FN Thomson Reuters Web of Science™ VR 1.0 PT S AU Song, SW Su, CY Rountree, B Cameron, KW AF Song, Shuaiwen Su, Chunyi Rountree, Barry Cameron, Kirk W. GP IEEE Comp Soc TI A Simplified and Accurate Model of Power-Performance Efficiency on Emergent GPU Architectures SO IEEE 27TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM (IPDPS 2013) SE International Parallel and Distributed Processing Symposium IPDPS LA English DT Proceedings Paper CT IEEE 27th International Parallel and Distributed Processing Symposium (IPDPS) CY MAY 20-24, 2013 CL Boston, MA SP IEEE, IEEE Comp Soc AB Emergent heterogeneous systems must be optimized for both power and performance at exascale. Massive parallelism combined with complex memory hierarchies form a barrier to efficient application and architecture design. These challenges are exacerbated with GPUs as parallelism increases orders of magnitude and power consumption can easily double. Models have been proposed to isolate power and performance bottlenecks and identify their root causes. However, no current models combine simplicity, accuracy, and support for emergent GPU architectures (e. g. NVIDIA Fermi). We combine hardware performance counter data with machine learning and advanced analytics to model power-performance efficiency for modern GPU-based systems. Our performance counter based approach is simpler than previous approaches and does not require detailed understanding of the underlying architecture. The resulting model is accurate for predicting power (within 2.1%) and performance (within 6.7%) for application kernels on modern GPUs. Our model can identify power-performance bottlenecks and their root causes for various complex computation and memory access patterns (e. g. global, shared, texture). We measure the accuracy of our power and performance models on a NVIDIA Fermi C2075 GPU for more than a dozen CUDA applications. We show our power model is more accurate and robust than the best available GPU power models - multiple linear regression models MLR and MLR+. We demonstrate how to use our models to identify power-performance bottlenecks and suggest optimization strategies for high-performance codes such as GEM, a biomolecular electrostatic analysis application. We verify our power-performance model is accurate on clusters of NVIDIA Fermi M2090s and useful for suggesting optimal runtime configurations on the Keeneland supercomputer at Georgia Tech. C1 [Song, Shuaiwen; Su, Chunyi; Cameron, Kirk W.] Virginia Tech, Blacksburg, VA 24061 USA. [Rountree, Barry] Lawrence Livermore Natl Lab, Livermore, CA USA. RP Song, SW (reprint author), Virginia Tech, Blacksburg, VA 24061 USA. EM s562673@vt.edu; sonicat@vt.edu; rountree@llnl.gov; cameron@cs.vt.edu FU National Science Foundation [0910784, 0905187, OCI-0910735]; DOEnOSCAR Beyond Standard Model [62855] FX This work is supported by the National Science Foundation under Grant No. 0910784 and 0905187, DOEnOSCAR Beyond Standard Model Project #62855. We also used resources of the Keeneland Computing Facility at the Georgia Institute of Technology, which is supported by the National Science Foundation under Contract OCI-0910735. NR 40 TC 14 Z9 14 U1 1 U2 4 PU IEEE COMPUTER SOC PI LOS ALAMITOS PA 10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA 90720-1264 USA SN 1530-2075 BN 978-0-7695-4971-2 J9 INT PARALL DISTRIB P PY 2013 BP 673 EP 686 DI 10.1109/IPDPS.2013.73 PG 14 WC Computer Science, Theory & Methods SC Computer Science GA BA1PT UT WOS:000332828000059 ER PT S AU Li, TL Zhou, XB Brandstatter, K Zhao, DF Wang, K Rajendran, A Zhang, Z Raicu, I AF Li, Tonglin Zhou, Xiaobing Brandstatter, Kevin Zhao, Dongfang Wang, Ke Rajendran, Anupam Zhang, Zhao Raicu, Ioan GP IEEE Comp Soc TI ZHT: A Light-weight Reliable Persistent Dynamic Scalable Zero-hop Distributed Hash Table SO IEEE 27TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM (IPDPS 2013) SE International Parallel and Distributed Processing Symposium IPDPS LA English DT Proceedings Paper CT IEEE 27th International Parallel and Distributed Processing Symposium (IPDPS) CY MAY 20-24, 2013 CL Boston, MA SP IEEE, IEEE Comp Soc DE Distributed hash tables; key/value stores; high-end computing ID NETWORK AB This paper presents ZHT, a zero-hop distributed hash table, which has been tuned for the requirements of high-end computing systems. ZHT aims to be a building block for future distributed systems, such as parallel and distributed file systems, distributed job management systems, and parallel programming systems. The goals of ZHT are delivering high availability, good fault tolerance, high throughput, and low latencies, at extreme scales of millions of nodes. ZHT has some important properties, such as being light-weight, dynamically allowing nodes join and leave, fault tolerant through replication, persistent, scalable, and supporting unconventional operations such as append (providing lock-free concurrent key/value modifications) in addition to insert/lookup/remove. We have evaluated ZHT's performance under a variety of systems, ranging from a Linux cluster with 512-cores, to an IBM Blue Gene/P supercomputer with 160K-cores. Using micro-benchmarks, we scaled ZHT up to 32K-cores with latencies of only 1.1ms and 18M operations/sec throughput. This work provides three real systems that have integrated with ZHT, and evaluate them at modest scales. 1) ZHT was used in the FusionFS distributed file system to deliver distributed meta-data management at over 60K operations (e. g. file create) per second at 2K-core scales. 2) ZHT was used in the IStore, an information dispersal algorithm enabled distributed object storage system, to manage chunk locations, delivering more than 500 chunks/sec at 32-nodes scales. 3) ZHT was also used as a building block to MATRIX, a distributed job scheduling system, delivering 5000 jobs/sec throughputs at 2K-core scales. We compared ZHT against other distributed hash tables and key/value stores and found it offers superior performance for the features and portability it supports. C1 [Li, Tonglin; Zhou, Xiaobing; Brandstatter, Kevin; Zhao, Dongfang; Wang, Ke; Rajendran, Anupam; Raicu, Ioan] IIT, Dept Comp Sci, Chicago, IL 60616 USA. [Zhang, Zhao] Univ Chicago, Dept Comp Sci, Chicago, IL 60637 USA. [Raicu, Ioan] Math & Comp Sci Div, Argonne Natl Lab, Argonne, IL USA. RP Li, TL (reprint author), IIT, Dept Comp Sci, Chicago, IL 60616 USA. EM tli13@hawk.iit.edu; xzhou40@hawk.iit.edu; kbrandst@iit.edu; dzhao8@hawk.iit.edu; kwang22@hawk.iit.edu; arajend5@hawk.iit.edu; zhaozhang@uchicago.edu; iraicu@cs.iit.edu FU National Science Foundation [NSF-1054974]; Argonne Leadership Computing Facility at Argonne National Laboratory; Office of Science of the U.S. Department of Energy [DEAC02-06CH11357] FX This work was supported in part by the National Science Foundation grant NSF-1054974. This research used resources of the Argonne Leadership Computing Facility at Argonne National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under contract DEAC02-06CH11357. NR 55 TC 22 Z9 22 U1 0 U2 3 PU IEEE COMPUTER SOC PI LOS ALAMITOS PA 10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA 90720-1264 USA SN 1530-2075 BN 978-0-7695-4971-2 J9 INT PARALL DISTRIB P PY 2013 BP 775 EP 787 DI 10.1109/IPDPS.2013.110 PG 13 WC Computer Science, Theory & Methods SC Computer Science GA BA1PT UT WOS:000332828000067 ER PT S AU Solomonik, E Matthews, D Hammond, JR Demmel, J AF Solomonik, Edgar Matthews, Devin Hammond, Jeff R. Demmel, James GP IEEE Comp Soc TI Cyclops Tensor Framework: reducing communication and eliminating load imbalance in massively parallel contractions SO IEEE 27TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM (IPDPS 2013) SE International Parallel and Distributed Processing Symposium IPDPS LA English DT Proceedings Paper CT IEEE 27th International Parallel and Distributed Processing Symposium (IPDPS) CY MAY 20-24, 2013 CL Boston, MA SP IEEE, IEEE Comp Soc ID COUPLED-CLUSTER THEORY; MATRIX MULTIPLICATION; QUANTUM-CHEMISTRY; MODEL; EXCITATIONS; SINGLES; TRIPLE AB Cyclops (cyclic-operations) Tensor Framework (CTF) (1) is a distributed library for tensor contractions. CTF aims to scale high-dimensional tensor contractions such as those required in the Coupled Cluster (CC) electronic structure method to massively-parallel supercomputers. The framework preserves tensor structure by subdividing tensors cyclically, producing a regular parallel decomposition. An internal virtualization layer provides completely general mapping support while maintaining ideal load balance. The mapping framework decides on the best mapping for each tensor contraction at run-time via explicit calculations of memory usage and communication volume. CTF employs a general redistribution kernel, which transposes tensors of any dimension between arbitrary distributed layouts, yet touches each piece of data only once. Sequential symmetric contractions are reduced to matrix multiplication calls via tensor index transpositions and partial unpacking. The user-level interface elegantly expresses arbitrary-dimensional generalized tensor contractions in the form of a domain specific language. We demonstrate performance of CC with single and double excitations on 8192 nodes of Blue Gene/Q and show that CTF outperforms NWChem on Cray XE6 supercomputers for benchmarked systems. C1 [Solomonik, Edgar; Demmel, James] Univ Calif Berkeley, Dept EECS, Berkeley, CA 94720 USA. [Matthews, Devin] Univ Texas Austin, Dept Chem & Biochem, Austin, TX 78712 USA. [Hammond, Jeff R.] Argonne Natl Lab, Comp Facil, Argonne, IL USA. RP Solomonik, E (reprint author), Univ Calif Berkeley, Dept EECS, Berkeley, CA 94720 USA. EM solomon@eecs.berkeley.edu RI Hammond, Jeff/G-8607-2013 OI Hammond, Jeff/0000-0003-3181-8190 FU Department of Energy Computational Science Graduate Fellowship [DE-FG02-97ER25308]; Microsoft [024263]; Intel [024894]; U.C. Discovery [DIG07-10227]; ParLab affiliates National Instruments; Nokia; NVIDIA; Oracle and Samsung; MathWorks; DOE [DE-SC0004938, DE-SC0005136, DE-SC0003959, DESC0008700, AC02-05CH11231]; DARPA [HR0011-12-2-0016]; Argonne Leadership Computing Facility (ALCF) at Argonne Na-tional Laboratory; Office of Science of the U.S. Department of Energy [DE-AC02-06CH11357, DE-AC02-05CH11231]; National Energy Research Scientific Computing Center (NERSC) FX ES and DM were supported by a Department of Energy Computational Science Graduate Fellowship, grant number DE-FG02-97ER25308. We acknowledge funding from Microsoft (Award #024263) and Intel (Award #024894), and matching funding by U.C. Discovery (Award #DIG07- 10227). Additional support comes from ParLab affiliates National Instruments, Nokia, NVIDIA, Oracle and Samsung, as well as MathWorks. Research is also supported by DOE grants DE-SC0004938, DE-SC0005136, DE-SC0003959, DESC0008700, and AC02-05CH11231, and DARPA grant HR0011-12-2-0016. This research used resources of the Argonne Leadership Computing Facility (ALCF) at Argonne Na-tional Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under contract DE-AC02-06CH11357. This research used resources of the National Energy Research Scientific Computing Center (NERSC), which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. NR 35 TC 13 Z9 13 U1 0 U2 3 PU IEEE COMPUTER SOC PI LOS ALAMITOS PA 10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA 90720-1264 USA SN 1530-2075 BN 978-0-7695-4971-2 J9 INT PARALL DISTRIB P PY 2013 BP 813 EP 824 DI 10.1109/IPDPS.2013.112 PG 12 WC Computer Science, Theory & Methods SC Computer Science GA BA1PT UT WOS:000332828000070 ER PT S AU Pearce, R Gokhale, M Amato, NM AF Pearce, Roger Gokhale, Maya Amato, Nancy M. GP IEEE Comp Soc TI Scaling Techniques for Massive Scale-Free Graphs in Distributed (External) Memory SO IEEE 27TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM (IPDPS 2013) SE International Parallel and Distributed Processing Symposium IPDPS LA English DT Proceedings Paper CT IEEE 27th International Parallel and Distributed Processing Symposium (IPDPS) CY MAY 20-24, 2013 CL Boston, MA SP IEEE, IEEE Comp Soc DE parallel algorithms; graph algorithms; big data; distributed computing ID ALGORITHMS; NETWORKS AB We present techniques to process large scale-free graphs in distributed memory. Our aim is to scale to trillions of edges, and our research is targeted at leadership class supercomputers and clusters with local non-volatile memory, e. g., NAND Flash. We apply an edge list partitioning technique, designed to accommodate high-degree vertices (hubs) that create scaling challenges when processing scale-free graphs. In addition to partitioning hubs, we use ghost vertices to represent the hubs to reduce communication hotspots. We present a scaling study with three important graph algorithms: Breadth-First Search (BFS), K-Core decomposition, and Triangle Counting. We also demonstrate scalability on BG/P Intrepid by comparing to best known Graph500 results [1]. We show results on two clusters with local NVRAM storage that are capable of traversing trillion-edge scale-free graphs. By leveraging node-local NAND Flash, our approach can process thirty-two times larger datasets with only a 39% performance degradation in Traversed Edges Per Second (TEPS). C1 [Pearce, Roger; Amato, Nancy M.] Texas A&M Univ, Parasol Lab, College Stn, TX 77843 USA. [Pearce, Roger; Gokhale, Maya] Lawrence Livermore Natl Lab, Ctr Appl Sci Comp, Livermore, CA USA. RP Pearce, R (reprint author), Texas A&M Univ, Parasol Lab, College Stn, TX 77843 USA. EM rpearce@llnl.gov; maya@llnl.gov; amato@cse.tamu.edu FU National Laboratory [DE-AC5207NA27344 (LLNL-CONF-5SS232)]; LDRD [11-ERD-00S]; Argonne Leadership Computing Facility (ALCF) at Argonne National Laboratory; Science of the U.S. Department of Energy [DE-AC0206CH11357]; Fault-Oblivious Exascale Computing Environment project; NSF [CNS-0615267, CCF-OS33199, CCF-0830753, IIS-0917266, IIS-0916053]; NSF/DNDO [2008-DN-077-ARI01802]; DOE [DE-AC0206CH11357, DE-FC520SNA2S616, B575363, B575366]; THECB NHARP [0005120097-2009]; Samsung; Chevron; IBM; Intel; Oracle/Sun; King Abdullah University of Science and Technology (KAUST) [KUS-C1016-04]; Lawrence Scholar fellowship at LLNL FX This work was partially performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC5207NA27344 (LLNL-CONF-5SS232). Funding was partially provided by LDRD 11-ERD-00S. Portions of experiments were performed at the Livermore Computing facility resources. This research used resources of the Argonne Leadership Computing Facility (ALCF) at Argonne National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under contract DE-AC0206CH11357. ALCF resources provided through an INCITE 2012 award for the Fault-Oblivious Exascale Computing Environment project. This research supported in part by NSF awards CNS-0615267, CCF-OS33199, CCF-0830753, IIS-0917266, IIS-0916053, NSF/DNDO award 2008-DN-077-ARI01802, by DOE awards DE-FC520SNA2S616, DE-AC0206CH11357, B575363, B575366, by THECB NHARP award 0005120097-2009, by Samsung, Chevron, IBM, Intel, Oracle/Sun and by Award KUS-C1016-04, made by King Abdullah University of Science and Technology (KAUST). Pearce is supported in part by a Lawrence Scholar fellowship at LLNL. NR 25 TC 5 Z9 5 U1 0 U2 2 PU IEEE COMPUTER SOC PI LOS ALAMITOS PA 10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA 90720-1264 USA SN 1530-2075 BN 978-0-7695-4971-2 J9 INT PARALL DISTRIB P PY 2013 BP 825 EP 836 DI 10.1109/IPDPS.2013.72 PG 12 WC Computer Science, Theory & Methods SC Computer Science GA BA1PT UT WOS:000332828000071 ER PT S AU Ballard, G Becker, D Demmel, J Dongarra, J Druinsky, A Peled, I Schwartz, O Toledo, S Yamazaki, I AF Ballard, Grey Becker, Dulceneia Demmel, James Dongarra, Jack Druinsky, Alex Peled, Inon Schwartz, Oded Toledo, Sivan Yamazaki, Ichitaro GP IEEE Comp Soc TI Implementing a Blocked Aasen's Algorithm with a Dynamic Scheduler on Multicore Architectures SO IEEE 27TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM (IPDPS 2013) SE International Parallel and Distributed Processing Symposium IPDPS LA English DT Proceedings Paper CT IEEE 27th International Parallel and Distributed Processing Symposium (IPDPS) CY MAY 20-24, 2013 CL Boston, MA SP IEEE, IEEE Comp Soc ID MATRICES; PARALLEL; SYSTEMS AB Factorization of a dense symmetric indefinite matrix is a key computational kernel in many scientific and engineering simulations. However, there is no scalable factorization algorithm that takes advantage of the symmetry and guarantees numerical stability through pivoting at the same time. This is because such an algorithm exhibits many of the fundamental challenges in parallel programming like irregular data accesses and irregular task dependencies. In this paper, we address these challenges in a tiled implementation of a blocked Aasen's algorithm using a dynamic scheduler. To fully exploit the limited parallelism in this left-looking algorithm, we study several performance enhancing techniques; e. g., parallel reduction to update a panel, tall-skinny LU factorization algorithms to factorize the panel, and a parallel implementation of symmetric pivoting. Our performance results on up to 48 AMD Opteron processors demonstrate that our implementation obtains speedups of up to 2.8 over MKL, while losing only one or two digits in the computed residual norms. C1 [Becker, Dulceneia; Dongarra, Jack; Yamazaki, Ichitaro] Univ Tennessee, Knoxville, TN 37996 USA. [Druinsky, Alex; Peled, Inon; Toledo, Sivan] Tel Aviv Univ, IL-69978 Tel Aviv, Israel. [Ballard, Grey; Demmel, James; Schwartz, Oded] Univ Calif Berkeley, Berkeley, CA USA. [Dongarra, Jack] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Dongarra, Jack] Univ Manchester, Manchester M13 9PL, Lancs, England. RP Yamazaki, I (reprint author), Univ Tennessee, Knoxville, TN 37996 USA. EM ballard@cs.berkeley.edu; dbecker7@eecs.utk.edu; demmel@cs.berkeley.edu; dongarra@eecs.utk.edu; alexdrui@post.tau.ac.il; inon.peled@gmail.com; odedsc@cs.berkeley.edu; stoledo@tau.ac.il; iyamazak@eecs.utk.edu FU NSF [CCF-1117062, CNS-0905188]; Microsoft Corporation Research Project Description "Exploring Novel Approaches for Achieving Scalable Performance on Emerging Hybrid and Multi-Core Architectures for Linear Algebra Algorithms and Software, [1045/09]; Israel Science Foundation (founded by the Israel Academy of Sciences and Humanities) [2010231]; US-Israel Bi-National Science Foundation; Microsoft [024263]; Intel [024894]; U.C. Discovery [DIG0710227]; DOE [DE-SC0004938, DE-SC0005136, DE-SC0003959, DE-SC0008700, AC0205CH11231]; DARPA [HR001112-20016] FX This research was supported in part by NSF CCF-1117062 and CNS-0905188, Microsoft Corporation Research Project Description Exploring Novel Approaches for Achieving Scalable Performance on Emerging Hybrid and Multi-Core Architectures for Linear Algebra Algorithms and Software, grant 1045/09 from the Israel Science Foundation (founded by the Israel Academy of Sciences and Humanities), and grant 2010231 from the US-Israel Bi-National Science Foundation, and by Microsoft (Award #024263) and Intel (Award #024894), and matching funding by U.C. Discovery (Award #DIG0710227). Additional support comes from ParLab affiliates National Instruments, Nokia, NVIDIA, Oracle and Samsung, as well as MathWorks. Research is also supported by DOE grants DE-SC0004938, DE-SC0005136, DE-SC0003959, DE-SC0008700, and AC0205CH11231, and DARPA grant HR001112-20016. NR 22 TC 4 Z9 4 U1 0 U2 3 PU IEEE COMPUTER SOC PI LOS ALAMITOS PA 10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA 90720-1264 USA SN 1530-2075 BN 978-0-7695-4971-2 J9 INT PARALL DISTRIB P PY 2013 BP 895 EP 907 DI 10.1109/IPDPS.2013.98 PG 13 WC Computer Science, Theory & Methods SC Computer Science GA BA1PT UT WOS:000332828000078 ER PT S AU Karlin, I Bhatele, A Keasler, J Chamberlain, BL Cohen, J DeVito, Z Haque, R Laney, D Luke, E Wang, F Richards, D Schulz, M Still, CH AF Karlin, Ian Bhatele, Abhinav Keasler, Jeff Chamberlain, Bradford L. Cohen, Jonathan DeVito, Zachary Haque, Riyaz Laney, Dan Luke, Edward Wang, Felix Richards, David Schulz, Martin Still, Charles H. GP IEEE Comp Soc TI Exploring Traditional and Emerging Parallel Programming Models using a Proxy Application SO IEEE 27TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM (IPDPS 2013) SE International Parallel and Distributed Processing Symposium IPDPS LA English DT Proceedings Paper CT IEEE 27th International Parallel and Distributed Processing Symposium (IPDPS) CY MAY 20-24, 2013 CL Boston, MA SP IEEE, IEEE Comp Soc DE parallel programming models; productivity; performance; co-design; proxy application ID LANGUAGE; ARRAYS; LOCI AB Parallel machines are becoming more complex with increasing core counts and more heterogeneous architectures. However, the commonly used parallel programming models, C/C++ with MPI and/or OpenMP, make it difficult to write source code that is easily tuned for many targets. Newer language approaches attempt to ease this burden by providing optimization features such as automatic load balancing, overlap of computation and communication, message-driven execution, and implicit data layout optimizations. In this paper, we compare several implementations of LULESH, a proxy application for shock hydrodynamics, to determine strengths and weaknesses of different programming models for parallel computation. We focus on four traditional (OpenMP, MPI, MPI+ OpenMP, CUDA) and four emerging (Chapel, Charm++, Liszt, Loci) programming models. In evaluating these models, we focus on programmer productivity, performance and ease of applying optimizations. C1 [Karlin, Ian; Bhatele, Abhinav; Keasler, Jeff; Cohen, Jonathan; Laney, Dan; Richards, David; Schulz, Martin; Still, Charles H.] Lawrence Livermore Natl Lab, POB 808, Livermore, CA 94551 USA. [Chamberlain, Bradford L.] Cray Res Inc, Washington, DC 98164 USA. [DeVito, Zachary] Stanford Univ, Stanford, CA 94305 USA. [Haque, Riyaz] Univ Calif Los Angeles, Los Angeles, CA 90095 USA. [Luke, Edward] Mississippi State Univ, Mississippi State, MS 39762 USA. [Wang, Felix] Univ Illinois, Urbana, IL 61801 USA. RP Karlin, I (reprint author), Lawrence Livermore Natl Lab, POB 808, Livermore, CA 94551 USA. EM karlin1@llnl.gov; bhatele@llnl.gov; keasler@llnl.gov FU U.S. Department of Energy by Lawrence Livermore National Laboratory [DE-AC5207NA27344 (LLNL-CONF-586774)]; Defense Advanced Research Projects Agency [HROO1107-90001]; DOE Office of Advanced Scientific Computing Research FX This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC5207NA27344 (LLNL-CONF-586774). This material is based upon work supported by the Defense Advanced Research Projects Agency under its Agreement No. HROO1107-90001. This work was partially supported by the DOE Office of Advanced Scientific Computing Research. Accordingly, the U.S. government retains a non-exclusive, royalty-free license to publish or reproduce the published form of this contribution, or allow others to do so, for U.S. government purposes. NR 32 TC 20 Z9 20 U1 1 U2 3 PU IEEE COMPUTER SOC PI LOS ALAMITOS PA 10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA 90720-1264 USA SN 1530-2075 BN 978-0-7695-4971-2 J9 INT PARALL DISTRIB P PY 2013 BP 919 EP 932 DI 10.1109/IPDPS.2013.115 PG 14 WC Computer Science, Theory & Methods SC Computer Science GA BA1PT UT WOS:000332828000080 ER PT S AU Randles, AP Kale, V Hammond, J Gropp, W Kaxiras, E AF Randles, Amanda Peters Kale, Vivek Hammond, Jeff Gropp, William Kaxiras, Efthimios GP IEEE Comp Soc TI Performance Analysis of the Lattice Boltzmann Model Beyond Navier-Stokes SO IEEE 27TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM (IPDPS 2013) SE International Parallel and Distributed Processing Symposium IPDPS LA English DT Proceedings Paper CT IEEE 27th International Parallel and Distributed Processing Symposium (IPDPS) CY MAY 20-24, 2013 CL Boston, MA SP IEEE, IEEE Comp Soc DE fluid dynamics; lattice Boltzmann; multicore optimization ID KINETIC-THEORY; FLOW; MICROCHANNELS AB The lattice Boltzmann method is increasingly important in facilitating large-scale fluid dynamics simulations. To date, these simulations have been built on discretized velocity models of up to 27 neighbors. Recent work has shown that higher order approximations of the continuum Boltzmann equation enable not only recovery of the Navier-Stokes hydrodynamics, but also simulations for a wider range of Knudsen numbers, which is especially important in micro-and nano-scale flows. These higher-order models have significant impact on both the communication and computational complexity of the application. We present a performance study of the higher-order models as compared to the traditional ones, on both the IBM Blue Gene/P and Blue Gene/Q architectures. We study the tradeoffs of many optimizations methods such as the use of deep halo level ghost cells that, alongside hybrid programming models, reduce the impact of extended models and enable efficient modeling of extreme regimes of computational fluid dynamics. C1 [Randles, Amanda Peters; Kaxiras, Efthimios] Harvard Univ, Sch Engn & Appl Sci, Cambridge, MA 02138 USA. [Hammond, Jeff] Argonne Natl Lab, Leadership Comp Faci, Argonne, IL 60439 USA. [Kale, Vivek; Gropp, William] Univ Illinois, Dept Comp Sci, Urbana, IL 61801 USA. RP Randles, AP (reprint author), Harvard Univ, Sch Engn & Appl Sci, Cambridge, MA 02138 USA. EM apeters@fas.harvard.edu RI Hammond, Jeff/G-8607-2013; OI Hammond, Jeff/0000-0003-3181-8190; Randles, Amanda/0000-0001-6318-3885; Gropp, William/0000-0003-2905-3029 FU Department of Energy's Computational Science Graduate Fellowship; DOE CSGF [DE-FG0297ER25308]; Office of Advanced Scientific Computing Research, Office of Science; U.S. Department of Energy [DE-SC0004131] FX This work was supported in part by the Department of Energy's Computational Science Graduate Fellowship, grant number DOE CSGF DE-FG0297ER25308, and in part by the Office of Advanced Scientific Computing Research, Office of Science, U.S. Department of Energy award DE-SC0004131. We would like to thank F. Mintzer and D. Singer for their help and support with use of the IBM Watson Blue Gene/P system and the LLNL Support Team for access to Blue Gene/Q. We also thank T. Gamblin, A. Bhatele, M. Schulz, and T. Spelce for their assistance. NR 24 TC 0 Z9 0 U1 3 U2 6 PU IEEE COMPUTER SOC PI LOS ALAMITOS PA 10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA 90720-1264 USA SN 1530-2075 BN 978-0-7695-4971-2 J9 INT PARALL DISTRIB P PY 2013 BP 1063 EP 1074 DI 10.1109/IPDPS.2013.109 PG 12 WC Computer Science, Theory & Methods SC Computer Science GA BA1PT UT WOS:000332828000091 ER PT S AU Bicer, T Yin, J Chiu, D Agrawal, G Schuchardt, K AF Bicer, Tekin Yin, Jian Chiu, David Agrawal, Gagan Schuchardt, Karen GP IEEE Comp Soc TI Integrating Online Compression to Accelerate Large-Scale Data Analytics Applications SO IEEE 27TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM (IPDPS 2013) SE International Parallel and Distributed Processing Symposium IPDPS LA English DT Proceedings Paper CT IEEE 27th International Parallel and Distributed Processing Symposium (IPDPS) CY MAY 20-24, 2013 CL Boston, MA SP IEEE, IEEE Comp Soc AB Compute cycles in high performance systems are increasing at a much faster pace than both storage and wide-area bandwidths. To continue improving the performance of large-scale data analytics applications, compression has therefore become promising approach. In this context, this paper makes the following contributions. First, we develop a new compression methodology, which exploits the similarities between spatial and/or temporal neighbors in a popular climate simulation dataset and enables high compression ratios and low decompression costs. Second, we develop a framework that can be used to incorporate a variety of compression and decompression algorithms. This framework also supports a simple API to allow integration with an existing application or data processing middleware. Once a compression algorithm is implemented, this framework automatically mechanizes multi-threaded retrieval, multi-threaded data decompression, and the use of informed prefetching and caching. By integrating this framework with a data-intensive middleware, we have applied our compression methodology and framework to three applications over two datasets, including the Global Cloud-Resolving Model (GCRM) climate dataset. We obtained an average compression ratio of 51.68%, and up to 53.27% improvement in execution time of data analysis applications by amortizing I/O time by moving compressed data. C1 [Bicer, Tekin; Agrawal, Gagan] Ohio State Univ, Columbus, OH 43210 USA. [Yin, Jian; Schuchardt, Karen] Pacific Northwest Natl Labs, Richland, WA USA. [Chiu, David] Washington State Univ, Olympia, WA 98504 USA. RP Bicer, T (reprint author), Ohio State Univ, Columbus, OH 43210 USA. EM bicer@cse.ohio-state.edu; jian.yin@pnnl.gov; david.chiu@wsu.edu; agrawal@cse.ohio-state.edu; karen.schuchardt@pnnl.gov OI Bicer, Tekin/0000-0002-8428-5159 FU Office of Biological and Environmental Research; Science, U.S. Department of Energy [DE-ACO2-O6CH1135] FX The authors would like to thank Robert L. Jacob from Argonne National Laboratory for his support and assistance. This work was supported in part by the Office of Biological and Environmental Research, Office of Science, U.S. Department of Energy, under contract DE-ACO2-O6CH1135 NR 36 TC 6 Z9 6 U1 0 U2 1 PU IEEE COMPUTER SOC PI LOS ALAMITOS PA 10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA 90720-1264 USA SN 1530-2075 BN 978-0-7695-4971-2 J9 INT PARALL DISTRIB P PY 2013 BP 1205 EP 1216 DI 10.1109/IPDPS.2013.81 PG 12 WC Computer Science, Theory & Methods SC Computer Science GA BA1PT UT WOS:000332828000103 ER PT S AU Morozov, V Kumaran, K Vishwanath, V Meng, JY Papka, ME AF Morozov, Vitali Kumaran, Kalyan Vishwanath, Venkatram Meng, Jiayuan Papka, Michael E. GP IEEE Comp Soc TI Early Experience on the Blue Gene/Q Supercomputing System SO IEEE 27TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM (IPDPS 2013) SE International Parallel and Distributed Processing Symposium IPDPS LA English DT Proceedings Paper CT IEEE 27th International Parallel and Distributed Processing Symposium (IPDPS) CY MAY 20-24, 2013 CL Boston, MA SP IEEE, IEEE Comp Soc AB The Argonne Leadership Computing Facility (ALCF) is home to Mira, a 10 PF Blue Gene/Q (BG/Q) system. The BG/Q system is the third generation in Blue Gene architecture from IBM and like its predecessors combines system-on-chip technology with a proprietary interconnect (5-D torus). Each compute node has 16 augmented PowerPC A2 processor cores with support for simultaneous multithreading, 4-wide double precision SIMD, and different data prefetching mechanisms. Mira offers several new opportunities for tuning and scaling scientific applications. This paper discusses our early experience with a subset of micro-benchmarks, MPI benchmarks, and a variety of science and engineering applications running at ALCF. Both performance and power are studied and results on BG/Q is compared with its predecessor BG/P. Several lessons gleaned from tuning applications on the BG/Q architecture for better performance and scalability are shared. C1 [Morozov, Vitali; Kumaran, Kalyan; Vishwanath, Venkatram; Meng, Jiayuan; Papka, Michael E.] Argonne Natl Lab, Argonne, IL 60439 USA. RP Morozov, V (reprint author), Argonne Natl Lab, 9700 S Cass Ave, Argonne, IL 60439 USA. EM morozov@anl.gov; kumaran@anl.gov; venkat@anl.gov; jmeng@anl.gov; papka@anl.gov NR 25 TC 0 Z9 0 U1 0 U2 0 PU IEEE COMPUTER SOC PI LOS ALAMITOS PA 10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA 90720-1264 USA SN 1530-2075 BN 978-0-7695-4971-2 J9 INT PARALL DISTRIB P PY 2013 BP 1229 EP 1240 DI 10.1109/IPDPS.2013.106 PG 12 WC Computer Science, Theory & Methods SC Computer Science GA BA1PT UT WOS:000332828000105 ER PT J AU Bhat, PC AF Bhat, Pushpalatha C. CA CMS Collaboration TI Observation of a Higgs-like Boson in CMS at the LHC SO NUCLEAR PHYSICS B-PROCEEDINGS SUPPLEMENTS LA English DT Proceedings Paper CT 16th International Conference on Quantum Chromodynamics CY JUL 02-06, 2012 CL Montpellier, FRANCE DE Higgs boson; Higgs-like boson; CMS experiment; Multivariate methods; Observation; LHC ID MASSLESS PARTICLES; BROKEN SYMMETRIES; MODEL AB After decades of pursuit at lepton and hadron colliders around the world, a Higgs-like boson has been observed at the Large Hadron Collider (LHC). We present results of searches by the CMS collaboration for the production of the standard model Higgs boson in proton-proton collisions, using data samples corresponding to integrated luminosities of 5.1 fb(-1) at root s = 7 TeV and 5.3 fb(-1) at root s = 8 TeV. The searches have been performed in five Higgs decay modes, gamma gamma, ZZ, WW, tau(+)tau(-), and b (b) over bar, in the mass range from 110 up to 160 GeV. Multivariate methods have been used in many aspects of the analyses to extract optimal results. An excess of events has been observed above the expected background, with a significance of 5.0 standard deviations. Most of the excess is in the high resolution gamma gamma and ZZ decay modes. A fit to the signal in these modes yields a mass for the boson of 125.3 +/- 0.4(stat.)+/- 0.5(syst.) GeV. Since the new boson decays into two photons, its spin can be inferred to be different from one. C1 [Bhat, Pushpalatha C.; CMS Collaboration] Fermilab Natl Accelerator Lab, Batavia, IL 60510 USA. RP Bhat, PC (reprint author), Fermilab Natl Accelerator Lab, Batavia, IL 60510 USA. EM pushpa@fnal.gov NR 34 TC 0 Z9 0 U1 1 U2 4 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0920-5632 EI 1873-3832 J9 NUCL PHYS B-PROC SUP JI Nucl. Phys. B-Proc. Suppl. PD JAN PY 2013 VL 234 BP 7 EP 14 DI 10.1016/j.nuclphysbps.2012.11.003 PG 8 WC Physics, Particles & Fields SC Physics GA 146IS UT WOS:000319085400002 ER PT S AU Morozov, V Meng, JY Vishwanath, V Kumaran, K Papka, ME AF Morozov, Vitali Meng, Jiayuan Vishwanath, Venkatram Kumaran, Kalyan Papka, Michael E. BE Malyshkin, V TI Characterization and Understanding Machine-Specific Interconnects SO PARALLEL COMPUTING TECHNOLOGIES (PACT 2013) SE Lecture Notes in Computer Science LA English DT Proceedings Paper CT 12th International Conference on Parallel Computing Technologies (PaCT) CY SEP 30-OCT 04, 2013 CL St Petersburg, RUSSIA SP Russian Acad Sci, Siberian Branch, Inst Computat Math & Math Geophys, Supercomputer Software Dept, St Petersburg State Polytechn Univ, Russian Fund Basic Res, Closed Joint Stock Co Intel A O DE interconnect; performance tuning; topology-aware; MPI AB The use of efficient communication patterns is becoming increasingly important to utilize high concurrency and achieve high throughput and low latency of modern high-performance supercomputers. Efficacy is not only dictated by an application communication pattern, but also driven by the interconnect properties, the node architecture, and the quality of runtime communication libraries. Different systems require different tradeoffs with respect to communication mechanisms, which can impact the choice of application implementations. We use the in-house MPI benchmark suite to study the communication behavior of the interconnects and guide the performance tuning of scientific applications. We report the results of our investigation of four supercomputer systems located at ALCF, and present lessons learned from our experience. C1 [Morozov, Vitali; Meng, Jiayuan; Vishwanath, Venkatram; Kumaran, Kalyan; Papka, Michael E.] Argonne Natl Lab, Argonne Leadership Comp Facil, Argonne, IL 60439 USA. RP Morozov, V (reprint author), Argonne Natl Lab, Argonne Leadership Comp Facil, 9700 S Cass Ave, Argonne, IL 60439 USA. EM morozov@anl.gov; jmeng@anl.gov; venkat@anl.gov; kumaran@anl.gov; papka@anl.gov NR 11 TC 0 Z9 0 U1 0 U2 0 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 0302-9743 BN 978-3-642-39957-2; 978-3-642-39958-9 J9 LECT NOTES COMPUT SC PY 2013 VL 7979 BP 90 EP 104 PG 15 WC Computer Science, Information Systems; Computer Science, Software Engineering; Computer Science, Theory & Methods SC Computer Science GA BA2HD UT WOS:000333402500008 ER PT J AU Omar, MA Mayyas, A Zhou, QL AF Omar, Mohammed A. Mayyas, Ahmad Zhou, Qilun BE Issa, G AlBahadili, H AlAkhras, M Maqousi, A Hasan, MA TI Knowledge based Systems KBS for Energy Efficiency Energy Aware Manufacturing SO 2013 1ST INTERNATIONAL CONFERENCE & EXHIBITION ON THE APPLICATIONS OF INFORMATION TECHNOLOGY TO RENEWABLE ENERGY PROCESSES AND SYSTEMS (IT-DREPS 2013) LA English DT Proceedings Paper CT 1st International Conference and Exhibition on the Applications of Information Technology to Renewable Energy Processes and Systems (IT-DREPS) CY MAY 29-31, 2013 CL Univ Petra, Amman, JORDAN SP Univ Petra, Fac Informat Technol, IEEE, Power Engn Grp, Assoc Arab Univ, Jordan Islam Bank, Canadian European Acad, Arab Potash Co, e Baheth Elect, Mazajnet, Standard Associates, IEEE Jordan Sect, IEEE Western Saudi Arabia Sect, ETA Max, Saudi Arabia Solar Ind Assoc HO Univ Petra DE component; Knowledge based Systems; Energy management; Energy optimization; Sustainable manufacturing AB This manuscript discusses the implementation of information technology tools; specifically, computerized Knowledge Based Systems KBS, in managing the energy flows, conversions, and expenditures within manufacturing environments; including renewable energy sources (namely, landfill gas). The study presents actual KBS embodiments in energy auditing, modeling, and optimization. Additionally, the text presents how IT tools can be used at a system level to integrate sustainability planning within manufacturing planning. The developed tool also addresses the question "how energy-efficient are renewable energy sources" using a novel simulation platform based on hybrid scheme. C1 [Omar, Mohammed A.] Masdar Inst Sci & Technol, Abu Dhabi, U Arab Emirates. [Omar, Mohammed A.; Zhou, Qilun] Clemson Univ, Automot Engn Dept, Clemson, SC 29631 USA. [Mayyas, Ahmad] Sustainable Transportat Res Ctr, Lawrence Berkeley Natl Lab, Berkeley, CA USA. RP Omar, MA (reprint author), Masdar Inst Sci & Technol, Abu Dhabi, U Arab Emirates. RI Mayyas, Ahmad/J-3671-2014 NR 9 TC 0 Z9 0 U1 0 U2 1 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-1-4799-0710-6 PY 2013 BP 149 EP 151 PG 3 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA1OR UT WOS:000332786400026 ER PT J AU Meyer, RM Coble, JB Ramuhalli, P AF Meyer, R. M. Coble, J. B. Ramuhalli, P. GP IEEE TI Requirements for Prognostic Health Management of Passive Components in Advanced Small Modular Reactors SO 2013 IEEE INTERNATIONAL CONFERENCE ON PROGNOSTICS AND HEALTH MANAGEMENT LA English DT Proceedings Paper CT IEEE International Conference on Prognostics and Health Management (PHM) CY JUN 24-27, 2013 CL Gaithersburg, MD SP IEEE, Reliabil Soc DE nuclear power plants; nondestructive evaluation; small modular reactors; PHM; reliability; passive components ID STRUCTURAL-MATERIALS; FATIGUE; RELIABILITY; SYSTEMS; DAMAGE; POWER; LIFE AB Advanced small modular reactors (aSMRs), which are based on modularization of advanced reactor concepts, may provide a longer-term alternative to traditional light-water reactors and near term small modular reactors (SMRs), which are based on integral pressurized water reactor (iPWR) concepts. aSMRs are conceived for applications in remote locations and for diverse missions that include providing process or district heating, water desalination, and hydrogen production. Several challenges exist with respect to cost-effective operations and maintenance (O&M) of aSMRs, including the impacts of aggressive operating environments and modularity, and limiting these costs and staffing needs will be essential to ensuring the economic feasibility of aSMR deployment. In this regard, prognostic health management (PHM) systems have the potential to play a vital role in supporting the deployment of aSMR systems. This paper identifies requirements and technical gaps associated with implementation of PHM systems for passive aSMR components. C1 [Meyer, R. M.; Coble, J. B.; Ramuhalli, P.] Pacific NW Natl Lab, Natl Secur Directorate, Appl Phys Grp, Richland, WA 99352 USA. RP Meyer, RM (reprint author), Pacific NW Natl Lab, Natl Secur Directorate, Appl Phys Grp, Richland, WA 99352 USA. EM Ryan.Meyer@pnnl.gov NR 45 TC 0 Z9 0 U1 0 U2 1 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-1-4673-5722-7 PY 2013 PG 8 WC Computer Science, Information Systems; Medical Informatics SC Computer Science; Medical Informatics GA BA1FZ UT WOS:000332461600016 ER PT S AU Cheah, YW Canon, R Plale, B Ramakrishnan, L AF Cheah, You-Wei Canon, Richard Plale, Beth Ramakrishnan, Lavanya GP IEEE TI Milieu: Lightweight and Configurable Big Data Provenance for Science SO 2013 IEEE INTERNATIONAL CONGRESS ON BIG DATA SE IEEE International Congress on Big Data LA English DT Proceedings Paper CT IEEE International Congress on Big Data CY JUN 27-JUL 02, 2013 CL Santa Clara, CA SP IEEE, IEEE Comp Soc DE Provenance; High Performance Computing; Database AB The volume and complexity of data produced and analyzed in scientific collaborations is growing exponentially. It is important to track scientific data-intensive analysis workflows to provide context and reproducibility as data is transformed in these collaborations. Provenance addresses this need and aids scientists by providing the lineage or history of how data is generated, used and modified. Provenance has traditionally been collected at the workflow level often making it hard to capture relevant information about resource characteristics and is difficult for users to easily incorporate in existing workflows. In this paper, we describe Milieu, a framework focused on the collection of provenance for scientific experiments in High Performance Computing systems. Our approach collects provenance in a minimally intrusive way without significantly impacting the performance of the execution of scientific workflows. We also provide fidelity to our provenance collection by allowing users to specify three levels of provenance collection. We evaluate our framework on systems at the National Energy Research Scientific Computing Center (NERSC) and show that the overhead is less than the variation already experienced by these applications in these shared environments. C1 [Cheah, You-Wei; Plale, Beth] Indiana Univ, Sch Informat & Comp, Bloomington, IN 47405 USA. [Canon, Richard; Ramakrishnan, Lavanya] Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Cheah, YW (reprint author), Indiana Univ, Sch Informat & Comp, Bloomington, IN 47405 USA. EM yocheah@cs.indiana.edu; plale@cs.indiana.edu; scanon@lbl.gov; lramakrishnan@lbl.gov OI Plale, Beth/0000-0003-2164-8132 FU U.S. Department of Energy NERSC [DE-AC02-05CH11231] FX This work was funded by the Office of Science of the U.S. Department of Energy under Contract Number DE-AC02-05CH11231 (including use of resources at NERSC). NR 17 TC 6 Z9 6 U1 1 U2 5 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 2379-7703 BN 978-0-7695-5006-0 J9 IEEE INT CONGR BIG PY 2013 BP 46 EP 53 DI 10.1109/BigData.Congress.2013.16 PG 8 WC Computer Science, Theory & Methods; Engineering, Electrical & Electronic SC Computer Science; Engineering GA BA1GT UT WOS:000332528300007 ER PT S AU Botterud, A Zhou, Z Wang, JH Sumaili, J Keko, H Mendes, J Bessa, R Miranda, V AF Botterud, Audun Zhou, Zhi Wang, Jianhui Sumaili, Jean Keko, Hrvoje Mendes, Joana Bessa, Ricardo Miranda, Vladimiro GP IEEE TI Demand Dispatch and Probabilistic Wind Power Forecasting in Unit Commitment and Economic Dispatch: A Case Study of Illinois SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc C1 [Botterud, Audun; Zhou, Zhi; Wang, Jianhui; Sumaili, Jean; Keko, Hrvoje; Mendes, Joana; Bessa, Ricardo; Miranda, Vladimiro] Argonne Natl Lab, Decis & Informat Sci Div, Argonne, IL 60439 USA. RP Botterud, A (reprint author), Argonne Natl Lab, Decis & Informat Sci Div, Argonne, IL 60439 USA. NR 0 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 1 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874303097 ER PT S AU Bravo, RJ Yinger, R Robles, S Eto, JH AF Bravo, Richard J. Yinger, Robert Robles, Steven Eto, Joe H. GP IEEE TI FIDVR in Distribution Circuits SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE FIDVR; residential air conditioner stalling; stalling characteristics of residential air conditioners in distribution circuits AB This paper presents Fault Induced Delayed Voltage Recovery (FIDVR) events captured in Southern California desert areas with residential distribution circuits. Southern California Edison (SCE) installed 22 power quality recorders in SCE's Valley Subtransmission network. These devices recorded both sinusoidal and rms data from events triggered by voltage excursions. The purpose of this project is to acquire FIDVR data to validate WECC's composite load model. This data will support the load composition analysis in the WECC composite load model as well. The sinusoidal data can be used to validate transient models of stalling residential air conditioners. This effort is part of an integrated program of FIDVR research sponsored by the U. S. Department of Energy to promote national awareness, improve understanding of potential grid impacts, and identify appropriate steps to ensure reliability of the power system. The key results presented are associated with the stalling behavior of the air conditioner units in SCE's Valley substation region. C1 [Bravo, Richard J.; Yinger, Robert; Robles, Steven] Southern Calif Edison, Adv Technol Org, Westminster, CA 92683 USA. [Eto, Joe H.] Lawrence Berkeley Natl Lab, Berkeley, CA USA. RP Bravo, RJ (reprint author), Southern Calif Edison, Adv Technol Org, Westminster, CA 92683 USA. NR 4 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 5 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874303164 ER PT S AU Chen, YS Jin, SS Rice, M Huang, ZY AF Chen, Yousu Jin, Shuangshuang Rice, Mark Huang, Zhenyu GP IEEE TI Parallel State Estimation Assessment with Practical Data SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE State Estimation; Preconditioned Conjugate Gradient; Orthogonal Decomposition; High Performance Computing ID SYSTEMS AB This paper presents a parallel state estimation (PSE) implementation using a preconditioned conjugate gradient algorithm and an orthogonal decomposition-based algorithm. Preliminary tests against a commercial Energy Management System (EMS) State Estimation (SE) tool using real-world data are performed. The results show that while the preconditioned conjugate gradient algorithm can solve the SE problem faster with the help of parallel computing techniques, it might not be good for real-world data due to the large condition number of its gain matrix introduced by the wide range of measurement weights. With the help of PETSc package, the orthogonal decomposition-based PSE algorithm can achieve 5-20 times speedup comparing against the commercial EMS tool. It is very promising that the developed PSE can solve the SE problem for large power systems at the SCADA rate, to improve grid reliability. C1 [Chen, Yousu; Jin, Shuangshuang] Pacific Northwest Natl Lab, Battelle Seattle Res Ctr, Seattle, WA 98109 USA. [Rice, Mark; Huang, Zhenyu] Pacific Northwest Natl Lab, Adv Power & Energy Syst, Richland, WA 99354 USA. RP Chen, YS (reprint author), Pacific Northwest Natl Lab, Battelle Seattle Res Ctr, Seattle, WA 98109 USA. EM yousu.chen@pnnl.gov; shuangshuang.jin@pnnl.gov; mark.rice@pnnl.gov; zhenyu.huang@pnnl.gov FU U.S. Department of Energy (DOE); Advanced Grid Modeling; Gil Bindewald; Pacific Northwest National Laboratory (PNNL); DOE [DE-AC05-76RL01830] FX This work is supported by the U.S. Department of Energy (DOE) through its Advanced Grid Modeling Program managed by Gil Bindewald. Pacific Northwest National Laboratory (PNNL) is operated by Battelle for the DOE under Contract DE-AC05-76RL01830. NR 18 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 5 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874302141 ER PT S AU Du, PW Makarov, YV AF Du, Pengwei Makarov, Y. V. GP IEEE TI PMU-Based Wide-Area Security Assessment: Concept, Method, and Implementation SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc C1 [Du, Pengwei] Pacific NW Natl Lab, Richland, WA 99352 USA. [Makarov, Y. V.] PNNL, Adv Power & Energy Syst, Richland, WA USA. RP Du, PW (reprint author), Pacific NW Natl Lab, Richland, WA 99352 USA. FU Bonneville Power Administration (BPA); Department of Energy (DOE); Pacific Northwest National Laboratory; U.S. Department of Energy; Battelle Memorial Institute [TSG-00470-2011] FX This work was jointly supported by Bonneville Power Administration (BPA) and Department of Energy (DOE).Pacific Northwest National Laboratory is operated for the U.S.Department of Energy by Battelle Memorial Institute. Paper no. TSG-00470-2011. NR 0 TC 0 Z9 0 U1 0 U2 1 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 1 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874300042 ER PT S AU Etingov, PV Makarov, YV Samaan, N Ma, J Loutan, C Rothleder, M Chowdhury, S AF Etingov, Pavel V. Makarov, Yuri V. Samaan, Nader Ma, Jian Loutan, Clyde Rothleder, Mark Chowdhury, Sirajul GP IEEE TI Prediction of Regulation Reserve Requirements in California ISO Balancing Authority Area based on BAAL SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE ACE; Regulation; Regulation Reserve; Control Performance; Balancing Authority ACE limit; BAAL AB This paper presents new methodologies developed at Pacific Northwest National Laboratory (PNNL) to estimate regulation capacity requirements in the California Independent System Operator (CAISO) balancing authority area (BAA). Two approaches have been developed: (1) an approach based on statistical analysis of actual historical area control error (ACE) and regulation data and (2) an approach based on balancing authority ACE limit control performance standard. The approaches predict regulation reserve requirements on a day-ahead basis including upward and downward requirements, for each operating hour of a day. California ISO data has been used to test the performance of the proposed algorithms. Results show that the software tool developed allows saving up to 30% on the regulation procurements cost(1). C1 [Etingov, Pavel V.; Makarov, Yuri V.; Samaan, Nader] Pacific NW Natl Lab, Richland, WA 99352 USA. [Ma, Jian] Burns & McDonnell, Kansas City, MO USA. [Loutan, Clyde; Rothleder, Mark; Chowdhury, Sirajul] California ISO, Folsom, CA USA. RP Etingov, PV (reprint author), Pacific NW Natl Lab, Richland, WA 99352 USA. EM yuri.makarov@pnnl.gov; nader.samaan@pnnl.gov; jma@burnsmcd.com; cloutan@caiso.com; mrothleder@caiso.com; schowdhury@caiso.com FU Public Interest Energy Research (PIER) program in renewable energy at the California Energy Commission; Pacific Northwest National Laboratory FX This work was funded by the Public Interest Energy Research (PIER) program in renewable energy at the California Energy Commission and managed by the California Institute for Energy and Environment. The authors would like to thank Mike Gravely, Pedro Gomez, and Jamie Patterson, California Energy Commission; Merwin Brown, Larry Miller, and Jim Cole, California Institute for Energy and Environment; and Zhijun (June) Xie, and Ajay Mannepalli, California Independent System Operator, for providing the project team with consultations, day-by-day support, and discussions essential to this work. The authors would also like to thank Carl Imhoff, Evan Jones, Dale King, Mark Morgan, Landis Kannberg, and Ryan Hafen, Pacific Northwest National Laboratory, for supporting this work. NR 10 TC 0 Z9 0 U1 1 U2 2 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 5 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874302037 ER PT S AU Feng, YH Gade, D Ryan, SM Watson, JP Wets, RJB Woodruff, DL AF Feng, Yonghan Gade, Dinakar Ryan, Sarah M. Watson, Jean-Paul Wets, Roger J-B Woodruff, David L. GP IEEE TI A New Approximation Method for Generating Day-Ahead Load Scenarios SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE Demand forecasting; Load modeling; Power system planning; Stochastic processes AB Unit commitment decisions made in the day-ahead market and resource adequacy assessment processes are based on forecasts of load, which depends strongly on weather. Two major sources of uncertainty in the load forecast are the errors in the day-ahead weather forecast and the variability in temporal patterns of electricity demand that is not explained by weather. We develop a stochastic model for hourly load on a given day, within a segment of similar days, based on a weather forecast available on the previous day. Identification of similar days in the past is based on weather forecasts and temporal load patterns. Trends and error distributions for the load forecasts are approximated by optimizing within a new class of functions specified by a finite number of parameters. Preliminary numerical results are presented based on data corresponding to a U.S. independent system operator. C1 [Feng, Yonghan; Gade, Dinakar; Ryan, Sarah M.] Iowa State Univ, Ames, IA 50011 USA. [Watson, Jean-Paul] Sandia Natl Labs, Albuquerque, NM 20024 USA. [Wets, Roger J-B; Woodruff, David L.] Univ Calif Davis, Davis, CA 95616 USA. RP Feng, YH (reprint author), Iowa State Univ, Ames, IA 50011 USA. EM yhfeng@iastate.edu; dgade@iastate.edu; smryan@iastate.edu; jwatson@sandia.gov; rjbwets@ucdavis.edu; dlwoodruff@ucdavis.edu FU U.S. Department of Energy under the ARPA-E Green Energy Network Integration (GENI); United States Department of Energy's National Nuclear Security Administration [DE-AC04-94-AL85000] FX This material is based on work sponsored by the U.S. Department of Energy under the ARPA-E Green Energy Network Integration (GENI) Program. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energys National Nuclear Security Administration under Contract DE-AC04-94-AL85000. NR 9 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 5 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874301200 ER PT S AU Holttinen, H Milligan, M Ela, E Menemenlis, N Dobschinski, J Rawn, B Bessa, RJ Flynn, D Lazaro, EG Detlefsen, N AF Holttinen, Hannele Milligan, Michael Ela, Erik Menemenlis, Nickie Dobschinski, Jan Rawn, Barry Bessa, Ricardo J. Flynn, Damian Lazaro, Emilio Gomez Detlefsen, Nina GP IEEE TI Methodologies to Determine Operating Reserves due to Increased Wind Power SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE operating reserves; power system operation; power system reliability; power systems; reserve requirements; wind power ID GENERATION; SYSTEMS AB Power systems with high wind penetration experience increased variability and uncertainty, such that determination of the required additional operating reserve is attracting a significant amount of attention and research. This paper presents methods used in recent wind integration analyses and operating practice, with key results that compare different methods or data. Wind integration analysis over the past several years has shown that wind variability need not be seen as a contingency event. The impact of wind will be seen in the reserves for non-event operation (normal operation dealing with deviations from schedules). Wind power will also result in some events of larger variability and large forecast errors that could be categorized as slow events. The level of operating reserve that is induced by wind is not constant during all hours of the year, so that dynamic allocation of reserves will reduce the amount of reserves needed in the system for most hours. The paper concludes with recent emerging trends. C1 [Holttinen, Hannele] VTT Tech Res Ctr Finland, POB 1000, Espoo 02044, Finland. [Milligan, Michael; Ela, Erik] Natl Renewable Energy Lab, Golden, CO 80401 USA. [Menemenlis, Nickie] Hydro Quebec, IREQ, Varennes, PQ J3X 1S1, Canada. [Dobschinski, Jan] Fraunhofer Inst Wind Energy & Energy Syst Technol, IWES, D-34119 Kassel, Germany. [Rawn, Barry] Delft Univ Technol, Dept Elect Sustainable Energy, NL-2628 CD Delft, Netherlands. [Bessa, Ricardo J.] Univ Porto, INESC TEC, Inst Engn Sistemas & Computadores, P-4200465 Oporto, Portugal. [Flynn, Damian] Univ Coll Dublin, Sch Elect Elect & Commun Engn, Dublin 4, Ireland. [Lazaro, Emilio Gomez] Univ Castilla La Mancha, Albacete 02071, Spain. [Detlefsen, Nina] Energinet Dk, DK-7000 Fredericia, Denmark. RP Holttinen, H (reprint author), VTT Tech Res Ctr Finland, POB 1000, Espoo 02044, Finland. EM hannele.holttinen@vtt.fi NR 40 TC 0 Z9 0 U1 1 U2 3 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 10 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874304030 ER PT S AU Jin, SS Huang, Z Diao, RS Wu, D Chen, YS AF Jin, Shuangshuang Huang, Zhenyu (Henry) Diao, Ruisheng Wu, Di Chen, Yousu GP IEEE TI Parallel Implementation of Power System Dynamic Simulation SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE dynamic simulation; differential algebraic equations; high-performance computing; look-ahead; power grid ID TRANSIENT STABILITY SIMULATION; INTEGRATION AB Dynamic simulation of power system transient stability is important for planning, monitoring, operation, and control of electric power systems. However, modeling the system dynamics and network involves the computationally intensive time-domain solution of numerous differential and algebraic equations. This results in a transient stability simulation implementation that does not satisfy the real-time constraints of online dynamic security assessment. This paper presents a parallel implementation of the dynamic simulation on a high-performance computing platform using parallel simulation algorithms and architectures. It enables the simulation to run even faster than real time, enabling the "look-ahead" capability to study pending stability problems in the power grid. C1 [Jin, Shuangshuang; Huang, Zhenyu (Henry); Diao, Ruisheng; Wu, Di; Chen, Yousu] Pacific NW Natl Lab, Seattle, WA 98109 USA. RP Jin, SS (reprint author), Pacific NW Natl Lab, Seattle, WA 98109 USA. EM shuangshuang.jin@pnnl.gov; zhenyu.huang@pnnl.gov; ruisheng.diao@pnnl.gov; di.wu@pnnl.gov; yousu.chen@pnnl.gov NR 21 TC 0 Z9 0 U1 0 U2 1 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 5 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874301201 ER PT S AU Lu, N Diao, RS Hafen, RP Samaan, N Makarov, YV AF Lu, Ning Diao, Ruisheng Hafen, Ryan P. Samaan, Nader Makarov, Yuri V. GP IEEE TI A Comparison of Forecast Error Generators for Modeling Wind and Load Uncertainty SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE load forecast error; stochastic simulation; wind forecast error; wind integration; wind statistics AB This paper presents four algorithms to generate random forecast error time series, including a truncated-normal distribution model, a state-space based Markov model, a seasonal autoregressive moving average (ARMA) model, and a stochastic-optimization based model. The error time series are used to create real-time (RT), hour-ahead (HA), and day-ahead (DA) wind and load forecast time series that statistically match historically observed forecasting data sets, used for variable generation integration studies. A comparison is made using historical DA load forecast and actual load values to generate new sets of DA forecasts with similar stoical forecast error characteristics. This paper discusses and compares the capabilities of each algorithm to preserve the characteristics of the historical forecast data sets. C1 [Lu, Ning] North Carolina State Univ, Dept Elect & Comp Engn, Raleigh, NC 27695 USA. [Diao, Ruisheng; Hafen, Ryan P.; Samaan, Nader; Makarov, Yuri V.] Pacific Northwest Natl Lab, Elect Infrastruct & Bldg Div, Richland, WA USA. RP Lu, N (reprint author), North Carolina State Univ, Dept Elect & Comp Engn, Raleigh, NC 27695 USA. EM Nlu2@ncsu.edu; ruisheng.diao@pnnl.gov; ryan.hafen@pnnl.gov; nader.samaan@pnnl.gov; yuri.makarov@pnnl.gov NR 15 TC 0 Z9 0 U1 1 U2 2 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 5 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874303159 ER PT S AU Mao, RK Li, HJ Xu, Y Li, HS AF Mao, Rukun Li, Huijuan Xu, Yan Li, Husheng GP IEEE TI Wireless Communication for Controlling Microgrids: Co-simulation and Performance Evaluation SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc AB A microgrid with wireless communication links for microgrid control has been designed and developed. The complete simulation model has been developed in MatLab SimuLink with seamless integration of the power subsystem and the communication subsystem. Unlike the conventional co-simulators that usually connect two existing simulators together by creating an interface, which has a steep learning curve, the proposed simulator is a compact single-unit model. Detailed modeling of the power subsystem and communication system is presented as well as the microgrid control architecture and strategies. The impact of different communication system performances on microgrid control has been studied and evaluated in the proposed simulator. The results help identify the cost effective communication solutions for microgrid applications. C1 [Mao, Rukun; Li, Husheng] Univ Tennessee, Dept Elect Engn & Comp Sci, Knoxville, TN 37996 USA. [Xu, Yan] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. [Li, Huijuan] Oak Ridge Associated Univ, Oak Ridge, TN 37831 USA. RP Mao, RK (reprint author), Univ Tennessee, Dept Elect Engn & Comp Sci, Knoxville, TN 37996 USA. FU UT-Battelle, LLC [DE-AC05-000R22725]; U.S. Department of Energy FX This manuscript has been authored by UT-Battelle, LLC, under Contract No. DE-AC05-000R22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a nonexclusive, paid-Up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. NR 6 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 5 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874304019 ER PT S AU Meng, D Zhou, N Lu, S Lin, G AF Meng, Da Zhou, Ning Lu, Shuai Lin, Guang GP IEEE TI An Expectation-Maximization Method for Calibrating Synchronous Machine Models SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE Extended Kalman Filter; EM Algorithms; State Estimation; Parameter Calibration ID MAXIMUM-LIKELIHOOD; GENERATOR AB The accuracy of a power system dynamic model is essential to its secure and efficient operation. Lower confidence in model accuracy usually leads to conservative operation and lowers asset usage. To improve model accuracy, this paper proposes an expectation-maximization (EM) method to calibrate the synchronous machine model using phasor measurement unit (PMU) data. First, an extended Kalman filter (EKF) is applied to estimate the dynamic states using measurement data. Then, the parameters are calculated based on the estimated states using the maximum likelihood estimation (MLE) method. The EM method iterates over the preceding two steps to improve estimation accuracy. The proposed EM method's performance is evaluated using a single-machine infinite bus system and compared with a method where both state and parameters are estimated using an EKF method. Sensitivity studies of the parameter calibration using the EM method also are presented to show the robustness of the proposed method for different levels of measurement noise and initial parameter uncertainty. C1 [Meng, Da; Zhou, Ning; Lu, Shuai; Lin, Guang] PNNL, Richland, WA 99354 USA. RP Meng, D (reprint author), PNNL, Richland, WA 99354 USA. EM da.meng@pnnl.gov; ning.zhou@pnnl.gov; Shuai.lu@pnnl.gov; guang.lin@pnnl.gov NR 17 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 5 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874303131 ER PT S AU Neely, JC Byrne, RH Elliott, RT Silva-Monroy, CA Schoenwald, DA Trudnowski, DJ Donnelly, MK AF Neely, Jason C. Byrne, Raymond H. Elliott, Ryan T. Silva-Monroy, Cesar A. Schoenwald, David A. Trudnowski, Daniel J. Donnelly, Matthew K. GP IEEE TI Damping of Inter-area Oscillations using Energy Storage SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE Inter-area oscillations; WECC; energy storage applications; damping control AB Low frequency inter-area oscillations have been identified as a significant problem in utility systems due to the potential for system damage and the resulting restrictions on power transmission over select lines. Previous research has identified real power injection by energy storage based damping control nodes as a promising approach to mitigate inter-area oscillations. In this paper, a candidate energy storage system based on UltraCapacitor technology is evaluated for damping control applications in the Western Electric Coordinating Council (WECC), and an analytical method for ensuring proper stability margins is also presented for inclusion in a future supervisory control algorithm. Dynamic simulations of the WECC were performed to validate the expected system performance. Finally, the Nyquist stability criteria was employed to derive safe operating regions in the gain, time delay space for a simple two-area system to provide guaranteed margins of stability. C1 [Neely, Jason C.; Byrne, Raymond H.; Elliott, Ryan T.; Silva-Monroy, Cesar A.; Schoenwald, David A.] Sandia Natl Labs, Albuquerque, NM 87123 USA. [Trudnowski, Daniel J.; Donnelly, Matthew K.] Montana Tech Univ, Elect Engn Dept, Butte, MT 59701 USA. RP Neely, JC (reprint author), Sandia Natl Labs, Albuquerque, NM 87123 USA. EM jneely@sandia.gov FU U.S.Department of Energy's National Nuclear Security Administration [DE-AC04-94AL85000] FX The research was performed with funding provided by the DOE Energy Storage Program managed by Dr. Imre Gyuk of the DOE Office of Electricity Delivery and Energy Reliability. We thank Dr. Gyuk for his support and guidance on this effort. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energys National Nuclear Security Administration, under contract DE-AC04-94AL85000. NR 10 TC 0 Z9 0 U1 0 U2 1 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 5 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874302174 ER PT S AU Rice, M Huang, ZY Chen, YS Allwardt, C Mackey, P AF Rice, Mark Huang, Zhenyu Chen, Yousu Allwardt, Craig Mackey, Patrick GP IEEE TI Alleviating Contingency Violations through Visual Analytics and Suggested Actions SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE Contingency Analysis; Operator Actions; Situational Awareness; Decision Support AB Contingency analysis (CA) is essential in maintaining a stable and secure power grid. Operating standards require that contingency violations are alleviated within 30 minutes. In today's practice, operators normally make decisions based on the information they have with limited support. This paper presents a new feature of suggested actions integrated in the graphical contingency analysis (GCA) tool, developed by the authors to help the operator's decision making process. This paper provides a few examples on showing how the decision support element of the GCA tool is further enhanced by this new feature to alleviate contingency violations for better grid reliability. C1 [Rice, Mark; Huang, Zhenyu; Allwardt, Craig; Mackey, Patrick] Pacific NW Natl Lab, Richland, WA 99354 USA. [Chen, Yousu] Seattle Biomed Res Inst, Seattle, WA 98109 USA. RP Rice, M (reprint author), Pacific NW Natl Lab, Richland, WA 99354 USA. EM mark.rice@pnnl.gov; zhenyu.huang@pnnl.gov; yousu.chen@pnnl.gov; craig.allwardt@pnnl.gov; patrick.mackey@pnnl.gov FU U.S. Department of Energy (DOE); Advanced Grid Modeling; Gil Bindewald; Pacific Northwest National Laboratory (PNNL); DOE [DE-AC05-76RL01830] FX This work is supported by the U.S. Department of Energy (DOE) through its Advanced Grid Modeling Program managed by Gil Bindewald. Pacific Northwest National Laboratory (PNNL) is operated by Battelle for the DOE under Contract DE-AC05-76RL01830. NR 10 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 5 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874302137 ER PT S AU Ryan, SM Wets, RJB Woodruff, DL Silva-Monroy, C Watson, JP AF Ryan, Sarah M. Wets, Roger J. -B. Woodruff, David L. Silva-Monroy, Cesar Watson, Jean-Paul GP IEEE TI Toward Scalable, Parallel Progressive Hedging for Stochastic Unit Commitment SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE Computation time; Optimization methods; Parallel algorithms; Power generation scheduling; Wind energy AB Given increasing penetration of variable generation units, there is significant interest in the power systems research community concerning the development of solution techniques that directly address the stochasticity of these sources in the unit commitment problem. Unfortunately, despite significant attention from the research community, stochastic unit commitment solvers have not made their way into practice, due in large part to the computational difficulty of the problem. In this paper, we address this issue, and focus on the development of a decomposition scheme based on the progressive hedging algorithm of Rockafellar and Wets. Our focus is on achieving solve times that are consistent with the requirements of ISO and utilities, on modest-scale instances, using reasonable numbers of scenarios. Further, we make use of modest-scale parallel computing, representing capabilities either presently deployed, or easily deployed in the near future. We demonstrate our progress to date on a test instance representing a simplified version of the US western interconnect (WECC-240). C1 [Ryan, Sarah M.] Iowa State Univ, Ames, IA 50011 USA. [Wets, Roger J. -B.; Woodruff, David L.] Univ Calif Davis, Davis, CA 95616 USA. [Silva-Monroy, Cesar; Watson, Jean-Paul] Sandia Natl Labs, Albuquerque, NM 87123 USA. RP Ryan, SM (reprint author), Iowa State Univ, Ames, IA 50011 USA. EM smryan@iastate.edu; dlwoodruff@ucdavis.edu; rjbwets@ucdavis.edu; casilv@sandia.gov; jwatson@sandia.gov FU US Department of Energy's ARPA-e Green Energy Network Integration (GENI); Sandia Corporation [DE-AC04-94-AL85000] FX This research was sponsored by the US Department of Energys ARPA-e Green Energy Network Integration (GENI) program. Sandia is a multi-program laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energys National Nuclear Security Administration under Contract DE-AC04-94-AL85000. NR 14 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 5 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874303191 ER PT S AU Schoene, J Zheglov, V Houseman, D Smith, JC Ellis, A AF Schoene, Jens Zheglov, Vadim Houseman, Douglas Smith, J. Charles Ellis, Abraham GP IEEE TI Photovoltaics in Distribution Systems - Integration Issues and Simulation Challenges SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE photovoltaics; integration; distribution systems AB High penetration of PVs in distribution systems can causes a number of issues on the system. Determining whether or not an issue exists for a given distribution circuit with PV is a non-trivial task. Accurate knowledge regarding the conditions under which issues can be positively ruled out would be immensely beneficial for solar projects as this would eliminate the need for a costly and time-consuming system impact study. In this paper, we focus on the challenges associated with evaluating the types of systems for which potential PV related problems turn into actual problems. In this context, we summarize utility experiences with PV on their system as discussed during UVIG meetings and reported in the pertinent literature. Furthermore, we present simulation results of a PV integration study we conducted for CEATI and discuss the implications of simulation challenges and simplifying assumption often associated with these types of studies. C1 [Schoene, Jens; Zheglov, Vadim; Houseman, Douglas] EnerNex, Knoxville, TN 37932 USA. [Smith, J. Charles] UVIG, Kitty Hawk, TN 37932 USA. [Ellis, Abraham] Sandia Natl Labs, Albuquerque, NM USA. RP Schoene, J (reprint author), EnerNex, Knoxville, TN 37932 USA. EM jens@enemex.com; Charlie@uwig.org; aellis@sandia.gov FU Centre for Energy Advancement through Technological Innovation (CEATI) FX The simulation results presented in this paper have been sponsored by the Centre for Energy Advancement through Technological Innovation (CEATI) NR 11 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 5 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874303065 ER PT S AU Silva-Monroy, C Neely, J Byrne, R Elliott, R Schoenwald, D AF Silva-Monroy, Cesar Neely, Jason Byrne, Raymond Elliott, Ryan Schoenwald, David GP IEEE TI Wind Generation Controls for Damping of Inter-area Oscillations SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE Control systems; Energy Storage; Interconnected power systems; Power system stability; Wind energy ID INERTIA AB Inter-area oscillations are one of the factors that limit transmission capacity in large interconnected systems. In this paper we investigate the effects of increasing wind generation on inter-area modes and propose the use of additional control schemes for wind plants for mitigation of inter-area oscillations. Control schemes include droop control and inertial emulation, which are originally aimed at improving transient stability. The sensitivities of inter-area modes to droop control and inertial emulation gains are identified. Implementation of suggested controls schemes via collocated energy storage devices is also explored. C1 [Silva-Monroy, Cesar; Neely, Jason; Byrne, Raymond; Elliott, Ryan; Schoenwald, David] Sandia Natl Labs, Energy Storage & Transmiss Anal Dept, Albuquerque, NM 87185 USA. RP Silva-Monroy, C (reprint author), Sandia Natl Labs, Energy Storage & Transmiss Anal Dept, POB 5800, Albuquerque, NM 87185 USA. EM casilv@sandia.gov NR 12 TC 0 Z9 0 U1 1 U2 1 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 5 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874301199 ER PT S AU Singhvi, V Pourbeik, P Bhatt, N Brooks, D Zhang, YC Gevorgian, V Ela, E Clark, K AF Singhvi, Vikas Pourbeik, Pouyan Bhatt, Navin Brooks, Daniel Zhang, Yingchen Gevorgian, Vahan Ela, Erik Clark, Kara GP IEEE TI Impact of Wind Active Power Control Strategies on Frequency Response of an InterconnectionYYYYY SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE Wind Generation; Primary Frequency response; Active Power Control; Inertial Control; Primary Frequency Control AB High penetrations of variable generation presents challenges for reliable operation of the power system. Ensuring adequate primary frequency response is one such concern as the generation mix changes with increasing penetration of variable generation and planned retirements of fossil-fired generation. However, inverter-coupled wind generation is capable of contributing to primary frequency response. The focus of the simulation work presented in this paper is to assess the impact of active power control strategies of wind generation on the primary frequency response of an interconnection. All simulations were conducted using the General Electric (GE) PSLF (R) simulation tool. The base case utilized was developed from the Western Electricity Coordinating Council (WECC) Transmission Expansion Planning Policy Committee (TEPPC) 2022 case with light spring load conditions with approximately 15% wind penetration. The 20, 30 and 40% wind penetration study cases were derived from the base case by strategically replacing thermal units throughout the WECC regions with wind generation. The results presented here are intended to develop a broad understanding of potential impact of changing generation mix and wind generation active power controls on the primary frequency response of an interconnection. The results are not intended to represent actual performance of the WECC since simplifying assumptions are used to serve the study purpose. C1 [Singhvi, Vikas; Pourbeik, Pouyan; Bhatt, Navin; Brooks, Daniel] Elect Power Res Inst, Knoxville, TN 37932 USA. [Zhang, Yingchen; Gevorgian, Vahan; Ela, Erik; Clark, Kara] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Singhvi, V (reprint author), Elect Power Res Inst, Knoxville, TN 37932 USA. NR 12 TC 0 Z9 0 U1 0 U2 2 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 5 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874303054 ER PT S AU Top, P Breneman, J AF Top, Philip Breneman, John GP IEEE TI Compressing Phasor Measurement Data SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE PMU; compression; szip; syncrhophasors AB Phasor Measurement units (PMU's) are becoming standard equipment in electrical grids around the world. They are capable of generating a significant amount of data on a continuous basis from distribution and transmission networks. Several months of data from 2 PMU's situated on a distribution network were captured in raw format. This data was separated by measurement type and compressed using a number of standard compression algorithms. The results show the compressibility of PMU data for these algorithms and are used to estimate the space requirements for storing a day of data from a single PMU. C1 [Top, Philip; Breneman, John] Lawrence Livermore Natl Lab, Dept Engn, Livermore, CA 94550 USA. RP Top, P (reprint author), Lawrence Livermore Natl Lab, Dept Engn, Livermore, CA 94550 USA. NR 11 TC 0 Z9 0 U1 0 U2 2 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 4 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874301113 ER PT S AU Vlachopoulou, M Ferryman, T Zhou, N Tong, JZ AF Vlachopoulou, Maria Ferryman, Tom Zhou, Ning Tong, Jianzhong GP IEEE TI A Stepwise Regression Method for Forecasting Net Interchange Schedule SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE explanatory variables; net interchange schedule; power grid operations; statistical significance; stepwise regression AB The net interchange schedule (NIS) is the sum of the transactions (MW) between an Independent System Operator (ISO)/Regional Transmission Organization (RTO) and its neighbors. Effective forecasting of the submitted NIS can improve grid operation efficiency. This paper presents a stepwise regression method for forecasting NIS. The stepwise regression method uses significance analysis to identify the most influential explanatory variables. Identifying the most influential explanatory variables can reduce model order and lead to better and faster prognostics. The performance of the stepwise regression method is evaluated using the field measurement data from PJM Interconnection (RTO). C1 [Vlachopoulou, Maria; Ferryman, Tom; Zhou, Ning] Pacific NW Natl Lab, Richland, WA 99352 USA. [Tong, Jianzhong] PJM Interconnet RTO, Maryville, MO USA. RP Vlachopoulou, M (reprint author), Pacific NW Natl Lab, Richland, WA 99352 USA. EM maria.vlachopoulou@pnnl.gov FU Laboratory Directed Research and Development funds from the Pacific Northwest National Laboratory; U. S. Department of Energy [DE-AC05-76RL01830] FX This work was supported by Laboratory Directed Research and Development funds from the Pacific Northwest National Laboratory. The Pacific Northwest National Laboratory is operated by Battelle for the U. S. Department of Energy under Contract DE-AC05-76RL01830. NR 11 TC 0 Z9 0 U1 0 U2 1 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 5 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874302162 ER PT S AU Vlachopoulou, M Gosink, L Pulsipher, TC Ferryman, T Zhou, N Tong, JZ AF Vlachopoulou, Maria Gosink, Luke Pulsipher, Trenton C. Ferryman, Tom Zhou, Ning Tong, Jianzhong GP IEEE TI An Ensemble Approach for Forecasting Net Interchange Schedule SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE Bayesian model averaging; ensemble approach; forecasting; net interchange schedule; power grid operations ID ARTIFICIAL NEURAL-NETWORKS; MODEL; REGRESSION AB The net interchange schedule (NIS) is the sum of the transactions (MW) between an Independent System Operator/Regional Transmission Organization (ISO/RTO) and its neighbors. Effective forecasting of the submitted NIS can improve grid operation efficiency. This paper applies a Bayesian model averaging (BMA) technique to forecast submitted NIS. As an ensemble approach, the BMA method aggregates different forecasting models in order to improve forecasting accuracy and consistency. In this study, the BMA method is compared to two alternative approaches: a stepwise regression method and an artificial neural network (ANN) trained for NIS forecasting. In our comparative analysis, we use field measurement data from the PJM Interconnection RTO to train and test each method. Our preliminary results indicate that ensemble-based methods can provide more accurate and consistent NIS forecasts in comparison to non-ensemble alternate methods. C1 [Vlachopoulou, Maria; Gosink, Luke; Pulsipher, Trenton C.; Ferryman, Tom; Zhou, Ning] Pacific NW Natl Lab, Richland, WA 99352 USA. [Tong, Jianzhong] PJM Interconnect RTO, Maryville, MO USA. RP Vlachopoulou, M (reprint author), Pacific NW Natl Lab, Richland, WA 99352 USA. EM maria.vlachopoulou@pnnl.gov FU Laboratory Directed Research and Development funds from the Pacific Northwest National Laboratory; U. S. Department of Energy [DE-AC05-76RL01830] FX This work was supported by Laboratory Directed Research and Development funds from the Pacific Northwest National Laboratory. The Pacific Northwest National Laboratory is operated by Battelle for the U. S. Department of Energy under Contract DE-AC05-76RL01830. NR 20 TC 0 Z9 0 U1 1 U2 1 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 5 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874302159 ER PT S AU Zhou, N Pierre, J Trudnowski, D AF Zhou, Ning Pierre, John Trudnowski, Daniel GP IEEE TI Some Considerations in Using Prony Analysis to Estimate Electromechanical Modes SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE least squares method; oscillation modes; phasor measurement unit (PMU); Prony analysis; singular value decomposition; total least squares method ID LINEAR PREDICTION; FREQUENCY; SINUSOIDS AB Prony analysis has been used to estimate oscillation modes from ringdown responses in a power grid. When applying Prony analysis, several factors must be considered to estimate the modes accurately. In this paper, a general prediction model is proposed for the Prony analysis. The influence of decimation factors, model orders, and linear solvers on estimation accuracy is studied using the Monte Carlo method with a goal of providing a reference for applying Prony analysis to estimate electromechanical modes. C1 [Zhou, Ning] Pacific NW Natl Lab, Richland, WA 99352 USA. [Pierre, John] Univ Wyoming, Laramie, WY 82071 USA. [Trudnowski, Daniel] Univ Montana, Missoula, MT 59812 USA. RP Zhou, N (reprint author), Pacific NW Natl Lab, Richland, WA 99352 USA. EM ning.zhou@pnnl.gov; pierre@uwyo.edu; dtrudnowski@mtech.edu FU U.S. Department of Energy (DOE) [DE-AC05-76RL01830] FX This paper was prepared as a result of work sponsored by the U.S. Department of Energy (DOE) through its Transmission Reliability Program. Pacific Northwest National Laboratory (PNNL) is operated by Battelle for DOE under contract DE-AC05-76RL01830. NR 14 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 5 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874303072 ER PT S AU Zhou, N AF Zhou, Ning GP IEEE TI A Coherence Method for Detecting and Analyzing Oscillations SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE coherence; power spectral density; phasor measurement unit (PMU); oscillations; power system dynamics ID ELECTROMECHANICAL OSCILLATIONS; POWER-SYSTEMS; IDENTIFICATION AB In this paper, a coherence method is proposed to detect and analyze forced oscillations from phasor measurement unit data. The calculation of coherence spectrum is reviewed, and forced oscillations are related to the peaks in the coherence spectrum. Using simulation and field measurement data, the proposed coherence method's performance is compared with the power spectral density method. When applied to detect and analyze forced oscillations under low signal noise ratio conditions, the proposed coherence method shows better performance. C1 Pacific NW Natl Lab, Richland, WA 99352 USA. RP Zhou, N (reprint author), Pacific NW Natl Lab, Richland, WA 99352 USA. EM ning.zhou@punl.gov NR 15 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 5 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874301073 ER PT S AU Zhou, Z Botterud, A AF Zhou, Zhi Botterud, Audun GP IEEE TI Price Responsive Demand for Operating Reserves and Energy in Electricity Markets with Wind Power SO 2013 IEEE POWER AND ENERGY SOCIETY GENERAL MEETING (PES) SE IEEE Power and Energy Society General Meeting PESGM LA English DT Proceedings Paper CT General Meeting of the IEEE-Power-and-Energy-Society (PES) CY JUL 21-25, 2013 CL Vancouver, CANADA SP IEEE Power & Energy Soc DE Demand response; operating reserves; electricity markets; wind power; forecast uncertainty AB Similar to demand response for energy, operating reserve can be elastic to prices given that minimal reliability criteria are satisfied. We present a probabilistic-based framework to estimate a demand curve for operating reserves. The operating reserve is estimated accounting for uncertainties from load, thermal unit contingencies, and wind power. The resulting demand for reserves is dynamically scheduled and co-optimized with energy in the market clearing. In a case study, the framework is applied to a two-settlement electricity market with centralized unit commitment, also considering demand response for energy. We find that the proposed demand curve for operating reserves contributes to improved handling of system uncertainties and more efficient pricing of operating reserves. Price elastic demand for energy has a similar effect on dispatch flexibility and cost, but has a less significant impact on the prices for spinning reserves. C1 [Zhou, Zhi; Botterud, Audun] Argonne Natl Lab, Decis & Informat Sci Div, Argonne, IL 60439 USA. RP Zhou, Z (reprint author), Argonne Natl Lab, Decis & Informat Sci Div, 9700 S Cass Ave, Argonne, IL 60439 USA. EM zzhou@anl.gov; abotterud@anl.gov NR 19 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1944-9925 BN 978-1-4799-1303-9 J9 IEEE POW ENER SOC GE PY 2013 PG 5 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA BA0LX UT WOS:000331874303195 ER PT S AU Cartes, D Chow, JH McCaugherty, D Widergren, S Venayagamoorthy, GK AF Cartes, David Chow, Joe H. McCaugherty, Dan Widergren, Steve Venayagamoorthy, G. Kumar GP IEEE TI The IEEE Computer Society Smart Grid Vision Project Opens Opportunites for Computational Intelligence SO PROCEEDINGS OF THE 2013 IEEE CONFERENCE ON EVOLVING AND ADAPTIVE INTELLIGENT SYSTEMS (EAIS) SE IEEE Conference on Evolving and Adaptive Intelligence Systems LA English DT Proceedings Paper CT IEEE Conference on Evolving and Adaptive Intelligent Systems (EAIS) CY APR 16-19, 2013 CL Singapore, SINGAPORE SP IEEE, IEEE Computat Intelligence Soc, Adapt & Evolving Fuzzy Syst Task Force, FSTC, CIS DE Adaptive critics; computers; computational intelligence; intelligent multi-agents; smart grid ID RENEWABLE ENERGY-SOURCES; COMMUNICATION; VEHICLES; BEHAVIOR; SYSTEMS; NETWORKS; COST AB The IEEE Computer Society Smart Grid Vision Project (CS-SGVP) was chartered to develop Smart Grid visions looking forward as far as 30 years into the future. At the completion of the project it was realized that to address the complexity of a Smart Grid with vast numbers of intelligent connected devices and systems, computational intelligence techniques must move from top-down to the lowest levels of architectures, with interactive cooperation between smart components, each with a level of autonomy. The CS-SGVP team emphasized creative thought leadership and "blue sky" thinking to identify future Smart Grid operational visions and the role of computing to achieve these visions. The CS-SGVP team developed its visions using a three-tiered approach. Architectural concepts describe Smart Grid goals and characteristics, general grid types, as well as computing concepts considered common across grid types. Functional concepts describe how the grid will operate. Technological concepts describe the roles of certain technologies within the Smart Grid. The CS-SGVP expects that over the course of many years, various visions will come to fruition. C1 [Cartes, David] Florida State Univ, Tallahassee, FL 32310 USA. [Chow, Joe H.] Rensselaer Polytech Inst, Troy, NY 12180 USA. [McCaugherty, Dan] Athena Sci Corp, Fairmont, WV 26554 USA. [Widergren, Steve] Pacific NW Natl Lab, Richland, WA 99352 USA. [Venayagamoorthy, G. Kumar] Clemson Univ, Clemson, SC 29631 USA. RP Cartes, D (reprint author), Florida State Univ, Tallahassee, FL 32310 USA. EM dave@eng.fsu.edu; chowj@rpi.edu; dan@athenasciences.com; Steve.widegren@pnnl.gov; gkumar@ieee.org NR 93 TC 0 Z9 0 U1 0 U2 1 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 2330-4863 BN 978-1-4673-5855-2 J9 IEEE CONF EVOL ADAPT PY 2013 BP 144 EP 150 PG 7 WC Computer Science, Artificial Intelligence; Computer Science, Information Systems SC Computer Science GA BA1HA UT WOS:000332538400020 ER PT S AU Boman, EG Wolf, MM AF Boman, Erik G. Wolf, Michael M. GP IEEE TI A Nested Dissection Partitioning Method for Parallel Sparse Matrix-Vector Multiplication SO 2013 IEEE CONFERENCE ON HIGH PERFORMANCE EXTREME COMPUTING (HPEC) SE IEEE High Performance Extreme Computing Conference LA English DT Proceedings Paper CT IEEE Conference on High Performance Extreme Computing (HPEC) CY SEP 10-12, 2013 CL Waltham, MA SP IEEE AB We consider how to map sparse matrices across processes to reduce communication costs in parallel sparse matrix-vector multiplication, an ubiquitous kernel in high performance computing. Our main contributions are: (i) an exact graph model for communication with general (two-dimensional) matrix distribution, and (ii) a recursive partitioning algorithm based on nested dissection that approximately solves this model. We have implemented our algorithm using hypergraph partitioning software to enable a fair comparison with existing methods. We present partitioning results for sparse structurally symmetric matrices from several application areas. Our new method is competitive with the best 2D algorithm (fine-grain hypergraph model) in terms of communication volume, but requires fewer messages. The nested dissection method is almost as fast to compute as 1D methods and the communication volume is significantly reduced (up to 97%) compared to 1D layout. Further improvements in quality may be possible by small modifications to existing nested dissection ordering software. C1 [Boman, Erik G.; Wolf, Michael M.] Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Boman, EG (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87185 USA. EM egboman@sandia.gov; michael.wolf@ll.mit.edu NR 22 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 2377-6943 BN 978-1-4799-1365-7; 978-1-4799-1364-0 J9 IEEE HIGH PERF EXTR PY 2013 PG 6 WC Computer Science, Hardware & Architecture; Computer Science, Theory & Methods SC Computer Science GA BA0SQ UT WOS:000332186600018 ER PT S AU Mattson, T Bader, D Berry, J Buluc, A Dongarra, J Faloutsos, C Feo, J Gilbert, J Gonzalez, J Hendrickson, B Kepner, J Leiserson, C Lumsdaine, A Padua, D Poole, S Reinhardt, S Stonebraker, M Wallach, S Yoo, A AF Mattson, Tim Bader, David Berry, Jon Buluc, Aydin Dongarra, Jack Faloutsos, Christos Feo, John Gilbert, John Gonzalez, Joseph Hendrickson, Bruce Kepner, Jeremy Leiserson, Charles Lumsdaine, Andrew Padua, David Poole, Stephen Reinhardt, Steve Stonebraker, Mike Wallach, Steve Yoo, Andrew GP IEEE TI Standards for Graph Algorithm Primitives SO 2013 IEEE CONFERENCE ON HIGH PERFORMANCE EXTREME COMPUTING (HPEC) SE IEEE High Performance Extreme Computing Conference LA English DT Proceedings Paper CT IEEE Conference on High Performance Extreme Computing (HPEC) CY SEP 10-12, 2013 CL Waltham, MA SP IEEE DE component; Graphs; Algorithms; Linear Algebra; Software Standards AB It is our view that the state of the art in constructing a large collection of graph algorithms in terms of linear algebraic operations is mature enough to support the emergence of a standard set of primitive building blocks. This paper is a position paper defining the problem and announcing our intention to launch an open effort to define this standard. C1 [Mattson, Tim] Intel Corp, Santa Clara, CA 95051 USA. [Bader, David] Georgia Inst Technol, Atlanta, GA 30332 USA. [Berry, Jon; Hendrickson, Bruce] Sandia Natl Labs, Albuquerque, NM 87123 USA. [Buluc, Aydin] Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. [Dongarra, Jack] Univ Tennessee, Knoxville, TN 37996 USA. [Faloutsos, Christos] Carnegie Mellon Univ, Pittsburgh, PA 15213 USA. [Feo, John] Pacific NW Natl Lab, Richland, WA 99354 USA. [Gilbert, John] Univ Calif Santa Barbara, Santa Barbara, CA 93106 USA. [Gonzalez, Joseph] Univ Calif Berkeley, Berkeley, CA 94720 USA. [Kepner, Jeremy; Leiserson, Charles; Stonebraker, Mike] MIT, Cambridge, MA 02139 USA. [Lumsdaine, Andrew] Indiana Univ, Bloomington, IN 47405 USA. [Padua, David] Univ Illinois, Urbana, IL 61801 USA. [Poole, Stephen] Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. [Reinhardt, Steve; Wallach, Steve] Cray Corp, Seattle, WA 98164 USA. [Yoo, Andrew] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. RP Mattson, T (reprint author), Intel Corp, Santa Clara, CA 95051 USA. RI Dongarra, Jack/E-3987-2014 NR 4 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 2377-6943 BN 978-1-4799-1365-7; 978-1-4799-1364-0 J9 IEEE HIGH PERF EXTR PY 2013 PG 2 WC Computer Science, Hardware & Architecture; Computer Science, Theory & Methods SC Computer Science GA BA0SQ UT WOS:000332186600023 ER PT S AU Zhang, GN Lu, D Ye, M Gunzburger, M Webster, C AF Zhang, Guannan Lu, Dan Ye, Ming Gunzburger, Max Webster, Clayton BE Simos, T Psihoyios, G Tsitouras, C TI An Efficient Surrogate Modeling Approach in Bayesian Uncertainty Analysis SO 11TH INTERNATIONAL CONFERENCE OF NUMERICAL ANALYSIS AND APPLIED MATHEMATICS 2013, PTS 1 AND 2 (ICNAAM 2013) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th International Conference of Numerical Analysis and Applied Mathematics (ICNAAM) CY SEP 21-27, 2013 CL GREECE SP European Soc Computat Methods Sci, Engn & Technol, Santilli Fdn DE Uncertainty quantification; Bayesian inference; sparse grids; importance sampling ID SPARSE GRIDS AB We develop an efficient sparse-grid Bayesian approach for quantifying parametric and predictive uncertainties of physical systems constrained by stochastic PDEs. An accurate surrogate posterior distribution is constructed using sparse-grid interpolation and integration. It improves the simulation efficiency by accelerating the evaluation of the posterior distribution without losing much accuracy, and by determining an appropriate importance density for importance sampling which is easily sampled and captures the main features of the exact posterior distribution. C1 [Zhang, Guannan; Webster, Clayton] Oak Ridge Natl Lab, Comp Sci & Math Div, Oak Ridge, TN 37831 USA. [Lu, Dan; Ye, Ming; Gunzburger, Max] Florida State Univ, Dept Sci Comp, Tallahassee, FL 32306 USA. RP Zhang, GN (reprint author), Oak Ridge Natl Lab, Comp Sci & Math Div, Oak Ridge, TN 37831 USA. OI Webster, Clayton/0000-0002-1375-0359; Zhang, Guannan/0000-0001-7256-150X NR 8 TC 0 Z9 0 U1 0 U2 3 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1185-2 J9 AIP CONF PROC PY 2013 VL 1558 BP 898 EP 901 DI 10.1063/1.4825643 PG 4 WC Mathematics, Applied; Physics, Applied SC Mathematics; Physics GA BA0IB UT WOS:000331472800213 ER PT S AU Archibald, R AF Archibald, Rick BE Simos, T Psihoyios, G Tsitouras, C TI Error Estimation in High Dimensional Space for Stochastic Collocation Methods on Arbitrary Sparse Samples SO 11TH INTERNATIONAL CONFERENCE OF NUMERICAL ANALYSIS AND APPLIED MATHEMATICS 2013, PTS 1 AND 2 (ICNAAM 2013) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th International Conference of Numerical Analysis and Applied Mathematics (ICNAAM) CY SEP 21-27, 2013 CL GREECE SP European Soc Computat Methods Sci, Engn & Technol, Santilli Fdn DE Uncertainty quantification; sampling ID PARTIAL-DIFFERENTIAL-EQUATIONS; RANDOM INPUT DATA; INTERPOLATION; CALIBRATION AB We have develop a fast method that can give high order error estimates of piecewise smooth functions in high dimensions with high order and low computational cost. This method can be used polynomial annihilation to estimate the smoothness of local regions of arbitrary samples in annihilation stochastic simulations. We compare the error estimation of this method to gaussian process error estimation techniques. C1 Oak Ridge Natl Lab, Comp Sci & Math Div, Oak Ridge, TN 37831 USA. RP Archibald, R (reprint author), Oak Ridge Natl Lab, Comp Sci & Math Div, Oak Ridge, TN 37831 USA. RI Archibald, Rick/I-6238-2016 OI Archibald, Rick/0000-0002-4538-9780 NR 12 TC 0 Z9 0 U1 0 U2 1 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1185-2 J9 AIP CONF PROC PY 2013 VL 1558 BP 906 EP 909 DI 10.1063/1.4825645 PG 4 WC Mathematics, Applied; Physics, Applied SC Mathematics; Physics GA BA0IB UT WOS:000331472800215 ER PT S AU Rupp, K Tillet, P Smith, BF Grasser, T Jungel, A AF Rupp, K. Tillet, Ph Smith, B. F. Grasser, T. Juengel, A. BE Simos, T Psihoyios, G Tsitouras, C TI A Note on the GPU Acceleration of Eigenvalue Computations SO 11TH INTERNATIONAL CONFERENCE OF NUMERICAL ANALYSIS AND APPLIED MATHEMATICS 2013, PTS 1 AND 2 (ICNAAM 2013) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th International Conference of Numerical Analysis and Applied Mathematics (ICNAAM) CY SEP 21-27, 2013 CL GREECE SP European Soc Computat Methods Sci, Engn & Technol, Santilli Fdn DE Linear Algebra; Eigenvalues; Krylov methods; GPU; CUDA; OpenCL; ViennaCL; PETSc; SLEPc AB Eigenvalue computations for large sparse matrices such as the Lanczos method are commonly based on Krylov subspace techniques. One of the dominant operations in such algorithms are iterated computations of inner products with the same vector in order to preserve orthogonality of the Krylov basis. These operations can be accelerated by existing BLAS functionality using GPUs. However, this is not fully efficient due to unnecessary memory transfers. We present improved implementations in CUDA and OpenCL, which are now available in ViennaCL, PETSc and SLEPc, and demonstrate an up to two-fold performance gain over existing GPU vendor libraries. C1 [Rupp, K.; Smith, B. F.] Argonne Natl Lab, 9700 S Cass Ave, Argonne, IL 60439 USA. [Rupp, K.; Juengel, A.] Vienna Univ Technol, Inst Anal & Sci Comp, A-1040 Vienna, Austria. [Tillet, Ph] Natl Chiao Tung Univ, Inst Elect & Comp Engn, Hsinchu 300, Taiwan. [Grasser, T.] Vienna Univ Technol, Inst Microelect, A-1040 Vienna, Austria. RP Rupp, K (reprint author), Argonne Natl Lab, 9700 S Cass Ave, Argonne, IL 60439 USA. FU Austrian Science Fund (FWF), [P23598]; FASTMath SciDAC Institute FX This work has been partially supported by the Austrian Science Fund (FWF), grant P23598, and the FASTMath SciDAC Institute. K. Rupp wishes to thank Paul Mullowney and Jose E. Roman for quick performance feedback on early versions of the implementations. NR 11 TC 1 Z9 1 U1 0 U2 2 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1185-2 J9 AIP CONF PROC PY 2013 VL 1558 BP 1536 EP 1539 DI 10.1063/1.4825816 PG 4 WC Mathematics, Applied; Physics, Applied SC Mathematics; Physics GA BA0IB UT WOS:000331472800363 ER PT S AU Liu, J AF Liu, Jun BE Simos, T Psihoyios, G Tsitouras, C TI Data Driven Analytic Continuation for One Particle Spectral Functions SO 11TH INTERNATIONAL CONFERENCE OF NUMERICAL ANALYSIS AND APPLIED MATHEMATICS 2013, PTS 1 AND 2 (ICNAAM 2013) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th International Conference of Numerical Analysis and Applied Mathematics (ICNAAM) CY SEP 21-27, 2013 CL GREECE SP European Soc Computat Methods Sci, Engn & Technol, Santilli Fdn DE one-particle spectral function; temperature Green function; imaginary time Green function; non-negative least square fit (NNLS); Tikhonov regularization; Pade approximant; global minimization; inverse problem ID QUANTUM MONTE-CARLO AB In this proceeding, an idea is outlined suggesting a generic treatment on any type of input data for a numerical analytic continuation problem, which is needed when dynamical information is to be extracted from a calculationally convenient one particle imaginary time Green function. The quality of the resulting spectral function will rely only on the data to be treated, viz, data-driven. This is different from the Maximum Entropy or the Stochastic method which relies on an entropy term to guide convergence of the resulting spectral function. C1 Iowa State Univ, Ames Lab DOE, Ames, IA 50010 USA. RP Liu, J (reprint author), Iowa State Univ, Ames Lab DOE, Ames, IA 50010 USA. RI Liu, Jun/F-1240-2014 NR 14 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1185-2 J9 AIP CONF PROC PY 2013 VL 1558 BP 1827 EP 1830 DI 10.1063/1.4825883 PG 4 WC Mathematics, Applied; Physics, Applied SC Mathematics; Physics GA BA0IB UT WOS:000331472800422 ER PT S AU Wu, Y Bamgbade, BA Burgess, WA Tapriyal, D Baled, HO Enick, RM McHugh, MA AF Wu, Yue Bamgbade, Babatunde A. Burgess, Ward A. Tapriyal, Deepak Baled, Hseen O. Enick, Robert M. McHugh, Mark A. BE Simos, T Psihoyios, G Tsitouras, C TI Equation of State Density Models for Hydrocarbons in Ultradeep Reservoirs at Extreme Temperature and Pressure Conditions SO 11TH INTERNATIONAL CONFERENCE OF NUMERICAL ANALYSIS AND APPLIED MATHEMATICS 2013, PTS 1 AND 2 (ICNAAM 2013) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th International Conference of Numerical Analysis and Applied Mathematics (ICNAAM) CY SEP 21-27, 2013 CL GREECE SP European Soc Computat Methods Sci, Engn & Technol, Santilli Fdn DE equation of state; high pressure; Peng-Robinson; volume-translated; PC-SAFT ID PERTURBED-CHAIN SAFT; PREDICTION AB The necessity of exploring ultradeep reservoirs requires the accurate prediction of hydrocarbon density data at extreme temperatures and pressures. In this study, three equations of state (EoS) models, Peng-Robinson (PR), high-temperature high-pressure volume-translated PR (HTHP VT-PR), and perturbed-chain statistical associating fluid theory (PC-SAFT) EoS are used to predict the density data for hydrocarbons in ultradeep reservoirs at temperatures to 523 K and pressures to 275 MPa. The calculated values are compared with experimental data. The results show that the HTHP VT-PR EoS and PC-SAFT EoS always perform better than the regular PR EoS for all the investigated hydrocarbons. C1 [Wu, Yue; Bamgbade, Babatunde A.; Burgess, Ward A.; Tapriyal, Deepak; Baled, Hseen O.; Enick, Robert M.; McHugh, Mark A.] US DOE, NETL, Off Res & Dev, Pittsburgh, PA 15236 USA. RP Wu, Y (reprint author), US DOE, NETL, Off Res & Dev, Pittsburgh, PA 15236 USA. NR 11 TC 1 Z9 1 U1 0 U2 5 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1185-2 J9 AIP CONF PROC PY 2013 VL 1558 BP 2423 EP 2426 DI 10.1063/1.4826030 PG 4 WC Mathematics, Applied; Physics, Applied SC Mathematics; Physics GA BA0IB UT WOS:000331472800566 ER PT S AU Tooker, A Madsen, TE Crowell, A Shah, KG Felix, S Mayberg, HS Pannu, S Rainnie, DG Tolosa, V AF Tooker, Angela Madsen, Teresa E. Crowell, Andrea Shah, Kedar G. Felix, Sarah Mayberg, Helen S. Pannu, Satinderpall Rainnie, Donald G. Tolosa, Vanessa GP IEEE TI Chronic, Multi-Contact, Neural Interface for Deep Brain Stimulation SO 2013 6TH INTERNATIONAL IEEE/EMBS CONFERENCE ON NEURAL ENGINEERING (NER) SE International IEEE EMBS Conference on Neural Engineering LA English DT Proceedings Paper CT 6th International IEEE EMBS Conference on Neural Engineering (NER) CY NOV 06-08, 2013 CL San Diego, CA SP IEEE EMBS, Battelle, Brain Vis LLC, Cortech Solut, Univ Minnesota, IGERT Program, Syst Neuroengineering, IOP Publishing, Ripple, Univ Minnesota, Inst Engn Med, Plexon ID TREATMENT-RESISTANT DEPRESSION; CONDITIONED FEAR; AMYGDALA; EXTINCTION; EXPRESSION AB Recent clinical studies show deep brain stimulation (DBS) as a promising therapy for the chronic treatment of major depression. Although an increasing number of studies have shown the clinical benefits of DBS in patients with major depressive disorder, little is known about the underlying mechanisms by which the treatment works. The neural interface described here consists of two multi-contact, polymer-based, microelectrode arrays that were specially-designed and fabricated. The first is for stimulation of the medial prefrontal cortex (mPFC) and the second is for recording local field potentials (LFPs) and event related potentials (ERPs) in the basolateral amygdala (BLA). Unlike conventional metal wire stimulating arrays, this stimulating array offers 144 spatial configurations, both monopolar and bipolar. We present here preliminary results involving stimulation of various contact points spanning the mPFC, with simultaneous recording from multiple contacts across the temporal lobe. C1 [Tooker, Angela; Shah, Kedar G.; Felix, Sarah; Pannu, Satinderpall; Tolosa, Vanessa] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. [Mayberg, Helen S.] Emory Univ, Dept Psychiat, Atlanta, GA 30322 USA. [Madsen, Teresa E.; Crowell, Andrea; Rainnie, Donald G.] Emory Univ, Sch Med, Atlanta, GA 30322 USA. RP Tooker, A (reprint author), Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. EM tooker1@llnl.gov; tmadsen@emory.edu; andrea.crowell@emory.edu; shah22@llnl.gov; felix5@llnl.gov; hmayber@emory.edu; pannu1@llnl.gov; drainni@emory.edu; tolosa1@llnl.gov RI Rainnie, Donald/L-3853-2016 OI Rainnie, Donald/0000-0003-0758-0530 FU Lawrence Livermore National Laboratory; U.S. Department of Energy by Lawrence Livermore National Laboratory [DE-AC52-07NA27344, LLNL-CONF-638803] FX This work has been funded by Lawrence Livermore National Laboratory. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-CONF-638803 NR 18 TC 0 Z9 0 U1 0 U2 1 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1948-3546 BN 978-1-4673-1969-0 J9 I IEEE EMBS C NEUR E PY 2013 BP 1198 EP 1201 PG 4 WC Engineering, Biomedical; Neurosciences SC Engineering; Neurosciences & Neurology GA BA0HI UT WOS:000331259200296 ER PT S AU Goteti, R Mitra, G Becene, A Sussman, A Lewis, C AF Goteti, Rajesh Mitra, Gautam Becene, Ahmet Sussman, Aviva Lewis, Claudia BE Hudson, MR Grauch, VJS TI Three-dimensional finite-element modeling of fault interactions in rift-scale normal fault systems: Implications for the late Cenozoic Rio Grande rift of north-central New Mexico SO NEW PERSPECTIVES ON RIO GRANDE RIFT BASINS: FROM TECTONICS TO GROUNDWATER SE Geological Society of America Special Papers LA English DT Article; Book Chapter ID CANYONLANDS NATIONAL-PARK; SEGMENTED NORMAL FAULTS; ESPANOLA BASIN; RELAY RAMPS; HYDROCARBON EXPLORATION; MECHANICAL MODELS; TRANSFER ZONES; THRUST SHEETS; EVOLUTION; GEOMETRY AB The late Cenozoic extension in the Rio Grande rift of north-central New Mexico was predominantly accommodated by the north-south-trending Pajarito and Sangre de Cristo normal faults and the intervening east-northeast striking predominantly strike-slip Embudo fault. Using this segment of the rift as our primary example, we have analyzed a series of three-dimensional nonlinear elastic-plastic finite-element models to assess the role of mechanical interactions between pairs of en echelon rift-scale listric normal faults in the evolution of intervening relay zones. The model results demonstrate that under orthogonal extension and an overall plane-strain deformation, relay zones may evolve in a three-dimensional strain field and along non-coaxial strain paths. The extent of non-plane strain and non-coaxial deformation depends on the fault overlap to spacing ratio, the relative orientations of the bounding faults, and the structural position within the relay zone. The model-derived minimum compressive stress vectors within the relay zone are oblique to the regional extension direction throughout the deformation. Within the Rio Grande rift of north-central New Mexico, the occurrence of northerly striking Neogene faults suggestive of east-west extension in the Espanola and the San Luis Basins, geographic variations in the vertical-axis rotations from paleomagnetic studies, and secondary fault patterns are consistent with the near-surface variations in the strain field predicted by the model. The model suggests that interaction between the Pajarito and the Sangre de Cristo faults may have played a major role in the evolution of this segment of the rift. C1 [Goteti, Rajesh; Mitra, Gautam] Univ Rochester, Dept Earth & Environm Sci, Rochester, NY 14627 USA. [Becene, Ahmet] Univ Rochester, Dept Mech Engn, Rochester, NY 14627 USA. [Sussman, Aviva; Lewis, Claudia] Los Alamos Natl Lab, Div Earth & Environm Sci, Los Alamos, NM 87545 USA. RP Goteti, R (reprint author), ExxonMobil Upstream Res Co, 3120 Buffalo Speedway, Houston, TX 77098 USA. NR 110 TC 5 Z9 5 U1 0 U2 3 PU GEOLOGICAL SOC AMER INC PI BOULDER PA 3300 PENROSE PL, PO BOX 9140, BOULDER, CO 80301 USA SN 0072-1077 BN 978-0-8137-2494-2 J9 GEOL SOC AM SPEC PAP PY 2013 VL 494 BP 157 EP 184 DI 10.1130/2013.2494(07) D2 10.1130/9780813724942 PG 28 WC Geology SC Geology GA BJS19 UT WOS:000329913600008 ER PT S AU Koning, DJ Grauch, VJS Connell, SD Ferguson, J McIntosh, W Slate, JL Wan, E Baldridge, WS AF Koning, Daniel J. Grauch, V. J. S. Connell, Sean D. Ferguson, John McIntosh, William Slate, Janet L. Wan, Elmira Baldridge, W. Scott BE Hudson, MR Grauch, VJS TI Structure and tectonic evolution of the eastern Espanola Basin, Rio Grande rift, north-central New Mexico SO NEW PERSPECTIVES ON RIO GRANDE RIFT BASINS: FROM TECTONICS TO GROUNDWATER SE Geological Society of America Special Papers LA English DT Article; Book Chapter ID JEMEZ MOUNTAINS; ALLUVIAL-FAN; SEDIMENTATION; STRATIGRAPHY; OLIGOCENE; VOLCANISM; BOUNDARY; GEOLOGY; STRESS; VALLEY AB We describe the structure of the eastern Espanola Basin and use stratigraphic and stratal attitude data to interpret its tectonic development. This area consists of a west-dipping half graben in the northern Rio Grande rift that includes several intrabasinal grabens, faults, and folds. The Embudo Santa Clara Pajarito fault system, a collection of northeast- and north-striking faults in the center of the Espanola Basin, defines the western boundary of the half graben and was active throughout rifting. Throw rates near the middle of the fault system (i.e., the Santa Clara and north Pajarito faults) and associated hanging-wall tilt rates progressively increased during the middle Miocene. East of Espanola, hanging-wall tilt rates decreased after 10-12 Ma, coinciding with increased throw rates on the Canada del Almagre fault. This fault may have temporarily shunted slip from the north Pajarito fault during ca. 8-11 Ala, resulting in lower strain rates on the Santa Clara fault. East of the Embudo Santa Clara Pajarito fault system, deformation of the southern Barrancos monocline and the Canada Ancha graben peaked during the early middle Miocene and effectively ceased by the late Pliocene. The north-striking Gabeldon faulted monocline lies at the base of the Sangre de Cristo Alountains, where stratal dip relations indicate late Oligocene and Miocene tilting. Shifting of strain toward the Embudo Santa Clara Pajarito fault system culminated during the late Pliocene Quaternary. Collectively, our data suggest that extensional tectonism in the eastern Espanola Basin increased in the early Miocene and probably peaked between 14-15 Ala and 9-10 Ma, preceding and partly accompanying major volcanism, and decreased in the Plio-Pleistocene. C1 [Koning, Daniel J.; McIntosh, William] New Mexico Inst Min & Technol, New Mexico Bur Geol & Mineral Resources, Socorro, NM 87801 USA. [Grauch, V. J. S.; Slate, Janet L.] US Geol Survey, Fed Ctr, Denver, CO 80225 USA. [Connell, Sean D.] New Mexico Inst Min & Technol, New Mexico Bur Geol & Mineral Resources, Albuquerque Off, Albuquerque, NM 87106 USA. [Ferguson, John] Univ Texas Dallas, Program Geosci, Richardson, TX 75083 USA. [Wan, Elmira] US Geol Survey, Menlo Pk, CA 94025 USA. [Baldridge, W. Scott] Los Alamos Natl Lab, Div Earth & Environm Sci, Los Alamos, NM 87545 USA. RP Koning, DJ (reprint author), New Mexico Inst Min & Technol, New Mexico Bur Geol & Mineral Resources, 801 Leroy Pl, Socorro, NM 87801 USA. EM seanconnell@chevron.com NR 120 TC 8 Z9 8 U1 1 U2 8 PU GEOLOGICAL SOC AMER INC PI BOULDER PA 3300 PENROSE PL, PO BOX 9140, BOULDER, CO 80301 USA SN 0072-1077 BN 978-0-8137-2494-2 J9 GEOL SOC AM SPEC PAP PY 2013 VL 494 BP 185 EP 219 DI 10.1130/2013.2494(08) D2 10.1130/9780813724942 PG 35 WC Geology SC Geology GA BJS19 UT WOS:000329913600009 ER PT S AU WoldeGabriel, G Koning, DJ Broxton, D Warren, RG AF WoldeGabriel, Giday Koning, Daniel J. Broxton, David Warren, Richard G. BE Hudson, MR Grauch, VJS TI Chronology of volcanism, tectonics, and sedimentation near the western boundary fault of the Espanola Basin, Rio Grande rift, New Mexico SO NEW PERSPECTIVES ON RIO GRANDE RIFT BASINS: FROM TECTONICS TO GROUNDWATER SE Geological Society of America Special Papers LA English DT Article; Book Chapter ID CHEMICAL CLASSIFICATION; JEMEZ MOUNTAINS; ALLUVIAL-FAN; EVOLUTION; SYSTEM; ROCKS AB New Ar-40/Ar-39 results from drill-hole cuttings of basaltic and basaltic andesite flows from the Guaje well field of the Pajarito Plateau along the western part of the Espanola Basin in north-central New Mexico yielded Middle Miocene ages (11.5-13.2 Ma). The volcanic eruptions were closely associated with intense faulting, subsidence, and sedimentation, and the results provide age constraints for the volcanic and tectonic processes along the western margin of the Espanola Basin. The Middle Miocene volcanic rocks are interbedded within the Santa Fe Group, which is divided into the Hernandez and Vallito Members of the Chamita Formation and the Chama El Rito Member of the Tesuque Formation, in descending stratigraphic order. New and published geochemical results from the Guaje well field and from other surface and subsurface mafic and intermediate lava flows within the Pajarito Plateau suggest that the volcanic rocks erupted from different magmatic sources and centers close to the Pajarito fault zone. Multiple pulses of volcanic eruptions mostly confined to the hanging wall of the Pajarito fault zone, which represents the current western boundary bull of the Espanola Basin, suggest that the Pajarito fault system has been sporadically reactivated several times, beginning at least in the Middle Miocene and continuing to the Plio-Pleistocene. Moreover, the volcanic, tectonic, and sedimentary records in the Pajarito Plateau suggest that there is no evidence for eastward migration of tectonic and volcanic activities from the Canada de Cochiti fault zone in the southern part of the Jemez Mountains to the Pajarito fault zone during the early Pliocene (4-5 Ma). C1 [WoldeGabriel, Giday; Broxton, David] Los Alamos Natl Lab, Div Earth & Environm Sci, Los Alamos, NM 87545 USA. [Koning, Daniel J.] New Mexico Inst Technol, New Mexico Bur Geol, Socorro, NM 87801 USA. [Warren, Richard G.] Comprehens Volcan Petrograph, Grand Junction, CO 81506 USA. RP WoldeGabriel, G (reprint author), Los Alamos Natl Lab, Div Earth & Environm Sci, Los Alamos, NM 87545 USA. NR 44 TC 4 Z9 4 U1 0 U2 2 PU GEOLOGICAL SOC AMER INC PI BOULDER PA 3300 PENROSE PL, PO BOX 9140, BOULDER, CO 80301 USA SN 0072-1077 BN 978-0-8137-2494-2 J9 GEOL SOC AM SPEC PAP PY 2013 VL 494 BP 221 EP 238 DI 10.1130/2013.2494(09) D2 10.1130/9780813724942 PG 18 WC Geology SC Geology GA BJS19 UT WOS:000329913600010 ER PT S AU Mishra, K AF Mishra, Kalanand BE Joni, IM Panatarani, C TI The Frontier of High Energy Physics and the Large Hadron Collider SO PADJADJARAN INTERNATIONAL PHYSICS SYMPOSIUM 2013 (PIPS-2013): CONTRIBUTION OF PHYSICS ON ENVIRONMENTAL AND ENERGY CONSERVATIONS SE AIP Conference Proceedings LA English DT Proceedings Paper CT Padjadjaran International Physics Symposium (PIPS) CY MAY 07-09, 2013 CL Univ Padjadjaran, Bandung, INDONESIA SP Univ Padjadjaran, Fac Math & Nat Sci, Dept Phys, Indonesian Phys Soc, Mat Res Soc Indonesia, Indonesian Opt Soc HO Univ Padjadjaran DE High Energy Physics; Large Hadron Collider; LHC AB High Energy Physics explores the most fundamental questions about the nature of the universe, e. g., basic building blocks of matter and energy, existence of the smallest sub-atomic particles, dark matter, dark energy etc. The Large Hadron Collider (LHC) is the most powerful accelerator on earth located near Geneva, Switzerland. It recreates the conditions just after the Big Bang by colliding two proton beams head-on at very high energy every 25-50 nanosecond. With the recent discovery of Higgs boson, the LHC is firmly marching on to explore the TeV energy scale. C1 Fermilab Natl Accelerator Lab, Batavia, IL 60510 USA. RP Mishra, K (reprint author), Fermilab Natl Accelerator Lab, POB 500, Batavia, IL 60510 USA. EM kalanand@fnal.gov NR 6 TC 0 Z9 0 U1 0 U2 1 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1180-7 J9 AIP CONF PROC PY 2013 VL 1554 BP 9 EP 11 DI 10.1063/1.4820273 PG 3 WC Geochemistry & Geophysics; Physics, Applied; Physics, Multidisciplinary SC Geochemistry & Geophysics; Physics GA BA0KI UT WOS:000331605700002 ER PT S AU Ben-Zvi, I AF Ben-Zvi, Ilan BE Milner, R Carlini, R Maas, F TI The 300 mA SRF ERL SO WORKSHOP TO EXPLORE PHYSICS OPPORTUNITIES WITH INTENSE, POLARIZED ELECTRON BEAMS AT 50-300 MEV SE AIP Conference Proceedings LA English DT Proceedings Paper CT Workshop on Explore Physics Opportunities with Intense, Polarized Electron Beams at 50-300 MeV CY MAR 14-16, 2013 CL Cambridge, MA SP Massachusetts Inst Technol, Johannes Gutenberg Univ, Jefferson Lab, Univ Mainz DE ERL SRF AB Energy Recovery Linacs (ERL) are important for a variety of applications, from high-power Free-Electron Lasers (FEL) to polarized-electron polarized-proton colliders. The ERL current is arguably the most important characteristic of ERLs for such applications. With that in mind, the Collider-Accelerator Department at Brookhaven National Laboratory embarked on the development of a 300 mA ERL to serve as an R&D test-bed for high-current ERL technologies. These include high-current, extremely well damped superconducting accelerating cavities, high-current superconducting laser-photocathode electron guns and high quantum-efficiency photocathodes. In this presentation I will cover these ERL related developments. C1 Brookhaven Natl Lab, Collider Accelerator Dept, Upton, NY 11973 USA. RP Ben-Zvi, I (reprint author), Brookhaven Natl Lab, Collider Accelerator Dept, Upton, NY 11973 USA. NR 13 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1191-3 J9 AIP CONF PROC PY 2013 VL 1563 BP 13 EP 19 DI 10.1063/1.4829370 PG 7 WC Astronomy & Astrophysics; Physics, Applied; Physics, Nuclear SC Astronomy & Astrophysics; Physics GA BA0KL UT WOS:000331657200002 ER PT S AU Chudakov, E AF Chudakov, E. BE Milner, R Carlini, R Maas, F TI Precision Electron Polarimetry SO WORKSHOP TO EXPLORE PHYSICS OPPORTUNITIES WITH INTENSE, POLARIZED ELECTRON BEAMS AT 50-300 MEV SE AIP Conference Proceedings LA English DT Proceedings Paper CT Workshop on Explore Physics Opportunities with Intense, Polarized Electron Beams at 50-300 MeV CY MAR 14-16, 2013 CL Cambridge, MA SP Massachusetts Inst Technol, Johannes Gutenberg Univ, Jefferson Lab, Univ Mainz DE Polarimetry ID BEAM POLARIZATION MEASUREMENTS; MOLLER POLARIMETER; ATOMIC-HYDROGEN; RELATIVISTIC ELECTRONS; COMPTON POLARIMETER; STORAGE-RING; SCATTERING; TARGET; ACCELERATOR; ASYMMETRY AB A new generation of precise Parity-Violating experiments will require a sub-percent accuracy of electron beam polanmetry. Compton polarimetry call provide such accuracy at high energies, but at a few hundred MeV the small analyzing power limits the sensitivity. Moller polarimetry provides a high analyzing power independent on the beam energy, but is limited by the properties of the polarized targets commonly used. Options for precision polarimetry at 300 MeV will be discussed, in particular a proposal to use ultra-cold atomic hydrogen traps to provide a 100%-polarized electron target for Moller polarimetry. C1 Jefferson Lab, Newport News, VA 23606 USA. RP Chudakov, E (reprint author), Jefferson Lab, 12000 Jefferson Ave,STE 16, Newport News, VA 23606 USA. NR 45 TC 0 Z9 0 U1 1 U2 2 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1191-3 J9 AIP CONF PROC PY 2013 VL 1563 BP 29 EP 36 DI 10.1063/14829372 PG 8 WC Astronomy & Astrophysics; Physics, Applied; Physics, Nuclear SC Astronomy & Astrophysics; Physics GA BA0KL UT WOS:000331657200004 ER PT S AU Douglas, DR Tennant, CD AF Douglas, David R. Tennant, Christopher D. BE Milner, R Carlini, R Maas, F TI The Jefferson Lab FEL Driver ERLs SO WORKSHOP TO EXPLORE PHYSICS OPPORTUNITIES WITH INTENSE, POLARIZED ELECTRON BEAMS AT 50-300 MEV SE AIP Conference Proceedings LA English DT Proceedings Paper CT Workshop on Explore Physics Opportunities with Intense, Polarized Electron Beams at 50-300 MeV CY MAR 14-16, 2013 CL Cambridge, MA SP Massachusetts Inst Technol, Johannes Gutenberg Univ, Jefferson Lab, Univ Mainz DE electron; linac; energy recovery; longitudinal dynamics; superconducting RF; internal target; polarization; operational-performance AB Jefferson Lab has - for over a decade - been operating high power IR and UV FELs using CW energy recovering linacs based on DC photocathode electron sources and CEBAF SRF technology. These machines have unique combinations of beam quality, power, and operational flexibility, and thus offer significant opportunity for experiments that use low and medium energy (several tens - few hundreds of MeV) electron beams. We will describe the systems and detail their present and near-term (potential) performance. Recent internal-target analysis and validation testing will be discussed, and schemes for single- and two-pass fixed target operation described. An introduction to subsequent discussions of beam quality(1) and upgrade paths to polarized operation/higher energy will be given. C1 [Douglas, David R.; Tennant, Christopher D.] Jefferson Lab, Newport News, VA 23606 USA. RP Douglas, DR (reprint author), Jefferson Lab, Newport News, VA 23606 USA. NR 25 TC 0 Z9 0 U1 0 U2 3 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1191-3 J9 AIP CONF PROC PY 2013 VL 1563 BP 37 EP 44 DI 10.1063/14829373 PG 8 WC Astronomy & Astrophysics; Physics, Applied; Physics, Nuclear SC Astronomy & Astrophysics; Physics GA BA0KL UT WOS:000331657200005 ER PT S AU Poelker, M AF Poelker, M. BE Milner, R Carlini, R Maas, F TI Polarized Electron Beams at Milliampere Average Current SO WORKSHOP TO EXPLORE PHYSICS OPPORTUNITIES WITH INTENSE, POLARIZED ELECTRON BEAMS AT 50-300 MEV SE AIP Conference Proceedings LA English DT Proceedings Paper CT Workshop on Explore Physics Opportunities with Intense, Polarized Electron Beams at 50-300 MeV CY MAR 14-16, 2013 CL Cambridge, MA SP Massachusetts Inst Technol, Johannes Gutenberg Univ, Jefferson Lab, Univ Mainz DE spin polarized electrons; polarized electron beams AB This contribution describes some of the challenges associated with developing a polarized electron source capable of uninterrupted days-long operation at milliAmpere average beam current with polarization greater than 80%. Challenges will be presented in the context of assessing the required level of extrapolation beyond the performance of today's CEBAF polarized source operating at similar to 200 uA average current. Estimates of performance at higher current will he based on hours-long demonstrations at I and 4 mA. Particular attention will be paid to beam-related lifetime-limiting mechanisms, and strategies to construct a photogun that operate reliably at bias voltage > 350kV. C1 Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. RP Poelker, M (reprint author), Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. NR 18 TC 0 Z9 0 U1 0 U2 1 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1191-3 J9 AIP CONF PROC PY 2013 VL 1563 BP 45 EP 50 DI 10.1063/14829374 PG 6 WC Astronomy & Astrophysics; Physics, Applied; Physics, Nuclear SC Astronomy & Astrophysics; Physics GA BA0KL UT WOS:000331657200006 ER PT S AU Marciano, WJ AF Marciano, William J. BE Milner, R Carlini, R Maas, F TI Polarized Electron Scattering, New Physics and Dark Parity Violation SO WORKSHOP TO EXPLORE PHYSICS OPPORTUNITIES WITH INTENSE, POLARIZED ELECTRON BEAMS AT 50-300 MEV SE AIP Conference Proceedings LA English DT Proceedings Paper CT Workshop on Explore Physics Opportunities with Intense, Polarized Electron Beams at 50-300 MeV CY MAR 14-16, 2013 CL Cambridge, MA SP Massachusetts Inst Technol, Johannes Gutenberg Univ, Jefferson Lab, Univ Mainz DE Polarized electron scattering; parity violation AB "New Physics" sensitivities of polarized electron scattering asymmetries, atomic parity violation, m(W) and sin(2) theta(W) (Z pole measurements) are compared. The utility of low Q(2) polarized electron scattering for probing parity violating "dark boson" effects is discussed. A possible determination of the weak charge Q(w)(C-12) to about +/- 0.3% via elastic e-Carbon scattering is advocated. C1 Brookhaven Natl Lab, Upton, NY 11973 USA. RP Marciano, WJ (reprint author), Brookhaven Natl Lab, Upton, NY 11973 USA. NR 13 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1191-3 J9 AIP CONF PROC PY 2013 VL 1563 BP 90 EP 93 DI 10.1063/14829382 PG 4 WC Astronomy & Astrophysics; Physics, Applied; Physics, Nuclear SC Astronomy & Astrophysics; Physics GA BA0KL UT WOS:000331657200014 ER PT S AU Hall, NL Blunden, PG Melnitchouk, W Thomas, AW Young, RD AF Hall, N. L. Blunden, P. G. Melnitchouk, W. Thomas, A. W. Young, R. D. BE Milner, R Carlini, R Maas, F TI Constrained gamma Z Correction to Parity-Violating Electron Scattering SO WORKSHOP TO EXPLORE PHYSICS OPPORTUNITIES WITH INTENSE, POLARIZED ELECTRON BEAMS AT 50-300 MEV SE AIP Conference Proceedings LA English DT Proceedings Paper CT Workshop on Explore Physics Opportunities with Intense, Polarized Electron Beams at 50-300 MeV CY MAR 14-16, 2013 CL Cambridge, MA SP Massachusetts Inst Technol, Johannes Gutenberg Univ, Jefferson Lab, Univ Mainz DE Radiative corrections; dispersion relations AB We update the calculation of gamma Z interference corrections to the weak charge of the proton. We show how constraints from parton distributions, together with new data on parity-violating electron scattering in the resonance region, significantly reduce the uncertainties on the corrections compared to previous estimates. C1 [Hall, N. L.; Thomas, A. W.; Young, R. D.] Univ Adelaide, ARC Ctr Excellence Particle Phys Terascale, Adelaide, SA 5005, Australia. [Blunden, P. G.] Univ Manitoba, Dept Phys & Astron, Winnipeg, MB R3T 2N2, Canada. [Melnitchouk, W.] Jefferson Lab, Newport News, VA 23606 USA. RP Hall, NL (reprint author), Univ Adelaide, ARC Ctr Excellence Particle Phys Terascale, Adelaide, SA 5005, Australia. OI Thomas, Anthony/0000-0003-0026-499X NR 14 TC 0 Z9 0 U1 0 U2 1 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1191-3 J9 AIP CONF PROC PY 2013 VL 1563 BP 94 EP 97 DI 10.1063/14829383 PG 4 WC Astronomy & Astrophysics; Physics, Applied; Physics, Nuclear SC Astronomy & Astrophysics; Physics GA BA0KL UT WOS:000331657200015 ER PT S AU Stepanyan, S AF Stepanyan, S. CA HPS Collaboration BE Milner, R Carlini, R Maas, F TI Heavy Photon Search Experiment at JLAB SO WORKSHOP TO EXPLORE PHYSICS OPPORTUNITIES WITH INTENSE, POLARIZED ELECTRON BEAMS AT 50-300 MEV SE AIP Conference Proceedings LA English DT Proceedings Paper CT Workshop on Explore Physics Opportunities with Intense, Polarized Electron Beams at 50-300 MeV CY MAR 14-16, 2013 CL Cambridge, MA SP Massachusetts Inst Technol, Johannes Gutenberg Univ, Jefferson Lab, Univ Mainz DE heavy photon; dark matter; electron positron; silicon tracker AB The Heavy Photon Search (HPS) experiment in Hall-B at Jefferson Lab will search for new heavy vector boson(s), aka "heavy photons", in the mass range of 20 MeV/c(2) to 1000 MeV/c(2) using the scattering of high energy, high intensity electron beams off a high Z target. The proposed measurements will cover the region of parameter space favored by the mum g-2 anomaly, and will explore a significant region of parameter space, not only at large couplings (alpha'/alpha > 10(-7)), but also in the regions of small couplings, down to alpha'/alpha similar to 10(-10). The excellent vertexing capability of the Si-tracker uniquely enables HPS to cover the small coupling region. Also, HPS will search for heavy photons in an alternative to the e(+)e(-) decay mode, in the heavy photon's decay to mu(+) mu(-). C1 [Stepanyan, S.; HPS Collaboration] Jefferson Lab, Newport News, VA 23606 USA. RP Stepanyan, S (reprint author), Jefferson Lab, Newport News, VA 23606 USA. NR 8 TC 3 Z9 3 U1 1 U2 1 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1191-3 J9 AIP CONF PROC PY 2013 VL 1563 BP 155 EP 158 DI 10.1063/1.4829398 PG 4 WC Astronomy & Astrophysics; Physics, Applied; Physics, Nuclear SC Astronomy & Astrophysics; Physics GA BA0KL UT WOS:000331657200030 ER PT S AU Deur, A AF Deur, A. BE Milner, R Carlini, R Maas, F TI Clean Measurements of the Nucleon Axial-Vector and Free-Neutron Magnetic Form Factors SO WORKSHOP TO EXPLORE PHYSICS OPPORTUNITIES WITH INTENSE, POLARIZED ELECTRON BEAMS AT 50-300 MEV SE AIP Conference Proceedings LA English DT Proceedings Paper CT Workshop on Explore Physics Opportunities with Intense, Polarized Electron Beams at 50-300 MeV CY MAR 14-16, 2013 CL Cambridge, MA SP Massachusetts Inst Technol, Johannes Gutenberg Univ, Jefferson Lab, Univ Mainz DE Axial form factor; electromagnetic form factors; beta decay; Inverse reaction; parity violation ID SCATTERING AB We discuss the feasibility of a weak charged current experiment using a low energy electron beam. A first goal is to measure the Q(2) dependence of the axial-vector form factor g(a)(Q(2)). It can be measured model-independently and as robustly as for electromagnetic form factors from typical electron scattering experiments, in contrast to the methods used so far to measure ga(Q(2)). If g(a)(Q(2)) follows a dipole form, the axial mass can be extracted with a better accuracy than the world data altogether. The most important detection equipment would be a segmented neutron detector with good momentum and angular resolution that is symmetric about the beam direction, and covers a moderate angular range. A high intensity beam (100 uA) is necessary. Beam polarization is highly desirable as it provides a clean measurement of the backgrounds. Beam energies between 70 and 110 MeV are ideal. This range would provide a Q(2) mapping of ga between 0.01 10(6)) transverse and longitudinal beam diagnostics can be used. We also present results of transverse beam profile measurements with the dynamic range approaching 10(5) and demonstrate the effect the increased dynamic range has on the beam characterization, i.e., emittance and Twiss parameters measurements. We also discuss near future work planned in this field and where the JLab FEL. facility will be used for beam tests of the developed of new diagnostics. C1 Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. RP Evtushenko, P (reprint author), Thomas Jefferson Natl Accelerator Facil, 12000 Jefferson Ave, Newport News, VA 23606 USA. NR 10 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1191-3 J9 AIP CONF PROC PY 2013 VL 1563 BP 264 EP 267 DI 10.1063/1.4829425 PG 4 WC Astronomy & Astrophysics; Physics, Applied; Physics, Nuclear SC Astronomy & Astrophysics; Physics GA BA0KL UT WOS:000331657200057 ER PT S AU Gaskell, D AF Gaskell, D. BE Milner, R Carlini, R Maas, F TI Electron Polarimetry at Low Energies in Hall C at JLab SO WORKSHOP TO EXPLORE PHYSICS OPPORTUNITIES WITH INTENSE, POLARIZED ELECTRON BEAMS AT 50-300 MEV SE AIP Conference Proceedings LA English DT Proceedings Paper CT Workshop on Explore Physics Opportunities with Intense, Polarized Electron Beams at 50-300 MeV CY MAR 14-16, 2013 CL Cambridge, MA SP Massachusetts Inst Technol, Johannes Gutenberg Univ, Jefferson Lab, Univ Mainz DE Moller polarimeter; Compton polarimeter; Electron beam polarimetry AB Although the majority of Jefferson Lab experiments require multi-GeV electron beams, there have been a few opportunities to make electron beam polarization measurements at rather low energies. This proceedings will discuss some of the practical difficulties encountered in performing electron polarimetry via Moller scattering at energies on the order of a few hundred MeV. Prospects for Compton polarimetry at very low energies will also be discussed. While Moller scattering is likely the preferred method for electron polarimetry at energies below 500 MeV, there are certain aspects of the polarimeter and experiment design that must be carefully considered. C1 Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. RP Gaskell, D (reprint author), Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. NR 7 TC 0 Z9 0 U1 0 U2 1 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1191-3 J9 AIP CONF PROC PY 2013 VL 1563 BP 268 EP 271 DI 10.1063/1.4829426 PG 4 WC Astronomy & Astrophysics; Physics, Applied; Physics, Nuclear SC Astronomy & Astrophysics; Physics GA BA0KL UT WOS:000331657200058 ER PT S AU Strasburg, C Basu, S Wong, JS AF Strasburg, Chris Basu, Samik Wong, Johnny S. GP IEEE TI S-MAIDS: A Semantic Model for Automated Tuning, Correlation, and Response Selection in Intrusion Detection Systems SO 2013 IEEE 37TH ANNUAL COMPUTER SOFTWARE AND APPLICATIONS CONFERENCE (COMPSAC) SE Proceedings International Computer Software and Applications Conference LA English DT Proceedings Paper CT IEEE 37th Annual Computer Software and Applications Conference (COMPSAC) CY JUL 22-26, 2013 CL Kyoto, JAPAN SP IEEE, IEEE Comp Soc, Informat Proc Soc Japan, Korean Inst Informat Scientists & Engineers, CCF, Tateisi Sci & Technol Fdn, Kyoto Univ, Iowa State Univ Sci & Technol DE Intrusion detection; Computer security; Knowledge based systems; Software measurement; Computer aided diagnosis AB As cyber threats increasingly utilize automated and adaptive attacks to bypass or overwhelm static defenses, the role of intrusion detection and response systems (IDRS) as an active defense layer is becoming more critical. To remain effective against current attacks IDRS must be capable of automating detection of, and response to, threats in their specific environment. Different operating characteristics, detection capabilities, and response actions all contribute to make each environment unique, complicating this automation. In this work we consider IDRS automation in three areas: detector tuning, detector correlation, and response selection. We motivate and present a novel, more finely-grained model of threats, detectors, and responses called S-MAIDS : A Semantic Model of Automated Intrusion Detection Systems. Based on the concept of a "signal" (an observable indicator of an attack), we show the utility of combining such a model with an existing measure of IDRS performance to facilitate automated tuning, cross-system correlation, and response selection. We support our claims through several case-studies demonstrating the application of this model, and provide the model as an OWL ontology. C1 [Strasburg, Chris] Iowa State Univ, Ames Lab, Ames, IA 50011 USA. [Basu, Samik; Wong, Johnny S.] Iowa State Univ, Dept Comp Sci, Ames, IA 50011 USA. RP Strasburg, C (reprint author), Iowa State Univ, Ames Lab, Ames, IA 50011 USA. EM cstras@ameslab.gov; sbasu@iastate.edu; wong@iastate.edu NR 18 TC 1 Z9 1 U1 0 U2 3 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 0730-3157 BN 978-0-7695-4986-6 J9 P INT COMP SOFTW APP PY 2013 BP 319 EP 328 DI 10.1109/COMPSAC.2013.57 PG 10 WC Computer Science, Software Engineering; Computer Science, Theory & Methods SC Computer Science GA BA0HA UT WOS:000331216500052 ER PT S AU Chang, H Borowsky, A Spellman, P Parvin, B AF Chang, Hang Borowsky, Alexander Spellman, Paul Parvin, Bahram GP IEEE TI Classification of Tumor Histology via Morphometric Context SO 2013 IEEE CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION (CVPR) SE IEEE Conference on Computer Vision and Pattern Recognition LA English DT Proceedings Paper CT 26th IEEE Conference on Computer Vision and Pattern Recognition (CVPR) CY JUN 23-28, 2013 CL Portland, OR SP IEEE, IEEE Comp Soc ID FEATURES; SPARSE; LEVEL AB Image-based classification of tissue histology, in terms of different components (e.g., normal signature, categories of aberrant signatures), provides a series of indices for tumor composition. Subsequently, aggregation of these indices in each whole slide image (WSI) from a large cohort can provide predictive models of clinical outcome. However, the performance of the existing techniques is hindered as a result of large technical and biological variations that are always present in a large cohort. In this paper, we propose two algorithms for classification of tissue histology based on robust representations of morphometric context, which are built upon nuclear level morphometric features at various locations and scales within the spatial pyramid matching (SPM) framework. These methods have been evaluated on two distinct datasets of different tumor types collected from The Cancer Genome Atlas (TCGA), and the experimental results indicate that our methods are (i) extensible to different tumor types; (ii) robust in the presence of wide technical and biological variations; (iii) invariant to different nuclear segmentation strategies; and (iv) scalable with varying training sample size. In addition, our experiments suggest that enforcing sparsity, during the construction of morphometric context, further improves the performance of the system. C1 [Chang, Hang; Parvin, Bahram] Lawrence Berkeley Natl Lab, Div Life Sci, Berkeley, CA 94720 USA. [Borowsky, Alexander] Univ Calif Davis, Ctr Comparat Med, Davis, CA USA. [Spellman, Paul] Oregon Hlth & Sci Univ, Ctr Spatial Syst Biomed, Portland, OR USA. RP Chang, H (reprint author), Lawrence Berkeley Natl Lab, Div Life Sci, Berkeley, CA 94720 USA. EM hchang@lbl.gov; adborowsky@ucdavis.edu; spellmap@ohsu.edu; bparvin@lbl.gov FU NIH [U24 CA1437991]; Lawrence Berkeley National Laboratory [DE-AC02-05CH11231] FX This work was supported by NIH U24 CA1437991 carried out at Lawrence Berkeley National Laboratory under Contract No. DE-AC02-05CH11231. NR 29 TC 4 Z9 4 U1 0 U2 1 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1063-6919 BN 978-0-7695-4989-7 J9 PROC CVPR IEEE PY 2013 BP 2203 EP 2210 DI 10.1109/CVPR.2013.286 PG 8 WC Computer Science, Artificial Intelligence SC Computer Science GA BA0ER UT WOS:000331094302034 ER PT B AU Bogen, PL Symons, CT McKenzie, A Patton, RM Gillen, RE AF Bogen, Paul Logasa, II Symons, Christopher T. McKenzie, Amber Patton, Robert M. Gillen, Robert E. BE Hu, X Lin, TY Raghavan, V Wah, B BaezaYates, R Fox, G Shahabi, C Smith, M Yang, Q Ghani, R Fan, W Lempel, R Nambiar, R TI Massively Scalable Near Duplicate Detection in Streams of Documents using MDSH SO 2013 IEEE INTERNATIONAL CONFERENCE ON BIG DATA LA English DT Proceedings Paper CT IEEE International Conference on Big Data (Big Data) CY OCT 06-09, 2013 CL Santa Clara, CA SP IEEE, IEEE Comp Soc, CCF, Yahoo Labs, CISCO DE Near Duplicate Detection; Big Data; Streaming Text; Open Source Intelligence; MDSH AB In a world where large-scale text collections are not only becoming ubiquitous but also are growing at increasing rates, near duplicate documents are becoming a growing concern that has the potential to hinder many different information filtering tasks. While others have tried to address this problem, prior techniques have only been used on limited collection sizes and static cases. We will briefly describe the problem in the context of Open Source analysis along with our additional constraints for performance. In this work we propose two variations on Multi-dimensional Spectral Hash (MDSH) tailored for working on extremely large, growing sets of text documents. We analyze the memory and runtime characteristics of our techniques and provide an informal analysis of the quality of the near-duplicate clusters produced by our techniques. C1 [Bogen, Paul Logasa, II; Symons, Christopher T.; McKenzie, Amber; Patton, Robert M.; Gillen, Robert E.] Oak Ridge Natl Lab, Computat Data Analyt Grp, Oak Ridge, TN 37831 USA. RP Bogen, PL (reprint author), Oak Ridge Natl Lab, Computat Data Analyt Grp, Oak Ridge, TN 37831 USA. EM orion-project@email.ornl.gov NR 32 TC 0 Z9 0 U1 0 U2 1 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-1-4799-1292-6; 978-1-4799-1293-3 PY 2013 PG 7 WC Computer Science, Information Systems; Computer Science, Theory & Methods; Engineering, Electrical & Electronic SC Computer Science; Engineering GA BA0BK UT WOS:000330831300067 ER PT B AU Endert, A Burtner, R Cramer, N Perko, R Hampton, S Cook, K AF Endert, Alex Burtner, Russ Cramer, Nick Perko, Ralph Hampton, Shawn Cook, Kristin BE Hu, X Lin, TY Raghavan, V Wah, B BaezaYates, R Fox, G Shahabi, C Smith, M Yang, Q Ghani, R Fan, W Lempel, R Nambiar, R TI Typograph: Multiscale Spatial Exploration of Text Documents SO 2013 IEEE INTERNATIONAL CONFERENCE ON BIG DATA LA English DT Proceedings Paper CT IEEE International Conference on Big Data (Big Data) CY OCT 06-09, 2013 CL Santa Clara, CA SP IEEE, IEEE Comp Soc, CCF, Yahoo Labs, CISCO DE Visual analytics; sensemaking; text analytics; spatialization AB Visualizing large document collections using a spatial layout of terms can enable quick overviews of information. These visual metaphors (e.g., word clouds, tag clouds, etc.) traditionally show a series of terms organized by space-filling algorithms. However, often lacking in these views is the ability to interactively explore the information to gain more detail, and the location and rendering of the terms are often not based on mathematical models that maintain relative distances from other information based on similarity metrics. In this paper, we present Typograph, a multi-scale spatial exploration visualization for large document collections. Based on the term-based visualization methods, Typograh enables multiple levels of detail (terms, phrases, snippets, and full documents) within the single spatialization. Further, the information is placed based on their relative similarity to other information to create the "near = similar" geographic metaphor. This paper discusses the design principles and functionality of Typograph and presents a use case analyzing Wikipedia to demonstrate usage. C1 [Endert, Alex; Burtner, Russ; Cramer, Nick; Perko, Ralph; Hampton, Shawn; Cook, Kristin] Pacific NW Natl Lab, Richland, WA 99352 USA. RP Endert, A (reprint author), Pacific NW Natl Lab, Richland, WA 99352 USA. NR 30 TC 0 Z9 0 U1 0 U2 1 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-1-4799-1292-6; 978-1-4799-1293-3 PY 2013 PG 8 WC Computer Science, Information Systems; Computer Science, Theory & Methods; Engineering, Electrical & Electronic SC Computer Science; Engineering GA BA0BK UT WOS:000330831300166 ER PT B AU Gomez, LAB Cappello, F AF Gomez, Leonardo A. Bautista Cappello, Franck BE Hu, X Lin, TY Raghavan, V Wah, B BaezaYates, R Fox, G Shahabi, C Smith, M Yang, Q Ghani, R Fan, W Lempel, R Nambiar, R TI Improving Floating Point Compression through Binary Masks SO 2013 IEEE INTERNATIONAL CONFERENCE ON BIG DATA LA English DT Proceedings Paper CT IEEE International Conference on Big Data (Big Data) CY OCT 06-09, 2013 CL Santa Clara, CA SP IEEE, IEEE Comp Soc, CCF, Yahoo Labs, CISCO AB Modern scientific technology such as particle accelerators, telescopes, and supercomputers are producing extremely large amounts of data. That scientific data needs to be processed by using systems with high computational capabilities such as supercomputers. Given that the scientific data is increasing in size at an exponential rate, storing and accessing the data are becoming expensive in both time and space. Most of this scientific data is stored by using floating point representation. Scientific applications executed on supercomputers spend a large amount of CPU cycles reading and writing floating point values, making data compression techniques an interesting way to increase computing efficiency. Given the accuracy requirements of scientific computing, we only focus on lossless data compression. In this paper we propose a masking technique that partially decreases the entropy of scientific datasets, allowing for a better compression ratio and higher throughput. We evaluate several data partitioning techniques for selective compression and compare these schemes with several existing compression strategies. Our approach shows up to 15% improvement in compression ratio while reducing the time spent in compression by half time in some cases. C1 [Gomez, Leonardo A. Bautista; Cappello, Franck] Argonne Natl Lab, Argonne, IL 60439 USA. RP Gomez, LAB (reprint author), Argonne Natl Lab, Argonne, IL 60439 USA. NR 16 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-1-4799-1292-6; 978-1-4799-1293-3 PY 2013 PG 6 WC Computer Science, Information Systems; Computer Science, Theory & Methods; Engineering, Electrical & Electronic SC Computer Science; Engineering GA BA0BK UT WOS:000330831300048 ER PT B AU Gu, W Choi, J Gu, M Simon, H Wu, KS AF Gu, William Choi, Jaesik Gu, Ming Simon, Horst Wu, Kesheng BE Hu, X Lin, TY Raghavan, V Wah, B BaezaYates, R Fox, G Shahabi, C Smith, M Yang, Q Ghani, R Fan, W Lempel, R Nambiar, R TI Fast Change Point Detection for Electricity Market Analysis SO 2013 IEEE INTERNATIONAL CONFERENCE ON BIG DATA LA English DT Proceedings Paper CT IEEE International Conference on Big Data (Big Data) CY OCT 06-09, 2013 CL Santa Clara, CA SP IEEE, IEEE Comp Soc, CCF, Yahoo Labs, CISCO ID CRISIS AB Electricity is a vital part of our daily life; therefore it is important to avoid irregularities such as the California Electricity Crisis of 2000 and 2001. In this work, we seek to predict anomalies using advanced machine learning algorithms, more specifically a Change Point Detection (CPD) algorithm on the electricity prices during the California Electricity Crisis. Such algorithms are effective, but computationally expensive when applied on a large amount of data. To address this challenge, we accelerate the Gaussian Process (GP) for 1-dimensional time series data. Since GP is at the core of many statistical learning techniques, this improvement could benefit many algorithms. In the specific Change Point Detection algorithm used in this study, we reduce the overall computational complexity from O(n(5)) to O(n(2)), where the amountized cost of solving a GP projet is O(1). Our efficient algorithm makes it possible to compute the Change Points using the hourly price data during the California Electricity Crisis. By comparing the detected Change Points with known events, we show that the Change Point Detection algorithm is indeed effective in detecting signals preceding major events. C1 [Gu, William; Choi, Jaesik; Gu, Ming; Simon, Horst; Wu, Kesheng] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Gu, W (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. EM wcgu@lbl.gov NR 27 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-1-4799-1292-6; 978-1-4799-1293-3 PY 2013 PG 8 WC Computer Science, Information Systems; Computer Science, Theory & Methods; Engineering, Electrical & Electronic SC Computer Science; Engineering GA BA0BK UT WOS:000330831300190 ER PT B AU Kim, Y Atchley, S Vallee, GR Shipman, GM AF Kim, Youngjae Atchley, Scott Vallee, Geoffroy R. Shipman, Galen M. BE Hu, X Lin, TY Raghavan, V Wah, B BaezaYates, R Fox, G Shahabi, C Smith, M Yang, Q Ghani, R Fan, W Lempel, R Nambiar, R TI Layout-Aware I/O Scheduling for Terabits Data Movement SO 2013 IEEE INTERNATIONAL CONFERENCE ON BIG DATA LA English DT Proceedings Paper CT IEEE International Conference on Big Data (Big Data) CY OCT 06-09, 2013 CL Santa Clara, CA SP IEEE, IEEE Comp Soc, CCF, Yahoo Labs, CISCO DE Storage Systems; I/O Scheduling; Networking AB Many science facilities, such as the Department of Energy's Leadership Computing Facilities and experimental facilities including the Spallation Neutron Source, Stanford Linear Accelerator Center, and Advanced Photon Source, produce massive amounts of experimental and simulation data. These data are often shared among the facilities and with collaborating institutions. Moving large datasets over the wide-area network (WAN) is a major problem inhibiting collaboration. Next-generation, terabit-networks will help alleviate the problem, however, the parallel storage systems on the end-system hosts at these institutions can become a bottleneck for terabit data movement. The parallel storage system (PFS) is shared by simulation systems, experimental systems, analysis and visualization clusters, in addition to wide-area data movers. These competing uses often induce temporary, but significant, I/O load imbalances on the storage system, which impact the performance of all the users. The problem is a serious concern because some resources are more expensive (e. g. super computers) or have time-critical deadlines (e. g. experimental data from a light source), but parallel file systems handle all requests fairly even if some storage servers are under heavy load. This paper investigates the problem of competing workloads accessing the parallel file system and how the performance of wide-area data movement can be improved in these environments. First, we study the I/O load imbalance problems using actual I/O performance data collected from the Spider storage system at the Oak Ridge Leadership Computing Facility. Second, we present I/O optimization solutions with layout-awareness on end-system hosts for bulk data movement. With our evaluation, we show that our I/O optimization techniques can avoid the I/O congested disk groups, improving storage I/O times on parallel storage systems for terabit data movement. C1 [Kim, Youngjae; Atchley, Scott; Vallee, Geoffroy R.; Shipman, Galen M.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. RP Kim, Y (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. EM kimy1@ornl.gov; atchleyes@ornl.gov; valleegr@ornl.gov; gshipman@ornl.gov NR 12 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-1-4799-1292-6; 978-1-4799-1293-3 PY 2013 PG 8 WC Computer Science, Information Systems; Computer Science, Theory & Methods; Engineering, Electrical & Electronic SC Computer Science; Engineering GA BA0BK UT WOS:000330831300118 ER PT B AU Morari, A Castellana, VG Haglin, D Feo, J Weaver, J Tumeo, A Villa, O AF Morari, Alessandro Castellana, Vito Giovanni Haglin, David Feo, John Weaver, Jesse Tumeo, Antonino Villa, Oreste BE Hu, X Lin, TY Raghavan, V Wah, B BaezaYates, R Fox, G Shahabi, C Smith, M Yang, Q Ghani, R Fan, W Lempel, R Nambiar, R TI Accelerating Semantic Graph Databases on Commodity Clusters SO 2013 IEEE INTERNATIONAL CONFERENCE ON BIG DATA LA English DT Proceedings Paper CT IEEE International Conference on Big Data (Big Data) CY OCT 06-09, 2013 CL Santa Clara, CA SP IEEE, IEEE Comp Soc, CCF, Yahoo Labs, CISCO AB We are developing a full software system for accelerating semantic graph databases on commodity cluster that scales to hundreds of nodes while maintaining constant query throughput. Our framework comprises a SPARQL to C++ compiler, a library of parallel graph methods and a custom multithreaded runtime layer, which provides a Partitioned Global Address Space (PGAS) programming model with fork/join parallelism and automatic load balancing over a commodity clusters. We present preliminary results for the compiler and for the runtime. C1 [Morari, Alessandro; Castellana, Vito Giovanni; Haglin, David; Feo, John; Weaver, Jesse; Tumeo, Antonino] Pacific NW Natl Lab, Richland, WA 99352 USA. [Villa, Oreste] NVIDIA, Santa Clara, CA USA. RP Morari, A (reprint author), Pacific NW Natl Lab, Richland, WA 99352 USA. EM alessandro.morari@pnnl.gov; vitoGiovanni.castellana@pnnl.gov; david.haglin@pnnl.gov; john.feo@pnnl.gov; jesse.weaver@pnnl.gov; antonino.tumeo@pnnl.gov; ovilla@nvidia.com RI Morari, Alessandro/J-8298-2014; Tumeo, Antonino/L-3106-2016 NR 4 TC 0 Z9 0 U1 0 U2 2 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-1-4799-1292-6; 978-1-4799-1293-3 PY 2013 PG 5 WC Computer Science, Information Systems; Computer Science, Theory & Methods; Engineering, Electrical & Electronic SC Computer Science; Engineering GA BA0BK UT WOS:000330831300107 ER PT B AU Tang, W Wilkening, J Desai, N Gerlach, W Wilke, A Meyer, F AF Tang, Wei Wilkening, Jared Desai, Narayan Gerlach, Wolfgang Wilke, Andreas Meyer, Folker BE Hu, X Lin, TY Raghavan, V Wah, B BaezaYates, R Fox, G Shahabi, C Smith, M Yang, Q Ghani, R Fan, W Lempel, R Nambiar, R TI A Scalable Data Analysis Platform for Metagenomics SO 2013 IEEE INTERNATIONAL CONFERENCE ON BIG DATA LA English DT Proceedings Paper CT IEEE International Conference on Big Data (Big Data) CY OCT 06-09, 2013 CL Santa Clara, CA SP IEEE, IEEE Comp Soc, CCF, Yahoo Labs, CISCO DE data management system; workflow; metagenomics; bioinformatics; data analysis platform; cloud computing ID SCIENTIFIC WORKFLOW; EXPERIENCE; GENOME AB With the advent of high-throughput DNA sequencing technology, the analysis and management of the increasing amount of biological sequence data has become a bottleneck for scientific progress. For example, MG-RAST, a metagenome annotation system serving a large scientific community worldwide, has experienced a sustained, exponential growth in data submissions for several years; and this trend is expected to continue. To address the computational challenges posed by this workload, we developed a new data analysis platform, including a data management system (Shock) for biological sequence data and a workflow management system (AWE) supporting scalable, fault-tolerant task and resource management. Shock and AWE can be used to build a scalable and reproducible data analysis infrastructure for upper-level biological data analysis services. C1 [Tang, Wei; Wilkening, Jared; Desai, Narayan; Gerlach, Wolfgang; Wilke, Andreas; Meyer, Folker] Argonne Natl Lab, Argonne, IL 60439 USA. RP Tang, W (reprint author), Argonne Natl Lab, 9700 S Cass Ave, Argonne, IL 60439 USA. EM wtang@mcs.anl.gov; jared@mcs.anl.gov; desai@mcs.anl.gov; wgerlach@mcs.anl.gov; wilke@mcs.anl.gov; folker@mcs.anl.gov NR 25 TC 0 Z9 0 U1 1 U2 3 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-1-4799-1292-6; 978-1-4799-1293-3 PY 2013 PG 6 WC Computer Science, Information Systems; Computer Science, Theory & Methods; Engineering, Electrical & Electronic SC Computer Science; Engineering GA BA0BK UT WOS:000330831300180 ER PT S AU Cardoso, G Stadler, M Bozchalui, MC Sharma, R Marnay, C Barbosa-Povoa, A Ferrao, P AF Cardoso, G. Stadler, M. Bozchalui, M. Chehreghani Sharma, R. Marnay, C. Barbosa-Povoa, A. Ferrao, P. GP IEEE TI Stochastic Programming of Vehicle to Building Interactions with Uncertainty in PEVs Driving for a Medium Office Building SO 39TH ANNUAL CONFERENCE OF THE IEEE INDUSTRIAL ELECTRONICS SOCIETY (IECON 2013) SE IEEE Industrial Electronics Society LA English DT Proceedings Paper CT 39th Annual Conference of the IEEE Industrial-Electronics-Society (IECON) CY NOV 10-14, 2013 CL Vienna, AUSTRIA SP IEEE Ind Elect Soc, Inst Elect & Elect Engineers, Austrian Inst Technol, Vienna Univ Technol DE microgrids; uncertainty; electric vehicles; electric storage; distributed energy resources; driving patterns ID ENERGY-SYSTEMS; OPERATION AB The large scale penetration of electric vehicles (EVs) will introduce technical challenges to the distribution grid, but also carries the potential for vehicle-to-grid services. Namely, if available in large enough numbers, EVs can be used as a distributed energy resource (DER) and their presence can influence optimal DER investment and scheduling decisions in microgrids. In this work, a novel EV fleet aggregator model is introduced in a stochastic formulation of DER-CAM [1], an optimization tool used to address DER investment and scheduling problems. This is used to assess the impact of EV interconnections on optimal DER solutions considering uncertainty in EV driving schedules. Optimization results indicate that EVs can have a significant impact on DER investments, particularly if considering short payback periods. Furthermore, results suggest that uncertainty in driving schedules carries little significance to total energy costs, which is corroborated by results obtained with the stochastic formulation of the problem. C1 [Cardoso, G.; Barbosa-Povoa, A.; Ferrao, P.] Univ Tecn Lisboa, Inst Super Tecn, Lisbon, Portugal. [Stadler, M.] Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. [Stadler, M.] Ctr Energy & Innovat Technol, Priel, Austria. [Bozchalui, M. Chehreghani; Sharma, R.] NEC labs Inc, Berkeley, CA USA. [Marnay, C.] Lawrence Berkeley Natl Lab, Microgrid Design Mendocin, LLC, Berkeley, CA 94720 USA. RP Cardoso, G (reprint author), Univ Tecn Lisboa, Inst Super Tecn, Lisbon, Portugal. EM goncalo.cardoso@ist.utl.pt; mstadler@lbl.gov; mohammad@nec-labs.com; ratnesh@nec-labs.com; chrismarnay@lbl.gov; apovoa@mail.ist.utl.pt; ferrao@ist.utl.pt RI Ferrao, Paulo/B-6065-2012; Barbosa-Povoa, Ana/A-8578-2012 OI Ferrao, Paulo/0000-0003-1357-9966; Barbosa-Povoa, Ana/0000-0001-6594-9653 FU Office of Electricity Delivery and Energy Reliability, Distributed Energy Program of the U.S. Department of Energy [DE-AC02-05CH11231]; NEC Laboratories America Inc - Fundacao para a Ciencia e Tecnologia [SFRH / BD / 35147 / 2007]; MIT-Portugal Program FX The work described in this paper was funded by the Office of Electricity Delivery and Energy Reliability, Distributed Energy Program of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 and with support of NEC Laboratories America Inc. Goncalo Cardoso was also funded by Fundacao para a Ciencia e Tecnologia under Grant SFRH / BD / 35147 / 2007 and the MIT-Portugal Program. The authors would also like to thank Professor Dr. Tomas Gomez and Ilan Momber for their very valuable contributions to previous versions of DER-CAM. NR 17 TC 5 Z9 5 U1 0 U2 4 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1553-572X BN 978-1-4799-0224-8 J9 IEEE IND ELEC PY 2013 BP 7648 EP 7653 PG 6 WC Automation & Control Systems; Engineering, Industrial; Engineering, Electrical & Electronic SC Automation & Control Systems; Engineering GA BA0GT UT WOS:000331149507074 ER PT S AU Ryzewski, K Herringer, S Bilheux, H Walker, L Sheldon, B Voisin, S Bilheux, JC Finocchiaro, V AF Ryzewski, K. Herringer, S. Bilheux, H. Walker, L. Sheldon, B. Voisin, S. Bilheux, J-C Finocchiaro, V. BE Hungler, PC TI Neutron imaging of archaeological bronzes at the Oak Ridge national laboratory SO 7TH INTERNATIONAL TOPICAL MEETING ON NEUTRON RADIOGRAPHY (ITMNR-7) SE Physics Procedia LA English DT Proceedings Paper CT 7th International Topical Meeting on Neutron Radiography (ITMNR) CY JUN 16-24, 2012 CL Kingston, CANADA DE neutron imaging; neutron radiography; neutron tomography; archaeology; archaeometry; cultural heritage; bronze ID TOMOGRAPHY; RADIOGRAPHY; OBJECTS AB This articl.e presents the initial results of 2-D and 3-D neutron imaging of bronze artifacts using the CG-1D prototype beamline at the High Flux Isotope Reactor (HFIR) located at the Oak Ridge National Laboratory (ORNL). Neutron imaging is a non-destructive technique capable of producing unprecedented three-dimensional. information on archaeomaterials, including qualitative, quantitative, and visual data on impurities, composition change, voids, and structure at macro-scale levels. The initial results presented in this publication highlight how information from neutron imaging can provide otherwise inaccessible details about the methods and materials that ancient craftspeople used in creating bronze objects. (C) 2013 The Authors. Published by Elsevier B.V. C1 [Bilheux, H.; Walker, L.; Bilheux, J-C] Oak Ridge Natl Lab, POB 2008, Oak Ridge, TN 37831 USA. [Ryzewski, K.] Wayne State Univ, Dept Anthropol, Detroit, MI 48202 USA. [Herringer, S.; Sheldon, B.] Brown Univ, Sch Engn, Providence, RI 02912 USA. [Finocchiaro, V.] Univ Messina, Dept Mat Phys & Elect, I-98122 Messina, Italy. RP Bilheux, H (reprint author), Oak Ridge Natl Lab, POB 2008, Oak Ridge, TN 37831 USA. EM bilheuxhn@ornl.gov RI Bilheux, Hassina/H-4289-2012; Bilheux, Jean/A-2823-2016 OI Bilheux, Hassina/0000-0001-8574-2449; Bilheux, Jean/0000-0003-2172-6487 FU Oak Ridge National Laboratory's High Flux Isotope; Office of Basic Energy Sciences; U. S. Department of Energy; UT-Battelle; LLC; National Science Foundation [DGE0228243] FX This research at the Oak Ridge National Laboratory's High Flux Isotope Reactor was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U. S. Department of Energy, which is managed by UT-Battelle, LLC. This material is based upon work supported by the National Science Foundation under Grant No. DGE0228243. The Authors are thankful for collection loans from Susan E. Alcock, Director of the Joukowsky Institute for Archaeology and the Ancient World, Brown University and editorial assistance from Emanuela Bocancea, Brown University. NR 12 TC 4 Z9 4 U1 0 U2 7 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA SARA BURGERHARTSTRAAT 25, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 1875-3892 J9 PHYSCS PROC PY 2013 VL 43 BP 343 EP 351 DI 10.1016/j.phpro.2013.03.041 PG 9 WC Physics, Applied SC Physics GA BA0HH UT WOS:000331257300041 ER PT J AU Graves, DT Colella, P Modiano, D Johnson, J Sjogreen, B Gao, XF AF Graves, Daniel T. Colella, Phillip Modiano, David Johnson, Jeffrey Sjogreen, Bjorn Gao, Xinfeng TI A CARTESIAN GRID EMBEDDED BOUNDARY METHOD FOR THE COMPRESSIBLE NAVIER-STOKES EQUATIONS SO COMMUNICATIONS IN APPLIED MATHEMATICS AND COMPUTATIONAL SCIENCE LA English DT Article DE Cartesian grid embedded boundaries; compressible Navier-Stokes; block-structured adaptive mesh refinement ID HYPERBOLIC CONSERVATION-LAWS; ADAPTIVE MESH REFINEMENT; POISSONS-EQUATION; HEAT-EQUATION; 3 DIMENSIONS; SHOCK-WAVES; RIGID RAMPS; FLOWS AB We present an unsplit method for the time-dependent compressible Navier-Stokes equations in two and three dimensions. We use a conservative, second-order Godunov algorithm. We use a Cartesian grid, embedded boundary method to resolve complex boundaries. We solve for viscous and conductive terms with a second-order semiimplicit algorithm. We demonstrate second-order accuracy in solutions of smooth problems in smooth geometries and demonstrate robust behavior for strongly discontinuous initial conditions in complex geometries. C1 [Graves, Daniel T.; Colella, Phillip; Johnson, Jeffrey] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Appl Numer Algorithms Grp, Berkeley, CA 94720 USA. [Modiano, David] Sanzaru Games Inc, Foster City, CA 94404 USA. [Sjogreen, Bjorn] Lawrence Livermore Natl Lab, Ctr Appl Sci Comp, Livermore, CA 94551 USA. [Gao, Xinfeng] Colorado State Univ, Dept Mech Engn, Ft Collins, CO 80523 USA. RP Graves, DT (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Appl Numer Algorithms Grp, 1 Cyclotron Rd,MS 50A-1148, Berkeley, CA 94720 USA. EM DTGraves@lbl.gov; PColella@lbl.gov; dave@alum.mit.edu; jjphatt@gmail.com; sjogreen2@llnl.gov; Xinfeng.Gao@colostate.edu RI Johnson, Jeffrey/J-5127-2014 OI Johnson, Jeffrey/0000-0002-0265-5241 FU Office of Advanced Scientific Computing Research of the US Department of Energy [DE-AC02-05CH11231]; U.S. Department of Energy by LBNL [DE-AC52-07NA27344] FX Colella's research at Lawrence Livermore National Laboratory (LBNL) was supported financially by the Office of Advanced Scientific Computing Research of the US Department of Energy under contract DE-AC02-05CH11231. Sjogreen's participation funded under the auspices of the U.S. Department of Energy by LBNL under contract DE-AC52-07NA27344. NR 32 TC 4 Z9 4 U1 3 U2 6 PU MATHEMATICAL SCIENCE PUBL PI BERKELEY PA UNIV CALIFORNIA, DEPT MATHEMATICS, BERKELEY, CA 94720-3840 USA SN 1559-3940 EI 2157-5452 J9 COMM APP MATH COM SC JI Commun. Appl. Math. Comput. Sci. PY 2013 VL 8 IS 1 BP 99 EP 122 DI 10.2140/camcos.2013.8.99 PG 24 WC Mathematics, Applied; Physics, Mathematical SC Mathematics; Physics GA AA8UU UT WOS:000331371300004 ER PT J AU Fagnan, K LeVeque, RJ Matula, TJ AF Fagnan, Kirsten LeVeque, Randall J. Matula, Thomas J. TI COMPUTATIONAL MODELS OF MATERIAL INTERFACES FOR THE STUDY OF EXTRACORPOREAL SHOCK WAVE THERAPY SO COMMUNICATIONS IN APPLIED MATHEMATICS AND COMPUTATIONAL SCIENCE LA English DT Article DE high-resolution finite volume methods; computational biology; shock wave therapy ID ADAPTIVE MESH REFINEMENT; TISSUE DIFFERENTIATION; PROPAGATION ALGORITHMS; BIOPHYSICAL STIMULI; HYPERBOLIC SYSTEMS; MECHANO-REGULATION; CONSERVATION-LAWS; FLUID-FLOW; BONE; FRACTURE AB Extracorporeal shock wave therapy (ESWT) is a noninvasive treatment for a variety of musculoskeletal ailments. A shock wave is generated in water and then focused using an acoustic lens or reflector so the energy of the wave is concentrated in a small treatment region where mechanical stimulation in principle enhances healing. In this work we have computationally investigated shock wave propagation in ESWT by solving a Lagrangian form of the isentropic Euler equations in the fluid and linear elasticity in the bone using high-resolution finite volume methods. We solve a full three-dimensional system of equations and use adaptive mesh refinement to concentrate grid cells near the propagating shock. We can model complex bone geometries, the reflection and mode conversion at interfaces, and the propagation of the resulting shear stresses generated within the bone. We discuss the validity of our simplified model and present results validating this approach. C1 [Fagnan, Kirsten] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, NERSC JGI, Berkeley, CA 94720 USA. [LeVeque, Randall J.] Univ Washington, Dept Appl Math, Seattle, WA 98195 USA. [Matula, Thomas J.] Univ Washington, Appl Phys Lab, Seattle, WA 98105 USA. RP Fagnan, K (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, NERSC JGI, 1 Cyclotron Rd,MS 943R0256, Berkeley, CA 94720 USA. EM kmfagnan@lbl.gov; rjl@amath.washington.edu; matula@apl.washington.edu RI Matula, Tom/I-5346-2012; OI LeVeque, Randall/0000-0003-1384-4504 FU NIH [5R01AR53652-2]; NSF [DMS-0609661, DMS-0914942]; Founders Term Professorship in Applied Mathematics at the University of Washington; National Science Foundation [TG-DMS090036T] FX This work was supported in part by NIH Grant 5R01AR53652-2, NSF Grants DMS-0609661 and DMS-0914942, and the Founders Term Professorship in Applied Mathematics at the University of Washington. The authors would like to thank Donna Calhoun and the ANAG group at Lawrence Berkeley Laboratory for their assistance with the ChomboClaw calculations. This research was supported in part by the National Science Foundation through TeraGrid resources provided by TACC under grant number TG-DMS090036T. NR 57 TC 1 Z9 1 U1 1 U2 11 PU MATHEMATICAL SCIENCE PUBL PI BERKELEY PA UNIV CALIFORNIA, DEPT MATHEMATICS, BERKELEY, CA 94720-3840 USA SN 1559-3940 EI 2157-5452 J9 COMM APP MATH COM SC JI Commun. Appl. Math. Comput. Sci. PY 2013 VL 8 IS 1 BP 159 EP 194 DI 10.2140/camcos.2013.8.159 PG 36 WC Mathematics, Applied; Physics, Mathematical SC Mathematics; Physics GA AA8UU UT WOS:000331371300006 ER PT S AU Colgan, J Kilcrease, DP Magee, NH Armstrong, GSJ Abdallah, J Sherrill, ME Fontes, CJ Zhang, HL Hakel, P AF Colgan, J. Kilcrease, D. P. Magee, N. H., Jr. Armstrong, G. S. J. Abdallah, J., Jr. Sherrill, M. E. Fontes, C. J. Zhang, H. L. Hakel, P. BE Gillaspy, JD Wiese, WL Podpaly, YA TI Light element opacities of astrophysical interest from ATOMIC SO EIGHTH INTERNATIONAL CONFERENCE ON ATOMIC AND MOLECULAR DATA AND THEIR APPLICATIONS (ICAMDATA-2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 8th International Conference on Atomic and Molecular Data and Their Applications (ICAMDATA) CY SEP 30-OCT 04, 2012 CL Gaithersburg, MD ID FREE ABSORPTION COEFFICIENT; STELLAR ENVELOPES; LINES; SCATTERING AB We present new calculations of local-thermodynamic-equilibrium (LTE) light element opacities from the Los Alamos ATOMIC code [1] for systems of astrophysical interest. ATOMIC is a multi-purpose code that can generate LTE or non-LTE quantities of interest at various levels of approximation. Our calculations, which include fine-structure detail, represent a systematic improvement over previous Los Alamos opacity calculations using the LEDCOP legacy code [2]. The ATOMIC code uses ab-initio atomic structure data computed from the CATS code, which is based on Cowan's atomic structure codes [3], and photoionization cross section data computed from the Los Alamos ionization code GIPPER [4]. ATOMIC also incorporates a new equation-of-state (EOS) model based on the chemical picture [5]. ATOMIC incorporates some physics packages from LEDCOP and also includes additional physical processes, such as improved free-free cross sections and additional scattering mechanisms. Our new calculations are made for elements of astrophysical interest and for a wide range of temperatures and densities. C1 [Colgan, J.; Kilcrease, D. P.; Magee, N. H., Jr.; Armstrong, G. S. J.; Abdallah, J., Jr.; Sherrill, M. E.] Los Alamos Natl Lab, Div Theoret, Los Alamos, NM 87545 USA. RP Colgan, J (reprint author), Los Alamos Natl Lab, Div Theoret, Los Alamos, NM 87545 USA. OI Colgan, James/0000-0003-1045-3858; Hakel, Peter/0000-0002-7936-4231; Kilcrease, David/0000-0002-2319-5934 NR 29 TC 4 Z9 4 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1170-8 J9 AIP CONF PROC PY 2013 VL 1545 BP 17 EP 26 DI 10.1063/1.4815837 PG 10 WC Physics, Applied; Physics, Atomic, Molecular & Chemical SC Physics GA BA0HJ UT WOS:000331261500002 ER PT S AU Kaganovich, I AF Kaganovich, Igor BE Gillaspy, JD Wiese, WL Podpaly, YA TI Data Needs for Low Temperature Plasmas and Accelerator Applications SO EIGHTH INTERNATIONAL CONFERENCE ON ATOMIC AND MOLECULAR DATA AND THEIR APPLICATIONS (ICAMDATA-2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 8th International Conference on Atomic and Molecular Data and Their Applications (ICAMDATA) CY SEP 30-OCT 04, 2012 CL Gaithersburg, MD AB The topic of the title is discussed briefly, and references to further details are provided. C1 Princeton Univ, Princeton Plasma Phys Lab, Princeton, NJ 08543 USA. RP Kaganovich, I (reprint author), Princeton Univ, Princeton Plasma Phys Lab, Princeton, NJ 08543 USA. NR 3 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1170-8 J9 AIP CONF PROC PY 2013 VL 1545 BP 212 EP 213 DI 10.1063/1.4815856 PG 2 WC Physics, Applied; Physics, Atomic, Molecular & Chemical SC Physics GA BA0HJ UT WOS:000331261500021 ER PT J AU Naulleau, PP Anderson, CN Bhattarai, S Neureuther, A AF Naulleau, Patrick P. Anderson, Christopher N. Bhattarai, Suchit Neureuther, Andrew TI EUV Extendibility: Challenges Facing EUV at 1x and beyond SO JOURNAL OF PHOTOPOLYMER SCIENCE AND TECHNOLOGY LA English DT Article DE photoresist; extreme ultraviolet; shot noise; line-edge roughness ID LINE-EDGE ROUGHNESS; RESIST AB Extreme ultraviolet chemically amplified resist performance has recently been extended to the 15-nm half pitch regime, yet line-edge roughness (LER) remains far from targets. Stochastic analysis, however, shows current LER performance to be material limited rather than photon limited. Interest in contact hole printing and contact size uniformity has dramatically increased over the past few years. As with line space printing, we find contact uniformity performance to be material limited rather than photon limited. Nevertheless, current resist parameters would lead to the photon noise alone exceeding the uniformity requirement by the 16-nm half pitch node with conventional masks. The use of phase shift masks is shown to provide a significant benefit. Combining phase shift masks with relatively modest improvements in resist is predicted to lead to target performance down to 12-nm half pitch and beyond. C1 [Naulleau, Patrick P.; Anderson, Christopher N.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Ctr Xray Opt, Berkeley, CA 94720 USA. [Bhattarai, Suchit; Neureuther, Andrew] Univ Calif Berkeley, EECS, Berkeley, CA 94720 USA. RP Naulleau, PP (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Ctr Xray Opt, Berkeley, CA 94720 USA. RI Anderson, Christopher/H-9526-2015 OI Anderson, Christopher/0000-0002-2710-733X FU SEMATECH; SEMATECH through the U.S. Department of Energy [DE-AC02-05CH11231] FX The authors are greatly indebted to the CXRO MET operations team including Gideon Jones, Lone-mae Baclea-an, Mark Binenbaum, Chanin King, Gayan Pothuhera, Jessica Ritland, and Jessalyn Sincher. We also thank Ken Maruyama of JSR, Shinji Tarutani of Fuji, and Mike Wagner of Dow for excellent resist support, and Mark Neisser of SEMATECH for valuable discussions and experimental data support. This work was funded by SEMATECH and the authors thank Dominic Ashworth, Kevin Cummings, and Stefan Wurm for continued support of the SEMATECH MET exposure facility at the Advanced Light Source. The work was performed at Lawrence Berkeley National Laboratory's Advanced Light Source synchrotron facility and was supported by SEMATECH through the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. NR 10 TC 2 Z9 2 U1 1 U2 5 PU TECHNICAL ASSOC PHOTOPOLYMERS,JAPAN PI CHIBA PA CHIBA UNIV, FACULTY ENGINEERING, YAYOICHO, CHIBA, 263-8522, JAPAN SN 0914-9244 J9 J PHOTOPOLYM SCI TEC JI J. Photopolym Sci. Technol. PY 2013 VL 26 IS 6 BP 697 EP 704 PG 8 WC Polymer Science SC Polymer Science GA AA8NS UT WOS:000331352800002 ER PT S AU Tranquada, JM AF Tranquada, John M. BE Avella, A Mancini, F TI Spins, Stripes, and Superconductivity in Hole-Doped Cuprates SO LECTURES ON THE PHYSICS OF STRONGLY CORRELATED SYSTEMS XVII SE AIP Conference Proceedings LA English DT Proceedings Paper CT 17th Training Course in the Physics of Strongly Correlated Systems CY OCT 01-12, 2012 CL Vietri sul Mare, ITALY SP Univ Studi Salerno, Dipartimento Fis E R Caianiello, Int Inst Adv Sci Studies E R Caianiello, European Sci Fdn, INTELBIOMAT Programme DE superconductivity; antiferromagnetism; charge order; stripes; cuprates; nickelates; neutron scattering ID HIGH-TEMPERATURE SUPERCONDUCTIVITY; T-C SUPERCONDUCTORS; X-RAY-ABSORPTION; COPPER-OXIDE SUPERCONDUCTORS; PHASE-SEPARATION; HEISENBERG-ANTIFERROMAGNET; ELECTRONIC-STRUCTURE; NEUTRON-SCATTERING; MAGNETIC ORDER; J MODEL AB One of the major themes in correlated electron physics over the last quarter century has been the problem of high-temperature superconductivity in hole-doped copper-oxide compounds. Fundamental to this problem is the competition between antiferromagnetic spin correlations, a symptom of strong Coulomb interactions, and the kinetic energy of the doped carriers, which favors delocalization. After discussing some of the early challenges in the field, I describe the experimental picture provided by a variety of spectroscopic and transport techniques. Then I turn to the technique of neutron scattering, and discuss how it is used to determine spin correlations, especially in model systems of quantum magnetism. Neutron scattering and complementary techniques have determined the extent to which antiferromagnetic spin correlations survive in the cuprate superconductors. One experimental case involves the ordering of spin and charge stripes. I first consider related measurements on model compounds, such as La2-xSrxNiO4+delta, and then discuss the case of La2-xBaxCuO4. In the latter system, recent transport studies have demonstrated that quasi-two-dimensional superconductivity coexists with the stripe order, but with frustrated phase order between the layers. This has led to new concepts for the coexistence of spin order and superconductivity. While the relevance of stripe correlations to high-temperature superconductivity remains a subject of controversy, there is no question that stripes are an intriguing example of electron matter that results from strong correlations. C1 [Tranquada, John M.] Brookhaven Natl Lab, Upton, NY 11973 USA. RP Tranquada, JM (reprint author), Brookhaven Natl Lab, Upton, NY 11973 USA. RI Tranquada, John/A-9832-2009 OI Tranquada, John/0000-0003-4984-8857 NR 169 TC 10 Z9 10 U1 2 U2 13 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1175-3 J9 AIP CONF PROC PY 2013 VL 1550 BP 114 EP 187 DI 10.1063/1.4818402 PG 74 WC Physics, Applied SC Physics GA BA0HG UT WOS:000331248800003 ER PT S AU Lewicki, JP Harley, SJ Finnie, JA Ashmore, M Bell, C Maxwell, RS AF Lewicki, James P. Harley, Stephen J. Finnie, Jasmine A. Ashmore, Michael Bell, Crystal Maxwell, Robert S. BE Clarson, SJ Owen, MJ Smith, SD Van Dyke, M Brook, M Mabry, J TI NMR Investigations of Network Formation and Motional Dynamics in Well-Defined Model Poly(dimethylsiloxane) Elastomers SO PROGRESS IN SILICONES AND SILICONE-MODIFIED MATERIALS SE ACS Symposium Series LA English DT Proceedings Paper CT Silicones and Silicone-Modified Materials Symposium / 243rd National Spring Meeting of the American-Chemical-Society CY MAR 25-29, 2012 CL San Diego, CA SP Amer Chem Soc, Div Polymer Chem ID NUCLEAR-MAGNETIC-RESONANCE; FILLED SILICONE ELASTOMER; IN-SITU PRECIPITATION; INDUCED CROSS-LINKING; SOLID-STATE NMR; INTEGRAL-EQUATIONS; CHAIN DYNAMICS; MQ-NMR; RADIATION; POLYMERS AB In this work, results of a study to optimize the structure of a series of model PDMS networks are reported. The study utilized H-1 Magic Angle Spinning (MAS), Magic Sandwich Echo (MSE) NMR methods and equilibrium solvent uptake analysis. The influence of inter-crosslink molar mass, vinyl to silane ratio and Pt chelation effects on the dynamics of network formation have been studied using low field NMR methodologies in real time. These comparatively simple solid-state NMR methodologies can be used to study the dynamics of network formation and the relationship between the chemical identity of key structural components and the final network structure of a silicone elastomer. C1 [Lewicki, James P.; Harley, Stephen J.; Finnie, Jasmine A.; Ashmore, Michael; Bell, Crystal; Maxwell, Robert S.] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. RP Lewicki, JP (reprint author), Lawrence Livermore Natl Lab, 7000 East Ave, Livermore, CA 94550 USA. EM lewicki1@llnl.gov NR 50 TC 2 Z9 2 U1 2 U2 8 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 SIXTEENTH ST NW, WASHINGTON, DC 20036 USA SN 0097-6156 BN 978-0-8412-2964-8 J9 ACS SYM SER JI ACS Symp. Ser. PY 2013 VL 1154 BP 133 EP 154 PG 22 WC Materials Science, Multidisciplinary; Polymer Science SC Materials Science; Polymer Science GA BA0KG UT WOS:000331591200010 ER PT S AU Ager, JW Lee, MH Javey, A AF Ager, Joel W. Lee, Min-Hyung Javey, Ali BE Sugiyama, M Fujii, K Nakamura, S TI Solar Fuels Production by Artificial Photosynthesis SO SOLAR CHEMICAL ENERGY STORAGE (SOLCHES) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 1st International Workshop on Solar Chemical Energy Storage (SolChES) CY JUL 23-28, 2012 CL Sendai, JAPAN SP Global Solar Initiat, KAITEKI Inst Inc, Sendai Tourism & Convent Bur DE photocathode; InP; photoelectrochemistry; artificial photosynthesis ID SURFACE RECOMBINATION VELOCITY; HYDROGEN-PRODUCTION; PHOTOELECTROCHEMICAL DEVICE; WATER; SEMICONDUCTORS; PHOTOCATHODES; CHALLENGES; CONVERSION; CATALYSTS; DESIGN AB A practical method to use sunlight to generate storable chemical energy could dramatically change the landscape of global energy generation. One of the fundamental requirements of such an "artificial photosynthesis" scheme is a light capture and conversion approach capable of generating the required chemical potentials (e.g. >1.23 V for splitting water into H-2 and O-2). An approach based on inorganic light absorbers coupled directly to oxidation and reduction catalysts is being developed in the Joint Center for Artificial Photosynthesis (JCAP). P-type III-V semiconductors with a high surface area can be used as high current density photocathodes. The longevity under operation of these photocathodes can be improved by the use of conformal metal oxides deposited by atomic layer deposition. C1 [Ager, Joel W.; Lee, Min-Hyung] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Joint Ctr Artificial Photosynth, Berkeley, CA 94720 USA. [Lee, Min-Hyung; Javey, Ali] Lawrence Berkeley Natl Lab, Div Sci Mat, Berkeley, CA 94720 USA. [Javey, Ali] Univ Calif Berkeley, Elect Engn & Comp Sci, Berkeley, CA 94720 USA. RP Ager, JW (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Joint Ctr Artificial Photosynth, Berkeley, CA 94720 USA. EM JWAger@lbl.gov OI Ager, Joel/0000-0001-9334-9751 FU Office of Science of the U.S. Department of Energy [DE-SC0004993] FX This material is based upon work performed by the Joint Center for Artificial Photosynthesis, a DOE Energy Innovation Hub, supported through the Office of Science of the U.S. Department of Energy under Award Number DE-SC0004993. NR 33 TC 1 Z9 1 U1 1 U2 9 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1196-8 J9 AIP CONF PROC PY 2013 VL 1568 BP 3 EP 6 DI 10.1063/1.4848078 PG 4 WC Energy & Fuels; Physics, Applied SC Energy & Fuels; Physics GA BA0HV UT WOS:000331393400001 ER PT S AU Yano, J Yachandra, V AF Yano, Junko Yachandra, Vittal BE Sugiyama, M Fujii, K Nakamura, S TI Water Oxidation Reaction in Natural and Artificial Photosynthetic Systems SO SOLAR CHEMICAL ENERGY STORAGE (SOLCHES) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 1st International Workshop on Solar Chemical Energy Storage (SolChES) CY JUL 23-28, 2012 CL Sendai, JAPAN SP Global Solar Initiat, KAITEKI Inst Inc, Sendai Tourism & Convent Bur DE Photosynthesis; Water oxidation; Manganese ID OXYGEN-EVOLVING COMPLEX; PHOTOSYSTEM-II; CATALYST AB Understanding the structure and mechanism of water oxidation catalysts is an essential component for developing artificial photosynthetic devices. In the natural water oxidation catalyst, the geometric and electronic structure of its inorganic core, the Mn4CaO5 cluster, has been studied by spectroscopic and diffraction measurements. In inorganic systems, metal oxides seem to be good candidates for water oxidation catalysts. Understanding the reaction mechanism in both natural and oxide-based catalysts will help in further developing efficient and robust water oxidation catalysts. C1 [Yano, Junko; Yachandra, Vittal] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA. RP Yano, J (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, 1 Cyclotron Rd, Berkeley, CA 94720 USA. NR 8 TC 0 Z9 0 U1 1 U2 5 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1196-8 J9 AIP CONF PROC PY 2013 VL 1568 BP 35 EP 36 DI 10.1063/1.4848086 PG 2 WC Energy & Fuels; Physics, Applied SC Energy & Fuels; Physics GA BA0HV UT WOS:000331393400009 ER PT S AU Wei, SH AF Wei, Su-Huai BE Sugiyama, M Fujii, K Nakamura, S TI Rational Design of Semiconductors for Photoelectrochemical Water Splitting SO SOLAR CHEMICAL ENERGY STORAGE (SOLCHES) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 1st International Workshop on Solar Chemical Energy Storage (SolChES) CY JUL 23-28, 2012 CL Sendai, JAPAN SP Global Solar Initiat, KAITEKI Inst Inc, Sendai Tourism & Convent Bur DE Water splitting; Solar; Photoelectrochemical; Semiconductors; First-principles design AB Using first-principles method as a tool, we discuss the general strategies for the rational design of semiconductors to simultaneously meet all of requirements for high-efficiency, solar-driven photoelectrochemical (PEC) water-splitting devices. Our studies demonstrate that theoretical calculations, which provided deep understanding of the underlying physics behind these PEC materials, can greatly accelerate scientific discovery of new PEC materials in this exciting field. C1 Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Wei, SH (reprint author), Natl Renewable Energy Lab, Golden, CO 80401 USA. NR 14 TC 0 Z9 0 U1 1 U2 6 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1196-8 J9 AIP CONF PROC PY 2013 VL 1568 BP 37 EP 39 DI 10.1063/1.4848087 PG 3 WC Energy & Fuels; Physics, Applied SC Energy & Fuels; Physics GA BA0HV UT WOS:000331393400010 ER PT S AU Dolan, DH Ao, T Seagle, CT AF Dolan, D. H. Ao, T. Seagle, C. T. BE Meyer, CW TI Reflectance Thermometry in Dynamic Compression Experiments SO TEMPERATURE: ITS MEASUREMENT AND CONTROL IN SCIENCE AND INDUSTRY, VOL 8 SE AIP Conference Proceedings LA English DT Proceedings Paper CT 9th International Temperature Symposium on Temperature - Its Measurement and Control in Science and Industry CY MAR 19-23, 2012 CL Los Angeles, CA SP US Natl Inst Standards & Technol, Measurement Sci Conf, Fluke Corp, Measurements Int, Chino Corp, ICL Calibrat Lab, INSCO Instrumentat Serv, Sensing Devices, Liu Res Lab, Thermoprobe, Rocky Mt Tissue Bank, Lake Shore Cryotron, Thermoworks, Tovey Engn, Palmer Wahl Instrumentat Grp DE reflectance; dynamic; gold ID GOLD; AU; LIQUID AB Ultrafast compression provides unique insights into material behavior at extreme conditions. Starting from ambient conditions, compressed samples can reach pressures of 1-100+ GPa, accompanied by temperature changes of 10(2)-10(5) K, within 10-100 ns. Dynamic temperature measurements of these states provide a wealth of thermodynamic information but are challenging in single-event experiments. Optical pyrometry can be used in some situations but becomes infeasible below 1000 K. Instead of inferring temperature based on light emitted by a sample, we propose to measure dynamic temperature states based on light reflected from a sample. As an active measurement, reflectance thermometry yields measurable optical signals at any temperature, potentially with nanosecond time resolution. C1 [Dolan, D. H.; Ao, T.; Seagle, C. T.] Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Dolan, DH (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87185 USA. NR 17 TC 1 Z9 1 U1 0 U2 3 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1178-4 J9 AIP CONF PROC PY 2013 VL 1552 BP 767 EP 770 DI 10.1063/1.4819639 PG 4 WC Thermodynamics; Physics, Applied SC Thermodynamics; Physics GA BA0HP UT WOS:000331284900134 ER PT S AU Allison, SW Gillies, GT AF Allison, S. W. Gillies, G. T. BE Meyer, CW TI Phosphor Thermometry Signal Analysis and Interpretation SO TEMPERATURE: ITS MEASUREMENT AND CONTROL IN SCIENCE AND INDUSTRY, VOL 8 SE AIP Conference Proceedings LA English DT Proceedings Paper CT 9th International Temperature Symposium on Temperature - Its Measurement and Control in Science and Industry CY MAR 19-23, 2012 CL Los Angeles, CA SP US Natl Inst Standards & Technol, Measurement Sci Conf, Fluke Corp, Measurements Int, Chino Corp, ICL Calibrat Lab, INSCO Instrumentat Serv, Sensing Devices, Liu Res Lab, Thermoprobe, Rocky Mt Tissue Bank, Lake Shore Cryotron, Thermoworks, Tovey Engn, Palmer Wahl Instrumentat Grp DE Fluorescence thermometry; Thermographic phosphors; Noncontact thermometry ID THERMOGRAPHIC PHOSPHORS AB Since the last International Temperature Symposium, phosphor thermometry has continued to mature with considerable attention given to combustion and turbine engine applications. More recently the utility to problems on the micro- and nano-scales has appreciated, particularly in regard to biological and biomedical situations. The method is therefore used for a wide range of situations. Signal interpretation is important and experience teaches that without sufficient care phosphor signals can be misleading. In order to advance the method, signal analysis investigations should prove fruitful. The specific aspect addressed here is the question of waveform sampling. A simple phenomenological approach is described that explores how the number of points digitized per waveform affects the measurement repeatability and accuracy. This is demonstrated for single shot signals and the average of 512 sequential waveforms. A bright temperature-independent luminescence signal from YVO4:Eu is sampled every 800 ps (1.25 GS/s) for a highly sampled condition and every 8 microseconds (125 kS/s) for a low sampled condition. When the average of 512 waveforms are compared for the two sampling conditions, they differ by only 0.4%. For the highly sampled case, a noisy single shot waveform compared to the averaged waveform differed by 1.8%. Future efforts on this subject will address intermediate and lower sampling rates. Also, variable window techniques should be explored that are especially important for non-log-linear signals. Investigations, such as this, give the developer the requisite information for designing analysis systems appropriate for the intended application in terms of precision, accuracy, and response time. C1 [Allison, S. W.] Oak Ridge Natl Lab, Sensors & Controls Grp, Oak Ridge, TN 37830 USA. [Gillies, G. T.] Univ Virginia, Mech & Biomed Engn, Charlottesville, VA 22903 USA. RP Allison, SW (reprint author), Oak Ridge Natl Lab, Sensors & Controls Grp, Oak Ridge, TN 37830 USA. FU Oak Ridge National Laboratory (ORNL) which is managed by UT-Battelle, LLC for the U.S. Department of Energy [DEAC05-00OR22725] FX This research was supported in part by Oak Ridge National Laboratory (ORNL) which is managed by UT-Battelle, LLC for the U.S. Department of Energy under contract no DEAC05-00OR22725 NR 8 TC 0 Z9 0 U1 3 U2 8 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1178-4 J9 AIP CONF PROC PY 2013 VL 1552 BP 863 EP 866 DI 10.1063/1.4819657 PG 4 WC Thermodynamics; Physics, Applied SC Thermodynamics; Physics GA BA0HP UT WOS:000331284900152 ER PT S AU Daw, JE Rempe, JL Knudson, DL Unruh, TC Chase, BM Davis, KL Palmer, AJ AF Daw, J. E. Rempe, J. L. Knudson, D. L. Unruh, T. C. Chase, B. M. Davis, K. L. Palmer, A. J. BE Meyer, CW TI Temperature Monitoring Options Available at the Idaho National Laboratory Advanced Test Reactor SO TEMPERATURE: ITS MEASUREMENT AND CONTROL IN SCIENCE AND INDUSTRY, VOL 8 SE AIP Conference Proceedings LA English DT Proceedings Paper CT 9th International Temperature Symposium on Temperature - Its Measurement and Control in Science and Industry CY MAR 19-23, 2012 CL Los Angeles, CA SP US Natl Inst Standards & Technol, Measurement Sci Conf, Fluke Corp, Measurements Int, Chino Corp, ICL Calibrat Lab, INSCO Instrumentat Serv, Sensing Devices, Liu Res Lab, Thermoprobe, Rocky Mt Tissue Bank, Lake Shore Cryotron, Thermoworks, Tovey Engn, Palmer Wahl Instrumentat Grp DE Advanced Test Reactor; Irradiation Testing; Temperature Monitoring AB As part of the Advanced Test Reactor National Scientific User Facility (ATR-NSUF) program, the Idaho National Laboratory (INL) has developed in-house capabilities to fabricate, test, and qualify new and enhanced temperature sensors for irradiation testing. Clearly, temperature sensor selection for irradiation tests will be determined based on the irradiation environment and budget. However, temperature sensors now offered by INL include a wide array of melt wires in small capsules, silicon carbide monitors, commercially available thermocouples, and specialized high temperature irradiation resistant thermocouples containing doped molybdenum and niobium alloy thermoelements. In addition, efforts have been initiated to develop and evaluate ultrasonic thermometers for irradiation testing. This array of temperature monitoring options now available to ATR and other Material and Test Reactor (MTR) users fulfills recent customer requests. C1 [Daw, J. E.; Rempe, J. L.; Knudson, D. L.; Unruh, T. C.; Chase, B. M.; Davis, K. L.; Palmer, A. J.] Idaho Natl Lab, Idaho Falls, ID 83404 USA. RP Daw, JE (reprint author), Idaho Natl Lab, POB 1625,MS 4112, Idaho Falls, ID 83404 USA. OI Rempe, Joy/0000-0001-5527-3549 NR 14 TC 0 Z9 0 U1 1 U2 4 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1178-4 J9 AIP CONF PROC PY 2013 VL 1552 BP 970 EP 975 DI 10.1063/1.4819675 PG 6 WC Thermodynamics; Physics, Applied SC Thermodynamics; Physics GA BA0HP UT WOS:000331284900170 ER PT S AU Heiken, G AF Heiken, Grant BE Bickford, ME TI From Kilauea Iki 1959 to Eyjafjallajokull 2010: How volcanology has changed! SO WEB OF GEOLOGICAL SCIENCES: ADVANCES, IMPACTS, AND INTERACTIONS SE Geological Society of America Special Papers LA English DT Article; Book Chapter ID MOUNT ST-HELENS; BASE-SURGE DEPOSITS; SUBMARINE LANDSLIDES; VOLCANIC-ERUPTIONS; CALDERA-COLLAPSE; BASALTIC VOLCANO; CENTRAL MEXICO; ANALOG MODELS; COLLI-ALBANI; LAVA FLOWS AB The field of volcanology has greatly changed during the last half century. The profession is now much more diverse and interdisciplinary, even including collaborating researchers from the social and medical sciences. This new mode of cooperation and working has been more successful in mitigating volcanic hazards and risks. There are fewer of the strong-willed lone rangers of the past and more of those who work with teams to more effectively understand how volcanoes work to protect those living on or near active or potentially active volcanoes. Moreover, there are more university departments with volcanology in their curricula and more international symposia and workshops focusing on mitigation of risk posed by volcano-related hazards. We all have respected colleagues and volcano observatories in many countries. The importance of understanding explosive volcanic eruptions and tracking of eruption plumes involves volcanologists, atmospheric physicists, and air-traffic controllers and is of great interest to the aviation industry. We now have the links in place between great science and practical applications. C1 [Heiken, Grant] NASA, Apollo Program, Lunar Receiving Lab, Washington, DC USA. [Heiken, Grant] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Heiken, G (reprint author), 331 Windantide Pl, Washington, DC USA. EM heiken@whidbey.com NR 237 TC 1 Z9 1 U1 0 U2 2 PU GEOLOGICAL SOC AMER INC PI BOULDER PA 3300 PENROSE PL, PO BOX 9140, BOULDER, CO 80301 USA SN 0072-1077 BN 978-0-8137-2500-0 J9 GEOL SOC AM SPEC PAP PY 2013 VL 500 BP 33 EP 63 DI 10.1130/2013.2500(02) D2 10.1130/9780813725000 PG 31 WC Geosciences, Multidisciplinary; History & Philosophy Of Science SC Geology; History & Philosophy of Science GA BJS00 UT WOS:000329864400003 ER PT J AU Nam, JM Ahmed, KM Costes, S Zhang, H Onodera, Y Olshen, AB Hatanaka, KC Kinoshita, R Ishikawa, M Sabe, H Shirato, H Park, CC AF Nam, Jin-Min Ahmed, Kazi M. Costes, Sylvain Zhang, Hui Onodera, Yasuhito Olshen, Adam B. Hatanaka, Kanako C. Kinoshita, Rumiko Ishikawa, Masayori Sabe, Hisataka Shirato, Hiroki Park, Catherine C. TI beta 1-integrin via NF-kappa B signaling is essential for acquisition of invasiveness in a model of radiation treated in situ breast cancer SO BREAST CANCER RESEARCH LA English DT Article DE ductal carcinoma in situ; DCIS; integrin; ionizing radiation ID IONIZING-RADIATION; 3-DIMENSIONAL CULTURE; BETA(1) INTEGRIN; MATRIX METALLOPROTEINASES; CELLS; EXPRESSION; FIBRONECTIN; TUMOR; INVASION; CARCINOMA AB Introduction: Ductal carcinoma in situ (DCIS) is characterized by non-invasive cancerous cell growth within the breast ducts. Although radiotherapy is commonly used in the treatment of DCIS, the effect and molecular mechanism of ionizing radiation (IR) on DCIS are not well understood, and invasive recurrence following radiotherapy remains a significant clinical problem. This study investigated the effects of IR on a clinically relevant model of Akt-driven DCIS and identified possible molecular mechanisms underlying invasive progression in surviving cells. Methods: We measured the level of phosphorylated-Akt (p-Akt) in a cohort of human DCIS specimens by immunohistochemistry (IHC) and correlated it with recurrence risk. To model human DCIS, we used Akt overexpressing human mammary epithelial cells (MCF10A-Akt) which, in three-dimensional laminin-rich extracellular matrix (lrECM) and in vivo, form organotypic DCIS-like lesions with lumina expanded by pleiomorphic cells contained within an intact basement membrane. In a population of cells that survived significant IR doses in three-dimensional lrECM, a malignant phenotype emerged creating a model for invasive recurrence. Results: P-Akt was up-regulated in clinical DCIS specimens and was associated with recurrent disease. MCF10A-Akt cells that formed DCIS-like structures in three-dimensional lrECM showed significant apoptosis after IR, preferentially in the luminal compartment. Strikingly, when cells that survived IR were repropagated in three-dimensional lrECM, a malignant phenotype emerged, characterized by invasive activity, up-regulation of fibronectin, alpha 5 beta 1-integrin, matrix metalloproteinase-9 (MMP-9) and loss of E-cadherin. In addition, IR induced nuclear translocation and binding of nuclear factor-kappa B (NF-kappa B) to the beta 1-integrin promoter region, associated with up-regulation of alpha 5 beta 1-integrins. Inhibition of NF-kappa B or beta 1-integrin signaling abrogated emergence of the invasive activity. Conclusions: P-Akt is up-regulated in some human DCIS lesions and is possibly associated with recurrence. MCF10A-Akt cells form organotypic DCIS-like lesions in three-dimensional lrECM and in vivo, and are a plausible model for some forms of human DCIS. A population of Akt-driven DCIS-like spheroids that survive IR progresses to an invasive phenotype in three-dimensional lrECM mediated by beta 1-integrin and NF-kappa B signaling. C1 [Nam, Jin-Min; Kinoshita, Rumiko; Shirato, Hiroki] Hokkaido Univ, Dept Radiat Med, Grad Sch Med, Sapporo, Hokkaido 0608638, Japan. [Ahmed, Kazi M.; Costes, Sylvain; Zhang, Hui; Park, Catherine C.] Ernest Orlando Lawrence Berkeley Natl Lab, Life Sci Div, Berkeley, CA 94720 USA. [Onodera, Yasuhito; Sabe, Hisataka] Hokkaido Univ, Dept Mol Biol, Grad Sch Med, Sapporo, Hokkaido 0608638, Japan. [Olshen, Adam B.] Univ Calif San Francisco, Dept Epidemiol & Biostat, San Francisco, CA 94158 USA. [Hatanaka, Kanako C.] Hokkaido Univ Hosp, Dept Surg Pathol, Sapporo, Hokkaido 0608638, Japan. [Ishikawa, Masayori] Hokkaido Univ, Dept Med Phys & Engn, Grad Sch Med, Sapporo, Hokkaido 0608638, Japan. [Park, Catherine C.] Univ Calif San Francisco, Calif Comprehens Canc Ctr, Dept Radiat Oncol, San Francisco, CA 94143 USA. RP Park, CC (reprint author), Ernest Orlando Lawrence Berkeley Natl Lab, Life Sci Div, 1 Cyclotron Rd, Berkeley, CA 94720 USA. EM cpark@radonc.ucsf.edu RI Shirato, Hiroki/A-7068-2010 FU NIH [1R01CA124891]; American Cancer Society [RSG-07-1110-01-CCE]; Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT); Japan Society for Young Scientists [23791376, 25861050] FX We thank Atsuko Saito and Mariko Sashika for their technical assistance and Keiko Kanno, Midori Tokuda and Etsuko Hayashi for their administrative work. We also thank Dr. Shigeru Hashimoto and Dr. Ari Hashimoto for support. We are grateful to the Department of Breast and Endocrine Surgery of Hokkaido University Hospital for providing us with the clinical specimens. This work was supported by NIH grant 1R01CA124891 to CP and by the American Cancer Society RSG-07-1110-01-CCE to CP. This work was supported in part by the Matching Program for Innovations in Future Drug Discovery and Medical Care from the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT) and by the Grant-in-Aid from the Japan Society for Young Scientists (B) (23791376 and 25861050) to JN. NR 39 TC 10 Z9 10 U1 0 U2 5 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1465-542X EI 1465-5411 J9 BREAST CANCER RES JI Breast Cancer Res. PY 2013 VL 15 IS 4 AR R60 DI 10.1186/bcr3454 PG 15 WC Oncology SC Oncology GA AB1HV UT WOS:000331543000009 PM 23883667 ER PT S AU Kruse, MKG AF Kruse, Michael Karl Gerhard BA Kruse, MKG BF Kruse, MKG TI Introduction to Low-Energy Nuclear Physics SO EXTENSIONS TO THE NO-CORE SHELL MODEL: IMPORTANCE-TRUNCATION, REGULATORS AND REACTIONS SE Springer Theses-Recognizing Outstanding PhD Research LA English DT Editorial Material; Book Chapter ID MONTE-CARLO CALCULATIONS; GROUND-STATE; SHELL-MODEL; SCATTERING; EQUATIONS C1 Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. RP Kruse, MKG (reprint author), Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. NR 27 TC 0 Z9 0 U1 1 U2 1 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 2190-5053 BN 978-3-319-01392-3 J9 SPRINGER THESES-RECO PY 2013 BP 1 EP 8 DI 10.1007/978-3-319-01393-0_1 D2 10.1007/978-3-319-01393-0 PG 8 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA BJQ88 UT WOS:000329742000002 ER PT S AU Kruse, MKG AF Kruse, Michael Karl Gerhard BA Kruse, MKG BF Kruse, MKG TI Extensions to the No-Core Shell Model Importance-Truncation, Regulators and Reactions Foreword SO EXTENSIONS TO THE NO-CORE SHELL MODEL: IMPORTANCE-TRUNCATION, REGULATORS AND REACTIONS SE Springer Theses-Recognizing Outstanding PhD Research LA English DT Editorial Material; Book Chapter C1 Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. RP Kruse, MKG (reprint author), Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. NR 0 TC 0 Z9 0 U1 0 U2 0 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 2190-5053 BN 978-3-319-01392-3 J9 SPRINGER THESES-RECO PY 2013 BP VII EP VIII D2 10.1007/978-3-319-01393-0 PG 2 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA BJQ88 UT WOS:000329742000001 ER PT S AU Kruse, MKG AF Kruse, Michael Karl Gerhard BA Kruse, MKG BF Kruse, MKG TI The No Core Shell Model SO EXTENSIONS TO THE NO-CORE SHELL MODEL: IMPORTANCE-TRUNCATION, REGULATORS AND REACTIONS SE Springer Theses-Recognizing Outstanding PhD Research LA English DT Article; Book Chapter ID CHIRAL PERTURBATION-THEORY; SPURIOUS STATES; FLOW-EQUATIONS; NUCLEAR-FORCES; LAGRANGIANS; HAMILTONIANS; RENORMALIZATION; BRACKETS; MASS C1 Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. RP Kruse, MKG (reprint author), Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. NR 59 TC 0 Z9 0 U1 0 U2 0 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 2190-5053 BN 978-3-319-01392-3 J9 SPRINGER THESES-RECO PY 2013 BP 9 EP 32 DI 10.1007/978-3-319-01393-0_2 D2 10.1007/978-3-319-01393-0 PG 24 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA BJQ88 UT WOS:000329742000003 ER PT S AU Kruse, MKG AF Kruse, Michael Karl Gerhard BA Kruse, MKG BF Kruse, MKG TI Importance Truncated No Core Shell Model SO EXTENSIONS TO THE NO-CORE SHELL MODEL: IMPORTANCE-TRUNCATION, REGULATORS AND REACTIONS SE Springer Theses-Recognizing Outstanding PhD Research LA English DT Article; Book Chapter ID CONFIGURATION-INTERACTION; PERTURBATION-THEORY C1 Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. RP Kruse, MKG (reprint author), Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. NR 32 TC 0 Z9 0 U1 0 U2 0 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 2190-5053 BN 978-3-319-01392-3 J9 SPRINGER THESES-RECO PY 2013 BP 33 EP 77 DI 10.1007/978-3-319-01393-0_3 D2 10.1007/978-3-319-01393-0 PG 45 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA BJQ88 UT WOS:000329742000004 ER PT S AU Kruse, MKG AF Kruse, Michael Karl Gerhard BA Kruse, MKG BF Kruse, MKG TI UV and IR Properties of the NCSM SO EXTENSIONS TO THE NO-CORE SHELL MODEL: IMPORTANCE-TRUNCATION, REGULATORS AND REACTIONS SE Springer Theses-Recognizing Outstanding PhD Research LA English DT Article; Book Chapter C1 Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. RP Kruse, MKG (reprint author), Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. NR 10 TC 0 Z9 0 U1 0 U2 0 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 2190-5053 BN 978-3-319-01392-3 J9 SPRINGER THESES-RECO PY 2013 BP 79 EP 91 DI 10.1007/978-3-319-01393-0_4 D2 10.1007/978-3-319-01393-0 PG 13 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA BJQ88 UT WOS:000329742000005 ER PT S AU Kruse, MKG AF Kruse, Michael Karl Gerhard BA Kruse, MKG BF Kruse, MKG TI Extending the NCSM with the RGM SO EXTENSIONS TO THE NO-CORE SHELL MODEL: IMPORTANCE-TRUNCATION, REGULATORS AND REACTIONS SE Springer Theses-Recognizing Outstanding PhD Research LA English DT Article; Book Chapter ID STATES; KNOCKOUT; ISOTOPES; BE-11; HE-9 C1 Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. RP Kruse, MKG (reprint author), Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. NR 19 TC 0 Z9 0 U1 0 U2 0 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 2190-5053 BN 978-3-319-01392-3 J9 SPRINGER THESES-RECO PY 2013 BP 93 EP 116 DI 10.1007/978-3-319-01393-0_5 D2 10.1007/978-3-319-01393-0 PG 24 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA BJQ88 UT WOS:000329742000006 ER PT S AU Kruse, MKG AF Kruse, Michael Karl Gerhard BA Kruse, MKG BF Kruse, MKG TI Extensions to the No-Core Shell Model Importance-Truncation, Regulators and Reactions Conclusion SO EXTENSIONS TO THE NO-CORE SHELL MODEL: IMPORTANCE-TRUNCATION, REGULATORS AND REACTIONS SE Springer Theses-Recognizing Outstanding PhD Research LA English DT Editorial Material; Book Chapter ID STATE C1 Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. RP Kruse, MKG (reprint author), Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. NR 12 TC 0 Z9 0 U1 0 U2 0 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 2190-5053 BN 978-3-319-01392-3 J9 SPRINGER THESES-RECO PY 2013 BP 117 EP 123 DI 10.1007/978-3-319-01393-0_6 D2 10.1007/978-3-319-01393-0 PG 7 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA BJQ88 UT WOS:000329742000007 ER PT J AU Onar, OC Campbell, S Ning, PQ Miller, JM Liang, ZX AF Onar, Omer C. Campbell, Steven Ning, Puqi Miller, John M. Liang, Zhenxian GP IEEE TI Fabrication and Evaluation of a High Performance SiC Inverter for Wireless Power Transfer Applications SO 2013 1ST IEEE WORKSHOP ON WIDE BANDGAP POWER DEVICES AND APPLICATIONS (WIPDA) LA English DT Proceedings Paper CT 1st Annual IEEE Workshop on Wide Bandgap Power Devices and Applications (WiPDA) CY OCT 27-29, 2013 CL Columbus, OH SP IEEE, Power Sources Manufacturers Assoc, IEEE Power Elect Soc, Electron Devices Soc AB In this study, a high power density SiC high efficiency wireless power transfer converter system via inductive coupling has been designed and developed. The detailed power module design, cooling system design and power stage development are presented. The successful operation of rated power converter system demonstrates the feasible wireless charging plan. One of the most important part of this study is the wind bandgap devices packaged at the Oak Ridge National Laboratory (ORNL) using the in-house packaging technologies by employing the bare SiC dies acquired from CREE, which are rated at 50 A / 1200 V each. These packaged devices are also in-house tested and characterized using ORNL's Device Characterization Facility. The successful operation of the proposed inverter is experimentally verified and the efficiency and operational characteristics of the inverter are also revealed. C1 [Onar, Omer C.; Campbell, Steven; Ning, Puqi; Miller, John M.; Liang, Zhenxian] Oak Ridge Natl Lab, Power Elect & Elect Machinery Grp, Oak Ridge, TN 37831 USA. RP Onar, OC (reprint author), Oak Ridge Natl Lab, Power Elect & Elect Machinery Grp, Oak Ridge, TN 37831 USA. EM onaroc@ornl.gov; campbellsl@ornl.gov; ningp@ornl.gov; millerjm@ornl.gov; liangz@ornl.gov OI Liang, Zhenxian/0000-0002-2811-0944 NR 8 TC 3 Z9 3 U1 0 U2 3 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-1-4799-1194-3 PY 2013 BP 125 EP 130 PG 6 WC Engineering, Electrical & Electronic SC Engineering GA BA0EW UT WOS:000331112200029 ER PT J AU Castellana, VG Tumeo, A Villa, O Haglin, D Feo, J AF Castellana, Vito Giovanni Tumeo, Antonino Villa, Oreste Haglin, David Feo, John GP IEEE Comp Soc Acad Sci & Engn TI Composing Data Parallel Code for a SPARQL Graph Engine SO 2013 ASE/IEEE INTERNATIONAL CONFERENCE ON SOCIAL COMPUTING (SOCIALCOM) LA English DT Proceedings Paper CT ASE/IEEE International Conference on Social Computing (SocialCom) CY SEP 08-14, 2013 CL Washington, DC SP Acad Sci Engn, IEEE, IEEE Comp Soc AB The emergence of petascale triple stores have motivated the investigation of alternates to traditional table-based relational methods. Since triple stores represent data as structured tuples, graphs are a natural data structure for encoding their information. The use of graph data structures, rather than tables, requires us to rethink the methods used to process queries on the store. We are developing a scalable, in-memory SPARQL graph engine that scales to hundreds of nodes while maintaining constant query throughput. Our framework comprises a SPARQL to data parallel C compiler, a library of parallel graph methods, and a custom multithreaded runtime layer for multinode commodity systems. Rather than transforming SPARQL queries into a series of select and join operations on tables, our front end compiles the queries into data parallel C code with calls to graph methods that walk internal data structures, constructing answers in their wake. In this paper, we describe the compilation process and give examples of the generated C code parallelized with OpenMP. We present performance numbers for the SP2Bench SPARQL benchmark queries on a 48-core shared-memory system. With respect to conventional relational database systems such as Virtuoso, our approach uses less memory and provides higher performance. C1 [Castellana, Vito Giovanni; Tumeo, Antonino; Villa, Oreste; Haglin, David; Feo, John] Pacific NW Natl Lab, Richland, WA 99354 USA. RP Castellana, VG (reprint author), Pacific NW Natl Lab, Richland, WA 99354 USA. EM vitogiovanni.castellana@pnnl.gov; antonino.tumeo@pnnl.gov; vcastellana@elet.polimi.it; david.haglin@pnnl.gov; john.feo@pnnl.gov RI Tumeo, Antonino/L-3106-2016 NR 17 TC 0 Z9 0 U1 0 U2 0 PU IEEE COMPUTER SOC PI LOS ALAMITOS PA 10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA 90720-1264 USA BN 978-0-7695-5137-1 PY 2013 BP 691 EP 699 DI 10.1109/SocialCom.2013.104 PG 9 WC Computer Science, Information Systems SC Computer Science GA BJU40 UT WOS:000330563800099 ER PT S AU Koch, MW AF Koch, Mark W. GP IEEE TI One-Class Multiple-Look Fusion: a theoretical comparison of different approaches with examples from infrared video SO 2013 IEEE CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION WORKSHOPS (CVPRW) SE IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops LA English DT Proceedings Paper CT 26th IEEE Conference on Computer Vision and Pattern Recognition (CVPR) CY JUN 23-28, 2013 CL Portland, OR SP IEEE, IEEE Comp Soc ID CLASSIFICATION AB Multiple-look fusion is quickly becoming more important in statistical pattern recognition. With increased computing power and memory one can make many measurements on an object of interest using, for example, video imagery or radar. By obtaining more views of an object, a system can make decisions with lower missed detection and false alarm errors. There are many approaches for combining information from multiple looks and we mathematically compare and contrast the sequential probability ratio test, Bayesian fusion, and Dempster-Shafer theory of evidence. Using a consistent probabilistic framework we demonstrate the differences and similarities between the approaches and show results for an application in infrared video classification. C1 Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Koch, MW (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87185 USA. EM mwkoch@sandia.gov NR 12 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 2160-7508 BN 978-0-7695-4990-3 J9 IEEE COMPUT SOC CONF PY 2013 BP 342 EP 347 DI 10.1109/CVPRW.2013.58 PG 6 WC Computer Science, Artificial Intelligence SC Computer Science GA BA0EZ UT WOS:000331116100055 ER PT B AU Hogan, E Hui, P Choudhury, S Halappanavar, M Oler, K Joslyn, C AF Hogan, Emilie Hui, Peter Choudhury, Sutanay Halappanavar, Mahantesh Oler, Kiri Joslyn, Cliff GP IEEE TI Towards a Multiscale Approach To Cybersecurity Modeling SO 2013 IEEE INTERNATIONAL CONFERENCE ON TECHNOLOGIES FOR HOMELAND SECURITY (HST) LA English DT Proceedings Paper CT 13th IEEE International Conference on Technologies for Homeland Security (HST) CY NOV 12-14, 2013 CL Waltham, MA SP IEEE, IEEE USA, IEEE Biometr Council, Massport, Govt Technol and Serv Coalit, Boston Prod Management Assoc, Massachusetts High Technol Council, Market Res Media, IEEE Women Engn, Domest Preparedness Com, DPJ Weekly Brief, DomPrep Journal, IEEE Boston Sect ID NETWORKS AB We propose a multiscale approach to modeling cyber networks, with the goal of capturing a view of the network and overall situational awareness with respect to a few key properties - connectivity, distance, and centrality - for a system under an active attack. We focus on theoretical and algorithmic foundations of multiscale graphs, coming from an algorithmic perspective, with the goal of modeling cyber system defense as a specific use case scenario. We first define a notion of multiscale graphs, in contrast with their well-studied single- scale counterparts. We develop multiscale analogs of paths and distance metrics. As a simple, motivating example of a common metric, we present a multiscale analog of the all-pairs shortest-path problem, along with a multiscale analog of a well-known algorithm which solves it. From a cyber defense perspective, this metric might be used to model the distance from an attacker's position in the network to a sensitive machine. In addition, we investigate probabilistic models of connectivity. These models exploit the hierarchy to quantify the likelihood that sensitive targets might be reachable from compromised nodes. We believe that our novel multiscale approach to modeling cyber-physical systems will advance several aspects of cyber defense, specifically allowing for a more efficient and agile approach to defending these systems. C1 [Hogan, Emilie; Hui, Peter; Choudhury, Sutanay; Halappanavar, Mahantesh; Oler, Kiri; Joslyn, Cliff] Pacific NW Natl Lab, Richland, WA 99352 USA. RP Hogan, E (reprint author), Pacific NW Natl Lab, Richland, WA 99352 USA. EM emilie.hogan@pnnl.gov; peter.hui@pnnl.gov; sutanay.choudhury@pnnl.gov; mahantesh.halappanavar@pnnl.gov; kiri.oler@pnnl.gov; cliff.joslyn@pnnl.gov NR 11 TC 1 Z9 1 U1 1 U2 4 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-1-4799-1535-4; 978-1-4799-3963-3 PY 2013 BP 80 EP 85 PG 6 WC Computer Science, Interdisciplinary Applications; Engineering, Electrical & Electronic; Operations Research & Management Science SC Computer Science; Engineering; Operations Research & Management Science GA BA0AD UT WOS:000330768500015 ER PT B AU Watkins, DM Sego, LH Holmes, AE Webb-Robertson, BJM White, AM Wunschel, DS Kreuzer, HW Corley, CD Tardiff, MF AF Watkins, Daniel M. Sego, Landon H. Holmes, Aimee E. Webb-Robertson, Bobbie-Jo M. White, Amanda M. Wunschel, David S. Kreuzer, Helen W. Corley, Courtney D. Tardiff, Mark F. GP IEEE TI Assessing Performance and Tradeoffs of Bioforensic Signature Systems SO 2013 IEEE INTERNATIONAL CONFERENCE ON TECHNOLOGIES FOR HOMELAND SECURITY (HST) LA English DT Proceedings Paper CT 13th IEEE International Conference on Technologies for Homeland Security (HST) CY NOV 12-14, 2013 CL Waltham, MA SP IEEE, IEEE USA, IEEE Biometr Council, Massport, Govt Technol and Serv Coalit, Boston Prod Management Assoc, Massachusetts High Technol Council, Market Res Media, IEEE Women Engn, Domest Preparedness Com, DPJ Weekly Brief, DomPrep Journal, IEEE Boston Sect DE multiattribute decision analysis; decision theory; Bayesian networks; microbial forensics; Yersinia pestis ID MICROBIAL FORENSICS AB Chemical and biological forensic programs rely on laboratory measurements to determine how a threat agent may have been produced. In addition to laboratory analyses, it may also be useful to identify institutions where the same threat agent has been produced by the same (or a similar) process, since the producer of the agent may have learned methods at a university or similar institution. In this paper, we evaluate a Bayesian network that combines the results of laboratory measurements with evidence from scientific literature to probabilistically rank institutions that have published papers on the agent of interest. We apply techniques from multiattribute decision science to assess and compare the performance of various implementations of the Bayesian network in terms of three attributes: fidelity, consumption of the forensic sample, and document curation intensity. The mathematical approach we use to compare the various implementations is generalizable to the evaluation of other signature systems. C1 [Watkins, Daniel M.; Sego, Landon H.; Holmes, Aimee E.; Wunschel, David S.; Kreuzer, Helen W.; Corley, Courtney D.; Tardiff, Mark F.] Pacific Northwest Natl Lab, Natl Secur Directorate, Richland, WA 99352 USA. [Watkins, Daniel M.] Univ Drexel, Dept Math, Philadelphia, PA USA. [Webb-Robertson, Bobbie-Jo M.; White, Amanda M.] Pacific Northwest Natl Lab, Fundamental & Computat Sci Directorat, Richland, WA USA. RP Sego, LH (reprint author), Pacific Northwest Natl Lab, Natl Secur Directorate, Richland, WA 99352 USA. EM danielmwatkins@gmail.com; landon.sego@pnnl.gov; aimee.holmes@pnnl.gov; bobbie-jo.webb-robertson@pnnl.gov; amanda.white@pnnl.gov; david.wunschel@pnnl.gov; helen.kreuzer@pnnl.gov; courtney.corley@pnnl.gov; mark.tardiff@pnnl.gov NR 15 TC 1 Z9 1 U1 1 U2 3 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-1-4799-1535-4; 978-1-4799-3963-3 PY 2013 BP 304 EP 309 PG 6 WC Computer Science, Interdisciplinary Applications; Engineering, Electrical & Electronic; Operations Research & Management Science SC Computer Science; Engineering; Operations Research & Management Science GA BA0AD UT WOS:000330768500049 ER PT B AU McKenzie, A Gillen, R Bogen, PL AF McKenzie, Amber Gillen, Rob Bogen, Paul Logasa, II GP IEEE TI Redeye Text Analysis Workbench Actionable intelligence from non-actionable data SO 2013 IEEE INTERNATIONAL CONFERENCE ON TECHNOLOGIES FOR HOMELAND SECURITY (HST) LA English DT Proceedings Paper CT 13th IEEE International Conference on Technologies for Homeland Security (HST) CY NOV 12-14, 2013 CL Waltham, MA SP IEEE, IEEE USA, IEEE Biometr Council, Massport, Govt Technol and Serv Coalit, Boston Prod Management Assoc, Massachusetts High Technol Council, Market Res Media, IEEE Women Engn, Domest Preparedness Com, DPJ Weekly Brief, DomPrep Journal, IEEE Boston Sect DE digital forensics; redeye; text analysis AB With the increase in digital data within the realm of law enforcement digital forensics comes significant challenges in the form of data discovery and analysis. The Redeye Text Analysis Workbench, produced by Oak Ridge National Laboratory, seeks to bridge the gap between existing data acquisition and higher-level data analysis systems in which forensic analysts must currently manually identify pertinent and relevant documents from possibly many terabytes of data that can then be used as input for further examination. The Redeye toolkit comprises two separate components: an ingestion pipeline and the workbench interface. Both of these components incorporate a number of tools - open source, proprietary, and custom-built - which have been integrated together to transcend the tools themselves. The final application is a means to facilitate the discovery of interesting, useful data within a digital forensics investigation. C1 [McKenzie, Amber; Gillen, Rob; Bogen, Paul Logasa, II] Oak Ridge Natl Lab, Computat Data Analyt Grp, Oak Ridge, TN 37831 USA. RP McKenzie, A (reprint author), Oak Ridge Natl Lab, Computat Data Analyt Grp, Oak Ridge, TN 37831 USA. EM redev@ornl.gov NR 17 TC 2 Z9 2 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-1-4799-1535-4; 978-1-4799-3963-3 PY 2013 BP 381 EP 385 PG 5 WC Computer Science, Interdisciplinary Applications; Engineering, Electrical & Electronic; Operations Research & Management Science SC Computer Science; Engineering; Operations Research & Management Science GA BA0AD UT WOS:000330768500063 ER PT B AU Sanfilippo, A Chikkagoudar, S AF Sanfilippo, Antonio Chikkagoudar, Satish GP IEEE TI Automated Detection of Anomalous Shipping Manifests to Identify Illicit Trade SO 2013 IEEE INTERNATIONAL CONFERENCE ON TECHNOLOGIES FOR HOMELAND SECURITY (HST) LA English DT Proceedings Paper CT 13th IEEE International Conference on Technologies for Homeland Security (HST) CY NOV 12-14, 2013 CL Waltham, MA SP IEEE, IEEE USA, IEEE Biometr Council, Massport, Govt Technol and Serv Coalit, Boston Prod Management Assoc, Massachusetts High Technol Council, Market Res Media, IEEE Women Engn, Domest Preparedness Com, DPJ Weekly Brief, DomPrep Journal, IEEE Boston Sect DE trade data; clustering; classification; visual analytics; illicit trafficking; detection of radiological threat materials; nuclear smuggling AB We describe an approach to analyzing anomalies in trade data based on the identification of cluster outliers. The approach uses unsupervised machine learning methods to discover semantically coherent clusters of shipping records in large collections of trade data. Trade data with cluster annotations are then used as input to a supervised machine learning algorithm to train and evaluate a classification model capable of identifying members of each cluster. The evaluation of this classification model provides an assessment of cluster coherence. Outliers are identified for each cluster by measuring the Euclidean distance from each member of the cluster to the cluster centroid, and then selecting a percentile threshold to identify shipping records with extreme distances from the cluster centroid. We describe a specific application of this approach to a dataset of 2.36M records for containerized shipments, with specific reference to the detection of anomalies potentially related to nuclear smuggling. Results show that this approach succeeds in finding semantically coherent clusters of shipping records, and identifying outliers that may help facilitate the detection of illicit trade. C1 [Sanfilippo, Antonio; Chikkagoudar, Satish] Pacific NW Natl Lab, Computat & Stat Div, Natl Secur Directorate, Richland, WA 99352 USA. RP Sanfilippo, A (reprint author), Pacific NW Natl Lab, Computat & Stat Div, Natl Secur Directorate, Richland, WA 99352 USA. EM antonio.sanfilippo@pnnl.gov; satish.chikkagoudar@pnnl.gov RI Sanfilippo, Antonio/B-6743-2016 OI Sanfilippo, Antonio/0000-0001-7097-4562 NR 14 TC 0 Z9 0 U1 1 U2 3 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-1-4799-1535-4; 978-1-4799-3963-3 PY 2013 BP 529 EP 534 PG 6 WC Computer Science, Interdisciplinary Applications; Engineering, Electrical & Electronic; Operations Research & Management Science SC Computer Science; Engineering; Operations Research & Management Science GA BA0AD UT WOS:000330768500088 ER PT B AU Ramuhalli, P Halappanavar, M Coble, J Dixit, M AF Ramuhalli, Pradeep Halappanavar, Mahantesh Coble, Jamie Dixit, Mukul GP IEEE TI Towards A Theory of Autonomous Reconstitution of Compromised Cyber-Systems SO 2013 IEEE INTERNATIONAL CONFERENCE ON TECHNOLOGIES FOR HOMELAND SECURITY (HST) LA English DT Proceedings Paper CT 13th IEEE International Conference on Technologies for Homeland Security (HST) CY NOV 12-14, 2013 CL Waltham, MA SP IEEE, IEEE USA, IEEE Biometr Council, Massport, Govt Technol and Serv Coalit, Boston Prod Management Assoc, Massachusetts High Technol Council, Market Res Media, IEEE Women Engn, Domest Preparedness Com, DPJ Weekly Brief, DomPrep Journal, IEEE Boston Sect DE resilient cyber-systems; reconstitution; recovery; evolution ID BYZANTINE AGREEMENT AB Effective reconstitution approaches for cyber systems are needed to keep critical infrastructure operational in the face of an intelligent adversary. The reconstitution response, including recovery and adaptation, may require significant reconfiguration of the system at all levels to render the cyber-system resilient to ongoing and future attacks or faults while maintaining continuity of operations. A theoretical basis for optimal dynamic reconstitution is needed to address the challenge of ensuring that dynamic reconstitution is optimal with respect to resilience metrics, and is being developed and evaluated in this project. Such a framework provides the technical basis for evaluating cyber-defense and reconstitution approaches. This paper describes a preliminary framework that may be used to develop and evaluate concepts for effective autonomous reconstitution of compromised cyber systems. C1 [Ramuhalli, Pradeep; Halappanavar, Mahantesh; Dixit, Mukul] Pacific Northwest Natl Lab, Richland, WA 99352 USA. [Coble, Jamie] Univ Tennessee, Knoxville, TN USA. RP Ramuhalli, P (reprint author), Pacific Northwest Natl Lab, Richland, WA 99352 USA. EM Pradeep.Ramuhalli@pnnl.gov; hala@pnnl.gov; jcoble1@utk.edu; Mukul.Dixit@pnnl.gov OI Ramuhalli, Pradeep/0000-0001-6372-1743 FU Asymmetric Resilient Cybersystems Initiative at the Pacific Northwest National Laboratory (PNNL); US Department of Energy [DE-AC0676RLO 1830] FX This work was supported by the Asymmetric Resilient Cybersystems Initiative at the Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated by Battelle Memorial Institute for the US Department of Energy under DE-AC0676RLO 1830. NR 22 TC 1 Z9 1 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-1-4799-1535-4; 978-1-4799-3963-3 PY 2013 BP 577 EP 583 PG 7 WC Computer Science, Interdisciplinary Applications; Engineering, Electrical & Electronic; Operations Research & Management Science SC Computer Science; Engineering; Operations Research & Management Science GA BA0AD UT WOS:000330768500096 ER PT B AU Nobles, MA Sego, LH Cooley, SK Gosink, LJ Anderson, RM Hays, SE Tardiff, MF AF Nobles, Mallory A. Sego, Landon H. Cooley, Scott K. Gosink, Luke J. Anderson, Richard M. Hays, Spencer E. Tardiff, Mark F. GP IEEE TI A Decision-Theoretic Approach to Evaluate Radiation Detection Algorithms SO 2013 IEEE INTERNATIONAL CONFERENCE ON TECHNOLOGIES FOR HOMELAND SECURITY (HST) LA English DT Proceedings Paper CT 13th IEEE International Conference on Technologies for Homeland Security (HST) CY NOV 12-14, 2013 CL Waltham, MA SP IEEE, IEEE USA, IEEE Biometr Council, Massport, Govt Technol and Serv Coalit, Boston Prod Management Assoc, Massachusetts High Technol Council, Market Res Media, IEEE Women Engn, Domest Preparedness Com, DPJ Weekly Brief, DomPrep Journal, IEEE Boston Sect DE multiattribute decision analysis; decision theory; signatures; assessment AB There are a variety of sensor systems deployed at border crossings and ports of entry throughout the world that scan for illicit nuclear material. These systems employ detection algorithms that interpret the output of the scans and determine whether additional investigation is warranted. In this work, we demonstrate an approach for comparing the performance of such detection algorithms. We optimize each algorithm by minimizing risk, which considers the probability distribution of threat sources and the consequence of detection errors. Our method is flexible and is easily adapted to many different assumptions regarding the probability of a conveyance containing illicit material and the relative consequences of false positive and false negative errors. This approach can help developers and decision makers identify optimal settings for these algorithms. We illustrate the method by comparing the risk from two families of detection algorithms and discuss the generalizability of the method. C1 [Nobles, Mallory A.] Carnegie Mellon Univ, HJ Heinz Coll 3, Pittsburgh, PA 15213 USA. RP Sego, LH (reprint author), Pacific NW Natl Lab, Appl Stat & Computat Modeling Grp, Richland, WA 99352 USA. EM mnobles@andrew.cmu.edu; landon.sego@pnnl.gov; scott.cooley@pnnl.gov; luke.gosink@pnnl.gov; rmanders@uw.edu; shays@vcu.edu; mark.tardiff@pnnl.gov NR 9 TC 0 Z9 0 U1 0 U2 4 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-1-4799-1535-4; 978-1-4799-3963-3 PY 2013 BP 683 EP 686 PG 4 WC Computer Science, Interdisciplinary Applications; Engineering, Electrical & Electronic; Operations Research & Management Science SC Computer Science; Engineering; Operations Research & Management Science GA BA0AD UT WOS:000330768500114 ER PT S AU Zhao, JK Robertson, L Herwig, K Crabb, D AF Zhao, J. K. Robertson, Lee Herwig, Ken Crabb, Donald BE Bourges, P Gillon, B Gukasov, A Klimko, S Longeville, S Mirebeau, I Ott, F TI Polarized neutron in structural biology - present and future outlook SO 9TH INTERNATIONAL CONFERENCE ON POLARISED NEUTRONS IN CONDENSED MATTER INVESTIGATIONS SE Physics Procedia LA English DT Proceedings Paper CT 9th International Conference on Polarised Neutrons in Condensed Matter Investigations (PNCMI) CY JUL 02-05, 2012 CL Paris, FRANCE SP CEA, CNRS, IRAMIS, LLB, ILL, HZB, JCNS, Swiss Neutron DE Polarized Neutron Scattering; Dynamic Nuclear Polarization; DNP ID DYNAMIC NUCLEAR-POLARIZATION; ESCHERICHIA-COLI RIBOSOMES; HYDROGENOUS MATERIALS; IN-SITU; SCATTERING; SUBUNIT; PROTEINS; CONTRAST AB Hydrogen has a strong polarization-dependent neutron scattering cross section. This property has been exploited in the study of soft matters, especially biological macromolecules. When a polarized neutron beam is scattered off a polarized hydrogenous sample, the otherwise large hydrogen incoherent cross section is drastically reduced while the coherent signal is significantly increased. Past experiments have demonstrated the potentials and benefits of polarized neutron scattering from soft materials. The main technical challenge of polarized neutron scattering from biological matters lies at sample polarization. Dynamic nuclear polarization is a proven yet rather sophisticated technique. Its complexity is one of the main reasons for the technique's slow adoption. The future of polarized neutron scattering in biology may rest largely in neutron protein crystallography. Polarization of protein crystals is much easier to accomplish, since protein crystals are typically rather small (<<1mm) and only require small and easy-to-operate polarization apparatuses. In addition, the high resolution nature of neutron protein crystallography means that we will be able to study individual atoms using the polarized neutron scattering technique. (c) 2013 The Authors. Published by Elsevier B.V. C1 [Zhao, J. K.; Robertson, Lee; Herwig, Ken] Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. [Crabb, Donald] Univ Virginia, Dept Phys, Charlottesville, VA 22904 USA. RP Zhao, JK (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. EM zhaoj@ornl.gov FU UT-Battelle; LLC [DE-AC05-00OR22725]; U.S.Department of Energy FX This manuscript has been authored by UT-Battelle, LLC,under Contract No. DE-AC05-00OR22725 with the U.S.Department of Energy. The United States Government retains,and the publisher, by accepting the article for publication,acknowledges that the United States Government retains a non-xclusive,paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. NR 19 TC 0 Z9 0 U1 0 U2 5 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA SARA BURGERHARTSTRAAT 25, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 1875-3892 J9 PHYSCS PROC PY 2013 VL 42 BP 39 EP 45 DI 10.1016/j.phpro.2013.03.173 PG 7 WC Physics, Applied; Physics, Condensed Matter SC Physics GA BA0GZ UT WOS:000331183800007 ER PT S AU Jiang, CY Tong, X Brown, DR Lee, WT Ambaye, H Craig, JW Crow, L Culbertson, H Goyette, R Graves-Brook, MK Hagen, ME Kadron, B Lauter, V McCollum, LW Robertson, JL Winn, B Vandegrift, AE AF Jiang, C. Y. Tong, X. Brown, D. R. Lee, W. T. Ambaye, H. Craig, J. W. Crow, L. Culbertson, H. Goyette, R. Graves-Brook, M. K. Hagen, M. E. Kadron, B. Lauter, V. McCollum, L. W. Robertson, J. L. Winn, B. Vandegrift, A. E. BE Bourges, P Gillon, B Gukasov, A Klimko, S Longeville, S Mirebeau, I Ott, F TI Polarized He-3 Neutron Spin Filters at Oak Ridge National Laboratory SO 9TH INTERNATIONAL CONFERENCE ON POLARISED NEUTRONS IN CONDENSED MATTER INVESTIGATIONS SE Physics Procedia LA English DT Proceedings Paper CT 9th International Conference on Polarised Neutrons in Condensed Matter Investigations (PNCMI) CY JUL 02-05, 2012 CL Paris, FRANCE SP CEA, CNRS, IRAMIS, LLB, ILL, HZB, JCNS, Swiss Neutron DE Helium-3; polarized; optical pumping; neutron spin filter AB The unique advantages of using polarized He-3 as neutron spin filters, such as broadband and wide angular acceptance of neutron beams, have made it widely used in most neutron facilities. Over the last several years, we have developed a polarized He-3 program to meet the increasing needs of He-3 based neutron spin filters at the Oak Ridge National Laboratory (ORNL) High Flux Isotope Reactor (HFIR) and Spallation Neutron Source (SNS). At ORNL, polarized He-3 is produced using Spin Exchange Optical Pumping (SEOP). We have constructed a He-3 cell fabrication station to produce He-3 cells of different pressures and dimensions. Two optical pumping stations have been built in the lab to perform ex situ pumping of He-3. A compact in situ He-3 analyzer has been constructed and installed for the Magnetism Reflectometer (MAGICS) at SNS. A novel polarized He-3 filling station for the Hybrid Spectrometer (HYSPEC) at SNS is under development. (C) 2012 Published by Elsevier B.V. C1 [Jiang, C. Y.; Tong, X.; Brown, D. R.; Ambaye, H.; Craig, J. W.; Crow, L.; Culbertson, H.; Goyette, R.; Graves-Brook, M. K.; Hagen, M. E.; Kadron, B.; Lauter, V.; McCollum, L. W.; Robertson, J. L.; Winn, B.; Vandegrift, A. E.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. [Lee, W. T.] Australian Nucl Sci & Technol Org, Menai, NSW 2234, Australia. RP Jiang, CY (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. EM tongx@ornl.gov RI Winn, Barry/A-5065-2016; Ambaye, Haile/D-1503-2016; tong, Xin/C-4853-2012; OI Winn, Barry/0000-0001-6383-4318; Ambaye, Haile/0000-0002-8122-9952; tong, Xin/0000-0001-6105-5345; Jiang, Chenyang/0000-0002-6321-3164 FU Scientific User Facilities Division; Office of Basic Energy Sciences; U.S. Department of Energy FX Research at Oak Ridge National Laboratory's Spallation Neutron Source was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy. We also want to give special thanks to Dr. Thomas Gentile and Dr. Wangchun Chen at the National Institute of Standards and Technology (NIST) for their advice and guidance to our program. NR 12 TC 8 Z9 8 U1 1 U2 6 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA SARA BURGERHARTSTRAAT 25, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 1875-3892 J9 PHYSCS PROC PY 2013 VL 42 BP 191 EP 199 DI 10.1016/j.phpro.2013.03.194 PG 9 WC Physics, Applied; Physics, Condensed Matter SC Physics GA BA0GZ UT WOS:000331183800028 ER PT S AU Ye, Q Gentile, TR Anderson, J Broholm, C Chen, WC DeLand, Z Erwin, RW Fu, CB Fuller, J Kirchhoff, A Rodriguez-Rivera, JA Thampy, V Walker, TG Watson, S AF Ye, Q. Gentile, T. R. Anderson, J. Broholm, C. Chen, W. C. DeLand, Z. Erwin, R. W. Fu, C. B. Fuller, J. Kirchhoff, A. Rodriguez-Rivera, J. A. Thampy, V. Walker, T. G. Watson, S. BE Bourges, P Gillon, B Gukasov, A Klimko, S Longeville, S Mirebeau, I Ott, F TI Wide Angle Polarization Analysis With Neutron Spin Filters SO 9TH INTERNATIONAL CONFERENCE ON POLARISED NEUTRONS IN CONDENSED MATTER INVESTIGATIONS SE Physics Procedia LA English DT Proceedings Paper CT 9th International Conference on Polarised Neutrons in Condensed Matter Investigations (PNCMI) CY JUL 02-05, 2012 CL Paris, FRANCE SP CEA, CNRS, IRAMIS, LLB, ILL, HZB, JCNS, Swiss Neutron DE Polarized He-3; He-3 neutron spin filter; Wide angle He-3 cell ID HE-3 AB We report substantial improvements in a compact wide angle neutron spin filter system that was recently employed on the Multi-Axis Crystal Spectrometer at the Center for Neutron Research at the U. S. National Institute of Standards and Technology. The apparatus consists of a cylindrical He-3 polarizer cell and wide-angle He-3 analyzer cells, a vertical solenoid to provide a uniform magnetic field, and a shielded radio-frequency solenoid for the polarizer cell. Nuclear magnetic resonance is employed to reverse the polarization in the polarizer cell and monitor the He-3 polarization in all cells. The first experiment using this apparatus was carried out with cylindrical analyzer cells with limited angular coverage due to low polarizations in fused quartz cells. We present results for aluminosilicate glass analyzer cells that cover 110. and have long relaxation times (100 h to 400 h). Using two 100 W diode bars spectrally narrowed with chirped volume Bragg gratings, we have obtained 65 % -80 % 3He polarization in these cells. The He-3 polarization has been measured by neutron transmission and electron paramagnetic resonance. Additional progress includes an improved holding field solenoid and decreased spin-flip losses.(C) 2012 Published by Elsevier B.V. C1 [Ye, Q.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. [Ye, Q.; Gentile, T. R.; Anderson, J.; Broholm, C.; Chen, W. C.; Erwin, R. W.; Fu, C. B.; Fuller, J.; Kirchhoff, A.; Rodriguez-Rivera, J. A.; Watson, S.] Natl Inst Stand & Technol, Gaithersburg, MD 20899 USA. [Broholm, C.; Thampy, V.] Johns Hopkins Univ, Baltimore, MD 21218 USA. [Chen, W. C.; Rodriguez-Rivera, J. A.] Univ Maryland, College Pk, MD 20742 USA. [Fu, C. B.] Indiana Univ, Bloomington, IN 47405 USA. [Walker, T. G.] Univ Wisconsin, Madison, WI 53706 USA. RP Ye, Q (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. EM qiang.ye@nist.gov RI Rodriguez-Rivera, Jose/A-4872-2013; Fu, Changbo/O-1550-2015 OI Rodriguez-Rivera, Jose/0000-0002-8633-8314; FU U. S. Department of Energy; National Science Foundation [DMR-0944772] FX We acknowledge M. Huber for assistance with the neutron transmission measurements on beamline NG6A. This work is supported in part by the U. S. Department of Energy, Basic Energy Sciences and utilized facilities supported in part by the National Science Foundation under Agreement No. DMR-0944772. NR 24 TC 4 Z9 4 U1 0 U2 4 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA SARA BURGERHARTSTRAAT 25, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 1875-3892 J9 PHYSCS PROC PY 2013 VL 42 BP 206 EP 212 DI 10.1016/j.phpro.2013.03.197 PG 7 WC Physics, Applied; Physics, Condensed Matter SC Physics GA BA0GZ UT WOS:000331183800030 ER PT S AU Hill, KK Smith, TJ AF Hill, Karen K. Smith, Theresa J. BE Rummel, A Binz, T TI Genetic Diversity Within Clostridium botulinum Serotypes, Botulinum Neurotoxin Gene Clusters and Toxin Subtypes SO BOTULINUM NEUROTOXINS SE Current Topics in Microbiology and Immunology LA English DT Review; Book Chapter DE Subtype; OrfX toxin gene cluster; Ha toxin gene cluster; Horizontal gene transfer; Phylogentic tree; Clostridium botulinum genome ID FRAGMENT LENGTH POLYMORPHISM; FIELD GEL-ELECTROPHORESIS; E STRAINS; GENOME SEQUENCE; COMPLEX GENES; PLASMID; INTERRELATIONSHIPS; IDENTIFICATION; BUTYRICUM; BACILLUS AB Clostridium botulinum is a species of spore-forming anaerobic bacteria defined by the expression of any one or two of seven serologically distinct botulinum neurotoxins (BoNTs) designated BoNT/A-G. This Gram-positive bacterium was first identified in 1897 and since then the paralyzing and lethal effects of its toxin have resulted in the recognition of different forms of the intoxication known as food-borne, infant, or wound botulism. Early microbiological and biochemical characterization of C. botulinum isolates revealed that the bacteria within the species had different characteristics and expressed different toxin types. To organize the variable bacterial traits within the species, Group I-IV designations were created. Interestingly, it was observed that isolates within different Groups could express the same toxin type and conversely a single Group could express different toxin types. This discordant phylogeny between the toxin and the host bacteria indicated that horizontal gene transfer of the toxin was responsible for the variation observed within the species. The recent availability of multiple C. botulinum genomic sequences has offered the ability to bioinformatically analyze the locations of the bont genes, the composition of their toxin gene clusters, and the genes flanking these regions to understand their variation. Comparison of the genomic sequences representing multiple serotypes indicates that the bont genes are not in random locations. Instead the analyses revealed specific regions where the toxin genes occur within the genomes representing serotype A, B, C, E, and F C. botulinum strains and C. butyricum type E strains. The genomic analyses have provided evidence of horizontal gene transfer, site-specific insertion, and recombination events. These events have contributed to the variation observed among the neurotoxins, the toxin gene clusters and the bacteria that contain them, and has supported the historical microbiological, and biochemical characterization of the Group classification within the species. C1 [Hill, Karen K.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. [Smith, Theresa J.] US Army, Med Res Inst Infect Dis, Ft Detrick, MD 21702 USA. RP Hill, KK (reprint author), Los Alamos Natl Lab, Mail Stop M 888, Los Alamos, NM 87545 USA. EM khill@lanl.gov; theresa.smith@amedd.army.mil NR 53 TC 79 Z9 79 U1 1 U2 27 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 0070-217X BN 978-3-642-33570-9; 978-3-642-33569-3 J9 CURR TOP MICROBIOL JI Curr.Top.Microbiol.Immunol. PY 2013 VL 364 BP 1 EP 20 DI 10.1007/978-3-642-33570-9_1 D2 10.1007/978-3-642-33570-9 PG 20 WC Immunology; Microbiology SC Immunology; Microbiology GA BJT57 UT WOS:000330226500002 PM 23239346 ER PT S AU Swaminathan, S AF Swaminathan, Subramanyam BE Rummel, A Binz, T TI Structure-Based Drug Discovery for Botulinum Neurotoxins SO BOTULINUM NEUROTOXINS SE Current Topics in Microbiology and Immunology LA English DT Review; Book Chapter DE Zink endoprotease; Light chain structure; Peptidic inhibitor; Pharmacophore model; Peptide analogs ID LIGHT-CHAIN PROTEASE; SUBSTRATE RECOGNITION; HEAVY-CHAIN; CRYSTAL-STRUCTURE; SEROTYPE-A; PROTEOLYTIC ACTIVITY; POTENT INHIBITORS; SNAP-25 SUBSTRATE; TETANUS TOXIN; HIGH-AFFINITY AB Clostridium botulinum neurotoxin is the most poisonous substance known to humans. It is a potential biowarfare threat and a public health hazard. The only therapeutics available is antibody treatment which will not be effective for post-exposure therapy. There are no drugs available for post-intoxication treatment. Accordingly, it is imperative to develop effective drugs to counter botulism. Available structural information on botulinum neurotoxins both alone and in complex with their substrates offers an efficient method for designing structure-based drugs to treat botulism. C1 Brookhaven Natl Lab, Dept Biol, Upton, NY 11973 USA. RP Swaminathan, S (reprint author), Brookhaven Natl Lab, Dept Biol, Upton, NY 11973 USA. EM swami@bnl.gov NR 71 TC 2 Z9 2 U1 1 U2 8 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 0070-217X BN 978-3-642-33570-9; 978-3-642-33569-3 J9 CURR TOP MICROBIOL JI Curr.Top.Microbiol.Immunol. PY 2013 VL 364 BP 197 EP 218 DI 10.1007/978-3-642-33570-9_10 D2 10.1007/978-3-642-33570-9 PG 22 WC Immunology; Microbiology SC Immunology; Microbiology GA BJT57 UT WOS:000330226500011 PM 23239355 ER PT S AU Daily, MD Yu, HB Phillips, GN Cui, Q AF Daily, Michael D. Yu, Haibo Phillips, George N., Jr. Cui, Qiang BE Klinman, J HammesSchiffer, S TI Allosteric Activation Transitions in Enzymes and Biomolecular Motors: Insights from Atomistic and Coarse-Grained Simulations SO DYNAMICS IN ENZYME CATALYSIS SE Topics in Current Chemistry LA English DT Review; Book Chapter DE Allostery; Molecular motors; Enzyme catalysis; Molecular dynamics; Coarse-grained models; Small angle X-ray scattering; Co-operativity; Protein evolution ID NORMAL-MODE ANALYSIS; MOLECULAR-DYNAMICS SIMULATIONS; FREE-ENERGY LANDSCAPES; ELASTIC NETWORK MODEL; APO-ADENYLATE KINASE; X-RAY-SCATTERING; CONFORMATIONAL TRANSITIONS; RECOVERY STROKE; MUSCLE-CONTRACTION; ATP HYDROLYSIS AB The chemical step in enzymes is usually preceded by a kinetically distinct activation step that involves large-scale conformational transitions. In "simple" enzymes this step corresponds to the closure of the active site; in more complex enzymes, such as biomolecular motors, the activation step is more complex and may involve interactions with other biomolecules. These activation transitions are essential to the function of enzymes and perturbations in the scale and/or rate of these transitions are implicated in various serious human diseases; incorporating key flexibilities into engineered enzymes is also considered a major remaining challenge in rational enzyme design. Therefore it is important to understand the underlying mechanism of these transitions. This is a significant challenge to both experimental and computational studies because of the allosteric and multi-scale nature of such transitions. Using our recent studies of two enzyme systems, myosin and adenylate kinase (AK), we discuss how atomistic and coarse-grained simulations can be used to provide insights into the mechanism of activation transitions in realistic systems. Collectively, the results suggest that although many allosteric transitions can be viewed as domain displacements mediated by flexible hinges, there are additional complexities and various deviations. For example, although our studies do not find any evidence for "cracking" in AK, our results do underline the contribution of intra-domain properties (e.g., dihedral flexibility) to the rate of the transition. The study of mechanochemical coupling in myosin highlights that local changes important to chemistry require stabilization from more extensive structural changes; in this sense, more global structural transitions are needed to activate the chemistry in the active site. These discussions further emphasize the importance of better understanding factors that control the degree of co-operativity for allosteric transitions, again hinting at the intimate connection between protein stability and functional flexibility. Finally, a number of topics of considerable future interest are briefly discussed. C1 [Daily, Michael D.] Pacific NW Natl Lab, Richland, WA 99352 USA. [Yu, Haibo] Univ Wollongong, Sch Chem, Wollongong, NSW 2522, Australia. [Phillips, George N., Jr.] Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA. [Phillips, George N., Jr.] Univ Wisconsin, Dept Comp Sci, Madison, WI 53706 USA. [Phillips, George N., Jr.] Rice Univ, Dept Biochem & Cell Biol, Houston, TX 77006 USA. [Phillips, George N., Jr.] Rice Univ, Dept Chem, Houston, TX 77006 USA. [Cui, Qiang] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. [Cui, Qiang] Univ Wisconsin, Inst Theoret Chem, Madison, WI 53706 USA. RP Cui, Q (reprint author), Univ Wisconsin, Dept Chem, 1101 Univ Ave, Madison, WI 53706 USA. EM cui@chem.wisc.edu RI Yu, Haibo/B-9750-2008 OI Yu, Haibo/0000-0002-1099-2803 FU NIGMS NIH HHS [R01GM071428, R01 GM071428, R01 GM084028, R01GM084028]; NLM NIH HHS [5T15LM007359, T15 LM007359] NR 133 TC 5 Z9 5 U1 5 U2 32 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 0340-1022 BN 978-3-642-38962-7; 978-3-642-38961-0 J9 TOP CURR CHEM JI Top. Curr. Chem. PY 2013 VL 337 BP 139 EP 164 DI 10.1007/128_2012_409 D2 10.1007/978-3-642-38962-7 PG 26 WC Chemistry, Multidisciplinary SC Chemistry GA BA0DT UT WOS:000331047400007 PM 23468286 ER PT J AU Hammonds, AS Bristow, CA Fisher, WW Weiszmann, R Wu, SQ Hartenstein, V Kellis, M Yu, B Frise, E Celniker, SE AF Hammonds, Ann S. Bristow, Christopher A. Fisher, William W. Weiszmann, Richard Wu, Siqi Hartenstein, Volker Kellis, Manolis Yu, Bin Frise, Erwin Celniker, Susan E. TI Spatial expression of transcription factors in Drosophila embryonic organ development SO GENOME BIOLOGY LA English DT Article ID IN-SITU HYBRIDIZATION; GENE-EXPRESSION; CAENORHABDITIS-ELEGANS; GLOBAL ANALYSIS; CELL-FATE; DATABASE; PROTEINS; ELEMENTS; PATTERNS; DOMAIN AB Background: Site-specific transcription factors (TFs) bind DNA regulatory elements to control expression of target genes, forming the core of gene regulatory networks. Despite decades of research, most studies focus on only a small number of TFs and the roles of many remain unknown. Results: We present a systematic characterization of spatiotemporal gene expression patterns for all known or predicted Drosophila TFs throughout embryogenesis, the first such comprehensive study for any metazoan animal. We generated RNA expression patterns for all 708 TFs by in situ hybridization, annotated the patterns using an anatomical controlled vocabulary, and analyzed TF expression in the context of organ system development. Nearly all TFs are expressed during embryogenesis and more than half are specifically expressed in the central nervous system. Compared to other genes, TFs are enriched early in the development of most organ systems, and throughout the development of the nervous system. Of the 535 TFs with spatially restricted expression, 79% are dynamically expressed in multiple organ systems while 21% show single-organ specificity. Of those expressed in multiple organ systems, 77 TFs are restricted to a single organ system either early or late in development. Expression patterns for 354 TFs are characterized for the first time in this study. Conclusions: We produced a reference TF dataset for the investigation of gene regulatory networks in embryogenesis, and gained insight into the expression dynamics of the full complement of TFs controlling the development of each organ system. C1 [Hammonds, Ann S.; Fisher, William W.; Weiszmann, Richard; Wu, Siqi; Frise, Erwin; Celniker, Susan E.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Dept Genome Dynam, Div Life Sci, Berkeley, CA 94720 USA. [Bristow, Christopher A.; Kellis, Manolis] MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA. [Bristow, Christopher A.; Kellis, Manolis] Broad Inst Massachusetts Inst Technol & Harvard, Cambridge, MA 02142 USA. [Wu, Siqi; Yu, Bin] Univ Calif Berkeley, Dept Stat, Berkeley, CA 94720 USA. [Hartenstein, Volker] Univ Calif Los Angeles, Dept Mol Cell & Dev Biol, Los Angeles, CA 90095 USA. RP Celniker, SE (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Dept Genome Dynam, Div Life Sci, Berkeley, CA 94720 USA. EM celniker@fruitfly.org FU NIH NRSA postdoctoral fellowship; NHGRI [1U01HG007031-01]; Center for Science of Information (CSoI), an NSF Science and Technology Center [CCF-0939370]; NIH [R01 GM076655, R01 GM097231]; Department of Energy [DEAC02-05CH11231] FX We are indebted to BDGP members for their advice and Kevin Peet for manuscript preparation. We also thank the anonymous reviewers for their insightful comments. We thank Caitlin Barale, Elaine Laguerta, and Ayesha Ghosh for imaging; Ben Brown, Marcus Stoiber, and Glenn Hammonds for statistical analysis; George Celniker and Ben Booth for RNA-seq visualization; and Bart Deplancke and Korneel Hens at Ecole Polytechnique Federale de Lausanne, Switzerland for five TF clones (CG7045, CG33557, slou, pb, Dbx) used in these studies. CAB was supported by a NIH NRSA postdoctoral fellowship. BY was partially supported by NHGRI grant 1U01HG007031-01 and by the Center for Science of Information (CSoI), an NSF Science and Technology Center, under grant agreement CCF-0939370. NIH Grants R01 GM076655 (SEC) and R01 GM097231 (EF) supported this work. Work at LBNL was conducted under Department of Energy contract DEAC02-05CH11231. NR 56 TC 30 Z9 31 U1 1 U2 8 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1465-6906 EI 1474-760X J9 GENOME BIOL JI Genome Biol. PY 2013 VL 14 IS 12 AR R140 DI 10.1186/gb-2013-14-12-r140 PG 15 WC Biotechnology & Applied Microbiology; Genetics & Heredity SC Biotechnology & Applied Microbiology; Genetics & Heredity GA AA8WR UT WOS:000331376200008 PM 24359758 ER PT J AU Zaremba-Niedzwiedzka, K Viklund, J Zhao, WZ Ast, J Sczyrba, A Woyke, T McMahon, K Bertilsson, S Stepanauskas, R Andersson, SGE AF Zaremba-Niedzwiedzka, Katarzyna Viklund, Johan Zhao, Weizhou Ast, Jennifer Sczyrba, Alexander Woyke, Tanja McMahon, Katherina Bertilsson, Stefan Stepanauskas, Ramunas Andersson, Siv G. E. TI Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade SO GENOME BIOLOGY LA English DT Article ID MULTIPLE SEQUENCE ALIGNMENT; PHYLOGENETIC ANALYSIS; MAXIMUM-LIKELIHOOD; EVOLUTION; BACTERIOPLANKTON; POPULATION; DIVERSITY; MODELS; PATHOGENS; SELECTION AB Background: The SAR11 group of Alphaproteobacteria is highly abundant in the oceans. It contains a recently diverged freshwater clade, which offers the opportunity to compare adaptations to salt-and freshwaters in a monophyletic bacterial group. However, there are no cultivated members of the freshwater SAR11 group and no genomes have been sequenced yet. Results: We isolated ten single SAR11 cells from three freshwater lakes and sequenced and assembled their genomes. A phylogeny based on 57 proteins indicates that the cells are organized into distinct microclusters. We show that the freshwater genomes have evolved primarily by the accumulation of nucleotide substitutions and that they have among the lowest ratio of recombination to mutation estimated for bacteria. In contrast, members of the marine SAR11 clade have one of the highest ratios. Additional metagenome reads from six lakes confirm low recombination frequencies for the genome overall and reveal lake-specific variations in microcluster abundances. We identify hypervariable regions with gene contents broadly similar to those in the hypervariable regions of the marine isolates, containing genes putatively coding for cell surface molecules. Conclusions: We conclude that recombination rates differ dramatically in phylogenetic sister groups of the SAR11 clade adapted to freshwater and marine ecosystems. The results suggest that the transition from marine to freshwater systems has purged diversity and resulted in reduced opportunities for recombination with divergent members of the clade. The low recombination frequencies of the LD12 clade resemble the low genetic divergence of host-restricted pathogens that have recently shifted to a new host. C1 [Zaremba-Niedzwiedzka, Katarzyna; Viklund, Johan; Zhao, Weizhou; Ast, Jennifer; Andersson, Siv G. E.] Uppsala Univ, Dept Mol Evolut, S-75124 Uppsala, Sweden. [Zaremba-Niedzwiedzka, Katarzyna; Viklund, Johan; Zhao, Weizhou; Ast, Jennifer; Andersson, Siv G. E.] Uppsala Univ, Sci Life Lab, S-75124 Uppsala, Sweden. [Sczyrba, Alexander] Univ Bielefeld, Ctr Biotechnol, D-33501 Bielefeld, Germany. [Woyke, Tanja] US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA. [McMahon, Katherina] Univ Wisconsin, Dept Civil & Environm Engn, Madison, WI 53706 USA. [McMahon, Katherina] Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA. [Bertilsson, Stefan] Uppsala Univ, Dept Ecol & Genet, Limnol & Sci Life Lab, S-75236 Uppsala, Sweden. [Stepanauskas, Ramunas] Bigelow Lab Ocean Sci, East Boothbay, ME 04544 USA. RP Andersson, SGE (reprint author), Uppsala Univ, Dept Mol Evolut, S-75124 Uppsala, Sweden. EM Siv.Andersson@icm.uu.se OI Stepanauskas, Ramunas/0000-0003-4458-3108; McMahon, Katherine D./0000-0002-7038-026X FU Swedish Research Council [349-2007-831, 621-2008-3259, 621-2011-4669-4669, 2009-3784, 2008-1923, 2012-3892]; European Union; Goran Gustafsson Foundation; Knut and Alice Wallenberg Foundation [KAW-2011.0148, KAW-2012.0075]; National Science Foundation [DEB-841933, OCE-821374, EF-0633142]; Office of Science of the US Department of Energy [DE-AC02-05CH11231]; SNIC through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) [p2006019, p2009043] FX Financial support from the Swedish Research Council (grant numbers 349-2007-831, 621-2008-3259, 621-2011-4669-4669 to SGEA, 2009-3784, 2008-1923, 2012-3892 to SB), the European Union, the Goran Gustafsson Foundation, the Knut and Alice Wallenberg Foundation (grant numbers KAW-2011.0148, KAW-2012.0075 to SGEA), the National Science Foundation (DEB-841933, OCE-821374, EF-0633142 to RS) is acknowledged. Sequencing of single amplified genomes was conducted by the US Department of Energy Joint Genome Institute, supported by the Office of Science of the US Department of Energy under contract number DE-AC02-05CH11231. TW was also funded under DE-AC02-05CH11231. Computational resources were provided by SNIC through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) under Project p2006019 and p2009043. NR 47 TC 17 Z9 17 U1 7 U2 25 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1465-6906 EI 1474-760X J9 GENOME BIOL JI Genome Biol. PY 2013 VL 14 IS 11 AR R130 DI 10.1186/gb-2013-14-11-r130 PG 14 WC Biotechnology & Applied Microbiology; Genetics & Heredity SC Biotechnology & Applied Microbiology; Genetics & Heredity GA 302PA UT WOS:000330616200009 PM 24286338 ER PT S AU DePaolo, DJ Cole, DR AF DePaolo, Donald J. Cole, David R. BE DePaolo, DJ Cole, DR Navrotsky, A Bourg, IC TI Geochemistry of Geologic Carbon Sequestration: An Overview SO GEOCHEMISTRY OF GEOLOGIC CO2 SEQUESTRATION SE Reviews in Mineralogy & Geochemistry LA English DT Editorial Material; Book Chapter ID REACTIVE TRANSPORT; CO2 INJECTION; SUPERCRITICAL CO2; SILICA SURFACES; MUTUAL SOLUBILITIES; WELLBORE INTEGRITY; CO2-H2O MIXTURES; NATURAL ANALOGS; SALINE AQUIFER; LEAKY WELLS C1 [DePaolo, Donald J.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. [Cole, David R.] Ohio State Univ, Sch Earth Sci, Columbus, OH 43210 USA. RP DePaolo, DJ (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Mail Stop 74R316C, Berkeley, CA 94720 USA. EM djdepaolo@lbl.gov; cole.618@osu.edu NR 82 TC 16 Z9 16 U1 2 U2 37 PU MINERALOGICAL SOC AMER PI CHANTILLY PA 3635 CONCORDE PKWY STE 500, CHANTILLY, VA 20151-1125 USA SN 1529-6466 BN 978-0-939950-92-8 J9 REV MINERAL GEOCHEM JI Rev. Mineral. Geochem. PY 2013 VL 77 BP 1 EP 14 DI 10.2138/rmg.2013.77.1 PG 14 WC Geochemistry & Geophysics; Mineralogy SC Geochemistry & Geophysics; Mineralogy GA BJU31 UT WOS:000330485200001 ER PT S AU Bodnar, RJ Steele-MacInnis, M Capobianco, RM Rimstidt, JD Dilmore, R Goodman, A Guthrie, G AF Bodnar, Robert J. Steele-MacInnis, Matthew Capobianco, Ryan M. Rimstidt, J. Donald Dilmore, Robert Goodman, Angela Guthrie, George BE DePaolo, DJ Cole, DR Navrotsky, A Bourg, IC TI PVTX Properties of H2O-CO2-"salt" at PTX Conditions Applicable to Carbon Sequestration in Saline Formations SO GEOCHEMISTRY OF GEOLOGIC CO2 SEQUESTRATION SE Reviews in Mineralogy & Geochemistry LA English DT Review; Book Chapter ID SYNTHETIC FLUID INCLUSIONS; EQUATION-OF-STATE; SODIUM-CHLORIDE SOLUTIONS; AQUEOUS CALCIUM-CHLORIDE; DIOXIDE-WATER MIXTURES; CO2 STORAGE CAPACITY; THERMODYNAMIC PROPERTIES; HIGH-TEMPERATURES; PHASE-EQUILIBRIA; SYSTEM H2O-NACL C1 [Bodnar, Robert J.; Steele-MacInnis, Matthew; Capobianco, Ryan M.; Rimstidt, J. Donald] Virginia Tech, Dept Geosci, Blacksburg, VA 24061 USA. [Dilmore, Robert; Goodman, Angela; Guthrie, George] US DOE, NETL, Pittsburgh, PA 15236 USA. RP Bodnar, RJ (reprint author), Virginia Tech, Dept Geosci, Blacksburg, VA 24061 USA. EM rjb@vt.edu; mjmaci@vt.edu; rcapobi@vt.edu; jdr02@vt.edu; Robert.Dilmore@NETL.DOE.GOV; Angela.Goodman@NETL.DOE.GOV; George.Guthrie@NETL.DOE.GOV NR 110 TC 12 Z9 12 U1 2 U2 16 PU MINERALOGICAL SOC AMER PI CHANTILLY PA 3635 CONCORDE PKWY STE 500, CHANTILLY, VA 20151-1125 USA SN 1529-6466 BN 978-0-939950-92-8 J9 REV MINERAL GEOCHEM JI Rev. Mineral. Geochem. PY 2013 VL 77 BP 123 EP 152 DI 10.2138/rmg.2013.77.4 PG 30 WC Geochemistry & Geophysics; Mineralogy SC Geochemistry & Geophysics; Mineralogy GA BJU31 UT WOS:000330485200004 ER PT S AU Hamm, LM Bourg, IC Wallace, AF Rotenberg, B AF Hamm, Laura M. Bourg, Ian C. Wallace, Adam F. Rotenberg, Benjamin BE DePaolo, DJ Cole, DR Navrotsky, A Bourg, IC TI Molecular Simulation of CO2- and CO3-Brine-Mineral Systems SO GEOCHEMISTRY OF GEOLOGIC CO2 SEQUESTRATION SE Reviews in Mineralogy & Geochemistry LA English DT Review; Book Chapter ID AMORPHOUS CALCIUM-CARBONATE; CONTACT-ANGLE MEASUREMENTS; PRESSURE PHASE-EQUILIBRIA; DENSITY-FUNCTIONAL THEORY; CACO3 POLYMORPHS CALCITE; MONTE-CARLO SIMULATIONS; SURFACE-CHARGE DENSITY; LIQUID PRECURSOR PHASE; X-RAY-SCATTERING; DYNAMICS SIMULATIONS C1 [Hamm, Laura M.; Bourg, Ian C.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. [Wallace, Adam F.] Univ Delaware, Dept Geol Sci, Newark, DC 19716 USA. [Rotenberg, Benjamin] CNRS, Lab PECSA, F-75005 Paris, France. [Rotenberg, Benjamin] Univ Paris 06, F-75005 Paris, France. RP Hamm, LM (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. EM icbourg@lbl.gov RI Rotenberg, Benjamin/C-5490-2014; Bourg, Ian/A-6405-2013 OI Rotenberg, Benjamin/0000-0001-5198-4650; NR 293 TC 20 Z9 20 U1 8 U2 57 PU MINERALOGICAL SOC AMER PI CHANTILLY PA 3635 CONCORDE PKWY STE 500, CHANTILLY, VA 20151-1125 USA SN 1529-6466 BN 978-0-939950-92-8 J9 REV MINERAL GEOCHEM JI Rev. Mineral. Geochem. PY 2013 VL 77 BP 189 EP 228 DI 10.2138/rmg.2013.77.6 PG 40 WC Geochemistry & Geophysics; Mineralogy SC Geochemistry & Geophysics; Mineralogy GA BJU31 UT WOS:000330485200006 ER PT S AU De Yoreo, JJ Waychunas, GA Jun, YS Fernandez-Martinez, A AF De Yoreo, James J. Waychunas, Glenn A. Jun, Young-Shin Fernandez-Martinez, Alejandro BE DePaolo, DJ Cole, DR Navrotsky, A Bourg, IC TI In situ Investigations of Carbonate Nucleation on Mineral and Organic Surfaces SO GEOCHEMISTRY OF GEOLOGIC CO2 SEQUESTRATION SE Reviews in Mineralogy & Geochemistry LA English DT Review; Book Chapter ID SELF-ASSEMBLED MONOLAYERS; X-RAY-SCATTERING; CO2 SEQUESTRATION CONDITIONS; GRAZING-INCIDENCE; INTERFACIAL ENERGIES; CALCITE NUCLEATION; CRYSTAL NUCLEATION; ORIENTED GROWTH; CACO3; MANGANESE C1 [De Yoreo, James J.] Pacific NW Natl Lab, Div Phys Sci, Richland, WA 99352 USA. [Waychunas, Glenn A.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. [Jun, Young-Shin] Washington Univ, Dept Energy Environm & Chem Engn, St Louis, MO 63130 USA. [Fernandez-Martinez, Alejandro] CNRS, ISTerre, F-38041 Grenoble 9, France. [Fernandez-Martinez, Alejandro] Univ Grenoble 1, F-38041 Grenoble 9, France. RP De Yoreo, JJ (reprint author), Pacific NW Natl Lab, Div Phys Sci, Richland, WA 99352 USA. EM James.DeYoreo@pnnl.gov RI Fernandez-Martinez, Alejandro/B-4042-2010 OI Fernandez-Martinez, Alejandro/0000-0001-5073-9629 NR 72 TC 10 Z9 10 U1 3 U2 31 PU MINERALOGICAL SOC AMER PI CHANTILLY PA 3635 CONCORDE PKWY STE 500, CHANTILLY, VA 20151-1125 USA SN 1529-6466 BN 978-0-939950-92-8 J9 REV MINERAL GEOCHEM JI Rev. Mineral. Geochem. PY 2013 VL 77 BP 229 EP 257 DI 10.2138/rmg.2013.77.7 PG 29 WC Geochemistry & Geophysics; Mineralogy SC Geochemistry & Geophysics; Mineralogy GA BJU31 UT WOS:000330485200007 ER PT S AU Steefel, CI Molins, S Trebotich, D AF Steefel, Carl I. Molins, Sergi Trebotich, David BE DePaolo, DJ Cole, DR Navrotsky, A Bourg, IC TI Pore Scale Processes Associated with Subsurface CO2 Injection and Sequestration SO GEOCHEMISTRY OF GEOLOGIC CO2 SEQUESTRATION SE Reviews in Mineralogy & Geochemistry LA English DT Review; Book Chapter ID MULTICOMPONENT IONIC-DIFFUSION; MAXIMAL INSCRIBED SPHERES; FILLED POROUS-MEDIA; REACTIVE TRANSPORT; SUPERCRITICAL CO2; DISSOLUTION KINETICS; CALCITE GROWTH; NETWORK MODELS; FREE-ENERGY; PRECIPITATION KINETICS C1 [Steefel, Carl I.; Molins, Sergi] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. [Trebotich, David] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA. RP Steefel, CI (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. EM cisteefel@lbl.gov; smolins@lbl.gov; DPTrebotich@lbl.gov RI Molins, Sergi/A-9097-2012; Steefel, Carl/B-7758-2010 OI Molins, Sergi/0000-0001-7675-3218; NR 164 TC 26 Z9 26 U1 7 U2 39 PU MINERALOGICAL SOC AMER PI CHANTILLY PA 3635 CONCORDE PKWY STE 500, CHANTILLY, VA 20151-1125 USA SN 1529-6466 BN 978-0-939950-92-8 J9 REV MINERAL GEOCHEM JI Rev. Mineral. Geochem. PY 2013 VL 77 BP 259 EP 303 DI 10.2138/rmg.2013.77.8 PG 45 WC Geochemistry & Geophysics; Mineralogy SC Geochemistry & Geophysics; Mineralogy GA BJU31 UT WOS:000330485200008 ER PT S AU Chialvo, AA Vlcek, L Cole, DR AF Chialvo, Ariel A. Vlcek, Lukas Cole, David R. BE DePaolo, DJ Cole, DR Navrotsky, A Bourg, IC TI Acid Gases in CO2-rich Subsurface Geologic Environments SO GEOCHEMISTRY OF GEOLOGIC CO2 SEQUESTRATION SE Reviews in Mineralogy & Geochemistry LA English DT Review; Book Chapter ID EQUATION-OF-STATE; VAPOR-LIQUID-EQUILIBRIUM; MONTE-CARLO-SIMULATION; INTERMOLECULAR POTENTIAL FUNCTIONS; DENSITY-TEMPERATURE MEASUREMENTS; MOLECULAR-DYNAMICS SIMULATIONS; SUPERCRITICAL CARBON-DIOXIDE; ACCOUNT DIPOLAR INTERACTIONS; PHASE COEXISTENCE PROPERTIES; WATER-ROCK INTERACTIONS C1 [Chialvo, Ariel A.; Vlcek, Lukas] Oak Ridge Natl Lab, Div Chem Sci, Geochem & Interfacial Sci Grp, Oak Ridge, TN 37831 USA. [Cole, David R.] Ohio State Univ, Sch Earth Sci, Columbus, OH 43210 USA. [Cole, David R.] Ohio State Univ, Dept Chem, Columbus, OH 43210 USA. RP Chialvo, AA (reprint author), Oak Ridge Natl Lab, Div Chem Sci, Geochem & Interfacial Sci Grp, Oak Ridge, TN 37831 USA. EM chialvoaa@ornl.gov; cole.618@osu.edu RI Vlcek, Lukas/N-7090-2013; OI Vlcek, Lukas/0000-0003-4782-7702; Chialvo, Ariel/0000-0002-6091-4563 NR 215 TC 10 Z9 10 U1 0 U2 23 PU MINERALOGICAL SOC AMER PI CHANTILLY PA 3635 CONCORDE PKWY STE 500, CHANTILLY, VA 20151-1125 USA SN 1529-6466 BN 978-0-939950-92-8 J9 REV MINERAL GEOCHEM JI Rev. Mineral. Geochem. PY 2013 VL 77 BP 361 EP 398 DI 10.2138/rmg.2013.77.10 PG 38 WC Geochemistry & Geophysics; Mineralogy SC Geochemistry & Geophysics; Mineralogy GA BJU31 UT WOS:000330485200010 ER PT S AU Tokunaga, TK Wan, JM AF Tokunaga, Tetsu K. Wan, Jiamin BE DePaolo, DJ Cole, DR Navrotsky, A Bourg, IC TI Capillary Pressure and Mineral Wettability Influences on Reservoir CO2 Capacity SO GEOCHEMISTRY OF GEOLOGIC CO2 SEQUESTRATION SE Reviews in Mineralogy & Geochemistry LA English DT Review; Book Chapter ID RELATIVE PERMEABILITY HYSTERESIS; CONTACT-ANGLE MEASUREMENTS; SUPERCRITICAL CO2; POROUS-MEDIA; INTERFACIAL-TENSION; CARBON-DIOXIDE; TEMPERATURE CONDITIONS; SEALING EFFICIENCY; HAMAKER CONSTANTS; WETTING PHENOMENA C1 [Tokunaga, Tetsu K.; Wan, Jiamin] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. RP Tokunaga, TK (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. EM tktokunaga@lbl.gov; jwan@lbl.gov RI Tokunaga, Tetsu/H-2790-2014; Wan, Jiamin/H-6656-2014 OI Tokunaga, Tetsu/0000-0003-0861-6128; NR 107 TC 16 Z9 16 U1 1 U2 18 PU MINERALOGICAL SOC AMER PI CHANTILLY PA 3635 CONCORDE PKWY STE 500, CHANTILLY, VA 20151-1125 USA SN 1529-6466 BN 978-0-939950-92-8 J9 REV MINERAL GEOCHEM JI Rev. Mineral. Geochem. PY 2013 VL 77 BP 481 EP 503 DI 10.2138/rmg.2013.77.14 PG 23 WC Geochemistry & Geophysics; Mineralogy SC Geochemistry & Geophysics; Mineralogy GA BJU31 UT WOS:000330485200014 ER PT S AU Carey, JW AF Carey, J. William BE DePaolo, DJ Cole, DR Navrotsky, A Bourg, IC TI Geochemistry of Wellbore Integrity in CO2 Sequestration: Portland Cement-Steel-Brine-CO2 Interactions SO GEOCHEMISTRY OF GEOLOGIC CO2 SEQUESTRATION SE Reviews in Mineralogy & Geochemistry LA English DT Review; Book Chapter ID CARBON-DIOXIDE; LABORATORY EXPERIMENTS; CEMENT CARBONATION; STORAGE-CONDITIONS; SUPERCRITICAL CO2; CO2-RICH BRINE; LEAKY WELLS; CORROSION; MODEL; DEGRADATION C1 Los Alamos Natl Lab, Div Earth & Environm Sci, Los Alamos, NM 87545 USA. RP Carey, JW (reprint author), Los Alamos Natl Lab, Div Earth & Environm Sci, Los Alamos, NM 87545 USA. EM bcarey@lanl.gov NR 87 TC 30 Z9 30 U1 3 U2 23 PU MINERALOGICAL SOC AMER PI CHANTILLY PA 3635 CONCORDE PKWY STE 500, CHANTILLY, VA 20151-1125 USA SN 1529-6466 BN 978-0-939950-92-8 J9 REV MINERAL GEOCHEM JI Rev. Mineral. Geochem. PY 2013 VL 77 BP 505 EP 539 DI 10.2138/rmg.2013.77.15 PG 35 WC Geochemistry & Geophysics; Mineralogy SC Geochemistry & Geophysics; Mineralogy GA BJU31 UT WOS:000330485200015 ER PT J AU Lichtenberger, J Clilverd, MA Heilig, B Vellante, M Manninen, J Rodger, CJ Collier, AB Jorgensen, AM Reda, J Holzworth, RH Friedel, R Simon-Wedlund, M AF Lichtenberger, Janos Clilverd, Mark A. Heilig, Balazs Vellante, Massimo Manninen, Jyrki Rodger, Craig J. Collier, Andrew B. Jorgensen, Anders M. Reda, Jan Holzworth, Robert H. Friedel, Reinhard Simon-Wedlund, Mea TI The plasmasphere during a space weather event: first results from the PLASMON project SO JOURNAL OF SPACE WEATHER AND SPACE CLIMATE LA English DT Article DE plasmasphere; whistler; FLR; data assimilation; relativistic electron precipitation ID FIELD LINE RESONANCE; RING CURRENT; PLASMAPAUSE; PARAMETERS; DEPLETION; DYNAMICS; MODEL AB The results of the first 18 months of the PLASMON project are presented. We have extended our three, existing ground-based measuring networks, AWDANet (VLF/whistlers), EMMA/SANSA (ULF/FLRs), and AARDDVARK (VLF/perturbations on transmitters' signal), by three, eight, and four new stations, respectively. The extended networks will allow us to achieve the four major scientific goals, the automatic retrieval of equatorial electron densities and density profiles of the plasmasphere by whistler inversion, the retrieval of equatorial plasma mass densities by EMMA and SANSA from FLRs, developing a new, data assimilative model of plasmasphere and validating the model predictions through comparison of modeled REP losses with measured data by AARDDVARK network. The first results on each of the four objectives are presented through a case study on a space weather event, a dual storm sudden commencement which occurred on August 3 and 4, 2010. C1 [Lichtenberger, Janos] Eotvos Lorand Univ, Space Res Grp, Dept Geophys & Space Sci, H-1117 Budapest, Hungary. [Lichtenberger, Janos] Hungarian Acad Sci, Geodet & Geophys Inst, Res Ctr Astron & Earth Sci, H-9400 Sopron, Hungary. [Clilverd, Mark A.] British Antarctic Survey, Cambridge CB3 0ET, England. [Heilig, Balazs] Geol & Geophys Inst Hungary, H-1143 Budapest, Hungary. [Vellante, Massimo] Univ Aquila, Dept Phys, I-67010 Coppito, Italy. [Manninen, Jyrki] Sodankyla Geophys Observ, Sodankyla 99600, Finland. [Rodger, Craig J.; Simon-Wedlund, Mea] Univ Otago, Dept Phys, Dunedin 9054, New Zealand. [Collier, Andrew B.] SANSA Space Sci, ZA-7200 Hermanus, South Africa. [Collier, Andrew B.] Univ KwaZulu Natal, Sch Phys, ZA-4001 Durban, South Africa. [Jorgensen, Anders M.] New Mexico Inst Min & Technol, Dept Elect Engn, Socorro, NM 87801 USA. [Reda, Jan] Inst Polish Acad Sci, PL-05622 Belsk Duzy, Poland. [Holzworth, Robert H.] Univ Washington, Dept Earth & Space Sci, Seattle, WA 98195 USA. [Friedel, Reinhard] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Lichtenberger, J (reprint author), Eotvos Lorand Univ, Space Res Grp, Dept Geophys & Space Sci, Pazmany P Setany 1-A, H-1117 Budapest, Hungary. EM lityi@sas.elte.hu RI Friedel, Reiner/D-1410-2012; Rodger, Craig/A-1501-2011; Heilig, Balazs/A-3903-2012 OI Friedel, Reiner/0000-0002-5228-0281; Rodger, Craig/0000-0002-6770-2707; Heilig, Balazs/0000-0002-7964-0048 FU European Union Seventh Framework Programme [FP7] [263218] FX The research leading to these results has received funding from the European Union Seventh Framework Programme [FP7/2007-2013] under Grant Agreement No. 263218 NR 43 TC 10 Z9 10 U1 1 U2 7 PU EDP SCIENCES S A PI LES ULIS CEDEX A PA 17, AVE DU HOGGAR, PA COURTABOEUF, BP 112, F-91944 LES ULIS CEDEX A, FRANCE SN 2115-7251 J9 J SPACE WEATHER SPAC JI J. Space Weather Space Clim. PY 2013 VL 3 AR A23 DI 10.1051/swsc/2013045 PG 13 WC Astronomy & Astrophysics; Geochemistry & Geophysics; Meteorology & Atmospheric Sciences SC Astronomy & Astrophysics; Geochemistry & Geophysics; Meteorology & Atmospheric Sciences GA 301YV UT WOS:000330569100024 ER PT S AU Li, DS Nielsen, MH De Yoreo, JJ AF Li, Dongsheng Nielsen, Michael H. De Yoreo, James J. BE Yoreo, JJD TI Design, Fabrication, and Applications of In Situ Fluid Cell TEM SO RESEARCH METHODS IN BIOMINERALIZATION SCIENCE SE Methods in Enzymology LA English DT Review; Book Chapter ID TRANSMISSION ELECTRON-MICROSCOPY; STRUCTURAL EVOLUTION; DIRECTED NUCLEATION; GROWTH; RESOLUTION; KINETICS; LIQUID; CACO3; ELECTRODEPOSITION; CRYSTALLIZATION AB In situ fluid cell TEM is a powerful new tool for understanding dynamic processes during liquid phase chemical reactions, including mineral formation. This technique, which operates in the high vacuum of a TEM chamber, provides information on crystal structure, phase, morphology, size, aggregation/segregation, and crystal growth mechanisms in real time. In situ TEM records both crystal structure and morphology at spatial resolutions down to the atomic level with high temporal resolution of up to 10(-6) s per image, giving it distinct advantages over other in situ techniques such as optical microscopy, AFM, or X-ray scattering or diffraction. This chapter addresses the design, fabrication, and assembly of TEM fluid cells and applications of fluid cell TEM to understanding mechanisms of mineralization. C1 [Li, Dongsheng; De Yoreo, James J.] Pacific NW Natl Lab, Div Phys Sci, Richland, WA 99352 USA. [Nielsen, Michael H.] Univ Calif Berkeley, Dept Mat Sci & Engn, Berkeley, CA 94720 USA. [Nielsen, Michael H.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Mat Sci, Berkeley, CA 94720 USA. RP Li, DS (reprint author), Pacific NW Natl Lab, Div Phys Sci, Richland, WA 99352 USA. EM dongsheng.li2@pnnl.gov; James.DeYoreo@pnnl.gov RI Nielsen, Michael/D-1881-2015 NR 35 TC 5 Z9 5 U1 12 U2 62 PU ELSEVIER ACADEMIC PRESS INC PI SAN DIEGO PA 525 B STREET, SUITE 1900, SAN DIEGO, CA 92101-4495 USA SN 0076-6879 BN 978-0-12-416617-2 J9 METHOD ENZYMOL JI Methods Enzymol. PY 2013 VL 532 BP 147 EP 164 DI 10.1016/B978-0-12-416617-2.00007-2 PG 18 WC Biochemical Research Methods; Biochemistry & Molecular Biology SC Biochemistry & Molecular Biology GA BA0CK UT WOS:000331016200007 PM 24188766 ER PT S AU Lee, JRI Bagge-Hansen, M Willey, TM Meulenberg, RW Nielsen, MH Tran, IC van Buuren, T AF Lee, Jonathan R. I. Bagge-Hansen, Michael Willey, Trevor M. Meulenberg, Robert W. Nielsen, Michael H. Tran, Ich C. van Buuren, Tony BE Yoreo, JJD TI X-ray Absorption Spectroscopy for the Structural Investigation of Self-Assembled-Monolayer-Directed Mineralization SO RESEARCH METHODS IN BIOMINERALIZATION SCIENCE SE Methods in Enzymology LA English DT Review; Book Chapter ID FINE-STRUCTURE; ALKYL-CHAIN; EDGE; ALKANETHIOLS; ELECTRON; GOLD; IRRADIATION; NUCLEATION; SURFACES; CALCITE AB Self-assembled monolayers (SAMs) of organothiol molecules prepared on noble metal substrates are known to exert considerable influence over biomineral nucleation and growth and, as such, offer model templates for investigation of the processes of directed biomineralization. Identifying the structural evolution of SAM/crystal systems is essential for a more comprehensive understanding of the mechanisms by which organic monolayers mediate mineral growth. X-ray absorption spectroscopy (XAS) provides the attractive ability to study SAM structure at critical stages throughout the processes of crystallization in SAM/mineral systems. Here, we discuss important theoretical and experimental considerations for designing and implementing XAS studies of SAM/mineral systems. C1 [Lee, Jonathan R. I.; Bagge-Hansen, Michael; Willey, Trevor M.; Tran, Ich C.; van Buuren, Tony] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. [Meulenberg, Robert W.] Univ Maine, Dept Phys & Astron, Lab Surface Sci & Technol, Orono, ME 04469 USA. [Nielsen, Michael H.] Univ Calif Berkeley, Dept Mat Sci & Engn, Berkeley, CA 94720 USA. RP Lee, JRI (reprint author), Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. EM lee204@llnl.gov RI Tran, Ich/C-9869-2014; Nielsen, Michael/D-1881-2015; Willey, Trevor/A-8778-2011; OI Willey, Trevor/0000-0002-9667-8830; Meulenberg, Robert/0000-0003-2696-8792 NR 23 TC 1 Z9 1 U1 0 U2 19 PU ELSEVIER ACADEMIC PRESS INC PI SAN DIEGO PA 525 B STREET, SUITE 1900, SAN DIEGO, CA 92101-4495 USA SN 0076-6879 BN 978-0-12-416617-2 J9 METHOD ENZYMOL JI Methods Enzymol. PY 2013 VL 532 BP 165 EP 187 DI 10.1016/B978-0-12-416617-2.00008-4 PG 23 WC Biochemical Research Methods; Biochemistry & Molecular Biology SC Biochemistry & Molecular Biology GA BA0CK UT WOS:000331016200008 PM 24188767 ER PT S AU Nielsen, MH Lee, JRI AF Nielsen, Michael H. Lee, Jonathan R. I. BE Yoreo, JJD TI Preparation of Organothiol Self-Assembled Monolayers for Use in Templated Crystallization SO RESEARCH METHODS IN BIOMINERALIZATION SCIENCE SE Methods in Enzymology LA English DT Review; Book Chapter ID CALCIUM-CARBONATE; DIRECTED NUCLEATION; GOLD; ALKANETHIOLS; CRYSTALS; SURFACES; GROWTH; SILVER; CACO3; BIOMINERALIZATION AB Organothiol self-assembled monolayers (SAMs) have garnered much interest as templates for oriented crystallization of biominerals. While, on the surface, SAM preparation appears to be straightforward, there are many subtleties that may yield films that lack the desired effect on the mineral component in subsequent use for templated mineralization. Herein, we discuss literature that uses organothiol SAMs to understand various principles in biomineralization, to motivate the following discussion of preparation procedures and pitfalls that may arise while working with SAMs. We provide a range of parameters for each element of a SAM-forming process, which have been shown in the literature to produce monolayers suitable for mineralization experiments, and close with a step-by-step procedure, based on findings in the cited literature, that yields functional SAMs with very high fidelity. C1 [Nielsen, Michael H.] Univ Calif Berkeley, Dept Mat Sci & Engn, Berkeley, CA 94720 USA. [Nielsen, Michael H.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Mat Sci, Berkeley, CA 94720 USA. [Lee, Jonathan R. I.] Lawrence Livermore Natl Lab, Livermore, CA USA. RP Nielsen, MH (reprint author), Univ Calif Berkeley, Dept Mat Sci & Engn, Berkeley, CA 94720 USA. EM mhnielsen@lbl.gov RI Nielsen, Michael/D-1881-2015 NR 31 TC 1 Z9 1 U1 1 U2 10 PU ELSEVIER ACADEMIC PRESS INC PI SAN DIEGO PA 525 B STREET, SUITE 1900, SAN DIEGO, CA 92101-4495 USA SN 0076-6879 BN 978-0-12-416617-2 J9 METHOD ENZYMOL JI Methods Enzymol. PY 2013 VL 532 BP 209 EP 224 DI 10.1016/B978-0-12-416617-2.00010-2 PG 16 WC Biochemical Research Methods; Biochemistry & Molecular Biology SC Biochemistry & Molecular Biology GA BA0CK UT WOS:000331016200010 PM 24188769 ER PT S AU Jin, HE Chung, WJ Lee, SW AF Jin, Hyo-Eon Chung, Woo-Jae Lee, Seung-Wuk BE Yoreo, JJD TI Phage Display for the Discovery of Hydroxyapatite-Associated Peptides SO RESEARCH METHODS IN BIOMINERALIZATION SCIENCE SE Methods in Enzymology LA English DT Review; Book Chapter ID BIOMIMETIC SYNTHESIS; CRYSTAL-STRUCTURE; BINDING PEPTIDES; CDNA SEQUENCE; SELECTION; CLONING; BONE; MINERALIZATION; NANOCRYSTALS; CONFORMATION AB In nature, proteins play a critical role in the biomineralization process. Understanding how different peptide or protein sequences selectively interact with the target crystal is of great importance. Identifying such protein structures is one of the critical steps in verifying the molecular mechanisms of biomineralization. One of the promising ways to obtain such information for a particular crystal surface is to screen combinatorial peptide libraries in a high-throughput manner. Among the many combinatorial library screening procedures, phage display is a powerful method to isolate such proteins and peptides. In this chapter, we will describe our established methods to perform phage display with inorganic crystal surfaces. Specifically, we will use hydroxyapatite as a model system for discovery of apatite-associated proteins in bone or tooth biomineralization studies. This model approach can be generalized to other desired crystal surfaces using the same experimental design principles with a little modification of the procedures. C1 [Jin, Hyo-Eon; Chung, Woo-Jae; Lee, Seung-Wuk] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. [Jin, Hyo-Eon; Chung, Woo-Jae; Lee, Seung-Wuk] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA. [Chung, Woo-Jae] Sungkyunkwan Univ, Coll Biotechnol & Bioengn, Suwon, South Korea. RP Lee, SW (reprint author), Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. EM leesw@berkeley.edu NR 39 TC 1 Z9 2 U1 7 U2 23 PU ELSEVIER ACADEMIC PRESS INC PI SAN DIEGO PA 525 B STREET, SUITE 1900, SAN DIEGO, CA 92101-4495 USA SN 0076-6879 BN 978-0-12-416617-2 J9 METHOD ENZYMOL JI Methods Enzymol. PY 2013 VL 532 BP 305 EP 323 DI 10.1016/B978-0-12-416617-2.00014-X PG 19 WC Biochemical Research Methods; Biochemistry & Molecular Biology SC Biochemistry & Molecular Biology GA BA0CK UT WOS:000331016200014 PM 24188773 ER PT S AU Tamura, N Gilbert, PUPA AF Tamura, Nobumichi Gilbert, Pupa U. P. A. BE Yoreo, JJD TI X-Ray Microdiffraction of Biominerals SO RESEARCH METHODS IN BIOMINERALIZATION SCIENCE SE Methods in Enzymology LA English DT Review; Book Chapter ID AMORPHOUS CALCIUM-CARBONATE; URCHIN LARVAL SPICULE; TEXTURE ANALYSIS; MICROBEAM DIFFRACTION; SYNCHROTRON-RADIATION; MECHANICAL-PROPERTIES; SPATIAL-RESOLUTION; RIETVELD METHOD; WAVE-GUIDES; BONE AB Biominerals have complex and heterogeneous architectures, hence diffraction experiments with spatial resolutions between 500 nm and 10 mu m are extremely useful to characterize them. X-ray beams in this size range are now routinely produced at many synchrotrons. This chapter provides a review of the different hard X-ray diffraction and scattering techniques, used in conjunction with efficient, state-of-the-art X-ray focusing optics. These include monochromatic X-ray microdiffraction, polychromatic (Laue) X-ray microdiffraction, and microbeam small-angle X-ray scattering. We present some of the most relevant discoveries made in the field of biomineralization using these approaches. C1 [Tamura, Nobumichi] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA. [Gilbert, Pupa U. P. A.] Univ Wisconsin, Dept Phys, Madison, WI 53706 USA. [Gilbert, Pupa U. P. A.] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA. RP Gilbert, PUPA (reprint author), Univ Wisconsin, Dept Phys, 1150 Univ Ave, Madison, WI 53706 USA. EM pupa@physics.wisc.edu RI Gilbert, Pupa/A-6299-2010 OI Gilbert, Pupa/0000-0002-0139-2099 NR 91 TC 3 Z9 3 U1 2 U2 39 PU ELSEVIER ACADEMIC PRESS INC PI SAN DIEGO PA 525 B STREET, SUITE 1900, SAN DIEGO, CA 92101-4495 USA SN 0076-6879 BN 978-0-12-416617-2 J9 METHOD ENZYMOL JI Methods Enzymol. PY 2013 VL 532 BP 501 EP 531 DI 10.1016/B978-0-12-416617-2.00021-7 PG 31 WC Biochemical Research Methods; Biochemistry & Molecular Biology SC Biochemistry & Molecular Biology GA BA0CK UT WOS:000331016200021 PM 24188780 ER PT S AU Tao, JH AF Tao, Jinhui BE Yoreo, JJD TI FTIR and Raman Studies of Structure and Bonding in Mineral and Organic-Mineral Composites SO RESEARCH METHODS IN BIOMINERALIZATION SCIENCE SE Methods in Enzymology LA English DT Review; Book Chapter ID AMORPHOUS CALCIUM-CARBONATE; URCHIN LARVAL SPICULE; VIBRATIONAL-SPECTRA; TERRESTRIAL ISOPODS; CRYSTAL NUCLEATION; PRECURSOR PHASE; PHOSPHATE; BIOMINERALIZATION; TRANSFORMATION; BONE AB Spectroscopy techniques, such as Fourier transform infrared (FTIR) and Raman, offer methodologies that overlap and expand X-ray diffraction and transmission electron microscopy (TEM) analyses and help gain new insight into mechanisms of biomineralization. FTIR and Raman spectroscopy techniques measure the molecular environment of asymmetrically and symmetrically vibrating bonds, respectively. As such, these techniques have widely been used to gain information on mineral content, phase, and orientation as well as chemical composition of associated organic matrices like collagen, chitin, or lipids. The traditional coupling of optical microscopes to the newer generation FTIR and Raman spectrometers has enabled these analyses to be performed on samples with 0.1-20 mu m spatial resolution. Herein, we briefly discuss the basis and protocol for effective measurements using vibrational spectroscopy by taking two systems from our own research as examples. C1 Pacific NW Natl Lab, Div Phys Sci, Richland, WA 99352 USA. RP Tao, JH (reprint author), Pacific NW Natl Lab, Div Phys Sci, Richland, WA 99352 USA. EM jtao@lbl.gov FU NIDDK NIH HHS [DK61673] NR 58 TC 2 Z9 2 U1 7 U2 34 PU ELSEVIER ACADEMIC PRESS INC PI SAN DIEGO PA 525 B STREET, SUITE 1900, SAN DIEGO, CA 92101-4495 USA SN 0076-6879 BN 978-0-12-416617-2 J9 METHOD ENZYMOL JI Methods Enzymol. PY 2013 VL 532 BP 533 EP 556 DI 10.1016/B978-0-12-416617-2.00022-9 PG 24 WC Biochemical Research Methods; Biochemistry & Molecular Biology SC Biochemistry & Molecular Biology GA BA0CK UT WOS:000331016200022 PM 24188781 ER PT S AU Ansong, C Deatherage, BL Hyduke, D Schmidt, B McDermott, JE Jones, MB Chauhan, S Charusanti, P Kim, YM Nakayasu, ES Li, J Kidwai, A Niemann, G Brown, RN Metz, TO McAteer, K Heffron, F Peterson, SN Motin, V Palsson, BO Smith, RD Adkins, JN AF Ansong, Charles Deatherage, Brooke L. Hyduke, Daniel Schmidt, Brian McDermott, Jason E. Jones, Marcus B. Chauhan, Sadhana Charusanti, Pep Kim, Young-Mo Nakayasu, Ernesto S. Li, Jie Kidwai, Afshan Niemann, George Brown, Roslyn N. Metz, Thomas O. McAteer, Kathleen Heffron, Fred Peterson, Scott N. Motin, Vladimir Palsson, Bernhard O. Smith, Richard D. Adkins, Joshua N. BE Katze, MG TI Studying Salmonellae and Yersiniae Host-Pathogen Interactions Using Integrated 'Omics and Modeling SO SYSTEMS BIOLOGY SE Current Topics in Microbiology and Immunology LA English DT Review; Book Chapter ID SCALE METABOLIC RECONSTRUCTIONS; MOUSE PERITONEAL-MACROPHAGES; GENOME ANNOTATION; ESCHERICHIA-COLI; GENE-EXPRESSION; III SECRETION; NETWORK INFERENCE; VIRULENCE FACTORS; PROTEOME ANALYSIS; PESTIS AB Salmonella and Yersinia are two distantly related genera containing species with wide host-range specificity and pathogenic capacity. The metabolic complexity of these organisms facilitates robust lifestyles both outside of and within animal hosts. Using a pathogen-centric systems biology approach, we are combining a multi-omics (transcriptomics, proteomics, metabolomics) strategy to define properties of these pathogens under a variety of conditions including those that mimic the environments encountered during pathogenesis. These high-dimensional omics datasets are being integrated in selected ways to improve genome annotations, discover novel virulence-related factors, and model growth under infectious states. We will review the evolving technological approaches toward understanding complex microbial life through multi-omic measurements and integration, while highlighting some of our most recent successes in this area. C1 [Ansong, Charles; Deatherage, Brooke L.; Kim, Young-Mo; Nakayasu, Ernesto S.; Brown, Roslyn N.; Metz, Thomas O.; Smith, Richard D.; Adkins, Joshua N.] Pacific NW Natl Lab, Biol Separat & Mass Spect Grp, Richland, WA 99352 USA. [Hyduke, Daniel; Schmidt, Brian; Charusanti, Pep; Palsson, Bernhard O.] Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA. [McDermott, Jason E.] Pacific NW Natl Lab, Computat Biol & Bioinformat Grp, Richland, WA 99352 USA. [Jones, Marcus B.; Peterson, Scott N.] J Craig Venter Inst, Rockville, MD USA. [Li, Jie; Kidwai, Afshan; Niemann, George; Heffron, Fred] Oregon Hlth & Sci Univ, Dept Mol Microbiol & Immunol, Portland, OR 97201 USA. [Chauhan, Sadhana; Motin, Vladimir] Univ Texas Med Branch, Dept Pathol, Galveston, TX 77555 USA. [Chauhan, Sadhana; Motin, Vladimir] Univ Texas Med Branch, Dept Microbiol & Immunol, Galveston, TX 77555 USA. [McAteer, Kathleen] Washington State Univ Tri Cities, Biol Program, Richland, WA USA. RP Adkins, JN (reprint author), Pacific NW Natl Lab, Biol Separat & Mass Spect Grp, POB 999,MSIN K8-98Richland, Richland, WA 99352 USA. EM Joshua.Adkins@pnnl.gov RI Adkins, Joshua/B-9881-2013; Smith, Richard/J-3664-2012; Kim, Young-Mo/D-3282-2009; Motin, Vladimir/O-1535-2013; OI Adkins, Joshua/0000-0003-0399-0700; Metz, Tom/0000-0001-6049-3968; Smith, Richard/0000-0002-2381-2349; Kim, Young-Mo/0000-0002-8972-7593; Charusanti, Pep/0000-0003-0009-6615 FU NIAID NIH HHS [R01 AI022933] NR 81 TC 6 Z9 6 U1 0 U2 19 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 0070-217X BN 978-3-642-33099-5; 978-3-642-33098-8 J9 CURR TOP MICROBIOL JI Curr.Top.Microbiol.Immunol. PY 2013 VL 363 BP 21 EP 41 DI 10.1007/82_2012_247 D2 10.1007/978-3-642-33099-5 PG 21 WC Mathematical & Computational Biology; Immunology; Microbiology SC Mathematical & Computational Biology; Immunology; Microbiology GA BJU56 UT WOS:000330590200004 PM 22886542 ER PT J AU Santini, D Zhou, Y Kim, N Gallagher, K Vyas, AD AF Santini, Danilo Zhou, Yan Kim, Namdoo Gallagher, Kevin Vyas, Anant D. TI Plug-In Electric Cars for Work Travel Evaluation of Four Electric Powertrains SO TRANSPORTATION RESEARCH RECORD LA English DT Article AB Vehicles with electrified powertrains such as hybrid electric vehicles, plug-in hybrid electric vehicles (PHEVs), and all-electric vehicles (AEVs, which use grid-supplied battery energy exclusively) are potentially marketable because of their low operating costs. However, each vehicle type incurs a significant initial cost penalty compared with a conventional vehicle powered by an internal combustion engine. Three PHEV cars and an AEV car are selected to assess cost-effectiveness from the consumers' perspective. Daily travel to and from work is isolated from other vehicle travel data from the U.S. National Household Travel Survey, and five daily distance categories are investigated. Three driving cycle runs are used: one developed by following cars in Los Angeles, California, in 1992, the Worldwide Harmonized Light-Duty Test Cycle, and a real driving record selected from the Kansas City metropolitan area in Kansas and Missouri. Probable charging patterns for each PHEV and the AEV are investigated for three of five daily distance categories. Overnight charging and workplace charging also are examined. The possibility for multiple charges at work is considered, as is the possibility of a charge after work, before the day's end. The degree of importance of spending a given pool of money to upgrade a residential (versus workplace) charging station is discussed. Two indicators of effectiveness of battery pack utilization are developed [a charge-depleting effectiveness factor and grid kilowatt-hours used per day per dollar of incremental vehicle expense (cost-effectiveness)], and target markets for cars used for work for each powertrain type are suggested. C1 [Santini, Danilo; Zhou, Yan; Kim, Namdoo; Gallagher, Kevin; Vyas, Anant D.] Argonne Natl Lab, Ctr Transportat Res, Argonne, IL 60439 USA. RP Zhou, Y (reprint author), Argonne Natl Lab, Ctr Transportat Res, Bldg 362,9700 South Cass Ave, Argonne, IL 60439 USA. EM yzhou@anl.gov FU Energy Storage Program of the Vehicle Technology Program, Office of Energy Efficiency and Renewable Energy, U.S. Department of Energy FX This work was supported by the Energy Storage Program of the Vehicle Technology Program, Office of Energy Efficiency and Renewable Energy, U.S. Department of Energy. The analysis draws heavily from Task 15, Study of Plug-In Hybrid Electric Vehicles of the International Energy Agency Hybrid and Electric Vehicle Implementing Agreement. The conceptual and collaborative contributions from experts in Germany and France, whose works are cited here, are greatly appreciated. NR 31 TC 0 Z9 0 U1 1 U2 5 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0361-1981 EI 2169-4052 J9 TRANSPORT RES REC JI Transp. Res. Record PY 2013 IS 2385 BP 53 EP 60 DI 10.3141/2385-07 PG 8 WC Engineering, Civil; Transportation; Transportation Science & Technology SC Engineering; Transportation GA AA3XK UT WOS:000331028300008 ER PT J AU Bremson, J Meier, A Lin, CYC Ogden, J AF Bremson, Joel Meier, Alan Lin, C-Y Cynthia Ogden, Joan TI New Approach to Modeling Large-Scale Transitions to Alternative Fuels and Vehicles SO TRANSPORTATION RESEARCH RECORD LA English DT Article ID MARKETS AB A large-scale transition to alternative fuels and vehicles is challenging. New modeling approaches are necessary to supplement existing models, such as MARKAL. One promising approach is simulation gaming. Simulation gaming has been used extensively in many fields, most conspicuously in military applications, to provide insights into the dynamics of uncertain processes. A large-scale game to simulate transitions to alternative fuels and vehicles was developed to explore the potential of this approach. Preliminary results of the game play suggest a possible counterintuitive dynamic: high energy prices can discourage the wide-scale adoption of alternative fuel vehicles because increased fuel costs reduce consumers' ability to pay for more costly alternative vehicle technologies. C1 [Bremson, Joel; Lin, C-Y Cynthia; Ogden, Joan] Univ Calif Davis, Inst Transportat Studies, Davis, CA 95616 USA. [Meier, Alan] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Bremson, J (reprint author), Univ Calif Davis, Inst Transportat Studies, 1605 Tilia St, Davis, CA 95616 USA. EM jbremson@ucdavis.edu RI Lin Lawell, C.-Y. Cynthia/M-6342-2014 OI Lin Lawell, C.-Y. Cynthia/0000-0003-1014-2101 NR 29 TC 0 Z9 0 U1 0 U2 3 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0361-1981 EI 2169-4052 J9 TRANSPORT RES REC JI Transp. Res. Record PY 2013 IS 2385 BP 61 EP 69 DI 10.3141/2385-08 PG 9 WC Engineering, Civil; Transportation; Transportation Science & Technology SC Engineering; Transportation GA AA3XK UT WOS:000331028300009 ER PT S AU Parkinson, B Turner, J AF Parkinson, Bruce Turner, John BE Lewerenz, HJ Peter, L TI The Potential Contribution of Photoelectrochemistry in the Global Energy Future SO PHOTOELECTROCHEMICAL WATER SPLITTING: MATERIALS, PROCESSES AND ARCHITECTURES SE RSC Energy and Environment Series LA English DT Article; Book Chapter ID HYDROGEN-PRODUCTION; SURFACE MODIFICATION; SEMICONDUCTING TIO2; OXYGEN EVOLUTION; SOLAR-CELL; WATER; EFFICIENCY; PHOTOELECTROLYSIS; OXIDE; ILLUMINATION C1 [Parkinson, Bruce] Univ Wyoming, Dept Chem, Laramie, WY 82071 USA. [Parkinson, Bruce] Univ Wyoming, Sch Energy Resources, Laramie, WY 82071 USA. [Turner, John] Natl Renewable Energy Lab, Golden, CO USA. RP Parkinson, B (reprint author), Univ Wyoming, Dept Chem, Laramie, WY 82071 USA. EM bparkin1@uwyo.edu; John.Turner@nrel.gov NR 42 TC 7 Z9 7 U1 0 U2 3 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, CAMBRIDGE CB4 4WF, CAMBS, ENGLAND SN 2044-0774 BN 978-1-84973-773-9; 978-1-84973-647-3 J9 RSC ENERGY ENVIRON S PY 2013 IS 9 BP 1 EP 18 D2 10.1039/9781849737739 PG 18 WC Electrochemistry; Energy & Fuels SC Electrochemistry; Energy & Fuels GA BHR71 UT WOS:000326503600002 ER PT S AU Nozik, AJ AF Nozik, Arthur J. BE Lewerenz, HJ Peter, L TI Novel Approaches to Water Splitting by Solar Photons SO PHOTOELECTROCHEMICAL WATER SPLITTING: MATERIALS, PROCESSES AND ARCHITECTURES SE RSC Energy and Environment Series LA English DT Article; Book Chapter ID MULTIPLE EXCITON GENERATION; SEMICONDUCTOR-ELECTROLYTE JUNCTIONS; HOT-CARRIER INJECTION; ENERGY-CONVERSION; QUANTUM DOTS; PHOTOELECTROLYSIS CELLS; LIQUID INTERFACES; EFFICIENCY; PHOTOELECTROCHEMISTRY; MULTIPLICATION C1 [Nozik, Arthur J.] Natl Renewable Energy Lab, Golden, CO 80401 USA. [Nozik, Arthur J.] Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA. RP Nozik, AJ (reprint author), Natl Renewable Energy Lab, Golden, CO 80401 USA. EM Arthur.Nozik@nrel.gov NR 82 TC 3 Z9 3 U1 0 U2 0 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, CAMBRIDGE CB4 4WF, CAMBS, ENGLAND SN 2044-0774 BN 978-1-84973-773-9; 978-1-84973-647-3 J9 RSC ENERGY ENVIRON S PY 2013 IS 9 BP 359 EP 388 D2 10.1039/9781849737739 PG 30 WC Electrochemistry; Energy & Fuels SC Electrochemistry; Energy & Fuels GA BHR71 UT WOS:000326503600014 ER PT S AU Liu, XB Wu, JW Johnson, C AF Liu, Xingbo Wu, Junwei Johnson, Christopher BE Ni, M Zhao, TS TI Interconnect Materials for SOFC Stacks SO SOLID OXIDE FUEL CELLS: FROM MATERIALS TO SYSTEM MODELING SE RSC Energy and Environment Series LA English DT Article; Book Chapter ID OXIDE FUEL-CELLS; FERRITIC STAINLESS-STEEL; DOPED LANTHANUM CHROMITES; OXYGEN PERMEATION FLUX; MN-CO ALLOYS; THERMAL-EXPANSION; METALLIC INTERCONNECTS; OXIDATION RESISTANCE; ELECTRICAL-CONDUCTIVITY; MECHANICAL-PROPERTIES C1 [Liu, Xingbo] W Virginia Univ, Dept Mech & Aerosp Engn, Morgantown, WV 26506 USA. [Wu, Junwei] Harbin Inst Technol, Shenzhen Grad Sch, Sch Mat Sci & Engn, Shenzhen 518055, Peoples R China. [Wu, Junwei] Shenzhen Key Lab Adv Mat, Shenzhen 518055, Peoples R China. [Johnson, Christopher] Natl Energy Technol Lab, Morgantown, WV 26507 USA. RP Liu, XB (reprint author), W Virginia Univ, Dept Mech & Aerosp Engn, Morgantown, WV 26506 USA. EM xingbo.liu@mail.wvu.edu NR 88 TC 1 Z9 1 U1 0 U2 1 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, CAMBRIDGE CB4 4WF, CAMBS, ENGLAND SN 2044-0774 BN 978-1-84973-777-7; 978-1-84973-654-1 J9 RSC ENERGY ENVIRON S PY 2013 IS 7 BP 106 EP 134 DI 10.1039/9781849737777-00106 D2 10.1039/9781849737777 PG 29 WC Energy & Fuels; Environmental Sciences SC Energy & Fuels; Environmental Sciences & Ecology GA BHW66 UT WOS:000326870100006 ER PT J AU Tchoua, R Choi, J Klasky, S Liu, Q Logan, J Moreland, K Mu, JQ Parashar, M Podhorszki, N Pugmire, D Wolf, M AF Tchoua, Roselyne Choi, Jong Klasky, Scott Liu, Qing Logan, Jeremy Moreland, Kenneth Mu, Jingqing Parashar, Manish Podhorszki, Norbert Pugmire, David Wolf, Matthew GP IEEE TI ADIOS Visualization Schema: A First Step towards Improving Interdisciplinary Collaboration in High Performance Computing SO 2013 IEEE 9TH INTERNATIONAL CONFERENCE ON E-SCIENCE (E-SCIENCE) LA English DT Proceedings Paper CT IEEE 9th International Conference on e-Science (e-Science) CY OCT 22-25, 2013 CL Beijing, PEOPLES R CHINA SP IEEE, IEEE Comp Soc, Chinese Acad Sci, Cyberinfrastructure Off, Natl Sci & Technol, Infrastructure Ctr, Microsoft Res, Chinese Acad Sci, Comp Network Informat Ctr DE collaboration; schema; visualization; simulation; experiments ID SCIENTIFIC COLLABORATION; SCIENCE; IMPACT AB Scientific communities have benefitted from a significant increase of available computing and storage resources in the last few decades. For science projects that have access to leadership scale computing resources, the capacity to produce data has been growing exponentially. Teams working on such projects must now include, in addition to the traditional application scientists, experts in various disciplines including applied mathematicians for development of algorithms, visualization specialists for large data, and I/O specialists. Sharing of knowledge and data is becoming a requirement for scientific discovery; providing useful mechanisms to facilitate this sharing is a key challenge for e-Science. Our hypothesis is that in order to decrease the time to solution for application scientists we need to lower the barrier of entry into related computing fields. We aim at improving users' experience when interacting with a vast software ecosystem and/or huge amount of data, while maintaining focus on their primary research field. In this context we present our approach to bridge the gap between the application scientists and the visualization experts through a visualization schema as a first step and proof of concept for a new way to look at interdisciplinary collaboration among scientists dealing with big data. The key to our approach is recognizing that our users are scientists who mostly work as islands. They tend to work in very specialized environment but occasionally have to collaborate with other researchers in order to take full advantage of computing innovations and get insight from big data. We present an example of identifying the connecting elements between one of such relationships and offer a liaison schema to facilitate their collaboration. C1 [Tchoua, Roselyne; Choi, Jong; Klasky, Scott; Liu, Qing; Podhorszki, Norbert; Pugmire, David] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. [Logan, Jeremy; Mu, Jingqing] Univ Tennessee, Knoxville, TN 37996 USA. [Parashar, Manish] Sandia Natl Labs, Albuquerque, NM USA. [Wolf, Matthew] Georgia Inst Technol, Atlanta, GA 30332 USA. RP Tchoua, R (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. FU National Center of Computation Science (NCCS); DOE SCIDAC: Center for Edge Physics Simulation (EPSi) FX The research and development of the ADIOS Schema has been partly supported by the National Center of Computation Science (NCCS) and by DOE SCIDAC: Center for Edge Physics Simulation (EPSi). We wish to thank our EPSi colleagues Choong-Seock Chang and Seung-Hoe Ku. NR 25 TC 4 Z9 4 U1 2 U2 6 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-0-7695-5083-1 PY 2013 BP 27 EP 34 DI 10.1109/eScience.2013.24 PG 8 WC Computer Science, Information Systems; Computer Science, Theory & Methods SC Computer Science GA BJT44 UT WOS:000330195500004 ER PT J AU Samak, T Egan, R Bushnell, B Gunter, D Copeland, A Wang, Z AF Samak, Taghrid Egan, Rob Bushnell, Brian Gunter, Daniel Copeland, Alex Wang, Zhong GP IEEE TI Automatic Outlier Detection for Genome Assembly Quality Assessment SO 2013 IEEE 9TH INTERNATIONAL CONFERENCE ON E-SCIENCE (E-SCIENCE) LA English DT Proceedings Paper CT IEEE 9th International Conference on e-Science (e-Science) CY OCT 22-25, 2013 CL Beijing, PEOPLES R CHINA SP IEEE, IEEE Comp Soc, Chinese Acad Sci, Cyberinfrastructure Off, Natl Sci & Technol, Infrastructure Ctr, Microsoft Res, Chinese Acad Sci, Comp Network Informat Ctr AB In this work we describe a method to automatically detect errors in de novo assembled genomes. The method extends a Bayesian assembly quality evaluation framework, ALE, which computes the likelihood of an assembly given a set of unassembled data. Starting from ALE output, this method applies outlier detection algorithms to identify the precise locations of assembly errors. We show results from a microbial genome with manually curated assembly errors. Our method detects all deletions, 82.3% of insertions, and 88.8% of single base substitutions. It was also able to detect an inversion error that spans more than 400 bases. C1 [Samak, Taghrid; Gunter, Daniel] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. [Egan, Rob; Bushnell, Brian; Copeland, Alex; Wang, Zhong] Lawrence Berkeley Natl Lab, Joint Genome Inst, Walnut Creek, CA USA. RP Samak, T (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. FU Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy [DE-AC02-05CH11231] FX This work was supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. NR 12 TC 0 Z9 0 U1 0 U2 1 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-0-7695-5083-1 PY 2013 BP 45 EP 52 DI 10.1109/eScience.2013.49 PG 8 WC Computer Science, Information Systems; Computer Science, Theory & Methods SC Computer Science GA BJT44 UT WOS:000330195500006 ER PT J AU Kugler, K Chard, K Caton, S Rana, O Katz, DS AF Kugler, Kai Chard, Kyle Caton, Simon Rana, Omer Katz, Daniel S. GP IEEE TI Constructing a Social Content Delivery Network for eScience SO 2013 IEEE 9TH INTERNATIONAL CONFERENCE ON E-SCIENCE (E-SCIENCE) LA English DT Proceedings Paper CT IEEE 9th International Conference on e-Science (e-Science) CY OCT 22-25, 2013 CL Beijing, PEOPLES R CHINA SP IEEE, IEEE Comp Soc, Chinese Acad Sci, Cyberinfrastructure Off, Natl Sci & Technol, Infrastructure Ctr, Microsoft Res, Chinese Acad Sci, Comp Network Informat Ctr AB Increases in the size of research data and the move towards citizen science, in which everyday users contribute data and analyses, have resulted in a research data deluge. Researchers must now carefully determine how to store, transfer and analyze "Big Data" in collaborative environments. This task is even more complicated when considering budget and locality constraints on data storage and access. In this paper we investigate the potential to construct a Social Content Delivery Network (S-CDN) based upon the social networks that exist between researchers. The S-CDN model builds upon the incentives of collaborative researchers within a given scientific community to address their data challenges collaboratively and in proven trusted settings. In this paper we present a prototype implementation of a S-CDN and investigate the performance of the data transfer mechanisms (using Globus Online) and the potential cost advantages of this approach. C1 [Kugler, Kai; Caton, Simon] Karlsruhe Inst Technol, Karlsruhe Serv Res Inst, D-76021 Karlsruhe, Germany. [Chard, Kyle; Katz, Daniel S.] Univ Chicago, Comp Inst, Chicago, IL 60637 USA. [Chard, Kyle; Katz, Daniel S.] Argonne Natl Lab, Comp Inst, Chicago, IL 60637 USA. [Rana, Omer] Cardiff Univ, Sch Comp Sci & Informat, Cardiff CF10 3AX, S Glam, Wales. RP Kugler, K (reprint author), Karlsruhe Inst Technol, Karlsruhe Serv Res Inst, D-76021 Karlsruhe, Germany. EM usblq@student.kit.edu; kyle@ci.uchicago.edu; simon.caton@kit.edu; o.f.rana@cs.cardiff.ac.uk; dsk@ci.uchicago.edu RI Rana, Omer/E-4314-2015; OI Rana, Omer/0000-0003-3597-2646; Katz, Daniel S./0000-0001-5934-7525 FU National Science Foundation FX Work by Katz was supported by the National Science Foundation while working at the Foundation; any opinion, finding, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. NR 17 TC 4 Z9 4 U1 0 U2 3 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-0-7695-5083-1 PY 2013 BP 350 EP 356 DI 10.1109/eScience.2013.52 PG 7 WC Computer Science, Information Systems; Computer Science, Theory & Methods SC Computer Science GA BJT44 UT WOS:000330195500043 ER PT J AU Reeve, W Drew, E Ballard, R Melino, V Tian, R De Meyer, S Brau, L Ninawi, M Teshima, H Goodwin, L Chain, P Liolios, K Pati, A Mavromatis, K Ivanova, N Markowitz, V Woyke, T Kyrpides, N AF Reeve, Wayne Drew, Elizabeth Ballard, Ross Melino, Vanessa Tian, Rui De Meyer, Sofie Brau, Lambert Ninawi, Mohamed Teshima, Hazuki Goodwin, Lynne Chain, Patrick Liolios, Konstantinos Pati, Amrita Mavromatis, Konstantinos Ivanova, Natalia Markowitz, Victor Woyke, Tanja Kyrpides, Nikos TI Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI565 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE root-nodule bacteria; nitrogen fixation; rhizobia; Alphaproteobacteria ID NATURALIZED SOIL RHIZOBIA; SYMBIOTIC EFFECTIVENESS; PASTURE LEGUMES; ACID-TOLERANCE; N-2 FIXATION; RNA GENES; PERFORMANCE; ANNOTATION; PREDICTION; PROSPECTS AB Rhizobium leguminosarum bv. trifolii SRDI565 (syn. N8-J) is an aerobic, motile, Gram-negative, non-spore-forming rod. SRDI565 was isolated from a nodule recovered from the roots of the annual clover Trifolium subterraneum subsp. subterraneum grown in the greenhouse and inoculated with soil collected from New South Wales, Australia. SRDI565 has a broad host range for nodulation within the clover genus, however N2-fixation is sub-optimal with some Trifolium species and ineffective with others. Here we describe the features of R. leguminosarum bv. trifolii strain SRDI565, together with genome sequence information and annotation. The 6,905,599 bp high-quality-draft genome is arranged into 7 scaffolds of 7 contigs, contains 6,750 protein-coding genes and 86 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project. C1 [Reeve, Wayne; Melino, Vanessa; Tian, Rui; De Meyer, Sofie; Ninawi, Mohamed] Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. [Drew, Elizabeth; Ballard, Ross] South Australian Res & Dev Inst, Urrbrae, SA, Australia. [Brau, Lambert] Deakin Univ, Fac Sci & Technol, Sch Life & Environm Sci, Melbourne, Vic, Australia. [Teshima, Hazuki; Goodwin, Lynne; Chain, Patrick] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Liolios, Konstantinos; Pati, Amrita; Mavromatis, Konstantinos; Ivanova, Natalia; Woyke, Tanja; Kyrpides, Nikos] DOE Joint Genome Inst, Walnut Creek, CA USA. [Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. RP Reeve, W (reprint author), Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. EM W.Reeve@murdoch.edu.au RI Melino, Vanessa/B-1920-2012; Kyrpides, Nikos/A-6305-2014; OI Melino, Vanessa/0000-0003-2742-5079; Kyrpides, Nikos/0000-0002-6131-0462; Chain, Patrick/0000-0003-3949-3634; Ivanova, Natalia/0000-0002-5802-9485 FU US Department of Energy's Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI); Centre for Rhizobium Studies (CRS) at Murdoch University; GRDC National Rhizobium Program [UMU00032]; Australia-China Joint Research Centre for Wheat Improvement (ACCWI); SuperSeed Technologies (SST) FX This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. We gratefully acknowledge the funding received from the Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI) and the Centre for Rhizobium Studies (CRS) at Murdoch University and the GRDC National Rhizobium Program (UMU00032). The authors would like to thank the Australia-China Joint Research Centre for Wheat Improvement (ACCWI) and SuperSeed Technologies (SST) for financially supporting Mohamed Ninawi's PhD project. NR 44 TC 0 Z9 0 U1 1 U2 3 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 2 BP 220 EP 231 DI 10.4056/sigs.4468250 PG 12 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 294JX UT WOS:000330042800001 PM 24976879 ER PT J AU Reeve, W Drew, E Ballard, R Melino, V Tian, R De Meyer, S Brau, L Ninawi, M Daligault, H Davenport, K Erkkila, T Goodwin, L Gu, W Munk, C Teshima, H Xu, Y Chain, P Kyrpides, N AF Reeve, Wayne Drew, Elizabeth Ballard, Ross Melino, Vanessa Tian, Rui De Meyer, Sofie Brau, Lambert Ninawi, Mohamed Daligault, Hajnalka Davenport, Karen Erkkila, Tracy Goodwin, Lynne Gu, Wei Munk, Christine Teshima, Hazuki Xu, Yan Chain, Patrick Kyrpides, Nikos TI Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI943 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE root-nodule bacteria; nitrogen fixation; rhizobia; Alphaproteobacteria ID SYMBIOTIC EFFECTIVENESS; ACID-TOLERANCE; SOIL RHIZOBIA; N-2 FIXATION; RNA GENES; PERFORMANCE; ANNOTATION; PREDICTION; PROSPECTS; REVISION AB Rhizobium leguminosarum bv. trifolii SRDI943 (strain syn. V2-2) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Trifolium michelianum Savi cv. Paradana that had been grown in soil collected from a mixed pasture in Victoria, Australia. This isolate was found to have a broad clover host range but was sub-optimal for nitrogen fixation with T. subterraneum (fixing 20-54% of reference inoculant strain WSM1325) and was found to be totally ineffective with the clover species T. polymorphum and T. pratense. Here we describe the features of R. leguminosarum bv. trifolii strain SRDI943, together with genome sequence information and annotation. The 7,412,387 bp high-quality-draft genome is arranged into 5 scaffolds of 5 contigs, contains 7,317 protein-coding genes and 89 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project. C1 [Reeve, Wayne; Melino, Vanessa; Tian, Rui; De Meyer, Sofie; Ninawi, Mohamed] Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. [Drew, Elizabeth; Ballard, Ross] South Australian Res & Dev Inst, Urrbrae, SA, Australia. [Brau, Lambert] Deakin Univ, Fac Sci & Technol, Sch Life & Environm Sci, Melbourne, Vic, Australia. [Daligault, Hajnalka; Davenport, Karen; Erkkila, Tracy; Gu, Wei; Munk, Christine; Teshima, Hazuki; Xu, Yan; Chain, Patrick] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Daligault, Hajnalka; Goodwin, Lynne; Kyrpides, Nikos] DOE Joint Genome Inst, Walnut Creek, CA USA. RP Reeve, W (reprint author), Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. EM W.Reeve@murdoch.edu.au RI Melino, Vanessa/B-1920-2012; Kyrpides, Nikos/A-6305-2014; OI Melino, Vanessa/0000-0003-2742-5079; Kyrpides, Nikos/0000-0002-6131-0462; Chain, Patrick/0000-0003-3949-3634 FU US Department of Energy's Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI); Centre for Rhizobium Studies (CRS) at Murdoch University; GRDC National Rhizobium Program [UMU00032]; Australia- China Joint Research Centre for Wheat Improvement (ACCWI); SuperSeed Technologies (SST) FX This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. We gratefully acknowledge the funding received from the Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI), the Centre for Rhizobium Studies (CRS) at Murdoch University and the GRDC National Rhizobium Program (UMU00032). The authors would like to thank the Australia- China Joint Research Centre for Wheat Improvement (ACCWI) and SuperSeed Technologies (SST) for financially supporting Mohamed Ninawi's PhD project. NR 44 TC 1 Z9 1 U1 1 U2 7 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 2 BP 232 EP 242 DI 10.4056/sigs.4478252 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 294JX UT WOS:000330042800002 PM 24976880 ER PT J AU Reeve, W Tian, R De Meyer, S Melino, V Terpolilli, J Ardley, J Tiwari, R Howieson, J Yates, R O'Hara, G Ninawi, M Teshima, H Bruce, D Detter, C Tapia, R Han, C Wei, CL Huntemann, M Han, J Chen, IM Mavromatis, K Markowitz, V Ivanova, N Ovchinnikova, G Pagani, I Pati, A Goodwin, L Pitluck, S Woyke, T Kyrpides, N AF Reeve, Wayne Tian, Rui De Meyer, Sofie Melino, Vanessa Terpolilli, Jason Ardley, Julie Tiwari, Ravi Howieson, John Yates, Ronald O'Hara, Graham Ninawi, Mohamed Teshima, Hazuki Bruce, David Detter, Chris Tapia, Roxanne Han, Cliff Wei, Chia-Lin Huntemann, Marcel Han, James Chen, I-Min Mavromatis, Konstantinos Markowitz, Victor Ivanova, Natalia Ovchinnikova, Galina Pagani, Ioanna Pati, Amrita Goodwin, Lynne Pitluck, Sam Woyke, Tanja Kyrpides, Nikos TI Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain TA1 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE root-nodule bacteria; nitrogen fixation; rhizobia; Alphaproteobacteria ID NITROGEN-FIXATION; LEGUME SEED; RNA GENES; TOLERANCE; IDENTIFICATION; ANNOTATION; PREDICTION; REVISION; BACTERIA; DATABASE AB Rhizobium leguminosarum bv. trifolii strain TA1 is an aerobic, motile, Gram-negative, non-spore-forming rod that is an effective nitrogen fixing microsymbiont on the perennial clovers originating from Europe and the Mediterranean basin. TA1 however is ineffective with many annual and perennial clovers originating from Africa and America. Here we describe the features of R. leguminosarum bv. trifolii strain TA1, together with genome sequence information and annotation. The 8,618,824 bp high-quality-draft genome is arranged in a 6 scaffold of 32 contigs, contains 8,493 protein-coding genes and 83 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program. C1 [Reeve, Wayne; Tian, Rui; De Meyer, Sofie; Melino, Vanessa; Terpolilli, Jason; Ardley, Julie; Tiwari, Ravi; Howieson, John; Yates, Ronald; O'Hara, Graham; Ninawi, Mohamed] Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. [Teshima, Hazuki; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Wei, Chia-Lin; Huntemann, Marcel; Han, James; Mavromatis, Konstantinos; Ivanova, Natalia; Ovchinnikova, Galina; Pagani, Ioanna; Pati, Amrita; Pitluck, Sam; Woyke, Tanja; Kyrpides, Nikos] DOE Joint Genome Inst, Walnut Creek, CA USA. [Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, I-Min; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. RP Reeve, W (reprint author), Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. EM W.Reeve@murdoch.edu.au RI Melino, Vanessa/B-1920-2012; Kyrpides, Nikos/A-6305-2014; OI Melino, Vanessa/0000-0003-2742-5079; Kyrpides, Nikos/0000-0002-6131-0462; Terpolilli, Jason/0000-0003-4306-3346 FU US Department of Energy's Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI); Centre for Rhizobium Studies (CRS) at Murdoch University; Australia-China Joint Research Centre for Wheat Improvement (ACCWI); SuperSeed Technologies (SST) FX This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. We gratefully acknowledge the funding received from the Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI) and the Centre for Rhizobium Studies (CRS) at Murdoch University. The authors would like to thank the Australia-China Joint Research Centre for Wheat Improvement (ACCWI) and SuperSeed Technologies (SST) for financially supporting Mohamed Ninawi's PhD project. NR 49 TC 2 Z9 2 U1 1 U2 10 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 2 BP 243 EP 253 DI 10.4056/sigs.4488254 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 294JX UT WOS:000330042800003 PM 24976881 ER PT J AU Reeve, W De Meyer, S Terpolilli, J Melino, V Ardley, J Tian, R Tiwari, R Howieson, J Yates, R O'Hara, G Ninawi, M Lu, MG Bruce, D Detter, C Tapia, R Han, C Wei, CL Huntemann, M Han, J Chen, IM Mavromatis, K Markowitz, V Ivanova, N Pagani, I Pati, A Goodwin, L Woyke, T Kyrpides, N AF Reeve, Wayne De Meyer, Sofie Terpolilli, Jason Melino, Vanessa Ardley, Julie Tian, Rui Tiwari, Ravi Howieson, John Yates, Ronald O'Hara, Graham Ninawi, Mohamed Lu, Megan Bruce, David Detter, Chris Tapia, Roxanne Han, Cliff Wei, Chia-Lin Huntemann, Marcel Han, James Chen, I-Min Mavromatis, Konstantinos Markowitz, Victor Ivanova, Natalia Pagani, Ioanna Pati, Amrita Goodwin, Lynne Woyke, Tanja Kyrpides, Nikos TI Genome sequence of the Ornithopus/Lupinus-nodulating Bradyrhizobium sp. strain WSM471 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE root-nodule bacteria; nitrogen fixation; rhizobia; Alphaproteobacteria ID ROOT-NODULE; RNA GENES; BACTERIA; ANNOTATION; PREDICTION; INITIATION; AUSTRALIA; DATABASE; LUPINUS; SYSTEM AB Bradyrhizobium sp. strain WSM471 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-(N-2) fixing root nodule formed on the annual legume Ornithopus pinnatus (Miller) Druce growing at Oyster Harbour, Albany district, Western Australia in 1982. This strain is in commercial production as an inoculant for Lupinus and Ornithopus. Here we describe the features of Bradyrhizobium sp. strain WSM471, together with genome sequence information and annotation. The 7,784,016 bp high-quality-draft genome is arranged in 1 scaffold of 2 contigs, contains 7,372 protein-coding genes and 58 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program. C1 [Reeve, Wayne; De Meyer, Sofie; Terpolilli, Jason; Melino, Vanessa; Ardley, Julie; Tian, Rui; Tiwari, Ravi; Howieson, John; Yates, Ronald; O'Hara, Graham; Ninawi, Mohamed] Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. [Lu, Megan; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Wei, Chia-Lin; Huntemann, Marcel; Han, James; Mavromatis, Konstantinos; Ivanova, Natalia; Pagani, Ioanna; Pati, Amrita; Woyke, Tanja; Kyrpides, Nikos] DOE Joint Genome Inst, Walnut Creek, CA USA. [Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, I-Min; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. RP Reeve, W (reprint author), Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. EM W.Reeve@murdoch.edu.au RI Melino, Vanessa/B-1920-2012; Kyrpides, Nikos/A-6305-2014; OI Melino, Vanessa/0000-0003-2742-5079; Kyrpides, Nikos/0000-0002-6131-0462; Terpolilli, Jason/0000-0003-4306-3346 FU US Department of Energy's Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI); Centre for Rhizobium Studies (CRS) at Murdoch University; Australia-China Joint Research Centre for Wheat Improvement (ACCWI); SuperSeed Technologies (SST) FX This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. We grate-fully acknowledge the funding received from the Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI) and the Centre for Rhizobium Studies (CRS) at Murdoch University. The authors would like to thank the Australia-China Joint Research Centre for Wheat Improvement (ACCWI) and SuperSeed Technologies (SST) for financially supporting Mohamed Ninawi's PhD project. NR 38 TC 1 Z9 1 U1 0 U2 3 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 2 BP 254 EP 263 DI 10.4056/sigs.4498256 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 294JX UT WOS:000330042800004 PM 24976882 ER PT J AU Reeve, W Terpolilli, J Melino, V Ardley, J Tian, R De Meyer, S Tiwari, R Yates, R O'Hara, G Howieson, J Ninawi, M Held, B Bruce, D Detter, C Tapia, R Han, C Wei, CL Huntemann, M Han, J Chen, IM Mavromatis, K Markowitz, V Ivanova, N Ovchinnikova, G Pagani, I Pati, A Goodwin, L Woyke, T Kyrpides, N AF Reeve, Wayne Terpolilli, Jason Melino, Vanessa Ardley, Julie Tian, Rui De Meyer, Sofie Tiwari, Ravi Yates, Ronald O'Hara, Graham Howieson, John Ninawi, Mohamed Held, Brittany Bruce, David Detter, Chris Tapia, Roxanne Han, Cliff Wei, Chia-Lin Huntemann, Marcel Han, James Chen, I-Min Mavromatis, Konstantinos Markowitz, Victor Ivanova, Natalia Ovchinnikova, Galina Pagani, Ioanna Pati, Amrita Goodwin, Lynne Woyke, Tanja Kyrpides, Nikos TI Genome sequence of the South American clover-nodulating Rhizobium leguminosarum bv. trifolii strain WSM597 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE root-nodule bacteria; nitrogen fixation; rhizobia; Alphaproteobacteria ID RNA GENES; ANNOTATION; PREDICTION; REVISION; BACTERIA; DATABASE; SYSTEM AB Rhizobium leguminosarum bv. trifolii strain WSM597 is an aerobic, motile, Gram-negative, non-spore-forming rod isolated from a root nodule of the annual clover Trifolium pallidum L. growing at Glencoe Research Station near Tacuarembo, Uruguay. This strain is generally ineffective for nitrogen (N-2) fixation with clovers of Mediterranean, North American and African origin, but is effective on the South American perennial clover T. polymorphum Poir. Here we describe the features of R. leguminosarum bv. trifolii strain WSM597, together with genome sequence information and annotation. The 7,634,384 bp high-quality-draft genome is arranged in 2 scaffolds of 53 contigs, contains 7,394 protein-coding genes and 87 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program. C1 [Reeve, Wayne; Terpolilli, Jason; Melino, Vanessa; Ardley, Julie; Tian, Rui; De Meyer, Sofie; Tiwari, Ravi; Yates, Ronald; O'Hara, Graham; Howieson, John; Ninawi, Mohamed] Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. [Held, Brittany; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Wei, Chia-Lin; Huntemann, Marcel; Han, James; Mavromatis, Konstantinos; Ivanova, Natalia; Ovchinnikova, Galina; Pagani, Ioanna; Pati, Amrita; Woyke, Tanja; Kyrpides, Nikos] DOE Joint Genome Inst, Walnut Creek, CA USA. [Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, I-Min; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. RP Reeve, W (reprint author), Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. EM W.Reeve@murdoch.edu.au RI Melino, Vanessa/B-1920-2012; Kyrpides, Nikos/A-6305-2014; OI Melino, Vanessa/0000-0003-2742-5079; Kyrpides, Nikos/0000-0002-6131-0462; Terpolilli, Jason/0000-0003-4306-3346 FU US Department of Energy's Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI); Centre for Rhizobium Studies (CRS) at Murdoch University; Australia-China Joint Research Centre for Wheat Improvement (ACCWI); SuperSeed Technologies (SST) FX This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. We grate-fully acknowledge the funding received from the Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI) and the Centre for Rhizobium Studies (CRS) at Murdoch University. The authors would like to thank the Australia-China Joint Research Centre for Wheat Improvement (ACCWI) and SuperSeed Technologies (SST) for financially supporting Mohamed Ninawi's PhD project. NR 38 TC 0 Z9 0 U1 0 U2 2 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 2 BP 264 EP 272 DI 10.4056/sigs.4508258 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 294JX UT WOS:000330042800005 PM 24976883 ER PT J AU Reeve, W Terpolilli, J Melino, V Ardley, J Tian, R De Meyer, S Tiwari, R Yates, R O'Hara, G Howieson, J Ninawi, M Teshima, H Bruce, D Detter, C Tapia, R Han, C Wei, CL Huntemann, M Han, J Chen, IM Mavrommatis, K Markowitz, V Ivanova, N Ovchinnikova, G Pagani, I Pati, A Goodwin, L Peters, L Woyke, T Kyrpides, N AF Reeve, Wayne Terpolilli, Jason Melino, Vanessa Ardley, Julie Tian, Rui De Meyer, Sofie Tiwari, Ravi Yates, Ronald O'Hara, Graham Howieson, John Ninawi, Mohamed Teshima, Hazuki Bruce, David Detter, Chris Tapia, Roxanne Han, Cliff Wei, Chia-Lin Huntemann, Marcel Han, James Chen, I-Min Mavrommatis, Konstantinos Markowitz, Victor Ivanova, Natalia Ovchinnikova, Galina Pagani, Ioanna Pati, Amrita Goodwin, Lynne Peters, Lin Woyke, Tanja Kyrpides, Nikos TI Genome sequence of the lupin-nodulating Bradyrhizobium sp. strain WSM1417 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE root-nodule bacteria; nitrogen fixation; rhizobia; Alphaproteobacteria ID ROOT-NODULE; RNA GENES; BACTERIA; ANNOTATION; PREDICTION; DATABASE; SYSTEM AB Bradyrhizobium sp. strain WSM1417 is an aerobic, motile, Gram-negative, non-sporeforming rod that was isolated from an effective nitrogen (N-2) fixing root nodule of Lupinus sp. collected in Papudo, Chile, in 1995. However, this microsymbiont is a poorly effective N2 fixer with the legume host Lupinus angustifolius L.; a lupin species of considerable economic importance in both Chile and Australia. The symbiosis formed with L. angustifolius produces less than half of the dry matter achieved by the symbioses with commercial inoculant strains such as Bradyrhizobium sp. strain WSM471. Therefore, WSM1417 is an important candidate strain with which to investigate the genetics of effective N2 fixation in the lupin-bradyrhizobia symbioses. Here we describe the features of Bradyrhizobium sp. strain WSM1417, together with genome sequence information and annotation. The 8,048,963 bp high-quality-draft genome is arranged in a single scaffold of 2 contigs, contains 7,695 protein-coding genes and 77 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program. C1 [Reeve, Wayne; Terpolilli, Jason; Melino, Vanessa; Ardley, Julie; Tian, Rui; De Meyer, Sofie; Tiwari, Ravi; Yates, Ronald; O'Hara, Graham; Howieson, John; Ninawi, Mohamed] Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. [Teshima, Hazuki; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Wei, Chia-Lin; Huntemann, Marcel; Han, James; Mavrommatis, Konstantinos; Ivanova, Natalia; Ovchinnikova, Galina; Pagani, Ioanna; Pati, Amrita; Peters, Lin; Woyke, Tanja; Kyrpides, Nikos] DOE Joint Genome Inst, Walnut Creek, CA USA. [Chen, I-Min; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. RP Reeve, W (reprint author), Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. EM W.Reeve@murdoch.edu.au RI Melino, Vanessa/B-1920-2012; Kyrpides, Nikos/A-6305-2014; OI Melino, Vanessa/0000-0003-2742-5079; Kyrpides, Nikos/0000-0002-6131-0462; Terpolilli, Jason/0000-0003-4306-3346 FU US Department of Energy's Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Livermore National Laboratory [DE-AC52- 07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI); Centre for Rhizobium Studies (CRS) at Murdoch University; Australia-China Joint Research Centre for Wheat Improvement (ACCWI); SuperSeed Technologies (SST) FX This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52- 07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. We gratefully acknowledge the funding received from the Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI) and the Centre for Rhizobium Studies (CRS) at Murdoch University. The authors would like to thank the Australia-China Joint Research Centre for Wheat Improvement (ACCWI) and SuperSeed Technologies (SST) for financially supporting Mohamed Ninawi's PhD project. NR 35 TC 0 Z9 0 U1 0 U2 4 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 2 BP 273 EP 282 DI 10.4056/sigs.4518260 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 294JX UT WOS:000330042800006 PM 24976884 ER PT J AU Reeve, W Melino, V Ardley, J Tian, R De Meyer, S Terpolilli, J Tiwari, R Yates, R O'Hara, G Howieson, J Ninawi, M Held, B Bruce, D Detter, C Tapia, R Han, C Wei, CL Huntemann, M Han, J Chen, IM Mavromatis, K Markowitz, V Szeto, E Ivanova, N Mikhailova, N Pagani, I Pati, A Goodwin, L Woyke, T Kyrpides, N AF Reeve, Wayne Melino, Vanessa Ardley, Julie Tian, Rui De Meyer, Sofie Terpolilli, Jason Tiwari, Ravi Yates, Ronald O'Hara, Graham Howieson, John Ninawi, Mohamed Held, Brittany Bruce, David Detter, Chris Tapia, Roxanne Han, Cliff Wei, Chia-Lin Huntemann, Marcel Han, James Chen, I-Min Mavromatis, Konstantinos Markowitz, Victor Szeto, Ernest Ivanova, Natalia Mikhailova, Natalia Pagani, Ioanna Pati, Amrita Goodwin, Lynne Woyke, Tanja Kyrpides, Nikos TI Genome sequence of the Trifolium rueppellianum - nodulating Rhizobium leguminosarum bv. trifolii strain WSM2012 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE root-nodule bacteria; nitrogen fixation; rhizobia; Alphaproteobacteria ID RNA GENES; ANNOTATION; PREDICTION; REVISION; BACTERIA; DATABASE; SYSTEM; NODULE; SPP.; TOOL AB Rhizobium leguminosarum bv. trifolii WSM2012 (syn. MAR1468) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an ineffective root nodule recovered from the roots of the annual clover Trifolium rueppellianum Fresen growing in Ethiopia. WSM2012 has a narrow, specialized host range for N-2-fixation. Here we describe the features of R. leguminosarum bv. trifolii strain WSM2012, together with genome sequence information and annotation. The 7,180,565 bp high-quality-draft genome is arranged into 6 scaffolds of 68 contigs, contains 7,080 protein-coding genes and 86 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program. C1 [Reeve, Wayne; Melino, Vanessa; Ardley, Julie; Tian, Rui; De Meyer, Sofie; Terpolilli, Jason; Tiwari, Ravi; Yates, Ronald; O'Hara, Graham; Howieson, John; Ninawi, Mohamed] Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. [Held, Brittany; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Wei, Chia-Lin; Huntemann, Marcel; Han, James; Mavromatis, Konstantinos; Ivanova, Natalia; Mikhailova, Natalia; Pagani, Ioanna; Pati, Amrita; Woyke, Tanja; Kyrpides, Nikos] DOE Joint Genome Inst, Walnut Creek, CA USA. [Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, I-Min; Markowitz, Victor; Szeto, Ernest] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. RP Reeve, W (reprint author), Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. EM W.Reeve@murdoch.edu.au RI Melino, Vanessa/B-1920-2012; Kyrpides, Nikos/A-6305-2014; OI Melino, Vanessa/0000-0003-2742-5079; Kyrpides, Nikos/0000-0002-6131-0462; Terpolilli, Jason/0000-0003-4306-3346 FU US Department of Energy's Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI); Centre for Rhizobium Studies (CRS) at Murdoch University; Australia-China Joint Research Centre for Wheat Improvement (ACCWI); SuperSeed Technologies (SST) FX This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. We grate-fully acknowledge the funding received from the Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI) and the Centre for Rhizobium Studies (CRS) at Murdoch University. The authors would like to thank the Australia-China Joint Research Centre for Wheat Improvement (ACCWI) and SuperSeed Technologies (SST) for financially supporting Mohamed Ninawi's PhD project. NR 42 TC 0 Z9 0 U1 0 U2 0 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 2 BP 283 EP 293 DI 10.4056/sigs.4528262 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 294JX UT WOS:000330042800007 PM 24976885 ER PT J AU Reeve, W Nandasena, K Yates, R Tiwari, R O'Hara, G Ninawi, M Chertkov, O Goodwin, L Bruce, D Detter, C Tapia, R Han, SS Woyke, T Pitluck, S Nolan, M Land, M Copeland, A Liolios, K Pati, A Mavromatis, K Markowitz, V Kyrpides, N Ivanova, N Goodwin, L Meenakshi, U Howieson, J AF Reeve, Wayne Nandasena, Kemanthi Yates, Ron Tiwari, Ravi O'Hara, Graham Ninawi, Mohamed Chertkov, Olga Goodwin, Lynne Bruce, David Detter, Chris Tapia, Roxanne Han, Shunseng Woyke, Tanja Pitluck, Sam Nolan, Matt Land, Miriam Copeland, Alex Liolios, Konstantinos Pati, Amrita Mavromatis, Konstantinos Markowitz, Victor Kyrpides, Nikos Ivanova, Natalia Goodwin, Lynne Meenakshi, Uma Howieson, John TI Complete genome sequence of Mesorhizobium opportunistum type strain WSM2075(T) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE root-nodule bacteria; nitrogen fixation; evolution; lateral gene transfer; integrative and conjugative elements; symbiosis; Alphaproteobacteria ID BISERRULA-PELECINUS L; ROOT-NODULE; LATERAL TRANSFER; RNA GENES; LEGUME; BACTERIA; ANNOTATION; PREDICTION; EVOLUTION; DATABASE AB Mesorhizobium opportunistum strain WSM2075(T) was isolated in Western Australia in 2000 from root nodules of the pasture legume Biserrula pelecinus that had been inoculated with M. ciceri bv. biserrulae WSM1271. WSM2075(T) is an aerobic, motile, Gram negative, non-spore-forming rod that has gained the ability to nodulate B. pelecinus but is completely ineffective in N-2 fixation with this host. This report reveals that the genome of M. opportunistum strain WSM2075(T) contains a chromosome of size 6,884,444 bp, encoding 6,685 protein-coding genes and 62 RNA-only encoding genes. The genome contains no plasmids, but does harbor a 455.7 kb genomic island from Mesorhizobium ciceri bv. biserrulae WSM1271 that has been integrated into a phenylalanine-tRNA gene. C1 [Reeve, Wayne; Nandasena, Kemanthi; Yates, Ron; Tiwari, Ravi; O'Hara, Graham; Ninawi, Mohamed; Meenakshi, Uma; Howieson, John] Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. [Chertkov, Olga; Goodwin, Lynne; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Shunseng] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Woyke, Tanja; Pitluck, Sam; Nolan, Matt; Copeland, Alex; Liolios, Konstantinos; Pati, Amrita; Mavromatis, Konstantinos; Kyrpides, Nikos; Ivanova, Natalia; Goodwin, Lynne] DOE Joint Genome Inst, Walnut Creek, CA USA. [Land, Miriam] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. RP Reeve, W (reprint author), Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. EM W.Reeve@murdoch.edu.au RI Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy's Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52- 07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Australian Research Council Discovery grant [DP0880896]; Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI); Centre for Rhizobium Studies (CRS) at Murdoch University; Australia-China Joint Research Centre for Wheat Improvement (ACCWI); SuperSeed Technologies (SST) FX This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52- 07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. We gratefully acknowledge the funding received from Australian Research Council Discovery grant (DP0880896), Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI) and the Centre for Rhizobium Studies (CRS) at Murdoch University. The authors would like to thank the Australia-China Joint Research Centre for Wheat Improvement (ACCWI) and SuperSeed Technologies (SST) for financially supporting Mohamed Ninawi's PhD project. NR 36 TC 4 Z9 4 U1 0 U2 6 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 2 BP 294 EP 303 DI 10.4056/sigs.4538264 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 294JX UT WOS:000330042800008 PM 24976886 ER PT J AU Tak, N Gehlot, HS Kaushik, M Choudhary, S Tiwari, R Tian, R Hill, Y Brau, L Goodwin, L Han, J Liolios, K Huntemann, M Palaniappan, K Pati, A Mavromatis, K Ivanova, N Markowitz, V Woyke, T Kyrpides, N Reeve, W AF Tak, Nisha Gehlot, Hukam S. Kaushik, Muskan Choudhary, Sunil Tiwari, Ravi Tian, Rui Hill, Yvette Braeu, Lambert Goodwin, Lynne Han, James Liolios, Konstantinos Huntemann, Marcel Palaniappan, Krishna Pati, Amrita Mavromatis, Konstantinos Ivanova, Natalia Markowitz, Victor Woyke, Tanja Kyrpides, Nikos Reeve, Wayne TI Genome sequence of Ensifer sp TW10; a Tephrosia wallichii (Biyani) microsymbiont native to the Indian Thar Desert SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE root-nodule bacteria; nitrogen fixation; rhizobia; Alphaproteobacteria ID BACTERIA; LEGUMES; SYSTEM AB Ensifer sp. TW10 is a novel N-2-fixing bacterium isolated from a root nodule of the perennial legume Tephrosia wallichii Graham (known locally as Biyani) found in the Great Indian (or Thar) desert, a large arid region in the northwestern part of the Indian subcontinent. Strain TW10 is a Gram-negative, rod shaped, aerobic, motile, non-spore forming, species of root nodule bacteria (RNB) that promiscuously nodulates legumes in Thar Desert alkaline soil. It is fast growing, acid-producing, and tolerates up to 2% NaCl and capable of growth at 40C. In this report we describe for the first time the primary features of this Thar Desert soil saprophyte together with genome sequence information and annotation. The 6,802,256 bp genome has a GC content of 62% and is arranged into 57 scaffolds containing 6,470 protein-coding genes, 73 RNA genes and a single rRNA operon. This genome is one of 100 RNB genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project. C1 [Tak, Nisha; Gehlot, Hukam S.; Kaushik, Muskan; Choudhary, Sunil] Jai Narain Vyas Univ, Dept Bot, BNF & Stress Biol Lab, Jodhpur, Rajasthan, India. [Tiwari, Ravi; Tian, Rui; Hill, Yvette; Reeve, Wayne] Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. [Braeu, Lambert] Deakin Univ, Sch Life & Environm Sci, Fac Sci Engn & Built Environm, Melbourne, Vic, Australia. [Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Han, James; Liolios, Konstantinos; Huntemann, Marcel; Pati, Amrita; Mavromatis, Konstantinos; Ivanova, Natalia; Woyke, Tanja; Kyrpides, Nikos] DOE Joint Genome Inst, Walnut Creek, CA USA. [Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. RP Reeve, W (reprint author), Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. EM W.Reeve@murdoch.edu.au RI Kyrpides, Nikos/A-6305-2014; OI Kyrpides, Nikos/0000-0002-6131-0462; Hill, Yvette/0000-0001-5810-7845 FU US Department of Energy's Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI); GRDC National Rhizobium Program [UMU00032]; Council of Scientific and Industrial Research (CSIR); Department of Biotechnology (India) [BT/PR11461/AGR/21/270/2008]; Commonwealth of Australia FX This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. We gratefully acknowledge funding received from the Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI), the GRDC National Rhizobium Program (UMU00032), the Council of Scientific and Industrial Research (CSIR) for a fellowship for Nisha Tak, the Department of Biotechnology (India) for a research grant (BT/PR11461/AGR/21/270/2008) and the Commonwealth of Australia for an Australia India Senior Visiting Fellowship for Ravi Tiwari. NR 30 TC 5 Z9 5 U1 0 U2 3 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 2 BP 304 EP 314 DI 10.4056/sigs.4598281 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 294JX UT WOS:000330042800009 PM 24976887 ER PT J AU Terpolilli, J Hill, Y Tian, R Howieson, J Brau, L Goodwin, L Han, J Liolios, K Huntemann, M Pati, A Woyke, T Mavromatis, K Markowitz, V Ivanova, N Kyrpides, N Reeve, W AF Terpolilli, Jason Hill, Yvette Tian, Rui Howieson, John Braeu, Lambert Goodwin, Lynne Han, James Liolios, Konstantinos Huntemann, Marcel Pati, Amrita Woyke, Tanja Mavromatis, Konstantinos Markowitz, Victor Ivanova, Natalia Kyrpides, Nikos Reeve, Wayne TI Genome sequence of Ensifer meliloti strain WSM1022; a highly effective microsymbiont of the model legume Medicago truncatula A17 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE root-nodule bacteria; nitrogen fixation; rhizobia; Alphaproteobacteria ID SINORHIZOBIUM-MELILOTI; RHIZOBIUM-MELILOTI; NITROGEN-FIXATION; ROOT-NODULE; BACTERIA; IDENTIFICATION; SYSTEM; GENES; SOIL AB Ensifer meliloti WSM1022 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago. WSM1022 was isolated in 1987 from a nodule recovered from the roots of the annual Medicago orbicularis growing on the Cyclades Island of Naxos in Greece. WSM1022 is highly effective at fixing nitrogen with M. truncatula and other annual species such as M. tornata and M. littoralis and is also highly effective with the perennial M. sativa (alfalfa or lucerne). In common with other characterized E. meliloti strains, WSM1022 will nodulate but fixes poorly with M. polymorpha and M. sphaerocarpos and does not nodulate M. murex. Here we describe the features of E. meliloti WSM1022, together with genome sequence information and its annotation. The 6,649,661 bp high-quality-draft genome is arranged into 121 scaffolds of 125 contigs containing 6,323 protein-coding genes and 75 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project. C1 [Terpolilli, Jason; Hill, Yvette; Tian, Rui; Howieson, John; Reeve, Wayne] Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. [Braeu, Lambert] Deakin Univ, Sch Life & Environm Sci, Geelong, Vic 3217, Australia. [Goodwin, Lynne; Ivanova, Natalia; Kyrpides, Nikos] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Han, James; Liolios, Konstantinos; Huntemann, Marcel; Woyke, Tanja] DOE Joint Genome Inst, Walnut Creek, CA USA. [Pati, Amrita; Mavromatis, Konstantinos; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. RP Reeve, W (reprint author), Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. EM W.Reeve@murdoch.edu.au RI Kyrpides, Nikos/A-6305-2014; OI Kyrpides, Nikos/0000-0002-6131-0462; Hill, Yvette/0000-0001-5810-7845; Terpolilli, Jason/0000-0003-4306-3346 FU US Department of Energy's Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI); Centre for Rhizobium Studies (CRS) at Murdoch University; School of Veterinary and Life Sciences at Murdoch University FX This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. We grate-fully acknowledge the funding received from the Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI) and the Centre for Rhizobium Studies (CRS) at Murdoch University. We also acknowledge ECR funding for J. Terpolilli awarded by the School of Veterinary and Life Sciences at Murdoch University. NR 38 TC 2 Z9 3 U1 0 U2 4 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 2 BP 315 EP 324 DI 10.4056/sigs.4608286 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 294JX UT WOS:000330042800010 PM 24976888 ER PT J AU Galardini, M Bazzicalupo, M Biondi, E Brambilla, E Brilli, M Bruce, D Chain, P Chen, A Daligault, H Davenport, KW Deshpande, S Detter, JC Goodwin, LA Han, C Han, J Huntemann, M Ivanova, N Klenk, HP Kyrpides, NC Markowitz, V Mavrommatis, K Mocali, S Nolan, M Pagani, I Pati, A Pini, F Pitluck, S Spini, G Szeto, E Teshima, H Woyke, T Mengoni, A AF Galardini, Marco Bazzicalupo, Marco Biondi, Emanuele Brambilla, Eveline Brilli, Matteo Bruce, David Chain, Patrick Chen, Amy Daligault, Hajnalka Davenport, Karen Walston Deshpande, Shweta Detter, John C. Goodwin, Lynne A. Han, Cliff Han, James Huntemann, Marcel Ivanova, Natalia Klenk, Hans-Peter Kyrpides, Nikos C. Markowitz, Victor Mavrommatis, Kostas Mocali, Stefano Nolan, Matt Pagani, Ioanna Pati, Amrita Pini, Francesco Pitluck, Sam Spini, Giulia Szeto, Ernest Teshima, Hazuki Woyke, Tanja Mengoni, Alessio TI Permanent draft genome sequences of the symbiotic nitrogen fixing Ensifer meliloti strains BO21CC and AK58 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Aerobic; motile; Gram-negative; mesophilic; chemoorganotrophic; chemoautotrophic; soil; plant symbiont; biological nitrogen fixation; Ensifer (Sinorhizobium) meliloti; legume yield ID SINORHIZOBIUM-MELILOTI; BACTERIA; ARCHAEA; SYSTEM; TOOL AB Ensifer (syn. Sinorhizobium) meliloti is an important symbiotic bacterial species that fixes nitrogen. Strains BO21CC and AK58 were previously investigated for their substrate utilization and their plant-growth promoting abilities showing interesting features. Here, we describe the complete genome sequence and annotation of these strains. BO21CC and AK58 genomes are 6,985,065 and 6,974,333 bp long with 6,746 and 6,992 genes predicted, respectively. C1 [Galardini, Marco; Bazzicalupo, Marco; Spini, Giulia; Mengoni, Alessio] Univ Florence, Dept Biol, I-50019 Sesto Fiorentino, Italy. [Biondi, Emanuele; Pini, Francesco] Interdisciplinary Res Inst CNRS, Villeneuve Dascq, France. [Brambilla, Eveline; Klenk, Hans-Peter] Leibniz Inst DSMZ German Collect Microorganisms &, Braunschweig, Germany. [Brilli, Matteo] Edmund Mach Fdn, San Michele All Adige, Italy. [Bruce, David; Chain, Patrick; Daligault, Hajnalka; Davenport, Karen Walston; Detter, John C.; Goodwin, Lynne A.; Han, Cliff; Teshima, Hazuki] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Deshpande, Shweta; Han, James; Huntemann, Marcel; Ivanova, Natalia; Kyrpides, Nikos C.; Markowitz, Victor; Mavrommatis, Kostas; Nolan, Matt; Pagani, Ioanna; Pati, Amrita; Pitluck, Sam; Szeto, Ernest; Woyke, Tanja] DOE Joint Genome Inst, Walnut Creek, CA USA. [Mocali, Stefano] Consiglio Ric & Sperimentaz Agr, Ctr Ric Agropedol & Pedol, Florence, Italy. RP Mengoni, A (reprint author), Univ Florence, Dept Biol, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy. EM alessio.mengoni@unifi.it RI Pini, Francesco/E-9630-2015; Kyrpides, Nikos/A-6305-2014; OI Pini, Francesco/0000-0001-5323-8395; Kyrpides, Nikos/0000-0002-6131-0462; Brilli, Matteo/0000-0001-9891-4617; Galardini, Marco/0000-0003-2018-8242; Chain, Patrick/0000-0003-3949-3634; Mocali, Stefano/0000-0002-1173-7206; Mengoni, Alessio/0000-0002-1265-8251 FU Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231] FX We are grateful to Dr. M. L. Roumiantseva and Dr. B. Simarov (Research Institute for Agricultural Microbiology, St-Petersburg-Puskin, Russia) for original isolation and the permission to use strain AK58 in this work. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy Under Contract No. DE-AC02-05CH11231. NR 30 TC 2 Z9 2 U1 1 U2 8 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 2 BP 325 EP 333 DI 10.4056/sigs.3797438 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 294JX UT WOS:000330042800011 PM 24976889 ER PT J AU Dogs, M Voget, S Teshima, H Petersen, J Davenport, K Dalingault, H Chen, A Pati, A Ivanova, N Goodwin, LA Chain, P Detter, JC Standfest, S Rohde, M Gronow, S Kyrpides, NC Woyke, T Simon, M Klenk, HP Goker, M Brinkhoff, T AF Dogs, Marco Voget, Sonja Teshima, Hazuki Petersen, Joern Davenport, Karen Dalingault, Hajnalka Chen, Amy Pati, Amrita Ivanova, Natalia Goodwin, Lynne A. Chain, Patrick Detter, John C. Standfest, Sonja Rohde, Manfred Gronow, Sabine Kyrpides, Nikos C. Woyke, Tanja Simon, Meinhard Klenk, Hans-Peter Goeker, Markus Brinkhoff, Thorsten TI Genome sequence of Phaeobacter inhibens type strain (T5(T)), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Anaerobic; motile; rod-shaped; tropodithietic acid; secondary metabolites; Rhodobacterales; Rhodobacteraceae ID STANDARD OPERATING PROCEDURE; SP-NOV.; ELECTROACTIVE BIOFILM; TROPODITHIETIC ACID; EMENDED DESCRIPTIONS; INHIBITORY-ACTIVITY; TIDAL FLAT; GEN. NOV.; SP. NOV.; RUEGERIA AB Strain T5(T) is the type strain of the species Phaeobacter inhibens Martens et al. 2006, a secondary metabolite producing bacterium affiliated to the Roseobacter clade. Strain T5(T) was isolated from a water sample taken at the German Wadden Sea, southern North Sea. Here we describe the complete genome sequence and annotation of this bacterium with a special focus on the secondary metabolism and compare it with the genomes of the Phaeobacter inhibens strains DSM 17395 and DSM 24588 (2.10), selected because of the close phylogenetic relationship based on the 16S rRNA gene sequences of these three strains. The genome of strain T5(T) comprises 4,130,897 bp with 3.923 protein-coding genes and shows high similarities in genetic and genomic characteristics compared to P. inhibens DSM 17395 and DSM 24588 (2.10). Besides the chromosome, strain T5(T) possesses four plasmids, three of which show a high similarity to the plasmids of the strains DSM 17395 and DSM 24588 (2.10). Analysis of the fourth plasmid suggested horizontal gene transfer. Most of the genes on this plasmid are not present in the strains DSM 17395 and DSM 24588 (2.10) including a nitrous oxide reductase, which allows strain T5(T) a facultative anaerobic lifestyle. The G+ C content was calculated from the genome sequence and differs significantly from the previously published value, thus warranting an emendation of the species description. C1 [Dogs, Marco; Standfest, Sonja; Simon, Meinhard; Brinkhoff, Thorsten] Inst Chem & Biol Marine Environm ICBM, Oldenburg, Germany. [Voget, Sonja] Univ Gottingen, Inst Microbiol & Genet, Dept Genom & Appl Microbiol, D-37073 Gottingen, Germany. [Voget, Sonja] Univ Gottingen, Inst Microbiol & Genet, Gottingen Genom Lab, D-37073 Gottingen, Germany. [Teshima, Hazuki; Davenport, Karen; Dalingault, Hajnalka; Goodwin, Lynne A.; Chain, Patrick; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Petersen, Joern; Gronow, Sabine; Klenk, Hans-Peter; Goeker, Markus] Leibniz Inst DSMZ German Collect Microorganisms &, Braunschweig, Germany. [Chen, Amy] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Pati, Amrita; Ivanova, Natalia; Goodwin, Lynne A.; Detter, John C.; Kyrpides, Nikos C.; Woyke, Tanja] DOE Joint Genome Inst, Walnut Creek, CA USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. RP Brinkhoff, T (reprint author), Inst Chem & Biol Marine Environm ICBM, Oldenburg, Germany. EM t.brinkhoff@icbm.de RI Kyrpides, Nikos/A-6305-2014; OI Kyrpides, Nikos/0000-0002-6131-0462; Chain, Patrick/0000-0003-3949-3634 FU Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]; German Research Foundation (DFG) [Transregio-SFB 51]; European Commission [222886] FX The authors gratefully acknowledge the assistance of Iljana Schroder for growing P. inhibens cultures and Evelyne-Marie Brambilla for DNA extraction and quality control (both at the DSMZ). The work conducted by the U.S. Department of Energy Joint Genome Institute was supported by the Office of Science of the U.S. Department of Energy under contract No. DE-AC02-05CH11231; the work conducted by members of the Roseobacter consortium was supported by the German Research Foundation (DFG) Transregio-SFB 51. We also thank the European Commission which supported phenotyping via the Microme project 222886 within the Framework 7 program. NR 80 TC 8 Z9 8 U1 0 U2 9 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 2 BP 334 EP 350 DI 10.4056/sigs.4448212 PG 17 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 294JX UT WOS:000330042800012 PM 24976890 ER PT J AU Khanna, N Ghosh, AK Huntemann, M Deshpande, S Han, J Chen, A Kyrpides, N Mavrommatis, K Szeto, E Markowitz, V Ivanova, N Pagani, I Pati, A Pitluck, S Nolan, M Woyke, T Teshima, H Chertkov, O Daligault, H Davenport, K Gu, W Munk, C Zhang, XJ Bruce, D Detter, C Xu, Y Quintana, B Reitenga, K Kunde, Y Green, L Erkkila, T Han, C Brambilla, EM Lang, EK Klenk, HP Goodwin, L Chain, P Das, D AF Khanna, Namita Ghosh, Ananta Kumar Huntemann, Marcel Deshpande, Shweta Han, James Chen, Amy Kyrpides, Nikos Mavrommatis, Kostas Szeto, Ernest Markowitz, Victor Ivanova, Natalia Pagani, Ioanna Pati, Amrita Pitluck, Sam Nolan, Matt Woyke, Tanja Teshima, Hazuki Chertkov, Olga Daligault, Hajnalka Davenport, Karen Gu, Wei Munk, Christine Zhang, Xiaojing Bruce, David Detter, Chris Xu, Yan Quintana, Beverly Reitenga, Krista Kunde, Yulia Green, Lance Erkkila, Tracy Han, Cliff Brambilla, Evelyne-Marie Lang, Elke Klenk, Hans-Peter Goodwin, Lynne Chain, Patrick Das, Debabrata TI Complete genome sequence of Enterobacter sp. IIT-BT 08: A potential microbial strain for high rate hydrogen production SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Enterobacter sp IIT-BT 08; genome sequence; facultative anaerobe; biohydrogen ID ESCHERICHIA-COLI; NUCLEOTIDE-SEQUENCE; SYSTEM; OPERON; EXPRESSION; PROPOSAL; BIOLOGY; TOOL AB Enterobacter sp. IIT-BT 08 belongs to Phylum: Proteobacteria, Class: Gammaproteobacteria, Order: Enterobacteriales, Family: Enterobacteriaceae. The organism was isolated from the leaves of a local plant near the Kharagpur railway station, Kharagpur, West Bengal, India. It has been extensively studied for fermentative hydrogen production because of its high hydrogen yield. For further enhancement of hydrogen production by strain development, complete genome sequence analysis was carried out. Sequence analysis revealed that the genome was linear, 4.67 Mbp long and had a GC content of 56.01%. The genome properties encode 4,393 protein-coding and 179 RNA genes. Additionally, a putative pathway of hydrogen production was suggested based on the presence of formate hydrogen lyase complex and other related genes identified in the genome. Thus, in the present study we describe the specific properties of the organism and the generation, annotation and analysis of its genome sequence as well as discuss the putative pathway of hydrogen production by this organism. C1 [Khanna, Namita; Ghosh, Ananta Kumar; Das, Debabrata] Indian Inst Technol Kharagpur, Kharagpur, W Bengal, India. [Huntemann, Marcel; Deshpande, Shweta; Han, James; Chen, Amy; Kyrpides, Nikos; Mavrommatis, Kostas; Szeto, Ernest; Markowitz, Victor; Ivanova, Natalia; Pagani, Ioanna; Pati, Amrita; Pitluck, Sam; Nolan, Matt; Woyke, Tanja] Joint Genome Inst, Dept Energy, Walnut Creek, CA USA. [Teshima, Hazuki; Chertkov, Olga; Daligault, Hajnalka; Davenport, Karen; Gu, Wei; Munk, Christine; Zhang, Xiaojing; Bruce, David; Detter, Chris; Xu, Yan; Quintana, Beverly; Reitenga, Krista; Kunde, Yulia; Green, Lance; Erkkila, Tracy; Han, Cliff; Goodwin, Lynne; Chain, Patrick] Lawrence Livermore Natl Lab, Livermore, CA USA. [Brambilla, Evelyne-Marie; Lang, Elke; Klenk, Hans-Peter] Leibniz Inst DSMZ German Collect Microorganisms &, Braunschweig, Germany. RP Das, D (reprint author), Indian Inst Technol Kharagpur, Kharagpur, W Bengal, India. EM ddas.iitkgp@gmail.com RI Kyrpides, Nikos/A-6305-2014 OI Kyrpides, Nikos/0000-0002-6131-0462 FU Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]; MNRE; Department of Biotechnology (DBT), Government of India FX The work was conducted by the U.S. Department of Energy Joint Genome Institute and is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Authors (DD and NK) are also thankful to MNRE for their financial assistance. NK also gratefully acknowledges Department of Biotechnology (DBT), Government of India, for senior research fellowship. The authors from IITKgp, India submitted the JGI-CSP project, analyzed the data and wrote the manuscript. The authors from DSMZ confirmed the strain identity and extracted high quality genomic DNA for sequencing. The authors from DoE-JGI, WC, USA, and LLNL, Livermore CA USA carried out the sequencing and annotation of the genome. NR 36 TC 5 Z9 5 U1 0 U2 6 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 2 BP 359 EP 369 DI 10.4056/sigs.4348035 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 294JX UT WOS:000330042800014 PM 24976892 ER PT J AU Reeve, W De Meyer, S Terpolilli, J Melino, V Ardley, J Rui, T Tiwari, R Howieson, J Yates, R O'Hara, G Lu, MG Bruce, D Detter, C Tapia, R Han, C Wei, CL Huntemann, M Han, J Chen, IM Mavromatis, K Markowitz, V Szeto, E Ivanova, N Mikhailova, N Ovchinnikova, G Pagani, I Pati, A Goodwin, L Peters, L Pitluck, S Woyke, T Kyrpides, N AF Reeve, Wayne De Meyer, Sofie Terpolilli, Jason Melino, Vanessa Ardley, Julie Rui, Tian Tiwari, Ravi Howieson, John Yates, Ron O'Hara, Graham Lu, Megan Bruce, David Detter, Chris Tapia, Roxanne Han, Cliff Wei, Chia-Lin Huntemann, Marcel Han, James Chen, I-Min Mavromatis, Konstantinos Markowitz, Victor Szeto, Ernest Ivanova, Natalia Mikhailova, Natalia Ovchinnikova, Galina Pagani, Ioanna Pati, Amrita Goodwin, Lynne Peters, Lin Pitluck, Sam Woyke, Tanja Kyrpides, Nikos TI Genome sequence of the Lebeckia ambigua-nodulating "Burkholderia sprentiae" strain WSM5005 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE root-nodule bacteria; nitrogen fixation; rhizobia; Alphaproteobacteria ID NITROGEN-FIXATION; SECT. LEBECKIA; RNA GENES; BACTERIA; GENUS; CROTALARIEAE; ANNOTATION; PREDICTION; FABACEAE; REVISION AB "Burkholderia sprentiae" strain WSM5005(T) is an aerobic, motile, Gram-negative, non-sporeforming rod that was isolated in Australia from an effective N-2-fixing root nodule of Lebeckia ambigua collected in Klawer, Western Cape of South Africa, in October 2007. Here we describe the features of "Burkholderia sprentiae" strain WSM5005T, together with the genome sequence and its annotation. The 7,761,063 bp high-quality-draft genome is arranged in 8 scaffolds of 236 contigs, contains 7,147 protein-coding genes and 76 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program. C1 [Reeve, Wayne; De Meyer, Sofie; Terpolilli, Jason; Melino, Vanessa; Ardley, Julie; Rui, Tian; Tiwari, Ravi; Howieson, John; Yates, Ron; O'Hara, Graham] Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. [Lu, Megan; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Wei, Chia-Lin; Huntemann, Marcel; Han, James; Mavromatis, Konstantinos; Ivanova, Natalia; Mikhailova, Natalia; Ovchinnikova, Galina; Pagani, Ioanna; Pati, Amrita; Peters, Lin; Pitluck, Sam; Woyke, Tanja; Kyrpides, Nikos] DOE Joint Genome Inst, Walnut Creek, CA USA. [Chen, I-Min; Markowitz, Victor; Szeto, Ernest; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. RP Reeve, W (reprint author), Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. EM W.Reeve@murdoch.edu.au RI Melino, Vanessa/B-1920-2012; Kyrpides, Nikos/A-6305-2014 OI Melino, Vanessa/0000-0003-2742-5079; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy's Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DEAC52- 07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI); Centre for Rhizobium Studies (CRS) at Murdoch University FX This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DEAC52- 07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. We gratefully acknowledge the funding received from the Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI) and the Centre for Rhizobium Studies (CRS) at Murdoch University. NR 41 TC 3 Z9 3 U1 1 U2 2 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 2 BP 385 EP 394 DI 10.4056/sigs.4558268 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 294JX UT WOS:000330042800016 PM 24976894 ER PT J AU Reeve, W Nandasena, K Yates, R Tiwari, R O'Hara, G Ninawi, M Gu, W Goodwin, L Detter, C Tapia, R Han, C Copeland, A Liolios, K Chen, A Markowitz, V Pati, A Mavromatis, K Woyke, T Kyrpides, N Ivanova, N Howieson, J AF Reeve, Wayne Nandasena, Kemanthi Yates, Ron Tiwari, Ravi O'Hara, Graham Ninawi, Mohamed Gu, Wei Goodwin, Lynne Detter, Chris Tapia, Roxanne Han, Cliff Copeland, Alex Liolios, Konstantinos Chen, Amy Markowitz, Victor Pati, Amrita Mavromatis, Konstantinos Woyke, Tanja Kyrpides, Nikos Ivanova, Natalia Howieson, John TI Complete genome sequence of Mesorhizobium australicum type strain (WSM2073(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE root-nodule bacteria; nitrogen fixation; evolution; lateral transfer of genes; integrative and conjugative elements; symbiosis; Alphaproteobacteria ID BISERRULA-PELECINUS L; LATERAL TRANSFER; ROOT-NODULE; RNA GENES; BACTERIA; ANNOTATION; PREDICTION; EVOLUTION; DATABASE; LEGUMES AB Mesorhizobium australicum strain WSM2073T was isolated from root nodules on the pasture legume Biserrula pelecinus growing in Australia in 2000. This aerobic, motile, gram negative, nonspore- forming rod is poorly effective in N2 fixation on B. pelecinus and has gained the ability to nodulate B. pelecinus following in situ lateral transfer of a symbiosis island from the original inoculant strain for this legume, Mesorhizobium ciceri bv. biserrulae WSM1271. We describe that the genome size of M. australicum strain WSM2073T is 6,200,534 bp encoding 6,013 proteincoding genes and 67 RNA-only encoding genes. This genome does not contain any plasmids but has a 455.7 kb genomic island from Mesorhizobium ciceri bv. biserrulae WSM1271 that has been integrated into a phenylalanine-tRNA gene. C1 [Reeve, Wayne; Nandasena, Kemanthi; Yates, Ron; Tiwari, Ravi; O'Hara, Graham; Ninawi, Mohamed; Howieson, John] Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. [Gu, Wei; Goodwin, Lynne; Detter, Chris; Tapia, Roxanne; Han, Cliff] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Copeland, Alex; Liolios, Konstantinos; Pati, Amrita; Mavromatis, Konstantinos; Woyke, Tanja; Kyrpides, Nikos; Ivanova, Natalia] DOE Joint Genome Inst, Walnut Creek, CA USA. [Chen, Amy; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. RP Reeve, W (reprint author), Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. EM W.Reeve@murdoch.edu.au RI Kyrpides, Nikos/A-6305-2014 OI Kyrpides, Nikos/0000-0002-6131-0462 FU University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DEAC52- 07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Australian Research Council [DP0880896]; Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI); Centre for Rhizobium Studies (CRS) at Murdoch University FX This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DEAC52- 07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. We gratefully acknowledge the funding received from Australian Research Council Discovery grant (DP0880896), Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI) and the Centre for Rhizobium Studies (CRS) at Murdoch University. The authors would like to thank the Australia-China Joint Research Centre for Wheat Improvement (ACCWI) and SuperSeed Technologies (SST) for financially supporting Mohamed Ninawi's PhD project. NR 39 TC 4 Z9 4 U1 0 U2 3 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 2 BP 410 EP 419 DI 10.4056/sigs.4568282 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 294JX UT WOS:000330042800018 PM 24976896 ER PT J AU Terpolilli, J Garau, G Hill, Y Tian, R Howieson, J Brau, L Goodwin, L Han, J Liolios, K Huntemann, M Pati, A Woyke, T Mavromatis, K Markowitz, V Ivanova, N Kyrpides, N Reeve, W AF Terpolilli, Jason Garau, Giovanni Hill, Yvette Tian, Rui Howieson, John Braeu, Lambert Goodwin, Lynne Han, James Liolios, Konstantinos Huntemann, Marcel Pati, Amrita Woyke, Tanja Mavromatis, Konstantinos Markowitz, Victor Ivanova, Natalia Kyrpides, Nikos Reeve, Wayne TI Genome sequence of Ensifer medicae strain WSM1369; an effective microsymbiont of the annual legume Medicago sphaerocarpos SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE root-nodule bacteria; nitrogen fixation; rhizobia; Alphaproteobacteria ID BIOLOGICAL NITROGEN-FIXATION; SINORHIZOBIUM-MELILOTI; RHIZOBIUM-MELILOTI; ROOT-NODULE; SP-NOV; BACTERIA; SYSTEM; SOIL AB Ensifer medicae WSM1369 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago. WSM1369 was isolated in 1993 from a nodule recovered from the roots of Medicago sphaerocarpos growing at San Pietro di Rudas, near Aggius in Sardinia (Italy). WSM1369 is an effective microsymbiont of the annual forage legumes M. polymorpha and M. sphaerocarpos. Here we describe the features of E. medicae WSM1369, together with genome sequence information and its annotation. The 6,402,557 bp standard draft genome is arranged into 307 scaffolds of 307 contigs containing 6,656 protein-coding genes and 79 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBARNB) project. C1 [Terpolilli, Jason; Hill, Yvette; Tian, Rui; Howieson, John; Reeve, Wayne] Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. [Garau, Giovanni] Univ Sassari, STAA, Dipartimento Agr, I-07100 Sassari, Italy. [Braeu, Lambert] Deakin Univ, Sch Life & Environm Sci, Geelong, Vic 3217, Australia. [Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Han, James; Liolios, Konstantinos; Huntemann, Marcel; Pati, Amrita; Woyke, Tanja; Ivanova, Natalia; Kyrpides, Nikos] DOE Joint Genome Inst, Walnut Creek, CA USA. [Mavromatis, Konstantinos; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. RP Reeve, W (reprint author), Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. EM W.Reeve@murdoch.edu.au RI Garau, Giovanni/J-5362-2014; Kyrpides, Nikos/A-6305-2014; OI Garau, Giovanni/0000-0001-8292-8336; Kyrpides, Nikos/0000-0002-6131-0462; Hill, Yvette/0000-0001-5810-7845; Terpolilli, Jason/0000-0003-4306-3346 FU US Department of Energy's Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DEAC52- 07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI); Centre for Rhizobium Studies (CRS) at Murdoch University FX This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DEAC52- 07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. We gratefully acknowledge the funding received from the Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI) and the Centre for Rhizobium Studies (CRS) at Murdoch University. NR 41 TC 1 Z9 1 U1 0 U2 3 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 2 BP 420 EP 430 DI 10.4056/sigs.4838624 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 294JX UT WOS:000330042800019 PM 24976897 ER PT J AU Vesth, T Ozen, A Andersen, SC Kaas, RS Lukjancenko, O Bohlin, J Nookaew, I Wassenaar, TM Ussery, DW AF Vesth, Tammi Ozen, Asli Andersen, Sandra C. Kaas, Rolf Sommer Lukjancenko, Oksana Bohlin, Jon Nookaew, Intawat Wassenaar, Trudy M. Ussery, David W. TI Veillonella, Firmicutes: Microbes disguised as Gram negatives SO STANDARDS IN GENOMIC SCIENCES LA English DT Article ID MULTIPLE SEQUENCE ALIGNMENT; IDENTIFICATION; SIGNATURE; BACTERIA; PLAQUE; LIFE AB The Firmicutes represent a major component of the intestinal microflora. The intestinal Firmicutes are a large, diverse group of organisms, many of which are poorly characterized due to their anaerobic growth requirements. Although most Firmicutes are Gram positive, members of the class Negativicutes, including the genus Veillonella, stain Gram negative. Veillonella are among the most abundant organisms of the oral and intestinal microflora of animals and humans, in spite of being strict anaerobes. In this work, the genomes of 24 Negativicutes, including eight Veillonella spp., are compared to 20 other Firmicutes genomes; a further 101 prokaryotic genomes were included, covering 26 phyla. Thus a total of 145 prokaryotic genomes were analyzed by various methods to investigate the apparent conflict of the Veillonella Gram stain and their taxonomic position within the Firmicutes. Comparison of the genome sequences confirms that the Negativicutes are distantly related to Clostridium spp., based on 16S rRNA, complete genomic DNA sequences, and a consensus tree based on conserved proteins. The genus Veillonella is relatively homogeneous: inter-genus pairwise comparison identifies at least 1,350 shared proteins, although less than half of these are found in any given Clostridium genome. Only 27 proteins are found conserved in all analyzed prokaryote genomes. Veillonella has distinct metabolic properties, and significant similarities to genomes of Proteobacteria are not detected, with the exception of a shared LPS biosynthesis pathway. The clade within the class Negativicutes to which the genus Veillonella belongs exhibits unique properties, most of which are in common with Gram-positives and some with Gram negatives. They are only distantly related to Clostridia, but are even less closely related to Gram-negative species. Though the Negativicutes stain Gram-negative and possess two membranes, the genome and proteome analysis presented here confirm their place within the (mainly) Gram positive phylum of the Firmicutes. Further studies are required to unveil the evolutionary history of the Veillonella and other Negativicutes. C1 [Vesth, Tammi; Ozen, Asli; Andersen, Sandra C.; Kaas, Rolf Sommer; Lukjancenko, Oksana] Tech Univ Denmark, Dept Syst Biol, Ctr Biol Sequence Anal, DK-2800 Lyngby, Denmark. [Bohlin, Jon] Norwegian Sch Vet Sci, Dept Food Safety & Infect Biol, Oslo, Norway. [Nookaew, Intawat] Chalmers, Dept Chem & Biol Engn, S-41296 Gothenburg, Sweden. [Wassenaar, Trudy M.] Mol Microbiol & Genom Consultants, Zotzenheim, Germany. [Ozen, Asli] Tech Univ Denmark, Novo Nordisk Fdn Ctr Biosustainabil, DK-2800 Lyngby, Denmark. [Ussery, David W.] Oak Ridge Natl Lab, Comparat Genom Grp, Biosci Div, Oak Ridge, TN 37831 USA. RP Ussery, DW (reprint author), Oak Ridge Natl Lab, Comparat Genom Grp, Biosci Div, Oak Ridge, TN 37831 USA. EM dave@cbs.dtu.dk OI Bohlin, Jon/0000-0002-0992-1311; Ussery, David/0000-0003-3632-5512; Kaas, Rolf Sommer/0000-0002-5050-8668 FU Danish Council for Strategic Research [09-067103/DSF]; Danish Research Council FX This research was supported by grants from the Danish Research Council, and in part by a grant 09-067103/DSF from the Danish Council for Strategic Research. NR 31 TC 9 Z9 9 U1 3 U2 15 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 2 BP 431 EP 448 DI 10.4056/sigs.2981345 PG 18 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 294JX UT WOS:000330042800020 PM 24976898 ER PT J AU Tittel, FK Lewicki, R Lascola, R McWhorter, S AF Tittel, Frank K. Lewicki, Rafal Lascola, Robert McWhorter, Scott BE Geiger, WM Raynor, MW TI EMERGING INFRARED LASER ABSORPTION SPECTROSCOPIC TECHNIQUES FOR GAS ANALYSIS SO TRACE ANALYSIS OF SPECIALTY AND ELECTRONIC GASES LA English DT Article; Book Chapter ID QUANTUM-CASCADE LASER; ENHANCED PHOTOACOUSTIC-SPECTROSCOPY; CAVITY OUTPUT SPECTROSCOPY; FREQUENCY COMB SPECTROSCOPY; QUARTZ TUNING FORKS; OPTICAL PARAMETRIC OSCILLATOR; HIGH-SENSITIVITY DETECTION; DIODE-LASER; MU-M; NITRIC-OXIDE C1 [Tittel, Frank K.; Lewicki, Rafal] Rice Univ, Dept Elect & Comp Engn, Houston, TX 77251 USA. [Lascola, Robert; McWhorter, Scott] Savannah River Natl Lab, Analyt Dev Div, Aiken, SC USA. RP Tittel, FK (reprint author), Rice Univ, Dept Elect & Comp Engn, POB 1892, Houston, TX 77251 USA. OI Lascola, Robert/0000-0002-6784-5644 NR 129 TC 2 Z9 2 U1 0 U2 2 PU BLACKWELL SCIENCE PUBL PI OXFORD PA OSNEY MEAD, OXFORD OX2 0EL, ENGLAND BN 978-1-118-06566-2 PY 2013 BP 71 EP 109 D2 10.1002/9781118642771 PG 39 WC Engineering, Chemical SC Engineering GA BJO96 UT WOS:000329443500005 ER PT S AU Jung, ES Maheshwari, K Kettimuthu, R AF Jung, Eun-Sung Maheshwari, Ketan Kettimuthu, Rajkumar GP IEEE TI Pipelining/Overlapping Data Transfer for Distributed Data-Intensive Job Execution SO 2013 42ND ANNUAL INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING (ICPP) SE Proceedings of the International Conference on Parallel Processing LA English DT Proceedings Paper CT 42nd Annual International Conference on Parallel Processing (ICPP) CY OCT 01-04, 2013 CL Ecole Normale Superieure Lyon, Lyon, FRANCE SP INRIA, LIP Lab, Univ Lyon, MILYON, IEEE Comp Soc HO Ecole Normale Superieure Lyon ID WORKFLOWS AB Scientific workflows are increasingly gaining attention as both data and compute resources are getting bigger, heterogeneous, and distributed. Many scientific workflows are both compute intensive and data intensive and use distributed resources. This situation poses significant challenges in terms of real-time remote analysis and dissemination of massive datasets to scientists across the community. These challenges will be exacerbated in the exascale era. Parallel jobs in scientific workflows are common, and such parallelism can be exploited by scheduling parallel jobs among multiple execution sites for enhanced performance. Previous scheduling algorithms such as heterogeneous earliest finish time (HEFT) did not focus on scheduling thousands of jobs often seen in contemporary applications. Some techniques, such as task clustering, have been proposed to reduce the overhead of scheduling a large number of jobs. However, scheduling massively parallel jobs in distributed environments poses new challenges as data movement becomes a nontrivial factor. We propose efficient parallel execution models through pipelined execution of data transfer, incorporating network bandwidth and reserved resources at an execution site. We formally analyze those models and suggest the best model with the optimal degree of parallelism. We implement our model in the Swift parallel scripting paradigm using GridFTP. Experiments on real distributed computing resources show that our model with optimal degrees of parallelism outperform the current parallel execution model by as much as 50% reduction of total execution time. C1 [Jung, Eun-Sung; Maheshwari, Ketan; Kettimuthu, Rajkumar] Argonne Natl Lab, Div Math & Comp Sci, Argonne, IL 60439 USA. RP Jung, ES (reprint author), Argonne Natl Lab, Div Math & Comp Sci, 9700 S Cass Ave, Argonne, IL 60439 USA. EM esjung@mcs.anl.gov; ketan@mcs.anl.gov; kettimut@mcs.anl.gov NR 20 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 0190-3918 BN 978-0-7695-5117-3 J9 PROC INT CONF PARAL PY 2013 BP 791 EP 797 DI 10.1109/ICPP.2013.93 PG 7 WC Computer Science, Hardware & Architecture SC Computer Science GA BJT04 UT WOS:000330046000084 ER PT S AU Hsu, CH Poole, SW AF Hsu, Chung-Hsing Poole, Stephen W. GP IEEE TI Revisiting Server Energy Proportionality SO 2013 42ND ANNUAL INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING (ICPP) SE Proceedings of the International Conference on Parallel Processing LA English DT Proceedings Paper CT 42nd Annual International Conference on Parallel Processing (ICPP) CY OCT 01-04, 2013 CL Ecole Normale Superieure Lyon, Lyon, FRANCE SP INRIA, LIP Lab, Univ Lyon, MILYON, IEEE Comp Soc HO Ecole Normale Superieure Lyon DE power analysis; energy proportionality AB Server energy proportionality refers to a proposed ideal that a server consumes energy proportional to its utilization level. Since its introduction in 2007, the ideal has been adopted by the server industry as a design goal to further optimize the energy efficiency of their servers. There have also been studies on how energy proportionality has evolved over time. However, most of these efforts assume linear proportionality. Must energy proportionality be linear? In this paper we look into this problem. We analyze 410 SPECpower_ssj2008 benchmark results published from 2007 to 2012, and find that modern servers have pushed server energy proportionality from linear to quadratic. We also observe a strong correlation in time between this change and dynamic over-clocking (such as Intel Turbo Boost). We present all these findings in the paper, along with discussions on the implications of super-linearity in server energy proportionality. C1 [Hsu, Chung-Hsing; Poole, Stephen W.] Oak Ridge Natl Lab, Comp Sci & Math Div, Oak Ridge, TN 37831 USA. RP Hsu, CH (reprint author), Oak Ridge Natl Lab, Comp Sci & Math Div, Oak Ridge, TN 37831 USA. EM hsuc@ornl.gov; spoole@ornl.gov NR 34 TC 2 Z9 2 U1 0 U2 2 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 0190-3918 BN 978-0-7695-5117-3 J9 PROC INT CONF PARAL PY 2013 BP 834 EP 840 DI 10.1109/ICPP.2013.99 PG 7 WC Computer Science, Hardware & Architecture SC Computer Science GA BJT04 UT WOS:000330046000088 ER PT S AU Engelmann, C Naughton, T AF Engelmann, Christian Naughton, Thomas GP IEEE TI Toward a Performance/Resilience Tool for Hardware/Software Co-Design of High-Performance Computing Systems SO 2013 42ND ANNUAL INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING (ICPP) SE Proceedings of the International Conference on Parallel Processing LA English DT Proceedings Paper CT 42nd Annual International Conference on Parallel Processing (ICPP) CY OCT 01-04, 2013 CL Ecole Normale Superieure Lyon, Lyon, FRANCE SP INRIA, LIP Lab, Univ Lyon, MILYON, IEEE Comp Soc HO Ecole Normale Superieure Lyon DE Fault Injection; Message Passing Interface; Parallel Discrete Event Simulation; High-performance Computing ID MIGRATION AB xSim is a simulation-based performance investigation toolkit that permits running high-performance computing (HPC) applications in a controlled environment with millions of concurrent execution threads, while observing application performance in a simulated extreme-scale system for hardware/software co-design. The presented work details newly developed features for xSim that permit the injection of MPI process failures, the propagation/detection/notification of such failures within the simulation, and their handling using application-level checkpoint/restart. These new capabilities enable the observation of application behavior and performance under failure within a simulated future-generation HPC system using the most common fault handling technique. C1 [Engelmann, Christian; Naughton, Thomas] Oak Ridge Natl Lab, Comp Sci & Math Div, Oak Ridge, TN 37831 USA. RP Engelmann, C (reprint author), Oak Ridge Natl Lab, Comp Sci & Math Div, Oak Ridge, TN 37831 USA. EM engelmannc@ornl.gov; naughtont@ornl.gov NR 45 TC 5 Z9 5 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 0190-3918 BN 978-0-7695-5117-3 J9 PROC INT CONF PARAL PY 2013 BP 960 EP 969 DI 10.1109/ICPP.2013.114 PG 10 WC Computer Science, Hardware & Architecture SC Computer Science GA BJT04 UT WOS:000330046000103 ER PT S AU Hilbrich, T Protze, J de Supinski, BR Schulz, M Muller, MS Nagel, WE AF Hilbrich, Tobias Protze, Joachim de Supinski, Bronis R. Schulz, Martin Mueller, Matthias S. Nagel, Wolfgang E. GP IEEE TI Intralayer Communication for Tree-Based Overlay Networks SO 2013 42ND ANNUAL INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING (ICPP) SE Proceedings of the International Conference on Parallel Processing LA English DT Proceedings Paper CT 42nd Annual International Conference on Parallel Processing (ICPP) CY OCT 01-04, 2013 CL Ecole Normale Superieure Lyon, Lyon, FRANCE SP INRIA, LIP Lab, Univ Lyon, MILYON, IEEE Comp Soc HO Ecole Normale Superieure Lyon AB While various HPC tools use Tree-Based Overlay Networks (TBONs) to increase their scalability, some use cases do not map well to a tree-based hierarchy. We provide the concept of intralayer communication to improve this situation, where nodes in a specific hierarchy layer may exchange messages directly with each other. This concept targets data preprocessing that allows tool developers to avoid load imbalances in higher hierarchy levels. We implement intralayer communication within the Generic Tools Infrastructure (GTI) that provides TBON services, as well as a high-level abstraction to ease the creation of scalable runtime tools. An extension of GTI's abstractions allows simple and efficient use of intralayer communication. We demonstrate this capability with a runtime message matching tool for MPI's point-to-point communication, which we evaluate in an application study with up to 16,384 processes. Low overheads for two benchmark suites show the applicability of our approach, while a stress test demonstrates close to constant overheads across scales. The stress test measurements demonstrate that intralayer communication reduces application slowdown by two orders of magnitude at 2,048 processes, compared to a previous TBON-based implementation. C1 [Hilbrich, Tobias; Nagel, Wolfgang E.] Tech Univ Dresden, D-01062 Dresden, Germany. [Protze, Joachim; Mueller, Matthias S.] Rhein Westfal TH Aachen, Aachen, Germany. [de Supinski, Bronis R.; Schulz, Martin] Lawrence Livermore Natl Lab, Livermore, CA USA. RP Hilbrich, T (reprint author), Tech Univ Dresden, D-01062 Dresden, Germany. EM tobias.hilbrich@tu-dresden.de; protze@rz.rwth-aachen.de; bronis@llnl.gov; schulzm@llnl.gov; mueller@rz.rwth-aachen.de; wolfgang.nagel@tu-dresden.de FU PERFCLOUD; FSN (Fond pour la Societe Numerique) FX This work is (integrated and) supported by the PERFCLOUD project. A French FSN (Fond pour la Societe Numerique) cooperative project that associates academics and industrials partners in order to design then provide building blocks for a new generation of HPC datacenters. NR 23 TC 2 Z9 2 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 0190-3918 BN 978-0-7695-5117-3 J9 PROC INT CONF PARAL PY 2013 BP 995 EP 1003 DI 10.1109/ICPP.2013.118 PG 9 WC Computer Science, Hardware & Architecture SC Computer Science GA BJT04 UT WOS:000330046000107 ER PT S AU Sen, S AF Sen, Satyabrata GP IEEE TI CONSTANT-ENVELOPE WAVEFORM DESIGN FOR OPTIMAL TARGET-DETECTION AND AUTOCORRELATION PERFORMANCES SO 2013 IEEE INTERNATIONAL CONFERENCE ON ACOUSTICS, SPEECH AND SIGNAL PROCESSING (ICASSP) SE International Conference on Acoustics Speech and Signal Processing ICASSP LA English DT Proceedings Paper CT IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP) CY MAY 26-31, 2013 CL Vancouver, CANADA SP Inst Elect & Elect Engineers, Inst Elect & Elect Engineers Signal Proc Soc DE Constant-envelope waveform; time-domain synthesis; optimal detection; energy spectral density; autocorrelation function ID SIGNAL-DEPENDENT INTERFERENCE; ENHANCED DETECTION; EXTENDED TARGET AB We propose an algorithm to directly synthesize in time-domain a constant-envelope transmit waveform that achieves the optimal performance in detecting an extended target in the presence of signal-dependent interference. This approach is in contrast to the traditional indirect methods that synthesize the transmit signal following the computation of the optimal energy spectral density. Additionally, we aim to maintain a good autocorrelation property of the designed signal. Therefore, our waveform design technique solves a bi-objective optimization problem in order to simultaneously improve the detection and autocorrelation performances, which are in general conflicting in nature. We demonstrate this compromising characteristics of the detection and autocorrelation performances with numerical examples. Furthermore, in the absence of the autocorrelation criterion, our designed signal is shown to achieve a near-optimum detection performance. C1 Oak Ridge Natl Lab, Ctr Engn Sci Adv Res, Comp Sci & Math Div, Oak Ridge, TN 37831 USA. RP Sen, S (reprint author), Oak Ridge Natl Lab, Ctr Engn Sci Adv Res, Comp Sci & Math Div, 1 Bethel Valley Rd, Oak Ridge, TN 37831 USA. EM sens@ornl.gov NR 19 TC 2 Z9 3 U1 0 U2 1 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1520-6149 BN 978-1-4799-0356-6 J9 INT CONF ACOUST SPEE PY 2013 BP 3851 EP 3855 PG 5 WC Acoustics; Engineering, Electrical & Electronic SC Acoustics; Engineering GA BJQ19 UT WOS:000329611504001 ER PT S AU Chartrand, R Wohlberg, B AF Chartrand, Rick Wohlberg, Brendt GP IEEE TI A NONCONVEX ADMM ALGORITHM FOR GROUP SPARSITY WITH SPARSE GROUPS SO 2013 IEEE INTERNATIONAL CONFERENCE ON ACOUSTICS, SPEECH AND SIGNAL PROCESSING (ICASSP) SE International Conference on Acoustics Speech and Signal Processing ICASSP LA English DT Proceedings Paper CT IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP) CY MAY 26-31, 2013 CL Vancouver, CANADA SP Inst Elect & Elect Engineers, Inst Elect & Elect Engineers Signal Proc Soc DE Sparse representations; group sparsity; shrinkage; nonconvex optimization; alternating direction method of multipliers ID RECONSTRUCTION; SIGNALS AB We present an efficient algorithm for computing sparse representations whose nonzero coefficients can be divided into groups, few of which are nonzero. In addition to this group sparsity, we further impose that the nonzero groups themselves be sparse. We use a nonconvex optimization approach for this purpose, and use an efficient ADMM algorithm to solve the nonconvex problem. The efficiency comes from using a novel shrinkage operator, one that minimizes nonconvex penalty functions for enforcing sparsity and group sparsity simultaneously. Our numerical experiments show that combining sparsity and group sparsity improves signal reconstruction accuracy compared with either property alone. We also find that using nonconvex optimization significantly improves results in comparison with convex optimization. C1 [Chartrand, Rick; Wohlberg, Brendt] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Chartrand, R (reprint author), Los Alamos Natl Lab, POB 1663, Los Alamos, NM 87545 USA. RI Wohlberg, Brendt/M-7764-2015 OI Wohlberg, Brendt/0000-0002-4767-1843 NR 21 TC 15 Z9 15 U1 0 U2 2 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1520-6149 BN 978-1-4799-0356-6 J9 INT CONF ACOUST SPEE PY 2013 BP 6009 EP 6013 PG 5 WC Acoustics; Engineering, Electrical & Electronic SC Acoustics; Engineering GA BJQ19 UT WOS:000329611506033 ER PT S AU Dong, J Ma, X Djouadi, SM Li, HS Kuruganti, T AF Dong, Jin Ma, Xiao Djouadi, Seddik M. Li, Husheng Kuruganti, Teja GP IEEE TI Real-Time Prediction of Power System Frequency in FNET: A State Space Approach SO 2013 IEEE INTERNATIONAL CONFERENCE ON SMART GRID COMMUNICATIONS (SMARTGRIDCOMM) SE International Conference on Smart Grid Communications LA English DT Proceedings Paper CT IEEE International Conference on Smart Grid Communications (SmartGridComm) CY OCT 21-24, 2013 CL Vancouver, CANADA SP IEEE, IEEE Commun Soc ID PARAMETER-ESTIMATION; MONITORING NETWORK; KALMAN FILTER; EQUATIONS; SIGNALS; PHASOR AB This paper proposes a novel approach to predict power frequency by applying a state-space model to describe the time-varying nature of power systems. It introduces the Expectation maximization (EM) and prediction error minimization (PEM) algorithms to dynamically estimate the parameters of the model. In this paper, we discuss how the proposed models can be used to ensure the efficiency and reliability of power systems in Frequency Monitoring Network (FNET), if serious frequency fluctuation or measurement failure occur at some nodes; this is achieved without requiring the exact model of complex power systems. Our approach leads to an easy online implementation with high precision and short response time that are key to effective frequency control. We randomly pick a set of frequency data for one power station in FNET and use it to estimate and predict the power frequency based on past measurements. Several computer simulations are provided to evaluate the method. Numerical results showed that the proposed technique could achieve good performance regarding the frequency monitoring with very limited measurement input information. C1 [Dong, Jin; Ma, Xiao; Djouadi, Seddik M.; Li, Husheng] Univ Tennessee, Dept Elect Engn & Comp Sci, Knoxville, TN 37996 USA. [Kuruganti, Teja] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. RP Dong, J (reprint author), Univ Tennessee, Dept Elect Engn & Comp Sci, Knoxville, TN 37996 USA. EM jdong@utk.edu; xma4@utk.edu; djouadi@eecs.utk.edu; husheng@eecs.utk.edu; kurugantipv@ornl.gov RI DONG, JIN/C-6060-2016; OI DONG, JIN/0000-0002-5753-1588 NR 32 TC 3 Z9 3 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 2373-6836 BN 978-1-4799-1526-2 J9 INT CONF SMART GRID PY 2013 BP 109 EP 114 PG 6 WC Computer Science, Hardware & Architecture; Computer Science, Theory & Methods; Engineering, Electrical & Electronic; Telecommunications SC Computer Science; Engineering; Telecommunications GA BJT39 UT WOS:000330174800019 ER PT S AU Huang, H Xu, J Peng, ZZ Yoo, S Yu, DT Huang, D Qin, H AF Huang, Hao Xu, Jin Peng, Zhenzhou Yoo, Shinjae Yu, Dantong Huang, Dong Qin, Hong GP IEEE TI Cloud Motion Estimation for Short Term Solar Irradiation Prediction SO 2013 IEEE INTERNATIONAL CONFERENCE ON SMART GRID COMMUNICATIONS (SMARTGRIDCOMM) SE International Conference on Smart Grid Communications LA English DT Proceedings Paper CT IEEE International Conference on Smart Grid Communications (SmartGridComm) CY OCT 21-24, 2013 CL Vancouver, CANADA SP IEEE, IEEE Commun Soc ID IMAGE REGISTRATION; FORECAST; OPERATOR AB Variability of solar energy is the most significant issue for integrating solar energy into the power Grid. There are pressing demands to develop methods to accurately estimate cloud motion that directly affects the stability of solar power output. We propose a solar prediction system that can detect cloud movements from the TSI (total sky imager) images, and then estimate the future cloud position over solar panels and subsequent solar irradiance fluctuations incurred by cloud transients. The experiment studies show that our proposed approach significantly improves the quality of cloud motion estimation within a time window (up to a few minutes) that is sufficient for grid operators to take actions to mitigate the solar power volatility. C1 [Huang, Hao; Xu, Jin; Peng, Zhenzhou; Qin, Hong] SUNY Stony Brook, 100 Nicolls Rd, Stony Brook, NY 11794 USA. [Yoo, Shinjae; Yu, Dantong; Huang, Dong] Brookhaven Natl Lab, Upton, NY USA. RP Huang, H (reprint author), SUNY Stony Brook, 100 Nicolls Rd, Stony Brook, NY 11794 USA. EM haohuang@cs.stonybrook.edu; jinxu@ece.sunysb.edu; zhenzhou.peng@stonybrook.edu; sjyoo@bnl.gov; dtyu@bnl.gov; dhuang@bnl.gov; qin@cs.stonybrook.edu FU DOE [DE-AC02-98CH10886] FX This research is part of A Public-Private-Academic Partnership to Advance Solar Power Forecasting. It is supported in part by DOE grants DE-AC02-98CH10886. NR 18 TC 10 Z9 10 U1 1 U2 3 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 2373-6836 BN 978-1-4799-1526-2 J9 INT CONF SMART GRID PY 2013 BP 696 EP 701 PG 6 WC Computer Science, Hardware & Architecture; Computer Science, Theory & Methods; Engineering, Electrical & Electronic; Telecommunications SC Computer Science; Engineering; Telecommunications GA BJT39 UT WOS:000330174800117 ER PT S AU Peng, ZZ Yoo, S Yu, DT Huang, D AF Peng, Zhenzhou Yoo, Shinjae Yu, Dantong Huang, Dong GP IEEE TI Solar Irradiance Forecast System Based on Geostationary Satellite SO 2013 IEEE INTERNATIONAL CONFERENCE ON SMART GRID COMMUNICATIONS (SMARTGRIDCOMM) SE International Conference on Smart Grid Communications LA English DT Proceedings Paper CT IEEE International Conference on Smart Grid Communications (SmartGridComm) CY OCT 21-24, 2013 CL Vancouver, CANADA SP IEEE, IEEE Commun Soc ID ARTIFICIAL NEURAL-NETWORK; RADIATION; IMAGES; TURKEY; MODEL AB Solar irradiance variability, left unmitigated, will threat the stability of grid system, and might incur significant economical impacts. This paper focuses on a pipeline to predict solar irradiance from 30 minutes to 5 hours using geostationary satellite. It consists of two parts: 1) cloud motion estimation and 2) solar irradiance prediction using the estimated satellite images. The main challenge is image noise at all levels of processing from motion estimation to irradiance prediction. To overcome this problem, we propose to use optical flow motion estimation, and subsequently combine multiple evidences together using robust support vector regression (SVR). Our systematic evaluation shows significant improvements over the baseline in both motion estimation and irradiance prediction. C1 [Peng, Zhenzhou] SUNY Stony Brook, 100 Nicolls Rd, Stony Brook, NY 11794 USA. [Huang, Dong] Brookhaven Natl Lab, Upton, NY USA. RP Peng, ZZ (reprint author), SUNY Stony Brook, 100 Nicolls Rd, Stony Brook, NY 11794 USA. EM zhenzhou.peng@stonybrook.edu; sjyoo@bnl.gov; dtyu@bnl.gov; dhuang@bnl.gov FU DOE [DE-AC02-98CH10886.] FX This research is part of A Public-Private-Academic Partnership to Advance Solar Power Forecasting. It is supported in part by DOE grants DE-AC02-98CH10886. NR 20 TC 4 Z9 4 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 2373-6836 BN 978-1-4799-1526-2 J9 INT CONF SMART GRID PY 2013 BP 708 EP 713 PG 6 WC Computer Science, Hardware & Architecture; Computer Science, Theory & Methods; Engineering, Electrical & Electronic; Telecommunications SC Computer Science; Engineering; Telecommunications GA BJT39 UT WOS:000330174800119 ER PT J AU Liu, JL Luo, ZP Bashir, S AF Liu, Jingbo Louise Luo, Zhiping Bashir, Sajid TI A progressive approach on inactivation of bacteria using silver-titania nanoparticles SO BIOMATERIALS SCIENCE LA English DT Article ID PHOTOCATALYTIC ACTIVITY; CELL WALL; TIO2; POWDERS; SULFADIAZINE; ABSORPTION; DEPENDENCE; SYSTEM; BURNS; FILMS AB A silver inserted metal oxide (Ag-TiO2) has been demonstrated to be an effective biocidal agent against prokaryotic microbes found in water. Transmission electron microscopy and electron energy loss spectroscopy indicated cellular damage after co-incubation with the nanocomposite, showing concomitant leakage of ions, which are critical for cell survival. C1 [Liu, Jingbo Louise; Bashir, Sajid] Texas A&I Univ, Dept Chem, Kingsville, TX 78363 USA. [Luo, Zhiping] Texas A&M Univ, Microscopy & Imaging Ctr, College Stn, TX 77843 USA. [Luo, Zhiping] Texas A&M Univ, Mat Sci & Engn Program, College Stn, TX 77843 USA. [Bashir, Sajid] Texas A&I Univ, Chem Biol Res Grp, Kingsville, TX 78363 USA. [Bashir, Sajid] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Adv Light Sources, Berkeley, CA 94720 USA. RP Liu, JL (reprint author), Texas A&I Univ, Dept Chem, MSC 161,700 Univ Blvd, Kingsville, TX 78363 USA. EM KFJLL00@tamuk.edu; luo@mic.tamu.edu; br9@tamuk.edu RI Luo, Zhiping/C-4435-2014; OI Luo, Zhiping/0000-0002-8264-6424; Bashir, Sajid/0000-0001-5356-8853 FU TAMUK University Research Award [160366-00002]; National Science Foundation, Major Research Instrumentation [CBET-0821370] FX Authors acknowledge the support from the TAMUK University Research Award (160366-00002) and the National Science Foundation, Major Research Instrumentation (CBET-0821370). Pilot work has been supported by Dr M. Gonzalez-Garcia for access to optical microscope and Dr Perez-Ballestero in instructing Mr Chamakura to conduct biological evaluation in the Department of Chemistry, TAMUK; ref. 24 including the R. Welch Foundation (Department Grant for Chemistry, AC 006). NR 53 TC 7 Z9 7 U1 0 U2 4 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 2047-4830 EI 2047-4849 J9 BIOMATER SCI-UK JI Biomater. Sci. PY 2013 VL 1 IS 2 BP 194 EP 201 DI 10.1039/c2bm00010e PG 8 WC Materials Science, Biomaterials SC Materials Science GA 295RL UT WOS:000330133100007 ER PT J AU Kumar, R Knight, C Voth, GA AF Kumar, Revati Knight, Chris Voth, Gregory A. TI Exploring the behaviour of the hydrated excess proton at hydrophobic interfaces SO FARADAY DISCUSSIONS LA English DT Article ID LIQUID WATER-SURFACE; VALENCE-BOND MODEL; MOLECULAR-DYNAMICS SIMULATIONS; AIR/WATER INTERFACE; COMPUTER-SIMULATION; BIOMOLECULAR SYSTEMS; CONDENSED-PHASE; TRANSPORT; IONS; SOLVATION AB The affinity of the excess proton for the aqueous solution-hydrophobic interface was examined for two specific examples, the air-water and hydrophobic wall-water cases, using a multiconfigurational molecular dynamics algorithm. The use of a reactive simulation method is important as it allows for a realistic description of the excess proton, namely, its propensity to hop between water molecules via the Grotthuss mechanism. The free energy profile reveals a minimum at these interfaces due to a favourable enthalpic term that outweighs the entropic penalty. The key factors that contribute to this enthalpic minimum were examined using a generalization of a scheme that decomposes the interaction energy into separate terms arising from various local environments [Otten et al., Proc. Natl. Acad. Sci. USA, 109, 701 (2012)] (coordination shell, bulk, and interface) and the delocalization energy (which allows the proton to hop). For both systems, it was observed that the energetic penalty for loss of coordinating water molecules as the excess proton moves toward the hydrophobic interface is more than compensated by the displacement of unfavourable interfacial water molecules. In addition, the ion becomes more delocalized, more Zundel-like, and therefore possesses a larger effective radius as it moves to the interface. The fluctuations of the instantaneous interface were reduced near the vicinity of the ion, thereby giving rise to an entropic penalty. This paper will discuss the application of energy decomposition schemes to multiconfigurational simulations and the resulting consequences realized for the excess proton at hydrophobic interfaces. C1 [Kumar, Revati; Knight, Chris; Voth, Gregory A.] Univ Chicago, James Franck Inst, Dept Chem, Computat Inst, Chicago, IL 60637 USA. [Kumar, Revati; Knight, Chris; Voth, Gregory A.] Argonne Natl Lab, Comp Environm & Life Sci Directorate, Argonne, IL 60439 USA. RP Voth, GA (reprint author), Univ Chicago, James Franck Inst, Dept Chem, Computat Inst, 5735 S Ellis Ave, Chicago, IL 60637 USA. EM gavoth@uchicago.edu RI Knight, Christopher/E-5570-2013; Kumar, Revati/E-7147-2014 OI Kumar, Revati/0000-0002-3272-8720 FU National Science Foundation (NSF) [CHE-1214087, OCI-1053575] FX This research was supported in part by the National Science Foundation (NSF grant CHE-1214087). The computations in this work utilized the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number OCI-1053575, with an allocation of time on TACC computing resources. The computations were also supported in part by a grant of computer time from the DOD High Performance Computing Modernization Program at the Air Force and Navy DOD Supercomputing Resource Centres. NR 57 TC 15 Z9 15 U1 1 U2 25 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1359-6640 EI 1364-5498 J9 FARADAY DISCUSS JI Faraday Discuss. PY 2013 VL 167 BP 263 EP 278 DI 10.1039/c3fd00087g PG 16 WC Chemistry, Physical SC Chemistry GA 292VZ UT WOS:000329932100011 PM 24640495 ER PT J AU Cox, SJ Raza, Z Kathmann, SM Slater, B Michaelides, A AF Cox, Stephen J. Raza, Zamaan Kathmann, Shawn M. Slater, Ben Michaelides, Angelos TI The microscopic features of heterogeneous ice nucleation may affect the macroscopic morphology of atmospheric ice crystals SO FARADAY DISCUSSIONS LA English DT Article ID MOLECULAR-DYNAMICS SIMULATION; SUPERCOOLED WATER; TROPOSPHERIC CLOUDS; FUNDAMENTAL-ASPECTS; KAOLINITE SURFACES; ELECTRIC-FIELDS; SOLID-SURFACES; ADSORPTION; GROWTH; CRYSTALLIZATION AB It is surprisingly difficult to freeze water. Almost all ice that forms under "mild" conditions (temperatures > -40 degrees C) requires the presence of a nucleating agent - a solid particle that facilitates the freezing process - such as clay mineral dust, soot or bacteria. In a computer simulation, the presence of such ice nucleating agents does not necessarily alleviate the difficulties associated with forming ice on accessible timescales. Nevertheless, in this work we present results from molecular dynamics simulations in which we systematically compare homogeneous and heterogeneous ice nucleation, using the atmospherically important clay mineral kaolinite as our model ice nucleating agent. From our simulations, we do indeed find that kaolinite is an excellent ice nucleating agent but that contrary to conventional thought, non-basal faces of ice can nucleate at the basal face of kaolinite. We see that in the liquid phase, the kaolinite surface has a drastic effect on the density profile of water, with water forming a dense, tightly bound first contact layer. Monitoring the time evolution of the water density reveals that changes away from the interface may play an important role in the nucleation mechanism. The findings from this work suggest that heterogeneous ice nucleating agents may not only enhance the ice nucleation rate, but also alter the macroscopic structure of the ice crystals that form. C1 [Cox, Stephen J.; Raza, Zamaan; Slater, Ben; Michaelides, Angelos] UCL, Thomas Young Ctr, London WC1E 6BT, England. [Cox, Stephen J.; Raza, Zamaan; Slater, Ben; Michaelides, Angelos] UCL, Dept Chem, London WC1E 6BT, England. [Cox, Stephen J.; Michaelides, Angelos] UCL, London Ctr Nanotechnol, London WC1H 0AH, England. [Kathmann, Shawn M.] Pacific NW Natl Lab, Div Phys Sci, Richland, WA 99352 USA. RP Cox, SJ (reprint author), UCL, Thomas Young Ctr, Mortimer St, London WC1E 6BT, England. RI Raza, Zamaan/F-7297-2014; OI Raza, Zamaan/0000-0002-3414-3590; Michaelides, Angelos/0000-0002-9169-169X; Slater, Ben/0000-0001-9738-5848 FU Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]; EPSRC [EP/F067496]; EPSRC's High End Computing Programme; U.S. Department of Energy, Office of Basic Energy Sciences (BES), Division of Chemical Sciences, Geosciences, and Biosciences; UCL; BES; European Research Council; Royal Society through a Royal Society Wolfson Research Merit Award FX The authors would like to thank Dr. Xiao-Liang Hu for many helpful discussions when commencing this work and for providing Fig. S2.dagger This research used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. We are grateful to the London Centre for Nanotechnology and UCL Research Computing for computational resources. Via our membership of the UK's HPC Materials Chemistry Consortium, which is funded by EPSRC (EP/F067496), this work made use of the facilities of HECToR, the UK's national high-performance computing service, which is provided by UoE HPCx Ltd. at the University of Edinburgh, Cray Inc., and NAG Ltd., and funded by EPSRC's High End Computing Programme. The authors also acknowledge the use of the UCL Legion High Performance Computing Facility, and associated support services, in the completion of this work. S. M. K. was supported fully by the U.S. Department of Energy, Office of Basic Energy Sciences (BES), Division of Chemical Sciences, Geosciences, and Biosciences. S.J.C. was supported by a student fellowship funded jointly by UCL and BES. A. M. is supported by the European Research Council and the Royal Society through a Royal Society Wolfson Research Merit Award. NR 82 TC 31 Z9 31 U1 10 U2 57 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1359-6640 EI 1364-5498 J9 FARADAY DISCUSS JI Faraday Discuss. PY 2013 VL 167 BP 389 EP 403 DI 10.1039/c3fd00059a PG 15 WC Chemistry, Physical SC Chemistry GA 292VZ UT WOS:000329932100018 PM 24640502 ER PT J AU Brodie, EL Lynch, SV AF Brodie, Eoin L. Lynch, Susan V. BE Fredricks, DN TI PHYLOARRAYS SO HUMAN MICROBIOTA: HOW MICROBIAL COMMUNITIES AFFECT HEALTH AND DISEASE LA English DT Article; Book Chapter ID OLIGONUCLEOTIDE MICROARRAYS; PHYLOGENETIC MICROARRAY; INTESTINAL MICROBIOTA; DIVERSITY; ENVIRONMENT; SEQUENCES; BACTERIA; ECOLOGY; DISEASE; ARRAYS C1 [Brodie, Eoin L.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Dept Ecol, Berkeley, CA 94720 USA. [Lynch, Susan V.] Univ Calif San Francisco, Dept Med, Div Gastroenterol, San Francisco, CA 94143 USA. RP Brodie, EL (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Dept Ecol, 1 Cyclotron Rd, Berkeley, CA 94720 USA. OI Brodie, Eoin/0000-0002-8453-8435 NR 30 TC 0 Z9 0 U1 0 U2 0 PU BLACKWELL SCIENCE PUBL PI OXFORD PA OSNEY MEAD, OXFORD OX2 0EL, ENGLAND BN 978-0-470-47989-6 PY 2013 BP 75 EP 84 D2 10.1002/9781118409855 PG 10 WC Microbiology; Virology SC Microbiology; Virology GA BJO88 UT WOS:000329433600004 ER PT J AU Fry, AT Wright, IG Simms, NJ McGhee, B Holcomb, GR AF Fry, A. T. Wright, I. G. Simms, N. J. McGhee, B. Holcomb, G. R. TI Steam oxidation of fossil power plant materials: collaborative research to enable advanced steam power cycles SO MATERIALS AT HIGH TEMPERATURES LA English DT Article DE steam oxidation; exfoliation; kinetics; steel ID BOILERS AB Research into improved materials systems and associated manufacturing and reliability issues is a major part of initiatives to produce cleaner and cheaper energy systems in the UK and the USA. Under the auspices of a Memorandum of Understanding on Energy R&D, a work programme concerned with steam oxidation has been conducted. The focus was on the generation of definitive information regarding the oxidation behaviour in steam of current and developmental ferritic steels, austenitic steels, and nickel-based alloys required to enable advanced steam power cycles. The results were intended to provide a basis for quantifying the rate of metal loss expected under advanced steam cycle conditions, as well as understanding of the evolution of oxide scale morphologies with time and temperature to identify features that could influence scale exfoliation characteristics. This understanding and acquired data were used to develop and validate models of oxide growth and loss by exfoliation. This paper provides an overview of the activity and highlights a selection of the results coming from the programme. C1 [Fry, A. T.] Natl Phys Lab, Teddington TW11 0LW, Middx, England. [Wright, I. G.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. [Simms, N. J.] Cranfield Univ, Energy Technol Ctr, Cranfield MK43 0AL, Beds, England. [Holcomb, G. R.] Natl Energy Technol Lab, Albany, OR 97321 USA. RP Fry, AT (reprint author), Natl Phys Lab, Teddington TW11 0LW, Middx, England. EM tony.fry@npl.co.uk RI Fry, Tony/E-3448-2014; Holcomb, Gordon/G-9070-2013 OI Fry, Tony/0000-0002-7925-1392; Holcomb, Gordon/0000-0003-3542-5319 FU Department for Innovation, Universities Skills; Department for Business, Enterprise and Regulatory Reform; US Department of Energy, Office of Fossil Energy Research; National Energy Technology Laboratory [DE-AC05-00OR22725]; UT-Battelle, LLC FX This work was carried out under the UK/US Collaboration on Advanced Materials for Low-Emission Power Plant, a programme of research whose UK activities were funded by the Department for Innovation, Universities & Skills and the Department for Business, Enterprise and Regulatory Reform. US activities were sponsored by the US Department of Energy, Office of Fossil Energy Research. The work at UT-Battelle LLC was supported by the National Energy Technology Laboratory under Contact DE-AC05-00OR22725 with UT-Battelle, LLC. NR 20 TC 1 Z9 1 U1 0 U2 11 PU MANEY PUBLISHING PI LEEDS PA STE 1C, JOSEPHS WELL, HANOVER WALK, LEEDS LS3 1AB, W YORKS, ENGLAND SN 0960-3409 EI 1878-6413 J9 MATER HIGH TEMP JI Mater. High Temp. PY 2013 VL 30 IS 4 BP 261 EP 270 DI 10.3184/096034013X13809076327729 PG 10 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering SC Materials Science; Metallurgy & Metallurgical Engineering GA 296LF UT WOS:000330185800002 ER PT J AU Holcomb, GR McGhee, BF Fry, AT Simms, NJ Davis, K Shim, HS Bullard, SJ AF Holcomb, Gordon R. McGhee, Barry F. Fry, Antony T. Simms, Nigel J. Davis, Kevin Shim, Hong-Shig Bullard, Sophie J. TI Boiler corrosion and monitoring SO MATERIALS AT HIGH TEMPERATURES LA English DT Article DE boiler; coal; air-firing; oxy-firing; waste-to-energy; fireside corrosion; corrosion sensors; electrochemical sensors; electrochemical noise AB Results of a collaborative effort to investigate and develop solutions for key material issues affecting the performance of large-scale coal-fired boilers operating at advanced conditions is presented. Advanced conditions include advanced steam temperatures, oxyfuel firing, and co-firing biomass materials. A series of laboratory experimental results are presented on fireside corrosion in environments representing air-, and oxy-fired conditions, and with coal and/or biomass as the fuel. The effects of fluctuating reducing atmospheres and heat flux effects were examined. A variety of boiler corrosion probes and sensors were developed and tested. The probes measured corrosion by section loss and the sensors by electrochemical techniques including electrochemical noise. The probes were tested in coal and waste-to-energy boilers. Correlations between section loss probes and electrochemical noise sensors allow for real-time corrosion rate measurements to be made that allow for changes in boiler operations to be tracked in terms of corrosion effects. C1 [Holcomb, Gordon R.; Bullard, Sophie J.] Natl Energy Technol Lab, Albany, OR 97321 USA. [McGhee, Barry F.] Doosan Babcock Energy Ltd, Renfrew PA4 8DJ, Lancs, England. [Fry, Antony T.] Natl Phys Lab, Teddington TW11 0LW, Middx, England. [Simms, Nigel J.] Cranfield Univ, Energy Technol Ctr, Cranfield MK43 0AL, Beds, England. [Davis, Kevin; Shim, Hong-Shig] React Engn Int, Salt Lake City, UT 84101 USA. RP Holcomb, GR (reprint author), Natl Energy Technol Lab, 1450 Queen Ave SW, Albany, OR 97321 USA. EM Gordon.holcomb@netl.doe.gov RI Holcomb, Gordon/G-9070-2013 OI Holcomb, Gordon/0000-0003-3542-5319 FU Department of Energy and Climate Change (DECC, formerly BERR and DTI) in Britain; Department of Energy (USDOE) in the United States FX The authors would like to acknowledge the support from the Department of Energy and Climate Change (DECC, formerly BERR and DTI) in Britain and the Department of Energy (USDOE) in the United States for establishment and oversight of the collaborations. NR 9 TC 3 Z9 3 U1 0 U2 6 PU SCIENCE REVIEWS 2000 LTD PI ST ALBANS PA PO BOX 314, ST ALBANS AL1 4ZG, HERTS, ENGLAND SN 0960-3409 EI 1878-6413 J9 MATER HIGH TEMP JI Mater. High Temp. PY 2013 VL 30 IS 4 BP 271 EP 286 DI 10.3184/096034013X13813935093793 PG 16 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering SC Materials Science; Metallurgy & Metallurgical Engineering GA 296LF UT WOS:000330185800003 ER PT S AU Lovergine, S Tumeo, A Villa, O Ferrandi, F AF Lovergine, Silvia Tumeo, Antonino Villa, Oreste Ferrandi, Fabrizio GP IEEE TI YAPPA: a Compiler-Based Parallelization Framework for Irregular Applications on MPSoCs SO RAPID SYSTEM PROTOTYPING: SHORTENING THE PATH FROM SPECIFICATION TO PROTOTYPE (RSP 2013) SE IEEE International Symposium on Rapid System Prototyping LA English DT Proceedings Paper CT International Symposium on Rapid System Prototyping / Embedded Systems Week CY OCT 03-04, 2013 CL Montreal, CANADA SP IEEE Reliabil Soc DE Irregular Applications; Compilers; Parallel Code Generation; Embedded Systems; HPC ID PERFORMANCE AB Modern embedded systems include hundreds of cores. Because of the difficulty in providing a fast, coherent memory architecture, these systems usually rely on non-coherent, non-uniform memory architectures with private memories for each core. However, programming these systems poses significant challenges. The developer must extract large amounts of parallelism, while orchestrating communication among cores to optimize application performance. These issues become even more significant with irregular applications, which present data sets difficult to partition, unpredictable memory accesses, unbalanced control flow and fine grained communication. Hand-optimizing every single aspect is hard and time-consuming, and it often does not lead to the expected performance. There is a growing gap between such complex and highly-parallel architectures and the high level languages used to describe the specification, which were designed for simpler systems and do not consider these new issues. In this paper we introduce YAPPA (Yet Another Parallel Programming Approach), a compilation framework for the automatic parallelization of irregular applications on modern MPSoCs based on LLVM. We start by considering an efficient parallel programming approach for irregular applications on distributed memory systems. We then propose a set of transformations that can reduce the development and optimization effort. The results of our initial prototype confirm the correctness of the proposed approach. C1 [Lovergine, Silvia; Tumeo, Antonino; Villa, Oreste] Pacific NW Natl Lab, Richland, WA 99352 USA. [Lovergine, Silvia; Ferrandi, Fabrizio] Politecn Milan, DEIB, Milan, Italy. RP Lovergine, S (reprint author), Pacific NW Natl Lab, Richland, WA 99352 USA. EM silvia.lovergine@pnnl.gov; antonino.tumeo@pnnl.gov; oreste.villa@pnnl.gov; ferrandi@elet.polimi.it RI Ferrandi, Fabrizio/K-7645-2015; Tumeo, Antonino/L-3106-2016 OI Ferrandi, Fabrizio/0000-0003-0301-4419; NR 15 TC 0 Z9 0 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1074-6005 BN 978-1-4799-2409-7 J9 P IEEE RAP SYST PROT PY 2013 BP 123 EP 129 PG 7 WC Computer Science, Hardware & Architecture; Computer Science, Software Engineering; Engineering, Electrical & Electronic SC Computer Science; Engineering GA BJS94 UT WOS:000330038200018 ER PT S AU Hsueh, HC Guo, GY Louie, SG AF Hsueh, Hung-Chung Guo, Guang-Yu Louie, Steven G. BE Li, H Wu, J Wang, ZM TI Electronic and Optical Properties of Silicon Carbide Nanostructures SO SILICON-BASED NANOMATERIALS SE Springer Series in Materials Science LA English DT Article; Book Chapter ID BORON-NITRIDE NANOTUBES; FUNCTIONAL PERTURBATION-THEORY; QUASI-PARTICLE ENERGIES; CARBON NANOTUBES; HOLE EXCITATIONS; BAND-GAPS; SEMICONDUCTORS; INSULATORS; STABILITY; SPECTRA AB The electronic and optical properties of quasi-one-dimensional single-walled zigzag/armchair silicon-carbide nantotubes (SiC-NTs) as well as a two-dimensional SiC monolayer are investigated by ab initio methods. In order to elucidate many-electron effects on SiC nanosystems, we apply the ab initio many-body Green's function approach to calculate the quasiparticle and optical properties of SiC nanostructures. The significant band gap correction, more than 1 eV, to the Kohn-Sham gap of density functional theory within the local density approximation of semiconducting SiC-NTs and a SiC monolayer is mainly due to the many-electron interaction effect, which is included in the GW approximation for the electron self energy. Furthermore, taking into account electron-hole interaction, the optical spectra of SiC-NTs are calculated by solving the Bethe-Salpeter equation (BSE) for the electron-hole amplitudes. Our GW+BSE calculations reveal the presence of excitons with a large binding energy as well as strong anisotropy in the optical properties in the low-dimensional SiC systems. The characteristics of the strongly bound electron-hole pairs or excitons in SiC nanostructures are also discussed in terms of the corresponding excitonic wavefunctions. C1 [Hsueh, Hung-Chung] Tamkang Univ, Dept Phys, Tamsui 25137, New Taipei, Taiwan. [Guo, Guang-Yu] Natl Taiwan Univ, Dept Phys, Taipei 10617, Taiwan. [Louie, Steven G.] Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA. [Louie, Steven G.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Hsueh, HC (reprint author), Tamkang Univ, Dept Phys, Tamsui 25137, New Taipei, Taiwan. EM hchsueh@mail.tku.edu.tw NR 65 TC 1 Z9 1 U1 0 U2 2 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 0933-033X BN 978-1-4614-8169-0; 978-1-4614-8168-3 J9 SPRINGER SER MATER S PY 2013 VL 187 BP 139 EP 159 DI 10.1007/978-1-4614-8169-0_7 D2 10.1007/978-1-4614-8169-0 PG 21 WC Nanoscience & Nanotechnology; Materials Science, Multidisciplinary; Physics, Applied SC Science & Technology - Other Topics; Materials Science; Physics GA BJN15 UT WOS:000329212600008 ER PT J AU Vimmerstedt, L Brown, A Heath, G Mai, T Melaina, M Newes, E Ruth, M Simpkins, T Warner, E Bertram, K Plotkin, S Patel, D Stephens, T Vyas, A AF Vimmerstedt, Laura Brown, Austin Heath, Garvin Mai, Trieu Melaina, Marc Newes, Emily Ruth, Mark Simpkins, Travis Warner, Ethan Bertram, Kenneth Plotkin, Steven Patel, Deena Stephens, Thomas Vyas, Anant TI Potential Reductions in Emissions and Petroleum Use in Transportation Perspectives from the Transportation Energy Futures Project SO TRANSPORTATION RESEARCH RECORD LA English DT Article AB The use of energy-efficient technologies and renewable energy sources in transportation could reduce petroleum use and greenhouse gas emissions, but these approaches may face challenges in consumer adoption, infrastructure requirements, and resource constraints. The Transportation Energy Futures project of the U.S. Department of Energy reviewed opportunities for significant reductions in petroleum use and greenhouse gas emissions. On the basis of that review, a diverse set of strategies is explored: reduced energy intensity of transportation modes, lower use intensity of motorized transport, and reduced carbon or petroleum intensity through the use of electricity and hydrogen from renewable energy as well as the use of biofuels. Energy efficiency and demand-side approaches could stop the growth in total transportation energy. lathe light-duty vehicle sector, growth in energy use already is projected to flatten; the deployment of technologies for energy efficiency could limit growth in the non-light-duty sector. Travel reduction and built environment changes could moderate personal transportation demand. Freight mass reductions and mode switching could slow or stabilize freight demand. Vehicles using electricity or hydrogen could enable access to renewable energy resources other than biomass. Challenges in fueling infrastructure expansion and market uptake of advanced vehicles are considered. Competition for biomass also is explored, considering markets for electricity, gasoline, diesel, jet fuel, and bunker fuel. The potential for the implementation of these strategies to displace U.S. petroleum use and reduce greenhouse gas emissions in the transportation sector is discussed along with the barriers to realizing this potential in the market. C1 [Vimmerstedt, Laura; Brown, Austin; Heath, Garvin; Mai, Trieu; Melaina, Marc; Newes, Emily; Ruth, Mark; Simpkins, Travis; Warner, Ethan] Natl Renewable Energy Lab, Golden, CO 80401 USA. [Bertram, Kenneth; Plotkin, Steven; Patel, Deena; Stephens, Thomas; Vyas, Anant] Argonne Natl Lab, Argonne, IL 60439 USA. RP Vimmerstedt, L (reprint author), Natl Renewable Energy Lab, 15013 Denver West Pkwy, Golden, CO 80401 USA. EM laura.vimmerstedt@nrel.gov NR 24 TC 1 Z9 1 U1 1 U2 6 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0361-1981 EI 2169-4052 J9 TRANSPORT RES REC JI Transp. Res. Record PY 2013 IS 2375 BP 37 EP 44 DI 10.3141/2375-05 PG 8 WC Engineering, Civil; Transportation; Transportation Science & Technology SC Engineering; Transportation GA 294XJ UT WOS:000330080900005 ER PT J AU Polyak, SJ Oberlies, NH Pecheur, EI Dahari, H Ferenci, P Pawlotsky, JM AF Polyak, Stephen J. Oberlies, Nicholas H. Pecheur, Eve-Isabelle Dahari, Harel Ferenci, Peter Pawlotsky, Jean-Michel TI Silymarin for HCV infection SO ANTIVIRAL THERAPY LA English DT Review ID CHRONIC HEPATITIS-C; MILK THISTLE EXTRACT; FATTY LIVER-DISEASE; LONG-TERM TREATMENT; IN-VIVO; PHASE-I; SILIBININ DIASTEREOMERS; COMBINATION THERAPY; SILYBUM-MARIANUM; RESCUE TREATMENT AB Silymarin, an extract of milk thistle seeds, and silymarinderived compounds have been considered hepatoprotective since the plant was first described in ancient times. Hepatoprotection is defined as several non-mutually exclusive biological activities including antiviral, antioxidant, anti-inflammatory and immunomodulatory functions. Despite clear evidence for silymarin-induced hepatoprotection in cell culture and animal models, evidence for beneficial effects in humans has been equivocal. This review will summarize the current state of knowledge on silymarin in the context of HCV infection. The information was collated from a recent workshop on silibinin in Germany. C1 [Polyak, Stephen J.] Univ Washington, Dept Lab Med, Seattle, WA 98195 USA. [Polyak, Stephen J.] Univ Washington, Dept Microbiol, Seattle, WA 98195 USA. [Polyak, Stephen J.] Univ Washington, Dept Global Hlth, Seattle, WA 98195 USA. [Oberlies, Nicholas H.] Univ N Carolina, Dept Chem & Biochem, Greensboro, NC 27412 USA. [Pecheur, Eve-Isabelle] CNRS 5286, UMR INSERM 1052, Lyon, France. [Dahari, Harel] Univ Illinois, Dept Med, Chicago, IL USA. [Dahari, Harel] Los Alamos Natl Lab, Los Alamos, NM USA. [Ferenci, Peter] Med Univ Vienna, Vienna, Austria. [Pawlotsky, Jean-Michel] Univ Paris Est, Henri Mondor Hosp, Dept Virol, Natl Reference Ctr Viral Hepatitis B C & Delta, Creteil, France. [Pawlotsky, Jean-Michel] Hop Henri Mondor, INSERM, U955, F-94010 Creteil, France. RP Polyak, SJ (reprint author), Univ Washington, Dept Lab Med, Seattle, WA 98195 USA. EM polyak@uw.edu OI Oberlies, Nicholas/0000-0002-0354-8464 FU NIH [R01AT006842, R56/R01-AI078881, P20-GM103452]; US Department of Energy; Agence Nationale pour la Recherche contre le SIDA et les hepatites virales (ANRS); ANRS; INSERM; Fondation pour la Recherche Medicale FX SJP and NHO are partially supported by NIH grant R01AT006842. HD is supported by the US Department of Energy and by NIH grants R56/R01-AI078881 and P20-GM103452. E-IP is supported by Agence Nationale pour la Recherche contre le SIDA et les hepatites virales (ANRS). J-MP is supported by ANRS, INSERM and the Fondation pour la Recherche Medicale. PF and J-MP have been consultants for Madaus/Rottapharm. NR 46 TC 25 Z9 25 U1 1 U2 11 PU INT MEDICAL PRESS LTD PI LONDON PA 2-4 IDOL LANE, LONDON EC3R 5DD, ENGLAND SN 1359-6535 J9 ANTIVIR THER JI Antivir. Ther. PY 2013 VL 18 IS 2 BP 141 EP 147 DI 10.3851/IMP2402 PG 7 WC Infectious Diseases; Pharmacology & Pharmacy; Virology SC Infectious Diseases; Pharmacology & Pharmacy; Virology GA 290LP UT WOS:000329759300001 PM 23011959 ER PT J AU Mei, F Setyan, A Zhang, Q Wang, J AF Mei, F. Setyan, A. Zhang, Q. Wang, J. TI CCN activity of organic aerosols observed downwind of urban emissions during CARES SO ATMOSPHERIC CHEMISTRY AND PHYSICS LA English DT Article ID CLOUD CONDENSATION NUCLEI; DROPLET GROWTH-KINETICS; SINGLE-PARAMETER REPRESENTATION; SIZE-RESOLVED MEASUREMENTS; HYGROSCOPIC GROWTH; MIXING STATE; MASS-SPECTROMETRY; HIGH-RESOLUTION; ACTIVATION KINETICS; PART 1 AB During the Carbonaceous Aerosols and Radiative Effects Study (CARES), activation fraction of size-resolved aerosol particles and aerosol chemical composition were characterized at the T1 site (similar to 60 km downwind of Sacramento, California) from 10 June to 28 June 2010. The hygroscopicity of cloud condensation nuclei (CCN)-active particles (kappa(CCN)) with diameter from 100 to 170 nm, derived from the size-resolved activated fraction, varied from 0.10 to 0.21, with an average of 0.15, which was substantially lower than that proposed for continental sites. The low kappa(CCN) value was due to the high organic volume fraction, averaged over 80% at the T1 site. The derived kappa(CCN) exhibited little diurnal variation, consistent with the relatively constant organic volume fraction observed. At any time, over 90% of the size-selected particles with diameter between 100 and 171 nm were CCN active, suggesting most particles within this size range were aged background particles. Due to the large organic volume fraction, organic hygroscopicity (kappa(org)) strongly impacted particle hygroscopicity and therefore calculated CCN concentration. For the vast majority of the cases, an increase of kappa(org) from 0.03 to 0.18, which are within the typical range, doubled the calculated CCN concentration. Organic hygroscopicity was derived from kappa(CCN) and aerosol chemical composition, and its variations with the fraction of total organic mass spectral signal at m/z 44 (f(44)) and O : C were compared to results from previous studies. Overall, the relationships between kappa(org) and f(44) are quite consistent for organic aerosol (OA) observed during field studies and those formed in a smog chamber. Compared to the relationship between kappa(org) and f(44), the relationship between kappa(org) and O: C exhibits more significant differences among different studies, suggesting kappa(org) may be better parameterized using f44. A least squares fit yielded kappa(org) = 2.10(+/- 0.07) x f(44) - 0.11(+/- 0.01) with a Pearson R-2 value of 0.71. One possible explanation for the stronger correlation between kappa(org) and f(44) is that the m/z 44 signal (mostly contributed by the CO2+ ion) is more closely related to organic acids, which may dominate the overall kappa(org) due to their relatively high water solubility and hygroscopicity. C1 [Mei, F.; Wang, J.] Brookhaven Natl Lab, Upton, NY 11973 USA. [Setyan, A.; Zhang, Q.] Univ Calif Davis, Dept Environm Toxicol, Davis, CA 95616 USA. RP Wang, J (reprint author), Brookhaven Natl Lab, Upton, NY 11973 USA. EM jian@bnl.gov RI Setyan, Ari/C-4025-2011; Zhang, Qi/F-9653-2010; Wang, Jian/G-9344-2011; OI Setyan, Ari/0000-0002-9078-6478; Mei, Fan/0000-0003-4285-2749 FU US Department of Energy Atmospheric System Research program [DE-AC02-98CH10866, DE-FG02-11ER65293] FX This research was performed with support from the US Department of Energy Atmospheric System Research program under contract number DE-AC02-98CH10866 and DE-FG02-11ER65293. We acknowledge the US Department of Energy Atmospheric Radiation Measurement program and Pacific Northwest National Laboratory for logistics support. NR 77 TC 20 Z9 20 U1 1 U2 47 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 1680-7316 EI 1680-7324 J9 ATMOS CHEM PHYS JI Atmos. Chem. Phys. PY 2013 VL 13 IS 24 BP 12155 EP 12169 DI 10.5194/acp-13-12155-2013 PG 15 WC Meteorology & Atmospheric Sciences SC Meteorology & Atmospheric Sciences GA 292VF UT WOS:000329930000001 ER PT J AU Smith, E AF Smith, Eric BE Lineweaver, CH Davies, PCW Ruse, M TI Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere SO COMPLEXITY AND THE ARROW OF TIME LA English DT Article; Book Chapter ID AUTOTROPHIC CARBON FIXATION; STATISTICAL-MECHANICS; INTERMEDIARY METABOLISM; REDUCTIVE CHEMOAUTOTROPH; IRREVERSIBLE-PROCESSES; RECIPROCAL RELATIONS; GENETICAL EVOLUTION; INFORMATION THEORY; CARNOT CYCLES; ENERGY-FLOW C1 [Smith, Eric] Santa Fe Inst, Santa Fe, NM USA. [Smith, Eric] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Smith, E (reprint author), Santa Fe Inst, Santa Fe, NM USA. NR 110 TC 1 Z9 1 U1 1 U2 5 PU CAMBRIDGE UNIV PRESS PI CAMBRIDGE PA THE PITT BUILDING, TRUMPINGTON ST, CAMBRIDGE CB2 1RP, CAMBS, ENGLAND BN 978-1-107-02725-1 PY 2013 BP 191 EP 223 D2 10.1017/CBO9781139225700 PG 33 WC History & Philosophy Of Science SC History & Philosophy of Science GA BJL26 UT WOS:000328818100009 ER PT J AU Wolpert, DH AF Wolpert, David H. BE Lineweaver, CH Davies, PCW Ruse, M TI Information width: a way for the second law to increase complexity SO COMPLEXITY AND THE ARROW OF TIME LA English DT Article; Book Chapter ID IRREVERSIBLE-PROCESSES; RECIPROCAL RELATIONS; ENERGY-FLOW; THERMODYNAMICS; ORGANIZATION; EVOLUTION; ATTRACTION; PRINCIPLE; CHEMISTRY; GROWTH C1 [Wolpert, David H.] Los Alamos Natl Lab, Ctr Nonlinear Studies, Los Alamos, NM 87545 USA. [Wolpert, David H.] NASA, Ames Res Ctr, Washington, DC USA. [Wolpert, David H.] Stanford Univ, Collect Intelligence Grp, Stanford, CA 94305 USA. RP Wolpert, DH (reprint author), Los Alamos Natl Lab, Informat Sci Div, Los Alamos, NM 87545 USA. NR 40 TC 1 Z9 1 U1 0 U2 1 PU CAMBRIDGE UNIV PRESS PI CAMBRIDGE PA THE PITT BUILDING, TRUMPINGTON ST, CAMBRIDGE CB2 1RP, CAMBS, ENGLAND BN 978-1-107-02725-1 PY 2013 BP 246 EP 275 D2 10.1017/CBO9781139225700 PG 30 WC History & Philosophy Of Science SC History & Philosophy of Science GA BJL26 UT WOS:000328818100011 ER PT J AU Feller, I AF Feller, Irwin BE Link, AN Vonortas, NS TI Peer review and expert panels as techniques for evaluating the quality of academic research SO HANDBOOK ON THE THEORY AND PRACTICE OF PROGRAM EVALUATION LA English DT Review; Book Chapter ID RESEARCH EXCELLENCE FRAMEWORK; INTERDISCIPLINARY RESEARCH; PROPOSALS; PERFORMANCE; ISSUES; IMPACT C1 [Feller, Irwin] Penn State Univ, Inst Policy Res & Evaluat, University Pk, PA 16802 USA. [Feller, Irwin] Natl Sci Fdn, Arlington, VA 22230 USA. [Feller, Irwin] US DOE, Washington, DC 20585 USA. NR 75 TC 2 Z9 2 U1 1 U2 4 PU EDWARD ELGAR PUBLISHING LTD PI CHELTENHAM PA GLENSANDA HOUSE, MONTPELLIER PARADE, CHELTENHAM GL50 1UA, GLOS, ENGLAND BN 978-0-85793-239-6 PY 2013 BP 115 EP 142 PG 28 WC Economics SC Business & Economics GA BJL29 UT WOS:000328820800005 ER PT J AU Jordan, GB AF Jordan, Gretchen B. BE Link, AN Vonortas, NS TI Logic modeling: a tool for designing program evaluations SO HANDBOOK ON THE THEORY AND PRACTICE OF PROGRAM EVALUATION LA English DT Article; Book Chapter C1 [Jordan, Gretchen B.] US DOE, Off Energy Efficiency & Renewable Energy, Washington, DC 20585 USA. [Jordan, Gretchen B.] US DOE, Off Sci, Washington, DC 20585 USA. RP Jordan, GB (reprint author), US DOE, Off Energy Efficiency & Renewable Energy, Washington, DC 20585 USA. NR 32 TC 0 Z9 0 U1 1 U2 1 PU EDWARD ELGAR PUBLISHING LTD PI CHELTENHAM PA GLENSANDA HOUSE, MONTPELLIER PARADE, CHELTENHAM GL50 1UA, GLOS, ENGLAND BN 978-0-85793-239-6 PY 2013 BP 143 EP 165 PG 23 WC Economics SC Business & Economics GA BJL29 UT WOS:000328820800006 ER PT J AU O'Connor, AC Gallaher, MP Loomis, RJ Casey, SE AF O'Connor, Alan C. Gallaher, Michael P. Loomis, Ross J. Casey, Sara E. BE Link, AN Vonortas, NS TI Estimating avoided environmental emissions and environmental health benefits SO HANDBOOK ON THE THEORY AND PRACTICE OF PROGRAM EVALUATION LA English DT Article; Book Chapter ID PARTICULATE AIR-POLLUTION; RESPIRATORY SYMPTOMS; HOSPITAL ADMISSIONS; FINE PARTICLES; POLLUTANTS; MORBIDITY; CHILDREN; SEATTLE C1 [O'Connor, Alan C.; Gallaher, Michael P.] RTI, Environm Technol & Energy Econ Program, Res Triangle Pk, NC 27709 USA. [O'Connor, Alan C.; Gallaher, Michael P.; Loomis, Ross J.] NIST, Gaithersburg, MD USA. [O'Connor, Alan C.] US DOE, Washington, DC 20585 USA. [O'Connor, Alan C.; Gallaher, Michael P.; Loomis, Ross J.] US EPA, Res Triangle Pk, NC USA. [O'Connor, Alan C.] Ctr Dis Control & Prevent, Atlanta, GA USA. [Gallaher, Michael P.] NSF, Arlington, VA USA. [Gallaher, Michael P.] NTIA, Washington, DC USA. [Loomis, Ross J.] RTI, Global Climate Change & Environm Sci Div, Res Triangle Pk, NC USA. [Loomis, Ross J.] Natl Pk Serv, Washington, DC USA. [Casey, Sara E.] RTI Int, Environm Technol & Energy Econ Program, Res Triangle Pk, NC USA. RP O'Connor, AC (reprint author), RTI, Environm Technol & Energy Econ Program, Res Triangle Pk, NC 27709 USA. NR 44 TC 0 Z9 0 U1 0 U2 0 PU EDWARD ELGAR PUBLISHING LTD PI CHELTENHAM PA GLENSANDA HOUSE, MONTPELLIER PARADE, CHELTENHAM GL50 1UA, GLOS, ENGLAND BN 978-0-85793-239-6 PY 2013 BP 247 EP 290 PG 44 WC Economics SC Business & Economics GA BJL29 UT WOS:000328820800009 ER PT J AU Tavener, S Wildey, T AF Tavener, Simon Wildey, Tim TI ADJOINT BASED A POSTERIORI ANALYSIS OF MULTISCALE MORTAR DISCRETIZATIONS WITH MULTINUMERICS SO SIAM JOURNAL ON SCIENTIFIC COMPUTING LA English DT Article DE mortar methods; multiscale; multinumerics; adjoint operators; error analysis; mixed finite elements; discontinuous Galerkin methods ID FINITE-ELEMENT METHODS; DISCONTINUOUS GALERKIN METHODS; ELLIPTIC PROBLEMS; ERROR ESTIMATION; DOMAIN DECOMPOSITION; POROUS-MEDIA; NONMATCHING GRIDS; MULTIPHASE FLOW; HEAT-TRANSFER; ADAPTIVITY AB In this paper we derive a posteriori error estimates for linear functionals of the solution to an elliptic problem discretized using a multiscale nonoverlapping domain decomposition method. The error estimates are based on the solution of an appropriately defined adjoint problem. We present a general framework that allows us to consider both primal and mixed formulations of the forward and adjoint problems within each subdomain. The primal subdomains are discretized using either an interior penalty discontinuous Galerkin method or a continuous Galerkin method with weakly imposed Dirichlet conditions. The mixed subdomains are discretized using Raviart-Thomas mixed finite elements. The a posteriori error estimate also accounts for the errors due to adjoint-inconsistent subdomain discretizations. The coupling between the subdomain discretizations is achieved via a mortar space. We show that the numerical discretization error can be broken down into subdomain and mortar components which may be used to drive adaptive refinement. C1 [Tavener, Simon] Colorado State Univ, Dept Math, Ft Collins, CO 80523 USA. [Wildey, Tim] Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Tavener, S (reprint author), Colorado State Univ, Dept Math, Ft Collins, CO 80523 USA. EM tavener@math.colostate.edu; tmwilde@sandia.gov FU King Abdullah University of Science and Technology (KAUST) [KUK-C1-013-04]; U.S. Department of Energy's National Nuclear Security Administration [DE-AC04-94AL85000] FX This research was supported in part by award KUK-C1-013-04, made by King Abdullah University of Science and Technology (KAUST).; Sandia National Laboratories is a multiprogram laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. NR 56 TC 1 Z9 1 U1 0 U2 2 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 1064-8275 EI 1095-7197 J9 SIAM J SCI COMPUT JI SIAM J. Sci. Comput. PY 2013 VL 35 IS 6 BP A2621 EP A2642 DI 10.1137/12089973X PG 22 WC Mathematics, Applied SC Mathematics GA 294FK UT WOS:000330028400009 ER PT J AU Womeldorff, G Peterson, J Gunzburger, M Ringler, T AF Womeldorff, G. Peterson, J. Gunzburger, M. Ringler, T. TI UNIFIED MATCHING GRIDS FOR MULTIDOMAIN MULTIPHYSICS SIMULATIONS SO SIAM JOURNAL ON SCIENTIFIC COMPUTING LA English DT Article DE grid generation; multiphysics and multidomain problems; domain decomposition ID CENTROIDAL VORONOI TESSELLATIONS; LAGRANGE MULTIPLIER AB Grid generation for multiple-domain multiple-physics problems in which the single-physics components are applied on disjoint abutting domains is considered. In general, grids that are separately constructed for each domain, as is the case when one uses legacy codes, may have overlaps and gaps and have grid points that do not match along the interface between the domains. Using very simple settings, the possible difficulties that can arise when using nonmatching grids are illustrated. Then, based on centroidal Voronoi tessellation gridding strategies, an algorithm is presented for the unified construction of grids in multiple domains that match perfectly, i.e., have no gaps or overlaps and have only common cell faces where they abut. Grid refinement is effected both to resolve boundaries, including interfaces, and to refine in regions of interest. The use of the matching grid construction algorithm is illustrated through its application to a simple example as well as to ocean-land gridding on the globe. C1 [Womeldorff, G.; Ringler, T.] Los Alamos Natl Lab, Div Theoret, Los Alamos, NM 87545 USA. [Peterson, J.; Gunzburger, M.] Florida State Univ, Dept Comp Sci, Tallahassee, FL 32306 USA. RP Womeldorff, G (reprint author), Los Alamos Natl Lab, Div Theoret, Los Alamos, NM 87545 USA. EM womeld@lanl.gov; jpeterson@fsu.edu; gunzburg@fsu.edu; ringler@lanl.gov OI Womeldorff, Geoff/0000-0003-0383-8100 FU U.S. Department of Energy Office of Science [DE-FG02-07ER64431, DE-FG02-07ER64432, DOE-07SCPF152]; U.S. Department of Energy [DE-AC52-06NA25396 (LA-UR-13-27843)] FX This work was supported by the U.S. Department of Energy Office of Science through grants DE-FG02-07ER64431, DE-FG02-07ER64432, and DOE-07SCPF152 and under the auspices of the U.S. Department of Energy under contract DE-AC52-06NA25396 (LA-UR-13-27843). NR 22 TC 1 Z9 1 U1 0 U2 2 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 1064-8275 EI 1095-7197 J9 SIAM J SCI COMPUT JI SIAM J. Sci. Comput. PY 2013 VL 35 IS 6 BP A2781 EP A2806 DI 10.1137/130906611 PG 26 WC Mathematics, Applied SC Mathematics GA 294FK UT WOS:000330028400016 ER PT J AU Kalchev, D Ketelsen, C Vassilevski, PS AF Kalchev, D. Ketelsen, C. Vassilevski, P. S. TI TWO-LEVEL ADAPTIVE ALGEBRAIC MULTIGRID FOR A SEQUENCE OF PROBLEMS WITH SLOWLY VARYING RANDOM COEFFICIENTS SO SIAM JOURNAL ON SCIENTIFIC COMPUTING LA English DT Article DE iterative methods; multigrid; algebraic multigrid; adaptive algebraic multigrid; Monte Carlo; Markov chain Monte Carlo; subsurface flow ID ELEMENT AGGLOMERATION; SMOOTHED AGGREGATION; AMGE AB This paper proposes an adaptive strategy for reusing a previously constructed coarse space by algebraic multigrid to construct a two-level solver for a problem with nearby characteristics. A main target application is the solution of the linear problems that appear throughout a sequence of Markov chain Monte Carlo simulations of subsurface flow with uncertain permeability field. The efficacy of the method is demonstrated with extensive set of numerical experiments. C1 [Kalchev, D.; Ketelsen, C.; Vassilevski, P. S.] Lawrence Livermore Natl Lab, Ctr Appl Sci Comp, Livermore, CA 94551 USA. RP Kalchev, D (reprint author), Lawrence Livermore Natl Lab, Ctr Appl Sci Comp, Livermore, CA 94551 USA. EM kalchev1@llnl.gov; ketelsen1@llnl.gov; vassilevski1@llnl.gov FU U.S. Department of Energy by Lawrence Livermore National Laboratory [DE-AC52-07NA27344 (LLNL-JRNL-589132)] FX This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 (LLNL-JRNL-589132). The U.S. Government retains a nonexclusive, royalty-free license to publish or reproduce the published form of this contribution, or allow others to do so, for U.S. Government purposes. Copyright is owned by SIAM to the extent not limited by these rights. NR 20 TC 1 Z9 1 U1 0 U2 0 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 1064-8275 EI 1095-7197 J9 SIAM J SCI COMPUT JI SIAM J. Sci. Comput. PY 2013 VL 35 IS 6 BP B1215 EP B1234 DI 10.1137/120895366 PG 20 WC Mathematics, Applied SC Mathematics GA 294FK UT WOS:000330028400028 ER PT J AU Wang, S Li, XS Xia, JL Situ, YC De Hoop, MV AF Wang, Shen Li, Xiaoye S. Xia, Jianlin Situ, Yingchong De Hoop, Maarten V. TI EFFICIENT SCALABLE ALGORITHMS FOR SOLVING DENSE LINEAR SYSTEMS WITH HIERARCHICALLY SEMISEPARABLE STRUCTURES SO SIAM JOURNAL ON SCIENTIFIC COMPUTING LA English DT Article DE HSS matrix; parallel HSS algorithm; low-rank property; compression; HSS construction; direct solver ID MATRICES; EQUATIONS; SOLVER; REPRESENTATIONS; FACTORIZATION AB Hierarchically semiseparable (HSS) matrix techniques are emerging in constructing superfast direct solvers for both dense and sparse linear systems. Here, we develop a set of novel parallel algorithms for key HSS operations that are used for solving large linear systems. These are parallel rank-revealing QR factorization, HSS constructions with hierarchical compression, ULV HSS factorization, and HSS solutions. The HSS tree-based parallelism is fully exploited at the coarse level. The BLACS and ScaLAPACK libraries are used to facilitate the parallel dense kernel operations at the fine-grained level. We appply our new solvers for discretized Helmholtz equations for multifrequency seismic imaging and iteratively solve time-harmonic seismic inverse boundary value problems. In particular, we use the HSS algorithms to solve the dense Schur complement systems associated with the root separator of the separator tree obtained from nested dissection of the graph of discretized Helmholtz equations. We demonstrate that the new approach is much faster and uses much less memory than the LU factorization algorithm for both two-dimensional and three-dimensional problems, using up to 8912 processing cores. This is the first work in parallelizing HSS algorithms and conducting detailed performance analysis on a large parallel machine. This also lays a good foundation for developing scalable sparse structured factorization algorithms for general sparse linear systems. C1 [Wang, Shen; Xia, Jianlin; De Hoop, Maarten V.] Purdue Univ, Dept Math, W Lafayette, IN 47907 USA. [Li, Xiaoye S.] Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. [Situ, Yingchong] Purdue Univ, Dept Comp Sci, W Lafayette, IN 47907 USA. RP Wang, S (reprint author), Purdue Univ, Dept Math, W Lafayette, IN 47907 USA. EM wang273@math.purdue.edu; xiaj@math.purdue.edu; xsli@lbl.gov; ysitu@cs.purdue.edu; mdehoop@math.purdue.edu FU Geo-Mathematical Imaging Group at Purdue University; BGP; ConocoPhillips; ExxonMobil; PGS; Statoil; Total FX We thank Francois-Henry Rouet for insightful discussions about the parallel performance bottleneck of the code and for providing the code for computing the residual. We thank the members of the Geo-Mathematical Imaging Group at Purdue University, BGP, ConocoPhillips, ExxonMobil, PGS, Statoil, and Total for partial financial support. NR 28 TC 19 Z9 19 U1 0 U2 3 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 1064-8275 EI 1095-7197 J9 SIAM J SCI COMPUT JI SIAM J. Sci. Comput. PY 2013 VL 35 IS 6 BP C519 EP C544 DI 10.1137/110848062 PG 26 WC Mathematics, Applied SC Mathematics GA 294FK UT WOS:000330028400036 ER PT S AU Holland, SA Mahan, CA Kuhn, MJ Rowe, NC AF Holland, Stephen A. Mahan, Cody A. Kuhn, Michael J. Rowe, Nathan C. BE Cullum, BM McLamore, ES TI Utilizing Metalized Fabrics for Liquid and Rip Detection and Localization SO SMART BIOMEDICAL AND PHYSIOLOGICAL SENSOR TECHNOLOGY X SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on Smart Biomedical and Physiological Sensor Technology X CY MAY 01-02, 2013 CL Baltimore, MD SP SPIE DE Conductive textile; distributed sensor; resistance grid; penetration; flexible; combat wound detection ID INFINITE NETWORKS; PERTURBATION; RESISTANCE; RESISTORS AB This paper proposes a novel technique for utilizing electrically conductive textiles as a distributed sensor for detecting and localizing liquids (e. g., blood), damage (e. g., rips, cuts, bullet holes) and, potentially, biosignals. The proposed technique is verified through both simulation and experimental measurements. Circuit theory is employed to depict conductive fabric as a bounded, near-infinite grid of resistors. Solutions to the well-known infinite resistance grid problem are used to confirm the accuracy and validity of this modeling approach. Simulations allow for discontinuities to be placed within the resistor matrix to illustrate the effects of bullet holes within the fabric. A real-time experimental system was developed that uses a multiplexed, Wheatstone bridge measurement approach to determine the resistances of a coarse electrode grid across the conductive fabric. Non-uniform resistance values of the grid infer the presence of liquids and rips in the fabric. The resistor-grid model is validated through a comparison of simulated and experimental results. Results suggest accuracy proportional to the electrode spacing in determining the presence and location of disturbances in conductive fabric samples. Future work is focused on refining the experimental system to provide more accuracy in detecting and localizing events (although just the knowledge of a penetration may be adequate for some intended applications) as well as developing a complete prototype that can be deployed for field testing. Potential applications include intelligent clothing, flexible, lightweight sensing systems, and combat wound detection. C1 [Holland, Stephen A.] Univ Tennessee, 1520 Middle Dr, Knoxville, TN 37916 USA. [Mahan, Cody A.] Western Kentucky Univ, Bowling Green, KY 42101 USA. [Kuhn, Michael J.; Rowe, Nathan C.] Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. RP Holland, SA (reprint author), Univ Tennessee, 1520 Middle Dr, Knoxville, TN 37916 USA. NR 22 TC 0 Z9 0 U1 1 U2 1 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9510-5 J9 PROC SPIE PY 2013 VL 8719 AR UNSP 87190J DI 10.1117/12.2018124 PG 12 WC Engineering, Biomedical; Optics; Physics, Applied SC Engineering; Optics; Physics GA BJQ21 UT WOS:000329624600011 ER PT S AU Mikhelson, IV Bakhtiari, S Elmer, TW Liao, S Sahakian, AV AF Mikhelson, Ilya V. Bakhtiari, Sasan Elmer, Thomas W., II Liao, Shaolin Sahakian, Alan V. BE Cullum, BM McLamore, ES TI Remote sensing of heart rate using millimeter-wave interferometry and probabilistic interpolation SO SMART BIOMEDICAL AND PHYSIOLOGICAL SENSOR TECHNOLOGY X SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on Smart Biomedical and Physiological Sensor Technology X CY MAY 01-02, 2013 CL Baltimore, MD SP SPIE DE Remote Sensing; Millimeter-Wave; Heartbeat Detection; Heart Rate; Ambulatory Monitoring ID AMBULATORY SUBJECT; NONCONTACT AB Using a 94-GHz homodyne interferometer employing a highly-directional quasi-optical lens antenna aimed at a human subject's chest, we can measure chest wall displacement from up to 10m away and through common clothing. Within the chest displacement signal are motions due to cardiac activity, respiration, and gross body movement. Our goal is to find the heart rate of the subject being monitored, which implies isolation of the minute movements due to cardiac activity from the much larger movements due to respiration and body movement. To accomplish this, we first find a subset of the true heartbeat temporal locations (called "confident" heartbeats) in the displacement signal using a multi-resolution wavelet approach, utilizing Symlet wavelets. Although the chest displacement due to cardiac activity is orders of magnitude smaller than that due to respiration and body movement, wavelets find those heartbeat locations due to several useful properties, such as shape matching, high-pass filtering, and vanishing moments. Using the assumption that the "confident" heartbeats are randomly selected from the set of all heartbeats, we are able to find the maximum a posteriori statistics of an inverse Gaussian probability distribution modeling the inter-heartbeat times. We then analyze the "confident" heartbeats and decide which heartbeats are probabilistically correct and which are not, based on the inverse Gaussian distribution we calculated earlier. The union of the "confident" set, after pruning, and the interpolated set forms a very close approximation to the true heartbeat temporal location set, and thus allows us to accurately calculate a heart rate. C1 [Mikhelson, Ilya V.; Sahakian, Alan V.] Northwestern Univ, Dept Elect Engn & Comp Sci, Evanston, IL 60208 USA. [Bakhtiari, Sasan; Elmer, Thomas W., II; Liao, Shaolin] Argonne Natl Lab, Nucl Engn Div, Argonne, IL 60439 USA. RP Mikhelson, IV (reprint author), Northwestern Univ, Dept Elect Engn & Comp Sci, Evanston, IL 60208 USA. EM sahakian@eecs.northwestern.edu RI Sahakian, Alan/B-7268-2009 NR 23 TC 0 Z9 0 U1 0 U2 1 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9510-5 J9 PROC SPIE PY 2013 VL 8719 AR UNSP 87190M DI 10.1117/12.2015282 PG 15 WC Engineering, Biomedical; Optics; Physics, Applied SC Engineering; Optics; Physics GA BJQ21 UT WOS:000329624600014 ER PT S AU Devereux, M AF Devereux, Michael GP IOP TI Testing Quantum Erasure and Reversible Quantum Measurement with Holladay's Simple Experiment SO 6TH INTERNATIONAL SYMPOSIUM ON QUANTUM THEORY AND SYMMETRIES (QTS6) SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 6th International Symposium on Quantum Theory and Symmetries (QTS) CY JUL 20-25, 2009 CL Univ Kentucky, Lexington, KY SP Dept Phys & Astronomy, Dept Math, Univ Kentucky, Ctr Computat Sci HO Univ Kentucky ID DELAYED CHOICE; ERASER; INTERFERENCE; MECHANICS AB Schrodinger's continuous differential equation, which, as far as we know, describes the time development of all physical systems, from microscopic to cosmological, is time-reversal invariant. It is the process of measurement of a system that von Neumann found to be irreversible, and may so account for the distinction between past and future. Developed over the last thirty years, quantum eraser theory has claimed that some quantum measurements are reversible. Holladay proposed a very simple double-slit quantum eraser experiment, hitherto never performed, which he said would refute von Neumann's measurement description and support the quantum erasure thesis. Now, that experiment can actually be implemented with inexpensive, easily accessible equipment. Remarkably, results of the experiment refute quantum eraser theory and confirm von Neumann's measurement reduction process instead. C1 [Devereux, Michael] Los Alamos Natl Lab, Los Alamos, NM 87544 USA. EM dbar_x@cybermesa.com NR 17 TC 1 Z9 1 U1 0 U2 1 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2013 VL 462 AR 012010 DI 10.1088/1742-6596/462/1/012010 PG 8 WC Physics, Multidisciplinary; Physics, Mathematical SC Physics GA BJO32 UT WOS:000329356700011 ER PT S AU Zachos, CK AF Zachos, Cosmas K. GP IOP TI Basics of Ternary Algebras and their underlying Nambu Brackets SO 6TH INTERNATIONAL SYMPOSIUM ON QUANTUM THEORY AND SYMMETRIES (QTS6) SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 6th International Symposium on Quantum Theory and Symmetries (QTS) CY JUL 20-25, 2009 CL Univ Kentucky, Lexington, KY SP Dept Phys & Astronomy, Dept Math, Univ Kentucky, Ctr Computat Sci HO Univ Kentucky AB Ternary algebras amount to closing systems of antisymmetrized trinomials of operators. The Filippov conditions ( FI, which are not identities) for ternary algebras are contrasted to Bremner's identities dictated by associativity of operator products, and thus analogous to Jacobi identities. Maps of the known FI-compliant ternary algebras to underlying classical Nambu brackets are constructed, which then explain this compliance: FI- compliant ternary algebras are essentially classical Nambu brackets in disguise. In some cases involving infinite algebras, we show the classical limit may be obtained by a contraction of the quantal ternary algebra, and then explicitly realized through classical Nambu brackets. We illustrate this classical-contraction method on our Virasoro-Witt ternary algebra paradigm. The content of the talk is in the following two references. C1 Argonne Natl Lab, Div High Energy Phys, Argonne, IL 60439 USA. RP Zachos, CK (reprint author), Argonne Natl Lab, Div High Energy Phys, Argonne, IL 60439 USA. EM zachos@anl.gov NR 2 TC 0 Z9 0 U1 0 U2 0 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2013 VL 462 AR 012060 DI 10.1088/1742-6596/462/1/012060 PG 1 WC Physics, Multidisciplinary; Physics, Mathematical SC Physics GA BJO32 UT WOS:000329356700061 ER PT J AU Chekanov, SV Erickson, M AF Chekanov, S. V. Erickson, M. TI A Nonparametric Peak Finder Algorithm and Its Application in Searches for New Physics SO ADVANCES IN HIGH ENERGY PHYSICS LA English DT Article ID SPECTRA; IDENTIFICATION AB We have developed an algorithm for nonparametric fitting and extraction of statistically significant peaks in the presence of statistical and systematic uncertainties. Applications of this algorithm for analysis of high-energy collision data are discussed. In particular, we illustrate how to use this algorithm in general searches for new physics in invariant-mass spectra using pp Monte Carlo simulations. C1 [Chekanov, S. V.; Erickson, M.] Argonne Natl Lab, HEP Div, Argonne, IL 60439 USA. [Erickson, M.] Coll New Jersey, Dept Phys, Ewing, NJ 08628 USA. RP Chekanov, SV (reprint author), Argonne Natl Lab, HEP Div, 9700 S Cass Ave, Argonne, IL 60439 USA. EM chekanov@anl.gov FU U.S. Department of Energy Office of Science Laboratory [DE-AC02-06CH11357] FX The authors would like to thank J. Proudfoot for discussion and comments. The submitted paper has been created by UChicago Argonne, LLC, Operator of Argonne National Laboratory (Argonne). Argonne, a U.S. Department of Energy Office of Science Laboratory, is operated under Contract no. DE-AC02-06CH11357. NR 21 TC 0 Z9 0 U1 1 U2 2 PU HINDAWI PUBLISHING CORPORATION PI NEW YORK PA 410 PARK AVENUE, 15TH FLOOR, #287 PMB, NEW YORK, NY 10022 USA SN 1687-7357 EI 1687-7365 J9 ADV HIGH ENERGY PHYS JI Adv. High. Energy Phys. PY 2013 AR 162986 DI 10.1155/2013/162986 PG 4 WC Physics, Particles & Fields SC Physics GA 290CS UT WOS:000329730800001 ER PT S AU Garrett, A New, J Chandler, T AF Garrett, Aaron New, Joshua Chandler, Theodore GP ASHRAE TI Evolutionary Tuning of Building Models to Monthly Electrical Consumption SO ASHRAE TRANSACTIONS 2013, VOL 119, PT 2 SE ASHRAE Transactions LA English DT Proceedings Paper CT ASHRAE Annual Conference CY JUN 22-26, 2013 CL Denver, CO SP ASHRAE ID COMPUTATION AB Building energy models of existing buildings are unreliable unless calibrated so they correlate well with actual energy use. Calibrating models is costly because it is currently an art that requires significant manual effort by an experienced and skilled professional. An automated methodology could significantly decrease this cost and facilitate greater adoption of energy simulation capabilities into the marketplace. The Autotune project is a novel methodology that leverages supercomputing, large databases of simulations, and machine learning to allow automatic calibration of simulations that match measured experimental data. This paper shares initial results from the automated methodology on commodity hardware applied to the calibration of building energy models (BEM) for EnergyPlus (E+) to provide error rates, as measured by the sumof absolute error, for matching monthly load and electrical data from a highly instrumented and automated ZEBRAlliance research home. C1 [Garrett, Aaron; Chandler, Theodore] Jacksonville State Univ, Dept Math Comp & Informat Sci, Jacksonville, AL 36265 USA. [New, Joshua] Oak Ridge Natl Lab, Whole Bldg & Comm Integrat Grp, Oak Ridge, TN USA. RP Garrett, A (reprint author), Jacksonville State Univ, Dept Math Comp & Informat Sci, Jacksonville, AL 36265 USA. FU Department of Energy Building Technology [CEBT105, BT0201000]; Oak Ridge National Laboratory; Office of Science of U.S. Department of Energy [DE-AC05-00OR22725]; RDAV (Remote Data Analysis and Visualization) Center of University of Tennessee, Knoxville; NSF [ARRA-NSF-OCI-0906324, NSF-OCI-1136246]; UTBattelle; LLC, for U.S. Dept. of Energy [DEAC05-00OR22725] FX This work was funded by field work proposal CEBT105 under the Department of Energy Building Technology Activity Number BT0201000. We would like to thank Amir Roth for his support and review of this project. This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725. Our work has been enabled and supported by data analysis and visualization experts at the RDAV (Remote Data Analysis and Visualization) Center of the University of Tennessee, Knoxville (NSF grant no. ARRA-NSF-OCI-0906324 and NSF-OCI-1136246). Oak Ridge National Laboratory is managed by UTBattelle, LLC, for the U.S. Dept. of Energy under contract DEAC05-00OR22725. This manuscript has been authored by UT-Battelle, LLC, under Contract Number DEAC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a nonexclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. NR 33 TC 1 Z9 1 U1 1 U2 1 PU AMER SOC HEATING, REFRIGERATING AND AIR-CONDITIONING ENGS PI ATLANTA PA 1791 TULLIE CIRCLE NE, ATLANTA, GA 30329 USA SN 0001-2505 BN 978-1-936504-54-1 J9 ASHRAE TRAN PY 2013 VL 119 BP 89 EP 100 PN 2 PG 12 WC Thermodynamics; Construction & Building Technology SC Thermodynamics; Construction & Building Technology GA BJM27 UT WOS:000329089700008 ER PT S AU Mohammed, AQ Wenning, T Sever, F Kissock, K AF Mohammed, Abdul Qayyum Wenning, Thomas Sever, Franc Kissock, Kelly GP ASHRAE TI Principles of Energy Efficient Ammonia Refrigeration Systems SO ASHRAE TRANSACTIONS 2013, VOL 119, PT 2 SE ASHRAE Transactions LA English DT Proceedings Paper CT ASHRAE Annual Conference CY JUN 22-26, 2013 CL Denver, CO SP ASHRAE AB Ammonia refrigeration systems are typically large energy users and hence good targets for energy efficiency improvements. Common opportunities to reduce energy use and improve energy efficiency include reducing refrigeration load, increasing suction pressure, employing dual suction, decreasing minimum head pressure setpoint, increasing evaporative condenser effectiveness, and reclaiming heat. Estimating savings from these measures is often difficult because of the complexity of the equipment and controls. However, the fundamental energy response of ammonia refrigeration systems to these measures can be estimated using a simplified model. An understanding of these responses is often an important first step to designing or optimizing the performance of actual systems. Thus, this paper develops a simplified model for simulating a single-stage ammonia refrigeration system and uses the model to estimate how energy use changes in response to the opportunities mentioned above. The results show how system energy use and potential energy savings vary with ambient wet-bulb temperature. The results give designers and operators insight into possible savings opportunities. C1 [Mohammed, Abdul Qayyum; Kissock, Kelly] Univ Dayton, Dept Mech & Aerosp Engn Renewable & Clean Energy, Dayton, OH 45469 USA. [Wenning, Thomas] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Sever, Franc] Go Sustainable Energy, Columbus, OH USA. RP Mohammed, AQ (reprint author), Univ Dayton, Dept Mech & Aerosp Engn Renewable & Clean Energy, Dayton, OH 45469 USA. RI Wenning, Thomas/J-4478-2016 OI Wenning, Thomas/0000-0002-7232-6822 FU U.S. Department of Energy FX The authors are grateful for support for thiswork from the U.S. Department of Energy through the Industrial Assessment Center program. The paper was improved from suggestions made by reviewers and others in the ammonia refrigeration industry. NR 10 TC 0 Z9 0 U1 0 U2 0 PU AMER SOC HEATING, REFRIGERATING AND AIR-CONDITIONING ENGS PI ATLANTA PA 1791 TULLIE CIRCLE NE, ATLANTA, GA 30329 USA SN 0001-2505 BN 978-1-936504-54-1 J9 ASHRAE TRAN PY 2013 VL 119 BP 222 EP 230 PN 2 PG 9 WC Thermodynamics; Construction & Building Technology SC Thermodynamics; Construction & Building Technology GA BJM27 UT WOS:000329089700018 ER PT S AU Tanner, RA Henze, GP Pless, S AF Tanner, Ryan A. Henze, Gregor P. Pless, Shanti GP ASHRAE TI Optimized Control of Automatic Windows for Energy Savings and Occupant Comfort2 SO ASHRAE TRANSACTIONS 2013, VOL 119, PT 2 SE ASHRAE Transactions LA English DT Proceedings Paper CT ASHRAE Annual Conference CY JUN 22-26, 2013 CL Denver, CO SP ASHRAE ID BEHAVIOR; MODEL AB In the context of optimizing controls for high-performance buildings to achieve energy savings while maintaining or improving occupant comfort, this study is aimed at finding incremental improvements in the existing control logic for an existing building. Through the use of parametric studies with a building energy simulation model that incorporates a stochastic model of occupant window use and automatic window control logic commensurate with the physical building, the performance of different natural ventilation control strategies is evaluated. Due to the inclusion of stochastic occupant behavior in the building model, results of simulations are presented as a distribution of potential outcomes, rather than a scalar value; however, the average of these distributions is used for simpler comparison between control strategies. The results show that annual HVAC electricity consumption can be reduced by 3% to 15%, depending upon the controls changes implemented. C1 [Tanner, Ryan A.; Henze, Gregor P.] Univ Colorado, Dept Civil Environm & Architectural Engn, Boulder, CO 80309 USA. [Pless, Shanti] Natl Renewable Energy Lab, Commercial Bldg Res Grp, Golden, CO USA. RP Tanner, RA (reprint author), Univ Colorado, Dept Civil Environm & Architectural Engn, Boulder, CO 80309 USA. RI Henze, Gregor/C-5505-2015 OI Henze, Gregor/0000-0002-4084-9709 NR 17 TC 0 Z9 0 U1 0 U2 0 PU AMER SOC HEATING, REFRIGERATING AND AIR-CONDITIONING ENGS PI ATLANTA PA 1791 TULLIE CIRCLE NE, ATLANTA, GA 30329 USA SN 0001-2505 BN 978-1-936504-54-1 J9 ASHRAE TRAN PY 2013 VL 119 BP 274 EP 287 PN 2 PG 14 WC Thermodynamics; Construction & Building Technology SC Thermodynamics; Construction & Building Technology GA BJM27 UT WOS:000329089700023 ER PT S AU Doebber, IR Lilya, D Henderson, HI AF Doebber, Ian R. Lilya, Dustin Henderson, Hugh I. GP ASHRAE TI Characterizing Supermarket's Thermal Demands for Integrating Combined Heat and Power Systems SO ASHRAE TRANSACTIONS 2013, VOL 119, PT 2 SE ASHRAE Transactions LA English DT Proceedings Paper CT ASHRAE Annual Conference CY JUN 22-26, 2013 CL Denver, CO SP ASHRAE AB Supermarkets installing combined heat and power (CHP) systems are looking to reduce utility electric consumption while applying the thermal output to offset service hot water, space heating, refrigeration subcooling, desiccant dehumidification and space cooling via an absorption chiller. Unfortunately, monitoring of supermarket CHP systems has shown that while the electric power was successfully applied, the waste heat was not properly utilized. Comparatively, CHP projects are highly successful in industry and manufacturing settings since the thermal load profiles are well understood and remain relatively constant throughout the year. For supermarket CHP systems to make economic sense and reduce carbon emissions, the thermal output needs to be nearly fully utilized throughout the year. The following paper summarizes the variation of thermal demands of stores in San Diego, CA and Boston, MA, which apply fuel cell waste heat to different thermal loads; two combined big box/grocery stores in Arkansas with no CHP system; and a supermarket in Raleigh, NC also with no CHP system. These concrete examples also provide insight into how thermal loads change when new stores or deep-dive retrofits implement increased on-site food preparation, secondary refrigeration systems, doors on medium temperature refrigerated display cases, and reduced lighting power densities. Each section is dedicated to a separate thermal demand. The authors use a combination of field monitored data and modeling to discuss in detail how to effectively apply CHP thermal output, focusing on how to maintain sufficient temperature differences (heat quality), attack persistent and large loads (heat quantity), and address fundamental design considerations. C1 [Doebber, Ian R.] Natl Renewable Energy Lab, Golden, CO 80401 USA. [Lilya, Dustin; Henderson, Hugh I.] CDH Energy Corp, DC Engn, Cazenovia, NY USA. RP Doebber, IR (reprint author), Natl Renewable Energy Lab, Golden, CO 80401 USA. NR 11 TC 0 Z9 0 U1 0 U2 1 PU AMER SOC HEATING, REFRIGERATING AND AIR-CONDITIONING ENGS PI ATLANTA PA 1791 TULLIE CIRCLE NE, ATLANTA, GA 30329 USA SN 0001-2505 BN 978-1-936504-54-1 J9 ASHRAE TRAN PY 2013 VL 119 BP 371 EP 378 PN 2 PG 8 WC Thermodynamics; Construction & Building Technology SC Thermodynamics; Construction & Building Technology GA BJM27 UT WOS:000329089700031 ER PT S AU Walker, I Faulkner, D Dickerhoff, D Turner, W AF Walker, Iain Faulkner, David Dickerhoff, Darryl Turner, Will GP ASHRAE TI Energy Implications of In-Line Filtration in California Homes SO ASHRAE TRANSACTIONS 2013, VOL 119, PT 2 SE ASHRAE Transactions LA English DT Proceedings Paper CT ASHRAE Annual Conference CY JUN 22-26, 2013 CL Denver, CO SP ASHRAE ID PERFORMANCE AB Furnace energy use and filter pressure drop was measured for forced-air heating/cooling systems in ten California homes. Each home was monitored for at least one year. Measurements were made of the blower energy, filter pressure drop, supply and return plenum pressures, and temperatures, as well as the indoor temperature. At least two filter types were installed, including a MERV 16 filter, in most houses. As the filter became dirty, in some homes the blower energy use increased, and in others the blower energy use decreased. Increasing blower energy use was associated with BPM blower motors, and decreasing blower energy was associated with PSC blower motors. There was a large pressure drop across the MERV 16 filter as compared to the lower-MERV filters. Many homeowners complained of noise because of the large pressure drop and air bypassing the filter. In addition to field measurements, simulations were made for a typical new home in six California climate zones, with combinations of PSC and BPM blowers, and low and high duct leakage. The results indicate that for MERV 10-13 filters, as compared to a baseline of MERV 5, the effects on blower energy use are moderate (<5%) over a wide range of performance conditions and climates. Using MERV 16 filters leads to problems in terms of noise, usability, and potential for significantly increased blower energy use (about 20%). In systems that are already close to blower performance limits with low-MERV filters, the addition of a MERV 16 filter pushed the blowers to their performance limits. The effect of filter loading on total HVAC system energy performance was small (<1%) for most homes. However, with high filter loading rates for MERV 16 filters, the performance deteriorated significantly (up to 20% increases in energy use for a system with a leaky duct and a BPM blower) indicating that a filter loading indicator should be required for MERV 16 filters. C1 [Walker, Iain; Faulkner, David; Dickerhoff, Darryl; Turner, Will] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Residential Bldg Syst Grp, Berkeley, CA 94720 USA. RP Walker, I (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Residential Bldg Syst Grp, Berkeley, CA 94720 USA. NR 27 TC 2 Z9 2 U1 2 U2 4 PU AMER SOC HEATING, REFRIGERATING AND AIR-CONDITIONING ENGS PI ATLANTA PA 1791 TULLIE CIRCLE NE, ATLANTA, GA 30329 USA SN 0001-2505 BN 978-1-936504-54-1 J9 ASHRAE TRAN PY 2013 VL 119 BP 399 EP 417 PN 2 PG 19 WC Thermodynamics; Construction & Building Technology SC Thermodynamics; Construction & Building Technology GA BJM27 UT WOS:000329089700034 ER PT S AU Elam, JW Mane, AU Libera, JA Hryn, JN Siegmund, OHW McPhate, J Wetstein, MJ Elagin, A Minot, MJ O'Mahony, A Wagner, RG Tong, WM Brodie, AD McCord, MA Bevis, CF AF Elam, Jeffrey W. Mane, Anil U. Libera, Joseph A. Hryn, John N. Siegmund, Oswald H. W. McPhate, Jason Wetstein, Matthew J. Elagin, Andrey Minot, Michael J. O'Mahony, Aileen Wagner, Robert G. Tong, William M. Brodie, Alan D. McCord, Mark A. Bevis, Christopher F. BE Roozeboom, F Delabie, A Londergan, A DeGendt, S Elam, JW VanDerStraten, O TI Synthesis, Characterization, and Application of Tunable Resistance Coatings Prepared by Atomic Layer Deposition SO ATOMIC LAYER DEPOSITION APPLICATIONS 9 SE ECS Transactions LA English DT Proceedings Paper CT 9th International Symposium on Atomic Layer Deposition Applications held during the 224th Meeting of the Electrochemical-Society (ECS) CY OCT 27-NOV 01, 2013 CL San Francisco, CA SP Electrochem Soc, Electrochem Soc, Dielectr Sci & Technol Div, Electrochem Soc, Elect & Photon Div ID QUARTZ-CRYSTAL MICROBALANCE; MICROCHANNEL PLATES; ALLOY-FILMS; DETECTORS; GROWTH AB We describe the synthesis, characterization, and application of nanocomposite, tunable resistance coatings consisting of conducting, metallic nanoparticles embedded in an amorphous dielectric matrix. These films are comprised of M:Al2O3 with M=Mo or W, and are prepared by atomic layer deposition (ALD) using alternating exposures to trimethyl aluminum and H2O for the Al2O3 ALD and alternating MF6/Si2H6 exposures for the metal ALD. By varying the ratio of ALD cycles for the metal and the Al2O3 components in the film, we can tune precisely the resistance of these coatings over a very broad range from 10(5)-10(12) Ohm. cm. These films exhibit ohmic behavior and resist breakdown even at high electric fields of 107 V/m. Moreover, the self-limiting nature of ALD allows us to grow these films inside of porous substrates and on complex 3D surfaces. As a result of these qualities, our nanocomposite films have proved exceptional as resistive coatings in microchannel plate electron multipliers and as charge drain coatings in electron-optical devices. C1 [Elam, Jeffrey W.; Mane, Anil U.; Libera, Joseph A.; Hryn, John N.; Wagner, Robert G.] Argonne Natl Lab, Argonne, IL 60439 USA. RP Elam, JW (reprint author), Argonne Natl Lab, 9700 S Cass Ave, Argonne, IL 60439 USA. NR 19 TC 8 Z9 8 U1 1 U2 9 PU ELECTROCHEMICAL SOC INC PI PENNINGTON PA 65 S MAIN ST, PENNINGTON, NJ 08534-2839 USA SN 1938-5862 BN 978-1-60768-455-8; 978-1-62332-101-7 J9 ECS TRANSACTIONS PY 2013 VL 58 IS 10 BP 249 EP 261 DI 10.1149/05810.0249ecst PG 13 WC Electrochemistry SC Electrochemistry GA BJQ28 UT WOS:000329647500025 ER PT J AU Gallagher, E Douglas, CG Kelly, DL Barth, S Kelleher, CT Hodkinson, TR AF Gallagher, E. Douglas, C. G. Kelly, D. L. Barth, S. Kelleher, C. T. Hodkinson, T. R. TI OLD AGE SEX: A PARENTAGE STUDY OF DIFFERENT AGE COHORTS IN A NATIVE VETERAN PEDUNCULATE OAK (QUERCUS ROBUR L.) WOODLAND USING MICROSATELLITE MARKERS SO BIOLOGY AND ENVIRONMENT-PROCEEDINGS OF THE ROYAL IRISH ACADEMY LA English DT Article ID SCALE GENETIC-STRUCTURE; HALF-SIB FAMILIES; FOREST FRAGMENTATION; PATERNITY INFERENCE; BUR OAK; POPULATION; PETRAEA; CHLOROPLAST; FLOW; SUCCESS AB To quantify levels of gene flow among and genetic variation within different age cohorts of pedunculate oak (Quercus robur L.) in a semi-natural oak woodland, diversity and parentage studies were undertaken on a stand in Ballytobin, Co. Kilkenny, Ireland. Trees were categorised into four size classes-seedlings, saplings, mature trees and veterans, and genetic differentiation was estimated for three microsatellite markers using AMOVA. Parentage was assessed using a likelihood assignment approach. Between nine and fourteen alleles were detected per locus (mean gene diversity, h, 0.8312). All samples from Ballytobin were heterozygous. AMOVA between age cohorts (veterans, mature, saplings and seedlings) estimated that only 2% of the variation was partitioned among age cohort and the mean F-ST was low (0.015) but significant (P = 0.034). Parent-pair analysis revealed that out of 24 candidate trees, fifteen were assigned as parents to at least one offspring and, out of these, five were veteran. The average pollination distance was estimated at 47.8m with seven out of the twelve parent-pairs being within 50m of each other. The measured range of distances between trees indicated in the analysis as parents was between 22m and 150m. The highest values for number of parent/offspring assignments were between 40m and 49m. Overall, veteran oak at the site were found to be reproductively successful and a low level of differentiation was found between age cohorts indicating that population genetic diversity has been maintained over time. C1 [Gallagher, E.; Kelly, D. L.; Hodkinson, T. R.] Trinity Coll Dublin, Sch Nat Sci, Dept Bot, Dublin 2, Ireland. [Gallagher, E.; Kelly, D. L.; Hodkinson, T. R.] Trinity Coll Dublin, Trinity Ctr Biodivers Res, Dublin 2, Ireland. [Douglas, C. G.] TEAGASC, Res Ctr, Dublin 17, Ireland. [Barth, S.] TEAGASC, Crops Environm & Land Use Programme, Oak Pk Res Ctr, Carlow, Ireland. [Kelleher, C. T.] Natl Bot Garden, DBN Plant Mol Lab, Dublin 9, Ireland. RP Gallagher, E (reprint author), Trinity Coll Dublin, Sch Nat Sci, Dept Bot, Dublin 2, Ireland. EM egallag@tcd.ie RI Hodkinson, Trevor/F-6850-2014; Barth, Susanne/P-3366-2014 OI Hodkinson, Trevor/0000-0003-1384-7270; Barth, Susanne/0000-0002-4104-5964 FU Teagasc Walsh Fellowship postgraduate programme FX We thank Michael Gabbett for allowing access to the oak wood on Ballytobin Estate. Funding information: this work was supported by the Teagasc Walsh Fellowship postgraduate programme. NR 53 TC 1 Z9 1 U1 1 U2 12 PU ROYAL IRISH ACAD PI DUBLIN PA 19 DAWSON STREET, DUBLIN 2, IRELAND SN 0791-7945 EI 2009-003X J9 BIOL ENVIRON JI Biol. Environ.-Proc. R. Irish Acad. PY 2013 VL 113B IS 2 BP 155 EP 167 DI 10.3318/BIOE.2013.15 PG 13 WC Biology; Environmental Sciences SC Life Sciences & Biomedicine - Other Topics; Environmental Sciences & Ecology GA 289ME UT WOS:000329685800003 ER PT S AU Soufli, R Fernandez-Perea, M Krzywinski, J Rich, DW Baker, SL Robinson, JC Hau-Riege, S Gullikson, EM Yashchuk, VV McKinney, WR Heimann, P Schlotter, WF Rowen, M Montanez, PA Boutet, S AF Soufli, Regina Fernandez-Perea, Monica Krzywinski, Jacek Rich, David W. Baker, Sherry L. Robinson, Jeff C. Hau-Riege, Stefan Gullikson, Eric M. Yashchuk, Valeriy V. McKinney, Wayne R. Heimann, Philip Schlotter, William F. Rowen, Michael Montanez, Paul A. Boutet, Sebastien BE Juha, L Bajt, S London, R Hudec, R Pina, L TI Development, experimental performance and damage properties of x-ray optics for the LCLS free-electron laser SO DAMAGE TO VUV, EUV, AND X-RAY OPTICS IV; AND EUV AND X-RAY OPTICS: SYNERGY BETWEEN LABORATORY AND SPACE III SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on Damage to VUV, EUV, and X-ray Optics IV; and EUV and X-ray Optics - Synergy between Laboratory and Space III CY APR 15-18, 2013 CL Prague, CZECH REPUBLIC SP SPIE DE free-electron lasers; x-ray optics; boron carbide; silicon carbide; damage; metrology; reflectivity ID LIGHT-SOURCE; MIRRORS; FILMS AB This manuscript presents an overview of recent work performed on x-ray optics development, metrology and calibration for the Soft X-ray Research (SXR) and the Coherent X-ray Imaging (CXI) instruments at the Linac Coherent Light Source (LCLS) free-electron laser. We also present results on the first LCLS exposures of boron carbide (B4C)-coated samples at photon energies near the carbon K edge and discuss relevant analysis and implications for future experiments. C1 [Soufli, Regina; Fernandez-Perea, Monica; Baker, Sherry L.; Robinson, Jeff C.; Hau-Riege, Stefan] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. RP Soufli, R (reprint author), Lawrence Livermore Natl Lab, 7000 East Ave, Livermore, CA 94550 USA. NR 27 TC 2 Z9 2 U1 1 U2 9 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9579-2 J9 PROC SPIE PY 2013 VL 8777 AR 877702 DI 10.1117/12.2019197 PG 10 WC Optics; Physics, Applied SC Optics; Physics GA BJQ06 UT WOS:000329577700001 ER PT B AU Gorman, ME Savage, NF Street, A AF Gorman, Michael E. Savage, Nora F. Street, Anita BE Savage, N Gorman, M Street, A TI Using Nanotechnology to Filter Water: A Hypothetical Case Study SO EMERGING TECHNOLOGIES: SOCIO-BEHAVIORAL LIFE CYCLE APPROACHES LA English DT Article; Book Chapter C1 [Gorman, Michael E.] Univ Virginia, Sch Engn & Appl Sci, Charlottesville, VA 22904 USA. [Savage, Nora F.] US EPA, Washington, DC 20460 USA. [Street, Anita] US DOE, Off Intelligence & Counterintelligence, Div Sci & Technol, Washington, DC 20585 USA. RP Gorman, ME (reprint author), Univ Virginia, Sch Engn & Appl Sci, 351 McCormick Rd,POB 400744,Thornton Hall, Charlottesville, VA 22904 USA. EM savage.nora@epa.gov NR 1 TC 0 Z9 0 U1 0 U2 0 PU PAN STANFORD PUBLISHING PTE LTD PI SINGAPORE PA PENTHOUSE LEVEL, SUNTEC TOWER 3, 8 TEMASEK BLVD, SINGAPORE, 038988, SINGAPORE BN 978-981-4411-01-1; 978-981-4411-00-4 PY 2013 BP 5 EP 9 PG 5 WC Multidisciplinary Sciences; Social Sciences, Interdisciplinary SC Science & Technology - Other Topics; Social Sciences - Other Topics GA BJJ89 UT WOS:000328539700003 ER PT B AU Gorman, ME Savage, NF Street, A AF Gorman, Michael E. Savage, Nora F. Street, Anita BE Savage, N Gorman, M Street, A TI Nanotechnology for Human Health SO EMERGING TECHNOLOGIES: SOCIO-BEHAVIORAL LIFE CYCLE APPROACHES LA English DT Article; Book Chapter C1 [Gorman, Michael E.] Univ Virginia, Sch Engn & Appl Sci, Charlottesville, VA 22904 USA. [Savage, Nora F.] US EPA, Washington, DC 20460 USA. [Street, Anita] US DOE, Off Intelligence & Counterintelligence, Div Sci & Technol, Washington, DC 20585 USA. RP Gorman, ME (reprint author), Univ Virginia, Sch Engn & Appl Sci, 351 McCormick Rd,POB 400744,Thornton Hall, Charlottesville, VA 22904 USA. EM meg3c@virginia.edu NR 0 TC 0 Z9 0 U1 0 U2 1 PU PAN STANFORD PUBLISHING PTE LTD PI SINGAPORE PA PENTHOUSE LEVEL, SUNTEC TOWER 3, 8 TEMASEK BLVD, SINGAPORE, 038988, SINGAPORE BN 978-981-4411-01-1; 978-981-4411-00-4 PY 2013 BP 11 EP 15 PG 5 WC Multidisciplinary Sciences; Social Sciences, Interdisciplinary SC Science & Technology - Other Topics; Social Sciences - Other Topics GA BJJ89 UT WOS:000328539700004 ER PT S AU Shenai, K AF Shenai, Krishna BE Shenai, K Dudley, M Bakowski, M Ohtani, N TI Voltage Switching Limits of Lateral GaN Power Devices SO GALLIUM NITRIDE AND SILICON CARBIDE POWER TECHNOLOGIES 3 SE ECS Transactions LA English DT Proceedings Paper CT 3rd Symposium on Gallium Nitride (GaN) and Silicon Carbide (SiC) Power Technologies as part of the Fall Meeting of the Electrochemical-Society (ECS) CY OCT 28-31, 2013 CL San Francisco, CA SP Electrochem Soc, Electrochem Soc, Elect & Photon Div, Electrochem Soc, Dielectr Sci & Technol Div, US Natl Sci Fdn, IEEE Power Elect Soc ID CIRCUIT SIMULATION-MODEL AB The dv/dt switching limitations of power semiconductor devices are evaluated in a boost (PFC) power converter using circuit simulations. State-of-the-art commercial silicon CoolMOS devices, commercial Silicon Carbide (SiC) Junction Barrier Schottky (JBS) diodes, and emerging Gallium Nitride (GaN) lateral power transistors are considered. It is shown that although SiC and GaN power devices have low stored charge and small capacitances, they experience high switching dv/dt stresses which may pose serious switching limitations especially in high-frequency power converters. This problem is likely to be further exacerbated by the presence of a high density of crystal defects in SiC and GaN materials which will manifest in the form of poor field-reliability. Specific guidelines for device selection are recommended in order to optimize both performance and field-reliability. C1 Argonne Natl Lab, Div Energy Syst, Argonne, IL 60439 USA. RP Shenai, K (reprint author), Argonne Natl Lab, Div Energy Syst, 9700 South Cass Ave,Bldg 362, Argonne, IL 60439 USA. NR 14 TC 0 Z9 0 U1 1 U2 8 PU ELECTROCHEMICAL SOC INC PI PENNINGTON PA 65 S MAIN ST, PENNINGTON, NJ 08534-2839 USA SN 1938-5862 BN 978-1-60768-449-7; 978-1-62332-095-9 J9 ECS TRANSACTIONS PY 2013 VL 58 IS 4 BP 179 EP 184 DI 10.1149/05804.0179ecst PG 6 WC Electrochemistry; Engineering, Electrical & Electronic; Physics, Applied SC Electrochemistry; Engineering; Physics GA BJO95 UT WOS:000329443400018 ER PT S AU Shenai, K AF Shenai, Krishna BE Shenai, K Dudley, M Bakowski, M Ohtani, N TI True "Figure of Merit (FOM)" of a Power Semiconductor Switch SO GALLIUM NITRIDE AND SILICON CARBIDE POWER TECHNOLOGIES 3 SE ECS Transactions LA English DT Proceedings Paper CT 3rd Symposium on Gallium Nitride (GaN) and Silicon Carbide (SiC) Power Technologies as part of the Fall Meeting of the Electrochemical-Society (ECS) CY OCT 28-31, 2013 CL San Francisco, CA SP Electrochem Soc, Electrochem Soc, Elect & Photon Div, Electrochem Soc, Dielectr Sci & Technol Div, US Natl Sci Fdn, IEEE Power Elect Soc ID HIGH-FREQUENCY APPLICATIONS; TRANSISTORS; PARAMETERS; DEVICES; SILICON; MODEL; GAN AB Wide Band Gap (WBG) semiconductors such as Silicon Carbide (SiC) and Gallium Nitride (GaN) are known to be superior materials for the fabrication of power electronics switching devices compared to the industry work-horse silicon. This advantage primarily stems from wider energy bandgap, higher electric field strength for avalanche breakdown, and improved thermal conductivity of SiC and GaN semiconductors compared to silicon. This paper reviews the various "Figures of Merit (FOM)" proposed in the literature for the WBG power semiconductors. Unipolar power transistors with MOS channel conduction as well as transistors that employ two-dimensional electron gas (2DEG) channels are considered. A true FOM for a power semiconductor switching device needs to take into account all electrical power losses and thermal limitations. A new Safe Operating Area (SOA) limit that relates material defect density (D-it) to the switching current density (J(on)) for a specified maximum junction temperature limit (T-jmax) is proposed as the true FOM for a power semiconductor switching device. C1 Argonne Natl Lab, Div Energy Syst, Argonne, IL 60439 USA. RP Shenai, K (reprint author), Argonne Natl Lab, Div Energy Syst, 9700 South Cass Ave,Bldg 362, Argonne, IL 60439 USA. NR 41 TC 0 Z9 0 U1 0 U2 6 PU ELECTROCHEMICAL SOC INC PI PENNINGTON PA 65 S MAIN ST, PENNINGTON, NJ 08534-2839 USA SN 1938-5862 BN 978-1-60768-449-7; 978-1-62332-095-9 J9 ECS TRANSACTIONS PY 2013 VL 58 IS 4 BP 199 EP 210 DI 10.1149/05804.0199ecst PG 12 WC Electrochemistry; Engineering, Electrical & Electronic; Physics, Applied SC Electrochemistry; Engineering; Physics GA BJO95 UT WOS:000329443400020 ER PT S AU Hughart, DR Flicker, JD DasGupta, SD Atcitty, S Kaplar, RJ Marinella, MJ AF Hughart, D. R. Flicker, J. D. DasGupta, S. D. Atcitty, S. Kaplar, R. J. Marinella, M. J. BE Shenai, K Dudley, M Bakowski, M Ohtani, N TI Progress in SiC MOSFET Reliability SO GALLIUM NITRIDE AND SILICON CARBIDE POWER TECHNOLOGIES 3 SE ECS Transactions LA English DT Proceedings Paper CT 3rd Symposium on Gallium Nitride (GaN) and Silicon Carbide (SiC) Power Technologies as part of the Fall Meeting of the Electrochemical-Society (ECS) CY OCT 28-31, 2013 CL San Francisco, CA SP Electrochem Soc, Electrochem Soc, Elect & Photon Div, Electrochem Soc, Dielectr Sci & Technol Div, US Natl Sci Fdn, IEEE Power Elect Soc ID DEVICES AB Bias-temperature stress experiments performed on two generations of SiC power MOSFETs from the same manufacturer show reductions in threshold voltage (V-T) shift at elevated temperatures from first- to second-generation. The negative V-T shift is reduced from a range of -1 V to -1.6 V to a range of -100 mV to -300 mV for temperatures from 125 degrees C to 175 degrees C. Plastic-packaged parts show a gate-bias-independent junction leakage current at temperatures above the rated temperature, suggesting that the plastic packaging introduces an extrinsic leakage path. Junction leakage in metal-packaged parts can be significantly reduced by applying a small negative gate bias at elevated temperatures. Switching gate bias temperature stresses show V-T shifts dependent on duty cycle, with a higher duty cycle resulting in a higher rate of V-T shift. Cumulative damage effects may be observed between switching gate bias stresses. C1 [Hughart, D. R.; Flicker, J. D.; DasGupta, S. D.; Atcitty, S.; Kaplar, R. J.; Marinella, M. J.] Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Hughart, DR (reprint author), Sandia Natl Labs, POB 5800,MS 1084, Albuquerque, NM 87185 USA. NR 13 TC 2 Z9 2 U1 3 U2 7 PU ELECTROCHEMICAL SOC INC PI PENNINGTON PA 65 S MAIN ST, PENNINGTON, NJ 08534-2839 USA SN 1938-5862 BN 978-1-60768-449-7; 978-1-62332-095-9 J9 ECS TRANSACTIONS PY 2013 VL 58 IS 4 BP 211 EP 220 DI 10.1149/05804.0211ecst PG 10 WC Electrochemistry; Engineering, Electrical & Electronic; Physics, Applied SC Electrochemistry; Engineering; Physics GA BJO95 UT WOS:000329443400021 ER PT S AU Shenai, K AF Shenai, Krishna BE Shenai, K Dudley, M Bakowski, M Ohtani, N TI Systems-Driven Power Semiconductor Education SO GALLIUM NITRIDE AND SILICON CARBIDE POWER TECHNOLOGIES 3 SE ECS Transactions LA English DT Proceedings Paper CT 3rd Symposium on Gallium Nitride (GaN) and Silicon Carbide (SiC) Power Technologies as part of the Fall Meeting of the Electrochemical-Society (ECS) CY OCT 28-31, 2013 CL San Francisco, CA SP Electrochem Soc, Electrochem Soc, Elect & Photon Div, Electrochem Soc, Dielectr Sci & Technol Div, US Natl Sci Fdn, IEEE Power Elect Soc ID CIRCUIT SIMULATION-MODEL; ELECTRONICS EDUCATION AB Today's power electronics curriculum practiced at most universities world-wide primarily focuses on power converters and power systems with little or no emphasis given to power electronics components and their interaction at the systems level. Consequently, graduates are trained to design power converters and power systems without adequate background on the physics and technology of power electronics components; graduate are often unable to understand and optimize component and systems technologies. The result is a widening disconnect that exists between the users and manufacturers of power electronics components. This paper discusses the challenges and approaches needed to bridge this educational gap and proposes a "systems-driven" power semiconductor educational curriculum in order to rapidly promote the power electronics industry. C1 Argonne Natl Lab, Div Energy Syst, Argonne, IL 60439 USA. RP Shenai, K (reprint author), Argonne Natl Lab, Div Energy Syst, 9700 South Cass Ave,Bldg 362, Argonne, IL 60439 USA. NR 17 TC 1 Z9 1 U1 0 U2 0 PU ELECTROCHEMICAL SOC INC PI PENNINGTON PA 65 S MAIN ST, PENNINGTON, NJ 08534-2839 USA SN 1938-5862 BN 978-1-60768-449-7; 978-1-62332-095-9 J9 ECS TRANSACTIONS PY 2013 VL 58 IS 4 BP 229 EP 235 DI 10.1149/05804.0229ecst PG 7 WC Electrochemistry; Engineering, Electrical & Electronic; Physics, Applied SC Electrochemistry; Engineering; Physics GA BJO95 UT WOS:000329443400023 ER PT S AU Shenai, K AF Shenai, Krishna BE Shenai, K Dudley, M Bakowski, M Ohtani, N TI Manufacturing Challenges in Wide Band Gap (WBG) Power Electronics SO GALLIUM NITRIDE AND SILICON CARBIDE POWER TECHNOLOGIES 3 SE ECS Transactions LA English DT Proceedings Paper CT 3rd Symposium on Gallium Nitride (GaN) and Silicon Carbide (SiC) Power Technologies as part of the Fall Meeting of the Electrochemical-Society (ECS) CY OCT 28-31, 2013 CL San Francisco, CA SP Electrochem Soc, Electrochem Soc, Elect & Photon Div, Electrochem Soc, Dielectr Sci & Technol Div, US Natl Sci Fdn, IEEE Power Elect Soc AB Wide Band Gap (WBG) semiconductors, Silicon Carbide (SiC) and Gallium Nitride (GaN), have enormous potential for transformative impact on electric utility and transportation infrastructures. However, commercialization of WBG power electronics switching devices has been slow primarily due to high cost and unproven field-reliability. This paper reviews the manufacturing challenges facing the WBG power electronics industry in order to "unlock" the true potential of this "game changing" solid-state energy conversion technology. C1 Argonne Natl Lab, Div Energy Syst, Argonne, IL 60439 USA. RP Shenai, K (reprint author), Argonne Natl Lab, Div Energy Syst, 9700 South Cass Ave,Bldg 362, Argonne, IL 60439 USA. NR 24 TC 0 Z9 0 U1 1 U2 5 PU ELECTROCHEMICAL SOC INC PI PENNINGTON PA 65 S MAIN ST, PENNINGTON, NJ 08534-2839 USA SN 1938-5862 BN 978-1-60768-449-7; 978-1-62332-095-9 J9 ECS TRANSACTIONS PY 2013 VL 58 IS 4 BP 301 EP 310 DI 10.1149/05804.0301ecst PG 10 WC Electrochemistry; Engineering, Electrical & Electronic; Physics, Applied SC Electrochemistry; Engineering; Physics GA BJO95 UT WOS:000329443400032 ER PT S AU Marinella, MJ DasGupta, S Kaplar, RJ Sun, M Atcitty, S Palacios, T AF Marinella, M. J. DasGupta, S. Kaplar, R. J. Sun, M. Atcitty, S. Palacios, T. BE Shenai, K Dudley, M Bakowski, M Ohtani, N TI Interaction of Defects with Quantum Well States: Electrostatic-Dependent Response Time for Traps in AlGaN/GaN HEMTs SO GALLIUM NITRIDE AND SILICON CARBIDE POWER TECHNOLOGIES 3 SE ECS Transactions LA English DT Proceedings Paper CT 3rd Symposium on Gallium Nitride (GaN) and Silicon Carbide (SiC) Power Technologies as part of the Fall Meeting of the Electrochemical-Society (ECS) CY OCT 28-31, 2013 CL San Francisco, CA SP Electrochem Soc, Electrochem Soc, Elect & Photon Div, Electrochem Soc, Dielectr Sci & Technol Div, US Natl Sci Fdn, IEEE Power Elect Soc ID MOBILITY TRANSISTORS; DC; CONVERTER; IMPACT; HFETS AB Recovery transients in high-voltage AlGaN/GaN HEMTs following both blocking voltage and ON-state stress show strong dependence on stress time. The defect time constant spectra exhibit a temperature-dependant component (TG1, E-a = 0.6 eV) and a temperature-independent component (TG2). With increased stress time and larger current collapse, the time constants for TG2 become progressively longer. The stress-time-dependent behavior of TG2 is shown to be consistent with the capture of trapped carriers in the AlGaN barrier directly by quantum well states, originating from the same defect giving rise to the 0.6 eV behavior. By modulating this alternate recombination pathway, the electric field normal to the AlGaN/GaN interface is shown to have a strong effect on reducing the response time of the trap to several orders of magnitude below its bulk response time. This demonstrates that barrier design may be utilized to tune the recovery characteristics of the HEMT. C1 [Marinella, M. J.; DasGupta, S.; Kaplar, R. J.; Atcitty, S.] Sandia Natl Labs, POB 5800,MS 1084, Albuquerque, NM 87185 USA. [Sun, M.; Palacios, T.] MIT, Cambridge, MA 02139 USA. RP Marinella, MJ (reprint author), Sandia Natl Labs, POB 5800,MS 1084, Albuquerque, NM 87185 USA. FU GaN Initiative for Grid Applications (GIGA); U.S. Department of Energy's Office of Electricity Sandia National Laboratories; U.S. Department of Energy's National Nuclear Security Administration [DE-AC0494AL85000] FX This work was supported by the GaN Initiative for Grid Applications (GIGA) program managed by Dr. G. Bindewald of the U.S. Department of Energy's Office of Electricity Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly-owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC0494AL85000. NR 21 TC 0 Z9 0 U1 1 U2 4 PU ELECTROCHEMICAL SOC INC PI PENNINGTON PA 65 S MAIN ST, PENNINGTON, NJ 08534-2839 USA SN 1938-5862 BN 978-1-60768-449-7; 978-1-62332-095-9 J9 ECS TRANSACTIONS PY 2013 VL 58 IS 4 BP 365 EP 374 DI 10.1149/05804.0365ecst PG 10 WC Electrochemistry; Engineering, Electrical & Electronic; Physics, Applied SC Electrochemistry; Engineering; Physics GA BJO95 UT WOS:000329443400039 ER PT S AU McDaniel, AH Chueh, W Shavorskiy, A Tyliszczak, T Bluhm, H McCarty, KF El Gabaly, F AF McDaniel, Anthony H. Chueh, William Shavorskiy, Andrey Tyliszczak, Tolek Bluhm, Hendrik McCarty, Kevin F. El Gabaly, Farid BE Jackson, G Opila, E Manivanan, A Markus, T Walker, R TI Probing Surface and Bulk States of Cathode Materials With Synchrotron-based Soft X-rays in a Functioning Solid Oxide Fuel Cell SO HIGH TEMPERATURE EXPERIMENTAL TECHNIQUES AND MEASUREMENTS SE ECS Transactions LA English DT Proceedings Paper CT Conference on High Temperature Experimental Techniques and Measurements at the 224th Electrochemical-Society Meeting (ECS) CY OCT 27-NOV 01, 2013 CL San Francisco, CA SP Electrochem Soc, Electrochem Soc, High Temp Mat Div, Electrochem Soc, Energy Technol Div, Electrochem Soc, Phys & Analyt Electrochemistry Div ID ELECTRODES; OXIDATION AB We discuss the development of a research platform designed to investigate surface and bulk properties of electrocatalysts in an operating solid oxide fuel cell using synchrotron-based soft X-ray spectroscopies. This novel platform realizes a fully functioning galvanic cell capable of supporting a Nernst potential, and incorporates both ambient pressure X-ray photoemission and X-ray absorption spectroscopies. Thus, surface compositions, surface electronic states, and bulk electronic states can be measured while manipulating the electrode environment; i.e., varying the gas composition, pressure, temperature, and cell potential. We will demonstrate the utility of this approach by presenting results of an experimental campaign focused on understanding what gives rise to the enhanced oxygen reduction reaction rates observed on a Ba0.5Sr0.5Co0.8Fe0.2O3 perovskite cathode. C1 [McDaniel, Anthony H.; Chueh, William; McCarty, Kevin F.; El Gabaly, Farid] Sandia Natl Labs, Livermore, CA 94551 USA. [Shavorskiy, Andrey; Tyliszczak, Tolek] Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA. [Bluhm, Hendrik] Lawrence Berkeley Natl Lab, Div Chem Sci, Berkeley, CA 94720 USA. RP McDaniel, AH (reprint author), Sandia Natl Labs, Livermore, CA 94551 USA. FU U.S. Department of Energy; Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy [DE-AC02-05CH11231]; Sandia Truman Fellowship; Office of Basic Energy Science; Division of Materials Sciences and Engineering; Lockheed Martin Company, for United States Department of Energy's National Nuclear Security Administration [DE-AC04-94AL85000] FX The research was supported by the U.S. Department of Energy through the Sandia Laboratory Directed research and Development program. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under contract no. DE-AC02-05CH11231. W. C. was supported by an appointment to the Sandia Truman Fellowship. F. E. G. and K. F. M. acknowledge support from the Office of Basic Energy Science, Division of Materials Sciences and Engineering. Sandia is a multi-program laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energys National Nuclear Security Administration under Contract DE-AC04-94AL85000. NR 13 TC 5 Z9 5 U1 0 U2 12 PU ELECTROCHEMICAL SOC INC PI PENNINGTON PA 65 S MAIN ST, PENNINGTON, NJ 08534-2839 USA SN 1938-5862 BN 978-1-60768-448-0; 978-1-62332-094-2 J9 ECS TRANSACTIONS PY 2013 VL 58 IS 3 BP 47 EP 53 DI 10.1149/05803.0047ecst PG 7 WC Electrochemistry SC Electrochemistry GA BJQ49 UT WOS:000329694100005 ER PT S AU Kiss, AM Harris, WM Nakajo, A Wang, S Vila-Comamala, J Deriy, A Chiu, WKS AF Kiss, Andrew M. Harris, William M. Nakajo, Arata Wang, Steve Vila-Comamala, Joan Deriy, Alex Chiu, Wilson K. S. BE Jackson, G Opila, E Manivanan, A Markus, T Walker, R TI Observation of Nickel Oxidation Using Transmission X-ray Microscopy SO HIGH TEMPERATURE EXPERIMENTAL TECHNIQUES AND MEASUREMENTS SE ECS Transactions LA English DT Proceedings Paper CT Conference on High Temperature Experimental Techniques and Measurements at the 224th Electrochemical-Society Meeting (ECS) CY OCT 27-NOV 01, 2013 CL San Francisco, CA SP Electrochem Soc, Electrochem Soc, High Temp Mat Div, Electrochem Soc, Energy Technol Div, Electrochem Soc, Phys & Analyt Electrochemistry Div ID FUEL-CELL ANODES; TRANSPORT PROCESSES; SOFC ANODES; OXIDE; TEMPERATURE; REDUCTION; PARTICLES; KINETICS AB Changes in the microstructure of solid oxide fuel cell electrodes have been known to contribute to performance degradation. One degradation mechanism is the conversion of the nickel to nickel oxide in the anode. This conversion causes a volume increase and can increase stresses in the anode which could lead to performance loss. In order to study the reaction kinetics for nickel oxidation, a full field transmission x-ray microscope was used to image the reaction in situ. The conversion can be monitored based on the optical density of the sample and complete conversion can be confirmed with x-ray absorption near edge spectroscopy. The conversion data is used to calculate reaction rates as a function of temperature and activation energies for the reactions. C1 [Kiss, Andrew M.; Harris, William M.; Nakajo, Arata; Chiu, Wilson K. S.] Univ Connecticut, Dept Mech Engn, Storrs, CT 06269 USA. [Wang, Steve; Vila-Comamala, Joan; Deriy, Alex] Argonne Natl Lab, Adv Photon Source, Argonne, IL 60439 USA. RP Chiu, WKS (reprint author), Univ Connecticut, Dept Mech Engn, Storrs, CT 06269 USA. EM wchiu@engr.uconn.edu RI Vila-Comamala, Joan/E-2106-2017; OI Kiss, Andrew/0000-0002-8515-5508 FU National Science Foundation [CBET- 1134052]; Energy Frontier Research Center on Science Based Nano-Structure Design and Synthesis of Heterogeneous Functional Materials for Energy Systems (HeteroFoaM Center); US Department of Energy, Office of Science; Office of Basic Energy Sciences [DE-SC0001061, DE-AC02-06CH11357] FX Financial support from the National Science Foundation (Award CBET- 1134052) and an Energy Frontier Research Center on Science Based Nano-Structure Design and Synthesis of Heterogeneous Functional Materials for Energy Systems (HeteroFoaM Center) funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences (Award DE-SC0001061) are gratefully acknowledged. Portions of this research were carried out at the Advanced Photon Source supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under contract No. DE-AC02-06CH11357. NR 21 TC 0 Z9 0 U1 1 U2 1 PU ELECTROCHEMICAL SOC INC PI PENNINGTON PA 65 S MAIN ST, PENNINGTON, NJ 08534-2839 USA SN 1938-5862 BN 978-1-60768-448-0; 978-1-62332-094-2 J9 ECS TRANSACTIONS PY 2013 VL 58 IS 3 BP 55 EP 62 DI 10.1149/05803.0055ecst PG 8 WC Electrochemistry SC Electrochemistry GA BJQ49 UT WOS:000329694100006 ER PT J AU Zhang, G Fu, PC Liang, FY AF Zhang, Ga Fu, Pengcheng Liang, Fayun TI Mathematical and Numerical Modeling in Geotechnical Engineering SO JOURNAL OF APPLIED MATHEMATICS LA English DT Editorial Material C1 [Zhang, Ga] Tsinghua Univ, Sch Civil Engn, Beijing 100084, Peoples R China. [Fu, Pengcheng] Lawrence Livermore Natl Lab, Atmospher Earth & Energy Div, Livermore, CA 94550 USA. [Liang, Fayun] Tongji Univ, Coll Civil Engn, Dept Geotech Engn, Shanghai 200092, Peoples R China. RP Zhang, G (reprint author), Tsinghua Univ, Sch Civil Engn, Beijing 100084, Peoples R China. EM zhangga@tsinghua.edu.cn NR 0 TC 0 Z9 0 U1 1 U2 10 PU HINDAWI PUBLISHING CORPORATION PI NEW YORK PA 410 PARK AVENUE, 15TH FLOOR, #287 PMB, NEW YORK, NY 10022 USA SN 1110-757X EI 1687-0042 J9 J APPL MATH JI J. Appl. Math. PY 2013 AR 123485 DI 10.1155/2013/123485 PG 1 WC Mathematics, Applied SC Mathematics GA 290ER UT WOS:000329737000001 ER PT J AU Wachtor, AJ Mocko, V Williams, DJ Goertz, MP Jebrail, FF AF Wachtor, Adam J. Mocko, Veronika Williams, Darrick J. Goertz, Matthew P. Jebrail, Farzaneh F. TI Buoyancy Driven Mixing of Miscible Fluids by Volumetric Energy Deposition of Microwaves SO JOURNAL OF MICROWAVE POWER AND ELECTROMAGNETIC ENERGY LA English DT Article DE Microwaves; Rayleigh-Taylor; unstable stratification; volumetric energy deposition ID RAYLEIGH-TAYLOR INSTABILITY; SMALL ATWOOD NUMBER AB An experiment that seeks to investigate buoyancy driven mixing of miscible fluids by microwave volumetric energy deposition is presented. The experiment involves the use of a light, non-polar fluid that initially rests on top of a heavier fluid which is more polar. Microwaves preferentially heat the polar fluid, and its density decreases due to thermal expansion. As the microwave heating continues, the density of the lower fluid eventually becomes less than that of the upper, and buoyancy driven Rayleigh-Taylor mixing ensues. The choice of fluids is crucial to the success of the experiment, and a description is given of numerous fluid combinations considered and characterized. After careful consideration, the miscible pair of toluene / tetrahydrofuran (THF) was determined as having the best potential for successful volumetric energy deposition buoyancy driven mixing. Various single fluid calibration experiments were performed to facilitate the development of a heating theory. Thereafter, results from two-fluid mixing experiments are presented that demonstrate the capability of this novel Rayleigh-Taylor driven experiment. Particular interest is paid to the onset of buoyancy driven mixing and unusual aspects of the experiment in the context of typical Rayleigh-Taylor driven mixing. C1 [Wachtor, Adam J.; Mocko, Veronika; Williams, Darrick J.; Goertz, Matthew P.; Jebrail, Farzaneh F.] Los Alamos Natl Lab, Los Alamos, NM 87544 USA. RP Wachtor, AJ (reprint author), Los Alamos Natl Lab, POB 1663, Los Alamos, NM 87544 USA. FU U.S. Department of Energy [DE-AC52-06NA25396] FX The authors appreciate the cooperation and coordination of Dr. Sergei Ivanov for use of his CEM Discover microwave and the Center for Integrated Nano-Technologies at Sandia and Los Alamos National Laboratories for the generous use of their facilities and equipment under RA2013A0001: Investigation experiment of buoyancy driven mixing due to volumetric energy deposition of microwaves. Additional thanks are due to Drs. Malcolm J. Andrews and Robert A. Gore for useful discussions and suggestions. This work was supported by the U.S. Department of Energy, subcontract #DE-AC52-06NA25396. NR 13 TC 1 Z9 1 U1 0 U2 1 PU INT MICROWAVE POWER INST PI MECHANICSVILLE PA PO BOX 1140, MECHANICSVILLE, VA 23111 USA SN 0832-7823 J9 J MICROWAVE POWER EE JI J. Microw. Power Electromagn. Energy PY 2013 VL 47 IS 3 BP 210 EP 223 PG 14 WC Engineering, Chemical; Engineering, Electrical & Electronic; Materials Science, Multidisciplinary SC Engineering; Materials Science GA 287WK UT WOS:000329572800006 PM 24779141 ER PT J AU Snyder, J Markovic, NM Stamenkovic, VR AF Snyder, Joshua Markovic, Nenad M. Stamenkovic, Vojislav R. TI Single crystalline thin films as a novel class of electrocatalysts SO JOURNAL OF THE SERBIAN CHEMICAL SOCIETY LA English DT Article DE thin films; magnetron sputtering; Pt-alloys; oxygen reduction reaction ID OXYGEN REDUCTION REACTION; SCANNING-TUNNELING-MICROSCOPY; SULFURIC-ACID-SOLUTION; IN-SITU STM; AU(111) ELECTRODE; HYDROGEN ADSORPTION; SURFACE-MORPHOLOGY; PT(111) ELECTRODES; OXIDE FORMATION; PLATINUM FILMS AB The ubiquitous Use of single crystal metal electrodes has gathered invaluable insight into the relationship between surface atomic structure and functional electrochemical properties. However, the sensitivity of their electrochemical response to surface orientation and the amount of precious metal required can limit their use. Herein, a generally applicable procedure for the production of thin metal films with a large proportion of atomically flat (111) terraces without the use of an epitaxial template is presented. Thermal annealing in a controlled atmosphere induces long-range ordering of magnetron sputtered thin metal films deposited on an amorphous substrate. The ordering transition in these thin metal films yields characteristic (111) electrochemical signatures using a minimal amount of material and provides an adequate replacement for oriented bulk single crystals'. This procedure could be generalized towards a novel class of practical multimetallic thin film-based electrocatalysts with tunable near-surface compositional profiles and morphologies. Annealing of atomically corrugated sputtered thin film Pt-alloy catalysts yields an atomically smooth structure with highly crystalline, (111)-like ordered and Pt segregated surface that displays superior functional properties, bridging the gap between extended/bulk surfaces and nanoscale systems. C1 [Snyder, Joshua; Markovic, Nenad M.; Stamenkovic, Vojislav R.] Argonne Natl Lab, Div Mat Sci, Argonne, IL 60439 USA. RP Stamenkovic, VR (reprint author), Argonne Natl Lab, Div Mat Sci, 9700 S Cass Ave, Argonne, IL 60439 USA. EM vrstamenkovic@anl.gov FU U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences [DE-AC02-06CH11357] FX This work was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. The authors are grateful to Dusan Tripkovic and Arvydas Paulikas (ANL) for support in experimental results obtained by STM, Mark Debe, Radoslav Atanasoski and Dennis van der Vliet (all from 3M) for providing the NSTF catalysts and support in the electrochemical characterizations. NR 63 TC 0 Z9 0 U1 5 U2 34 PU SERBIAN CHEMICAL SOC PI BELGRADE PA KARNEGIJEVA 4, 11 120 BELGRADE, SERBIA SN 0352-5139 J9 J SERB CHEM SOC JI J. Serb. Chem. Soc. PY 2013 VL 78 IS 11 BP 1689 EP 1702 DI 10.2298/JSC130916119S PG 14 WC Chemistry, Multidisciplinary SC Chemistry GA 283RT UT WOS:000329265400006 ER PT J AU Dimitrijevic, NM AF Dimitrijevic, Nada M. TI Investigation of the charge-transfer in photo-excited nanoparticles for CO2 reduction in non-aqueous media SO JOURNAL OF THE SERBIAN CHEMICAL SOCIETY LA English DT Article DE carbon dioxide reduction; photocatalysis; titanium dioxide; cuprous oxide ID ELECTRON-PARAMAGNETIC-RES; CARBON-DIOXIDE; IONIC LIQUIDS; PHOTOCATALYTIC REDUCTION; COLLOIDAL TIO2; NANOCOMPOSITES; ABSORPTION; CONVERSION; CHEMISTRY; FIXATION AB Photo-induced charge separation in TiO2 and Cu2O semiconductor nanoparticles was examined using electron paramagnetic resonance spectroscopy in order to obtain insight into the photocatalytic reduction of CO2 in nonaqueous media. For dissolution/grafting of CO2, carboxy-PEG(4)-amine was used with poly(ethylene glycol) 200 as the solvent. It was found that the reduction of CO2 in this system starts at a potential of 0.5 V vs. Ag/AgCl, which is significantly more positive than the potential for electrochemical reduction of CO2 in most organic solvents and water (-2.0 V vs. Ag/AgCl). The electron transfer from excited nanoparticles to CO2 is governed by both thermodynamic and kinetic parameters, namely by the redox potential of conduction band electrons and adsorption/binding of CO2 on the surface of the nanoparticles. C1 [Dimitrijevic, Nada M.] Argonne Natl Lab, Chem Sci & Engn Div, Argonne, IL 60439 USA. [Dimitrijevic, Nada M.] Argonne Natl Lab, Nrinosci & Technol Div, Argonne, IL 60439 USA. RP Dimitrijevic, NM (reprint author), Argonne Natl Lab, Chem Sci & Engn Div, 9700 S Cass Ave, Argonne, IL 60439 USA. EM Dimitrijevic@anl.gov FU Department of Energy, Office of Science, Office of Basic Energy Sciences [DE-AC02-06CH11357] FX This work was supported by the Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. NR 27 TC 0 Z9 0 U1 6 U2 44 PU SERBIAN CHEMICAL SOC PI BELGRADE PA KARNEGIJEVA 4, 11 120 BELGRADE, SERBIA SN 0352-5139 J9 J SERB CHEM SOC JI J. Serb. Chem. Soc. PY 2013 VL 78 IS 11 BP 1797 EP 1807 DI 10.2298/JSC130726093D PG 11 WC Chemistry, Multidisciplinary SC Chemistry GA 283RT UT WOS:000329265400013 ER PT S AU Lohn, AJ Stevens, JE Mickel, PR Hughart, DR Marinella, MJ AF Lohn, A. J. Stevens, J. E. Mickel, P. R. Hughart, D. R. Marinella, M. J. BE Shingubara, S Karim, Z TI A CMOS Compatible, Forming Free TaOx ReRAM SO NONVOLATILE MEMORIES 2 SE ECS Transactions LA English DT Proceedings Paper CT 2nd Symposium on Nonvolatile Memories held at the 224th Meeting of the Electrochemical-Society CY OCT 30-31, 2013 CL San Francisco, CA SP Electrochem Soc, Electrochem Soc, Dielectr Sci & Technol Div, Electrochem Soc, Elect & Photon Div AB Resistive random access memory (ReRAM) has become a promising candidate for next-generation high-performance nonvolatile memory that operates by electrically tuning resistance states via modulating vacancy concentrations. We demonstrate a wafer-scale process for resistive switching in tantalum oxide that is completely CMOS compatible. The resulting devices are forming-free and with greater than 1x10(5) cycle endurance. C1 [Lohn, A. J.; Stevens, J. E.; Mickel, P. R.; Hughart, D. R.; Marinella, M. J.] Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Lohn, AJ (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87185 USA. EM mmarine@sandia.gov NR 11 TC 13 Z9 13 U1 0 U2 10 PU ELECTROCHEMICAL SOC INC PI PENNINGTON PA 65 S MAIN ST, PENNINGTON, NJ 08534-2839 USA SN 1938-5862 BN 978-1-60768-450-3; 978-1-62332-096-6 J9 ECS TRANSACTIONS PY 2013 VL 58 IS 5 BP 59 EP 65 DI 10.1149/05805.0059ecst PG 7 WC Electrochemistry SC Electrochemistry GA BJQ27 UT WOS:000329646100009 ER PT J AU Sathekge, M Wagener, J Smith, SV Soni, N Marjanovic-Painter, B Zinn, C Van de Wiele, C D'Asseler, Y Perkins, G Zeevaart, JR AF Sathekge, M. Wagener, J. Smith, S. V. Soni, N. Marjanovic-Painter, B. Zinn, C. Van de Wiele, C. D'Asseler, Y. Perkins, G. Zeevaart, J. R. TI Biodistribution and dosimetry of Pt-195m-cisplatin in normal volunteers SO NUKLEARMEDIZIN-NUCLEAR MEDICINE LA English DT Article DE Pt-195m-cisplatin; normal volunteers; biodistribution ID CISPLATIN; METABOLISM; ADDUCTS; CANCER AB Pt-195m-cisplatin is regarded as a promising imaging agent for optimizing dosage in; patients receiving cisplatin chemotherapy. Methods: We investigated the whole-body distribution and radiation dosimetry of Pt-195m-cisplatin in humans. Whole-body scans were obtained up to 144 h after intravenous injection of 112.4 MBq Pt-195m-cisplatin in each of five subjects. Blood samples were taken at various times up to 144 h after injection. Urine was collected up to 114 h after injection for calculation of renal clearance and whole-body Clearance. Time/activity curves were generated by fitting the organ-specific geometric mean counts, obtained from regions of interest, on the respective images as a function of the time after injection. OLINDA software package was applied to calculate the absorbed radiation dose for various organs. Results: Most of the activity (32 +/- 4%) was excreted in the urine during the first 5 h. The effective clearance half-life derived; from extrapolation of the whole-body curve was 40 hours (1.7 days). On average, the highest dose was received by the kidneys (mean dose received 2.68 +/- 1.5 mGy/MB9), followed by the spleen (mean dose received 1.6 +/- 0.8 mGy/MBq) followed by the liver (mean dose received 1.45 +/- 0.38 inGy/MBq). The estimated Mean effective dase for the adult subject was 0.185 +/- 0.034 mSv/MBq. Conclusion: Pt-195m-cisplatin proved a safe radiopharmaceutical with a favourable biodistribution for early and delayed imaging of pathology above the diaphragm. The ED obtained was,0.185 +/- 0.034 mSv/MBq. The highest organ dose was received by the kidneys (2.68 +/- 1.5 mGy/ MBq). C1 [Sathekge, M.; Soni, N.; Zinn, C.] Univ Pretoria, ZA-0001 Pretoria, South Africa. [Sathekge, M.; Soni, N.; Zinn, C.] Steve Biko Acad Hosp, Pretoria, South Africa. [Wagener, J.; Marjanovic-Painter, B.] Necsa, Radiochem, Pretoria, South Africa. [Smith, S. V.; Perkins, G.] ANSTO, Menai, NSW, Australia. [Smith, S. V.] Brookhaven Natl Lab, Upton, NY 11973 USA. [Van de Wiele, C.; D'Asseler, Y.] Univ Hosp Ghent, Dept Nucl Med, Ghent, Belgium. [Zeevaart, J. R.] North West Univ, DST NWU Preclin Drug Dev Platform, Potchefstroom, South Africa. RP Sathekge, M (reprint author), Univ Pretoria, Steve Biko Acad Hosp, Private Bag X169, ZA-0001 Pretoria, South Africa. EM mike.sathekge@up.ac.za NR 25 TC 5 Z9 5 U1 0 U2 11 PU SCHATTAUER GMBH-VERLAG MEDIZIN NATURWISSENSCHAFTEN PI STUTTGART PA HOLDERLINSTRASSE 3, D-70174 STUTTGART, GERMANY SN 0029-5566 J9 NUKLEARMED-NUCL MED JI Nuklearmedizin PY 2013 VL 52 IS 6 BP 222 EP 227 DI 10.3413/Nukmed-0599-13-06 PG 6 WC Radiology, Nuclear Medicine & Medical Imaging SC Radiology, Nuclear Medicine & Medical Imaging GA 287RP UT WOS:000329560200004 PM 24108524 ER PT J AU Haynes, R Shiao, M Liu, KC AF Haynes, R. Shiao, M. Liu, K. C. BE Bakis, CE TI Probabilistic Investigation of Composite Damage Progression and Failure Predictions SO PROCEEDINGS OF THE AMERICAN SOCIETY FOR COMPOSITES LA English DT Proceedings Paper CT 28th Technical Conference of the American-Society-for-Composites CY SEP 09-11, 2013 CL Penn State Univ, Dept Engn Sci & Mech, State College, PA SP Amer Soc Composites HO Penn State Univ, Dept Engn Sci & Mech ID SENSITIVITY-ANALYSIS; SIMULATIONS AB In this work, the uncertainty in progressive failure of a composite is studied. Damage progression and failure of a composite is analyzed deterministically using the Generalized Method of Cells. Monte Carlo simulations are performed to determine the probabilistic distribution of the failure load and associated reliability. A new probabilistic methodology is employed that uses a single set of sample results to conduct a probabilistic sensitivity analysis, which can identify parameters that have significant or negligible influence on failure load. The accuracy of this approach is investigated. The methodology is verified using Monte Carlo simulation. C1 [Haynes, R.; Shiao, M.] US Army Res Lab, 4603 Flare Loop, Aberdeen Proving Ground, MD 21005 USA. [Liu, K. C.] ORISE, Aberdeen Proving Ground, MD 21005 USA. RP Haynes, R (reprint author), US Army Res Lab, 4603 Flare Loop, Aberdeen Proving Ground, MD 21005 USA. NR 12 TC 0 Z9 0 U1 0 U2 1 PU DESTECH PUBLICATIONS, INC PI LANCASTER PA 439 DUKE STREET, LANCASTER, PA 17602-4967 USA BN 978-1-60595-107-2 PY 2013 PG 10 WC Materials Science, Composites SC Materials Science GA BJN63 UT WOS:000329309500051 ER PT J AU Nguyen, BN Kunc, V Jin, X Tucker, CL Costa, F AF Nguyen, B. N. Kunc, V. Jin, X. Tucker, C. L., III Costa, F. BE Bakis, CE TI Injection-Molded Long-Fiber Thermoplastic Composites: From Process Modeling to Prediction of Mechanical Properties SO PROCEEDINGS OF THE AMERICAN SOCIETY FOR COMPOSITES LA English DT Proceedings Paper CT 28th Technical Conference of the American-Society-for-Composites CY SEP 09-11, 2013 CL Penn State Univ, Dept Engn Sci & Mech, State College, PA SP Amer Soc Composites HO Penn State Univ, Dept Engn Sci & Mech ID ELASTIC PROPERTIES; ORIENTATION; SUSPENSIONS AB This article illustrates the predictive capabilities for long-fiber thermoplastic (LFT) composites that first simulate the injection molding of LFT structures by Autodesk (R) Simulation Moldflow (R) Insight (ASMI) to accurately predict fiber orientation and length distributions in these structures. After validating fiber orientation and length predictions against the experimental data, the predicted results are used by ASMI to compute distributions of elastic properties in the molded structures. In addition, local stress-strain responses and damage accumulation under tensile loading are predicted by an elastic-plastic damage model of EMTA-NLA, a nonlinear analysis tool implemented in ABAQUS (R) via user-subroutines using an incremental Eshelby-Mori-Tanaka approach. Predicted stress-strain responses up to failure and damage accumulations are compared to the experimental results to validate the model. C1 [Nguyen, B. N.] Pacific NW Natl Lab, Richland, WA 99352 USA. RP Nguyen, BN (reprint author), Pacific NW Natl Lab, POB 999, Richland, WA 99352 USA. EM ba.nguyen@pnnl.gov RI Kunc, Vlastimil/E-8270-2017 OI Kunc, Vlastimil/0000-0003-4405-7917 NR 28 TC 0 Z9 0 U1 1 U2 11 PU DESTECH PUBLICATIONS, INC PI LANCASTER PA 439 DUKE STREET, LANCASTER, PA 17602-4967 USA BN 978-1-60595-107-2 PY 2013 PG 18 WC Materials Science, Composites SC Materials Science GA BJN63 UT WOS:000329309500029 ER PT J AU Hubbard, SS AF Hubbard, Susan S. BA Revil, A Jardani, A BF Revil, A Jardani, A TI Fundamentals of the self-potential method SO SELF-POTENTIAL METHOD: THEORY AND APPLICATIONS IN ENVIRONMENTAL GEOSCIENCES LA English DT Article; Book Chapter C1 Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Hubbard, SS (reprint author), Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. NR 0 TC 0 Z9 0 U1 0 U2 1 PU CAMBRIDGE UNIV PRESS PI CAMBRIDGE PA THE PITT BUILDING, TRUMPINGTON ST, CAMBRIDGE CB2 1RP, CAMBS, ENGLAND BN 978-1-107-01927-0 PY 2013 BP 1 EP 22 D2 10.1017/CBO9781139094252 PG 22 WC Geochemistry & Geophysics; Geosciences, Multidisciplinary SC Geochemistry & Geophysics; Geology GA BJL25 UT WOS:000328817700003 ER PT J AU Hubbard, SS AF Hubbard, Susan S. BA Revil, A Jardani, A BF Revil, A Jardani, A TI THE SELF-POTENTIAL METHOD Theory and Applications in Environmental Geosciences Foreword SO SELF-POTENTIAL METHOD: THEORY AND APPLICATIONS IN ENVIRONMENTAL GEOSCIENCES LA English DT Editorial Material; Book Chapter C1 Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Hubbard, SS (reprint author), Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. NR 0 TC 0 Z9 0 U1 0 U2 0 PU CAMBRIDGE UNIV PRESS PI CAMBRIDGE PA THE PITT BUILDING, TRUMPINGTON ST, CAMBRIDGE CB2 1RP, CAMBS, ENGLAND BN 978-1-107-01927-0 PY 2013 BP IX EP X D2 10.1017/CBO9781139094252 PG 2 WC Geochemistry & Geophysics; Geosciences, Multidisciplinary SC Geochemistry & Geophysics; Geology GA BJL25 UT WOS:000328817700001 ER PT J AU Hubbard, SS AF Hubbard, Susan S. BA Revil, A Jardani, A BF Revil, A Jardani, A TI THE SELF-POTENTIAL METHOD Theory and Applications in Environmental Geosciences Preface SO SELF-POTENTIAL METHOD: THEORY AND APPLICATIONS IN ENVIRONMENTAL GEOSCIENCES LA English DT Editorial Material; Book Chapter C1 Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Hubbard, SS (reprint author), Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. NR 0 TC 0 Z9 0 U1 0 U2 0 PU CAMBRIDGE UNIV PRESS PI CAMBRIDGE PA THE PITT BUILDING, TRUMPINGTON ST, CAMBRIDGE CB2 1RP, CAMBS, ENGLAND BN 978-1-107-01927-0 PY 2013 BP XI EP + D2 10.1017/CBO9781139094252 PG 23 WC Geochemistry & Geophysics; Geosciences, Multidisciplinary SC Geochemistry & Geophysics; Geology GA BJL25 UT WOS:000328817700002 ER PT J AU Hubbard, SS AF Hubbard, Susan S. BA Revil, A Jardani, A BF Revil, A Jardani, A TI Development of a fundamental theory SO SELF-POTENTIAL METHOD: THEORY AND APPLICATIONS IN ENVIRONMENTAL GEOSCIENCES LA English DT Article; Book Chapter C1 Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Hubbard, SS (reprint author), Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. NR 0 TC 0 Z9 0 U1 0 U2 0 PU CAMBRIDGE UNIV PRESS PI CAMBRIDGE PA THE PITT BUILDING, TRUMPINGTON ST, CAMBRIDGE CB2 1RP, CAMBS, ENGLAND BN 978-1-107-01927-0 PY 2013 BP 23 EP 81 D2 10.1017/CBO9781139094252 PG 59 WC Geochemistry & Geophysics; Geosciences, Multidisciplinary SC Geochemistry & Geophysics; Geology GA BJL25 UT WOS:000328817700004 ER PT J AU Hubbard, SS AF Hubbard, Susan S. BA Revil, A Jardani, A BF Revil, A Jardani, A TI Laboratory investigations SO SELF-POTENTIAL METHOD: THEORY AND APPLICATIONS IN ENVIRONMENTAL GEOSCIENCES LA English DT Article; Book Chapter C1 Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Hubbard, SS (reprint author), Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. NR 0 TC 0 Z9 0 U1 0 U2 0 PU CAMBRIDGE UNIV PRESS PI CAMBRIDGE PA THE PITT BUILDING, TRUMPINGTON ST, CAMBRIDGE CB2 1RP, CAMBS, ENGLAND BN 978-1-107-01927-0 PY 2013 BP 82 EP 109 D2 10.1017/CBO9781139094252 PG 28 WC Geochemistry & Geophysics; Geosciences, Multidisciplinary SC Geochemistry & Geophysics; Geology GA BJL25 UT WOS:000328817700005 ER PT J AU Hubbard, SS AF Hubbard, Susan S. BA Revil, A Jardani, A BF Revil, A Jardani, A TI Forward and inverse modeling SO SELF-POTENTIAL METHOD: THEORY AND APPLICATIONS IN ENVIRONMENTAL GEOSCIENCES LA English DT Article; Book Chapter C1 Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Hubbard, SS (reprint author), Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. NR 0 TC 0 Z9 0 U1 0 U2 0 PU CAMBRIDGE UNIV PRESS PI CAMBRIDGE PA THE PITT BUILDING, TRUMPINGTON ST, CAMBRIDGE CB2 1RP, CAMBS, ENGLAND BN 978-1-107-01927-0 PY 2013 BP 110 EP 153 D2 10.1017/CBO9781139094252 PG 44 WC Geochemistry & Geophysics; Geosciences, Multidisciplinary SC Geochemistry & Geophysics; Geology GA BJL25 UT WOS:000328817700006 ER PT J AU Hubbard, SS AF Hubbard, Susan S. BA Revil, A Jardani, A BF Revil, A Jardani, A TI Applications to geohazards SO SELF-POTENTIAL METHOD: THEORY AND APPLICATIONS IN ENVIRONMENTAL GEOSCIENCES LA English DT Article; Book Chapter C1 Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Hubbard, SS (reprint author), Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. NR 0 TC 0 Z9 0 U1 0 U2 0 PU CAMBRIDGE UNIV PRESS PI CAMBRIDGE PA THE PITT BUILDING, TRUMPINGTON ST, CAMBRIDGE CB2 1RP, CAMBS, ENGLAND BN 978-1-107-01927-0 PY 2013 BP 154 EP 191 D2 10.1017/CBO9781139094252 PG 38 WC Geochemistry & Geophysics; Geosciences, Multidisciplinary SC Geochemistry & Geophysics; Geology GA BJL25 UT WOS:000328817700007 ER PT J AU Hubbard, SS AF Hubbard, Susan S. BA Revil, A Jardani, A BF Revil, A Jardani, A TI Application to water resources SO SELF-POTENTIAL METHOD: THEORY AND APPLICATIONS IN ENVIRONMENTAL GEOSCIENCES LA English DT Article; Book Chapter C1 Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Hubbard, SS (reprint author), Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. NR 0 TC 0 Z9 0 U1 0 U2 0 PU CAMBRIDGE UNIV PRESS PI CAMBRIDGE PA THE PITT BUILDING, TRUMPINGTON ST, CAMBRIDGE CB2 1RP, CAMBS, ENGLAND BN 978-1-107-01927-0 PY 2013 BP 192 EP 244 D2 10.1017/CBO9781139094252 PG 53 WC Geochemistry & Geophysics; Geosciences, Multidisciplinary SC Geochemistry & Geophysics; Geology GA BJL25 UT WOS:000328817700008 ER PT J AU Hubbard, SS AF Hubbard, Susan S. BA Revil, A Jardani, A BF Revil, A Jardani, A TI Application to hydrothermal systems SO SELF-POTENTIAL METHOD: THEORY AND APPLICATIONS IN ENVIRONMENTAL GEOSCIENCES LA English DT Article; Book Chapter C1 Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Hubbard, SS (reprint author), Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. NR 0 TC 0 Z9 0 U1 0 U2 0 PU CAMBRIDGE UNIV PRESS PI CAMBRIDGE PA THE PITT BUILDING, TRUMPINGTON ST, CAMBRIDGE CB2 1RP, CAMBS, ENGLAND BN 978-1-107-01927-0 PY 2013 BP 245 EP 283 D2 10.1017/CBO9781139094252 PG 39 WC Geochemistry & Geophysics; Geosciences, Multidisciplinary SC Geochemistry & Geophysics; Geology GA BJL25 UT WOS:000328817700009 ER PT J AU Hubbard, SS AF Hubbard, Susan S. BA Revil, A Jardani, A BF Revil, A Jardani, A TI Seismoelectric coupling SO SELF-POTENTIAL METHOD: THEORY AND APPLICATIONS IN ENVIRONMENTAL GEOSCIENCES LA English DT Article; Book Chapter C1 Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Hubbard, SS (reprint author), Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. NR 0 TC 0 Z9 0 U1 0 U2 0 PU CAMBRIDGE UNIV PRESS PI CAMBRIDGE PA THE PITT BUILDING, TRUMPINGTON ST, CAMBRIDGE CB2 1RP, CAMBS, ENGLAND BN 978-1-107-01927-0 PY 2013 BP 284 EP 341 D2 10.1017/CBO9781139094252 PG 58 WC Geochemistry & Geophysics; Geosciences, Multidisciplinary SC Geochemistry & Geophysics; Geology GA BJL25 UT WOS:000328817700010 ER PT J AU Roach, D AF Roach, D. BE Chang, FK TI Validation and Verification Processes to Certify SHM Solutions for Commercial Aircraft Applications SO STRUCTURAL HEALTH MONITORING 2013, VOLS 1 AND 2 LA English DT Proceedings Paper CT 9th International Workshop on Structural Health Monitoring (IWSHM) CY SEP 10-12, 2013 CL Stanford Univ, Stanford, CA SP AF Off Sci Res, Army Res Lab, Off Naval Res, Boeing, Airbus, Embraer HO Stanford Univ AB Reliable Structural Health Monitoring (SHM) systems can automatically process data, assess structural condition and signal the need for human intervention. While ad-hoc efforts to introduce SHM into routine aircraft maintenance practices are valuable in leading the way for more widespread SHM use, there is a significant need for formal SHM technology validation and certification processes to uniformly and comprehensively support the evolution and adoption of SHM practices. Such a plan must contain input from aircraft manufacturers, regulators, operators and research organizations so that the full spectrum of issues including design, deployment, performance and certification is appropriately considered. Currently, there are no guidelines for SHM system designers or agreed-upon procedures for assessing the performance of SHM systems. Through the operation of the FAA's Airworthiness Assurance Nondestructive Inspection Validation Center (AANC), the FAA secured its mission to provide independent validation of technologies intended to enhance the structural inspection of aircraft. A natural extension of this mission is to incorporate SHM in these validation efforts. The AANC's validation approach is designed to address the equipment, the inspection task, the resolution required, the inspection procedures, the conditions under which the inspection will occur, and the potential inspector population. To carry out the validation process, knowledge of aircraft maintenance practices must be coupled with an unbiased, independent evaluation. The AANC has designed, implemented, and analyzed the results from a wide range of statistically-relevant experimental programs to quantify the reliability of inspection methods as deployed at commercial aircraft maintenance facilities. Much of this methodology to quantify NDI performance can be adapted to the validation of SHM systems. However, it is important to recognize the unique validation and verification tasks that arise from distinct differences between SHM and NDI deployment and flaw detection. An important element in developing SHM validation processes is a clear understanding of the regulatory measures needed to adopt SHM solutions along with the knowledge of the structural and maintenance characteristics that may impact the operational performance of an SHM system C1 Sandia Natl Labs, FAA Airworthiness Assurance Ctr, Albuquerque, NM 87185 USA. RP Roach, D (reprint author), Sandia Natl Labs, FAA Airworthiness Assurance Ctr, Box 5800, Albuquerque, NM 87185 USA. NR 9 TC 0 Z9 0 U1 0 U2 0 PU DESTECH PUBLICATIONS, INC PI LANCASTER PA 439 DUKE STREET, LANCASTER, PA 17602-4967 USA BN 978-1-60595-115-7 PY 2013 BP 519 EP 527 PG 9 WC Engineering, Civil; Engineering, Mechanical SC Engineering GA BJN59 UT WOS:000329292700063 ER PT J AU Taylor, SG Raby, EY Park, G Farinholt, KM Todd, MD AF Taylor, S. G. Raby, E. Y. Park, G. Farinholt, K. M. Todd, M. D. BE Chang, FK TI Wireless Active Sensing Platform for Structural Infrastructure Monitoring SO STRUCTURAL HEALTH MONITORING 2013, VOLS 1 AND 2 LA English DT Proceedings Paper CT 9th International Workshop on Structural Health Monitoring (IWSHM) CY SEP 10-12, 2013 CL Stanford Univ, Stanford, CA SP AF Off Sci Res, Army Res Lab, Off Naval Res, Boeing, Airbus, Embraer HO Stanford Univ AB Embedded sensing for structural health monitoring (SHM) is a rapidly expanding field, propelled by algorithmic advances in SHM and the ever-shrinking size and cost of electronic hardware necessary for its implementation. Although commercial systems are available to perform the relevant tasks, they are usually bulky and/or expensive because of their high degree of general utility to a wider range of applications. As a result, multiple separate devices may be required in order to obtain the same results that could be obtained with an SHM-specific device. This work presents the development and deployment of a versatile, wireless active sensing platform (WASP), designed for the particular needs of embedded sensing for multiscale SHM. The WASP combines the conventional data acquisition ability to record voltage output (e.g. from strain or acceleration transducers) with ultrasonic guided wave-based active sensing, and a seamlessly integrated impedance measurement mode, enabling impedance-based SHM and piezoelectric sensor diagnostics to reduce the potential for false positives in damage identification. The unique combination of sensing modalities makes the WASP an excellent new platform for embedded SHM. The motivation, capabilities, and hardware design for the WASP are reviewed, and deployment examples are presented, each demonstrating an important aspect of embedded sensing for SHM. C1 [Taylor, S. G.; Raby, E. Y.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Taylor, SG (reprint author), Los Alamos Natl Lab, Los Alamos, NM 87545 USA. NR 21 TC 0 Z9 0 U1 0 U2 1 PU DESTECH PUBLICATIONS, INC PI LANCASTER PA 439 DUKE STREET, LANCASTER, PA 17602-4967 USA BN 978-1-60595-115-7 PY 2013 BP 561 EP 568 PG 8 WC Engineering, Civil; Engineering, Mechanical SC Engineering GA BJN59 UT WOS:000329292700068 ER PT J AU Mascarenas, D Choi, Y Kim, HC Pekedis, M Yildiz, H Plont, CA Brown, C Cowell, M Park, G Hahn, H Lee, JR Farrar, C AF Mascarenas, D. Choi, Y. Kim, H. C. Pekedis, M. Yildiz, H. Plont, C. A. Brown, C. Cowell, M. Park, G. Hahn, H. Lee, J. -R. Farrar, C. BE Chang, FK TI A Vibro-Haptic Human-Machine Interface for Structural Health Monitoring SO STRUCTURAL HEALTH MONITORING 2013, VOLS 1 AND 2 LA English DT Proceedings Paper CT 9th International Workshop on Structural Health Monitoring (IWSHM) CY SEP 10-12, 2013 CL Stanford Univ, Stanford, CA SP AF Off Sci Res, Army Res Lab, Off Naval Res, Boeing, Airbus, Embraer HO Stanford Univ AB The goal of the structural health monitoring (SHM) community has been to endow physical systems with a nervous system not unlike those commonly found in living organisms. Typically the SHM community has attempted to do this by instrumenting structures with a variety of sensors, and then applying various signal processing and classification procedures to the data in order to detect the presence of damage, the location of damage, the severity of damage, and to estimate the remaining useful life of the structure. This procedure has had some success, but we are still a long ways from achieving the performance of the nervous systems found in biology. Primarily because contemporary classification algorithms do not have the performance required. In many cases expert judgment is superior to automated classification. This work introduces a new paradigm. Instead of trying to build a nervous system from scratch, we propose interfacing the human nervous system to the distributed sensor network located on the structure and developing new techniques to enable human-machine cooperation. Results from the field of sensor substitution suggest this should be possible. Sensor substitution is a process by which a human can partially regain the use of a lost sense using a different sense as a surrogate. The plasticity of the human brain allows the human to interpret the stimuli to the alternative sense as coming from the original sense that was lost. Recent advances in smart structures haptic technology have enabled a wide range of new human-machine interfaces to facilitate sensory substitution. Examples of these interfaces include force feedback for robotic applications, refreshable Braille displays, and prosthesis devices. Thus far, haptic devices have mainly been limited to physical applications. It is possible that haptic devices may allow humans a new interface to interact with abstract entities such as the data from a wireless sensor network, the topography of a high dimensional cost function, or the structural health of a wind farm. This study investigates vibro-haptic human-machine interfaces for SHM. The investigation was performed using a surrogate three-story structure. The structure features three nonlinearity-inducing bumpers to simulate damage. Accelerometers are placed on each floor to measure the response of the structure to a harmonic base excitation. The accelerometer measurements are preprocessed using Principal Component Analysis (PCA) via Singular Value Decomposition (SVD) and the fast Fourier transform. The preprocessed data is then encoded as a vibro-tactile stimulus. Human subjects will be subjected to the vibro-tactile stimulus and asked to characterize the damage in the structure. C1 [Mascarenas, D.; Choi, Y.; Kim, H. C.; Pekedis, M.; Yildiz, H.; Plont, C. A.; Brown, C.; Cowell, M.; Park, G.; Hahn, H.; Lee, J. -R.; Farrar, C.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Mascarenas, D (reprint author), Los Alamos Natl Lab, POB 1663,MS T001, Los Alamos, NM 87545 USA. NR 9 TC 2 Z9 2 U1 0 U2 1 PU DESTECH PUBLICATIONS, INC PI LANCASTER PA 439 DUKE STREET, LANCASTER, PA 17602-4967 USA BN 978-1-60595-115-7 PY 2013 BP 1171 EP 1178 PG 8 WC Engineering, Civil; Engineering, Mechanical SC Engineering GA BJN59 UT WOS:000329292700143 ER PT J AU Flynn, EB Jarmer, GS AF Flynn, E. B. Jarmer, G. S. BE Chang, FK TI High-Speed, Non-Contact, Baseline-Free Imaging of Hidden Defects Using Scanning Laser Measurements of Steady-State Ultrasonic Vibration SO STRUCTURAL HEALTH MONITORING 2013, VOLS 1 AND 2 LA English DT Proceedings Paper CT 9th International Workshop on Structural Health Monitoring (IWSHM) CY SEP 10-12, 2013 CL Stanford Univ, Stanford, CA SP AF Off Sci Res, Army Res Lab, Off Naval Res, Boeing, Airbus, Embraer HO Stanford Univ AB We present an approach to visualize damage through rapid, full-field measurements of a plate-like structure's steady-state response to a single-tone ultrasonic excitation. In our setup, a piezoelectric transducer provides the excitation while a 2D scanning laser Doppler vibrometer (LDV) makes the full-field response measurement. In taking measurements of a structure's relatively high amplitude single-tone steady-state response, we enable significantly faster scans by avoiding many of the signal-to-noise ratio issues typically associated with LDV ultrasonic measurements. Damage is visualized by making automated estimates, on a pixel-by-pixel basis, of the wavenumber of the excited response through wavenumber-domain processing. We provide sample imaging results for hidden corrosion spots in a metallic plate and delamination in two composite specimens. C1 [Flynn, E. B.; Jarmer, G. S.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Flynn, EB (reprint author), Los Alamos Natl Lab, MS T001, Los Alamos, NM 87545 USA. NR 5 TC 3 Z9 3 U1 0 U2 2 PU DESTECH PUBLICATIONS, INC PI LANCASTER PA 439 DUKE STREET, LANCASTER, PA 17602-4967 USA BN 978-1-60595-115-7 PY 2013 BP 1186 EP 1193 PG 8 WC Engineering, Civil; Engineering, Mechanical SC Engineering GA BJN59 UT WOS:000329292700145 ER PT S AU Wiens, RC AF Wiens, Roger C. BE MacEwen, HA Breckinridge, JB TI Zapping Rocks on Mars: Exploring the Red Planet with Curiosity and its Laser (Presentation Video) SO UV/OPTICAL/IR SPACE TELESCOPES AND INSTRUMENTS: INNOVATIVE TECHNOLOGIES AND CONCEPTS VI SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on UV/Optical/IR Space Telescopes and Instruments - Innovative Technologies and Concepts VI CY AUG 25-26, 2013 CL San Diego, CA SP SPIE C1 Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Wiens, RC (reprint author), Los Alamos Natl Lab, Los Alamos, NM 87545 USA. NR 0 TC 0 Z9 0 U1 0 U2 1 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9710-9 J9 PROC SPIE PY 2013 VL 8860 AR 88601E DI 10.1117/12.2050969 PG 1 WC Engineering, Aerospace; Instruments & Instrumentation; Optics SC Engineering; Instruments & Instrumentation; Optics GA BIA02 UT WOS:000327125100034 ER PT S AU Cai, ZH Liu, WJ Tischler, JZ Shu, DM Xu, RQ Schmidt, O AF Cai, Zhonghou Liu, Wenjun Tischler, Jonathan Z. Shu, Deming Xu, Ruqing Schmidt, Oliver BE Lai, B TI Preliminary design of a zone plate based hard X-ray monochromatic diffraction nanoprobe for materials studies at APS SO X-RAY NANOIMAGING: INSTRUMENTS AND METHODS SE Proceedings of SPIE LA English DT Proceedings Paper CT SPIE X-ray Nanoimaging Conference - Instruments and Methods CY AUG 28-29, 2013 CL San Diego, CA SP SPIE DE Hard X-ray microscopy; X-ray diffraction nanoprobe AB Aiming at studies of the micro/nano-structures of a broad range materials and electronic devices, Advance Photon Source (APS) is developing a dedicated diffraction nanoprobe (DNP) beamline for the needs arising from a multidiscipline research community. As a part of the APS Upgrade Project, the planed facility, named Sub-micron 3-D Diffraction (S3DD) beamline(1), integrates the K-B mirror based polychromatic Laue diffraction and the Fresnel zone-plate based monochromatic diffraction techniques that currently support 3D/2D microdiffraction programs at the 34-ID-E and 2-ID-D of the APS, respectively. Both diffraction nanoprobes are designed to have a 50-nm or better special resolution. The zone-plate based monochromatic DNP has been preliminarily designed and will be constructed at the sector 34-ID. It uses an APS-3.0-cm period or APS-3.3-cm period undulator, a liquid-nitrogen cooled mirror as its first optics, and a water cooled small gap silicon double-crystal monochromator with an energy range of 5-30 keV. A set of zone plates have been designed to optimize for focusing efficiency and the working distance based on the attainable beamline length and the beam coherence. To ensure the nanoprobe performance, high stiffness and high precision flexure stage systems have been designed or demonstrated for optics mounting and sample scanning, and high precision temperature control of the experimental station will be implemented to reduce thermal instability. Designed nanoprobe beamline has a good management on thermal power loading on optical components and allows high degree of the preservation of beam brilliance for high focal flux and coherence. Integrated with variety of X-ray techniques, planed facility provides nano-XRD capability with the maximum reciprocal space accessibility and allows micro/nano-spectroscopy studies with K-edge electron binding energies of most elements down to Vanadium in the periodic table. We will discuss the preliminary design of the zone-plate based monochromatic DNP and its technical relevance to a broad range of scientific applications. C1 [Cai, Zhonghou; Liu, Wenjun; Tischler, Jonathan Z.; Shu, Deming; Xu, Ruqing; Schmidt, Oliver] Argonne Natl Lab, Adv Photon Source, Argonne, IL 60439 USA. RP Cai, ZH (reprint author), Argonne Natl Lab, Adv Photon Source, Argonne, IL 60439 USA. RI Xu, Ruqing/K-3586-2012 OI Xu, Ruqing/0000-0003-1037-0059 NR 18 TC 0 Z9 0 U1 0 U2 6 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9701-7 J9 PROC SPIE PY 2013 VL 8851 AR 88510M DI 10.1117/12.2025900 PG 6 WC Nanoscience & Nanotechnology; Optics; Imaging Science & Photographic Technology SC Science & Technology - Other Topics; Optics; Imaging Science & Photographic Technology GA BJQ07 UT WOS:000329578700014 ER PT S AU Chen, B Abbey, B Balaur, E van Riessen, G Junker, M Jones, MWM Peele, AG Putkunz, CT Vine, D Quiney, HM Nugent, KA AF Chen, Bo Abbey, Brian Balaur, Eugeniu van Riessen, Grant Junker, Mark Jones, Michael W. M. Peele, Andrew G. Putkunz, Corey T. Vine, David Quiney, Harry M. Nugent, Keith A. BE Lai, B TI A Universal Measure for Coherence Requirements in Diffractive Imaging SO X-RAY NANOIMAGING: INSTRUMENTS AND METHODS SE Proceedings of SPIE LA English DT Proceedings Paper CT SPIE X-ray Nanoimaging Conference - Instruments and Methods CY AUG 28-29, 2013 CL San Diego, CA SP SPIE DE coherent diffraction imaging; X-ray; partial coherence AB The requirements on the spatial and temporal coherence for conventional Coherent Diffractive Imaging (CDI) have been well-established in the literature based on Shannon sampling of the diffracted intensities. The spatial coherence length of the illumination must be larger than twice the lateral dimensions of the sample whilst the temporal coherence length must be larger than the maximum optical path length difference between the two edges of the sample for the highest order diffraction peaks. However, recent approaches to CDI which have included knowledge of the spatial and temporal coherence information in the image reconstruction have allowed us to relax these conventional coherence constraints, extending the applicability of the technique to less coherent sources. In light of these developments it is useful to revisit the idea of a coherence limit in partially coherent CDI and establish a 'universal' limit on the partial coherence that can be tolerated without any loss of information. In this paper we present a simple and straightforward description of the limit of spatial and temporal coherence in partially coherent CDI. C1 [Chen, Bo; Abbey, Brian; Balaur, Eugeniu; van Riessen, Grant; Junker, Mark; Jones, Michael W. M.; Peele, Andrew G.; Nugent, Keith A.] La Trobe Univ, Dept Phys, ARC Ctr Excellence Coherent Xray Sci CXS, Bundoora, Vic 3083, Australia. [Putkunz, Corey T.; Quiney, Harry M.] Univ Melbourne, ARC Ctr Excellence Coherent Xray Sci CXS, Sch Phys, Melbourne, Vic 3010, Australia. [Peele, Andrew G.] Australian Synchrotron, Clayton, Vic 3168, Australia. [Vine, David] Argonne Natl Lab, Adv Photon Source, Argonne, IL 60439 USA. RP Chen, B (reprint author), La Trobe Univ, Dept Phys, ARC Ctr Excellence Coherent Xray Sci CXS, Bundoora, Vic 3083, Australia. EM b.abbey@latrobe.edu.au RI Abbey, Brian/D-3274-2011; van Riessen, Grant/H-3840-2011; Nugent, Keith/I-4154-2016; Balaur, Eugeniu/J-5865-2016 OI Jones, Michael/0000-0002-0720-8715; Abbey, Brian/0000-0001-6504-0503; van Riessen, Grant/0000-0002-6240-7143; Nugent, Keith/0000-0002-4281-3478; Balaur, Eugeniu/0000-0003-4029-2055 FU Australian Reseach Council Centre of Excellence for Coherent X-ray Science; US Department of Energy; Office of Science; Office of Basic Energy Sciences [DE-AC02-06CH11357] FX The authors acknowledge the support of the Australian Reseach Council Centre of Excellence for Coherent X-ray Science. Use of the Advanced Photon Source was supported by the US Department of Energy, Office of Science,Office of Basic Energy Sciences(contract no. DEAC0206CH11357). NR 17 TC 1 Z9 1 U1 0 U2 8 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9701-7 J9 PROC SPIE PY 2013 VL 8851 AR UNSP 88510T DI 10.1117/12.2027269 PG 7 WC Nanoscience & Nanotechnology; Optics; Imaging Science & Photographic Technology SC Science & Technology - Other Topics; Optics; Imaging Science & Photographic Technology GA BJQ07 UT WOS:000329578700017 ER PT S AU Chen, S Yuan, Y Deng, JJ Mak, R Jin, QL Paunesku, T Gleber, SC Vine, D Flachenecker, C Hornberger, B Shu, DM Lai, B Maser, J Finney, L Roehrig, C VonOsinski, J Bolbat, M Brister, K Jacobsen, C Woloschak, G Vogt, S AF Chen, Si Yuan, Ye Deng, Junjing Mak, Rachel Jin, Qiaoling Paunesku, Tatjana Gleber, Sophie C. Vine, David Flachenecker, Claus Hornberger, Benjamin Shu, Deming Lai, Barry Maser, Joerg Finney, Lydia Roehrig, Christian VonOsinski, Jay Bolbat, Michael Brister, Keith Jacobsen, Chris Woloschak, Gayle Vogt, Stefan BE Lai, B TI Sub-100-nm 3D-elemental mapping of frozen-hydrated cells using the Bionanoprobe SO X-RAY NANOIMAGING: INSTRUMENTS AND METHODS SE Proceedings of SPIE LA English DT Proceedings Paper CT SPIE X-ray Nanoimaging Conference - Instruments and Methods CY AUG 28-29, 2013 CL San Diego, CA SP SPIE DE hard X-ray fluorescence microscopy; the Bionanoprobe; cryogenic capabilities; tomography ID NANOPROBE BEAMLINE; ZONE PLATES; MICROSCOPY AB Hard X-ray fluorescence microscopy is one of the most sensitive techniques to perform trace elemental analysis of unsectioned biological samples, such as cells and tissues. As the spatial resolution increases beyond sub-micron scale, conventional sample preparation method, which involves dehydration, may not be sufficient for preserving subcellular structures in the context of radiation-induced artifacts. Imaging of frozen-hydrated samples under cryogenic conditions is the only reliable way to fully preserve the three dimensional structures of the samples while minimizing the loss of diffusible ions. To allow imaging under this hydrated "natural-state" condition, we have developed the Bionanoprobe (BNP), a hard X-ray fluorescence nanoprobe with cryogenic capabilities, dedicated to studying trace elements in frozen-hydrated biological systems. The BNP is installed at an undulator beamline at Life Sciences Collaboration Access Team at the Advanced Photon Source. It provides a spatial resolution of 30 nm for fluorescence imaging by using Fresnel zone plates as nanofocusing optics. Differential phase contrast imaging is carried out in parallel to fluorescence imaging by using a quadrant photodiode mounted downstream of the sample. By employing a liquid-nitrogen-cooled sample stage and cryo specimen transfer mechanism, the samples are well maintained below 110 K during both transfer and X-ray imaging. The BNP is capable for automated tomographic dataset collection, which enables visualization of internal structures and composition of samples in a nondestructive manner. In this presentation, we will describe the instrument design principles, quantify instrument performance, and report the early results that were obtained from frozen-hydrated whole cells. C1 [Chen, Si; Gleber, Sophie C.; Vine, David; Shu, Deming; Lai, Barry; Maser, Joerg; Finney, Lydia; Roehrig, Christian; Jacobsen, Chris; Vogt, Stefan] Argonne Natl Lab, Adv Photon Source, Xray Sci Div, Argonne, IL 60439 USA. [Yuan, Ye; Paunesku, Tatjana] Northwestern Univ, Dept Radiat Oncol, Chicago, IL 60611 USA. [Deng, Junjing] Northwestern Univ, Appl Phys, Evanston, IL 60208 USA. [Mak, Rachel; Jin, Qiaoling] Northwestern Univ, Dept Phys & Astron, Evanston, IL 60208 USA. [Flachenecker, Claus; Hornberger, Benjamin] Carl Zeiss X Ray Microscop Inc, Pleasanton, CA 94588 USA. [VonOsinski, Jay; Bolbat, Michael; Brister, Keith] Northwestern Synchrotron Res Ctr, Argonne, IL 60439 USA. RP Chen, S (reprint author), Argonne Natl Lab, Adv Photon Source, Xray Sci Div, Argonne, IL 60439 USA. EM sichen@aps.anl.gov RI Jacobsen, Chris/E-2827-2015; Paunesku, Tatjana/A-3488-2017; Woloschak, Gayle/A-3799-2017 OI Jacobsen, Chris/0000-0001-8562-0353; Paunesku, Tatjana/0000-0001-8698-2938; Woloschak, Gayle/0000-0001-9209-8954 FU NIH/NCRR High End Instrumentation (HEI) [1S10RR029272- 01]; Argonne National Laboratory [2010-183-N0]; NIH [2 R01 GM064846-05]; U.S. DOE [DE-AC02-06CH11357]; [2010-193-N0] FX This research was made possible by ARRA: NIH/NCRR High End Instrumentation (HEI) grant (1S10RR029272- 01). We thank Argonne National Laboratory for support under Laboratory Directed Research and Development programs 2010-183-N0 for cryogenic X-ray microscope development and 2010-193-N0 for cryogenic sample preparation facility development, as well as NIH grant 2 R01 GM064846-05 for some of the cryogenic sample preparation equipment used. Use of the Advanced Photon Source, an Office of Science User Facility operated for the U.S. Department of Energy (DOE) Office of Science by Argonne National Laboratory, was supported by the U.S. DOE under Contract No. DE-AC02-06CH11357. NR 16 TC 0 Z9 0 U1 0 U2 8 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9701-7 J9 PROC SPIE PY 2013 VL 8851 AR UNSP 885102 DI 10.1117/12.2025169 PG 7 WC Nanoscience & Nanotechnology; Optics; Imaging Science & Photographic Technology SC Science & Technology - Other Topics; Optics; Imaging Science & Photographic Technology GA BJQ07 UT WOS:000329578700002 ER PT S AU Chen-Wiegart, YCK Wang, JJ Wang, J AF Chen-Wiegart, Yu-chen Karen Wang, Jiajun Wang, Jun BE Lai, B TI Development of In situ Full Field Spectroscopic Imaging Analysis and Application on Li-ion Battery using Transmission X-ray Microscopy SO X-RAY NANOIMAGING: INSTRUMENTS AND METHODS SE Proceedings of SPIE LA English DT Proceedings Paper CT SPIE X-ray Nanoimaging Conference - Instruments and Methods CY AUG 28-29, 2013 CL San Diego, CA SP SPIE DE Transmission X-ray Microscopy; TXM; Spectroscopic Imaging; XANES imaging; battery ID NANO-TOMOGRAPHY; NANOPOROUS GOLD; EVOLUTION AB This paper presents the advance in spectroscopic imaging technique and analysis method from the newly developed transmission x-ray microscopy (TXM) at the beamline X8C of National Synchrotron Light Source. Through leastsquares linear combination fitting we developed on the in situ spectroscopic images, a time-dependent and spatially resolved chemical composition mapping can be obtained and quantitatively analyzed undergone chemical/ electrochemical reactions. A correlation of morphological evolution, chemical state distribution changes and reaction conditions can be revealed. We successfully applied this method to study the electrochemical evolution of CuO, an anode material of Li-ion battery, during the lithiation-delitiation cycling. C1 [Chen-Wiegart, Yu-chen Karen; Wang, Jiajun; Wang, Jun] Brookhaven Natl Lab, Photon Sci Directorate, Upton, NY 11973 USA. RP Chen-Wiegart, YCK (reprint author), Brookhaven Natl Lab, Photon Sci Directorate, 744 Ring Rd, Upton, NY 11973 USA. EM junwang@bnl.gov RI wang, jiajun/H-3315-2012; wang, jiajun/H-5683-2016 NR 8 TC 1 Z9 1 U1 5 U2 8 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9701-7 J9 PROC SPIE PY 2013 VL 8851 AR 88510C DI 10.1117/12.2027095 PG 5 WC Nanoscience & Nanotechnology; Optics; Imaging Science & Photographic Technology SC Science & Technology - Other Topics; Optics; Imaging Science & Photographic Technology GA BJQ07 UT WOS:000329578700009 ER PT S AU Eng, C Chen-Wiegart, YCK Wang, J AF Eng, Christopher Chen-Wiegart, Yu-chen K. Wang, Jun BE Lai, B TI Development of in-line furnace for in situ nanoscale resolution x-ray microscopy SO X-RAY NANOIMAGING: INSTRUMENTS AND METHODS SE Proceedings of SPIE LA English DT Proceedings Paper CT SPIE X-ray Nanoimaging Conference - Instruments and Methods CY AUG 28-29, 2013 CL San Diego, CA SP SPIE DE in situ; energy storage materials; transmission x-ray microscopy; high resolution; full field TXM; environmental cell; furnace; morphological evolution; nanoscale; reactor AB Full field transmission x-ray microscopy (TXM) is a newly developed x-ray imaging technique to provide quantitative and non-destructive 3D characterization of the complex microstructure of materials at nanometer resolution. A key missing component is an in situ apparatus enabling the imaging of the complex structural evolution of the materials and to correlate the structural change with a material's functionality under real operating conditions. This work describes the design of an environmental cell which satisfies the requirements for in situ TXM studies. The limited space within the TXM presents a spatial constraint which prohibits the use of conventional heaters, as well as requiring consideration in designing for safe and controlled operation of the system and alignment of the cell with the beam. A gravity drip-fed water cooling jacket was installed in place around the heating module to maintain critical components of the microscope at safe operating temperatures. A motion control system consisting of pulse width modulated DC motor driven XYZ translation stages was developed to facilitate fine alignment of the cell. Temperature of the sample can be controlled remotely and accurately through a controller to temperatures as high as 1200 K. Heating zone measurement was carried out and shows a 500 x 500 x 500 mu m3 homogeneous zone volume for sample area, which is a critical parameter to ensure accurate observation of structural evolution at nanometer scale with a sample in size of tens of microns. Application on Ni particles for in situ oxidation experiment and dehydrogenation of aluminum hydride is also discussed. C1 [Eng, Christopher; Chen-Wiegart, Yu-chen K.; Wang, Jun] Brookhaven Natl Lab, Upton, NY 11973 USA. RP Eng, C (reprint author), Brookhaven Natl Lab, Upton, NY 11973 USA. NR 10 TC 0 Z9 0 U1 1 U2 3 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9701-7 J9 PROC SPIE PY 2013 VL 8851 AR 88510D DI 10.1117/12.2025842 PG 7 WC Nanoscience & Nanotechnology; Optics; Imaging Science & Photographic Technology SC Science & Technology - Other Topics; Optics; Imaging Science & Photographic Technology GA BJQ07 UT WOS:000329578700010 ER PT S AU Maser, J Lai, B Buonassisi, T Cai, ZH Chen, S Finney, L Gleber, SC Harder, R Jacobsen, C Liu, WJ Murray, C Preissner, C Roehrig, C Rose, V Shu, DM Vine, D Vogt, S AF Maser, Joerg Lai, Barry Buonassisi, Tonio Cai, Zhonghou Chen, Si Finney, Lydia Gleber, Sophie-Charlotte Harder, Ross Jacobsen, Chris Liu, Wenjun Murray, Conal Preissner, Curt Roehrig, Chris Rose, Volker Shu, Deming Vine, David Vogt, Stefan BE Lai, B TI A Next-Generation In-Situ Nanoprobe Beamline for the Advanced Photon Source SO X-RAY NANOIMAGING: INSTRUMENTS AND METHODS SE Proceedings of SPIE LA English DT Proceedings Paper CT SPIE X-ray Nanoimaging Conference - Instruments and Methods CY AUG 28-29, 2013 CL San Diego, CA SP SPIE DE x-ray; nanofocusing; x-ray nanoprobe; energy science; materials science; x-ray optics ID ZONE PLATES; MICROSCOPY; DIFFRACTION; OPTICS AB The Advanced Photon Source is currently developing a suite of new hard x-ray beamlines, aimed primarily at the study of materials and devices under real conditions. One of the flagship beamlines of the APS Upgrade is the In-Situ Nanoprobe beamline (ISN beamline), which will provide in-situ and operando characterization of advanced energy materials and devices under change of temperature and gases, under applied fields, in 3D. The ISN beamline is designed to deliver spatially coherent x-rays with photon energies between 4 keV and 30 keV to the ISN instrument. As an x-ray source, a revolver-type undulator with two interchangeable magnetic structures, optimized to provide high brilliance throughout the range of photon energies of 4 keV - 30 keV, will be used. The ISN instrument will provide a smallest hard x-ray spot of 20 nm using diffractive optics, with sensitivity to sub-10 nm sample structures using coherent diffraction. Using nanofocusing mirrors in Kirkpatrick-Baez geometry, the ISN will also provide a focus of 50 nm with a flux of 8.10(11) Photons/s at a photon energy of 10 keV, several orders of magnitude larger than what is currently available. This will allow imaging of trace amounts of most elements in the periodic table, with a sensitivity to well below 100 atoms for most metals in thin samples. It will also enable nanospectroscopic studies of the chemical state of most materials relevant to energy science. The ISN beamline will be primarily used to study inorganic and organic photovoltaic systems, advanced batteries and fuel cells, nanoelectronics devices, and materials and systems designed to reduce the environmental impact of combustion. C1 [Maser, Joerg; Lai, Barry; Cai, Zhonghou; Chen, Si; Finney, Lydia; Gleber, Sophie-Charlotte; Harder, Ross; Jacobsen, Chris; Liu, Wenjun; Preissner, Curt; Roehrig, Chris; Rose, Volker; Shu, Deming; Vine, David; Vogt, Stefan] Argonne Natl Lab, 9700 S Cass Ave, Argonne, IL 60439 USA. [Buonassisi, Tonio] MIT, Cambridge, MA 02139 USA. [Murray, Conal] IBM TJ Watson Res Ctr, Yorktown Hts, NY USA. RP Maser, J (reprint author), Argonne Natl Lab, 9700 S Cass Ave, Argonne, IL 60439 USA. RI Rose, Volker/B-1103-2008; Jacobsen, Chris/E-2827-2015 OI Rose, Volker/0000-0002-9027-1052; Jacobsen, Chris/0000-0001-8562-0353 FU U.S. Department of Energy SunShot Initiative [DE-EE0005314, DE-EE0005329, DE-EE0005948]; US Department of Energy; Office of Science; Office of Basic Energy Sciences [DE-AC02-06CH11357] FX T.B.acknowledges funding from U.S. Department of Energy SunShot Initiative under Contracts No.DE-EE0005314, DE-EE0005329, and DE-EE0005948.Use of the Advanced Photon Source (APS) at Argonne National Laboratory was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02- 06CH11357. NR 18 TC 2 Z9 2 U1 1 U2 7 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9701-7 J9 PROC SPIE PY 2013 VL 8851 AR UNSP 885106 DI 10.1117/12.2026418 PG 6 WC Nanoscience & Nanotechnology; Optics; Imaging Science & Photographic Technology SC Science & Technology - Other Topics; Optics; Imaging Science & Photographic Technology GA BJQ07 UT WOS:000329578700004 ER PT S AU Ryan, CG Siddons, DP Kirkham, R Li, ZY de Jonge, MD Paterson, D Cleverley, JS Kuczewski, A Dunn, PA Jensen, M De Geronimo, G Howard, DL Godel, B Dyl, KA Fisher, LA Hough, RH Barnes, SJ Bland, PA Moorhead, G James, SA Spiers, KM Falkenberg, G Boesenberg, U Wellenreuther, G AF Ryan, C. G. Siddons, D. P. Kirkham, R. Li, Z. Y. de Jonge, M. D. Paterson, D. Cleverley, J. S. Kuczewski, A. Dunn, P. A. Jensen, M. De Geronimo, G. Howard, D. L. Godel, B. Dyl, K. A. Fisher, L. A. Hough, R. H. Barnes, S. J. Bland, P. A. Moorhead, G. James, S. A. Spiers, K. M. Falkenberg, G. Boesenberg, U. Wellenreuther, G. BE Lai, B TI The Maia detector array and X-ray fluorescence imaging system: Locating rare precious metal phases in complex samples SO X-RAY NANOIMAGING: INSTRUMENTS AND METHODS SE Proceedings of SPIE LA English DT Proceedings Paper CT SPIE X-ray Nanoimaging Conference - Instruments and Methods CY AUG 28-29, 2013 CL San Diego, CA SP SPIE DE Maia detector; X-ray fluorescence microscopy; synchrotron X-ray fluorescence; real-time element imaging; quantitative SXRF analysis; depth mapping; platinum group minerals; Allende meteorite ID QUANTITATIVE PIXE MICROANALYSIS; NUCLEAR MICROPROBE; PROTON MICROPROBE; SYNCHROTRON; SPECIATION; COWPEA; ROOTS; MICROSCOPY; AUSTRALIA; GENESIS AB X-ray fluorescence images acquired using the Maia large solid-angle detector array and integrated real-time processor on the X-ray Fluorescence Microscopy (XFM) beamline at the Australian Synchrotron capture fine detail in complex natural samples with images beyond 100M pixels. Quantitative methods permit real-time display of deconvoluted element images and for the acquisition of large area XFM images and 3D datasets for fluorescence tomography and chemical state (XANES) imaging. This paper outlines the Maia system and analytical methods and describes the use of the large detector array, with a wide range of X-ray take-off angles, to provide sensitivity to the depth of features, which is used to provide an imaging depth contrast and to determine the depth of rare precious metal particles in complex geological samples. C1 [Ryan, C. G.; Cleverley, J. S.; Godel, B.; Dyl, K. A.; Fisher, L. A.; Hough, R. H.; Barnes, S. J.] CSIRO Earth Sci & Resource Engn, 26 Dick Perry Ave, Kensington, WA 6151, Australia. [Siddons, D. P.; Li, Z. Y.; Kuczewski, A.; De Geronimo, G.] Brookhaven Natl Lab, Upton, NY USA. [Dunn, P. A.; Jensen, M.; Moorhead, G.] CISRO Mat Sci & Engn, Clayton, Vic 3168, Australia. [de Jonge, M. D.; Paterson, D.; Howard, D. L.; James, S. A.; Spiers, K. M.] Australian Synchrotron, Clayton, Vic, Australia. [Falkenberg, G.; Boesenberg, U.; Wellenreuther, G.] HASYLAB, DESY, D-22603 Hamburg, Germany. [Dyl, K. A.; Bland, P. A.] Curtin Univ, Dept Appl Geol, Perth, WA 6845, Australia. RP Ryan, CG (reprint author), CSIRO Earth Sci & Resource Engn, 26 Dick Perry Ave, Kensington, WA 6151, Australia. EM chris.ryan@csiro.au RI Kirkham, Robin/C-9786-2010; Moorhead, Gareth/B-6634-2009; James, Simon/J-5320-2012 OI Kirkham, Robin/0000-0003-1012-3496; Moorhead, Gareth/0000-0002-9299-9549; James, Simon/0000-0001-9369-3288 NR 45 TC 7 Z9 7 U1 0 U2 12 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9701-7 J9 PROC SPIE PY 2013 VL 8851 AR UNSP 88510Q DI 10.1117/12.2027195 PG 11 WC Nanoscience & Nanotechnology; Optics; Imaging Science & Photographic Technology SC Science & Technology - Other Topics; Optics; Imaging Science & Photographic Technology GA BJQ07 UT WOS:000329578700016 ER PT S AU Ahmed, S Bokhari, SH Khan, LA Amin, F Hussain, Z AF Ahmed, S. Bokhari, S. H. Khan, L. A. Amin, F. Hussain, Z. BE Syed, AS TI Parallel Planar-Processed and Ion-Induced Electrically Isolated Future Generation AlGaN/GaN HEMT for Gas Sensing and Opto-Telecommunication Applications SO 1ST INTERNATIONAL CONFERENCE ON SENSING FOR INDUSTRY, CONTROL, COMMUNICATIONS, & SECURITY TECHNOLOGIES (ICSICCST 2013) SE IOP Conference Series-Materials Science and Engineering LA English DT Proceedings Paper CT 1st International Conference on Sensing for Industry, Control, Communications, and Security Technologies (ICSICCST) CY JUN 24-26, 2013 CL Indus Univ, Karachi, PAKISTAN SP Univ Karachi, H E J Res Inst Chem, Ctr Emerging Sci, Engn & Technol, Inst Phys, Natl ICT R & D Fund, Al Riaz Green Syst, Hilton Pharma Ltd HO Indus Univ ID IRRADIATION; LAYERS; INGAASN; GAAS AB Ion-implanted AlGaN/GaN High Electron Mobility Transistors (HEMT) devices were studied thoroughly to look into the possibilities of enhancing efficiency for high-power and high-frequency electronic and gas sensing applications. A dedicated experimental design was created in order to study the influence of the physical parameters in response to high energy (by virtue of in-situ beam heating due to highly energetic implantation) ion implantation to the active device regions in nitride HEMT structures. Disorder or damage created in the HEMT structure was then studied carefully with electrical characterization techniques such as Hall, I-V and G-V measurements. The evolution of the electrical characteristics affecting the high-power, high-frequency and ultra-high efficiency gas sensing operations were also analyzed by subjecting the HEMT active device regions to progressive time-temperature annealing cycles. Our suggested model can also provide a functional process engineering window to control the extent of 2D Electron mobility in AlGaN/GaN HEMT devices undergoing a full cycle of thermal impact (i.e. from a desirable conductive region to a highly compensated one). C1 [Ahmed, S.; Bokhari, S. H.; Amin, F.] Int Islamic Univ, Fac Engn & Technol, Adv Elect Lab, Islamabad 44000, Pakistan. [Ahmed, S.; Khan, L. A.; Amin, F.] Ctr Emerging Sci Engn & Technol, Islamabad 44000, Pakistan. [Hussain, Z.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Ahmed, S (reprint author), Int Islamic Univ, Fac Engn & Technol, Adv Elect Lab, Islamabad 44000, Pakistan. EM ahmed.shuja@iiu.edu.pk NR 20 TC 0 Z9 0 U1 2 U2 5 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1757-8981 J9 IOP CONF SER-MAT SCI PY 2013 VL 51 AR UNSP 012008 DI 10.1088/1757-899X/51/1/012008 PG 10 WC Automation & Control Systems; Engineering, Electrical & Electronic; Materials Science, Multidisciplinary; Telecommunications SC Automation & Control Systems; Engineering; Materials Science; Telecommunications GA BJO20 UT WOS:000329345300008 ER PT S AU Walker, SI Callahan, BJ Arya, G Barry, JD Bhattacharya, T Grigoryev, S Pellegrini, M Rippe, K Rosenberg, SM AF Walker, Sara Imari Callahan, Benjamin J. Arya, Gaurav Barry, J. David Bhattacharya, Tanmoy Grigoryev, Sergei Pellegrini, Matteo Rippe, Karsten Rosenberg, Susan M. GP New York Acad Sci TI Evolutionary dynamics and information hierarchies in biological systems SO CONFERENCE REPORTS: EVOLUTIONARY DYNAMICS AND INFORMATION HIERARCHIES IN BIOLOGICAL SYSTEMS: ASPEN CENTER FOR PHYSICS WORKSHOP AND CRACKING THE NEURAL CODE: THIRD ANNUAL ASPEN BRAIN FORUMS SE Annals of the New York Academy of Sciences LA English DT Article; Proceedings Paper CT Workshop on Evolutionary Dynamics and Information Hierarchies in Biological Systems CY AUG 19-SEP 09, 2012 CL Aspen Ctr Phys, Aspen, CO HO Aspen Ctr Phys DE evolution; information hierarchy; chromatin; epigenetics; viruses; networks ID IMMUNODEFICIENCY-VIRUS TYPE-1; STRAND-BREAK REPAIR; TRYPANOSOMA-BRUCEI; ANTIGENIC VARIATION; DNA BREAKS; CHROMATIN ORGANIZATION; ESCHERICHIA-COLI; MUTAGENIC REPAIR; IN-VIVO; MUTATION AB The study of evolution has entered a revolutionary new era, where quantitative and predictive methods are transforming the traditionally qualitative and retrospective approaches of the past. Genomic sequencing and modern computational techniques are permitting quantitative comparisons between variation in the natural world and predictions rooted in neo-Darwinian theory, revealing the shortcomings of current evolutionary theory, particularly with regard to large-scale phenomena like macroevolution. Current research spanning and uniting diverse fields and exploring the physical and chemical nature of organisms across temporal, spatial, and organizational scales is replacing the model of evolution as a passive filter selecting for random changes at the nucleotide level with a paradigm in which evolution is a dynamic process both constrained and driven by the informational architecture of organisms across scales, from DNA and chromatin regulation to interactions within and between species and the environment. C1 [Walker, Sara Imari] Arizona State Univ, BEYOND Ctr Fundamental Concepts Sci, Tempe, AZ USA. [Walker, Sara Imari] Blue Marble Space Inst Sci, Seattle, WA USA. [Callahan, Benjamin J.] Stanford Univ, Dept Appl Phys, Stanford, CA 94305 USA. [Arya, Gaurav] Univ Calif San Diego, Dept NanoEngn, La Jolla, CA 92093 USA. [Barry, J. David] Univ Glasgow, Wellcome Trust Ctr Mol Parasitol, Inst Infect Immun & Inflammat, Glasgow, Lanark, Scotland. [Bhattacharya, Tanmoy] Sante Fe Inst, Santa Fe, NM USA. [Bhattacharya, Tanmoy] Los Alamos Natl Lab, Grp T 2, Los Alamos, NM USA. [Grigoryev, Sergei] Penn State Univ, Coll Med, Dept Biochem & Mol Biol, Hershey, PA USA. [Pellegrini, Matteo] Univ Calif Los Angeles, Dept Mol Cell & Dev Biol, Los Angeles, CA USA. [Rippe, Karsten] Deutsch Krebsforschungszentrum DKFZ, Heidelberg, Germany. [Rippe, Karsten] BioQuant, Res Grp Genome Org & Funct, Heidelberg, Germany. [Rosenberg, Susan M.] Baylor Coll Med, Dept Mol & Human Genet, Houston, TX 77030 USA. [Rosenberg, Susan M.] Baylor Coll Med, Dept Biochem & Mol Biol, Houston, TX 77030 USA. [Rosenberg, Susan M.] Baylor Coll Med, Dept Mol Virol & Microbiol, Houston, TX 77030 USA. [Rosenberg, Susan M.] Baylor Coll Med, Dan L Duncan Canc Ctr, Houston, TX 77030 USA. RP Walker, SI (reprint author), BEYOND Ctr Fundamental Concepts Sci, POB 871504, Tempe, AZ 85287 USA. EM sara.i.walker@asu.edu RI Rippe, Karsten/A-3562-2012; Walker, Sara/J-5829-2015; Bhattacharya, Tanmoy/J-8956-2013 OI Rippe, Karsten/0000-0001-9951-9395; Walker, Sara/0000-0001-5779-2772; Bhattacharya, Tanmoy/0000-0002-1060-652X FU National Science Foundation [PHY-1066293] FX The Evolutionary Dynamics and Information Hierarchies workshop was held on August 19-September 9, 2012 at the Aspen Center for Physics in Aspen, CO. The authors wish to thank the hospitality of the Aspen Center for Physics for hosting the workshop, which was supported in part by the National Science Foundation under Grant no. PHY-1066293. The workshop was organized by Gyan Bhanot (Rutgers University), Lynn Caporale (St. John's University), Sebastian Doniach (Stanford University), Alexandre Morozov (Rutgers University), and Matteo Pellegrini (University of California, Los Angeles). NR 66 TC 2 Z9 2 U1 2 U2 13 PU BLACKWELL SCIENCE PUBL PI OXFORD PA OSNEY MEAD, OXFORD OX2 0EL, ENGLAND SN 0077-8923 J9 ANN NY ACAD SCI JI Ann.NY Acad.Sci. PY 2013 VL 1305 BP 1 EP 17 DI 10.1111/nyas.12140 PG 17 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA BJQ04 UT WOS:000329568700001 PM 23691975 ER PT J AU Percival, CJ Welz, O Eskola, AJ Savee, JD Osborn, DL Topping, DO Lowe, D Utembe, SR Bacak, A McFiggans, G Cooke, MC Xiao, P Archibald, AT Jenkin, ME Derwent, RG Riipinen, I Mok, DWK Lee, EPF Dyke, JM Taatjes, CA Shallcross, DE AF Percival, Carl J. Welz, Oliver Eskola, Arkke J. Savee, John D. Osborn, David L. Topping, David O. Lowe, Douglas Utembe, Steven R. Bacak, Asan McFiggans, Gordon Cooke, Michael C. Xiao, Ping Archibald, Alexander T. Jenkin, Michael E. Derwent, Richard G. Riipinen, Ilona Mok, Daniel W. K. Lee, Edmond P. F. Dyke, John M. Taatjes, Craig A. Shallcross, Dudley E. TI Regional and global impacts of Criegee intermediates on atmospheric sulphuric acid concentrations and first steps of aerosol formation SO FARADAY DISCUSSIONS LA English DT Article ID SECONDARY ORGANIC AEROSOL; GAS-PHASE OZONOLYSIS; TORCH 2003 CAMPAIGN; PARTICLE FORMATION; CRI MECHANISM; SOUTHERN UK; TROPOSPHERIC OZONE; BETA-PINENE; MODEL; NUCLEATION AB Carbonyl oxides ("Criegee intermediates"), formed in the ozonolysis of alkenes, are key species in tropospheric oxidation of organic molecules and their decomposition provides a non-photolytic source of OH in the atmosphere (Johnson and Marston, Chem. Soc. Rev., 2008, 37, 699, Harrison et al., Sci. Total Environ., 2006, 360, 5, Gab et al., Nature, 1985, 316, 535, ref. 1-3). Recently it was shown that small Criegee intermediates, C.I.'s, react far more rapidly with SO2 than typically represented in tropospheric models, (Welz, Science, 2012, 335, 204, ref. 4) which suggested that carbonyl oxides could have a substantial influence on the atmospheric oxidation of SO2. Oxidation of SO2 is the main atmospheric source of sulphuric acid (H2SO4), which is a critical contributor to aerosol formation, although questions remain about the fundamental nucleation mechanism (Sipila et al., Science, 2010, 327, 1243, Metzger et al., Proc. Natl. Acad. Sci. U. S. A., 2010 107, 6646, Kirkby et al., Nature, 2011, 476, 429, ref. 5-7). Non-absorbing atmospheric aerosols, by scattering incoming solar radiation and acting as cloud condensation nuclei, have a cooling effect on climate (Intergovernmental Panel on Climate Change (IPCC), Climate Change 2007: The Physical Science Basis, Cambridge University Press, 2007, ref. 8). Here we explore the effect of the Criegees on atmospheric chemistry, and demonstrate that ozonolysis of alkenes via the reaction of Criegee intermediates potentially has a large impact on atmospheric sulphuric acid concentrations and consequently the first steps in aerosol production. Reactions of Criegee intermediates with SO2 will compete with and in places dominate over the reaction of OH with SO2 (the only other known gas-phase source of H2SO4) in many areas of the Earth's surface. In the case that the products of Criegee intermediate reactions predominantly result in H2SO4 formation, modelled particle nucleation rates can be substantially increased by the improved experimentally obtained estimates of the rate coefficients of Criegee intermediate reactions. Using both regional and global scale modelling, we show that this enhancement is likely to be highly variable spatially with local hot-spots in e. g. urban outflows. This conclusion is however contingent on a number of remaining uncertainties in Criegee intermediate chemistry. C1 [Percival, Carl J.; Topping, David O.; Lowe, Douglas; Utembe, Steven R.; Bacak, Asan; McFiggans, Gordon] Univ Manchester, Sch Earth Atmospher & Environm Sci, Ctr Atmospher Sci, Manchester M13 9PL, Lancs, England. [Welz, Oliver; Eskola, Arkke J.; Savee, John D.; Osborn, David L.; Taatjes, Craig A.] Sandia Natl Labs, Combust Res Facil, Livermore, CA 94551 USA. [Cooke, Michael C.; Xiao, Ping; Archibald, Alexander T.; Jenkin, Michael E.; Shallcross, Dudley E.] Univ Bristol, Sch Chem, Biogeochem Res Ctr, Bristol BS8 1TS, Avon, England. [Jenkin, Michael E.] Atmospher Chem Serv, Okehampton EX20 1FB, Devon, England. [Derwent, Richard G.] Rdscientific, Newbury, Berks, England. [Riipinen, Ilona] Univ Stockholm, Dept Appl Environm Sci, Stockholm, Sweden. [Mok, Daniel W. K.; Lee, Edmond P. F.] Hong Kong Polytech Univ, Dept Appl Biol & Chem Technol, Hong Kong, Hong Kong, Peoples R China. [Lee, Edmond P. F.; Dyke, John M.] Univ Southampton, Sch Chem, Southampton SO17 1BJ, Hants, England. RP Percival, CJ (reprint author), Univ Manchester, Sch Earth Atmospher & Environm Sci, Ctr Atmospher Sci, Simon Bldg,Brunswick St, Manchester M13 9PL, Lancs, England. EM c.percival@manchester.ac.uk; d.e.shallcross@bristol.ac.uk RI Riipinen, Ilona/I-9379-2012; Welz, Oliver/C-1165-2013; McFiggans, Gordon/B-8689-2011; Utembe, Steven/C-4713-2016; Topping, David/B-8643-2011; OI Welz, Oliver/0000-0003-1978-2412; McFiggans, Gordon/0000-0002-3423-7896; Utembe, Steven/0000-0002-2741-3142; Topping, David/0000-0001-8247-9649; Archibald, Alexander/0000-0001-9302-4180; percival, carl/0000-0003-2525-160X; Derwent, Richard/0000-0003-4498-645X; Mok, Daniel Kam-Wah/0000-0002-6677-2949 FU Division of Chemical Sciences, Geosciences, and Biosciences, the Office of Basic Energy Sciences; U.S. Department of Energy; Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy [DE-AC02-05CH11231]; National Nuclear Security Administration [DE-AC04-94-AL85000]; Research Grant Council (RGC) of the Hong Kong Special Administrative Region (HKSAR) [Polyu 5019/11P] FX The participation of OW, AJE, JDS, DLO, and CAT are funded by the Division of Chemical Sciences, Geosciences, and Biosciences, the Office of Basic Energy Sciences, the U.S. Department of Energy. DES, JMD, GMcF and CJP thank NERC for funding. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U. S. Department of Energy under Contract DE-AC02-05CH11231 at Lawrence Berkeley National Laboratory. Sandia is a multi-program laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the National Nuclear Security Administration under contract DE-AC04-94-AL85000. DKWM, JMD, CJP and EPFL acknowledge support from the Research Grant Council (RGC) of the Hong Kong Special Administrative Region (HKSAR, Grant No Polyu 5019/11P). NR 95 TC 29 Z9 29 U1 8 U2 80 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1359-6640 EI 1364-5498 J9 FARADAY DISCUSS JI Faraday Discuss. PY 2013 VL 165 BP 45 EP 73 DI 10.1039/c3fd00048f PG 29 WC Chemistry, Physical SC Chemistry GA 280ZF UT WOS:000329068600003 PM 24600996 ER PT J AU Nguyen, TB Laskin, A Laskin, J Nizkorodov, SA AF Nguyen, Tran B. Laskin, Alexander Laskin, Julia Nizkorodov, Sergey A. TI Brown carbon formation from ketoaldehydes of biogenic monoterpenes SO FARADAY DISCUSSIONS LA English DT Article ID GAS-PHASE OZONOLYSIS; POLYCYCLIC AROMATIC-HYDROCARBONS; RESOLUTION MASS-SPECTROMETRY; CONTAINING ORGANIC-COMPOUNDS; SULFURIC-ACID-SOLUTIONS; AQUEOUS AEROSOL MIMICS; DIELS-ALDER REACTION; LIGHT-ABSORPTION; OXIDATIVE CLEAVAGE; REACTION-PRODUCTS AB Sources and chemical composition of brown carbon are poorly understood, and even less is known about the mechanisms of its atmospheric transformations. This work presents molecular-level investigations of the reactive compound ketolimononaldehyde (KLA, C9H14O3), a second-generation ozonolysis product of limonene (C10H16), as a potent brown carbon precursor in secondary organic aerosol (SOA) through its reactions with reduced nitrogen compounds, such as ammonium ion (NH4+), ammonia, and amino acids. The reactions of synthesized and purified KLA with NH4+ and glycine resulted in the formation of chromophores nearly identical in spectral properties and formation rates to those found in similarly-aged limonene/O-3 SOA. Similar chemical reaction processes of limononaldehyde (LA, C10H16O2) and pinonaldehyde (PA, C10H16O2), the first-generation ozonolysis products of limonene and a-pinene, respectively, were also studied, but the resulting products did not exhibit the light absorption properties of brown carbon, suggesting that the unique molecular structure of KLA produces visiblelight- absorbing compounds. The KLA/NH4+ and KLA/GLY reactions produce watersoluble, hydrolysis-resilient chromophores with high mass absorption coefficients (MAC = 2000-4000 cm(2) g(-1)) at lambda similar to 500 nm, precisely at the maximum of the solar emission spectrum. Liquid chromatography was used to isolate the light-absorbing fraction, and UV-Vis, FTIR, NMR and high-resolution mass spectrometry (HR-MS) techniques were used to investigate the structures and chemical properties of the light-absorbing compounds. The KLA browning reaction generates a diverse mixture of light-absorbing compounds, with the majority of the observable products containing 1-4 units of KLA and 0-2 nitrogen atoms. Based on the HR-MS product distribution, conjugated aldol condensates, secondary imines (Schiff bases), and N-heterocycles like pyrroles may contribute in varying degree to the light-absorbing properties of the KLA brown carbon. The results of this study demonstrate the high degree of selectivity of organic compound structures on the light-absorbing properties of SOA. C1 [Nguyen, Tran B.; Nizkorodov, Sergey A.] Univ Calif Irvine, Dept Chem, Irvine, CA 92697 USA. [Laskin, Alexander] Pacific NW Natl Lab, Environm Mol Sci Lab, Richland, WA 99352 USA. [Laskin, Julia] Pacific NW Natl Lab, Phys Sci Div, Richland, WA 99352 USA. RP Nguyen, TB (reprint author), CALTECH, Div Geol & Planetary Sci, Pasadena, CA 91125 USA. EM tbn@calech.edu RI Laskin, Julia/H-9974-2012; Laskin, Alexander/I-2574-2012; Nizkorodov, Sergey/I-4120-2014 OI Laskin, Julia/0000-0002-4533-9644; Laskin, Alexander/0000-0002-7836-8417; Nizkorodov, Sergey/0000-0003-0891-0052 FU NSF [CHE-0909227, AGS-1227579]; UCI for the Chancellors Club fellowship; US DOE by Battelle Memorial Institute [DE-AC06-76RL0 1830] FX The authors would also like to thank the following people for helpful discussions: Dr John DeLorbe, Dr Phil Dennison, Dr Hyun Ji (Julie) Lee, Dr Jiri Misek, Dr Theresa McIntire, Dr John Greaves, Prof. Richard Chamberlain, and Prof. James Nowick. The UCI group acknowledges support by the NSF grants CHE-0909227 and AGS-1227579. TBN thanks UCI for the Chancellors Club fellowship. The PNNL group acknowledges support from the Chemical Sciences Division (JL), Office of Basic Energy Sciences of the U. S. DOE, and the W. R. Wiley Environmental Molecular Sciences Laboratory (EMSL) -a national scientific user facility located at PNNL, and sponsored by the Office of Biological and Environmental Research of the U. S. PNNL is operated for US DOE by Battelle Memorial Institute under Contract No. DE-AC06-76RL0 1830. NR 83 TC 24 Z9 25 U1 6 U2 74 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1359-6640 EI 1364-5498 J9 FARADAY DISCUSS JI Faraday Discuss. PY 2013 VL 165 BP 473 EP 494 DI 10.1039/c3fd00036b PG 22 WC Chemistry, Physical SC Chemistry GA 280ZF UT WOS:000329068600025 PM 24601018 ER PT J AU Daemen, A Griffith, OL Heiser, LM Wang, NJ Enache, OM Sanborn, Z Pepin, F Durinck, S Korkola, JE Griffith, M Hur, JS Huh, N Chung, J Cope, L Fackler, MJ Umbricht, C Sukumar, S Seth, P Sukhatme, VP Jakkula, LR Lu, YL Mills, GB Cho, RJ Collisson, EA van't Veer, LJ Spellman, PT Gray, JW AF Daemen, Anneleen Griffith, Obi L. Heiser, Laura M. Wang, Nicholas J. Enache, Oana M. Sanborn, Zachary Pepin, Francois Durinck, Steffen Korkola, James E. Griffith, Malachi Hur, Joe S. Huh, Nam Chung, Jongsuk Cope, Leslie Fackler, Mary Jo Umbricht, Christopher Sukumar, Saraswati Seth, Pankaj Sukhatme, Vikas P. Jakkula, Lakshmi R. Lu, Yiling Mills, Gordon B. Cho, Raymond J. Collisson, Eric A. van't Veer, Laura J. Spellman, Paul T. Gray, Joe W. TI Modeling precision treatment of breast cancer SO GENOME BIOLOGY LA English DT Article ID DRUG-SENSITIVITY; NEOADJUVANT CHEMOTHERAPY; MOLECULAR SUBTYPES; PHASE-II; PREDICTION; INHIBITORS; MUTATIONS; RESPONSES; CELLS; CHEMOSENSITIVITY AB Background: First-generation molecular profiles for human breast cancers have enabled the identification of features that can predict therapeutic response; however, little is known about how the various data types can best be combined to yield optimal predictors. Collections of breast cancer cell lines mirror many aspects of breast cancer molecular pathobiology, and measurements of their omic and biological therapeutic responses are well-suited for development of strategies to identify the most predictive molecular feature sets. Results: We used least squares-support vector machines and random forest algorithms to identify molecular features associated with responses of a collection of 70 breast cancer cell lines to 90 experimental or approved therapeutic agents. The datasets analyzed included measurements of copy number aberrations, mutations, gene and isoform expression, promoter methylation and protein expression. Transcriptional subtype contributed strongly to response predictors for 25% of compounds, and adding other molecular data types improved prediction for 65%. No single molecular dataset consistently out-performed the others, suggesting that therapeutic response is mediated at multiple levels in the genome. Response predictors were developed and applied to TCGA data, and were found to be present in subsets of those patient samples. Conclusions: These results suggest that matching patients to treatments based on transcriptional subtype will improve response rates, and inclusion of additional features from other profiling data types may provide additional benefit. Further, we suggest a systems biology strategy for guiding clinical trials so that patient cohorts most likely to respond to new therapies may be more efficiently identified. C1 [Daemen, Anneleen; Griffith, Obi L.; Heiser, Laura M.; Wang, Nicholas J.; Enache, Oana M.; Pepin, Francois; Durinck, Steffen; Korkola, James E.; Jakkula, Lakshmi R.; Collisson, Eric A.; Spellman, Paul T.; Gray, Joe W.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Life Sci, Dept Canc & DNA Damage Responses, Berkeley, CA 94720 USA. [Daemen, Anneleen; Collisson, Eric A.; van't Veer, Laura J.] Univ Calif San Francisco, San Francisco, CA 94115 USA. [Griffith, Obi L.; Spellman, Paul T.] Oregon Hlth & Sci Univ, Dept Mol & Med Genet, Portland, OR 97239 USA. [Heiser, Laura M.; Wang, Nicholas J.; Korkola, James E.; Gray, Joe W.] Oregon Hlth & Sci Univ, Knight Canc Inst, Ctr Spatial Syst Biomed, Dept Biomed Engn, Portland, OR 97239 USA. [Sanborn, Zachary] Five3 Genom, Santa Cruz, CA 95060 USA. [Griffith, Obi L.; Griffith, Malachi] Washington Univ, Sch Med, Genome Inst, St Louis, MO 63105 USA. [Hur, Joe S.] Samsung Elect Headquarters, Seoul 137857, South Korea. [Huh, Nam; Chung, Jongsuk] Samsung Adv Inst Technol, Emerging Technol Res Ctr, Kyonggi Do 446712, South Korea. [Cope, Leslie; Fackler, Mary Jo; Umbricht, Christopher; Sukumar, Saraswati] Johns Hopkins Univ, Sch Med, Dept Oncol, Baltimore, MD 21205 USA. [Seth, Pankaj; Sukhatme, Vikas P.] Harvard Univ, Beth Israel Deaconess Med Ctr, Sch Med, Dept Med, Boston, MA 02215 USA. [Lu, Yiling; Mills, Gordon B.] Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Houston, TX 77030 USA. [Cho, Raymond J.] Univ Calif San Francisco, Dept Dermatol, San Francisco, CA 94115 USA. RP Daemen, A (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Life Sci, Dept Canc & DNA Damage Responses, Berkeley, CA 94720 USA. EM daemena@gene.com; ogriffit@genome.wustl.edu; grayjo@ohsu.edu OI Griffith, Obi/0000-0002-0843-4271 FU Director, Office of Science, Office of Biological and Environmental Research, of the US Department of Energy [DE-AC02-05CH11231]; National Institutes of Health, National Cancer Institute [P50 CA 58207, U54 CA 112970, CA 126551]; GSK [SU2C-AACR-DT0409]; Pfizer Corporation; Prospect Creek Foundation FX We thank Michael Kellen, Brian Bot, and Steven Friend at Sage Bionetworks for their assistance in porting the R Toolbox into Synapse. This work was supported by the Director, Office of Science, Office of Biological and Environmental Research, of the US Department of Energy under contract number DE-AC02-05CH11231; by the National Institutes of Health, National Cancer Institute grants P50 CA 58207 (LJV, JWG), U54 CA 112970, CA 126551, the SU2C-AACR-DT0409 and research grants from GSK, Pfizer Corporation and Prospect Creek Foundation grants to JWG. The content of the information does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred. NR 37 TC 50 Z9 50 U1 2 U2 8 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1465-6906 EI 1474-760X J9 GENOME BIOL JI Genome Biol. PY 2013 VL 14 IS 10 AR R110 DI 10.1186/gb-2013-14-10-r110 PG 14 WC Biotechnology & Applied Microbiology; Genetics & Heredity SC Biotechnology & Applied Microbiology; Genetics & Heredity GA 285IN UT WOS:000329387500003 PM 24176112 ER PT J AU Brioude, J Arnold, D Stohl, A Cassiani, M Morton, D Seibert, P Angevine, W Evan, S Dingwell, A Fast, JD Easter, RC Pisso, I Burkhart, J Wotawa, G AF Brioude, J. Arnold, D. Stohl, A. Cassiani, M. Morton, D. Seibert, P. Angevine, W. Evan, S. Dingwell, A. Fast, J. D. Easter, R. C. Pisso, I. Burkhart, J. Wotawa, G. TI The Lagrangian particle dispersion model FLEXPART-WRF version 3.1 SO GEOSCIENTIFIC MODEL DEVELOPMENT LA English DT Article ID ATMOSPHERIC DISPERSION; NUMBER GENERATOR; FREE TROPOSPHERE; FOREST-FIRES; STILT MODEL; TRANSPORT; EMISSIONS; MESOSCALE; CAMPAIGN; PLUME AB The Lagrangian particle dispersion model FLEXPART was originally designed for calculating long-range and mesoscale dispersion of air pollutants from point sources, such that occurring after an accident in a nuclear power plant. In the meantime, FLEXPART has evolved into a comprehensive tool for atmospheric transport modeling and analysis at different scales. A need for further multiscale modeling and analysis has encouraged new developments in FLEXPART. In this paper, we present a FLEXPART version that works with the Weather Research and Forecasting (WRF) mesoscale meteorological model. We explain how to run this new model and present special options and features that differ from those of the preceding versions. For instance, a novel turbulence scheme for the convective boundary layer has been included that considers both the skewness of turbulence in the vertical velocity as well as the vertical gradient in the air density. To our knowledge, FLEXPART is the first model for which such a scheme has been developed. On a more technical level, FLEXPART-WRF now offers effective parallelization, and details on computational performance are presented here. FLEXPART-WRF output can either be in binary or Network Common Data Form (NetCDF) format, both of which have efficient data compression. In addition, test case data and the source code are provided to the reader as a Supplement. This material and future developments will be accessible at http://www.flexpart.eu. C1 [Brioude, J.; Angevine, W.; Evan, S.] Univ Colorado, Cooperat Inst Res Environm Sci, Boulder, CO 80309 USA. [Brioude, J.; Angevine, W.; Evan, S.] NOAA, Chem Sci Div, Earth Syst Res Lab, Boulder, CO USA. [Arnold, D.] Tech Univ Catalonia, INTE Inst Energy Technol, Barcelona, Spain. [Arnold, D.; Wotawa, G.] Cent Inst Meteorol & Geodynam, Vienna, Austria. [Stohl, A.; Cassiani, M.; Pisso, I.; Burkhart, J.] NILU Norwegian Inst Air Res, Kjeller, Norway. [Morton, D.] Univ Alaska, ARSC, Fairbanks, AK 99701 USA. [Seibert, P.] Univ Nat Resources & Life Sci, Inst Meteorol, Vienna, Austria. [Dingwell, A.] Uppsala Univ, Dept Earth Sci, Uppsala, Sweden. [Fast, J. D.; Easter, R. C.] Pacific NW Natl Lab, Washington, DC USA. [Burkhart, J.] Univ Calif, Sch Engn, Merced, CA USA. RP Brioude, J (reprint author), Univ Colorado, Cooperat Inst Res Environm Sci, Boulder, CO 80309 USA. EM jerome.brioude@noaa.gov RI Brioude, Jerome/E-4629-2011; Evan, Stephanie/C-2213-2013; Angevine, Wayne/H-9849-2013; Stohl, Andreas/A-7535-2008; Burkhart, John/B-7095-2008; Manager, CSD Publications/B-2789-2015; OI Angevine, Wayne/0000-0002-8021-7116; Stohl, Andreas/0000-0002-2524-5755; Burkhart, John/0000-0002-5587-1693; Dingwell, Adam/0000-0001-7909-0640; Arnold, Delia/0000-0003-1204-234X FU US Department of Energy (DOE) Atmospheric System Research Program at PNNL [DE-AC06-76RLO 1830] FX Jerome Fast and Richard Easter were supported by the US Department of Energy (DOE) Atmospheric System Research Program under Contract DE-AC06-76RLO 1830 at PNNL. PNNL is operated for the US DOE by Battelle Memorial Institute. NR 61 TC 48 Z9 48 U1 5 U2 38 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 1991-959X EI 1991-9603 J9 GEOSCI MODEL DEV JI Geosci. Model Dev. PY 2013 VL 6 IS 6 BP 1889 EP 1904 DI 10.5194/gmd-6-1889-2013 PG 16 WC Geosciences, Multidisciplinary SC Geology GA 280SG UT WOS:000329050500003 ER PT J AU Fang, Y Huang, M Liu, C Li, H Leung, LR AF Fang, Y. Huang, M. Liu, C. Li, H. Leung, L. R. TI A generic biogeochemical module for Earth system models: Next Generation BioGeoChemical Module (NGBGC), version 1.0 SO GEOSCIENTIFIC MODEL DEVELOPMENT LA English DT Article ID CARBON; PHOSPHORUS; NITROGEN; TRANSPORT; DYNAMICS; CLIMATE; SOILS; RESPIRATION; SIMULATION; VEGETATION AB Physical and biogeochemical processes regulate soil carbon dynamics and CO2 flux to and from the atmosphere, influencing global climate changes. Integration of these processes into Earth system models (e.g., community land models (CLMs)), however, currently faces three major challenges: (1) extensive efforts are required to modify modeling structures and to rewrite computer programs to incorporate new or updated processes as new knowledge is being generated, (2) computational cost is prohibitively expensive to simulate biogeochemical processes in land models due to large variations in the rates of biogeochemical processes, and (3) various mathematical representations of biogeochemical processes exist to incorporate different aspects of fundamental mechanisms, but systematic evaluation of the different mathematical representations is difficult, if not impossible. To address these challenges, we propose a new computational framework to easily incorporate physical and biogeochemical processes into land models. The new framework consists of a new biogeochemical module, Next Generation BioGeoChemical Module (NGBGC), version 1.0, with a generic algorithm and reaction database so that new and updated processes can be incorporated into land models without the need to manually set up the ordinary differential equations to be solved numerically. The reaction database consists of processes of nutrient flow through the terrestrial ecosystems in plants, litter, and soil. This framework facilitates effective comparison studies of biogeochemical cycles in an ecosystem using different conceptual models under the same land modeling framework. The approach was first implemented in CLM and benchmarked against simulations from the original CLM-CN code. A case study was then provided to demonstrate the advantages of using the new approach to incorporate a phosphorus cycle into CLM. To our knowledge, the phosphorus-incorporated CLM is a new model that can be used to simulate phosphorus limitation on the productivity of terrestrial ecosystems. The method presented here could in theory be applied to simulate biogeochemical cycles in other Earth system models. C1 [Fang, Y.; Li, H.] Pacific NW Natl Lab, Energy & Environm Directorate, Hydrol Grp, Richland, WA 99352 USA. [Huang, M.; Leung, L. R.] Pacific NW Natl Lab, Climate Phys Grp, Fundamental & Computat Sci Directorate, Richland, WA 99352 USA. [Liu, C.] Pacific NW Natl Lab, Fundamental & Computat Sci Directorate, Geochem Grp, Richland, WA 99352 USA. RP Fang, Y (reprint author), Pacific NW Natl Lab, Energy & Environm Directorate, Hydrol Grp, Richland, WA 99352 USA. EM yilin.fang@pnnl.gov RI Li, Hong-Yi/C-9143-2014; Liu, Chongxuan/C-5580-2009; Huang, Maoyi/I-8599-2012; Fang, Yilin/J-5137-2015 OI Li, Hong-Yi/0000-0001-5690-3610; Huang, Maoyi/0000-0001-9154-9485; FU Pacific Northwest National Laboratory's Laboratory Directed Research and Development Program; US Department of Energy [DE-AC05-76RL01830] FX This research has been accomplished through funding support from Pacific Northwest National Laboratory's Laboratory Directed Research and Development Program. A portion of this research was performed using PNNL Institutional Computing at Pacific Northwest National Laboratory. PNNL is operated by Battelle for the US Department of Energy under Contract DE-AC05-76RL01830. NR 33 TC 5 Z9 5 U1 1 U2 16 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 1991-959X EI 1991-9603 J9 GEOSCI MODEL DEV JI Geosci. Model Dev. PY 2013 VL 6 IS 6 BP 1977 EP 1988 DI 10.5194/gmd-6-1977-2013 PG 12 WC Geosciences, Multidisciplinary SC Geology GA 280SG UT WOS:000329050500008 ER PT J AU Huntzinger, DN Schwalm, C Michalak, AM Schaefer, K King, AW Wei, Y Jacobson, A Liu, S Cook, RB Post, WM Berthier, G Hayes, D Huang, M Ito, A Lei, H Lu, C Mao, J Peng, CH Peng, S Poulter, B Riccuito, D Shi, X Tian, H Wang, W Zeng, N Zhao, F Zhu, Q AF Huntzinger, D. N. Schwalm, C. Michalak, A. M. Schaefer, K. King, A. W. Wei, Y. Jacobson, A. Liu, S. Cook, R. B. Post, W. M. Berthier, G. Hayes, D. Huang, M. Ito, A. Lei, H. Lu, C. Mao, J. Peng, C. H. Peng, S. Poulter, B. Riccuito, D. Shi, X. Tian, H. Wang, W. Zeng, N. Zhao, F. Zhu, Q. TI The North American Carbon Program Multi-Scale Synthesis and Terrestrial Model Intercomparison Project - Part 1: Overview and experimental design SO GEOSCIENTIFIC MODEL DEVELOPMENT LA English DT Article ID CLIMATE; CYCLE; CO2; BIOGEOCHEMISTRY; BALANCE AB Terrestrial biosphere models (TBMs) have become an integral tool for extrapolating local observations and understanding of land-atmosphere carbon exchange to larger regions. The North American Carbon Program (NACP) Multi-scale synthesis and Terrestrial Model Intercomparison Project (MsTMIP) is a formal model intercomparison and evaluation effort focused on improving the diagnosis and attribution of carbon exchange at regional and global scales. MsTMIP builds upon current and past synthesis activities, and has a unique framework designed to isolate, interpret, and inform understanding of how model structural differences impact estimates of carbon uptake and release. Here we provide an overview of the MsTMIP effort and describe how the MsTMIP experimental design enables the assessment and quantification of TBM structural uncertainty. Model structure refers to the types of processes considered (e.g., nutrient cycling, disturbance, lateral transport of carbon), and how these processes are represented (e.g., photosynthetic formulation, temperature sensitivity, respiration) in the models. By prescribing a common experimental protocol with standard spin-up procedures and driver data sets, we isolate any biases and variability in TBM estimates of regional and global carbon budgets resulting from differences in the models themselves (i.e., model structure) and model-specific parameter values. An initial intercomparison of model structural differences is represented using hierarchical cluster diagrams (a.k.a. dendrograms), which highlight similarities and differences in how models account for carbon cycle, vegetation, energy, and nitrogen cycle dynamics. We show that, despite the standardized protocol used to derive initial conditions, models show a high degree of variation for GPP, total living biomass, and total soil carbon, underscoring the influence of differences in model structure and parameterization on model estimates. C1 [Huntzinger, D. N.; Schwalm, C.] No Arizona Univ, Sch Earth Sci & Environm Sustainabil, Flagstaff, AZ 86011 USA. [Huntzinger, D. N.] No Arizona Univ, Dept Civil Engn Construct Management & Environm E, Flagstaff, AZ 86011 USA. [Michalak, A. M.] Carnegie Inst Sci, Dept Global Ecol, Stanford, CA USA. [Schaefer, K.; Jacobson, A.] Natl Snow & Ice Data Ctr, Boulder, CO USA. [Schaefer, K.] Univ Colorado, Cooperat Inst Res Environm Sci, Boulder, CO 80309 USA. [King, A. W.; Wei, Y.; Liu, S.; Cook, R. B.; Post, W. M.; Hayes, D.; Mao, J.; Riccuito, D.; Shi, X.] Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA. [Jacobson, A.] NOAA, Earth Syst Res Lab, Global Monitoring Div, Boulder, CO USA. [Berthier, G.; Peng, S.; Poulter, B.] LSCE, Gif Sur Yvette, France. [Huang, M.] Pacific NW Natl Lab, Richland, WA 99352 USA. [Ito, A.] Natl Inst Environm Studies, Tsukuba, Ibaraki, Japan. [Lei, H.] Pacific NW Natl Lab, Atmospher Sci & Global Change Div, Richland, WA 99352 USA. [Lei, H.] Tsinghua Univ, Dept Hydraul Engn, State Key Lab Hydrosci & Engn, Beijing 100084, Peoples R China. [Lu, C.; Tian, H.] Auburn Univ, Int Ctr Climate & Global Change Res, Auburn, AL 36849 USA. [Lu, C.; Tian, H.] Auburn Univ, Sch Forestry & Wildlife Sci, Auburn, AL 36849 USA. [Peng, C. H.] Univ Quebec, Inst Environm Sci, Dept Biol Sci, Montreal, PQ H3C 3P8, Canada. [Peng, C. H.; Zhu, Q.] Northwest A&F Univ, Coll Forestry, Lab Ecol Forecasting & Global Change, Yangling 712100, Shaanxi, Peoples R China. [Wang, W.] NASA, Ames Res Ctr, Moffett Field, CA 94035 USA. [Zeng, N.; Zhao, F.] Univ Maryland, Dept Atmospher & Ocean Sci, College Pk, MD 20742 USA. RP Huntzinger, DN (reprint author), No Arizona Univ, Sch Earth Sci & Environm Sustainabil, POB 5694, Flagstaff, AZ 86011 USA. EM deborah.huntzinger@nau.edu RI Zeng, Ning/A-3130-2008; Tian, Hanqin/A-6484-2012; Huang, Maoyi/I-8599-2012; Lei, Huimin/H-9596-2015; Peng, Shushi/J-4779-2014; Ricciuto, Daniel/I-3659-2016; Mao, Jiafu/B-9689-2012 OI Cook, Robert/0000-0001-7393-7302; Zeng, Ning/0000-0002-7489-7629; Tian, Hanqin/0000-0002-1806-4091; Poulter, Benjamin/0000-0002-9493-8600; Huang, Maoyi/0000-0001-9154-9485; Lei, Huimin/0000-0002-1175-2334; Peng, Shushi/0000-0001-5098-726X; Ricciuto, Daniel/0000-0002-3668-3021; Mao, Jiafu/0000-0002-2050-7373 FU NASA ROSES Grant [NNX10AG01A, NNH10AN68I]; US Department of Energy (DOE), Office of Science, Biological and Environmental Research; DOE [DE-AC05-00OR22725]; US DOE by Battelle Memorial Institute [DE-AC06-76RLO1830]; NASA; NASA Land Cover/Land Use Change Program (LCLUC); NASA Terrestrial Ecology Program; NASA Atmospheric Composition Modeling and Analysis Program (ACMAP); NSF Dynamics of Coupled Natural-Human System Program (CNH); Decadal and Regional Climate Prediction using Earth System Models (EaSM); DOE National Institute for Climate Change Research; USDA AFRI Program; EPA STAR Program; GhG Europe FP7 grant; National Basic Research Program of China [2013CB956602]; National Science and Engineering Research Council of Canada (NSERC) FX Funding for this project was provided through NASA ROSES Grant # NNX10AG01A. Data management support for preparing, documenting, and distributing model driver and output data was performed by the Modeling and Synthesis Thematic Data Center at Oak Ridge National Laboratory (http://nacp.ornl.gov), with funding through NASA ROSES Grant # NNH10AN68I. Finalized MsTMIP data products will be archived at the ORNL DAAC (http://daac.ornl.gov). This is MsTMIP contribution #1. Acknowledgments for specific MsTMIP participating models follow.; CLM: This research is supported in part by the US Department of Energy (DOE), Office of Science, Biological and Environmental Research. Oak Ridge National Laboratory is managed by UT-BATTELLE for DOE under contract DE-AC05-00OR22725.; CLM4-VIC: This research is supported in part by the US Department of Energy (DOE), Office of Science, Biological and Environmental Research. PNNL is operated for the US DOE by Battelle Memorial Institute under Contract DE-AC06-76RLO1830.; DLEM: The Dynamic Land Ecosystem Model (DLEM) developed in the International Center for Climate and Global Change Research at Auburn University has been supported by NASA Interdisciplinary Science Program (IDS), NASA Land Cover/Land Use Change Program (LCLUC), NASA Terrestrial Ecology Program, NASA Atmospheric Composition Modeling and Analysis Program (ACMAP); NSF Dynamics of Coupled Natural-Human System Program (CNH), Decadal and Regional Climate Prediction using Earth System Models (EaSM); DOE National Institute for Climate Change Research; USDA AFRI Program and EPA STAR Program.; ORCHIDEE-LSCE: ORCHIDEE is a global land surface model developed at the IPSL institute in France. The simulations were performed with the support of the GhG Europe FP7 grant with computing facilities provided by "LSCE" or "TGCC".; TRIPLEX-GHG: TRIPLEX-GHG developed at University of Quebec at Montreal (Canada) and Northwest A&F University (China) has been supported by the National Basic Research Program of China (2013CB956602) and the National Science and Engineering Research Council of Canada (NSERC) Discover Grant. NR 24 TC 41 Z9 41 U1 3 U2 33 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 1991-959X EI 1991-9603 J9 GEOSCI MODEL DEV JI Geosci. Model Dev. PY 2013 VL 6 IS 6 BP 2121 EP 2133 DI 10.5194/gmd-6-2121-2013 PG 13 WC Geosciences, Multidisciplinary SC Geology GA 280SG UT WOS:000329050500016 ER PT J AU Vukmirovic, MB Zhang, Y Wang, JX Buceta, D Wu, LJ Adzic, RR AF Vukmirovic, Miomir B. Zhang, Yu Wang, Jia X. Buceta, David Wu, Lijun Adzic, Radoslav R. TI Pt monolayer shell on hollow Pd core electrocatalysts: scale up synthesis, structure, and activity for the oxygen reduction reaction SO JOURNAL OF THE SERBIAN CHEMICAL SOCIETY LA English DT Article DE platinum overlayer; electrocatalysis; fuel cells; surface strain ID O-2 REDUCTION; CATALYTIC-ACTIVITY; PLATINUM; SURFACES AB The synthesis, characterization and kinetics of the oxygen reduction reaction (ORR) of a Pt monolayer shell on Pd(hollow), or Pd-Au(hollow) core electrocatalysts are reported. Comparisons between the ORR catalytic activity of the electrocatalysts with hollow cores and those of Pt solid and Pt hollow nanoparticles were obtained using the rotating disk electrode technique. Hollow nanopartieles were made using Ni or Cu nanoparticles as sacrificial templates. The Pt ORR specific and mass activities of the electrocatalysts with hollow cores were found to be considerably higher than those of the electrocatalysts with solid cores. This enhanced Pt activity is attributed to the smooth surface morphology and hollow-induced lattice contraction. In addition, the hollow particles have a mass-saving geometry. C1 [Vukmirovic, Miomir B.; Zhang, Yu; Wang, Jia X.; Buceta, David; Adzic, Radoslav R.] Brookhaven Natl Lab, Dept Chem, Upton, NY 11973 USA. [Wu, Lijun] Brookhaven Natl Lab, Condensed Matter Phys & Mat Sci Dept, Upton, NY 11973 USA. RP Adzic, RR (reprint author), Brookhaven Natl Lab, Dept Chem, Upton, NY 11973 USA. EM adzic@bnl.gov RI Wang, Jia/B-6346-2011; Buceta, David/I-1337-2015; OI Buceta, David/0000-0002-3297-6695; Zhang, Yu/0000-0002-0814-2965 FU US Department of Energy, Division of Chemical Sciences, Geosciences and Biosciences Division [DE-AC02-98CH10886]; US Department of Energy, Office of Basic Energy Science, Division of Materials Science and Engineering [DE-AC02-98CH10886]; MICINN, Spain [MAT2010-20442, MAT2011-28673-C02-01] FX Work at Brookhaven National Laboratory was supported by the US Department of Energy, Division of Chemical Sciences, Geosciences and Biosciences Division, under Contract No. DE-AC02-98CH10886. LW was supported by the US Department of Energy, Office of Basic Energy Science, Division of Materials Science and Engineering, under Contract No. DE-AC02-98CH10886. DB thanks the MICINN, Spain (MAT2010-20442 and MAT2011-28673-C02-01) for an FPU grant. NR 20 TC 1 Z9 1 U1 0 U2 52 PU SERBIAN CHEMICAL SOC PI BELGRADE PA KARNEGIJEVA 4, 11 120 BELGRADE, SERBIA SN 0352-5139 J9 J SERB CHEM SOC JI J. Serb. Chem. Soc. PY 2013 VL 78 IS 12 BP 1983 EP 1992 DI 10.2298/JSC131024117V PG 10 WC Chemistry, Multidisciplinary SC Chemistry GA 283QD UT WOS:000329261200012 ER PT J AU Atanasoska, LL Cullen, DA Atanasoski, RT AF Atanasoska, Ljiljana L. Cullen, David A. Atanasoski, Radoslav T. TI XPS and STEM study of the interface formation between ultra-thin Ru and Ir OER catalyst layers and Perylene Red support whiskers SO JOURNAL OF THE SERBIAN CHEMICAL SOCIETY LA English DT Article DE fuel cell; catalyst; surface properties; deposition ID RAY PHOTOELECTRON-SPECTROSCOPY AB The interface formation between nano-structured Perylene Red (PR) whiskers and the oxygen evolution reaction (OER) catalysts ruthenium and iridium was studied systematically by XPS and STEM. The OER catalyst over-layers with thicknesses ranging from approximate to 0.1 to approximate to 50 nm were vapor deposited onto PR ex situ. STEM images demonstrated that, with increasing thickness, Ru and Ir transform from amorphous clusters to crystalline nanoparticles, which agglomerate with increased over-layer thickness. XPS data showed a strong interaction between Ru and PR. Ir also interacts with PR although not to the extent seen for Ru. At low coverages, the entire Ru deposit was in the reacted state while a small portion of the deposited Ir remained metallic. Ru and Ir bonding occur at the PR carbonyl sites as evidenced by the attenuation of carbonyl photoemission and the emergence of new peak assigned to C-O single bonds. Curve fitting analysis and the derived stoichiometry indicated the formation of metallo organic bonds. The co-existence of oxide bonds was also apparent. C1 [Atanasoska, Ljiljana L.; Atanasoski, Radoslav T.] 3M Co, 3M Ctr, St Paul, MN 55144 USA. [Cullen, David A.] Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. RP Atanasoska, LL (reprint author), 3M Co, 3M Ctr, St Paul, MN 55144 USA. EM rtatanasoski@mmm.com RI Cullen, David/A-2918-2015 OI Cullen, David/0000-0002-2593-7866 FU DOE Fuel Cell Technology Office [DE-EE0000456]; Oak Ridge National Laboratory's Shared Research Equipment (ShaRE) User Program; Office of Basic Energy Sciences, U.S. DOE FX This work was supported by the DOE Fuel Cell Technology Office, Award No. DE-EE0000456 and the Oak Ridge National Laboratory's Shared Research Equipment (ShaRE) User Program, sponsored by the Office of Basic Energy Sciences, U.S. DOE. NR 9 TC 2 Z9 2 U1 2 U2 25 PU SERBIAN CHEMICAL SOC PI BELGRADE PA KARNEGIJEVA 4, 11 120 BELGRADE, SERBIA SN 0352-5139 J9 J SERB CHEM SOC JI J. Serb. Chem. Soc. PY 2013 VL 78 IS 12 BP 1993 EP 2005 DI 10.2298/JSC130927111A PG 13 WC Chemistry, Multidisciplinary SC Chemistry GA 283QD UT WOS:000329261200013 ER PT J AU Danilovic, N Subbaraman, R Strmcnik, D Stamenkovic, VR Markovic, NM AF Danilovic, Nemanja Subbaraman, Ram Strmcnik, Dusan Stamenkovic, Vojislav R. Markovic, Nenad M. TI Electrocatalysis of the HER in acid and alkaline media SO JOURNAL OF THE SERBIAN CHEMICAL SOCIETY LA English DT Article DE volcano plot; HER; hydrogen evolution reaction; acid; alkaline ID ELECTROLYTIC HYDROGEN EVOLUTION; FUNCTIONAL THEORY CALCULATIONS; SINGLE-CRYSTAL SURFACES; PLATINUM; ADSORPTION; TRENDS; ELECTROCHEMISTRY; OXIDATION; PT(111); METALS AB Trends in the HER were studied on selected metals (M = Cu, Ag, Au, Pt, Ru, Ir. and Ti) in acid and alkaline environments. It was found that with the exception of Pt, Ir and Au, due to high coverage by spectator species on non-noble metal catalysts, the experimentally established positions of Cu, Ag, Ru and Ti in the observed volcano relations are still uncertain. It was also found that while the M-H-upd binding energy most likely controls the activity trends in acidic solutions, the trends in activity in alkaline solutions are controlled by a delicate balance between two descriptors: the M-H-ad interaction and the energetics required to dissociate water molecules. The importance of the second descriptor was confirmed by introducing bifunctional catalysts such as M modified by Ni(OH); e.g., while the latter serves to enhance the catalytic decomposition of water, the metal sites are required for collecting and recombining the produced hydrogen intermediates. C1 [Danilovic, Nemanja; Subbaraman, Ram; Strmcnik, Dusan; Stamenkovic, Vojislav R.; Markovic, Nenad M.] Argonne Natl Lab, Div Mat Sci, Argonne, IL 60439 USA. RP Markovic, NM (reprint author), Argonne Natl Lab, Div Mat Sci, 9700 S Cass Ave, Argonne, IL 60439 USA. EM nmmarkovic@anl.gov FU Office of Science, Office of Basic Energy Sciences, Division of Materials Science, U.S. Department of Energy [DE-AC0-06CH11357] FX This work was supported by the Office of Science, Office of Basic Energy Sciences, Division of Materials Science, U.S. Department of Energy, under contract DE-AC0-06CH11357. NR 24 TC 15 Z9 15 U1 18 U2 104 PU SERBIAN CHEMICAL SOC PI BELGRADE PA KARNEGIJEVA 4, 11 120 BELGRADE, SERBIA SN 0352-5139 J9 J SERB CHEM SOC JI J. Serb. Chem. Soc. PY 2013 VL 78 IS 12 BP 2007 EP 2015 DI 10.2298/JSC131118136D PG 9 WC Chemistry, Multidisciplinary SC Chemistry GA 283QD UT WOS:000329261200014 ER PT S AU Bochove, EJ Nair, N Aceves, AB Zunoubi, MR AF Bochove, Erik J. Nair, Niketh Aceves, Alejandro B. Zunoubi, Mohammad R. BE Exarhos, GJ Gruzdev, VE Menapace, JA Ristau, D Soileau, MJ TI New Tools for the Dynamical Description of Laser Arrays and Other Complex Systems SO LASER-INDUCED DAMAGE IN OPTICAL MATERIALS: 2013 SE Proceedings of SPIE LA English DT Proceedings Paper CT 45th Annual Laser Damage Symposium on Laser-Induced Damage in Optical Materials CY SEP 22-25, 2013 CL Boulder, CO SP SPIE, Lawrence Livermore Natl Lab, Spica Technologies Inc DE Phased Laser Arrays; Laser Beam Quality; Neural Nets; Dynamical Systems ID COHERENCE AB We propose a systematic approach that may apply to many complex interactive networks, such as biological or electronic neural assemblies, which was partly inspired by mathematical features of phased laser arrays. Using an appropriate quasi-logarithmic transformation, a Fox-Li integral equation of linearly coupled phased laser arrays is mapped to a semi-equivalent coupled oscillator description, of which the interaction term is decomposed into orthogonal projections. Based on traditional ideas of symmetry, orthogonality, completeness, and the physical concept of criticality, techniques are proposed for the description of the dynamics and organization of massively nonlinearly interconnected networks, which may serve as memories, or perform computational operations in biological neuron assemblies, or models of evolution, pathology, ecological and social networks, individual and collective behavior, etc. C1 [Bochove, Erik J.] Air Force Res Lab, Directed Energy Directorate, Kirtland AFB, NM 87117 USA. [Nair, Niketh] Univ Tennessee, Dept Mech Engn, Knoxville, TN 37996 USA. [Nair, Niketh] Oak Ridge Natl Lab, Div Comp Sci & Math, Oak Ridge, TN 37831 USA. [Aceves, Alejandro B.] So Methodist Univ, Dept Math, Dallas, TX 75275 USA. [Zunoubi, Mohammad R.] SUNY Coll New Paltz, Dept Elect & Comp Engn, New Paltz, NY 12561 USA. RP Bochove, EJ (reprint author), Air Force Res Lab, Directed Energy Directorate, Kirtland AFB, NM 87117 USA. FU AFOSR FX This project was funded by the AFOSR (program of A. Nachman). NR 16 TC 0 Z9 0 U1 0 U2 1 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9753-6 J9 PROC SPIE PY 2013 VL 8885 AR UNSP 88851H DI 10.1117/12.2031604 PG 8 WC Optics; Physics, Applied SC Optics; Physics GA BJM57 UT WOS:000329160900029 ER PT S AU Demos, SG Negres, RA Raman, RN Rubenchik, AM Feit, MD AF Demos, Stavros G. Negres, Raluca A. Raman, Rajesh N. Rubenchik, Alexander M. Feit, Michael D. BE Exarhos, GJ Gruzdev, VE Menapace, JA Ristau, D Soileau, MJ TI Comparison of material response in fused silica and KDP following exit surface laser-induced breakdown SO LASER-INDUCED DAMAGE IN OPTICAL MATERIALS: 2013 SE Proceedings of SPIE LA English DT Proceedings Paper CT 45th Annual Laser Damage Symposium on Laser-Induced Damage in Optical Materials CY SEP 22-25, 2013 CL Boulder, CO SP SPIE, Lawrence Livermore Natl Lab, Spica Technologies Inc DE Fused silica; SiO2; KDP; DKDP; laser-induced damage; laser-induced breakdown; material ejection; laser ablation ID INDUCED DAMAGE; CRYSTALS; DEFECTS; PULSES; GROWTH AB Crater formation that accompanies laser-induced damage is the result of material ejection following the rapid, localized heating to temperatures on the order of 1 eV. The objective of this work is to compare the material ejection behavior in fused silica and KDP crystals as captured using time-resolved shadowgraphy. These two materials are of fundamental importance in ICF class laser systems but they also represent materials with significantly different physical properties. We hypothesize that these different properties can affect the material ejection process. C1 [Demos, Stavros G.; Negres, Raluca A.; Raman, Rajesh N.; Rubenchik, Alexander M.; Feit, Michael D.] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. RP Demos, SG (reprint author), Lawrence Livermore Natl Lab, 7000 East Ave, Livermore, CA 94550 USA. EM demos1@llnl.gov RI Feit, Michael/A-4480-2009 NR 16 TC 2 Z9 2 U1 0 U2 12 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9753-6 J9 PROC SPIE PY 2013 VL 8885 AR UNSP 88850W DI 10.1117/12.2030481 PG 6 WC Optics; Physics, Applied SC Optics; Physics GA BJM57 UT WOS:000329160900019 ER PT S AU Field, ES Bellum, JC Kletecka, DE AF Field, Ella S. Bellum, John C. Kletecka, Damon E. BE Exarhos, GJ Gruzdev, VE Menapace, JA Ristau, D Soileau, MJ TI Laser Damage Comparisons of Broad-Bandwidth, High-Reflection Optical Coatings Containing TiO2, Nb2O5, or Ta2O5 High Index Layers SO LASER-INDUCED DAMAGE IN OPTICAL MATERIALS: 2013 SE Proceedings of SPIE LA English DT Proceedings Paper CT 45th Annual Laser Damage Symposium on Laser-Induced Damage in Optical Materials CY SEP 22-25, 2013 CL Boulder, CO SP SPIE, Lawrence Livermore Natl Lab, Spica Technologies Inc DE Laser Induced Damage Threshold; High Reflection; Broad Bandwidth; Optical Coatings; E-Beam Evaporation; TiO2; Nb2O5; Ta2O5 AB Broad bandwidth coatings allow angle of incidence flexibility and accommodate spectral shifts due to aging and water absorption. Higher refractive index materials in optical coatings, such as TiO2, Nb2O5, and Ta2O5, can be used to achieve broader bandwidths compared to coatings that contain HfO2 high index layers. We have identified the deposition settings that lead to the highest index, lowest absorption layers of TiO2, Nb2O5, and Ta2O5, via e-beam evaporation using ion-assisted deposition. We paired these high index materials with SiO2 as the low index material to create broad bandwidth high reflection coatings centered at 1054 nm for 45 degrees angle of incidence and P polarization. High reflection bandwidths as large as 231 nm were realized. Laser damage tests of these coatings using the ISO 11254 and NIF-MEL protocols are presented, which revealed that the Ta2O5/SiO2 coating exhibits the highest resistance to laser damage, at the expense of lower bandwidth compared to the TiO2/SiO2 and Nb2O5/SiO2 coatings. C1 [Field, Ella S.; Bellum, John C.; Kletecka, Damon E.] Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Field, ES (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87185 USA. EM efield@sandia.gov NR 10 TC 2 Z9 2 U1 2 U2 7 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9753-6 J9 PROC SPIE PY 2013 VL 8885 AR UNSP 88851X DI 10.1117/12.2030068 PG 8 WC Optics; Physics, Applied SC Optics; Physics GA BJM57 UT WOS:000329160900040 ER PT S AU Folta, J Nostrand, M Honig, J Wong, N Ravizza, F Geraghty, P Taranowski, M Johnson, G Larkin, G Ravizza, D Peterson, J Welday, B Wegner, P AF Folta, James Nostrand, Mike Honig, John Wong, Nan Ravizza, Frank Geraghty, Paul Taranowski, Mike Johnson, Gary Larkin, Glenn Ravizza, Doug Peterson, John Welday, Brian Wegner, Paul BE Exarhos, GJ Gruzdev, VE Menapace, JA Ristau, D Soileau, MJ TI Mitigation of Laser Damage on National Ignition Facility Optics in Volume Production SO LASER-INDUCED DAMAGE IN OPTICAL MATERIALS: 2013 SE Proceedings of SPIE LA English DT Proceedings Paper CT 45th Annual Laser Damage Symposium on Laser-Induced Damage in Optical Materials CY SEP 22-25, 2013 CL Boulder, CO SP SPIE, Lawrence Livermore Natl Lab, Spica Technologies Inc DE National Ignition Facility; optics; laser damage; laser damage mitigation; laser damage repair ID FUSED-SILICA; CO2-LASER; GROWTH; PERFORMANCE; RELAXATION; MICROSCOPY AB The National Ignition Facility has recently achieved the milestone of delivering over 1.8 MJ and 500 TW of 351 nm laser energy and power on target, which required average fluences up to 9 J/cm(2) (3 ns equivalent) in the final optics system. Commercial fused silica laser-grade UV optics typically have a maximum operating threshold of 5 J/cm(2). We have developed an optics recycling process which enables NIF to operate above the laser damage initiation and growth thresholds. We previously reported a method to mitigate laser damage with laser ablation of the damage site to leave benign cone shaped pits. We have since developed a production facility with four mitigation systems capable of performing the mitigation protocols on full-sized (430 mm) optics in volume production. We have successfully repaired over 700 NIF optics (unique serial numbers), some of which have been recycled as many as 11 times. We describe the mitigation systems, the optics recycle loop process, and optics recycle production data. C1 [Folta, James; Nostrand, Mike; Honig, John; Wong, Nan; Ravizza, Frank; Geraghty, Paul; Taranowski, Mike; Johnson, Gary; Larkin, Glenn; Ravizza, Doug; Peterson, John; Welday, Brian; Wegner, Paul] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. RP Folta, J (reprint author), Lawrence Livermore Natl Lab, 7000 East Ave, Livermore, CA 94550 USA. NR 23 TC 4 Z9 4 U1 1 U2 5 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9753-6 J9 PROC SPIE PY 2013 VL 8885 AR UNSP 88850Z DI 10.1117/12.2030475 PG 9 WC Optics; Physics, Applied SC Optics; Physics GA BJM57 UT WOS:000329160900020 ER PT S AU Hobbs, DS MacLeod, BD Sabatino, E Britten, JA Stolz, CJ AF Hobbs, Douglas S. MacLeod, Bruce D. Sabatino, Ernest, III Britten, Jerald A. Stolz, Christopher J. BE Exarhos, GJ Gruzdev, VE Menapace, JA Ristau, D Soileau, MJ TI Contamination resistant antireflection nano-textures in fused silica for laser optics. SO LASER-INDUCED DAMAGE IN OPTICAL MATERIALS: 2013 SE Proceedings of SPIE LA English DT Proceedings Paper CT 45th Annual Laser Damage Symposium on Laser-Induced Damage in Optical Materials CY SEP 22-25, 2013 CL Boulder, CO SP SPIE, Lawrence Livermore Natl Lab, Spica Technologies Inc DE Nano-Textures; Anti-reflection; AR; Motheye; Laser Damage; Organic Adsorption; Sol-Gel Coatings; Grating Debris Shields ID COATINGS; DAMAGE AB Anti-reflecting (AR) surface relief nano-textures have been integrated with fused silica diffraction gratings to demonstrate the potential of stable diffractive 3 omega beam samplers with increased energy to target at the National Ignition Facility (NIF). TelAztec's AR texturing process was used to etch Random-type AR (RAR) microstructures in sub-scale NIF Grating Debris Shields consisting of large pitch, shallow line gratings. This superposition yielded the desired similar to 3.5% increase in zero-order transmission uniformly over the full aperture without compromising the grating function. Another fused silica window fabricated with RAR nano-textures in both faces for a 3 omega (351nm) transmission of 99.5%, was subjected to capillary condensation tests to evaluate the resistance of the RAR texture to the adsorption of organic compounds. It was found that for a one day exposure time to a surrogate suite of organic contaminants, the RAR textured fused silica surfaces adsorbed less than one fourth the amount of organic contaminants found on a NIF baseline hardened sol-gel AR coated optic. In two additional exposure cycles, further RAR process refinement reduced the amount of adsorbed organics to a level nearly 200 times below the current NIF baseline. Significantly, the 3 omega transmission of the RAR textured window remained unchanged after all three exposure cycles, whereas the sol-gel coated windows showed losses up to 4.9% for the highest contaminant concentration. Large beam pulsed laser damage testing of RAR textured fused silica windows was conducted with the Optical Sciences Laser (OSL) at NIF. The RAR sample damage resistance was found to be equivalent to the current NIF baseline - even after multiple aggressive chemical cleaning cycles. Lastly, a series of RAR textured and sol-gel AR coated windows were subjected to commercial 3 omega pulsed laser damage testing at Quantel. The results indicate an average RAR damage threshold of 26 J/cm(2), a level about 80% of the two NIF fused silica samples tested, two times higher than the best performing ion beam sputtered thin-film AR coatings reported in the literature, and six times higher than catalog high power laser window coating specifications. C1 [Hobbs, Douglas S.; MacLeod, Bruce D.; Sabatino, Ernest, III] TelAztec LLC, 15 A St, Burlington, MA 01803 USA. [Britten, Jerald A.; Stolz, Christopher J.] Lawrence Livermore Natl Lab, Livermore, CA 94551 USA. RP Hobbs, DS (reprint author), TelAztec LLC, 15 A St, Burlington, MA 01803 USA. EM dshobbs@telaztec.com; britten1@llnl.gov FU U.S. Department of Energy [DE-AC52-07NA27344] FX Work at LLNL was performed under the auspices of the U.S. Department of Energy under Contract DE-AC52-07NA27344. Jeff Runkel of Quantel USA (JRunkel@quantelusa.com) is also gratefully acknowledged for his fast and thorough work providing the certified, NIST traceable pulsed LiDT testing at 355nm. NR 22 TC 3 Z9 3 U1 3 U2 9 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9753-6 J9 PROC SPIE PY 2013 VL 8885 AR UNSP 88850J DI 10.1117/12.2042888 PG 11 WC Optics; Physics, Applied SC Optics; Physics GA BJM57 UT WOS:000329160900010 ER PT S AU Matthews, MJ Elhadj, S Guss, GM Sridharan, A Nielsen, ND Yoo, JH Lee, D Grigoropoulos, C AF Matthews, Manyalibo J. Elhadj, Selim Guss, Gabe M. Sridharan, Arun Nielsen, Norman D. Yoo, Jae Hyuck Lee, Daeho Grigoropoulos, Costas BE Exarhos, GJ Gruzdev, VE Menapace, JA Ristau, D Soileau, MJ TI Localized planarization of optical damage using laser-based chemical vapor deposition SO LASER-INDUCED DAMAGE IN OPTICAL MATERIALS: 2013 SE Proceedings of SPIE LA English DT Proceedings Paper CT 45th Annual Laser Damage Symposium on Laser-Induced Damage in Optical Materials CY SEP 22-25, 2013 CL Boulder, CO SP SPIE, Lawrence Livermore Natl Lab, Spica Technologies Inc DE Damage repair; chemical vapor deposition; additive processing; surfaces; lasers ID TETRAETHOXYSILANE; GROWTH; SIO2 AB We present a method to repair damaged optics using laser-based chemical vapor deposition (L-CVD). A CO2 laser is used to heat damaged silica regions and polymerize a gas precursor to form SiO2. Measured deposition rates and morphologies agree well with finite element modeling of a two-phase reaction. Along with optimizing deposition rates and morphology, we also show that the deposited silica is structurally identical to high-grade silica substrate and possesses high UV laser damage thresholds. Successful application of such a method could reduce processing costs, extend optic lifetime, and lead to more damage resistant laser optics used in high power applications. C1 [Matthews, Manyalibo J.; Elhadj, Selim; Guss, Gabe M.; Sridharan, Arun; Nielsen, Norman D.] Lawrence Livermore Natl Lab, Natl Ignit Facil, Livermore, CA 94550 USA. [Yoo, Jae Hyuck; Lee, Daeho; Grigoropoulos, Costas] Univ Calif Berkeley, Dept Engn Mech, Berkeley, CA 94704 USA. RP Matthews, MJ (reprint author), Lawrence Livermore Natl Lab, Natl Ignit Facil, Livermore, CA 94550 USA. EM ibo@llnl.gov FU UCFR [12-LR-237713]; U.S. Department of Energy by Lawrence Livermore National Laboratory [DE-AC52-07NA27344, LLNL-PROC-646682] FX S. Elhadj and M. Matthews kindly acknowledge support from UCFR grant #12-LR-237713. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-PROC-646682 NR 17 TC 1 Z9 1 U1 1 U2 3 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9753-6 J9 PROC SPIE PY 2013 VL 8885 AR UNSP 888526 DI 10.1117/12.2030506 PG 9 WC Optics; Physics, Applied SC Optics; Physics GA BJM57 UT WOS:000329160900048 ER PT S AU Matthews, MJ Shen, N Rubenchik, AM Honig, J Bude, JD AF Matthews, Manyalibo J. Shen, Nan Rubenchik, Alexander M. Honig, John Bude, Jeff D. BE Exarhos, GJ Gruzdev, VE Menapace, JA Ristau, D Soileau, MJ TI Phase modulation in high power optical systems caused by pulsed laser-driven particle ablation events SO LASER-INDUCED DAMAGE IN OPTICAL MATERIALS: 2013 SE Proceedings of SPIE LA English DT Proceedings Paper CT 45th Annual Laser Damage Symposium on Laser-Induced Damage in Optical Materials CY SEP 22-25, 2013 CL Boulder, CO SP SPIE, Lawrence Livermore Natl Lab, Spica Technologies Inc DE Fourier optics; damage; surfaces; lasers ID FUSED-SILICA; SURFACE AB Surface modification of fused silica windows caused by the laser ablation of surface-bound microparticles is investigated. Using optical and electron microscopies between laser pulses, we detail the ablation, fragmentation and dispersal of 2-150 mu m diameter particles of various materials. Following complete ablation and ejection of all debris material, surface pitting was found to be highly dependent on material type and particle size. Subsequent light propagation modeling based on pit morphology indicates up to similar to 4x intensification. Understanding this class of non-local, debris-generated damage is argued to be important for effective design of high-power optical windows and debris-mitigation strategies. C1 [Matthews, Manyalibo J.; Shen, Nan; Rubenchik, Alexander M.; Honig, John; Bude, Jeff D.] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. RP Matthews, MJ (reprint author), Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. EM ibo@llnl.gov NR 12 TC 0 Z9 0 U1 1 U2 7 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9753-6 J9 PROC SPIE PY 2013 VL 8885 AR UNSP 88850T DI 10.1117/12.2030507 PG 8 WC Optics; Physics, Applied SC Optics; Physics GA BJM57 UT WOS:000329160900018 ER PT S AU Rubenchik, AM Feit, MD Demos, SG AF Rubenchik, Alexander M. Feit, Michael D. Demos, Stavros G. BE Exarhos, GJ Gruzdev, VE Menapace, JA Ristau, D Soileau, MJ TI Interaction of laser pulse with confined plasma during exit surface nanosecond laser damage SO LASER-INDUCED DAMAGE IN OPTICAL MATERIALS: 2013 SE Proceedings of SPIE LA English DT Proceedings Paper CT 45th Annual Laser Damage Symposium on Laser-Induced Damage in Optical Materials CY SEP 22-25, 2013 CL Boulder, CO SP SPIE, Lawrence Livermore Natl Lab, Spica Technologies Inc DE Laser-induced damage; laser-induced breakdown; laser ablation ID FUSED-SILICA AB Interpretation of spatial and time resolved images of rear surface ns laser damage in dielectrics requires understanding of the dynamic interaction of the incoming laser beam with the confined expanding plasma in the material. The detailed kinetics of the plasma, involving both expansion and retraction, depends on details of reflection and absorption in the hot material. The growth of the hot region is treated using a model previously developed to understand laser peening. The pressure is found to scale as the square root of laser intensity and drops off slowly after energy deposition is complete. For the conditions of our experimental observations in fused silica, our model predicts a pressure of about 9 GPa and a surface expansion velocity of about 1.5 km/sec, in good agreement with experimental observation. C1 [Rubenchik, Alexander M.; Feit, Michael D.; Demos, Stavros G.] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. RP Rubenchik, AM (reprint author), Lawrence Livermore Natl Lab, 7000 East Ave, Livermore, CA 94550 USA. RI Feit, Michael/A-4480-2009 NR 13 TC 0 Z9 0 U1 0 U2 6 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9753-6 J9 PROC SPIE PY 2013 VL 8885 AR UNSP 88851D DI 10.1117/12.2030482 PG 6 WC Optics; Physics, Applied SC Optics; Physics GA BJM57 UT WOS:000329160900027 ER PT S AU Stolz, CJ Runkel, J AF Stolz, Christopher J. Runkel, Jeff BE Exarhos, GJ Gruzdev, VE Menapace, JA Ristau, D Soileau, MJ TI Brewster Angle Thin Film Polarizing Beamsplitter Laser Damage Competition: "S" Polarization SO LASER-INDUCED DAMAGE IN OPTICAL MATERIALS: 2013 SE Proceedings of SPIE LA English DT Proceedings Paper CT 45th Annual Laser Damage Symposium on Laser-Induced Damage in Optical Materials CY SEP 22-25, 2013 CL Boulder, CO SP SPIE, Lawrence Livermore Natl Lab, Spica Technologies Inc DE damage testing; polarizer; thin film; Brewster angle; multilayer; 1064 nm laser; nanosecond pulse length; and ISO21254-2 AB This Brewster angle thin film polarizer damage competition is a continuation of last year's test with "P" polarization results published in 2012 and "S" polarization results in this study. This competition allows a direct laser resistance comparison between polarizations because the samples were laser damage tested under identical conditions. The requirements of the coatings are a minimum transmission of 95% at "P" polarization and minimum reflection of 99% at "S" polarization at 1064 nm and 56.4 degrees angle of incidence. The choice of coating materials, design, and deposition method were left to the participant. Laser damage testing was performed according to the ISO 11254 standard utilizing a 1064 nm wavelength laser with a 10 ns pulse length operating at 20 Hz. A double blind test assured sample and submitter anonymity. In addition to the laser resistance results, details of deposition processes, coating materials and layer count, and spectral results are shared. C1 [Stolz, Christopher J.] Lawrence Livermore Natl Lab, 7000 East Ave,L-460, Livermore, CA 94550 USA. [Runkel, Jeff] Quantel USA, Bozeman 59715, MT USA. RP Stolz, CJ (reprint author), Lawrence Livermore Natl Lab, 7000 East Ave,L-460, Livermore, CA 94550 USA. NR 8 TC 1 Z9 1 U1 1 U2 5 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9753-6 J9 PROC SPIE PY 2013 VL 8885 AR UNSP 888509 DI 10.1117/12.2030476 PG 8 WC Optics; Physics, Applied SC Optics; Physics GA BJM57 UT WOS:000329160900005 ER PT S AU Stolz, CJ Wolfe, JE Mirkarimi, PB Folta, JA Adams, JJ Menor, MG Teslich, NE Soufli, R Menoni, C Patel, D AF Stolz, Christopher J. Wolfe, Justin E. Mirkarimi, Paul B. Folta, James A. Adams, John J. Menor, Marlon G. Teslich, Nick E. Soufli, Regina Menoni, Carmen Patel, Dinesh BE Exarhos, GJ Gruzdev, VE Menapace, JA Ristau, D Soileau, MJ TI Defect insensitive 100 J/cm(2) multilayer mirror coating process SO LASER-INDUCED DAMAGE IN OPTICAL MATERIALS: 2013 SE Proceedings of SPIE LA English DT Proceedings Paper CT 45th Annual Laser Damage Symposium on Laser-Induced Damage in Optical Materials CY SEP 22-25, 2013 CL Boulder, CO SP SPIE, Lawrence Livermore Natl Lab, Spica Technologies Inc DE damage testing; 1064-nm laser; nanosecond pulse length; thin film; multilayer mirror; ion beam sputtering ID LASER DAMAGE AB Multilayer mirrors are fluence-limited by nodular defects. Such defects originate from the deposition source, inadequate cleaning, transport, pump down, heating, shedding from rotating hardware, etc. These overcoated inclusions behave as micro-lenses resulting in light intensification within the multilayer structure. To minimize the impact of these defects, a planarization process has been developed to reduce geometric-induced light intensification. By exploiting the angle-dependent etching rate of materials, a deposit-and-etch process reduces nodular defect height and diameter. Planarized defects demonstrate a greater than 20x increase in laser resistance at a wavelength of 1064 nm and pulse length of 10 ns. Process parameters were explored such as planarization efficiency of the coating materials, discrete versus continuous etching, thick planarization layers for substrate defects, and etching throughout the multilayer to planarize coating defects. C1 [Stolz, Christopher J.; Wolfe, Justin E.; Mirkarimi, Paul B.; Folta, James A.; Adams, John J.; Menor, Marlon G.; Teslich, Nick E.; Soufli, Regina] Lawrence Livermore Natl Lab, 7000 East Ave,L-460, Livermore, CA 94550 USA. [Menoni, Carmen; Patel, Dinesh] Colorado State Univ, Dept Elect & Comp Engn, Colorado Springs 80523, CO USA. RP Stolz, CJ (reprint author), Lawrence Livermore Natl Lab, 7000 East Ave,L-460, Livermore, CA 94550 USA. EM Carmen.Menoni@colostate.edu FU U.S. Department of Energy [W-7405-ENG-48]; Office of Naval Research [N00014-06-1-0523] FX This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. W-7405-ENG-48. The work at Colorado State University used facilities developed with support of the Office of Naval Research through grant N00014-06-1-0523. C. J. Stolz acknowledges the help of administrative assistant Terrie Goodwin with formatting of the manuscript and preparation of the presentation shown at the Boulder Damage Symposium. NR 14 TC 4 Z9 4 U1 1 U2 6 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9753-6 J9 PROC SPIE PY 2013 VL 8885 AR UNSP 888502 DI 10.1117/12.2030477 PG 7 WC Optics; Physics, Applied SC Optics; Physics GA BJM57 UT WOS:000329160900001 ER PT S AU Yan, CS Fan, JL Xu, CC AF Yan, Chengshi Fan, Jilian Xu, Changcheng BE Yang, H Li, P TI Analysis of Oil Droplets in Microalgae SO LIPID DROPLETS SE Methods in Cell Biology LA English DT Review; Book Chapter ID ALGA CHLAMYDOMONAS-REINHARDTII; LIPID DROPLETS; NILE RED; METABOLISM; FLUORESCENCE; VARIABILITY; BODIES AB Microalgae are diverse groups of eukaryotic organisms capable of efficiently converting sunlight into chemical energy through photosynthesis with carbohydrates and oils as major storage products. Like other eukaryotes, microalgae store oils in dynamic subcellular organelles named oil droplets. In this chapter, we present a detailed description of basic procedures that can be followed for the isolation of mutants defective in oil droplet biogenesis and for the imaging and analysis of oil droplets in the model unicellular green alga Chlamydomonas reinhardtii. Several commonly used methods for isolating and purifying oil droplets in microalgae are discussed. C1 [Yan, Chengshi; Fan, Jilian; Xu, Changcheng] Brookhaven Natl Lab, Dept Biosci, Upton, NY 11973 USA. RP Yan, CS (reprint author), Brookhaven Natl Lab, Dept Biosci, Upton, NY 11973 USA. RI Yan, Chengshi/O-5639-2014 NR 39 TC 5 Z9 5 U1 0 U2 15 PU ELSEVIER ACADEMIC PRESS INC PI SAN DIEGO PA 525 B STREET, SUITE 1900, SAN DIEGO, CA 92101-4495 USA SN 0091-679X BN 978-0-12-408051-5 J9 METHOD CELL BIOL JI Methods Cell Biol. PY 2013 VL 116 BP 71 EP 82 DI 10.1016/B978-0-12-408051-5.00005-X PG 12 WC Cell Biology SC Cell Biology GA BJN44 UT WOS:000329254900006 PM 24099288 ER PT S AU Leong, K Foster, ME Wong, BM Spoerke, ED Gough, D Deaton, JC Allendorf, MD AF Leong, Kirsty Foster, Michael E. Wong, Bryan M. Spoerke, Erik D. Gough, Dara Deaton, Joseph C. Allendorf, Mark D. BE Tao, M Deligianni, H Overberg, ME Rajeshwar, K Claeys, C Fenton, JM Park, JG Sunkara, M TI Nano-Ordering of Donor-Acceptor Interactions Using Metal-Organic Frameworks as Scaffolds SO PHOTOVOLTAICS FOR THE 21ST CENTURY 9 SE ECS Transactions LA English DT Proceedings Paper CT Electrochemical-Society (ECS) 9th Symposium on Photovoltaics for the 21st Century CY OCT, 2013 CL San Francisco, CA SP Electrochem Soc, Electrochem Soc, Dielectr Sci & Technol Div, Electrochem Soc, Electrodeposit Div, Electrochem Soc, Elect & Photon Div, Electrochem Soc, Energy Technol Div, Electrochem Soc, Ind Electrochemistry & Electrochem Engn Div ID HETEROJUNCTION PHOTOVOLTAIC CELLS; SOLAR-CELLS; PORE-SIZE; EFFICIENT; DESIGN; FUNCTIONALITY AB Metal-Organic Frameworks (MOFs) are nanoporous materials with tunable pore sizes that can accommodate and stabilize small molecules. Because of their long-range order and well-understood pore environment, the nano-confinement of donor-acceptor materials within MOFs offers a new methodology for creating uniform phase-segregated donor-acceptor interfaces. Phase segregation and the photo-physical effects of confining alpha,omega-Dihexylsexithiophene (DH-6T) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) in several MOFs and the potential role of the MOF in creating a nano-heterojunction for organic photovoltaics are discussed. We demonstrate infiltration of both molecules into MOF pores and use luminescence and absorption spectroscopies to characterize the MOF-guest energy transfer processes. Comparison with density functional theory allows us to determine the energetics and band alignment within the MOF. The results demonstrate the utility of MOFs as scaffolds for sub-nanoscale ordering of donor and acceptor species within a highly uniform environment, allowing both the interaction and separation distance to be much more controlled than in the classical bulk heterojunction. C1 [Leong, Kirsty; Foster, Michael E.; Wong, Bryan M.; Allendorf, Mark D.] Sandia Natl Labs, Livermore, CA 94551 USA. [Spoerke, Erik D.; Gough, Dara] Sandia Natl Labs, Albuquerque, NM 87185 USA. [Deaton, Joseph C.] Bowling Green State Univ, Dept Chem, Bowling Green, OH 43403 USA. RP Leong, K (reprint author), Sandia Natl Labs, Livermore, CA 94551 USA. EM mdallen@sandia.gov NR 13 TC 0 Z9 0 U1 1 U2 24 PU ELECTROCHEMICAL SOC INC PI PENNINGTON PA 65 S MAIN ST, PENNINGTON, NJ 08534-2839 USA SN 1938-5862 BN 978-1-62332-102-4; 978-1-60768-456-5 J9 ECS TRANSACTIONS PY 2013 VL 58 IS 11 BP 21 EP 28 DI 10.1149/05811.0021ecst PG 8 WC Electrochemistry; Energy & Fuels SC Electrochemistry; Energy & Fuels GA BJO98 UT WOS:000329445000003 ER PT B AU Rahman, R Hollenberg, LCL Klimeck, G AF Rahman, Rajib Hollenberg, Lloyd C. L. Klimeck, Gerhard BE Prati, E Shinada, T TI Theory and Simulations of Controlled Electronic States Bound to a Single Dopant in Silicon SO SINGLE-ATOM NANOELECTRONICS LA English DT Article; Book Chapter ID QUANTUM DOTS; NEMO 3-D; ATOM; SEMICONDUCTORS; SPECTROSCOPY C1 [Rahman, Rajib] Sandia Natl Labs, Albuquerque, NM 87185 USA. [Hollenberg, Lloyd C. L.; Klimeck, Gerhard] Purdue Univ, Sch Elect & Comp Engn, Network Computat Nanotechnol, W Lafayette, IN 47907 USA. RP Rahman, R (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87185 USA. EM rrahman@purdue.edu OI Rahman, Rajib/0000-0003-1649-823X NR 32 TC 0 Z9 0 U1 0 U2 1 PU PAN STANFORD PUBLISHING PTE LTD PI SINGAPORE PA PENTHOUSE LEVEL, SUNTEC TOWER 3, 8 TEMASEK BLVD, SINGAPORE, 038988, SINGAPORE BN 978-981-4316-69-9; 978-981-4316-31-6 PY 2013 BP 41 EP 59 PG 19 WC Engineering, Electrical & Electronic; Nanoscience & Nanotechnology SC Engineering; Science & Technology - Other Topics GA BJH99 UT WOS:000328280800004 ER PT B AU Schenkel, T Lo, CC Weis, CD Bokor, J Tyryshkin, AM Lyon, SA AF Schenkel, Thomas Lo, Cheuk Chi Weis, Christoph D. Bokor, Jeffrey Tyryshkin, Alexei M. Lyon, Stephen A. BE Prati, E Shinada, T TI A Spin Quantum Bit Architecture with Coupled Donors and Quantum Dots in Silicon SO SINGLE-ATOM NANOELECTRONICS LA English DT Article; Book Chapter ID SINGLE-SHOT READOUT; ELECTRON-SPIN; ION-IMPLANTATION; NUCLEAR-SPIN; COMPUTATION; TRANSISTOR; DIFFUSION; COMPUTER; SURFACE; QUBITS C1 [Schenkel, Thomas; Lo, Cheuk Chi; Weis, Christoph D.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Accelerator & Fus Res, Ion Beam Technol Grp, Berkeley, CA 94720 USA. [Lo, Cheuk Chi; Bokor, Jeffrey] Univ Calif Berkeley, Dept Elect Engn & Comp Sci, Berkeley, CA 94720 USA. [Tyryshkin, Alexei M.; Lyon, Stephen A.] Princeton Univ, Dept Elect Engn, Princeton, NJ 08544 USA. RP Schenkel, T (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Accelerator & Fus Res, Ion Beam Technol Grp, Berkeley, CA 94720 USA. EM T_schenkel@lbl.gov RI Bokor, Jeffrey/A-2683-2011 NR 80 TC 3 Z9 3 U1 0 U2 6 PU PAN STANFORD PUBLISHING PTE LTD PI SINGAPORE PA PENTHOUSE LEVEL, SUNTEC TOWER 3, 8 TEMASEK BLVD, SINGAPORE, 038988, SINGAPORE BN 978-981-4316-69-9; 978-981-4316-31-6 PY 2013 BP 255 EP 279 PG 25 WC Engineering, Electrical & Electronic; Nanoscience & Nanotechnology SC Engineering; Science & Technology - Other Topics GA BJH99 UT WOS:000328280800012 ER PT J AU White, JR AF White, J. R. BE Chang, FK TI Passive Damage Monitoring of Wind Turbine Rotor Blades Using Cyclic Signal Processing SO STRUCTURAL HEALTH MONITORING 2011: CONDITION-BASED MAINTENANCE AND INTELLIGENT STRUCTURES, VOL 2 SE Structural Health Monitoring LA English DT Proceedings Paper CT 8th International Workshop on Structural Health Monitoring CY SEP 13-15, 2011 CL Stanford Univ, Stanford, CA SP AF Off Sci Res, Army Res Off, Natl Sci Fdn, Off Naval Res HO Stanford Univ AB As of Q1 2011, 41,400 MW of wind energy had been installed in the US and those installations are on pace to achieve the US DOE goal of 20% wind energy by 2030. With this increased level of penetration from wind generation, the stability of the electrical grid will become dependent on the reliability of offshore and terrestrial wind turbines. Structural health monitoring (SHM) integrated into the Operations & Maintenance (O&M) strategy of wind plants has the ability to both increase reliability and reduce O&M costs. Sandia National Laboratories Wind Energy Technologies Department (SNL) has been actively researching SHM technologies at the sub-component, component, and full system levels in both computational and experimental efforts for both terrestrial and offshore wind plants. SNL commissioned the fabrication of a Sensored rotor blade during Spring 2008 as a test bed for promising wind rotor monitoring technologies, including strain gages, fiber Bragg gratings, RTD temperature sensors and accelerometers. Following operational testing, the rotor blade was shipped to the National Renewable Energy Laboratory National Wind Technology Center to test structural health monitoring techniques during a fatigue to failure rotor blade test. To understand the structural state of the rotor blade, a method was devised to estimate Frequency Response Functions from the fatigue excitation and response. The results showed that the method for estimating FRFs could be used to monitor the fatigue test magnitude, phase and structural characteristics throughout the 2M cycle test. C1 Sandia Natl Labs, Albuquerque, NM 87123 USA. RP White, JR (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87123 USA. NR 6 TC 0 Z9 0 U1 0 U2 1 PU DESTECH PUBLICATIONS, INC PI LANCASTER PA 439 DUKE STREET, LANCASTER, PA 17602-4967 USA BN 978-1-60595-053-2 J9 STRUCT HLTH MONIT PY 2013 BP 1648 EP 1655 PG 8 WC Engineering, Multidisciplinary SC Engineering GA BJH31 UT WOS:000328194500037 ER PT J AU Sheng, S AF Sheng, S. BE Chang, FK TI Investigation of Various Condition Monitoring Techniques Based on a Damaged Wind Turbine Gearbox SO STRUCTURAL HEALTH MONITORING 2011: CONDITION-BASED MAINTENANCE AND INTELLIGENT STRUCTURES, VOL 2 SE Structural Health Monitoring LA English DT Proceedings Paper CT 8th International Workshop on Structural Health Monitoring CY SEP 13-15, 2011 CL Stanford Univ, Stanford, CA SP AF Off Sci Res, Army Res Off, Natl Sci Fdn, Off Naval Res HO Stanford Univ AB The National Renewable Energy Laboratory presented an investigation of various wind turbine drivetrain condition monitoring (CM) techniques at the 7th International Workshop on Structural Health Monitoring held in 2009. The study contained in this report is a continuation of the 2009 paper and focuses on results obtained by various CM techniques from a damaged Gearbox Reliability Collaborative test gearbox. The purpose of the study is to demonstrate the capabilities and limitations of each technique. In order to provide the audience a relatively complete picture, a brief discussion of CM system implementation is provided first. The dynamometer test setup, along with some failure information on the damaged gearbox obtained during its disassembly, is presented next, followed by the CM results obtained during the retest of the damaged gearbox. For comparison and discussion purposes, earlier results obtained from a test gearbox under healthy condition will also be included. Finally, the paper will conclude with some observations obtained during the tests. C1 Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Sheng, S (reprint author), Natl Renewable Energy Lab, 1617 Cole Blvd, Golden, CO 80401 USA. NR 7 TC 0 Z9 0 U1 0 U2 1 PU DESTECH PUBLICATIONS, INC PI LANCASTER PA 439 DUKE STREET, LANCASTER, PA 17602-4967 USA BN 978-1-60595-053-2 J9 STRUCT HLTH MONIT PY 2013 BP 1664 EP 1671 PG 8 WC Engineering, Multidisciplinary SC Engineering GA BJH31 UT WOS:000328194500039 ER PT J AU Park, G Farinholt, KM Taylor, SG Farrar, CR AF Park, G. Farinholt, K. M. Taylor, S. G. Farrar, C. R. BE Chang, FK TI A Full-Scale Fatigue Test of 9-m CX-100 Wind Turbine Blades SO STRUCTURAL HEALTH MONITORING 2011: CONDITION-BASED MAINTENANCE AND INTELLIGENT STRUCTURES, VOL 2 SE Structural Health Monitoring LA English DT Proceedings Paper CT 8th International Workshop on Structural Health Monitoring CY SEP 13-15, 2011 CL Stanford Univ, Stanford, CA SP AF Off Sci Res, Army Res Off, Natl Sci Fdn, Off Naval Res HO Stanford Univ ID VALIDATION AB This paper presents the SHM result of a 9m CX-100 wind turbine blade under full-scale fatigue loads. The test was performed at the National Renewable Energy Laboratory. The 9-meter blade was instrumented with piezoelectric transducers, accelerometers, acoustic emission sensors, and foil strain gauges on the surface of the blade. The blade underwent fatigue excitation at 1.8 Hz for defined intervals, and data from the sensors were collected between and during fatigue loading sessions. The data were measured at multi-scale, high frequency ranges for identifying fatigue damage initiation, and low-frequency ranges for assessing damage progression. High and Low frequency response functions, time series based methods, and Lamb wave date measured by piezoelectric transducers were utilized to analyze the condition of the turbine blade, along with other sensing systems (acoustic emission). A specially designed hardware developed by Los Alamos National Laboratory was also implemented for performance comparison. This paper summarizes considerations needed to design such SHM systems, experimental procedures and results, and additional issues that can be used as guidelines for future investigations. C1 [Park, G.; Farinholt, K. M.; Taylor, S. G.; Farrar, C. R.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Park, G (reprint author), Los Alamos Natl Lab, Los Alamos, NM 87545 USA. NR 6 TC 0 Z9 0 U1 1 U2 2 PU DESTECH PUBLICATIONS, INC PI LANCASTER PA 439 DUKE STREET, LANCASTER, PA 17602-4967 USA BN 978-1-60595-053-2 J9 STRUCT HLTH MONIT PY 2013 BP 2655 EP 2662 PG 8 WC Engineering, Multidisciplinary SC Engineering GA BJH31 UT WOS:000328194500158 ER PT J AU Phillips, CL McFarlane, KJ Risk, D Desai, AR AF Phillips, C. L. McFarlane, K. J. Risk, D. Desai, A. R. TI Biological and physical influences on soil (CO2)-C-14 seasonal dynamics in a temperate hardwood forest SO BIOGEOSCIENCES LA English DT Article ID GAS-DIFFUSION COEFFICIENT; CO2 EFFLUX; CARBON-DIOXIDE; PARTITIONING SOURCES; NORTHERN WISCONSIN; ORGANIC-CARBON; BOREAL FOREST; RESPIRED CO2; RESPIRATION; RADIOCARBON AB While radiocarbon (C-14) abundances in standing stocks of soil carbon have been used to evaluate rates of soil carbon turnover on timescales of several years to centuries, soil-respired (CO2)-C-14 measurements are an important tool for identifying more immediate responses to disturbance and climate change. Soil Delta(CO2)-C-14 data, however, are often temporally sparse and could be interpreted better with more context for typical seasonal ranges and trends. We report on a semi-high-frequency sampling campaign to distinguish physical and biological drivers of soil Delta(CO2)-C-14 at a temperate forest site in northern Wisconsin, USA. We sampled (CO2)-C-14 profiles every three weeks during snow-free months through 2012 in three intact plots and one trenched plot that excluded roots. Respired Delta(CO2)-C-14 declined through the summer in intact plots, shifting from an older C composition that contained more bomb C-14 to a younger composition more closely resembling present C-14 levels in the atmosphere. In the trenched plot, respired Delta(CO2)-C-14 was variable but remained comparatively higher than in intact plots, reflecting older bomb-enriched C-14 sources. Although respired Delta(CO2)-C-14 from intact plots correlated with soil moisture, related analyses did not support a clear cause-and-effect relationship with moisture. The initial decrease in Delta(CO2)-C-14 from spring to midsummer could be explained by increases in C-14-deplete root respiration; however, Delta(CO2)-C-14 continued to decline in late summer after root activity decreased. We also investigated whether soil moisture impacted vertical partitioning of CO2 production, but found this had little effect on respired Delta(CO2)-C-14 because CO2 contained modern bomb C at depth, even in the trenched plot. This surprising result contrasted with decades to centuries-old pre-bomb CO2 produced in lab incubations of the same soils. Our results suggest that root-derived C and other recent C sources had dominant impacts on respired Delta(CO2)-C-14 in situ, even at depth. We propose that Delta(CO2)-C-14 may have declined through late summer in intact plots because of continued microbial turnover of root-derived C, following declines in root respiration. Our results agree with other studies showing declines in the C-14 content of soil respiration over the growing season, and suggest inputs of new photosynthates through roots are an important driver. C1 [Phillips, C. L.; McFarlane, K. J.] Lawrence Livermore Natl Lab, Ctr Accelerator Mass Spectrometry, Livermore, CA 94550 USA. [Risk, D.] St Francis Xavier Univ, Dept Earth Sci, Antigonish, NS B2G 1C0, Canada. [Desai, A. R.] Univ Wisconsin, Dept Atmospher & Ocean Sci, Madison, WI USA. RP Phillips, CL (reprint author), Oregon State Univ, Dept Crops & Soil Sci, Corvallis, OR 97331 USA. EM claire.phillips@oregonstate.edu RI Desai, Ankur/A-5899-2008; OI Desai, Ankur/0000-0002-5226-6041; McFarlane, Karis/0000-0001-6390-7863 FU US Department of Energy by Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Lawrence Livermore National Laboratory [LDRD 11-ERD-053]; Wisconsin Focus on Energy Environmental and Economic Research and Development (EERD) [10-06. LLNL-JRNL-637140] FX Field assistance was provided by J. Thom (UW) and D. Baumann (USGS), and laboratory assistance was provided by P. Zermeno and L. Larson (LLNL). This work was performed under the auspices of the US Department of Energy by Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344, with support from Lawrence Livermore National Laboratory (LDRD 11-ERD-053) and the Wisconsin Focus on Energy Environmental and Economic Research and Development (EERD) grant# 10-06. LLNL-JRNL-637140. NR 40 TC 11 Z9 11 U1 1 U2 21 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 1726-4170 EI 1726-4189 J9 BIOGEOSCIENCES JI Biogeosciences PY 2013 VL 10 IS 12 BP 7999 EP 8012 DI 10.5194/bg-10-7999-2013 PG 14 WC Ecology; Geosciences, Multidisciplinary SC Environmental Sciences & Ecology; Geology GA 280TV UT WOS:000329054600014 ER PT J AU Torn, MS Kleber, M Zavaleta, ES Zhu, B Field, CB Trumbore, SE AF Torn, M. S. Kleber, M. Zavaleta, E. S. Zhu, B. Field, C. B. Trumbore, S. E. TI A dual isotope approach to isolate soil carbon pools of different turnover times SO BIOGEOSCIENCES LA English DT Article ID ORGANIC-MATTER TURNOVER; PHYSICAL FRACTIONATION; MICROBIAL BIOMASS; NATURAL-ABUNDANCE; FOREST SOILS; RADIOCARBON MEASUREMENTS; NITROGEN MINERALIZATION; DENSITY FRACTIONATION; TEMPERATE SOILS; AGE CALIBRATION AB Soils are globally significant sources and sinks of atmospheric CO2. Increasing the resolution of soil carbon turnover estimates is important for predicting the response of soil carbon cycling to environmental change. We show that soil carbon turnover times can be more finely resolved using a dual isotope label like the one provided by elevated CO2 experiments that use fossil CO2. We modeled each soil physical fraction as two pools with different turnover times using the atmospheric C-14 bomb spike in combination with the label in C-14 and C-13 provided by an elevated CO2 experiment in a California annual grassland. In sandstone and serpentine soils, the light fraction carbon was 21-54% fast cycling with 2-9 yr turnover, and 36-79% slow cycling with turnover slower than 100 yr. This validates model treatment of the light fraction as active and intermediate cycling carbon. The dense, mineral-associated fraction also had a very dynamic component, consisting of similar to 7% fast-cycling carbon and similar to 93% very slow cycling carbon. Similarly, half the microbial biomass carbon in the sandstone soil was more than 5 yr old, and 40% of the carbon respired by microbes had been fixed more than 5 yr ago. Resolving each density fraction into two pools revealed that only a small component of total soil carbon is responsible for most CO2 efflux from these soils. In the sandstone soil, 11% of soil carbon contributes more than 90% of the annual CO2 efflux. The fact that soil physical fractions, designed to isolate organic material of roughly homogeneous physico-chemical state, contain material of dramatically different turnover times is consistent with recent observations of rapid isotope incorporation into seemingly stable fractions and with emerging evidence for hot spots or micro-site variation of decomposition within the soil matrix. Predictions of soil carbon storage using a turnover time estimated with the assumption of a single pool per density fraction would greatly overestimate the near-term response to changes in productivity or decomposition rates. Therefore, these results suggest a slower initial change in soil carbon storage due to environmental change than has been assumed by simpler (one-pool) mass balance calculations. C1 [Torn, M. S.; Zhu, B.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. [Torn, M. S.] Univ Calif Berkeley, Energy & Resources Grp, Berkeley, CA 94720 USA. [Kleber, M.] Oregon State Univ, Dept Crop & Soil Sci, Corvallis, OR 97331 USA. [Zavaleta, E. S.] Univ Calif Santa Cruz, Dept Environm Studies, Santa Cruz, CA 95064 USA. [Field, C. B.] Carnegie Inst Sci, Dept Global Ecol, Stanford, CA 94305 USA. [Trumbore, S. E.] Max Planck Inst Biogeochem, Dept Biogeochem Proc, D-07745 Jena, Germany. RP Torn, MS (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. EM mstorn@lbl.gov RI Zhu, Biao/F-8712-2010; Torn, Margaret/D-2305-2015 OI Zhu, Biao/0000-0001-9858-7943; FU Laboratory Directed Research and Development Program at Lawrence Berkeley National Laboratory, US Department of Energy [DE-AC03-76SF00098]; Office of Science, US Department of Energy [DE-AC02-05CH11231]; US National Science Foundation FX This work was supported by the Laboratory Directed Research and Development Program at Lawrence Berkeley National Laboratory, US Department of Energy under contract no. DE-AC03-76SF00098 and by the Office of Science, US Department of Energy under contract no. DE-AC02-05CH11231. The Jasper Ridge elevated CO2 experiment was supported by grants from the US National Science Foundation to the Carnegie Institution for Science, Stanford University, and University of California, Berkeley. We thank two anonymous reviewers for their valuable comments that improved this manuscript. NR 66 TC 8 Z9 8 U1 4 U2 87 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 1726-4170 EI 1726-4189 J9 BIOGEOSCIENCES JI Biogeosciences PY 2013 VL 10 IS 12 BP 8067 EP 8081 DI 10.5194/bg-10-8067-2013 PG 15 WC Ecology; Geosciences, Multidisciplinary SC Environmental Sciences & Ecology; Geology GA 280TV UT WOS:000329054600017 ER PT J AU Tang, JY Riley, WJ AF Tang, J. Y. Riley, W. J. TI A total quasi-steady-state formulation of substrate uptake kinetics in complex networks and an example application to microbial litter decomposition SO BIOGEOSCIENCES LA English DT Article ID SOIL ORGANIC-MATTER; MICHAELIS-MENTEN KINETICS; NUTRIENT-UPTAKE; ENZYME-KINETICS; LEAF-LITTER; TEMPERATURE SENSITIVITY; CHEMICAL-REACTIONS; NITROGEN DYNAMICS; ACTIVATED COMPLEX; FOREST ECOSYSTEMS AB We demonstrate that substrate uptake kinetics in any consumer-substrate network subject to the total quasi-steady-state assumption can be formulated as an equilibrium chemistry (EC) problem. If the consumer-substrate complexes equilibrate much faster than other metabolic processes, then the relationships between consumers, substrates, and consumer-substrate complexes are in quasi-equilibrium and the change of a given total substrate (free plus consumer-bounded) is determined by the degradation of all its consumer-substrate complexes. In this EC formulation, the corresponding equilibrium reaction constants are the conventional Michaelis-Menten (MM) substrate affinity constants. When all of the elements in a given network are either consumer or substrate (but not both), we derived a first-order accurate EC approximation (ECA). The ECA kinetics is compatible with almost every existing extension of MM kinetics. In particular, for microbial organic matter decomposition modeling, ECA kinetics explicitly predicts a specific microbe's uptake for a specific substrate as a function of the microbe's affinity for the substrate, other microbes' affinity for the substrate, and the shielding effect on substrate uptake by environmental factors, such as mineral surface adsorption. By taking the EC solution as a reference, we evaluated MM and ECA kinetics for their abilities to represent several differently configured enzyme-substrate reaction networks. In applying the ECA and MM kinetics to microbial models of different complexities, we found (i) both the ECA and MM kinetics accurately reproduced the EC solution when multiple microbes are competing for a single substrate; (ii) ECA outperformed MM kinetics in reproducing the EC solution when a single microbe is feeding on multiple substrates; (iii) the MM kinetics failed, while the ECA kinetics succeeded, in reproducing the EC solution when multiple consumers (i.e., microbes and mineral surfaces) were competing for multiple substrates. We then applied the EC and ECA kinetics to a guild based C-only microbial litter decomposition model and found that both approaches successfully simulated the commonly observed (i) two-phase temporal evolution of the decomposition dynamics; (ii) final asymptotic convergence of the lignocellulose index to a constant that depends on initial litter chemistry and microbial community structure; and (iii) microbial biomass proportion of total organic biomass (litter plus microbes). In contrast, the MM kinetics failed to realistically predict these metrics. We therefore conclude that the ECA kinetics are more robust than the MM kinetics in representing complex microbial, C substrate, and mineral surface interactions. Finally, we discuss how these concepts can be applied to other consumer-substrate networks. C1 [Tang, J. Y.; Riley, W. J.] Lawrence Berkeley Natl Lab LBL, Div Earth Sci, Berkeley, CA 94720 USA. RP Tang, JY (reprint author), Lawrence Berkeley Natl Lab LBL, Div Earth Sci, Berkeley, CA 94720 USA. EM jinyuntang@lbl.gov RI Tang, Jinyun/M-4922-2013; Riley, William/D-3345-2015 OI Tang, Jinyun/0000-0002-4792-1259; Riley, William/0000-0002-4615-2304 FU Office of Science, Office of Biological and Environmental Research of the US Department of Energy [DE-AC02-05CH11231]; Next-Generation Ecosystem Experiments (NGEE Arctic) project; Office of Biological and Environmental Research in the DOE Office of Science [DE-AC02-05CH11231] FX This research was supported by the Director, Office of Science, Office of Biological and Environmental Research of the US Department of Energy, under contract no. DE-AC02-05CH11231, as part of their Regional and Global Climate Modeling Program; and by the Next-Generation Ecosystem Experiments (NGEE Arctic) project, supported by the Office of Biological and Environmental Research in the DOE Office of Science under contract no. DE-AC02-05CH11231. NR 115 TC 15 Z9 15 U1 6 U2 25 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 1726-4170 EI 1726-4189 J9 BIOGEOSCIENCES JI Biogeosciences PY 2013 VL 10 IS 12 BP 8329 EP 8351 DI 10.5194/bg-10-8329-2013 PG 23 WC Ecology; Geosciences, Multidisciplinary SC Environmental Sciences & Ecology; Geology GA 280TV UT WOS:000329054600033 ER PT J AU Durden, DJ Nappo, CJ Leclerc, MY Duarte, HF Zhang, G Parker, MJ Kurzeja, RJ AF Durden, D. J. Nappo, C. J. Leclerc, M. Y. Duarte, H. F. Zhang, G. Parker, M. J. Kurzeja, R. J. TI On the impact of wave-like disturbances on turbulent fluxes and turbulence statistics in nighttime conditions: a case study SO BIOGEOSCIENCES LA English DT Article ID NOCTURNAL BOUNDARY-LAYER; INTERNAL GRAVITY-WAVES; EDDY COVARIANCE; ANTARCTICA; EXCHANGE; NETWORK; LEVEL; FLOW AB The interpretation of flux measurements in nocturnal conditions is typically fraught with challenges. This paper reports on how the presence of wave-like disturbances in a time series, can lead to an overestimation of turbulence statistics, errors when calculating the stability parameter, erroneous estimation of the friction velocity u* used to screen flux data, and errors in turbulent flux calculations. Using time series of the pressure signal from a microbarograph, wavelike disturbances at an AmeriFlux site are identified. The wave-like disturbances are removed during the calculation of turbulence statistics and turbulent fluxes. Our findings suggest that filtering eddy-covariance data in the presence of wave-like events prevents both an overestimation of turbulence statistics and errors in turbulent flux calculations. Results show that large-amplitude wave-like events, events surpassing three standard deviations, occurred on 18% of the nights considered in the present study. Remarkably, on flux towers located in a very stably stratified boundary-layer regime, the presence of a gravity wave can enhance turbulence statistics more than 50 %. In addition, the presence of the disturbance modulates the calculated turbulent fluxes of CO2 resulting in erroneous turbulent flux calculations of the order of 10% depending on averaging time and pressure perturbation threshold criteria. Furthermore, the friction velocity u* was affected by the presence of the wave, and in at least one case, a 10% increase caused u* to exceed the arbitrary 0.25 m s(-1) threshold used in many studies. This results in an unintended bias in the data selected for analysis in the flux calculations. The impact of different averaging periods was also examined and found to be variable specific. These early case study results provide an insight into errors introduced when calculating "purely" turbulent fluxes. These results could contribute to improving modeling efforts by providing more accurate inputs of both turbulent kinetic energy, and isolating the turbulent component of u* for flux selection in the stable nocturnal boundary layer. C1 [Durden, D. J.; Leclerc, M. Y.; Duarte, H. F.; Zhang, G.] Univ Georgia, Lab Environm Phys, Griffin, GA 30223 USA. [Nappo, C. J.] CJN Res Meteorol, Knoxville, TN 37919 USA. [Parker, M. J.; Kurzeja, R. J.] Savannah River Natl Lab, Aiken, SC 29802 USA. RP Leclerc, MY (reprint author), Univ Georgia, Lab Environm Phys, Griffin, GA 30223 USA. EM mleclerc@uga.edu OI Durden, David/0000-0001-9572-8325 FU US Dept. of Energy, Office of Science, Terrestrial Carbon Processes [ER64321] FX We wish to extend our thanks for D. Cotten for his input and useful comments on the manuscript as well. The present study was conducted thanks to a grant from the US Dept. of Energy, Office of Science, Terrestrial Carbon Processes grant no. ER64321. NR 34 TC 6 Z9 6 U1 1 U2 8 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 1726-4170 EI 1726-4189 J9 BIOGEOSCIENCES JI Biogeosciences PY 2013 VL 10 IS 12 BP 8433 EP 8443 DI 10.5194/bg-10-8433-2013 PG 11 WC Ecology; Geosciences, Multidisciplinary SC Environmental Sciences & Ecology; Geology GA 280TV UT WOS:000329054600040 ER PT J AU Pesce, LL Lee, HC Hereld, M Visser, S Stevens, RL Wildeman, A van Drongelen, W AF Pesce, Lorenzo L. Lee, Hyong C. Hereld, Mark Visser, Sid Stevens, Rick L. Wildeman, Albert van Drongelen, Wim TI Large-Scale Modeling of Epileptic Seizures: Scaling Properties of Two Parallel Neuronal Network Simulation Algorithms SO COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE LA English DT Article ID IN-VITRO; DYNAMICS; NEUROSCIENCE; FRAMEWORK; NEOCORTEX AB Our limited understanding of the relationship between the behavior of individual neurons and large neuronal networks is an important limitation in current epilepsy research and may be one of the main causes of our inadequate ability to treat it. Addressing this problem directly via experiments is impossibly complex; thus, we have been developing and studying medium-large-scale simulations of detailed neuronal networks to guide us. Flexibility in the connection schemas and a complete description of the cortical tissue seem necessary for this purpose. In this paper we examine some of the basic issues encountered in these multiscale simulations. We have determined the detailed behavior of two such simulators on parallel computer systems. The observed memory and computation-time scaling behavior for a distributed memory implementation were very good over the range studied, both in terms of network sizes (2,000 to 400,000 neurons) and processor pool sizes (1 to 256 processors). Our simulations required between a few megabytes and about 150 gigabytes of RAM and lasted between a few minutes and about a week, well within the capability of most multinode clusters. Therefore, simulations of epileptic seizures on networks with millions of cells should be feasible on current supercomputers. C1 [Pesce, Lorenzo L.; Lee, Hyong C.; Visser, Sid; Wildeman, Albert; van Drongelen, Wim] Univ Chicago, Dept Pediat, Chicago, IL 60637 USA. [Pesce, Lorenzo L.; Hereld, Mark; Stevens, Rick L.] Univ Chicago, Computat Inst, Argonne, IL 60439 USA. [Pesce, Lorenzo L.; Hereld, Mark; Stevens, Rick L.] Argonne Natl Labs, Argonne, IL 60439 USA. [Hereld, Mark; Stevens, Rick L.] Argonne Natl Labs, Math & Comp Sci Div, Argonne, IL 60439 USA. [van Drongelen, Wim] Univ Chicago, Dept Neurol, Chicago, IL 60637 USA. [van Drongelen, Wim] Univ Chicago, Comm Computat Neurosci, Chicago, IL 60637 USA. RP Pesce, LL (reprint author), Univ Chicago, Dept Pediat, Chicago, IL 60637 USA. EM lpesce@uchicago.edu OI van Drongelen, Wim/0000-0001-8950-5424; Hereld, Mark/0000-0002-0268-2880 FU Dr. Ralph and Marian Falk Medical Research Trust; NIH [S10 RR029030-01]; Office of Advanced Scientific Computing Research, Office of Science, U.S. Department of Energy [DE-AC02-06CH11357] FX This work was supported by the Dr. Ralph and Marian Falk Medical Research Trust. This research was supported in part by NIH through resources provided by the Computation Institute and the Biological Sciences Division of the University of Chicago and Argonne National Laboratory, under Grant S10 RR029030-01, and in part by the Office of Advanced Scientific Computing Research, Office of Science, U.S. Department of Energy, under Contract DE-AC02-06CH11357. The authors specifically acknowledge the assistance of Greg Cross. NR 34 TC 0 Z9 0 U1 1 U2 6 PU HINDAWI PUBLISHING CORPORATION PI NEW YORK PA 410 PARK AVENUE, 15TH FLOOR, #287 PMB, NEW YORK, NY 10022 USA SN 1748-670X EI 1748-6718 J9 COMPUT MATH METHOD M JI Comput. Math. Method Med. PY 2013 AR UNSP 182145 DI 10.1155/2013/182145 PG 10 WC Mathematical & Computational Biology SC Mathematical & Computational Biology GA 279TW UT WOS:000328983300001 ER PT J AU Gudavalli, R Katsenovich, Y Wellman, D Lagos, L Tansel, B AF Gudavalli, Ravi Katsenovich, Yelena Wellman, Dawn Lagos, Leonel Tansel, Berrin TI Quantification of kinetic rate law parameters of uranium release from sodium autunite as a function of aqueous bicarbonate concentrations SO ENVIRONMENTAL CHEMISTRY LA English DT Article ID SOLUTION SATURATION STATE; DISSOLUTION KINETICS; META-AUTUNITE; PH; CARBONATE; TEMPERATURE; MINERALS; PHASES; WASTE AB Hydrogen carbonate (also known as bicarbonate) is one of the most significant components within the uranium geochemical cycle. In aqueous solutions, bicarbonate forms strong complexes with uranium. As such, aqueous bicarbonate may significantly increase the rate of uranium release from uranium minerals. Quantifying the relationship of aqueous bicarbonate solutions to the rate of uranium release during dissolution is critical to understanding the long-term fate of uranium within the environment. Single-pass flow-through experiments were conducted to estimate the rate of uranium release from Na meta-autunite as a function of bicarbonate solutions (0.0005-0.003M) over the pH range of 6-11 and temperatures of 5-60 degrees C. Consistent with the results of previous investigations, the rate of uranium release from sodium autunite exhibited minimal dependency on temperature, but was strongly dependent on pH and increasing concentrations of bicarbonate solutions. Most notably at pH 7, the rate of uranium release exhibited a 370-fold increase relative to the rate of uranium release in the absence of bicarbonate. However, the effect of increasing concentrations of bicarbonate solutions on the release of uranium was significantly less under higher pH conditions. It is postulated that at high pH values, surface sites are saturated with carbonate, thus the addition of more bicarbonate would have less effect on uranium release. Results indicate that the activation energies were unaffected by temperature and bicarbonate concentration variations, but were strongly dependent on pH conditions. As the pH increased from 6 to 11, the activation energy values were observed to decrease from 29.94 to 13.07kJmol(-1). The calculated activation energies suggest a surface controlled dissolution mechanism. C1 [Gudavalli, Ravi; Katsenovich, Yelena; Lagos, Leonel] Florida Int Univ, Appl Res Ctr, Miami, FL 33174 USA. [Gudavalli, Ravi; Tansel, Berrin] Florida Int Univ, Dept Civil & Environm Engn, Miami, FL 33174 USA. [Wellman, Dawn] US DOE, Pacific NW Natl Lab, Richland, WA 99352 USA. RP Katsenovich, Y (reprint author), Florida Int Univ, Appl Res Ctr, 10555 W Flagler St,Suite 2100, Miami, FL 33174 USA. EM katsenov@fiu.edu FU US Department of Energy, Office of Environmental Management; EM-30 Technology Innovation and Development Office [DE-EM0000598] FX Funding for this project was provided by the US Department of Energy, Office of Environmental Management, EM-30 Technology Innovation and Development Office under Grant DE-EM0000598. The authors gratefully acknowledge the efforts of K. Parker from Pacific Northwest National Laboratory for his help with the surface area analysis of synthetic autunite; as well as A. Henao and M. Iddaraga for their assistance in conducting KPA and ICP-OES analysis. The authors also acknowledge P. Shoffner for her comments and suggestions and Dr Y. Liu from the FIU Advanced Materials Engineering Research Institute (AMERI) for his assistance with the SEM/EDS analysis of synthetic autunite. Authors thank two anonymous reviewers for their valuable comments and suggestions that helped to improve this manuscript. NR 35 TC 1 Z9 1 U1 3 U2 9 PU CSIRO PUBLISHING PI COLLINGWOOD PA 150 OXFORD ST, PO BOX 1139, COLLINGWOOD, VICTORIA 3066, AUSTRALIA SN 1448-2517 EI 1449-8979 J9 ENVIRON CHEM JI Environ. Chem. PY 2013 VL 10 IS 6 BP 475 EP 485 DI 10.1071/EN13117 PG 11 WC Chemistry, Analytical; Environmental Sciences SC Chemistry; Environmental Sciences & Ecology GA 275BP UT WOS:000328650700004 ER PT J AU Sun, Y Hou, Z Huang, M Tian, F Leung, LR AF Sun, Y. Hou, Z. Huang, M. Tian, F. Leung, L. Ruby TI Inverse modeling of hydrologic parameters using surface flux and runoff observations in the Community Land Model SO HYDROLOGY AND EARTH SYSTEM SCIENCES LA English DT Article ID SOIL-MOISTURE; UNCERTAINTY ASSESSMENT; METROPOLIS ALGORITHM; IMPROVED CALIBRATION; GLOBAL OPTIMIZATION; SEISMIC AVA; CSEM DATA; RAINFALL; PREDICTION; CHRONOSEQUENCE AB This study demonstrates the possibility of inverting hydrologic parameters using surface flux and runoff observations in version 4 of the Community Land Model (CLM4). Previous studies showed that surface flux and runoff calculations are sensitive to major hydrologic parameters in CLM4 over different watersheds, and illustrated the necessity and possibility of parameter calibration. Both deterministic least-square fitting and stochastic Markov-chain Monte Carlo (MCMC)-Bayesian inversion approaches are evaluated by applying them to CLM4 at selected sites with different climate and soil conditions. The unknowns to be estimated include surface and subsurface runoff generation parameters and vadose zone soil water parameters. We find that using model parameters calibrated by the sampling-based stochastic inversion approaches provides significant improvements in the model simulations compared to using default CLM4 parameter values, and that as more information comes in, the predictive intervals (ranges of posterior distributions) of the calibrated parameters become narrower. In general, parameters that are identified to be significant through sensitivity analyses and statistical tests are better calibrated than those with weak or nonlinear impacts on flux or runoff observations. Temporal resolution of observations has larger impacts on the results of inverse modeling using heat flux data than runoff data. Soil and vegetation cover have important impacts on parameter sensitivities, leading to different patterns of posterior distributions of parameters at different sites. Overall, the MCMC-Bayesian inversion approach effectively and reliably improves the simulation of CLM under different climates and environmental conditions. Bayesian model averaging of the posterior estimates with different reference acceptance probabilities can smooth the posterior distribution and provide more reliable parameter estimates, but at the expense of wider uncertainty bounds. C1 [Sun, Y.; Hou, Z.; Huang, M.; Leung, L. Ruby] Pacific NW Natl Lab, Richland, WA 99352 USA. [Sun, Y.; Tian, F.] Tsinghua Univ, Dept Hydraul Engn, State Key Lab Hydrosci & Engn, Beijing 100084, Peoples R China. RP Hou, Z (reprint author), Pacific NW Natl Lab, POB 999, Richland, WA 99352 USA. EM zhangshuan.hou@pnnl.gov RI Huang, Maoyi/I-8599-2012; Tian, Fuqiang/M-9958-2013; Hou, Zhangshuan/B-1546-2014 OI Huang, Maoyi/0000-0001-9154-9485; Tian, Fuqiang/0000-0001-9414-7019; Hou, Zhangshuan/0000-0002-9388-6060 FU project Climate Science for a Sustainable Energy Future; Office of Science of the US DOE through the Earth System Modeling Program; US DOE by Battelle Memorial Institute [DE-AC05-76RLO1830]; National Science Foundation of China [NSFC51190092, 51222901]; foundation of the State Key Laboratory of Hydroscience and Engineering of Tsinghua University [2012-KY-03] FX This work is supported by the project Climate Science for a Sustainable Energy Future, funded by the Office of Science of the US DOE through the Earth System Modeling Program. The Pacific Northwest National Laboratory (PNNL) Platform for Regional Integrated Modeling and Analysis (PRIMA) Initiative provided support for the model configuration and data sets used in the numerical experiments. PNNL is operated for the US DOE by Battelle Memorial Institute under Contract DE-AC05-76RLO1830. Yu Sun and Fuqiang Tian would like to acknowledge the support from the National Science Foundation of China (NSFC51190092, 51222901) and the foundation of the State Key Laboratory of Hydroscience and Engineering of Tsinghua University (2012-KY-03). NR 42 TC 8 Z9 8 U1 1 U2 18 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 1027-5606 EI 1607-7938 J9 HYDROL EARTH SYST SC JI Hydrol. Earth Syst. Sci. PY 2013 VL 17 IS 12 BP 4995 EP 5011 DI 10.5194/hess-17-4995-2013 PG 17 WC Geosciences, Multidisciplinary; Water Resources SC Geology; Water Resources GA 280WL UT WOS:000329061400019 ER PT S AU Patton-Mallory, M Skog, KE Dale, VH AF Patton-Mallory, Marcia Skog, Kenneth E. Dale, Virginia H. BE Christopher, L TI Integrated Forest Biorefineries: Sustainability Considerations for Forest Biomass Feedstocks SO INTEGRATED FOREST BIOREFINERIES SE RSC Green Chemistry Series LA English DT Article; Book Chapter C1 [Patton-Mallory, Marcia] US Forest Serv, USDA, Pacific NW Res Stn, Seattle, WA 98103 USA. [Skog, Kenneth E.] US Forest Serv, USDA, Forest Prod Lab, Madison, WI 53726 USA. [Dale, Virginia H.] Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA. RP Patton-Mallory, M (reprint author), US Forest Serv, USDA, Pacific NW Res Stn, 400 N 34th St,Suite 201, Seattle, WA 98103 USA. EM mpattonmallory@fs.fed.us NR 21 TC 1 Z9 1 U1 0 U2 1 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, CAMBRIDGE CB4 4WF, CAMBS, ENGLAND SN 1757-7039 BN 978-1-84973-506-3; 978-1-84973-321-2 J9 RSC GREEN CHEM SER PY 2013 IS 18 BP 80 EP 97 DI 10.1039/9781849735063-00080 D2 10.1039/9781849735063 PG 18 WC Biotechnology & Applied Microbiology; Materials Science, Paper & Wood SC Biotechnology & Applied Microbiology; Materials Science GA BJJ32 UT WOS:000328484600004 ER PT S AU Levin, DB Job, JH Maness, PC AF Levin, David B. Job, Ji Hye Maness, Pin-Ching BE Christopher, L TI Biohydrogen Production from Cellulosic Biomass SO INTEGRATED FOREST BIOREFINERIES SE RSC Green Chemistry Series LA English DT Article; Book Chapter ID FERMENTATIVE HYDROGEN-PRODUCTION; THERMOCELLUM ATCC 27405; THERMOPHILE CALDICELLULOSIRUPTOR-SACCHAROLYTICUS; IMMOBILIZED ANAEROBIC SLUDGE; CLOSTRIDIUM-THERMOCELLUM; ENTEROBACTER-AEROGENES; MICROBIAL-PRODUCTION; DARK FERMENTATION; FLUIDIZED-BED; WASTE-WATER C1 [Levin, David B.] Univ Manitoba, Dept Biosyst Engn, Winnipeg, MB R3T 5V6, Canada. [Job, Ji Hye; Maness, Pin-Ching] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Levin, DB (reprint author), Univ Manitoba, Dept Biosyst Engn, Winnipeg, MB R3T 5V6, Canada. EM levindb@ad.umanitoba.ca NR 105 TC 0 Z9 0 U1 0 U2 0 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, CAMBRIDGE CB4 4WF, CAMBS, ENGLAND SN 1757-7039 BN 978-1-84973-506-3; 978-1-84973-321-2 J9 RSC GREEN CHEM SER PY 2013 IS 18 BP 256 EP 275 DI 10.1039/9781849735063-00256 D2 10.1039/9781849735063 PG 20 WC Biotechnology & Applied Microbiology; Materials Science, Paper & Wood SC Biotechnology & Applied Microbiology; Materials Science GA BJJ32 UT WOS:000328484600011 ER PT J AU Brown, MJ Gowardhan, AA Nelson, MA Williams, MD Pardyjak, ER AF Brown, Michael J. Gowardhan, Akshay A. Nelson, Mathew A. Williams, Michael D. Pardyjak, Eric R. TI QUIC transport and dispersion modelling of two releases from the Joint Urban 2003 field experiment SO INTERNATIONAL JOURNAL OF ENVIRONMENT AND POLLUTION LA English DT Article DE urban dispersion; fast-response plume modelling; random walk dispersion modelling; flow around buildings; validation; Joint Urban 2003 tracer field experiment ID ULTRAFINE PARTICLES; FLOW; SIMULATIONS; AREA; SCALE AB An in-depth comparison of plume calculations from the Quick Urban and Industrial Complex (QUIC) dispersion model to street- and roof-level concentration measurements for a daytime and night time release taken during the Joint Urban 2003 field experiment held in downtown Oklahoma City is presented. A number of improvements to the empirical-diagnostic wind solver to better account for high-rise buildings and dense urban areas will be discussed. Traditional plume statistical performance measures reveal that the code is performing as well as computational fluid dynamics models and meets the criteria proposed by Hanna and Chang (2012) for urban dispersion models. Statistics for the day and night release are fairly similar, and model performance drops slightly after the release is turned off in the flushing phase. Scatterplots indicate that rooftop measurements were generally well predicted, although the percentage of outliers (false negatives, large over predictions) was greater as compared to street-level measurements. Using all tracer data within a kilometre of the release, including rooftop samplers, from 39 to 46% of the model-computed concentrations were within a factor of two of the observations when broken up into four cases stratified by day or night and release on or off. C1 [Brown, Michael J.; Gowardhan, Akshay A.; Nelson, Mathew A.; Williams, Michael D.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. [Gowardhan, Akshay A.] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. [Pardyjak, Eric R.] Univ Utah, Dept Mech Engn, Salt Lake City, UT 84112 USA. RP Brown, MJ (reprint author), Los Alamos Natl Lab, Los Alamos, NM 87545 USA. EM mbrown@lanl.gov; gowardhan1@llnl.gov; nelsonm@lanl.gov; mdw@lanl.gov; pardyjak@gmail.com OI Brown, Michael J./0000-0002-8069-0835 NR 49 TC 7 Z9 7 U1 3 U2 9 PU INDERSCIENCE ENTERPRISES LTD PI GENEVA PA WORLD TRADE CENTER BLDG, 29 ROUTE DE PRE-BOIS, CASE POSTALE 856, CH-1215 GENEVA, SWITZERLAND SN 0957-4352 EI 1741-5101 J9 INT J ENVIRON POLLUT JI Int. J. Environ. Pollut. PY 2013 VL 52 IS 3-4 BP 263 EP 287 DI 10.1504/IJEP.2013.058458 PG 25 WC Environmental Sciences SC Environmental Sciences & Ecology GA 282JV UT WOS:000329168200009 ER PT J AU Aartsen, MG Abbasi, R Abdou, Y Ackermann, M Adams, J Aguilar, JA Ahlers, M Altmann, D Auffenberg, J Bai, X Baker, M Barwick, SW Baum, V Bay, R Beatty, JJ Bechet, S Becker, KH Tjus, JB Bell, M Benabderrahmane, ML BenZvi, S Berdermann, J Berghaus, P Berley, D Bernardini, E Bernhard, A Bertrand, D Besson, DZ Binder, G Bindig, D Bissok, M Blaufuss, E Blumenthal, J Boersma, DJ Bohaichuk, S Bohm, C Bose, D Boser, S Botner, O Brayeur, L Bretz, HP Brown, AM Bruijn, R Brunner, J Carson, M Casey, J Casier, M Cherwinka, J Chirkin, D Christov, A Christy, B Clark, K Clevermann, F Coenders, S Cohen, S Cowen, DF Silva, AHC Danninger, M Daughhetee, J Davis, JC De Clercq, C De Ridder, S Desiati, P de With, M DeYoung, T Diaz-Velez, JC Dunkman, M Eagan, R Eberhardt, B Eisch, J Ellsworth, RW Euler, S Evenson, PA Fadiran, O Fazely, AR Fedynitch, A Feintzeig, J Feusels, T Filimonov, K Finley, C Fischer-Wasels, T Flis, S Franckowiak, A Franke, R Frantzen, K Fuchs, T Gaisser, TK Gallagher, J Gerhardt, L Gladstone, L Glusenkamp, T Goldschmidt, A Golup, G Gonzalez, JG Goodman, JA Gora, D Grant, D Gross, A Gurtner, M Ha, C Ismail, AH Hallen, P Hallgren, A Halzen, F Hanson, K Heereman, D Heinen, D Helbing, K Hellauer, R Hickford, S Hill, GC Hoffman, KD Hoffmann, R Homeier, A Hoshina, K Huelsnitz, W Hulth, PO Hultqvist, K Hussain, S Ishihara, A Jacobi, E Jacobsen, J Jagielski, K Japaridze, GS Jero, K Jlelati, O Kaminsky, B Kappes, A Karg, T Karle, A Kelley, JL Kiryluk, J Kislat, F Klas, J Klein, SR Kohne, JH Kohnen, G Kolanoski, H Kopke, L Kopper, C Kopper, S Koskinen, DJ Kowalski, M Krasberg, M Krings, K Kroll, G Kunnen, J Kurahashi, N Kuwabara, T Labare, M Landsman, H Larson, MJ Lesiak-Bzdak, M Leuermann, M Leute, J Lunemann, J Madsen, J Maruyama, R Mase, K Matis, HS McNally, F Meagher, K Merck, M Meszaros, P Meures, T Miarecki, S Midden, E Milke, N Miller, J Mohrmann, L Montaruli, T Morse, R Nahnhauer, R Naumann, U Niederhausen, H Nowicki, SC Nygren, DR Obertacke, A Odrowski, S Olivas, A Olivo, M O'Murchadha, A Paul, L Pepper, JA de los Heros, CP Pfendner, C Pieloth, D Pinat, E Pirk, N Posselt, J Price, PB Przybylski, GT Radel, L Rameez, M Rawlins, K Red, P Reimann, R Resconi, E Rhode, W Ribordy, M Richman, M Riede, B Rodrigues, JP Rott, C Ruhe, T Ruzybayev, B Ryckbosch, D Saba, SM Salameh, T Sander, HG Santander, M Sarkar, S Schatto, K Scheel, M Scheriau, F Schmidt, T Schmitz, M Schoenen, S Schoneberg, S Schonwald, A Schukraft, A Schulte, L Schulz, O Seckel, D Sestayo, Y Seunarine, S Sheremata, C Smith, MWE Soiron, M Soldin, D Spiczak, GM Spiering, C Stamatikos, M Stanev, T Stasik, A Stezelberger, T Stokstad, RG Stossl, A Strahler, EA Strom, R Sullivan, GW Taavola, H Taboada, I Tamburro, A Ter-Antonyan, S Tesic, G Tilay, S Toale, PA Toscano, S Tosi, D Usner, M van der Drift, D van Eijndhoven, N Van Overloop, A van Santen, J Vehring, M Voge, M Vraeghe, M Walck, C Waldenmaier, T Wallraff, M Wasserman, R Weaver, C Wellons, M Wendt, C Westerhoff, S Whitehorn, N Wiebe, K Wiebusch, CH Williams, DR Wissing, H Wolf, M Wood, TR Woschnagg, K Xu, C Xu, DL Xu, XW Yanez, JP Yodh, G Yoshida, S Zarzhitsky, P Ziemann, J Zierke, S Zilles, A Zoll, M AF Aartsen, M. G. Abbasi, R. Abdou, Y. Ackermann, M. Adams, J. Aguilar, J. A. Ahlers, M. Altmann, D. Auffenberg, J. Bai, X. Baker, M. Barwick, S. W. Baum, V. Bay, R. Beatty, J. J. Bechet, S. Becker, K-H. Tjus, J. Becker Bell, M. Benabderrahmane, M. L. BenZvi, S. Berdermann, J. Berghaus, P. Berley, D. Bernardini, E. Bernhard, A. Bertrand, D. Besson, D. Z. Binder, G. Bindig, D. Bissok, M. Blaufuss, E. Blumenthal, J. Boersma, D. J. Bohaichuk, S. Bohm, C. Bose, D. Boeser, S. Botner, O. Brayeur, L. Bretz, H. -P. Brown, A. M. Bruijn, R. Brunner, J. Carson, M. Casey, J. Casier, M. Cherwinka, J. Chirkin, D. Christov, A. Christy, B. Clark, K. Clevermann, F. Coenders, S. Cohen, S. Cowen, D. F. Silva, A. H. Cruz Danninger, M. Daughhetee, J. Davis, J. C. De Clercq, C. De Ridder, S. Desiati, P. de With, M. DeYoung, T. Diaz-Velez, J. C. Dunkman, M. Eagan, R. Eberhardt, B. Eisch, J. Ellsworth, R. W. Euler, S. Evenson, P. A. Fadiran, O. Fazely, A. R. Fedynitch, A. Feintzeig, J. Feusels, T. Filimonov, K. Finley, C. Fischer-Wasels, T. Flis, S. Franckowiak, A. Franke, R. Frantzen, K. Fuchs, T. Gaisser, T. K. Gallagher, J. Gerhardt, L. Gladstone, L. Gluesenkamp, T. Goldschmidt, A. Golup, G. Gonzalez, J. G. Goodman, J. A. Gora, D. Grant, D. Gross, A. Gurtner, M. Ha, C. Ismail, A. Haj Hallen, P. Hallgren, A. Halzen, F. Hanson, K. Heereman, D. Heinen, D. Helbing, K. Hellauer, R. Hickford, S. Hill, G. C. Hoffman, K. D. Hoffmann, R. Homeier, A. Hoshina, K. Huelsnitz, W. Hulth, P. O. Hultqvist, K. Hussain, S. Ishihara, A. Jacobi, E. Jacobsen, J. Jagielski, K. Japaridze, G. S. Jero, K. Jlelati, O. Kaminsky, B. Kappes, A. Karg, T. Karle, A. Kelley, J. L. Kiryluk, J. Kislat, F. Klaes, J. Klein, S. R. Koehne, J-H. Kohnen, G. Kolanoski, H. Koepke, L. Kopper, C. Kopper, S. Koskinen, D. J. Kowalski, M. Krasberg, M. Krings, K. Kroll, G. Kunnen, J. Kurahashi, N. Kuwabara, T. Labare, M. Landsman, H. Larson, M. J. Lesiak-Bzdak, M. Leuermann, M. Leute, J. Luenemann, J. Madsen, J. Maruyama, R. Mase, K. Matis, H. S. McNally, F. Meagher, K. Merck, M. Meszaros, P. Meures, T. Miarecki, S. Midden, E. Milke, N. Miller, J. Mohrmann, L. Montaruli, T. Morse, R. Nahnhauer, R. Naumann, U. Niederhausen, H. Nowicki, S. C. Nygren, D. R. Obertacke, A. Odrowski, S. Olivas, A. Olivo, M. O'Murchadha, A. Paul, L. Pepper, J. A. de los Heros, C. Perez Pfendner, C. Pieloth, D. Pinat, E. Pirk, N. Posselt, J. Price, P. B. Przybylski, G. T. Raedel, L. Rameez, M. Rawlins, K. Red, P. Reimann, R. Resconi, E. Rhode, W. Ribordy, M. Richman, M. Riede, B. Rodrigues, J. P. Rott, C. Ruhe, T. Ruzybayev, B. Ryckbosch, D. Saba, S. M. Salameh, T. Sander, H-G. Santander, M. Sarkar, S. Schatto, K. Scheel, M. Scheriau, F. Schmidt, T. Schmitz, M. Schoenen, S. Schoeneberg, S. Schoenwald, A. Schukraft, A. Schulte, L. Schulz, O. Seckel, D. Sestayo, Y. Seunarine, S. Sheremata, C. Smith, M. W. E. Soiron, M. Soldin, D. Spiczak, G. M. Spiering, C. Stamatikos, M. Stanev, T. Stasik, A. Stezelberger, T. Stokstad, R. G. Stoessl, A. Strahler, E. A. Strom, R. Sullivan, G. W. Taavola, H. Taboada, I. Tamburro, A. Ter-Antonyan, S. Tesic, G. Tilay, S. Toale, P. A. Toscano, S. Tosi, D. Usner, M. van der Drift, D. van Eijndhoven, N. Van Overloop, A. van Santen, J. Vehring, M. Voge, M. Vraeghe, M. Walck, C. Waldenmaier, T. Wallraff, M. Wasserman, R. Weaver, Ch. Wellons, M. Wendt, C. Westerhoff, S. Whitehorn, N. Wiebe, K. Wiebusch, C. H. Williams, D. R. Wissing, H. Wolf, M. Wood, T. R. Woschnagg, K. Xu, C. Xu, D. L. Xu, X. W. Yanez, J. P. Yodh, G. Yoshida, S. Zarzhitsky, P. Ziemann, J. Zierke, S. Zilles, A. Zoll, M. CA IceCube Collaboration TI South Pole glacial climate reconstruction from multi-borehole laser particulate stratigraphy SO JOURNAL OF GLACIOLOGY LA English DT Article ID EPICA-DOME-C; ANTARCTIC ICE-SHEET; DEEP ICE; OPTICAL-PROPERTIES; EAST ANTARCTICA; VOLCANIC WINTER; SIPLE DOME; CORE; DUST; VOSTOK AB The IceCube Neutrino Observatory and its prototype, AMANDA, were built in South Pole ice, using powerful hot-water drills to cleanly bore >100 holes to depths up to 2500 m. The construction of these particle physics detectors provided a unique opportunity to examine the deep ice sheet using a variety of novel techniques. We made high-resolution particulate profiles with a laser dust logger in eight of the boreholes during detector commissioning between 2004 and 2010. The South Pole laser logs are among the most clearly resolved measurements of Antarctic dust strata during the last glacial period and can be used to reconstruct paleoclimate records in exceptional detail. Here we use manual and algorithmic matching to synthesize our South Pole measurements with ice-core and logging data from Dome C, East Antarctica. We derive impurity concentration, precision chronology, annual-layer thickness, local spatial variability, and identify several widespread volcanic ash depositions useful for dating. We also examine the interval around similar to 74 ka recently isolated with radiometric dating to bracket the Toba (Sumatra) supereruption. C1 [Bissok, M.; Blumenthal, J.; Coenders, S.; Euler, S.; Hallen, P.; Heinen, D.; Jagielski, K.; Krings, K.; Leuermann, M.; Paul, L.; Raedel, L.; Reimann, R.; Scheel, M.; Schoenen, S.; Schukraft, A.; Soiron, M.; Vehring, M.; Wallraff, M.; Wiebusch, C. H.; Zierke, S.; Zilles, A.] Rhein Westfal TH Aachen, Phys Inst 3, Aachen, Germany. [Aartsen, M. G.; Hill, G. C.] Univ Adelaide, Sch Chem & Phys, Adelaide, SA, Australia. [Rawlins, K.] Univ Alaska Anchorage, Dept Phys & Astron, Anchorage, AK USA. [Japaridze, G. S.] Clark Atlanta Univ, CTSPS, Atlanta, GA 30314 USA. [Casey, J.; Daughhetee, J.; Huelsnitz, W.; Taboada, I.] Georgia Inst Technol, Sch Phys, Atlanta, GA 30332 USA. [Casey, J.; Daughhetee, J.; Huelsnitz, W.; Taboada, I.] Georgia Inst Technol, Ctr Relativist Astrophys, Atlanta, GA 30332 USA. [Fazely, A. R.; Ter-Antonyan, S.; Xu, X. W.] Southern Univ, Dept Phys, Baton Rouge, LA USA. [Bay, R.; Binder, G.; Filimonov, K.; Gerhardt, L.; Ha, C.; Klein, S. R.; Miarecki, S.; Price, P. B.; Tosi, D.; van der Drift, D.; Woschnagg, K.] Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA. [Binder, G.; Gerhardt, L.; Goldschmidt, A.; Ha, C.; Klein, S. R.; Matis, H. S.; Miarecki, S.; Nygren, D. R.; Przybylski, G. T.; Stezelberger, T.; Stokstad, R. G.; van der Drift, D.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. [Altmann, D.; de With, M.; Kappes, A.; Kolanoski, H.; Waldenmaier, T.] Humboldt Univ, Inst Phys, D-10099 Berlin, Germany. [Tjus, J. Becker; Fedynitch, A.; Olivo, M.; Saba, S. M.; Schoeneberg, S.] Ruhr Univ Bochum, Fak Phys & Astron, Bochum, Germany. [Boeser, S.; Franckowiak, A.; Homeier, A.; Kowalski, M.; Schulte, L.; Stasik, A.; Usner, M.; Voge, M.] Univ Bonn, Inst Phys, Bonn, Germany. [Bechet, S.; Bertrand, D.; Hanson, K.; Heereman, D.; Meures, T.; O'Murchadha, A.; Pinat, E.] Univ Libre Bruxelles, Sci Fac CP230, Brussels, Belgium. [Bose, D.; Brayeur, L.; Casier, M.; De Clercq, C.; Golup, G.; Kunnen, J.; Labare, M.; Miller, J.; Strahler, E. A.; van Eijndhoven, N.] Vrije Univ Brussel, Dienst ELEM, Brussels, Belgium. [Ishihara, A.; Mase, K.; Yoshida, S.] Chiba Univ, Dept Phys, Chiba 260, Japan. [Adams, J.; Brown, A. M.; Hickford, S.] Univ Canterbury, Dept Phys & Astron, Christchurch 1, New Zealand. [Berley, D.; Blaufuss, E.; Christy, B.; Ellsworth, R. W.; Goodman, J. A.; Hellauer, R.; Hoffman, K. D.; Huelsnitz, W.; Meagher, K.; Olivas, A.; Red, P.; Richman, M.; Schmidt, T.; Sullivan, G. W.; Wissing, H.] Univ Maryland, Dept Phys, College Pk, MD 20742 USA. [Beatty, J. J.; Davis, J. C.; Pfendner, C.; Rott, C.; Stamatikos, M.] Ohio State Univ, Dept Phys, Columbus, OH 43210 USA. [Beatty, J. J.; Davis, J. C.; Pfendner, C.; Rott, C.; Stamatikos, M.] Ohio State Univ, Ctr Cosmol & Astroparticle Phys, Columbus, OH 43210 USA. [Beatty, J. J.] Ohio State Univ, Dept Astron, Columbus, OH 43210 USA. [Clevermann, F.; Frantzen, K.; Fuchs, T.; Koehne, J-H.; Milke, N.; Pieloth, D.; Rhode, W.; Ruhe, T.; Scheriau, F.; Schmitz, M.; Ziemann, J.] TU Dortmund Univ, Dept Phys, Dortmund, Germany. [Bohaichuk, S.; Grant, D.; Nowicki, S. C.; Sheremata, C.; Wood, T. R.] Univ Alberta, Dept Phys, Edmonton, AB, Canada. [Aguilar, J. A.; Christov, A.; Montaruli, T.; Rameez, M.] Univ Geneva, Dept Phys Nucl & Corpusculaire, Geneva, Switzerland. [Abdou, Y.; Carson, M.; De Ridder, S.; Feusels, T.; Ismail, A. Haj; Jlelati, O.; Ryckbosch, D.; Van Overloop, A.; Vraeghe, M.] Univ Ghent, Dept Phys & Astron, B-9000 Ghent, Belgium. [Barwick, S. W.; Yodh, G.] Univ Calif Irvine, Dept Phys & Astron, Irvine, CA USA. [Bruijn, R.; Cohen, S.; Ribordy, M.] Ecole Polytech Fed Lausanne, High Energy Phys Lab, Lausanne, Switzerland. [Besson, D. Z.] Univ Kansas, Dept Phys & Astron, Lawrence, KS 66045 USA. [Gallagher, J.] Univ Wisconsin, Dept Astron, Madison, WI 53706 USA. [Abbasi, R.; Ahlers, M.; Auffenberg, J.; Baker, M.; BenZvi, S.; Cherwinka, J.; Chirkin, D.; Desiati, P.; Diaz-Velez, J. C.; Eisch, J.; Fadiran, O.; Feintzeig, J.; Gladstone, L.; Halzen, F.; Hoshina, K.; Jacobsen, J.; Jero, K.; Karle, A.; Kelley, J. L.; Kopper, C.; Krasberg, M.; Kurahashi, N.; Landsman, H.; Maruyama, R.; McNally, F.; Merck, M.; Morse, R.; Riede, B.; Rodrigues, J. P.; Santander, M.; Toscano, S.; van Santen, J.; Weaver, Ch.; Wellons, M.; Wendt, C.; Westerhoff, S.; Whitehorn, N.] Univ Wisconsin, Dept Phys, Madison, WI 53706 USA. [Abbasi, R.; Ahlers, M.; Auffenberg, J.; Baker, M.; BenZvi, S.; Cherwinka, J.; Chirkin, D.; Desiati, P.; Diaz-Velez, J. C.; Eisch, J.; Fadiran, O.; Feintzeig, J.; Gladstone, L.; Halzen, F.; Hoshina, K.; Jacobsen, J.; Jero, K.; Karle, A.; Kelley, J. L.; Kopper, C.; Krasberg, M.; Kurahashi, N.; Landsman, H.; Maruyama, R.; McNally, F.; Merck, M.; Morse, R.; Riede, B.; Rodrigues, J. P.; Santander, M.; Toscano, S.; van Santen, J.; Weaver, Ch.; Wellons, M.; Wendt, C.; Westerhoff, S.; Whitehorn, N.] Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI USA. [Baum, V.; Eberhardt, B.; Koepke, L.; Kroll, G.; Luenemann, J.; Sander, H-G.; Schatto, K.; Wiebe, K.] Johannes Gutenberg Univ Mainz, Inst Phys, Mainz, Germany. [Kohnen, G.] Univ Mons, B-7000 Mons, Belgium. [Bernhard, A.; Gross, A.; Leute, J.; Odrowski, S.; Resconi, E.; Schulz, O.; Sestayo, Y.] Tech Univ Munich, Garching, Germany. [Bai, X.; Evenson, P. A.; Gaisser, T. K.; Gonzalez, J. G.; Hussain, S.; Kuwabara, T.; Ruzybayev, B.; Seckel, D.; Stanev, T.; Tamburro, A.; Tilay, S.; Xu, C.] Univ Delaware, Bartol Res Inst, Newark, DE 19716 USA. [Bai, X.; Evenson, P. A.; Gaisser, T. K.; Gonzalez, J. G.; Hussain, S.; Kuwabara, T.; Ruzybayev, B.; Seckel, D.; Stanev, T.; Tamburro, A.; Tilay, S.; Xu, C.] Univ Delaware, Dept Phys & Astron, Newark, DE 19716 USA. [Sarkar, S.] Univ Oxford, Dept Phys, Oxford, England. [Madsen, J.; Seunarine, S.; Spiczak, G. M.] Univ Wisconsin, Dept Phys, River Falls, WI 54022 USA. [Bohm, C.; Danninger, M.; Finley, C.; Flis, S.; Hulth, P. O.; Hultqvist, K.; Walck, C.; Wolf, M.; Zoll, M.] Stockholm Univ, Oskar Klein Ctr, S-10691 Stockholm, Sweden. [Bohm, C.; Danninger, M.; Finley, C.; Flis, S.; Hulth, P. O.; Hultqvist, K.; Walck, C.; Wolf, M.; Zoll, M.] Stockholm Univ, Dept Phys, S-10691 Stockholm, Sweden. [Kiryluk, J.; Lesiak-Bzdak, M.; Niederhausen, H.] SUNY Stony Brook, Dept Phys & Astron, Stony Brook, NY 11794 USA. [Larson, M. J.; Pepper, J. A.; Toale, P. A.; Williams, D. R.; Xu, D. L.] Univ Alabama, Dept Phys & Astron, Tuscaloosa, AL 35487 USA. [Cowen, D. F.; Meszaros, P.] Penn State Univ, Dept Astron & Astrophys, University Pk, PA 16802 USA. [Bell, M.; Clark, K.; Cowen, D. F.; DeYoung, T.; Dunkman, M.; Eagan, R.; Koskinen, D. J.; Meszaros, P.; Salameh, T.; Smith, M. W. E.; Tesic, G.; Wasserman, R.] Penn State Univ, Dept Phys, University Pk, PA 16802 USA. [Boersma, D. J.; Botner, O.; Hallgren, A.; de los Heros, C. Perez; Strom, R.; Taavola, H.; Zarzhitsky, P.] Uppsala Univ, Dept Phys & Astron, Uppsala, Sweden. [Becker, K-H.; Bindig, D.; Fischer-Wasels, T.; Gurtner, M.; Helbing, K.; Hoffmann, R.; Klaes, J.; Kopper, S.; Naumann, U.; Obertacke, A.; Posselt, J.; Soldin, D.] Univ Wuppertal, Dept Phys, Wuppertal, Germany. [Ackermann, M.; Benabderrahmane, M. L.; Berdermann, J.; Berghaus, P.; Bernardini, E.; Bretz, H. -P.; Brunner, J.; Silva, A. H. Cruz; Franke, R.; Gluesenkamp, T.; Gora, D.; Jacobi, E.; Kaminsky, B.; Karg, T.; Kislat, F.; Midden, E.; Mohrmann, L.; Nahnhauer, R.; Pirk, N.; Schoenwald, A.; Spiering, C.; Stoessl, A.; Yanez, J. P.] DESY, Zeuthen, Germany. [Bai, X.] South Dakota Sch Mines & Technol, Dept Phys, Rapid City, SD USA. Los Alamos Natl Lab, Los Alamos, NM USA. [Montaruli, T.] Dipartimento Fis, Sez INFN, Bari, Italy. [Rott, C.] Sungkyunkwan Univ, Dept Phys, Suwon, South Korea. [Stamatikos, M.] NASA, Goddard Space Flight Ctr, Greenbelt, MD 20771 USA. RP Aartsen, MG (reprint author), Univ Adelaide, Sch Chem & Phys, Adelaide, SA, Australia. RI Wiebusch, Christopher/G-6490-2012; Auffenberg, Jan/D-3954-2014; Tjus, Julia/G-8145-2012; Koskinen, David/G-3236-2014; Brunner, Juergen/G-3540-2015; Aguilar Sanchez, Juan Antonio/H-4467-2015; Maruyama, Reina/A-1064-2013; Beatty, James/D-9310-2011; Sarkar, Subir/G-5978-2011; OI Benabderrahmane, Mohamed Lotfi/0000-0003-4410-5886; Wiebusch, Christopher/0000-0002-6418-3008; Auffenberg, Jan/0000-0002-1185-9094; Koskinen, David/0000-0002-0514-5917; Brunner, Juergen/0000-0002-5052-7236; Aguilar Sanchez, Juan Antonio/0000-0003-2252-9514; Maruyama, Reina/0000-0003-2794-512X; Beatty, James/0000-0003-0481-4952; Sarkar, Subir/0000-0002-3542-858X; Carson, Michael/0000-0003-0400-7819; Perez de los Heros, Carlos/0000-0002-2084-5866 FU US National Science Foundation (NSF) Office of Polar Programs; NSF Physics Division, University of Wisconsin Alumni Research Foundation; Grid Laboratory Of Wisconsin (GLOW) grid infrastructure at the University of Wisconsin-Madison, Open Science Grid (OSG) grid infrastructure; US Department of Energy, National Energy Research Scientific Computing Center, Louisiana Optical Network Initiative (LONI) grid computing resources; Natural Sciences and Engineering Research Council of Canada; Compute Canada; Compute West High Performance Computing; Swedish Research Council; Swedish Polar Research Secretariat; Swedish. National Infrastructure for Computing (SNIC); Knut and Alice Wallenberg Foundation, Sweden; German Ministry for Education and Research (BMBF); Deutsche Forschungsgemeinschaft (DFG); Helmholtz Alliance for Astroparticle Physics (HAP); Research Department of Plasmas with Complex Interactions (Bochum), Germany; Fund for Scientific Research (FNRS-FWO); FWO Odysseus programme; Flanders Institute to encourage scientific and technological research in industry (IWT); Belgian Federal Science Policy Office (Belspo); University of Oxford, UK; Marsden Fund, New Zealand; Australian Research Council; Japan Society for Promotion of Science (JSPS); Swiss National Science Foundation (SNSF), Switzerland FX We thank Nathan Bramall, Robert Rohde, Andres Morey, Tom Ham, Kurt Cuffey, Dave Ferris, Michael Solarz, the EPICA Collaboration, the WAIS Divide Project members and the US National Ice Core Laboratory. We acknowledge the support from the following agencies: US National Science Foundation (NSF) Office of Polar Programs, NSF Physics Division, University of Wisconsin Alumni Research Foundation, Grid Laboratory Of Wisconsin (GLOW) grid infrastructure at the University of Wisconsin-Madison, Open Science Grid (OSG) grid infrastructure; US Department of Energy, National Energy Research Scientific Computing Center, Louisiana Optical Network Initiative (LONI) grid computing resources; Natural Sciences and Engineering Research Council of Canada, Compute Canada and Compute West High Performance Computing; Swedish Research Council, Swedish Polar Research Secretariat, Swedish. National Infrastructure for Computing (SNIC), Knut and Alice Wallenberg Foundation, Sweden; German Ministry for Education and Research (BMBF), Deutsche Forschungsgemeinschaft (DFG), Helmholtz Alliance for Astroparticle Physics (HAP), Research Department of Plasmas with Complex Interactions (Bochum), Germany; Fund for Scientific Research (FNRS-FWO), FWO Odysseus programme, Flanders Institute to encourage scientific and technological research in industry (IWT), Belgian Federal Science Policy Office (Belspo); University of Oxford, UK; Marsden Fund, New Zealand; Australian Research Council; Japan Society for Promotion of Science (JSPS); Swiss National Science Foundation (SNSF), Switzerland. NR 63 TC 4 Z9 4 U1 1 U2 20 PU CAMBRIDGE UNIV PRESS PI CAMBRIDGE PA EDINBURGH BLDG, SHAFTESBURY RD, CB2 8RU CAMBRIDGE, ENGLAND SN 0022-1430 EI 1727-5652 J9 J GLACIOL JI J. Glaciol. PY 2013 VL 59 IS 218 BP 1117 EP 1128 DI 10.3189/2013JoG13J068 PG 12 WC Geography, Physical; Geosciences, Multidisciplinary SC Physical Geography; Geology GA 280FI UT WOS:000329013700011 ER PT B AU Checco, A AF Checco, Antonio BE Ondarcuhu, T Aime, JP TI Droplet Morphology at Nanometer Scale SO NANOSCALE LIQUID INTERFACES: WETTING, PATTERNING, AND FORCE MICROSCOPY AT THE MOLECULAR SCALE LA English DT Article; Book Chapter ID SCANNING FORCE MICROSCOPY; SELF-ASSEMBLED MONOLAYERS; WETTING PROPERTIES; SURFACES; NANOSCALE; CAPILLARY; GRAPHITE; LIQUIDS; FILMS; MICA C1 Brookhaven Natl Lab, Condensed Matter Phys & Mat Sci Dept, Upton, NY 11973 USA. RP Checco, A (reprint author), Brookhaven Natl Lab, Condensed Matter Phys & Mat Sci Dept, Upton, NY 11973 USA. EM checco@bnl.gov NR 37 TC 0 Z9 0 U1 2 U2 6 PU PAN STANFORD PUBLISHING PTE LTD PI SINGAPORE PA PENTHOUSE LEVEL, SUNTEC TOWER 3, 8 TEMASEK BLVD, SINGAPORE, 038988, SINGAPORE BN 978-981-4364-48-5; 978-981-4316-45-3 PY 2013 BP 235 EP 257 D2 10.1201/b14789 PG 23 WC Nanoscience & Nanotechnology; Microscopy SC Science & Technology - Other Topics; Microscopy GA BJH15 UT WOS:000328156600007 ER PT J AU Yu, Y Koller, J Morley, SK AF Yu, Y. Koller, J. Morley, S. K. TI Quantifying the effect of magnetopause shadowing on electron radiation belt dropouts SO ANNALES GEOPHYSICAE LA English DT Article DE Magnetospheric physics; Solar wind-magnetosphere interactions ID GEOMAGNETIC STORMS; MAGNETIC STORM; GEOSYNCHRONOUS ORBIT; PHASE; DIFFUSION; DENSITY; TIMES AB Energetic radiation belt electron fluxes can undergo sudden dropouts in response to different solar wind drivers. Many physical processes contribute to the electron flux dropout, but their respective roles in the net electron depletion remain a fundamental puzzle. Some previous studies have qualitatively examined the importance of magnetopause shadowing in the sudden dropouts either from observations or from simulations. While it is difficult to directly measure the electron flux loss into the solar wind, radial diffusion codes with a fixed boundary location (commonly utilized in the literature) are not able to explicitly account for magnetopause shadowing. The exact percentage of its contribution has therefore not yet been resolved. To overcome these limitations and to determine the exact contribution in percentage, we carry out radial diffusion simulations with the magnetopause shadowing effect explicitly accounted for during a superposed solar wind stream interface passage, and quantify the relative contribution of the magnetopause shadowing coupled with outward radial diffusion by comparing with GPS- observed total flux dropout. Results indicate that during high- speed solar wind stream events, which are typically preceded by enhanced dynamic pressure and hence a compressed magnetosphere, magnetopause shadowing coupled with the outward radial diffusion can explain about 6099% of the main- phase radiation belt electron depletion near the geosynchronous orbit. While the outer region (L* > 5) can nearly be explained by the above coupled mechanism, additional loss mechanisms are needed to fully explain the energetic electron loss for the inner region (L* <= 5). While this conclusion confirms earlier studies, our quantification study demonstrates its relative importance with respect to other mechanisms at different locations. C1 [Yu, Y.; Koller, J.; Morley, S. K.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Yu, Y (reprint author), Los Alamos Natl Lab, Los Alamos, NM 87545 USA. EM yiqun@lanl.gov RI Morley, Steven/A-8321-2008; Yu, Yiqun/E-2710-2012; Koller, Josef/C-5591-2009 OI Morley, Steven/0000-0001-8520-0199; Yu, Yiqun/0000-0002-1013-6505; Koller, Josef/0000-0002-6770-4980 FU Los Alamos National Laboratory Directed Research and Development program FX This work was conducted under the auspices of the US Department of Energy, with support from the Los Alamos National Laboratory Directed Research and Development program. The authors would like to acknowledge Yue Chen for providing the phase space density data for conducting the DREAM data assimilation in order to obtain the initial conditions used in this study. NR 57 TC 13 Z9 13 U1 1 U2 6 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 0992-7689 EI 1432-0576 J9 ANN GEOPHYS-GERMANY JI Ann. Geophys. PY 2013 VL 31 IS 11 BP 1929 EP 1939 DI 10.5194/angeo-31-1929-2013 PG 11 WC Astronomy & Astrophysics; Geosciences, Multidisciplinary; Meteorology & Atmospheric Sciences SC Astronomy & Astrophysics; Geology; Meteorology & Atmospheric Sciences GA 263NZ UT WOS:000327816600004 ER PT J AU Dougal, ER Nykyri, K Moore, TW AF Dougal, E. R. Nykyri, K. Moore, T. W. TI Mapping of the quasi-periodic oscillations at the flank magnetopause into the ionosphere SO ANNALES GEOPHYSICAE LA English DT Article DE Magnetospheric physics; Magnetopause; cusp and boundary layers; Magnetosphere-ionosphere interactions; MHD waves and instabilities ID KELVIN-HELMHOLTZ INSTABILITY; HIGH-LATITUDE CONVECTION; MAGNETIC-FIELD; MAGNETOSPHERIC BOUNDARY; MAGNETOTAIL BOUNDARY; EARTHS MAGNETOSPHERE; GEOTAIL OBSERVATIONS; GROUND OBSERVATIONS; MAGNETOHYDRODYNAMICS; SIMULATION AB We have estimated the ionospheric location, area, and travel time of quasi-periodic oscillations originating from the magnetospheric flanks. This was accomplished by utilizing global and local MHD models and Tsyganenko semi-empirical magnetic field model on multiple published and four new cases believed to be caused by the KelvinHelmholtz Instability. Finally, we used auroral, magnetometer, and radar instruments to observe the ionospheric signatures. The ionospheric magnetic latitude determined using global MHD and Tsyganenko models ranged from 58.3-80.2 degrees in the Northern Hemisphere and -59.6 degrees to -83.4 degrees in the Southern Hemisphere. The ionospheric magnetic local time ranged between 5.0-13.8 h in the Northern Hemisphere and 1.3-11.9 h in the Southern Hemisphere. Typical Alfven wave travel time from spacecraft location to the closest ionosphere ranged between 0.6-3.6 min. The projected ionospheric size calculated at an altitude of 100 km ranged from 47-606 km, the same order of magnitude as previously determined ionospheric signature sizes. Stationary and traveling convection vortices were observed in SuperDARN radar data in both hemispheres. The vortices were between 1000-1800 km in size. Some events were located within the ionospheric footprint ranges. Pc5 magnetic oscillations were observed in SuperMAG magnetometer data in both hemispheres. The oscillations had periods between 410 min with amplitudes of 3-25 nT. They were located within the ionospheric footprint ranges. Some ground magnetometer data power spectral density peaked at frequencies within one tenth of a mHz of the peaks found in the corresponding Cluster data. These magnetometer observations were consistent with previously published results. C1 [Dougal, E. R.] Sandia Natl Labs, Albuquerque, NM 87185 USA. [Dougal, E. R.; Nykyri, K.; Moore, T. W.] Embry Riddle Aeronaut Univ, Dept Phys Sci, Daytona Beach, FL USA. RP Dougal, ER (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87185 USA. EM dougale@my.erau.edu OI Nykyri, Katariina/0000-0002-6905-9487 FU National Science Foundation [0847120] FX This research was performed during E. Dougal's undergraduate and graduate studies at Embry-Riddle Aeronautical University. E. Dougal's, K. Nykyri's and T. Moore's research is funded by National Science Foundation Grant 0847120. Global MHD simulations have been provided by the Community Coordinated Modeling Center at Goddard Space Flight Center through their public runs on request system (http://ccmc.gsfc.nasa.gov). The CCMC is a multi-agency partnership between NASA, AFMC, AFOSR, AFRL, AFWA, NOAA, NSF and ONR. The OpenGGCM Model was developed by Joachim Raeder at University of New Hampshire and Timothy Fuller-Rowell at NOAA. The BATS-R-US Model was developed by Tamas Gombosi et al. at the University of Michigan. The TS89 4D Orbit Viewer software was provided by NASA Goddard Space Flight Center Space Physics Data Facility, plotted with TIPSOD Version 3.1.28. The original 2-D MHD code was developed by A. Otto. We acknowledge all Cluster instrument teams and the ESA Cluster Active Archive for providing processed science-level data for download. We acknowledge NASA Goddard Space Flight Center Satellite Situation Center Web for providing coordinate system transformations. NR 46 TC 4 Z9 4 U1 1 U2 8 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 0992-7689 EI 1432-0576 J9 ANN GEOPHYS-GERMANY JI Ann. Geophys. PY 2013 VL 31 IS 11 BP 1993 EP 2011 DI 10.5194/angeo-31-1993-2013 PG 19 WC Astronomy & Astrophysics; Geosciences, Multidisciplinary; Meteorology & Atmospheric Sciences SC Astronomy & Astrophysics; Geology; Meteorology & Atmospheric Sciences GA 263NZ UT WOS:000327816600009 ER PT J AU D'Andrea, SD Hakkinen, SAK Westervelt, DM Kuang, C Levin, EJT Kanawade, VP Leaitch, WR Spracklen, DV Riipinen, I Pierce, JR AF D'Andrea, S. D. Hakkinen, S. A. K. Westervelt, D. M. Kuang, C. Levin, E. J. T. Kanawade, V. P. Leaitch, W. R. Spracklen, D. V. Riipinen, I. Pierce, J. R. TI Understanding global secondary organic aerosol amount and size-resolved condensational behavior SO ATMOSPHERIC CHEMISTRY AND PHYSICS LA English DT Article ID NUCLEATION EVENTS; PARTICLE FORMATION; ATMOSPHERIC NUCLEATION; ULTRAFINE PARTICLES; CCN CONCENTRATIONS; BOUNDARY-LAYER; SULFURIC-ACID; GROWTH-RATES; NUCLEI; MODEL AB Recent research has shown that secondary organic aerosols (SOA) are major contributors to ultrafine particle growth to climatically relevant sizes, increasing global cloud condensation nuclei (CCN) concentrations within the continental boundary layer (BL). However, there are three recent developments regarding the condensation of SOA that lead to uncertainties in the contribution of SOA to particle growth and CCN concentrations: (1) while many global models contain only biogenic sources of SOA (with annual production rates generally 10-30 Tg yr(-1)), recent studies have shown that an additional source of SOA around 100 Tg yr(-1) correlated with anthropogenic carbon monoxide (CO) emissions may be required to match measurements. (2) Many models treat SOA solely as semi-volatile, which leads to condensation of SOA proportional to the aerosol mass distribution; however, recent closure studies with field measurements show nucleation mode growth can be captured only if it is assumed that a significant fraction of SOA condenses proportional to the Fuchs-corrected aerosol surface area. This suggests a very low volatility of the condensing vapors. (3) Other recent studies of particle growth show that SOA con-densation at sizes smaller than 10 nm and that size-dependent growth rate parameterizations (GRP) are needed to match measurements. We explore the significance of these three findings using GEOS-Chem-TOMAS global aerosol microphysics model and observations of aerosol size distributions around the globe. The change in the concentration of particles of size D-p > 40 nm (N40) within the BL assuming surface-area condensation compared to mass-distribution net condensation yielded a global increase of 11% but exceeded 100% in biogenically active regions. The percent change in N40 within the BL with the inclusion of the additional 100 Tg SOAyr(-1) compared to the base simulation solely with biogenic SOA emissions (19 Tg yr-1) both using surface area condensation yielded a global increase of 13.7 %, but exceeded 50% in regions with large CO emissions. The inclusion of two different GRPs in the additional-SOA case both yielded a global increase in N40 of < 1 %, however exceeded 5% in some locations in the most extreme case. All of the model simulations were compared to measured data obtained from diverse locations around the globe and the results confirmed a decrease in the model-measurement bias and improved slope for comparing modeled to measured CCN number concentration when non-volatile SOA was assumed and the extra SOA was included. C1 [D'Andrea, S. D.; Pierce, J. R.] Dalhousie Univ, Dept Phys & Atmospher Sci, Halifax, NS, Canada. [D'Andrea, S. D.; Levin, E. J. T.; Pierce, J. R.] Colorado State Univ, Dept Atmospher Sci, Ft Collins, CO 80523 USA. [Hakkinen, S. A. K.] Univ Helsinki, Dept Phys, Helsinki, Finland. [Hakkinen, S. A. K.] Columbia Univ, Dept Chem Engn, New York, NY USA. [Westervelt, D. M.] Carnegie Mellon Univ, Ctr Atmospher Particle Studies, Pittsburgh, PA 15213 USA. [Kuang, C.] Brookhaven Natl Lab, Div Atmospher Sci, Upton, NY 11973 USA. [Kanawade, V. P.] Indian Inst Technol, Dept Civil Engn, Kanpur 208016, Uttar Pradesh, India. [Leaitch, W. R.] Environm Canada, Toronto, ON, Canada. [Spracklen, D. V.] Univ Leeds, Sch Earth & Environm, Leeds, W Yorkshire, England. [Riipinen, I.] Stockholm Univ, Dept Appl Environm Sci, S-10691 Stockholm, Sweden. [Riipinen, I.] Stockholm Univ, Bert Bolin Ctr Climate Res, S-10691 Stockholm, Sweden. RP D'Andrea, SD (reprint author), Dalhousie Univ, Dept Phys & Atmospher Sci, Halifax, NS, Canada. EM sdandrea@atmos.colostate.edu RI Levin, Ezra/F-5809-2010; Spracklen, Dominick/B-4890-2014; Chem, GEOS/C-5595-2014; Pierce, Jeffrey/E-4681-2013; Riipinen, Ilona/I-9379-2012; Kanawade, Vijay Punjaji/C-9848-2015; OI Pierce, Jeffrey/0000-0002-4241-838X; Kanawade, Vijay Punjaji/0000-0001-5611-3029; Hame, Silja/0000-0002-3763-0407 FU Natural Sciences and Engineering Research Council (NSERC) of Canada through the Network on Climate and Aerosols (NETCARE) network; Environment Canada's Clean Air and Regulatory Agenda; aerosol measurements at Kent State University FX We thank the Atlantic Computational Excellence Network (ACENet) for the computational resources used in this study. The authors acknowledge Natural Sciences and Engineering Research Council (NSERC) of Canada for funding through the Network on Climate and Aerosols (NETCARE) network. We are grateful to A. M. Macdonald, S. Sharma and D. Toom-Sauntry for their support of the aerosol measurements at Whistler and Alert, and we acknowledge financial support from Environment Canada's Clean Air and Regulatory Agenda. We would also like to thank S. Lee for support of the aerosol measurements at Kent State University. NR 57 TC 26 Z9 26 U1 1 U2 40 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 1680-7316 EI 1680-7324 J9 ATMOS CHEM PHYS JI Atmos. Chem. Phys. PY 2013 VL 13 IS 22 BP 11519 EP 11534 DI 10.5194/acp-13-11519-2013 PG 16 WC Meteorology & Atmospheric Sciences SC Meteorology & Atmospheric Sciences GA 263NX UT WOS:000327816400024 ER PT J AU Liou, KN Gu, Y Leung, LR Lee, WL Fovell, RG AF Liou, K. N. Gu, Y. Leung, L. R. Lee, W. L. Fovell, R. G. TI A WRF simulation of the impact of 3-D radiative transfer on surface hydrology over the Rocky Mountains and Sierra Nevada SO ATMOSPHERIC CHEMISTRY AND PHYSICS LA English DT Article ID WESTERN UNITED-STATES; REGIONAL CLIMATE SIMULATION; PART I; MODEL; PARAMETERIZATION; HYDROCLIMATE; SENSITIVITY; SNOWPACK; WEATHER; LAYER AB We investigate 3-D mountains/snow effects on solar flux distributions and their impact on surface hydrology over the western United States, specifically the Rocky Mountains and Sierra Nevada. The Weather Research and Forecasting (WRF) model, applied at a 30 km grid resolution, is used in conjunction with a 3-D radiative transfer parameterization covering a time period from 1 November 2007 to 31 May 2008, during which abundant snowfall occurred. A comparison of the 3-D WRF simulation with the observed snow water equivalent (SWE) and precipitation from Snowpack Telemetry (SNOTEL) sites shows reasonable agreement in terms of spatial patterns and daily and seasonal variability, although the simulation generally has a positive precipitation bias. We show that 3-D mountain features have a profound impact on the diurnal and monthly variation of surface radiative and heat fluxes, and on the consequent elevation-dependence of snowmelt and precipitation distributions. In particular, during the winter months, large deviations (3-DPP, in which PP denotes the plane-parallel approach) of the monthly mean surface solar flux are found in the morning and afternoon hours due to shading effects for elevations below 2.5 km. During spring, positive deviations shift to the earlier morning. Over mountaintops higher than 3 km, positive deviations are found throughout the day, with the largest values of 40-60 W m(-2) occurring at noon during the snowmelt season of April to May. The monthly SWE deviations averaged over the entire domain show an increase in lower elevations due to reduced snowmelt, which leads to a reduction in cumulative runoff. Over higher elevation areas, positive SWE deviations are found because of increased solar radiation available at the surface. Overall, this study shows that deviations of SWE due to 3-D radiation effects range from an increase of 18% at the lowest elevation range (1.5-2 km) to a decrease of 8% at the highest elevation range (above 3 km). Since lower elevation areas occupy larger fractions of the land surface, the net effect of 3-D radiative transfer is to extend snowmelt and snowmelt-driven runoff into the warm season. Because 60-90% of water resources originate from mountains worldwide, the aforementioned differences in simulated hydrology due solely to 3-D interactions between solar radiation and mountains/snow merit further investigation in order to understand the implications of modeling mountain water resources, and these resources' vulnerability to climate change and air pollution. C1 [Liou, K. N.; Gu, Y.; Fovell, R. G.] Univ Calif Los Angeles, Dept Atmospher & Ocean Sci, Joint Inst Reg Earth Syst Sci & Engn, Los Angeles, CA 90095 USA. [Leung, L. R.] Pacific NW Natl Lab, Richland, WA 99352 USA. [Lee, W. L.] Acad Sinica, Res Ctr Environm Changes, Taipei 115, Taiwan. RP Gu, Y (reprint author), Univ Calif Los Angeles, Dept Atmospher & Ocean Sci, Joint Inst Reg Earth Syst Sci & Engn, Los Angeles, CA 90095 USA. EM gu@atmos.ucla.edu FU Office of Science of the US Department of Energy as part of the Earth System Modeling program through DOE [DESC0006742]; DOE [DE-AC05-76RLO1830] FX This research was supported by the Office of Science of the US Department of Energy as part of the Earth System Modeling program through DOE Grant DESC0006742 to UCLA and separate funding to PNNL. PNNL is operated for DOE by Battelle Memorial Institute under contract DE-AC05-76RLO1830. NR 36 TC 4 Z9 4 U1 1 U2 7 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 1680-7316 EI 1680-7324 J9 ATMOS CHEM PHYS JI Atmos. Chem. Phys. PY 2013 VL 13 IS 23 BP 11709 EP 11721 DI 10.5194/acp-13-11709-2013 PG 13 WC Meteorology & Atmospheric Sciences SC Meteorology & Atmospheric Sciences GA 274OV UT WOS:000328616800007 ER PT J AU Friedman, B Zelenyuk, A Beranek, J Kulkarni, G Pekour, M Hallar, AG McCubbin, IB Thornton, JA Cziczo, DJ AF Friedman, B. Zelenyuk, A. Beranek, J. Kulkarni, G. Pekour, M. Hallar, A. Gannet McCubbin, I. B. Thornton, J. A. Cziczo, D. J. TI Aerosol measurements at a high-elevation site: composition, size, and cloud condensation nuclei activity SO ATMOSPHERIC CHEMISTRY AND PHYSICS LA English DT Article ID CCN CONCENTRATIONS; PARTICLE FORMATION; HYGROSCOPIC PROPERTIES; NUMBER CONCENTRATION; SOLUBLE ORGANICS; ARCTIC AEROSOL; MIXING STATE; ACTIVATION; CAPABILITIES; CHEMISTRY AB Measurements of cloud condensation nuclei (CCN) concentrations, single particle composition and size distributions at a high-elevation research site from March 2011 are presented. The temporal evolution of detailed single particle composition is compared with changes in CCN activation on four days, two of which include new particle formation and growth events. Sulfate-containing particles dominated the single particle composition by number; biomass burning particles, sea salt particles, and particles containing organic components were also present. CCN activation largely followed the behavior of the sulfate-containing particle types; biomass burning particle types also likely contained hygroscopic material that impacted CCN activation. Newly formed particles also may contribute to CCN activation at higher supersaturation conditions. Derived aerosol hygroscopicity parameters from the size distribution and CCN concentration measurements are within the range of previous reports of remote continental kappa values. C1 [Friedman, B.; Thornton, J. A.] Univ Washington, Dept Atmospher Sci, Seattle, WA 98195 USA. [Zelenyuk, A.; Beranek, J.; Kulkarni, G.; Pekour, M.] Pacific NW Natl Lab, Richland, WA 99352 USA. [Hallar, A. Gannet; McCubbin, I. B.] Desert Res Inst, Storm Peak Lab, Steamboat Springs, CO USA. [Cziczo, D. J.] MIT, Dept Earth Atmospher & Planetary Sci, Cambridge, MA USA. RP Friedman, B (reprint author), Univ Washington, Dept Atmospher Sci, Seattle, WA 98195 USA. EM bfriedma@uw.edu RI Hallar, Anna Gannet/I-9104-2012 OI Hallar, Anna Gannet/0000-0001-9972-0056 FU DOE-OBER and located at Pacific Northwest National Laboratory; Office of Biological and Environmental Research of the U.S. Department of Energy as part of the Atmospheric Radiation Measurement Climate Research Facility; Department of Energy (DOE) Office of Science Graduate Fellowship Program (DOE SCGF); DOE [DE-AC05-06OR23100] FX The authors would like to thank the Desert Research Institute's Storm Peak Laboratory staff, the Steamboat Springs ski area for logistic support. We furthermore thank the US Department of Energy's Office of Biological and Environmental Research (DOE-OBER) Atmospheric Radiation Measurement (ARM) StormVEx project, Atmospheric Research Program (ASR), and EMSL, a national scientific user facility sponsored by the DOE-OBER and located at Pacific Northwest National Laboratory for funding. DRI is an equal opportunity service provider and employer and a permittee of the Medicine-Bow Routt National Forest. The StormVEx campaign and all measurements included in this study were supported by the Office of Biological and Environmental Research of the U.S. Department of Energy as part of the Atmospheric Radiation Measurement Climate Research Facility. B. Friedman gratefully acknowledges support from the Department of Energy (DOE) Office of Science Graduate Fellowship Program (DOE SCGF). The DOE SCGF Program was made possible in part by the American Recovery and Reinvestment Act of 2009. The DOE SCGF program is administered by the Oak Ridge Institute for Science and Education for the DOE. ORISE is managed by Oak Ridge Associated Universities (ORAU) under DOE contract number DE-AC05-06OR23100. All opinions expressed in this paper are the author's and do not necessarily reflect the policies and views of DOE, ORAU, or ORISE. NR 62 TC 7 Z9 7 U1 4 U2 33 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 1680-7316 EI 1680-7324 J9 ATMOS CHEM PHYS JI Atmos. Chem. Phys. PY 2013 VL 13 IS 23 BP 11839 EP 11851 DI 10.5194/acp-13-11839-2013 PG 13 WC Meteorology & Atmospheric Sciences SC Meteorology & Atmospheric Sciences GA 274OV UT WOS:000328616800015 ER PT J AU Johnston, MS Eliasson, S Eriksson, P Forbes, RM Wyser, K Zelinka, MD AF Johnston, M. S. Eliasson, S. Eriksson, P. Forbes, R. M. Wyser, K. Zelinka, M. D. TI Diagnosing the average spatio-temporal impact of convective systems - Part 1: A methodology for evaluating climate models SO ATMOSPHERIC CHEMISTRY AND PHYSICS LA English DT Article ID UPPER-TROPOSPHERIC HUMIDITY; TROPICAL UPPER TROPOSPHERE; COUPLED EQUATORIAL WAVES; LARGE-SCALE MODELS; DEEP CONVECTION; DIURNAL CYCLE; WATER-VAPOR; WESTERN PACIFIC; LIFE-CYCLE; WARM POOL AB An earlier method to determine the mean response of upper-tropospheric water to localised deep convective systems (DC systems) is improved and applied to the EC-Earth climate model. Following Zelinka and Hartmann (2009), several fields related to moist processes and radiation from various satellites are composited with respect to the local maxima in rain rate to determine their spatio-temporal evolution with deep convection in the central Pacific Ocean. Major improvements to the earlier study are the isolation of DC systems in time so as to prevent multiple sampling of the same event, and a revised definition of the mean background state that allows for better characterisation of the DC-system-induced anomalies. The observed DC systems in this study propagate westward at similar to 4 ms(-1). Both the upper-tropospheric relative humidity and the outgoing longwave radiation are substantially perturbed over a broad horizontal extent and for periods > 30 h. The cloud fraction anomaly is fairly constant with height but small maximum can be seen around 200 hPa. The cloud ice water content anomaly is mostly confined to pressures greater than 150 hPa and reaches its maximum around 450 hPa, a few hours after the peak convection. Consistent with the large increase in upper-tropospheric cloud ice water content, albedo increases dramatically and persists about 30 h after peak convection. Applying the compositing technique to EC-Earth allows an assessment of the model representation of DC systems. The model captures the large-scale responses, most notably for outgoing longwave radiation, but there are a number of important differences. DC systems appear to propagate east-ward in the model, suggesting a strong link to Kelvin waves instead of equatorial Rossby waves. The diurnal cycle in the model is more pronounced and appears to trigger new convection further to the west each time. Finally, the modelled ice water content anomaly peaks at pressures greater than 500 hPa and in the upper troposphere between 250 hPa and 500 hPa, there is less ice than the observations and it does not persist as long after peak convection. The modelled upper-tropospheric cloud fraction anomaly, however, is of a comparable magnitude and exhibits a similar longevity as the observations. C1 [Johnston, M. S.; Eriksson, P.] Chalmers, Dept Earth & Space Sci, S-41296 Gothenburg, Sweden. [Eliasson, S.] Lulea Univ Technol, Dept Comp Sci Elect & Space Engn, Div Space Technol, Kiruna, Sweden. [Zelinka, M. D.] Lawrence Livermore Natl Lab, Program Climate Model Diag & Intercomparison, Livermore, CA USA. [Johnston, M. S.; Eliasson, S.; Wyser, K.] Swedish Meteorol & Hydrol Inst, S-60176 Norrkoping, Sweden. [Forbes, R. M.] European Ctr Medium Range Weather Forecasts, Reading RG2 9AX, Berks, England. RP Johnston, MS (reprint author), Chalmers, Dept Earth & Space Sci, S-41296 Gothenburg, Sweden. EM shejo284@gmail.com RI Eriksson, Patrick/A-5321-2009; Johnston, Marston/E-6838-2015; Zelinka, Mark/C-4627-2011 OI Eriksson, Patrick/0000-0002-8475-0479; Johnston, Marston/0000-0003-3788-8659; Zelinka, Mark/0000-0002-6570-5445 FU US Department of Energy (DOE) [DE-AC52-07NA27344]; LLNL Institutional Postdoctoral Program; Regional and Global Climate Modeling Program of the Office of Science at the DOE; Swedish National Space Board FX The authors would like to thank Jean-Jacques Morcrette and Peter Bechtold from the European Centre for Medium-Range Weather Forecasts (ECMWF), Martin Evaldsson (Swedish Meteorological and Hydrological Institute, SMHI), Andreas Skyman, and Ole-Martin Christensen for their technical and scientific help with this study. The authors would also like to thank Stefan Buehler at Lulea University of Technology for his input on the UTH retrievals and satellite sampling. The TMPA data were provided by the NASA/Goddard Space Flight Center's Mesoscale Atmospheric Processes Laboratory and PPS, which develop and compute the TMPA as a contribution to TRMM. In addition the CERES data were obtained from the NASA Langley Research Center Atmospheric Science Data Center. Also we would like to acknowledge the NASA CloudSat project that provided the CloudSat-CALIPSO dataset used in this project. The contribution of Mark D. Zelinka was performed under the auspices of the US Department of Energy (DOE) by Lawrence Livermore National Laboratory (LLNL) under contract DE-AC52-07NA27344 and was supported by the LLNL Institutional Postdoctoral Program and by the Regional and Global Climate Modeling Program of the Office of Science at the DOE. Salomon Eliasson and Patrick Eriksson were supported by the Swedish National Space Board. Finally, the authors would like to thank the anonymous reviewers and Benjamin Grandey for their critique and comments that significantly contributed in improving this paper. NR 45 TC 1 Z9 1 U1 1 U2 12 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 1680-7316 EI 1680-7324 J9 ATMOS CHEM PHYS JI Atmos. Chem. Phys. PY 2013 VL 13 IS 23 BP 12043 EP 12058 DI 10.5194/acp-13-12043-2013 PG 16 WC Meteorology & Atmospheric Sciences SC Meteorology & Atmospheric Sciences GA 274OV UT WOS:000328616800029 ER PT J AU Mernild, SH Lipscomb, WH Bahr, DB Radic, V Zemp, M AF Mernild, S. H. Lipscomb, W. H. Bahr, D. B. Radic, V. Zemp, M. TI Global glacier changes: a revised assessment of committed mass losses and sampling uncertainties SO CRYOSPHERE LA English DT Article ID SEA-LEVEL RISE; MOUNTAIN GLACIERS; ICE CAPS; BALANCE AB Most glaciers and ice caps (GIC) are out of balance with the current climate. To return to equilibrium, GIC must thin and retreat, losing additional mass and raising sea level. Because glacier observations are sparse and geographically biased, there is an undersampling problem common to all global assessments. Here, we further develop an assessment approach based on accumulation-area ratios (AAR) to estimate committed mass losses and analyze the undersampling problem. We compiled all available AAR observations for 144 GIC from 1971 to 2010, and found that most glaciers and ice caps are farther from balance than previously believed. Accounting for regional and global undersampling errors, our model suggests that GIC are committed to additional losses of 32 +/- 12% of their area and 38 +/- 16% of their volume if the future climate resembles the climate of the past decade. These losses imply global mean sea-level rise of 163 +/- 69 mm, assuming total glacier volume of 430 mm sea-level equivalent. To reduce the large uncertainties in these projections, more long-term glacier measurements are needed in poorly sampled regions. C1 [Mernild, S. H.; Lipscomb, W. H.] Los Alamos Natl Lab, Climate Ocean & Sea Ice Modeling Grp, Los Alamos, NM 87545 USA. [Mernild, S. H.] Ctr Estudios Cient, Glaciol & Climate Change Lab, Ctr Sci Studies, Valdivia, Chile. [Bahr, D. B.] Univ Colorado, Inst Arctic & Alpine Res, Boulder, CO 80309 USA. [Bahr, D. B.] Univ Innsbruck, Inst Geog, A-6020 Innsbruck, Austria. [Radic, V.] Univ British Columbia, Dept Earth & Ocean Sci, Vancouver, BC V5Z 1M9, Canada. [Zemp, M.] Univ Zurich, Dept Geog, Zurich, Switzerland. RP Mernild, SH (reprint author), Los Alamos Natl Lab, Climate Ocean & Sea Ice Modeling Grp, POB 1663, Los Alamos, NM 87545 USA. EM mernild@cecs.cl FU National Nuclear Security Administration of the US Department of Energy [DE-AC52-06NA25396]; European Community [262693]; Los Alamos National Laboratory (LANL); Earth System Modeling program of the Office of Biological and Environmental Research within the US Department of Energ's Office of Science FX We thank principal investigators and their teams, along with the WGMS staff, for providing AAR and mass-balance data. We also thank Daniel Farinotti, Ben Marzeion, and Mauri Pelto for insightful reviews, and we thank Graham Cogley, Alex Gardner, Matthias Huss, and Georg Kaser for helpful data and feedback. This work was supported partly by a Los Alamos National Laboratory (LANL) Director's Fellowship and by the Earth System Modeling program of the Office of Biological and Environmental Research within the US Department of Energ's Office of Science. LANL is operated under the auspices of the National Nuclear Security Administration of the US Department of Energy under contract No. DE-AC52-06NA25396, and partly by the European Community's Seventh Framework Programme under grant agreement No. 262693. NR 31 TC 19 Z9 19 U1 2 U2 13 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 1994-0416 EI 1994-0424 J9 CRYOSPHERE JI Cryosphere PY 2013 VL 7 IS 5 BP 1565 EP 1577 DI 10.5194/tc-7-1565-2013 PG 13 WC Geography, Physical; Geosciences, Multidisciplinary SC Physical Geography; Geology GA 273OM UT WOS:000328544800018 ER PT J AU Morriss, BF Hawley, RL Chipman, JW Andrews, LC Catania, GA Hoffman, MJ Luthi, MP Neumann, TA AF Morriss, B. F. Hawley, R. L. Chipman, J. W. Andrews, L. C. Catania, G. A. Hoffman, M. J. Luethi, M. P. Neumann, T. A. TI A ten-year record of supraglacial lake evolution and rapid drainage in West Greenland using an automated processing algorithm for multispectral imagery SO CRYOSPHERE LA English DT Article ID ICE-SHEET; ACCELERATION; ISBRAE AB The rapid drainage of supraglacial lakes introduces large pulses of meltwater to the subglacial environment and creates moulins, surface-to-bed conduits for future melt. Introduction of water to the subglacial system has been shown to affect ice flow, and modeling suggests that variability in water supply and delivery to the subsurface play an important role in the development of the subglacial hydrologic system and its ability to enhance or mitigate ice flow. We developed a fully automated method for tracking meltwater and rapid drainages in large (>0.125 km(2)) perennial lakes and applied it to a 10 yr time series of ETM+ and MODIS imagery of an outlet glacier flow band in West Greenland. Results indicate interannual variability in maximum coverage and spatial evolution of total lake area. We identify 238 rapid drainage events, occurring most often at low (< 900 m) and middle (900-1200 m) elevations during periods of net filling or peak lake coverage. We observe a general progression of both lake filling and draining from lower to higher elevations but note that the timing of filling onset, peak coverage, and dissipation are also variable. Lake coverage is sensitive to air temperature, and warm years exhibit greater variability in both coverage evolution and rapid drainage. Mid-elevation drainages in 2011 coincide with large surface velocity increases at nearby GPS sites, though the relationships between ice-shed-scale dynamics and meltwater input are still unclear. C1 [Morriss, B. F.; Hawley, R. L.; Chipman, J. W.] Dartmouth Coll, Hanover, NH 03755 USA. [Andrews, L. C.; Catania, G. A.] Univ Texas Austin, Austin, TX 78712 USA. [Hoffman, M. J.] Los Alamos Natl Lab, Los Alamos, NM USA. [Luethi, M. P.] Swiss Fed Inst, Zurich, Switzerland. [Neumann, T. A.] NASA Goddard Space Flight Ctr, Green Belt, MD USA. RP Morriss, BF (reprint author), Dartmouth Coll, Hanover, NH 03755 USA. EM bfm@dartmouth.edu RI Catania, Ginny/B-9787-2008; Neumann, Thomas/D-5264-2012; Andrews, Lauren/D-8274-2017; OI Andrews, Lauren/0000-0003-3727-4737; Luthi, Martin Peter/0000-0003-4419-8496 FU National Science Foundation (NSF) [NSF-OPP 0908156] FX This work was made possible by National Science Foundation (NSF) grant NSF-OPP 0908156 awarded to R. L. Hawley. Special thanks to the National to Aeronautics and Space Administration (NASA) and Konrad Steffen's group at the Cooperative Institute for Research in Environmental Science (CIRES) for freely supplying imagery and climate data, respectively. Thanks also to CH2M Hill Polar Field Services and Air Greenland for logistical support in the field. Additional thanks are due to all those friends and colleagues who offered support and insight throughout the project. NR 27 TC 10 Z9 10 U1 1 U2 16 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 1994-0416 EI 1994-0424 J9 CRYOSPHERE JI Cryosphere PY 2013 VL 7 IS 6 BP 1869 EP 1877 DI 10.5194/tc-7-1869-2013 PG 9 WC Geography, Physical; Geosciences, Multidisciplinary SC Physical Geography; Geology GA 273OY UT WOS:000328546300014 ER PT J AU Blazey, BA Holland, MM Hunke, EC AF Blazey, B. A. Holland, M. M. Hunke, E. C. TI Arctic Ocean sea ice snow depth evaluation and bias sensitivity in CCSM SO CRYOSPHERE LA English DT Article ID THICKNESS DISTRIBUTION; THERMAL-CONDUCTIVITY; MODEL; CLIMATE; VARIABILITY; ATMOSPHERE; EVOLUTION; ALBEDO; COVER AB Sea ice cover in the Arctic Ocean is a continued focus of attention. This study investigates the impact of the snow overlying the sea ice in the Arctic Ocean. The impact of snow depth biases in the Community Climate System Model (CCSM) is shown to impact not only the sea ice, but also the overall Arctic climate. Following the identification of seasonal biases produced in CCSM simulations, the thermodynamic transfer through the snow-ice column is perturbed to determine model sensitivity to these biases. This study concludes that perturbations on the order of the observed biases result in modification of the annual mean conductive flux through the snow-ice column of 0.5 W m(2) relative to an unmodified simulation. The results suggest that the ice has a complex response to snow characteristics, with ice of different thicknesses producing distinct reactions. Our results indicate the importance of an accurate simulation of snow on the Arctic sea ice. Consequently, future work investigating the impact of current precipitation biases and missing snow processes, such as blowing snow, densification, and seasonal changes, is warranted. C1 [Blazey, B. A.] Univ Bremen, Ctr Marine Environm Sci MARUM, D-28359 Bremen, Germany. [Blazey, B. A.] Univ Colorado, Dept Atmospher & Ocean Sci, Boulder, CO 80309 USA. [Holland, M. M.] Natl Ctr Atmospher Res, Boulder, CO 80307 USA. [Hunke, E. C.] Los Alamos Natl Lab, Los Alamos, NM USA. RP Blazey, BA (reprint author), Univ Bremen, Ctr Marine Environm Sci MARUM, D-28359 Bremen, Germany. EM bblazey@marum.de FU NSF Office of Polar Programs [OPP-0229473]; NASA Cryospheric Sciences Program [NNX07AR21G, NNX11AI48G]; Biological and Environmental Research division of the US Department of Energy Office of Science; National Nuclear Security Administration of the US Department of Energy [DE-AC52-06NA25396] FX The authors thank J. Maslanik for his support, both as faculty advisor and through funding support through NSF Office of Polar Programs, grant OPP-0229473, and NASA Cryospheric Sciences Program, grants NNX07AR21G and NNX11AI48G. Funding from the Biological and Environmental Research division of the US Department of Energy Office of Science is gratefully acknowledged. Los Alamos National Laboratory is operated by the National Nuclear Security Administration of the US Department of Energy under Contract No. DE-AC52-06NA25396. NR 59 TC 4 Z9 4 U1 1 U2 4 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 1994-0416 EI 1994-0424 J9 CRYOSPHERE JI Cryosphere PY 2013 VL 7 IS 6 BP 1887 EP 1900 DI 10.5194/tc-7-1887-2013 PG 14 WC Geography, Physical; Geosciences, Multidisciplinary SC Physical Geography; Geology GA 273OY UT WOS:000328546300017 ER PT J AU Voisin, N Liu, L Hejazi, M Tesfa, T Li, H Huang, M Liu, Y Leung, LR AF Voisin, N. Liu, L. Hejazi, M. Tesfa, T. Li, H. Huang, M. Liu, Y. Leung, L. R. TI One-way coupling of an integrated assessment model and a water resources model: evaluation and implications of future changes over the US Midwest SO HYDROLOGY AND EARTH SYSTEM SCIENCES LA English DT Article ID SHARED SOCIOECONOMIC PATHWAYS; ASSIMILATION SYSTEM NLDAS; CLIMATE-CHANGE IMPACTS; DAILY SOLAR-RADIATION; COMMUNITY LAND MODEL; RIVER-BASIN; ELECTRICITY-GENERATION; WASHINGTON-STATE; SURFACE; MANAGEMENT AB An integrated model is being developed to advance our understanding of the interactions between human activities, terrestrial system and water cycle, and to evaluate how system interactions will be affected by a changing climate at the regional scale. As a first step towards that goal, a global integrated assessment model, which includes a water-demand model driven by socioeconomics at regional and global scales, is coupled in a one-way fashion with a land surface hydrology-routing-water resources management model. To reconcile the scale differences between the models, a spatial and temporal disaggregation approach is developed to downscale the annual regional water demand simulations into a daily time step and subbasin representation. The model demonstrates reasonable ability to represent the historical flow regulation and water supply over the US Midwest (Missouri, Upper Mississippi, and Ohio river basins). Implications for future flow regulation, water supply, and supply deficit are investigated using climate change projections with the B1 and A2 emission scenarios, which affect both natural flow and water demand. Although natural flow is projected to increase under climate change in both the B1 and A2 scenarios, there is larger uncertainty in the changes of the regulated flow. Over the Ohio and Upper Mississippi river basins, changes in flow regulation are driven by the change in natural flow due to the limited storage capacity. However, both changes in flow and demand have effects on the Missouri River Basin summer regulated flow. Changes in demand are driven by socioeconomic factors, energy and food demands, global markets and prices with rainfed crop demand handled directly by the land surface modeling component. Even though most of the changes in supply deficit (unmet demand) and the actual supply (met demand) are driven primarily by the change in natural flow over the entire region, the integrated framework shows that supply deficit over the Missouri River Basin sees an increasing sensitivity to changes in demand in future periods. It further shows that the supply deficit is six times as sensitive as the actual supply to changes in flow and demand. A spatial analysis of the supply deficit demonstrates vulnerabilities of urban areas located along mainstream with limited storage. C1 [Voisin, N.; Tesfa, T.; Li, H.; Huang, M.; Liu, Y.; Leung, L. R.] Pacific NW Natl Lab, Richland, WA 99352 USA. [Liu, L.; Hejazi, M.] Pacific NW Natl Lab, Joint Global Change Res Inst, College Pk, MD USA. RP Voisin, N (reprint author), Pacific NW Natl Lab, Richland, WA 99352 USA. EM nathalie.voisin@pnnl.gov RI Li, Hong-Yi/C-9143-2014; Voisin, Nathalie/D-8845-2014; Huang, Maoyi/I-8599-2012; Liu, Lu/J-4551-2015; OI Li, Hong-Yi/0000-0001-5690-3610; Huang, Maoyi/0000-0001-9154-9485; Liu, Lu/0000-0002-4939-5432; Voisin, Nathalie/0000-0002-6848-449X FU PNNL's Platform for Regional Integrated Modeling and Analysis (PRIMA); US DOE [DE-AC05-76RL01830] FX The authors would like to thank S. Siebert at the University of Bonn, Germany for providing the global gridded monthly irrigation water requirements data for crops, and Duane Ward at the Pacific Northwest National Laboratory (PNNL) for his assistance with the WM dependence database set up over the US Midwest. We thank two anonymous reviewers and editor W. Buytaert for their constructive criticism that significantly improved the manuscript. This study was supported by PNNL's Platform for Regional Integrated Modeling and Analysis (PRIMA). The authors wish to express appreciation to the Integrated Assessment Research Program in the Office of Science of the US Department of Energy (DOE) for long-term support that enabled the development of the Global Change Assessment Model, which was used in the conduct of this research. PNNL is operated by Battelle for the US DOE under contract DE-AC05-76RL01830. The views and opinions expressed in this paper are those of the authors alone. NR 64 TC 15 Z9 15 U1 4 U2 31 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 1027-5606 EI 1607-7938 J9 HYDROL EARTH SYST SC JI Hydrol. Earth Syst. Sci. PY 2013 VL 17 IS 11 BP 4555 EP 4575 DI 10.5194/hess-17-4555-2013 PG 21 WC Geosciences, Multidisciplinary; Water Resources SC Geology; Water Resources GA 263IG UT WOS:000327800700019 ER PT J AU Kent, AD Liebrock, LM AF Kent, Alexander D. Liebrock, Lorie M. GP IEEE TI Differentiating User Authentication Graphs SO IEEE CS SECURITY AND PRIVACY WORKSHOPS (SPW 2013) LA English DT Proceedings Paper CT 2nd IEEE CS Security and Privacy Workshops (SPW) CY MAY 23-24, 2013 CL San Francisco, CA SP IEEE, IEEE Comp Soc, IBM, Cisco, Silent Circle, Microsoft Res AB Authentication using centralized methods is a primary trust mechanism within most large-scale, enterprise computer networks. This paper proposes using graphs to represent user authentication activity within the network. Using this mechanism over a real enterprise network dataset, we find that non-privileged users and users with system administration privileges have distinguishable graph attributes in terms of size and complexity. In addition, we find that user authentication graphs provide intuitive insights into network user behavior. We believe that understanding these differences in even greater detail will lead to improved user behavior profiling and the elusive detection of authentication credential misuse. C1 [Kent, Alexander D.; Liebrock, Lorie M.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Kent, AD (reprint author), Los Alamos Natl Lab, Los Alamos, NM 87545 USA. EM alex@lanl.gov; liebrock@nmt.edu NR 6 TC 1 Z9 1 U1 0 U2 1 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-1-4799-0458-7 PY 2013 BP 72 EP 75 DI 10.1109/SPW.2013.38 PG 4 WC Computer Science, Theory & Methods SC Computer Science GA BJK70 UT WOS:000328702000013 ER PT J AU Bhalla, A Limpijumnong, S Priya, S Yimnirun, R Saxena, A Guo, RY AF Bhalla, Amar Limpijumnong, Sukit Priya, Shashank Yimnirun, Rattikorn Saxena, Avadh Guo, Ruyan TI Untitled SO INTEGRATED FERROELECTRICS LA English DT Article; Proceedings Paper CT International Network of Advanced and Multifunctional Materials (INAMM) Symposium CY DEC 09-10, 2012 CL Pattaya, THAILAND C1 [Bhalla, Amar; Guo, Ruyan] Univ Texas San Antonio, San Antonio, TX USA. [Limpijumnong, Sukit; Yimnirun, Rattikorn] Suranaree Univ, Nakhon Ratchasima, Thailand. [Priya, Shashank] Virginia Tech, Blacksburg, VA USA. [Saxena, Avadh] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Bhalla, A (reprint author), Univ Texas San Antonio, San Antonio, TX USA. NR 0 TC 0 Z9 0 U1 1 U2 7 PU TAYLOR & FRANCIS LTD PI ABINGDON PA 2-4 PARK SQUARE, MILTON PARK, ABINGDON OR14 4RN, OXON, ENGLAND SN 1058-4587 EI 1607-8489 J9 INTEGR FERROELECTR JI Integr. Ferroelectr. PD JAN 1 PY 2013 VL 148 IS 1 BP VII EP VIII DI 10.1080/10584587.2013.864179 PG 2 WC Engineering, Electrical & Electronic; Physics, Applied; Physics, Condensed Matter SC Engineering; Physics GA 269NL UT WOS:000328247900021 ER PT J AU Yi, J Sopori, B Lan, CW Kim, D Bremner, S AF Yi, Junsin Sopori, Bhushan Lan, C. W. Kim, Donghwan Bremner, Stephen TI Si-Related Solar Cells for a Low Cost and High Efficiency 2013 SO INTERNATIONAL JOURNAL OF PHOTOENERGY LA English DT Editorial Material C1 [Yi, Junsin] Sungkyunkwan Univ, Dept Elect & Elect Engn, Suwon 440746, South Korea. [Sopori, Bhushan] Natl Renewable Energy Lab, Golden, CO USA. [Lan, C. W.] Natl Taiwan Univ, Dept Chem Engn, Taipei 106, Taiwan. [Kim, Donghwan] Korea Univ, Dept Mat Sci & Engn, Seoul 136713, South Korea. [Bremner, Stephen] Univ New S Wales, Sch Photovolta & Renewable Energy Engn, Sydney, NSW 2052, Australia. RP Yi, J (reprint author), Sungkyunkwan Univ, Dept Elect & Elect Engn, 300 Chunchun Dong, Suwon 440746, South Korea. EM yi@yurim.skku.ac.kr OI Lan, Chung-wen/0000-0003-4141-2741 NR 0 TC 0 Z9 0 U1 0 U2 4 PU HINDAWI PUBLISHING CORPORATION PI NEW YORK PA 410 PARK AVENUE, 15TH FLOOR, #287 PMB, NEW YORK, NY 10022 USA SN 1110-662X EI 1687-529X J9 INT J PHOTOENERGY JI Int. J. Photoenergy PY 2013 AR 596973 DI 10.1155/2013/596973 PG 1 WC Chemistry, Physical; Energy & Fuels; Optics; Physics, Atomic, Molecular & Chemical SC Chemistry; Energy & Fuels; Optics; Physics GA 276RB UT WOS:000328766300001 ER PT J AU Ryan, SD Berlyand, L Haines, BM Karpeev, DA AF Ryan, S. D. Berlyand, L. Haines, B. M. Karpeev, D. A. TI A KINETIC MODEL FOR SEMIDILUTE BACTERIAL SUSPENSIONS SO MULTISCALE MODELING & SIMULATION LA English DT Article DE collective motion; effective viscosity; coupled PDE/ODE system; kinetic theory ID PARTICLES; COMPUTER; MOTION; FLUID AB Suspensions of self-propelled microscopic particles, such as swimming bacteria, exhibit collective motion leading to remarkable experimentally observable macroscopic properties. Rigorous mathematical analysis of this emergent behavior can provide significant insight into the mechanisms behind these experimental observations; however, there are many theoretical questions remaining unanswered. In this paper, we study a coupled PDE/ODE system first introduced in the physics literature and used to investigate numerically the effective viscosity of a bacterial suspension. We then examine the kinetic theory associated with the coupled system, which is designed to capture the long-time behavior of a Stokesian suspension of point force dipoles (infinitesimal spheroids representing self-propelled particles) with Lennard-Jones-type repulsion. A planar shear background flow is imposed on the suspension through the novel use of Lees-Edwards quasi-periodic boundary conditions applied to a representative volume. We show the existence and uniqueness of solutions for all time to the equations of motion for particle configurations-dipole orientations and relative positions. This result follows from first establishing the regularity of the solution to the fluid equations. The existence and uniqueness result allows us to define the Liouville equation for the probability density of configurations. We show that this probability density defines the average bulk stress in the suspension underlying the definition of many macroscopic quantities of interest, in particular the effective viscosity. These effective properties are determined by microscopic interactions highlighting the multiscale nature of this work. C1 [Ryan, S. D.; Berlyand, L.; Haines, B. M.] Penn State Univ, Dept Math, University Pk, PA 16802 USA. [Haines, B. M.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. [Karpeev, D. A.] Argonne Natl Lab, Math & Comp Sci Div, Argonne, IL 60439 USA. RP Ryan, SD (reprint author), Penn State Univ, Dept Math, University Pk, PA 16802 USA. EM ryan@math.psu.edu; berlyand@math.psu.edu; brianmhaines@gmail.com; karpeev@mcs.anl.gov OI Haines, Brian/0000-0002-3889-7074 FU Department of Energy [DE-FG02-08ER25862] FX The work of these authors was supported by Department of Energy grant DE-FG02-08ER25862. NR 38 TC 5 Z9 5 U1 0 U2 5 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 1540-3459 EI 1540-3467 J9 MULTISCALE MODEL SIM JI Multiscale Model. Simul. PY 2013 VL 11 IS 4 BP 1176 EP 1196 DI 10.1137/120900575 PG 21 WC Mathematics, Interdisciplinary Applications; Physics, Mathematical SC Mathematics; Physics GA 278OE UT WOS:000328898800008 ER PT J AU Hauck, CD McClarren, RG AF Hauck, Cory D. McClarren, Ryan G. TI A COLLISION-BASED HYBRID METHOD FOR TIME-DEPENDENT, LINEAR, KINETIC TRANSPORT EQUATIONS SO MULTISCALE MODELING & SIMULATION LA English DT Article DE hybrid method; kinetic equations; multiscale equations ID ASYMPTOTIC PRESERVING SCHEME; SMOOTH TRANSITION MODEL; MEAN FREE PATHS; DIFFUSION-LIMIT; DOMAIN DECOMPOSITION; RADIATIVE-TRANSFER; MONTE-CARLO; NEUTRON-TRANSPORT; ITERATIVE METHODS; BOLTZMANN AB We present a hybrid method for simulating kinetic equations with multiscale phenomena in the context of linear transport. The method consists of (i) partitioning the kinetic equation into collisional and noncollisional components, (ii) applying a different numerical method to each component, and (iii) repartitioning the kinetic distribution after each time step in the algorithm. Preliminary results show that, for a wide range of test problems, the combination of a low-fidelity method for the collisional component and a high-fidelity method for the noncollisional component provides a level of accuracy that is comparable to a uniform high-fidelity treatment of the entire system. C1 [Hauck, Cory D.] Oak Ridge Natl Lab, Computat Math Grp, Comp Sci & Math Div, Oak Ridge, TN 37831 USA. [McClarren, Ryan G.] Texas A&M Univ, Dept Nucl Engn, College Stn, TX 77843 USA. RP Hauck, CD (reprint author), Oak Ridge Natl Lab, Computat Math Grp, Comp Sci & Math Div, Oak Ridge, TN 37831 USA. EM hauckc@ornl.gov; rgm@tamu.edu FU Office of Advanced Scientific Computing Research, U.S. Department of Energy; UT-Battelle, LLC [De-AC05-00OR22725] FX This research is sponsored by the Office of Advanced Scientific Computing Research, U.S. Department of Energy. Oak Ridge National Laboratory is managed by UT-Battelle, LLC under contract De-AC05-00OR22725. This work was performed by an employee of the U.S. Government or under U. S. Government contract. The U. S. Government retains a nonexclusive, royalty-free license to publish or reproduce the published form of this contribution, or allow others to do so, for U.S. Government purposes. Copyright is owned by SIAM to the extent not limited by these rights. NR 56 TC 2 Z9 2 U1 1 U2 5 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 1540-3459 EI 1540-3467 J9 MULTISCALE MODEL SIM JI Multiscale Model. Simul. PY 2013 VL 11 IS 4 BP 1197 EP 1227 DI 10.1137/110846610 PG 31 WC Mathematics, Interdisciplinary Applications; Physics, Mathematical SC Mathematics; Physics GA 278OE UT WOS:000328898800009 ER PT S AU Lopatina, LM Reichhardt, C Reichhardt, CJO AF Lopatina, L. M. Reichhardt, C. Reichhardt, C. J. Olson BE Dholakia, K Spalding, GC TI Self-Driven Particles on Asymmetric Trap Arrays SO OPTICAL TRAPPING AND OPTICAL MICROMANIPULATION X SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on Optical Trapping and Optical Micromanipulation X CY AUG 25-29, 2013 CL San Diego, CA SP SPIE, Elliot Sci Ltd, nPoint Inc, Thorlabs Inc DE Active matter; ratchet effect; optical traps ID VORTEX LATTICES; BACTERIA; MOTORS AB Active matter or self driven particle systems include swimming bacteria, crawling cells and artificial swimmers. These systems often exhibit run and tumble dynamics; however, there are also examples of particles that move or swim in circles, such as bacteria near surfaces. Circular swimmers have also been experimentally realized using chiral colloidal particles. Here we examine how a substrate can be used to direct the motion of circle swimmers and separate particles with different swimming chiralities. The combination of the time reversal symmetry breaking by the circular motion as well as the breaking of detailed balance when the particles interact with the barriers leads to the directed motion. We examine this effect for different types of substrate geometries and also consider the effects of temperature. Such substrates could be created using various optical techniques. C1 [Lopatina, L. M.; Reichhardt, C.; Reichhardt, C. J. Olson] Los Alamos Natl Lab, Ctr Nonlinear Studies, Los Alamos, NM 87545 USA. RP Lopatina, LM (reprint author), Los Alamos Natl Lab, Ctr Nonlinear Studies, Los Alamos, NM 87545 USA. EM reichhardt@lanl.gov NR 55 TC 0 Z9 0 U1 1 U2 4 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9660-7 J9 PROC SPIE PY 2013 VL 8810 AR 881016 DI 10.1117/12.2027325 PG 11 WC Nanoscience & Nanotechnology; Optics SC Science & Technology - Other Topics; Optics GA BJJ20 UT WOS:000328460400019 ER PT S AU McDermott, D Libal, A Chern, GW Reichhardt, C Reichhardt, CJO AF McDermott, D. Libal, A. Chern, G. W. Reichhardt, C. Reichhardt, C. J. Olson BE Dholakia, K Spalding, GC TI Frustration Effects and Grain Boundaries in Colloidal Particle Orderings on Optical Substrates SO OPTICAL TRAPPING AND OPTICAL MICROMANIPULATION X SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on Optical Trapping and Optical Micromanipulation X CY AUG 25-29, 2013 CL San Diego, CA SP SPIE, Elliot Sci Ltd, nPoint Inc, Thorlabs Inc DE Active matter; ratchet effect; optical traps ID ARTIFICIAL SPIN-ICE; GEOMETRICAL FRUSTRATION; STATES; CRYSTALS; LATTICE; ARRAYS; SYSTEM AB Optical traps have been extensively employed to create tailored colloidal crystalline structures where the crystals can have long range order. Here we discuss how colloidal particles on periodic substrates can be used to understand how frustration can produce partially ordered states. We demonstrate how to create artificial spin ice systems using colloidal particles and describe variations on this system that include geometries in which a random loop model can be realized. We also discuss how frustration effects can be used to control grain boundary formation by creating energetic defects in the ground state ordering of these systems. C1 [McDermott, D.; Chern, G. W.; Reichhardt, C.; Reichhardt, C. J. Olson] Los Alamos Natl Lab, Ctr Nonlinear Studies, Los Alamos, NM 87545 USA. RP McDermott, D (reprint author), Los Alamos Natl Lab, Ctr Nonlinear Studies, Los Alamos, NM 87545 USA. EM reichhardt@lanl.gov FU NNSA of the U.S. Department of Energy at Los Alamos National Laboratory [DE-AC52-06NA25396] FX This work was carried out under the auspices of the NNSA of the U.S. Department of Energy at Los Alamos National Laboratory under Contract No. DE-AC52-06NA25396. NR 51 TC 0 Z9 0 U1 0 U2 2 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9660-7 J9 PROC SPIE PY 2013 VL 8810 AR 881013 DI 10.1117/12.2026935 PG 10 WC Nanoscience & Nanotechnology; Optics SC Science & Technology - Other Topics; Optics GA BJJ20 UT WOS:000328460400017 ER PT S AU Vasdekis, AE Scott, EA O'Neil, CP Psaltis, D Hubbell, JA AF Vasdekis, A. E. Scott, E. A. O'Neil, C. P. Psaltis, D. Hubbell, J. A. BE Dholakia, K Spalding, GC TI Optical Manipulation of Vesicles for Optofluidic Applications SO OPTICAL TRAPPING AND OPTICAL MICROMANIPULATION X SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on Optical Trapping and Optical Micromanipulation X CY AUG 25-29, 2013 CL San Diego, CA SP SPIE, Elliot Sci Ltd, nPoint Inc, Thorlabs Inc ID DRUG-DELIVERY SYSTEMS; MICROFLUIDIC SYSTEMS; TRIGGERED RELEASE; LIPID VESICLES; CANCER-THERAPY; POLYMERSOMES; LASERS; MEMBRANES; LIGHT; POLY(DIMETHYLSILOXANE) AB In this report, we review our recent results in the optical micromanipulation of vesicles. Traditionally, vesicle manipulation has been possible by employing photon momentum and optical trapping, giving rise to unique observations of vesicle shape changes and soft matter mechanics. Contrary to these attempts, we employ photon energy rather than momentum, by sensitizing vesicles with an oxidizing moiety. The later converts incident photons to reactive oxygen species, which in turn attack and compromise the stability of the vesicle membrane. Both coherent and incoherent radiation was employed. Polymersome re-organization into smaller diameter vesicles was possible by focusing the excitation beam in the vicinity of the polymersomes. Extended vesicle illumination with a collimated beam lead to their complete destabilization and micelle formation. Single particle analysis revealed that payload release takes place within seconds of illumination in an explosive burst. We will discuss the destabilization and payload release kinetics, as revealed by high resolution microscopy at the single particle level, as well as potential applications in single cell biomodulation. C1 [Vasdekis, A. E.; Psaltis, D.] Pacific Northwestern Natl Lab, Environm Mol Sci Lab, POB 999, Richland, WA 99354 USA. [Scott, E. A.; O'Neil, C. P.; Hubbell, J. A.] Ecole Polytech Fed Lausanne, Inst Bioengn, CH-1015 Lausanne, Switzerland. [Hubbell, J. A.] Ecole Polytech Fed Lausanne, Inst Chem Sci Engn, CH-1015 Lausanne, Switzerland. RP Vasdekis, AE (reprint author), Pacific Northwestern Natl Lab, Environm Mol Sci Lab, POB 999, Richland, WA 99354 USA. OI Vasdekis, Andreas/0000-0003-4315-1047 NR 47 TC 0 Z9 0 U1 0 U2 10 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9660-7 J9 PROC SPIE PY 2013 VL 8810 AR 88101R DI 10.1117/12.2026583 PG 9 WC Nanoscience & Nanotechnology; Optics SC Science & Technology - Other Topics; Optics GA BJJ20 UT WOS:000328460400028 ER PT S AU Benk, MP Goldberg, KA Mochi, I Chao, WL Anderson, EH AF Benk, Markus P. Goldberg, Kenneth A. Mochi, Iacopo Chao, Weilun Anderson, Erik H. BE Faure, TB Ackmann, PW TI Increased depth of field through wave-front coding: using an off-axis zone plate lens with cubic phase modulation in an EUV microscope SO PHOTOMASK TECHNOLOGY 2013 SE Proceedings of SPIE LA English DT Proceedings Paper CT SPIE Conference on Photomask Technology held as part of the 33rd International Symposium on Photomask Technology CY SEP 10-12, 2013 CL Monterey, CA SP SPIE, Bay Area Chrome Users Soc DE Wave front coding; cubic phase modulation; depth of focus; depth of field; EUV; microscopy; zone plate AB The authors are extending the capabilities of the SHARP microscope (SEMATECH High-NA Actinic Reticle review Project) by implementing wave front coding as a complementary imaging mode. SHARP, using a single off-axis lens has a tilted focal plane, reducing the instrument's field of view to a few micrometers. Wave-front coding increases the depth of field of an incoherent imaging system without affecting its resolution and light gathering power, rendering clear, large-field images for navigation and analysis. The resolution of the resulting image is close to the diffraction limit of the unmodified system. The authors have designed and nanofabricated zone plate lenses with a modified pattern that combines focusing power and wave front coding in a single optical element. The study clears the path to further applications of wave front coded zone plates in lab-and synchrotron-based microscopes and metrology tools. The authors have demonstrated wave-front coding in visible-light optical systems using Fresnel zone plate lenses in an off-axis configuration similar to SHARP. Simulations complementing the visible light experiments assess the performance of wave-front coded zone plates in the SHARP microscope. C1 [Benk, Markus P.; Goldberg, Kenneth A.; Mochi, Iacopo; Chao, Weilun; Anderson, Erik H.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Benk, MP (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, 1 Cyclotron Rd, Berkeley, CA 94720 USA. EM mpbenk@lbl.gov NR 7 TC 0 Z9 0 U1 2 U2 2 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9545-7 J9 PROC SPIE PY 2013 VL 8880 AR 88801R DI 10.1117/12.2025954 PG 9 WC Optics; Imaging Science & Photographic Technology SC Optics; Imaging Science & Photographic Technology GA BJJ93 UT WOS:000328542900056 ER PT S AU Chao, R Gullikson, E Goldstein, M Goodwin, F Teki, R Neureuther, A Naulleau, P AF Chao, Rikon Gullikson, Eric Goldstein, Michael Goodwin, Frank Teki, Ranganath Neureuther, Andy Naulleau, Patrick BE Faure, TB Ackmann, PW TI EUV scatterometry-based measurement method for the determination of phase roughness SO PHOTOMASK TECHNOLOGY 2013 SE Proceedings of SPIE LA English DT Proceedings Paper CT SPIE Conference on Photomask Technology held as part of the 33rd International Symposium on Photomask Technology CY SEP 10-12, 2013 CL Monterey, CA SP SPIE, Bay Area Chrome Users Soc DE Phase roughness; power spectral density; scatterometry; extreme ultraviolet lithography; metrology AB AFM-based roughness measurement reveals the topography of EUV masks, but is only sensitive to the top surface [1]. Scatterometry provides a more accurate approach to characterize the effective phase roughness of the multilayer, and it becomes important to determine the valid metrology for roughness characterization. In this work, the power spectral density calculated from scatterometry is compared to that from AFM for measurements before and after coating of substrates with a range of roughness levels. Results show noticeable discrepancies between AFM- and scatterometry-measured roughness, and indicates that when the physical surface roughness increases with deposition the EUV penetration into the multilayer tends to mitigate this effect. In this paper, we describe an EUV scatterometry-based measurement method for the determination of phase roughness with the goal of minimizing the amount of physical scattering data to be collected and rendering the method compatible with potential future standalone EUV reflectometer tools. C1 [Chao, Rikon; Gullikson, Eric; Naulleau, Patrick] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Ctr Xray Opt, Berkeley, CA 94720 USA. RP Chao, R (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Ctr Xray Opt, Berkeley, CA 94720 USA. NR 8 TC 1 Z9 1 U1 0 U2 1 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9545-7 J9 PROC SPIE PY 2013 VL 8880 AR 88801B DI 10.1117/12.2027695 PG 4 WC Optics; Imaging Science & Photographic Technology SC Optics; Imaging Science & Photographic Technology GA BJJ93 UT WOS:000328542900040 ER PT S AU Goldberg, KA Mochi, I Benk, MP Lin, CC Allezy, A Dickinson, M Cork, CW Macdougall, JB Anderson, EH Chao, WL Salmassi, F Gullikson, EM Zehm, D Vytla, V Cork, W DePonte, J Picchi, G Pekedis, A Katayanagi, T Jones, MG Martin, E Naulleau, PP Rekawa, SB AF Goldberg, Kenneth A. Mochi, Iacopo Benk, Markus P. Lin, Chihcheng Allezy, Arnaud Dickinson, Michael Cork, Carl W. Macdougall, James B. Anderson, Erik H. Chao, Weilun Salmassi, Farhad Gullikson, Eric. M. Zehm, Daniel Vytla, Vamsi Cork, William DePonte, Jason Picchi, Gino Pekedis, Ahmet Katayanagi, Takeshi Jones, Michael G. Martin, Elizabeth Naulleau, Patrick P. Rekawa, Senajith B. BE Faure, TB Ackmann, PW TI The SEMATECH high-NA actinic reticle review project (SHARP) EUV mask-imaging microscope SO PHOTOMASK TECHNOLOGY 2013 SE Proceedings of SPIE LA English DT Proceedings Paper CT SPIE Conference on Photomask Technology held as part of the 33rd International Symposium on Photomask Technology CY SEP 10-12, 2013 CL Monterey, CA SP SPIE, Bay Area Chrome Users Soc DE extreme ultraviolet; EUV; mask; microscope; coherence; imaging AB The SEMATECH High Numerical Aperture Actinic Reticle Review Project (SHARP) is a newly commissioned, synchrotron-based extreme ultraviolet (EUV) microscope dedicated to photomask research. SHARP offers several major advances including objective lenses with 4xNA values from 0.25 to 0.625, flexible, lossless coherence control through a Fourier-synthesis illuminator, a rotating azimuthal plane of incidence up to +/- 25 degrees, illumination central ray angles from 6 to 10, and a continuously tunable, EUV illumination wavelength. SHARP is now being used to study programmed and native mask defects, defect repairs, mask architecture, optical proximity correction, and the influence of mask substrate roughness on imaging. SHARP has the ability to emulate a variety of current and future lithography tool numerical apertures, and illumination properties. Here, we present various performance studies and examples where SHARP's unique capabilities are used in EUV mask research. C1 [Goldberg, Kenneth A.; Mochi, Iacopo; Benk, Markus P.; Allezy, Arnaud; Dickinson, Michael; Cork, Carl W.; Macdougall, James B.; Anderson, Erik H.; Chao, Weilun; Salmassi, Farhad; Gullikson, Eric. M.; Zehm, Daniel; Vytla, Vamsi; Cork, William; DePonte, Jason; Picchi, Gino; Pekedis, Ahmet; Katayanagi, Takeshi; Jones, Michael G.; Martin, Elizabeth; Naulleau, Patrick P.; Rekawa, Senajith B.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Goldberg, KA (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, 1 Cyclotron Rd, Berkeley, CA 94720 USA. EM KAGoldberg@lbl.gov NR 8 TC 6 Z9 6 U1 0 U2 1 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9545-7 J9 PROC SPIE PY 2013 VL 8880 AR 88800T DI 10.1117/12.2026496 PG 9 WC Optics; Imaging Science & Photographic Technology SC Optics; Imaging Science & Photographic Technology GA BJJ93 UT WOS:000328542900023 ER PT S AU Mochi, I Goldberg, KA Benk, MP Naulleau, PP AF Mochi, Iacopo Goldberg, Kenneth A. Benk, Markus P. Naulleau, Patrick P. BE Faure, TB Ackmann, PW TI Pupil shaping and coherence control in an EUV mask-imaging microscope SO PHOTOMASK TECHNOLOGY 2013 SE Proceedings of SPIE LA English DT Proceedings Paper CT SPIE Conference on Photomask Technology held as part of the 33rd International Symposium on Photomask Technology CY SEP 10-12, 2013 CL Monterey, CA SP SPIE, Bay Area Chrome Users Soc DE EUV lithography; EUV microscopy; mask inspection; coherence; pupil-fill AB We are investigating the effect of pupil-fill patterns and partial coherence settings on EUV reticle images on the new SEMATECH High-NA Actinic Reticle review Project (SHARP), to deepen our understanding of its performance, and improve the emulation of image formation in arbitrary printing tools. SHARP is an EUV mask microscope developed as the successor of the SEMATECH Berkeley Actinic Inspection Tool (AIT). It is equipped with a unique, MEMS-based Fourier synthesis illuminator that generates arbitrary, customized pupil fill patterns to control the illumination partial coherence. The high-magnification objective lenses are an array of interchangeable Fresnel zoneplates with 4xNA values ranging from 0.25 to 0.625. We have used SHARP to inspect isolated and dense features with half pitch as low as 55 nm using lenses with a range of NA values, and common illumination patterns, such as annular, dipole and QUASAR (TM). We will show the effect of illumination on important, measured pattern parameters, including contrast, normalized image log-slope, and depth of focus. We have also studied the effect of partial coherence on the imaging of on multilayer roughness observed in bright mask regions, a topic important for expanding our understanding of the causes of LER. C1 [Mochi, Iacopo; Goldberg, Kenneth A.; Benk, Markus P.; Naulleau, Patrick P.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Mochi, I (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, 1 Cyclotron Rd, Berkeley, CA 94720 USA. NR 14 TC 0 Z9 0 U1 0 U2 0 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9545-7 J9 PROC SPIE PY 2013 VL 8880 AR 888022 DI 10.1117/12.2026498 PG 10 WC Optics; Imaging Science & Photographic Technology SC Optics; Imaging Science & Photographic Technology GA BJJ93 UT WOS:000328542900066 ER PT J AU Felmy, AR Moore, DA Qafoku, O Buck, E Conradson, SD Ilton, ES AF Felmy, A. R. Moore, D. A. Qafoku, O. Buck, E. Conradson, S. D. Ilton, E. S. TI Heterogeneous reduction of (PuO2)-Pu-239 by aqueous Fe(II) in the presence of hematite SO RADIOCHIMICA ACTA LA English DT Article DE Plutonium dioxide; Hematite; Ferrous iron; Reduction; Radiolysis ID URANIUM(VI); SURFACE; IRON; MINERALS; U(VI); 25-DEGREES-C; NEPTUNIUM(V); DISSOLUTION; SOLUBILITY; RADIOLYSIS AB The reduction of PuO2(am) by Fen in the presence and absence of hematite was studied over a range of pH values and oxidation/reduction potentials. In contrast to thermodynamic predictions, the presence of hematite did not have a major effect on the overall reduction of PuO2(am) to aqueous Pu(III). Instead the aqueous Pu(111) concentrations at longer time frames were accurately predicted using the measured Fe(II) concentration and existing thermodynamic data for the reaction: H2O + H+ + Fe2+ + PuO2(am) (sic) Pu3+ + Fe(OH)(3)(am) with log K = -0.6. The accuracy of this approach in all solutions containing aqueous Fe(II), coupled with the apparent lack of oxidation of Fe(II) by O-2(g), suggests that the Fe(OH)(3)(am) is formed by the oxidation of Fe(II) to Fe(III) by radiolysis. The continued generation of reactive amorphous iron hydroxide by radiolysis prevents thermodynamic equilibrium from being reached with more stable ferric oxide compounds, except possibly under acidic conditions where amorphous ferric hydroxide is soluble. The use of measured pe values, instead of aqueous Fe(II) measurements, also yields reasonable predictions of the final Pu(III) concentrations although the predictions are more uncertain. C1 [Felmy, A. R.; Moore, D. A.; Qafoku, O.; Buck, E.; Ilton, E. S.] Pacific NW Natl Lab, Richland, WA 99352 USA. [Conradson, S. D.] Los Alamos Natl Lab, Los Alamos, NM USA. RP Felmy, AR (reprint author), Pacific NW Natl Lab, Richland, WA 99352 USA. EM ar.felmy@pnnl.gov FU U.S. Department of Energy's Office of Biological and Environmental Research, as part of the Subsurface Biogeochemical Research (SBR) Science Focus Area (SFA) at the Pacific Northwest National Laboratory; U.S. Department of Energy's Office of Biological and environmental Research FX This work was supported by the U.S. Department of Energy's Office of Biological and Environmental Research, as part of the Subsurface Biogeochemical Research (SBR) Science Focus Area (SFA) at the Pacific Northwest National Laboratory. A portion of this research was performed using EMSL, a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and environmental Research and located at the Pacific Northwest National Laboratory. The XAFS measurements were made at the Stanford Synchrotron Radiation Lightsource, a national user facility operated by Stanford University on behalf of the U.S. Department of Energy, Office of Basic Energy Sciences. NR 33 TC 1 Z9 1 U1 3 U2 13 PU WALTER DE GRUYTER GMBH PI BERLIN PA GENTHINER STRASSE 13, D-10785 BERLIN, GERMANY SN 0033-8230 J9 RADIOCHIM ACTA JI Radiochim. Acta PY 2013 VL 101 IS 11 BP 701 EP 710 DI 10.1524/ract.2013.2091 PG 10 WC Chemistry, Inorganic & Nuclear; Nuclear Science & Technology SC Chemistry; Nuclear Science & Technology GA 275GF UT WOS:000328663600003 ER PT J AU Camarillo, MK Stringfellow, WT Hanlon, JS Basha, E AF Camarillo, Mary Kay Stringfellow, William T. Hanlon, Jeremy S. Basha, Elizabeth TI Performance of sanitary sewer collection system odour control devices operating in diverse conditions SO WATER SCIENCE AND TECHNOLOGY LA English DT Article DE collection system; hydrogen sulphide; manhole; odour control; sanitary sewer ID VENTILATION MODEL; SULFIDE; SCALE AB Controlling odours from sanitary sewer systems is challenging as a result of the expansive nature of these systems. Addition of oxidizing chemicals is often practiced as a mitigation strategy. One alternative is to remove odorous compounds in the gases vented from manholes using adsorptive media. In this study, odour control devices located at manholes were observed to determine the ability of these systems to reduce hydrogen sulphide from vented gases. The odour control devices incorporated pressure regulation to control gas flow out of manhole covers and adsorptive media to remove hydrogen sulphide in the vented gases prior to release. Pressure regulation was accomplished using a variable volume bladder and two pressure relief valves that permitted gas flow when pressures exceeded 1.3 to 2.5 cm water column. The reduction in gas flow vented from manholes was intended to extend the service life of the adsorptive media, as compared with odour control devices that do not incorporate pressure modulation. Devices were deployed at four locations and three adsorptive media were tested. Although measured collection system hydrogen sulphide concentrations varied from zero to over 1,000 ppm, the removal rates observed using odour control devices were typically above 90%. The lower removal rates observed at one of the sites (50.5 +/- 36.1%) appeared related to high gas flow rates being emitted at this location. Activated carbon was used in most of the tests, although use of iron media resulted in the highest removal observed: 97.8 +/- 3.6%. The expected service life of the adsorptive media contained within the odour control devices is a function of site-specific hydrogen sulphide concentrations and gas flow rates. The units used in this study were in service for more than 8 to 12 months prior to requiring media replacement. C1 [Camarillo, Mary Kay; Stringfellow, William T.; Hanlon, Jeremy S.; Basha, Elizabeth] Univ Pacific, Sch Engn & Comp Sci, Stockton, CA 95211 USA. [Stringfellow, William T.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Stringfellow, WT (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. EM wstringfellow@lbl.gov RI Stringfellow, William/O-4389-2015 OI Stringfellow, William/0000-0003-3189-5604 FU University of the Pacific School of Engineering and Computer Science FX Funding was provided by the University of the Pacific School of Engineering and Computer Science. NR 18 TC 1 Z9 1 U1 1 U2 13 PU IWA PUBLISHING PI LONDON PA ALLIANCE HOUSE, 12 CAXTON ST, LONDON SW1H0QS, ENGLAND SN 0273-1223 EI 1996-9732 J9 WATER SCI TECHNOL JI Water Sci. Technol. PY 2013 VL 68 IS 12 BP 2527 EP 2533 DI 10.2166/wst.2013.492 PG 7 WC Engineering, Environmental; Environmental Sciences; Water Resources SC Engineering; Environmental Sciences & Ecology; Water Resources GA 276HR UT WOS:000328741000002 PM 24355837 ER PT J AU Willert, J Kelley, CT Knoll, DA Park, H AF Willert, Jeffrey Kelley, C. T. Knoll, D. A. Park, H. BE Khaddaj, S TI Scalable Hybrid Deterministic/Monte Carlo Neutronics Simulations in Two Space Dimensions SO 2013 12TH INTERNATIONAL SYMPOSIUM ON DISTRIBUTED COMPUTING AND APPLICATIONS TO BUSINESS, ENGINEERING & SCIENCE (DCABES) LA English DT Proceedings Paper CT 12th International Symposium on Distributed Computing and Applications to Business, Engineering and Science (DCABES) CY SEP 02-04, 2012 CL Kingston Univ, London, ENGLAND SP Univ Greenwich, Kingston Univ, Component & Distributed Syst Res Grp, BCS Chartered Inst IT, Distributed & Scalable Comp Specialist Grp, Wuhan Univ Technol, Univ Wyoming, Enterprise Europe Network, London Math Soc HO Kingston Univ DE Neutron Transport; Jacobian-Free Newton-Krylov; NDA; Monte Carlo ID K-EIGENVALUE PROBLEMS; NEWTON-KRYLOV METHOD; ACCELERATION; TRANSPORT AB In this paper we discuss a parallel hybrid deterministic/Monte Carlo (MC) method for the solution of the neutron transport equation in two space dimensions. The algorithm uses an NDA formulation of the transport equation, with a MC solver for the high-order equation. The scalability arises from the concentration of work in the MC phase of the algorithm, while the overall run-time is a consequence of the deterministic phase. C1 [Willert, Jeffrey; Kelley, C. T.] North Carolina State Univ, Dept Math, Box 8205, Raleigh, NC 27695 USA. [Knoll, D. A.; Park, H.] Los Alamos Nat Lab, Theor Div, Los Alamos, NM USA. RP Willert, J (reprint author), North Carolina State Univ, Dept Math, Box 8205, Raleigh, NC 27695 USA. EM jawiller@ncsu.edu; tim_kelley@ncsu.edu; nol@lanl.gov; hkpark@lanl.gov FU Consortium for Advanced Simulation of Light Water Reactors; Modeling and Simulation of Nuclear Reactors under U.S. Department of Energy [DE-AC05-00OR22725]; Los Alamos National Laboratory [172092-1] FX This work was been partially supported by the Consortium for Advanced Simulation of Light Water Reactors (www.casl.gov), an Energy Innovation Hub (http://www.energy.gov/hubs) for Modeling and Simulation of Nuclear Reactors under U.S. Department of Energy Contract No. DE-AC05-00OR22725 and Los Alamos National Laboratory contract No. 172092-1. NR 20 TC 1 Z9 1 U1 0 U2 1 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-0-7695-5060-2 PY 2013 BP 7 EP 10 DI 10.1109/DCABES.2013.8 PG 4 WC Computer Science, Interdisciplinary Applications; Computer Science, Theory & Methods SC Computer Science GA BJG80 UT WOS:000328118300002 ER PT S AU Nayak, N Chang, H Borowsky, A Spellman, P Parvin, B AF Nayak, Nandita Chang, Hang Borowsky, Alexander Spellman, Paul Parvin, Bahram GP IEEE TI CLASSIFICATION OF TUMOR HISTOPATHOLOGY VIA SPARSE FEATURE LEARNING SO 2013 IEEE 10TH INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING (ISBI) SE IEEE International Symposium on Biomedical Imaging LA English DT Proceedings Paper CT IEEE 10th International Symposium on Biomedical Imaging - From Nano to Macro (ISBI) CY APR 07-11, 2013 CL San Francisco, CA SP IEEE, IEEE Signal Processing Soc, Engn Med Biol Soc DE Tumor characterization; whole slide imaging; feature learning; sparse coding ID CANCER AB Our goal is to decompose whole slide images (WSI) of histology sections into distinct patches (e. g., viable tumor, necrosis) so that statistics of distinct histopathology can be linked with the outcome. Such an analysis requires a large cohort of histology sections that may originate from different laboratories, which may not use the same protocol in sample preparation. We have evaluated a method based on a variation of the restricted Boltzmann machine (RBM) that learns intrinsic features of the image signature in an unsupervised fashion. Computed code, from the learned representation, is then utilized to classify patches from a curated library of images. The system has been evaluated against a dataset of small image blocks of 1k-by-1k that have been extracted from glioblastoma multiforme (GBM) and clear cell kidney carcinoma (KIRC) from the cancer genome atlas (TCGA) archive. The learned model is then projected on each whole slide image (e. g., of size 20k-by-20k pixels or larger) for characterizing and visualizing tumor architecture. In the case of GBM, each WSI is decomposed into necrotic, transition into necrosis, and viable. In the case of the KIRC, each WSI is decomposed into tumor types, stroma, normal, and others. Evaluation of 1400 and 2500 samples of GBM and KIRC indicates a performance of 84% and 81%, respectively. C1 [Nayak, Nandita; Chang, Hang; Parvin, Bahram] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Life Sci, Berkeley, CA 94720 USA. [Borowsky, Alexander] Univ Calif Davis, Ctr Comparat Med, Davis, CA USA. [Spellman, Paul] Oregon Hlth & Sci Univ, Ctr Spatial Syst Biomed, Portland, OR USA. RP Nayak, N (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Life Sci, Berkeley, CA 94720 USA. FU NIH [U24 CA1437991]; Lawrence Berkeley National Laboratory [DE-AC02-05CH11231] FX This work was supported in part by NIH grant U24 CA1437991 carried out at Lawrence Berkeley National Laboratory under Contract No. DE-AC02-05CH11231. NR 24 TC 6 Z9 6 U1 0 U2 2 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1945-7928 BN 978-1-4673-6455-3 J9 I S BIOMED IMAGING PY 2013 BP 410 EP 413 PG 4 WC Engineering, Biomedical; Radiology, Nuclear Medicine & Medical Imaging SC Engineering; Radiology, Nuclear Medicine & Medical Imaging GA BHX19 UT WOS:000326900100103 ER PT S AU Nayak, N Chang, H Borowsky, A Spellman, P Parvin, B AF Nayak, Nandita Chang, Hang Borowsky, Alexander Spellman, Paul Parvin, Bahram GP IEEE TI CLASSIFICATION OF TUMOR HISTOPATHOLOGY VIA SPARSE FEATURE LEARNING SO 2013 IEEE 10TH INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING (ISBI) SE IEEE International Symposium on Biomedical Imaging LA English DT Proceedings Paper CT IEEE 10th International Symposium on Biomedical Imaging - From Nano to Macro (ISBI) CY APR 07-11, 2013 CL San Francisco, CA SP IEEE, IEEE Signal Processing Soc, Engn Med Biol Soc DE Tumor characterization; whole slide imaging; feature learning; sparse coding ID CANCER AB Our goal is to decompose whole slide images (WSI) of histology sections into distinct patches (e. g., viable tumor, necrosis) so that statistics of distinct histopathology can be linked with the outcome. Such an analysis requires a large cohort of histology sections that may originate from different laboratories, which may not use the same protocol in sample preparation. We have evaluated a method based on a variation of the restricted Boltzmann machine (RBM) that learns intrinsic features of the image signature in an unsupervised fashion. Computed code, from the learned representation, is then utilized to classify patches from a curated library of images. The system has been evaluated against a dataset of small image blocks of 1k-by-1k that have been extracted from glioblastoma multiforme (GBM) and clear cell kidney carcinoma (KIRC) from the cancer genome atlas (TCGA) archive. The learned model is then projected on each whole slide image (e. g., of size 20k-by-20k pixels or larger) for characterizing and visualizing tumor architecture. In the case of GBM, each WSI is decomposed into necrotic, transition into necrosis, and viable. In the case of the KIRC, each WSI is decomposed into tumor types, stroma, normal, and others. Evaluation of 1400 and 2500 samples of GBM and KIRC indicates a performance of 84% and 81%, respectively. C1 [Nayak, Nandita; Chang, Hang; Parvin, Bahram] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Life Sci, Berkeley, CA 94720 USA. [Borowsky, Alexander] Univ Calif Berkeley, Ctr Comparat Med, Berkeley, CA 94720 USA. [Spellman, Paul] Oregon Hlth & Sci Univ, Ctr Spatial Syst Biomed, Portland, OR USA. RP Nayak, N (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Life Sci, Berkeley, CA 94720 USA. FU NIH [U24 CA1437991]; Lawrence Berkeley National Laboratory [DE-AC02-05CH11231] FX This work was supported in part by NIH grant U24 CA1437991 carried out at Lawrence Berkeley National Laboratory under Contract No. DE-AC02-05CH11231. NR 24 TC 3 Z9 3 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA SN 1945-7928 BN 978-1-4673-6455-3 J9 I S BIOMED IMAGING PY 2013 BP 1348 EP 1351 PG 4 WC Engineering, Biomedical; Radiology, Nuclear Medicine & Medical Imaging SC Engineering; Radiology, Nuclear Medicine & Medical Imaging GA BHX19 UT WOS:000326900100337 ER PT B AU Rangaswamy, P Lewis, MW AF Rangaswamy, P. Lewis, M. W. BE GilNegrete, N Alonso, A TI Testing and validation of finite element modeling for silicone based elastomeric foam materials SO CONSTITUTIVE MODELS FOR RUBBER VIII LA English DT Proceedings Paper CT 8th European Conference on Constitutive Models for Rubbers (ECCMR) CY JUN 25-28, 2013 CL Univ Navarra, CEIT Tecnun, San Sebastian, SPAIN SP Endurica, Leartiker, Eusko Jaurlaritza Gobierno Vasco, Dept Educ Politica Linguistica & Cultura, Univ Navarra, Tecnun HO Univ Navarra, CEIT Tecnun AB In this study an Ogden hyperfoam and a user-developed six parameter hyperelastic material model are compared for uniaxial compression loading and uniaxial compression loading followed by shear. It was observed the change in normal stress (loading direction) showed dramatic differences with increasing shear angle as the depth of uniaxial compression was increased. At smaller compression the normal stress decreases in magnitude, with a reversal of this trend as the compressive depth is progressively increased. An analytical solution for this loading path (compression followed by shear) was developed and verified with finite element simulations. A compression-torsion experiment has been developed to obtain shear response upon compressive loading. These results are to be validated from the finite element models using uniaxial stress data. The presentation of these results will also include the effect of friction between the loading platens and the sample surfaces. C1 [Rangaswamy, P.; Lewis, M. W.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Rangaswamy, P (reprint author), Los Alamos Natl Lab, Los Alamos, NM 87545 USA. NR 6 TC 0 Z9 0 U1 0 U2 2 PU CRC PRESS-TAYLOR & FRANCIS GROUP PI BOCA RATON PA 6000 BROKEN SOUND PARKWAY NW, STE 300, BOCA RATON, FL 33487-2742 USA BN 978-1-315-88484-4; 978-1-138-00072-8 PY 2013 BP 233 EP 238 PG 6 WC Physics, Applied; Polymer Science SC Physics; Polymer Science GA BJG78 UT WOS:000328115500035 ER PT B AU Lewis, MW Rangaswamy, P AF Lewis, M. W. Rangaswamy, P. BE GilNegrete, N Alonso, A TI Toward a hyperelastic model for foamed rubber with matrix compressibility and pore gas effects SO CONSTITUTIVE MODELS FOR RUBBER VIII LA English DT Proceedings Paper CT 8th European Conference on Constitutive Models for Rubbers (ECCMR) CY JUN 25-28, 2013 CL Univ Navarra, CEIT Tecnun, San Sebastian, SPAIN SP Endurica, Leartiker, Eusko Jaurlaritza Gobierno Vasco, Dept Educ Politica Linguistica & Cultura, Univ Navarra, Tecnun HO Univ Navarra, CEIT Tecnun AB A hyperelastic strain energy function for foamed rubber introduced by Lewis and Rangaswamy (2011) is in the process of being improved and extended. The model is now unconditionally polyconvex. Recent extensions will be presented, including the effect of matrix compressibility, which will remove a singularity present in the original model. Additionally, the effects of pore gas compressibility are rigorously included for bounding conditions of isothermal and adiabatic compression. C1 [Lewis, M. W.; Rangaswamy, P.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Lewis, MW (reprint author), Los Alamos Natl Lab, Los Alamos, NM 87545 USA. NR 2 TC 0 Z9 0 U1 0 U2 0 PU CRC PRESS-TAYLOR & FRANCIS GROUP PI BOCA RATON PA 6000 BROKEN SOUND PARKWAY NW, STE 300, BOCA RATON, FL 33487-2742 USA BN 978-1-315-88484-4; 978-1-138-00072-8 PY 2013 BP 239 EP 244 PG 6 WC Physics, Applied; Polymer Science SC Physics; Polymer Science GA BJG78 UT WOS:000328115500036 ER PT J AU Scott, BR Gott, KM Potter, CA Wilder, J AF Scott, B. R. Gott, K. M. Potter, C. A. Wilder, J. TI A COMPARISON OF IN VIVO CELLULAR RESPONSES TO CS-137 GAMMA RAYS AND 320-KV X RAYS SO DOSE-RESPONSE LA English DT Article DE X rays; gamma rays; RBE; cytotoxicity; bone marrow; splenocytes ID SURVIVAL CURVES; RADIATION AB Research reported here relates to comparing the relative effectiveness of 320-kV X rays compared to Cs-137 gamma rays for two in vivo endpoints in C. B-17 mice after whole-body exposure: (1) cytotoxicity to bone marrow cells and splenocytes evaluated at 24-hours post exposure and (2) bone marrow and spleen reconstitution deficits (repopulation shortfalls) evaluated at 6 weeks post exposure. We show that cytotoxicity dose-response relationships for bone marrow cells and splenocytes are complex, involving negative curvature (decreasing slope as dose increases), presumably implicating a mixed cell population comprised of large numbers of hypersensitive, modestly radiosensitive, and resistant cells. The radiosensitive cells appear to respond with 50% being killed by a dose < 0.5 Gy. The X-ray relative biological effectiveness (RBE), relative to gamma rays, for destroying bone marrow cells in vivo is > 1, while for destroying splenocytes it is < 1. In contrast, dose-response relationships for reconstitution deficits in the bone marrow and spleen of C. B-17 mice at 6 weeks after radiation exposure were of the threshold type with gamma rays being more effective in causing reconstitution deficit. C1 [Scott, B. R.; Gott, K. M.; Wilder, J.] Lovelace Resp Res Inst, Albuquerque, NM 87108 USA. [Potter, C. A.] Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Scott, BR (reprint author), Lovelace Resp Res Inst, 2425 Ridgecrest Dr SE, Albuquerque, NM 87108 USA. EM bscott@LRRI.org FU Office of Science (BER), U.S. Department of Energy [DE-FG02-09ER64783]; [SL11-RadBio-PD13] FX This work was performed under project number SL11-RadBio-PD13 and with partial support from the Office of Science (BER), U.S. Department of Energy, Grant No. DE-FG02-09ER64783. The authors would like to express their appreciation to the U. S. Department of Energy, NA-22, Radiation Source Replacement Program and Frances Keel (DOE/NA-221). We are also grateful to Susan Longley of Sandia National Laboratories who had a major role in the acquisition and initiation of this project and to the reviewers of the paper. NR 14 TC 2 Z9 2 U1 0 U2 0 PU INT DOSE-RESPONSE SOC PI AMHERST PA UNIV MASSACHUSETTS SPH, MORRILL SCI CTR 1, N344, 639 N PLEASANT ST, AMHERST, MA 01003-9298 USA SN 1559-3258 J9 DOSE-RESPONSE JI Dose-Response PY 2013 VL 11 IS 4 BP 444 EP 459 DI 10.2203/dose-response.12-050.Scott PG 16 WC Pharmacology & Pharmacy; Radiology, Nuclear Medicine & Medical Imaging; Toxicology SC Pharmacology & Pharmacy; Radiology, Nuclear Medicine & Medical Imaging; Toxicology GA 270RR UT WOS:000328336800002 PM 24298223 ER PT J AU Dernburg, AF AF Dernburg, Abby F. TI Pushing the (nuclear) envelope into meiosis SO GENOME BIOLOGY LA English DT Editorial Material ID C. ELEGANS; ATTACHMENT; PROTEINS; MICE AB A recent study shows that a short isoform of a mammalian nuclear lamin is important for homologous chromosome interactions during meiotic prophase in mice. C1 [Dernburg, Abby F.] Univ Calif Berkeley, Dept Mol & Cell Biol, Berkeley, CA 94720 USA. [Dernburg, Abby F.] Howard Hughes Med Inst, Chevy Chase, MD 20815 USA. [Dernburg, Abby F.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Life Sci, Dept Genome Dynam, Berkeley, CA 94720 USA. [Dernburg, Abby F.] Calif Inst Quantitat Biosci, Berkeley, CA 94720 USA. RP Dernburg, AF (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Life Sci, Dept Genome Dynam, Berkeley, CA 94720 USA. EM afdernburg@lbl.gov NR 9 TC 1 Z9 1 U1 1 U2 4 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1465-6906 EI 1474-760X J9 GENOME BIOL JI Genome Biol. PY 2013 VL 14 IS 3 AR 110 DI 10.1186/gb-2013-14-3-110 PG 3 WC Biotechnology & Applied Microbiology; Genetics & Heredity SC Biotechnology & Applied Microbiology; Genetics & Heredity GA 268TP UT WOS:000328193700013 PM 23651872 ER PT J AU Olama, MM Djouadi, SM Li, YY Fathy, A AF Olama, Mohammed M. Djouadi, Seddik M. Li, Yanyan Fathy, Aly TI Modeling, Real-Time Estimation, and Identification of UWB Indoor Wireless Channels SO INTERNATIONAL JOURNAL OF ANTENNAS AND PROPAGATION LA English DT Article ID ULTRAWIDEBAND PROPAGATION CHANNELS; STOCHASTIC DIFFERENTIAL-EQUATIONS; STATISTICAL-MODEL; SIMULATION; NUMBER; RADAR; NOISE AB Stochastic differential equations (SDEs) are used to model ultrawideband (UWB) indoor wireless channels. We show that the impulse responses for time-varying indoor wireless channels can be approximated in a mean-square sense as close as desired by impulse responses that can be realized by SDEs. The state variables represent the inphase and quadrature components of the UWB channel. The expected maximization and extended Kalman filter are employed to recursively identify and estimate the channel parameters and states, respectively, fromonline received signal strength measured data. Both resolvable and nonresolvable multipath received signals are considered and represented as small-scaled Nakagami fading. The proposed models together with the estimation algorithm are tested using UWB indoor measurement data demonstrating the method's viability and the results are presented. C1 [Olama, Mohammed M.] Oak Ridge Natl Lab, Computat Sci & Engn Div, Oak Ridge, TN 37831 USA. [Djouadi, Seddik M.; Li, Yanyan; Fathy, Aly] Univ Tennessee, Elect Engn & Comp Sci Dept, Knoxville, TN 37996 USA. RP Olama, MM (reprint author), Oak Ridge Natl Lab, Computat Sci & Engn Div, POB 2008,MS 6085, Oak Ridge, TN 37831 USA. EM olamahussemm@ornl.gov FU US Department of Energy [DE-AC05-00OR22725]; NSF [CMMI-1334094] FX This paper has been authored by employees of UT-Battelle, LLC, under Contract no. DE-AC05-00OR22725 with the US Department of Energy. Also, this work was supported in part by NSF Grant no. CMMI-1334094. NR 33 TC 0 Z9 0 U1 1 U2 5 PU HINDAWI PUBLISHING CORPORATION PI NEW YORK PA 410 PARK AVENUE, 15TH FLOOR, #287 PMB, NEW YORK, NY 10022 USA SN 1687-5869 EI 1687-5877 J9 INT J ANTENN PROPAG JI Int. J. Antennas Propag. PY 2013 AR 467670 DI 10.1155/2013/467670 PG 8 WC Engineering, Electrical & Electronic; Telecommunications SC Engineering; Telecommunications GA 271MB UT WOS:000328394900001 ER PT J AU Sopori, B Emery, K Rupnowski, P Shet, S AF Sopori, Bhushan Emery, Keith Rupnowski, Peter Shet, Sudhakar TI Photovoltaic Materials and Devices 2013 SO INTERNATIONAL JOURNAL OF PHOTOENERGY LA English DT Editorial Material C1 [Sopori, Bhushan; Emery, Keith] Natl Renewable Energy Lab, Golden, CO 80401 USA. [Shet, Sudhakar] Princeton Optron, Trenton, NJ 08619 USA. RP Sopori, B (reprint author), Natl Renewable Energy Lab, 1617 Cole Blvd, Golden, CO 80401 USA. EM bhushan.sopori@nrel.gov OI Rupnowski, Przemyslaw/0000-0003-0040-418X NR 0 TC 0 Z9 0 U1 0 U2 7 PU HINDAWI PUBLISHING CORPORATION PI NEW YORK PA 410 PARK AVENUE, 15TH FLOOR, #287 PMB, NEW YORK, NY 10022 USA SN 1110-662X EI 1687-529X J9 INT J PHOTOENERGY JI Int. J. Photoenergy PY 2013 AR 306463 DI 10.1155/2013/306463 PG 1 WC Chemistry, Physical; Energy & Fuels; Optics; Physics, Atomic, Molecular & Chemical SC Chemistry; Energy & Fuels; Optics; Physics GA 271RC UT WOS:000328408300001 ER PT J AU Meier-Kolthoff, JP Lu, M Huntemann, M Lucas, S Lapidus, A Copeland, A Pitluck, S Goodwin, LA Han, C Tapia, R Potter, G Land, M Ivanova, N Rohde, M Goker, M Detter, JC Woyke, T Kyrpides, NC Klenk, HP AF Meier-Kolthoff, Jan P. Lu, Megan Huntemann, Marcel Lucas, Susan Lapidus, Alla Copeland, Alex Pitluck, Sam Goodwin, Lynne A. Han, Cliff Tapia, Roxanne Poetter, Gabriele Land, Miriam Ivanova, Natalia Rohde, Manfred Goeker, Markus Detter, John C. Woyke, Tanja Kyrpides, Nikos C. Klenk, Hans-Peter TI Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE draft genome; aerobic; chemoheterotrophic; Gram-positive; vegetative and aerial mycelia; spore-forming; non-motile; soil bacterium; Pseudonocardiaceae; CSP 2010 ID STANDARD OPERATING PROCEDURE; SP-NOV.; HALOPHILIC ACTINOMYCETE; CLASSIFICATION; PROPOSAL; SYSTEM; ACTINOBACTERIA; NOMENCLATURE; PHYLOGENY; ALGORITHM AB Saccharomonospora cyanea Runmao et al. 1988 is a member of the genus Saccharomonospora in the family Pseudonocardiaceae that is moderately well characterized at the genome level thus far. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as soil, leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they probably play a role in the primary degradation of plant material by attacking hemicellulose. Species of the genus Saccharomonospora are usually Gram-positive, non-acid fast, and are classified among the actinomycetes. S. cyanea is characterized by a dark blue (= cyan blue) aerial mycelium. After S. viridis, S. azurea, and S. marina, S. cyanea is only the fourth member in the genus for which a completely sequenced (non-contiguous finished draft status) type strain genome will be published. Here we describe the features of this organism, together with the draft genome sequence, and annotation. The 5,408,301 bp long chromosome with its 5,139 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI). C1 [Meier-Kolthoff, Jan P.; Goeker, Markus; Klenk, Hans-Peter] Leibniz Inst, DSMZ German Collect Microorganisms & Cell Cultur, Braunschweig, Germany. [Lu, Megan; Goodwin, Lynne A.; Han, Cliff; Tapia, Roxanne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Huntemann, Marcel; Lucas, Susan; Copeland, Alex; Pitluck, Sam; Goodwin, Lynne A.; Han, Cliff; Tapia, Roxanne; Land, Miriam; Ivanova, Natalia; Detter, John C.; Woyke, Tanja; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Lapidus, Alla] St Petersburg State Univ, Theodosius Dobzhansky Ctr Genome Bionformat, St Petersburg 199034, Russia. [Lapidus, Alla] St Petersburg Acad Univ, Algorithm Biol Lab, St Petersburg, Russia. [Land, Miriam] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. RP Klenk, HP (reprint author), Leibniz Inst, DSMZ German Collect Microorganisms & Cell Cultur, Braunschweig, Germany. RI Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Fac Sci, KAU, Biol Sci Dept/L-4228-2013; Lapidus, Alla/I-4348-2013 OI Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Meier-Kolthoff, Jan Philipp/0000-0001-9105-9814; Lapidus, Alla/0000-0003-0427-8731 FU Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231] FX We would like to gratefully acknowledge the help of Gabriele Potter for growing S. cyanea cultures, and Evelyne-Marie Brambilla for DNA extraction and quality control (both at DSMZ). The work conducted by the U.S. Department of Energy Joint Genome Institute was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. NR 54 TC 17 Z9 17 U1 0 U2 1 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 1 BP 28 EP 41 DI 10.4056/sigs.4207886 PG 14 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 270MV UT WOS:000328323400003 PM 24501643 ER PT J AU Palaniappan, K Meier-Kolthoff, JP Teshima, H Nolan, M Lapidus, A Tice, H Del Rio, TG Cheng, JF Han, C Tapia, R Goodwin, LA Pitluck, S Liolios, K Mavromatis, K Pagani, I Ivanova, N Mikhailova, N Pati, A Chen, A Rohde, M Mayilraj, S Spring, S Detter, JC Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Woyke, T AF Palaniappan, Krishna Meier-Kolthoff, Jan P. Teshima, Hazuki Nolan, Matt Lapidus, Alla Tice, Hope Del Rio, Tijana Glavina Cheng, Jan-Fang Han, Cliff Tapia, Roxanne Goodwin, Lynne A. Pitluck, Sam Liolios, Konstantinos Mavromatis, Konstantinos Pagani, Ioanna Ivanova, Natalia Mikhailova, Natalia Pati, Amrita Chen, Amy Rohde, Manfred Mayilraj, Shanmugam Spring, Stefan Detter, John C. Goeker, Markus Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Woyke, Tanja TI Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701(T)) and emended description of the genus Thermanaerovibrio SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE obligate anaerobic; motile; curved rods; organotrophic; S-0-reduction; cyanobacterial mat; Synergistaceae; Synergistetes; GEBA ID STANDARD OPERATING PROCEDURE; DATABASE; ARCHAEA; ACIDAMINOVORANS; ALGORITHM; PROPOSAL; SYSTEM; GRAPHS; NOV.; TOOL AB Thermanaerovibrio velox Zavarzina et al. 2000 is a member of the Synergistaceae, a family in the phylum Synergistetes that is already well-characterized at the genome level. Members of this phylum were described as Gram-negative staining anaerobic bacteria with a rod/vibrioid cell shape and possessing an atypical outer cell envelope. They inhabit a large variety of anaerobic environments including soil, oil wells, wastewater treatment plants and animal gastrointestinal tracts. They are also found to be linked to sites of human diseases such as cysts, abscesses, and areas of periodontal disease. The moderately thermophilic and organotrophic T. velox shares most of its morphologic and physiologic features with the closely related species, T. acidaminovorans. In addition to Su883(T), the type strain of T. acidaminovorans, stain Z-9701(T) is the second type strain in the genus Thermanaerovibrio to have its genome sequence published. Here we describe the features of this organism, together with the non-contiguous genome sequence and annotation. The 1,880,838 bp long chromosome (non-contiguous finished sequence) with its 1,751 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Palaniappan, Krishna; Teshima, Hazuki; Nolan, Matt; Tice, Hope; Del Rio, Tijana Glavina; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mikhailova, Natalia; Pati, Amrita; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Woyke, Tanja] DOE Joint Genome Inst, Walnut Creek, CA USA. [Meier-Kolthoff, Jan P.; Spring, Stefan; Goeker, Markus; Klenk, Hans-Peter] Leibniz Inst, DSMZ German Collect Microorganisms & Cell Cultur, Braunschweig, Germany. [Teshima, Hazuki; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Lapidus, Alla] St Petersburg State Univ, T Dobzhansky Ctr Genome Bionformat, St Petersburg 199034, Russia. [Lapidus, Alla] St Petersburg Acad Univ, Algorithm Biol Lab, St Petersburg, Russia. [Chen, Amy] Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Mayilraj, Shanmugam] CSIR Inst Microbial Technol, MTCC Microbial Type Culture Collect & Gene Bank, Chandigarh, India. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. [Hugenholtz, Philip] Univ Queensland, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Klenk, HP (reprint author), Leibniz Inst, DSMZ German Collect Microorganisms & Cell Cultur, Braunschweig, Germany. EM hpk@dsmz.de RI Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013; Lapidus, Alla/I-4348-2013; OI Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938; Lapidus, Alla/0000-0003-0427-8731; Eisen, Jonathan A./0000-0002-0159-2197; Meier-Kolthoff, Jan Philipp/0000-0001-9105-9814 FU US Department of Energy Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2]; Russian Ministry of Science [11.G34.31.0068]; Council of Scientific and Industrial Research (CSIR, India); DAAD, Germany FX We would like to gratefully acknowledge the help of Maren Schroder for growing T. velox cultures, and Evelyne-Marie Brambilla for DNA extraction and quality control (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725. The work was further supported by German Research Foundation (DFG) INST 599/1-2 (for DNA generation) and in part by the Russian Ministry of Science Mega-grant no. 11.G34.31.0068; SJ O'Brien Principal Investigator. The Council of Scientific and Industrial Research (CSIR, India) and DAAD, Germany, provided a Fellowship to Shanmugam Mayilraj. NR 40 TC 2 Z9 2 U1 1 U2 7 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 1 BP 57 EP 70 DI 10.4056/sigs.4237901 PG 14 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 270MV UT WOS:000328323400005 PM 24501645 ER PT J AU Rawat, SR Mannisto, MK Starovoytov, V Goodwin, L Nolan, M Hauser, LJ Land, M Davenport, KW Woyke, T Haggblom, MM AF Rawat, Suman R. Mannisto, Minna K. Starovoytov, Valentin Goodwin, Lynne Nolan, Matt Hauser, Loren J. Land, Miriam Davenport, Karen Walston Woyke, Tanja Haeggblom, Max M. TI Complete genome sequence of Granulicella mallensis type strain MP5ACTX8(T), an acidobacterium from tundra soil SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE cold adapted; acidophile; tundra soil; Acidobacteria ID RIBOSOMAL-RNA GENES; SP-NOV.; BACTERIAL COMMUNITIES; PHYLUM ACIDOBACTERIA; ARCTIC TUNDRA; DIVERSITY; ANNOTATION; PREDICTION; DATABASE; SYSTEM AB Granulicella mallensis MP5ACTX8(T) is a novel species of the genus Granulicella in subdivision 1 of Acidobacteria. G. mallensis is of ecological interest being a member of the dominant soil bacterial community active at low temperatures and nutrient limiting conditions in Arctic alpine tundra. G. mallensis is a cold-adapted acidophile and a versatile heterotroph that hydrolyzes a suite of sugars and complex polysaccharides. Genome analysis revealed metabolic versatility with genes involved in metabolism and transport of carbohydrates. These include gene modules encoding the carbohydrate-active enzyme (CAZyme) family involved in breakdown, utilization and biosynthesis of diverse structural and storage polysaccharides including plant based carbon polymers. The genome of Granulicella mallensis MP5ACTX8(T) consists of a single replicon of 6,237,577 base pairs (bp) with 4,907 protein-coding genes and 53 RNA genes. C1 [Rawat, Suman R.; Haeggblom, Max M.] Rutgers State Univ, Dept Biochem & Microbiol, New Brunswick, NJ 08903 USA. [Mannisto, Minna K.] Finnish Forest Res Inst, Rovaniemi, Finland. [Starovoytov, Valentin] Rutgers State Univ, Dept Cell Biol & Neurosci, New Brunswick, NJ 08903 USA. [Goodwin, Lynne; Davenport, Karen Walston] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Nolan, Matt; Woyke, Tanja] DOE Joint Genome Inst, Walnut Creek, CA USA. [Hauser, Loren J.; Land, Miriam] Oak Ridge Natl Lab, Oak Ridge, TN USA. RP Haggblom, MM (reprint author), Rutgers State Univ, Dept Biochem & Microbiol, New Brunswick, NJ 08903 USA. EM haggblom@sebs.rutgers.edu RI Haggblom, Max/E-7597-2010; Land, Miriam/A-6200-2011 OI Haggblom, Max/0000-0001-6307-7863; Land, Miriam/0000-0001-7102-0031 FU Office of Science of the US Department of Energy [DE-AC02-05CH11231]; Academy of Finland; New Jersey Agricultural Experiment Station FX The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy Under Contract No. DE-AC02-05CH11231. This work was funded in part by the Academy of Finland and the New Jersey Agricultural Experiment Station. NR 57 TC 3 Z9 3 U1 0 U2 12 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 1 BP 71 EP 82 DI 10.4056/sigs.4328031 PG 12 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 270MV UT WOS:000328323400006 PM 24501646 ER PT J AU Anderson, I Teshima, H Nolan, M Lapidus, A Tice, H Del Rio, TG Cheng, JF Han, C Tapia, R Goodwin, LA Pitluck, S Liolios, K Mavromatis, K Pagani, I Ivanova, N Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Rohde, M Lang, EK Detter, JC Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Anderson, Iain Teshima, Huzuki Nolan, Matt Lapidus, Alla Tice, Hope Del Rio, Tijana Glavina Cheng, Jan-Fang Han, Cliff Tapia, Roxanne Goodwin, Lynne A. Pitluck, Sam Liolios, Konstantinos Mavromatis, Konstantinos Pagani, Ioanna Ivanova, Natalia Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Rohde, Manfred Lang, Elke Detter, John C. Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Genome sequence of Frateuria aurantia type strain (Kondo 67(T)), a xanthomonade isolated from Lilium auratium Lindl. SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE strictly aerobic; motile; rod-shaped; acetogenic; mesophilic; 'Acetobacter aurantius'; Xanthomonadaceae; GEBA ID BACTERIA; ARCHAEA; ALGORITHM; DATABASE; SYSTEM; GRAPHS; GENUS; TOOL AB Frateuria aurantia (ex Kondo and Ameyama 1958) Swings et al. 1980 is a member of the bispecific genus Frateuria in the family Xanthomonadaceae, which is already heavily targeted for non-type strain genome sequencing. Strain Kondo 67(T) was initially (1958) identified as a member of 'Acetobacter aurantius', a name that was not considered for the approved list. Kondo 67(T) was therefore later designated as the type strain of the newly proposed acetogenic species Frateuria aurantia. The strain is of interest because of its triterpenoids (hopane family). F. aurantia Kondo 67(T) is the first member of the genus Frateura whose genome sequence has been deciphered, and here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,603,458-bp long chromosome with its 3,200 protein-coding and 88 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Anderson, Iain; Teshima, Huzuki; Nolan, Matt; Tice, Hope; Del Rio, Tijana Glavina; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mikhailova, Natalia; Pati, Amrita; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Teshima, Huzuki; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Lapidus, Alla] St Petersburg State Univ, Theodosius Dobzhansky Ctr Genome Bionformat, St Petersburg 199034, Russia. [Lapidus, Alla] St Petersburg Acad Univ, Algorithm Biol Lab, St Petersburg, Russia. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Lang, Elke; Goeker, Markus; Klenk, Hans-Peter] Leibniz Inst DSMZ German Collect Microorganisms &, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. [Hugenholtz, Philip] Univ Queensland, Australian Ctr Ecogenom, Sch Chem & Mol Biosci, Brisbane, Qld, Australia. RP Klenk, HP (reprint author), Leibniz Inst DSMZ German Collect Microorganisms &, Braunschweig, Germany. EM hpk@dsmz.de RI Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Lapidus, Alla/I-4348-2013; OI Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731; Eisen, Jonathan A./0000-0002-0159-2197 FU US Department of Energy Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2]; Russian Ministry of Science [11.G34.31.0068] FX We would like to gratefully acknowledge the help of Markus Kopitz for growing F. aurantia cultures and Susanne Schneider for DNA extractions and quality control (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2 and in part by the Russian Ministry of Science Mega-grant no. 11.G34.31.0068; SJ O'Brien Principal Investigator. NR 37 TC 0 Z9 0 U1 2 U2 4 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 1 BP 83 EP 92 DI 10.4056/sigs.4338002 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 270MV UT WOS:000328323400007 PM 24501647 ER PT J AU Nakatsu, CH Barabote, R Thompson, S Bruce, D Detter, C Brettin, T Han, C Beasley, F Chen, WM Konopka, A Xie, G AF Nakatsu, Cindy H. Barabote, Ravi Thompson, Sue Bruce, David Detter, Chris Brettin, Thomas Han, Cliff Beasley, Federico Chen, Weimin Konopka, Allan Xie, Gary TI Complete genome sequence of Arthrobacter sp strain FB24 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article ID COMMUNITY; CLASSIFICATION; PROPOSAL; SYSTEM; SOIL; ACTINOBACTERIA; IDENTIFICATION; MICROCOSMS; RESPONSES; BACTERIA AB Arthrobacter sp. strain FB24 is a species in the genus Arthrobacter Conn and Dimmick 1947, in the family Micrococcaceae and class Actinobacteriaceae. A number of Arthrobacter genome sequences have been completed because of their important role in soil, especially bioremediation. This isolate is of special interest because it is tolerant to multiple metals and it is extremely resistant to elevated concentrations of chromate. The genome consists of a 4,698,945 bp circular chromosome and three plasmids (96,488, 115,507, and 159,536 bp, a total of 5,070,478 bp), coding 4,536 proteins of which 1,257 are without known function. This genome was sequenced as part of the DOE Joint Genome Institute Program. C1 [Nakatsu, Cindy H.; Beasley, Federico; Chen, Weimin] Purdue Univ, Dept Agron, W Lafayette, IN 47907 USA. [Barabote, Ravi; Thompson, Sue; Bruce, David; Detter, Chris; Brettin, Thomas; Han, Cliff; Xie, Gary] Los Alamos Natl Labs, Los Alamos, NM USA. [Konopka, Allan] Pacific NW Natl Lab, Richland, WA 99352 USA. RP Nakatsu, CH (reprint author), Purdue Univ, Dept Agron, W Lafayette, IN 47907 USA. EM cnakatsu@purdue.edu RI Barabote, Ravi/C-1299-2017; OI Barabote, Ravi/0000-0002-0403-246X; xie, gary/0000-0002-9176-924X NR 34 TC 2 Z9 3 U1 5 U2 9 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 1 BP 106 EP 116 DI 10.4056/sigs.4438185 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 270MV UT WOS:000328323400009 PM 24501649 ER PT J AU Riedel, T Fiebig, A Petersen, J Gronow, S Kyrpides, NC Goker, M Klenk, HP AF Riedel, Thomas Fiebig, Anne Petersen, Joern Gronow, Sabine Kyrpides, Nikos C. Goeker, Markus Klenk, Hans-Peter TI Genome sequence of the Litoreibacter arenae type strain (DSM 19593(T)), a member of the Roseobacter clade isolated from sea sand SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE marine; rod-shaped; sea sand; sediment; motile; strictly aerobic; mesophile; chemoorganotrophic; halophilic; virus-like structures; carbon monoxide utilization; sulfur oxidation; Rhodobacteraceae; Alphaproteobacteria; Thalassobacter arenae ID SP NOV.; THALASSOBACTER-ARENAE; EMENDED DESCRIPTION; GEN. NOV.; BACTERIA; TOOL; ALPHAPROTEOBACTERIA; IDENTIFICATION; RECOGNITION; ALIGNMENTS AB Litoreibacter arenae Kim et al. 2012 is a member of the genomically well-characterized Rhodobacteraceae clade within the Roseobacter clade. Representatives of this clade are known to be metabolically versatile and involved in marine carbon-producing and biogeochemical processes. They form a physiologically heterogeneous group of Alphaproteobacteria and were mostly found in coastal or polar waters, especially in symbiosis with algae, in microbial mats, in sediments or together with invertebrates and vertebrates. Here we describe the features of L. arenae DSM 19593(T), including novel aspects of its phenotype, together with the draft genome sequence and annotation. The 3,690,113 bp long genome consists of 17 scaffolds with 3,601 protein-coding and 56 RNA genes. This genome was sequenced as part of the activities of the Transregional Collaborative Research Centre 51 funded by the German Research Foundation (DFG). C1 [Riedel, Thomas] Univ Paris 06, Observ Oceanol, UMR 7621, Banyuls Sur Mer, France. [Riedel, Thomas] CNRS, Observ Oceanol, UMR 7621, LOMIC, Banyuls Sur Mer, France. [Fiebig, Anne; Petersen, Joern; Gronow, Sabine; Goeker, Markus; Klenk, Hans-Peter] Leibniz Inst DSMZ German Collect Microorganisms &, Braunschweig, Germany. [Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. RP Goker, M (reprint author), Leibniz Inst DSMZ German Collect Microorganisms &, Braunschweig, Germany. EM mgo08@dsmz.de RI Kyrpides, Nikos/A-6305-2014 OI Kyrpides, Nikos/0000-0002-6131-0462 FU German Research Foundation (DFG) [Transregio-SFB 51] FX The authors gratefully acknowledge the assistance of Iljana Schroder for technical assistance and Evelyne-Marie Brambilla for DNA extraction and quality control (both at the DSMZ). This study was supported by the German Research Foundation (DFG) Transregio-SFB 51. NR 49 TC 4 Z9 4 U1 0 U2 6 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 1 BP 117 EP 127 DI 10.4056/sigs.4258318 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 270MV UT WOS:000328323400010 PM 24501650 ER PT J AU Buddruhs, N Chertkov, O Petersen, J Fiebig, A Chen, A Pati, A Ivanova, N Lapidus, A Goodwin, LA Chain, P Detter, JC Gronow, S Kyrpides, NC Woyke, T Goker, M Brinkhoff, T Klenk, HP AF Buddruhs, Nora Chertkov, Olga Petersen, Joern Fiebig, Anne Chen, Amy Pati, Amrita Ivanova, Natalia Lapidus, Alla Goodwin, Lynne A. Chain, Patrick Detter, John C. Gronow, Sabine Kyrpides, Nikos C. Woyke, Tanja Goeker, Markus Brinkhoff, Thorsten Klenk, Hans-Peter TI Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336T), a representative of the Roseobacter clade SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Methylotrophy; methyl halides; extrachromosomal elements; Alphaproteobacteria; Rhodobacteraceae; Roseobacter clade; aerobe ID STANDARD OPERATING PROCEDURE; SP NOV.; PHAEOBACTER-GALLAECIENSIS; EMENDED DESCRIPTIONS; GEN. NOV.; DIVERSITY; PHENOTYPE; ECOLOGY; BIOLOGY; SYSTEMS AB Leisingera methylohalidivorans Schaefer et al. 2002 emend. Vandecandelaere et al. 2008 is the type species of the genus Leisingera. The genus belongs to the Roseobacter clade (Rhodobacteraceae, Alphaproteobacteria), a widely distributed lineage in marine environments. Leisingera and particularly L. methylohalidivorans strain MB2(T) is of special interest due to its methylotrophy. Here we describe the complete genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. The 4,650,996 bp long genome with its 4,515 protein-coding and 81 RNA genes consists of three replicons, a single chromosome and two extrachromosomal elements with sizes of 221 kb and 285 kb. C1 [Buddruhs, Nora; Petersen, Joern; Fiebig, Anne; Gronow, Sabine; Klenk, Hans-Peter] Leibniz Inst DSMZ German Collect Microorganisms &, Braunschweig, Germany. [Chertkov, Olga; Goodwin, Lynne A.; Chain, Patrick; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Goeker, Markus] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Pati, Amrita; Ivanova, Natalia; Goodwin, Lynne A.; Detter, John C.; Kyrpides, Nikos C.; Woyke, Tanja] DOE Joint Genome Inst, Walnut Creek, CA USA. [Lapidus, Alla] St Petersburg State Univ, Theodosius Dobzhansky Ctr Genome Bioinformat, St Petersburg 199034, Russia. [Lapidus, Alla] St Petersburg Acad Univ, Algorithm Biol Lab, St Petersburg, Russia. [Brinkhoff, Thorsten] Inst Chem & Biol Marine Environm ICMB, Oldenburg, Germany. RP Goker, M (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. EM markus.goeker@dsmz.de RI Kyrpides, Nikos/A-6305-2014; Lapidus, Alla/I-4348-2013; OI Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731; Chain, Patrick/0000-0003-3949-3634 FU Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]; Russian Ministry of Science [11.G34.31.0068]; German Research Foundation (DFG) [Transregio-SFB 51]; European Commission [222886] FX The authors would like to gratefully acknowledge the assistance of Iljana Schroeder for growing L. methylohalidivorans cultures and Evelyne-Marie Brambilla for DNA extraction and quality control (both at the DSMZ). The work conducted by the U.S. Department of Energy Joint Genome Institute was supported by the Office of Science of the U.S. Department of Energy under contract No. DE-AC02-05CH11231; AL was supported by Russian Ministry of Science Mega-grant no. 11.G34.31.0068; SJ O'Brien Principal Investigator. The work conducted by the members of the Roseobacter consortium was supported by the German Research Foundation (DFG) Transregio-SFB 51 with PhD stipends for NB and AF. We also thank the European Commission which supported phenotyping via the Microme project 222886 within the Framework 7 program. NR 50 TC 8 Z9 8 U1 1 U2 6 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 1 BP 128 EP 141 DI 10.4056/sigs.4297965 PG 14 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 270MV UT WOS:000328323400011 PM 24501651 ER PT J AU Dogs, M Teshima, H Petersen, J Fiebig, A Chertkov, O Dalingault, H Chen, A Pati, A Goodwin, LA Chain, P Detter, JC Ivanova, N Lapidus, A Rohde, M Gronow, S Kyrpides, NC Woyke, T Simon, M Goker, M Klenk, HP Brinkhoff, T AF Dogs, Marco Teshima, Hazuki Petersen, Joern Fiebig, Anne Chertkov, Olga Dalingault, Hajnalka Chen, Amy Pati, Amrita Goodwin, Lynne A. Chain, Patrick Detter, John C. Ivanova, Natalia Lapidus, Alla Rohde, Manfred Gronow, Sabine Kyrpides, Nikos C. Woyke, Tanja Simon, Meinhard Goeker, Markus Klenk, Hans-Peter Brinkhoff, Thorsten TI Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Marine microbiology; facultative anaerobe; indigoidine; Rhodobacteraceae; Roseobacter clade ID STANDARD OPERATING PROCEDURE; NANHAIENSIS SP NOV.; SOUTH CHINA SEA; ROSEOBACTER CLADE; GEN. NOV.; ELECTROACTIVE BIOFILM; EMENDED DESCRIPTIONS; TIDAL FLAT; LEISINGERA; SYSTEM AB TF-218(T) is the type strain of the species Phaeobacter daeponensis Yoon et al. 2007, a facultatively anaerobic Phaeobacter species isolated from tidal flats. Here we describe the draft genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. We analyzed the genome for genes involved in secondary metabolite production and its anaerobic lifestyle, which have also been described for its closest relative Phaeobacter caeruleus. The 4,642,596 bp long genome of strain TF-218(T) contains 4,310 protein-coding genes and 78 RNA genes including four rRNA operons and consists of five replicons: one chromosome and four extrachromosomal elements with sizes of 276 kb, 174 kb, 117 kb and 90 kb. Genome analysis showed that TF-218(T) possesses all of the genes for indigoidine biosynthesis, and on specific media the strain showed a blue pigmentation. We also found genes for dissimilatory nitrate reduction, gene-transfer agents, NRPS/PKS genes and signaling systems homologous to the LuxR/I system. C1 [Dogs, Marco; Simon, Meinhard; Brinkhoff, Thorsten] Carl von Ossietzky Univ Oldenburg, Inst Chem & Biol Marine Environm, D-26111 Oldenburg, Germany. [Teshima, Hazuki; Chertkov, Olga; Dalingault, Hajnalka; Goodwin, Lynne A.; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Petersen, Joern; Fiebig, Anne; Gronow, Sabine; Goeker, Markus; Klenk, Hans-Peter] Leibniz Inst DSMZ German Collect Microorganisms &, Braunschweig, Germany. [Chen, Amy] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Pati, Amrita; Goodwin, Lynne A.; Chain, Patrick; Detter, John C.; Ivanova, Natalia; Lapidus, Alla; Kyrpides, Nikos C.; Woyke, Tanja] DOE Joint Genome Inst, Walnut Creek, CA USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. RP Goker, M (reprint author), Leibniz Inst DSMZ German Collect Microorganisms &, Braunschweig, Germany. EM mgo08@dsmz.du RI Kyrpides, Nikos/A-6305-2014; Lapidus, Alla/I-4348-2013 OI Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731 FU Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]; German Research Foundation (DFG) [Transregio-SFB 51]; European Commission [222886] FX The authors would like to gratefully acknowledge the assistance of Iljana Schroder for growing P. daeponensis cultures and Evelyne-Marie Brambilla for DNA extraction and quality control (both at DSMZ). The work conducted by the U.S. Department of Energy Joint Genome Institute was supported by the Office of Science of the U.S. Department of Energy under contract No. DE-AC02-05CH11231; the work conducted by members of the Roseobacter consortium was supported by the German Research Foundation (DFG) Transregio-SFB 51. We also thank the European Commission which supported phenotyping via the Microme project 222886 within the Framework 7 program. NR 66 TC 5 Z9 5 U1 0 U2 7 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 9 IS 1 BP 142 EP 159 DI 10.4056/sigs.4287962 PG 18 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 270MV UT WOS:000328323400012 PM 24501652 ER PT J AU Kruse, T Maillard, J Goodwin, L Woyke, T Teshima, H Bruce, D Detter, C Tapia, R Han, C Huntemann, M Wei, CL Han, J Chen, A Kyrpides, N Szeto, E Markowitz, V Ivanova, N Pagani, I Pati, A Pitluck, S Nolan, M Holliger, C Smidt, H AF Kruse, Thomas Maillard, Julien Goodwin, Lynne Woyke, Tanja Teshima, Hazuki Bruce, David Detter, Chris Tapia, Roxanne Han, Cliff Huntemann, Marcel Wei, Chia-Lin Han, James Chen, Amy Kyrpides, Nikos Szeto, Ernest Markowitz, Victor Ivanova, Natalia Pagani, Ioanna Pati, Amrita Pitluck, Sam Nolan, Matt Holliger, Christof Smidt, Hauke TI Complete genome sequence of Dehalobacter restrictus PER-K23(T) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Dehalobacter restrictus type strain; anaerobe; organohalide respiration; PCE; TCE; reductive dehalogenases ID TETRACHLOROETHENE REDUCTIVE DEHALOGENASE; HAFNIENSE STRAIN TCE1; DESULFITOBACTERIUM-HAFNIENSE; DEHALOCOCCOIDES-ETHENOGENES; RNA GENES; BACTERIA; RESPIRATION; GEOBACTER; PROTEIN; HALORESPIRATION AB Dehalobacter restrictus strain PER-K23 (DSM 9455) is the type strain of the species Dehalobacter restrictus. D. restrictus strain PER-K23 grows by organohalide respiration, coupling the oxidation of H-2 to the reductive dechlorination of tetra-or trichloroethene. Growth has not been observed with any other electron donor or acceptor, nor has fermentative growth been shown. Here we introduce the first full genome of a pure culture within the genus Dehalobacter. The 2,943,336 bp long genome contains 2,826 protein coding and 82 RNA genes, including 5 16S rRNA genes. Interestingly, the genome contains 25 predicted reductive dehalogenase genes, the majority of which appear to be full length. The reductive dehalogenase genes are mainly located in two clusters, suggesting a much larger potential for organohalide respiration than previously anticipated. C1 [Kruse, Thomas; Smidt, Hauke] Wageningen Univ, Microbiol Lab, NL-6703 HB Wageningen, Netherlands. [Maillard, Julien; Holliger, Christof] Ecole Polytech Fed Lausanne, Sch Architecture Civil & Environm Engn, Lab Environm Biotechnol, CH-1015 Lausanne, Switzerland. [Goodwin, Lynne; Woyke, Tanja; Teshima, Hazuki; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Huntemann, Marcel; Wei, Chia-Lin; Han, James; Chen, Amy; Kyrpides, Nikos; Szeto, Ernest; Markowitz, Victor; Ivanova, Natalia; Pagani, Ioanna; Pati, Amrita; Pitluck, Sam; Nolan, Matt] DOE Joint Genome Inst, Walnut Creek, CA USA. [Goodwin, Lynne; Teshima, Hazuki; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. RP Kruse, T (reprint author), Wageningen Univ, Microbiol Lab, Dreijenplein 10, NL-6703 HB Wageningen, Netherlands. EM thomas@theviking.dk RI Kyrpides, Nikos/A-6305-2014; OI Kyrpides, Nikos/0000-0002-6131-0462; Kruse, Thomas/0000-0002-7551-1505; Smidt, Hauke/0000-0002-6138-5026; Maillard, Julien/0000-0002-7498-7202 FU Netherlands Genomics Initiative; European Community [211684, 222625]; Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231] FX The work of Thomas Kruse and Hauke Smidt were supported by the Netherlands Genomics Initiative as well as the European Community's Seventh Framework Programme (FP7/2007-2013) through the Ecogenomics program and the BACSIN and METAEXPLORE projects (grant agreements No. 211684 and 222625), respectively. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract No. DE-AC02-05CH11231. NR 58 TC 10 Z9 10 U1 1 U2 7 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 8 IS 3 BP 375 EP 388 DI 10.4056/sigs.3787426 PG 14 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 270ML UT WOS:000328322400001 PM 24501624 ER PT J AU Riedel, T Teshima, H Petersen, J Fiebig, A Davenport, K Daligault, H Erkkila, T Gu, W Munk, C Xu, Y Chen, A Pati, A Ivanova, N Goodwin, LA Chain, P Detter, JC Rohde, M Gronow, S Kyrpides, NC Woyke, T Goker, M Brinkhoff, T Klenk, HP AF Riedel, Thomas Teshima, Hazuki Petersen, Joern Fiebig, Anne Davenport, Karen Daligault, Hajnalka Erkkila, Tracy Gu, Wei Munk, Christine Xu, Yan Chen, Amy Pati, Amrita Ivanova, Natalia Goodwin, Lynne A. Chain, Patrick Detter, John C. Rohde, Manfred Gronow, Sabine Kyrpides, Nikos C. Woyke, Tanja Goeker, Markus Brinkhoff, Thorsten Klenk, Hans-Peter TI Genome sequence of the Leisingera aquimarina type strain (DSM 24565(T)), a member of the marine Roseobacter clade rich in extrachromosomal elements SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE marine; biofilm; ovoid-shaped; halotolerant; heterotrophic; quorum sensing; plasmid; thiosulfate oxidation; carbon monoxide utilization; Rhodobacteraceae; Alphaproteobacteria ID STANDARD OPERATING PROCEDURE; SP NOV.; PHAEOBACTER-GALLAECIENSIS; EMENDED DESCRIPTIONS; GEN. NOV.; PLASMIDS; SYSTEM; ALGORITHM; DATABASE; GRAPHS AB Leisingera aquimarina Vandecandelaere et al. 2008 is a member of the genomically well characterized Roseobacter clade within the family Rhodobacteraceae. Representatives of the marine Roseobacter clade are metabolically versatile and involved in carbon fixation and biogeochemical processes. They form a physiologically heterogeneous group, found predominantly in coastal or polar waters, especially in symbiosis with algae, in microbial mats, in sediments or associated with invertebrates. Here we describe the features of L. aquimarina DSM 24565T together with the permanent-draft genome sequence and annotation. The 5,344,253 bp long genome consists of one chromosome and an unusually high number of seven extrachromosomal elements and contains 5,129 protein-coding and 89 RNA genes. It was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2010 and of the activities of the Transregional Collaborative Research Centre 51 funded by the German Research Foundation (DFG). C1 [Riedel, Thomas; Rohde, Manfred] HZI, Helmholtz Ctr Infect Res, Braunschweig, Germany. [Teshima, Hazuki; Davenport, Karen; Daligault, Hajnalka; Erkkila, Tracy; Gu, Wei; Munk, Christine; Xu, Yan; Goodwin, Lynne A.; Chain, Patrick; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Petersen, Joern; Fiebig, Anne; Gronow, Sabine; Goeker, Markus; Klenk, Hans-Peter] Leibniz Inst DSMZ German Collect Microorganisms &, Braunschweig, Germany. [Chen, Amy] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Pati, Amrita; Ivanova, Natalia; Goodwin, Lynne A.; Detter, John C.; Kyrpides, Nikos C.; Woyke, Tanja] DOE Joint Genome Inst, Walnut Creek, CA USA. [Brinkhoff, Thorsten] Inst Chem & Biol Marine Environm ICBM, Oldenburg, Germany. RP Goker, M (reprint author), Leibniz Inst DSMZ German Collect Microorganisms &, Braunschweig, Germany. EM markus.goeker@dsmz.de RI Kyrpides, Nikos/A-6305-2014; OI Kyrpides, Nikos/0000-0002-6131-0462; Chain, Patrick/0000-0003-3949-3634 FU Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]; German Research Foundation (DFG) [Transregio-SFB 51]; European Commission [222886] FX The authors would like to gratefully acknowledge the assistance of Iliana Schroder for growing L. aquamarina cultures and Evelyne-Marie Brambilla for DNA extraction and quality control (both at the DSMZ). The work conducted by the U.S. Department of Energy Joint Genome Institute was supported by the Office of Science of the U.S. Department of Energy under contract No. DE-AC02-05CH11231; the work conducted by the members of the Roseobacter consortium was supported by the German Research Foundation (DFG) Transregio-SFB 51. We also thank the European Commission which supported phenotyping via the Microme project 222886 within the Framework 7 program. NR 52 TC 14 Z9 14 U1 0 U2 3 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 8 IS 3 BP 389 EP 402 DI 10.4056/sigs.3858183 PG 14 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 270ML UT WOS:000328322400002 PM 24501625 ER PT J AU Beyersmann, PG Chertkov, O Petersen, J Fiebig, A Chen, A Pati, A Ivanova, N Lapidus, A Goodwin, LA Chain, P Detter, JC Rohde, M Gronow, S Kyrpides, NC Woyke, T Simon, M Goker, M Klenk, HP Brinkhoff, T AF Beyersmann, Paul G. Chertkov, Olga Petersen, Joern Fiebig, Anne Chen, Amy Pati, Amrita Ivanova, Natalia Lapidus, Alla Goodwin, Lynne A. Chain, Patrick Detter, John C. Rohde, Manfred Gronow, Sabine Kyrpides, Nikos C. Woyke, Tanja Simon, Meinhard Goeker, Markus Klenk, Hans-Peter Brinkhoff, Thorsten TI Genome sequence of Phaeobacter caeruleus type strain (DSM 24564(T)), a surface-associated member of the marine Roseobacter clade SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE biofilm; motile; indigoidine; quorum sensing; siderophores; Rhodobacteraceae; Alphaproteobacteria ID STANDARD OPERATING PROCEDURE; SOUTH CHINA SEA; SP-NOV.; ELECTROACTIVE BIOFILM; GEN. NOV.; EMENDED DESCRIPTIONS; TIDAL FLAT; GALLAECIENSIS; LEISINGERA; BACTERIA AB In 2009 Phaeobacter caeruleus was described as a novel species affiliated with the marine Roseobacter clade, which, in turn, belongs to the class Alphaproteobacteria. The genus Phaeobacter is well known for members that produce various secondary metabolites. Here we report of putative quorum sensing systems, based on the finding of six N-acyl-homoserine lactone synthetases, and show that the blue color of P. caeruleus is probably due to the production of the secondary metabolite indigoidine. Therefore, P. caeruleus might have inhibitory effects on other bacteria. In this study the genome of the type strain DSM 24564(T) was sequenced, annotated and characterized. The 5,344,419 bp long genome with its seven plasmids contains 5,227 protein-coding genes (3,904 with a predicted function) and 108 RNA genes. C1 [Beyersmann, Paul G.; Simon, Meinhard; Brinkhoff, Thorsten] Chem & Biol Marine Environm ICMB, Oldenburg, Germany. [Chertkov, Olga; Chain, Patrick; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Petersen, Joern; Fiebig, Anne; Gronow, Sabine; Goeker, Markus; Klenk, Hans-Peter] Leibniz Inst DSMZ German Collect Microorganisms &, Braunschweig, Germany. [Chen, Amy] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Pati, Amrita; Ivanova, Natalia; Lapidus, Alla; Goodwin, Lynne A.; Detter, John C.; Kyrpides, Nikos C.; Woyke, Tanja] DOE Joint Genome Inst, Walnut Creek, CA USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. RP Goker, M (reprint author), Leibniz Inst DSMZ German Collect Microorganisms &, Braunschweig, Germany. EM markus.goeker@dsmz.de RI Kyrpides, Nikos/A-6305-2014; Lapidus, Alla/I-4348-2013; OI Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731; Chain, Patrick/0000-0003-3949-3634 FU Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]; German Research Foundation (DFG) [Transregio-SFB 51]; European Commission [222886] FX The authors would like to gratefully acknowledge the assistance of Iliana Schroder for growing P. caeruleus cultures and Evelyne-Marie Brambilla for DNA extraction and quality control (both at the DSMZ). The work conducted by the U.S. Department of Energy Joint Genome Institute was supported by the Office of Science of the U.S. Department of Energy under contract No. DE-AC02-05CH11231; the work conducted by the members of the Roseobacter consortium was supported by the German Research Foundation (DFG) Transregio-SFB 51. We also thank the European Commission which supported phenotyping via the Microme project 222886 within the Framework 7 program. NR 61 TC 11 Z9 11 U1 2 U2 8 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 8 IS 3 BP 403 EP 419 DI 10.4056/sigs.3927623 PG 17 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 270ML UT WOS:000328322400003 PM 24501626 ER PT J AU Neupane, S Goodwin, LA Hogberg, N Kyrpides, NC Alstrom, S Bruce, D Quintana, B Munk, C Daligault, H Teshima, H Davenport, K Reitenga, K Green, L Chain, P Erkkila, T Gu, W Zhang, XJ Xu, Y Kunde, Y Chertkov, O Han, J Han, C Detter, JC Ivanova, N Pati, A Chen, A Szeto, E Mavromatis, K Huntemann, M Nolan, M Pitluck, S Deshpande, S Markowitz, V Pagani, I Klenk, HP Woyke, T Finlay, RD AF Neupane, Saraswoti Goodwin, Lynne A. Hogberg, Nils Kyrpides, Nikos C. Alstrom, Sadhna Bruce, David Quintana, Beverly Munk, Christine Daligault, Hajnalka Teshima, Hazuki Davenport, Karen Reitenga, Krista Green, Lance Chain, Patrick Erkkila, Tracy Gu, Wei Zhang, Xiaojing Xu, Yan Kunde, Yulia Chertkov, Olga Han, James Han, Cliff Detter, John C. Ivanova, Natalia Pati, Amrita Chen, Amy Szeto, Ernest Mavromatis, Kostas Huntemann, Marcel Nolan, Matt Pitluck, Sam Deshpande, Shweta Markowitz, Victor Pagani, Ioanna Klenk, Hans-Peter Woyke, Tanja Finlay, Roger D. TI Non-contiguous finished genome sequence of plant-growth promoting Serratia proteamaculans S4 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Facultative aerobe; gram-negative; motile; non-sporulating; mesophilic; chemoor-ganotrophic; agriculture ID STANDARD OPERATING PROCEDURE; GENUS SERRATIA; RNA GENES; DATABASE; ANNOTATION; PREDICTION; SYSTEM; TOOL AB Serratia proteamaculans S4 (previously Serratia sp. S4), isolated from the rhizosphere of wild Equisetum sp., has the ability to stimulate plant growth and to suppress the growth of several soil-borne fungal pathogens of economically important crops. Here we present the non-contiguous, finished genome sequence of S. proteamaculans S4, which consists of a 5,324,944 bp circular chromosome and a 129,797 bp circular plasmid. The chromosome contains 5,008 predicted genes while the plasmid comprises 134 predicted genes. In total, 4,993 genes are assigned as protein-coding genes. The genome consists of 22 rRNA genes, 82 tRNA genes and 58 pseudogenes. This genome is a part of the project "Genomics of four rapeseed plant growth-promoting bacteria with antagonistic effect on plant pathogens" awarded through the 2010 DOE-JGI's Community Sequencing Program. C1 [Neupane, Saraswoti; Hogberg, Nils; Alstrom, Sadhna; Finlay, Roger D.] Swedish Univ Agr Sci, Uppsala BioCtr, Dept Forest Mycol & Plant Pathol, Uppsala, Sweden. [Goodwin, Lynne A.; Bruce, David; Quintana, Beverly; Munk, Christine; Daligault, Hajnalka; Teshima, Hazuki; Davenport, Karen; Reitenga, Krista; Green, Lance; Chain, Patrick; Erkkila, Tracy; Gu, Wei; Zhang, Xiaojing; Xu, Yan; Kunde, Yulia; Chertkov, Olga; Han, Cliff; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Kyrpides, Nikos C.; Han, James; Ivanova, Natalia; Pati, Amrita; Chen, Amy; Szeto, Ernest; Mavromatis, Kostas; Huntemann, Marcel; Nolan, Matt; Pitluck, Sam; Deshpande, Shweta; Markowitz, Victor; Pagani, Ioanna; Woyke, Tanja] DOE Joint Genome Inst, Walnut Creek, CA USA. [Klenk, Hans-Peter] Leibniz Inst DSMZ German Collect Microorganisms &, Braunschweig, Germany. RP Neupane, S (reprint author), Swedish Univ Agr Sci, Uppsala BioCtr, Dept Forest Mycol & Plant Pathol, Uppsala, Sweden. EM Saraswoti.Neupane@slu.se RI Finlay, Roger/B-4731-2009; Kyrpides, Nikos/A-6305-2014; OI Finlay, Roger/0000-0002-3652-2930; Kyrpides, Nikos/0000-0002-6131-0462; Chain, Patrick/0000-0003-3949-3634 FU Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231] FX The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. NR 38 TC 4 Z9 4 U1 0 U2 6 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 8 IS 3 BP 441 EP 449 DI 10.4056/sigs.4027757 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 270ML UT WOS:000328322400006 PM 24501629 ER PT J AU Freese, HM Dalingault, H Petersen, J Pradella, S Davenport, K Teshima, H Chen, A Pati, A Ivanova, N Goodwin, LA Chain, P Detter, JC Rohde, M Gronow, S Kyrpides, NC Woyke, T Brinkhoff, T Goker, M Overmann, J Klenk, HP AF Freese, Heike M. Dalingault, Hajnalka Petersen, Joern Pradella, Silke Davenport, Karen Teshima, Hazuki Chen, Amy Pati, Amrita Ivanova, Natalia Goodwin, Lynne A. Chain, Patrick Detter, John C. Rohde, Manfred Gronow, Sabine Kyrpides, Nikos C. Woyke, Tanja Brinkhoff, Thorsten Goeker, Markus Overmann, Joerg Klenk, Hans-Peter TI Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566(T) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE aerobic; psychrophilic; motile; high-quality draft; prophage-like structures; extrachromosomal elements; assimilatory nitrate reduction; Alphaproteobacteria; Roseobacter clade ID STANDARD OPERATING PROCEDURE; SEARCH TOOL; SP-NOV.; DATABASE; ROSEOBACTER; BACTERIA; ALGORITHM; SYSTEM; GRAPHS AB Phaeobacter arcticus Zhang et al. 2008 belongs to the marine Roseobacter clade whose members are phylogenetically and physiologically diverse. In contrast to the type species of this genus, Phaeobacter gallaeciensis, which is well characterized, relatively little is known about the characteristics of P. arcticus. Here, we describe the features of this organism including the annotated high-quality draft genome sequence and highlight some particular traits. The 5,049,232 bp long genome with its 4,828 protein-coding and 81 RNA genes consists of one chromosome and five extrachromosomal elements. Prophage sequences identified via PHAST constitute nearly 5% of the bacterial chromosome and included a potential Mu-like phage as well as a gene-transfer agent (GTA). In addition, the genome of strain DSM 23566(T) encodes all of the genes necessary for assimilatory nitrate reduction. Phylogenetic analysis and intergenomic distances indicate that the classification of the species might need to be reconsidered. C1 [Freese, Heike M.; Petersen, Joern; Pradella, Silke; Gronow, Sabine; Goeker, Markus; Overmann, Joerg; Klenk, Hans-Peter] Leibniz Inst DSMZ German Collect Microorganisms &, Braunschweig, Germany. [Dalingault, Hajnalka; Davenport, Karen; Teshima, Hazuki; Goodwin, Lynne A.; Chain, Patrick; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Pati, Amrita; Ivanova, Natalia; Goodwin, Lynne A.; Detter, John C.; Kyrpides, Nikos C.; Woyke, Tanja] DOE Joint Genome Inst, Walnut Creek, CA USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Brinkhoff, Thorsten] Inst Chem & Biol Marine Environm, Oldenburg, Germany. RP Goker, M (reprint author), Leibniz Inst DSMZ German Collect Microorganisms &, Braunschweig, Germany. EM markus.goeker@dsmz.de RI Kyrpides, Nikos/A-6305-2014; OI Kyrpides, Nikos/0000-0002-6131-0462; Chain, Patrick/0000-0003-3949-3634 FU Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]; German Research Foundation (DFG) [Transregio-SFB 51] FX The authors would like to gratefully acknowledge the assistance of Iliana Schroder for growing P. arcticus cultures and Evelyne-Marie Brambilla for DNA extraction and quality control (both at the DSMZ). The work conducted by the U.S. Department of Energy Joint Genome Institute was supported by the Office of Science of the U.S. Department of Energy under contract No. DE-AC02-05CH11231; the work conducted by the members of the Roseobacter consortium was supported by the German Research Foundation (DFG) Transregio-SFB 51. NR 52 TC 7 Z9 7 U1 0 U2 4 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 8 IS 3 BP 450 EP 464 DI 10.4056/sigs.383362 PG 15 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 270ML UT WOS:000328322400007 PM 24501630 ER PT J AU Shogan, BD Smith, DP Packman, AI Kelley, ST Landon, EM Bhangar, S Vora, GJ Jones, RM Keegan, K Stephens, B Ramos, T Kirkup, BC Levin, H Rosenthal, M Foxman, B Chang, EB Siegel, J Cobey, S An, G Alverdy, JC Olsiewski, PJ Martin, MO Marrs, R Hernandez, M Christley, S Morowitz, M Weber, S Gilbert, J AF Shogan, Benjamin D. Smith, Daniel P. Packman, Aaron I. Kelley, Scott T. Landon, Emily M. Bhangar, Seema Vora, Gary J. Jones, Rachael M. Keegan, Kevin Stephens, Brent Ramos, Tiffanie Kirkup, Benjamin C., Jr. Levin, Hal Rosenthal, Mariana Foxman, Betsy Chang, Eugene B. Siegel, Jeffrey Cobey, Sarah An, Gary Alverdy, John C. Olsiewski, Paula J. Martin, Mark O. Marrs, Rachel Hernandez, Mark Christley, Scott Morowitz, Michael Weber, Stephen Gilbert, Jack TI The Hospital Microbiome Project: Meeting report for the 2nd Hospital Microbiome Project, Chicago, USA, January 15th, 2013 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article AB This report details the outcome of the 2nd Hospital Microbiome Project workshop held on January 15th at the University of Chicago, USA. This workshop was the final planning meeting prior to the start of the Hospital Microbiome Project, an investigation to measure and characterize the development of a microbial community within a newly built hospital at the University of Chicago. The main goals of this workshop were to bring together experts in various disciplines to discuss the potential hurdles facing the implementation of the project, and to allow brainstorming of potential synergistic project opportunities. C1 [Shogan, Benjamin D.; An, Gary; Alverdy, John C.; Christley, Scott] Univ Chicago Med, Dept Surg, Chicago, IL 60637 USA. [Smith, Daniel P.; Keegan, Kevin; Gilbert, Jack] Argonne Natl Lab, Argonne, IL 60439 USA. [Packman, Aaron I.] Northwestern Univ, Dept Civil & Environm Engn, Evanston, IL 60208 USA. [Kelley, Scott T.] San Diego State Univ, Dept Biol, San Diego, CA 92182 USA. [Landon, Emily M.; Marrs, Rachel; Weber, Stephen] Univ Chicago Med, Dept Med, Sect Infect Dis & Global Hlth, Chicago, IL 60637 USA. [Bhangar, Seema] Univ Calif Berkeley, Dept Civil & Environm Engn, Berkeley, CA 94720 USA. [Vora, Gary J.] Naval Res Lab, Ctr Bio Mol Sci & Engn, Washington, DC 20375 USA. [Jones, Rachael M.] Univ Illinois, Sch Publ Hlth, Div Environm & Occupat Hlth Sci, Chicago, IL 60612 USA. [Stephens, Brent; Ramos, Tiffanie] IIT, Dept Civil Architectural & Environm Engn, Chicago, IL 60616 USA. [Kirkup, Benjamin C., Jr.] Walter Reed Army Inst Res, Dept Wound Infect, Silver Spring, MD 20910 USA. [Kirkup, Benjamin C., Jr.] Uniformed Serv Univ Hlth Sci, Dept Med, Bethesda, MD 20814 USA. [Levin, Hal] Bldg Ecol Res Grp, Santa Cruz, CA 95060 USA. [Rosenthal, Mariana; Foxman, Betsy] Univ Michigan, Sch Publ Hlth, Dept Epidemiol, Ann Arbor, MI 48109 USA. [Chang, Eugene B.] Univ Chicago Med, Dept Med, Chicago, IL 60637 USA. [Siegel, Jeffrey] Univ Toronto, Dept Civil Engn, Toronto, ON M5S 1A1, Canada. [Cobey, Sarah; Gilbert, Jack] Univ Chicago, Dept Ecol & Evolut, Chicago, IL 60637 USA. [Olsiewski, Paula J.] Alfred P Sloan Fdn, New York, NY 10111 USA. [Martin, Mark O.] Univ Puget Sound, Dept Biol, Tacoma, WA 98416 USA. [Hernandez, Mark] Univ Colorado, Dept Civil Environm & Architectural Engn, Boulder, CO 80309 USA. [Morowitz, Michael] Univ Pittsburgh, Childrens Hosp Pittsburgh UPMC, Sch Med, Pittsburgh, PA 15224 USA. RP Shogan, BD (reprint author), Univ Chicago Med, Dept Surg, Chicago, IL 60637 USA. RI Packman, Aaron/B-7085-2009; Foxman, Betsy/E-1836-2015; Kirkup, Benjamin/C-3610-2009; OI Kirkup, Benjamin/0000-0002-8722-6218; Vora, Gary/0000-0002-0657-8597 FU APSF; U.S. Dept. of Energy [DE-AC02-06CH11357] FX We acknowledge the APSF for funding this workshop. This work was supported in part by the U.S. Dept. of Energy under contract DE-AC02-06CH11357. NR 5 TC 3 Z9 3 U1 1 U2 21 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2013 VL 8 IS 3 BP 571 EP 579 DI 10.4056/sigs.4187859 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 270ML UT WOS:000328322400017 PM 24501640 ER PT S AU Pennington, MR AF Pennington, M. R. BE Fleming, B TI Understanding the baryon and meson spectra SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE Baryons; mesons; spectrum; decays; coupled channels; QCD ID PARTIAL-WAVE ANALYSIS; NUCLEON RESONANCES; MODEL; QCD; HADRONS; EBAC AB A brief overview is given of what we know of the baryon and meson spectra, with a focus on what are the key internal degrees of freedom and how these relate to strong coupling QCD. The challenges, experimental, theoretical and phenomenological, for the future are outlined, with particular reference to a program at Jefferson Lab to extract hadronic states in which glue unambiguously contributes to their quantum numbers. C1 Jefferson Lab, Ctr Theory, Newport News, VA 23606 USA. RP Pennington, MR (reprint author), Jefferson Lab, Ctr Theory, 12000 Jefferson Ave, Newport News, VA 23606 USA. NR 50 TC 2 Z9 2 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 11 EP 20 DI 10.1063/1.4826708 PG 10 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000002 ER PT S AU Morse, WM AF Morse, William M. CA Storage Ring EDM Collaboration BE Fleming, B TI Storage Ring Electric Dipole Moment Experiments SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE EDM; Time Reversal Invariance; Parity Violation; Hadron; Storage Ring AB Dedicated electric dipole moment (edm) searches have been done only for neutral systems. We discuss in this talk dedicated storage ring proposals for measuring edms of charged particles. The statistical error dominates over the systematic error for the neutron and mercury atom edm searches. Large numbers of particles are available today from modern polarized sources at several accelerators. A proposed proton edm experiment at BNL would improve the present proton edm limit by a factor of 10(4). A "precursor" deuteron edm experiment has been proposed at COSY, Juelich, Germany. This would be the first measurement of the deuteron edm. C1 [Morse, William M.] Brookhaven Natl Lab, Dept Phys, Upton, NY 11973 USA. RP Morse, WM (reprint author), Brookhaven Natl Lab, Dept Phys, Upton, NY 11973 USA. NR 5 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 131 EP 133 DI 10.1063/1.4826736 PG 3 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000030 ER PT S AU Fomin, N AF Fomin, Nadia CA NPDGamma Collaboration BE Fleming, B TI First results from the NPDGamma experiment at the Spallation Neutron Source SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE parity violation; fundamental symmetries; electroweak interactions ID PARITY; CAPTURE; CL-35 AB The NPDGamma experiment aims to measure the parity-odd correlation between the neutron spin and the direction of the emitted photon in neutron-proton capture. A parity violating asymmetry (to be measured to 10(-8)) from this process can be directly related to the strength of the hadronic weak interaction between nucleons, specifically the Delta I=1 contribution. As part of the commissioning runs on the Fundamental Neutron Physics beamline at the Spallation Neutron Source (SNS) at ORNL, the gamma-ray asymmetries from the parity-violating capture of cold neutrons on Cl-35 and Al-27 were measured, to check for systematic effects, false asymmetries, and backgrounds. Early this year, the parahydrogen target for the production run of NPDGamma was commissioned. Preliminary results for the commissioning measurements with Cl-35 and Al-27 will be presented as well as first results of the hydrogen run. C1 [Fomin, Nadia; NPDGamma Collaboration] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Fomin, N (reprint author), Los Alamos Natl Lab, POB 1663, Los Alamos, NM 87545 USA. NR 8 TC 3 Z9 3 U1 0 U2 2 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 145 EP 148 DI 10.1063/1.4826740 PG 4 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000034 ER PT S AU Ling, JJ AF Ling, Jiajie CA Daya Bay Collaboration BE Fleming, B TI Observation of Electron-antineutrino Disappearance at Daya Bay SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE neutrino oscillation; neutrino mixing; reactor; Daya Bay ID LOADED LIQUID SCINTILLATOR; OSCILLATIONS; SPECTRA AB The Daya Bay Reactor Neutrino Experiment has measured a nonzero value of.13 with significance of 5.2 standard deviations. Antineutrinos from six 2.9 GW(th) reactors were detected in six antineutrino detectors deployed in two near and one far underground experimental halls. With a 43,000 ton-GWth-day live-time exposure in 55 days, 10,416 (80,376) electron-antineutrino candidates were detected at the far hall (near halls). The ratio of the observed to expected number of antineutrinos at the far hall is R = 0.940 +/- 0.011(stat) +/- 0.004(syst). A rate-only analysis finds sin2 2.13 = 0.092 +/- 0.016(stat) +/- 0.005(syst) in a three-neutrino framework. C1 [Ling, Jiajie] Brookhaven Natl Lab, Upton, NY 11973 USA. RP Ling, JJ (reprint author), Brookhaven Natl Lab, POB 5000,Bldg 510E, Upton, NY 11973 USA. RI Ling, Jiajie/I-9173-2014 OI Ling, Jiajie/0000-0003-2982-0670 NR 17 TC 0 Z9 0 U1 3 U2 13 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 206 EP 210 DI 10.1063/1.4826754 PG 5 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000048 ER PT S AU Osta, J AF Osta, Jyotsna CA MINERvA Collaboration BE Fleming, B TI The MINERvA Experiment - A Status Report SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE neutrinos; scattering AB MINER nu A (Main INjector ExpeRiment v-A) is a few-GeV neutrino-nucleus scattering experiment, stationed in the high intensity NuMI (Neutrinos at the Main Injector) beam line at Fermilab. It has been taking data since November 2009 and completed construction in March 2010. MINERvA aims to make precision measurements of low energy neutrino interactions, both in support of neutrino oscillation experiments and as a pure weak probe of the nuclear medium. For this, the experiment employs a fine-grained, high-resolution detector. The active target region is composed of plastic scintillator. There are additional nuclear targets of helium, carbon, iron, lead and water placed upstream of the fully active region. These targets will be used for measuring the A-dependence of nuclear effects in neutrino scattering. We present our preliminary results, from analyses probing the nuclear effects on charged current events in the iron, lead and plastic of the detector to results from analyses studying charged current quasi-elastic scattering on the active plastic target using both neutrinos and anti-neutrinos. C1 [Osta, Jyotsna; MINERvA Collaboration] Fermilab Natl Accelerator Lab, Batavia, IL 60510 USA. RP Osta, J (reprint author), Fermilab Natl Accelerator Lab, POB 500, Batavia, IL 60510 USA. NR 8 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 227 EP 231 DI 10.1063/1.4826760 PG 5 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000054 ER PT S AU VanDevender, BA Asner, DM Bahr, M Bradley, RF Doelman, S Jones, AM Fernandes, J Formaggio, JA Furse, D Kelly, JF Kofron, J LaRoque, BH Leber, ML McBride, L Monreal, B Oblath, N Patterson, R Rogers, A Robertson, RGH Rosenberg, L Rybka, G Thummler, T AF VanDevender, B. A. Asner, D. M. Bahr, M. Bradley, R. F. Doelman, S. Jones, A. M. Fernandes, J. Formaggio, J. A. Furse, D. Kelly, J. F. Kofron, J. LaRoque, B. H. Leber, M. L. McBride, L. Monreal, B. Oblath, N. Patterson, R. Rogers, A. Robertson, R. G. H. Rosenberg, L. Rybka, G. Thuemmler, T. BE Fleming, B TI Project 8: Precision Electron Specroscopy to Measure the Mass of the Neutrino SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE neutrino; tritium; beta decay; krypton-83; conversion electron; electron spectroscopy; cyclotron radiation; waveguide AB The Project 8 Collaboration is exploring a new technique for the spectroscopy of medium-energy electrons (similar to 1 - 100 keV) with the ultimate goal of measuring the effective mass of the electron antineutrino by the tritium endpoint method. Our method is based on the detection of microwave-frequency cyclotron radiation emitted by magnetically trapped electrons. The immediate goal of Project 8 is to demonstrate the utility of this technique for a tritium endpoint experiment through a high-precision measurement of the conversion electron spectrum of Kr-83m. We present concepts for detecting this cyclotron radiation, focusing on a guided wave design currently being implemented in a prototype apparatus at the University of Washington. C1 [VanDevender, B. A.; Asner, D. M.; Jones, A. M.; Fernandes, J.; Kelly, J. F.] Pacific NW Natl Lab, Richland, WA 99352 USA. [Bahr, M.; LaRoque, B. H.; Leber, M. L.; Monreal, B.] Univ Calif Santa Barbara, Santa Barbara, CA USA. [Bradley, R. F.] Natl Radio Astron Observ, Charlottesville, VA USA. [Doelman, S.; Rogers, A.] MIT, Haystack Observ, Westford, MA USA. [Formaggio, J. A.; Furse, D.; Oblath, N.] MIT, Cambridge, MA USA. [Kofron, J.; McBride, L.; Robertson, R. G. H.; Rosenberg, L.; Rybka, G.] Univ Washington, Ctr Expt Nucl Phys & Astrophys, Seattle, WA USA. [Patterson, R.] CALTECH, Pasadena, CA USA. [Thuemmler, T.] Karlsruhe Inst Technol, Karlsruhe, Germany. RP VanDevender, BA (reprint author), Pacific NW Natl Lab, Richland, WA 99352 USA. FU NSF; DOE Office of Nuclear Physics; MIT Wade Award and the Laboratory Directed Research and Development Program; Pacific Northwest National Laboratory; multiprogram national laboratory; U.S. Department of Energy [DE-AC05-76RL01830] FX Project 8 research is supported by the NSF, DOE Office of Nuclear Physics, an MIT Wade Award and the Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory, a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy under Contract DE-AC05-76RL01830 NR 6 TC 0 Z9 0 U1 0 U2 1 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 237 EP 239 DI 10.1063/1.4826762 PG 3 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000056 ER PT S AU Varouchas, D AF Varouchas, Dimitris CA ATLAS Collaboration BE Fleming, B TI Physics with tau lepton final states in ATLAS SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE Tau lepton; W -> tau nu; Z -> tau tau; Standard Model Higgs Boson; H -> tau tau; ATLAS; CERN AB Physics involving tau lepton signatures form an integral part of the ATLAS physics program. This article reviews the status of searches for Higgs bosons with tau lepton final states. In addition, measurements from Standard Model processes of W, Z with tau leptons are presented, along with a brief overview of the performance of the tau reconstruction algorithm in ATLAS. C1 [Varouchas, Dimitris] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Phys, Berkeley, CA 94720 USA. RP Varouchas, D (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Phys, Berkeley, CA 94720 USA. NR 8 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 257 EP 261 DI 10.1063/1.4826768 PG 5 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000062 ER PT S AU Bardayan, DW Ahn, S Blackmon, JC Chae, KY Chipps, KA Cizewski, JA Hardy, S Howard, ME Jones, KL Kozub, RL O'Malley, PD Manning, B Matos, M Nesaraja, CD Pain, SD Peters, WA Pittman, ST Ratkiewicz, A Schmitt, KT Smith, MS Spassova, I Strauss, S AF Bardayan, D. W. Ahn, S. Blackmon, J. C. Chae, K. Y. Chipps, K. A. Cizewski, J. A. Hardy, S. Howard, M. E. Jones, K. L. Kozub, R. L. O'Malley, P. D. Manning, B. Matos, M. Nesaraja, C. D. Pain, S. D. Peters, W. A. Pittman, S. T. Ratkiewicz, A. Schmitt, K. T. Smith, M. S. Spassova, I. Strauss, S. BE Fleming, B TI HRIBF studies of r-process nuclei and first results with the new SuperORRUBA detector SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE r-process; exotic beams; silicon detectors AB The astrophysical rapid neutron-capture process (r-process) is believed to have produced approximately half of the nuclear species more massive than Fe. Unfortunately, almost nothing is known about the structure of the majority of the extremely neutron-rich nuclei involved in the reaction flow. At exotic beam facilities such as the Holifield Radioactive Ion Beam Facility (HRIBF), measurements with accelerated beams of fission fragments have provided some of the first spectroscopic information on many r-process nuclei. The new SuperORRUBA (Oak Ridge Rutgers University Barrel Array) detector has been constructed at the HRIBF to study such nuclei, and first results are presented. C1 [Bardayan, D. W.; Chae, K. Y.; Nesaraja, C. D.; Pain, S. D.; Pittman, S. T.; Schmitt, K. T.; Smith, M. S.] Oak Ridge Natl Lab, Div Phys, Oak Ridge, TN 37831 USA. [Ahn, S.; Jones, K. L.] Univ Tennessee, Dept Phys & Astron, Knoxville, TN 37996 USA. [Blackmon, J. C.; Matos, M.] Louisiana State Univ, Dept Phys & Astron, Baton Rouge, LA 70803 USA. [Chae, K. Y.] Sungkyunkwan Univ, Dept Phys, Suwon 440746, South Korea. [Chipps, K. A.] Colorado Sch Mines, Dept Phys, Golden, CO 80401 USA. [Cizewski, J. A.; Hardy, S.; Howard, M. E.; O'Malley, P. D.; Manning, B.; Ratkiewicz, A.; Strauss, S.] Rutgers State Univ, Dept Phys & Astron, Piscataway, NJ 08854 USA. [Kozub, R. L.] Tennessee Technol Univ, Dept Phys, Cookeville, TN 38505 USA. [Peters, W. A.; Spassova, I.] Oak Ridge Associated Univ, Oak Ridge, TN 37830 USA. RP Bardayan, DW (reprint author), Oak Ridge Natl Lab, Div Phys, Oak Ridge, TN 37831 USA. RI Jones, Katherine/B-8487-2011; Pain, Steven/E-1188-2011; OI Jones, Katherine/0000-0001-7335-1379; Pain, Steven/0000-0003-3081-688X; Nesaraja, Caroline/0000-0001-5571-8341; Chipps, Kelly/0000-0003-3050-1298 NR 11 TC 0 Z9 0 U1 1 U2 2 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 330 EP 332 DI 10.1063/1.4826785 PG 3 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000079 ER PT S AU Ha, CH AF Ha, Chang Hyon CA IceCube Collaboration BE Fleming, B TI Detection of Cascades induced by Atmospheric Neutrinos in the 79-string IceCube Detector SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE DeepCore; IceCube; neutrino; cascades AB Neutrino production and oscillation physics can be studied by utilizing the very high flux of atmospheric neutrinos observed with IceCube. In a Cherenkov medium such as ice, atmospheric muon neutrino interactions create tracks while cascades (showers) are produced by atmospheric electron neutrinos and by neutral current interactions of all flavors. We present the first detection of atmospheric neutrino-induced cascades at energies between 30 GeV and 10 TeV using the DeepCore array of the IceCube detector. Using 281 days of data, 1029 events are observed with 59% predicted to be cascades. C1 [Ha, Chang Hyon] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Ha, CH (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. NR 14 TC 0 Z9 0 U1 0 U2 1 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 347 EP 349 DI 10.1063/1.4826790 PG 3 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000084 ER PT S AU Gabrielyan, M Raue, B Carman, DS Park, K AF Gabrielyan, Marianna Raue, Brian Carman, Daniel S. Park, Kijun BE Fleming, B TI Induced Polarization of Lambda(1116) in Kaon Electroproduction with CLAS SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE kaon; hyperon; electroproduction; polarization ID BARYON RESONANCES; DECAYS AB The CLAS Collaboration is using the p(e, e' K+ p)pi(-) reaction to perform a measurement of the induced polarization of the electroproduced Lambda(1116). The parity-violating weak decay of the. into p pi(-) (64%) allows extraction of the recoil polarization of the Lambda. This study uses the CEBAF Large Acceptance Spectrometer (CLAS) to detect the scattered electron, the kaon, and the decay proton. CLAS allows for a large kinematic acceptance with 0.8 <= Q(2) <= 3.5 GeV2, 1.6 <= W <= 3.0 GeV, as well as the kaon scattering angle. In this experiment a 5.5 GeV electron beam was incident upon an unpolarized liquid-hydrogen target. The goal is to map out the kinematic dependencies for this polarization observable to provide new constraints for theoretical models of the electromagnetic production of kaon-hyperon final states. Along with previously published photo-and electroproduction cross sections and polarization observables from CLAS, SAPHIR, and GRAAL, these data are needed in a coupled-channel analysis to identify previously unobserved s-channel resonances. C1 [Gabrielyan, Marianna; Raue, Brian] Florida Int Univ, Miami, FL 33199 USA. [Carman, Daniel S.; Park, Kijun] Jefferson Lab, Newport News, VA 23606 USA. RP Gabrielyan, M (reprint author), Florida Int Univ, Miami, FL 33199 USA. NR 9 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 410 EP 412 DI 10.1063/1.4826805 PG 3 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000099 ER PT S AU Lee, TSH AF Lee, T. -S. H. BE Fleming, B TI Status of Dynamical Coupled-Channel Analysis by Collaboration@EBAC SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE Nucleon resonance analysis ID MODEL AB The development and results of the Dynamical Coupled-Channels analysis by a collaboration at the Excited Baryon Analysis Center (EBAC) are reported. C1 Argonne Natl Lab, Div Phys, Argonne, IL 60439 USA. RP Lee, TSH (reprint author), Argonne Natl Lab, Div Phys, Argonne, IL 60439 USA. NR 12 TC 1 Z9 1 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 413 EP 417 DI 10.1063/1.4826806 PG 5 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000100 ER PT S AU Sandorfi, AM Hoblit, S AF Sandorfi, A. M. Hoblit, S. BE Fleming, B TI Extraction Of Reaction Amplitudes From Complete Photo-Production Experiments SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE meson photo-production; baryon resonances; multipole analysis; polarization AB A new generation of complete experiments in pseudoscalar meson photo-production is being pursued at several laboratories. Here the designation of complete refers to measurements of most if not all of the possible reaction observables, of which there are 16 involving spins of the beam, target and recoil baryon. Hyperon production to Lambda or Sigma(+) final states affords attractive opportunities, since their weak decays provide an efficient self-analysis of their spin. When the beam and target are also polarized, the resulting triple polarization measurements determine the full suite of observables with a single target orientation. This has been a focus at Jefferson Lab in the recently completed g9/FROST and g14/HDice experiments now under analysis. Multipole analyses of gamma p -> K+ Lambda have been carried out with recently published (incomplete) polarization data, and the uniqueness of the extracted amplitudes has been studied. Experiments with realistically achievable uncertainties require a significantly larger number of spin asymmetries than the in-principle minimum needed for a mathematical solution of the amplitude. C1 [Sandorfi, A. M.] Thomas Jefferson Natl Accelerator Lab, Dept Phys, Newport News, VA 23606 USA. [Hoblit, S.] Brookhaven Natl Lab, Natl Nucl Data Ctr, Upton, NY 11973 USA. RP Sandorfi, AM (reprint author), Thomas Jefferson Natl Accelerator Lab, Dept Phys, Newport News, VA 23606 USA. FU US Department of Energy [DE-AC05-06OR23177, DE-AC02-98CH10886] FX This work was supported by the US Department of Energy, Office of Nuclear Physics Division, under contract DE-AC05-06OR23177 under which Jefferson Science Associates operate Jefferson Laboratory, and also US Department of Energy contracts DE-AC02-98CH10886. NR 12 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 424 EP 428 DI 10.1063/1.4826809 PG 5 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000103 ER PT S AU Fomin, N AF Fomin, Nadia BE Fleming, B TI New analysis of the common nuclear dependence of the EMC effect and short-range correlations SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE short-range correlations; EMC effect; electron scattering AB The strong repulsive core of the nucleon-nucleon (NN) interaction at short distances prevents nucleons from becoming close to each other. This gives rise to high-momentum nucleons in the nucleus that cannot be explained in the context of the mean field and are commonly called short-range correlations (SRCs). They are responsible for the strength seen in momentum distribution tails seen in all nuclei, and we can obtain a relative measure of SRCs via cross section ratios to light nuclei. Recent inclusive scattering data from Jefferson Lab have allowed a precise determination of the A-dependence of SRCs in nuclei and suggests that, like the EMC effect, it is especially sensitive to the nuclear local density. These new results, as well as a new analysis of the relationship between SRCs and the EMC effect, will be presented and discussed. C1 Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Fomin, N (reprint author), Los Alamos Natl Lab, POB 1663, Los Alamos, NM 87545 USA. NR 13 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 516 EP 518 DI 10.1063/1.4826831 PG 3 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000125 ER PT S AU Arrington, J AF Arrington, J. BE Fleming, B TI New measurements of the proton's size and structure using polarized photons SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE nucleon electromagnetic form factors; charge radius; elastic scattering ID ELECTROMAGNETIC FORM-FACTORS; ELECTRON-SCATTERING; NUCLEON; 2-PHOTON-EXCHANGE AB Improved measurements of the proton's structure are now possible thanks to significant technical advances that allow us to probe the proton with polarized photons. These measurements have shown that the proton is not as simple as previously believed: quark orbital angular momentum and relativistic effects play an important role and the spatial distribution of charge and magnetization do not simply mimic the spatial distribution of the quarks. Even more recently, the large scale structure and size of the proton have been examined more carefully, and a significant discrepancy has been observed between the charge radius of the proton as measured in the Lamb shift of muonic hydrogen and measurements using the electron-proton interaction. C1 Argonne Natl Lab, Div Phys, Argonne, IL 60439 USA. RP Arrington, J (reprint author), Argonne Natl Lab, Div Phys, Argonne, IL 60439 USA. RI Arrington, John/D-1116-2012 OI Arrington, John/0000-0002-0702-1328 NR 55 TC 0 Z9 0 U1 0 U2 1 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 525 EP 532 DI 10.1063/1.4826834 PG 8 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000128 ER PT S AU Nadel-Turonski, P Guidal, M Horn, T Paremuzyan, R Stepanyan, S AF Nadel-Turonski, P. Guidal, M. Horn, T. Paremuzyan, R. Stepanyan, S. BE Fleming, B TI Timelike Compton Scattering at JLab 12 GeV SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE Timelike; Compton; DVCS; J/psi; GPD AB A major goal of Jefferson Lab at 12 GeV is to map out the 3-D structure of the proton through Generalized Parton Distributions (GPDs). An important tool in this endeavor is Deeply Virtual Compton Scattering, traditionally performed in kinematics where the incoming photon has a spacelike virtuality and the outgoing photon is real. However, measuring the corresponding timelike process, known as Timlike Compton Scattering (TCS), where the incoming photon is real and the outgoing one timelike, offers a unique opportunity to test the universality of GPDs. It also allows to take advantage of the straightforward access in TCS to the real part of the Compton Form Factors, providing constraints on global GPD fits. In addition, the experiment will provide a high-statistics measurement of the J/psi photoproduction cross section near threshold, as this process shares the same final state. C1 [Nadel-Turonski, P.; Stepanyan, S.] Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. [Guidal, M.; Paremuzyan, R.] Inst Phys Nucl, IN2P3, F-91406 Orsay, France. [Horn, T.] Catholic Univ Amer, Washington, DC 20064 USA. [Paremuzyan, R.] Yerevan Phys Inst, Yerevan 375036, Armenia. RP Nadel-Turonski, P (reprint author), Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. NR 3 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 557 EP 559 DI 10.1063/1.4826840 PG 3 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000134 ER PT S AU Kubarovsky, V AF Kubarovsky, Valery CA CLAS Collaboration BE Fleming, B TI Deeply Virtual Meson Production with CLAS and CLAS12 SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE Meson electroproduction; Generalized Parton Distributions; nucleon structure ID ELECTROPRODUCTION; DISTRIBUTIONS; TRANSVERSITY AB Deeply virtual exclusive reactions offer a unique opportunity to study the structure of the nucleon at the parton level as one varies both the size of the probe, i.e. the photon virtuality Q(2), and the momentum transfer to the nucleon t. The mapping of the nucleon's structure in terms of the generalized parton distributions is one of the major objectives of the Jefferson Lab. In this article we focus on deeply virtual pseudoscalar meson production gamma*p -> p pi(0) at 6 GeV. The Jefferson Lab upgrade will significantly extend the available Q(2) and t range for the meson electroproduction. The CLAS12 performance is demonstrated on the example of the phi electroproduction gamma*p -> p phi. C1 [Kubarovsky, Valery; CLAS Collaboration] Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. RP Kubarovsky, V (reprint author), Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. NR 15 TC 0 Z9 0 U1 0 U2 1 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 566 EP 570 DI 10.1063/1.4826843 PG 5 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000137 ER PT S AU Quinn, BP Collaboration, S AF Quinn, B. P. Collaboration, S. B. S. BE Fleming, B TI Nucleon Elastic Form Factors at High Q(2) SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE nucleon; electromagnetic; form factors; neutron; proton AB Electron scattering allows precise determination of the form factors of the proton and neutron, providing insight into their electromagnetic structure. The energy upgrade of Jefferson Lab's CE-BAF accelerator, in combination with large acceptance spectrometers and high rate detectors, will make it possible to push the range of high precision measurements to higher Q(2), probing the small-scale structure of the quark distribution within the nucleon. C1 [Quinn, B. P.] Carnegie Mellon Univ, Pittsburgh, PA 15213 USA. [Collaboration, S. B. S.] Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. RP Quinn, BP (reprint author), Carnegie Mellon Univ, Pittsburgh, PA 15213 USA. RI Quinn, Brian/N-7343-2014 OI Quinn, Brian/0000-0003-2800-986X NR 13 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 571 EP 575 DI 10.1063/1.4826844 PG 5 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000138 ER PT S AU Knecht, A Alexander, ZT Bagdasarova, Y Cope, TM Delbridge, BG Flechard, X Garcia, A Hong, R Lienard, E Mueller, P Naviliat-Cuncic, O Palmer, ASC Robertson, RGH Storm, DW Swanson, HE Utsuno, S Wauters, F Williams, W Wrede, C Zumwalt, DW AF Knecht, A. Alexander, Z. T. Bagdasarova, Y. Cope, T. M. Delbridge, B. G. Flechard, X. Garcia, A. Hong, R. Lienard, E. Mueller, P. Naviliat-Cuncic, O. Palmer, A. S. C. Robertson, R. G. H. Storm, D. W. Swanson, H. E. Utsuno, S. Wauters, F. Williams, W. Wrede, C. Zumwalt, D. W. BE Fleming, B TI Weak Interaction Studies with He-6 SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE helium-6; nuclear beta decay; half-life; weak axial coupling constant ID NUCLEAR BETA-DECAY; HALF-LIFE; TESTS; HE6 AB The He-6 nucleus is an ideal candidate to study the weak interaction. To this end we have built a high-intensity source of He-6 delivering similar to 10(10) atoms/s to experiments. Taking full advantage of that available intensity we have performed a high-precision measurement of the He-6 half-life that directly probes the axial part of the nuclear Hamiltonian. Currently, we are preparing a measurement of the beta-neutrino angular correlation in He-6 beta decay that will allow to search for new physics beyond the Standard Model in the form of tensor currents. C1 [Knecht, A.; Alexander, Z. T.; Bagdasarova, Y.; Cope, T. M.; Delbridge, B. G.; Garcia, A.; Hong, R.; Palmer, A. S. C.; Robertson, R. G. H.; Storm, D. W.; Swanson, H. E.; Utsuno, S.; Wauters, F.; Zumwalt, D. W.] Univ Washington, Dept Phys, Seattle, WA 98195 USA. [Flechard, X.; Lienard, E.] Univ Caen, ENSICAEN, CNRS IN2P3 ENSI, LPC Caen, Caen, France. [Mueller, P.; Williams, W.] Argonne Natl Lab, Div Phys, Argonne, IL 60439 USA. [Naviliat-Cuncic, O.; Wrede, C.] Michigan State Univ, Dept Phys & Astron, Natl Superconducting Cyclotron Lab, E Lansing, MI 48824 USA. RP Knecht, A (reprint author), Univ Washington, Dept Phys, Seattle, WA 98195 USA. RI Mueller, Peter/E-4408-2011; Naviliat-Cuncic, Oscar/H-5697-2016; OI Mueller, Peter/0000-0002-8544-8191; Hong, Ran/0000-0002-8984-7501; Garcia, Alejandro/0000-0001-6056-6645 FU US Department of Energy [DEFG02-97ER41020, DEAC02-06CH11357] FX We thank the excellent staff at the Center for Experimental Nuclear Physics and Astrophysics. This work has been supported by the US Department of Energy under DEFG02- 97ER41020 and under Contract No. DEAC02-06CH11357. NR 23 TC 6 Z9 6 U1 0 U2 5 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 636 EP 640 DI 10.1063/1.4826859 PG 5 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000153 ER PT S AU Schenke, B Tribedy, P Venugopalan, R AF Schenke, Bjoern Tribedy, Prithwish Venugopalan, Raju BE Fleming, B TI Glasma fluctuations in heavy-ion collisions SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE relativistic heavy-ion collisions; fluctuations; particle production ID NUCLEUS-NUCLEUS COLLISIONS AB We present calculations of event-by-event gluon multiplicities and energy densities within the glasma model by solving classical Yang-Mills equations. The model naturally yields negative binomial fluctuations of multiplicities and energies. We further present results for the average eccentricities of the glasma initial state and compare them to another Color-Glass-Condensate based model. C1 [Schenke, Bjoern; Venugopalan, Raju] Brookhaven Natl Lab, Dept Phys, Upton, NY 11973 USA. [Tribedy, Prithwish] Ctr Variable Energy Cyclotron, Kolkata 700064, W Bengal, India. RP Schenke, B (reprint author), Brookhaven Natl Lab, Dept Phys, Upton, NY 11973 USA. FU US Department of Energy under DOE [DE-AC02-98CH10886]; BNL [10-043]; Brookhaven Science Associates FX BPS and RV are supported by the US Department of Energy under DOE Contract No. DE-AC02-98CH10886 and acknowledge additional support from a BNL"Lab Directed Research and Development" grant LDRD 10-043. BPS gratefully acknowledges a Goldhaber Distinguished Fellowship from Brookhaven Science Associates. NR 21 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 650 EP 654 DI 10.1063/1.4826862 PG 5 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000156 ER PT S AU Debbe, R AF Debbe, Ramiro CA ATLAS Collaboration BE Fleming, B TI Measurement of Harmonic Flow from Heavy Ion Collisions in ATLAS SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE Relativistic Heavy ions; Hydrodynamical flow; Viscosity AB The ATLAS Collaboration has measured the flow of charged particles as the medium formed in Pb-Pb collisions at root s(NN) = 2.76 TeV expands after the interaction. The Fourier expansion of distributions in azimuth angle constructed with two different methods have been measured over a large range of p(T), eta and centrality and are found to be consistent with an acoustic harmonic expansion of a system with very low viscosity. The power spectrum of such a flow is shown up to 15th order. For n>6 the coefficients are consistent with zero. C1 [Debbe, Ramiro; ATLAS Collaboration] Brookhaven Natl Lab, Dept Phys, Upton, NY 11973 USA. RP Debbe, R (reprint author), Brookhaven Natl Lab, Dept Phys, Upton, NY 11973 USA. NR 4 TC 0 Z9 0 U1 0 U2 1 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 666 EP 668 DI 10.1063/1.4826866 PG 3 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000160 ER PT S AU Debbe, R AF Debbe, R. CA ATLAS Collaboration BE Fleming, B TI Particle and Jet Production in Heavy-Ion Collisions with the ATLAS Detector at LHC SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE Relativistic Heavy Ion; Jet Energy loss AB The ATLAS Collaboration embarked on a detailed study of the dense and opaque extended system formed in Pb-Pb collisions at LHC. Comparisons of jet yields obtained in different classes of events confirm the presence of strong energy loss of partons in the medium at this energy. The study of jet shapes provides detailed information on the flow of energy as partons traverse the medium. C1 [Debbe, R.; ATLAS Collaboration] Brookhaven Natl Lab, Dept Phys, Upton, NY 11973 USA. RP Debbe, R (reprint author), Brookhaven Natl Lab, Dept Phys, Upton, NY 11973 USA. NR 7 TC 0 Z9 0 U1 0 U2 1 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 680 EP 682 DI 10.1063/1.4826870 PG 3 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000164 ER PT S AU Pinkenburg, C AF Pinkenburg, Christopher BE Fleming, B TI sPHENIX: the upgraded PHENIX detector for the next decade SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE Instrumentation Jets Calorimetry Simulations AB The PHENIX collaboration proposes a major upgrade, referred to as sPHENIX, to the PHENIX detector at the Relativistic Heavy Ion Collider (RHIC). This upgrade will bring new capabilities to the RHIC program by opening new and important channels for experimental investigation of the quark gluon plasma near 1-2 T-c utilizing fully the luminosity of the recently upgraded RHIC facility. The baseline conceptual design consists of a tungsten based compact electromagnetic calorimeter and a hadronic calorimeter covering the full azimuth in |eta| < 1.1. The existing silicon vertex detectors provides the tracking layers. C1 Brookhaven Natl Lab, Dept Phys, Upton, NY 11973 USA. RP Pinkenburg, C (reprint author), Brookhaven Natl Lab, Dept Phys, Bldg 510 C, Upton, NY 11973 USA. NR 4 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 691 EP 693 DI 10.1063/1.4826873 PG 3 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000167 ER PT S AU Somov, A AF Somov, A. CA GlueX Collaboration JLab Fast Elect Grp BE Fleming, B TI Development of Level-1 triggers for experiments at Jefferson Lab SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE Level-1 trigger systems; GlueX experiment AB The upgrade of the CEBAF electron beam energy from 6 GeV to 12 GeV will expand the physics program at Jefferson Lab and result in upgrading three existing experimental halls and constructing a new detector GlueX in a fourth experimental Hall-D. This experiment requires a Level-1 trigger capable of running dead-timeless at 200 kHz total trigger rate. We have developed general-purpose custom-build electronics modules that meet these requirements. These modules are being implemented for other Jefferson Lab experiments. Description of the Level-1 triggers being developed at Jefferson Lab will be presented. C1 [Somov, A.; GlueX Collaboration; JLab Fast Elect Grp] Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. RP Somov, A (reprint author), Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. NR 3 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 700 EP 702 DI 10.1063/1.4826876 PG 3 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000170 ER PT S AU Qiang, Y Zorn, C Barbosa, F Smith, E AF Qiang, Yi Zorn, Carl Barbosa, Fernando Smith, Elton BE Fleming, B TI Neutron Radiation Hardness Tests of SiPMs SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE Silicon photomultiplier; SiPM; MPPC; Radiation damage ID DAMAGE AB Hall D at Jefferson Laboratory is building its new GlueX spectrometer to study QCD gluonic excitations. The hermetic detector includes a scintillating fiber-lead barrel calorimeter where the photodetectors must operate in a high magnetic field. The silicon photomultiplier (SiPM) array manufactured by Hamamatsu Corporation was chosen for the photodetector of the BCAL. We report on the measurement of neutron radiation hardness of SiPMs at Jefferson Lab. C1 [Qiang, Yi; Zorn, Carl; Barbosa, Fernando; Smith, Elton] Jefferson Lab, Newport News, VA 23606 USA. RP Qiang, Y (reprint author), Jefferson Lab, Newport News, VA 23606 USA. OI Qiang, Yi/0000-0001-7026-7841 NR 5 TC 0 Z9 0 U1 0 U2 2 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 703 EP 705 DI 10.1063/1.4826877 PG 3 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000171 ER PT S AU Mashnik, SG Bull, JS Hughes, HG Prael, RE Sierk, AJ AF Mashnik, S. G. Bull, J. S. Hughes, H. G. Prael, R. E. Sierk, A. J. BE Fleming, B TI Current status of MCNP6 as a simulation tool useful for space and accelerator applications SO 11TH CONFERENCE ON THE INTERSECTIONS OF PARTICLE AND NUCLEAR PHYSICS (CIPANP 2012) SE AIP Conference Proceedings LA English DT Proceedings Paper CT 11th Conference on the Intersections of Particle and Nuclear Physics (CIPANP) CY MAY 29-JUN 03, 2012 CL St Petersburg, FL SP US Dept Energy, US Natl Sci Fdn, Jefferson Natl Accelerator Lab, Fermi Natl Accelerator Lab, Brookhaven Natl Lab, TRIUMF Lab, SNOLAB Lab, Canadian Inst Nucl Phys, Los Alamos Natl Lab DE MCNP6; Monte-Carlo method; spallation; fragmentation; evaporation; fission; CEM03.03; LAQGSM03.03; INCL plus ABLA; ISABEL; Bertini plus MPM plus Dresner plus RAL ID INTRANUCLEAR-CASCADE CALCULATION AB For the past several years, a major effort has been undertaken at Los Alamos National Laboratory (LANL) to develop the transport code MCNP6, the latest LANL Monte-Carlo transport code representing a merger and improvement of MCNP5 and MCNPX. We emphasize a description of the latest developments of MCNP6 at higher energies to improve its reliability in calculating rare-isotope production, high-energy cumulative particle production, and a gamut of reactions important for space-radiation shielding, cosmic-ray propagation, and accelerator applications. We present several examples of validation and verification of MCNP6 compared to a wide variety of intermediate-and high-energy experimental data on reactions induced by photons, mesons, nucleons, and nuclei at energies from tens of MeV to about 1 TeV/nucleon, and compare to results from other modern simulation tools. C1 [Mashnik, S. G.; Bull, J. S.; Hughes, H. G.; Prael, R. E.; Sierk, A. J.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Mashnik, SG (reprint author), Los Alamos Natl Lab, POB 1663, Los Alamos, NM 87545 USA. NR 26 TC 0 Z9 0 U1 0 U2 2 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-1188-3 J9 AIP CONF PROC PY 2013 VL 1560 BP 706 EP 708 DI 10.1063/1.4826878 PG 3 WC Physics, Applied; Physics, Nuclear; Physics, Particles & Fields SC Physics GA BID33 UT WOS:000327656000172 ER PT S AU Gleber, SC Weinhausen, B Koster, S Ward, J Vine, D Finney, L Vogt, S AF Gleber, Sophie-Charlotte Weinhausen, Britta Koester, Sarah Ward, Jesse Vine, David Finney, Lydia Vogt, Stefan BE Xu, H Wu, Z Tai, R TI New Developments in Hard X-ray Fluorescence Microscopy for In-situ Investigations of Trace Element Distributions in Aqueous Systems of Soil Colloids SO 11TH INTERNATIONAL CONFERENCE ON X-RAY MICROSCOPY (XRM2012) SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 11th International Conference on X-ray Microscopy (XRM) CY AUG 05-10, 2012 CL Shanghai Synchrotron Radiat Facil, Shanghai, PEOPLES R CHINA SP Natl Synchrotron Radiat Lab, Chinese Acad Sci, Natl Nat Sci Fdn China, BRUKER, xradia HO Shanghai Synchrotron Radiat Facil AB The distribution, binding and release of trace elements on soil colloids determine matter transport through the soil matrix, and necessitates an aqueous environment and short length and time scales for their study. However, not many microscopy techniques allow for that. We previously showed hard x-ray fluorescence microscopy capabilities to image aqueous colloidal soil samples [1]. As this technique provides attogram sensitivity for transition elements like Cu, Zn, and other geochemically relevant trace elements at sub micrometer spatial resolution (currently down to 150 nm at 2-ID-E [2]; below 50 nm at Bionanoprobe, cf. G. Woloschak et al, this volume) combined with the capability to penetrate tens of micrometer of water, it is ideally suited for imaging the elemental content of soil colloids. To address the question of binding and release processes of trace elements on the surface of soil colloids, we developed a microfluidics based XRF flow cytometer, and expanded the applied methods of hard x-ray fluorescence microscopy towards three dimensional imaging. Here, we show (a) the 2-D imaged distributions of Si, K and Fe on soil colloids of Pseudogley samples; (b) how the trace element distribution is a dynamic, pH-dependent process; and (c) x-ray tomographic applications to render the trace elemental distributions in 3-D. We conclude that the approach presented here shows the remarkable potential to image and quantitate elemental distributions from samles within their natural aqueous microenvironment, particularly important in the environmental, medical, and biological sciences. C1 [Gleber, Sophie-Charlotte; Ward, Jesse; Vine, David; Finney, Lydia; Vogt, Stefan] Argonne Natl Lab, Xray Sci Div, Argonne, IL 60304 USA. RP Gleber, SC (reprint author), Argonne Natl Lab, Xray Sci Div, Argonne, IL 60304 USA. EM gleber@aps.anl.gov NR 4 TC 1 Z9 1 U1 0 U2 8 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2013 VL 463 AR UNSP 012005 DI 10.1088/1742-6596/463/1/012005 PG 4 WC Microscopy; Physics, Applied SC Microscopy; Physics GA BIE98 UT WOS:000327949000005 ER PT S AU Shu, DM Nazaretski, E Kim, J Yan, HF Lauer, K Mullany, B Kuhne, D Maser, J Chu, YS AF Shu, Deming Nazaretski, Evgeny Kim, Jungdae Yan, Hanfei Lauer, Kenneth Mullany, Brian Kuhne, Dennis Maser, Joerg Chu, Yong S. BE Xu, H Wu, Z Tai, R TI Optomechanical Design of a Multilayer Laue Lens Test Bed for 10-nm Focusing of Hard X-rays SO 11TH INTERNATIONAL CONFERENCE ON X-RAY MICROSCOPY (XRM2012) SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 11th International Conference on X-ray Microscopy (XRM) CY AUG 05-10, 2012 CL Shanghai Synchrotron Radiat Facil, Shanghai, PEOPLES R CHINA SP Natl Synchrotron Radiat Lab, Chinese Acad Sci, Natl Nat Sci Fdn China, BRUKER, xradia HO Shanghai Synchrotron Radiat Facil AB A multilayer Laue lens (MLL) test bed was designed at the Argonne National Laboratory for the National Synchrotron Light Source-II (NSLS-II) project at Brookhaven National Laboratory. Argonne and Brookhaven scientists and engineers collaborated to carry out this work in order to achieve NSLS-II's R&D goals of 10-nm focusing of hard x-rays. The test-bed design was based on the experience gained from the Argonne nanopositioning system designed for the CNM/APS hard x-ray nanoprobe project and an MLL test bed at Advanced Photon Source (APS) beamline 26-ID [1-3]. Optomechanical design of the MLL test bed, as well as the preliminary test results for the alignment apparatus and sample base stages' mechanical vibration performances are presented in this paper. C1 [Shu, Deming; Maser, Joerg] Argonne Natl Lab, Adv Photon Source, Argonne, IL 60439 USA. RP Shu, DM (reprint author), Argonne Natl Lab, Adv Photon Source, Argonne, IL 60439 USA. EM shu@aps.anl.gov RI Yan, Hanfei/F-7993-2011 OI Yan, Hanfei/0000-0001-6824-0367 NR 7 TC 4 Z9 4 U1 1 U2 6 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2013 VL 463 AR UNSP 012029 DI 10.1088/1742-6596/463/1/012029 PG 4 WC Microscopy; Physics, Applied SC Microscopy; Physics GA BIE98 UT WOS:000327949000029 ER PT S AU Thieme, J Kilcoyne, D Tyliszczak, T Haselwandter, K AF Thieme, J. Kilcoyne, D. Tyliszczak, T. Haselwandter, K. BE Xu, H Wu, Z Tai, R TI Spatially resolved NEXAFS spectroscopy of siderophores in biological matrices SO 11TH INTERNATIONAL CONFERENCE ON X-RAY MICROSCOPY (XRM2012) SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 11th International Conference on X-ray Microscopy (XRM) CY AUG 05-10, 2012 CL Shanghai Synchrotron Radiat Facil, Shanghai, PEOPLES R CHINA SP Natl Synchrotron Radiat Lab, Chinese Acad Sci, Natl Nat Sci Fdn China, BRUKER, xradia HO Shanghai Synchrotron Radiat Facil ID ADVANCED LIGHT-SOURCE; FUNGI AB Iron is an essential nutrient for almost all forms of life. In the presence of oxygen iron is present in its ferric form which precipitates under formation of rather insoluble oxide-hydroxide polymers. Hence the bioavailability of iron is extremely low (< 10(-17) M at pH 7 for Fe3+). Under such conditions almost all microorganisms synthesize siderophores as iron chelating agents, thus solubilizing ferric iron from rather insoluble iron sources. Siderophores form soluble complexes with Fe3+. The present study aims at developing a methodology that would allow for the specific detection and localization of such iron chelators in their natural environment. The applicability of spatially resolved NEXAFS spectroscopy in the soft X-ray energy (E < 1 keV) range was evaluated for localization of typical fungal hydroxamate siderophores like ferrichrome or coprogen, which can be present in various biological materials. Results obtained with the scanning transmission X-ray microscopes at beamlines 11.0.2 and 5.3.2 of the ALS have shown characteristic signatures for siderophores. Thus NEXAFS spectroscopy at the carbon K-edge, nitrogen K-edge and iron L-edge with high spatial resolution has proven to be extremely useful for their identification in their natural environment. Spectra of different siderophores as well as spectra and images of biological material containing siderophores are presented. C1 [Thieme, J.] Brookhaven Natl Lab, Upton, NY 11973 USA. RP Thieme, J (reprint author), Brookhaven Natl Lab, NSLS 2, Upton, NY 11973 USA. EM jthieme@bnl.gov RI Kilcoyne, David/I-1465-2013 NR 10 TC 0 Z9 0 U1 0 U2 7 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2013 VL 463 AR UNSP 012037 DI 10.1088/1742-6596/463/1/012037 PG 4 WC Microscopy; Physics, Applied SC Microscopy; Physics GA BIE98 UT WOS:000327949000037 ER PT S AU Wang, S Shapiro, D Kaznatcheev, K AF Wang, S. Shapiro, D. Kaznatcheev, K. BE Xu, H Wu, Z Tai, R TI X-ray ptychography with highly-curved wavefront SO 11TH INTERNATIONAL CONFERENCE ON X-RAY MICROSCOPY (XRM2012) SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 11th International Conference on X-ray Microscopy (XRM) CY AUG 05-10, 2012 CL Shanghai Synchrotron Radiat Facil, Shanghai, PEOPLES R CHINA SP Natl Synchrotron Radiat Lab, Chinese Acad Sci, Natl Nat Sci Fdn China, BRUKER, xradia HO Shanghai Synchrotron Radiat Facil ID FREE-ELECTRON LASER; DIFFRACTION MICROSCOPY AB The recent development of scanning coherent x-ay diffraction microscopy (also known as ptychography) eliminates several constraints exerted by coherent imaging. In particular, an illuminating wave (the probe) can have an arbitrary shape, as a diffraction data redundancy due to multiple measurements at overlapping neighboring probe positions permits its independent reconstruction along with the scattering potential (the object wave). A priori knowledge, such as a finite sample support, is reduced to a recording of sequential probe positions and a plausible guess to be used as a starting estimate for iterative phase retrieval. Using a focusing probe, such as one produced by a zone plate, we investigate the effectiveness of the reconstruction algorithm and find that it is significantly less successful at reconstructing wavefronts with large curvature (extended phase variation) than the wavefronts with almost flat phase structure. Our simulations show that when the actual probe has large phase variation, the amount of overlap required for a successful reconstruction of both object and probe depends upon the phase difference between the actual probe and the probe used as a starting estimate for the reconstruction. We quantitatively define the circumstances for successful reconstruction of an object placed away from focus. We use an experimental dataset measured with a moderate amount of overlap to show that a successful reconstruction of the test sample can be done using a curved probe as an initial guess. C1 [Wang, S.; Kaznatcheev, K.] Brookhaven Natl Lab, NSLSII, Upton, NY 11973 USA. RP Wang, S (reprint author), Brookhaven Natl Lab, NSLSII, Upton, NY 11973 USA. EM shellywang@bnl.gov NR 21 TC 0 Z9 0 U1 0 U2 5 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2013 VL 463 AR UNSP 012040 DI 10.1088/1742-6596/463/1/012040 PG 4 WC Microscopy; Physics, Applied SC Microscopy; Physics GA BIE98 UT WOS:000327949000040 ER PT J AU Ciraci, S Sozer, H Tekinerdogan, B AF Ciraci, Selim Sozer, Hasan Tekinerdogan, Bedir GP IEEE TI A Run-Time Verification Framework for Smart Grid Applications Implemented on Simulation Frameworks SO 2013 2ND INTERNATIONAL WORKSHOP ON SOFTWARE ENGINEERING CHALLENGES FOR THE SMART GRID (SE4SG) LA English DT Proceedings Paper CT 2nd International Workshop on Software Engineering Challenges for the Smart Grid (SE4SG) CY MAY 18, 2013 CL San Francisco, CA AB Smart grid applications are implemented and tested with simulation frameworks as the developers usually do not have access to large sensor networks to be used as a test bed. The developers are forced to map the implementation onto these frameworks which results in a deviation between the architecture and the code. On its turn this deviation makes it hard to verify behavioral constraints that are described at the architectural level. We have developed the ConArch toolset to support the automated verification of architecture-level behavioral constraints. A key feature of ConArch is programmable mapping for architecture to the implementation. Here, developers implement queries to identify the points in the target program that correspond to architectural interactions. ConArch generates runtime observers that monitor the flow of execution between these points and verifies whether this flow conforms to the behavioral constraints. We illustrate how the programmable mappings can be exploited for verifying behavioral constraints of a smart grid application that is implemented with two simulation frameworks. C1 [Ciraci, Selim] Pacific NW Natl Lab, Richland, WA 99352 USA. [Sozer, Hasan] Ozyegin Univ, Istanbul, Turkey. [Tekinerdogan, Bedir] Bilkent Univ, Ankara, Turkey. RP Ciraci, S (reprint author), Pacific NW Natl Lab, Richland, WA 99352 USA. EM selim.ciraci@pnnl.gov; hasan.sozer@ozyegin.edu.tr; bedir@cs.bilkent.edu.tr NR 17 TC 1 Z9 1 U1 0 U2 0 PU IEEE PI NEW YORK PA 345 E 47TH ST, NEW YORK, NY 10017 USA BN 978-1-4673-6280-1 PY 2013 BP 1 EP 8 PG 8 WC Computer Science, Software Engineering; Computer Science, Theory & Methods; Engineering, Electrical & Electronic SC Computer Science; Engineering GA BIE94 UT WOS:000327944900001 ER PT J AU Dharap, A Pokrzywa, C Vemuganti, R AF Dharap, Ashutosh Pokrzywa, Courtney Vemuganti, Raghu TI Increased binding of stroke-induced long non-coding RNAs to the transcriptional corepressors Sin3A and coREST SO ASN NEURO LA English DT Article DE cerebral ischemia; corepressor; genomics; long non-coding RNA; REST; Sin3A; transcription factor ID GENE-EXPRESSION; FOCAL ISCHEMIA; CHROMATIN; GENOME AB LncRNAs (long non-coding RNAs) are thought to play a significant role in cellular homeostasis during development and disease by interacting with CMPs (chromatin-modifying proteins). We recently showed that following transient focal ischemia, the expression of many lncRNAs was altered significantly in rat brain. We currently analyzed whether focal ischemia also alters the association of lncRNAs with the CMPs Sin3A and coREST (corepressors of the RE-1 silencing transcription factor). RIP (RNA immunoprecipitation) combined with lncRNA microarray analysis showed that 177 of the 2497 lncRNAs expressed in rat cerebral cortex showed significantly increased binding to either Sin3A or coREST following ischemia compared with sham. Of these, 26 lncRNAs enriched with Sin3A and 11 lncRNAs enriched with coREST were also up-regulated in their expressions after ischemia. A majority of the lncRNAs enriched with these CMPs were intergenic in origin. Evaluation of the expression profiles of corresponding protein-coding genes showed that their expression levels correlate with those of the lncRNAs with which they shared a common locus. This is the first study to show that stroke-induced lncRNAs might associate with CMPs to modulate the post-ischemic epigenetic landscape. C1 [Dharap, Ashutosh; Pokrzywa, Courtney; Vemuganti, Raghu] Univ Wisconsin, Dept Neurol Surg, Madison, WI USA. [Dharap, Ashutosh] Los Alamos Natl Lab, Los Alamos, NM USA. RP Vemuganti, R (reprint author), Univ Wisconsin, Dept Neurol Surg, Madison, WI USA. EM Dharap.wisc@gmail.com; vemuganti@neurosurgery.wisc.edu RI Dharap, Ashutosh/H-7466-2013 FU National Institutes of Health [NS074444, NS079585] FX This work was supported by the National Institutes of Health [grant numbers NS074444 and NS079585]. NR 25 TC 15 Z9 20 U1 0 U2 5 PU PORTLAND PRESS LTD PI LONDON PA THIRD FLOOR, EAGLE HOUSE, 16 PROCTER STREET, LONDON WC1V 6 NX, ENGLAND SN 1759-0914 J9 ASN NEURO JI ASN Neuro PY 2013 VL 5 IS 4 BP 283 EP U65 AR e00124 DI 10.1042/AN20130029 PG 11 WC Neurosciences SC Neurosciences & Neurology GA 269SQ UT WOS:000328262600005 PM 24063527 ER PT S AU Lister, TE Dufek, EJ Stone, SG AF Lister, T. E. Dufek, E. J. Stone, S. G. BE Zhou, XD Mogensen, MB Staser, JA Brisard, G Mustain, WE Williams, MC TI Electrochemical Systems for Production of Syngas and Co-Products SO ELECTROCHEMICAL SYNTHESIS OF FUELS 2 SE ECS Transactions LA English DT Proceedings Paper CT 2nd International Symposium on Electrochemical Synthesis of Fuels (ESF) CY OCT 27-NOV 01, 2013 CL San Francisco, CA SP Electrochem Soc Inc, High Temp Mat Div, Electrochem Soc Inc, Phys & Analyt Electrochemistry Div, Electrochem Soc Inc, Energy Technol Div, Electrochem Soc Inc, Ind Electrochemistry & Electrochem Engn Div, New Technol Subcommittee ID GAS-DIFFUSION ELECTRODES; CARBON-DIOXIDE; METAL-ELECTRODES; CO2 REDUCTION; LOW-TEMPERATURE; AG ELECTRODES; HIGH-PRESSURE; CELL; SELECTIVITY; OPERATION AB This paper describes the development of bench-scale systems for the electrochemical reduction of CO2 to synthesis gas (syngas). Syngas is a significant building block chemical currently derived from fossil energy. Conventional methods create syngas using fossil resources which releases carbon into the atmosphere. Electrochemical reduction of CO2 is a process that could integrate intermittent alternative energy sources into the electric grid by using excess electricity to convert CO2 and H2O to a useful product. The paper describes applied electrochemical development of systems to reduce CO2 and H2O using technical data from previous work. This paper will describe three developed processes: 1) ambient pressure production of syn-gas, 2) pressurized CO2 reduction and 3) Cl-2 and syngas co-production. C1 [Lister, T. E.; Dufek, E. J.] Idaho Natl Lab, Energy & Environm Sci & Technol Div, Idaho Falls, ID 83415 USA. [Stone, S. G.] Giner Inc, Newton, MA 02466 USA. RP Lister, TE (reprint author), Idaho Natl Lab, Energy & Environm Sci & Technol Div, Idaho Falls, ID 83415 USA. RI Dufek, Eric/B-8847-2017 OI Dufek, Eric/0000-0003-4802-1997 FU Battelle Energy Alliance, LLC [DE-AC07-05ID14517]; U.S. Department of Energy FX Work supported through the INL Laboratory Directed Research and Development (LDRD) Program under DOE Idaho Operations Office. This manuscript has been authored by Battelle Energy Alliance, LLC under Contract No. DE-AC07-05ID14517 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a nonexclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. NR 30 TC 0 Z9 0 U1 0 U2 5 PU ELECTROCHEMICAL SOC INC PI PENNINGTON PA 65 S MAIN ST, PENNINGTON, NJ 08534-2839 USA SN 1938-5862 BN 978-1-60768-447-3; 978-1-62332-093-5 J9 ECS TRANSACTIONS PY 2013 VL 58 IS 2 BP 125 EP 137 DI 10.1149/05802.0125ecst PG 13 WC Electrochemistry; Energy & Fuels SC Electrochemistry; Energy & Fuels GA BJH38 UT WOS:000328212000013 ER PT S AU Haussener, S Hu, S Xiang, CX Weber, AZ Lewis, NS AF Haussener, Sophia Hu, Shu Xiang, Chengxiang Weber, Adam Z. Lewis, Nathan S. BE Zhou, XD Mogensen, MB Staser, JA Brisard, G Mustain, WE Williams, MC TI Simulations of the Irradiation and Temperature Dependence of the Efficiency of Tandem Photoelectrochemical Water-splitting Systems SO ELECTROCHEMICAL SYNTHESIS OF FUELS 2 SE ECS Transactions LA English DT Proceedings Paper CT 2nd International Symposium on Electrochemical Synthesis of Fuels (ESF) CY OCT 27-NOV 01, 2013 CL San Francisco, CA SP Electrochem Soc Inc, High Temp Mat Div, Electrochem Soc Inc, Phys & Analyt Electrochemistry Div, Electrochem Soc Inc, Energy Technol Div, Electrochem Soc Inc, Ind Electrochemistry & Electrochem Engn Div, New Technol Subcommittee ID ACID-SOLUTIONS; EVOLUTION REACTION; OXYGEN EVOLUTION; HYDROGEN; PLATINUM; ELECTRODES; SURFACES; KINETICS; CELL AB The efficiency of an operating photoelectrochemical solar-fuels-generator system is determined by the system design, the properties and morphology of the system's components, and the operational conditions. We used a previously developed model comprising of i) the detailed balance limit to describe the currentpotential performance of the photoabsorber component, and ii) the detailed multi-physics device model solving for the governing conservation equations (mass, momentum, species and charge) spatially resolved in the device, to quantify the performance of photoelectrochemical devices. The investigated the performance and its variations as a function of operational conditions, i.e. daily and seasonal irradiation variations, concentration factor of irradiation, and isothermal device temperature. Additionally, the difference in performance of an integrated photoelectrochemical system and a photovoltaic array connected electrically to a standalone electrolyzer system was quantified. C1 [Haussener, Sophia] Ecole Polytech Fed Lausanne, Inst Engn Mech, CH-1015 Lausanne, Switzerland. [Hu, Shu; Xiang, Chengxiang; Lewis, Nathan S.] CALTECH, Joint Ctr Artificial Photosynthesis, Pasadena, CA 91125 USA. [Weber, Adam Z.] Lawrence Berkeley Natl Lab, Joint Ctr Artificial Photosynthesis, Berkeley, CA 94720 USA. RP Haussener, S (reprint author), Ecole Polytech Fed Lausanne, Inst Engn Mech, CH-1015 Lausanne, Switzerland. FU DOE Energy Innovation Hub; Office of Science; U.S. Department of Energy [DE-SC0004993] FX We acknowledge the Joint Center for Artificial Photosynthesis, a DOE Energy Innovation Hub, supported through the Office of Science of the U.S. Department of Energy under Award Number DE-SC0004993. We thank Harry Atwater for fruitful discussions on temperature-dependent analysis of realistic systems. NR 30 TC 0 Z9 0 U1 0 U2 7 PU ELECTROCHEMICAL SOC INC PI PENNINGTON PA 65 S MAIN ST, PENNINGTON, NJ 08534-2839 USA SN 1938-5862 BN 978-1-60768-447-3; 978-1-62332-093-5 J9 ECS TRANSACTIONS PY 2013 VL 58 IS 2 BP 293 EP 303 DI 10.1149/05802.0293ecst PG 11 WC Electrochemistry; Energy & Fuels SC Electrochemistry; Energy & Fuels GA BJH38 UT WOS:000328212000031 ER PT J AU Lee, E Helt, GA Reese, JT Munoz-Torres, MC Childers, CP Buels, RM Stein, L Holmes, IH Elsik, CG Lewis, SE AF Lee, Eduardo Helt, Gregg A. Reese, Justin T. Munoz-Torres, Monica C. Childers, Chris P. Buels, Robert M. Stein, Lincoln Holmes, Ian H. Elsik, Christine G. Lewis, Suzanna E. TI Web Apollo: a web-based genomic annotation editing platform SO GENOME BIOLOGY LA English DT Article DE GENOME; COLLABORATIVE; EDITOR ID COMMUNITY ANNOTATION; GENE ANNOTATION; LIFE SCIENCES; RNA-SEQ; SEQUENCE; DATABASE; EVOLUTION; RESOURCE; INSIGHTS; BROWSER AB Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current advances in sequencing technology is that there are more and more researchers sequencing new genomes. These researchers require tools to describe the functional features of their newly sequenced genomes. With Web Apollo researchers can use any of the common browsers (for example, Chrome or Firefox) to jointly analyze and precisely describe the features of a genome in real time, whether they are in the same room or working from opposite sides of the world. C1 [Lee, Eduardo; Helt, Gregg A.; Munoz-Torres, Monica C.; Holmes, Ian H.; Lewis, Suzanna E.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Genom Div, Berkeley, CA 94720 USA. [Reese, Justin T.; Childers, Chris P.; Elsik, Christine G.] Univ Missouri, Div Anim Sci, Columbia, MO 65211 USA. [Buels, Robert M.; Holmes, Ian H.] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. [Stein, Lincoln] MaRS Ctr, Ontario Inst Canc Res, Toronto, ON M5G 0A3, Canada. [Stein, Lincoln] Univ Toronto, Dept Mol Genet, Toronto, ON M5R 0A3, Canada. [Elsik, Christine G.] Univ Missouri, Div Plant Sci, Columbia, MO 65211 USA. RP Lewis, SE (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Genom Div, Berkeley, CA 94720 USA. EM selewis@lbl.gov RI Elsik, Christine/C-4120-2017; OI Elsik, Christine/0000-0002-4248-7713; Lewis, Suzanna/0000-0002-8343-612X; Childers, Chris/0000-0002-1253-5550; Holmes, Ian/0000-0001-7639-5369 FU National Institutes of Health from National Institute of General Medical Sciences [5R01GM080203]; National Institutes of Health from National Human Genome Research Institute [5R01HG004483]; Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy [DE-AC02-05CH11231] FX This work was supported by the National Institutes of Health grant numbers 5R01GM080203 from the National Institute of General Medical Sciences and 5R01HG004483 from the National Human Genome Research Institute, and by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. NR 61 TC 44 Z9 44 U1 3 U2 13 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1465-6906 EI 1474-760X J9 GENOME BIOL JI Genome Biol. PY 2013 VL 14 IS 8 AR R93 DI 10.1186/gb-2013-14-8-r93 PG 13 WC Biotechnology & Applied Microbiology; Genetics & Heredity SC Biotechnology & Applied Microbiology; Genetics & Heredity GA 268UF UT WOS:000328195400011 PM 24000942 ER PT S AU Hjalmarson, HP Nguyen, DD Kambour, KE Kouhestani, C Devine, RAB AF Hjalmarson, H. P. Nguyen, D. D. Kambour, K. E. Kouhestani, C. Devine, R. A. B. BE Kar, S VanElshocht, S Kita, K Jagannathan, H Houssa, M Misra, D Landheer, D TI Similarities between Ionizing Radiation Effects and Negative-Bias Temperature Instability (NBTI) in MOSFET Devices SO SEMICONDUCTORS, DIELECTRICS, AND METALS FOR NANOELECTRONICS 11 SE ECS Transactions LA English DT Proceedings Paper CT Symposium on Semiconductors, Dielectrics, and Metals for Nanoelectronics 11 held during the 224th Meeting of the Electrochemical-Society CY OCT 27-NOV 01, 2013 CL San Francisco, CA SP Electrochem Soc, Electrochem Soc, Dielectr Sci & Technol Div, Electrochem Soc, Elect & Photon Div ID SWITCHING OXIDE TRAPS; DOSE-RATE SENSITIVITY; BIPOLAR-TRANSISTORS; CENTERS AB The equivalent role of hydrogen cracking in radiation effects and Negative Bias Temperature Instability (NBTI) is described. A prediction concerning thickness dependence is compared with data. The temperature dependence of interface trap density is explained. C1 [Hjalmarson, H. P.] Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Hjalmarson, HP (reprint author), Sandia Natl Labs, MS-1179, Albuquerque, NM 87185 USA. NR 9 TC 0 Z9 0 U1 1 U2 2 PU ELECTROCHEMICAL SOC INC PI PENNINGTON PA 65 S MAIN ST, PENNINGTON, NJ 08534-2839 USA SN 1938-5862 BN 978-1-60768-452-7; 978-1-62332-098-0 J9 ECS TRANSACTIONS PY 2013 VL 58 IS 7 BP 49 EP 54 DI 10.1149/05807.0049ecst PG 6 WC Electrochemistry; Engineering, Electrical & Electronic; Physics, Applied SC Electrochemistry; Engineering; Physics GA BJG28 UT WOS:000328065400005 ER PT S AU Fiorucci, S Gilchriese, MG Lesko, KT AF Fiorucci, S. Gilchriese, M. G. Lesko, K. T. CA Sanford Underground Res Facility GP IOP TI The Sanford Underground Research Facility at Homestake SO SIXTH SYMPOSIUM ON LARGE TPCS FOR LOW ENERGY RARE EVENT DETECTION SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 6th International Symposium on Large TPCs for Low-Energy Rare-Event Detection CY DEC 17-19, 2012 CL Paris, FRANCE AB The Sanford Underground Research Facility (SURF) at Homestake is presented. The Davis campus is described in detail including the two laboratory modules at the 4850-foot level (>4200 mwe). These modules house the LUX dark matter and MAJORANA DEMONSTRATOR neutrinoless double-beta decay experiments. The Long Baseline Neutrino Experiment plans to place their far detector at SURF. The facility is managed for the US Department of Energy (DOE) by Lawrence Berkeley National Laboratory. The South Dakota Science and Technology Authority (SDSTA) owns and operates the facility. SURF is a dedicated science facility with significant expansion capability. C1 [Fiorucci, S.] Brown Univ, Dept Phys, 182 Hope St, Providence, RI 02912 USA. [Gilchriese, M. G.; Lesko, K. T.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Fiorucci, S (reprint author), Brown Univ, Dept Phys, 182 Hope St, Providence, RI 02912 USA. EM fiorucci@brown.edu NR 8 TC 0 Z9 0 U1 0 U2 1 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2013 VL 460 AR UNSP 012018 DI 10.1088/1742-6596/460/1/012018 PG 5 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA BIF04 UT WOS:000327954400018 ER PT S AU Nygren, DR AF Nygren, D. R. GP IOP TI Columnar recombination: a tool for nuclear recoil directional sensitivity in a xenon-based direct detection WIMP search SO SIXTH SYMPOSIUM ON LARGE TPCS FOR LOW ENERGY RARE EVENT DETECTION SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 6th International Symposium on Large TPCs for Low-Energy Rare-Event Detection CY DEC 17-19, 2012 CL Paris, FRANCE AB A robust signal for sidereal anisotropy in nuclear recoils would support, perhaps more decisively than any other evidence, a discovery claim for a WIMP component of Dark Matter. I present a concept based on columnar recombination in dense xenon gas, sensing nuclear recoil direction relative to a TPC drift field. The central advance is that nuclear recoil directionality information is obtained through a comparison, event-by-event, of the ionization signal and recombination signal that are produced prior to drifting the track ionization. The optimum xenon density for this concept may be near ten bars, unlike conventional techniques that employ track visualization - with severe restrictions on gas density to about 1/10 bar. No restriction is imposed by diffusion during drift, facilitating the realization of a large monolithic room temperature xenon gas Time Projection Chamber at the ton-scale, with unprecedented sensitivity for both directionality and cross-section. Remarkably, the desired operating conditions for 0-nu beta beta Xe-136 experiment may be identical. C1 Lawrence Berkeley Natl Lab, Berkeley, CA 94705 USA. RP Nygren, DR (reprint author), Lawrence Berkeley Natl Lab, MS 50R5008,1 Cyclotron Rd, Berkeley, CA 94705 USA. EM drnygren@lbl.gov NR 4 TC 27 Z9 27 U1 0 U2 0 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2013 VL 460 AR UNSP 012006 DI 10.1088/1742-6596/460/1/012006 PG 7 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA BIF04 UT WOS:000327954400006 ER PT S AU Oliveira, CAB AF Oliveira, C. A. B. CA NEXT Collaboration GP IOP TI Results from the NEXT prototypes SO SIXTH SYMPOSIUM ON LARGE TPCS FOR LOW ENERGY RARE EVENT DETECTION SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 6th International Symposium on Large TPCs for Low-Energy Rare-Event Detection CY DEC 17-19, 2012 CL Paris, FRANCE ID HIGH-PRESSURE XENON AB NEXT-100 is an electroluminescent high pressure Time Projection Chamber currently under construction. It will search for the neutrino-less double beta decay in Xe-136 at the Canfranc Underground Laboratory. NEXT-100 aims to achieve nearly intrinsic energy resolution and to highly suppress background events by taking advantage of the unique properties of xenon in the gaseous phase as the detection medium. In order to prove the principle of operation and to study which are the best operational conditions, two prototypes were constructed: NEXT-DEMO and NEXT-DBDM. In this paper we present the latest results from both prototypes. We report the improvement in terms of light collection (similar to 3x) achieved by coating the walls of NEXT-DEMO with tetraphenyl butadiene (TPB), the outstanding energy resolution of 1 % (Full Width Half Maximum) from NEXT-DBDM as well as the tracking capabilities of this prototype (2.1 mm RMS error for point-like depositions) achieved by using a square array of 8 x 8 SiPMs. C1 [Oliveira, C. A. B.; NEXT Collaboration] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Oliveira, CAB (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, 1 Cyclotron Rd, Berkeley, CA 94720 USA. EM cabdoliveira@lbl.gov NR 12 TC 2 Z9 2 U1 0 U2 0 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2013 VL 460 AR UNSP 012011 DI 10.1088/1742-6596/460/1/012011 PG 8 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA BIF04 UT WOS:000327954400011 ER PT S AU Norman, AG France, RM McMahon, WE Geisz, JF Romero, MJ AF Norman, A. G. France, R. M. McMahon, W. E. Geisz, J. F. Romero, M. J. GP IOP BE Walther, T Hutchison, JL TI The influence of atomic ordering on strain relaxation during the growth of metamorphic solar cells SO 18TH MICROSCOPY OF SEMICONDUCTING MATERIALS CONFERENCE (MSM XVIII) SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 18th International Conference on Microscopy of Semiconducting Materials CY APR 07-11, 2013 CL Univ Oxford, St Catherines Coll, Oxford, ENGLAND SP Royal Microscop Soc HO Univ Oxford, St Catherines Coll ID LAYERS; SEMICONDUCTORS; DISLOCATIONS; GAINP; GA0.5IN0.5P; SURFACTANT; NUCLEATION; EPITAXY AB The occurrence of single variant CuPtB ordering during growth of InGaP graded buffer layer structures on offcut (001) GaAs substrates for inverted metamorphic solar cells is found to have a strong influence on strain relaxation mechanisms. Since the surface-induced CuPtB ordering is metastable in the bulk of the material, a strong preference is observed for the nucleation and glide of 60 degrees type misfit dislocations with Burgers vectors that introduce an antiphase boundary into the ordered structure. This results in an overall epitaxial layer tilt in the opposite sense to that normally observed for the direction of substrate offcut. Furthermore, in InGaP buffer layers graded to InP, a switch in the dislocation glide plane preference back to that normally observed for the direction of substrate offcut is observed as the degree of atomic ordering falls below a critical value. This results in the nucleation and glide of new misfit dislocations resulting in an increase in the threading dislocation density that is found to have a deleterious effect on device efficiency. Understanding the materials science behind this behavior will enable the engineering of more effective, lower threading dislocation density strain relief buffer layers resulting in improved performance of subsequently grown devices. C1 [Norman, A. G.; France, R. M.; McMahon, W. E.; Geisz, J. F.; Romero, M. J.] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Norman, AG (reprint author), Natl Renewable Energy Lab, 15013 Denver West Pkwy, Golden, CO 80401 USA. EM andrew.norman@nrel.gov RI Norman, Andrew/F-1859-2010 OI Norman, Andrew/0000-0001-6368-521X NR 30 TC 1 Z9 1 U1 0 U2 6 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2013 VL 471 AR UNSP 012006 DI 10.1088/1742-6596/471/1/012006 PG 10 WC Microscopy; Physics, Applied SC Microscopy; Physics GA BIF09 UT WOS:000327967600006 ER PT J AU Xue, Q Som, S Senecal, PK Pomraning, E AF Xue, Q. Som, S. Senecal, P. K. Pomraning, E. TI LARGE EDDY SIMULATION OF FUEL-SPRAY UNDER NON-REACTING IC ENGINE CONDITIONS SO ATOMIZATION AND SPRAYS LA English DT Article DE computational fluid dynamics (CFD); grid resolution; internal combustion engines (ICEs); Lagrangian-Eulerian; LES; spray ID DIESEL SPRAY; COMBUSTION CHARACTERISTICS; MESH REFINEMENT; FLOWS; MODEL AB This work examines the Subgrid-scale (SGS) model performance and effects of grid resolution for fuel spray simulations within a Lagrangian-Eulerian framework. The widely studied SGS models for large eddy simulation (LES), namely, (1) Smagorinsky model, (2) one-equation dynamic structure model, and (3) no SGS model, are investigated and compared with the Reynolds averaged Navier-Stokes (RANS) approach using the RNG k - epsilon model. The simulation results are also compared against experimental data. For each turbulence model, simulations are performed with different smallest grid sizes ranging from 500 to 31.25 mu m using adaptive mesh refinement with a base grid size of 1 mm. The corresponding smallest grid size to nozzle diameter ratios are 5-0.3. Two diesel surrogates, namely, n-heptane and n-dodecane, are studied under nonreacting conditions relevant for compression ignition engine applications. Experimental data from Sandia National Laboratory through the Engine Combustion Network (ECN) are used for validation purposes. The qualitative comparisons are conducted for the instantaneous mixture fraction and temperature contours. Quantitatively, predicted global spray characteristics of liquid spray and vapor penetration, as well as radial and axial mixture fraction and axial velocity profiles at different locations, are compared against the measurements. Additionally, five different injection realizations are simulated for all the models, with a smallest grid size of 62.5 mu m to capture cycle-to-cycle variations. The required grid resolution for grid convergence for LES spray simulations is discussed based on the experimental comparisons. With the dramatic increase in computational resources in the past decade, this study indicates that LES is a viable alternative to RANS for engine sprays, since it is more predictive in capturing flow structure and local spray characteristics, with reasonable wall-clock times. C1 [Xue, Q.; Som, S.] Argonne Natl Lab, Div Energy Syst, Argonne, IL 60439 USA. [Senecal, P. K.; Pomraning, E.] Convergent Sci Inc, Middleton, WI 53562 USA. RP Xue, Q (reprint author), Argonne Natl Lab, Div Energy Syst, 9700 S Cass Ave, Argonne, IL 60439 USA. EM qxue@anl.gov FU Argonne, a U.S. Department of Energy Office of Science laboratory [DE-AC02-06CH11357] FX The submitted manuscript has been created by UChicago Argonne, LLC, operator of Argonne National Laboratory (Argonne). Argonne, a U.S. Department of Energy Office of Science laboratory, is operated under Contract No. DE-AC02-06CH11357. The U.S. Government retains for itself, and others acting on its behalf, a paid-up, nonexclusive, irrevocable worldwide license in said article to reproduce, prepare derivative works, distribute copies to the public, and perform publicly and display publicly, by or on behalf of the Government. NR 69 TC 22 Z9 22 U1 2 U2 18 PU BEGELL HOUSE INC PI REDDING PA 50 CROSS HIGHWAY, REDDING, CT 06896 USA SN 1044-5110 EI 1936-2684 J9 ATOMIZATION SPRAY JI Atom. Sprays PY 2013 VL 23 IS 10 BP 925 EP 955 PG 31 WC Engineering, Multidisciplinary; Engineering, Chemical; Engineering, Mechanical; Materials Science, Multidisciplinary; Physics, Applied SC Engineering; Materials Science; Physics GA 264UG UT WOS:000327905900003 ER PT J AU Stoy, PC Dietze, MC Richardson, AD Vargas, R Barr, AG Anderson, RS Arain, MA Baker, IT Black, TA Chen, JM Cook, RB Gough, CM Grant, RF Hollinger, DY Izaurralde, RC Kucharik, CJ Lafleur, P Law, BE Liu, S Lokupitiya, E Luo, Y Munger, JW Peng, C Poulter, B Price, DT Ricciuto, DM Riley, WJ Sahoo, AK Schaefer, K Schwalm, CR Tian, H Verbeeck, H Weng, E AF Stoy, P. C. Dietze, M. C. Richardson, A. D. Vargas, R. Barr, A. G. Anderson, R. S. Arain, M. A. Baker, I. T. Black, T. A. Chen, J. M. Cook, R. B. Gough, C. M. Grant, R. F. Hollinger, D. Y. Izaurralde, R. C. Kucharik, C. J. Lafleur, P. Law, B. E. Liu, S. Lokupitiya, E. Luo, Y. Munger, J. W. Peng, C. Poulter, B. Price, D. T. Ricciuto, D. M. Riley, W. J. Sahoo, A. K. Schaefer, K. Schwalm, C. R. Tian, H. Verbeeck, H. Weng, E. TI Evaluating the agreement between measurements and models of net ecosystem exchange at different times and timescales using wavelet coherence: an example using data from the North American Carbon Program Site-Level Interim Synthesis SO BIOGEOSCIENCES LA English DT Article ID GLOBAL VEGETATION MODEL; DIOXIDE EXCHANGE; BOREAL FORESTS; INTERANNUAL VARIABILITY; PRIMARY PRODUCTIVITY; ATMOSPHERE EXCHANGE; MULTISCALE ANALYSIS; CANOPY NITROGEN; CO2; TEMPERATE AB Earth system processes exhibit complex patterns across time, as do the models that seek to replicate these processes. Model output may or may not be significantly related to observations at different times and on different frequencies. Conventional model diagnostics provide an aggregate view of model-data agreement, but usually do not identify the time and frequency patterns of model-data disagreement, leaving unclear the steps required to improve model response to environmental drivers that vary on characteristic frequencies. Wavelet coherence can quantify the times and timescales at which two time series, for example time series of models and measurements, are significantly different. We applied wavelet coherence to interpret the predictions of 20 ecosystem models from the North American Carbon Program (NACP) Site-Level Interim Synthesis when confronted with eddy-covariance-measured net ecosystem exchange (NEE) from 10 ecosystems with multiple years of available data. Models were grouped into classes with similar approaches for incorporating phenology, the calculation of NEE, the inclusion of foliar nitrogen (N), and the use of model-data fusion. Models with prescribed, rather than prognostic, phenology often fit NEE observations better on annual to interannual timescales in grassland, wetland and agricultural ecosystems. Models that calculated NEE as net primary productivity (NPP) minus heterotrophic respiration (HR) rather than gross ecosystem productivity (GPP) minus ecosystem respiration (ER) fit better on annual timescales in grassland and wetland ecosystems, but models that calculated NEE as GPP minus ER were superior on monthly to seasonal timescales in two coniferous forests. Models that incorporated foliar nitrogen (N) data were successful at capturing NEE variability on interannual (multiple year) timescales at Howland Forest, Maine. The model that employed a model-data fusion approach often, but not always, resulted in improved fit to data, suggesting that improving model parameterization is important but not the only step for improving model performance. Combined with previous findings, our results suggest that the mechanisms driving daily and annual NEE variability tend to be correctly simulated, but the magnitude of these fluxes is often erroneous, suggesting that model parameterization must be improved. Few NACP models correctly predicted fluxes on seasonal and interannual timescales where spectral energy in NEE observations tends to be low, but where phenological events, multi-year oscillations in climatological drivers, and ecosystem succession are known to be important for determining ecosystem function. Mechanistic improvements to models must be made to replicate observed NEE variability on seasonal and interannual timescales. C1 [Stoy, P. C.] Dept Land Resources & Environm Sci, Bozeman, MT 59717 USA. [Dietze, M. C.] Boston Univ, Dept Earth & Environm, Boston, MA 02215 USA. [Richardson, A. D.] Harvard Univ, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USA. [Vargas, R.] Univ Delaware, Delaware Environm Inst, Dept Plant & Soil Sci, Newark, DE 19717 USA. [Barr, A. G.] Atmospher Sci & Technol Directorate, Div Climate Res, Saskatoon, SK S7N 3H5, Canada. [Anderson, R. S.] Univ Montana, Numer Terradynam Simulat Grp, Missoula, MT 59812 USA. [Arain, M. A.] McMaster Univ, Sch Geog & Earth Sci, Hamilton, ON L8S 4K1, Canada. [Arain, M. A.] McMaster Univ, McMaster Ctr Climate Change, Hamilton, ON L8S 4K1, Canada. [Baker, I. T.] Colorado State Univ, Dept Atmospher Sci, Ft Collins, CO 80523 USA. [Black, T. A.] Univ British Columbia, Fac Land & Food Syst, Vancouver, BC V6T 1Z4, Canada. [Chen, J. M.] Univ Toronto, Dept Geog, Toronto, ON M5S 3G3, Canada. [Chen, J. M.] Univ Toronto, Program Planning, Toronto, ON M5S 3G3, Canada. [Cook, R. B.; Ricciuto, D. M.] Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA. [Gough, C. M.] Virginia Commonwealth Univ, Dept Biol, Richmond, VA 23284 USA. [Grant, R. F.] Univ Alberta, Dept Renewable Resources, Edmonton, AB T6G 2E3, Canada. [Hollinger, D. Y.] US Forest Serv, No Res Stn, USDA, Durham, NH 03824 USA. [Izaurralde, R. C.] Pacific NW Natl Lab, College Pk, MD 20740 USA. [Izaurralde, R. C.] Univ Maryland, College Pk, MD 20740 USA. [Kucharik, C. J.] Univ Wisconsin, Dept Agron, Madison, WI 53706 USA. [Kucharik, C. J.] Univ Wisconsin, Nelson Inst, Ctr Sustainabil & Global Environm, Madison, WI 53706 USA. [Lafleur, P.] Trent Univ, Dept Geog, Peterborough, ON K9J 7B8, Canada. [Law, B. E.] Oregon State Univ, Dept Forest Ecosyst & Soc, Corvallis, OR 97331 USA. [Liu, S.] US Geol Survey USGS, Earth Resources Observat & Sci EROS Ctr, Sioux Falls, SD 57198 USA. [Lokupitiya, E.] Univ Colombo, Dept Zool, Colombo 03, Sri Lanka. [Luo, Y.] Univ Oklahoma, Dept Bot & Microbiol, Norman, OK 73019 USA. [Munger, J. W.] Harvard Univ, Sch Engn & Appl Sci, Cambridge, MA 02138 USA. [Munger, J. W.] Harvard Univ, Dept Earth & Planetary Sci, Cambridge, MA 02138 USA. [Peng, C.] Univ Quebec, Dept Biol Sci, Montreal, PQ H3C 3P8, Canada. [Poulter, B.] Lab Sci Climat & Environm, Gif Sur Yvette, France. [Price, D. T.] Canadian Forest Serv, No Forestry Ctr, Edmonton, AB T6H 3S5, Canada. [Riley, W. J.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. [Sahoo, A. K.] Princeton Univ, Dept Civil & Environm Engn, Princeton, NJ 08544 USA. [Schaefer, K.] Univ Colorado, Natl Snow & Ice Data Ctr NSIDC, Boulder, CO 80309 USA. [Schwalm, C. R.] No Arizona Univ, Sch Earth Sci & Environm Sustainabil, Flagstaff, AZ 86001 USA. [Tian, H.] Auburn Univ, Sch Forestry & Wildlife Sci, Auburn, AL 36849 USA. [Verbeeck, H.] Univ Ghent, Lab Plant Ecol, B-9000 Ghent, Belgium. [Weng, E.] Princeton Univ, Dept Ecol & Evolutionary Biol, Princeton, NJ 08544 USA. RP Stoy, PC (reprint author), Dept Land Resources & Environm Sci, Bozeman, MT 59717 USA. EM paul.stoy@montana.edu RI Dietze, Michael/A-5834-2009; Weng, Ensheng/E-4390-2012; Richardson, Andrew/F-5691-2011; Tian, Hanqin/A-6484-2012; Munger, J/H-4502-2013; Vargas, Rodrigo/C-4720-2008; Law, Beverly/G-3882-2010; Hollinger, David/G-7185-2012; Barr, Alan/H-9939-2014; Riley, William/D-3345-2015; Ricciuto, Daniel/I-3659-2016 OI Cook, Robert/0000-0001-7393-7302; Poulter, Benjamin/0000-0002-9493-8600; Dietze, Michael/0000-0002-2324-2518; Weng, Ensheng/0000-0002-1858-4847; Richardson, Andrew/0000-0002-0148-6714; Tian, Hanqin/0000-0002-1806-4091; Munger, J/0000-0002-1042-8452; Vargas, Rodrigo/0000-0001-6829-5333; Law, Beverly/0000-0002-1605-1203; Grant, Robert/0000-0002-8890-6231; Riley, William/0000-0002-4615-2304; Ricciuto, Daniel/0000-0002-3668-3021 FU US National Aeronautics and Space Administration (NASA) [NNX06AE65G]; US National Oceanic and Atmospheric Administration (NOAA) [NA07OAR4310115]; US National Science Foundation (NSF) [OPP-0352957] FX First and foremost, we wish to thank all of the researchers involved in eddy covariance data collection and curation, and in model development and testing. P. C. Stoy thanks Matteo Detto and Aslak Grinsted for helpful discussions and code examples regarding wavelet coherence and the National Science Foundation (Scaling ecosystem function: Novel Approaches from MaxEnt and Multiresolution, DBI # 1021095). We would like to thank the North American Carbon Program Site-Level Interim Synthesis team, the Modeling and Synthesis Thematic Data Center, and the Oak Ridge National Laboratory Distributed Active Archive Center, and Larry Flanagan for collecting, organizing, and distributing the model output and flux observations required for this analysis. We also thank Robert Bemis for creating the MATLAB code that followed the suggestions of Light and Bartlein (2004) for improved use of color in images. This study was in part supported by the US National Aeronautics and Space Administration (NASA) grant NNX06AE65G, the US National Oceanic and Atmospheric Administration (NOAA) grant NA07OAR4310115, and the US National Science Foundation (NSF) grant OPP-0352957 to the University of Colorado at Boulder. This study was part of the North American Carbon Program. NR 87 TC 9 Z9 9 U1 5 U2 45 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 1726-4170 EI 1726-4189 J9 BIOGEOSCIENCES JI Biogeosciences PY 2013 VL 10 IS 11 BP 6893 EP 6909 DI 10.5194/bg-10-6893-2013 PG 17 WC Ecology; Geosciences, Multidisciplinary SC Environmental Sciences & Ecology; Geology GA 263NG UT WOS:000327814700010 ER PT J AU Koven, CD Riley, WJ Subin, ZM Tang, JY Torn, MS Collins, WD Bonan, GB Lawrence, DM Swenson, SC AF Koven, C. D. Riley, W. J. Subin, Z. M. Tang, J. Y. Torn, M. S. Collins, W. D. Bonan, G. B. Lawrence, D. M. Swenson, S. C. TI The effect of vertically resolved soil biogeochemistry and alternate soil C and N models on C dynamics of CLM4 SO BIOGEOSCIENCES LA English DT Article ID EARTH SYSTEM MODELS; ORGANIC-MATTER; CARBON-CYCLE; TEMPERATURE SENSITIVITY; TERRESTRIAL BIOSPHERE; ROOT DISTRIBUTIONS; GENERALIZED-MODEL; RESIDENCE TIMES; GRASSLAND SOILS; STEADY-STATE AB Soils are a crucial component of the Earth system; they comprise a large portion of terrestrial carbon stocks, mediate the supply and demand of nutrients, and influence the overall response of terrestrial ecosystems to perturbations. In this paper, we develop a new soil biogeochemistry model for the Community Land Model, version 4 (CLM4). The new model includes a vertical dimension to carbon (C) and nitrogen (N) pools and transformations, a more realistic treatment of mineral N pools, flexible treatment of the dynamics of decomposing carbon, and a radiocarbon (C-14) tracer. We describe the model structure, compare it with site-level and global observations, and discuss the overall effect of the revised soil model on Community Land Model (CLM) carbon dynamics. Site-level comparisons to radiocarbon and bulk soil C observations support the idea that soil C turnover is reduced at depth beyond what is expected from environmental controls for temperature, moisture, and oxygen that are considered in the model. In better agreement with observations, the revised soil model predicts substantially more and older soil C, particularly at high latitudes, where it resolves a permafrost soil C pool. In addition, the 20th century-C dynamics of the model are more realistic than those of the baseline model, with more terrestrial C uptake over the 20th century due to reduced N downregulation and longer turnover times for decomposing C. C1 [Koven, C. D.; Riley, W. J.; Subin, Z. M.; Tang, J. Y.; Torn, M. S.; Collins, W. D.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. [Bonan, G. B.; Lawrence, D. M.; Swenson, S. C.] Natl Ctr Atmospher Res, Boulder, CO 80307 USA. RP Koven, CD (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. EM cdkoven@lbl.gov RI Lawrence, David/C-4026-2011; Collins, William/J-3147-2014; Tang, Jinyun/M-4922-2013; Riley, William/D-3345-2015; Torn, Margaret/D-2305-2015; Koven, Charles/N-8888-2014 OI Lawrence, David/0000-0002-2968-3023; Collins, William/0000-0002-4463-9848; Tang, Jinyun/0000-0002-4792-1259; Riley, William/0000-0002-4615-2304; Koven, Charles/0000-0002-3367-0065 FU Office of Science, Office of Biological and Environmental Research of the US Department of Energy [DE-AC02-05CH11231]; Office of Science of the US Department of Energy [DE-AC02-05CH11231] FX This research was supported by the Director, Office of Science, Office of Biological and Environmental Research of the US Department of Energy under Contract No. DE-AC02-05CH11231 as part of their Climate and Earth System Modeling Program and used resources of the National Energy Research Scientific Computing Center (NERSC), also supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. Thanks to Abby Swann for discussion about improving model spinup performance, and to Peter Thornton for several discussions about the CLM-CN model. Thanks to Chris Jones, Philippe Ciais, and an anonymous reviewer for comments that improved the manuscript. NR 91 TC 77 Z9 77 U1 10 U2 81 PU COPERNICUS GESELLSCHAFT MBH PI GOTTINGEN PA BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY SN 1726-4170 EI 1726-4189 J9 BIOGEOSCIENCES JI Biogeosciences PY 2013 VL 10 IS 11 BP 7109 EP 7131 DI 10.5194/bg-10-7109-2013 PG 23 WC Ecology; Geosciences, Multidisciplinary SC Environmental Sciences & Ecology; Geology GA 263NG UT WOS:000327814700023 ER PT J AU Dong, YC Kapilashrami, M Zhang, YF Guo, JH AF Dong, Yucai Kapilashrami, Mukes Zhang, Yanfeng Guo, Jinghua TI Morphology change and band gap narrowing of hierarchical TiO2 nanostructures induced by fluorine doping SO CRYSTENGCOMM LA English DT Article ID ENHANCED PHOTOCATALYTIC ACTIVITY; VISIBLE-LIGHT PHOTOCATALYSIS; HOLLOW MICROSPHERES; TITANIUM-DIOXIDE; SONOCHEMICAL FABRICATION; ANATASE TIO2; MECHANISM; NANORODS; SURFACE; GROWTH AB A series of TiO2 hierarchical nanostructures were synthesized by a facile template-free hydrothermal method in the presence of sodium fluoride (NaF) using titanium tetrachloride (TiCl4) as precursor. The pompon-like and football-like TiO2 hierarchical microspheres are composed of aligned rutile and anatase nanoparticles. The TiO2 nanostructures are comprised of oriented anatase nanoparticles. It is found that the doping concentration of NaF plays an important role in controlling the morphology and structure of the hierarchical nanoarchitectures. A sequential phase transition is observed with increasing dopant concentration: rutile. rutile -> anatase + anatase -> X-ray photoelectron spectroscopy (XPS) and X-ray absorption near edge structure (XANES) results indicated that F ions physically absorbed on the surface of TiO2 and incorporated into TiO2 crystal lattice. For the first time, a sequential red shift of absorption band edge of F-doped TiO2 is observed with increasing the concentration of NaF as compared to pure TiO2. The band gap could be tuned from 3.0 eV to 2.2 eV, which depends on the fluorine doping concentration. It is found that F-doped TiO2 nanostructures exhibit higher photocatalytic activity than that of pure TiO2 under visible light irradiation. C1 [Dong, Yucai; Zhang, Yanfeng] Hebei Normal Univ, Coll Chem & Mat Sci, Hebei 050024, Peoples R China. [Kapilashrami, Mukes; Zhang, Yanfeng; Guo, Jinghua] Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Dong, YC (reprint author), Hebei Normal Univ, Coll Chem & Mat Sci, Hebei 050024, Peoples R China. EM zhangyanfeng@mail.hebtu.edu.cn; jguo@lbl.gov FU National Nature Science Foundation of China [11179029]; National Synchrotron Radiation Laboratory of China; Service Center for Experts and Scholars of Hebei Province of China; Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy [DE-AC02-05CH11231] FX This work was supported by Large Scientific Facilities Joint Fund of the National Nature Science Foundation of China (no. 11179029), National Synchrotron Radiation Laboratory of China and the Service Center for Experts and Scholars of Hebei Province of China. The work at the Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under contract no. DE-AC02-05CH11231. NR 42 TC 8 Z9 8 U1 4 U2 41 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1466-8033 J9 CRYSTENGCOMM JI Crystengcomm PY 2013 VL 15 IS 48 BP 10657 EP 10664 DI 10.1039/c3ce41390j PG 8 WC Chemistry, Multidisciplinary; Crystallography SC Chemistry; Crystallography GA 258GE UT WOS:000327446500033 ER PT S AU Ma, BH Narayanan, M Liu, SS Hu, ZQ Balachandran, U AF Ma, Beihai Narayanan, Manoj Liu, Shanshan Hu, Zhongqiang Balachandran, Uthamalingam GP IOP TI Development of PLZT film-on-foil capacitors with high energy density SO DIELECTRICS 2013 SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 42nd Dielectrics-Group Conference CY APR 10-12, 2013 CL Univ Reading, Reading, ENGLAND SP Dielectr Grp, Inst Phys HO Univ Reading ID THIN-FILMS; DIELECTRIC-PROPERTIES; METAL FOILS; STORAGE; BREAKDOWN AB Ceramic thin films with high dielectric constant and high breakdown strength hold special promise for advanced electronics applications. We deposited lanthanum-doped lead zirconate titanate (PLZT) on base metal foils (film-on-foils) by chemical solution deposition. The PLZT film-on-foils were characterized over a wide temperature range between room temperature and 200 C. For approximate to 2-mu m-thick PLZT films grown on LaNO3-buffered nickel foils at room temperature, we measured a dielectric constant of approximate to 1300, dielectric loss of approximate to 0.07, remanent polarization of approximate to 26 mu C/cm(2), coercive field of approximate to 29 kV/cm, leakage current density of approximate to 9.2 x 10(-9) A/cm(2), and energy density of approximate to 67 J/cm(3). Dielectric breakdown strength was determined to be approximate to 2.6 x 10(6) V/cm by Weibull analysis. These and other results reported here indicate that electronic devices with film-on-foil capacitors would possess higher performance, improved reliability, and enhanced volumetric and gravimetric efficiencies compared with traditional dielectric capacitors. C1 [Ma, Beihai; Narayanan, Manoj; Liu, Shanshan; Hu, Zhongqiang; Balachandran, Uthamalingam] Argonne Natl Lab, Div Energy Syst, Argonne, IL 60439 USA. RP Ma, BH (reprint author), Argonne Natl Lab, Div Energy Syst, 9700 S Cass Ave, Argonne, IL 60439 USA. EM bma@anl.gov RI Hu, Zhongqiang/I-2528-2012; Ma, Beihai/I-1674-2013 OI Hu, Zhongqiang/0000-0002-7534-0427; Ma, Beihai/0000-0003-3557-2773 NR 19 TC 1 Z9 1 U1 1 U2 17 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2013 VL 472 DI 10.1088/1742-6596/472/1/012004 PG 6 WC Engineering, Electrical & Electronic; Physics, Applied SC Engineering; Physics GA BIF02 UT WOS:000327951700004 ER PT J AU Pavuk, M Dutton, N AF Pavuk, Marian Dutton, Nina BE Carpenter, DO TI Cardiovascular Disease and Hypertension SO EFFECTS OF PERSISTENT AND BIOACTIVE ORGANIC POLLUTANTS ON HUMAN HEALTH LA English DT Article; Book Chapter ID NUTRITION EXAMINATION SURVEY; ENDOTHELIUM-DEPENDENT CONTRACTIONS; PERSISTENT ORGANIC POLLUTANTS; TOXIC EQUIVALENCY FACTORS; CAUSE-SPECIFIC MORTALITY; CHEMICAL CORPS VIETNAM; AGENT-ORANGE EXPOSURE; 15-YEAR FOLLOW-UP; POLYCHLORINATED-BIPHENYLS; CANCER INCIDENCE AB Background: Persistent organic pollutants (POPs) have been implicated in altering a variety of physiological processes related to cardiovascular function. Occupationally and accidentally exposed cohorts have been studied for mortality from cardiovascular disease (CVD) and exposure to dioxins since the 1970s. Recently, relationships between hypertension and low-level exposure to polychlorinated biphenyls (PCBs) and other POPs have been intensely studied. Objectives: This chapter reviews evidence for relationships between dioxin exposure and morbidity from CVD and ischemic heart disease (IHD), focusing on recent cohort updates. Associations between hypertension and exposure to PCBs and other POPs are evaluated in studies of the general U. S. population and populations near contaminated sites. Discussion: Results of CVD mortality studies in dioxin-exposed cohorts using external comparisons found little evidence of association. In internal comparison studies with detailed exposure assessments, more evidence of increased IHD and CVD mortality was reported. Two cohort studies with proper adjustment for major CVD risk factors showed little or no association with CVD mortality. In hypertension studies, effects of dioxin-like or non-dioxin-like PCB congeners could not be separated clearly. Conclusions: Mixed results of studies in dioxin-exposed cohorts do not support a strong association between dioxin exposure and cardiovascular mortality in humans. Suggestive findings on PCBs and other POPs and hypertension require confirmation in follow-up studies. C1 [Pavuk, Marian] CDC Atlanta, ATSDR CDC, Atlanta, GA USA. [Dutton, Nina] Oak Ridge Inst Sci & Educ, Res Participat Program, Atlanta, GA USA. [Dutton, Nina] ATSDR CDC, Atlanta, GA USA. RP Pavuk, M (reprint author), CDC Atlanta, ATSDR CDC, Atlanta, GA USA. NR 90 TC 0 Z9 0 U1 0 U2 1 PU BLACKWELL SCIENCE PUBL PI OXFORD PA OSNEY MEAD, OXFORD OX2 0EL, ENGLAND BN 978-1-118-15926-2 PY 2013 BP 143 EP 173 D2 10.1002/9781118679654 PG 31 WC Public, Environmental & Occupational Health; Toxicology SC Public, Environmental & Occupational Health; Toxicology GA BID81 UT WOS:000327747000007 ER PT J AU Abdel-Fattah, TM Williams, PA Wincheski, RA Shams, QA AF Abdel-Fattah, Tarek M. Williams, Phillip A. Wincheski, Russell A. Shams, Qamar A. TI Catalyst Design Using Nanoporous Iron for the Chemical Vapor Deposition Synthesis of Single-Walled Carbon Nanotubes SO JOURNAL OF NANOMATERIALS LA English DT Article ID MOLECULAR-SIEVES AB Single-walled carbon nanotubes (SWNTs) have been synthesized via a novel chemical vapor deposition (CVD) approach utilizing nanoporous, iron-supported catalysts. Stable aqueous dispersions of the CVD-grown nanotubes using an anionic surfactant were also obtained. The properties of the as-produced SWNTs were characterized through atomic force microscopy and Raman spectroscopy and compared with purified SWNTs produced via the high-pressure CO (HiPCO) method as a reference, and the nanotubes were observed with greater lengths than those of similarly processed HiPCO SWNTs. C1 [Abdel-Fattah, Tarek M.] Christopher Newport Univ, Thomas Jefferson Natl Accelerator Facil, Appl Res Ctr, Newport News, VA 23606 USA. [Abdel-Fattah, Tarek M.] Christopher Newport Univ, Dept Mol Biol & Chem, Newport News, VA 23606 USA. [Williams, Phillip A.; Wincheski, Russell A.] NASA, Langley Res Ctr, Nondestruct Evaluat Sci Branch, Hampton, VA 23681 USA. [Shams, Qamar A.] NASA, Langley Res Ctr, Aeronaut Syst Engn Branch, Hampton, VA 23681 USA. RP Abdel-Fattah, TM (reprint author), Christopher Newport Univ, Thomas Jefferson Natl Accelerator Facil, Appl Res Ctr, Newport News, VA 23606 USA. EM fattah@cnu.edu NR 27 TC 0 Z9 0 U1 1 U2 7 PU HINDAWI PUBLISHING CORPORATION PI NEW YORK PA 410 PARK AVENUE, 15TH FLOOR, #287 PMB, NEW YORK, NY 10022 USA SN 1687-4110 EI 1687-4129 J9 J NANOMATER JI J. Nanomater. PY 2013 AR 421503 DI 10.1155/2013/421503 PG 7 WC Nanoscience & Nanotechnology; Materials Science, Multidisciplinary SC Science & Technology - Other Topics; Materials Science GA 265OP UT WOS:000327961800001 ER PT S AU Xie, JQ Demarteau, M Wagner, R May, E Jiang, Z Ruiz-Oses, M Liang, X Ben-Zvi, I Attenkofer, K Schubert, S Smedley, J Wong, J Padmore, H AF Xie, Junqi Demarteau, Marcel Wagner, Robert May, Edward Jiang, Zhang Ruiz-Oses, Miguel Liang, Xue Ben-Zvi, Ilan Attenkofer, Klaus Schubert, Susan Smedley, John Wong, Jared Padmore, Howard BE Yin, S Guo, R TI Real Time Evolution of Antimony Deposition for High Performance Alkali Photocathode Development SO PHOTONIC FIBER AND CRYSTAL DEVICES: ADVANCES IN MATERIALS AND INNOVATIONS IN DEVICE APPLICATIONS VII SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on Photonic Fiber and Crystal Devices - Advances in Materials and Innovations in Device Applications VII CY AUG 25-26, 2013 CL San Diego, CA SP SPIE DE Photomultiplier tubes; PMTs; Photocathode; Antimony; Alkali Antimonide; X-ray scattering AB The development of X-ray techniques opens new opportunities for real-time in-situ study of photocathode growth process in details. The initial ultra thin Sb films during photocathode process were investigated on multiple substrates based on different applications. The real-time X-ray scattering and post-growth X-ray reflectivity and diffraction measurement were performed and analyzed. Experiment results indicate that Sb deposition performs a phase change from amorphous to crystalline, the critical thicknesses are different on B33 float glass, Si and Mo. Two methods were applied for film thickness calculation from X-ray scattering data, and they agree well with thickness monitor result. Sb films deposited on different substrates show similar final film roughnesses. The real time x-ray study indicates that the initial Sb layer deposition process on different substrate has different structure during deposition, the optimized thickness of the initial Sb layer may varies depends on the substrate. This study also paved the road for further study of the more complex alkali metal vapor diffusion process in photocathode growth. C1 [Xie, Junqi; Demarteau, Marcel; Wagner, Robert; May, Edward; Jiang, Zhang] Argonne Natl Lab, Lemont, IL 60439 USA. RP Xie, JQ (reprint author), Argonne Natl Lab, 9700 S Cass Ave, Lemont, IL 60439 USA. EM jxie@anl.gov RI Jiang, Zhang/A-3297-2012 OI Jiang, Zhang/0000-0003-3503-8909 NR 12 TC 1 Z9 1 U1 0 U2 4 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-9697-3 J9 PROC SPIE PY 2013 VL 8847 AR 884705 DI 10.1117/12.2024424 PG 7 WC Crystallography; Optics SC Crystallography; Optics GA BHV63 UT WOS:000326750500005 ER PT J AU Huang, Q Choi, DW Cosimbescu, L Lemmon, JP AF Huang, Qian Choi, Daiwon Cosimbescu, Lelia Lemmon, John P. TI Multi-electron redox reaction of an organic radical cathode induced by a mesopore carbon network with nitroxide polymers SO PHYSICAL CHEMISTRY CHEMICAL PHYSICS LA English DT Article ID RECHARGEABLE LITHIUM BATTERIES; ELECTROCHEMICAL PROPERTIES; ELECTRODE MATERIALS; ION BATTERIES; PTMA CATHODE; KETJEN BLACK; PERFORMANCE; INTERFACE; LAYER AB An organic radical based composite cathode comprised of poly(2,2,6,6-tetramethylpiperidinyloxy-4-yl methacrylate) (PTMA)-Ketjenblack was developed by a simple solvent-less electrode fabrication method. The composite cathode demonstrated a two-electron redox reaction of PTMA that is from an aminoxy anion (n-type) via a radical to an oxoammonium cation (p-type) with the corresponding redox potential at 2.8-3.1 V and 3.5-3.7 V vs. Li/Li+ when evaluated in lithium half cells. Moreover, the PTMAKetjenblack composite electrode exhibits fast electrode reaction kinetics and an enhanced solid electrolyte interface by cyclic voltammetry and electrochemical impedance spectroscopy measurements. These improved electrochemical properties contribute to increased capacity (300 mA h g(-1)), a high rate (50% capacity retention after 100 C rate excursions) and a long cycle life in the cell performance evaluations. Morphological and compositional characterization indicates a unique mesopore network of Ketjenblack with the PTMA matrix, which highly facilitates the interaction between the conductive media and the radical species, resulting in the performance enhancement of the PTMA-Ketjenblack composite cathode. C1 [Huang, Qian; Choi, Daiwon; Cosimbescu, Lelia; Lemmon, John P.] Pacific NW Natl Lab, Richland, WA 99354 USA. RP Lemmon, JP (reprint author), Pacific NW Natl Lab, 908 Battelle Blvd,POB 999, Richland, WA 99354 USA. EM John.Lemmon@pnnl.gov RI Choi, Daiwon/B-6593-2008 FU Defense Advanced Research Projects Agency (DARPA) of the U. S. Department of Defense [hr001132084] FX This work was supported by the Defense Advanced Research Projects Agency (DARPA) of the U. S. Department of Defense under Contract No. hr001132084. The authors would thank Zimin Nie of the Pacific Northwest National Laboratory (PNNL) for the BET measurement, thank Chongmin Wang, Vijayakumar Murugesan and Manjula Nandasiri of the Environmental Molecular Sciences Laboratory (EMSL) for the TEM and XPS characterization, and thank In-tae Bae of the State University of New York at Binghamton for the SEM characterization. NR 27 TC 11 Z9 11 U1 1 U2 35 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1463-9076 EI 1463-9084 J9 PHYS CHEM CHEM PHYS JI Phys. Chem. Chem. Phys. PY 2013 VL 15 IS 48 BP 20921 EP 20928 DI 10.1039/c3cp54358g PG 8 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 258NW UT WOS:000327467000016 PM 24202318 ER PT J AU Haranczyk, M Lin, LC Lee, K Martin, RL Neaton, JB Smit, B AF Haranczyk, Maciej Lin, Li-Chiang Lee, Kyuho Martin, Richard L. Neaton, Jeffrey B. Smit, Berend TI Methane storage capabilities of diamond analogues SO PHYSICAL CHEMISTRY CHEMICAL PHYSICS LA English DT Article ID METAL-ORGANIC FRAMEWORKS; GENERALIZED GRADIENT APPROXIMATION; CRYSTALLINE POROUS MATERIALS; AUGMENTED-WAVE METHOD; HIGH-SURFACE-AREA; POLYMER NETWORKS; MOLECULAR SIMULATIONS; CARBON-DIOXIDE; DESIGN; ENERGY AB Methane can be an alternative fuel for vehicular usage provided that new porous materials are developed for its efficient adsorption-based storage. Herein, we search for materials for this application within the family of diamond analogues. We used density functional theory to investigate structures in which tetrahedral C atoms of diamond are separated by-CC-or-BN-groups, as well as ones involving substitution of tetrahedral C atoms with Si and Ge atoms. The adsorptive and diffusive properties of methane are studied using classical molecular simulations. Our results suggest that the all-carbon structure has the highest volumetric methane uptake of 280 VSTP/V at p = 35 bar and T = 298 K. However, it suffers from limited methane diffusion. Alternatively, the considered Si and Ge-containing analogies have fast diffusive properties but their adsorption is lower, ca. 172-179 VSTP/V, at the same conditions. C1 [Haranczyk, Maciej; Martin, Richard L.; Smit, Berend] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. [Lin, Li-Chiang; Lee, Kyuho; Smit, Berend] Univ Calif Berkeley, Dept Chem & Biomol Engn, Berkeley, CA 94720 USA. [Lee, Kyuho; Neaton, Jeffrey B.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Mol Foundry, Berkeley, CA 94720 USA. [Smit, Berend] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. RP Haranczyk, M (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, 1 Cyclotron Rd,MS 50F-1650, Berkeley, CA 94720 USA. EM mharanczyk@lbl.gov RI Smit, Berend/B-7580-2009; Haranczyk, Maciej/A-6380-2014; Martin, Richard/C-7129-2013; Lee, Kyuho/B-9370-2008; Lin, Li-Chiang/J-8120-2014; Neaton, Jeffrey/F-8578-2015; Foundry, Molecular/G-9968-2014; OI Smit, Berend/0000-0003-4653-8562; Haranczyk, Maciej/0000-0001-7146-9568; Martin, Richard/0000-0001-9858-2608; Lee, Kyuho/0000-0001-9325-3717; Neaton, Jeffrey/0000-0001-7585-6135; Lin, Li-Chiang/0000-0002-2821-9501 FU ARPA-E MOVE program [DE-AR0000249]; U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences [DE-FG0212ER16362]; Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy [DE-AC02-05CH11231]; Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231] FX The authors would like to thank Dr James Stewart for providing the MOPAC license. M. H. and R. L. M. were supported by ARPA-E MOVE program under Award Number DE-AR0000249 while L.-C.L., K.L., and B. S. were supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences under Award DE-FG0212ER16362. Portions of this work was done at the Lawrence Berkeley National Laboratory and at the Molecular Foundry, which are supported by the Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. This research used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. NR 33 TC 4 Z9 4 U1 0 U2 11 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1463-9076 EI 1463-9084 J9 PHYS CHEM CHEM PHYS JI Phys. Chem. Chem. Phys. PY 2013 VL 15 IS 48 BP 20937 EP 20942 DI 10.1039/c3cp53814a PG 6 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 258NW UT WOS:000327467000018 PM 24202112 ER PT J AU Kim, JB Weichman, ML Neumark, DM AF Kim, Jongjin B. Weichman, Marissa L. Neumark, Daniel M. TI High-resolution anion photoelectron spectra of TiO2-, ZrO2-, and HfO2- obtained by slow electron velocity- map imaging SO PHYSICAL CHEMISTRY CHEMICAL PHYSICS LA English DT Article ID METAL-OXIDE CLUSTERS; EFFECTIVE CORE POTENTIALS; TITANIUM OXYGEN CLUSTERS; AB-INITIO; VIBRATIONAL SPECTROSCOPY; MOLECULAR-STRUCTURES; ROTATIONAL SPECTRUM; (TIO2)(N) N=1-4; NEGATIVE-IONS; TRANSITION AB High- resolution anion photoelectron spectra of the Group 4 metal dioxides TiO2-, ZrO2-, and HfO2- are reported, using slow electron velocity- map imaging (SEVI) combined with ion trapping and cryogenic cooling. The resulting spectra exhibit sub- meV resolution with no congestion from hot bands. Electron affinities are obtained with greater precision than in previous photodetachment experiments, with values of 1.5892(5) eV, 1.6397(5) eV, and 2.1045(5) eV, for TiO2, ZrO2, and HfO2, respectively. We obtain precise values for all of the vibrational frequencies of the neutral X(-1)A(1) ground states, except for the n3 mode of HfO2. Weak activity observed in the forbidden n(3) mode for TiO2 and ZrO2 is attributed to Herzberg- Teller coupling to the A(-2)B(2) excited state. C1 [Kim, Jongjin B.; Weichman, Marissa L.; Neumark, Daniel M.] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. [Neumark, Daniel M.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Chem Sci, Berkeley, CA 94720 USA. RP Neumark, DM (reprint author), Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. EM dneumark@berkeley.edu RI Neumark, Daniel/B-9551-2009; OI Neumark, Daniel/0000-0002-3762-9473; Weichman, Marissa/0000-0002-2551-9146 FU Air Force Office of Scientific Research [FA9550-12-1-0160]; Defense University Research Instrumentation Program [FA9550-11-1-0300] FX This research is funded by the Air Force Office of Scientific Research under Grant No. FA9550-12-1-0160 and the Defense University Research Instrumentation Program under Grant No. FA9550-11-1-0300. M. L. W. thanks the National Science Foundation for a graduate research fellowship. NR 87 TC 13 Z9 13 U1 2 U2 27 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1463-9076 EI 1463-9084 J9 PHYS CHEM CHEM PHYS JI Phys. Chem. Chem. Phys. PY 2013 VL 15 IS 48 BP 20973 EP 20981 DI 10.1039/c3cp54084g PG 9 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 258NW UT WOS:000327467000023 PM 24213351 ER PT J AU Mukherjee, A Kokhan, O Huang, J Niklas, J Chen, LX Tiede, DM Mulfort, KL AF Mukherjee, Anusree Kokhan, Oleksandr Huang, Jier Niklas, Jens Chen, Lin X. Tiede, David M. Mulfort, Karen L. TI Detection of a charge-separated catalyst precursor state in a linked photosensitizer-catalyst assembly SO PHYSICAL CHEMISTRY CHEMICAL PHYSICS LA English DT Article ID ELECTROCATALYTIC HYDROGEN EVOLUTION; PHOTOSYNTHETIC REACTION-CENTER; ELECTRON-TRANSFER; PHOTOCATALYTIC SYSTEMS; COBALOXIME CATALYSTS; MOLECULAR-HYDROGEN; FUNCTIONAL MODELS; COMPLEXES; COBALT; WATER AB We have designed two new supramolecular assemblies based on Co(II)-templated coordination of Ru(bpy)(3)(2+) (bpy = 2,2'-bipyridyl) analogues as photosensitizers and electron donors to a cobaloxime macrocycle, which are of interest as proton reduction catalysts. The self-assembled photocatalyst precursors were structurally characterized by Co K-edge X-ray absorption spectroscopy and solution-phase X-ray scattering. Visible light excitation of one of the assemblies has yielded instantaneous electron transfer and charge separation to form a transient Co(I) state which persists for 26 ps. The development of a linked photosensitizer-cobaloxime architecture supporting efficient Co(I) charge transfer is significant since it is mechanistically critical as the first photo-induced electron transfer step for hydrogen production, and has not been detected in previous photosensitizer-cobaloxime linked dyad assemblies. X-band EPR spectroscopy has revealed that the Co(II) centres of both assemblies are high spin, in contrast to most previously described cobaloximes, and likely plays an important role in facilitating photoinduced charge separation. Based on the results obtained from ultrafast and nanosecond transient absorption optical spectroscopies, we propose that charge recombination occurs through multiple ligand states present within the photosensitizer modules. The studies presented here will enhance our understanding of supramolecular photocatalyst assembly and direct new designs for artificial photosynthesis. C1 [Mukherjee, Anusree; Kokhan, Oleksandr; Huang, Jier; Niklas, Jens; Chen, Lin X.; Tiede, David M.; Mulfort, Karen L.] Argonne Natl Lab, Div Chem Sci & Engn, Argonne, IL 60439 USA. [Chen, Lin X.] Northwestern Univ, Dept Chem, Evanston, IL 60208 USA. RP Chen, LX (reprint author), Argonne Natl Lab, Div Chem Sci & Engn, 9700 S Cass Ave, Argonne, IL 60439 USA. EM lchen@anl.gov; mulfort@anl.gov RI Niklas, Jens/I-8598-2016; OI Niklas, Jens/0000-0002-6462-2680; Kokhan, Oleksandr/0000-0001-9867-8044 FU Division of Chemical Sciences, Biosciences, Office of Basic Energy Sciences of the U.S. Department of Energy [DE-AC02-06CH11357]; U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences [DE-AC02-06CH11357]; U.S. DOE [DE-AC02-06CH11357] FX We acknowledge funding from the Division of Chemical Sciences, Biosciences, Office of Basic Energy Sciences of the U.S. Department of Energy through Grant DE-AC02-06CH11357 for support of this work. Use of the Center for Nanoscale Materials was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. We thank Dr David J. Gosztola for his expert assistance at the transient absorption facility at CNM. Use of beamlines 12-BM (XAS) and 12-ID-B (X-ray scattering)