FN Thomson Reuters Web of Science™ VR 1.0 PT J AU Zipper, LE Aristide, X Bishop, DP Joshi, I Kharzeev, J Patel, KB Santiago, BM Joshi, K Dorsinvil, K Sweet, RM Soares, AS AF Zipper, Lauren E. Aristide, Xavier Bishop, Dylan P. Joshi, Ishita Kharzeev, Julia Patel, Krishna B. Santiago, Brianna M. Joshi, Karan Dorsinvil, Kahille Sweet, Robert M. Soares, Alexei S. TI A simple technique to reduce evaporation of crystallization droplets by using plate lids with apertures for adding liquids SO ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS LA English DT Article ID X-RAY-DIFFRACTION; THROUGHPUT PROTEIN CRYSTALLIZATION; DATA-COLLECTION; REFINEMENT; MICROBATCH; CRYSTALS; SYSTEM; CHIP AB A method is described for using plate lids to reduce evaporation in low-volume vapor-diffusion crystallization experiments. The plate lids contain apertures through which the protein and precipitants were added to different crystallization microplates (the reservoir was filled before fitting the lids). Plate lids were designed for each of these commonly used crystallization microplates. This system minimizes the dehydration of crystallization droplets containing just a few nanolitres of protein and precipitant, and results in more reproducible diffraction from the crystals. For each lid design, changes in the weight of the plates were used to deduce the rate of evaporation under different conditions of temperature, air movement, droplet size and precipitant. For comparison, the state of dehydration was also visually assessed throughout the experiment. Finally, X-ray diffraction methods were used to compare the diffraction of protein crystals that were conventionally prepared against those that were prepared on plates with plate lids. The measurements revealed that the plate lids reduced the rate of evaporation by 63-82%. Crystals grown in 5 nl drops that were set up with plate lids diffracted to higher resolution than similar crystals from drops that were set up without plate lids. The results demonstrate that plate lids can be instrumental for improving few-nanolitre crystallizations. C1 [Zipper, Lauren E.; Aristide, Xavier; Bishop, Dylan P.; Joshi, Ishita; Kharzeev, Julia; Patel, Krishna B.; Santiago, Brianna M.; Joshi, Karan; Dorsinvil, Kahille] Brookhaven Natl Lab, Off Educ Programs, Upton, NY 11973 USA. [Zipper, Lauren E.] SUNY Binghamton, Dept Mech Engn, Vestal, NY 13902 USA. [Aristide, Xavier] North Babylon High Sch, Babylon, NY 11703 USA. [Bishop, Dylan P.] Northport High Sch, Northport, NY 11768 USA. [Joshi, Ishita] St Augustine Catholic High Sch, Markham, ON L6C 1S3, Canada. [Kharzeev, Julia] Earl L Vandermeulen High Sch, Port Jefferson, NY 11777 USA. [Patel, Krishna B.] John P Stevens High Sch, Edison, NJ 08820 USA. [Santiago, Brianna M.] Connetquot High Sch, Bohemia, NY 11716 USA. [Joshi, Karan] PEC Univ Technol, Dept Elect & Elect Commun Engn, Chandigarh, India. [Sweet, Robert M.; Soares, Alexei S.] Brookhaven Natl Lab, Photon Sci Directorate, Upton, NY 11973 USA. [Sweet, Robert M.] Brookhaven Natl Lab, Biosci Dept, Upton, NY 11973 USA. RP Soares, AS (reprint author), Brookhaven Natl Lab, Photon Sci Directorate, Upton, NY 11973 USA. EM soares@bnl.gov FU US Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists (WDTS); Brookhaven National Laboratory/US Department of Energy, Laboratory Directed Research and Development [11-008]; Offices of Biological and Environmental Research and of Basic Energy Sciences of the US Department of Energy; National Center for Research Resources [P41RR012408]; National Institute of General Medical Sciences of the National Institutes of Health [P41GM103473] FX Personnel for this study were recruited largely through the 2014 summer session of the Science Undergraduate Laboratory Internships Program (SULI), supported through the US Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists (WDTS). Major ongoing financial support for acoustic droplet ejection applications was through the Brookhaven National Laboratory/US Department of Energy, Laboratory Directed Research and Development Grant 11-008 and from the Offices of Biological and Environmental Research and of Basic Energy Sciences of the US Department of Energy and from the National Center for Research Resources (P41RR012408) and the National Institute of General Medical Sciences (P41GM103473) of the National Institutes of Health. Data for this study were measured at beamline X12b of the National Synchrotron Light Source. Author contributions: ASS designed the experiment and wrote the paper. XA, DPB, IJ, JK, KBP, BMS and AS grew crystals, obtained data and analyzed data. ASS, LZ and KJ designed and built the labware. ASS, RMS and KD trained and supervised student interns. NR 27 TC 4 Z9 4 U1 0 U2 9 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 1744-3091 J9 ACTA CRYSTALLOGR F JI Acta Crystallogr. F-Struct. Biol. Commun. PD DEC PY 2014 VL 70 BP 1707 EP 1713 DI 10.1107/S2053230X14025126 PN 12 PG 7 WC Biochemical Research Methods; Biochemistry & Molecular Biology; Biophysics; Crystallography SC Biochemistry & Molecular Biology; Biophysics; Crystallography GA AU8JS UT WOS:000345843300030 PM 25484231 ER PT J AU Johnson, MS Yates, EL Iraci, LT Loewenstein, M Tadic, JM Wecht, KJ Jeong, S Fischer, ML AF Johnson, Matthew S. Yates, Emma L. Iraci, Laura T. Loewenstein, Max Tadic, Jovan M. Wecht, Kevin J. Jeong, Seongeun Fischer, Marc L. TI Analyzing source apportioned methane in northern California during Discover-AQ-CA using airborne measurements and model simulations SO ATMOSPHERIC ENVIRONMENT LA English DT Article DE Methane; Source apportionment; Emission inventory; Livestock emissions ID ATMOSPHERIC METHANE; ANTHROPOGENIC EMISSIONS; AIRCRAFT AB This study analyzes source apportioned methane (CH4) emissions and atmospheric mixing ratios in northern California during the Discover-AQ-CA field campaign using airborne measurement data and model simulations. Source apportioned CH4 emissions from the Emissions Database for Global Atmospheric Research (EDGAR) version 4.2 were applied in the 3-D chemical transport model GEOS-Chem and analyzed using airborne measurements taken as part of the Alpha Jet Atmospheric eXperiment over the San Francisco Bay Area (SFBA) and northern San Joaquin Valley (SJV). During the time period of the Discover-AQ-CA field campaign EDGAR inventory CH4 emissions were similar to 5.30 Gg day(-1) (Gg = 1.0 x 10(9) g) (equating to similar to 1.90 x 10(3) Gg yr(-1)) for all of California. According to EDGAR, the SFBA and northern SJV region contributes similar to 30% of total CH4 emissions from California. Source apportionment analysis during this study shows that CH4 mixing ratios over this area of northern California are largely influenced by global emissions from wetlands and local/global emissions from gas and oil production and distribution, waste treatment processes, and livestock management. Model simulations, using EDGAR emissions, suggest that the model under-estimates CH4 mixing ratios in northern California (average normalized mean bias (NMB) = -5.2% and linear regression slope = 0.20). The largest negative biases in the model were calculated on days when large amounts of CH4 were measured over local emission sources and atmospheric CH4 mixing ratios reached values >2.5 parts per million. Sensitivity emission studies conducted during this research suggest that local emissions of CH4 from livestock management processes are likely the primary source of the negative model bias. These results indicate that a variety, and larger quantity, of measurement data needs to be obtained and additional research is necessary to better quantify source apportioned CH4 emissions in California. Published by Elsevier Ltd. C1 [Johnson, Matthew S.; Yates, Emma L.; Iraci, Laura T.; Loewenstein, Max; Tadic, Jovan M.] NASA, Ames Res Ctr, Div Earth Sci, Moffett Field, CA 94035 USA. [Wecht, Kevin J.] Harvard Univ, Dept Earth & Planetary Sci, Cambridge, MA 02138 USA. [Jeong, Seongeun; Fischer, Marc L.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Dept Global Ecol, Berkeley, CA 94720 USA. [Tadic, Jovan M.] Carnegie Inst Sci, Dept Global Ecol, Stanford, CA USA. RP Johnson, MS (reprint author), NASA, Ames Res Ctr, Div Earth Sci, Moffett Field, CA 94035 USA. EM matthew.s.johnson@nasa.gov RI Tadic, Jovan/P-3677-2016; OI Tadic, Jovan/0000-0003-4655-5063 FU NASA High-End Computing (HEC) Program through the NASA Advanced Supercomputing (NAS) Division at NASA Ames Research Center; University of California; California Energy Commission; California Air Resources Board [DE-AC02-05CH11231]; NASA's Earth Science Division at Ames Research Center; H211 L. L. C. FX The authors gratefully recognize the support and partnership of H211 L. L. C., with particular thanks to K. Ambrose, R. Simone, B. Quiambao, J. Lee, and R. Fisher. Technical contributions from W. Gore, A. Trias, M. Roby, E. Quigley, R. Walker, R. Belme, L Sharma, and B. Pierce made this project possible. Matthew Johnson would also like to thank D. Jacob and the Harvard University Atmospheric Chemistry Modeling Group for providing the base model GEOS-Chem used during our research. Resources supporting this work were provided by the NASA High-End Computing (HEC) Program through the NASA Advanced Supercomputing (NAS) Division at NASA Ames Research Center. Further thanks are due to D. Kokron for assisting in the installation of GEOS-Chem on NAS. Effort by LBNL was supported by the University of California, the California Energy Commission, and the California Air Resources Board under contract number DE-AC02-05CH11231. All the authors express gratitude to the support from NASA's Earth Science Division at Ames Research Center. Finally, the views, opinions, and findings contained in this report are those of the authors and should not be construed as an official NASA or United States Government position, policy, or decision. NR 30 TC 3 Z9 3 U1 1 U2 14 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 1352-2310 EI 1873-2844 J9 ATMOS ENVIRON JI Atmos. Environ. PD DEC PY 2014 VL 99 BP 248 EP 256 DI 10.1016/j.atmosenv.2014.09.068 PG 9 WC Environmental Sciences; Meteorology & Atmospheric Sciences SC Environmental Sciences & Ecology; Meteorology & Atmospheric Sciences GA AU7TS UT WOS:000345804400027 ER PT J AU Jing, P Lu, ZF Xing, J Streets, DG Tan, Q O'Brien, T Kamberos, J AF Jing, Ping Lu, Zifeng Xing, Jia Streets, David G. Tan, Qian O'Brien, Timothy Kamberos, Joseph TI Response of the summertime ground-level ozone trend in the Chicago area to emission controls and temperature changes, 2005-2013 SO ATMOSPHERIC ENVIRONMENT LA English DT Article DE Ozone trend; Temperature dependence of ozone; NOx and VOC emission control; Chicago ID UNITED-STATES; MONITORING INSTRUMENT; NOX EMISSIONS; URBAN AREAS; POWER-PLANTS; MEXICO-CITY; METEOROLOGY; RETRIEVALS; STRATEGIES; INDUSTRIAL AB Despite strenuous efforts to reduce the emissions of ozone precursors such as nitrogen oxides (NOx), concentrations of ground-level ozone (O-3) still often exceed the National Ambient Air Quality Standard in U.S. cities in summertime, including Chicago. Furthermore, studies have projected a future increase in O-3 formation due to global climate change. This study examines the response of summertime O-3 to emission controls and temperature change in the Chicago area from 2005 to 2013 by employing observations of O-3, O-3 precursors, and meteorological variables. We find that meteorology explains about 53% of the O-3 variance in Chicago. O-3 mixing ratios over Chicago are found to show no clear decline over the 2005-2013 period. The summertime ground-level O-3 trend consists of a decrease of 0.08 ppb/year between 2005 and 2009 and an increase of 1.49 ppb/year between 2009 and 2013. Emissions of NOx and concentrations of NO2 have been decreasing steadily from 2005 to 2013 in the Chicago area. Concentrations of volatile organic compounds (VOCs) in Chicago, however, have more than doubled since 2009, even though emission inventories suggest that VOC emissions have decreased. We believe that O-3 production in Chicago became more sensitive to VOCs starting in 2008/2009 and may have switched from being NOx-limited to VOC-limited. The warmer climate since 2008 has also contributed to the increasing ozone trend in the Chicago area. Increased attention should be paid to improving the quantification of VOC sources, enhancing the monitoring of reactive VOC concentrations, and designing VOC mitigation measures. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Jing, Ping; Kamberos, Joseph] Loyola Univ, Inst Environm Sustainabil, Chicago, IL 60660 USA. [Lu, Zifeng; Streets, David G.] Argonne Natl Lab, Decis & Informat Sci Div, Argonne, IL 60439 USA. [Xing, Jia] US EPA, Res Triangle Pk, NC 27711 USA. [Tan, Qian] NASA, Goddard Earth Sci Technol & Res GESTAR Studies &, Goddard Space Flight Ctr, Greenbelt, MD 20771 USA. [O'Brien, Timothy] Loyola Univ, Dept Math & Stat, Chicago, IL 60660 USA. RP Jing, P (reprint author), Loyola Univ, Inst Environm Sustainabil, Chicago, IL 60660 USA. EM pjing@luc.edu RI xing, jia/O-1784-2014 FU Loyola University Chicago Summer Research Stipends FX This work was funded by the Loyola University Chicago Summer Research Stipends. We thank Gao Chen from NASA's Langley Research Center for helpful comments. NR 37 TC 5 Z9 5 U1 7 U2 39 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 1352-2310 EI 1873-2844 J9 ATMOS ENVIRON JI Atmos. Environ. PD DEC PY 2014 VL 99 BP 630 EP 640 DI 10.1016/j.atmosenv.2014.10.035 PG 11 WC Environmental Sciences; Meteorology & Atmospheric Sciences SC Environmental Sciences & Ecology; Meteorology & Atmospheric Sciences GA AU7TS UT WOS:000345804400066 ER PT J AU Messick, CE Galan, JJ AF Messick, C. E. Galan, J. J. TI US-Origin Nuclear Material Removal Program SO ATW-INTERNATIONAL JOURNAL FOR NUCLEAR POWER LA English DT Article AB The United States (U.S.) Department of Energy (DOE) Global Threat Reduction Initiative's (GTRI) U.S.-Origin Nuclear Material Removal program, also known as the Foreign Research Reactor Spent Nuclear Fuel Acceptance Program (FRR SNF AP), was established by the U.S. Department of Energy in May 1996. The program's mission provides a disposition pathway for certain U.S. origin spent nuclear fuel and other weaponsgrade nuclear material. The program will continue until May 2016 with an additional three year window for fuel cooldown and transportation. This paper provides an update on recent program accomplishments, current program initiatives and future activities. C1 [Messick, C. E.; Galan, J. J.] US DOE, US Origin Nucl Mat Removal Program, Natl Nucl Secur Adm, Off Global Threat Reduct, Washington, DC 20585 USA. RP Messick, CE (reprint author), US DOE, US Origin Nucl Mat Removal Program, Natl Nucl Secur Adm, Off Global Threat Reduct, Washington, DC 20585 USA. NR 0 TC 0 Z9 0 U1 0 U2 1 PU INFORUM VERLAGS-VERWALTUNGSGESELLSCHAFT MBH PI BERLIN PA ROBERT-KOCH-PLATZ 4, BERLIN, 10115, GERMANY SN 1431-5254 J9 ATW-INT J NUCL POWER JI ATW-Int. J. Nucl. Power PD DEC PY 2014 VL 59 IS 12 BP 682 EP + PG 4 WC Nuclear Science & Technology SC Nuclear Science & Technology GA AW0CW UT WOS:000345958800006 ER PT J AU Knapik, JJ Steelman, R Hoedebecke, K Rankin, S Klug, K Collier, K Jones, BH AF Knapik, Joseph J. Steelman, Ryan Hoedebecke, Kyle Rankin, Shawn Klug, Kevin Collier, Keith Jones, Bruce H. TI Injury incidence with T-10 and T-11 Parachutes in Military Airborne Operations SO AVIATION SPACE AND ENVIRONMENTAL MEDICINE LA English DT Article DE wind; temperature; night; combat load; aircraft entanglement ID RISK-FACTORS; ALTITUDE; SYSTEM AB Background: The T-10 parachute has been the U.S. Army standard parachute since 1952 and is now being replaced by the T-11, which has a capacity for heavier loads. This investigation compared injury rates between the two parachute systems during mass tactical parachute training exercises at Fort Bragg, NC. Methods: Investigators were on the drop zone for all parachute operations. Data on injured jumpers were collected on the drop zone and supplemented with medical records. Operational data were collected from standard reports and weather data were obtained using a Kestrel Model 4500 pocket weather tracker. Results: There were a total of 131,747 jumps resulting in 1101 injured service members for a crude incidence of 8.4 injuries/1000 jumps. Most injuries (88%) with a known injury mechanism were associated with ground impact. In univariate analysis, risk of injury with the T-10 was 9.1/1000 jumps and that with the T-11 was 5.2/1000 jumps [odds ratio (T-10/T-11) = 1.72, 95% confidence interval (95%CI) = 1.45-2.08, P<0.011. Other factors that independently increased injury risk included night jumps, combat loads, higher wind speeds, higher temperatures, certain aircraft, and entanglements. After controlling for these factors in a multivariate analysis, injury risk was still higher for the T-10 parachute when compared to the T-11 [odds ratio (T-10/T-11) = 1.56, 95%CI = 1.28-1.89, P<0.01). For virtually all strata of the independent risk factors, the T-11 had a lower injury rate. Conclusion: Compared to the T-10, the T-11 parachute had a lower injury incidence under virtually all the operational conditions examined. C1 US Army, Inst Publ Hlth, Aberdeen Proving Ground, MD 21010 USA. Womack Army Med Ctr, Ft Bragg, NC USA. Concurrent Technol Corp, Fayetteville, NC USA. Program Management Off, Ft Belvoir, VA USA. Oak Ridge Inst Sci & Educ, Belcamp, MD USA. RP Knapik, JJ (reprint author), US Army, Inst Publ Hlth, ATTN MCHB IP DI, Aberdeen Proving Ground, MD 21010 USA. EM joseph.j.knapik.ctr@mail.mil FU Office of the Assistant Secretary of the Army (Installations, Energy and Environment) [W74V8H-04-D-0005 Tasks 0517, 0568] FX We would like to thank the numerous personnel from the 82nd Airborne Division and XVIII Airborne Corps who supported this effort. These included LTC Robert Malsby, LTC Michael Sassano, COL Michael Smith, Dr. Ellen Segan, Mr. Tommie Brown, Mr. Earl Jefferson, CPT King Cooper, MSG Todd Winhoven, CW3 Thompson, CW4 Lewis, Mr. Nick Weidler, Mr. Terence Hensey, CW5 Frazier, CW3 Rojas, and SFC Jess Brown. Data collection work was funded through the Office of the Assistant Secretary of the Army (Installations, Energy and Environment) and conducted under contract W74V8H-04-D-0005 Tasks 0517 and 0568. This project was supported in part by an appointment to the Research Participation Program for the U.S. Army Public for Health Command administered by the Oak Ridge Institute for Science and Education through an agreement between the U.S. Department of Energy and the USAPHC. NR 33 TC 3 Z9 3 U1 1 U2 2 PU AEROSPACE MEDICAL ASSOC PI ALEXANDRIA PA 320 S HENRY ST, ALEXANDRIA, VA 22314-3579 USA SN 0095-6562 EI 1943-4448 J9 AVIAT SPACE ENVIR MD JI Aviat. Space Environ. Med. PD DEC PY 2014 VL 85 IS 12 BP 1159 EP 1169 DI 10.3357/ASEM.4012.2014 PG 11 WC Public, Environmental & Occupational Health; Medicine, General & Internal; Sport Sciences SC Public, Environmental & Occupational Health; General & Internal Medicine; Sport Sciences GA AU8BA UT WOS:000345820500001 PM 25479257 ER PT J AU Boscoboinik, JA Shaikhutdinov, S AF Boscoboinik, J. Anibal Shaikhutdinov, Shamil TI Exploring Zeolite Chemistry with the Tools of Surface Science: Challenges, Opportunities, and Limitations SO CATALYSIS LETTERS LA English DT Article DE Heterogeneous catalysis; Zeolites; Bronsted acid catalysis; Thin films; Oxide supports; MTH ID 2-DIMENSIONAL ZEOLITES; ALUMINOSILICATE FILMS; ACID STRENGTH; SILICA FILMS; SOLID ACIDS; CATALYSTS; MECHANISMS; HYDROXYLS; MOLECULES; KINETICS AB The complexity of catalysts that the surface science community has been able to address has increased substantially in a systematic manner, starting with metal and oxide single crystal surfaces and evolving to an atomistic description of clusters and nanoparticles on well-defined, planar supports. The next step in adding complexity is now to address surfaces of porous oxide materials, in particular of zeolites, which are the most extensively used catalysts in the industry. The recently reported successful fabrication of well-ordered thin films, consisting of planar arrangement of aluminosilicate polygonal prisms on a metal substrate counting with highly acidic bridging hydroxyl groups on the surface, represents the limiting case of infinitely large pore and cages in zeolites. This model system allows one to study reactions catalyzed by zeolites using the toolkit of surface science. In this Perspective, we describe the zeolitic model system, with its virtues and limitations, as well as the challenges, opportunities and expectations for the future in modelling porous catalysts by a surface science approach. . C1 [Boscoboinik, J. Anibal] Brookhaven Natl Lab, Ctr Funct Nanomat, Upton, NY 11973 USA. [Shaikhutdinov, Shamil] Max Planck Gesell, Fritz Haber Inst, D-14195 Berlin, Germany. RP Boscoboinik, JA (reprint author), Brookhaven Natl Lab, Ctr Funct Nanomat, Upton, NY 11973 USA. EM jboscoboinik@bnl.gov RI Boscoboinik, Jorge/E-8110-2010 OI Boscoboinik, Jorge/0000-0002-5090-7079 FU Center for Functional Nanomaterials at BNL, under DOE [DE-AC02-98CH10886] FX We gratefully thank Prof. H.-J. Freund and all our coworkers cited in the references, in particular the theory group of Prof. J. Sauer, for their tremendous contribution to the work presented here. J.A.B thanks the A. von Humboldt Foundation and the Center for Functional Nanomaterials at BNL, under DOE contract No. DE-AC02-98CH10886. NR 43 TC 4 Z9 4 U1 3 U2 37 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1011-372X EI 1572-879X J9 CATAL LETT JI Catal. Lett. PD DEC PY 2014 VL 144 IS 12 BP 1987 EP 1995 DI 10.1007/s10562-014-1369-3 PG 9 WC Chemistry, Physical SC Chemistry GA AU8JX UT WOS:000345843700001 ER PT J AU Mander, BA Rao, V Lu, B Saletin, JM Ancoli-Israel, S Jagust, WJ Walker, MP AF Mander, Bryce A. Rao, Vikram Lu, Brandon Saletin, Jared M. Ancoli-Israel, Sonia Jagust, William J. Walker, Matthew P. TI Impaired Prefrontal Sleep Spindle Regulation of Hippocampal-Dependent Learning in Older Adults SO CEREBRAL CORTEX LA English DT Article DE aging; fMRI; hippocampus; learning; sleep ID FUNCTIONAL CONNECTIVITY; RECOGNITION MEMORY; MODEL SELECTION; AGE; YOUNG; ACTIVATION; FMRI AB A hallmark feature of cognitive aging is a decline in the ability to form new memories. Parallel to these cognitive impairments are marked disruptions in sleep physiology. Despite recent evidence in young adults establishing a role for sleep spindles in restoring hippocampal-dependent memory formation, the possibility that disrupted sleep physiology contributes to age-related decline in hippocampal-dependent learning remains unknown. Here, we demonstrate that reduced prefrontal sleep spindles by over 40% in older adults statistically mediates the effects of old age on next day episodic learning, such that the degree of impaired episodic learning is explained by the extent of impoverished prefrontal sleep spindles. In addition, prefrontal spindles significantly predicted the magnitude of impaired next day hippocampal activation, thereby determining the influence of spindles on post-sleep learning capacity. These data support the hypothesis that disrupted sleep physiology contributes to age-related cognitive decline in later life, the consequence of which has significant treatment intervention potential. C1 [Mander, Bryce A.; Rao, Vikram; Saletin, Jared M.; Walker, Matthew P.] Univ Calif Berkeley, Sleep & Neuroimaging Lab, Berkeley, CA 94720 USA. [Jagust, William J.; Walker, Matthew P.] Univ Calif Berkeley, Helen Wills Neurosci Inst, Berkeley, CA 94720 USA. [Walker, Matthew P.] Univ Calif Berkeley, Dept Psychol, Berkeley, CA 94720 USA. [Jagust, William J.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Life Sci, Berkeley, CA 94720 USA. [Lu, Brandon] Calif Pacific Med Ctr, Div Pulm & Crit Care Med, San Francisco, CA 94115 USA. [Ancoli-Israel, Sonia] Univ Calif San Diego, Dept Psychiat, La Jolla, CA 92093 USA. RP Walker, MP (reprint author), Univ Calif Berkeley, Dept Psychol, 3210 Tolman Hall, Berkeley, CA 94720 USA. EM mpwalker@berkeley.edu RI Rao, Vikram/J-6931-2016; OI Saletin, Jared/0000-0002-8547-0161 FU National Institutes of Health [R01-AG031164, R01-AG034570, R01-AG08415, F32-AG039170] FX This work was supported by awards R01-AG031164 (M.P.W.), R01-AG034570 (W.J.), R01-AG08415 (S.A.), and F32-AG039170 (B.A.M.) from the National Institutes of Health. NR 59 TC 16 Z9 16 U1 2 U2 16 PU OXFORD UNIV PRESS INC PI CARY PA JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA SN 1047-3211 EI 1460-2199 J9 CEREB CORTEX JI Cereb. Cortex PD DEC PY 2014 VL 24 IS 12 BP 3301 EP 3309 DI 10.1093/cercor/bht188 PG 9 WC Neurosciences SC Neurosciences & Neurology GA AU8HX UT WOS:000345838300018 PM 23901074 ER PT J AU Walters, AD May, CK Dauster, ES Cinquin, BP Smith, EA Robellet, X D'Amours, D Larabell, CA Cohen-Fix, O AF Walters, Alison D. May, Christopher K. Dauster, Emma S. Cinquin, Bertrand P. Smith, Elizabeth A. Robellet, Xavier D'Amours, Damien Larabell, Carolyn A. Cohen-Fix, Orna TI The Yeast Polo Kinase Cdc5 Regulates the Shape of the Mitotic Nucleus SO CURRENT BIOLOGY LA English DT Article ID SISTER-CHROMATID SEPARATION; CHROMOSOME CONDENSATION; BUDDING-YEAST; SACCHAROMYCES-CEREVISIAE; GENOME STABILITY; IN-VIVO; ENVELOPE; EXIT; PHOSPHORYLATION; NETWORK AB Abnormal nuclear size and shape are hallmarks of aging and cancer [1, 2]. However, the mechanisms regulating nuclear morphology and nuclear envelope (NE) expansion are poorly understood. In metazoans, the NE disassembles prior to chromosome segregation and reassembles at the end of mitosis [3]. In budding yeast, the NE remains intact. The nucleus elongates as chromosomes segregate and then divides at the end of mitosis to form two daughter nuclei without NE disassembly. The budding yeast nucleus also undergoes remodeling during a mitotic arrest; the NE continues to expand despite the pause in chromosome segregation, forming a nuclear extension, or "flare," that encompasses the nucleolus [4]. The distinct nucleolar localization of the mitotic flare indicates that the NE is compartmentalized and that there is a mechanism by which NE expansion is confined to the region adjacent to the nucleolus. Here we show that mitotic flare formation is dependent on the yeast polo kinase Cdc5. This function of Cdc5 is independent of its known mitotic roles, including rDNA condensation. High-resolution imaging revealed that following Cdc5 inactivation, nuclei expand isometrically rather than forming a flare, indicating that Cdc5 is needed for NE compartmentalization. Even in an uninterrupted cell cycle, a small NE expansion occurs adjacent to the nucleolus prior to anaphase in a Cdc5-dependent manner. Our data provide the first evidence that polo kinase, a key regulator of mitosis [5], plays a role in regulating nuclear morphology and NE expansion. C1 [Walters, Alison D.; May, Christopher K.; Dauster, Emma S.; Cohen-Fix, Orna] NIDDK, Mol & Cellular Biol Lab, NIH, Bethesda, MD 20892 USA. [Cinquin, Bertrand P.; Smith, Elizabeth A.; Larabell, Carolyn A.] Univ Calif San Francisco, Dept Anat, San Francisco, CA 94158 USA. [Cinquin, Bertrand P.; Smith, Elizabeth A.; Larabell, Carolyn A.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA. [Robellet, Xavier; D'Amours, Damien] Univ Montreal, Inst Res Immunol & Canc, Montreal, PQ H3C 3J7, Canada. [Robellet, Xavier; D'Amours, Damien] Univ Montreal, Dept Pathol & Biol Cellulaire, Montreal, PQ H3C 3J7, Canada. RP Cohen-Fix, O (reprint author), NIDDK, Mol & Cellular Biol Lab, NIH, Bethesda, MD 20892 USA. EM ornac@helix.nih.gov FU National Institute of Diabetes and Digestive and Kidney Diseases; National Institute of General Medical Science of the NIH [P41GM103445]; U.S. Department of Energy, Office of Biological and Environmental Research [DE-AC02-05CH11231]; Canadian Institutes of Health Research [MOP 82912, MOP 136788]; Canada Research Chair in Cell Cycle Regulation and Genomic Integrity FX We thank D. Reynolds, A. Hoyt, T. Eng, D. Koshland, A. Amon, S. Lacefield, and J. Diffley for yeast strains and plasmids and M. Lichten, W. Prinz, F. Chang, and members of the O.C.-F. laboratory for discussions on the manuscript. A.D.W., C.K.M., E.S.D., and O.C.-F. are funded by an intramural National Institute of Diabetes and Digestive and Kidney Diseases grant. C.A.L., B.P.C., and E.A.S. are funded by the National Institute of General Medical Science of the NIH (P41GM103445) and the U.S. Department of Energy, Office of Biological and Environmental Research (DE-AC02-05CH11231). Research in D.D.'s laboratory is supported by the Canadian Institutes of Health Research (MOP 82912 and MOP 136788). D.D. is a recipient of a Tier II Canada Research Chair in Cell Cycle Regulation and Genomic Integrity. NR 31 TC 7 Z9 7 U1 2 U2 9 PU CELL PRESS PI CAMBRIDGE PA 600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USA SN 0960-9822 EI 1879-0445 J9 CURR BIOL JI Curr. Biol. PD DEC 1 PY 2014 VL 24 IS 23 BP 2861 EP 2867 DI 10.1016/j.cub.2014.10.029 PG 7 WC Biochemistry & Molecular Biology; Cell Biology SC Biochemistry & Molecular Biology; Cell Biology GA AU7WH UT WOS:000345808700032 PM 25454593 ER PT J AU Poust, S Hagen, A Katz, L Keasling, JD AF Poust, Sean Hagen, Andrew Katz, Leonard Keasling, Jay D. TI Narrowing the gap between the promise and reality of polyketide synthases as a synthetic biology platform SO CURRENT OPINION IN BIOTECHNOLOGY LA English DT Review ID ESCHERICHIA-COLI; HETEROLOGOUS EXPRESSION; 6-DEOXYERYTHRONOLIDE-B SYNTHASE; METAGENOMIC LIBRARIES; SUBSTRATE-SPECIFICITY; KETOSYNTHASE DOMAINS; MASS-SPECTROMETRY; NATURAL-PRODUCTS; RATIONAL DESIGN; SHUTTLE VECTORS AB Engineering modular polyketide synthases (PKSs) has the potential to be an effective methodology to produce existing and novel chemicals. However, this potential has only just begun to be realized. We propose the adoption of an iterative design-build-test-learn paradigm to improve PKS engineering. We suggest methods to improve engineered PKS design by learning from laboratory-based selection; adoption of DNA design software and automation to build constructs and libraries more easily; tools for the expression of engineered proteins in a variety of heterologous hosts; and mass spectrometry-based high-throughput screening methods. Finally, lessons learned during iterations of the design-build-test-learn cycle can serve as a knowledge base for the development of a single retrosynthesis algorithm usable by both PKS experts and non-experts alike. C1 [Poust, Sean; Keasling, Jay D.] Univ Calif Berkeley, Dept Biomol & Chem Engn, Berkeley, CA 94270 USA. [Hagen, Andrew] Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94270 USA. [Poust, Sean; Hagen, Andrew; Keasling, Jay D.] Joint BioEnergy Inst, Emeryville, CA 94608 USA. [Katz, Leonard; Keasling, Jay D.] Univ Calif Berkeley, Inst QB3, Berkeley, CA 94270 USA. [Hagen, Andrew; Katz, Leonard; Keasling, Jay D.] Synthet Biol Engn Res Ctr, Emeryville, CA 94608 USA. [Keasling, Jay D.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94270 USA. RP Keasling, JD (reprint author), Univ Calif Berkeley, Dept Biomol & Chem Engn, Berkeley, CA 94270 USA. EM keasling@berkeley.edu OI Hagen, Andrew/0000-0002-2691-157X FU Joint BioEnergy Institute - Office of Science, Office of Biological and Environmental Research of the U.S. Department of Energy [DE-AC02-05CH11231]; National Science Foundation [EEC-0540879]; Department of Energy, ARPA-E Electrofuels Program [DE-0000206-1577]; National Science Foundation Graduate Research Fellowship Program [DGE 1106400] FX This work was supported by the Joint BioEnergy Institute which is funded by the Office of Science, Office of Biological and Environmental Research of the U.S. Department of Energy (Contract No. DE-AC02-05CH11231); by the National Science Foundation, award No. EEC-0540879 to the Synthetic Biology Research Center, by the Department of Energy, ARPA-E Electrofuels Program (Contract No. DE-0000206-1577); and by the National Science Foundation Graduate Research Fellowship Program (Grant No. DGE 1106400). We thank Brian Fong for expert assistance in the preparation of figures. NR 56 TC 26 Z9 26 U1 1 U2 60 PU CURRENT BIOLOGY LTD PI LONDON PA 84 THEOBALDS RD, LONDON WC1X 8RR, ENGLAND SN 0958-1669 EI 1879-0429 J9 CURR OPIN BIOTECH JI Curr. Opin. Biotechnol. PD DEC PY 2014 VL 30 BP 32 EP 39 DI 10.1016/j.copbio.2014.04.011 PG 8 WC Biochemical Research Methods; Biotechnology & Applied Microbiology SC Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology GA AU8BS UT WOS:000345822300007 PM 24816568 ER PT J AU Biswas, K Abhari, R AF Biswas, Kaushik Abhari, Ramin TI Low-cost phase change material as an energy storage medium in building envelopes: Experimental and numerical analyses SO ENERGY CONVERSION AND MANAGEMENT LA English DT Article DE Phase change materials; Low-cost PCM; PCM modeling; Finite element analysis; COMSOL ID CHANGE MATERIALS PCMS; THERMAL PERFORMANCE; CONCRETE WALLS; SIMULATION; WALLBOARD; SAVINGS; OIL AB A promising approach to increasing the energy efficiency of buildings is the implementation of a phase change material (PCM) in the building envelope. Numerous studies over the last two decades have reported the energy saving potential of PCMs in building envelopes, but their wide application has been inhibited, in part, by their high cost. This article describes a novel PCM made of naturally occurring fatty acids/glycerides trapped into high density polyethylene (HDPE) pellets and its performance in a building envelope application. The PCM-HDPE pellets were mixed with cellulose insulation and then added to an exterior wall of a test building in a hot and humid climate, and tested over a period of several months. To demonstrate the efficacy of the PCM-enhanced cellulose insulation in reducing the building envelope heat gains and losses, a side-by-side comparison was performed with another wall section filled with cellulose-only insulation. Further, numerical modeling of the test wall was performed to determine the actual impact of the PCM-HDPE pellets on wall-generated heating and cooling loads and the associated electricity consumption. The model was first validated using experimental data and then used for annual simulations using typical meteorological year (TMY3) weather data. This article presents the experimental data and numerical analyses showing the energy-saving potential of the new PCM. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Biswas, Kaushik] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. [Abhari, Ramin] Renewable Energy Grp Inc, REG Synthet Fuels LLC, Tulsa, OK 74135 USA. RP Biswas, K (reprint author), One Bethel Valley Rd,Bldg 3147,POB 2008,MS-6070, Oak Ridge, TN 37831 USA. EM biswask@ornl.gov OI Biswas, Kaushik/0000-0002-4177-6230 FU United States Department of Energy as part of the American Recovery and Reinvestment Act [DE-EE0003924] FX The authors gratefully acknowledge the funding support for this work from the United States Department of Energy as part of the American Recovery and Reinvestment Act, as Contract No. DE-EE0003924. The authors are also thankful to Jerald Atchley and Phillip Childs of ORNL for their contributions in installing and instrumenting the test wall, data gathering and troubleshooting, Drs. Keith Rice and Bo Shen (ORNL) for the heat pump coefficient of performance-related calculations, and Dr. Som Shrestha for providing the weather data used for the annual simulations. NR 32 TC 13 Z9 14 U1 4 U2 47 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0196-8904 EI 1879-2227 J9 ENERG CONVERS MANAGE JI Energy Conv. Manag. PD DEC PY 2014 VL 88 BP 1020 EP 1031 DI 10.1016/j.enconman.2014.09.003 PG 12 WC Thermodynamics; Energy & Fuels; Mechanics SC Thermodynamics; Energy & Fuels; Mechanics GA AU6PU UT WOS:000345725400099 ER PT J AU Gregoire, P Engelbrektson, A Hubbard, CG Metlagel, Z Csencsits, R Auer, M Conrad, ME Thieme, J Northrup, P Coates, JD AF Gregoire, Patrick Engelbrektson, Anna Hubbard, Christopher G. Metlagel, Zoltan Csencsits, Roseann Auer, Manfred Conrad, Mark E. Thieme, Juergen Northrup, Paul Coates, John D. TI Control of sulfidogenesis through bio-oxidation of H2S coupled to (per) chlorate reduction SO ENVIRONMENTAL MICROBIOLOGY REPORTS LA English DT Article ID SULFATE-REDUCING CONDITIONS; POLYCYCLIC AROMATIC-HYDROCARBONS; MICROBIAL PERCHLORATE REDUCTION; ANAEROBIC DEGRADATION; HARBOR SEDIMENTS; ELEMENTAL SULFUR; OXIDATION; BACTERIUM; SULFIDE; AQUIFER AB We investigated H2S attenuation by dissimilatory perchlorate-reducing bacteria (DPRB). All DPRB tested oxidized H2S coupled to (per)chlorate reduction without sustaining growth. H2S was preferentially utilized over organic electron donors resulting in an enriched (S-34)-elemental sulfur product. Electron microscopy revealed elemental sulfur production in the cytoplasm and on the cell surface of the DPRB Azospira suillum. Based on our results, we propose a novel hybrid enzymatic-abiotic mechanism for H2S oxidation similar to that recently proposed for nitrate-dependent Fe(II) oxidation. The results of this study have implications for the control of biosouring and biocorrosion in a range of industrial environments. C1 [Gregoire, Patrick; Engelbrektson, Anna; Coates, John D.] Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA. [Hubbard, Christopher G.; Conrad, Mark E.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. [Metlagel, Zoltan; Csencsits, Roseann; Auer, Manfred] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Life Sci, Berkeley, CA 94720 USA. [Thieme, Juergen; Northrup, Paul] Brookhaven Natl Lab, Upton, NY 11973 USA. RP Coates, JD (reprint author), Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA. EM jdcoates@berkeley.edu RI Conrad, Mark/G-2767-2010; Hubbard, Christopher/J-6150-2014; Foundry, Molecular/G-9968-2014 OI Hubbard, Christopher/0000-0002-8217-8122; FU Energy Biosciences Institute; Office of Science, Office of Basic Energy Sciences of the U.S. Department of Energy [DE-AC02-05CH11231] FX Funding for research on (per)chlorate reduction and sulfur redox cycling was provided to J. D. C. by the Energy Biosciences Institute. Electron microscopy work at the Molecular Foundry was supported by the Office of Science, Office of Basic Energy Sciences of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. NR 43 TC 11 Z9 11 U1 2 U2 26 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 1758-2229 J9 ENV MICROBIOL REP JI Environ. Microbiol. Rep. PD DEC PY 2014 VL 6 IS 6 BP 558 EP 564 DI 10.1111/1758-2229.12156 PG 7 WC Environmental Sciences; Microbiology SC Environmental Sciences & Ecology; Microbiology GA AU6GU UT WOS:000345702700003 PM 25756108 ER PT J AU Liu, YM Wang, ZM Liu, J Levar, C Edwards, MJ Babauta, JT Kennedy, DW Shi, Z Beyenal, H Bond, DR Clarke, TA Butt, JN Richardson, DJ Rosso, KM Zachara, JM Fredrickson, JK Shi, L AF Liu, Yimo Wang, Zheming Liu, Juan Levar, Caleb Edwards, Marcus J. Babauta, Jerome T. Kennedy, David W. Shi, Zhi Beyenal, Haluk Bond, Daniel R. Clarke, Thomas A. Butt, Julea N. Richardson, David J. Rosso, Kevin M. Zachara, John M. Fredrickson, James K. Shi, Liang TI A trans-outer membrane porin-cytochrome protein complex for extracellular electron transfer by Geobacter sulfurreducens PCA SO ENVIRONMENTAL MICROBIOLOGY REPORTS LA English DT Article ID C-TYPE CYTOCHROME; SHEWANELLA-ONEIDENSIS MR-1; II SECRETION SYSTEM; CRYSTAL-STRUCTURE; COMPARATIVE GENOMICS; FE(III) REDUCTION; OXIDE REDUCTION; IRON; SURFACE; OMCA AB The multi-heme, outer membrane c-type cytochrome (c-Cyt) OmcB of Geobacter sulfurreducens was previously proposed to mediate electron transfer across the outer membrane. However, the underlying mechanism has remained uncharacterized. In G.sulfurreducens, the omcB gene is part of two tandem four-gene clusters, each is predicted to encode a transcriptional factor (OrfR/OrfS), a porin-like outer membrane protein (OmbB/OmbC), a periplasmic c-type cytochrome (OmaB/OmaC) and an outer membrane c-Cyt (OmcB/OmcC) respectively. Here, we showed that OmbB/OmbC, OmaB/OmaC and OmcB/OmcC of G.sulfurreducensPCA formed the porin-cytochrome (Pcc) protein complexes, which were involved in transferring electrons across the outer membrane. The isolated Pcc protein complexes reconstituted in proteoliposomes transferred electrons from reduced methyl viologen across the lipid bilayer of liposomes to Fe(III)-citrate and ferrihydrite. The pcc clusters were found in all eight sequenced Geobacter and 11 other bacterial genomes from six different phyla, demonstrating a widespread distribution of Pcc protein complexes in phylogenetically diverse bacteria. Deletion of ombB-omaB-omcB-orfS-ombC-omaC-omcC gene clusters had no impact on the growth of G.sulfurreducensPCA with fumarate but diminished the ability of G.sulfurreducensPCA to reduce Fe(III)-citrate and ferrihydrite. Complementation with the ombB-omaB-omcB gene cluster restored the ability of G.sulfurreducensPCA to reduce Fe(III)-citrate and ferrihydrite. C1 [Liu, Yimo; Wang, Zheming; Liu, Juan; Kennedy, David W.; Shi, Zhi; Rosso, Kevin M.; Zachara, John M.; Fredrickson, James K.; Shi, Liang] Pacific NW Natl Lab, Fundamental & Computat Sci Directorate, Richland, WA 99352 USA. [Levar, Caleb; Bond, Daniel R.] Univ Minnesota, Dept Microbiol, St Paul, MN 55108 USA. [Edwards, Marcus J.; Clarke, Thomas A.; Butt, Julea N.; Richardson, David J.] Univ E Anglia, Sch Biol Sci, Ctr Mol & Struct Biochem, Norwich NR4 7TJ, Norfolk, England. [Edwards, Marcus J.; Clarke, Thomas A.; Butt, Julea N.; Richardson, David J.] Univ E Anglia, Sch Chem, Norwich NR4 7TJ, Norfolk, England. [Babauta, Jerome T.; Beyenal, Haluk] Washington State Univ, Gene & Linda Voiland Sch Chem Engn & Bioengn, Pullman, WA 99164 USA. RP Shi, L (reprint author), Pacific NW Natl Lab, Fundamental & Computat Sci Directorate, Richland, WA 99352 USA. EM liang.shi@pnnl.gov RI clarke, tom/D-1837-2009; Wang, Zheming/E-8244-2010; Liu, Juan/G-6035-2016; Butt, Julea/E-2133-2011; OI clarke, tom/0000-0002-6234-1914; Wang, Zheming/0000-0002-1986-4357; Butt, Julea/0000-0002-9624-5226; Bond, Daniel/0000-0001-8083-7107; Kennedy, David/0000-0003-0763-501X FU Subsurface Biogeochemical Research program (SBR)/Office of Biological and Environmental Research (BER), U.S. Department of Energy (DOE); Genome Science Program (GSP)/BER [DE-SC0007229]; DOE-BER; DOE by Battelle [DE-AC05-76RLO 1830] FX This work was supported by the Subsurface Biogeochemical Research program (SBR)/Office of Biological and Environmental Research (BER), U.S. Department of Energy (DOE), and is a contribution of the Pacific Northwest National Laboratory (PNNL) Scientific Focus Area. Y. L. was supported by the Genome Science Program (GSP)/BER (DE-SC0007229). We are grateful for experimental assistance from Dr G. Saalbach (John Innes Centre proteomics facility, UK). A portion of the research was performed at the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by DOE-BER and located at PNNL. Pacific Northwest National Laboratory is operated for the DOE by Battelle under contract DE-AC05-76RLO 1830. NR 49 TC 30 Z9 30 U1 14 U2 70 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 1758-2229 J9 ENV MICROBIOL REP JI Environ. Microbiol. Rep. PD DEC PY 2014 VL 6 IS 6 BP 776 EP 785 DI 10.1111/1758-2229.12204 PG 10 WC Environmental Sciences; Microbiology SC Environmental Sciences & Ecology; Microbiology GA AU6GU UT WOS:000345702700027 PM 25139405 ER PT J AU Moran, JJ Doll, CG Bernstein, HC Renslow, RS Cory, AB Hutchison, JR Lindemann, SR Fredrickson, JK AF Moran, James J. Doll, Charles G. Bernstein, Hans C. Renslow, Ryan S. Cory, Alexandra B. Hutchison, Janine R. Lindemann, Stephen R. Fredrickson, James K. TI Spatially tracking C-13-labelled substrate (bicarbonate) accumulation in microbial communities using laser ablation isotope ratio mass spectrometry SO ENVIRONMENTAL MICROBIOLOGY REPORTS LA English DT Article ID TREE-RINGS; MATS; CARBON; DELTA-C-13; DIVERSITY; OXYGEN AB Microbial mats are characterized by extensive metabolic interactions, rapidly changing internal geochemical gradients, and prevalent microenvironments within tightly constrained physical structures. We present laser ablation isotope ratio mass spectrometry (LA-IRMS) as a culture-independent, spatially specific technology for tracking the accumulation of C-13-labelled substrate into heterogeneous microbial mat communities. This study demonstrates the novel LA-IRMS approach by tracking labeled bicarbonate incorporation into a cyanobacteria-dominated microbial mat system. The spatial resolution of 50m was sufficient for distinguishing different mat strata and the approach effectively identified regions of greatest label incorporation. Sample preparation for LA-IRMS is straightforward and the spatial selectivity of LA-IRMS minimizes the volume of mat consumed, leaving material for complimentary analyses. We present analysis of DNA extracted from a sample post-ablation and suggest pigments, lipids or other biomarkers could similarly be extracted following ablation. LA-IRMS is well positioned to spatially resolve the accumulation of any C-13-labelled substrate provided to a mat, making this a versatile tool for studying carbon transfer and interspecies exchanges within the limited spatial confines of such systems. C1 [Moran, James J.; Doll, Charles G.; Bernstein, Hans C.] Pacific NW Natl Lab, Natl Secur Directorate, Signatures Sci & Technol Div, Richland, WA 99352 USA. [Renslow, Ryan S.] Pacific NW Natl Lab, William R Wiley Environm Mol Sci Lab, Sci Resources Div, Richland, WA 99352 USA. [Cory, Alexandra B.] Lawrence Univ, Dept Geol, Appleton, WI 54911 USA. [Hutchison, Janine R.; Lindemann, Stephen R.; Fredrickson, James K.] Pacific NW Natl Lab, Fundamental & Computat Sci Directorate, Biol Sci Div, Richland, WA 99352 USA. RP Moran, JJ (reprint author), Pacific NW Natl Lab, Natl Secur Directorate, Signatures Sci & Technol Div, Richland, WA 99352 USA. EM James.Moran@pnnl.gov RI Lindemann, Steve/H-6088-2016; OI Lindemann, Steve/0000-0002-3788-5389; Moran, James/0000-0001-9081-9017; Bernstein, Hans/0000-0003-2913-7708 FU Genomic Science Program (GSP), Office of Biological and Environmental Research (OBER), U.S. Department of Energy (DOE); Lawrence University (Appleton, WI) LUR1 program; Linus Pauling Distinguished Post-doctoral Fellowship program FX This research was supported by the Genomic Science Program (GSP), Office of Biological and Environmental Research (OBER), U.S. Department of Energy (DOE) and is a contribution of the Pacific Northwest National Laboratory (PNNL) Foundational Scientific Focus Area. Alexandra B. Cory was supported by the Lawrence University (Appleton, WI) LUR1 program. A portion of the research described in this paper was conducted under the Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory, a multiprogramme national laboratory operated by Battelle for the U.S. Department of Energy. Hans C. Bernstein and Ryan S. Renslow are grateful for the support of the Linus Pauling Distinguished Post-doctoral Fellowship program. We thank William Chrisler for his assistance in microscope sample photography and Dr. Helen Kreuzer for insightful discussions regarding data interpretation. NR 22 TC 4 Z9 4 U1 1 U2 16 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 1758-2229 J9 ENV MICROBIOL REP JI Environ. Microbiol. Rep. PD DEC PY 2014 VL 6 IS 6 BP 786 EP 791 DI 10.1111/1758-2229.12211 PG 6 WC Environmental Sciences; Microbiology SC Environmental Sciences & Ecology; Microbiology GA AU6GU UT WOS:000345702700028 PM 25155264 ER PT J AU Earl, D Nguyen, N Hickey, G Harris, RS Fitzgerald, S Beal, K Seledtsov, I Molodtsov, V Raney, BJ Clawson, H Kim, J Kemena, C Chang, JM Erb, L Poliakov, A Hou, M Herrero, J Kent, WJ Solovyev, V Darling, AE Ma, J Notredame, C Brudno, M Dubchak, I Haussler, D Paten, B AF Earl, Dent Nguyen, Ngan Hickey, Glenn Harris, Robert S. Fitzgerald, Stephen Beal, Kathryn Seledtsov, Igor Molodtsov, Vladimir Raney, Brian J. Clawson, Hiram Kim, Jaebum Kemena, Carsten Chang, Jia-Ming Erb, Ionas Poliakov, Alexander Hou, Minmei Herrero, Javier Kent, William James Solovyev, Victor Darling, Aaron E. Ma, Jian Notredame, Cedric Brudno, Michael Dubchak, Inna Haussler, David Paten, Benedict TI Alignathon: a competitive assessment of whole-genome alignment methods SO GENOME RESEARCH LA English DT Article ID MULTIPLE SEQUENCE ALIGNMENT; EVOLUTION; SIMULATION; ELEMENTS; BROWSER; GENES; UNCERTAINTY; RELIABILITY; BENCHMARKS; CHALLENGES AB Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments and then assessments were performed collectively after all the submissions were received. Three data sets were used: Two were simulated and based on primate and mammalian phylogenies, and one was comprised of 20 real fly genomes. In total, 35 submissions were assessed, submitted by 10 teams using 12 different alignment pipelines. We found agreement between independent simulation-based and statistical assessments, indicating that there are substantial accuracy differences between contemporary alignment tools. We saw considerable differences in the alignment quality of differently annotated regions and found that few tools aligned the duplications analyzed. We found that many tools worked well at shorter evolutionary distances, but fewer performed competitively at longer distances. We provide all data sets, submissions, and assessment programs for further study and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments. C1 [Earl, Dent; Nguyen, Ngan; Raney, Brian J.; Clawson, Hiram; Kent, William James; Haussler, David; Paten, Benedict] Univ Calif Santa Cruz, Ctr Biomol Sci & Engn, Santa Cruz, CA 95064 USA. [Earl, Dent; Nguyen, Ngan; Kent, William James; Haussler, David; Paten, Benedict] Univ Calif Santa Cruz, Dept Biomol Engn, Santa Cruz, CA 95064 USA. [Hickey, Glenn] McGill Univ, Sch Comp Sci, Montreal, PQ H3A 0G4, Canada. [Harris, Robert S.] Penn State Univ, Dept Biol, University Pk, PA 16801 USA. [Fitzgerald, Stephen; Beal, Kathryn; Herrero, Javier] European Bioinformat Inst, European Mol Biol Lab, Cambridge CB10 1SD, England. [Seledtsov, Igor; Molodtsov, Vladimir; Solovyev, Victor] Softberry Inc, Mt Kisco, NY 10549 USA. [Kim, Jaebum] Konkuk Univ, Dept Anim Biotechnol, Seoul 143701, South Korea. [Kemena, Carsten; Chang, Jia-Ming; Erb, Ionas; Notredame, Cedric] Ctr Genom Regulat CRG, Barcelona 08003, Spain. [Kemena, Carsten; Chang, Jia-Ming; Erb, Ionas; Notredame, Cedric] UPF, Barcelona 08003, Spain. [Kemena, Carsten] Univ Munster, Inst Evolut & Biodivers, D-48149 Munster, Germany. [Chang, Jia-Ming] CNRS, UPR 1142, Inst Human Genet IGH, Montpellier, France. [Poliakov, Alexander; Dubchak, Inna] Dept Energy Joint Genome Inst, Walnut Creek, CA 94598 USA. [Hou, Minmei] No Illinois Univ, Dept Comp Sci, De Kalb, IL 60115 USA. [Herrero, Javier] Genome Anal Ctr, Norwich NR4 7UH, Norfolk, England. [Darling, Aaron E.] Univ Technol Sydney, I Inst 3, Sydney, NSW 2007, Australia. [Ma, Jian] Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA. [Ma, Jian] Univ Illinois, Inst Genom Biol, Urbana, IL 61801 USA. [Brudno, Michael] Univ Toronto, Dept Comp Sci, Toronto, ON M5S 3G4, Canada. [Brudno, Michael] Univ Toronto, Donnelly Ctr, Toronto, ON M5S 3G4, Canada. [Brudno, Michael] Hosp Sick Children, Ctr Computat Med, Toronto, ON M5G 1X8, Canada. [Brudno, Michael] Hosp Sick Children, Genet & Genome Biol Program, Toronto, ON M5G 1X8, Canada. [Dubchak, Inna] Lawrence Berkeley Natl Lab, Berkeley, CA 94710 USA. [Haussler, David] Howard Hughes Med Inst, Chevy Chase, MD 20815 USA. RP Paten, B (reprint author), Univ Calif Santa Cruz, Ctr Biomol Sci & Engn, Santa Cruz, CA 95064 USA. EM benedict@soe.ucsc.edu RI Chang, Jia-Ming/A-5642-2008; Notredame, Cedric/G-3868-2010; OI Chang, Jia-Ming/0000-0002-6711-1739; Notredame, Cedric/0000-0003-1461-0988; Erb, Ionas/0000-0002-2331-9714; Herrero, Javier/0000-0001-7313-717X; Darling, Aaron/0000-0003-2397-7925; Solovyev, Victor/0000-0001-8885-493X FU Howard Hughes Medical Institute; NIH [2U41 HG002371-13, R21HG006464, R01HG007352, R15HG005913]; NHGRI/NIH [5U01HG004695]; NSF grant [1054309, 1262575]; Spanish Ministry of Economy and Competitiveness [BFU2011-28575]; Secretariat of Universities and Research; Department of Economy and Knowledge of the Government of Catalonia [SGR 951]; "la Caixa" International Fellowship Programme for a predoctoral fellowship at the CRG; European Research Council [232947]; Spanish Ministry of Economy and Competitiveness, "Centro de Excelencia Severo Ochoa" [SEV-2012-0208]; Wellcome Trust [WT095908]; European Molecular Biology Laboratory; European Community's Seventh Framework Programme (FP7) [222664] FX We would like to thank the Howard Hughes Medical Institute, Dr. and Mrs. Gordon Ringold, the NIH (grant 2U41 HG002371-13), and the NHGRI/NIH (grant 5U01HG004695) for providing funding. We would like to thank the Genome 10K organizers for providing a venue to discuss an early version of these findings. J.M. is supported by NIH grant R21HG006464, NIH grant R01HG007352, NSF grant 1054309, and NSF grant 1262575. M.H. is supported by NIH grant R15HG005913. O.K., J.-M.C., I.E., and C.N. were supported by the Spanish Ministry of Economy and Competitiveness (grant no. BFU2011-28575); the Secretariat of Universities and Research, Department of Economy and Knowledge of the Government of Catalonia (2009 SGR 951); the "la Caixa" International Fellowship Programme for a predoctoral fellowship at the CRG (to J.-M.C.); the European Research Council (ERC-2008-AdG no. 232947 to J.-M.C.); and the Spanish Ministry of Economy and Competitiveness, "Centro de Excelencia Severo Ochoa 2013-2017," SEV-2012-0208. This work was supported by the Wellcome Trust (grant no. WT095908) and the European Molecular Biology Laboratory. The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 222664 ("Quantomics"). This publication reflects only the authors' views and the European Community is not liable for any use that may be made of the information contained herein. We thank three anonymous referees who provided a great deal of helpful feedback and suggestions. NR 63 TC 14 Z9 14 U1 4 U2 13 PU COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT PI COLD SPRING HARBOR PA 1 BUNGTOWN RD, COLD SPRING HARBOR, NY 11724 USA SN 1088-9051 EI 1549-5469 J9 GENOME RES JI Genome Res. PD DEC PY 2014 VL 24 IS 12 BP 2077 EP 2089 DI 10.1101/gr.174920.114 PG 13 WC Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Genetics & Heredity SC Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Genetics & Heredity GA AU7XB UT WOS:000345810600016 PM 25273068 ER PT J AU Mernild, SH Hanna, E Yde, JC Seidenkrantz, MS Wilson, R Knudsen, NT AF Mernild, Sebastian H. Hanna, Edward Yde, Jacob C. Seidenkrantz, Marit-Solveig Wilson, Ryan Knudsen, Niels Tvis TI ATMOSPHERIC AND OCEANIC INFLUENCE ON MASS BALANCE OF NORTHERN NORTH ATLANTIC REGION LAND-TERMINATING GLACIERS SO GEOGRAFISKA ANNALER SERIES A-PHYSICAL GEOGRAPHY LA English DT Article DE Atlantic multidecadal oscillation; climate change; climate indices; glaciers and ice caps; Greenland Blocking Index; North Atlantic oscillation ID MITTIVAKKAT GLETSCHER; SOUTHEAST GREENLAND; EAST GREENLAND; OSCILLATION; CLIMATE; VARIABILITY; TEMPERATURE; CIRCULATION; PATTERNS; WASHINGTON AB In this study, observed annual mass-balance data series from 1970 to 2009 for 29 land-terminating glaciers and ice caps in the northern North Atlantic region are presented to highlight their spatio-temporal variability. The glaciers and ice caps mass-balance data are compared with various zonal latitude bands of regional near-surface air temperature time series, large-scale atmospheric and oceanic circulation indices, as well as with North Icelandic sea-surface temperature records, since variations in mass-balance conditions are related both to variations in surface weather conditions and to atmospheric and oceanic circulations. The purpose is to explore statistical and physical relations based on the hypothesis that the general atmospheric and sea-surface warming trends are potential drivers of the ongoing regional glaciers and ice caps mass change. Our analysis shows that the mean observed northern North Atlantic glaciers and ice caps annual mass balance was mostly negative during the first decade of the twenty-first century, with a variability in glaciers and ice caps loss from c. 860mm water equivalent yr(-1) for Southeast Greenland and Iceland to c. 380mm water equivalent yr(-1) for Svalbard and Scandinavia. For Iceland and Scandinavia, variations in the North Atlantic oscillation seem to be important for mass-balance conditions, whereas overall for the entire northern North Atlantic region the mass-balance time series was significantly correlated with both NASA's Goddard Institute for Space Studies regional near-surface air temperature and Atlantic multidecadal oscillation time series, individually. C1 [Mernild, Sebastian H.; Wilson, Ryan] Ctr Estudios Cient, Ctr Sci Studies, Glaciol & Climate Change Lab, Valdivia 5110466, Chile. [Mernild, Sebastian H.] Los Alamos Natl Lab, Climate Ocean & Sea Ice Modeling Grp, Los Alamos, NM 87545 USA. [Hanna, Edward] Univ Sheffield, Dept Geog, Sheffield S10 2TN, S Yorkshire, England. [Yde, Jacob C.] Sogn Fjordane Univ Coll, Fac Sci & Engn, Sogndal, Norway. [Seidenkrantz, Marit-Solveig] Aarhus Univ, Dept Geosci, Ctr Climate Studies, DK-8000 Aarhus, Denmark. [Seidenkrantz, Marit-Solveig] Aarhus Univ, Dept Geosci, Arctic Res Ctr, DK-8000 Aarhus, Denmark. [Knudsen, Niels Tvis] Aarhus Univ, Dept Geosci, DK-8000 Aarhus C, Denmark. RP Mernild, SH (reprint author), Ctr Estudios Cient, Ctr Sci Studies, Glaciol & Climate Change Lab, Av Arturo Prat 514, Valdivia 5110466, Chile. EM mernild@cecs.cl; e.hanna@sheffield.ac.uk; jacob.yde@hisf.no; mss@geo.au.dk; rwilson@cecs.cl; ntk@geo.au.dk RI Seidenkrantz, Marit-Solveig/A-3451-2012; Knudsen, Niels Tvis/A-2461-2014; Hanna, Edward/H-2219-2016; OI Seidenkrantz, Marit-Solveig/0000-0002-1973-5969; Hanna, Edward/0000-0002-8683-182X; Yde, Jacob Clement/0000-0002-6211-2601 FU Chilean Government through the Centers of Excellence Base Financing Program of CONICYT; Earth System Modeling program by the Scientific Discovery for Advanced Computing (SciDAC) program within the US Department of Energy's Office of Science; Los Alamos National Laboratory; National Nuclear Security Administration of the US Department of Energy [DE-AC52-06NA25396]; European Community [262693]; Danish Council for Independent Research Natural Science [12-126709/FNU]; EU [243908] FX This work was supported by the Chilean Government through the Centers of Excellence Base Financing Program of CONICYT, the Earth System Modeling program by the Scientific Discovery for Advanced Computing (SciDAC) program within the US Department of Energy's Office of Science and by the Los Alamos National Laboratory. 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 from the European Community's Seventh Framework Programme under grant agreement No. 262693 (project GLAMOSEG-II). It is also a contribution to the OCEANHEAT project funded by the Danish Council for Independent Research Natural Science (Project No. 12-126709/FNU), and the EU FP7 project "Past4Future" (Project No. 243908). Thanks are given to reviewers for their valuable comments and to the World Glacier Monitoring Service for providing GIC mass-balance data. We thank the Icelandic Meteorological Office and Trausti Jonsson for help in updating the NIceSST dataset and data used therein. NASA GISS data can be downloaded from http://data.giss.nasa.gov/gistemp/tabledata/ZonAnn. Ts+dSST.txt, AMO: http://www.esrl.noaa.gov/psd/data/timeseries/AMO/, NAO: http://gcmd.nasa.gov/records/GCMD_NCAR_NAO.html, and AO: http://www.cpc.ncep.noaa.gov/products/precip/CWlink/daily_ao_index/ao.sh tml. NR 68 TC 5 Z9 5 U1 0 U2 18 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 0435-3676 EI 1468-0459 J9 GEOGR ANN A JI Geogr. Ann. Ser. A-Phys. Geogr. PD DEC PY 2014 VL 96 IS 4 SI SI BP 561 EP 577 DI 10.1111/geoa.12053 PG 17 WC Geography, Physical; Geology SC Physical Geography; Geology GA AU7HG UT WOS:000345770800010 ER PT J AU Ondondo, B Clutton, G McMichael, A Korber, B Hanke, T AF Ondondo, B. Clutton, G. McMichael, A. Korber, B. Hanke, T. TI The 2nd generation of a T-cell vaccine against HIV based on conserved region mosaics SO IMMUNOLOGY LA English DT Meeting Abstract C1 [Ondondo, B.; Clutton, G.; McMichael, A.; Hanke, T.] Univ Oxford, Jenner Inst, Oxford, England. [Korber, B.] Los Alamos Natl Lab, Los Alamos, NM USA. NR 0 TC 0 Z9 0 U1 0 U2 1 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 0019-2805 EI 1365-2567 J9 IMMUNOLOGY JI Immunology PD DEC PY 2014 VL 143 SU 2 SI SI MA 677 BP 146 EP 146 PG 1 WC Immunology SC Immunology GA AU6GT UT WOS:000345702600439 ER PT J AU Brant, JA dela Cruz, C Yao, JL Douvalis, AP Bakas, T Sorescu, M Aitken, JA AF Brant, Jacilynn A. dela Cruz, Clarina Yao, Jinlei Douvalis, Alexios P. Bakas, Thomas Sorescu, Monica Aitken, Jennifer A. TI Field-Induced Spin-Flop in Antiferromagnetic Semiconductors with Commensurate and Incommensurate Magnetic Structures: Li2FeGeS4 (LIGS) and Li2FeSnS4 (LITS) SO INORGANIC CHEMISTRY LA English DT Article ID DIAMOND-LIKE SEMICONDUCTOR; ELECTRONIC BAND-STRUCTURE; RAY-POWDER DIFFRACTION; X-RAY; MOSSBAUER-SPECTRA; CRYSTAL-STRUCTURE; STRUCTURE REFINEMENT; STANNITE; CU2FESNS4; SYSTEM AB Li2FeGeS4 (LIGS) and Li2FeSnS4 (LITS), which are among the first magnetic semiconductors with the wurtz-kesterite structure, exhibit antiferromagnetism with TN 6 and 4 K, respectively. Both compounds undergo a conventional metamagnetic transition that is accompanied by a hysteresis; a reversible spin-flop transition is dominant. On the basis of constant-wavelength neutron powder diffraction data, we propose that LIGS and LITS exhibit collinear magnetic structures that are commensurate and incommensurate with propagation vectors k(m) = [(1)/(2), (1)/(2), (1)/(2)] and [0, 0, 0.546(1)], respectively. The two compounds exhibit similar magnetic phase diagrams, as the critical fields are temperature-dependent. The nuclear structures of the bulk powder samples were verified using time-of-flight neutron powder diffraction along with synchrotron X-ray powder diffraction. (57)Fe and (119)Sn Mossbauer spectroscopy confirmed the presence of Fe2+ and Sn4+ as well as the number of crystallographically unique positions. LIGS and LITS are semiconductors with indirect and direct bandgaps of 1.42 and 1.86 eV, respectively, according to optical diffuse-reflectance UV-vis-NIR spectroscopy. C1 [Brant, Jacilynn A.; Aitken, Jennifer A.] Duquesne Univ, Dept Chem & Biochem, Pittsburgh, PA 15282 USA. [dela Cruz, Clarina] Oak Ridge Natl Lab, Quantum Condensed Matter Div, Oak Ridge, TN 37381 USA. [Yao, Jinlei] Suzhou Univ Sci & Technol, Sch Math & Phys, Res Ctr Solid State Phys & Mat, Suzhou 215009, Peoples R China. [Douvalis, Alexios P.; Bakas, Thomas] Univ Ioannina, Dept Phys, GR-45110 Ioannina, Greece. [Sorescu, Monica] Duquesne Univ, Dept Phys, Pittsburgh, PA 15282 USA. RP Aitken, JA (reprint author), Duquesne Univ, Dept Chem & Biochem, Pittsburgh, PA 15282 USA. EM aitkenj@duq.edu RI Yao, Jinlei/D-4977-2012; dela Cruz, Clarina/C-2747-2013; OI dela Cruz, Clarina/0000-0003-4233-2145; Brant, Jacilynn/0000-0001-7825-8667 FU National Science Foundation [DMR-1201729, DMR-0645304]; Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy [IFTS-6435, IPTS-8267, IPTS-10859]; U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences [DE-AC02-06CH11357 (GUP-33598)] FX This work was supported by the National Science Foundation (Grants DMR-1201729 and DMR-0645304). A portion of this research at Oak Ridge National Laboratory's High Flux Isotope Reactor and Spallation Neutron Source was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy (IFTS-6435, IPTS-8267, and IPTS-10859). Use of the Advanced Photon Source at Argonne National Laboratory was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract DE-AC02-06CH11357 (GUP-33598). We thank Jason Hodges, Ashfia Huq, and Mike Shatruk for help with data collections and for valuable discussions. NR 95 TC 6 Z9 6 U1 1 U2 26 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0020-1669 EI 1520-510X J9 INORG CHEM JI Inorg. Chem. PD DEC 1 PY 2014 VL 53 IS 23 BP 12265 EP 12274 DI 10.1021/ic5011693 PG 10 WC Chemistry, Inorganic & Nuclear SC Chemistry GA AU6OZ UT WOS:000345723300009 PM 25397682 ER PT J AU Boyle, TJ Yonemoto, DT Doan, TQ Alam, TM AF Boyle, Timothy J. Yonemoto, Daniel T. Doan, Thu Q. Alam, Todd M. TI Synthesis and Structural Characterization of Group 4 Metal Carboxylates for Nanowire Production SO INORGANIC CHEMISTRY LA English DT Article ID CLUSTERS; METHACRYLATE; NANOFIBERS; REACTIVITY; FIBERS; LIGAND AB The synthesis and characterization of a series of group 4 carboxylate derivatives ([M(ORc)(4)] where M = Ti, Zr, Hf) was undertaken for potential utility as precursors to ceramic nanowires. The attempted syntheses of the [M(ORc())4] precursors were undertaken from the reaction of [M(OBut)(4)] with a select set of carboxylic acids (H-ORc where ORc = OPc (O2CCH(CH3)(2)), OBc (O2CC(CH3)(3)), ONc (O2CCH2C(CH3)(3))). The products were identified by single-crystal X-ray diffraction studies as [Ti(eta(2)-OBc)(3)(OBut] (1), [Zr-2(mu(3)-O)(mu-OPc)(4)(mu,eta(2)-OPc)eta(2)-OPc)](2) (2), [H](2)[Zr eta(2)-OBc)(2)(OBc)(2)(OBc)(2)] (3), [Zr(mu-ONc)(2)eta(2)-ONc)(2)](2) (4), or [Hf(mu-ORc)(2)eta(2)-ORc)(2)](2) [ORc = OPc (5), OBc (6, shown), ONc (7)]. The majority of compounds (4-7) were isolated as dinuclear species with a dodecahedral-like (CN-8) bonding mode around the metals due to chelation and bridging of the ORc ligand. The two monomers (1 and 3) were found to adopt a capped trigonal prismatic and CN-8 geometry, respectively, due to chelating ORc and terminal ORc or OBu(t) ligands. The metals of the oxo-species 2 were isolated in octahedral and CN-8 arrangements. These compounds were then processed by electrospinning methods (applied voltage 10 kV, flow rate 30-60 mu L/min, electric field 0.5 kV/cm), and wire-like morphologies were isolated using compounds 4, 6 (shown), and 7. C1 [Boyle, Timothy J.; Yonemoto, Daniel T.; Doan, Thu Q.; Alam, Todd M.] Sandia Natl Labs, Adv Mat Lab, Albuquerque, NM 87106 USA. RP Boyle, TJ (reprint author), Sandia Natl Labs, Adv Mat Lab, 1001 Univ Blvd SE, Albuquerque, NM 87106 USA. EM tjboyle@sandia.gov FU Laboratory Directed Research and Development (LDRD) program at Sandia National Laboratories; U.S. Department of Energy, Office of Electricity [DE-AC04-94AL85000] FX For support of this research, the authors thank Dr. N. S. Bell for assistance with the viscosity measurements and the Laboratory Directed Research and Development (LDRD) program at Sandia National Laboratories and the U.S. Department of Energy, Office of Electricity, under Contract DE-AC04-94AL85000. Sandia is a multiprogramming laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy. NR 39 TC 3 Z9 3 U1 0 U2 16 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0020-1669 EI 1520-510X J9 INORG CHEM JI Inorg. Chem. PD DEC 1 PY 2014 VL 53 IS 23 BP 12449 EP 12458 DI 10.1021/ic501904m PG 10 WC Chemistry, Inorganic & Nuclear SC Chemistry GA AU6OZ UT WOS:000345723300029 PM 25402557 ER PT J AU Wu, LC Thomsen, MK Madsen, SR Schmoekel, M Jorgensen, MRV Cheng, MC Peng, SM Chen, YS Overgaard, J Iversen, BB AF Wu, Lai-Chin Thomsen, Maja K. Madsen, Solveig R. Schmoekel, Mette Jorgensen, Mads R. V. Cheng, Ming-Chuan Peng, Shie-Ming Chen, Yu-Sheng Overgaard, Jacob Iversen, Bo B. TI Chemical Bonding in a Linear Chromium Metal String Complex SO INORGANIC CHEMISTRY LA English DT Article ID EXPERIMENTAL ELECTRON-DENSITY; RAY CHARGE-DENSITY; AVERAGED FERMI HOLES; MN-MN BOND; CRYSTAL-STRUCTURE; X-RAY; TRICHROMIUM COMPLEXES; COORDINATION POLYMER; MAGNETIC-PROPERTIES; STRETCH ISOMERISM AB A combined experimental and theoretical electron density study of the shortest trichromium metal wire, Cr-3(dpa)(4)Cl-2 (C2H5OC2H5)x(CH2Cl2)(1-x) (1, dpa = bis(2-pyridyl)amido), is reported. High resolution X-ray diffraction data has been collected both at 100 K using a conventional X-ray source (DS1) and at 15 K using a synchrotron X-ray source (DS2). The linear chromium string is terminated by Cl- ions at both ends, and each Cr atom is also coordinated by four N atoms from bridging dpa ligands. The two Cr-Cr bond distances are unequal at 100 K (with d(Cr-1-Cr-2) being 0.029 angstrom shorter than d(Cr-2-Cr-3)) but at 15 K they are almost equal (0.002 angstrom difference). Analysis of the slightly elongated thermal ellipsoids of the Cr-2 atom suggests that it is not due to disorder, but the presence of a shallow potential energy surface. Laplacian maps clearly show local valence shell charge concentration (VSCC) in the electron density along the bisector of the equatorial Cr-N bonds. Integration over the atomic basins indicates that Cr-2 has smaller atomic charge and volume than Cr-1 and Cr-3. The topological characterization of the Cr-Cr bonds indicates partly covalent characters with electron density at the bond critical point of similar to 0.3 e angstrom(-3) and negative total energy density. The delocalization index of Cr-Cr is 0.8 for Cr-1-Cr-2 and 0.08 for Cr-1-Cr-3. Second-order perturbation analysis shows high stabilization energy of the Cr-Cr bonds (E-2 similar to 190 kcal mol(-1). Delocalization indices and source function and natural bond orbital analyses are all indicative of localized Cr-Cr bonding interactions. C1 [Wu, Lai-Chin; Thomsen, Maja K.; Madsen, Solveig R.; Schmoekel, Mette; Jorgensen, Mads R. V.; Overgaard, Jacob; Iversen, Bo B.] Aarhus Univ, Dept Chem & INANO, Ctr Mat Crystallog, DK-8000 Aarhus, Denmark. [Cheng, Ming-Chuan; Peng, Shie-Ming] Acad Sinica, Dept Chem, Taipei 115, Taiwan. [Chen, Yu-Sheng] Univ Chicago, ChemMatCARS Beam Iine, Adv Photon Source, Argonne, IL 60439 USA. RP Overgaard, J (reprint author), Aarhus Univ, Dept Chem & INANO, Ctr Mat Crystallog, Langelandsgade 140, DK-8000 Aarhus, Denmark. EM jacobo@chem.au.dk; bo@chem.au.dk RI Jorgensen, Mads Ry Vogel/C-6109-2017; OI Jorgensen, Mads Ry Vogel/0000-0001-5507-9615; Overgaard, Jacob/0000-0001-6492-7962 FU Danish Research Council (Danscatt); Danish National Research Foundation [DNRF93] FX We gratefully acknowledge the beam time obtained at beamline 15-ID-E, ChemMatCARS beamline, The University of Chicago, Advanced Photon Source. The work was supported by the Danish Research Council (Danscatt) and by the Danish National Research Foundation (DNRF93) NR 104 TC 3 Z9 3 U1 4 U2 32 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0020-1669 EI 1520-510X J9 INORG CHEM JI Inorg. Chem. PD DEC 1 PY 2014 VL 53 IS 23 BP 12489 EP 12498 DI 10.1021/ic501603x PG 10 WC Chemistry, Inorganic & Nuclear SC Chemistry GA AU6OZ UT WOS:000345723300033 PM 25383889 ER PT J AU De Sio, SM Wilson, RE AF De Sio, Stephanie M. Wilson, Richard E. TI EXAFS Study of the Speciation of Protactinium(V) in Aqueous Hydrofluoric Acid Solutions SO INORGANIC CHEMISTRY LA English DT Article ID ABSORPTION FINE-STRUCTURE; CRYSTAL-STRUCTURE; FLUORO-COMPLEXES; SPECTROSCOPY; TEMPERATURES; IFEFFIT; RAMAN; IONS AB The speciation of protactinium(V) in hydrofluoric acid (HF) solutions was studied using X-ray absorption spectroscopy. Extended X-ray absorption fine structure measurements were performed on an aqueous solution of 0.05 M protactinium(V) with various HF concentrations ranging from 0.5 to 27 M in order to probe the protactinium coordination sphere with respect to the identity and number of coordinating ligands. The resulting fits to the spectra suggest the presence of an eight-coordinate homoleptic fluoro complex in highly concentrated fluoride solutions (27 M), with equilibrium between seven- and eight-coordinate fluoro complexes at moderate acidities, and in more dilute solutions, results indicate that one water molecule is likely to replace a fluoride in the first coordination sphere, at a distance of 2.54-2.57 angstrom. Comparisons of this chemistry with group V metals, niobium and tantalum, are presented, and the potential implications for these results on the hydrolytic behavior of protactinium in aqueous systems are discussed. C1 [De Sio, Stephanie M.; Wilson, Richard E.] Argonne Natl Lab, Chem Sci & Engn Div, Argonne, IL 60439 USA. RP Wilson, RE (reprint author), Argonne Natl Lab, Chem Sci & Engn Div, 9700 S Cass Ave, Argonne, IL 60439 USA. EM rewilson@anl.gov RI De Sio, Stephanie/I-7327-2013; Wilson, Richard/H-1763-2011 OI De Sio, Stephanie/0000-0001-7724-3498; Wilson, Richard/0000-0001-8618-5680 FU United States Department of Energy, Office of Science, Basic Energy Sciences, Early Career Research Award Program [DE-AC02-06CH11357] FX This work was performed at Argonne National Laboratory, operated by UChicagoArgonne LLC, for the United States Department of Energy, Office of Science, Basic Energy Sciences, Early Career Research Award Program, under Contract DE-AC02-06CH11357. NR 36 TC 5 Z9 5 U1 4 U2 18 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0020-1669 EI 1520-510X J9 INORG CHEM JI Inorg. Chem. PD DEC 1 PY 2014 VL 53 IS 23 BP 12643 EP 12649 DI 10.1021/ic502376m PG 7 WC Chemistry, Inorganic & Nuclear SC Chemistry GA AU6OZ UT WOS:000345723300050 PM 25389749 ER PT J AU Duros, V Sartzi, H Teat, SJ Sanakis, Y Roubeau, O Perlepes, SP AF Duros, Vasilios Sartzi, Harikleia Teat, Simon J. Sanakis, Yiannis Roubeau, Olivier Perlepes, Spyros P. TI Tris{2,4-bis(2-pyridyl)-1,3,5-triazapentanedienato}manganese(III), a complex derived from a unique metal ion-assisted transformation of pyridine-2-amidoxime SO INORGANIC CHEMISTRY COMMUNICATIONS LA English DT Article DE EPR spectra; Manganese(III) complex; Metal-ion-assisted ligand's transformation; Pyridine-2-amidoxime; 2,4-Bis(2-pyridyl)-1,3,5-triazapentanedienate(-1) ligand ID CRYSTAL; TRIS(2,4-PENTANEDIONATO)MANGANESE(III) AB A novel metal ion-mediated reaction of pyridine-2-amidoxime has led to a 1:3 mononuclear Mn(III) complex containing the 2,4-bis(2-pyridyI)-1,3,5-triazapentanedienate(-1) ligand; the high-spin Mn-III in the complex is "EPR silent" at X-band. (C) 2014 Elsevier B.V. All rights reserved. C1 [Duros, Vasilios; Sartzi, Harikleia; Perlepes, Spyros P.] Univ Patras, Dept Chem, Patras 26504, Greece. [Sartzi, Harikleia] Univ Glasgow, WestCHEM, Dept Chem, Glasgow C12 8QQ, Lanark, Scotland. [Teat, Simon J.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA. [Sanakis, Yiannis] NCSR Demokritos, Inst Adv Mat Physicochem Proc Nanotechnol & Micro, Dept Mat Sci, Aghia Paraskevi 15310, Greece. [Roubeau, Olivier] Univ Zaragoza, Fac Ciencias, CSIC, Inst Ciencia Mat Aragon, Zaragoza 50009, Spain. [Perlepes, Spyros P.] Fdn Res & Technol Hellas FORTH ICE HT, Inst Chem Engn Sci, Patras 26504, Greece. RP Sanakis, Y (reprint author), NCSR Demokritos, Inst Adv Mat Physicochem Proc Nanotechnol & Micro, Dept Mat Sci, Aghia Paraskevi 15310, Greece. EM sanakis@ims.demokritos.gr; roubeau@unizar.es; perlepes@patreas.upatras.gr RI Roubeau, Olivier/A-6839-2010 OI Roubeau, Olivier/0000-0003-2095-5843 FU European Union (European Social Fund-ESF); Greek National Funds through the Operational Programme "Education and Lifelong Learning" of the National Strategic Reference Framework (NSRF)-Research Funding Programme: THALFS; Office of Science, Office of Basic Energy Sciences of the U.S. Department of Energy [DE-AC02-05CH11231] FX This research has been co-financed by the European Union (European Social Fund-ESF) and Greek National Funds through the Operational Programme "Education and Lifelong Learning" of the National Strategic Reference Framework (NSRF)-Research Funding Programme: THALFS. Investing in knowledge society through the European Social Fund (to S.P.P.). The Advance 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 22 TC 3 Z9 3 U1 1 U2 6 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 1387-7003 EI 1879-0259 J9 INORG CHEM COMMUN JI Inorg. Chem. Commun. PD DEC PY 2014 VL 50 BP 117 EP 121 DI 10.1016/j.inoche.2014.10.017 PG 5 WC Chemistry, Inorganic & Nuclear SC Chemistry GA AU8BX UT WOS:000345822700029 ER PT J AU Qian, M Anderson, IE AF Qian, Ma Anderson, Iver E. TI PREFACE: PM TITANIUM SO INTERNATIONAL JOURNAL OF POWDER METALLURGY LA English DT Editorial Material C1 [Qian, Ma] RMIT Univ, Sch Aerosp Mech & Mfg Engn, Melbourne, Vic 3001, Australia. [Qian, Ma] Univ Queensland, Sch Mech & Min Engn, Brisbane, Qld 4072, Australia. [Anderson, Iver E.] Iowa State Univ, Ames Lab, Ames, IA 50011 USA. RP Qian, M (reprint author), RMIT Univ, Sch Aerosp Mech & Mfg Engn, GPO Box 2476, Melbourne, Vic 3001, Australia. EM rna.qian@rmit.edu.au; andersoni@ameslab.gov NR 0 TC 0 Z9 0 U1 0 U2 2 PU AMER POWDER METALLURGY INST PI PRINCETON PA 105 COLLEGE ROAD EAST, PRINCETON, NJ 08540 USA SN 0888-7462 J9 INT J POWDER METALL JI Int. J. Powder Metall. PD WIN PY 2014 VL 50 IS 1 BP 23 EP 24 PG 2 WC Metallurgy & Metallurgical Engineering SC Metallurgy & Metallurgical Engineering GA AW1IZ UT WOS:000346044500004 ER PT J AU Dabritz, HA Hill, KK Barash, JR Ticknor, LO Helma, CH Dover, N Payne, JR Arnon, SS AF Dabritz, Haydee A. Hill, Karen K. Barash, Jason R. Ticknor, Lawrence O. Helma, Charles H. Dover, Nir Payne, Jessica R. Arnon, Stephen S. TI Molecular Epidemiology of Infant Botulism in California and Elsewhere, 1976-2010 SO JOURNAL OF INFECTIOUS DISEASES LA English DT Article DE botulinum toxin; clinical spectrum; Clostridium baratii; Clostridium botulinum; Clostridium butyricum; honey; infant botulism; molecular epidemiology; sudden infant death ID FRAGMENT LENGTH POLYMORPHISM; TANDEM-REPEAT ANALYSIS; CLOSTRIDIUM-BOTULINUM; GENETIC-CHARACTERIZATION; NEUROTOXIN GENES; DEATH-SYNDROME; A STRAINS; TOXIN; DIFFERENTIATION; OUTBREAK AB Background. Infant botulism (IB), first identified in California in 1976, results from Clostridium botulinum spores that germinate, multiply, and produce botulinum neurotoxin (BoNT) in the immature intestine. From 1976 to 2010 we created an archive of 1090 BoNT-producing isolates consisting of 1012 IB patient ( 10 outpatient, 985 hospitalized, 17 sudden death), 25 food, 18 dust/soils, and 35 other strains. Methods. The mouse neutralization assay determined isolate toxin type (56% BoNT/A, 32% BoNT/B). Amplified fragment-length polymorphism (AFLP) analysis of the isolates was combined with epidemiologic information. Results. The AFLP dendrogram, the largest to date, contained 154 clades; 52% of isolates clustered in just 2 clades, 1 BoNT/A (n = 418) and 1 BoNT/B (n = 145). These clades constituted an endemic C. botulinum population that produced the entire clinical spectrum of IB. Isolates from the patient's home environment (dust/soil, honey) usually located to the same AFLP clade as the patient's isolate, thereby identifying the likely source of infective spores. C. botulinum A(B) strains were identified in California for the first time. Conclusions. Combining molecular methods and epidemiological data created an effective tool that yielded novel insights into the genetic diversity of C. botulinum and the clinical spectrum, occurrence, and distribution of IB in California. C1 [Dabritz, Haydee A.; Barash, Jason R.; Dover, Nir; Payne, Jessica R.; Arnon, Stephen S.] Calif Dept Publ Hlth, Infant Botulism Treatment & Prevent Program, Div Communicable Dis Control, Ctr Infect Dis, Richmond, CA 94804 USA. [Hill, Karen K.; Helma, Charles H.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM 87545 USA. [Ticknor, Lawrence O.] Los Alamos Natl Lab, Comp Computat & Stat Sci Div, Los Alamos, NM 87545 USA. RP Arnon, SS (reprint author), Calif Dept Publ Hlth, Infant Botulism Treatment & Prevent Program, 850 Marina Bay Pkwy E-361, Richmond, CA 94804 USA. EM stephen.arnon@cdph.ca.gov OI Ticknor, Lawrence/0000-0002-7967-7908 FU US Department of Homeland Security Science and Technology Directorate; Infant Botulism Treatment and Prevention Fund of the California Department of Public Health FX The RT-PCR assay development work was supported by the US Department of Homeland Security Science and Technology Directorate. This work was otherwise supported by the Infant Botulism Treatment and Prevention Fund of the California Department of Public Health. NR 50 TC 5 Z9 5 U1 2 U2 14 PU OXFORD UNIV PRESS INC PI CARY PA JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA SN 0022-1899 EI 1537-6613 J9 J INFECT DIS JI J. Infect. Dis. PD DEC 1 PY 2014 VL 210 IS 11 BP 1711 EP 1722 DI 10.1093/infdis/jiu331 PG 12 WC Immunology; Infectious Diseases; Microbiology SC Immunology; Infectious Diseases; Microbiology GA AU7HI UT WOS:000345771000005 PM 24924163 ER PT J AU Zuo, SM Zhou, XG Chen, MS Zhang, SL Schwessinger, B Ruan, DL Yuan, C Wang, J Chen, XW Ronald, PC AF Zuo, Shimin Zhou, Xiaogang Chen, Mawsheng Zhang, Shilu Schwessinger, Benjamin Ruan, Deling Yuan, Can Wang, Jing Chen, Xuewei Ronald, Pamela C. TI OsSERK1 regulates rice development but not immunity to Xanthomonas oryzae pv. oryzae or Magnaporthe oryzae SO JOURNAL OF INTEGRATIVE PLANT BIOLOGY LA English DT Article DE Oryza sativa; OsSERK1; somatic embryogenesis receptor kinase; Xanthomonas oryzae pv. Oryzae; Magnaporthe oryzae ID SOMATIC-EMBRYOGENESIS; PLANT ARCHITECTURE; INNATE IMMUNITY; CELL-DEATH; DISEASE RESISTANCE; NEGATIVE REGULATOR; ARABIDOPSIS; KINASE; BAK1; GENE AB Somatic embryogenesis receptor kinase (SERK) proteins play pivotal roles in regulation of plant development and immunity. The rice genome contains two SERK genes, OsSerk1 and OsSerk2. We previously demonstrated that OsSerk2 is required for rice Xa21-mediated resistance to Xanthomonas oryzae pv. oryzae (Xoo) and for normal development. Here we report the molecular characterization of OsSerk1. Overexpression of OsSerk1 results in a semi-dwarf phenotype whereas silencing of OsSerk1 results in a reduced angle of the lamina joint. OsSerk1 is not required for rice resistance to Xoo or Magnaporthe oryzae. Overexpression of OsSerk1 in OsSerk2-silenced lines complements phenotypes associated with brassinosteroid (BR) signaling defects, but not the disease resistance phenotype mediated by Xa21. In yeast, OsSERK1 interacts with itself forming homodimers, and also interacts with the kinase domains of OsSERK2 and BRI1, respectively. OsSERK1 is a functional protein kinase capable of autophosphorylation in vitro. We conclude that, whereas OsSERK2 regulates both rice development and immunity, OsSERK1 functions in rice development but not immunity to Xoo and M. oryzae. C1 [Zuo, Shimin; Chen, Mawsheng; Zhang, Shilu; Schwessinger, Benjamin; Ruan, Deling; Ronald, Pamela C.] Univ Calif Davis, Dept Plant Pathol, Davis, CA 95616 USA. [Zuo, Shimin; Chen, Mawsheng; Zhang, Shilu; Schwessinger, Benjamin; Ruan, Deling; Ronald, Pamela C.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. [Zuo, Shimin; Schwessinger, Benjamin; Ruan, Deling; Ronald, Pamela C.] Joint Bioenergy Inst, Emeryville, CA 94710 USA. [Zuo, Shimin] Yangzhou Univ, Coll Agr, Key Lab Crop Genet & Physiol Jiangsu Prov, Yangzhou 225009, Peoples R China. [Zuo, Shimin] Yangzhou Univ, Coll Agr, Minist Educ, Key Lab Plant Funct Genom, Yangzhou 225009, Peoples R China. [Zhou, Xiaogang; Yuan, Can; Wang, Jing; Chen, Xuewei] Sichuan Agr Univ Wenjiang, Rice Res Inst, Chengdu 611130, Peoples R China. RP Chen, XW (reprint author), Sichuan Agr Univ Wenjiang, Rice Res Inst, Chengdu 611130, Peoples R China. EM xwchen88@163.com; pcronald@ucdavis.edu OI Schwessinger, Benjamin/0000-0002-7194-2922 FU National Institutes of Health [GM59962]; Jiangsu Government scholarship for overseas study; fund for short-term visit of foreign research fellows; National Science Fund of China [31171622, 31371705]; Sichuan 'Hundred Talents Plan' fund; EMBO (European Molecular Biology Organization) long-term post-doctoral fellowship [ALTF 1290-2011]; Human Frontiers Science Program long-term post-doctoral fellowship [LT000674/2012] FX We are grateful to Dr. Bo Ding and Professor Wende Liu from Institution of Plant Protection of Chinese Academic of Agricultural Science for their helpful discussions on this manuscript. We also thank Professor Zhihui Xia from Hainan University, China, for kindly providing the Xoo strain Xoo-4. This work was supported by a National Institutes of Health grant (GM59962) to Pamela C. Ronald, Jiangsu Government scholarship for overseas study and the fund for short-term visit of foreign research fellows to Shimin Zuo, National Science Fund of China (31171622 and 31371705) and Sichuan 'Hundred Talents Plan' fund to Xuewei Chen, and an EMBO (European Molecular Biology Organization) long-term post-doctoral fellowship (ALTF 1290-2011) and a Human Frontiers Science Program long-term post-doctoral fellowship (LT000674/2012) to Benjamin Schwessinger. NR 38 TC 6 Z9 6 U1 4 U2 27 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 1672-9072 EI 1744-7909 J9 J INTEGR PLANT BIOL JI J. Integr. Plant Biol. PD DEC PY 2014 VL 56 IS 12 BP 1179 EP 1192 DI 10.1111/jipb.12290 PG 14 WC Biochemistry & Molecular Biology; Plant Sciences SC Biochemistry & Molecular Biology; Plant Sciences GA AU8KK UT WOS:000345845200007 PM 25266270 ER PT J AU Krishnamoorthy, S Ramanujam, J Sadayappan, P AF Krishnamoorthy, Sriram Ramanujam, J. Sadayappan, P. TI Introduction to the JPDC Special Issue on Domain-Specific Languages and High-Level Frameworks for High-Performance Computing SO JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING LA English DT Editorial Material C1 [Krishnamoorthy, Sriram] Pacific NW Natl Lab, Richland, WA 99352 USA. [Ramanujam, J.] Louisiana State Univ, Baton Rouge, LA 70803 USA. [Sadayappan, P.] Ohio State Univ, Columbus, OH 43210 USA. RP Krishnamoorthy, S (reprint author), Pacific NW Natl Lab, Richland, WA 99352 USA. EM sriram@pnnl.gov; jxr@ece.lsu.edu; sadayappan.1@osu.edu NR 0 TC 0 Z9 0 U1 1 U2 3 PU ACADEMIC PRESS INC ELSEVIER SCIENCE PI SAN DIEGO PA 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA SN 0743-7315 EI 1096-0848 J9 J PARALLEL DISTR COM JI J. Parallel Distrib. Comput. PD DEC PY 2014 VL 74 IS 12 SI SI BP 3175 EP 3175 DI 10.1016/j.jpdc.2014.09.011 PG 1 WC Computer Science, Theory & Methods SC Computer Science GA AU6SZ UT WOS:000345733300001 ER PT J AU Solomonik, E Matthews, D Hammond, JR Stanton, JF Demmel, J AF Solomonik, Edgar Matthews, Devin Hammond, Jeff R. Stanton, John F. Demmel, James TI A massively parallel tensor contraction framework for coupled-cluster computations SO JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING LA English DT Article DE Coupled-cluster; Tensor contractions; Matrix multiplication; Topology-aware mapping; Communication-avoiding algorithms ID MANY-BODY PERTURBATION; MATRIX MULTIPLICATION; CONFIGURATION-INTERACTION; QUANTUM-CHEMISTRY; MODEL; ALGORITHMS; IMPLEMENTATION; EXCITATIONS; SINGLES; TRIPLE AB Precise calculation of molecular electronic wavefunctions by methods such as coupled-cluster requires the computation of tensor contractions, the cost of which has polynomial computational scaling with respect to the system and basis set sizes. Each contraction may be executed via matrix multiplication on a properly ordered and structured tensor. However, data transpositions are often needed to reorder the tensors for each contraction. Writing and optimizing distributed-memory kernels for each transposition and contraction is tedious since the number of contractions scales combinatorially with the number of tensor indices. We present a distributed-memory numerical library (Cyclops Tensor Framework (CTF)) that automatically manages tensor blocking and redistribution to perform any user-specified contractions. CTF serves as the distributed-memory contraction engine in Aquarius, a new program designed for high-accuracy and massively-parallel quantum chemical computations. Aquarius implements a range of coupled-cluster and related methods such as CCSD and CCSDT by writing the equations on top of a C++ templated domain-specific language. This DSL calls CTF directly to manage the data and perform the contractions. Our CCSD and CCSDT implementations achieve high parallel scalability on the BlueGene/Q and Cray XC30 supercomputer architectures showing that accurate electronic structure calculations can be effectively carried out on top of general distributed-memory tensor primitives. (C) 2014 Elsevier Inc. All rights reserved. C1 [Solomonik, Edgar; Demmel, James] Univ Calif Berkeley, Dept Elect Engn & Comp Sci, Berkeley, CA 94720 USA. [Matthews, Devin; Stanton, John F.] Univ Texas Austin, Dept Chem & Biochem, Austin, TX 78712 USA. [Hammond, Jeff R.] Argonne Natl Lab, Leadership Comp Facil, Argonne, IL 60439 USA. RP Solomonik, E (reprint author), Univ Calif Berkeley, Dept Elect Engn & Comp Sci, Berkeley, CA 94720 USA. EM solomon@eecs.berkeley.edu; dmatthews@utexas.edu; jeff_hammond@acm.org; jfstanton@mail.utexas.edu; demmel@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]; DOE [DE-SC0004938, DE-SC0005136, DE-SC0003959, DE-SC0008700, AC02-05CH11231]; DARPA [HR0011-12-2-0016]; Office of Science of the US Department of Energy [DE-AC02-06CH11357, DE-AC02-05CH11231]; ParLab affiliates National Instruments; Nokia; NVIDIA; Oracle; Samsung; MathWorks 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, DE-SC0008700, and AC02-05CH11 231, and DARPA grant HR0011-12-2-0016. 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 US 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 US Department of Energy under Contract No. DE-AC02-05CH11231. NR 54 TC 10 Z9 10 U1 1 U2 16 PU ACADEMIC PRESS INC ELSEVIER SCIENCE PI SAN DIEGO PA 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA SN 0743-7315 EI 1096-0848 J9 J PARALLEL DISTR COM JI J. Parallel Distrib. Comput. PD DEC PY 2014 VL 74 IS 12 SI SI BP 3176 EP 3190 DI 10.1016/j.jpdc.2014.06.002 PG 15 WC Computer Science, Theory & Methods SC Computer Science GA AU6SZ UT WOS:000345733300002 ER PT J AU Edwards, HC Trott, CR Sunderland, D AF Edwards, H. Carter Trott, Christian R. Sunderland, Daniel TI Kokkos: Enabling manycore performance portability through polymorphic memory access patterns SO JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING LA English DT Article DE Parallel computing; Thread parallelism; Manycore; GPU; Performance portability; Multidimensional array; Mini-application ID EMBEDDED ANALYSIS CAPABILITIES; MANAGING SOFTWARE COMPLEXITY; MULTIPHYSICS SIMULATION; FRAMEWORK AB The manycore revolution can be characterized by increasing thread counts, decreasing memory per thread, and diversity of continually evolving manycore architectures. High performance computing (HPC) applications and libraries must exploit increasingly finer levels of parallelism within their codes to sustain scalability on these devices. A major obstacle to performance portability is the diverse and conflicting set of constraints on memory access patterns across devices. Contemporary portable programming models address manycore parallelism (e.g., OpenMP, OpenACC, OpenCL) but fail to address memory access patterns. The Kokkos C++ library enables applications and domain libraries to achieve performance portability on diverse manycore architectures by unifying abstractions for both fine-grain data parallelism and memory access patterns. In this paper we describe Kokkos' abstractions, summarize its application programmer interface (API), present performance results for unit-test kernels and mini-applications, and outline an incremental strategy for migrating legacy C++ codes to Kokkos. The Kokkos library is under active research and development to incorporate capabilities from new generations of manycore architectures, and to address a growing list of applications and domain libraries. (C) 2014 Elsevier Inc. All rights reserved. C1 [Edwards, H. Carter; Trott, Christian R.; Sunderland, Daniel] Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Edwards, HC (reprint author), Sandia Natl Labs, POB 5800,MS 1318, Albuquerque, NM 87185 USA. EM hcedwar@sandia.gov; crtrott@sandia.gov; dsunder@sandia.gov RI Trott, Christian/B-6757-2011 OI Trott, Christian/0000-0003-0661-5594 FU US Department of Energy's National Nuclear Security Administration [DE-AC04-94AL85000] FX Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the US Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. This paper is cross-referenced at Sandia as SAND2013-5603J. NR 29 TC 11 Z9 12 U1 1 U2 9 PU ACADEMIC PRESS INC ELSEVIER SCIENCE PI SAN DIEGO PA 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA SN 0743-7315 EI 1096-0848 J9 J PARALLEL DISTR COM JI J. Parallel Distrib. Comput. PD DEC PY 2014 VL 74 IS 12 SI SI BP 3202 EP 3216 DI 10.1016/j.jpdc.2014.07.003 PG 15 WC Computer Science, Theory & Methods SC Computer Science GA AU6SZ UT WOS:000345733300004 ER PT J AU Dubey, A Almgren, A Bell, J Berzins, M Brandt, S Bryan, G Colella, P Graves, D Lijewski, M Loffler, F O'Shea, B Schnetter, E Van Straalen, B Weide, K AF Dubey, Anshu Almgren, Ann Bell, John Berzins, Martin Brandt, Steve Bryan, Greg Colella, Phillip Graves, Daniel Lijewski, Michael Loeffler, Frank O'Shea, Brian Schnetter, Erik Van Straalen, Brian Weide, Klaus TI A survey of high level frameworks in block-structured adaptive mesh refinement packages SO JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING LA English DT Article DE SAMR; BoxLib; Chombo; FLASH; Cactus; Enzo; Uintah ID FLUID-STRUCTURE INTERACTION; RADIATION HYDRODYNAMICS; CONSTRAINED-TRANSPORT; NUMERICAL RELATIVITY; SHOCK HYDRODYNAMICS; MACH NUMBER; CODE; SIMULATION; INFRASTRUCTURE; ALGORITHMS AB Over the last decade block-structured adaptive mesh refinement (SAMR) has found increasing use in large, publicly available codes and frameworks. SAMR frameworks have evolved along different paths. Some have stayed focused on specific domain areas, others have pursued a more general functionality, providing the building blocks for a larger variety of applications. In this survey paper we examine a representative set of SAMR packages and SAMR-based codes that have been in existence for half a decade or more, have a reasonably sized and active user base outside of their home institutions, and are publicly available. The set consists of a mix of SAMR packages and application codes that cover a broad range of scientific domains. We look at their high-level frameworks, their design trade-offs and their approach to dealing with the advent of radical changes in hardware architecture. The codes included in this survey are BoxLib, Cactus, Chombo, Enzo, FLASH, and Uintah. Published by Elsevier Inc. C1 [Dubey, Anshu; Almgren, Ann; Bell, John; Colella, Phillip; Graves, Daniel; Lijewski, Michael; Van Straalen, Brian] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA. [Weide, Klaus] Univ Chicago, Flash Ctr Computat Sci, Chicago, IL 60637 USA. [O'Shea, Brian] Michigan State Univ, Dept Phys & Astron, E Lansing, MI 48824 USA. [O'Shea, Brian] Michigan State Univ, Lyman Briggs Coll, E Lansing, MI 48824 USA. [O'Shea, Brian] Michigan State Univ, Inst Cyber Enabled Res, E Lansing, MI 48824 USA. [Brandt, Steve; Schnetter, Erik] Louisiana State Univ, Ctr Computat & Technol, Baton Rouge, LA 70803 USA. [Brandt, Steve] Louisiana State Univ, Dept Comp Sci, Baton Rouge, LA 70803 USA. [Schnetter, Erik] Perimeter Inst Theoret Phys, Waterloo, ON N2L 2Y5, Canada. [Schnetter, Erik] Univ Guelph, Dept Phys, Guelph, ON N1G 2W1, Canada. [Berzins, Martin] Univ Utah, Math & Sch Comp, Salt Lake City, UT 84112 USA. [Bryan, Greg] Columbia Univ, Dept Astron, New York, NY 10025 USA. [Colella, Phillip] Univ Calif Berkeley, Dept Comp Sci, Berkeley, CA 94720 USA. RP Dubey, A (reprint author), One Cyclotron Rd,Mailstop 50A1148, Berkeley, CA 94720 USA. EM adubey@lbl.gov OI Loffler, Frank/0000-0001-6643-6323; Weide, Klaus/0000-0001-9869-9750; Schnetter, Erik/0000-0002-4518-9017 FU US DOE Office of Science at LBNL [DE-AC02-05CH11231]; Office of Science of the US DOE [DE-AC02-05CH11231, DE-AC05-00OR22725]; US National Science Foundation [0903973, 0903782, 0904015, 1212401, 1212426, 1212433, 1212460, 0905046, 1047956]; German Deutsche Forschungsgemeinschaft [SFB/Transregio 7]; Canada NSERC grant; NASA Computation Technologies Project; NSF Office of Cyber-Infrastructure through the PRAC program [OCI-0832662]; US DOE [B523820, B524196]; US DOE NNSA ASC through the Argonne Institute for Computing in Science [57789]; NSF Peta-apps grant [5-27429]; National Science Foundation [OCI0721659, OCI 0905068]; DOE INCITE awards [CMB015, CMB021]; DOE NETL [NET DE-EE0004449]; DOE; NSF FX BoxLib Much of the Box Lib development over the past 20+ years has been supported by the Applied Mathematics Program and the SciDAC program under the US DOE Office of Science at LBNL under contract No. DE-AC02-05CH11231. Scaling studies of BoxLib have used resources of NERSC and OLCF, which are supported by the Office of Science of the US DOE under Contract No. DE-AC02-05CH11231, and DE-AC05-00OR22725 respectively.; Cactus Cactus is developed with direct and indirect support from a number of different sources, including support by the US National Science Foundation under the grant numbers 0903973, 0903782, 0904015 (CIGR) and 1212401, 1212426, 1212433, 1212460 (Einstein Toolkit), 0905046 (PetaCactus), 1047956 (Eclipse/PTP), a German Deutsche Forschungsgemeinschaft grant SFB/Transregio 7 (Gravitational Wave Astronomy), and a Canada NSERC grant. Computational resources are provided by Louisiana State University (allocation hpc_cactus), by the Louisiana Optical Network Initiative (allocations loni_cactus), by the US National Science Foundation through XSEDE resources (allocations TG-ASC120003 and TG-SEE100004), the Argonne National Laboratory, NERSC, and Compute Canada.; Chombo Chombo was started in 1998 and has been in continuous development since then at Lawrence Berkeley National Laboratory, primarily supported by the US DOE Office of Science at LBNL under Contract No. DE-AC02-05CH11231, and supported for a short time by the NASA Computation Technologies Project (2002-2004).; Enzo The Enzo code has been continuously developed since 1995 by the NSF, NASA, and DOE, as well as by the National Center for Supercomputing Applications, the San Diego Supercomputing Center, and several individual universities. Please consult [14] for the full list of funding sources-notably, Enzo has been funded by the NSF Office of Cyber-Infrastructure through the PRAC program (grant OCI-0832662).; FLASH The FLASH code was in part developed by the US DOE-supported ASC/Alliance Center for Astrophysical Thermonuclear Flashes at the University of Chicago under grant B523820. The continued development has been supported in part by the US DOE NNSA ASC through the Argonne Institute for Computing in Science under field work proposal 57789, and by NSF Peta-apps grant 5-27429.; Uintah Uintah was originally developed at the University of Utah's Center for the Simulation of Accidental Fires and Explosions (C-SAFE) funded by the US DOE, under Subcontract No. B524196. Subsequent support was provided by the National Science Foundation under Subcontract No. OCI0721659, Award No. OCI 0905068 and by DOE INCITE awards CMB015 and CMB021 and DOE NETL for funding under NET DE-EE0004449. Applications development of Uintah has been supported by a broad range of funding from NSF and DOE. NR 90 TC 8 Z9 9 U1 1 U2 6 PU ACADEMIC PRESS INC ELSEVIER SCIENCE PI SAN DIEGO PA 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA SN 0743-7315 EI 1096-0848 J9 J PARALLEL DISTR COM JI J. Parallel Distrib. Comput. PD DEC PY 2014 VL 74 IS 12 SI SI BP 3217 EP 3227 DI 10.1016/j.jpdc.2014.07.001 PG 11 WC Computer Science, Theory & Methods SC Computer Science GA AU6SZ UT WOS:000345733300005 ER PT J AU Haas, NA O'Connor, BL Hayse, JW Bevelhimer, MS Endreny, TA AF Haas, Nicholas A. O'Connor, Ben L. Hayse, John W. Bevelhimer, Mark S. Endreny, Theodore A. TI ANALYSIS OF DAILY PEAKING AND RUN-OF-RIVER OPERATIONS WITH FLOW VARIABILITY METRICS, CONSIDERING SUBDAILY TO SEASONAL TIME SCALES SO JOURNAL OF THE AMERICAN WATER RESOURCES ASSOCIATION LA English DT Article DE rivers and streams; flow variability; environmental flows; ecological flow assessment; hydropower operations; environmental impacts; time series analysis ID HYDROLOGIC ALTERATION; ENVIRONMENTAL FLOWS; REGULATED RIVER; DAM OPERATIONS; HYDROPEAKING; HYDROPOWER; ECOSYSTEMS; STREAMFLOW; FRAMEWORK; HABITAT AB Environmental flows are an important consideration in licensing hydropower projects as operational flow releases can result in adverse conditions for downstream ecological communities. Flow variability assessments have typically focused on pre- and post-dam conditions using metrics based on daily averaged flow values. This study used subdaily and daily flow data to assess environmental flow response to changes in hydropower operations from daily peaking to run-of-river. An analysis tool was developed to quantify flow variability metrics and was applied to four hydropower projects. Significant differences were observed between operations at the 99% confidence level in the median flow values using hourly averaged flow datasets. Median daily rise and fall rates decreased on average 34.5 and 27.9%, respectively, whereas median hourly rise and fall rates decreased on average 50.1 and 50.6%, respectively. Differences in operational flow regimes were more pronounced in the hourly averaged flow datasets and less pronounced or nonexistent in the daily averaged flow datasets. These outcomes have implications for the development of ecology-flow relationships that quantify effects of flow on processes such as fish stranding and displacement, along with habitat stability. Results indicate that flow variability statistics should be quantified using subdaily datasets to accurately represent the nature of hydropower operations, especially for daily peaking facilities. C1 [Haas, Nicholas A.; O'Connor, Ben L.; Hayse, John W.] Argonne Natl Lab, Div Environm Sci, Argonne, IL 60439 USA. [Bevelhimer, Mark S.] Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA. [Endreny, Theodore A.] SUNY Coll Environm Sci & Forestry, Dept Environm Resources Engn, Syracuse, NY 13210 USA. RP Haas, NA (reprint author), Argonne Natl Lab, Div Environm Sci, Bldg 240,9700 South Cass Ave, Argonne, IL 60439 USA. EM nhaas@anl.gov FU U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Water Power Program [DE-AC02-06CH11357, DE-AC05-00OR22725] FX This study was performed while N.A. Haas held a co-op student position at Argonne National Laboratory. Argonne National Laboratory's and Oak Ridge National Laboratory's work was supported by the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Water Power Program under contracts DE-AC02-06CH11357 and DE-AC05-00OR22725, respectively. The authors would like to extend gracious thanks to the three anonymous reviewers of the article; their constructive reviews were helpful and appreciated. NR 40 TC 9 Z9 10 U1 2 U2 29 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 1093-474X EI 1752-1688 J9 J AM WATER RESOUR AS JI J. Am. Water Resour. Assoc. PD DEC PY 2014 VL 50 IS 6 BP 1622 EP 1640 DI 10.1111/jawr.12228 PG 19 WC Engineering, Environmental; Geosciences, Multidisciplinary; Water Resources SC Engineering; Geology; Water Resources GA AU7IJ UT WOS:000345773900019 ER PT J AU Yamazoe, K Mochi, I Goldberg, KA AF Yamazoe, Kenji Mochi, Iacopo Goldberg, Kenneth A. TI Gradient descent algorithm applied to wavefront retrieval from through-focus images by an extreme ultraviolet microscope with partially coherent source SO JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION LA English DT Article ID PHASE-RETRIEVAL; LITHOGRAPHY AB The wavefront retrieval by gradient descent algorithm that is typically applied to coherent or incoherent imaging is extended to retrieve a wavefront from a series of through-focus images by partially coherent illumination. For accurate retrieval, we modeled partial coherence as well as object transmittance into the gradient descent algorithm. However, this modeling increases the computation time due to the complexity of partially coherent imaging simulation that is repeatedly used in the optimization loop. To accelerate the computation, we incorporate not only the Fourier transform but also an eigenfunction decomposition of the image. As a demonstration, the extended algorithm is applied to retrieve a field-dependent wavefront of a microscope operated at extreme ultraviolet wavelength (13.4 nm). The retrieved wavefront qualitatively matches the expected characteristics of the lens design. (C) 2014 Optical Society of America C1 [Yamazoe, Kenji] Canon USA Inc, Cambridge, MA 02139 USA. [Mochi, Iacopo; Goldberg, Kenneth A.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Ctr Xray Opt, Berkeley, CA 94720 USA. RP Yamazoe, K (reprint author), Canon USA Inc, 210 Broadway 3rd Floor, Cambridge, MA 02139 USA. EM kyamazoe@cusa.canon.com FU SEMATECH; Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy [DE-AC02-05CH11231]; U.S. Department of Energy FX This work started while Yamazoe was a visiting industrial fellow at the University of California, Berkeley, and we thank Professor Andrew R. Neureuther for organizing this collaboration. Yamazoe continued this work at Canon Inc., Japan, and Canon U.S.A. Inc. We thank Yoshinari Higaki, Yoshiyuki Sekine of Canon Inc., and Tokuyuki Honda of Canon U.S.A. Inc. for their technical discussion. Measurements performed on the AIT microscope were conducted by the Center for X-Ray Optics. Portions of this work were funded by SEMATECH and performed by the University of California Lawrence Berkeley National Laboratory under the auspices of the U.S. Department of Energy. 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. The EUV photomask used in these experiments was created by Intel for the Microfield Exposure Tool (MET) project, also at LBNL. NR 29 TC 1 Z9 2 U1 1 U2 2 PU OPTICAL SOC AMER PI WASHINGTON PA 2010 MASSACHUSETTS AVE NW, WASHINGTON, DC 20036 USA SN 1084-7529 EI 1520-8532 J9 J OPT SOC AM A JI J. Opt. Soc. Am. A-Opt. Image Sci. Vis. PD DEC PY 2014 VL 31 IS 12 BP B34 EP B43 DI 10.1364/JOSAA.31.000B34 PG 10 WC Optics SC Optics GA AU9HK UT WOS:000345902400005 PM 25606778 ER PT J AU Hendrickson, SM Foster, AC Camacho, RM Clader, BD AF Hendrickson, S. M. Foster, A. C. Camacho, R. M. Clader, B. D. TI Integrated nonlinear photonics: emerging applications and ongoing challenges [Invited] SO JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS LA English DT Article ID SILICON WAVE-GUIDES; OPTICAL WAVELENGTH CONVERSION; RADIOFREQUENCY SPECTRUM ANALYZER; MICRO-RING-RESONATOR; ULTRA-LOW POWER; XOR LOGIC GATE; FREQUENCY-CONVERSION; DPSK SIGNALS; PULSE CHARACTERIZATION; QUANTUM INTERFERENCE AB We provide a review of recent progress in integrated nonlinear photonics with a focus on emerging applications in all-optical signal processing, ultra-low-power all-optical switching, and quantum information processing. (C) 2014 Optical Society of America C1 [Hendrickson, S. M.; Clader, B. D.] Johns Hopkins Univ, Appl Phys Lab, Laurel, MD 20723 USA. [Foster, A. C.] Johns Hopkins Univ, Dept Elect & Comp Engn, Baltimore, MD 21218 USA. [Camacho, R. M.] Sandia Natl Labs, Albuquerque, NM 87123 USA. RP Hendrickson, SM (reprint author), Johns Hopkins Univ, Appl Phys Lab, Johns Hopkins Rd, Laurel, MD 20723 USA. EM scott.hendrickson@jhuapl.edu FU DARPA ZOE program [W31P4Q-09-C-0566]; Johns Hopkins University Applied Physics Laboratory; DARPA Young Faculty Award program [N66001-12-1-4248]; U.S. Department of Energy's National Nuclear Security Administration [DE-AC04-94AL85000] FX S. M. H. and B. D. C. acknowledge funding from the DARPA ZOE program (Contract No. W31P4Q-09-C-0566) as well as internal research and development funds provided by The Johns Hopkins University Applied Physics Laboratory. A. C. F. acknowledges support from the DARPA Young Faculty Award program under award number N66001-12-1-4248. 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 131 TC 4 Z9 4 U1 0 U2 25 PU OPTICAL SOC AMER PI WASHINGTON PA 2010 MASSACHUSETTS AVE NW, WASHINGTON, DC 20036 USA SN 0740-3224 EI 1520-8540 J9 J OPT SOC AM B JI J. Opt. Soc. Am. B-Opt. Phys. PD DEC PY 2014 VL 31 IS 12 BP 3193 EP 3203 DI 10.1364/JOSAB.31.003193 PG 11 WC Optics SC Optics GA AU9HC UT WOS:000345901500034 ER PT J AU Rubin, BER Sanders, JG Hampton-Marcell, J Owens, SM Gilbert, JA Moreau, CS AF Rubin, Benjamin E. R. Sanders, Jon G. Hampton-Marcell, Jarrad Owens, Sarah M. Gilbert, Jack A. Moreau, Corrie S. TI DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure SO MICROBIOLOGYOPEN LA English DT Article DE 16S rRNA; ants; DNA extraction; Earth Microbiome Project; host-associated bacteria; insects; microbiome ID GUT BACTERIAL COMMUNITIES; HUMAN MICROBIOME PROJECT; DIVERSITY; INSECTS; ANTS; SOIL; PATTERNS; READS; DIET; BEES AB The recent development of methods applying next-generation sequencing to microbial community characterization has led to the proliferation of these studies in a wide variety of sample types. Yet, variation in the physical properties of environmental samples demands that optimal DNA extraction techniques be explored for each new environment. The microbiota associated with many species of insects offer an extraction challenge as they are frequently surrounded by an armored exoskeleton, inhibiting disruption of the tissues within. In this study, we examine the efficacy of several commonly used protocols for extracting bacterial DNA from ants. While bacterial community composition recovered using Illumina 16S rRNA amplicon sequencing was not detectably biased by any method, the quantity of bacterial DNA varied drastically, reducing the number of samples that could be amplified and sequenced. These results indicate that the concentration necessary for dependable sequencing is around 10,000 copies of target DNA per microliter. Exoskeletal pulverization and tissue digestion increased the reliability of extractions, suggesting that these steps should be included in any study of insect-associated microorganisms that relies on obtaining microbial DNA from intact body segments. Although laboratory and analysis techniques should be standardized across diverse sample types as much as possible, minimal modifications such as these will increase the number of environments in which bacterial communities can be successfully studied. C1 [Rubin, Benjamin E. R.] Univ Chicago, Comm Evolutionary Biol, Chicago, IL 60637 USA. [Rubin, Benjamin E. R.; Moreau, Corrie S.] Field Museum Nat Hist, Dept Sci & Educ, Chicago, IL 60605 USA. [Sanders, Jon G.] Harvard Univ, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USA. [Hampton-Marcell, Jarrad; Owens, Sarah M.; Gilbert, Jack A.] Argonne Natl Lab, Inst Genom & Syst Biol, Lemont, IL USA. [Hampton-Marcell, Jarrad; Gilbert, Jack A.] Univ Chicago, Dept Ecol & Evolut, Chicago, IL 60637 USA. [Owens, Sarah M.] Univ Chicago, Computat Inst, Chicago, IL 60637 USA. RP Rubin, BER (reprint author), Univ Chicago, Comm Evolutionary Biol, Culver Hall 402,1025 E 57th St, Chicago, IL 60637 USA. EM brubin@fieldmuseum.org OI Moreau, Corrie/0000-0003-1139-5792 FU U.S. Dept. of Energy [DE-AC02-06CH11357]; National Science Foundation DEB [1050243]; Grainger Foundation; Negaunee Foundation; NSF Graduate Research Fellowship; Field Museum Brown Family Graduate Fellowship; NSF [1311417] FX This work was supported in part by the U.S. Dept. of Energy under Contract DE-AC02-06CH11357, National Science Foundation DEB Grant no. 1050243 to Corrie S. Moreau, a Grainger Foundation grant to Corrie S. Moreau, and a Negaunee Foundation grant to Corrie S. Moreau. Benjamin E. R. Rubin was supported in part by an NSF Graduate Research Fellowship, the Field Museum Brown Family Graduate Fellowship, and NSF Doctoral Dissertation Improvement Grant no. 1311417. NR 51 TC 18 Z9 19 U1 5 U2 69 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 2045-8827 J9 MICROBIOLOGYOPEN JI MicrobiologyOpen PD DEC PY 2014 VL 3 IS 6 BP 910 EP 921 DI 10.1002/mbo3.216 PG 12 WC Microbiology SC Microbiology GA AW0MM UT WOS:000345986700008 PM 25257543 ER PT J AU Guo, J Nguyen, AY Dai, ZY Su, DA Gaffrey, MJ Moore, RJ Jacobs, JM Monroe, ME Smith, RD Koppenaal, DW Pakrasi, HB Qian, WJ AF Guo, Jia Nguyen, Amelia Y. Dai, Ziyu Su, Dian Gaffrey, Matthew J. Moore, Ronald J. Jacobs, Jon M. Monroe, Matthew E. Smith, Richard D. Koppenaal, David W. Pakrasi, Himadri B. Qian, Wei-Jun TI Proteome-wide Light/Dark Modulation of Thiol Oxidation in Cyanobacteria Revealed by Quantitative Site-specific Redox Proteomics SO MOLECULAR & CELLULAR PROTEOMICS LA English DT Article ID SYNECHOCYSTIS SP PCC-6803; SP STRAIN PCC-6803; SYNECHOCOCCUS SP PCC-7942; SP. PCC 6803; S-NITROSYLATION; MASS-SPECTROMETRY; GENE-EXPRESSION; IN-VIVO; PROTOCHLOROPHYLLIDE OXIDOREDUCTASE; DIRECTED MUTAGENESIS AB Reversible protein thiol oxidation is an essential regulatory mechanism of photosynthesis, metabolism, and gene expression in photosynthetic organisms. Herein, we present proteome-wide quantitative and site-specific profiling of in vivo thiol oxidation modulated by light/dark in the cyanobacterium Synechocystis sp. PCC 6803, an oxygenic photosynthetic prokaryote, using a resin-assisted thiol enrichment approach. Our proteomic approach integrates resin-assisted enrichment with isobaric tandem mass tag labeling to enable site-specific and quantitative measurements of reversibly oxidized thiols. The redox dynamics of similar to 2,100 Cys-sites from 1,060 proteins under light, dark, and 3-(3,4-dichlorophenyl)1,1-dimethylurea (a photosystem II inhibitor) conditions were quantified. In addition to relative quantification, the stoichiometry or percentage of oxidation (reversibly oxidized/total thiols) for similar to 1,350 Cys-sites was also quantified. The overall results revealed broad changes in thiol oxidation in many key biological processes, including photosynthetic electron transport, carbon fixation, and glycolysis. Moreover, the redox sensitivity along with the stoichiometric data enabled prediction of potential functional Cys-sites for proteins of interest. The functional significance of redox-sensitive Cyssites in NADP-dependent glyceraldehyde-3-phosphate dehydrogenase, peroxiredoxin (AhpC/TSA family protein Sll1621), and glucose 6-phosphate dehydrogenase was further confirmed with site-specific mutagenesis and biochemical studies. Together, our findings provide significant insights into the broad redox regulation of photosynthetic organisms. C1 [Guo, Jia; Su, Dian; Gaffrey, Matthew J.; Moore, Ronald J.; Jacobs, Jon M.; Monroe, Matthew E.; Smith, Richard D.; Qian, Wei-Jun] Pacific NW Natl Lab, Div Biol Sci, Richland, WA 99352 USA. [Nguyen, Amelia Y.; Pakrasi, Himadri B.] Washington Univ, Dept Biol, St Louis, MO 63130 USA. [Smith, Richard D.; Koppenaal, David W.] Pacific NW Natl Lab, Environm Mol Sci Lab, Richland, WA 99352 USA. RP Qian, WJ (reprint author), Pacific NW Natl Lab, Div Biol Sci, POB 999,MSIN K8-98, Richland, WA 99352 USA. EM weijun.qian@pnnl.gov RI Smith, Richard/J-3664-2012 OI Smith, Richard/0000-0002-2381-2349 FU DOE [DE-AC05-76RLO-1830, DE-FG02-99ER20350]; DOE Early Career Research Award; Environmental Molecular Science Laboratory (EMSL) Research Campaign project; DOE Office of Biological and Environmental Research Genome Sciences Program under the Panomics project; NSF Graduate Research Fellowship FX Portions of experimental work were performed in the Environmental Molecular Science Laboratory, a DOE/BER national scientific user facility at PNNL in Richland, WA. PNNL is operated by Battelle for the DOE under Contract No. DE-AC05-76RLO-1830.; Portions of this work were supported by the DOE Early Career Research Award (to W.J.Q.), DOE Grant No. DE-FG02-99ER20350 (to H.B.P.), the Environmental Molecular Science Laboratory (EMSL) Research Campaign project, and the DOE Office of Biological and Environmental Research Genome Sciences Program under the Panomics project. A.N. has been supported by an NSF Graduate Research Fellowship. NR 81 TC 21 Z9 22 U1 2 U2 35 PU AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC PI BETHESDA PA 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3996 USA SN 1535-9476 EI 1535-9484 J9 MOL CELL PROTEOMICS JI Mol. Cell. Proteomics PD DEC PY 2014 VL 13 IS 12 BP 3270 EP 3285 DI 10.1074/mcp.M114.041160 PG 16 WC Biochemical Research Methods SC Biochemistry & Molecular Biology GA AU5DC UT WOS:000345626400004 PM 25118246 ER PT J AU Webb-Robertson, BJM Matzke, MM Datta, S Payne, SH Kang, JY Bramer, LM Nicora, CD Shukla, AK Metz, TO Rodland, KD Smith, RD Tardiff, MF McDermott, JE Pounds, JG Waters, KM AF Webb-Robertson, Bobbie-Jo M. Matzke, Melissa M. Datta, Susmita Payne, Samuel H. Kang, Jiyun Bramer, Lisa M. Nicora, Carrie D. Shukla, Anil K. Metz, Thomas O. Rodland, Karin D. Smith, Richard D. Tardiff, Mark F. McDermott, Jason E. Pounds, Joel G. Waters, Katrina M. TI Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements SO MOLECULAR & CELLULAR PROTEOMICS LA English DT Article ID MASS-SPECTROMETRY; QUANTITATIVE-ANALYSIS; SOFTWARE PACKAGE; SHARED PEPTIDES; ACCURATE MASS; IDENTIFICATION; THROUGHPUT; BIOMARKERS; INTENSITIES; DISCOVERY AB As the capability of mass spectrometry-based proteomics has matured, tens of thousands of peptides can be measured simultaneously, which has the benefit of offering a systems view of protein expression. However, a major challenge is that, with an increase in throughput, protein quantification estimation from the native measured peptides has become a computational task. A limitation to existing computationally driven protein quantification methods is that most ignore protein variation, such as alternate splicing of the RNA transcript and post-translational modifications or other possible proteoforms, which will affect a significant fraction of the proteome. The consequence of this assumption is that statistical inference at the protein level, and consequently downstream analyses, such as network and pathway modeling, have only limited power for biomarker discovery. Here, we describe a Bayesian Proteoform Quantification model (BP-Quant) 1 that uses statistically derived peptides signatures to identify peptides that are outside the dominant pattern or the existence of multiple overexpressed patterns to improve relative protein abundance estimates. It is a research-driven approach that utilizes the objectives of the experiment, defined in the context of a standard statistical hypothesis, to identify a set of peptides exhibiting similar statistical behavior relating to a protein. This approach infers that changes in relative protein abundance can be used as a surrogate for changes in function, without necessarily taking into account the effect of differential post-translational modifications, processing, or splicing in altering protein function. We verify the approach using a dilution study from mouse plasma samples and demonstrate that BP-Quant achieves similar accuracy as the current state-of-the-art methods at proteoform identification with significantly better specificity. BP-Quant is available as a MatLab (R) and R packages. C1 [Webb-Robertson, Bobbie-Jo M.; Matzke, Melissa M.; Payne, Samuel H.; Kang, Jiyun; Bramer, Lisa M.; Nicora, Carrie D.; Shukla, Anil K.; Metz, Thomas O.; Rodland, Karin D.; Smith, Richard D.; Tardiff, Mark F.; McDermott, Jason E.; Pounds, Joel G.; Waters, Katrina M.] Pacific NW Natl Lab, Richland, WA 99354 USA. [Datta, Susmita] Univ Louisville, Louisville, KY 40202 USA. RP Webb-Robertson, BJM (reprint author), Pacific NW Natl Lab, 3300 Stevens Dr,K7-20, Richland, WA 99354 USA. EM bj@pnnl.gov RI Smith, Richard/J-3664-2012; Bramer, Lisa/L-9184-2016; OI Smith, Richard/0000-0002-2381-2349; Bramer, Lisa/0000-0002-8384-1926; Metz, Tom/0000-0001-6049-3968; Payne, Samuel/0000-0002-8351-1994 FU Laboratory Directed Research and Development at Pacific Northwest National Laboratory (PNNL) under the Signature Discovery Initiative; National Institutes of Health(NIH)/National Cancer Institute [U01-1CA184783]; NIH/National Institute of Environmental Health Sciences [U54-016015]; NIH [DK071283]; NIH/National Institute of General Medical Sciences from the National Institutes of Health [8 P41 GM103493-10]; U.S. Department of Energy Office of Biological and Environmental Research; U.S. Department of Energy [DE-AC06-76RL01830] FX Computational work was supported by Laboratory Directed Research and Development at Pacific Northwest National Laboratory (PNNL) under the Signature Discovery Initiative (K.D.R., J.E.M) and the National Institutes of Health(NIH)/National Cancer Institute through grant U01-1CA184783 (B.M.W). The mouse plasma proteomics data were generated through NIH/National Institute of Environmental Health Sciences grant U54-016015 (J.G.P.). The SIGT plasma proteomics data were generated through NIH grant DK071283 (R.D.S. and T.O.M.). Proteomics datasets originated from samples analyzed using capabilities developed under the support from the NIH/National Institute of General Medical Sciences (8 P41 GM103493-10) from the National Institutes of Health, and from the U.S. Department of Energy Office of Biological and Environmental Research (R.D.S). Proteomics data were collected and processed in the Environmental Molecular Sciences Laboratory (EMSL). EMSL is a national scientific user facility supported by the Department of Energy. All work was performed at PNNL, which is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy under contract DE-AC06-76RL01830. NR 34 TC 8 Z9 8 U1 2 U2 8 PU AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC PI BETHESDA PA 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3996 USA SN 1535-9476 EI 1535-9484 J9 MOL CELL PROTEOMICS JI Mol. Cell. Proteomics PD DEC PY 2014 VL 13 IS 12 BP 3639 EP 3646 DI 10.1074/mcp.M113.030932 PG 8 WC Biochemical Research Methods SC Biochemistry & Molecular Biology GA AU5DC UT WOS:000345626400033 PM 25433089 ER PT J AU Hodges, M Belle, JH Carlton, EJ Liang, S Li, HZ Luo, W Freeman, MC Liu, Y Gao, Y Hess, JJ Remais, JV AF Hodges, Maggie Belle, Jessica H. Carlton, Elizabeth J. Liang, Song Li, Huazhong Luo, Wei Freeman, Matthew C. Liu, Yang Gao, Yang Hess, Jeremy J. Remais, Justin V. TI Delays in reducing waterborne and water-related infectious diseases in China under climate change SO NATURE CLIMATE CHANGE LA English DT Article ID COMPARATIVE RISK-ASSESSMENT; BURDEN; HEALTH; MODEL; TEMPERATURE; SANITATION; CMIP5; AIR AB Despite China's rapid progress in improving water, sanitation and hygiene (WSH) access, in 2011. 471 million people lacked access to improved sanitation and 401 million to household piped water. As certain infectious diseases are sensitive to changes in both climate and WSH conditions, we projected impacts of climate change on WSH-attributable diseases in China in 2020 and 2030 by coupling estimates of the temperature sensitivity of diarrhoeal diseases and three vector-borne diseases, temperature projections from global climate models, WSH-infrastructure development scenarios, and projected demographic changes. By 2030, climate change is projected to delay China's rapid progress towards reducing WSH-attributable infectious disease burden by 8-85 months. This development delay summarizes the adverse impact of climate change on WSH-attributable infectious diseases in China, and can be used in other settings where a significant health burden may accompany future changes in climate even as the total burden of disease falls owing to non-climate reasons. C1 [Hodges, Maggie; Belle, Jessica H.; Freeman, Matthew C.; Liu, Yang; Hess, Jeremy J.; Remais, Justin V.] Emory Univ, Dept Environm Hlth, Rollins Sch Publ Hlth, Atlanta, GA 30322 USA. [Hodges, Maggie; Hess, Jeremy J.] Emory Univ, Sch Med, Atlanta, GA 30322 USA. [Carlton, Elizabeth J.] Univ Colorado, Dept Environm & Occupat Hlth, Colorado Sch Publ Hlth, Aurora, CO 80045 USA. [Liang, Song] Univ Florida, Dept Environm & Global Hlth, Coll Publ Hlth & Hlth Profess, Gainesville, FL 32610 USA. [Liang, Song] Univ Florida, Emerging Pathogens Inst, Gainesville, FL 32610 USA. [Li, Huazhong] China Ctr Dis Control & Prevent, Off Dis Control & Emergency Response, Beijing 102206, Peoples R China. [Luo, Wei] Chinese Acad Sci, Ecoenvironm Sci Res Ctr, Beijing 100085, Peoples R China. [Gao, Yang] Pacific NW Natl Lab, Atmospher Sci & Global Change Div, Richland, WA 99352 USA. RP Remais, JV (reprint author), Emory Univ, Dept Environm Hlth, Rollins Sch Publ Hlth, 1518 Clifton Rd NE, Atlanta, GA 30322 USA. EM justin.remais@emory.edu OI Belle, Jessica/0000-0002-3134-9219 FU Chemical, Broengineerrng. Environmental, and Transport Systems Division of the National Science Foundation [1249250]; Division of Earth Sciences of the National Science Foundation [1360330]; National Institute for Allergy and Infectious Disease [K01AI091864]; Global Health Institute at Emory University; Centers for Disease Control and Prevention [U01EH000405]; National institutes of Health [R21ES020225]; IS EPA Science to Achieve Results grant [RD835192010]; Emerging Pathogens Institute, University of Florida; Office of Science of the U.S. Department of Energy as part of the Regional and Global Climate Modeling Program; DOE [DE-AC05-76RL01830] FX This work was supported in part by the Chemical, Broengineerrng. Environmental, and Transport Systems Division of the National Science Foundation under grant no. 1249250, by the Division of Earth Sciences of the National Science Foundation under grant no 1360330, by the National Institute for Allergy and Infectious Disease (K01AI091864) and by the Global Health Institute at Emory University. Y.L. was supported in part by the Centers for Disease Control and Prevention (U01EH000405) and the National institutes of Health (R21ES020225). SI. was supported in part by IS EPA Science to Achieve Results grant (RD835192010) and by Emerging Pathogens Institute, University of Florida. VG. was supported in part by the Office of Science of the U.S. Department of Energy as part of the Regional and Global Climate Modeling Program. The Pacific Northwest National Laboratory is operated for DOE by Battelle Memorial Institute (DE-AC05-76RL01830) NR 45 TC 6 Z9 6 U1 6 U2 37 PU NATURE PUBLISHING GROUP PI LONDON PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND SN 1758-678X EI 1758-6798 J9 NAT CLIM CHANGE JI Nat. Clim. Chang. PD DEC PY 2014 VL 4 IS 12 BP 1109 EP 1115 DI 10.1038/NCLIMATE2428 PG 7 WC Environmental Sciences; Environmental Studies; Meteorology & Atmospheric Sciences SC Environmental Sciences & Ecology; Meteorology & Atmospheric Sciences GA AU4ZT UT WOS:000345617500022 PM 25530812 ER PT J AU Hantke, MF Hasse, D Maia, FRNC Ekeberg, T John, K Svenda, M Loh, ND Martin, AV Timneanu, N Larsson, DSD van der Schot, G Carlsson, GH Ingelman, M Andreasson, J Westphal, D Liang, MN Stellato, F DePonte, DP Hartmann, R Kimmel, N Kirian, RA Seibert, MM Muhlig, K Schorb, S Ferguson, K Bostedt, C Carron, S Bozek, JD Rolles, D Rudenko, A Epp, S Chapman, HN Barty, A Hajdu, J Andersson, I AF Hantke, Max F. Hasse, Dirk Maia, Filipe R. N. C. Ekeberg, Tomas John, Katja Svenda, Martin Loh, N. Duane Martin, Andrew V. Timneanu, Nicusor Larsson, Daniel S. D. van der Schot, Gijs Carlsson, Gunilla H. Ingelman, Margareta Andreasson, Jakob Westphal, Daniel Liang, Mengning Stellato, Francesco DePonte, Daniel P. Hartmann, Robert Kimmel, Nils Kirian, Richard A. Seibert, M. Marvin Muhlig, Kerstin Schorb, Sebastian Ferguson, Ken Bostedt, Christoph Carron, Sebastian Bozek, John D. Rolles, Daniel Rudenko, Artem Epp, Sascha Chapman, Henry N. Barty, Anton Hajdu, Janos Andersson, Inger TI High-throughput imaging of heterogeneous cell organelles with an X-ray laser SO NATURE PHOTONICS LA English DT Article ID FREE-ELECTRON LASER; DIFFRACTION DATA; SINGLE-PARTICLES; CARBOXYSOMES; RECONSTRUCTION; PHASE; CRYOMICROSCOPY; ALGORITHM; SOFTWARE; PROTEINS AB We overcome two of the most daunting challenges in single-particle diffractive imaging: collecting many high-quality diffraction patterns on a small amount of sample and separating components from mixed samples. We demonstrate this on carboxysomes, which are polyhedral cell organelles that vary in size and facilitate up to 40% of Earth's carbon fixation. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min with the Linac Coherent Light Source running at 120 Hz. We separate different structures directly from the diffraction data and show that the size distribution is preserved during sample delivery. We automate phase retrieval and avoid reconstruction artefacts caused by missing modes. We attain the highest-resolution reconstructions on the smallest single biological objects imaged with an X-ray laser to date. These advances lay the foundations for accurate, high-throughput structure determination by flash-diffractive imaging and offer a means to study structure and structural heterogeneity in biology and elsewhere. C1 [Hantke, Max F.; Hasse, Dirk; Maia, Filipe R. N. C.; Ekeberg, Tomas; John, Katja; Svenda, Martin; Timneanu, Nicusor; Larsson, Daniel S. D.; van der Schot, Gijs; Carlsson, Gunilla H.; Ingelman, Margareta; Andreasson, Jakob; Westphal, Daniel; Seibert, M. Marvin; Muhlig, Kerstin; Hajdu, Janos; Andersson, Inger] Uppsala Univ, Dept Cell & Mol Biol, Lab Mol Biophys, SE-75124 Uppsala, Sweden. [Maia, Filipe R. N. C.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, NERSC, Berkeley, CA 94720 USA. [Loh, N. Duane] Natl Univ Singapore, Ctr BioImaging Sci, Singapore 117557, Singapore. [Martin, Andrew V.] Univ Melbourne, Sch Phys, ARC Ctr Excellence Coherent Xray Sci, Melbourne, Vic 3010, Australia. [Liang, Mengning; Stellato, Francesco; Kirian, Richard A.; Rolles, Daniel; Epp, Sascha; Chapman, Henry N.; Barty, Anton] DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany. [Stellato, Francesco] Univ Roma Tor Vergata, Ist Nazl Fis Nucl, I-00133 Rome, Italy. [Stellato, Francesco] Univ Roma Tor Vergata, Dept Phys, I-00133 Rome, Italy. [DePonte, Daniel P.; Seibert, M. Marvin; Schorb, Sebastian; Ferguson, Ken; Bostedt, Christoph; Carron, Sebastian; Bozek, John D.] SLAC Natl Accelerator Lab, LCLS, Menlo Pk, CA 94025 USA. [Hartmann, Robert] PNSensor GmbH, D-80803 Munich, Germany. [Kimmel, Nils] Max Planck Inst Extraterr Phys, D-85741 Garching, Germany. [Rudenko, Artem] Kansas State Univ, Dept Phys, Manhattan, KS 66506 USA. [Hajdu, Janos] European XFEL GmbH, D-22761 Hamburg, Germany. RP Hantke, MF (reprint author), Uppsala Univ, Dept Cell & Mol Biol, Lab Mol Biophys, Husargatan 3 Box 596, SE-75124 Uppsala, Sweden. EM janos@xray.bmc.uu.se RI Rudenko, Artem/C-7412-2009; Larsson, Daniel/G-3699-2012; Barty, Anton/K-5137-2014; Timneanu, Nicusor/C-7691-2012; Loh, Duane/I-7371-2013; Chapman, Henry/G-2153-2010; Bozek, John/E-9260-2010 OI Rudenko, Artem/0000-0002-9154-8463; Rocha Neves Couto Maia, Filipe/0000-0002-2141-438X; MARTIN, ANDREW/0000-0003-3704-1829; Epp, Sascha/0000-0001-6366-9113; Barty, Anton/0000-0003-4751-2727; Timneanu, Nicusor/0000-0001-7328-0400; Loh, Duane/0000-0002-8886-510X; Chapman, Henry/0000-0002-4655-1743; Bozek, John/0000-0001-7486-7238 FU Swedish Research Council; Knut and Alice Wallenberg Foundation; European Research Council; Rontgen-Angstrom Cluster; Stiftelsen Olle Engkvist Byggmastare; Max Planck Society FX This work was supported by the Swedish Research Council, the Knut and Alice Wallenberg Foundation, the European Research Council, the Rontgen-Angstrom Cluster and Stiftelsen Olle Engkvist Byggmastare. Portions of this research were carried out at the Linac Coherent Light Source, a national user facility operated by Stanford University on behalf of the US Department of Energy, Office of Basic Energy Sciences. The authors thank the scientific and technical staff of the LCLS for support. The authors thank the CAMP collaboration for giving access to their experimental set-up and for supporting the experiment at the LCLS. The authors also acknowledge the Max Planck Society for funding the development and operation of the CAMP instrument. NR 46 TC 33 Z9 33 U1 4 U2 43 PU NATURE PUBLISHING GROUP PI LONDON PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND SN 1749-4885 EI 1749-4893 J9 NAT PHOTONICS JI Nat. Photonics PD DEC PY 2014 VL 8 IS 12 BP 943 EP 949 DI 10.1038/NPHOTON.2014.270 PG 7 WC Optics; Physics, Applied SC Optics; Physics GA AU8AG UT WOS:000345818600014 ER PT J AU Helml, W Maier, AR Schweinberger, W Grguras, I Radcliffe, P Doumy, G Roedig, C Gagnon, J Messerschmidt, M Schorb, S Bostedt, C Gruner, F DiMauro, LF Cubaynes, D Bozek, JD Tschentscher, T Costello, JT Meyer, M Coffee, R Dusterer, S Cavalieri, AL Kienberger, R AF Helml, W. Maier, A. R. Schweinberger, W. Grguras, I. Radcliffe, P. Doumy, G. Roedig, C. Gagnon, J. Messerschmidt, M. Schorb, S. Bostedt, C. Gruener, F. DiMauro, L. F. Cubaynes, D. Bozek, J. D. Tschentscher, Th. Costello, J. T. Meyer, M. Coffee, R. Duesterer, S. Cavalieri, A. L. Kienberger, R. TI Measuring the temporal structure of few-femtosecond free-electron laser X-ray pulses directly in the time domain SO NATURE PHOTONICS LA English DT Article ID EXTREME-ULTRAVIOLET; MAGNETIC-FIELD; RADIATION; OPERATION; LCLS AB Short-wavelength free-electron lasers are now well established as essential and unrivalled sources of ultrabright coherent X-ray radiation. One of the key characteristics of these intense X-ray pulses is their expected few-femtosecond duration. No measurement has succeeded so far in directly determining the temporal structure or even the duration of these ultrashort pulses in the few-femtosecond range. Here, by deploying the so-called streaking spectroscopy technique at the Linac Coherent Light Source, we demonstrate a non-invasive scheme for temporal characterization of X-ray pulses with sub-femtosecond resolution. This method is independent of photon energy, decoupled from machine parameters, and provides an upper bound on the X-ray pulse duration. We measured the duration of the shortest X-ray pulses currently available to be on average no longer than 4.4 fs. Analysing the pulse substructure indicates a small percentage of the free-electron laser pulses consisting of individual high-intensity spikes to be on the order of hundreds of attoseconds. C1 [Helml, W.; Kienberger, R.] Tech Univ Munich, Dept Phys E11, D-85748 Garching, Germany. [Helml, W.; Schweinberger, W.; Gagnon, J.; Kienberger, R.] Max Planck Inst Quantum Opt, D-85748 Garching, Germany. [Maier, A. R.; Grguras, I.; Gruener, F.; Cavalieri, A. L.] Ctr Free Electron Laser Sci CFEL, D-22607 Hamburg, Germany. [Maier, A. R.; Gruener, F.] Univ Hamburg, Grp Beschleunigerphys, Inst Expt Phys, D-22761 Hamburg, Germany. [Maier, A. R.; Gruener, F.] Ctr Xray Free Electron Laser Sci, D-22761 Hamburg, Germany. [Grguras, I.; Cavalieri, A. L.] Max Planck Inst Struct & Dynam Matter, D-22761 Hamburg, Germany. [Radcliffe, P.; Tschentscher, Th.; Meyer, M.] European XFEL, D-22761 Hamburg, Germany. [Doumy, G.] Argonne Natl Lab, Argonne, IL 60439 USA. [Doumy, G.; Roedig, C.; DiMauro, L. F.] Ohio State Univ, Dept Phys, Columbus, OH 43210 USA. [Messerschmidt, M.; Schorb, S.; Bostedt, C.; Bozek, J. D.] Linac Coherent Light Source, Menlo Pk, CA 94025 USA. [Cubaynes, D.; Meyer, M.] Univ Paris 11, CNRS, UMR 8214, Inst Sci Mol Orsay, F-91405 Orsay, France. [Costello, J. T.] Dublin City Univ, Sch Phys Sci, Dublin 9, Ireland. [Costello, J. T.] Dublin City Univ, Natl Ctr Plasma Sci & Technol, Dublin 9, Ireland. [Duesterer, S.] DESY, D-22607 Hamburg, Germany. RP Helml, W (reprint author), Tech Univ Munich, Dept Phys E11, James Franck Str, D-85748 Garching, Germany. EM reinhard.kienberger@tum.de RI Messerschmidt, Marc/F-3796-2010; Maier, Andreas/L-5741-2016; Gruner, Florian/M-1212-2016; Bozek, John/E-9260-2010; Helml, Wolfram/D-1005-2017; OI Messerschmidt, Marc/0000-0002-8641-3302; Maier, Andreas/0000-0003-3361-4247; Gruner, Florian/0000-0001-8382-9225; Bozek, John/0000-0001-7486-7238; Gagnon, Justin/0000-0001-9133-9541; Costello, John/0000-0003-4677-9999 FU German cluster of excellence 'Munich-Centre for Advanced Photonics'; BACATEC programme; The International Max Planck Research School on Advanced Photon Science; Marie Curie fellowship; US DOE [DE-FG02-04ER15614]; National Science Foundation (NSF) [PHY-1004778]; US Department of Energy/Basic Energy Sciences (US DOE/BES) [DE-AC02-06CH11357]; Science Foundation Ireland [12/IA/1742]; European Research Council Starting Grant FX Portions of this research were carried out at the Linac Coherent Light Source (LCLS) at SLAC National Accelerator Laboratory. LCLS is an Office of Science User Facility operated for the US Department of Energy (DOE) Office of Science by Stanford University. The work was partly supported from the German cluster of excellence 'Munich-Centre for Advanced Photonics'. W.H., W.S. and R.K. acknowledge financial support by the BACATEC programme. W.H., ARM. and W.S. acknowledge 'The International Max Planck Research School on Advanced Photon Science' for funding and continued inspiring support. W.H. acknowledges financial support from a Marie Curie fellowship. A.R.M. thanks S. Reiche for fruitful discussions and help with GENESIS simulations. C.R. and G.D. acknowledge partial support from the US DOE (DE-FG02-04ER15614) and the National Science Foundation (NSF; PHY-1004778). G.D. also acknowledges support from US Department of Energy/Basic Energy Sciences (US DOE/BES; DE-AC02-06CH11357). J.T.C. acknowledges support from Science Foundation Ireland (grant no. 12/IA/1742). RE. acknowledges funding from an European Research Council Starting Grant. The authors thank T. Schatz for comments on the manuscript. The authors thank P. Emma, Y. Ding, J.B. Hastings and W. White for their support, C. Behrens and H.-D. Nuhn for their expertise and advice on FEL-related questions, and to the whole scientific and technical team at LCLS for their dedication and unrelenting work during our beam time, in particular to the machine operators. NR 37 TC 24 Z9 24 U1 3 U2 52 PU NATURE PUBLISHING GROUP PI LONDON PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND SN 1749-4885 EI 1749-4893 J9 NAT PHOTONICS JI Nat. Photonics PD DEC PY 2014 VL 8 IS 12 BP 950 EP 957 DI 10.1038/NPHOTON.2014.278 PG 8 WC Optics; Physics, Applied SC Optics; Physics GA AU8AG UT WOS:000345818600015 ER PT J AU Bozovic, I Ahn, C AF Bozovic, Ivan Ahn, Charles TI A new frontier for superconductivity SO NATURE PHYSICS LA English DT Editorial Material ID HIGH-TEMPERATURE SUPERCONDUCTIVITY; FESE FILMS; ENHANCEMENT; OXIDES; ORIGIN; STRAIN; SRTIO3 C1 [Bozovic, Ivan] Brookhaven Natl Lab, Upton, NY 11973 USA. [Bozovic, Ivan; Ahn, Charles] Yale Univ, Dept Appl Phys, New Haven, CT 06511 USA. RP Bozovic, I (reprint author), Brookhaven Natl Lab, Upton, NY 11973 USA. NR 24 TC 27 Z9 28 U1 7 U2 116 PU NATURE PUBLISHING GROUP PI LONDON PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND SN 1745-2473 EI 1745-2481 J9 NAT PHYS JI Nat. Phys. PD DEC PY 2014 VL 10 IS 12 BP 892 EP 895 PG 4 WC Physics, Multidisciplinary SC Physics GA AU7BI UT WOS:000345755100002 ER PT J AU Lin, SZ Wang, XY Kamiya, Y Chern, GW Fan, F Fan, D Casas, B Liu, Y Kiryukhin, V Zurek, WH Batista, CD Cheong, SW AF Lin, Shi-Zeng Wang, Xueyun Kamiya, Yoshitomo Chern, Gia-Wei Fan, Fei Fan, David Casas, Brian Liu, Yue Kiryukhin, Valery Zurek, Wojciech H. Batista, Cristian D. Cheong, Sang-Wook TI Topological defects as relics of emergent continuous symmetry and Higgs condensation of disorder in ferroelectrics SO NATURE PHYSICS LA English DT Article ID SUPERCONDUCTING PHASE-TRANSITION; SUPERFLUID HE-3; 3 DIMENSIONS; VORTICES; BREAKING; CRYSTALS; DYNAMICS; MODEL; RENORMALIZATION; UNIVERSE AB Lars Onsager and Richard Feynman envisaged that the three-dimensional (3D) superfluid-to-normal lambda transition in He-4 occurs through the proliferation of vortices. This process should hold for every phase transition in the same universality class. The role of topological defects in symmetry-breaking phase transitions has become a prime topic in cosmology and high-temperature superconductivity, even though direct imaging of these defects is challenging. Here we show that the U(1) continuous symmetry that emerges at the ferroelectric critical point of multiferroic hexagonal manganites leads to a similar proliferation of vortices. Moreover, the disorder field (vortices) is coupled to an emergent U(1) gauge field, which becomes massive by means of the Higgs mechanism when vortices condense (span the whole system) on heating above the ferroelectric transition temperature. Direct imaging of the vortex network in hexagonal manganites offers unique experimental access to this dual description of the ferroelectric transition, while enabling tests of the Kibble-Zurek mechanism. C1 [Lin, Shi-Zeng; Kamiya, Yoshitomo; Chern, Gia-Wei; Zurek, Wojciech H.; Batista, Cristian D.] Los Alamos Natl Lab, Div Theoret, Los Alamos, NM 87545 USA. [Lin, Shi-Zeng; Chern, Gia-Wei; Zurek, Wojciech H.; Batista, Cristian D.] Los Alamos Natl Lab, CNLS, Los Alamos, NM 87545 USA. [Wang, Xueyun; Fan, Fei; Fan, David; Casas, Brian; Liu, Yue; Kiryukhin, Valery; Cheong, Sang-Wook] Rutgers State Univ, Rutgers Ctr Emergent Mat, Piscataway, NJ 08854 USA. [Wang, Xueyun; Fan, Fei; Fan, David; Casas, Brian; Liu, Yue; Kiryukhin, Valery; Cheong, Sang-Wook] Rutgers State Univ, Dept Phys & Astron, Piscataway, NJ 08854 USA. [Kamiya, Yoshitomo] RIKEN, iTHES Res Grp, Wako, Saitama 3510198, Japan. [Kamiya, Yoshitomo] RIKEN, Condensed Matter Theory Lab, Wako, Saitama 3510198, Japan. [Fan, Fei] Northwestern Polytech Univ, Sch Sci, Shaanxi Key Lab Condensed Matter Struct & Propert, Xian 710129, Peoples R China. [Fan, David] Montgomery High Sch, Skillman, NJ 08558 USA. [Casas, Brian] Univ S Florida, Dept Phys, Funct Mat Lab, Tampa, FL 33613 USA. [Liu, Yue] Nankai Univ, MOE Key Lab Weak Light Nonlinear Photon, Tianjin 300457, Peoples R China. [Liu, Yue] Nankai Univ, TEDA Appl Phys Sch, Tianjin 300457, Peoples R China. RP Cheong, SW (reprint author), Rutgers State Univ, Rutgers Ctr Emergent Mat, 136 Frelinghuysen Rd, Piscataway, NJ 08854 USA. EM sangc@physics.rutgers.edu RI Kamiya, Yoshitomo/B-6307-2012; Lin, Shi-Zeng/B-2906-2008; Batista, Cristian/J-8008-2016; OI Kamiya, Yoshitomo/0000-0002-0758-0234; Lin, Shi-Zeng/0000-0002-4368-5244; Fan, David/0000-0002-9217-5451 FU DOE under the LDRD program at the Los Alamos National Laboratory; DOE [DE-FG02-07ER46382]; RIKEN iTHES Project; China Scholarship Council FX We thank S. C. Chae, A. del campo and V. Zapf for stimulating discussion. This project was in part supported by the DOE under the LDRD program at the Los Alamos National Laboratory. The work at Rutgers University was supported by the DOE under Grant No. DE-FG02-07ER46382. Y.K. acknowledges the financial support by the RIKEN iTHES Project. The work was also supported by China Scholarship Council. NR 46 TC 20 Z9 20 U1 7 U2 57 PU NATURE PUBLISHING GROUP PI LONDON PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND SN 1745-2473 EI 1745-2481 J9 NAT PHYS JI Nat. Phys. PD DEC PY 2014 VL 10 IS 12 BP 970 EP 977 DI 10.1038/NPHYS3142 PG 8 WC Physics, Multidisciplinary SC Physics GA AU7BI UT WOS:000345755100022 ER PT J AU Baxamusa, S Miller, PE Wong, L Steele, R Shen, N Bude, J AF Baxamusa, S. Miller, P. E. Wong, L. Steele, R. Shen, N. Bude, J. TI Mitigation of organic laser damage precursors from chemical processing of fused silica SO OPTICS EXPRESS LA English DT Article ID 351 NM; OPTICAL-MATERIALS; SURFACES; CONTAMINATION; PULSES; BULK AB Increases in the laser damage threshold of fused silica have been driven by the successive elimination of near-surface damage precursors such as polishing residue, fractures, and inorganic salts. In this work, we show that trace impurities in ultrapure water used to process fused silica optics may be responsible for the formation of carbonaceous deposits. We use surrogate materials to show that organic compounds precipitated onto fused silica surfaces form discrete damage precursors. Following a standard etching process, solvent-free oxidative decomposition using oxygen plasma or high-temperature thermal treatments in air reduced the total density of damage precursors to as low as <50 cm(-2). Finally, we show that inorganic compounds are more likely to cause damage when they are tightly adhered to a surface, which may explain why high-temperature thermal treatments have been historically unsuccessful at removing extrinsic damage precursors from fused silica. (C)2014 Optical Society of America C1 [Baxamusa, S.] Lawrence Livermore Natl Lab, Phys & Life Sci Directorate, Livermore, CA 94550 USA. Lawrence Livermore Natl Lab, Natl Ignit Facil, Livermore, CA 94550 USA. RP Baxamusa, S (reprint author), Lawrence Livermore Natl Lab, Phys & Life Sci Directorate, 7000 East Ave, Livermore, CA 94550 USA. EM baxamusa1@llnl.gov FU U.S. Department of Energy by Lawrence Livermore National Laboratory within the LDRD program [DE-AC52-07NA27344] FX Authors acknowledge the assistance of N. Teslich (SEM and EDX analyses); D. VanBlarcom (UV-O3 treatment); J. Hayes and C. Alford (O2 plasma treatment); and W. Carr, M. Norton, and D. Cross for large-area damage testing. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344 within the LDRD program. NR 21 TC 10 Z9 11 U1 2 U2 24 PU OPTICAL SOC AMER PI WASHINGTON PA 2010 MASSACHUSETTS AVE NW, WASHINGTON, DC 20036 USA SN 1094-4087 J9 OPT EXPRESS JI Opt. Express PD DEC 1 PY 2014 VL 22 IS 24 BP 29568 EP 29577 DI 10.1364/OE.22.029568 PG 10 WC Optics SC Optics GA AU7HD UT WOS:000345770500027 PM 25606889 ER PT J AU Poovaiah, CR Nageswara-Rao, M Soneji, JR Baxter, HL Stewart, CN AF Poovaiah, Charleson R. Nageswara-Rao, Madhugiri Soneji, Jaya R. Baxter, Holly L. Stewart, Charles N., Jr. TI Altered lignin biosynthesis using biotechnology to improve lignocellulosic biofuel feedstocks SO PLANT BIOTECHNOLOGY JOURNAL LA English DT Review DE bioenergy; biomass; fermentable sugars; genetic manipulation; lignin biosynthetic pathway; transcription factors ID CINNAMYL ALCOHOL-DEHYDROGENASE; BICOLOR L. MOENCH; CYTOCHROME P450-DEPENDENT MONOOXYGENASE; DOMAIN TRANSCRIPTION FACTORS; PHENYLALANINE AMMONIA-LYASE; FERMENTABLE SUGAR YIELDS; SECONDARY WALL SYNTHESIS; BROWN-MIDRIB MUTANTS; PANICUM-VIRGATUM L.; MEDICAGO-SATIVA L. AB Lignocellulosic feedstocks can be converted to biofuels, which can conceivably replace a large fraction of fossil fuels currently used for transformation. However, lignin, a prominent constituent of secondary cell walls, is an impediment to the conversion of cell walls to fuel: the recalcitrance problem. Biomass pretreatment for removing lignin is the most expensive step in the production of lignocellulosic biofuels. Even though we have learned a great deal about the biosynthesis of lignin, we do not fully understand its role in plant biology, which is needed for the rational design of engineered cell walls for lignocellulosic feedstocks. This review will recapitulate our knowledge of lignin biosynthesis and discuss how lignin has been modified and the consequences for the host plant. C1 [Poovaiah, Charleson R.; Nageswara-Rao, Madhugiri; Baxter, Holly L.; Stewart, Charles N., Jr.] Univ Tennessee, Dept Plant Sci, Knoxville, TN 37996 USA. [Poovaiah, Charleson R.; Baxter, Holly L.; Stewart, Charles N., Jr.] Oak Ridge Natl Lab, BioEnergy Sci Ctr, Oak Ridge, TN USA. [Nageswara-Rao, Madhugiri] New Mexico State Univ, Dept Biol, Las Cruces, NM 88003 USA. [Soneji, Jaya R.] New Mexico State Univ, Dept Entomol Plant Pathol & Weed Sci, Las Cruces, NM 88003 USA. RP Stewart, CN (reprint author), Univ Tennessee, Dept Plant Sci, Knoxville, TN 37996 USA. EM nealstewart@utk.edu RI Poovaiah, Charleson/C-6777-2012; OI Poovaiah, Charleson/0000-0001-7157-5176 FU USDA NIFA Biotechnology Risk Assessment Grants (BRAG) Program [2010-39211-21699]; BioEnergy Science Center, a Bioenergy Research Center - Office of Biological and Environmental Research in the US Department of Energy Office of Science FX This project was made possible through funding from USDA NIFA Biotechnology Risk Assessment Grants (BRAG) Program grant # 2010-39211-21699 and the BioEnergy Science Center, a Bioenergy Research Center supported by the Office of Biological and Environmental Research in the US Department of Energy Office of Science. NR 119 TC 23 Z9 23 U1 7 U2 68 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 1467-7644 EI 1467-7652 J9 PLANT BIOTECHNOL J JI Plant Biotechnol. J. PD DEC PY 2014 VL 12 IS 9 BP 1163 EP 1173 DI 10.1111/pbi.12225 PG 11 WC Biotechnology & Applied Microbiology; Plant Sciences SC Biotechnology & Applied Microbiology; Plant Sciences GA AU6GS UT WOS:000345702500003 PM 25051990 ER PT J AU Kalluri, UC Yin, HF Yang, XH Davison, BH AF Kalluri, Udaya C. Yin, Hengfu Yang, Xiaohan Davison, Brian H. TI Systems and synthetic biology approaches to alter plant cell walls and reduce biomass recalcitrance SO PLANT BIOTECHNOLOGY JOURNAL LA English DT Review DE biomass; biofuels; recalcitrance; plant cell wall; synthetic biology; systems biology ID TARGETED GENOME MODIFICATION; NAC TRANSCRIPTION FACTORS; FERMENTABLE SUGAR YIELDS; ZINC-FINGER NUCLEASES; LIGNIN BIOSYNTHESIS; CELLULOSE SYNTHASE; BIOFUEL PRODUCTION; ARABIDOPSIS; PROTEIN; DOMAIN AB Fine-tuning plant cell wall properties to render plant biomass more amenable to biofuel conversion is a colossal challenge. A deep knowledge of the biosynthesis and regulation of plant cell wall and a high-precision genome engineering toolset are the two essential pillars of efforts to alter plant cell walls and reduce biomass recalcitrance. The past decade has seen a meteoric rise in use of transcriptomics and high-resolution imaging methods resulting in fresh insights into composition, structure, formation and deconstruction of plant cell walls. Subsequent gene manipulation approaches, however, commonly include ubiquitous mis-expression of a single candidate gene in a host that carries an intact copy of the native gene. The challenges posed by pleiotropic and unintended changes resulting from such an approach are moving the field towards synthetic biology approaches. Synthetic biology builds on a systems biology knowledge base and leverages high-precision tools for high-throughput assembly of multigene constructs and pathways, precision genome editing and site-specific gene stacking, silencing and/or removal. Here, we summarize the recent breakthroughs in biosynthesis and remodelling of major secondary cell wall components, assess the impediments in obtaining a systems-level understanding and explore the potential opportunities in leveraging synthetic biology approaches to reduce biomass recalcitrance. C1 [Kalluri, Udaya C.; Davison, Brian H.] Oak Ridge Natl Lab, BioEnergy Sci Ctr, Oak Ridge, TN 37831 USA. [Kalluri, Udaya C.; Yin, Hengfu; Yang, Xiaohan; Davison, Brian H.] Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA. RP Kalluri, UC (reprint author), Oak Ridge Natl Lab, BioEnergy Sci Ctr, Oak Ridge, TN 37831 USA. EM kalluriudayc@ornl.gov RI Davison, Brian/D-7617-2013; Yin, Hengfu/H-1695-2012; Yang, Xiaohan/A-6975-2011; OI Davison, Brian/0000-0002-7408-3609; Yin, Hengfu/0000-0002-0720-5311; Yang, Xiaohan/0000-0001-5207-4210; KALLURI, UDAYA/0000-0002-5963-8370 FU U.S. Department of Energy (DOE) BioEnergy Science Center project; Office of Biological and Environmental Research in the DOE Office of Science; U.S. Department of Energy [DE-AC05-00OR22725] FX The authors would like to thank Dr. Jerry Tuskan for his valuable comments on this manuscript. This work was funded by the U.S. Department of Energy (DOE) BioEnergy Science Center project. The BioEnergy Science Center is a Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science. ORNL is managed by UT-Battelle, LLC for the U.S. Department of Energy under Contract Number DE-AC05-00OR22725. NR 114 TC 15 Z9 15 U1 3 U2 57 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 1467-7644 EI 1467-7652 J9 PLANT BIOTECHNOL J JI Plant Biotechnol. J. PD DEC PY 2014 VL 12 IS 9 BP 1207 EP 1216 DI 10.1111/pbi.12283 PG 10 WC Biotechnology & Applied Microbiology; Plant Sciences SC Biotechnology & Applied Microbiology; Plant Sciences GA AU6GS UT WOS:000345702500006 PM 25363806 ER PT J AU Furtado, A Lupoi, JS Hoang, NV Healey, A Singh, S Simmons, BA Henry, RJ AF Furtado, Agnelo Lupoi, Jason S. Hoang, Nam V. Healey, Adam Singh, Seema Simmons, Blake A. Henry, Robert J. TI Modifying plants for biofuel and biomaterial production SO PLANT BIOTECHNOLOGY JOURNAL LA English DT Review DE biomass; biofuels; biomaterials ID CINNAMYL ALCOHOL-DEHYDROGENASE; ACIDOTHERMUS-CELLULOLYTICUS ENDOGLUCANASE; CELL-WALL; DOWN-REGULATION; LIGNOCELLULOSIC BIOMASS; LIGNIN BIOSYNTHESIS; ENZYMATIC-HYDROLYSIS; TRANSCRIPTION FACTOR; TRANSGENIC TOBACCO; HYBRID POPLAR AB The productivity of plants as biofuel or biomaterial crops is established by both the yield of plant biomass per unit area of land and the efficiency of conversion of the biomass to biofuel. Higher yielding biofuel crops with increased conversion efficiencies allow production on a smaller land footprint minimizing competition with agriculture for food production and biodiversity conservation. Plants have traditionally been domesticated for food, fibre and feed applications. However, utilization for biofuels may require the breeding of novel phenotypes, or new species entirely. Genomics approaches support genetic selection strategies to deliver significant genetic improvement of plants as sources of biomass for biofuel manufacture. Genetic modification of plants provides a further range of options for improving the composition of biomass and for plant modifications to assist the fabrication of biofuels. The relative carbohydrate and lignin content influences the deconstruction of plant cell walls to biofuels. Key options for facilitating the deconstruction leading to higher monomeric sugar release from plants include increasing cellulose content, reducing cellulose crystallinity, and/or altering the amount or composition of noncellulosic polysaccharides or lignin. Modification of chemical linkages within and between these biomass components may improve the ease of deconstruction. Expression of enzymes in the plant may provide a cost-effective option for biochemical conversion to biofuel. C1 [Furtado, Agnelo; Lupoi, Jason S.; Hoang, Nam V.; Healey, Adam; Simmons, Blake A.; Henry, Robert J.] Univ Queensland, Queensland Alliance Agr & Food Innovat, Brisbane, Qld, Australia. [Lupoi, Jason S.; Singh, Seema; Simmons, Blake A.] Joint BioEnergy Inst, Emeryville, CA USA. RP Henry, RJ (reprint author), Univ Queensland, Queensland Alliance Agr & Food Innovat, Brisbane, Qld, Australia. EM robert.henry@uq.edu.au RI Henry, Robert/B-5824-2008; OI Henry, Robert/0000-0002-4060-0292; Hoang, Nam V/0000-0003-0782-2835; Simmons, Blake/0000-0002-1332-1810 FU Queensland Government; University of Queensland; US Department of Energy; Office of Science, Office of Biological and Environmental Research, of the U.S. Department of Energy [DE-AC02-05CH11231] FX This research is supported by the Queensland Government, University of Queensland and US Department of Energy. The work conducted by the Joint BioEnergy Institute was supported by the Office of Science, Office of Biological and Environmental Research, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. NR 135 TC 11 Z9 11 U1 5 U2 68 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 1467-7644 EI 1467-7652 J9 PLANT BIOTECHNOL J JI Plant Biotechnol. J. PD DEC PY 2014 VL 12 IS 9 BP 1246 EP 1258 DI 10.1111/pbi.12300 PG 13 WC Biotechnology & Applied Microbiology; Plant Sciences SC Biotechnology & Applied Microbiology; Plant Sciences GA AU6GS UT WOS:000345702500009 PM 25431201 ER PT J AU Peng, YH Allen, S Millwood, RJ Stewart, CN AF Peng, Yanhui Allen, Sara Millwood, Reginald J. Stewart, C. Neal, Jr. TI 'Fukusensor:' a genetically engineered plant for reporting DNA damage in response to gamma radiation SO PLANT BIOTECHNOLOGY JOURNAL LA English DT Article DE transgenic plants; radiation biosensor; green fluorescence protein; DNA repair mutant; Arabidopsis thaliana ID ATM; GENOTOXICITY; CHERNOBYL; SILENCE; REPAIR AB Transgenic plants can be designed to be phytosensors' for detection of environmental contaminants and pathogens. In this study, we describe the design and testing of a radiation phytosensor in the form of green fluorescence protein (GFP)-transgenic Arabidopsis plant utilizing a DNA repair deficiency mutant background as a host. Mutant lines of Arabidopsis AtATM (At3g48190), which are hypersensitive to gamma irradiation, were used to generate stable GFP transgenic plants in which a gfp gene was under the control of a strong constitutive CaMV 35S promoter. Mutant and nonmutant genetic background transgenic plants were treated with 0, 1, 5, 10 and 100Gy radiation doses, respectively, using a Co-60 source. After 1week, the GFP expression levels were drastically reduced in young leaves of mutant background plants (treated by 10 and 100Gy), whereas there were scant visible differences in the fluorescence of the nonmutant background plants. These early results indicate that transgenic plants could serve in a relevant sensor system to report radiation dose and the biological effects to organisms in response to radionuclide contamination. C1 [Peng, Yanhui; Allen, Sara; Millwood, Reginald J.; Stewart, C. Neal, Jr.] Univ Tennessee, Dept Plant Sci, Knoxville, TN 37996 USA. [Stewart, C. Neal, Jr.] Oak Ridge Natl Lab, Oak Ridge, TN USA. RP Stewart, CN (reprint author), Univ Tennessee, Dept Plant Sci, Knoxville, TN 37996 USA. EM nealstewart@utk.edu FU National Academies Keck Futures Initiative; Oak Ridge National Laboratory; University of Tennessee FX Thanks to Larry Avens, Denise Lee and Nan Zhao at ORNL for assistance in radiation assays of the transgenic plants. All biosafety regulations were adhered to in this research. We appreciate funding from the National Academies Keck Futures Initiative, Oak Ridge National Laboratory and the University of Tennessee. NR 15 TC 1 Z9 1 U1 2 U2 20 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 1467-7644 EI 1467-7652 J9 PLANT BIOTECHNOL J JI Plant Biotechnol. J. PD DEC PY 2014 VL 12 IS 9 BP 1329 EP 1332 DI 10.1111/pbi.12247 PG 4 WC Biotechnology & Applied Microbiology; Plant Sciences SC Biotechnology & Applied Microbiology; Plant Sciences GA AU6GS UT WOS:000345702500017 PM 25196148 ER PT J AU Duff, MC Kuhne, WW Halverson, NV Chang, CS Kitamura, E Hawthorn, L Martinez, NE Stafford, C Milliken, CE Caldwell, EF Stieve-Caldwell, E AF Duff, M. C. Kuhne, W. W. Halverson, N. V. Chang, C. -S. Kitamura, E. Hawthorn, L. Martinez, N. E. Stafford, C. Milliken, C. E. Caldwell, E. F. Stieve-Caldwell, E. TI mRNA Transcript abundance during plant growth and the influence of Li+ exposure SO PLANT SCIENCE LA English DT Article DE Arabidopsis thaliana; Microarray; Next generation sequencing; Lithium exposure; Hydroponics; Soil ID GENE-EXPRESSION; ARABIDOPSIS-THALIANA; 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE; MYOINOSITOL MONOPHOSPHATASE; INOSITOL MONOPHOSPHATASE; HYDROGEN-PEROXIDE; LITHIUM TREATMENT; OXIDATIVE STRESS; MAIZE SEEDLINGS; TOXICITY AB Lithium (Li) toxicity in plants is, at a minimum, a function of Li+ concentration, exposure time, species and growth conditions. Most plant studies with Li+ focus on short-term acute exposures. This study examines short- and long-term effects of Li+ exposure in Arabidopsis with Li+ uptake studies and measured shoot mRNA transcript abundance levels in treated and control plants. Stress, pathogen-response and arabinogalactan protein genes were typically more up-regulated in older (chronic, low level) Li+-treatment plants and in the much younger plants from acute high-level exposures. The gene regulation behavior of high-level Li+ resembled prior studies due to its influence on: inositol synthesis, 1-aminocyclopropane1-carboxylate synthases and membrane ion transport. In contrast, chronically-exposed plants had gene regulation responses that were indicative of pathogen, cold, and heavy-metal stress, cell wall degradation, ethylene production, signal transduction, and calcium-release modulation. Acute Li+ exposure phenocopies magnesium-deficiency symptoms and is associated with elevated expression of stress response genes that could lead to consumption of metabolic and transcriptional energy reserves and the dedication of more resources to cell development. In contrast, chronic Li+ exposure increases expression signal transduction genes. The identification of new Li+-sensitive genes and a gene-based "response plan" for acute and chronic Li+ exposure are delineated. (C) 2014 Elsevier Ireland Ltd. All rights reserved. C1 [Duff, M. C.; Kuhne, W. W.; Halverson, N. V.; Martinez, N. E.; Stafford, C.; Milliken, C. E.; Caldwell, E. F.; Stieve-Caldwell, E.] Savannah River Natl Lab, Aiken, SC 29808 USA. [Chang, C. -S.; Kitamura, E.; Hawthorn, L.] Georgia Regents Univ, Ctr Canc, Integrated Genom Core, Augusta, GA 30912 USA. [Martinez, N. E.] Colorado State Univ, Dept Environm & Radiol Hlth Sci, Ft Collins, CO 80523 USA. [Stafford, C.] Univ S Carolina, Sch Med, Columbia, SC 29208 USA. RP Duff, MC (reprint author), Savannah River Natl Lab, Aiken, SC 29808 USA. EM Martine.Duff@srnl.doe.gov RI Martinez, Nicole/M-7538-2015 OI Martinez, Nicole/0000-0002-7184-3043 FU U.S. Dept. of Energy [DE-AC09-08SR22470]; U.S. DOE-National Nuclear Security Administration through the Office of Defense Nuclear Nonproliferation Research and Development-NA-22 [DE-FG52-05NA27035] FX This project was conducted in conjunction with work accomplished under Contract No. DE-AC09-08SR22470 with the U.S. Dept. of Energy. This work was supported by U.S. DOE-National Nuclear Security Administration through the Office of Defense Nuclear Nonproliferation Research and Development-NA-22 (Grant No. DE-FG52-05NA27035). NR 62 TC 1 Z9 1 U1 3 U2 25 PU ELSEVIER IRELAND LTD PI CLARE PA ELSEVIER HOUSE, BROOKVALE PLAZA, EAST PARK SHANNON, CO, CLARE, 00000, IRELAND SN 0168-9452 J9 PLANT SCI JI Plant Sci. PD DEC PY 2014 VL 229 BP 262 EP 279 DI 10.1016/j.plantsci.2014.10.004 PG 18 WC Biochemistry & Molecular Biology; Plant Sciences SC Biochemistry & Molecular Biology; Plant Sciences GA AU7UY UT WOS:000345807800025 PM 25443852 ER PT J AU Woo, S Cha, SW Na, S Guest, C Liu, T Smith, RD Rodland, KD Payne, S Bafna, V AF Woo, Sunghee Cha, Seong Won Na, Seungjin Guest, Clark Liu, Tao Smith, Richard D. Rodland, Karin D. Payne, Samuel Bafna, Vineet TI Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data SO PROTEOMICS LA English DT Article DE Cancer; MS; Mutated peptide identification; Ovarian cancer; Proteogenomics ID RNA-SEQ DATA; PROTEIN IDENTIFICATION; MASS-SPECTROMETRY; MESSENGER-RNA; DISCOVERY; TRANSCRIPTOMES; DATABASES; FRAMEWORK; ABUNDANCE; SEARCH AB Cancer is driven by the acquisition of somatic DNA lesions. Distinguishing the early driver mutations from subsequent passenger mutations is key to molecular subtyping of cancers, understanding cancer progression, and the discovery of novel biomarkers. The advances of genomics technologies (whole-genome exome, and transcript sequencing, collectively referred to as NGS (next-generation sequencing)) have fueled recent studies on somatic mutation discovery. However, the vision is challenged by the complexity, redundancy, and errors in genomic data, and the difficulty of investigating the proteome translated portion of aberrant genes using only genomic approaches. Combination of proteomic and genomic technologies are increasingly being employed. Various strategies have been employed to allow the usage of large-scale NGS data for conventional MS/MS searches. This paper provides a discussion of applying different strategies relating to large database search, and FDR (false discovery rate) -based error control, and their implication to cancer proteogenomics. Moreover, it extends and develops the idea of a unified genomic variant database that can be searched by any MS sample. A total of 879 BAM files downloaded from TCGA repository were used to create a 4.34GB unified FASTA database that contained 2787062 novel splice junctions, 38464 deletions, 1105 insertions, and 182302 substitutions. Proteomic data from a single ovarian carcinoma sample (439858 spectra) was searched against the database. By applying the most conservative FDR measure, we have identified 524 novel peptides and 65578 known peptides at 1% FDR threshold. The novel peptides include interesting examples of doubly mutated peptides, frame-shifts, and nonsample-recruited mutations, which emphasize the strength of our approach. C1 [Woo, Sunghee; Cha, Seong Won; Guest, Clark; Bafna, Vineet] Univ Calif San Diego, Dept Elect & Comp Engn, San Diego, CA 92103 USA. [Na, Seungjin; Bafna, Vineet] Univ Calif San Diego, Dept Comp Sci & Engn, San Diego, CA 92103 USA. [Liu, Tao; Smith, Richard D.; Rodland, Karin D.; Payne, Samuel] Pacific NW Natl Lab, Washington, DC USA. RP Bafna, V (reprint author), Univ Calif San Diego, Dept Elect & Comp Engn, San Diego, CA 92103 USA. EM vbafna@cs.ucsd.edu RI Smith, Richard/J-3664-2012 OI Smith, Richard/0000-0002-2381-2349 FU NIH [P41-RR024851]; NSF IGERT Plant Systems Biology training grant [DGE-0504645]; National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC) [U24-CA-160019]; DOE [DE-AC05-76RL01830]; DOE early career grant; [P41GM103493] FX V. B. and S. W. were supported by a grant from the NIH (P41-RR024851). S. C. was supported in part by the NSF IGERT Plant Systems Biology training grant # DGE-0504645. This work was supported by grant U24-CA-160019 (to R.D.S. and K.R.N.) from the National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). The authors acknowledge partial support for proteomics analyses from P41GM103493 (to R.D.S.). The experimental work described herein was performed in the Environmental Molecular Sciences Laboratory (EMSL), a U.S. Department of Energy (DOE) national scientific user facility located at PNNL in Richland, Washington. PNNL is a multi-program national laboratory operated by Battelle Memorial Institute for the DOE under Contract DE-AC05-76RL01830. N. S. is supported by an DOE early career grant (to S. H. P.). NR 25 TC 14 Z9 15 U1 3 U2 9 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 1615-9853 EI 1615-9861 J9 PROTEOMICS JI Proteomics PD DEC PY 2014 VL 14 IS 23-24 SI SI BP 2719 EP 2730 DI 10.1002/pmic.201400206 PG 12 WC Biochemical Research Methods; Biochemistry & Molecular Biology SC Biochemistry & Molecular Biology GA AU9LU UT WOS:000345915200010 PM 25263569 ER PT J AU Osei-Kuffuor, D Maxwell, RM Woodward, CS AF Osei-Kuffuor, D. Maxwell, R. M. Woodward, C. S. TI Improved numerical solvers for implicit coupling of subsurface and overland flow SO ADVANCES IN WATER RESOURCES LA English DT Article DE Overland flow; Preconditioning; Newton-Krylov; Implicit flow coupling; Parallel scalability ID LARGE-SCALE; HYDROLOGIC-RESPONSE; KRYLOV METHODS; SURFACE; MODEL; SIMULATIONS; CATCHMENT; EQUATIONS; FRAMEWORK; PARALLEL AB Due to complex dynamics inherent in the physical models, numerical formulation of subsurface and overland flow coupling can be challenging to solve. ParFlow is a subsurface flow code that utilizes a structured grid discretization in order to benefit from fast and efficient structured solvers. Implicit coupling between subsurface and overland flow modes in ParFlow is obtained by prescribing an overland boundary condition at the top surface of the computational domain. This form of implicit coupling leads to the activation and deactivation of the overland boundary condition during simulations where ponding or drying events occur. This results in a discontinuity in the discrete system that can be challenging to resolve. Furthermore, the coupling relies on unstructured connectivities between the subsurface and surface components of the discrete system, which makes it challenging to use structured solvers to effectively capture the dynamics of the coupled flow. We present a formulation of the discretized algebraic system that enables the use of an analytic form of the Jacobian for the Newton-Krylov solver, while preserving the structured properties of the discretization. An effective multigrid preconditioner is extracted from the analytic Jacobian and used to precondition the Jacobian linear system solver. We compare the performance of the new solver against one that uses a finite difference approximation to the Jacobian within the Newton-Krylov approach, previously used in the literature. Numerical results explores the effectiveness of using the analytic Jacobian for the Newton-Krylov solver, and highlights the performance of the new preconditioner and its cost. The results indicate that the new solver is robust and generally outperforms the solver that is based on the finite difference approximation to the Jacobian, for problems where the overland boundary condition is activated and deactivated during the simulation. A parallel weak scaling study highlights the efficiency of the new solver. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Osei-Kuffuor, D.; Woodward, C. S.] Lawrence Livermore Natl Lab, Livermore, CA 94551 USA. [Maxwell, R. M.] Colorado Sch Mines, Dept Geol & Geol Engn, Golden, CO 80401 USA. [Maxwell, R. M.] Colorado Sch Mines, Integrated Ground Water Modeling Ctr, Golden, CO 80401 USA. RP Osei-Kuffuor, D (reprint author), Lawrence Livermore Natl Lab, POB 808,L-561, Livermore, CA 94551 USA. EM oseikuffuor1@llnl.gov; rmaxwell@mines.edu; cswoodward@llnl.gov RI Woodward, Carol/M-4008-2014; Maxwell, Reed/D-7980-2013 OI Maxwell, Reed/0000-0002-1364-4441 FU Lawrence Livermore National Laboratory LDRD Program; United States Department of Energy SciDAC Program FX This work was supported by the Lawrence Livermore National Laboratory LDRD Program and by the United States Department of Energy SciDAC Program. NR 29 TC 7 Z9 7 U1 1 U2 9 PU ELSEVIER SCI LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND SN 0309-1708 EI 1872-9657 J9 ADV WATER RESOUR JI Adv. Water Resour. PD DEC PY 2014 VL 74 BP 185 EP 195 DI 10.1016/j.advwatres.2014.09.006 PG 11 WC Water Resources SC Water Resources GA AU3PE UT WOS:000345525000015 ER PT J AU Huang, K Fu, JS Hodson, EL Dong, XY Cresko, J Prikhodko, VY Storey, JM Cheng, MD AF Huang, Kan Fu, Joshua S. Hodson, Elke L. Dong, Xinyi Cresko, Joe Prikhodko, Vitaly Y. Storey, John M. Cheng, Meng-Dawn TI Identification of Missing Anthropogenic Emission Sources in Russia: Implication for Modeling Arctic Haze SO AEROSOL AND AIR QUALITY RESEARCH LA English DT Article DE Russia; EDAGR; Emission underestimation; Arctic ID BLACK CARBON; ATMOSPHERIC TRANSPORT; POLLUTION; AEROSOLS; WINTER AB Any comprehensive simulation of air pollution in the Arctic requires an accurate emission inventory. Using a community global emission inventory EDGAR v4.2 (Emissions Database for Global Atmospheric Research), GEOS-Chem modeling underestimated aerosol optical depth by 150-300% when compared to ground-based sites in Russia. Emissions from power plants, gas flaring, and mining were found significantly underestimated or even missing in EDGAR's Russian emission inventory. Approximately 70% of Russian provinces had lower NOx and PM10 emission from power plants in EDGAR as compared to a Russian federal emission inventory. Emissions from gas flaring dominated in Russia's main oil and gas producing regions. However, it is completely missing in EDGAR. In addition, EDGAR underestimated Russia's mining emissions in most of its remote areas. Overall, we find EDGAR underestimated Russia's emissions especially at high latitudes and this could overlook the impact of Russian emissions on the Arctic if EDGAR is used as input for models. C1 [Huang, Kan; Fu, Joshua S.; Dong, Xinyi] Univ Tennessee, Dept Civil & Environm Engn, Knoxville, TN 37996 USA. [Hodson, Elke L.; Cresko, Joe] US DOE, Washington, DC USA. [Prikhodko, Vitaly Y.; Storey, John M.; Cheng, Meng-Dawn] Oak Ridge Natl Lab, Energy & Environm Sci Directorate, Oak Ridge, TN USA. RP Fu, JS (reprint author), Univ Tennessee, Dept Civil & Environm Engn, Knoxville, TN 37996 USA. EM jsfu@utk.edu RI Huang, Kan/E-4824-2011; OI Cheng, Meng-Dawn/0000-0003-1407-9576 FU U.S. Department of State [S-OES-11_IAA-0027]; U.S. Department of Energy Office of Policy and International Affairs; U. S. Department of Energy [DE-AC05-00OR22725] FX This work is supported by Interagency Acquisition Agreement S-OES-11_IAA-0027 from the U.S. Department of State to the U.S. Department of Energy. Meng-Dawn Cheng, John M. Storey, and Vitaly Y. Prikhodko were supported by the U.S. Department of Energy Office of Policy and International Affairs, and performed at Oak Ridge National Laboratory (ORNL). ORNL is managed by UT-Battelle, LLC, for the U. S. Department of Energy under contract DE-AC05-00OR22725. This work does not reflect the official views or policies of the United States Government or any agency thereof, including the funding entities. The mention of any computer software, data products, and or computational hardware does not represent endorsement by the authors nor organizations that the authors are associated with. NR 39 TC 4 Z9 4 U1 1 U2 23 PU TAIWAN ASSOC AEROSOL RES-TAAR PI TAICHUNG COUNTY PA CHAOYANG UNIV TECH, DEPT ENV ENG & MGMT, PROD CTR AAQR, NO 168, JIFONG E RD, WUFONG TOWNSHIP, TAICHUNG COUNTY, 41349, TAIWAN SN 1680-8584 EI 2071-1409 J9 AEROSOL AIR QUAL RES JI Aerosol Air Qual. Res. PD DEC PY 2014 VL 14 IS 7 BP 1799 EP U25 DI 10.4209/aaqr.2014.08.0165 PG 18 WC Environmental Sciences SC Environmental Sciences & Ecology GA AU0EX UT WOS:000345297400001 ER PT J AU Wang, YG Hopke, PK AF Wang, Yungang Hopke, Philip K. TI Is Alaska Truly the Great Escape from Air Pollution? - Long Term Source Apportionment of Fine Particulate Matter in Fairbanks, Alaska SO AEROSOL AND AIR QUALITY RESEARCH LA English DT Article DE Air pollution; Fine particular matter; Source apportionment; Positive matrix factorization; Wood combustion; Alaska ID SOURCE IDENTIFICATION; ATMOSPHERIC AEROSOL; EMISSIONS; PARTICLES AB Alaska is generally considered to be a place that is one of the last great escapes from air pollution. However, they have not spent a winter in Fairbanks or the nearby village of North Pole, where the daily average PM2.5 concentration was 170 mu g/m(3) in December 2012 according to the Alaska Department of Environmental Conservation (DEC) Air Monitoring Network. In this study, source apportionment using Positive Factorization Matrix (EPA PMF 5.0) has been conducted based on the 2005 to 2012 Fairbanks PM2.5 compositional data including elements, sulfate, nitrate, ammonia, elemental carbon (EC), and organic carbon (OC) from the U.S. Environmental Protection Agency speciation network. Seven sources were identified: soil, gasoline, sulfate, diesel, wood smoke, road salt, and nitrate. The average contributions to PM2.5 of these seven sources were 3.4%, 16.3%, 19.5%, 14.3%, 40.5%, 1.5%, and 4.5%, respectively. Wood smoke provided the highest contributions to PM2.5. Its contributions were the lowest in 2007 (3.5 mu g/m(3)) and peaked in 2009 (5.7 mu g/m(3)). The winter contributions of sulfate, nitrate, diesel, road salt, and wood smoke were all substantially higher compared to other seasons. Wood smoke is the only source with weekend's contribution greater than the weekdays' corresponding to the times when residential wood combustion is more likely to occur. The contributions of diesel, wood smoke, and sulfate were approximately doubled on violation days (daily average PM2.5 higher than 35 mu g/m(3)) compared to all days. This finding indicates that winter heating is the most important factor affecting the air quality in Fairbanks In the future, additional source apportionment using other receptor models and tracers will need to be conducted to confirm these results. C1 [Wang, Yungang] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Environm Energy Technol Div, Berkeley, CA 94720 USA. [Hopke, Philip K.] Clarkson Univ, Ctr Air Resource Engn & Sci, Potsdam, NY 13699 USA. RP Wang, YG (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Environm Energy Technol Div, Berkeley, CA 94720 USA. EM yungangwang@lbl.gov RI Hopke, Philip/C-6020-2008 OI Hopke, Philip/0000-0003-2367-9661 FU Sylvia Schultz of Clean Air Fairbanks FX The authors gratefully acknowledge Sylvia Schultz of Clean Air Fairbanks for the support of this project. NR 20 TC 2 Z9 2 U1 3 U2 19 PU TAIWAN ASSOC AEROSOL RES-TAAR PI TAICHUNG COUNTY PA CHAOYANG UNIV TECH, DEPT ENV ENG & MGMT, PROD CTR AAQR, NO 168, JIFONG E RD, WUFONG TOWNSHIP, TAICHUNG COUNTY, 41349, TAIWAN SN 1680-8584 EI 2071-1409 J9 AEROSOL AIR QUAL RES JI Aerosol Air Qual. Res. PD DEC PY 2014 VL 14 IS 7 BP 1875 EP U101 DI 10.4209/aaqr.2014.03.0047 PG 13 WC Environmental Sciences SC Environmental Sciences & Ecology GA AU0EX UT WOS:000345297400007 ER PT J AU Zhang, GC Kong, II Kim, H Liu, JJ Cate, JHD Jin, YS AF Zhang, Guo-Chang Kong, In Iok Kim, Heejin Liu, Jing-Jing Cate, Jamie H. D. Jin, Yong-Su TI Construction of a Quadruple Auxotrophic Mutant of an Industrial Polyploid Saccharomyces cerevisiae Strain by Using RNA-Guided Cas9 Nuclease SO APPLIED AND ENVIRONMENTAL MICROBIOLOGY LA English DT Article ID YEAST STRAINS; RESISTANCE MARKERS; SYSTEM; VECTORS; FERMENTATION; EXPRESSION; KNOCKOUT; TALENS; PLOIDY; CELLS AB Industrial polyploid yeast strains harbor numerous beneficial traits but suffer from a lack of available auxotrophic markers for genetic manipulation. Here we demonstrated a quick and efficient strategy to generate auxotrophic markers in industrial polyploid yeast strains with the RNA-guided Cas9 nuclease. We successfully constructed a quadruple auxotrophic mutant of a popular industrial polyploid yeast strain, Saccharomyces cerevisiae ATCC 4124, with ura3, trp1, leu2, and his3 auxotrophies through RNA-guided Cas9 nuclease. Even though multiple alleles of auxotrophic marker genes had to be disrupted simultaneously, we observed knockouts in up to 60% of the positive colonies after targeted gene disruption. In addition, growth-based spotting assays and fermentation experiments showed that the auxotrophic mutants inherited the beneficial traits of the parental strain, such as tolerance of major fermentation inhibitors and high temperature. Moreover, the auxotrophic mutants could be transformed with plasmids containing selection marker genes. These results indicate that precise gene disruptions based on the RNA-guided Cas9 nuclease now enable metabolic engineering of polyploid S. cerevisiae strains that have been widely used in the wine, beer, and fermentation industries. C1 [Zhang, Guo-Chang; Kong, In Iok; Kim, Heejin; Liu, Jing-Jing; Jin, Yong-Su] Univ Illinois, Inst Genom Biol, Urbana, IL 61801 USA. [Kong, In Iok; Kim, Heejin; Jin, Yong-Su] Univ Illinois, Dept Food Sci & Human Nutr, Urbana, IL USA. [Cate, Jamie H. D.] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. [Cate, Jamie H. D.] Univ Calif Berkeley, Dept Mol & Cell Biol, Berkeley, CA 94720 USA. [Cate, Jamie H. D.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA. RP Jin, YS (reprint author), Univ Illinois, Inst Genom Biol, Urbana, IL 61801 USA. EM ysjin@illinois.edu FU Energy Biosciences Institute FX This work was supported by funding from the Energy Biosciences Institute. NR 35 TC 20 Z9 20 U1 6 U2 26 PU AMER SOC MICROBIOLOGY PI WASHINGTON PA 1752 N ST NW, WASHINGTON, DC 20036-2904 USA SN 0099-2240 EI 1098-5336 J9 APPL ENVIRON MICROB JI Appl. Environ. Microbiol. PD DEC PY 2014 VL 80 IS 24 BP 7694 EP 7701 DI 10.1128/AEM.02310-14 PG 8 WC Biotechnology & Applied Microbiology; Microbiology SC Biotechnology & Applied Microbiology; Microbiology GA AT9BS UT WOS:000345223500027 PM 25281382 ER PT J AU Cantrell, KJ Carroll, KC Buck, EC Neiner, D Geiszler, KN AF Cantrell, Kirk J. Carroll, Kenneth C. Buck, Edgar C. Neiner, Doinita Geiszler, Keith N. TI Single-pass flow-through test elucidation of weathering behavior and evaluation of contaminant release models for Hanford tank residual radioactive waste (vol 28, pg 119, 2013) SO APPLIED GEOCHEMISTRY LA English DT Correction C1 [Cantrell, Kirk J.; Carroll, Kenneth C.; Buck, Edgar C.; Neiner, Doinita; Geiszler, Keith N.] Pacific NW Natl Lab, Richland, WA 99352 USA. RP Cantrell, KJ (reprint author), Pacific NW Natl Lab, POB 999,Mail Stop K6-81, Richland, WA 99352 USA. EM kirk.cantrell@pnnl.gov RI Buck, Edgar/N-7820-2013 OI Buck, Edgar/0000-0001-5101-9084 NR 1 TC 0 Z9 0 U1 0 U2 8 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0883-2927 J9 APPL GEOCHEM JI Appl. Geochem. PD DEC PY 2014 VL 51 BP 327 EP 327 DI 10.1016/j.apgeochem.2014.08.007 PG 1 WC Geochemistry & Geophysics SC Geochemistry & Geophysics GA AU1UL UT WOS:000345405400030 ER PT J AU Noh, JH Stanford, MG Lewis, BB Fowlkes, JD Plank, H Rack, PD AF Noh, J. H. Stanford, M. G. Lewis, B. B. Fowlkes, J. D. Plank, H. Rack, P. D. TI Nanoscale electron beam-induced deposition and purification of ruthenium for extreme ultraviolet lithography mask repair SO APPLIED PHYSICS A-MATERIALS SCIENCE & PROCESSING LA English DT Article ID PLATINUM; NANOSTRUCTURES; PT(PF3)(4); TRANSMISSION; FABRICATION; PRECURSOR; GROWTH AB One critical area for the adoption of extreme ultraviolet (EUV) lithography is the development of appropriate mask repair strategies. To this end, we have explored focused electron beam-induced deposition of the ruthenium capping or protective layer. Electron beam-induced deposition (EBID) was used to deposit a ruthenium capping/protective film using the liquid bis(ethylcyclopentyldienyl) ruthenium(II) precursor. The carbon to ruthenium atomic ratio in the as-deposited material was estimated to be similar to 9/1. Subsequent to deposition, we demonstrate an electron stimulated purification process to remove carbon by-products from the deposit. Results indicate that high-fidelity nanoscale ruthenium repairs can be realized. C1 [Noh, J. H.; Stanford, M. G.; Lewis, B. B.; Rack, P. D.] Univ Tennessee, Dept Mat Sci & Engn, Knoxville, TN 37996 USA. [Fowlkes, J. D.; Rack, P. D.] Oak Ridge Natl Lab, Ctr Nanophase Mat Sci, Oak Ridge, TN 37831 USA. [Plank, H.] Graz Univ Technol, Inst Electron Microscopy & Nanoanal, A-8010 Graz, Austria. [Plank, H.] Ctr Electron Microscopy, A-8010 Graz, Austria. RP Rack, PD (reprint author), Univ Tennessee, Dept Mat Sci & Engn, Knoxville, TN 37996 USA. EM prack@utk.edu OI Rack, Philip/0000-0002-9964-3254 FU Scientific User Facilities Division, Office of Basic Energy Sciences, US Department of Energy; Austrian Cooperative Research (ACR); Graz University of Technology in Austria; University of Tennessee Chancellor's Fellowship program; National Defense Science and Engineering Graduate Fellowship through the AFOSR; Intel Corporation at the Semiconductor Research Corporation [SRC-2012-In-2310] FX A portion of this research was conducted at the Center for Nanophase Materials Sciences, which is sponsored at Oak Ridge National Laboratory by the Scientific User Facilities Division, Office of Basic Energy Sciences, US Department of Energy. HP acknowledges the support from Prof. Ferdinand Hofer and the Austrian Cooperative Research (ACR) and the Graz University of Technology in Austria. BBL acknowledges support via the University of Tennessee Chancellor's Fellowship program. MGS acknowledges support from the National Defense Science and Engineering Graduate Fellowship funded through the AFOSR. PDR and JHN acknowledge support from Intel Corporation (and Ted Liang as program mentor) via the direct funding program at the Semiconductor Research Corporation (SRC-2012-In-2310). PDR and JDF acknowledge Cheryl Hartfield at Omniprobe, Inc. (an Oxford Instruments Company) for assistance with the OmniGIS gas injection system. NR 44 TC 4 Z9 4 U1 1 U2 19 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 0947-8396 EI 1432-0630 J9 APPL PHYS A-MATER JI Appl. Phys. A-Mater. Sci. Process. PD DEC PY 2014 VL 117 IS 4 BP 1705 EP 1713 DI 10.1007/s00339-014-8745-0 PG 9 WC Materials Science, Multidisciplinary; Physics, Applied SC Materials Science; Physics GA AU0DI UT WOS:000345293200011 ER PT J AU Asad, AH Chan, S Morandeau, L Cryer, D Smith, SV Price, RI AF Asad, Ali H. Chan, Sun Morandeau, Laurence Cryer, David Smith, Suzanne V. Price, Roger I. TI Excitation functions of Zn-nat(p,x) nuclear reactions with proton beam energy below 18 MeV SO APPLIED RADIATION AND ISOTOPES LA English DT Article DE Excitation function; Natural zinc; Stacked-foils activation; Proton beam; Isochronous cyclotron; Zn-nat(p,x) reactions ID CROSS-SECTION; PET TRACER; ZN-NAT; YIELDS; GA-66; CYCLOTRON; CU-67 AB We measured the excitation functions of Zn-nat (p,x) reactions up to 17.6 MeV, using the stacked-foils activation technique. High-purity natural zinc (and copper) foils were irradiated with proton beams generated by an 18 MeV isochronous cyclotron. Activated foils were measured using high-purity Ge gamma spectroscopy to quantify the radionuclides Cu-61, Ga-66, Ga-67, and Zn-65 produced from the reactions. Thick-target integral yields were also deduced from the measured excitation functions of the produced radioisotopes. These results were compared with the published literature and were found to be in good agreement with most reports, particularly those most recently compiled. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Asad, Ali H.; Chan, Sun; Morandeau, Laurence; Cryer, David; Price, Roger I.] Sir Charles Gairdner Hosp, Radiopharmaceut Prod & Dev RAPID Lab, Perth, WA 6009, Australia. [Asad, Ali H.] Curtin Univ, Dept Imaging & Appl Phys, Perth, WA 6845, Australia. [Smith, Suzanne V.] Brookhaven Natl Lab, Collider Accelerator Dept, Upton, NY 11973 USA. [Smith, Suzanne V.] Australian Natl Univ, Res Sch Phys & Engn, Ctr Excellence Antimatter Matter Studies CAMS, Canberra, ACT 0200, Australia. [Price, Roger I.] Univ Western Australia, Sch Phys, Nedlands, WA 6009, Australia. RP Asad, AH (reprint author), Sir Charles Gairdner Hosp, Hosp Ave, Nedlands, WA 6009, Australia. EM ali.asad@health.wa.gov.au NR 28 TC 3 Z9 3 U1 0 U2 3 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0969-8043 J9 APPL RADIAT ISOTOPES JI Appl. Radiat. Isot. PD DEC PY 2014 VL 94 BP 67 EP 71 DI 10.1016/j.apradiso.2014.07.008 PG 5 WC Chemistry, Inorganic & Nuclear; Nuclear Science & Technology; Radiology, Nuclear Medicine & Medical Imaging SC Chemistry; Nuclear Science & Technology; Radiology, Nuclear Medicine & Medical Imaging GA AU2XK UT WOS:000345477700012 PM 25108597 ER PT J AU Slowey, AJ Vandehey, NT O'Neil, JP Boutchko, R Moses, WW Nico, PS AF Slowey, Aaron J. Vandehey, Nicholas T. O'Neil, James P. Boutchko, Rostyslav Moses, William W. Nico, Peter S. TI Chemical stability of Tc-99m-DTPA under aerobic and microbially mediated Fe(III)-reducing conditions in porous media SO APPLIED RADIATION AND ISOTOPES LA English DT Article DE Technetium; Chromium; Groundwater; Radiotracer; SPECT; Tomography ID SHEWANELLA-PUTREFACIENS; DIETHYLENETRIAMINEPENTAACETIC ACID; EMISSION-TOMOGRAPHY; DEGRADATION RATES; ADSORPTION; REDUCTION; IRON; DISSOLUTION; FE(III); EDTA AB Tc-99m-DTPA has been used as a conservative tracer to quantify water transport through porous media. However, more information on the reactivity of this Tc-99m compound under varying geochemical conditions is desirable to better understand its potential uses. We measured the speciation of Tc following amendment of Tc-99m-DTPA to batch systems spanning a range of controlled biogeochemical conditions. Our results suggest that Tc-99m-DTPA is stable under the reducing conditions tested. However, freshly precipitated Al-ferrihydrite may displace Tc(IV) from DTPA in the absence of Fe(III)-reducing conditions. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Slowey, Aaron J.; Nico, Peter S.] Lawrence Berkeley Natl Lab, Div Earth Sci, Dept Geochem, Berkeley, CA 94207 USA. [Vandehey, Nicholas T.; O'Neil, James P.; Boutchko, Rostyslav; Moses, William W.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Life Sci, Dept Radiotracer Dev & Imaging Technol, Berkeley, CA 94720 USA. RP Nico, PS (reprint author), Lawrence Berkeley Natl Lab, Div Earth Sci, Dept Geochem, 1 Cyclotron Rd, Berkeley, CA 94207 USA. EM psnico@lbl.gov RI Nico, Peter/F-6997-2010; OI Nico, Peter/0000-0002-4180-9397; Vandehey, Nicholas/0000-0003-0286-7532 FU Subsurface Science and Radiochemistry and Instrumentation Scientific Focus Areas - U.S. Department of Energy (DoE), Office of Science, Office of Biological and Environmental Research [DE-AC02-05CH11231]; United States Government FX Support from the Subsurface Science and Radiochemistry and Instrumentation Scientific Focus Areas funded by the U.S. Department of Energy (DoE), Office of Science, Office of Biological and Environmental Research under Award number DE-AC02-05CH11231. This document was prepared as an account of work sponsored by the United States Government. While this document is believed to contain correct information, neither the United States Government nor any agency thereof, nor the Regents of the University of California, nor any of their employees, makes any warranty, express or implied, or assumes any legal responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or the Regents of the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof or the Regents of the University of California. NR 35 TC 0 Z9 0 U1 1 U2 9 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0969-8043 J9 APPL RADIAT ISOTOPES JI Appl. Radiat. Isot. PD DEC PY 2014 VL 94 BP 175 EP 181 DI 10.1016/j.apradiso.2014.08.005 PG 7 WC Chemistry, Inorganic & Nuclear; Nuclear Science & Technology; Radiology, Nuclear Medicine & Medical Imaging SC Chemistry; Nuclear Science & Technology; Radiology, Nuclear Medicine & Medical Imaging GA AU2XK UT WOS:000345477700030 PM 25213084 ER PT J AU Kim, D Alexoff, DL Schueller, M Babst, B Ferrieri, R Fowler, JS Schlyer, DJ AF Kim, Dohyun Alexoff, David L. Schueller, Mike Babst, Ben Ferrieri, Richard Fowler, Joanna S. Schlyer, David J. TI The design and performance of a portable handheld (CO2)-C-11 delivery system SO APPLIED RADIATION AND ISOTOPES LA English DT Article DE [C-11]CO2; Radiochemistry; Portable; Miniature; PET ID C-11 CARBON-DIOXIDE; MOLECULAR-SIEVES; GAS STREAMS; TRANSPORT; POPULUS; TRAP; CO2 AB We constructed a hand-held device to efficiently trap [C-11]CO2 from the cyclotron target, safely transport up to 3.7 GBq (100 mCi) doses to remote sites and release it without the need for a liquid cryogen. The system consists of a 180 W furnace and a miniature molecular sieve trap (80-100 mg; 80-100 mesh 13 x) placed inside a lead pig weighing 11.1 kg. The overall [C-11]CO2 delivery efficiency of the device is similar to 82% (> 99% trapping efficiency). Radiation dose rates measured at 30 cm from the surface of the pig are <43.5 mu Sv/h (5 mR/h) up to 2.59 GBq (70 mCi). (C) 2014 Elsevier Ltd. All rights reserved. C1 [Kim, Dohyun; Alexoff, David L.; Schueller, Mike; Babst, Ben; Ferrieri, Richard; Fowler, Joanna S.; Schlyer, David J.] Brookhaven Natl Lab, Dept Biosci, Upton, NY 11973 USA. RP Alexoff, DL (reprint author), Brookhaven Natl Lab, Dept Biosci, Upton, NY 11973 USA. EM dohkim@bnl.gov; alexoff@bnl.gov; mschueller@bnl.gov; bbabst@bnl.gov; ferrieri@bnl.gov; fowler@bnl.gov; schlyer@bnl.gov FU U. S. Department of Energy, Office of Biological and Environmental Research [DE-AC02-98CH10886] FX This work was supported in part by the U. S. Department of Energy, Office of Biological and Environmental Research under Contract DE-AC02-98CH10886. The authors thank Abhijit Karve for his many helpful discussions. NR 23 TC 3 Z9 3 U1 0 U2 2 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0969-8043 J9 APPL RADIAT ISOTOPES JI Appl. Radiat. Isot. PD DEC PY 2014 VL 94 BP 338 EP 343 DI 10.1016/j.apradiso.2014.09.008 PG 6 WC Chemistry, Inorganic & Nuclear; Nuclear Science & Technology; Radiology, Nuclear Medicine & Medical Imaging SC Chemistry; Nuclear Science & Technology; Radiology, Nuclear Medicine & Medical Imaging GA AU2XK UT WOS:000345477700052 PM 25305526 ER PT J AU Guo, LJ Huang, YM Bhattacharjee, A Innes, DE AF Guo, L. -J. Huang, Y. -M. Bhattacharjee, A. Innes, D. E. TI RAYLEIGH-TAYLOR TYPE INSTABILITIES IN THE RECONNECTION EXHAUST JET AS A MECHANISM FOR SUPRA-ARCADE DOWNFLOWS IN THE SUN SO ASTROPHYSICAL JOURNAL LETTERS LA English DT Article DE instabilities; magnetic reconnection; Sun: flares ID SOLAR-FLARES; CURRENT SHEETS; MAGNETIC RECONNECTION; MOTIONS AB Supra-arcade downflows (hereafter referred to as SADs) are low-emission, elongated, finger-like features observed in active region coronae above post-eruption flare arcades. Observations exhibit downward moving SADs intertwined with bright upward growing spikes. Whereas SADs are dark voids, spikes are brighter, denser structures. Although SADs have been observed for more than a decade, the mechanism of the formation of SADs remains an open issue. Using three-dimensional resistive magnetohydrodynamic simulations, we demonstrate that Rayleigh-Taylor-type instabilities develop in the downstream region of a reconnecting current sheet. The instabilities result in the formation of low-density coherent structures that resemble SADs, and high-density structures that appear to be spike-like. Comparison between the simulation results and observations suggests that Rayleigh-Taylor-type instabilities in the exhaust of reconnecting current sheets provide a plausible mechanism for observed SADs. C1 [Guo, L. -J.; Huang, Y. -M.; Bhattacharjee, A.] Univ New Hampshire, Ctr Space Sci, Durham, NH 03824 USA. [Guo, L. -J.; Huang, Y. -M.; Bhattacharjee, A.] Princeton Univ, Dept Astrophys Sci, Ctr Heliosphys, Princeton, NJ 08540 USA. [Guo, L. -J.; Huang, Y. -M.; Bhattacharjee, A.] Princeton Univ, Princeton Plasma Phys Lab, Princeton, NJ 08540 USA. [Guo, L. -J.; Huang, Y. -M.; Bhattacharjee, A.; Innes, D. E.] Max Planck Princeton Ctr Plasma Phys, Princeton, NJ 08540 USA. [Guo, L. -J.; Innes, D. E.] Max Planck Inst Solar Syst Res, D-37077 Gottingen, Germany. RP Guo, LJ (reprint author), Univ New Hampshire, Ctr Space Sci, Durham, NH 03824 USA. EM guol@mps.mpg.de; yiminh@princeton.edu; amitava@princeton.edu; innes@mps.mpg.de RI Huang, Yi-Min/G-6926-2011 OI Huang, Yi-Min/0000-0002-4237-2211 FU Department of Energy [DE-FG02-07ER46372]; National Science Foundation [PHY-0215581]; NASA [NNX09AJ86G, NNX10AC04G]; NSF [ATM-0802727, ATM-090315, AGS-0962698] FX This work was supported by the Department of Energy, grant No. DE-FG02-07ER46372 and the National Science Foundation, grant No. PHY-0215581, NASA grant Nos. NNX09AJ86G and NNX10AC04G, and NSF grant Nos. ATM-0802727, ATM-090315, and AGS-0962698. NR 27 TC 5 Z9 5 U1 2 U2 3 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 2041-8205 EI 2041-8213 J9 ASTROPHYS J LETT JI Astrophys. J. Lett. PD DEC 1 PY 2014 VL 796 IS 2 AR L29 DI 10.1088/2041-8205/796/2/L29 PG 6 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA AU3HP UT WOS:000345503400008 ER PT J AU Ballinger, MY Larson, TV AF Ballinger, Marcel Y. Larson, Timothy V. TI Source apportionment of stack emissions from research and development facilities using positive matrix factorization SO ATMOSPHERIC ENVIRONMENT LA English DT Article DE Positive matrix factorization; Measured stack emissions; Bootstrapping; Volatile organic compounds AB Research and development (R&D) facility emissions are difficult to characterize due to their variable processes, changing nature of research, and large number of chemicals. Positive matrix factorization (PMF) was applied to volatile organic compound (VOC) concentrations measured in the main exhaust stacks of four different R&D buildings to identify the number and composition of major contributing sources. PMF identified between 9 and 11 source-related factors contributing to stack emissions, depending on the building. Similar factors between buildings were major contributors to trichloroethylene (TCE), acetone, and ethanol emissions; other factors had similar profiles for two or more buildings but not all four. At least one factor for each building was identified that contained a broad mix of many species and constraints were used in PMF to modify the factors to resemble more closely the off-shift concentration profiles. PMF accepted the constraints with little decrease in model fit. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Ballinger, Marcel Y.] Seattle Biomed Res Inst, Pacific NW Natl Lab, Seattle, WA 98109 USA. [Larson, Timothy V.] Univ Washington, Dept Civil & Environm Engn, Seattle, WA 98195 USA. RP Ballinger, MY (reprint author), Seattle Biomed Res Inst, Pacific NW Natl Lab, 1100 Dexter Ave North,Suite 400, Seattle, WA 98109 USA. EM marcel.ballinger@pnnl.gov FU PNNL FX The authors would like to acknowledge PNNL for supporting this work. The authors thank Cheryl Duchsherer and Rodger Woodruff at PNNL and Professor Christopher Simpson at the University of Washington for their review of the manuscript and suggestions for improvements. NR 22 TC 1 Z9 1 U1 5 U2 21 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 1352-2310 EI 1873-2844 J9 ATMOS ENVIRON JI Atmos. Environ. PD DEC PY 2014 VL 98 BP 59 EP 65 DI 10.1016/j.atmosenv.2014.08.041 PG 7 WC Environmental Sciences; Meteorology & Atmospheric Sciences SC Environmental Sciences & Ecology; Meteorology & Atmospheric Sciences GA AU2WI UT WOS:000345475000008 ER PT J AU de Foy, B Wilkins, JL Lu, ZF Streets, DG Duncan, BN AF de Foy, Benjamin Wilkins, Joseph L. Lu, Zifeng Streets, David G. Duncan, Bryan N. TI Model evaluation of methods for estimating surface emissions and chemical lifetimes from satellite data SO ATMOSPHERIC ENVIRONMENT LA English DT Article DE Emission inventory; Satellite retrieval; Chemical lifetime; Air quality model; Emissions estimation ID NOX EMISSIONS; POWER-PLANTS; NITROGEN-OXIDES; SPACE; RETRIEVALS; COLUMNS AB Column densities from satellite retrievals can provide valuable information for estimating emissions and chemical lifetimes objectively across the globe. To better understand the uncertainties associated with these estimates, we test four methods using simulated column densities from a point source: a box model approach, a 2D Gaussian fit, an Inverse Radius fit and an Exponentially-Modified Gaussian fit. The model results were simulated using the WRF and CAMx models for the year 2005, for a single point source outside Atlanta in Georgia, USA with specified emissions and three chemical scenarios: no chemical reactions, 12 h chemical lifetime and 1 h chemical lifetime. No other sources were included in the simulations. We find that the box model provides reliable estimates irrespective of plume speed and plume direction, if the plume speed and the chemical lifetime are known accurately. The 2D Gaussian fit was found to be sensitive to plume speed and direction, and requires omnidirectional dispersion in order to have a decent fit. However, the 2D Gaussian fit is only an approximate fit to the data, and the discrepancies mean that the results are dependent on the geographical domain used for the optimization. An Inverse Radius fit is introduced to correct this issue, which is found to provide improved emissions and lifetime estimates. The Exponentially-Modified Gaussian fit also gave improved estimates. It is however dependent on accurate plume rotation such that reported chemical lifetimes with this method could be significantly underestimated. (C) 2014 Elsevier Ltd. All rights reserved. C1 [de Foy, Benjamin; Wilkins, Joseph L.] St Louis Univ, Dept Earth & Atmospher Sci, St Louis, MO 63103 USA. [Lu, Zifeng; Streets, David G.] Argonne Natl Lab, Decis & Informat Sci Div, Argonne, IL 60439 USA. [Duncan, Bryan N.] NASA, Goddard Space Flight Ctr, Atmospher Chem & Dynam Lab, Greenbelt, MD 20771 USA. RP de Foy, B (reprint author), St Louis Univ, Dept Earth & Atmospher Sci, St Louis, MO 63103 USA. EM bdefoy@slu.edu RI de Foy, Benjamin/A-9902-2010; Duncan, Bryan/A-5962-2011 OI de Foy, Benjamin/0000-0003-4150-9922; FU NASA [NNX11AJ63G] FX This research was funded by the NASA Air Quality Applied Sciences Team (AQAST) program, NASA grant #NNX11AJ63G, including funding for the AQAST Tiger Team "Relationships and trends among satellite NO2 columns, NOx emissions, and air quality in North America." We are grateful for valuable comments and discussion from the team members and the team leader and assistant leader, Daniel J. Jacob and Tracey Holloway. We are also grateful for detailed reviewer comments that improved the quality of the paper. NR 33 TC 9 Z9 9 U1 3 U2 22 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 1352-2310 EI 1873-2844 J9 ATMOS ENVIRON JI Atmos. Environ. PD DEC PY 2014 VL 98 BP 66 EP 77 DI 10.1016/j.atmosenv.2014.08.051 PG 12 WC Environmental Sciences; Meteorology & Atmospheric Sciences SC Environmental Sciences & Ecology; Meteorology & Atmospheric Sciences GA AU2WI UT WOS:000345475000009 ER PT J AU Situ, S Wang, XM Guenther, A Zhang, YL Wang, XM Huang, MJ Fan, Q Xiong, Z AF Situ, Shuping Wang, Xuemei Guenther, Alex Zhang, Yanli Wang, Xinming Huang, Minjuan Fan, Qi Xiong, Zhe TI Uncertainties of isoprene emissions in the MEGAN model estimated for a coniferous and broad-leaved mixed forest in Southern China SO ATMOSPHERIC ENVIRONMENT LA English DT Article DE MEGAN; Isoprene emission; Uncertainty; Monte Carlo; Dinghushan; Biogenic VOCs ID PEARL RIVER-DELTA; ORGANIC-COMPOUND EMISSIONS; HYDROCARBONS; PREDICTIONS; CAMPAIGN; SUBURBAN; DROUGHT; REGION; DOMAIN; URBAN AB With local observed emission factor and meteorological data, this study constrained the Model of Emissions of Gases and Aerosols from Nature (MEGAN) v2.1 to estimate isoprene emission from the Dinghushan forest during fall 2008 and quantify the uncertainties associated with MEGAN parameters using Monte Carlo approach. Compared with observation-based isoprene emission data originated from a campaign during this period at this site, the local constrained MEGAN tends to reproduce the diurnal variations and magnitude of isoprene emission reasonably well, with correlation coefficient of 0.7 and mean bias of 47.5%. The results also indicate high uncertainties in isoprene emission estimated, with the relative error varied from -89.0-111.0% at the 95% confidence interval. The key uncertainty sources include emission factors, gamma(TLD), photosynthetically active radiation (PAR) and temperature. This implies that accurate input of emission factor, PAR and temperature is a key approach to reduce uncertainties in isoprene emission estimation. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Situ, Shuping; Wang, Xuemei; Huang, Minjuan; Fan, Qi] Sun Yat Sen Univ, Sch Environm Sci & Engn, Guangzhou 510275, Guangdong, Peoples R China. [Guenther, Alex] Pacific NW Natl Lab, Richland, WA 99352 USA. [Zhang, Yanli; Wang, Xinming] Chinese Acad Sci, Guangzhou Inst Geochem, State Key Lab Organ Geochem, Guangzhou 510640, Guangdong, Peoples R China. [Xiong, Zhe] Chinese Acad Sci, Inst Atmospher Phys, Key Lab Climate Environm East Asia, Beijing 100029, Peoples R China. RP Wang, XM (reprint author), Sun Yat Sen Univ, Sch Environm Sci & Engn, Guangzhou 510275, Guangdong, Peoples R China. EM eeswxm@mail.sysu.edu.cn RI ZHANG, Yanli/A-3225-2015; Wang, Xuemei/B-4521-2012; Wang, Xinming/A-7388-2014 OI ZHANG, Yanli/0000-0003-0614-2096; Wang, Xinming/0000-0002-1982-0928 FU National Natural Science Foundation of Guangdong Province [S2012020011044]; public sector (meteorological) Scientific research project [GYHY201406031]; European Union [3206429]; Jiangsu Collaborative Innovation Center for Climate Change; Sun Yat-sen University FX This research was supported by the National Natural Science Foundation of Guangdong Province as key project (S2012020011044), the public sector (meteorological) Scientific research project (GYHY201406031) and the European Union FP7 project PANDA (3206429). This work was also partly supported by the Jiangsu Collaborative Innovation Center for Climate Change and the high-performance grid-computing platform of Sun Yat-sen University. The authors thank the South China Institute of Botany for experiment, and thank Dr. Keding Lu for providing the detail OH concentration in PRD. NR 46 TC 5 Z9 5 U1 4 U2 26 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 1352-2310 EI 1873-2844 J9 ATMOS ENVIRON JI Atmos. Environ. PD DEC PY 2014 VL 98 BP 105 EP 110 DI 10.1016/j.atmosenv.2014.08.023 PG 6 WC Environmental Sciences; Meteorology & Atmospheric Sciences SC Environmental Sciences & Ecology; Meteorology & Atmospheric Sciences GA AU2WI UT WOS:000345475000013 ER PT J AU Fisher, N Kramer, DM AF Fisher, Nicholas Kramer, David M. TI Non-photochemical reduction of thylakoid photosynthetic redox carriers in vitro: Relevance to cyclic electron flow around photosystem I? SO BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS LA English DT Article DE Photosynthesis; Chlorophyll fluorescence; Cyclic electron flow; Photosystem II; PGR5; Plastoquinone ID FERREDOXIN-PLASTOQUINONE REDUCTASE; A FLUORESCENCE INDUCTION; WATER-SPLITTING SYSTEM; SPINACH-CHLOROPLASTS; CHLOROPHYLL-A; NAD(P)H DEHYDROGENASE; CYTOCHROME B-559; REACTION CENTERS; PRIMARY ACCEPTOR; HIGHER-PLANTS AB Non-photochemical (dark) increases in chlorophyll a fluorescence yield associated with non-photochemical reduction of redox carriers (F-npr) have been attributed to the reduction of plastoquinone (PQ) related to cyclic electron flow (CEF) around photosystem I. In vivo, this rise in fluorescence is associated with activity of the chloroplast plastoquinone reductase (plastid NAD(P)H:plastoquinone oxidoreductase) complex. In contrast, this signal measured in isolated thylakoids has been attributed to the activity of the protein gradient regulation-5 (PGR5)/PGR5-like (PGRL1)-associated CEF pathway. Here, we report a systematic experimentation on the origin of F-npr in isolated thylakoids. Addition of NADPH and ferredoxin to isolated spinach thylakoids resulted in the reduction of the PQ pool, but neither its kinetics nor its inhibitor sensitivities matched those of Notably, F-npr was more rapid than PQ reduction, and completely insensitive to inhibitors of the PSII Q(B) site and oxygen evolving complex as well as inhibitors of the cytochrome b(6)f complex. We thus conclude that Fnpr in isolated thylakoids is not a result of redox equilibrium with bulk PQ. Redox titrations and fluorescence emission spectra imply that F-npr is dependent on the reduction of a low potential redox component (Em about -340 mV) within photosystem II (PSII), and is likely related to earlier observations of low potential variants of Q(A) within a subpopulation of PSII that is directly reducible by ferredoxin. The implications of these results for our understanding of CEF and other photosynthetic processes are discussed. (C) 2014 Elsevier B.V. All rights reserved. C1 [Fisher, Nicholas; Kramer, David M.] Michigan State Univ, MSU DOE Plant Res Lab, E Lansing, MI 48824 USA. [Kramer, David M.] Michigan State Univ, Dept Biochem & Mol Biol, E Lansing, MI 48824 USA. RP Kramer, DM (reprint author), Michigan State Univ, MSU DOE Plant Res Lab, E Lansing, MI 48824 USA. EM kramerd8@msu.edu FU Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the US Department of Energy [DE-FG02-11ER16220] FX This work was supported by the grant DE-FG02-11ER16220 (to D.M.K.) from the Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the US Department of Energy. We would like to thank Prof. Charles Yocum (University of Michigan), Prof. William Rutherford (Imperial College), Prof. William Cramer (Purdue University), Dr. Derek Bendall (University of Cambridge) and Deserah Strand (Michigan State University) for useful discussions during the preparation of this manuscript. NR 101 TC 14 Z9 14 U1 2 U2 38 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0005-2728 EI 0006-3002 J9 BBA-BIOENERGETICS JI Biochim. Biophys. Acta-Bioenerg. PD DEC PY 2014 VL 1837 IS 12 BP 1944 EP 1954 DI 10.1016/j.bbabio.2014.09.005 PG 11 WC Biochemistry & Molecular Biology; Biophysics SC Biochemistry & Molecular Biology; Biophysics GA AU6RO UT WOS:000345729800004 PM 25251244 ER PT J AU Wendt, LM Bonner, IJ Hoover, AN Emerson, RM Smith, WA AF Wendt, Lynn M. Bonner, Ian J. Hoover, Amber N. Emerson, Rachel M. Smith, William A. TI Influence of Airflow on Laboratory Storage of High Moisture Corn Stover SO BIOENERGY RESEARCH LA English DT Article DE Biomass; Corn stover; Aerobic storage; Aeration rate; Dry matter loss; Composition ID AERATION RATE; AEROBIC STABILITY; NUTRITIVE-VALUE; SINGLE-PASS; HARVEST; FERMENTATION; KINETICS; COMPOST; DIGESTIBILITY; ADDITIVES AB Storing high moisture biomass for bioenergy use is a reality in many areas of the country where wet harvest conditions and environmental factors prevent dry storage from being feasible. Aerobic storage of high moisture biomass leads to microbial degradation and self-heating, but oxygen limitation can aid in material preservation. To understand the influence of oxygen presence on high moisture biomass (50 %, wet basis), three airflow rates were tested on corn stover stored in laboratory reactors. Temperature, carbon dioxide production, dry matter loss, chemical composition, fungal abundance, pH, and organic acids were used to monitor the effects of airflow on storage conditions. The results of this work indicate that oxygen availability impacts both the duration of self-heating and the severity of dry matter loss. High airflow systems experienced the greatest initial rates of loss but a shortened microbially active period that limited total dry matter loss (19 %). Intermediate airflow had improved preservation in short-term storage compared to high airflow systems but accumulated the greatest dry matter loss over time (up to 27 %) as a result of an extended microbially active period. Low airflow systems displayed the best performance with the lowest rates of loss and total loss (10 %) in storage at 50 days. Total structural sugar levels of the stored material were preserved, although glucan enrichment and xylan loss were documented in the high and intermediate flow conditions. By understanding the role of oxygen availability on biomass storage performance, the requirements for high moisture storage solutions may begin to be experimentally defined. C1 [Wendt, Lynn M.; Smith, William A.] Idaho Natl Lab, Biol & Chem Proc Dept, Idaho Falls, ID 83415 USA. [Bonner, Ian J.; Hoover, Amber N.; Emerson, Rachel M.] Idaho Natl Lab, Biofuels & Renewable Energy Technol Dept, Idaho Falls, ID 83415 USA. RP Wendt, LM (reprint author), Idaho Natl Lab, Biol & Chem Proc Dept, POB 1625, Idaho Falls, ID 83415 USA. EM lynn.wendt@inl.gov RI Hoover, Amber/B-8373-2017 OI Hoover, Amber/0000-0001-8584-3995 FU U.S. Department of Energy, under DOE Idaho Operations Office [DE-AC07-05ID14517] FX The authors thank Karen Delezene-Briggs and Sabrina Morgan of the Idaho National Laboratory for their efforts in sample analysis and Kevin Kenney for his critical review of the manuscript. This work is supported by the U.S. Department of Energy, under DOE Idaho Operations Office Contract DE-AC07-05ID14517. Accordingly, 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. NR 46 TC 0 Z9 0 U1 3 U2 13 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1939-1234 EI 1939-1242 J9 BIOENERG RES JI BioEnergy Res. PD DEC PY 2014 VL 7 IS 4 BP 1212 EP 1222 DI 10.1007/s12155-014-9455-3 PG 11 WC Energy & Fuels; Environmental Sciences SC Energy & Fuels; Environmental Sciences & Ecology GA AU4MF UT WOS:000345584500014 ER PT J AU Zhou, C Ma, Q Mao, XZ Liu, BQ Yin, YB Xu, Y AF Zhou, Chuan Ma, Qin Mao, Xizeng Liu, Bingqiang Yin, Yanbin Xu, Ying TI New Insights into Clostridia Through Comparative Analyses of Their 40 Genomes SO BIOENERGY RESEARCH LA English DT Article DE Clostridium; Comparative genomics; Pan-genome; Phylogeny; CAZyme; Motif ID MICROBIAL PAN-GENOME; RIBOSOMAL-RNA; BIOFUEL PRODUCTION; WEB SERVER; SEQUENCE; IDENTIFICATION; DATABASE; STRAINS; ACETOBUTYLICUM; CELLULOVORANS AB The Clostridium genus of bacteria contains the most widely studied biofuel-producing organisms such as Clostridium thermocellum and also some human pathogens, plus a few less characterized strains. Here, we present a comparative genomic analysis of 40 fully sequenced clostridial genomes, paying a particular attention to the biomass degradation ones. Our analysis indicates that some of the Clostridium botulinum strains may have been incorrectly classified in the current taxonomy and hence should be renamed according to the 16S ribosomal RNA (rRNA) phylogeny. A core-genome analysis suggests that only 169 orthologous gene groups are shared by all the strains, and the strain-specific gene pool consists of 22,668 genes, which is consistent with the fact that these bacteria live in very diverse environments and have evolved a very large number of strain-specific genes to adapt to different environments. Across the 40 genomes, 1.4-5.8 % of genes fall into the carbohydrate active enzyme (CAZyme) families, and 20 out of the 40 genomes may encode cellulosomes with each genome having 1 to 76 genes bearing the cellulosome-related modules such as dockerins and cohesins. A phylogenetic footprinting analysis identified cis-regulatory motifs that are enriched in the promoters of the CAZyme genes, giving rise to 32 statistically significant motif candidates. C1 [Zhou, Chuan; Liu, Bingqiang] Shandong Univ, Sch Math, Jinan 250100, Shandong, Peoples R China. [Ma, Qin; Mao, Xizeng; Xu, Ying] Univ Georgia, Dept Biochem & Mol Biol, Computat Syst Biol Lab, Athens, GA 30602 USA. [Ma, Qin; Mao, Xizeng; Xu, Ying] Univ Georgia, Inst Bioinformat, Athens, GA 30602 USA. [Ma, Qin; Mao, Xizeng; Xu, Ying] BioEnergy Sci Ctr, Oak Ridge, TN USA. [Yin, Yanbin] No Illinois Univ, Dept Biol Sci, De Kalb, IL 60115 USA. [Xu, Ying] Jilin Univ, Coll Comp Sci & Technol, Changchun 130023, Jilin, Peoples R China. RP Xu, Y (reprint author), Univ Georgia, Dept Biochem & Mol Biol, Computat Syst Biol Lab, Athens, GA 30602 USA. EM yyin@niu.edu; xyn@bmb.uga.edu RI Ma, Qin/O-1525-2013; Yin, Yanbin/C-9788-2010 OI Ma, Qin/0000-0002-3264-8392; Yin, Yanbin/0000-0001-7667-881X FU National Science Foundation [NSF DEB-0830024, NSF MCB-0958172]; US Department of Energy's BioEnergy Science Center (BESC) grant through the Office of Biological and Environmental Research; National Science Foundation of China [NSFC 61272016, 61303084]; Office of Biological and Environmental Research in the DOE Office of Science; US Department of Energy's BioEnergy Science Center (BESC) FX This research was supported in part by the National Science Foundation (#NSF DEB-0830024 and NSF MCB-0958172), the US Department of Energy's BioEnergy Science Center (BESC) grant through the Office of Biological and Environmental Research, and National Science Foundation of China (NSFC 61272016 and 61303084). The BioEnergy Science Center is a US Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science. Funding for open access charge was provided by the US Department of Energy's BioEnergy Science Center (BESC). NR 65 TC 5 Z9 5 U1 3 U2 23 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1939-1234 EI 1939-1242 J9 BIOENERG RES JI BioEnergy Res. PD DEC PY 2014 VL 7 IS 4 BP 1481 EP 1492 DI 10.1007/s12155-014-9486-9 PG 12 WC Energy & Fuels; Environmental Sciences SC Energy & Fuels; Environmental Sciences & Ecology GA AU4MF UT WOS:000345584500038 ER PT J AU Yazdanpanah, F Sokhansanj, S Lim, CJ Lau, A Bi, X Melin, S AF Yazdanpanah, F. Sokhansanj, S. Lim, C. J. Lau, A. Bi, X. Melin, S. TI Stratification of off-gases in stored wood pellets SO BIOMASS & BIOENERGY LA English DT Article DE Wood pellet; Storage; Purging; Off-gassing; Gas stratification; Storage temperature ID VOLATILE ORGANIC-COMPOUNDS; CARBON-MONOXIDE; OXYGEN DEPLETION; EMISSIONS; STORAGE; TRANSPORTATION AB Wood pellets emit gases such as CO, CO2 and CH4 during storage especially under high temperature conditions. This study investigates the stratification of the evolved gases in a sealed storage container of 1.2 m diameter and 4.6 m height. The data recorded include the concentration of off-gasses (CO2, CO and CH4), temperature and relative humidity profiles in vertical and horizontal directions. The results obtained clearly show high concentration of gases as well as fast depletion of oxygen. The emitted gases showed to have higher emission factor compared to work done with white wood pellets in small scale. Some stratification was observed for CO2 and CH4 over the first days of storage. However for CO the stratification was much clear and related to high uptake of CO by wood pellets over time. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Yazdanpanah, F.; Sokhansanj, S.; Lim, C. J.; Lau, A.; Bi, X.; Melin, S.] Univ British Columbia, Chem & Biol Engn Dept, Vancouver, BC V6T 1Z3, Canada. [Sokhansanj, S.] Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA. [Melin, S.] Delta Res Corp, Delta, BC, Canada. RP Yazdanpanah, F (reprint author), Univ British Columbia, Chem & Biol Engn Dept, Vancouver, BC V6T 1Z3, Canada. EM fyazdanpanah@chbe.ubc.ca RI Lau, Anthony/J-8519-2015 FU Wood Pellet Association of Canada; Natural Sciences and Engineering Research Council of Canada (NSERC Collaborative Research and Development Project CRDPJ) [342219-06] FX Authors acknowledge the funding sources from Wood Pellet Association of Canada and Natural Sciences and Engineering Research Council of Canada (NSERC Collaborative Research and Development Project CRDPJ 342219-06). The authors are also thankful to Premium Pellet Ltd., British Columbia, Canada and OPI Systems Inc., Calgary, Alberta for providing the wood pellet samples and nine temperature cables respectively. NR 24 TC 8 Z9 8 U1 2 U2 17 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0961-9534 EI 1873-2909 J9 BIOMASS BIOENERG JI Biomass Bioenerg. PD DEC PY 2014 VL 71 BP 1 EP 11 DI 10.1016/j.biombioe.2014.04.019 PG 11 WC Agricultural Engineering; Biotechnology & Applied Microbiology; Energy & Fuels SC Agriculture; Biotechnology & Applied Microbiology; Energy & Fuels GA AU0ZA UT WOS:000345349500001 ER PT J AU Kim, S Dale, BE Heijungs, R Azapagic, A Darlington, T Kahlbaum, D AF Kim, Seungdo Dale, Bruce E. Heijungs, Reinout Azapagic, Adisa Darlington, Tom Kahlbaum, Dennis TI Indirect land use change and biofuels: Mathematical analysis reveals a fundamental flaw in the regulatory approach SO BIOMASS & BIOENERGY LA English DT Article DE Biofuel policy; Corn ethanol; Indirect land use change; Renewable fuel standard; Soybean Biodiesel; Sugarcane ethanol ID IMPROVING ANALYTICAL METHODOLOGIES; TESTING PREDICTIONS; EMISSIONS; DALE; KIM AB In the Renewable Fuel Standard (RFS2) program, the United States Environmental Protection Agency (U.S. EPA) has used partial equilibrium models to estimate the overall indirect land use change (iLUC) associated with the biofuel scenario mandated by the Energy Independence and Security Act of 2007 (EISA). For regulatory purposes, the U.S. EPA "shocks" (changes) the amount of each biofuel in the economic models one at a time to estimate the threshold values for specific biofuels (single-shock analysis). The primary assumption in the single-shock analysis is that iLUC is a linear process with respect to biofuels, i.e., that interactions between different biofuels are trivially small. However, the assumption of linearity in the single-shock analysis is not appropriate for estimating the threshold values for specific biofuels when the interactions between different biofuels are not small. Numerical results from the RFS2 program show that the effects of interactions between different biofuels are too large to be ignored. Thus, the threshold values for specific biofuels determined by the U.S. EPA are scenario-dependent and value choice-driven. They do not reflect real impacts of specific biofuels. Using scenario-dependent values for regulation is arbitrary and inappropriate. Failure to deal appropriately with interactions between different biofuels when assigning iLUC values to specific biofuels is a mathematical and systematic flaw; it is not an "uncertainty" issue. The U. S. EPA should find better ways to differentiate the contribution of one biofuel versus another when assigning iLUC values or find better means of regulating the land use change impact of biofuel production. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Kim, Seungdo; Dale, Bruce E.] Michigan State Univ, DOE Great Lakes Bioenergy Res Ctr, Lansing, MI 48910 USA. [Kim, Seungdo; Dale, Bruce E.] Michigan State Univ, Dept Chem Engn & Mat Sci, Lansing, MI 48910 USA. [Heijungs, Reinout] Vrije Univ Amsterdam, Dept Econometr & Operat Res, NL-1081 HV Amsterdam, Netherlands. [Heijungs, Reinout] Leiden Univ, Inst Environm Sci, Leiden, Netherlands. [Azapagic, Adisa] Univ Manchester, Sch Sustainable Chem Engn & Analyt Sci, Manchester M13 9PL, Lancs, England. [Darlington, Tom; Kahlbaum, Dennis] Air Improvement Resource Inc, Novi, MI 48374 USA. RP Dale, BE (reprint author), Michigan State Univ, Dept Chem Engn & Mat Sci, 3815 Technol Blvd, Lansing, MI 48910 USA. EM bdale@egr.msu.edu OI Azapagic, Adisa/0000-0003-2380-918X; Heijungs, Reinout/0000-0002-0724-5962 FU DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science) [DE-FC02-07ER64494]; DOE OBP Office of Energy Efficiency and Renewable Energy [DE-AC05-76RL01830] FX This work was funded by the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science DE-FC02-07ER64494) and DOE OBP Office of Energy Efficiency and Renewable Energy DE-AC05-76RL01830). NR 21 TC 2 Z9 2 U1 2 U2 24 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0961-9534 EI 1873-2909 J9 BIOMASS BIOENERG JI Biomass Bioenerg. PD DEC PY 2014 VL 71 BP 408 EP 412 DI 10.1016/j.biombioe.2014.09.015 PG 5 WC Agricultural Engineering; Biotechnology & Applied Microbiology; Energy & Fuels SC Agriculture; Biotechnology & Applied Microbiology; Energy & Fuels GA AU0ZA UT WOS:000345349500041 ER PT J AU Guo, ZY Kobayashi, T Wang, LL Goh, TW Xiao, CX Caporini, MA Rosay, M Johnson, DD Pruski, M Huang, WY AF Guo, Zhiyong Kobayashi, Takeshi Wang, Lin-Lin Goh, Tian Wei Xiao, Chaoxian Caporini, Marc A. Rosay, Melanie Johnson, Duane D. Pruski, Marek Huang, Wenyu TI Selective Host-Guest Interaction between Metal Ions and Metal-Organic Frameworks Using Dynamic Nuclear Polarization Enhanced Solid-State NMR Spectroscopy SO CHEMISTRY-A EUROPEAN JOURNAL LA English DT Article DE density functional calculations; dynamic nuclear polarization; metal-organic frameworks; solid-state NMR spectroscopy; X-ray absorption spectroscopy ID TOTAL-ENERGY CALCULATIONS; WAVE BASIS-SET; DRUG-DELIVERY; IFEFFIT; CAPTURE; ADSORPTION; CISPLATIN; CATALYSIS; ARTEMIS; ATHENA AB The host-guest interaction between metal ions (Pt2+ and Cu2+) and a zirconium metal-organic framework (UiO-66-NH2) was explored using dynamic nuclear polarization-enhanced N-15{H-1} CPMAS NMR spectroscopy supported by X-ray absorption spectroscopy and density functional calculations. The combined experimental results conclude that each Pt2+ coordinates with two NH2 groups from the MOF and two Cl- from the metal precursor, whereas Cu2+ do not form chemical bonds with the NH2 groups of the MOF framework. Density functional calculations reveal that Pt2+ prefers a square-planar structure with the four ligands and resides in the octahedral cage of the MOF in either cis or trans configurations. C1 [Guo, Zhiyong; Goh, Tian Wei; Xiao, Chaoxian; Pruski, Marek; Huang, Wenyu] Iowa State Univ, Dept Chem, Ames, IA 50011 USA. [Kobayashi, Takeshi; Wang, Lin-Lin; Johnson, Duane D.; Pruski, Marek; Huang, Wenyu] US DOE, Ames Lab, Ames, IA 50011 USA. [Caporini, Marc A.; Rosay, Melanie] Bruker BioSpin Corp, Billerica, MA 01821 USA. [Johnson, Duane D.] Iowa State Univ, Dept Mat Sci & Engn, Ames, IA 50011 USA. RP Pruski, M (reprint author), Iowa State Univ, Dept Chem, Ames, IA 50011 USA. EM mpruski@iastate.edu; whuang@iastate.edu RI Xiao, Chaoxian/E-7339-2013; Guo, Zhiyong/L-5541-2014; Goh, Tian Wei/G-3463-2016; Huang, Wenyu/L-3784-2014 OI Johnson, Duane/0000-0003-0794-7283; Xiao, Chaoxian/0000-0002-4012-0539; Goh, Tian Wei/0000-0002-4141-3392; Huang, Wenyu/0000-0003-2327-7259 FU U.S. Department of Energy, Office of Basic Energy Sciences (BES), Division of Chemical Sciences, Geosciences, and Biosciences through the Ames Laboratory; Ames Laboratory; Iowa State University; Laboratory Research and Development Program of The Ames Laboratory; U.S. Department of Energy by Iowa State University [DE-AC02-07CH11358]; U.S. DOE-BES [DE-AC02-06CH11357] FX This research was supported by the U.S. Department of Energy, Office of Basic Energy Sciences (BES), Division of Chemical Sciences, Geosciences, and Biosciences through the Ames Laboratory (T.K., L.-L. W., D.D.J., M.P.) and by the Ames Laboratory Royalty Account and Iowa State University startup funds (Z.G., T.W.G., C.X., W.H.). This work was also supported by the Laboratory Research and Development Program of The Ames Laboratory. The Ames Laboratory is operated for the U.S. Department of Energy by Iowa State University under Contract No. DE-AC02-07CH11358. Use of the Advanced Photon Source was supported by the U.S. DOE-BES under Contract No. DE-AC02-06CH11357. We thank Gordon J. Miller for use of his XRD and XPS, and Igor I. Slowing for use of his gas adsorption analyzer and ICP-OES. NR 55 TC 7 Z9 7 U1 10 U2 119 PU WILEY-V C H VERLAG GMBH PI WEINHEIM PA BOSCHSTRASSE 12, D-69469 WEINHEIM, GERMANY SN 0947-6539 EI 1521-3765 J9 CHEM-EUR J JI Chem.-Eur. J. PD DEC 1 PY 2014 VL 20 IS 49 BP 16308 EP 16313 DI 10.1002/chem.201403884 PG 6 WC Chemistry, Multidisciplinary SC Chemistry GA AU3LW UT WOS:000345515700037 PM 25297002 ER PT J AU Winkler, B Friedrich, A Morgenroth, W Haussuhl, E Milman, V Stanek, CR McClellan, KJ AF Winkler, Bjoern Friedrich, Alexandra Morgenroth, Wolfgang Haussuehl, Eiken Milman, Victor Stanek, Chris R. McClellan, Kenneth J. TI Compression behavior of Sm2Ti2O7-pyrochlore up to 50 GPa: single-crystal X-ray diffraction and density functional theory calculations SO CHINESE SCIENCE BULLETIN LA English DT Article DE Pyrochlore; High pressure; Single crystal; X-ray diffraction; Density functional theory ID HIGH-PRESSURES; PYROCHLORE; TITANATES; OXIDES AB Single-crystal X-ray diffraction at pressures up to 50 GPa has been employed to study the compression behavior of Sm2Ti2O7-pyrochlore. In contrast to earlier reports, we observed no pressure-induced amorphization or pressure-induced anion disorder up to 50 GPa. The experimental study has been complemented by density functional theory-based calculations. A combination of the theoretical and experimental data yields a bulk modulus of 185 GPa, significantly higher than a value which had been reported earlier. In comparison to earlier work, the current study provides more reliable data due to the use of neon as a pressure medium, which provides a more hydrostatic pressure than the aluminum, which had been employed as a pressure medium in the earlier studies. An analysis of the compressibility of AlBO pyrochlores shows an approximately linear dependence of the bulk modulus on the unit cell volume. C1 [Winkler, Bjoern; Friedrich, Alexandra; Morgenroth, Wolfgang; Haussuehl, Eiken] Goethe Univ Frankfurt, D-60438 Frankfurt, Germany. [Milman, Victor] Dassault Syst BIOVIA, Cambridge CB4 0WN, England. [Stanek, Chris R.; McClellan, Kenneth J.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Winkler, B (reprint author), Goethe Univ Frankfurt, Altenhoferallee 1, D-60438 Frankfurt, Germany. EM b.winkler@kristall.uni-frankfurt.de RI Milman, Victor/M-6117-2015; OI Milman, Victor/0000-0003-2258-1347; Morgenroth, Wolfgang/0000-0001-8921-0052 FU DFG, Germany [SPP1236 (FR-2491/2-1)]; BMBF, Germany [05KS7RF1, 05K10RFA]; DESY, Germany FX This work was supported by the DFG, Germany, within SPP1236 (FR-2491/2-1), the BMBF, Germany (05KS7RF1, 05K10RFA), and DESY, Germany. Portions of this research were carried out at the light source PETRA III at DESY, a member of the Helmholtz Association (HGF). We thank H.-P. Liermann (PETRA III) for support at the beamline. NR 28 TC 2 Z9 2 U1 2 U2 15 PU SCIENCE PRESS PI BEIJING PA 16 DONGHUANGCHENGGEN NORTH ST, BEIJING 100717, PEOPLES R CHINA SN 1001-6538 EI 1861-9541 J9 CHINESE SCI BULL JI Chin. Sci. Bull. PD DEC PY 2014 VL 59 IS 36 BP 5278 EP 5282 DI 10.1007/s11434-014-0635-5 PG 5 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA AU1LF UT WOS:000345381500018 ER PT J AU LaKind, JS Sobus, JR Goodman, M Barr, DB Furst, P Albertini, RJ Arbuckle, TE Schoeters, G Tan, YM Teeguarden, J Tornero-Velez, R Weisel, CP AF LaKind, Judy S. Sobus, Jon R. Goodman, Michael Barr, Dana Boyd Fuerst, Peter Albertini, Richard J. Arbuckle, Tye E. Schoeters, Greet Tan, Yu-Mei Teeguarden, Justin Tornero-Velez, Rogelio Weisel, Clifford P. TI A proposal for assessing study quality: Biomonitoring, Environmental Epidemiology, and Short-lived Chemicals (BEES-C) instrument SO ENVIRONMENT INTERNATIONAL LA English DT Article DE BEES-C; Biomonitoring; Ubiquitous chemicals; Short physiologic half-life; Evaluation instrument; Environmental epidemiology ID NUTRITION EXAMINATION SURVEY; 24-H URINE SAMPLES; BISPHENOL-A; NONDIFFERENTIAL MISCLASSIFICATION; TEMPORAL VARIABILITY; UNITED-STATES; MOLECULAR EPIDEMIOLOGY; PYRETHROID METABOLITES; HYPOTHESIS GENERATION; PHTHALATE METABOLITES AB The quality of exposure assessment is a major determinant of the overall quality of any environmental epidemiology study. The use of biomonitoring as a tool for assessing exposure to ubiquitous chemicals with short physiologic half-lives began relatively recently. These chemicals present several challenges, including their presence in analytical laboratories and sampling equipment, difficulty in establishing temporal order in cross-sectional studies, short- and long-term variability in exposures and biomarker concentrations, and a paucity of information on the number of measurements required for proper exposure classification. To date, the scientific community has not developed a set of systematic guidelines for designing, implementing and interpreting studies of short-lived chemicals that use biomonitoring as,the exposure metric or for evaluating the quality of this type of research for WOE assessments or for peer review of grants or publications. We describe key issues that affect epidemiology studies using biomonitoring data on short-lived chemicals and propose a systematic instrument - the Biomonitoring, Environmental Epidemiology, and Short-lived Chemicals (BEES-C) instrument - for evaluating the quality of research proposals and studies that incorporate biomonitoring data on short-lived chemicals. Quality criteria for three areas considered fundamental to the evaluation of epidemiology studies that include biological measurements of short-lived chemicals are described: 1) biomarker selection and measurement, 2) study design and execution, and 3) general epidemiological study design considerations. We recognize that the development of an evaluative tool such as BEES-C is neither simple nor non-controversial. We hope and anticipate that the instrument will initiate further discussion/debate on this topic. (C) 2014 The Authors. Published by Elsevier Ltd. C1 [LaKind, Judy S.] LaKind Associates LLC, Catonsville, MD 21228 USA. [LaKind, Judy S.] Univ Maryland, Dept Epidemiol & Publ Hlth, Sch Med, College Pk, MD USA. [LaKind, Judy S.] Penn State Univ, Dept Pediat, Coll Med, Milton S Hershey Med Ctr, University Pk, PA 16802 USA. [Sobus, Jon R.; Tan, Yu-Mei; Tornero-Velez, Rogelio] US EPA, Natl Exposure Res Lab, Human Exposure & Atmospher Sci Div, Res Triangle Pk, NC 27711 USA. [Goodman, Michael] Emory Univ, Rollins Sch Publ Hlth, Dept Epidemiol, Atlanta, GA 30322 USA. [Barr, Dana Boyd] Emory Univ, Rollins Sch Publ Hlth, Dept Environm & Occupat Hlth, Atlanta, GA 30322 USA. [Fuerst, Peter] Munsterland Emscher Lippe CVUA MEL, Chem & Vet Analyt Inst, D-48151 Munster, Germany. [Albertini, Richard J.] Univ Vermont, Coll Med, Underhill Ctr, VT 05490 USA. [Arbuckle, Tye E.] Hlth Canada, Populat Studies Div, Hlth Environm & Consumer Safety Branch, Ottawa, ON K1A 0K9, Canada. [Schoeters, Greet] VITO, Environm Risk & Hlth Unit, B-2400 Mol, Belgium. [Schoeters, Greet] Univ Antwerp, Dept Biomed Sci, Antwerp, Belgium. [Teeguarden, Justin] Pacific NW Natl Lab, Richland, WA 99352 USA. [Weisel, Clifford P.] UMDNJ, Environm & Occupat Hlth Sci Inst, Robert Wood Johnson Med Sch, Piscataway, NJ 08854 USA. RP LaKind, JS (reprint author), LaKind Associates LLC, 106 Oakdale Ave, Catonsville, MD 21228 USA. EM lakindassoc@gmail.com; Sobus.Jon@epa.gov; mgoodm2@emory.edu; dbbarr@emory.edu; Peter.Fuerst@cvua-mel.de; Ralbert315@aol.com; Tye.Arbuckle@hc-sc.gc.ca; greet.schoeters@vito.be; Tan.Cecilia@epa.gov; jt@pnnl.gov; Tornero-Velez.Rogelio@epa.gov; weisel@eohsi.rutgers.edu OI Teeguarden, Justin/0000-0003-3817-4391 FU Polycarbonate/BPA Global Group of the American Chemistry Council (ACC) FX The Workshop was sponsored by Polycarbonate/BPA Global Group of the American Chemistry Council (ACC). ACC was not involved in the design, management, or development of the Workshop or in the preparation or approval of the manuscript Workshop participants or their affiliated organizations received an honorarium (except JSL, ES, GS, JS, JT, Y-MT, RT-V, TA) and travel support (except TA, Y-MT, DB, ES). JSL received support for Workshop development and facilitation; JSL consults to governmental and private sectors. MG regularly serves as a consultant for the government and for the private sector. No other competing interests are declared. NR 122 TC 11 Z9 11 U1 1 U2 17 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0160-4120 EI 1873-6750 J9 ENVIRON INT JI Environ. Int. PD DEC PY 2014 VL 73 BP 195 EP 207 DI 10.1016/j.envint.2014.07.011 PG 13 WC Environmental Sciences SC Environmental Sciences & Ecology GA AU3WE UT WOS:000345540700023 PM 25137624 ER PT J AU Wang, YG Ying, Q Hu, JL Zhang, HL AF Wang, Yungang Ying, Qi Hu, Jianlin Zhang, Hongliang TI Spatial and temporal variations of six criteria air pollutants in 31 provincial capital cities in China during 2013-2014 SO ENVIRONMENT INTERNATIONAL LA English DT Article DE Spatial variation; Temporal variation; Criteria pollutants; PM2.5; Provincial capital cities; China ID RESOLUTION EMISSION INVENTORY; PARTICULATE MATTER; SEASONAL-VARIATIONS; PM2.5 NITRATE; RIVER DELTA; HONG-KONG; POLLUTION; PM10; TRANSPORT; SENSITIVITY AB Long-term air pollution data with high temporal and spatial resolutions are needed to support the research of physical and chemical processes that affect the air quality, and the corresponding health risks. However, such datasets were not available in China until recently. For the first time, this study examines the spatial and temporal variations of PM2.5, PM10, CO, SO2, NO2, and 8 h 03 in 31 capital cities in China between March 2013 and February 2014 using hourly data released by the Ministry of Environmental Protection (MEP) of China. The annual mean concentrations of PM2.5 and PM10 exceeded the Chinese Ambient Air Quality Standards (CAAQS), Grade I standards (15 and 40 mu g/m(3) for PM2.5 and PM10, respectively) for all cities, and only Haikou, Fuzhou and Lasa met the CAAQS Grade II standards (35 and 70 mu g/m(3) for PM2.5 and PM10, respectively). Observed PM2.5, PM10, CO and SO2 concentrations were higher in cities located in the North region than those in the West and the South-East regions. The number of non-attainment days was highest in the winter, but high pollution days were also frequently observed in the South-East region during the fall and in the West region during the spring. PM2.5 was the largest contributor to the air pollution in China based on the number of non-attainment days, followed by PM10, and O-3. Strong correlation was found between different pollutants except for O-3. These results suggest great impacts of coal combustion and biomass burning in the winter, long range transport of windblown dust in the spring, and secondary aerosol formation throughout the year. Current air pollution in China is caused by multiple pollutants, with great variations among different regions and different seasons. Future studies should focus on improving the understanding of the associations between air quality and meteorological conditions, variations of emissions in different regions, and transport and transformation of pollutants in both intra-and inter-regional contexts. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Wang, Yungang] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Environm Energy Technol Div, Berkeley, CA 94720 USA. [Ying, Qi] Texas A&M Univ, Dept Civil Engn, College Stn, TX 77843 USA. [Hu, Jianlin] Univ Calif Davis, Dept Civil & Environm Engn, Davis, CA 95616 USA. [Zhang, Hongliang] Louisiana State Univ, Dept Civil & Environm Engn, Baton Rouge, LA 70803 USA. RP Hu, JL (reprint author), Univ Calif Davis, Dept Civil & Environm Engn, Davis, CA 95616 USA. EM jjlhu@ucdavis.edu; hlzhang@lsu.edu RI Zhang, Hongliang/C-2499-2012; Hu, Jianlin/C-2023-2014; OI Hu, Jianlin/0000-0001-7709-439X; Zhang, Hongliang/0000-0002-1797-2311 NR 35 TC 44 Z9 47 U1 24 U2 127 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0160-4120 EI 1873-6750 J9 ENVIRON INT JI Environ. Int. PD DEC PY 2014 VL 73 BP 413 EP 422 DI 10.1016/j.envint.2014.08.016 PG 10 WC Environmental Sciences SC Environmental Sciences & Ecology GA AU3WE UT WOS:000345540700046 PM 25244704 ER PT J AU French, SW Romanowicz, BA AF French, S. W. Romanowicz, B. A. TI Whole-mantle radially anisotropic shear velocity structure from spectral-element waveform tomography SO GEOPHYSICAL JOURNAL INTERNATIONAL LA English DT Article DE Inverse theory; Body waves; Surface waves and free oscillations; Seismic anisotropy; Seismic tomography; Computational seismology ID SEISMIC TOMOGRAPHY; ADJOINT METHODS; CRUSTAL CORRECTIONS; CLUSTER-ANALYSIS; EARTH STRUCTURE; INVERSION; MODELS; PROPAGATION; CONVECTION; HETEROGENEITY AB The radially anisotropic shear velocity structure of the Earth's mantle provides a critical window on the interior dynamics of the planet, with isotropic variations that are interpreted in terms of thermal and compositional heterogeneity and anisotropy in terms of flow. While significant progress has been made in the more than 30 yr since the advent of global seismic tomography, many open questions remain regarding the dual roles of temperature and composition in shaping mantle convection, as well as interactions between different dominant scales of convective phenomena. We believe that advanced seismic imaging techniques, such as waveform inversion using accurate numerical simulations of the seismic wavefield, represent a clear path forwards towards addressing these open questions through application to whole-mantle imaging. To this end, we employ a 'hybrid' waveform-inversion approach, which combines the accuracy and generality of the spectral finite element method (SEM) for forward modelling of the global wavefield, with non-linear asymptotic coupling theory for efficient inverse modelling. The resulting whole-mantle model (SEMUCB-WM1) builds on the earlier successful application of these techniques for global modelling at upper mantle and transition-zone depths (<= 800 km) which delivered the models SEMum and SEMum2. Indeed, SEMUCB-WM1 is the first whole-mantle model derived from fully numerical SEM-based forward modelling. Here, we detail the technical aspects of the development of our whole-mantle model, as well as provide a broad discussion of isotropic and radially anisotropic model structure. We also include an extensive discussion of model uncertainties, specifically focused on assessing our results at transition-zone and lower-mantle depths. C1 [French, S. W.; Romanowicz, B. A.] Univ Calif Berkeley, Berkeley Seismol Lab, Berkeley, CA 94720 USA. [Romanowicz, B. A.] Inst Phys Globe Paris, F-752382 Paris 05, France. [Romanowicz, B. A.] Coll France, F-75005 Paris, France. RP French, SW (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Natl Energy Res Sci Comp Ctr NERSC, Berkeley, CA 94720 USA. EM sfrench@seismo.berkeley.edu OI romanowicz, Barbara/0000-0002-6208-6044 FU National Science Foundation [EAR-0738284]; NSF; US Department of Energy Office of Science [DE-AC02-05CH11231] FX The authors would like to thank Andreas Fichtner and one anonymous reviewer for their constructive comments on the manuscript, from which the latter benefitted greatly. The authors would also like to thank Vedran Lekic for valuable discussions and Huaiyu Yuan for assistance in collecting the supplementary waveform data set. In addition, the authors would like to thank Masayuki Obayashi for kindly providing access to the GAP-P4 model in electronic form. The authors acknowledge support from the National Science Foundation (grant EAR-0738284) and SWF acknowledges additional support from the NSF Graduate Research Fellowship Programme. All waveform data used in this study are available from the Incorporated Research Institutions for Seismology (http://www.iris.edu). Computations were performed at the National Energy Research Scientific Computing Center, supported by the US Department of Energy Office of Science (Contract No. DE-AC02-05CH11231). NR 85 TC 34 Z9 34 U1 5 U2 44 PU OXFORD UNIV PRESS PI OXFORD PA GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND SN 0956-540X EI 1365-246X J9 GEOPHYS J INT JI Geophys. J. Int. PD DEC PY 2014 VL 199 IS 3 BP 1303 EP 1327 DI 10.1093/gji/ggu334 PG 25 WC Geochemistry & Geophysics SC Geochemistry & Geophysics GA AU3JT UT WOS:000345509800001 ER PT J AU Guedj, J Rotman, Y Cotler, SJ Koh, C Schmid, P Albrecht, J Haynes-Williams, V Liang, TJ Hoofnagle, JH Heller, T Dahari, H AF Guedj, Jeremie Rotman, Yaron Cotler, Scott J. Koh, Christopher Schmid, Peter Albrecht, Jeff Haynes-Williams, Vanessa Liang, T. Jake Hoofnagle, Jay H. Heller, Theo Dahari, Harel TI Understanding Early Serum Hepatitis D Virus and Hepatitis B Surface Antigen Kinetics During Pegylated Interferon-alpha Therapy Via Mathematical Modeling SO HEPATOLOGY LA English DT Article ID N-LINKED GLYCANS; C-VIRUS; ENVELOPE GLYCOPROTEIN; NEUTRALIZING ANTIBODIES; GLUCOSIDASE INHIBITORS; ANTIVIRAL ACTIVITY; HCV INFECTION; RNA KINETICS; EFFICACY; CELLS AB There is little information on the early kinetics of hepatitis delta virus (HDV) and hepatitis B surface antigen (HBsAg) during interferon-a therapy. Here a mathematical model was developed and fitted to frequent HDV and HBsAg kinetic data from 10 patients during the first 28 weeks of pegylated-interferon-alpha 2a (peg-IFN) therapy. Three patients achieved a complete virological response (CVR), defined as undetectable HDV 6 months after treatment stopped with loss of HBsAg and anti-HBsAg seroconversion. After initiation of therapy, a median delay of 9 days (interquartile range [IQR]: 5-15) was observed with no significant changes in HDV level. Thereafter, HDV declined in a biphasic manner, where a rapid first phase lasting for 25 days (IQR: 23-58) was followed by a slower or plateau second phase. The model predicts that the main effect of peg-IFN is to reduce HDV production/release with a median effectiveness of 96% (IQR: 93-99.8). Median serum HDV half-life (t1/2) was estimated as 2.9 days (IQR: 1.5-5.3) corresponding to a pretreatment production and clearance of about 10(10) (IQR: 10(9.7)-10(10.7)) virions/day. None of the patients with flat second phase in HDV achieved CVR. HBsAg kinetics of decline paralleled the second phase of HDV decline consistent with HBsAg-productive-infected cells being the main source of production of HDV, with a median t(1/2) of 135 days (IQR: 20-460). The interferon lambda-3 polymorphism (rs12979860) was not associated with kinetic parameters. Conclusion: Modeling results provide insights into HDV-host dynamics, the relationship between serum HBsAg levels and HBsAg-infected cells, IFN's mode of action, and its effectiveness. The observation that a flat second phase in HDV and HBsAg kinetics was associated with failure to achieve CVR provides the basis to develop early stopping rules during peg-IFN treatment in HDV-infected patients. C1 [Guedj, Jeremie; Dahari, Harel] Los Alamos Natl Lab, Los Alamos, NM USA. [Guedj, Jeremie] Univ Paris 07, INSERM, UMR 1137, IAME, F-75018 Paris, France. [Guedj, Jeremie] Univ Paris 07, Sorbonne Paris Cite, UMR 1137, IAME, F-75018 Paris, France. [Rotman, Yaron; Koh, Christopher; Haynes-Williams, Vanessa; Liang, T. Jake; Hoofnagle, Jay H.; Heller, Theo] NIDDK, Liver Dis Branch, NIH, Bethesda, MD 20892 USA. [Cotler, Scott J.; Dahari, Harel] Loyola Univ, Med Ctr, Dept Med, Program Expt & Theoret Modeling,Div Hepatol, Maywood, IL 60153 USA. [Schmid, Peter; Albrecht, Jeff] Natl Inst Genet, Los Angeles, CA USA. RP Dahari, H (reprint author), Loyola Univ, Med Ctr, Dept Med, Program Expt & Theoret Modeling,Div Hepatol, Maywood, IL 60153 USA. EM theoh@intra.niddk.nih.gov; hdahari@lumc.edu RI Guedj, Jeremie/A-6842-2017 OI Guedj, Jeremie/0000-0002-5534-5482 FU NIGMS NIH HHS [P20-GM103452, P30 GM110907, P20 GM103452] NR 33 TC 12 Z9 12 U1 0 U2 4 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 0270-9139 EI 1527-3350 J9 HEPATOLOGY JI Hepatology PD DEC PY 2014 VL 60 IS 6 BP 1902 EP 1910 DI 10.1002/hep.27357 PG 9 WC Gastroenterology & Hepatology SC Gastroenterology & Hepatology GA AU3MI UT WOS:000345517000055 PM 25098971 ER PT J AU Chen, C Wang, JH Zhu, H AF Chen, Chen Wang, Jianhui Zhu, Hao TI Effects of Phasor Measurement Uncertainty on Power Line Outage Detection SO IEEE JOURNAL OF SELECTED TOPICS IN SIGNAL PROCESSING LA English DT Article DE Bayesian criterion; error probability; multi-hypothesis test; PMU; power line outage detection; uncertainty AB Phasor measurement unit (PMU) technology provides an effective tool to enhance the wide-area monitoring systems (WAMSs) in power grids. Although extensive studies have been conducted to develop several PMU applications in power systems (e.g., state estimation, oscillation detection and control, voltage stability analysis, and line outage detection), the uncertainty aspects of PMUs have not been adequately investigated. This paper focuses on quantifying the impact of PMU uncertainty on power line outage detection and identification, in which a limited number of PMUs installed at a subset of buses are utilized to detect and identify the line outage events. Specifically, the line outage detection problem is formulated as a multi-hypothesis test, and a general Bayesian criterion is used for the detection procedure, in which the PMU uncertainty is analytically characterized. We further apply the minimum detection error criterion for the multi-hypothesis test and derive the expected detection error probability in terms of PMU uncertainty. The framework proposed provides fundamental guidance for quantifying the effects of PMU uncertainty on power line outage detection. Case studies are provided to validate our analysis and show how PMU uncertainty influences power line outage detection. C1 [Chen, Chen; Wang, Jianhui] Argonne Natl Lab, Decis & Informat Sci Div, Argonne, IL 60049 USA. [Zhu, Hao] Univ Illinois, Dept Elect & Comp Engn, Urbana, IL 61801 USA. RP Chen, C (reprint author), Argonne Natl Lab, Decis & Informat Sci Div, Argonne, IL 60049 USA. EM morningchen@anl.gov; jianhui.wang@anl.gov; haozhu@illinois.edu FU 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 non-exclusive, 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 25 TC 5 Z9 5 U1 0 U2 4 PU IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC PI PISCATAWAY PA 445 HOES LANE, PISCATAWAY, NJ 08855-4141 USA SN 1932-4553 EI 1941-0484 J9 IEEE J-STSP JI IEEE J. Sel. Top. Signal Process. PD DEC PY 2014 VL 8 IS 6 BP 1127 EP 1139 DI 10.1109/JSTSP.2014.2333493 PG 13 WC Engineering, Electrical & Electronic SC Engineering GA AU3MQ UT WOS:000345517900010 ER PT J AU Davoudi, A Guerrero, JM Lewis, F Balog, R Johnson, B Weaver, W Wang, LW Edrington, C Blasco-Gimenez, R Dominguez-Garcia, A Chow, MY AF Davoudi, Ali Guerrero, Josep M. Lewis, Frank Balog, Robert Johnson, Brian Weaver, Wayne Wang, Liwei Edrington, Chris Blasco-Gimenez, Ramon Dominguez-Garcia, Alejandro Chow, Mo-Yuen TI Advanced Distributed Control of Energy Conversion Devices and Systems SO IEEE TRANSACTIONS ON ENERGY CONVERSION LA English DT Editorial Material C1 [Davoudi, Ali; Lewis, Frank] Univ Texas Arlington, Arlington, TX 76019 USA. [Guerrero, Josep M.] Aalborg Univ, DK-9100 Aalborg, Denmark. [Balog, Robert] Texas A&M Univ, College Stn, TX 77843 USA. [Johnson, Brian] Natl Renewable Energy Lab, Golden, CO 80401 USA. [Weaver, Wayne] Michigan Technol Univ, Houghton, MI 49931 USA. [Wang, Liwei] Univ British Columbia, Vancouver, BC V6T 1Z4, Canada. [Edrington, Chris] Florida State Univ, Tallahassee, FL 32306 USA. [Blasco-Gimenez, Ramon] Univ Politecn Valencia, Valencia 46021, Spain. [Dominguez-Garcia, Alejandro] Univ Illinois, Champaign, IL 61820 USA. [Chow, Mo-Yuen] N Carolina State Univ, Raleigh, NC 27695 USA. RP Davoudi, A (reprint author), Univ Texas Arlington, Arlington, TX 76019 USA. EM davoudi@uta.edu RI Guerrero, Josep/D-5519-2014 OI Guerrero, Josep/0000-0001-5236-4592 NR 0 TC 1 Z9 1 U1 0 U2 8 PU IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC PI PISCATAWAY PA 445 HOES LANE, PISCATAWAY, NJ 08855-4141 USA SN 0885-8969 EI 1558-0059 J9 IEEE T ENERGY CONVER JI IEEE Trans. Energy Convers. PD DEC PY 2014 VL 29 IS 4 BP 819 EP 822 DI 10.1109/TEC.2014.2364751 PG 4 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA AU4KC UT WOS:000345578600003 ER PT J AU Dall'Anese, E Dhople, SV Johnson, BB Giannakis, GB AF Dall'Anese, Emiliano Dhople, Sairaj V. Johnson, Brian B. Giannakis, Georgios B. TI Decentralized Optimal Dispatch of Photovoltaic Inverters in Residential Distribution Systems SO IEEE TRANSACTIONS ON ENERGY CONVERSION LA English DT Article DE Alternating direction method of multipliers (ADMM); decentralized optimization; distribution systems; optimal power flow (OPF); photovoltaic systems; sparsity; voltage regulation ID OPTIMAL POWER-FLOW; SPARSITY AB Decentralized methods for computing optimal real and reactive power setpoints for residential photovoltaic (PV) inverters are developed in this paper. It is known that conventional PV inverter controllers, which are designed to extract maximum power at unity power factor, cannot address secondary performance objectives such as voltage regulation and network loss minimization. Optimal power flow techniques can be utilized to select which inverters will provide ancillary services and to compute their optimal real and reactive power setpoints according to well-defined performance criteria and economic objectives. Lever-aging advances in sparsity-promoting regularization techniques and semidefinite relaxation, this paper shows how such problems can be solved with reduced computational burden and optimality guarantees. To enable large-scale implementation, a novel algorithmic framework is introduced-based on the so-called alternating direction method of multipliers-by which optimal power flow-type problems in this setting can be systematically decomposed into subproblems that can be solved in a decentralized fashion by the utility and customer-owned PV systems with limited exchanges of information. Since the computational burden is shared among multiple devices and the requirement of all-to-all communication can be circumvented, the proposed optimization approach scales favorably to large distribution networks. C1 [Dall'Anese, Emiliano; Dhople, Sairaj V.; Giannakis, Georgios B.] Univ Minnesota, Dept Elect & Comp Engn, Minneapolis, MN 55455 USA. [Dall'Anese, Emiliano; Dhople, Sairaj V.; Giannakis, Georgios B.] Univ Minnesota, Digital Technol Ctr, Minneapolis, MN 55455 USA. [Johnson, Brian B.] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Dall'Anese, E (reprint author), Univ Minnesota, Dept Elect & Comp Engn, Minneapolis, MN 55455 USA. EM emiliano@umn.edu; sdhople@umn.edu; brian.johnson@nrel.gov; georgios@umn.edu FU National Science Foundation-Computing and Communication Foundations (NSF-CCF) [1423316, CyberSEES 1442686]; Institute of Renewable Energy and the Environment, University of Minnesota [RL-0010-13]; Laboratory Directed Research and Development Program at the National Renewable Energy Laboratory FX This work was supported by National Science Foundation-Computing and Communication Foundations (NSF-CCF) under Grant 1423316 and Grant CyberSEES 1442686; by the Institute of Renewable Energy and the Environment, University of Minnesota, under Grant RL-0010-13; and by the Laboratory Directed Research and Development Program at the National Renewable Energy Laboratory. Paper no. TEC-00174-2014. NR 34 TC 17 Z9 17 U1 1 U2 4 PU IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC PI PISCATAWAY PA 445 HOES LANE, PISCATAWAY, NJ 08855-4141 USA SN 0885-8969 EI 1558-0059 J9 IEEE T ENERGY CONVER JI IEEE Trans. Energy Convers. PD DEC PY 2014 VL 29 IS 4 BP 957 EP 967 DI 10.1109/TEC.2014.2357997 PG 11 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA AU4KC UT WOS:000345578600017 ER PT J AU Sulc, P Backhaus, S Chertkov, M AF Sulc, Petr Backhaus, Scott Chertkov, Michael TI Optimal Distributed Control of Reactive Power Via the Alternating Direction Method of Multipliers SO IEEE TRANSACTIONS ON ENERGY CONVERSION LA English DT Article DE Alternating direction method of multiplier (ADMM); distributed algorithms; distributed control; dual-ascent method; photovoltaic (PV) power generation; power flow; reactive power control ID DISTRIBUTION-SYSTEMS AB We formulate the control of reactive power generation by photovoltaic inverters in a power distribution circuit as a constrained optimization that aims to minimize power losses subject to finite inverter capacity and upper and lower voltage limits at all nodes in the circuit. When voltage variations along the circuit are small and losses of both real and reactive powers are small compared with the respective flows, the resulting optimization problem is convex. Moreover, the cost function is separable enabling a distributed online implementation with node-local computations using only local measurements augmented with limited information from the neighboring nodes communicated over cyber channels. Such an approach lies between the fully centralized and local policy approaches previously considered. We explore protocols based on the dual-ascent method and on the alternating direction method of multipliers (ADMMs), and find that the ADMM protocol performs significantly better. C1 [Sulc, Petr] Univ Oxford, Rudolf Peierls Ctr Theoret Phys, Oxford OX1 3NP, England. [Backhaus, Scott] Los Alamos Natl Lab, Mat Phys & Applicat Div, Los Alamos, NM 87545 USA. [Backhaus, Scott; Chertkov, Michael] New Mexico Consortium, Los Alamos, NM 87544 USA. [Chertkov, Michael] Los Alamos Natl Lab, Ctr Nonlinear Studies, Los Alamos, NM 87545 USA. [Chertkov, Michael] Los Alamos Natl Lab, Theoret Div, Los Alamos, NM 87545 USA. RP Sulc, P (reprint author), Rockefeller Univ, Ctr Studies Phys & Biol, New York, NY 10065 USA. EM petr.sulc@rockefeller.edu; backhaus@lanl.gov; chertkov@lanl.gov RI Chertkov, Michael/O-8828-2015; OI Backhaus, Scott/0000-0002-0344-6791; Chertkov, Michael/0000-0002-6758-515X FU Advanced Grid Modeling Program in the Office of Electricity at the U.S. Department of Energy; National Nuclear Security Administration of the U.S. Department of Energy at Los Alamos National Laboratory [DE-AC52-06NA25396]; National Science Foundation [1128501] FX The work at Los Alamos National Laboratory, Los Alamos, NM, USA, was supported by the Advanced Grid Modeling Program in the Office of Electricity at the U.S. Department of Energy and was carried out under the auspices of the National Nuclear Security Administration of the U.S. Department of Energy at Los Alamos National Laboratory under Contract DE-AC52-06NA25396. The work at New Mexico Consortium was supported by the National Science Foundation Award 1128501, Electrical Engineering and Computer Science Collaborative Research "Power Grid Spectroscopy." Paper no. TEC-00114-2014. NR 27 TC 27 Z9 27 U1 1 U2 8 PU IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC PI PISCATAWAY PA 445 HOES LANE, PISCATAWAY, NJ 08855-4141 USA SN 0885-8969 EI 1558-0059 J9 IEEE T ENERGY CONVER JI IEEE Trans. Energy Convers. PD DEC PY 2014 VL 29 IS 4 BP 968 EP 977 DI 10.1109/TEC.2014.2363196 PG 10 WC Energy & Fuels; Engineering, Electrical & Electronic SC Energy & Fuels; Engineering GA AU4KC UT WOS:000345578600018 ER PT J AU Massoudi, M Sanchez, G Soltau, S Vaidya, A Varner, J AF Massoudi, M. Sanchez, G. Soltau, S. Vaidya, A. Varner, J. TI Some experimental observations on the pressure driven flow of biomass suspensions SO INTERNATIONAL JOURNAL OF ENGINEERING SCIENCE LA English DT Article DE Pipeline transport; Suspension flow; Pressure drop; Biomass AB This paper is devoted to the experimental investigation of the pipeline flow of low volume fraction suspensions. Our experimental observations of low volume fraction biomass suspensions such as mulch, coffee powder, crushed leaves, in water, show an unusual, non-linear relationship between flow rate and pressure drop which is not observed in homogeneous systems. While it is well known that in Newtonian liquids, the flow rate increases monotonically with the pressure drop, our experiments indicate that increasing pressure drop across the pipe can cause the flow rate to drop at an exponential rate. The observations are seen to be consistent for the varying concentrations and for different kinds of solute particles. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Massoudi, M.] US DOE, Natl Energy Technol Lab, Pittsburgh, PA 15236 USA. [Sanchez, G.; Soltau, S.; Vaidya, A.; Varner, J.] Montclair State Univ, Dept Math Sci, Complex Fluids Lab, Montclair, NJ 07043 USA. RP Vaidya, A (reprint author), Montclair State Univ, Dept Math Sci, Complex Fluids Lab, Montclair, NJ 07043 USA. EM vaidyaa@mail.montclair.edu NR 17 TC 0 Z9 0 U1 1 U2 4 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0020-7225 EI 1879-2197 J9 INT J ENG SCI JI Int. J. Eng. Sci. PD DEC PY 2014 VL 85 BP 58 EP 65 DI 10.1016/j.ijengsci.2014.08.001 PG 8 WC Engineering, Multidisciplinary SC Engineering GA AU2XC UT WOS:000345476900006 ER PT J AU Roberts, SA Schunk, PR AF Roberts, Scott A. Schunk, P. Randall TI A reduced-order model for porous flow through thin, structured materials SO INTERNATIONAL JOURNAL OF MULTIPHASE FLOW LA English DT Article DE Porous media; Lubrication; Reduced-order model; Shell element; Finite element method; Nano-manufacturing ID FLASH IMPRINT LITHOGRAPHY; STEP; FORMULATION; SIMULATION; IMBIBITION; CYLINDERS; DYNAMICS; ARRAYS; MEDIA AB Darcy's equations are frequently used as a coarse-grained numerical expedient for modeling multiphase flow through complex porous materials. In some applications, the porous material may be quite thin, allowing the possibility of further simplification of the equations. In this paper we derive a reduced-order shell finite-element model for flow through thin porous materials using an approach similar to that taken to derive the Reynolds' lubrication equation. We advance first a formulation that addresses generalized unstructured porous materials and then specialize the equations for certain structured cases. We also extend the model to account for multiphase, confined lubrication flow in an adjoining layer and gas transport within the pores. We apply the model to several problems of topical interest in micro- and nano-manufacturing processes. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Roberts, Scott A.; Schunk, P. Randall] Sandia Natl Labs, Engn Sci Ctr, Albuquerque, NM 87185 USA. RP Roberts, SA (reprint author), Sandia Natl Labs, Engn Sci Ctr, POB 5800, Albuquerque, NM 87185 USA. EM sarober@sandia.gov; prschun@sandia.gov RI Roberts, Scott/C-1158-2009 OI Roberts, Scott/0000-0002-4196-6771 FU U.S. Department of Energy's National Nuclear Security Administration [DE-AC04-94AL85000] FX 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-AC04-94AL85000. NR 35 TC 0 Z9 0 U1 2 U2 8 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0301-9322 EI 1879-3533 J9 INT J MULTIPHAS FLOW JI Int. J. Multiph. Flow PD DEC PY 2014 VL 67 BP 25 EP 36 DI 10.1016/j.ijmultiphaseflow.2014.07.013 PG 12 WC Mechanics SC Mechanics GA AU2WP UT WOS:000345475700003 ER PT J AU Jeanne, P Rutqvist, J Dobson, PF Walters, M Hartline, C Garcia, J AF Jeanne, Pierre Rutqvist, Jonny Dobson, Patrick F. Walters, Mark Hartline, Craig Garcia, Julio TI The impacts of mechanical stress transfers caused by hydromechanical and thermal processes on fault stability during hydraulic stimulation in a deep geothermal reservoir SO INTERNATIONAL JOURNAL OF ROCK MECHANICS AND MINING SCIENCES LA English DT Article DE Induced seismicity; Shear reactivation; Thermohydromechanical simulation; Mechanical stress transfer; Enhanced geothermal systems; The Geysers ID FLUID-FLOW; CALIFORNIA; GEYSERS; SEISMICITY; ROCK; INJECTION; PRESSURE; SYSTEM; FIELD; SLIP AB We performed a series of 3D thermo-hydro-mechanical (THM) simulations to study the influences of hydromechanical and thermal processes on the development of an enhanced geothermal system, strongly influenced by a network of short fault zones. The model we developed was calibrated by comparing the simulated THM responses to field observations, including ground-surface deformations, well pressure, and microseismic activity. Of particular importance was the comparison between the observed temporal and spatial distribution of microseismic activity, and the calculated shear reactivation of preexisting fractures inferred from simulated elasto-plastic mechanical responses in the short fault zones. Using this approach, we could identify when fault zones were reactivated (as manifested in the field by a surge of local microseismic activity within the fault zone), and we could back-calculate the in situ stress field as being close to the stress conditions required for shear reactivation. Our results show that the main mechanisms of inducing seismicity are related to injection-induced pressure increase and cooling. During injection, the reservoir expansion caused by the pressure increase led to mechanical stress transfer through the reservoir, which prevented or delayed the reactivation of preexisting fractures. After injection stopped, there was an inversion of the mechanical stress transfers that favored shear reactivation, which may explain why microseismic activity occurred after the cessation of the injection. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Jeanne, Pierre; Rutqvist, Jonny; Dobson, Patrick F.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. [Walters, Mark; Hartline, Craig; Garcia, Julio] Calpine Corp, Middletown, CA 95461 USA. RP Jeanne, P (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. EM pjeanne@lbl.gov RI Dobson, Patrick/D-8771-2015; Rutqvist, Jonny/F-4957-2015; Jeanne, Pierre/I-2996-2015; OI Dobson, Patrick/0000-0001-5031-8592; Rutqvist, Jonny/0000-0002-7949-9785; Jeanne, Pierre/0000-0003-1487-8378; Walters, Mark/0000-0001-8458-4813 FU Assistant Secretary for Energy Efficiency and Renewable Energy, Geothermal Technologies Program, of the U.S. Department under the U.S. Department of Energy [DE-AC02-05CH11231] FX This work was conducted with funding provided by the Assistant Secretary for Energy Efficiency and Renewable Energy, Geothermal Technologies Program, of the U.S. Department under the U.S. Department of Energy Contract no. DE-AC02-05CH11231. The authors are grateful for the constructive comments made by the two anonymous reviewers, who helped to improve this paper. NR 37 TC 8 Z9 8 U1 2 U2 36 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 1365-1609 EI 1873-4545 J9 INT J ROCK MECH MIN JI Int. J. Rock Mech. Min. Sci. PD DEC PY 2014 VL 72 BP 149 EP 163 DI 10.1016/j.ijrmms.2014.09.005 PG 15 WC Engineering, Geological; Mining & Mineral Processing SC Engineering; Mining & Mineral Processing GA AU4LZ UT WOS:000345583900017 ER PT J AU Zubelewicz, A Rougier, E Ostoja-Starzewski, M Knight, EE Bradley, C Viswanathan, HS AF Zubelewicz, A. Rougier, E. Ostoja-Starzewski, M. Knight, E. E. Bradley, C. Viswanathan, H. S. TI A mechanisms-based model for dynamic behavior and fracture of geomaterials SO INTERNATIONAL JOURNAL OF ROCK MECHANICS AND MINING SCIENCES LA English DT Article DE Dynamic fracture; Rate-dependent frictional plasticity; Anisotropy ID MICROPLANE MODEL; ROCK; STRESS AB A mechanisms based fracture model applicable to a broad class of earth and earth like materials is presented. The key features the model captures are: (1) material anisotropy; (2) rate sensitive directional fracture; (3) dilatational friction; (4) dynamic overstress in loading extremes, where the rate of supplied energy is not fully compensated by the rate of the energy redistribution and release and, lastly, (5) spatial stochasticity due to material heterogeneity. In comparison with more traditional phenomenological descriptions, the contribution of the proposed approach is the utilization of tensor representation theory; the theory is suitable for converting observed deformation and fracture mechanisms into a precise mathematical description of the material's behavior. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Zubelewicz, A.] Alek Res Associates LLC, Los Alamos, NM 87545 USA. [Zubelewicz, A.; Rougier, E.; Knight, E. E.; Bradley, C.; Viswanathan, H. S.] Los Alamos Natl Lab, Los Alamos, NM USA. [Ostoja-Starzewski, M.] Univ Illinois, Dept Mech Sci & Engn, Urbana, IL USA. RP Zubelewicz, A (reprint author), Alek Res Associates LLC, Los Alamos, NM 87545 USA. EM Alek.Zubelewicz@gmail.com RI Rougier, Esteban/C-9946-2015; OI Rougier, Esteban/0000-0002-4624-2844; Ostoja-Starzewski, Martin/0000-0002-3493-363X; Knight, Earl/0000-0003-0461-0714 FU U.S. DOE [DE-AC52-06NA25396]; Lawrence Livermore National Laboratory (LLNL); Los Alamos National Laboratory (LANL); Sandia National Laboratories (SNL); Defense Threat Reduction Agency (DTRA); Air Force Technical Applications Center (AFTAC) FX This project has been performed under the auspices of the US Department of Energy. The Los Alamos National Laboratory is operated by Los Alamos National Security, LLC for the NNSA of the U.S. DOE under Contract no. DE-AC52-06NA25396. The authors wish to express their gratitude to Scott Broome of Sandia National Laboratories for providing experimental data for granite. The experimental study was sponsored by the SPE multi-institutional and interdisciplinary group of scientists and engineers from National Security Technologies (NSTec), Lawrence Livermore National Laboratory (LLNL), Los Alamos National Laboratory (LANL), Sandia National Laboratories (SNL), the Defense Threat Reduction Agency (DTRA), and the Air Force Technical Applications Center (AFTAC). NR 22 TC 6 Z9 6 U1 2 U2 14 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 1365-1609 EI 1873-4545 J9 INT J ROCK MECH MIN JI Int. J. Rock Mech. Min. Sci. PD DEC PY 2014 VL 72 BP 277 EP 282 DI 10.1016/j.ijrmms.2014.09.015 PG 6 WC Engineering, Geological; Mining & Mineral Processing SC Engineering; Mining & Mineral Processing GA AU4LZ UT WOS:000345583900027 ER PT J AU Reedy, ED AF Reedy, E. D., Jr. TI Cohesive zone finite element analysis of crack initiation from a butt joint's interface corner SO INTERNATIONAL JOURNAL OF SOLIDS AND STRUCTURES LA English DT Article DE Cohesive zone; Bonded joint; Interface corner; Interfacial fracture ID ADHESIVELY-BONDED JOINTS; FRACTURE ANALYSES; INTENSITY AB Cohesive zone (CZ) fracture analysis techniques are used to predict the initiation of crack growth from the interface corner of an adhesively bonded butt joint. In this plane strain analysis, a thin linear elastic adhesive layer is sandwiched between rigid adherends. There is no preexisting crack in the problem analyzed, and the focus is on how the shape of the traction-separation (T-U) relationship affects the predicted joint strength. Unlike the case of a preexisting interfacial crack, the calculated results clearly indicate that the predicted joint strength depends on the shape of the T-U relationship. Most of the calculations used a rectangular T-U relationship whose shape (aspect ratio) is defined by two parameters: the interfacial strength sigma*. and the work of separation/unit area Gamma. The principal finding of this study is that for a specified adhesive layer thickness, there is any number of sigma*, Gamma combinations that generate the same predicted joint strength. Each combination corresponds to a different CZ length. An approximate CZ-like elasticity solution was developed to show how such combinations arise and their connection with the CZ length. (C) 2014 Elsevier Ltd. All rights reserved. C1 Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Reedy, ED (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87185 USA. EM edreedy@sandia.gov FU Laboratory Directed Research and Development Program at Sandia National Laboratories; US Department of Energy's National Nuclear Security Administration [DE-AC04-94AL85000] FX This work was supported by the Laboratory Directed Research and Development Program at Sandia National Laboratories. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the US Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. NR 18 TC 2 Z9 2 U1 2 U2 6 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0020-7683 EI 1879-2146 J9 INT J SOLIDS STRUCT JI Int. J. Solids Struct. PD DEC PY 2014 VL 51 IS 25-26 BP 4336 EP 4344 DI 10.1016/j.ijsolstr.2014.08.020 PG 9 WC Mechanics SC Mechanics GA AU2TM UT WOS:000345470400013 ER PT J AU Closek, CJ Sunagawa, S DeSalvo, MK Piceno, YM DeSantis, TZ Brodie, EL Weber, MX Voolstra, CR Andersen, GL Medina, M AF Closek, Collin J. Sunagawa, Shinichi DeSalvo, Michael K. Piceno, Yvette M. DeSantis, Todd Z. Brodie, Eoin L. Weber, Michele X. Voolstra, Christian R. Andersen, Gary L. Medina, Monica TI Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata SO ISME JOURNAL LA English DT Article DE 16S rRNA gene; Orbicella faveolata; Montastraea faveolata; PhyloChip; coral reefs; yellow band blotch disease ID REEF-BUILDING CORALS; ANNULARIS SPECIES COMPLEX; NITROGEN-FIXING BACTERIA; ANEMONE ACTINIA-EQUINA; MONTASTRAEA-FAVEOLATA; CARIBBEAN CORALS; GENE-EXPRESSION; METAGENOMIC ANALYSIS; DIVERSITY; POPULATIONS AB Coral diseases impact reefs globally. Although we continue to describe diseases, little is known about the etiology or progression of even the most common cases. To examine a spectrum of coral health and determine factors of disease progression we examined Orbicella faveolata exhibiting signs of Yellow Band Disease (YBD), a widespread condition in the Caribbean. We used a novel combined approach to assess three members of the coral holobiont: the coral-host, associated Symbiodinium algae, and bacteria. We profiled three conditions: (1) healthy-appearing colonies (HH), (2) healthy-appearing tissue on diseased colonies (HD), and (3) diseased lesion (DD). Restriction fragment length polymorphism analysis revealed health state-specific diversity in Symbiodinium clade associations. 16S ribosomal RNA gene microarrays (PhyloChips) and O. faveolata complimentary DNA microarrays revealed the bacterial community structure and host transcriptional response, respectively. A distinct bacterial community structure marked each health state. Diseased samples were associated with two to three times more bacterial diversity. HD samples had the highest bacterial richness, which included components associated with HH and DD, as well as additional unique families. The host transcriptome under YBD revealed a reduced cellular expression of defense- and metabolism-related processes, while the neighboring HD condition exhibited an intermediate expression profile. Although HD tissue appeared visibly healthy, the microbial communities and gene expression profiles were distinct. HD should be regarded as an additional (intermediate) state of disease, which is important for understanding the progression of YBD. C1 [Closek, Collin J.; Weber, Michele X.; Medina, Monica] Penn State Univ, Dept Biol, University Pk, PA 16802 USA. [Closek, Collin J.; Weber, Michele X.; Medina, Monica] Univ Calif, Sch Nat Sci, Merced, CA USA. [Sunagawa, Shinichi] European Mol Biol Lab, Struct & Computat Biol Unit, D-69012 Heidelberg, Germany. [DeSalvo, Michael K.] Phalanx Biotech Grp Inc, San Diego, CA USA. [Piceno, Yvette M.; Andersen, Gary L.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Ctr Environm Biotechnol, Berkeley, CA 94720 USA. [DeSantis, Todd Z.] Second Genome Inc, San Francisco, CA USA. [Voolstra, Christian R.] KAUST, Red Sea Res Ctr, Thuwal, Saudi Arabia. RP Closek, CJ (reprint author), Penn State Univ, Dept Biol, 208 Mueller Lab Bldg, University Pk, PA 16802 USA. EM closek@gmail.com; monicamedina@psu.edu RI Sunagawa, Shinichi/D-9715-2011; Andersen, Gary/G-2792-2015; Brodie, Eoin/A-7853-2008; Piceno, Yvette/I-6738-2016; Voolstra, Christian R./H-7158-2014 OI Sunagawa, Shinichi/0000-0003-3065-0314; Andersen, Gary/0000-0002-1618-9827; Brodie, Eoin/0000-0002-8453-8435; Piceno, Yvette/0000-0002-7915-4699; Voolstra, Christian R./0000-0003-4555-3795 FU NSF [IOS 0644438, IOS 0926906] FX We would like to thank the Instituto de Ciencias del Mar y Limnologia (ICML), the Universidad Nacional Autonoma de Mexico for providing facilities and collection permits. Additionally we would like to thank those at the ICML, as well as the Medina & Andersen Lab members who provided assistance in collecting the sample, and in experimental and analytical methods. Especially, Adan Guillermo Jordan-Garza, Julia Schnetzer and Erika M Diaz-Almeyda for helping with the sample collection. Nicholas R Polato & Elizabeth Green for genotyping coral colonies. Lauren M Tom for assistance with the analyses. Justin L Matthews for statistical input. Bishoy SK Kamel and Erika M Diaz-Almeyda for additional draft comments. This study was supported by NSF awards IOS 0644438 and IOS 0926906 from NSF to MM. NR 81 TC 24 Z9 24 U1 4 U2 42 PU NATURE PUBLISHING GROUP PI LONDON PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND SN 1751-7362 EI 1751-7370 J9 ISME J JI ISME J. PD DEC PY 2014 VL 8 IS 12 BP 2411 EP 2422 DI 10.1038/ismej.2014.85 PG 12 WC Ecology; Microbiology SC Environmental Sciences & Ecology; Microbiology GA AU3FP UT WOS:000345498200007 PM 24950107 ER PT J AU Ghylin, TW Garcia, SL Moya, F Oyserman, BO Schwientek, P Forest, KT Mutschler, J Dwulit-Smith, J Chan, LK Martinez-Garcia, M Sczyrba, A Stepanauskas, R Grossart, HP Woyke, T Warnecke, F Malmstrom, R Bertilsson, S McMahon, KD AF Ghylin, Trevor W. Garcia, Sarahi L. Moya, Francisco Oyserman, Ben O. Schwientek, Patrick Forest, Katrina T. Mutschler, James Dwulit-Smith, Jeffrey Chan, Leong-Keat Martinez-Garcia, Manuel Sczyrba, Alexander Stepanauskas, Ramunas Grossart, Hans-Peter Woyke, Tanja Warnecke, Falk Malmstrom, Rex Bertilsson, Stefan McMahon, Katherine D. TI Comparative single-cell genomics reveals potential ecological niches for the freshwater acl Actinobacteria lineage SO ISME JOURNAL LA English DT Article ID BACTERIAL COMMUNITY COMPOSITION; CYANOPHYCIN-DEGRADING BACTERIA; CODON USAGE BIAS; ORGANIC-CARBON; SEQUENCE DATA; BACTERIOPLANKTON POPULATIONS; ACTINORHODOPSIN GENES; PROTEIN FAMILIES; LAKE BACTERIA; HUMIC LAKE AB Members of the acI lineage of Actinobacteria are the most abundant microorganisms in most freshwater lakes; however, our understanding of the keys to their success and their role in carbon and nutrient cycling in freshwater systems has been hampered by the lack of pure cultures and genomes. We obtained draft genome assemblies from 11 single cells representing three acI tribes (acI-A1, acI-A7, acI-B1) from four temperate lakes in the United States and Europe. Comparative analysis of acI SAGs and other available freshwater bacterial genomes showed that acI has more gene content directed toward carbohydrate acquisition as compared to Polynucleobacter and LD12 Alphaproteobacteria, which seem to specialize more on carboxylic acids. The acI genomes contain actinorhodopsin as well as some genes involved in anaplerotic carbon fixation indicating the capacity to supplement their known heterotrophic lifestyle. Genome-level differences between the acI-A and acI-B clades suggest specialization at the clade level for carbon substrate acquisition. Overall, the acI genomes appear to be highly streamlined versions of Actinobacteria that include some genes allowing it to take advantage of sunlight and N-rich organic compounds such as polyamines, di-and oligopeptides, branched-chain amino acids and cyanophycin. This work significantly expands the known metabolic potential of the cosmopolitan freshwater acI lineage and its ecological and genetic traits. C1 [Ghylin, Trevor W.; Moya, Francisco; Oyserman, Ben O.; McMahon, Katherine D.] Univ Wisconsin, Dept Civil & Environm Engn, Madison, WI 53706 USA. [Garcia, Sarahi L.; Forest, Katrina T.; Mutschler, James; Dwulit-Smith, Jeffrey; McMahon, Katherine D.] Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA. [Garcia, Sarahi L.; Warnecke, Falk] Univ Jena, JSMC, Jena, Germany. [Garcia, Sarahi L.; Warnecke, Falk] Univ Jena, Microbial Ecol Grp, Jena, Germany. [Schwientek, Patrick; Chan, Leong-Keat; Sczyrba, Alexander; Woyke, Tanja; Malmstrom, Rex] DOE Joint Genome Inst, Walnut Creek, CA USA. [Martinez-Garcia, Manuel; Stepanauskas, Ramunas] Bigelow Lab Ocean Sci, East Boothbay, ME USA. [Sczyrba, Alexander] Univ Bielefeld, Ctr Biotechnol CeBiTec, D-33615 Bielefeld, Germany. [Grossart, Hans-Peter] Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Limnol Stratified Lakes, Stechlin, Germany. [Grossart, Hans-Peter] Univ Potsdam, Inst Biochem & Biol, Potsdam, Germany. [Bertilsson, Stefan] Uppsala Univ, Dept Ecol & Genet, Limnol & Sci Life Lab, Uppsala, Sweden. RP McMahon, KD (reprint author), Univ Wisconsin, Dept Civil & Environm Engn, 1550 Linden Dr Room 5552, Madison, WI 53706 USA. EM kdmcmahon@wisc.edu FU Join Genome Institute; Biotechnology Training Program of the National Institutes of Health at the University of Wisconsin-Madison [5T32GM08349]; Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]; United States National Science Foundation Microbial Observatories program [MCB-0702395]; Long Term Ecological Research program [NTL-LTER DEB-0822700]; INSPIRE award [DEB-1344254]; Swedish Wenner-Gren Foundation; National Institute of Food and Agriculture, United States Department of Agriculture [WIS01516]; United States National Science Foundation [DEB-0841933, OCE-0821374, EF-0633142, MCB-0738232]; Swedish Research Council; German Science Foundation [DFG GR1540/17-1]; JSMC FX We thank Dr Todd Miller and Sara Yeo for collecting the original water samples used to retrieve single cells from Lake Mendota and Sparkling Lake. We thank the Join Genome Institute for supporting this work through the Community Sequencing Program, performing the bioinformatics and providing technical support. We would also like to acknowledge the Biotechnology Training Program of the National Institutes of Health at the University of Wisconsin-Madison for providing financial support for TWG's research and training (grant #5T32GM08349). 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. KDM acknowledges funding from the United States National Science Foundation Microbial Observatories program (MCB-0702395), the Long Term Ecological Research program (NTL-LTER DEB-0822700), an INSPIRE award (DEB-1344254) and the Swedish Wenner-Gren Foundation. This material is based upon work supported by the National Institute of Food and Agriculture, United States Department of Agriculture, under ID number WIS01516 (to KDM). RS acknowledges funding from the United States National Science Foundation (DEB-0841933, OCE-0821374, EF-0633142, and MCB-0738232). SB acknowledges funding from the Swedish Research Council and H-PG acknowledges funding from the German Science Foundation (DFG GR1540/17-1). SLG thanks JSMC for funding. NR 68 TC 24 Z9 25 U1 4 U2 39 PU NATURE PUBLISHING GROUP PI LONDON PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND SN 1751-7362 EI 1751-7370 J9 ISME J JI ISME J. PD DEC PY 2014 VL 8 IS 12 BP 2503 EP 2516 DI 10.1038/ismej.2014.135 PG 14 WC Ecology; Microbiology SC Environmental Sciences & Ecology; Microbiology GA AU3FP UT WOS:000345498200015 PM 25093637 ER PT J AU Clingenpeel, S Schwientek, P Hugenholtz, P Woyke, T AF Clingenpeel, Scott Schwientek, Patrick Hugenholtz, Philip Woyke, Tanja TI Effects of sample treatments on genome recovery via single-cell genomics SO ISME JOURNAL LA English DT Article ID IN-SITU HYBRIDIZATION; AMPLIFICATION; INSIGHTS AB Single-cell genomics is a powerful tool for accessing genetic information from uncultivated microorganisms. Methods of handling samples before single-cell genomic amplification may affect the quality of the genomes obtained. Using three bacterial strains we show that, compared to cryopreservation, lower-quality single-cell genomes are recovered when the sample is preserved in ethanol or if the sample undergoes fluorescence in situ hybridization, while sample preservation in paraformaldehyde renders it completely unsuitable for sequencing. C1 [Clingenpeel, Scott; Schwientek, Patrick; Woyke, Tanja] DOE Joint Genome Inst, Walnut Creek, CA 94598 USA. [Hugenholtz, Philip] Univ Queensland, Australian Ctr Ecogen, Sch Chem & Mol Biosci, Brisbane, Qld, Australia. RP Woyke, T (reprint author), DOE Joint Genome Inst, 2800 Mitchell Dr, Walnut Creek, CA 94598 USA. EM twoyke@lbl.gov RI Hugenholtz, Philip/G-9608-2011; OI hugenholtz, philip/0000-0001-5386-7925 FU Office of Science of the US Department of Energy [DEAC02-05CH11231]; Australian Research Council [LE120100025, DP120103498] 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. PH was supported by grants from the Australian Research Council (LE120100025 and DP120103498). We also thank Suzan Yilmaz for helpful discussions. NR 14 TC 10 Z9 10 U1 0 U2 17 PU NATURE PUBLISHING GROUP PI LONDON PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND SN 1751-7362 EI 1751-7370 J9 ISME J JI ISME J. PD DEC PY 2014 VL 8 IS 12 BP 2546 EP 2549 DI 10.1038/ismej.2014.92 PG 4 WC Ecology; Microbiology SC Environmental Sciences & Ecology; Microbiology GA AU3FP UT WOS:000345498200019 PM 24926860 ER PT J AU Wu, MY Singh, AK AF Wu, Meiye Singh, Anup K. TI Microfluidic Molecular Assay Platform for the Detection of miRNAs, mRNAs, Proteins, and Posttranslational Modifications at Single-Cell Resolution SO JALA LA English DT Article DE protein; mRNA; microRNA; PTM; multiplex; single cell; microfluidics; flow cytometry; imaging ID MACROPHAGE RESPONSE AB Cell signaling is a dynamic and complex process. A typical signaling pathway may begin with activation of cell surface receptors, leading to activation of a kinase cascade that culminates in induction of messenger RNA (mRNA) and noncoding microRNA (miRNA) production in the nucleus, followed by modulation of mRNA expression by miRNAs in the cytosol, and end with production of proteins in response to the signaling pathway. Signaling pathways involve proteins, miRNA, and mRNAs, along with various forms of transient posttranslational modifications, and detecting each type of signaling molecule requires categorically different sample preparation methods such as Western blotting for proteins, PCR for nucleic acids, and flow cytometry for posttranslational modifications. Since we know that cells in populations behave heterogeneously,(1) especially in the cases of stem cells, cancer, and hematopoiesis, there is need for a new technology that provides capability to detect and quantify multiple categories of signaling molecules in intact single cells to provide a comprehensive view of the cell's physiological state. In this Technology Brief, we describe our automated microfluidic platform with a portfolio of customized molecular assays that can detect nucleic acids, proteins, and posttranslational modifications in single intact cells with >95% reduction in reagent requirement in under 8 h. C1 [Wu, Meiye; Singh, Anup K.] Sandia Natl Labs, Livermore, CA 94550 USA. RP Wu, MY (reprint author), Sandia Natl Labs, Biotechnol & Bioengn Dept, POB 969,MS 9671, Livermore, CA 94550 USA. EM meiwu@sandia.gov OI Wu, Meiye/0000-0003-3712-1554 FU NIDCR [R01 DE020891]; MISL Grand Challenge Laboratory Directed Research and Development program at Sandia National Laboratories; NIGMS [P50GM085273] FX The authors disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: Financial support for preparation and some of the work included was provided by the grants: R01 DE020891, funded by the NIDCR; The MISL Grand Challenge Laboratory Directed Research and Development program at Sandia National Laboratories. Part of this research was paid by P50GM085273 (the New Mexico Spatiotemporal Modeling Center) funded by the NIGMS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. NR 9 TC 1 Z9 1 U1 1 U2 34 PU SAGE PUBLICATIONS INC PI THOUSAND OAKS PA 2455 TELLER RD, THOUSAND OAKS, CA 91320 USA SN 2211-0682 EI 1540-2452 J9 JALA-J LAB AUTOM JI JALA PD DEC PY 2014 VL 19 IS 6 BP 587 EP 592 DI 10.1177/2211068214542247 PG 6 WC Biochemical Research Methods; Chemistry, Analytical SC Biochemistry & Molecular Biology; Chemistry GA AU2SN UT WOS:000345468000009 PM 25027027 ER PT J AU Pint, BA Dryepondt, S Unocic, KA Hoelzer, DT AF Pint, B. A. Dryepondt, S. Unocic, K. A. Hoelzer, D. T. TI Development of ODS FeCrAl for Compatibility in Fusion and Fission Energy Applications SO JOM LA English DT Article ID HIGH-TEMPERATURE OXIDATION; CLADDING CANDIDATE MATERIALS; ALUMINA SCALE FORMATION; MECHANICAL-PROPERTIES; PROTECTIVE SCALES; FORMING ALLOYS; FERRITIC STEEL; PB-LI; OXIDE; ADDITIONS AB Oxide dispersion strengthened (ODS) FeCrAl alloys with 12-15% Cr are being evaluated for improved compatibility with Pb-Li for a fusion energy application and with high temperature steam for a more accident-tolerant light water reactor fuel cladding application. A 12% Cr content alloy showed low mass losses in static Pb-Li at 700 degrees C, where a LiAlO2 surface oxide formed and inhibited dissolution into the liquid metal. All the evaluated compositions formed a protective scale in steam at 1200 degrees C, which is not possible with ODS FeCr alloys. However, most of the compositions were not protective at 1400 degrees C, which is a general and somewhat surprising problem with ODS FeCrAl alloys that is still being studied. More work is needed to optimize the alloy composition, microstructure and oxide dispersion, but initial promising tensile and creep results have been obtained with mixed oxide additions, i.e. Y2O3 with ZrO2, HfO2 or TiO2. C1 [Pint, B. A.; Dryepondt, S.; Unocic, K. A.; Hoelzer, D. T.] Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. RP Pint, BA (reprint author), Oak Ridge Natl Lab, Div Mat Sci & Technol, POB 2008, Oak Ridge, TN 37831 USA. EM pintba@ornl.gov RI Pint, Bruce/A-8435-2008; Hoelzer, David/L-1558-2016 OI Pint, Bruce/0000-0002-9165-3335; FU U.S. Department of Energy's Office of Nuclear Energy, Advanced Fuel Campaign of the Fuel Cycle RD program; Office of Fusion Energy Sciences, Fusion Energy Materials Program FX The experimental work was conducted by M. Howell, M. Stephens, C. Stevens, J. Moser, D. Harper, T. Lowe, H. Longmire, J. Mayotte, T. Geer and T. Jordan. K. A. Terrani, P. F. Tortorelli and R. B. Rebak provided useful comments on the manuscript. This research was funded by the U.S. Department of Energy's Office of Nuclear Energy, Advanced Fuel Campaign of the Fuel Cycle R&D program and by the Office of Fusion Energy Sciences, Fusion Energy Materials Program under a proposal written by Dr. Peng Dou while he was at ORNL. NR 55 TC 7 Z9 7 U1 4 U2 46 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1047-4838 EI 1543-1851 J9 JOM-US JI JOM PD DEC PY 2014 VL 66 IS 12 BP 2458 EP 2466 DI 10.1007/s11837-014-1200-z PG 9 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing SC Materials Science; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing GA AU1RF UT WOS:000345397200011 ER PT J AU Yablinsky, CA Tippey, KE Vaynman, S Anderoglu, O Fine, ME Chung, YW Speer, JG Findley, KO Dogan, ON Jablonski, PD Maloy, SA Hackenberg, RE Clarke, AJ Clarke, KD AF Yablinsky, C. A. Tippey, K. E. Vaynman, S. Anderoglu, O. Fine, M. E. Chung, Y. -W. Speer, J. G. Findley, K. O. Dogan, Oe. N. Jablonski, P. D. Maloy, S. A. Hackenberg, R. E. Clarke, A. J. Clarke, K. D. TI Concepts for the Development of Nanoscale Stable Precipitation-Strengthened Steels Manufactured by Conventional Methods SO JOM LA English DT Article ID FERRITIC/MARTENSITIC STEELS; MECHANICAL-PROPERTIES; ELEVATED-TEMPERATURE; RADIATION-DAMAGE; IRRADIATION; REACTORS; ALLOYS AB The development of oxide dispersion strengthened ferrous alloys has shown that microstructures designed for excellent irradiation resistance and thermal stability ideally contain stable nanoscale precipitates and dislocation sinks. Based upon this understanding, the microstructures of conventionally manufactured ferritic and ferritic-martensitic steels can be designed to include controlled volume fractions of fine, stable precipitates and dislocation sinks via specific alloying and processing paths. The concepts proposed here are categorized as advanced high-Cr ferritic-martensitic (AHCr-FM) and novel tailored precipitate ferritic (TPF) steels, which have the potential to improve the in-reactor performance of conventionally manufactured alloys. AHCr-FM steels have modified alloy content relative to current reactor materials (such as alloy NF616/P92) to maximize desirable precipitates and control phase stability. TPF steels are designed to incorporate nickel aluminides, in addition to microalloy carbides, in a ferritic matrix to produce fine precipitate arrays with good thermal stability. Both alloying concepts may also benefit from thermomechanical processing to establish dislocation sinks and modify phase transformation behaviors. Alloying and processing paths toward designed microstructures are discussed for both AHCr-FM and TPF material classes. C1 [Yablinsky, C. A.; Anderoglu, O.; Maloy, S. A.; Hackenberg, R. E.; Clarke, A. J.; Clarke, K. D.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. [Tippey, K. E.; Speer, J. G.; Findley, K. O.] Colorado Sch Mines, Adv Steel Proc & Prod Res Ctr, Golden, CO 80401 USA. [Vaynman, S.; Fine, M. E.; Chung, Y. -W.] Northwestern Univ, Dept Mat Sci & Engn, Evanston, IL 60208 USA. [Dogan, Oe. N.; Jablonski, P. D.] Natl Energy Technol Lab, Albany, OR 97321 USA. RP Yablinsky, CA (reprint author), Los Alamos Natl Lab, MS G770,POB 1663, Los Alamos, NM 87545 USA. EM rizz@lanl.gov RI Findley, Kip/H-8845-2013; Chung, Yip-Wah/B-7506-2009; Maloy, Stuart/A-8672-2009; Clarke, Kester/R-9976-2016; OI Findley, Kip/0000-0001-7068-9446; Maloy, Stuart/0000-0001-8037-1319; Hackenberg, Robert/0000-0002-0380-5723; Yablinsky, Clarissa/0000-0001-6162-0949 FU U.S. Department of Energy-Nuclear Energy, Nuclear Energy Enabling Technology Program [DE-FOA-0000426]; U.S. Department of Energy [DE-AC52-06NA25396] FX This work is funded by the U.S. Department of Energy-Nuclear Energy, Nuclear Energy Enabling Technology Program: DE-FOA-0000426. This work was performed, in part, at the Center for Integrated Nanotechnologies, an Office of Science User Facility operated for the U.S. Department of Energy (DOE) Office of Science. Los Alamos National Laboratory, an affirmative action equal opportunity employer, is operated by Los Alamos National Security, LLC, for the National Nuclear Security Administration of the U.S. Department of Energy under contract DE-AC52-06NA25396. NR 35 TC 0 Z9 0 U1 0 U2 20 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1047-4838 EI 1543-1851 J9 JOM-US JI JOM PD DEC PY 2014 VL 66 IS 12 BP 2467 EP 2475 DI 10.1007/s11837-014-1204-8 PG 9 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing SC Materials Science; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing GA AU1RF UT WOS:000345397200012 ER PT J AU Unocic, KA Shingledecker, JP Tortorelli, PF AF Unocic, K. A. Shingledecker, J. P. Tortorelli, P. F. TI Microstructural Changes in Inconel (R) 740 After Long-Term Aging in the Presence and Absence of Stress SO JOM LA English DT Article ID POWER-PLANTS; CREEP AB The Ni-based alloy, Inconel (R) 740, is being extensively examined for use in advanced ultrasupercritical steam boilers because its precipitation-strengthened microstructure appears to offer the necessary creep strength under the high temperatures and pressures (up to 760 degrees C and 35 MPa) needed for high efficiency power generation. However, because this application requires extremely long lifetimes under these conditions (up to 30 years), long-term microstructure stability is a major concern. In this paper, results from microstructural analyses of Inconel 740 specimens aged at 700 and 750 degrees C in the presence and absence of creep loading for times up to similar to 31,000 h are presented. The primary focus was on the development of the eta eta (Ni3Ti) phase and coarsening of coherent gamma'-Ni-3(Al,Ti) precipitates and its depletion near eta/matrix interfaces. However, despite these processes, Inconel 740 showed adequate long-term microstructural stability to assure adequate creep strength for the intended application. C1 [Unocic, K. A.; Tortorelli, P. F.] Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. [Shingledecker, J. P.] Elect Power Res Inst, Charlotte, NC 28262 USA. RP Unocic, KA (reprint author), Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. EM unocicka@ornl.gov FU U.S. Department of Energy (DOE), Office of Fossil Energy FX This research was sponsored by the U.S. Department of Energy (DOE), Office of Fossil Energy, Crosscutting Research Program in support of the DOE project on boiler materials for advanced ultrasupercritical steam conditions. G.J. Pillitiere, T. Lowe, T. Geer, K. S. Reeves, K. Powers, and J. Moser assisted with the experimental work. The authors thank D. T. Hoelzer and Y. Yamamoto for comments on the results and manuscript. NR 24 TC 2 Z9 2 U1 1 U2 18 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1047-4838 EI 1543-1851 J9 JOM-US JI JOM PD DEC PY 2014 VL 66 IS 12 BP 2535 EP 2542 DI 10.1007/s11837-014-1208-4 PG 8 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing SC Materials Science; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing GA AU1RF UT WOS:000345397200020 ER PT J AU Bai, XM AF Bai, Xian-Ming TI Recent Progress in Using Advanced Characterization and Modeling Approaches to Study Radiation Effects in Oxide Ceramics SO JOM LA English DT Editorial Material ID CRYSTAL C1 Idaho Natl Lab, Idaho Falls, ID 83415 USA. RP Bai, XM (reprint author), Idaho Natl Lab, 2525 N Fremont Ave,POB 1625,MS 3835, Idaho Falls, ID 83415 USA. EM xianming.bai@inl.gov RI Bai, Xianming/E-2376-2017 OI Bai, Xianming/0000-0002-4609-6576 NR 8 TC 0 Z9 0 U1 0 U2 6 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1047-4838 EI 1543-1851 J9 JOM-US JI JOM PD DEC PY 2014 VL 66 IS 12 BP 2543 EP 2545 DI 10.1007/s11837-014-1162-1 PG 3 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing SC Materials Science; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing GA AU1RF UT WOS:000345397200021 ER PT J AU He, LF Gupta, M Kirk, MA Pakarinen, J Gan, J Allen, TR AF He, L. F. Gupta, M. Kirk, M. A. Pakarinen, J. Gan, J. Allen, T. R. TI In Situ TEM Observation of Dislocation Evolution in Polycrystalline UO2 SO JOM LA English DT Article ID MOLECULAR-DYNAMICS SIMULATIONS; URANIUM-DIOXIDE; RADIATION-DAMAGE; IRRADIATED UO2; MICROSTRUCTURE EVOLUTION; THERMAL-CONDUCTIVITY; BURN-UP; TEMPERATURE; CERAMICS; CRYSTALS AB In situ transmission electron microscopy observation of polycrystalline UO2 (with average grain size of about 5 mu m) irradiated with Kr ions at 600 degrees C and 800 degrees C was conducted to understand the radiation-induced dislocation evolution under the influence of grain boundaries. The dislocation evolution in the grain interior of polycrystalline UO2 was similar under Kr irradiation at different ion energies and temperatures. As expected, it was characterized by the nucleation and growth of dislocation loops at low irradiation doses, followed by transformation to extended dislocation lines and tangles at high doses. For the first time, a dislocation-denuded zone was observed near a grain boundary in the 1-MeV Kr-irradiated UO2 sample at 800 degrees C. The denuded zone in the vicinity of grain boundary was not found when the irradiation temperature was at 600 degrees C. The suppression of dislocation loop formation near the boundary is likely due to the enhanced interstitial diffusion toward grain boundary at the high temperature. C1 [He, L. F.; Gupta, M.; Pakarinen, J.; Allen, T. R.] Univ Wisconsin, Dept Engn Phys, Madison, WI 53706 USA. [Kirk, M. A.] Argonne Natl Lab, Argonne, IL 60439 USA. [He, L. F.; Gan, J.; Allen, T. R.] Idaho Natl Lab, Idaho Falls, ID 83415 USA. RP He, LF (reprint author), Idaho Natl Lab, POB 1625, Idaho Falls, ID 83415 USA. EM lfhechina@gmail.com OI Allen, Todd/0000-0002-2372-7259; He, Lingfeng/0000-0003-2763-1462 FU Center for Materials Science of Nuclear Fuel, an Energy Frontier Research Center - U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences; U.S. Department of Energy Office of Science Laboratory by UChicago Argonne, LLC [DE-AC02-06CH11357]; Center for Advanced Energy Studies located in Idaho Falls, Idaho; Advanced Test Reactor National Scientific User Facility U.S. Department of Energy, Office of Nuclear Energy under DOE Idaho Operations Office [DE-AC07-051D14517] FX This work was supported as part of the Center for Materials Science of Nuclear Fuel, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. The electron microscopy was accomplished at the Electron Microscopy Center for Materials Research at Argonne National Laboratory, a U.S. Department of Energy Office of Science Laboratory operated under Contract No. DE-AC02-06CH11357 by UChicago Argonne, LLC, and the Center for Advanced Energy Studies located in Idaho Falls, Idaho, the Advanced Test Reactor National Scientific User Facility U.S. Department of Energy, Office of Nuclear Energy under DOE Idaho Operations Office Contract DE-AC07-051D14517. The authors would like to thank Dr. Xianming Bai at Idaho National Laboratory for previewing the manuscript and for his important comments and suggestions. We also thank Dr. Andrew Nelson for providing the UO2 samples used in this study and Peter M. Baldo of Argonne National Laboratory for his help in performing the irradiations. NR 33 TC 5 Z9 5 U1 2 U2 46 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1047-4838 EI 1543-1851 J9 JOM-US JI JOM PD DEC PY 2014 VL 66 IS 12 BP 2553 EP 2561 DI 10.1007/s11837-014-1186-6 PG 9 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing SC Materials Science; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing GA AU1RF UT WOS:000345397200023 ER PT J AU Valderrama, B He, LF Henderson, HB Pakarinen, J Jaques, B Gan, J Butt, DP Allen, TR Manuel, MV AF Valderrama, Billy He, Lingfeng Henderson, Hunter B. Pakarinen, Janne Jaques, Brian Gan, Jian Butt, Darryl P. Allen, Todd R. Manuel, Michele V. TI Effect of Grain Boundaries on Krypton Segregation Behavior in Irradiated Uranium Dioxide SO JOM LA English DT Article ID GAS-RELEASE; PLAUSIBLE CONCEPTS; HIGH-TEMPERATURE; DIFFUSION; UO2; SUFFICIENT; CERAMICS AB Fission products, such as krypton (Kr), are known to be insoluble within UO2, segregating toward grain boundaries and eventually leading to a lowering in thermal conductivity and fuel swelling. Recent computational studies have identified that differences in grain boundary structure have a significant effect on the segregation behavior of fission products. However, experimental work supporting these simulations is lacking. Atom probe tomography was used to measure the Kr distribution across grain boundaries in UO2. Polycrystalline depleted UO2 samples were irradiated with 0.7 MeV and 1.8 MeV Kr-ions and annealed to 1000 degrees C, 1300 degrees C, and 1600 degrees C for 1 h to produce a Kr-bubble dominated microstructure. The results of this work indicate a strong dependence of Kr concentration as a function of grain boundary structure. Temperature also influences grain boundary chemistry with greater Kr concentration evident at higher temperatures, resulting in a reduced Kr concentration in the bulk. Although Kr segregation takes place at elevated temperatures, no change in grain size or texture was observed in the irradiated UO2 samples. C1 [Valderrama, Billy; Henderson, Hunter B.; Manuel, Michele V.] Univ Florida, Dept Mat Sci & Engn, Gainesville, FL 32611 USA. [He, Lingfeng; Pakarinen, Janne; Allen, Todd R.] Univ Wisconsin, Dept Engn Phys, Madison, WI USA. [Jaques, Brian; Butt, Darryl P.] Boise State Univ, Dept Mat Sci & Engn, Boise, ID 83725 USA. [Gan, Jian; Allen, Todd R.] Idaho Natl Lab, Idaho Falls, ID 83415 USA. RP Valderrama, B (reprint author), Univ Florida, Dept Mat Sci & Engn, Gainesville, FL 32611 USA. EM mmanuel@mse.ufl.edu RI Manuel, Michele/A-8795-2009; OI Manuel, Michele/0000-0002-3495-7826; Allen, Todd/0000-0002-2372-7259; He, Lingfeng/0000-0003-2763-1462; Pakarinen, Janne/0000-0001-8944-8757; Jaques, Brian/0000-0002-5324-555X FU Center for Materials Science of Nuclear Fuel, an Energy Frontier Research Center - U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences [FWP 1356]; U.S. Department of Energy, Office of Nuclear Energy under DOE Idaho Operations Office [DE-AC07-051D14517] FX This work is supported as part of the Center for Materials Science of Nuclear Fuel, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number FWP 1356. Use of the FIB and atom probe instrumentation at the Center for Advanced Energy Studies was supported by the U.S. Department of Energy, Office of Nuclear Energy under DOE Idaho Operations Office Contract DE-AC07-051D14517. The authors would also like to thank Dr. Andrew Nelson for providing the UO2 samples used in this study and Dr. Yaqaio Wu for assistance in running the atom probe. The Kr irradiation was carried out in the Frederick Seitz Materials Research Laboratory Central Facilities at the University of Illinois-Urbana Champaign, and the authors would like to thank Doug Jeffers for his assistance in performing the irradiation. NR 24 TC 3 Z9 3 U1 3 U2 21 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1047-4838 EI 1543-1851 J9 JOM-US JI JOM PD DEC PY 2014 VL 66 IS 12 BP 2562 EP 2568 DI 10.1007/s11837-014-1182-x PG 7 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing SC Materials Science; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing GA AU1RF UT WOS:000345397200024 ER PT J AU Teague, MC Fromm, BS Tonks, MR Field, DP AF Teague, Melissa C. Fromm, Bradley S. Tonks, Michael R. Field, David P. TI Using Coupled Mesoscale Experiments and Simulations to Investigate High Burn-Up Oxide Fuel Thermal Conductivity SO JOM LA English DT Article ID FINITE-ELEMENT-METHOD; PHASE-FIELD; THERMOPHYSICAL PROPERTIES; MICROSTRUCTURE; MIXTURES; POROSITY; BUBBLES AB Nuclear energy is a mature technology with a small carbon footprint. However, work is needed to make current reactor technology more accident tolerant and to allow reactor fuel to be burned in a reactor for longer periods of time. Optimizing the reactor fuel performance is essentially a materials science problem. The current understanding of fuel microstructure have been limited by the difficulty in studying the structure and chemistry of irradiated fuel samples at the mesoscale. Here, we take advantage of recent advances in experimental capabilities to characterize the microstructure in 3D of irradiated mixed oxide (MOX) fuel taken from two radial positions in the fuel pellet. We also reconstruct these microstructures using Idaho National Laboratory's MARMOT code and calculate the impact of microstructure heterogeneities on the effective thermal conductivity using mesoscale heat conduction simulations. The thermal conductivities of both samples are higher than the bulk MOX thermal conductivity because of the formation of metallic precipitates and because we do not currently consider phonon scattering due to defects smaller than the experimental resolution. We also used the results to investigate the accuracy of simple thermal conductivity approximations and equations to convert 2D thermal conductivities to 3D. It was found that these approximations struggle to predict the complex thermal transport interactions between metal precipitates and voids. C1 [Teague, Melissa C.; Fromm, Bradley S.; Tonks, Michael R.] Idaho Natl Lab, Idaho Falls, ID 83415 USA. [Fromm, Bradley S.] Washington State Univ, Mat Sci & Engn Program, Pullman, WA 99164 USA. [Field, David P.] Washington State Univ, Sch Mech & Mat Engn, Pullman, WA 99164 USA. RP Teague, MC (reprint author), Idaho Natl Lab, POB 1625, Idaho Falls, ID 83415 USA. EM michael.tonks@inl.gov OI Field, David/0000-0001-9415-0795 FU Idaho National Laboratory Directed Research and Development project; Fuel Cycle Research and Development program; Battelle Energy Alliance, LLC [DE-AC07-05ID14517]; U.S. Department of Energy FX This work was funded by an Idaho National Laboratory Directed Research and Development project and by the Fuel Cycle Research and Development program. This manuscript has been authored by Battelle Energy Alliance, LLC under Contract No. DE-AC07-05ID14517 with the U.S. Department of Energy. The U.S. government retains and the publisher, by accepting the article for publication, acknowledges that the U.S. government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for U.S. government purposes. NR 30 TC 3 Z9 3 U1 4 U2 26 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1047-4838 EI 1543-1851 J9 JOM-US JI JOM PD DEC PY 2014 VL 66 IS 12 BP 2569 EP 2577 DI 10.1007/s11837-014-1160-3 PG 9 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing SC Materials Science; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing GA AU1RF UT WOS:000345397200025 ER PT J AU Uberuaga, BP Jiang, C Stanek, CR Sickafus, KE Scott, C Smith, R AF Uberuaga, B. P. Jiang, C. Stanek, C. R. Sickafus, K. E. Scott, C. Smith, R. TI Prediction of Irradiation Spectrum Effects in Pyrochlores SO JOM LA English DT Article ID RADIATION TOLERANCE; OXIDES; AMORPHIZATION; CERAMICS AB The formation energy of cation antisites in pyrochlores (A(2)B(2)O(7)) has been correlated with the susceptibility to amorphize under irradiation, and thus, density functional theory calculations of antisite energetics can provide in-sights into the radiation tolerance of pyrochlores. Here, we show that the formation energy of antisite pairs in titanate pyrochlores, as opposed to other families of pyrochlores (B = Zr, Hf, or Sn), exhibits a strong dependence on the separation distance between the antisites. Classical molecular dynamics simulations of collision cascades in Er2Ti2O7 show that the average separation of antisite pairs is a function of the primary knock-on atom energy that creates the collision cascades. Together, these results suggest that the radiation tolerance of titanate pyrochlores may be sensitive to the irradiation conditions and might be controllable via the appropriate selection of ion beam parameters. C1 [Uberuaga, B. P.; Jiang, C.; Stanek, C. R.] Los Alamos Natl Lab, Div Mat Sci & Technol, Los Alamos, NM 87545 USA. [Sickafus, K. E.] Univ Tennessee, Dept Mat Sci & Engn, Knoxville, TN 37996 USA. [Scott, C.; Smith, R.] Univ Loughborough, Dept Math Sci, Loughborough LE11 3TU, Leics, England. RP Uberuaga, BP (reprint author), Los Alamos Natl Lab, Div Mat Sci & Technol, Los Alamos, NM 87545 USA. EM blas@lanl.gov RI Smith, Roger/C-2550-2013 FU U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division; National Nuclear Security Administration of the (U.S.) Department of Energy [DE-AC52-06NA25396] FX This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division. Los Alamos National Laboratory is operated by Los Alamos National Security, LLC, for the National Nuclear Security Administration of the (U.S.) Department of Energy under contract DE-AC52-06NA25396. We thank Arthur F. Voter for helpful discussions. NR 15 TC 4 Z9 4 U1 5 U2 24 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1047-4838 EI 1543-1851 J9 JOM-US JI JOM PD DEC PY 2014 VL 66 IS 12 BP 2578 EP 2582 DI 10.1007/s11837-014-1158-x PG 5 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing SC Materials Science; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing GA AU1RF UT WOS:000345397200026 ER PT J AU Brady, MP Keiser, JR Leonard, DN Whitmer, L Thomson, JK AF Brady, M. P. Keiser, J. R. Leonard, D. N. Whitmer, L. Thomson, J. K. TI Corrosion Considerations for Thermochemical Biomass Liquefaction Process Systems in Biofuel Production SO JOM LA English DT Article ID BIO-OIL; FAST PYROLYSIS; BOILERS; DIESEL; FUELS; STEEL; ACIDS AB Thermochemical liquefaction processing of biomass to produce bio-derived fuels (e. g., gasoline, jet fuel, diesel, home heating oil, etc.) is of great recent interest as a renewable energy source. Approaches under investigation include direct liquefaction, hydrothermal liquefaction, hydropyrolysis, fast pyrolysis, etc., to produce energy dense liquids that can be utilized as produced or further processed to provide products of higher value. An issue with bio-oils is that they tend to contain significant concentrations of organic oxygenates, including acids, which make the bio-oil a potential source of corrosion issues in transport, storage, and use. Efforts devoted to modified/further processing of bio-oils to make them less corrosive are currently being widely pursued. Another issue that must also be addressed in bio-oil liquefaction is potential corrosion issues in the process equipment. Depending on the specific process, bio-oil liquefaction production temperatures are typically in the 300-600 degrees C range, and the process environment can contain aggressive sulfur and halide species from both the biomass used and/or process additives. Detailed knowledge of the corrosion resistance of candidate process equipment alloys in these bio-oil production environments is currently lacking. This paper summarizes recent, ongoing efforts to assess the extent of corrosion of bio-oil process equipment, with the ultimate goal of providing a basis for the selection of the lowest cost alloy grades capable of providing the long-term corrosion resistance needed for future bio-oil production plants. C1 [Brady, M. P.; Keiser, J. R.; Leonard, D. N.; Thomson, J. K.] Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. [Whitmer, L.] Iowa State Univ, BioCentury Res Farm, Boone, IA 50036 USA. RP Brady, MP (reprint author), Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. EM bradymp@ornl.gov; keiserjr@ornl.gov RI Brady, Michael/A-8122-2008 OI Brady, Michael/0000-0003-1338-4747 FU U.S. Department of Energy's Bioenergy Technologies Office FX Component examinations were performed by Tyson Jordan (metallographic preparation and LM), Tracie Lowe (SEM), and Adam Willoughby (corrosion test sample design). Dane Wilson, Maggie Connatser, Bruce Pint, and Tim Theiss provided helpful comments on this manuscript. This research was funded by the U.S. Department of Energy's Bioenergy Technologies Office. NR 32 TC 2 Z9 2 U1 0 U2 23 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1047-4838 EI 1543-1851 J9 JOM-US JI JOM PD DEC PY 2014 VL 66 IS 12 BP 2583 EP 2592 DI 10.1007/s11837-014-1201-y PG 10 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing SC Materials Science; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing GA AU1RF UT WOS:000345397200027 ER PT J AU Antonaglia, J Xie, X Tang, Z Tsai, CW Qiao, JW Zhang, Y Laktionova, MO Tabachnikova, ED Carroll, R Yeh, JW Senkov, ON Gao, MC Uhl, JT Liaw, PK Dahmen, KA AF Antonaglia, J. Xie, X. Tang, Z. Tsai, C. -W. Qiao, J. W. Zhang, Y. Laktionova, M. O. Tabachnikova, E. D. Carroll, R. Yeh, J. W. Senkov, O. N. Gao, M. C. Uhl, J. T. Liaw, P. K. Dahmen, K. A. TI Temperature Effects on Deformation and Serration Behavior of High-Entropy Alloys (HEAs) (vol 66, pg 2002, 2014) SO JOM LA English DT Correction C1 [Antonaglia, J.; Carroll, R.; Dahmen, K. A.] Univ Illinois, Dept Phys, Urbana, IL 61801 USA. [Xie, X.; Tang, Z.; Liaw, P. K.] Univ Tennessee, Dept Mat Sci & Engn, Knoxville, TN 37996 USA. [Tsai, C. -W.; Yeh, J. W.] Natl Tsing Hua Univ, Dept Mat Sci & Engn, Hsinchu 30013, Taiwan. [Qiao, J. W.] Taiyuan Univ Technol, Coll Mat Sci & Engn, Taiyuan 030024, Peoples R China. [Zhang, Y.] Univ Sci & Technol Beijing, State Key Lab Adv Met & Mat, Beijing 100083, Peoples R China. [Laktionova, M. O.; Tabachnikova, E. D.] Natl Acad Sci Ukraine, BI Verkin Inst Low Temp Phys & Engn, UA-61103 Kharkov, Ukraine. [Senkov, O. N.] Air Force Res Lab, Mat & Mfg Directorate, Wright Patterson AFB, OH 45433 USA. [Gao, M. C.] Natl Energy Technol Lab, Albany, OR 97321 USA. [Gao, M. C.] USR Corp, Albany, OR 97321 USA. RP Antonaglia, J (reprint author), Univ Illinois, Dept Phys, Urbana, IL 61801 USA. EM dahmen@illinois.edu NR 1 TC 0 Z9 0 U1 3 U2 52 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1047-4838 EI 1543-1851 J9 JOM-US JI JOM PD DEC PY 2014 VL 66 IS 12 BP 2593 EP 2593 DI 10.1007/s11837-014-1190-x PG 1 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing SC Materials Science; Metallurgy & Metallurgical Engineering; Mineralogy; Mining & Mineral Processing GA AU1RF UT WOS:000345397200028 ER PT J AU Meyer, KM Tufts, JA Calfee, MW Oudejans, L AF Meyer, K. M. Tufts, J. A. Calfee, M. W. Oudejans, L. TI Efficacy of sporicidal wipes for inactivation of a Bacillus anthracis surrogate SO JOURNAL OF APPLIED MICROBIOLOGY LA English DT Article DE anthrax; Bacillus anthracis; Bacillus atrophaeus; biological agent; decontamination; sporicidal wipe ID CLOSTRIDIUM-DIFFICILE SPORES; MICROBICIDAL ACTIVITIES; ENVIRONMENTAL SURFACES; DISINFECTION METHODS; LABORATORY-SCALE; DECONTAMINATION; CONTAMINATION AB AimsTo evaluate five commercially available sporicidal wipes and two disinfecting wipes for their ability to inactivate Bacillus atrophaeus spores deposited onto various material surfaces. Methods and ResultsDecontamination efficacy of the wipes was initially tested on glass Petri dishes (150mm diameter). Following exposure for a specified time of contact, survival of the spores was assessed by quantification of the remaining viable spores, both on the coupon surface and on the towelette itself, with efficacy quantified in terms of mean log reduction. Based on these data, five wipes were down-selected for evaluation on a larger scale, using 36x36cm coupons of five different material types. ConclusionsResults suggest that sodium hypochlorite-based sporicidal wipes were most effective, having completely inactivated the Bacillus spores on the glass Petri dish and several materials. Additionally, results demonstrate that the manufacturer-prescribed contact times for Clostridium difficile achieved a 6 log(10) reduction of B.atrophaeus spores. Moreover, commercially available disinfecting wipes were not able to kill Bacillus spores as evaluated. Significance and Impact of the StudyThese data show the potential of sporicidal wipes for decontamination of small, contained areas of biological contamination and may help on-scene coordinators develop remediation plans following a biological terrorism event. C1 [Meyer, K. M.; Tufts, J. A.] Oak Ridge Inst Sci & Educ, Res Triangle Pk, NC USA. [Calfee, M. W.; Oudejans, L.] US EPA, Off Res & Dev, Natl Homeland Secur Res Ctr, Res Triangle Pk, NC 27711 USA. RP Oudejans, L (reprint author), US EPA, MD E343-06,109 TW Alexander Dr, Res Triangle Pk, NC 27711 USA. EM oudejans.lukas@epa.gov OI Calfee, Michael/0000-0001-6544-329X FU U.S. Department of Energy; EPA FX This research was supported in part by an appointment to the Research Participation Program for the U.S. Environmental Protection Agency, Office of Research and Development, administered by the Oak Ridge Institute for Science and Education through an interagency agreement between the U.S. Department of Energy and EPA. The authors gratefully acknowledge the critical reviews by Shannon Serre (EPA's Office of Research and Development on detail with EPA's Office of Emergency Management) and Frank Schaefer (EPA's Office of Research and Development). This manuscript has been subject to an administrative review; the views expressed here are those of the authors and do not reflect the view or policies of the Agency. No official endorsement should be inferred, as the EPA does not endorse the purchase or sale of any commercial products or services. NR 40 TC 2 Z9 2 U1 1 U2 19 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 1364-5072 EI 1365-2672 J9 J APPL MICROBIOL JI J. Appl. Microbiol. PD DEC PY 2014 VL 117 IS 6 BP 1634 EP 1644 DI 10.1111/jam.12648 PG 11 WC Biotechnology & Applied Microbiology; Microbiology SC Biotechnology & Applied Microbiology; Microbiology GA AU3JZ UT WOS:000345510300010 PM 25220421 ER PT J AU Harun, NF Tucker, D Adams, TA AF Harun, Nor Farida Tucker, David Adams, Thomas A., II TI Fuel Composition Transients in Fuel Cell Turbine Hybrid for Polygeneration Applications SO JOURNAL OF FUEL CELL SCIENCE AND TECHNOLOGY LA English DT Article ID POWER; FLEXIBILITY; HYDROGEN; SYSTEM; DESIGN AB Transient impacts on the performance of solid oxide fuel cell/gas turbine (SOFC/GT) hybrid systems were investigated using hardware-in-the-loop simulations (HiLSs) at a test facility located at the U. S. Department of Energy, National Energy Technology Laboratory. The work focused on applications relevant to polygeneration systems, which require significant fuel flexibility. Specifically, the dynamic response of implementing a sudden change in fuel composition from syngas to methane was examined. The maximum range of possible fuel composition allowable within the constraints of carbon deposition in the SOFC and stalling/surging of the turbine compressor system was determined. It was demonstrated that the transient response was significantly impact the fuel cell dynamic performance, which mainly drives the entire transient in SOFC/GT hybrid systems. This resulted in severe limitations on the allowable methane concentrations that could be used in the final fuel composition when switching from syngas to methane. Several system performance parameters were analyzed to characterize the transient impact over the course of 2 h from the composition change. C1 [Harun, Nor Farida; Adams, Thomas A., II] McMaster Univ, Dept Chem Engn, Hamilton, ON L8S 4L7, Canada. [Tucker, David] US DOE, Natl Energy Technol Lab, Morgantown, WV 26507 USA. RP Harun, NF (reprint author), McMaster Univ, Dept Chem Engn, 1280 Main St West, Hamilton, ON L8S 4L7, Canada. EM adfarimie@yahoo.com; David.Tucker@NETL.DOE.GOV; tadams@mcmaster.ca FU Universiti Teknologi Malaysia; Ministry of Higher Education Malaysia; U.S. Department of Energy (DOE) Crosscutting Research program FX The authors would like to thanks all people involved in this collaboration work between NETL and McMaster University, Paolo Pezzini and Nana Zhou from NETL for their contribution in the execution of the experimentation and also greatly acknowledge Universiti Teknologi Malaysia and Ministry of Higher Education Malaysia for the financial support. This work was funded by the U.S. Department of Energy (DOE) Crosscutting Research program, administered through the National Energy Technology Laboratory (NETL). NR 18 TC 2 Z9 2 U1 0 U2 2 PU ASME PI NEW YORK PA TWO PARK AVE, NEW YORK, NY 10016-5990 USA SN 1550-624X EI 1551-6989 J9 J FUEL CELL SCI TECH JI J. Fuel Cell Sci. Technol. PD DEC PY 2014 VL 11 IS 6 AR 061001 DI 10.1115/1.4028159 PG 8 GA AU2QL UT WOS:000345462800001 ER PT J AU Tsai, A Tucker, D Emami, T AF Tsai, Alex Tucker, David Emami, Tooran TI Adaptive Control of a Nonlinear Fuel Cell-Gas Turbine Balance of Plant Simulation Facility SO JOURNAL OF FUEL CELL SCIENCE AND TECHNOLOGY LA English DT Article AB A 300 kW solid oxide fuel cell gas turbine (SOFC-GT) power plant simulator is evaluated with the use of a model reference adaptive control (MRAC) scheme, implemented for a set of nonlinear empirical transfer functions. The SOFC-GT simulator allows testing of various fuel cell models under a hardware-in-the-loop configuration that incorporates a 120 kW auxiliary power unit and balance-of-plant components in hardware, and a fuel cell model in software. The adaptation technique is beneficial to plants having a wide range of operation, and strong coupling interaction. The practical implementation of the adaptive methodology is presented through simulation in the MATLAB/SIMULINK environment. C1 [Tsai, Alex; Emami, Tooran] US Coast Guard Acad, New London, CT 06320 USA. [Tucker, David] US DOE, Natl Energy Technol Lab, Morgantown, WV 26507 USA. RP Tsai, A (reprint author), US Coast Guard Acad, New London, CT 06320 USA. EM alex.j.tsai@gmail.com; david.tucker@netl.doe.gov; tooran.emami@uscga.edu NR 17 TC 4 Z9 4 U1 1 U2 5 PU ASME PI NEW YORK PA TWO PARK AVE, NEW YORK, NY 10016-5990 USA SN 1550-624X EI 1551-6989 J9 J FUEL CELL SCI TECH JI J. Fuel Cell Sci. Technol. PD DEC PY 2014 VL 11 IS 6 AR 061002 DI 10.1115/1.4028157 PG 8 GA AU2QL UT WOS:000345462800002 ER PT J AU Islam, TZ Bagchi, S Eigenmann, R AF Islam, Tanzima Zerin Bagchi, Saurabh Eigenmann, Rudolf TI Reliable and Efficient Distributed Checkpointing System for Grid Environments SO JOURNAL OF GRID COMPUTING LA English DT Article DE Checkpoint; Checkpointing; Recovery; Reliability; Cycle sharing system; FGCS; Condor; Efficient; Data parallel checkpointing; Erasure encoding; Checkpoint/Restart AB In Fine-Grained Cycle Sharing (FGCS) systems, machine owners voluntarily share their unused CPU cycles with guest jobs, as long as their performance degradation is tolerable. However, unpredictable evictions of guest jobs lead to fluctuating completion times. Checkpoint-recovery is an attractive mechanism for recovering from such "failures". Today's FGCS systems often use expensive, high-performance dedicated checkpoint servers. However, in geographically distributed clusters, this may incur high checkpoint transfer latencies. In this paper we present a distributed checkpointing system called Falcon that uses available disk resources of the FGCS machines as shared checkpoint repositories. However, an unavailable storage host may lead to loss of checkpoint data. Therefore, we model the failures of a storage host and develop a prediction algorithm for choosing reliable checkpoint repositories. We experiment with Falcon in the university-wide Condor testbed at Purdue and show improved and consistent performance for guest jobs in the presence of irregular resource availability. C1 [Islam, Tanzima Zerin] Lawrence Livermore Natl Lab, Livermore, CA 94551 USA. [Bagchi, Saurabh; Eigenmann, Rudolf] Lawrence Livermore Natl Lab, CASC, Livermore, CA 94551 USA. RP Islam, TZ (reprint author), Lawrence Livermore Natl Lab, Box 808,L-560, Livermore, CA 94551 USA. EM islam3@llnl.gov; sbagchi@purdue.edu; eigenman@purdue.edu FU National Science Foundation [0751153-CNS, 0707931-CNS, 0833115-CCF]; Purdue Research Foundation through a Special Initiative Research Grant (SIRG); U.S. Department of Energy by Lawrence Livermore National Laboratory [DE-AC52-07NA27344] FX We thank Mohammed Sayeed and Preston Smith of Rosen Center for Advanced Computing (RCAC) at Purdue for their help with BoilerGrid. We thank Mohammad Sajjad Hossain for the C version of the erasure encoding software. This work was supported, in part, by the National Science Foundation under grants No. 0751153-CNS, 0707931-CNS, and 0833115-CCF and by the Purdue Research Foundation through a Special Initiative Research Grant (SIRG). This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. Document #LLNL-JRNL-649440. NR 20 TC 1 Z9 1 U1 0 U2 4 PU SPRINGER PI DORDRECHT PA VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS SN 1570-7873 EI 1572-9184 J9 J GRID COMPUT JI J. Comput. PD DEC PY 2014 VL 12 IS 4 BP 593 EP 613 DI 10.1007/s10723-014-9297-4 PG 21 WC Computer Science, Information Systems; Computer Science, Theory & Methods SC Computer Science GA AU5DA UT WOS:000345626100002 ER PT J AU Endert, A Hossain, MS Ramakrishnan, N North, C Fiaux, P Andrews, C AF Endert, Alex Hossain, M. Shahriar Ramakrishnan, Naren North, Chris Fiaux, Patrick Andrews, Christopher TI The human is the loop: new directions for visual analytics SO JOURNAL OF INTELLIGENT INFORMATION SYSTEMS LA English DT Article DE Visual analytics; Clustering; Spatialization; Semantic interaction; Storytelling ID GENE-EXPRESSION DATA; VISUALIZATION; ALGORITHMS; NETWORKS; MODEL AB Visual analytics is the science of marrying interactive visualizations and analytic algorithms to support exploratory knowledge discovery in large datasets. We argue for a shift from a 'human in the loop' philosophy for visual analytics to a 'human is the loop' viewpoint, where the focus is on recognizing analysts' work processes, and seamlessly fitting analytics into that existing interactive process. We survey a range of projects that provide visual analytic support contextually in the sensemaking loop, and outline a research agenda along with future challenges. C1 [Endert, Alex] Pacific NW Natl Lab, Richland, WA 99352 USA. [Hossain, M. Shahriar] Univ Texas El Paso, Dept Comp Sci, El Paso, TX 79968 USA. [Ramakrishnan, Naren; North, Chris; Fiaux, Patrick] Virginia Tech, Dept Comp Sci, Blacksburg, VA 24060 USA. [Andrews, Christopher] Mt Holyoke Coll, Dept Comp Sci, S Hadley, MA 01075 USA. RP Ramakrishnan, N (reprint author), Virginia Tech, Dept Comp Sci, Blacksburg, VA 24060 USA. EM alex.endert@pnnl.gov; mhossain@utep.edu; naren@cs.vt.edu; north@cs.vt.edu; pfiaux@vt.edu; andrews@mtholyoke.edu FU Institute for Critical Technology and Applied Science, Virginia Tech; US National Science Foundation [CCF-0937133] FX This work is supported in part by the Institute for Critical Technology and Applied Science, Virginia Tech, and the US National Science Foundation through grant CCF-0937133. NR 75 TC 6 Z9 6 U1 0 U2 7 PU SPRINGER PI DORDRECHT PA VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS SN 0925-9902 EI 1573-7675 J9 J INTELL INF SYST JI J. Intell. Inf. Syst. PD DEC PY 2014 VL 43 IS 3 SI SI BP 411 EP 435 DI 10.1007/s10844-014-0304-9 PG 25 WC Computer Science, Artificial Intelligence; Computer Science, Information Systems SC Computer Science GA AU4OM UT WOS:000345590900002 ER PT J AU Jia, JY AF Jia, Jiangyong TI Event-shape fluctuations and flow correlations in ultra-relativistic heavy-ion collisions SO JOURNAL OF PHYSICS G-NUCLEAR AND PARTICLE PHYSICS LA English DT Article DE heavy ion collisions; event by event flow; event-shape fluctuations ID INITIAL-STATE FLUCTUATIONS; PB-PB COLLISIONS; PLANE CORRELATIONS; ANISOTROPIC FLOW; ROOT-S(NN)=2.76 TEV; NUCLEAR COLLISIONS; COLLECTIVE FLOW; VISCOSITY; ALICE AB I review recent measurements of a large set of flow observables associated with event-shape fluctuations and collective expansion in heavy ion collisions. First, these flow observables are classified and experiment methods are introduced. The experimental results for each type of observables are then presented and compared to theoretical calculations. A coherent picture of initial condition and collective flow based on linear and nonlinear hydrodynamic responses is derived, which qualitatively describe most experimental results. I discuss new types of fluctuation measurements that can further our understanding of the event- shape fluctuations and collective expansion dynamics. C1 [Jia, Jiangyong] SUNY Stony Brook, Dept Chem, Stony Brook, NY 11794 USA. [Jia, Jiangyong] Brookhaven Natl Lab, Dept Phys, Upton, NY 11796 USA. RP Jia, JY (reprint author), SUNY Stony Brook, Dept Chem, Stony Brook, NY 11794 USA. EM jjia@bnl.gov FU NSF [PHY-1305037]; DOE through BNL [DE-AC02-98CH10886] FX I appreciate fruitful discussions with S Mohapatra and comments from J Liao, B Schenke, R Snellings and F Wang. This research is supported by NSF under grant number PHY-1305037 and by DOE through BNL under grant number DE-AC02-98CH10886. NR 77 TC 15 Z9 15 U1 0 U2 7 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0954-3899 EI 1361-6471 J9 J PHYS G NUCL PARTIC JI J. Phys. G-Nucl. Part. Phys. PD DEC PY 2014 VL 41 IS 12 AR 124003 DI 10.1088/0954-3899/41/12/124003 PG 27 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA AU4FO UT WOS:000345565600006 ER PT J AU Kodama, T Stocker, H Xu, N AF Kodama, Takeshi Stocker, Horst Xu, Nu TI 40 years of collective flow in relativistic heavy ion collisions-the barometer for primordial hot and dense QCD matter SO JOURNAL OF PHYSICS G-NUCLEAR AND PARTICLE PHYSICS LA English DT Editorial Material ID NUCLEAR-MATTER; MODELS C1 [Kodama, Takeshi] Univ Fed Rio de Janeiro, BR-21941 Rio De Janeiro, Brazil. [Stocker, Horst] Goethe Univ Frankfurt, Frankfurt, Germany. [Xu, Nu] Cent China Normal Univ, Wuhan, Peoples R China. [Xu, Nu] Lawrence Berkeley Natl Lab, Berkeley, CA USA. RP Kodama, T (reprint author), Univ Fed Rio de Janeiro, BR-21941 Rio De Janeiro, Brazil. RI Kodama, Takeshi/H-2381-2011 OI Kodama, Takeshi/0000-0001-7718-9874 NR 24 TC 1 Z9 1 U1 0 U2 0 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0954-3899 EI 1361-6471 J9 J PHYS G NUCL PARTIC JI J. Phys. G-Nucl. Part. Phys. PD DEC PY 2014 VL 41 IS 12 AR 120301 DI 10.1088/0954-3899/41/12/120301 PG 3 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA AU4FO UT WOS:000345565600001 ER PT J AU Liu, J Ru, P Zhang, WN Wong, CY AF Liu, Jie Ru, Peng Zhang, Wei-Ning Wong, Cheuk-Yin TI Chaoticity parameter lambda in two-pion interferometry in an expanding boson gas model SO JOURNAL OF PHYSICS G-NUCLEAR AND PARTICLE PHYSICS LA English DT Article DE pion interferometry; source coherence; relativistic heavy ion collisions; Bose-Einstein condensation ID HEAVY-ION COLLISIONS AB We investigate the chaoticity parameter lambda in two-pion interferometry in an expanding boson gas model. The degree of Bose-Einstein condensation of identical pions, density distributions, and Hanbury-Brown-Twiss (HBT) correlation functions are calculated for expanding gas within the mean-field description with a harmonic oscillator potential. The results indicate that a source with thousands of identical pions may exhibit a degree of Bose-Einstein condensation at the temperatures encountered during the hadronic phase in relativistic heavy-ion collisions. This finite condensation may decrease the chaoticity parameter lambda in two-pion interferometry measurements at low pion-pair momenta, but influence only slightly the lambda value at high pion-pair momentum. C1 [Liu, Jie; Ru, Peng; Zhang, Wei-Ning] Dalian Univ Technol, Sch Phys & Optoelect Technol, Dalian 116024, Liaoning, Peoples R China. [Wong, Cheuk-Yin] Oak Ridge Natl Lab, Div Phys, Oak Ridge, TN 37831 USA. RP Liu, J (reprint author), Dalian Univ Technol, Sch Phys & Optoelect Technol, Dalian 116024, Liaoning, Peoples R China. EM wnzhang@dlut.edu.cn FU National Natural Science Foundation of China [11275037] FX This research was supported by the National Natural Science Foundation of China under Grant No. 11275037. NR 23 TC 1 Z9 1 U1 0 U2 6 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0954-3899 EI 1361-6471 J9 J PHYS G NUCL PARTIC JI J. Phys. G-Nucl. Part. Phys. PD DEC PY 2014 VL 41 IS 12 AR 125101 DI 10.1088/0954-3899/41/12/125101 PG 14 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA AU4FO UT WOS:000345565600016 ER PT J AU Ritter, HG Stock, R AF Ritter, Hans Georg Stock, Reinhard TI Collective flow of QCD matter: a historical introduction SO JOURNAL OF PHYSICS G-NUCLEAR AND PARTICLE PHYSICS LA English DT Article DE radial and non-isotropic flow; partonic hydrodynamics; event-by-event analysis ID HEAVY-ION COLLISIONS; RELATIVISTIC NUCLEAR COLLISIONS; QUARK-GLUON PLASMA; PLUS AU COLLISIONS; EQUATION-OF-STATE; ELLIPTIC FLOW; AU+AU COLLISIONS; CENTRALITY DEPENDENCE; AZIMUTHAL ANISOTROPY; HIGH-ENERGIES C1 [Ritter, Hans Georg] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Nucl Sci, Berkeley, CA 94720 USA. [Stock, Reinhard] Goethe Univ Frankfurt, Inst Nucl Phys, Frankfurt, Germany. [Stock, Reinhard] Goethe Univ Frankfurt, Frankfurt Inst Adv Studies, Frankfurt, Germany. RP Ritter, HG (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Nucl Sci, 1 Cyclotron Rd, Berkeley, CA 94720 USA. EM hgritter@lbl.gov; stock@ikf.uni-frankfurt.de FU Deutsche Forschungsgemeinschaft (DFG); office of NP within the US DOE Office of Science FX We would like to thank Julian Book for his invaluable contributions to realizing this manuscript. We thank Art Poskanzer and Alexander Schmah for valuable discussions and suggestions, and our referee from journal J. Phys. G for a critical reading, resulting in substantial revision. This work was supported in part by Deutsche Forschungsgemeinschaft (DFG), HIC for Fair and by the office of NP within the US DOE Office of Science. NR 124 TC 6 Z9 6 U1 0 U2 8 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0954-3899 EI 1361-6471 J9 J PHYS G NUCL PARTIC JI J. Phys. G-Nucl. Part. Phys. PD DEC PY 2014 VL 41 IS 12 AR 124002 DI 10.1088/0954-3899/41/12/124002 PG 36 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA AU4FO UT WOS:000345565600005 ER PT J AU Stratakis, D Neuffer, DV AF Stratakis, Diktys Neuffer, David V. TI Compact muon production and collection scheme for high-energy physics experiments SO JOURNAL OF PHYSICS G-NUCLEAR AND PARTICLE PHYSICS LA English DT Article DE muon source; muon accelerator; high-power target AB The relative immunity of muons to synchrotron radiation suggests that they might be used in place of electrons as probes in fundamental high-energy physics experiments. Muons are commonly produced indirectly through pion decay by interaction of a charged particle beam with a target. However, the large angle and energy dispersion of the initial beams as well as the short muon lifetime limits many potential applications. Here, we describe a fast method for manipulating the longitudinal and transverse phase-space of a divergent pion-muon beam to enable efficient capture and downstream transport with minimum losses. We also discuss the design of a handling system for the removal of unwanted secondary particles from the target region and thus reduce activation of the machine. The compact muon source we describe can be used for fundamental physics research in neutrino experiments. C1 [Stratakis, Diktys] Brookhaven Natl Lab, Upton, NY 11973 USA. [Neuffer, David V.] Fermilab Natl Accelerator Lab, Batavia, IL 60510 USA. RP Stratakis, D (reprint author), Brookhaven Natl Lab, Upton, NY 11973 USA. EM diktys@bnl.gov FU US Department of Energy [DE-AC02-98CH10886] FX The authors are grateful to J S Berg, H Kirk, H K Sayed, and R B Palmer for useful discussions. This work is supported by the US Department of Energy, Contract no. DE-AC02-98CH10886 NR 27 TC 0 Z9 0 U1 2 U2 6 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0954-3899 EI 1361-6471 J9 J PHYS G NUCL PARTIC JI J. Phys. G-Nucl. Part. Phys. PD DEC PY 2014 VL 41 IS 12 AR 125002 DI 10.1088/0954-3899/41/12/125002 PG 12 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA AU4FO UT WOS:000345565600012 ER PT J AU Tang, ZB Xu, N Zhou, K Zhuang, PF AF Tang, Zebo Xu, Nu Zhou, Kai Zhuang, Pengfei TI Charmonium transverse momentum distribution in high energy nuclear collisions SO JOURNAL OF PHYSICS G-NUCLEAR AND PARTICLE PHYSICS LA English DT Article DE quarkonium production; quark-gluon plasma; heavy ion collisions ID HEAVY-ION COLLISIONS; QUARK-GLUON PLASMA; PB-PB COLLISIONS; J/PSI-PRODUCTION; S-32-U COLLISIONS; MESON PRODUCTION; PP INTERACTIONS; CROSS-SECTIONS; ROOT-S=7 TEV; DRELL-YAN AB The charmonium transverse momentum distribution is more sensitive to the nature of the hot quantum chromodynamic matter created in high energy nuclear collisions compared with the yield. Taking a detailed transport approach for charmonium motion together with a hydrodynamic description for the medium evolution, the cancellation between the two hot nuclear matter effects, the dissociation and the regeneration, controls the charmonium transverse momentum distribution. In particular, the second moment of the distribution can be used to differentiate between the hot mediums produced at SPS, RHIC and LHC energies. C1 [Tang, Zebo] Univ Sci & Technol China, Dept Modern Phys, Hefei 230026, Peoples R China. [Xu, Nu] Cent China Normal Univ, Key Lab Quark & Lepton Phys MOE, Wuhan 430079, Peoples R China. [Xu, Nu] Cent China Normal Univ, Inst Particle Phys, Wuhan 430079, Peoples R China. [Xu, Nu] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Nucl Sci, Berkeley, CA 94720 USA. [Zhou, Kai; Zhuang, Pengfei] Tsinghua Univ, Dept Phys, Beijing 100084, Peoples R China. [Zhou, Kai; Zhuang, Pengfei] Collaborat Innovat Ctr Quantum Matter, Beijing 100084, Peoples R China. RP Tang, ZB (reprint author), Univ Sci & Technol China, Dept Modern Phys, Hefei 230026, Peoples R China. EM zhuangpf@mail.tsinghua.edu.cn OI Tang, Zebo/0000-0002-4247-0081 FU NSFC; MOST [11335005, 11221504, 2013CB922000, 2014CB845400]; DOE [DE-AC03-76SF00098] FX The work is supported by the NSFC and the MOST under grant nos. 11335005, 11221504, 2013CB922000, 2014CB845400, and the DOE under grant no. DE-AC03-76SF00098. NR 97 TC 5 Z9 5 U1 3 U2 20 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0954-3899 EI 1361-6471 J9 J PHYS G NUCL PARTIC JI J. Phys. G-Nucl. Part. Phys. PD DEC PY 2014 VL 41 IS 12 AR 124006 DI 10.1088/0954-3899/41/12/124006 PG 20 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA AU4FO UT WOS:000345565600009 ER PT J AU Rodriguez, JN Miller, MW Boyle, A Horn, J Yang, CK Wilson, TS Ortega, JM Small, W Nash, L Skoog, H Maitland, DJ AF Rodriguez, Jennifer N. Miller, Matthew W. Boyle, Anthony Horn, John Yang, Cheng-Kang Wilson, Thomas S. Ortega, Jason M. Small, Ward Nash, Landon Skoog, Hunter Maitland, Duncan J. TI Reticulation of low density shape memory polymer foam with an in vivo demonstration of vascular occlusion SO JOURNAL OF THE MECHANICAL BEHAVIOR OF BIOMEDICAL MATERIALS LA English DT Article ID ANEURYSMS; MODEL AB Predominantly closed-cell low density shape memory polymer (SMP) foam was recently reported to be an effective aneurysm filling device in a porcine model (Rodriguez et al., Journal of Biomedical Materials Research Part A 2013: (http://www.dx.doLorg/10.1002/jbm.a.34782)). Because healing involves blood clotting and cell migration throughout the foam volume, a more open-cell structure may further enhance the healing response. This research sought to develop a non-destructive reticulation process for this SMP foam to disrupt the membranes between pore cells. Non-destructive mechanical reticulation was achieved using a gravity-driven floating nitinol pin array coupled with vibratory agitation of the foam and supplemental chemical etching. Reticulation resulted in a reduced elastic modulus and increased permeability, but did not impede the shape memory behavior. Reticulated foams were capable of achieving rapid vascular occlusion in an in vivo porcine model. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Rodriguez, Jennifer N.; Boyle, Anthony; Horn, John; Nash, Landon; Skoog, Hunter; Maitland, Duncan J.] Texas A&M Univ, Dept Biomed Engn, College Stn, TX 77843 USA. [Wilson, Thomas S.; Ortega, Jason M.; Small, Ward] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. [Miller, Matthew W.] Texas A&M Univ, Texas Inst Preclin Studies, College Stn, TX 77845 USA. [Yang, Cheng-Kang] Texas A&M Univ, Dept Mech Engn, College Stn, TX 77843 USA. RP Maitland, DJ (reprint author), Texas A&M Univ, Dept Biomed Engn, MS 3120,5057 Emerging Technol Bldg, College Stn, TX 77843 USA. EM djmaitland@tamu.edu FU National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering [R01EB000462]; U.S. Department of Energy by Lawrence Livermore National Laboratory [DE-AC52-07NA27344] FX This work was supported by the National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering Grant R01EB000462 and partially performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. The authors would like to thank Carl Johnson and Todd Landsman for their assistance in fabrication of the reticulation devices. NR 12 TC 11 Z9 11 U1 5 U2 39 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 1751-6161 EI 1878-0180 J9 J MECH BEHAV BIOMED JI J. Mech. Behav. Biomed. Mater. PD DEC PY 2014 VL 40 BP 102 EP 114 DI 10.1016/j.jmbbm.2014.07.037 PG 13 WC Engineering, Biomedical; Materials Science, Biomaterials SC Engineering; Materials Science GA AU2SU UT WOS:000345468700011 PM 25222869 ER PT J AU Datta, MK Ramanathan, M Jampani, P Saha, P Epur, R Kadakia, K Chung, SJ Patel, P Gattu, B Manivannan, A Kumta, PN AF Datta, Moni Kanchan Ramanathan, Madhumati Jampani, Prashanth Saha, Partha Epur, Rigved Kadakia, Karan Chung, Sung Jae Patel, Prasad Gattu, Bharat Manivannan, Ayyakkannu Kumta, Prashant N. TI High energy mechano-chemical milling: Convenient approach to synthesis of LiMn1.5Ni0.5O4 high voltage cathode for lithium ion batteries SO MATERIALS SCIENCE AND ENGINEERING B-ADVANCED FUNCTIONAL SOLID-STATE MATERIALS LA English DT Article DE Nanostructured LiMn1.5Ni0.5O4; High energy mechanical milling; Li-ion batteries; High voltage cathode ID ELECTROCHEMICAL PROPERTIES; SPINEL CATHODES; RATE CAPABILITY; PERFORMANCE; LINI0.5MN1.5O4; STABILITY; STORAGE AB The high voltage spinel form of LiMn1.5Ni0.5O4 (LMNO) with a particle size similar to 10-40 nm has been synthesized for the first time using high energy mechanical milling (HEMM) followed by low temperature thermal treatments using Li2O, MnO2 and NiO as the starting precursors. The nanostructured LMNO cathode, synthesized by the simple, but effective HEMM process followed by thermal treatments to refine the structure in the temperature range similar to 573-1073 K, exhibits a reversible capacity similar to 120-110 mAh/g when cycled at a rate of similar to 20 mA/g in the potential window similar to 3.6-5.1 V. The electrochemical results are comparable to capacity values reported in the literature for LMNO derived using various other methods suggesting the efficacy of HEMM as an attractive and viable alternative approach for synthesizing battery grade high voltage spinel phase, LMNO. (c) 2014 Elsevier B.V. All rights reserved. C1 [Datta, Moni Kanchan; Ramanathan, Madhumati; Jampani, Prashanth; Saha, Partha; Epur, Rigved; Kadakia, Karan; Chung, Sung Jae; Patel, Prasad; Gattu, Bharat; Kumta, Prashant N.] Univ Pittsburgh, Swanson Sch Engn, Pittsburgh, PA 15261 USA. [Datta, Moni Kanchan; Kumta, Prashant N.] Univ Pittsburgh, Ctr Complex Engn Multifunct Mat, Pittsburgh, PA 15261 USA. [Manivannan, Ayyakkannu] US DOE, Natl Energy Technol Lab, Morgantown, WV 26507 USA. [Kumta, Prashant N.] Univ Pittsburgh, Sch Dent Med, Pittsburgh, PA 15261 USA. RP Datta, MK (reprint author), Univ Pittsburgh, Swanson Sch Engn, Pittsburgh, PA 15261 USA. EM mkd16@pitt.edu; pkumta@pitt.edu RI SAHA, PARTHA/D-5508-2011; Jampani Hanumantha, Prashanth/A-9840-2013 OI SAHA, PARTHA/0000-0002-0309-8387; Jampani Hanumantha, Prashanth/0000-0001-7159-1993 FU DOE-BATT (Batteries for Advanced Transportation Technology) program [DE-AC02-05CHl1231]; National Science Foundation [NSF-CBET-0933141]; Ford Foundation; Edward R. Weidlein Chair Professorship funds; Center for Complex Engineered Materials (CCEMM) FX The authors gratefully acknowledge the financial support of the DOE-BATT (Batteries for Advanced Transportation Technology) program (Contract DE-AC02-05CHl1231), the National Science Foundation (NSF-CBET-0933141) and partial support of the Ford Foundation. PNK also acknowledges the Edward R. Weidlein Chair Professorship funds and the Center for Complex Engineered Materials (CCEMM) administered by the Swanson School of Engineering, University of Pittsburgh for partial support of this research. NR 38 TC 1 Z9 1 U1 5 U2 39 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0921-5107 EI 1873-4944 J9 MATER SCI ENG B-ADV JI Mater. Sci. Eng. B-Adv. Funct. Solid-State Mater. PD DEC PY 2014 VL 190 BP 119 EP 125 DI 10.1016/j.mseb.2014.09.015 PG 7 WC Materials Science, Multidisciplinary; Physics, Condensed Matter SC Materials Science; Physics GA AU2UQ UT WOS:000345473300018 ER PT J AU Leishear, RA AF Leishear, Robert A. TI FROM WATER HAMMER TO IGNITION SO MECHANICAL ENGINEERING LA English DT Article C1 Savannah River Natl Lab, Aiken, SC 29803 USA. RP Leishear, RA (reprint author), Savannah River Natl Lab, Aiken, SC 29803 USA. NR 0 TC 0 Z9 0 U1 0 U2 1 PU ASME PI NEW YORK PA TWO PARK AVE, NEW YORK, NY 10016-5990 USA SN 0025-6501 EI 1943-5649 J9 MECH ENG JI Mech. Eng. PD DEC PY 2014 VL 136 IS 12 BP 44 EP 47 PG 4 WC Engineering, Mechanical SC Engineering GA AT9SN UT WOS:000345266500023 ER PT J AU Migdisov, AA Williams-Jones, AE AF Migdisov, Art A. Williams-Jones, A. E. TI Hydrothermal transport and deposition of the rare earth elements by fluorine-bearing aqueous liquids SO MINERALIUM DEPOSITA LA English DT Article ID MOLAL THERMODYNAMIC PROPERTIES; 500 DEGREES-C; STRANGE LAKE; ELEVATED-TEMPERATURES; NEODYMIUM(III) COMPLEXATION; ACTIVITY-COEFFICIENTS; CHLORIDE SOLUTIONS; HYDROFLUORIC-ACID; FLUID INCLUSION; QUEBEC LABRADOR AB New technologies, particularly those designed to address environmental concerns, have created a great demand for the rare earth elements (REE), and focused considerable attention on the processes by which they are concentrated to economically exploitable levels in the Earth's crust. There is widespread agreement that hydrothermal fluids played an important role in the formation of the world's largest economic REE deposit, i.e. Bayan Obo, China. Until recently, many researchers have assumed that hydrothermal transport of the REE in fluorine-bearing ore-forming systems occurs mainly due to the formation of REE-fluoride complexes. Consequently, hydrothermal models for REE concentration have commonly involved depositional mechanisms based on saturation of the fluid with REE minerals due to destabilization of REE-fluoride complexes. Here, we demonstrate that these complexes are insignificant in REE transport, and that the above models are therefore flawed. The strong association of H+ and F- as HF degrees and low solubility of REE-F solids greatly limit transport of the REE as fluoride complexes. However, this limitation does not apply to REE-chloride complexes. Because of this, the high concentration of Cl- in the ore fluids, and the relatively high stability of REE-chloride complexes, the latter can transport appreciable concentrations of REE at low pH. The limitation also does not apply to sulphate complexes and in some fluids, the concentration of sulphate may be sufficient to transport significant concentrations of REE as sulphate complexes, particularly at weakly acidic pH. This article proposes new models for hydrothermal REE deposition based on the transport of the REE as chloride and sulphate complexes. C1 [Migdisov, Art A.; Williams-Jones, A. E.] McGill Univ, Dept Earth & Planetary Sci, Montreal, PQ H3A 0E8, Canada. RP Migdisov, AA (reprint author), Los Alamos Natl Lab, Earth & Environm Div, MS J535,POB 1663, Los Alamos, NM 87545 USA. EM artas65@gmail.com OI Migdisov, Artaches/0000-0001-7734-2082 FU NSERC; FQRNT FX This research was made possible through grants from NSERC and FQRNT to AEW-J. The authors are grateful to D. Huston and three anonymous referees for their thoughtful and constructive reviews. NR 53 TC 28 Z9 28 U1 3 U2 45 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 0026-4598 EI 1432-1866 J9 MINER DEPOSITA JI Miner. Depos. PD DEC PY 2014 VL 49 IS 8 SI SI BP 987 EP 997 DI 10.1007/s00126-014-0554-z PG 11 WC Geochemistry & Geophysics; Mineralogy SC Geochemistry & Geophysics; Mineralogy GA AU1OZ UT WOS:000345391200006 ER PT J AU Gardner, JG Crouch, L Labourel, A Forsberg, Z Bukhman, YV Vaaje-Kolstad, G Gilbert, HJ Keating, DH AF Gardner, Jeffrey G. Crouch, Lucy Labourel, Aurore Forsberg, Zarah Bukhman, Yury V. Vaaje-Kolstad, Gustav Gilbert, Harry J. Keating, David H. TI Systems biology defines the biological significance of redox-active proteins during cellulose degradation in an aerobic bacterium SO MOLECULAR MICROBIOLOGY LA English DT Article ID CELL WALL DEGRADATION; LYTIC POLYSACCHARIDE MONOOXYGENASES; FLUORESCENS SUBSP CELLULOSA; CLOSTRIDIUM-THERMOCELLUM; CELLVIBRIO-JAPONICUS; ESCHERICHIA-COLI; CELLOBIOSE DEHYDROGENASE; NEUROSPORA-CRASSA; ENZYMES; OLIGOSACCHARIDES AB Microbial depolymerization of plant cell walls contributes to global carbon balance and is a critical component of renewable energy. The genomes of lignocellulose degrading microorganisms encode diverse classes of carbohydrate modifying enzymes, although currently there is a paucity of knowledge on the role of these proteins in vivo. We report the comprehensive analysis of the cellulose degradation system in the saprophytic bacterium Cellvibrio japonicus. Gene expression profiling of C. japonicus demonstrated that three of the 12 predicted -1,4 endoglucanases (cel5A, cel5B, and cel45A) and the sole predicted cellobiohydrolase (cel6A) showed elevated expression during growth on cellulose. Targeted gene disruptions of all 13 predicted cellulase genes showed that only cel5B and cel6A were required for optimal growth on cellulose. Our analysis also identified three additional genes required for cellulose degradation: lpmo10B encodes a lytic polysaccharide monooxygenase (LPMO), while cbp2D and cbp2E encode proteins containing carbohydrate binding modules and predicted cytochrome domains for electron transfer. CjLPMO10B oxidized cellulose and Cbp2D demonstrated spectral properties consistent with redox function. Collectively, this report provides insight into the biological role of LPMOs and redox proteins in cellulose utilization and suggests that C. japonicus utilizes a combination of hydrolytic and oxidative cleavage mechanisms to degrade cellulose. C1 [Gardner, Jeffrey G.] Univ Maryland Baltimore Cty, Dept Biol Sci, Baltimore, MD 21250 USA. [Crouch, Lucy; Labourel, Aurore; Gilbert, Harry J.] Newcastle Univ, Inst Cell & Mol Biosci, Newcastle Upon Tyne NE2 4HH, Tyne & Wear, England. [Forsberg, Zarah; Vaaje-Kolstad, Gustav] Norwegian Univ Life Sci NMBU, Dept Chem Biotechnol & Food Sci, N-1432 As, Norway. [Bukhman, Yury V.; Keating, David H.] Univ Wisconsin, DOE Great Lakes Bioenergy Res Ctr, Madison, WI 53706 USA. RP Gardner, JG (reprint author), Univ Maryland Baltimore Cty, Dept Biol Sci, 324 Biol Sci Bldg,1000 Hilltop Circle, Baltimore, MD 21250 USA. EM jgardner@umbc.edu; dkeating@glbrc.wisc.edu OI Bukhman, Yury/0000-0002-8111-7651 FU College of Natural and Mathematical Sciences at the University of Maryland Baltimore County; BBSRC; Norwegian Academy of Science and Letters Vista Program [6505]; Norwegian Research Council [214138]; US Department of Energy (DOE BER Office of Science) [DE-FC02-07ER64494] FX We thank R. Zinkel and I. Ong for assistance in transcriptomic sample processing and bioinformatic analysis respectively. We also thank Robert Landick for assistance with the design of the Roche Nimblegen Microarray. We thank James Moyer (University of York, UK) for providing us with the pST2 plasmid used to express the cbp2D and Achim Treumann for assistance with the mass spectrometry (NUPPA, Newcastle University, UK). JGG was supported by the College of Natural and Mathematical Sciences at the University of Maryland Baltimore County. HJG, LC and AL were supported by BBSRC funding. ZF and GV-K were supported by the Norwegian Academy of Science and Letters Vista Program Grant 6505 and the Norwegian Research Council grant 214138 respectively. Work at the GLBRC was supported by the US Department of Energy (DOE BER Office of Science DE-FC02-07ER64494). NR 43 TC 18 Z9 18 U1 4 U2 45 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 0950-382X EI 1365-2958 J9 MOL MICROBIOL JI Mol. Microbiol. PD DEC PY 2014 VL 94 IS 5 BP 1121 EP 1133 DI 10.1111/mmi.12821 PG 13 WC Biochemistry & Molecular Biology; Microbiology SC Biochemistry & Molecular Biology; Microbiology GA AU4PX UT WOS:000345595100009 ER PT J AU Goldman, N AF Goldman, Nir TI ACCELERATED REACTION SIMULATIONS A virtual squeeze on chemistry SO NATURE CHEMISTRY LA English DT News Item ID AMINO-ACIDS; EARLY EARTH; IMPACTS; ANALOGS C1 Lawrence Livermore Natl Lab, Div Mat Sci, Livermore, CA 94550 USA. RP Goldman, N (reprint author), Lawrence Livermore Natl Lab, Div Mat Sci, 7000 East Ave,L-288, Livermore, CA 94550 USA. EM goldman14@llnl.gov NR 9 TC 1 Z9 1 U1 1 U2 23 PU NATURE PUBLISHING GROUP PI LONDON PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND SN 1755-4330 EI 1755-4349 J9 NAT CHEM JI Nat. Chem. PD DEC PY 2014 VL 6 IS 12 BP 1033 EP 1034 DI 10.1038/nchem.2118 PG 3 WC Chemistry, Multidisciplinary SC Chemistry GA AU2EN UT WOS:000345429200004 PM 25411877 ER PT J AU Lai, YT Reading, E Hura, GL Tsai, KL Laganowsky, A Asturias, FJ Tainer, JA Robinson, CV Yeates, TO AF Lai, Yen-Ting Reading, Eamonn Hura, Greg L. Tsai, Kuang-Lei Laganowsky, Arthur Asturias, Francisco J. Tainer, John A. Robinson, Carol V. Yeates, Todd O. TI Structure of a designed protein cage that self-assembles into a highly porous cube SO NATURE CHEMISTRY LA English DT Article ID MACROMOLECULAR ASSEMBLIES; COMPUTATIONAL DESIGN; CRYSTAL-STRUCTURE; ESCHERICHIA-COLI; DNA; SYMMETRY; NANOMATERIALS; TRANSMISSION; OCTAHEDRON; COMPLEXES AB Natural proteins can be versatile building blocks for multimeric, self-assembling structures. Yet, creating protein-based assemblies with specific geometries and chemical properties remains challenging. Highly porous materials represent particularly interesting targets for designed assembly. Here, we utilize a strategy of fusing two natural protein oligomers using a continuous alpha-helical linker to design a novel protein that self assembles into a 750 kDa, 225 angstrom diameter, cubeshaped cage with large openings into a 130 angstrom diameter inner cavity. A crystal structure of the cage showed atomic-level agreement with the designed model, while electron microscopy, native mass spectrometry and small angle X-ray scattering revealed alternative assembly forms in solution. These studies show that accurate design of large porous assemblies with specific shapes is feasible, while further specificity improvements will probably require limiting flexibility to select against alternative forms. These results provide a foundation for the design of advanced materials with applications in bionanotechnology, nanomedicine and material sciences. C1 [Lai, Yen-Ting; Yeates, Todd O.] Univ Calif Los Angeles, UCLA DOE Inst Genom & Prote, Los Angeles, CA 90095 USA. [Reading, Eamonn; Laganowsky, Arthur; Robinson, Carol V.] Univ Oxford, Dept Chem, Oxford OX1 3QZ, England. [Hura, Greg L.; Tainer, John A.] Lawrence Berkeley Natl Lab, Berkeley, CA 94704 USA. [Hura, Greg L.] Univ Calif Santa Cruz, Dept Chem & Biochem, Santa Cruz, CA 95064 USA. [Tsai, Kuang-Lei; Asturias, Francisco J.; Tainer, John A.] Scripps Res Inst, Dept Integrat Struct & Computat Biol, La Jolla, CA 92037 USA. [Tainer, John A.] Scripps Res Inst, Skaggs Inst Chem Biol, La Jolla, CA 92037 USA. [Yeates, Todd O.] Univ Calif Los Angeles, Dept Chem & Biochem, Los Angeles, CA 90095 USA. [Yeates, Todd O.] Univ Calif Los Angeles, Calif Nanosyst Inst, Los Angeles, CA 90095 USA. RP Yeates, TO (reprint author), Univ Calif Los Angeles, UCLA DOE Inst Genom & Prote, Los Angeles, CA 90095 USA. EM yeates@mbi.ucla.edu OI Reading, Eamonn/0000-0001-8219-0052; Yeates, Todd/0000-0001-5709-9839 FU National Science Foundation [CHE-1332907]; Department of Energy Office of Science; National Institutes of Health (NIH) [R01GM067167]; Department of Energy [DE-AC02-05CH11231]; NIH MINOS [R01GM105404]; National Resource for Automated Macromolecular Microscopy (NRAMM) FX This work was supported by the National Science Foundation (grant CHE-1332907, T.O.Y.), the BER programme of the Department of Energy Office of Science, and the National Institutes of Health (NIH, grant R01GM067167, F. J. A.). The authors thank M. Sawaya, D. Cascio, D. McNamara and D. Leibly for X-ray data collection at the Advanced Photon Source (APS), the staff at APS beamline 24-ID-C and the National Resource for Automated Macromolecular Microscopy (NRAMM) for support. The authors thank D. Woolfson, N. King and members of the D. Baker laboratory for discussions and T. Goddard for advice on modelling in UCSF Chimera. SAXS data collection and analysis at BL12.3.1 at the Advanced Light Source (ALS) was supported by the Integrated Diffraction Analysis Technologies (IDAT) program (DOE/ BER), by the Department of Energy (contract DE-AC02-05CH11231) and by NIH MINOS (R01GM105404). NR 49 TC 49 Z9 49 U1 15 U2 133 PU NATURE PUBLISHING GROUP PI LONDON PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND SN 1755-4330 EI 1755-4349 J9 NAT CHEM JI Nat. Chem. PD DEC PY 2014 VL 6 IS 12 BP 1065 EP 1071 DI 10.1038/NCHEM.2107 PG 7 WC Chemistry, Multidisciplinary SC Chemistry GA AU2EN UT WOS:000345429200012 PM 25411884 ER PT J AU Ugeda, MM Bradley, AJ Shi, SF da Jornada, FH Zhang, Y Qiu, DY Ruan, W Mo, SK Hussain, Z Shen, ZX Wang, F Louie, SG Crommie, MF AF Ugeda, Miguel M. Bradley, Aaron J. Shi, Su-Fei da Jornada, Felipe H. Zhang, Yi Qiu, Diana Y. Ruan, Wei Mo, Sung-Kwan Hussain, Zahid Shen, Zhi-Xun Wang, Feng Louie, Steven G. Crommie, Michael F. TI Giant bandgap renormalization and excitonic effects in a monolayer transition metal dichalcogenide semiconductor SO NATURE MATERIALS LA English DT Article ID SINGLE-LAYER MOS2; QUASI-PARTICLE; VALLEY POLARIZATION; PHOTOLUMINESCENCE AB Two-dimensional (2D) transition metal dichalcogenides (TMDs) are emerging as a new platform for exploring 2D semiconductor physics(1-9). Reduced screening in two dimensions results in markedly enhanced electron-electron interactions, which have been predicted to generate giant bandgap renormalization and excitonic effects(10-13). Here we present a rigorous experimental observation of extraordinarily large exciton binding energy in a 2D semiconducting TMD. We determine the single-particle electronic bandgap of single-layer MoSe2 by means of scanning tunnelling spectroscopy (STS), as well as the two-particle exciton transition energy using photoluminescence (PL) spectroscopy. These yield an exciton binding energy of 0.55 eV for monolayer MoSe2 on graphene-orders of magnitude larger than what is seen in conventional 3D semiconductors and significantly higher than what we see for MoSe2 monolayers in more highly screening environments. This finding is corroborated by our ab initio GW and Bethe-Salpeter equation calculations(14,15) which include electron correlation effects. The renormalized bandgap and large exciton binding observed here will have a profound impact on electronic and optoelectronic device technologies based on single-layer semiconducting TMDs. C1 [Ugeda, Miguel M.; Bradley, Aaron J.; Shi, Su-Fei; da Jornada, Felipe H.; Qiu, Diana Y.; Ruan, Wei; Wang, Feng; Louie, Steven G.; Crommie, Michael F.] Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA. [da Jornada, Felipe H.; Qiu, Diana Y.; Wang, Feng; Louie, Steven G.; Crommie, Michael F.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Mat Sci, Berkeley, CA 94720 USA. [Zhang, Yi; Mo, Sung-Kwan; Hussain, Zahid] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA. [Zhang, Yi; Shen, Zhi-Xun] SLAC Natl Accelerator Lab, Stanford Inst Mat & Energy Sci, Menlo Pk, CA 94025 USA. [Ruan, Wei] Tsinghua Univ, Dept Phys, State Key Lab Low Dimens Quantum Phys, Beijing 100084, Peoples R China. [Shen, Zhi-Xun] Stanford Univ, Geballe Lab Adv Mat, Dept Phys, Stanford, CA 94305 USA. [Shen, Zhi-Xun] Stanford Univ, Dept Appl Phys, Stanford, CA 94305 USA. [Wang, Feng; Crommie, Michael F.] Univ Calif Berkeley, Kavli Energy NanoSci Inst, Berkeley, CA 94720 USA. [Wang, Feng; Crommie, Michael F.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Ugeda, MM (reprint author), Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA. EM mmugeda@berkeley.edu; crommie@berkeley.edu RI Zhang, Yi/J-9025-2013; Mo, Sung-Kwan/F-3489-2013; Moreno Ugeda, Miguel/N-3006-2016; wang, Feng/I-5727-2015 OI Zhang, Yi/0000-0003-1204-8717; Mo, Sung-Kwan/0000-0003-0711-8514; FU Office of Basic Energy Sciences, Department of Energy Early Career Award [DE-SC0003949]; sp2 Program (STM instrumentation development and operation); Theory Program (GW-BSE calculations); SciDAC Program on Excited State Phenomena in Energy Materials - US Department of Energy, Office of Basic Energy Sciences and of Advanced Scientific Computing Research [DE-AC02-05CH11231]; National Science Foundation [1235361, DMR10-1006184]; Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program; Chinese Scholarship Council [201306210202]; NSF Graduate Research Fellowship [DGE 1106400]; Simons Foundation Fellowship in Theoretical Physics FX Research supported by Office of Basic Energy Sciences, Department of Energy Early Career Award No. DE-SC0003949 (optical measurements), and by the sp2 Program (STM instrumentation development and operation), the Theory Program (GW-BSE calculations), and the SciDAC Program on Excited State Phenomena in Energy Materials (algorithms and codes) which are funded by the US Department of Energy, Office of Basic Energy Sciences and of Advanced Scientific Computing Research, under Contract No. DE-AC02-05CH11231. Support also provided by National Science Foundation award no. 1235361 (image analysis) and National Science Foundation award no. DMR10-1006184 (substrate screening theory and calculations). Computational resources have been provided by the NSF through XSEDE resources at NICS and DOE at NERSC. A.J.B. was supported by the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program. W. R acknowledges support from the Chinese Scholarship Council (No. 201306210202). D.Y.Q. acknowledges support from NSF Graduate Research Fellowship Grant No. DGE 1106400 and S.G.L. acknowledges support of a Simons Foundation Fellowship in Theoretical Physics. STM/STS data were analysed and rendered using WSxM software31. S-F.S. and F.W. acknowledge X. Hong and J. Kim for technical help. NR 31 TC 253 Z9 253 U1 89 U2 427 PU NATURE PUBLISHING GROUP PI LONDON PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND SN 1476-1122 EI 1476-4660 J9 NAT MATER JI Nat. Mater. PD DEC PY 2014 VL 13 IS 12 BP 1091 EP 1095 DI 10.1038/NMAT4061 PG 5 WC Chemistry, Physical; Materials Science, Multidisciplinary; Physics, Applied; Physics, Condensed Matter SC Chemistry; Materials Science; Physics GA AU2FQ UT WOS:000345432200009 PM 25173579 ER PT J AU Kappera, R Voiry, D Yalcin, SE Branch, B Gupta, G Mohite, AD Chhowalla, M AF Kappera, Rajesh Voiry, Damien Yalcin, Sibel Ebru Branch, Brittany Gupta, Gautam Mohite, Aditya D. Chhowalla, Manish TI Phase-engineered low-resistance contacts for ultrathin MoS2 transistors SO NATURE MATERIALS LA English DT Article ID SINGLE-LAYER MOS2; TRANSITION-METAL DICHALCOGENIDES; FIELD-EFFECT TRANSISTORS; LITHIUM INTERCALATION; MOLYBDENUM-DISULFIDE; MONOLAYER MOS2; TRANSPORT-PROPERTIES; INTEGRATED-CIRCUITS; RESTACKED MOS2; BILAYER MOS2 AB Ultrathin molybdenum disulphide (MoS2) has emerged as an interesting layered semiconductor because of its finite energy bandgap and the absence of dangling bonds. However, metals deposited on the semiconducting 2H phase usually form high-resistance (0.7 k Omega mu m-10 k Omega mu m) contacts, leading to Schottky-limited transport. In this study, we demonstrate that the metallic 1T phase of MoS2 can be locally induced on semiconducting 2H phase nanosheets, thus decreasing contact resistances to 200-300 Omega mu m at zero gate bias. Field-effect transistors (FETs) with 1T phase electrodes fabricated and tested in air exhibit mobility values of similar to 50 cm(2)V(-1)s(-1), subthreshold swing values below 100mV per decade, on/of ratios of >10(7), drive currents approaching similar to 100 mu A mu m(-1), and excellent current saturation. The deposition of different metals has limited influence on the FET performance, suggesting that the 1T/2H interface controls carrier injection into the channel. An increased reproducibility of the electrical characteristics is also obtained with our strategy based on phase engineering of MoS2. C1 [Kappera, Rajesh; Voiry, Damien; Chhowalla, Manish] Rutgers State Univ, Piscataway, NJ 08854 USA. [Yalcin, Sibel Ebru; Branch, Brittany; Gupta, Gautam; Mohite, Aditya D.] Los Alamos Natl Lab, MPA Mat Synth & Integrated Devices 11, Los Alamos, NM 87545 USA. RP Mohite, AD (reprint author), Los Alamos Natl Lab, MPA Mat Synth & Integrated Devices 11, POB 1663, Los Alamos, NM 87545 USA. EM amohite@lanl.gov; manish1@rci.rutgers.edu RI Voiry, Damien/G-3541-2016; OI Voiry, Damien/0000-0002-1664-2839; Kappera, Rajesh/0000-0003-1792-4405 FU NSF DGE [0903661]; NSF ECCS [1128335] FX M. C., R. K. and D. V. acknowledge financial support from NSF DGE 0903661 and NSF ECCS 1128335. R. K. acknowledges support and discussions with E. Garfunkel. We acknowledge T. Fujita for the EELS data and B. Yakshinskiy for NRA. This work was done in part at the Center for Integrated Nanotechnologies, an Office of Science User Facility. NR 54 TC 222 Z9 222 U1 90 U2 408 PU NATURE PUBLISHING GROUP PI LONDON PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND SN 1476-1122 EI 1476-4660 J9 NAT MATER JI Nat. Mater. PD DEC PY 2014 VL 13 IS 12 BP 1128 EP 1134 DI 10.1038/NMAT4080 PG 7 WC Chemistry, Physical; Materials Science, Multidisciplinary; Physics, Applied; Physics, Condensed Matter SC Chemistry; Materials Science; Physics GA AU2FQ UT WOS:000345432200015 PM 25173581 ER PT J AU Gong, YJ Lin, JH Wang, XL Shi, G Lei, SD Lin, Z Zou, XL Ye, GL Vajtai, R Yakobson, BI Terrones, H Terrones, M Tay, BK Lou, J Pantelides, ST Liu, Z Zhou, W Ajayan, PM AF Gong, Yongji Lin, Junhao Wang, Xingli Shi, Gang Lei, Sidong Lin, Zhong Zou, Xiaolong Ye, Gonglan Vajtai, Robert Yakobson, Boris I. Terrones, Humberto Terrones, Mauricio Tay, Beng Kang Lou, Jun Pantelides, Sokrates T. Liu, Zheng Zhou, Wu Ajayan, Pulickel M. TI Vertical and in-plane heterostructures from WS2/MoS2 monolayers SO NATURE MATERIALS LA English DT Article ID HEXAGONAL BORON-NITRIDE; MOLYBDENUM-DISULFIDE; LAYERED MATERIALS; GRAPHENE; GROWTH; WS2; ELECTRONICS; DIODES; WSE2 AB Layer-by-layer stacking or lateral interfacing of atomic monolayers has opened up unprecedented opportunities to engineer two-dimensional heteromaterials. Fabrication of such artificial heterostructures with atomically clean and sharp interfaces, however, is challenging. Here, we report a one-step growth strategy for the creation of high-quality vertically stacked as well as in-plane interconnected heterostructures ofWS(2)/MoS2 via control of the growth temperature. Vertically stacked bilayers with WS2 epitaxially grown on top of the MoS2 monolayer are formed with preferred stacking order at high temperature. A strong interlayer excitonic transition is observed due to the type II band alignment and to the clean interface of these bilayers. Vapour growth at low temperature, on the other hand, leads to lateral epitaxy of WS2 on MoS2 edges, creating seamless and atomically sharp in-plane heterostructures that generate strong localized photoluminescence enhancement and intrinsic p-n junctions. The fabrication of heterostructures from monolayers, using simple and scalable growth, paves the way for the creation of unprecedented two-dimensional materials with exciting properties. C1 [Gong, Yongji; Ajayan, Pulickel M.] Rice Univ, Dept Chem, Houston, TX 77005 USA. [Gong, Yongji; Shi, Gang; Lei, Sidong; Zou, Xiaolong; Ye, Gonglan; Vajtai, Robert; Yakobson, Boris I.; Lou, Jun; Ajayan, Pulickel M.] Rice Univ, Dept Mat Sci & NanoEngn, Houston, TX 77005 USA. [Lin, Junhao; Pantelides, Sokrates T.; Zhou, Wu] Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. [Lin, Junhao; Pantelides, Sokrates T.] Vanderbilt Univ, Dept Phys & Astron, Nashville, TN 37235 USA. [Wang, Xingli; Tay, Beng Kang; Liu, Zheng] Nanyang Technol Univ, Sch Mat Sci & Engn, Singapore 639798, Singapore. [Wang, Xingli; Tay, Beng Kang; Liu, Zheng] Nanyang Technol Univ, Sch Elect & Elect Engn, Singapore 639798, Singapore. [Lin, Zhong; Terrones, Mauricio] Penn State Univ, Dept Phys, University Pk, PA 16802 USA. [Lin, Zhong; Terrones, Mauricio] Penn State Univ, Ctr Dimens & Layered Mat 2, University Pk, PA 16802 USA. [Terrones, Humberto] Rensselaer Polytech Inst, Johnson Rowland Sci Ctr, Dept Phys Appl Phys & Astron, Troy, NY 12180 USA. [Terrones, Mauricio] Penn State Univ, Dept Chem, University Pk, PA 16802 USA. [Terrones, Mauricio] Penn State Univ, Dept Mat Sci & Engn, University Pk, PA 16802 USA. [Terrones, Mauricio] Penn State Univ, Inst Mat Res, University Pk, PA 16802 USA. RP Zhou, W (reprint author), Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. EM wu.zhou.stem@gmail.com; ajayan@rice.edu RI Liu, Zheng/C-1813-2014; Lin, Junhao/D-7980-2015; Lin, Zhong/O-4339-2014; Tay, Beng Kang/A-5077-2011; Zhou, Wu/D-8526-2011; Lei, Sidong/A-8600-2016; Gong, Yongji/L-7628-2016 OI Liu, Zheng/0000-0002-8825-7198; Lin, Junhao/0000-0002-2195-2823; Tay, Beng Kang/0000-0002-3776-3648; Zhou, Wu/0000-0002-6803-1095; Lei, Sidong/0000-0001-9129-2202; FU Army Research Office MURI grant [W911NF-11-1-0362]; US DOE grant [DE-FG02-09ER46554]; Wigner Fellowship through the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory (ORNL); FAME Center, one of six centres of STARnet, a Semiconductor Research Corporation program - MARCO; DARPA; US Office of Naval Research MURI grant [N000014-09-1-1066]; NSF grant [ECCS-1327093]; MOE Academic Research Fund (AcRF) Tier 1 project Singapore [RG81/12]; Si-COE project, Singapore; ORNL's Center for Nanophase Materials Sciences (CNMS) - Scientific User Facilities Division, Office of Basic Energy Sciences, US DOE; Office of Science of the US Department of Energy [DE-AC02-05CH11231]; Singapore National Research Foundation under NRF RF Award [NRF-RF2013-02]; Nanyang Technological University [M4081137.070] FX We thank A. Lupini for providing the script for STEM image quantification. This work was supported by the Army Research Office MURI grant W911NF-11-1-0362, US DOE grant DE-FG02-09ER46554 (J.L., S.T.P.), a Wigner Fellowship through the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory (ORNL), managed by UT-Battelle, LLC, for the US DOE (W.Z.), the FAME Center, one of six centres of STARnet, a Semiconductor Research Corporation program sponsored by MARCO and DARPA, the US Office of Naval Research MURI grant N000014-09-1-1066, NSF grant ECCS-1327093 and MOE Academic Research Fund (AcRF) Tier 1 RG81/12 project Singapore and Si-COE project, Singapore. This research was also supported through a user project supported by ORNL's Center for Nanophase Materials Sciences (CNMS), which is sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, US DOE. This research used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. This work was also supported by the Singapore National Research Foundation under NRF RF Award No. NRF-RF2013-02, the start-up funding from Nanyang Technological University (M4081137.070) NR 35 TC 350 Z9 351 U1 161 U2 729 PU NATURE PUBLISHING GROUP PI LONDON PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND SN 1476-1122 EI 1476-4660 J9 NAT MATER JI Nat. Mater. PD DEC PY 2014 VL 13 IS 12 BP 1135 EP 1142 DI 10.1038/NMAT4091 PG 8 WC Chemistry, Physical; Materials Science, Multidisciplinary; Physics, Applied; Physics, Condensed Matter SC Chemistry; Materials Science; Physics GA AU2FQ UT WOS:000345432200017 PM 25262094 ER PT J AU Li, YY El Gabaly, F Ferguson, TR Smith, RB Bartelt, NC Sugar, JD Fenton, KR Cogswell, DA Kilcoyne, ALD Tyliszczak, T Bazant, MZ Chueh, WC AF Li, Yiyang El Gabaly, Farid Ferguson, Todd R. Smith, Raymond B. Bartelt, Norman C. Sugar, Joshua D. Fenton, Kyle R. Cogswell, Daniel A. Kilcoyne, A. L. David Tyliszczak, Tolek Bazant, Martin Z. Chueh, William C. TI Current-induced transition from particle-by-particle to concurrent intercalation in phase-separating battery electrodes SO NATURE MATERIALS LA English DT Article ID ADVANCED LIGHT-SOURCE; DOMINO-CASCADE MODEL; SOFT-X-RAY; LIFEPO4 NANOPARTICLES; NONEQUILIBRIUM THERMODYNAMICS; POROUS-ELECTRODES; MISCIBILITY GAP; OLIVINE LIFEPO4; LITHIUM CELLS; ION BATTERIES AB Many battery electrodes contain ensembles of nanoparticles that phase-separate on (de) intercalation. In such electrodes, the fraction of actively intercalating particles directly impacts cycle life: a vanishing population concentrates the current in a small number of particles, leading to current hotspots. Reports of the active particle population in the phase-separating electrode lithium iron phosphate (LiFePO4; LFP) vary widely, ranging from near 0% (particle-by-particle) to 100% (concurrent intercalation). Using synchrotron-based X-ray microscopy, we probed the individual state-of-charge for over 3,000 LFP particles. We observed that the active population depends strongly on the cycling current, exhibiting particle-by-particle-like behaviour at low rates and increasingly concurrent behaviour at high rates, consistent with our phase-field porous electrode simulations. Contrary to intuition, the current density, or current per active internal surface area, is nearly invariant with the global electrode cycling rate. Rather, the electrode accommodates higher current by increasing the active particle population. This behaviour results from thermodynamic transformation barriers in LFP, and such a phenomenon probably extends to other phase-separating battery materials. We propose that modifying the transformation barrier and exchange current density can increase the active population and thus the current homogeneity. This could introduce new paradigms to enhance the cycle life of phase-separating battery electrodes. C1 [Li, Yiyang; Chueh, William C.] Stanford Univ, Dept Mat Sci & Engn, Stanford, CA 94305 USA. [El Gabaly, Farid; Bartelt, Norman C.; Sugar, Joshua D.] Sandia Natl Labs, Livermore, CA 94551 USA. [Ferguson, Todd R.; Smith, Raymond B.; Bazant, Martin Z.] MIT, Dept Chem Engn, Cambridge, MA 02139 USA. [Fenton, Kyle R.] Sandia Natl Labs, Albuquerque, NM 87185 USA. [Cogswell, Daniel A.] Samsung Adv Inst Technol Amer, Cambridge, MA 02142 USA. [Kilcoyne, A. L. David; Tyliszczak, Tolek] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA. [Bazant, Martin Z.] MIT, Dept Math, Cambridge, MA 02139 USA. [Chueh, William C.] Stanford Inst Mat & Energy Sci, Menlo Pk, CA 94025 USA. RP Chueh, WC (reprint author), Stanford Inst Mat & Energy Sci, Menlo Pk, CA 94025 USA. EM wchueh@stanford.edu RI Cogswell, Daniel/I-1740-2012; Kilcoyne, David/I-1465-2013 OI Cogswell, Daniel/0000-0001-8027-9635; FU Samsung Advanced Institute of Technology Global Research Outreach Program; Stanford School of Engineering and Precourt Institute for Energy; Samsung-MIT Program for Materials Design in Energy Applications; Office of Basic Energy Sciences, Division of Materials and Engineering Sciences, US Department of Energy [DE-AC04-94AL85000]; US Department of Energy through the Sandia Laboratory Directed Research and Development program [DE-AC04-94AL85000]; Office of Science, Office of Basic Energy Sciences, of the US Department of Energy [DE-AC02-05CH11231]; King Abdullah University of Science and Technology; National Science Foundation Graduate Research Fellowship [DGE-114747] FX The research at Stanford was supported by the Samsung Advanced Institute of Technology Global Research Outreach Program, and by startup funding from Stanford School of Engineering and Precourt Institute for Energy. Support for the research at MIT was provided by the Samsung-MIT Program for Materials Design in Energy Applications. F. E. G. and N.C.B. were supported by the Office of Basic Energy Sciences, Division of Materials and Engineering Sciences, US Department of Energy, under contract DE-AC04-94AL85000. J.D.S. and K. R. F. were supported by US Department of Energy through the Sandia Laboratory Directed Research and Development program under contract DE-AC04-94AL85000. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the US Department of Energy under Contract No. DE-AC02-05CH11231. Beam line 5.3.2.1 at the Advanced Light Source was funded through a donation by the King Abdullah University of Science and Technology. Y.L. was supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-114747. We acknowledge M. Homer of Sandia and J. Perrino of Stanford for ultramicrotoming. We thank J. Nelson Weker of the Stanford Synchrotron Radiation Lightsource for insightful discussions. NR 53 TC 50 Z9 50 U1 23 U2 217 PU NATURE PUBLISHING GROUP PI LONDON PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND SN 1476-1122 EI 1476-4660 J9 NAT MATER JI Nat. Mater. PD DEC PY 2014 VL 13 IS 12 BP 1149 EP 1156 DI 10.1038/NMAT4084 PG 8 WC Chemistry, Physical; Materials Science, Multidisciplinary; Physics, Applied; Physics, Condensed Matter SC Chemistry; Materials Science; Physics GA AU2FQ UT WOS:000345432200019 PM 25218062 ER PT J AU Ahn, JW Maingi, R Canik, JM Gan, KF Gray, TK McLean, AG AF Ahn, J. W. Maingi, R. Canik, J. M. Gan, K. F. Gray, T. K. McLean, A. G. TI Broadening of divertor heat flux profile with increasing number of ELM filaments in NSTX SO NUCLEAR FUSION LA English DT Article DE ELM filament; divertor heat flux; NSTX ID PEDESTAL; TOKAMAKS; PLASMAS AB Edge localized modes (ELMs) represent a challenge to future fusion devices, owing to cyclical high peak heat fluxes on divertor plasma facing surfaces. One ameliorating factor has been that the heat flux characteristic profile width has been observed to broaden with the size of the ELM, as compared with the inter-ELM heat flux profile. In contrast, the heat flux profile has been observed to narrow during ELMs under certain conditions in NSTX. Here we show that the ELM heat flux profile width increases with the number of filamentary striations observed, i.e. profile narrowing is observed with zero or very few striations. Because NSTX often lies on the long wavelength current-driven mode side of ideal MHD instabilities, few filamentary structures can be expected under many conditions. ITER is also projected to lie on the current driven low-n stability boundary, and therefore detailed projections of the unstable modes expected in ITER and the heat flux driven in ensuing filamentary structures is needed. C1 [Ahn, J. W.; Canik, J. M.; Gray, T. K.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. [Maingi, R.] Princeton Plasma Phys Lab, Princeton, NJ 08543 USA. [Gan, K. F.] Chinese Acad Sci, Inst Plasma Phys, Hefei, Peoples R China. [McLean, A. G.] Lawrence Livermore Natl Lab, Livermore, CA USA. RP Ahn, JW (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. EM jahn@pppl.gov OI Canik, John/0000-0001-6934-6681 FU U.S. Department of Energy [DE-AC05-00OR22725 (ORNL), DE-AC02-09CH11466 (PPPL), DE-AC52-07NA27344 (LLNL)]; National Magnetic Confinement Fusion Science Program of China [2011GB107001] FX This work was supported by the U.S. Department of Energy under contract DE-AC05-00OR22725 (ORNL), DE-AC02-09CH11466 (PPPL) and DE-AC52-07NA27344 (LLNL). K.F. Gan was supported by the National Magnetic Confinement Fusion Science Program of China under contract 2011GB107001. The authors acknowledge the international collaboration with CCFE and help from Drs A. Kirk and E. Delchambre that allowed us to install the original version of TACOfor the implementation at PPPL, and fruitful discussions with Dr Richard Pitts of the ITER Organization. NR 31 TC 2 Z9 2 U1 2 U2 16 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0029-5515 EI 1741-4326 J9 NUCL FUSION JI Nucl. Fusion PD DEC PY 2014 VL 54 IS 12 AR 122004 DI 10.1088/0029-5515/54/12/122004 PG 7 WC Physics, Fluids & Plasmas SC Physics GA AU4KN UT WOS:000345579800004 ER PT J AU Gorelenkov, NN Pinches, SD Toi, K AF Gorelenkov, N. N. Pinches, S. D. Toi, K. TI Energetic particle physics in fusion research in preparation for burning plasma experiments SO NUCLEAR FUSION LA English DT Review DE energetic particles; burning plasmas; toroidal fusion devices; Alfven instabilities ID TOROIDAL ALFVEN EIGENMODES; ION-CYCLOTRON EMISSION; JOINT EUROPEAN TORUS; LARGE HELICAL DEVICE; DEUTERIUM-TRITIUM EXPERIMENTS; KINETIC BALLOONING MODES; NEUTRAL BEAM INJECTION; DIII-D TOKAMAK; FAST MAGNETOACOUSTIC EIGENMODES; COLLECTIVE THOMSON SCATTERING AB The area of energetic particle (EP) physics in fusion research has been actively and extensively researched in recent decades. The progress achieved in advancing and understanding EP physics has been substantial since the last comprehensive review on this topic by Heidbrink and Sadler (1994 Nucl. Fusion 34 535). That review coincided with the start of deuterium-tritium (DT) experiments on the Tokamak Fusion Test Reactor (TFTR) and full scale fusion alphas physics studies. Fusion research in recent years has been influenced by EP physics in many ways including the limitations imposed by the 'sea' of Alfven eigenmodes (AEs), in particular by the toroidicity-induced AE (TAE) modes and reversed shear AEs (RSAEs). In the present paper we attempt a broad review of the progress that has been made in EP physics in tokamaks and spherical tori since the first DT experiments on TFTR and JET (Joint European Torus), including stellarator/helical devices. Introductory discussions on the basic ingredients of EP physics, i.e., particle orbits in STs, fundamental diagnostic techniques of EPs and instabilities, wave particle resonances and others, are given to help understanding of the advanced topics of EP physics. At the end we cover important and interesting physics issues related to the burning plasma experiments such as ITER (International Thermonuclear Experimental Reactor). C1 [Gorelenkov, N. N.] Princeton Univ, Princeton Plasma Phys Lab, Princeton, NJ 08543 USA. [Pinches, S. D.] ITER Org, F-13115 St Paul Les Durance, France. [Toi, K.] Natl Inst Nat Sci, Natl Inst Fus Sci, Toki, Gifu 5095292, Japan. RP Gorelenkov, NN (reprint author), Princeton Univ, Princeton Plasma Phys Lab, POB 451, Princeton, NJ 08543 USA. FU JSPS [21360457, 24360386]; U S DOE [DE-AC02-09CH11466] FX The work on this review is supported in part (KT) by the Grant-in-Aid for Scientific Research from JSPS (grant no's 21360457 and 24360386) and in part (NNG) under contract number DE-AC02-09CH11466 with the U S DOE. The views and opinions expressed herein do not necessarily reflect those of the ITER organization. NR 572 TC 43 Z9 45 U1 6 U2 54 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0029-5515 EI 1741-4326 J9 NUCL FUSION JI Nucl. Fusion PD DEC PY 2014 VL 54 IS 12 AR 125001 DI 10.1088/0029-5515/54/12/125001 PG 79 WC Physics, Fluids & Plasmas SC Physics GA AU4KN UT WOS:000345579800029 ER PT J AU Hahm, TS Lee, J Wang, WX Diamond, PH Choi, GJ Na, DH Na, YS Chung, KJ Hwang, YS AF Hahm, T. S. Lee, J. Wang, W. X. Diamond, P. H. Choi, G. J. Na, D. H. Na, Y. S. Chung, K. J. Hwang, Y. S. TI Turbulent equipartition pinch of toroidal momentum in spherical torus SO NUCLEAR FUSION LA English DT Article DE momentum transport; pinch; spherical torus ID TRANSPORT; TOKAMAKS; ROTATION AB We present a new analytic expression for turbulent equipartition (TEP) pinch of toroidal angular momentum originating from magnetic field inhomogeneity of spherical torus (ST) plasmas. Starting from a conservative modern nonlinear gyrokinetic equation (Hahm et al 1988 Phys. Fluids 31 2670), we derive an expression for pinch to momentum diffusivity ratio without using a usual tokamak approximation of B proportional to 1/R which has been previously employed for TEP momentum pinch derivation in tokamaks (Hahm et al 2007 Phys. Plasmas 14 072302). Our new formula is evaluated for model equilibria of National Spherical Torus eXperiment (NSTX) (Ono et al 2001 Nucl. Fusion 41 1435) and Versatile Experiment Spherical Torus (VEST) (Chung et al 2013 Plasma Sci. Technol. 15 244) plasmas. Our result predicts stronger inward pinch for both cases, as compared to the prediction based on the tokamak formula. C1 [Hahm, T. S.; Lee, J.; Choi, G. J.; Na, D. H.; Na, Y. S.; Chung, K. J.; Hwang, Y. S.] Seoul Natl Univ, Dept Nucl Engn, Seoul, South Korea. [Wang, W. X.] Princeton Plasma Phys Lab, Princeton, NJ 08543 USA. [Diamond, P. H.] NFRI, WCI Ctr Fus Theory, Taejon 305333, South Korea. [Diamond, P. H.] Univ Calif San Diego, CMTFO, La Jolla, CA 92093 USA. [Diamond, P. H.] Univ Calif San Diego, CASS, La Jolla, CA 92093 USA. RP Hahm, TS (reprint author), Seoul Natl Univ, Dept Nucl Engn, Seoul, South Korea. FU International Research & Development Program of the National Research Foundation of Korea(NRF) grant - Korea government(MSIP) [20110030459]; World Class Institute (WCI) Program of the National Research Foundation (NRF) - Ministry of Science, ICT & Future Planning (MSIP) [WCI-2009-0001]; National Research Foundation of Korea (NRF) grant - Korea government (MSIP) [20080061900]; Brain Korea 21 Plus Project [21A2013 0012821] FX This work was supported by the International Research & Development Program of the National Research Foundation of Korea(NRF) grant funded by the Korea government(MSIP) (No 20110030459), the World Class Institute (WCI) Program of the National Research Foundation (NRF) funded by the Ministry of Science, ICT & Future Planning (MSIP) (No. WCI-2009-0001) and the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIP) (No. 20080061900). In addition, this work was partly supported by the Brain Korea 21 Plus Project (No 21A2013 0012821). NR 35 TC 1 Z9 1 U1 0 U2 9 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0029-5515 EI 1741-4326 J9 NUCL FUSION JI Nucl. Fusion PD DEC PY 2014 VL 54 IS 12 AR 123012 DI 10.1088/0029-5515/54/12/123012 PG 4 WC Physics, Fluids & Plasmas SC Physics GA AU4KN UT WOS:000345579800018 ER PT J AU Melnikov, AV Ochando, M Ascasibar, E Castejon, F Cappa, A Eliseev, LG Hidalgo, C Krupnik, LI Lopez-Fraguas, A Liniers, M Lysenko, SE de Pablos, JL Perfilov, SV Sharapov, SE Spong, DA Jimenez, JA Ufimtsev, MV Breizman, BN AF Melnikov, A. V. Ochando, M. Ascasibar, E. Castejon, F. Cappa, A. Eliseev, L. G. Hidalgo, C. Krupnik, L. I. Lopez-Fraguas, A. Liniers, M. Lysenko, S. E. de Pablos, J. L. Perfilov, S. V. Sharapov, S. E. Spong, D. A. Jimenez, J. A. Ufimtsev, M. V. Breizman, B. N. CA HIBP Grp TJ-II Team TI Effect of magnetic configuration on frequency of NBI-driven Alfven modes in TJ-II SO NUCLEAR FUSION LA English DT Article DE stellarator; Alfven modes; rotational transformation ID MAGNETOHYDRODYNAMIC INSTABILITIES; WAVE CASCADES; T-10 TOKAMAK; STELLARATOR; PLASMAS; DIAGNOSTICS; EIGENMODES; ECRH AB Excitation of modes in the Alfvenic frequency range, 30 kHz < f(AE) < 300 kHz, was observed in hydrogen plasma heated by hydrogen neutral beam injection (NBI) in the TJ-II heliac. Co-field and counter-field NBI were injected, and the components of the poloidal magnetic field were varied one by one and in combinations, in order to investigate the beam-driven modes over an extended range of the rotational transform values, 1.51 < t(0) < 1.67. Taking advantage of the unique TJ-II capabilities, a dynamic magnetic configuration experiment with t(rho, t) variation during discharges has shown strong effects on the mode frequency via both vacuum t changes and induced net plasma current. A drastic frequency increase from similar to 50 to similar to 250 kHz was observed for some modes when plasma current as low as +/- 2 kA was induced by small (10%) changes in the vertical field. A comprehensive set of diagnostics including a heavy ion beam probe, magnetic probes and a multi-chord bolometer made it possible to identify the spatial spread of the modes and deduce the internal amplitudes of their plasma density and magnetic field perturbations. A simple analytical model for f(AE), based on the local Alfven eigenmode (AE) dispersion relation, was proposed to characterize the observation. It was shown that all the observations, including vacuum iota and plasma current variations, may be fitted by the model, so the linear mode frequency dependence on t (plasma current) and one over square root density dependence present the major features of the NBI-induced AEs in TJ-II, and provide the framework for further experiment-to-theory comparison. C1 [Melnikov, A. V.; Eliseev, L. G.; Lysenko, S. E.; Perfilov, S. V.] NRC Kurchatov Inst, Inst Tokamak Phys, Moscow 123182, Russia. [Melnikov, A. V.] Natl Res Nucl Univ MEPhI, Moscow 115409, Russia. [Ochando, M.; Ascasibar, E.; Castejon, F.; Cappa, A.; Hidalgo, C.; Lopez-Fraguas, A.; Liniers, M.; de Pablos, J. L.; Jimenez, J. A.] CIEMAT, Fus Natl Lab, E-28040 Madrid, Spain. [Krupnik, L. I.; HIBP Grp] NSC KIPT, Inst Plasma Phys, UA-310108 Kharkov, Ukraine. [Sharapov, S. E.] CCFE, Culham Sci Ctr, Abingdon OX14 3DB, Oxon, England. [Spong, D. A.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. [Ufimtsev, M. V.] Moscow MV Lomonosov State Univ, Dept Computat Math & Cybernet, Moscow, Russia. [Breizman, B. N.] Univ Texas Austin, Inst Fus Studies, Austin, TX 78712 USA. RP Melnikov, AV (reprint author), NRC Kurchatov Inst, Inst Tokamak Phys, Moscow 123182, Russia. EM melnikov_07@yahoo.com RI Jimenez, Juan/A-5245-2017; Liniers, Macarena/C-4593-2017; Hidalgo, Carlos/H-6109-2015; Lopez-Fraguas, Antonio/L-8104-2014; Cappa, Alvaro/C-5614-2017; Ascasibar, Enrique/B-7498-2014; OI Jimenez, Juan/0000-0003-3453-2470; Liniers, Macarena/0000-0003-2101-0112; Lopez-Fraguas, Antonio/0000-0002-0277-8137; Cappa, Alvaro/0000-0002-2250-9209; Ascasibar, Enrique/0000-0001-8124-0994; Castejon, Francisco/0000-0002-4654-0542 FU Spanish National Research Plan [ENE2012-38620-C02-01, STCU P-507]; RSCF [14-22-00193] FX The authors acknowledge the long-term cooperation between participating institutes, which was supported by the Spanish National Research Plan ref ENE2012-38620-C02-01 and STCU P-507.; The Kurchatov team warmly acknowledges the very important and timely support of RSCF. The detailed modelling, essential for this paper, was carried out by RSCF project no. 14-22-00193. NR 41 TC 8 Z9 8 U1 3 U2 6 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0029-5515 EI 1741-4326 J9 NUCL FUSION JI Nucl. Fusion PD DEC PY 2014 VL 54 IS 12 AR 123002 DI 10.1088/0029-5515/54/12/123002 PG 11 WC Physics, Fluids & Plasmas SC Physics GA AU4KN UT WOS:000345579800008 ER PT J AU Zhu, J Ma, ZW Fu, GY AF Zhu, J. Ma, Z. W. Fu, G. Y. TI Nonlinear frequency chirping of toroidal Alfven eigenmodes in tokamak plasmas SO NUCLEAR FUSION LA English DT Article DE frequency chirping; TAE; energetic particles; KAM surfaces; wave-particle interaction; hole-clump ID CLUMP PAIR CREATION; WAVES; INSTABILITY; PARTICLES; DRIVEN; MODES AB Nonlinear frequency chirping of toroidal Alfen eigenmodes (TAE) driven by energetic particles is investigated by kinetic simulations in toroidal plasmas. It is found that the up-down symmetry of the frequency chirping of a TAE is broken due to an anisotropic pitch-angle distribution with dominant co-passing energetic particles. The nonuniform distribution of the free energy associated with the initial energetic particle distribution causes biased driving forces that result in a strongly asymmetric frequency chirping. The evolution of the perturbed distribution function in the phase space shows that a hole-clump pair moves together towards the magnetic axis for the small pitch-angle parameter cases. The downward chirping of the mode frequency is associated with the negative drift of the phase island in the KAM surfaces or the resonance delta f structures in the radial direction. On the other hand, the energetic particle distribution with larger pitch-angle parameters leads to upward chirping of the TAE frequency. The upward chirping is due to the drifting of the resonance structure towards the boundary of the simulation region and overlapping of different poloidal resonances in the (Lambda, E) phase space at the late stage. The phase space dynamics provides a key mechanism for understanding the wave chirping direction and particle transport process. C1 [Zhu, J.; Ma, Z. W.] Zhejiang Univ, Inst Fus Theory & Simulat, Hangzhou 310027, Zhejiang, Peoples R China. [Fu, G. Y.] Princeton Univ, Princeton Plasma Phys Lab, Princeton, NJ 08543 USA. RP Zhu, J (reprint author), Zhejiang Univ, Inst Fus Theory & Simulat, Hangzhou 310027, Zhejiang, Peoples R China. EM zwma@zju.edu.cn FU National Natural Science Foundation of China [11175156, 41074105]; China ITER Program [2013GB104004, 2013GB111004]; US Department of Energy [DE-AC02-09CH11466] FX The authors would like to thank Professor Liu Chen and Professor Jiaqi Dong for helpful comments. This work is supported by the National Natural Science Foundation of China under Grants No 11175156 and 41074105, the China ITER Program under Grants No 2013GB104004 and 2013GB111004, and US Department of Energy under DE-AC02-09CH11466. NR 22 TC 2 Z9 2 U1 4 U2 6 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0029-5515 EI 1741-4326 J9 NUCL FUSION JI Nucl. Fusion PD DEC PY 2014 VL 54 IS 12 AR 123020 DI 10.1088/0029-5515/54/12/123020 PG 11 WC Physics, Fluids & Plasmas SC Physics GA AU4KN UT WOS:000345579800026 ER PT J AU Leclaire, N Duhamel, I Le Dauphin, FX Briggs, B Piot, J Rennesson, M Laville, A AF Leclaire, Nicolas Duhamel, Isabelle Le Dauphin, Francois-Xavier Briggs, Blair Piot, Jerome Rennesson, Malvina Laville, Arnaud TI The MIRTE Experimental Program: An Opportunity to Test Structural Materials in Various Configurations in Thermal Energy Spectrum SO NUCLEAR SCIENCE AND ENGINEERING LA English DT Article AB The MIRTE (Materials in Interacting and Reflecting configurations, all Thicknesses) program was established to answer the needs of criticality safety practitioners in terms of experimental validation of structural materials and to possibly contribute to nuclear data improvement, which ultimately supports reactor safety analysis as well. MIRTE took the shape of a collaboration between the AREVA and ANDRA French industrialists and a noncommercial international funding partner such as the U.S. Department of Energy. The aim of this paper is to present the configurations of the MIRTE 1 and MIRTE 2 programs and to highlight the results of the titanium experiments recently published in the International Handbook of Evaluated Criticality Safety Benchmark Experiments. C1 [Leclaire, Nicolas; Duhamel, Isabelle; Le Dauphin, Francois-Xavier] IRSN, F-92262 Fontenay Aux Roses, France. [Briggs, Blair] Idaho Natl Lab, Idaho Falls, ID 83415 USA. [Piot, Jerome] Commissariat Energie Atom & Energies Alternat CEA, Ctr Valduc, F-21120 Is Sur Tille, France. [Rennesson, Malvina] AREVA, Direct Rech & Innovat, Tour AREVA, F-92084 Paris, France. [Laville, Arnaud] ANDRA, F-92298 Chatenay Malabry, France. RP Leclaire, N (reprint author), IRSN, BP 17, F-92262 Fontenay Aux Roses, France. EM nicolas.leclaire@irsn.fr NR 12 TC 1 Z9 1 U1 0 U2 0 PU AMER NUCLEAR SOC PI LA GRANGE PK PA 555 N KENSINGTON AVE, LA GRANGE PK, IL 60526 USA SN 0029-5639 EI 1943-748X J9 NUCL SCI ENG JI Nucl. Sci. Eng. PD DEC PY 2014 VL 178 IS 4 BP 429 EP 445 PG 17 WC Nuclear Science & Technology SC Nuclear Science & Technology GA AU3FA UT WOS:000345496700002 ER PT J AU Marshall, MA AF Marshall, Margaret A. TI Reactor Physics Measurements and Benchmark Specifications for Oak Ridge Highly Enriched Uranium Sphere (ORSphere) SO NUCLEAR SCIENCE AND ENGINEERING LA English DT Article ID DELAYED NEUTRON FRACTION; NUCLEAR-DATA LIBRARY; METAL SPHERES; PLUTONIUM; FISSION AB In the early 1970s, J. T. Mihalczo (team leader), J. J. Lynn, and J. R. Taylor performed experiments at the Oak Ridge Critical Experiments Facility with highly enriched uranium (HEU) metal (called Oak Ridge Alloy or ORALLOY) in an effort to recreate GODIVA I results with greater accuracy than those performed at Los Alamos National Laboratory in the 1950s. The purpose of the Oak Ridge ORALLOY Sphere experiments was to estimate the unreflected and unmoderated critical mass of an idealized sphere of uranium metal corrected to a density, purity, and enrichment such that it could be compared with the GODIVA I experiments. Additionally, various material reactivity worths, the surface material worth coefficient, the delayed neutron fraction, the prompt neutron decay constant, relative fission density, and relative neutron importance were all measured. The critical assembly, material reactivity worths, the surface material worth coefficient, and the delayed neutron fraction were all evaluated as benchmark experiment measurements. The reactor physics measurements are the focus of this paper; although for clarity the critical assembly benchmark specifications are briefly discussed. C1 Idaho Natl Lab, Idaho Falls, ID 83415 USA. RP Marshall, MA (reprint author), Idaho Natl Lab, 2525 North Fremont, Idaho Falls, ID 83415 USA. EM margaret.marshall@inl.gov NR 22 TC 0 Z9 0 U1 1 U2 3 PU AMER NUCLEAR SOC PI LA GRANGE PK PA 555 N KENSINGTON AVE, LA GRANGE PK, IL 60526 USA SN 0029-5639 EI 1943-748X J9 NUCL SCI ENG JI Nucl. Sci. Eng. PD DEC PY 2014 VL 178 IS 4 BP 446 EP 458 PG 13 WC Nuclear Science & Technology SC Nuclear Science & Technology GA AU3FA UT WOS:000345496700003 ER PT J AU Marshall, MA AF Marshall, Margaret A. TI Evaluation of Cadmium Ratio and Foil Activation Measurements for a Beryllium-Reflected Assembly of U(93.15)O-2 Fuel Rods (1.506-cm Triangular Pitch) SO NUCLEAR SCIENCE AND ENGINEERING LA English DT Article ID NUCLEAR-DATA LIBRARY AB A series of small, compact critical assembly experiments was completed from 1962 to 1965 at Oak Ridge National Laboratory's Critical Experiments Facility in support of the Medium-Power Reactor Experiments program. Initial experiments, performed in November and December 1962, consisted of a core of unmoderated stainless steel tubes surrounded by a graphite reflector. Later experiments included beryllium-reflected assemblies with the fuel in a 1.506-cm triangular lattice and in seven-tube clusters. Once the critical configurations had been achieved, various measurements of reactivity, relative axial and radial activation rates of U-235, and cadmium ratios were performed. The critical configurations, the cadmium ratio, and activation rate measurements for the beryllium-reflected 1.506-cm-array critical configuration have been evaluated and are described in this paper. It was found that these measurements are acceptable as benchmark experiments and have been included in the International Handbook of Evaluated Reactor Physics Benchmark Experiments and the International Handbook of Evaluated Criticality Safety Benchmark Experiments. C1 Idaho Natl Lab, Idaho Falls, ID 83415 USA. RP Marshall, MA (reprint author), Idaho Natl Lab, 2525 North Fremont Ave, Idaho Falls, ID 83415 USA. EM margaret.marshall@inl.gov NR 16 TC 0 Z9 0 U1 0 U2 0 PU AMER NUCLEAR SOC PI LA GRANGE PK PA 555 N KENSINGTON AVE, LA GRANGE PK, IL 60526 USA SN 0029-5639 EI 1943-748X J9 NUCL SCI ENG JI Nucl. Sci. Eng. PD DEC PY 2014 VL 178 IS 4 BP 479 EP 495 PG 17 WC Nuclear Science & Technology SC Nuclear Science & Technology GA AU3FA UT WOS:000345496700005 ER PT J AU Snoj, L Kodeli, I Remec, I AF Snoj, Luka Kodeli, Ivan Remec, Igor TI Evaluation of the KRITZ-2 Criticality and Reaction Rate Benchmark Experiments SO NUCLEAR SCIENCE AND ENGINEERING LA English DT Article AB A complete evaluation of the experimental uncertainties of the KRITZ-2 series of critical and relative fission rate experiments was performed within the International Reactor Physics Experiment Evaluation Project. The uncertainties in the benchmark model k(eff) are mainly due to uranium enrichment, plutonium content [mixed oxide (MOX) fuel], pitch, and boron isotopic composition. The largest contribution to the uncertainty in the benchmark model k(eff) is from the uncertainty in the bias due to the homogenization of the particulate MOX fuel. In addition, uncertainties due to nuclear data libraries are presented. The k(eff)'s calculated with various nuclear data libraries systematically under predict the benchmark model k(eff) by one to three times the standard experimental uncertainties. When taking into account uncertainties in nuclear data estimated using SCALE-6.0 and JENDL-4.0m covariances, the benchmark and calculated k(eff)'s agree within 1 sigma of the total-experimental plus calculational-uncertainties. In contrast to the criticality benchmark data, the calculated relative fission rates agree very well with the experimental ones, especially when eliminating systematic errors due to normalization. C1 [Snoj, Luka; Kodeli, Ivan] Jozef Stefan Inst, Reactor Phys Div F8, SI-1000 Ljubljana, Slovenia. [Remec, Igor] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. RP Snoj, L (reprint author), Jozef Stefan Inst, Reactor Phys Div F8, Jamova Cesta 39, SI-1000 Ljubljana, Slovenia. EM luka.snoj@ijs.si OI Snoj, Luka/0000-0003-3097-5928 NR 22 TC 1 Z9 1 U1 0 U2 3 PU AMER NUCLEAR SOC PI LA GRANGE PK PA 555 N KENSINGTON AVE, LA GRANGE PK, IL 60526 USA SN 0029-5639 EI 1943-748X J9 NUCL SCI ENG JI Nucl. Sci. Eng. PD DEC PY 2014 VL 178 IS 4 BP 496 EP 508 PG 13 WC Nuclear Science & Technology SC Nuclear Science & Technology GA AU3FA UT WOS:000345496700006 ER PT J AU Bess, JD Maddock, TL Smolinski, AT Marshall, MA AF Bess, John D. Maddock, Thomas L. Smolinski, Andrew T. Marshall, Margaret A. TI Evaluation of Neutron Radiography Reactor LEU-Core Start-Up Measurements SO NUCLEAR SCIENCE AND ENGINEERING LA English DT Article ID II BENCHMARK EXPERIMENT; CARLO CODE MCNP; MONTE-CARLO AB Benchmark models were developed to evaluate the cold-critical start-up measurements performed during the fresh core reload of the neutron radiography (NRAD) reactor with low-enriched uranium fuel. Experiments include criticality, control rod worth measurements, shutdown margin, and excess reactivity for four core loadings with 56, 60, 62, and 64 fuel elements. The worths of four graphite reflector block assemblies and an empty dry tube used for experiment irradiations were also measured and evaluated for the 60-fuel-element core configuration. Dominant uncertainties in the experimental k(eff) come from uncertainties in the manganese content and impurities in the stainless steel fuel cladding as well as the U-236 and erbium poison content in the fuel matrix. Calculations with MCNP5 (Monte Carlo N-Particle version 5-1.60) and ENDF/B-VII.0 neutron nuclear data are similar to 1.4% (9 sigma) greater than the benchmark model eigenvalues, which is commonly seen in Monte Carlo simulations of other TRIGA (Training, Research, Isotopes, General Atomics) reactors. Simulations of the worth measurements are within the 2 sigma uncertainty for most of the benchmark experiment worth values. The complete benchmark evaluation details are available in the 2014 edition of the International Handbook of Evaluated Reactor Physics Benchmark Experiments. C1 [Bess, John D.; Maddock, Thomas L.; Smolinski, Andrew T.; Marshall, Margaret A.] Idaho Natl Lab, Idaho Falls, ID 83415 USA. RP Bess, JD (reprint author), Idaho Natl Lab, POB 1625,MS 3855, Idaho Falls, ID 83415 USA. EM john.bess@inl.gov RI Smolinski, Andrew/C-5979-2017 OI Bess, John/0000-0002-4936-9103; Smolinski, Andrew/0000-0002-3774-9467 FU U.S. Department of Energy [DE-AC07-05ID14517] FX The authors would like to thank L. Montierth, N. Zhang, A. M. Phillips, K. Schreck, B. Briggs, and E. Woolstenhulme from INL; J. Bolin and A. Veca from General Atomics; and R. McKnight and R. Lell from Argonne National Laboratory for their review and support in developing a comprehensive benchmark evaluation. Additional gratitude is expressed to C. White from INL for generating graphical representations. Further appreciation is expressed to all the international participants in the International Reactor Physics Experiment Evaluation Project for all their well-spent time and effort. This paper was prepared at INL for the U.S. Department of Energy under contract DE-AC07-05ID14517. NR 24 TC 0 Z9 0 U1 1 U2 1 PU AMER NUCLEAR SOC PI LA GRANGE PK PA 555 N KENSINGTON AVE, LA GRANGE PK, IL 60526 USA SN 0029-5639 EI 1943-748X J9 NUCL SCI ENG JI Nucl. Sci. Eng. PD DEC PY 2014 VL 178 IS 4 BP 550 EP 561 PG 12 WC Nuclear Science & Technology SC Nuclear Science & Technology GA AU3FA UT WOS:000345496700010 ER PT J AU Poston, DI McClure, PR Dixon, DD Gibson, MA Mason, LS AF Poston, David I. McClure, Patrick R. Dixon, David D. Gibson, Marc A. Mason, Lee S. TI EXPERIMENTAL DEMONSTRATION OF A HEAT PIPE-STIRLING ENGINE NUCLEAR REACTORLE SO NUCLEAR TECHNOLOGY LA English DT Article DE space nuclear power; heat pipe reactor; fission power system AB Los Alamos National Laboratory and Glenn Research Center with the help of National Security Technologies demonstrated the use of a nuclear fission system as a power source that transferred heat via a water-based heat pipe to a small Stirling engine-based power converter to produce electricity. This experimental setup demonstrated that a small reactor based on heat pipes and Stirling engines is possible and produces a system with well-characterized nuclear feedback between the reactor and the power conversion system. This paper describes the experimental setup, modeling of the system, and results that confirm the basic physics of the experiment. C1 [Poston, David I.; McClure, Patrick R.; Dixon, David D.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. [Gibson, Marc A.; Mason, Lee S.] Glenn Res Ctr, Natl Aeronaut & Space Adm, Cleveland, OH 44135 USA. RP Poston, DI (reprint author), Los Alamos Natl Lab, POB 1663, Los Alamos, NM 87545 USA. EM poston@lanl.gov NR 11 TC 2 Z9 2 U1 0 U2 3 PU AMER NUCLEAR SOC PI LA GRANGE PK PA 555 N KENSINGTON AVE, LA GRANGE PK, IL 60526 USA SN 0029-5450 EI 1943-7471 J9 NUCL TECHNOL JI Nucl. Technol. PD DEC PY 2014 VL 188 IS 3 BP 229 EP 237 PG 9 WC Nuclear Science & Technology SC Nuclear Science & Technology GA AU3CC UT WOS:000345489400001 ER PT J AU George, NM Maldonado, I Terrani, K Godfrey, A Gehin, J Powers, J AF George, Nathan Michael Maldonado, Ivan Terrani, Kurt Godfrey, Andrew Gehin, Jess Powers, Jeff TI NEUTRONICS STUDIES OF URANIUM-BEARING FULLY CERAMIC MICROENCAPSULATED FUEL FOR PRESSURIZED WATER REACTORS SO NUCLEAR TECHNOLOGY LA English DT Article DE fully ceramic microencapsulated; TRISO; uranium mononitride ID ANALYSIS CAPABILITIES; SCALE AB This study evaluated the neutronics and some of the fuel cycle characteristics of using uranium-based fully ceramic microencapsulated (FCM) fuel in a pressurized water reactor (PWR). Specific PWR lattice designs with FCM fuel have been developed that are expected to achieve higher specific burnup levels in the fuel while also increasing the tolerance to reactor accidents. The SCALE software system was the primary analysis tool used to model the lattice designs. A parametric study was peiformed by varying tristructural isotropic particle design features (e.g., kernel diameter, coating layer thicknesses, and packing fraction) to understand the impact on reactivity and resulting operating cycle length. To match the lifetime of an 18month PWR cycle, the FCM particle fuel design required roughly 10% additional fissile material at beginning of life compared with that of a standard uranium dioxide (UO2) rod. Uranium mononitride proved to be a favorable fuel for the fuel kernel due to its higher heavy metal loading density compared with UO2. The FCM fuel designs evaluated maintain acceptable neutronics design features for fuel lifetime, lattice peaking factors, and nonproliferation figure of merit. C1 [George, Nathan Michael; Maldonado, Ivan] Univ Tennessee, Dept Nucl Engn, Knoxville, TN 37996 USA. [Terrani, Kurt; Godfrey, Andrew; Gehin, Jess; Powers, Jeff] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. RP George, NM (reprint author), Univ Tennessee, Dept Nucl Engn, Knoxville, TN 37996 USA. EM ngeorge3@utk.edu OI Gehin, Jess/0000-0001-8337-9551; Powers, Jeffrey/0000-0003-3653-3880 FU UT-Battelle, LLC [DE-ACO5-000R22725]; Advanced Fuels Campaign of the Fuel Cycle Research and Development program in the DOE Office of Nuclear Energy FX This manuscript has been authored by UT-Battelle, LLC, under contract DE-ACO5-000R22725 with the U.S. Department of Energy (DOE). This work was supported by the Advanced Fuels Campaign of the Fuel Cycle Research and Development program in the DOE Office of Nuclear Energy. NR 21 TC 2 Z9 2 U1 0 U2 8 PU AMER NUCLEAR SOC PI LA GRANGE PK PA 555 N KENSINGTON AVE, LA GRANGE PK, IL 60526 USA SN 0029-5450 EI 1943-7471 J9 NUCL TECHNOL JI Nucl. Technol. PD DEC PY 2014 VL 188 IS 3 BP 238 EP 251 PG 14 WC Nuclear Science & Technology SC Nuclear Science & Technology GA AU3CC UT WOS:000345489400002 ER PT J AU Scaglione, JM Mueller, DE Wagner, JC AF Scaglione, J. M. Mueller, D. E. Wagner, J. C. TI AN APPROACH FOR VALIDATING ACTINIDE AND FISSION PRODUCT BURNUP CREDIT CRITICALITY SAFETY ANALYSES: CRITICALITY (k(eff)) PREDICTIONS SO NUCLEAR TECHNOLOGY LA English DT Article DE criticality; bumup; validation AB One of the most significant remaining challenges associated with expanded implementation of burnup credit in the United States is the validation of depletion and criticality calculations used in the safety evaluation in particular, the availability and use of applicable measured data to support validation, especially for fission products (FP s). Applicants and regulatory reviewers have been constrained by both a scarcity of data and a lack of clear technical basis or approach for use of the data. This paper describes a validation approach for commercial spent nuclear fuel (SNF) criticality safety (k(eff)) evaluations based on best-available data and methods and applies the approach for representative SNF storage and transport configurations/ conditions to demonstrate its usage and applicability, as well as to provide reference bias results. The criticality validation approach utilizes not only available laboratory critical experiment (LCE) data from the International Handbook of Evaluated Criticality Safety Benchmark Experiments and the French Haut Taux de Combustion program to support validation of the principal actinides but also calculated sensitivities, nuclear data uncertainties, and limited available FP LCE data to predict w and verify individual biases for relevant minor actinides and FP s. The results demonstrate that (a) sufficient critical experiment data exist to adequately validate k(eff) calculations via conventional validation approaches for the primary actinides, (b) sensitivity-based critical experiment selection is more appropriate for generating accurate application model bias and uncertainty, and (c) calculated sensitivities and nuclear data uncertainties can be used for generating conservative estimates of bias for minor actinides and FP s. Results based on the SCALE 6.1 and the ENDFIB-VII.0 cross-section libraries indicate that a conservative estimate of the bias for the minor actinides and FP s is 1.5% of their worth within the application model. This paper provides a detailed description of the approach and its technical bases, describes the application of the approach for representative pressurized water reactor and boiling water reactor safety analysis models, and provides reference bias results based on the prerelease SCALE 6.1 code package and ENDF IBVII nuclear cross-section data. C1 [Scaglione, J. M.; Mueller, D. E.; Wagner, J. C.] Oak Ridge Natl Lab, Reactor & Nucl Syst Div, Oak Ridge, TN 37831 USA. RP Scaglione, JM (reprint author), Oak Ridge Natl Lab, Reactor & Nucl Syst Div, POB 2008,Bldg 5700, Oak Ridge, TN 37831 USA. EM scaglionejm@ornl.gov RI Wagner, John/K-3644-2015 OI Wagner, John/0000-0003-0257-4502 FU UT-Battelle, LLC [DE-ACO5-000R22725]; U.S. Department of Energy. FX This manuscript has been authored by UT-Battelle, LLC, under contract DE-ACO5-000R22725 with the U.S. Department of Energy. NR 28 TC 0 Z9 0 U1 0 U2 4 PU AMER NUCLEAR SOC PI LA GRANGE PK PA 555 N KENSINGTON AVE, LA GRANGE PK, IL 60526 USA SN 0029-5450 EI 1943-7471 J9 NUCL TECHNOL JI Nucl. Technol. PD DEC PY 2014 VL 188 IS 3 BP 266 EP 279 PG 14 WC Nuclear Science & Technology SC Nuclear Science & Technology GA AU3CC UT WOS:000345489400004 ER PT J AU Kim, WC Kim, JY Ko, JH Kang, H Kim, J Han, KH AF Kim, Won-Chan Kim, Joo-Yeol Ko, Jae-Heung Kang, Hunseung Kim, Jungmook Han, Kyung-Hwan TI AtC3H14, a plant-specific tandem CCCH zinc-finger protein, binds to its target mRNAs in a sequence-specific manner and affects cell elongation in Arabidopsis thaliana SO PLANT JOURNAL LA English DT Article DE CCCH-type zinc-finger; post-transcriptional regulation; RNA binding ID SECONDARY WALL BIOSYNTHESIS; AVOCADO PERSEA-AMERICANA; GENOME-WIDE ANALYSIS; TRANSCRIPTION FACTOR; PECTIN METHYLESTERASES; GENE-EXPRESSION; CELLULOSE SYNTHASES; GROWTH; TRISTETRAPROLIN; FAMILY AB AtC3H14 (At1 g66810) is a plant-specific tandem CCCH zinc-finger (TZF) protein that belongs to the 68-member CCCH family in Arabidopsis thaliana. In animals, TZFs have been shown to bind and recruit target mRNAs to the cytoplasmic foci where mRNA decay enzymes are active. However, it is not known whether plant TZF proteins such as AtC3H14 function. So far, no mRNA targets of plant TZFs have been identified. We have obtained several lines of experimental evidence in support of our hypothesis that AtC3H14 isinvolved in post-transcriptional regulation of its target genes. Nucleic acid binding assays using [S-35]-labeled AtC3H14 protein showed that AtC3H14 could bind to ssDNA, dsDNA, and ribohomopolymers, suggesting its RNA-binding activity. RNA immunoprecipitation (RIP) assay identified several putative target RNAs of AtC3H14, including a polygalacturonase, a well-known cell wall modifying gene. RNA electrophoretic mobility shift assays (RNA-EMSA) were used to confirm the RIP results and demonstrate that the TZF domain of AtC3H14 is required for the target RNA binding. Microarray analysis of 35S::AtC3H14 plants revealed that many of the cell wall elongation and/or modification-associated genes were differentially expressed, which is consistent with the cell elongation defect phenotype and the changes in the cell wall monosaccharide composition. In addition, yeast activation assay showed that AtC3H14 also function as a transcriptional activator, which is consistent with the previous finding that AtC3H14 activate the secondary wall biosynthesis genes. Taken together, we conclude that AtC3H14 may play a key role in both transcriptional and post-transcriptional regulation. C1 [Kim, Won-Chan; Kim, Joo-Yeol; Han, Kyung-Hwan] Michigan State Univ, Dept Hort, E Lansing, MI 48824 USA. [Kim, Won-Chan; Kim, Joo-Yeol; Han, Kyung-Hwan] Michigan State Univ, Dept Forestry, E Lansing, MI 48824 USA. [Kim, Won-Chan; Kim, Joo-Yeol; Han, Kyung-Hwan] Michigan State Univ, DOE Great Lakes Bioenergy Res Ctr, E Lansing, MI 48824 USA. [Ko, Jae-Heung] Kyung Hee Univ, Dept Plant & Environm New Resources, Yongin 446701, Gyeonggi Do, South Korea. [Ko, Jae-Heung] Kyung Hee Univ, Bioenergy Ctr, Yongin 446701, South Korea. [Kang, Hunseung] Chonnam Natl Univ, Dept Plant Biotechnol, Kwangju 500757, South Korea. [Kim, Jungmook] Chonnam Natl Univ, Dept Bioenergy Sci & Technol, Kwangju 500757, South Korea. RP Ko, JH (reprint author), Kyung Hee Univ, Dept Plant & Environm New Resources, 1732 Deogyeong Daero, Yongin 446701, Gyeonggi Do, South Korea. EM jhko@khu.ac.kr; hanky@msu.edu FU DOE Great Lakes Bioenergy Research Center (DOE Office of Science BER) [DR-FC02-07ER64494]; Ministry of Education, Science and Technology of Korea via World Class University Project at Chonnam National University [R31-2009-000-20025-0]; Basic Science Research Program through National Research Foundation of Korea (NRF) [2011-0008840]; Korea Forest Service [S111213L080110]; National Research Foundation of Korea [2011-0017357] FX This work was funded by the DOE Great Lakes Bioenergy Research Center (DOE Office of Science BER DR-FC02-07ER64494), in part a grant to K-H Han and J Kim by the Ministry of Education, Science and Technology of Korea via the World Class University Project at Chonnam National University (R31-2009-000-20025-0), a grant to J-H Ko by Basic Science Research Program through the National Research Foundation of Korea (NRF) (2011-0008840) and a grant to J-H Ko from the Korea Forest Service (S111213L080110), and a grant to HS Kang by Mid-Career Researcher Program through the National Research Foundation of Korea (2011-0017357). NR 77 TC 7 Z9 9 U1 2 U2 26 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 0960-7412 EI 1365-313X J9 PLANT J JI Plant J. PD DEC PY 2014 VL 80 IS 5 BP 772 EP 784 DI 10.1111/tpj.12667 PG 13 WC Plant Sciences SC Plant Sciences GA AU3KI UT WOS:000345511500003 PM 25228083 ER PT J AU Budhraja, V Sopori, B Ravindra, N Misra, D AF Budhraja, Vinay Sopori, Bhushan Ravindra, Nuggehalli Misra, Durgamadhab TI Improved dislocation model of silicon solar cells with the effect of front and back surface recombination velocity SO PROGRESS IN PHOTOVOLTAICS LA English DT Article DE dislocations; Si solar cells ID MULTICRYSTALLINE SILICON; PERFORMANCE; EFFICIENCY; DEFECTS AB We have extended a previous model for calculating the effects of dislocations on the characteristics of a Si solar cell to include the effects of front and back surface recombination. This improved dislocation model uses Green's function approach to solve the three-dimensional continuity equation of the minority carriers with suitable boundary conditions corresponding to surface recombination at the n and p sides. The dislocations are considered to be localized lines, extending perpendicular to the front and back surfaces of the cell and having a recombination velocity. We discuss effect of several parameters such as bulk dislocation density, minority carrier diffusion length in p and n regions on the J-V characteristics, and spectral response of the cell. It is shown that these results agree well with previously published, experimental data. Copyright (c) 2013 John Wiley & Sons, Ltd. C1 [Budhraja, Vinay; Sopori, Bhushan] Natl Renewable Energy Lab, Golden, CO 80401 USA. [Budhraja, Vinay; Ravindra, Nuggehalli; Misra, Durgamadhab] New Jersey Inst Technol, Newark, NJ 07102 USA. RP Sopori, B (reprint author), Natl Renewable Energy Lab, Golden, CO 80401 USA. EM bhushan.sopori@nrel.gov NR 15 TC 0 Z9 0 U1 1 U2 16 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 1062-7995 EI 1099-159X J9 PROG PHOTOVOLTAICS JI Prog. Photovoltaics PD DEC PY 2014 VL 22 IS 12 BP 1256 EP 1266 DI 10.1002/pip.2412 PG 11 WC Energy & Fuels; Materials Science, Multidisciplinary; Physics, Applied SC Energy & Fuels; Materials Science; Physics GA AU4IZ UT WOS:000345575500007 ER PT J AU Drury, E Lopez, A Denholm, P Margolis, R AF Drury, Easan Lopez, Anthony Denholm, Paul Margolis, Robert TI Relative performance of tracking versus fixed tilt photovoltaic systems in the USA SO PROGRESS IN PHOTOVOLTAICS LA English DT Article DE tracking PV; PV economics; photovoltaics ID SATELLITE-DERIVED IRRADIANCES AB Tracking systems can increase the amount of electricity generated by photovoltaic (PV) modules, by actively orienting each module to intercept more solar energy. We find that horizontal one-axis tracking systems can increase PV generation by 12-25% relative to south-facing fixed mount PV systems with 25 degrees tilts in the contiguous USA, and two-axis tracking systems can increase PV generation by 30-45% relative to fixed mount systems. Tracking systems increase PV generation more significantly in arid regions such as the southwest USA than in humid regions with persistent cloud cover such as the Pacific Northwest and coastal Atlantic states. We find that fixed and tracking PV systems have similar interannual variability in their generation profiles, and this variability is primarily driven by project location. Tracking PV projects cost more than fixed tilt systems, per unit capacity, and we explore how much more tracking projects could cost while generating similar levelized costs of energy as fixed tilt systems. We define this as the breakeven additional cost of tracking and find that it is primarily driven by three factors: (i) regional tracking performance, (ii) fixed tilt system costs that tracking projects compete against, and (iii) additional tracking operation and maintenance costs. Using this framework, we explore the relative competitiveness of tracking systems for a range of fixed and tracking PV prices and evaluate how tracking competitiveness varies by region. Copyright (c) 2013 John Wiley & Sons, Ltd. C1 [Drury, Easan; Lopez, Anthony; Denholm, Paul] Natl Renewable Energy Lab, Golden, CO 80401 USA. [Margolis, Robert] Natl Renewable Energy Lab, Washington, DC 20024 USA. RP Drury, E (reprint author), Natl Renewable Energy Lab, 15013 Denver West Pkwy,RSF300, Golden, CO 80401 USA. EM Easan.drury@nrel.gov FU US Department of Energy [DE-AC36-08GO28308] FX We thank Aron Dobos, Alan Goodrich, Chris Gueymard, Ted James, Richard Perez, and Steve Wilcox for comments and input. This work was supported by the US Department of Energy under contract number DE-AC36-08GO28308. NR 22 TC 12 Z9 12 U1 0 U2 11 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 1062-7995 EI 1099-159X J9 PROG PHOTOVOLTAICS JI Prog. Photovoltaics PD DEC PY 2014 VL 22 IS 12 BP 1302 EP 1315 DI 10.1002/pip.2373 PG 14 WC Energy & Fuels; Materials Science, Multidisciplinary; Physics, Applied SC Energy & Fuels; Materials Science; Physics GA AU4IZ UT WOS:000345575500013 ER PT J AU Qi, SQ O'Hayre, M Gutkind, JS Hurley, JH AF Qi, Shiqian O'Hayre, Morgan Gutkind, J. Silvio Hurley, James H. TI Insights into beta 2-adrenergic receptor binding from structures of the N-terminal lobe of ARRDC3 SO PROTEIN SCIENCE LA English DT Article DE protein crystallography; ubiquitin ligase; arrestin; coimmunoprecipitation; asthma ID DOMAIN-CONTAINING PROTEINS; CRYSTAL-STRUCTURE; BETA-ARRESTINS; TRAFFICKING; LIGASE; UBIQUITINATION; RECRUITMENT; ENDOCYTOSIS; RETROMER; FAMILY AB ARRDC3 is one of six known human -arrestins, and has been implicated in the downregulation of the 2-adrenergic receptor (2AR). ARRDC3 consists of a two-lobed arrestin fold and a C-terminal tail containing two PPYX motifs. In the current model for receptor downregulation by ARRDC3, the arrestin fold portion is thought to bind the receptor, while the PPXY motifs recruit ubiquitin ligases of the NEDD4 family. Here we report the crystal structures of the N-terminal lobe of human ARRDC3 in two conformations, at 1.73 and 2.8 angstrom resolution, respectively. The structures reveal a large electropositive region that is capable of binding phosphate ions of crystallization. Residues within the basic patch were shown to be important for binding to 2AR, similar to the situation with -arrestins. This highlights potential parallels in receptor recognition between - and -arrestins. C1 [Qi, Shiqian; Hurley, James H.] Univ Calif Berkeley, Dept Mol & Cell Biol, Berkeley, CA 94720 USA. [Qi, Shiqian; Hurley, James H.] Univ Calif Berkeley, Calif Inst Quantitat Biosci, Berkeley, CA 94720 USA. [O'Hayre, Morgan; Gutkind, J. Silvio] NIDR, Oral & Pharyngeal Canc Branch, NIH, Bethesda, MD 20892 USA. [Hurley, James H.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Life Sci, Berkeley, CA 94720 USA. RP Hurley, JH (reprint author), Univ Calif Berkeley, Dept Mol & Cell Biol, 229 Stanley Hall, Berkeley, CA 94720 USA. EM jimhurley@berkeley.edu RI Qi, Shiqian/P-9177-2014 FU American Asthma Foundation [AAF 2011-0228]; NIH Intramural program, NIDCR FX Grant sponsor: American Asthma Foundation AAF 2011-0228 and NIH Intramural program, NIDCR. NR 31 TC 5 Z9 6 U1 2 U2 9 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 0961-8368 EI 1469-896X J9 PROTEIN SCI JI Protein Sci. PD DEC PY 2014 VL 23 IS 12 BP 1708 EP 1716 DI 10.1002/pro.2549 PG 9 WC Biochemistry & Molecular Biology SC Biochemistry & Molecular Biology GA AU0QW UT WOS:000345329800006 PM 25220262 ER PT J AU Jang, DH Anderson-Cook, CM AF Jang, Dae-Heung Anderson-Cook, Christine M. TI Firework Plot as a Graphical Exploratory Data Analysis Tool for Evaluating the Impact of Outliers in Data Exploration and Regression SO QUALITY AND RELIABILITY ENGINEERING INTERNATIONAL LA English DT Article DE outliers; influential observations; mean-standard deviation firework plot; mean-correlation firework plot; 3-D firework plot; pairwise firework plot matrix AB Outliers can distort many measures for data analysis. We propose a new set of graphical summaries, called firework plots, as simple tools for evaluating the impact of outliers in data exploration and regression assessment. One variation of the plot focuses on the impact of extreme observations on the mean and standard deviation by using curves that trace the relative contribution to the overall summary as weights for individual observations are changed from 1 to 0 in a univariate data set. Similarly, other variations for bivariate data allow examination of the impact of changing weights on combinations of the correlation coefficient and mean with two- or three-dimensional firework plots. One variation of the plot focuses on the impact on the estimated intercept, the estimated slope, and the estimated standard deviation by using curves based on the relative contribution to the overall summary as weights for individual observations are changed from 1 to 0 in a simple linear regression analysis. Similarly, other variations for a multiple regression allow the practitioner to examine the impact of changing weights on combinations of the estimated regression coefficients and the standard error with the pairwise firework plot matrix. Copyright (c) 2013 John Wiley & Sons, Ltd. C1 [Jang, Dae-Heung] Pukyong Natl Univ, Dept Stat, Pusan, South Korea. [Anderson-Cook, Christine M.] Los Alamos Natl Lab, Stat Sci Grp, Los Alamos, NM 87545 USA. RP Anderson-Cook, CM (reprint author), Los Alamos Natl Lab, Los Alamos, NM 87545 USA. EM candcook@lanl.gov NR 8 TC 0 Z9 0 U1 1 U2 4 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 0748-8017 EI 1099-1638 J9 QUAL RELIAB ENG INT JI Qual. Reliab. Eng. Int. PD DEC PY 2014 VL 30 IS 8 BP 1409 EP 1425 DI 10.1002/qre.1563 PG 17 WC Engineering, Multidisciplinary; Engineering, Industrial; Operations Research & Management Science SC Engineering; Operations Research & Management Science GA AU3JA UT WOS:000345507500026 ER PT J AU Buck, EC Moore, DA Czerwinski, KR Conradson, SD Batuk, ON Felmy, AR AF Buck, Edgar C. Moore, Dean A. Czerwinski, Kenneth R. Conradson, Steven D. Batuk, Olga N. Felmy, Andrew R. TI Nature of nano-sized plutonium particles in soils at the Hanford Site SO RADIOCHIMICA ACTA LA English DT Article DE Electron Microscopy; EELS; XAS; Plutonium; Hanford; Soil Contamination ID ENERGY-LOSS SPECTROSCOPY; NEVADA TEST-SITE; HYDROUS OXIDE; FAR-FIELD; SOLUBILITY; MINERALS; BEHAVIOR; EELS; NANOPARTICLES; DISSOLUTION AB The occurrence of plutoniumdioxide (PuO2) either from direct deposition or from the precipitation of plutonium-bearing solutions in contaminated soils and sediments is well described, particularly for the Hanford site in Washington State. However, past research has suggested that plutonium at the Hanford site may exist in chemical forms in addition to PuO2. Although the majority of the plutonium is present as oxide, we present evidence for the formation of nano-sized mixed plutonium-iron phosphate hydroxide structurally related to the rhabdophane group minerals in 216-Z9 crib sediments from Hanford using both transmission electron microscopy (TEM) and X-ray absorption spectroscopy (XAS). The iron-plutonium phosphate formation may depend on the local microenvironment in the sediments, availability of phosphate, and hence the distribution of these minerals may control long-term migration of plutonium in the soil. C1 [Buck, Edgar C.] Pacific NW Natl Lab, Energy & Environm Directorate, Richland, WA 99352 USA. [Moore, Dean A.; Felmy, Andrew R.] Pacific NW Natl Lab, Fundamental Sci Directorate, Richland, WA 99352 USA. [Czerwinski, Kenneth R.] Univ Nevada, Harry Reid Ctr Environm Studies, Las Vegas, NV 89154 USA. [Conradson, Steven D.; Batuk, Olga N.] Los Alamos Natl Lab, Los Alamos, NM 87544 USA. RP Buck, EC (reprint author), Pacific NW Natl Lab, Energy & Environm Directorate, POB 999,Mail Stop P7-27, Richland, WA 99352 USA. EM edgar.buck@pnnl.gov RI Buck, Edgar/N-7820-2013 OI Buck, Edgar/0000-0001-5101-9084 FU U.S. Department of Energy's Office of Biological and Environmental Research, Subsurface Biogeochemical Research (SBR) Science Focus Area (SFA); U.S. Department of Energy's Office of Biological and Environmental Research (BER) at the PNNL 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). A portion of this research was performed using the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research (BER) and located at the PNNL. We would like to thank Dr. Longzhou Ma for providing access to the FEI Tecnai G230 Transmission Electron Microscope. NR 43 TC 3 Z9 3 U1 3 U2 45 PU WALTER DE GRUYTER GMBH PI BERLIN PA GENTHINER STRASSE 13, D-10785 BERLIN, GERMANY SN 0033-8230 J9 RADIOCHIM ACTA JI Radiochim. Acta PD DEC PY 2014 VL 102 IS 12 BP 1059 EP 1068 DI 10.1515/ract-2013-2103 PG 10 WC Chemistry, Inorganic & Nuclear; Nuclear Science & Technology SC Chemistry; Nuclear Science & Technology GA AU4HE UT WOS:000345570400001 ER PT J AU Even, J Yakushev, A Dullmann, CE Dvorak, J Eichler, R Gothe, O Hartmann, W Hild, D Jager, E Khuyagbaatar, J Kindler, B Kratz, JV Krier, J Lommel, B Niewisch, L Nitsche, H Pysmenetska, I Schadel, M Schausten, B Turler, A Wiehl, N Wittwer, D AF Even, Julia Yakushev, Alexander Duellmann, Christoph Emanuel Dvorak, Jan Eichler, Robert Gothe, Oliver Hartmann, Willy Hild, Daniel Jaeger, Egon Khuyagbaatar, Jadambaa Kindler, Birgit Kratz, Jens Volker Krier, Joerg Lommel, Bettina Niewisch, Lorenz Nitsche, Heino Pysmenetska, Inna Schaedel, Matthias Schausten, Brigitta Tuerler, Andreas Wiehl, Norbert Wittwer, David TI In-situ formation, thermal decomposition, and adsorption studies of transition metal carbonyl complexes with short-lived radioisotopes SO RADIOCHIMICA ACTA LA English DT Article DE Carbonyl Complexes; Short-lived Isotopes; Carbonyl Synthesis; In-Situ Synthesis; Adsorption Studies; Thermochromatography; Isothermal Chromatography; Thermal Stability; Fission Products; Superheavy Elements; Physical Preseparation ID BOND-DISSOCIATION ENERGY; CRYSTAL-STRUCTURE; PHYSICAL PRESEPARATION; CHROMIUM HEXACARBONYL; SUPERHEAVY ELEMENT; HASSIUM Z=108; M(CO)(6) M=CR; CHEMISTRY; SEPARATOR; ISOTOPES AB We report on the in-situ synthesis of metal carbonyl complexes with short-lived isotopes of transition metals. Complexes of molybdenum, technetium, ruthenium and rhodium were synthesized by thermalisation of products of neutron-induced fission of Cf-249 in a carbon monoxide-nitrogen mixture. Complexes of tungsten, rhenium, osmium, and iridium were synthesized by thermalizing short-lived isotopes produced in 24 Mg-induced fusion evaporation reactions in a carbon monoxide containing atmosphere. The chemical reactions took place at ambient temperature and pressure conditions. The complexes were rapidly transported in a gas stream to collection setups or gas phase chromatography devices. The physisorption of the complexes on Au and SiO2 surfaces was studied. We also studied the stability of some of the complexes, showing that these start to decompose at temperatures above 300 degrees C in contact with a quartz surface. Our studies lay a basis for the investigation of such complexes with transactinides. C1 [Even, Julia; Duellmann, Christoph Emanuel; Dvorak, Jan; Khuyagbaatar, Jadambaa; Wiehl, Norbert] Helmholtz Inst Mainz, D-55099 Mainz, Germany. [Even, Julia; Duellmann, Christoph Emanuel; Hild, Daniel; Kratz, Jens Volker; Niewisch, Lorenz; Pysmenetska, Inna; Wiehl, Norbert] Johannes Gutenberg Univ Mainz, D-55099 Mainz, Germany. [Yakushev, Alexander; Duellmann, Christoph Emanuel; Hartmann, Willy; Jaeger, Egon; Khuyagbaatar, Jadambaa; Kindler, Birgit; Krier, Joerg; Lommel, Bettina; Schaedel, Matthias; Schausten, Brigitta] Schwerionenforsch GmbH, GSI Helmholtzzentrum, D-64192 Darmstadt, Germany. [Eichler, Robert; Tuerler, Andreas; Wittwer, David] Paul Scherrer Inst, CH-5232 Villigen, Switzerland. [Eichler, Robert; Tuerler, Andreas; Wittwer, David] Univ Bern, CH-3012 Bern, Switzerland. [Gothe, Oliver; Nitsche, Heino] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Even, J (reprint author), Helmholtz Inst Mainz, D-55099 Mainz, Germany. EM j.even@gsi.de RI Eichler, Robert/G-5130-2011; Even, Julia/K-1186-2016; Turler, Andreas/D-3913-2014 OI Even, Julia/0000-0002-6314-9094; Turler, Andreas/0000-0002-4274-1056 FU Helmholtz Institute Mainz; Research Center Elementary Forces and Mathematical Foundations (EMG); BMBF [06MZ223I, 06MZ7164]; Helmholtz association [VH-NG-723]; Swiss National Science Foundation [200020, 126639, 200020_244511] FX We thank the staff from the TRIGA Mainz reactor and the mechanical and electronics workshops at the Institut fur Kernchemie at the University of Mainz as well as the GSI target laboratory for their support. We thank the GSI ion source and accelerator staff for stable beams. We thank Valeria Pershina and Josef Anton for their support with theoretical calculations and fruitful discussion. We gratefully acknowledge financial support of the Helmholtz Institute Mainz, the Research Center Elementary Forces and Mathematical Foundations (EMG), the BMBF under contract No. 06MZ223I and 06MZ7164, the Helmholtz association under contract No. VH-NG-723, and the Swiss National Science Foundation under contract No. 200020, 126639 and 200020_244511. NR 60 TC 9 Z9 9 U1 3 U2 18 PU WALTER DE GRUYTER GMBH PI BERLIN PA GENTHINER STRASSE 13, D-10785 BERLIN, GERMANY SN 0033-8230 J9 RADIOCHIM ACTA JI Radiochim. Acta PD DEC PY 2014 VL 102 IS 12 BP 1093 EP 1110 DI 10.1515/ract-2013-2198 PG 18 WC Chemistry, Inorganic & Nuclear; Nuclear Science & Technology SC Chemistry; Nuclear Science & Technology GA AU4HE UT WOS:000345570400005 ER PT J AU Appel, AA Ibarra, V Garson, AB Guan, H Zhong, Z Anastasio, MA Opara, EC Brey, EM AF Appel, A. A. Ibarra, V. Garson, A. B., III Guan, H. Zhong, Z. Anastasio, M. A. Opara, E. C. Brey, E. M. TI X-Ray Phase Contrast Imaging of Encapsulated Cells and Foreign Body Response SO TISSUE ENGINEERING PART A LA English DT Meeting Abstract CT TERMIS-AM Conference CY DEC 13-16, 2014 CL Washington, DC SP TERMIS AM C1 [Appel, A. A.; Ibarra, V.; Brey, E. M.] IIT, Chicago, IL 60616 USA. [Garson, A. B., III; Guan, H.; Anastasio, M. A.] Washington Univ, St Louis, MO USA. [Zhong, Z.] Brookhaven Natl Lab, Natl Synchrotron Light Source, Upton, NY 11973 USA. [Opara, E. C.] Wake Forest Sch Med, Inst Regenerat Med, Winston Salem, NC USA. NR 0 TC 0 Z9 0 U1 0 U2 0 PU MARY ANN LIEBERT, INC PI NEW ROCHELLE PA 140 HUGUENOT STREET, 3RD FL, NEW ROCHELLE, NY 10801 USA SN 1937-3341 EI 1937-335X J9 TISSUE ENG PT A JI Tissue Eng. Part A PD DEC 1 PY 2014 VL 20 SU 1 MA O-110 BP S10 EP S10 PG 1 WC Cell & Tissue Engineering; Biotechnology & Applied Microbiology; Cell Biology SC Cell Biology; Biotechnology & Applied Microbiology GA AU6AK UT WOS:000345684300030 ER PT J AU Kacher, J Minor, AM AF Kacher, Josh Minor, Andrew M. TI Twin boundary interactions with grain boundaries investigated in pure rhenium SO ACTA MATERIALIA LA English DT Article DE Twinning; Rhenium; Mechanical behavior; Electron backscatter diffraction; Transmission electron microscopy ID DEFORMATION; NUCLEATION; DISLOCATIONS; MAGNESIUM; CRYSTALS AB The mechanical behavior of pure rhenium was investigated using uniaxial compression tests, transmission electron microscopy and electron backscatter diffraction characterization. The plasticity was characterized by a large amount of twin formation and propagation, including twin transmission across grain boundaries. In-depth analysis of the interactions of {1 1 (2) over bar 1}<(1) over bar (1) over bar 2 6 > twins with grain boundaries found that grain boundaries with misorientation angles below similar to 25 degrees allowed twin transmission, while grain boundaries with higher angles did not. Similar to dislocation interactions with grain boundaries, twin transmission was largely dictated by the minimization of the angle between the shear vectors of the incoming and outgoing twins. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved. C1 [Kacher, Josh; Minor, Andrew M.] Univ Calif Berkeley, Dept Mat Sci & Engn, Berkeley, CA 94709 USA. [Kacher, Josh; Minor, Andrew M.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Natl Ctr Electron Microscopy, Berkeley, CA 94720 USA. RP Kacher, J (reprint author), Univ Calif Berkeley, Dept Mat Sci & Engn, Berkeley, CA 94709 USA. EM jkacher@berkeley.edu RI Foundry, Molecular/G-9968-2014 FU US Office of Naval Research [N00014-11-1-0886]; US Department of Energy [DE-AC02-05CH11231] FX The authors gratefully acknowledge funding from the US Office of Naval Research under Grant No. N00014-11-1-0886. Portions of this work were performed as a user project at the National Center for Electron Microscopy at Lawrence Berkeley National Laboratory, which is supported by the US Department of Energy under Contract # DE-AC02-05CH11231. EBSD work was done at the EDAX-TSL facilities in Draper, UT. NR 19 TC 10 Z9 11 U1 1 U2 51 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 1359-6454 EI 1873-2453 J9 ACTA MATER JI Acta Mater. PD DEC PY 2014 VL 81 BP 1 EP 8 DI 10.1016/j.actamat.2014.08.013 PG 8 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering SC Materials Science; Metallurgy & Metallurgical Engineering GA AT8JM UT WOS:000345179800001 ER PT J AU Smilauerova, J Harcuba, P Strasky, J Straska, J Janecek, M Pospisil, J Kuzel, R Brunatova, T Holy, V Ilavsky, J AF Smilauerova, J. Harcuba, P. Strasky, J. Straska, J. Janecek, M. Pospisil, J. Kuzel, R. Brunatova, T. Holy, V. Ilavsky, J. TI Ordered array of omega particles in beta-Ti matrix studied by small-angle X-ray scattering SO ACTA MATERIALIA LA English DT Article DE omega-Ti phase; Ti alloys; Small-angle X-ray scattering; Self-ordering ID PHASE-TRANSFORMATIONS; TITANIUM-ALLOY; PRECIPITATION; MO; INSTABILITIES; EXAMPLE; GROWTH AB Nanosized particles of omega phase in a beta-Ti alloy were investigated by small-angle X-ray scattering using synchrotron radiation. We demonstrated that the particles are spontaneously weakly ordered in a three-dimensional cubic array along the < 1 0 0 >-directions in the beta-Ti matrix. The small-angle scattering data fit well to a three-dimensional short-range-order model; from the fit we determined the evolution of the mean particle size and mean distance between particles during ageing. The self-ordering of the particles is explained by elastic interaction between the particles, since the relative positions of the particles coincide with local minima of the interaction energy. We performed numerical Monte Carlo simulation of the particle ordering and we obtained a good agreement with the experimental data. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved. C1 [Smilauerova, J.; Harcuba, P.; Strasky, J.; Straska, J.; Janecek, M.; Pospisil, J.; Kuzel, R.; Brunatova, T.; Holy, V.] Charles Univ Prague, Fac Math & Phys, Prague, Czech Republic. [Ilavsky, J.] Argonne Natl Lab, Argonne, IL 60439 USA. RP Smilauerova, J (reprint author), Charles Univ Prague, Fac Math & Phys, Prague, Czech Republic. EM jana.smilauerova@gmail.com; Petr.Harcuba@mff.cuni.cz; josef.strasky@gmail.com; straska.jitka@gmail.com; janecek@met.mff.cuni.cz; jiri.pospisil@centrum.cz; kuzel@karlov.mff.cuni.cz; brunatovat@centrum.cz; holy@mag.mff.cuni.cz; ilavsky@aps.anl.gov RI Pospisil, Jiri/M-9882-2016; Ilavsky, Jan/D-4521-2013; Harcuba, Petr/P-6279-2016; Smilauerova, Jana/P-6399-2016; Holy, Vaclav/E-1508-2017 OI Ilavsky, Jan/0000-0003-1982-8900; Harcuba, Petr/0000-0002-9910-9158; Smilauerova, Jana/0000-0002-9554-9578; Holy, Vaclav/0000-0002-0370-6928 FU Ministry of Education, Youth and Sports of Czech Republic [LH13005]; Czech Science Foundation [P204/11/0785, 14-08124S, 14-36566G]; Grant Agency of Charles University in Prague [106-10/251403]; Czech Research Infrastructures [LM2011025]; National Science Foundation/Department of Energy [NSF/CHE-0822838]; US DOE [DE-AC02-06CH11357] FX The authors gratefully acknowledge Prof. Henry J. Rack for helpful comments on phase transformations in Ti alloys and for the idea of their investigation by the means of SAXS. The work was supported by the Ministry of Education, Youth and Sports of Czech Republic (Project LH13005), by the Czech Science Foundation (Projects P204/11/0785, 14-08124S and 14-36566G), and by the Grant Agency of Charles University in Prague (Project 106-10/251403). The single-crystal growth was performed in MLTL (http://mltl.eu/) within the program of Czech Research Infrastructures (Project No. LM2011025). The ChemMatCARS Sector 15 of the synchrotron source APS is principally supported by the National Science Foundation/Department of Energy under Grant No. NSF/CHE-0822838. Use of the Advanced Photon Source, an Office of Science User Facility operated for the US Department of Energy (DOE) Office of Science by Argonne National Laboratory, was supported by the US DOE under Contract No. DE-AC02-06CH11357. NR 33 TC 10 Z9 10 U1 1 U2 30 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 1359-6454 EI 1873-2453 J9 ACTA MATER JI Acta Mater. PD DEC PY 2014 VL 81 BP 71 EP 82 DI 10.1016/j.actamat.2014.06.042 PG 12 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering SC Materials Science; Metallurgy & Metallurgical Engineering GA AT8JM UT WOS:000345179800008 ER PT J AU Qin, W Szpunar, JA Kumar, NAPK Kozinski, J AF Qin, W. Szpunar, J. A. Kumar, N. A. P. Kiran Kozinski, J. TI Microstructural criteria for abrupt ductile-to-brittle transition induced by delta-hydrides in zirconium alloys SO ACTA MATERIALIA LA English DT Article DE Zirconium alloys; Hydride; Microstructure; Ductile-to-brittle transition ID HYDROGEN EMBRITTLEMENT; MECHANICAL-PROPERTIES; FRACTURE INITIATION; CRACK-TIP; ZIRCALOY-4; TITANIUM; MISFIT; PRECIPITATION; ORIENTATION; SOLUBILITY AB Hydride-induced ductile-to-brittle transition is an important feature for the failure of hydride-forming materials. Although this problem has been studied for many years, its relation to microstructure remains unclear. The degree of hydride-induced embrittlement depends on the hydride network. In this study, the formation mechanism of the hydride network with a high degree of continuity and its influence on the ductile-to-brittle transition of zirconium alloys are investigated. A criterion is proposed to determine the critical hydrogen content for the formation of an interlinked hydride configuration by considering the local stress-induced changes in hydrogen concentration and terminal solid solubility in the vicinity of the hydride tip. The theoretical results are in good agreement with the experimental observations. The propagation path of the hydride network and its dependence on microstructure are analyzed using electron backscatter diffraction and thermodynamic modeling. The results show that the grain-boundary structure, the grain-boundary misorientation and the angle of hydride inclination toward the grain-boundary plane control the formation and the growth direction of the hydride network. Although this work focuses on zirconium alloys, the obtained results are also of significance for other hydride-foiming materials. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved. C1 [Qin, W.; Szpunar, J. A.; Kozinski, J.] Univ Saskatchewan, Dept Mech Engn, Saskatoon, SK S7N 5A9, Canada. [Kozinski, J.] York Univ, Fac Sci & Engn, Toronto, ON M3J 1P3, Canada. [Kumar, N. A. P. Kiran] Oak Ridge Natl Lab, Mat Sci & Technol Div, Oak Ridge, TN USA. RP Qin, W (reprint author), Univ Saskatchewan, Dept Mech Engn, Saskatoon, SK S7N 5A9, Canada. EM wenqin68@hotmail.com NR 48 TC 8 Z9 8 U1 7 U2 37 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 1359-6454 EI 1873-2453 J9 ACTA MATER JI Acta Mater. PD DEC PY 2014 VL 81 BP 219 EP 229 DI 10.1016/j.actamat.2014.08.010 PG 11 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering SC Materials Science; Metallurgy & Metallurgical Engineering GA AT8JM UT WOS:000345179800022 ER PT J AU Barnard, L Young, GA Swoboda, B Choudhury, S Van der Ven, A Morgan, D Tucker, JD AF Barnard, L. Young, G. A. Swoboda, B. Choudhury, S. Van der Ven, A. Morgan, D. Tucker, J. D. TI Atomistic modeling of the order-disorder phase transformation in the Ni2Cr model alloy SO ACTA MATERIALIA LA English DT Article DE Nickel alloys; Monte Carlo; Phase transformations; Long-range ordering; Atomistic modeling ID TOTAL-ENERGY CALCULATIONS; WAVE BASIS-SET; NI-CR ALLOYS; HYDROGEN EMBRITTLEMENT; METALS; SYSTEM AB Mechanical property degradation due to the disorder order phase transformation is of potential concern for alloys based on the Ni-Cr binary system, particularly in nuclear power applications, where component lifetimes can exceed 80 years. In the present research, a disorder order phase transformation has been studied in the Ni-33 at.% Cr model alloy by a combined experimental and computational approach. The multiscale modeling framework utilizes grand canonical and kinetic Monte Carlo simulation techniques based upon density functional theory calculations to treat both the thermodynamic and kinetic aspects of the phase transformation. The simulation results are used to generate a simple model for the ordering kinetics based upon the Kolmogorov-Johnson-Mehl-Avrami equation. Experimental measurements of the change in lattice parameter as a function of aging time and temperature are obtained in order to assess the model accuracy. The resulting model shows reasonable agreement with experimental data at 470 and 418 C; however, additional experimental data at longer aging times are needed to confirm the accuracy of the model at lower temperatures. The model predicts that the initiation of the ordering transformation will occur in Ni-33Cr at temperatures and timescales relevant to nuclear power systems, though longer times are required for the transformation to proceed to completion. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved. C1 [Barnard, L.; Swoboda, B.; Morgan, D.] Univ Wisconsin, Madison, WI 53706 USA. [Young, G. A.] Knolls Atom Power Lab, Niskayuna, NY 12309 USA. [Choudhury, S.] Los Alamos Natl Lab, Div Mat Sci & Technol, Los Alamos, NM 87545 USA. [Van der Ven, A.] Univ Calif Santa Barbara, Dept Mat, Santa Barbara, CA 93106 USA. [Tucker, J. D.] Oregon State Univ, Corvallis, OR 97331 USA. RP Barnard, L (reprint author), Univ Wisconsin, 1509 Univ Ave, Madison, WI 53706 USA. EM lmbarnard@wisc.edu RI Choudhury, Samrat/B-4115-2009 FU DOE Nuclear Engineering University Program (NEUP) [10-888]; NSF DMR-Award [110564]; National Science Foundation [OCI-1053575] FX Research from L.B. was conducted under appointment to the Rickover Graduate Fellowship Program. Financial support for D.M. and for equipment and travel for L.B. was provided by the DOE Nuclear Engineering University Program (NEUP) under Grant Number 10-888 and NSF DMR-Award 110564. This work benefitted from the use of the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant number OCI-1053575. NR 53 TC 3 Z9 3 U1 2 U2 30 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 1359-6454 EI 1873-2453 J9 ACTA MATER JI Acta Mater. PD DEC PY 2014 VL 81 BP 258 EP 271 DI 10.1016/j.actamat.2014.08.017 PG 14 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering SC Materials Science; Metallurgy & Metallurgical Engineering GA AT8JM UT WOS:000345179800026 ER PT J AU Zhang, F Ji, M Fang, XW Sun, Y Wang, CZ Mendelev, MI Kramer, MJ Napolitano, RE Ho, KM AF Zhang, Feng Ji, Min Fang, Xiao-Wei Sun, Yang Wang, Cai-Zhuang Mendelev, Mikhail I. Kramer, M. J. Napolitano, Ralph E. Ho, Kai-Ming TI Composition-dependent stability of the medium-range order responsible for metallic glass formation SO ACTA MATERIALIA LA English DT Article DE Metallic glass; Medium-range order; Genetic algorithm ID TOTAL-ENERGY CALCULATIONS; WAVE BASIS-SET; CU-ZR ALLOYS; MECHANICAL-PROPERTIES; FORMING ABILITY; CRYSTAL STRUCTURE; QUASI-CRYSTALS; TRANSITION; LIQUID; POTENTIALS AB The competition between the characteristic medium-range order corresponding to amorphous alloys and that in ordered crystalline phases is central to phase selection and morphology evolution under various processing conditions. We examine the stability of a model glass system, Cu-Zr, by comparing the energetics of various medium-range structural motifs over a wide range of compositions using first-principles calculations. We focus specifically on motifs that represent possible building blocks for competing glassy and crystalline phases, and we employ a genetic algorithm to efficiently identify the energetically favored decorations of each motif for specific compositions. Our results show that a Bergman-type motif with crystallization-resisting icosahedral symmetry is energetically most favorable in the composition range 0.63 < x(Cu) < 0.68, and is the underlying motif for one of the three optimal glass-forming ranges observed experimentally for this binary system (Li et al., 2008). This work establishes an energy-based methodology to evaluate specific medium-range structural motifs which compete with stable crystalline nuclei in deeply undercooled liquids. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved. C1 [Zhang, Feng; Ji, Min; Fang, Xiao-Wei; Sun, Yang; Wang, Cai-Zhuang; Mendelev, Mikhail I.; Kramer, M. J.; Napolitano, Ralph E.; Ho, Kai-Ming] US DOE, Ames Lab, Ames, IA 50011 USA. [Zhang, Feng; Ji, Min; Fang, Xiao-Wei; Sun, Yang; Wang, Cai-Zhuang; Ho, Kai-Ming] Iowa State Univ, Dept Phys & Astron, Ames, IA 50011 USA. [Fang, Xiao-Wei] Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, Hefei 230026, Anhui, Peoples R China. [Fang, Xiao-Wei] Univ Sci & Technol China, Dept Phys, Hefei 230026, Anhui, Peoples R China. [Kramer, M. J.; Napolitano, Ralph E.] Iowa State Univ, Dept Mat Sci & Engn, Ames, IA 50011 USA. RP Zhang, F (reprint author), US DOE, Ames Lab, Ames, IA 50011 USA. EM fzhang@ameslab.gov OI Sun, Yang/0000-0002-4344-2920 FU US Department of Energy, Basic Energy Sciences, Division of Materials Science and Engineering [DE-AC02-07CH11358] FX Work at Ames Laboratory was supported by the US Department of Energy, Basic Energy Sciences, Division of Materials Science and Engineering, under Contract No. DE-AC02-07CH11358, including a grant of computer time at the National Energy Research Supercomputing Center (NERSC) in Berkeley, CA. F.Z. thanks S.H. Zhou for preparing the Cu-Zr phase diagram. NR 50 TC 2 Z9 2 U1 9 U2 49 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 1359-6454 EI 1873-2453 J9 ACTA MATER JI Acta Mater. PD DEC PY 2014 VL 81 BP 337 EP 344 DI 10.1016/j.actamat.2014.08.041 PG 8 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering SC Materials Science; Metallurgy & Metallurgical Engineering GA AT8JM UT WOS:000345179800033 ER PT J AU Wu, Z Bei, H Pharr, GM George, EP AF Wu, Z. Bei, H. Pharr, G. M. George, E. P. TI Temperature dependence of the mechanical properties of equiatomic solid solution alloys with face-centered cubic crystal structures SO ACTA MATERIALIA LA English DT Article DE High entropy alloy; Face-centered cubic crystals; Solid solution strengthening; Mechanical properties; Temperature ID HIGH-ENTROPY ALLOY; STACKING-FAULT ENERGY; RESOLVED SHEAR-STRESS; SINGLE-CRYSTALS; STATISTICAL-THEORY; STRAIN-RATE; FCC ALLOYS; COMPUTER-SIMULATION; ALUMINUM-ALLOYS; PHASE-STABILITY AB Compared to decades-old theories of strengthening in dilute solid solutions, the mechanical behavior of concentrated solid solutions is relatively poorly understood. A special subset of these materials includes alloys in which the constituent elements are present in equal atomic proportions, including the high-entropy alloys of recent interest. A unique characteristic of equiatomic alloys is the absence of "solvent" and "solute" atoms, resulting in a breakdown of the textbook picture of dislocations moving through a solvent lattice and encountering discrete solute obstacles. To clarify the mechanical behavior of this interesting new class of materials, we investigate here a family of equiatomic binary, ternary and quaternary alloys based on the elements Fe, Ni, Co, Cr and Mn that were previously shown to be single-phase face-centered cubic (fcc) solid solutions. The alloys were arc-melted, drop-cast, homogenized, cold-rolled and recrystallized to produce equiaxed microstructures with comparable grain sizes. Tensile tests were performed at an engineering strain rate of 10(-3) s(-1) at temperatures in the range 77-673 K. Unalloyed fcc Ni was processed similarly and tested for comparison. The flow stresses depend to varying degrees on temperature, with some (e.g. NiCoCr, NiCoCrMn and FeNiCoCr) exhibiting yield and ultimate strengths that increase strongly with decreasing temperature, while others (e.g. NiCo and Ni) exhibit very weak temperature dependencies. To better understand this behavior, the temperature dependencies of the yield strength and strain hardening were analyzed separately. Lattice friction appears to be the predominant component of the temperature-dependent yield stress, possibly because the Peierls barrier height decreases with increasing temperature due to a thermally induced increase of dislocation width. In the early stages of plastic flow (5-13% strain, depending on material), the temperature dependence of strain hardening is due mainly to the temperature dependence of the shear modulus. In all the equiatomic alloys, ductility and strength increase with decreasing temperature down to 77 K. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved. C1 [Wu, Z.; Pharr, G. M.; George, E. P.] Univ Tennessee, Mat Sci & Engn Dept, Knoxville, TN 37996 USA. [Bei, H.; Pharr, G. M.; George, E. P.] Oak Ridge Natl Lab, Mat Sci & Technol Div, Oak Ridge, TN 37831 USA. RP George, EP (reprint author), Oak Ridge Natl Lab, Mat Sci & Technol Div, Oak Ridge, TN 37831 USA. EM egeorge@utk.edu OI Bei, Hongbin/0000-0003-0283-7990 FU US Department of Energy, Office of Basic Energy Sciences, Materials Sciences and Engineering Division FX This research was supported by the US Department of Energy, Office of Basic Energy Sciences, Materials Sciences and Engineering Division. The authors thank Dr Fei Ren for measuring the temperature dependence of the shear modulus of the quaternary alloy FeNiCoCr (Table 4). NR 90 TC 77 Z9 78 U1 47 U2 210 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 1359-6454 EI 1873-2453 J9 ACTA MATER JI Acta Mater. PD DEC PY 2014 VL 81 BP 428 EP 441 DI 10.1016/j.actamat.2014.08.026 PG 14 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering SC Materials Science; Metallurgy & Metallurgical Engineering GA AT8JM UT WOS:000345179800041 ER PT J AU Liu, JP Wang, YD Hao, YL Wang, HL Wang, Y Nie, ZH Su, R Wang, D Ren, Y Lu, ZP Wang, JG Hui, XD Yang, R AF Liu, J. P. Wang, Y. D. Hao, Y. L. Wang, H. L. Wang, Y. Nie, Z. H. Su, R. Wang, D. Ren, Y. Lu, Z. P. Wang, J. G. Hui, X. D. Yang, R. TI High-energy X-ray diffuse scattering studies on deformation-induced spatially confined martensitic transformations in multifunctional Ti-24Nb-4Zr-8Sn alloy SO ACTA MATERIALIA LA English DT Article DE Titanium alloys; Martensitic transformation; Nanodomains; Synchrotron diffraction; Nonlinear superelastic behavior ID SHAPE-MEMORY ALLOYS; GUM METAL; PLASTIC-DEFORMATION; ELECTRON-MICROSCOPY; ALPHA'' MARTENSITE; TITANIUM-ALLOYS; ELASTIC-MODULUS; SUPERELASTICITY; MECHANISM; BEHAVIOR AB Two main explanations exist for the deformation mechanisms in Ti-Nb-based gum metals, i.e. the formation of reversible nanodisturbance and reversible stress-induced martensitic transformation. In this work, we used the in situ synchrotron-based high-energy X-ray diffuse-scattering technique to reveal the existence of a specific deformation mechanism, i.e. deformation-induced spatially confined martensitic transformations, in Ti-24Nb-4Zr-8Sn-0.10O single crystals with cubic 13 parent phase, which explains well some anomalous mechanical properties of the alloy such as low elastic modulus and nonlinear superelasticity. Two kinds of nanosized martensites with different crystal structures were found during uniaxial tensile loading along the [11 0](beta) axis at room temperature and 190 K, respectively. The detailed changes in the martensitic phase transformation characteristics and the transformation kinetics were experimentally observed at different temperatures. The domain switch from non-modulated martensite to a modulated one occurred at 190 K, with its physical origin attributed to the heterogeneity of local phonon softening depending on temperature and inhomogeneous composition in the parent phase. An in-depth understanding of the formation of stress-induced spatially confined nanosized martensites with a large gradient in chemical composition may benefit designs of high-strength and high-ductility alloys. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved. C1 [Liu, J. P.; Nie, Z. H.; Su, R.; Lu, Z. P.; Hui, X. D.] Beijing Inst Technol, Sch Mat Sci & Engn, Beijing 100081, Peoples R China. [Liu, J. P.; Wang, Y. D.; Su, R.] Univ Sci & Technol Beijing, State Key Lab Adv Met & Mat, Beijing 100083, Peoples R China. [Hao, Y. L.; Wang, H. L.; Yang, R.] Chinese Acad Sci, Inst Met Res, Shenyang Natl Lab Mat Sci, Shenyang 110016, Peoples R China. [Wang, Y.; Wang, D.] Ohio State Univ, Dept Mat Sci & Engn, Columbus, OH 43210 USA. [Wang, Y.; Wang, D.] Xi An Jiao Tong Univ, Frontier Inst Sci & Technol, State Key Lab Mech Behav Mat, Xian 710049, Peoples R China. [Ren, Y.] Argonne Natl Lab, Xray Sci Div, Argonne, IL 60439 USA. [Wang, J. G.] Univ Texas Richardson, Dept Mat Sci & Engn, Dallas, TX 75080 USA. RP Wang, YD (reprint author), Univ Sci & Technol Beijing, State Key Lab Adv Met & Mat, Beijing 100083, Peoples R China. EM ydwang@mail.neu.edu.cn; ylhao@imr.ac.cn; wang.363@osu.edu RI Lu, Zhao-Ping/A-2718-2009; Wang, Yunzhi/B-2557-2010; wang, yandong/G-9404-2013; Nie, Zhihua/G-9459-2013 OI Nie, Zhihua/0000-0002-2533-933X FU National Basic Research Program of China (973 Program) [2012CB619405, 2012CB619103]; National Natural Science Foundation of China [51231002, 51271180, 51201125]; Fundamental Research Funds for the Central Universities [06111020]; State Key Laboratory for Advanced Metals and Materials [2014Z-01]; US Department of Energy, Office of Science, Office of Basic Energy Science, [DE-AC02-06CH11357]; US Natural Science Foundation [DMR-1008349]; National Basic Research Program of China [2012CB619402, 2010CB631003] FX This study was supported by the National Basic Research Program of China (973 Program) (Grant Nos. 2012CB619405 and 2012CB619103), the National Natural Science Foundation of China (Grant Nos. 51231002 and 51271180), the Fundamental Research Funds for the Central Universities (Grant No. 06111020) and the financial support (Grant No. 2014Z-01) by the State Key Laboratory for Advanced Metals and Materials. Use of the Advanced Photon Source was supported by the US Department of Energy, Office of Science, Office of Basic Energy Science, under Contract No. DE-AC02-06CH11357. This work was also partially supported by the US Natural Science Foundation Grant No. DMR-1008349, National Basic Research Program of China (Grants Nos. 2012CB619402 and 2010CB631003) and National Natural Science Foundation of China (Grant No. 51201125). NR 45 TC 6 Z9 6 U1 5 U2 66 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 1359-6454 EI 1873-2453 J9 ACTA MATER JI Acta Mater. PD DEC PY 2014 VL 81 BP 476 EP 486 DI 10.1016/j.actamat.2014.08.019 PG 11 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering SC Materials Science; Metallurgy & Metallurgical Engineering GA AT8JM UT WOS:000345179800045 ER PT J AU Ekiz, EH Lach, TG Averback, RS Mara, NA Beyerlein, IJ Pouryazdan, M Hahn, H Bellon, P AF Ekiz, E. H. Lach, T. G. Averback, R. S. Mara, N. A. Beyerlein, I. J. Pouryazdan, M. Hahn, H. Bellon, P. TI Microstructural evolution of nanolayered Cu-Nb composites subjected to high pressure torsion (vol 72, pg 178, 2014) SO ACTA MATERIALIA LA English DT Correction C1 [Ekiz, E. H.; Lach, T. G.; Averback, R. S.; Bellon, P.] Univ Illinois, Dept Mat Sci & Engn, Urbana, IL 61801 USA. [Mara, N. A.; Beyerlein, I. J.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. [Pouryazdan, M.; Hahn, H.] Karlsruhe Inst Technol, Inst Nanotechnol, D-76021 Karlsruhe, Germany. [Pouryazdan, M.; Hahn, H.] Tech Univ Darmstadt, Joint Res Lab Nanomat, D-64287 Darmstadt, Germany. RP Bellon, P (reprint author), Univ Illinois, Dept Mat Sci & Engn, 1304 West Green St, Urbana, IL 61801 USA. EM bellon@uiuc.edu RI Mara, Nathan/J-4509-2014; Hahn, Horst/G-9018-2011 OI Hahn, Horst/0000-0001-9901-3861 NR 1 TC 1 Z9 1 U1 1 U2 30 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 1359-6454 EI 1873-2453 J9 ACTA MATER JI Acta Mater. PD DEC PY 2014 VL 81 BP 528 EP 528 DI 10.1016/j.actamat.2014.05.012 PG 1 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering SC Materials Science; Metallurgy & Metallurgical Engineering GA AT8JM UT WOS:000345179800050 ER PT J AU Adedinsewo, DA Wei, SC Robertson, M Rose, C Johnson, CH Dombrowski, J Skarbinski, J AF Adedinsewo, Demilade A. Wei, Stanley C. Robertson, McKaylee Rose, Charles Johnson, Christopher H. Dombrowski, Julie Skarbinski, Jacek TI Timing of Antiretroviral Therapy Initiation in a Nationally Representative Sample of HIV-Infected Adults Receiving Medical Care in the United States SO AIDS PATIENT CARE AND STDS LA English DT Article ID INJECTION-DRUG USERS; MONITORING PROJECT; TRENDS; INDIVIDUALS; DISPARITIES; PREVALENCE; MEN; RNA; SEX AB Early antiretroviral therapy (ART) initiation reduces the risk of disease progression and HIV transmission, but data on time from HIV care entry to ART initiation are lacking. Using data from the Medical Monitoring Project (MMP), a population-based probability sample of HIV-infected adults receiving medical care in the United States, we assessed time from care entry to ART initiation among persons diagnosed May 2004-April 2009 and used multivariable Cox proportional-hazards models to identify factors associated with time to ART initiation. Among 1094 MMP participants, 83.9% reported initiating ART, with median time to ART initiation of 10 months. In multivariable models, blacks compared to whites [hazard ratio (HR) 0.82; 95% confidence interval (CI) 0.70-0.98], persons without continuous health insurance (HR 0.82; CI 0.70-0.97), heterosexual women and men who have sex with men compared to heterosexual men (HR 0.66; CI 0.51-0.85 and HR 0.71; CI 0.60-0.84, respectively), and persons without AIDS at care entry (HR 0.37; CI 0.31-0.43) had significantly longer times to ART initiation. Overall, time to ART initiation was suboptimal by current standards and significant disparities were noted among certain subgroups. Efforts to encourage prompt ART initiation should address delays among those without health insurance and among certain sociodemographic subgroups. C1 [Adedinsewo, Demilade A.; Robertson, McKaylee] Oak Ridge Inst Sci & Educ, Oak Ridge, TN USA. [Adedinsewo, Demilade A.; Wei, Stanley C.; Robertson, McKaylee; Rose, Charles; Johnson, Christopher H.; Skarbinski, Jacek] Ctr Dis Control & Prevent, Natl Ctr HIV AIDS Viral Hepatitis STD & TB Preven, Atlanta, GA 30329 USA. [Wei, Stanley C.] US PHS, Atlanta, GA USA. [Dombrowski, Julie] Univ Washington, Dept Med, Seattle, WA USA. [Dombrowski, Julie] Publ Hlth Seattle & King Cty HIV STD Program, Seattle, WA USA. RP Skarbinski, J (reprint author), Ctr Dis Control & Prevent, Div HIV AIDS Prevent, 1600 Clifton Rd NE,Mailstop E-46, Atlanta, GA 30329 USA. EM jskarbinski@cdc.gov OI Adedinsewo, Demilade/0000-0002-8629-2029 FU Research Participation Program at the Centers for Disease Control and Prevention; Centers for Disease Control and Prevention [PS09-937] FX This research was supported in part by an appointment to the Research Participation Program at the Centers for Disease Control and Prevention administered by the Oak Ridge Institute for Science and Education through an agreement between the US Department of Energy and CDC. Funding for the Medical Monitoring Project is provided by a cooperative agreement (PS09-937) from the Centers for Disease Control and Prevention. NR 31 TC 6 Z9 6 U1 0 U2 4 PU MARY ANN LIEBERT, INC PI NEW ROCHELLE PA 140 HUGUENOT STREET, 3RD FL, NEW ROCHELLE, NY 10801 USA SN 1087-2914 EI 1557-7449 J9 AIDS PATIENT CARE ST JI Aids Patient Care STDS PD DEC 1 PY 2014 VL 28 IS 12 BP 613 EP 621 DI 10.1089/apc.2014.0194 PG 9 WC Public, Environmental & Occupational Health; Infectious Diseases SC Public, Environmental & Occupational Health; Infectious Diseases GA AU4FI UT WOS:000345564900001 PM 25329710 ER PT J AU Noguera, DR Wright, ES Camejo, P Yilmaz, LS AF Noguera, Daniel R. Wright, Erik S. Camejo, Pamela Yilmaz, L. Safak TI Mathematical tools to optimize the design of oligonucleotide probes and primers SO APPLIED MICROBIOLOGY AND BIOTECHNOLOGY LA English DT Review DE Oligonucleotides; DNA probes; FISH; PCR; Microarrays; Mismatch stability; Microbial diversity; Primer design ID 16S RIBOSOMAL-RNA; IN-SITU HYBRIDIZATION; POLYMERASE-CHAIN-REACTION; CATALYZED REPORTER DEPOSITION; SULFATE-REDUCING PROKARYOTES; AMMONIA-OXIDIZING ARCHAEA; REAL-TIME PCR; THERMODYNAMIC PARAMETERS; SECONDARY STRUCTURE; DNA AMPLIFICATION AB The identification and quantification of specific organisms in mixed microbial communities often relies on the ability to design oligonucleotide probes and primers with high specificity and sensitivity. The design of these oligonucleotides (or "oligos" for short) shares many of the same principles in spite of their widely divergent applications. Three common molecular biology technologies that require oligonucleotide design are polymerase chain reaction (PCR), fluorescence in situ hybridization (FISH), and DNA microarrays. This article reviews techniques and software available for the design and optimization of oligos with the goal of targeting a specific group of organisms within mixed microbial communities. Strategies for enhancing specificity without compromising sensitivity are described, as well as design tools well suited for this purpose. C1 [Noguera, Daniel R.; Camejo, Pamela] Univ Wisconsin, Dept Civil & Environm Engn, Madison, WI 53706 USA. [Noguera, Daniel R.] Univ Wisconsin, Great Lakes Bioenergy Res Ctr, Madison, WI USA. [Wright, Erik S.] Univ Wisconsin, Wisconsin Inst Discovery, Madison, WI USA. [Wright, Erik S.] Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA. [Yilmaz, L. Safak] Univ Massachusetts, Sch Med, Program Syst Biol, Worcester, MA USA. RP Noguera, DR (reprint author), 1415 Engn Dr, Madison, WI 53706 USA. EM noguera@engr.wisc.edu FU Becas Chile (Conicyt) FX The authors would like to thank Alexander Steinbuchel for the invitation to write this review. This research was partially supported by a fellowship from Becas Chile (Conicyt) to Pamela Camejo. NR 108 TC 3 Z9 3 U1 3 U2 48 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 0175-7598 EI 1432-0614 J9 APPL MICROBIOL BIOT JI Appl. Microbiol. Biotechnol. PD DEC PY 2014 VL 98 IS 23 BP 9595 EP 9608 DI 10.1007/s00253-014-6165-x PG 14 WC Biotechnology & Applied Microbiology SC Biotechnology & Applied Microbiology GA AT7TN UT WOS:000345140200006 PM 25359473 ER PT J AU Aartsen, MG Ackermann, M Adams, J Aguilar, JA Ahlers, M Ahrens, M Altmann, D Anderson, T Arguelles, C Arlen, TC Auffenberg, J Bai, X Barwick, SW Baum, V Beatty, JJ Tjus, JB Becker, KH BenZvi, S Berghaus, P Berley, D Bernardini, E Bernhard, A Besson, DZ Binder, G Bindig, D Bissok, M Blaufuss, E Blumenthal, J Boersma, DJ Bohm, C Bos, F Bose, D Boser, S Botner, O Brayeur, L Bretz, HP Brown, AM Casey, J Casier, M Cheung, E Chirkin, D Christov, A Christy, B Clark, K Classen, L Clevermann, F Coenders, S Cowen, DF Silva, AHC Danninger, M Daughhetee, J Davis, JC Day, M de Andre, JPAM De Clercq, C De Ridder, S Desiati, P de Vries, KD de With, M DeYoung, T Diaz-Velez, JC Dunkman, M Eagan, R Eberhardt, B Eichmann, B Eisch, J Euler, S Evenson, PA Fadiran, O Fazely, AR Fedynitch, A Feintzeig, J Felde, J Feusels, T Filimonov, K Finley, C Fischer-Wasels, T Flis, S Franckowiak, A Frantzen, K Fuchs, T Gaisser, TK Gallagher, J Gerhardt, L Gier, D Gladstone, L Glusenkamp, T Goldschmidt, A Golup, G Gonzalez, JG Goodman, JA Gora, D Grandmont, DT Grant, D Gretskov, P Groh, JC Gross, A Ha, C Haack, C Ismail, AH Hallen, P Hallgren, A Halzen, F Hanson, K Hebecker, D Heereman, D Heinen, D Helbing, K Hellauer, R Hellwig, D Hickford, S Hill, GC Hoffman, KD Hoffmann, R Homeier, A Hoshina, K Huang, F Huelsnitz, W Hulth, PO Hultqvist, K Hussain, S Ishihara, A Jacobi, E Jacobsen, J Jagielski, K Japaridze, GS Jero, K Jlelati, O Jurkovic, M Kaminsky, B Kappes, A Karg, T Karle, A Kauer, M Kelley, JL Kheirandish, A Kiryluk, J Klas, J Klein, SR Kohne, JH Kohnen, G Kolanoski, H Koob, A Kopke, L Kopper, C Kopper, S Koskinen, DJ Kowalski, M Kriesten, A Krings, K Kroll, G Kroll, M Kunnen, J Kurahashi, N Kuwabara, T Labare, M Larsen, DT Larson, MJ Lesiak-Bzdak, M Leuermann, M Leute, J Lunemann, J Macias, O Madsen, J Maggi, G Maruyama, R Mase, K Matis, HS Maunu, R McNally, F Meagher, K Medici, M Meli, A Meures, T Miarecki, S Middell, E Middlemas, 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 Omairat, A O'Murchadha, A Palczewski, T Paul, L Penek, O Pepper, JA Heros, CPD Pfendner, C Pieloth, D Pinat, E Posselt, J Price, PB Przybylski, GT Putz, J Quinnan, M Radel, L Rameez, M Rawlins, K Redl, P Rees, I Reimann, R Resconi, E Rhode, W Richman, M Riedel, B Robertson, S Rodrigues, JP Rongen, M Rott, C Ruhe, T Ruzybayev, B Ryckbosch, D Saba, SM Sander, HG Sandroos, J Santander, M Sarkar, S Schatto, K Scheriau, F Schmidt, T Schmitz, M Schoenen, S Schoneberg, S Schonwald, A Schukraft, A Schulte, L Schulz, O Seckel, D Sestayo, Y Seunarine, S Shanidze, R Sheremata, C Smith, MWE Soldin, D Spiczak, GM Spiering, C Stamatikos, M Stanev, T Stanisha, NA Stasik, A Stezelberger, T Stokstad, RG Stossl, A Strahler, EA Strom, R Strotjohann, NL Sullivan, GW Taavola, H Taboada, I Tamburro, A Tepe, A Ter-Antonyan, S Terliuk, A Tesic, G Tilav, S Toale, PA Tobin, MN Tosi, D Tselengidou, M Unger, E Usner, M Vallecorsa, S van Eijndhoven, N Vandenbroucke, J van Santen, J Vehring, M Voge, M Vraeghe, M Walck, C Wallraff, M Weaver, C Wellons, M Wendt, C Westerhoff, S Whelan, BJ Whitehorn, N Wichary, C Wiebe, K Wiebusch, CH Williams, DR Wissing, H Wolf, M Wood, TR Woschnagg, K Xu, DL Xu, XW Yanez, JP Yodh, G Yoshida, S Zarzhitsky, P Ziemann, J Zierke, S Zoll, M AF Aartsen, M. G. Ackermann, M. Adams, J. Aguilar, J. A. Ahlers, M. Ahrens, M. Altmann, D. Anderson, T. Arguelles, C. Arlen, T. C. Auffenberg, J. Bai, X. Barwick, S. W. Baum, V. Beatty, J. J. Tjus, J. Becker Becker, K. -H. BenZvi, S. Berghaus, P. Berley, D. Bernardini, E. Bernhard, A. Besson, D. Z. Binder, G. Bindig, D. Bissok, M. Blaufuss, E. Blumenthal, J. Boersma, D. J. Bohm, C. Bos, F. Bose, D. Boeser, S. Botner, O. Brayeur, L. Bretz, H. -P. Brown, A. M. Casey, J. Casier, M. Cheung, E. Chirkin, D. Christov, A. Christy, B. Clark, K. Classen, L. Clevermann, F. Coenders, S. Cowen, D. F. Silva, A. H. Cruz Danninger, M. Daughhetee, J. Davis, J. C. Day, M. de Andre, J. P. A. M. De Clercq, C. De Ridder, S. Desiati, P. de Vries, K. D. de With, M. DeYoung, T. Diaz-Velez, J. C. Dunkman, M. Eagan, R. Eberhardt, B. Eichmann, B. Eisch, J. Euler, S. Evenson, P. A. Fadiran, O. Fazely, A. R. Fedynitch, A. Feintzeig, J. Felde, J. Feusels, T. Filimonov, K. Finley, C. Fischer-Wasels, T. Flis, S. Franckowiak, A. Frantzen, K. Fuchs, T. Gaisser, T. K. Gallagher, J. Gerhardt, L. Gier, D. Gladstone, L. Gluesenkamp, T. Goldschmidt, A. Golup, G. Gonzalez, J. G. Goodman, J. A. Gora, D. Grandmont, D. T. Grant, D. Gretskov, P. Groh, J. C. Gross, A. Ha, C. Haack, C. Ismail, A. Haj Hallen, P. Hallgren, A. Halzen, F. Hanson, K. Hebecker, D. Heereman, D. Heinen, D. Helbing, K. Hellauer, R. Hellwig, D. Hickford, S. Hill, G. C. Hoffman, K. D. Hoffmann, R. Homeier, A. Hoshina, K. Huang, F. Huelsnitz, W. Hulth, P. O. Hultqvist, K. Hussain, S. Ishihara, A. Jacobi, E. Jacobsen, J. Jagielski, K. Japaridze, G. S. Jero, K. Jlelati, O. Jurkovic, M. Kaminsky, B. Kappes, A. Karg, T. Karle, A. Kauer, M. Kelley, J. L. Kheirandish, A. Kiryluk, J. Klaes, J. Klein, S. R. Koehne, J. -H. Kohnen, G. Kolanoski, H. Koob, A. Koepke, L. Kopper, C. Kopper, S. Koskinen, D. J. Kowalski, M. Kriesten, A. Krings, K. Kroll, G. Kroll, M. Kunnen, J. Kurahashi, N. Kuwabara, T. Labare, M. Larsen, D. T. Larson, M. J. Lesiak-Bzdak, M. Leuermann, M. Leute, J. Luenemann, J. Macias, O. Madsen, J. Maggi, G. Maruyama, R. Mase, K. Matis, H. S. Maunu, R. McNally, F. Meagher, K. Medici, M. Meli, A. Meures, T. Miarecki, S. Middell, E. Middlemas, 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. Omairat, A. O'Murchadha, A. Palczewski, T. Paul, L. Penek, O. Pepper, J. A. Heros, C. Perez De Los Pfendner, C. Pieloth, D. Pinat, E. Posselt, J. Price, P. B. Przybylski, G. T. Puetz, J. Quinnan, M. Raedel, L. Rameez, M. Rawlins, K. Redl, P. Rees, I. Reimann, R. Resconi, E. Rhode, W. Richman, M. Riedel, B. Robertson, S. Rodrigues, J. P. Rongen, M. Rott, C. Ruhe, T. Ruzybayev, B. Ryckbosch, D. Saba, S. M. Sander, H. -G. Sandroos, J. Santander, M. Sarkar, S. Schatto, K. Scheriau, F. Schmidt, T. Schmitz, M. Schoenen, S. Schoeneberg, S. Schoenwald, A. Schukraft, A. Schulte, L. Schulz, O. Seckel, D. Sestayo, Y. Seunarine, S. Shanidze, R. Sheremata, C. Smith, M. W. E. Soldin, D. Spiczak, G. M. Spiering, C. Stamatikos, M. Stanev, T. Stanisha, N. A. Stasik, A. Stezelberger, T. Stokstad, R. G. Stoessl, A. Strahler, E. A. Strom, R. Strotjohann, N. L. Sullivan, G. W. Taavola, H. Taboada, I. Tamburro, A. Tepe, A. Ter-Antonyan, S. Terliuk, A. Tesic, G. Tilav, S. Toale, P. A. Tobin, M. N. Tosi, D. Tselengidou, M. Unger, E. Usner, M. Vallecorsa, S. van Eijndhoven, N. Vandenbroucke, J. van Santen, J. Vehring, M. Voge, M. Vraeghe, M. Walck, C. Wallraff, M. Weaver, Ch. Wellons, M. Wendt, C. Westerhoff, S. Whelan, B. J. Whitehorn, N. Wichary, C. Wiebe, K. Wiebusch, C. H. Williams, D. R. Wissing, H. Wolf, M. Wood, T. R. Woschnagg, K. Xu, D. L. Xu, X. W. Yanez, J. P. Yodh, G. Yoshida, S. Zarzhitsky, P. Ziemann, J. Zierke, S. Zoll, M. CA IceCube Collaboration TI SEARCHES FOR EXTENDED AND POINT-LIKE NEUTRINO SOURCES WITH FOUR YEARS OF ICECUBE DATA SO ASTROPHYSICAL JOURNAL LA English DT Article DE astroparticle physics; galaxies: active; galaxies: clusters: general; galaxies: starburst; ISM: supernova remnants; neutrinos ID HIGH-ENERGY NEUTRINOS; ACTIVE GALACTIC NUCLEI; GAMMA-RAY EMISSION; SUPERNOVA-REMNANTS; PARTICLE-ACCELERATION; COSMIC-RAYS; FERMI LAT; TELESCOPE; ASTRONOMY; MILAGRO AB We present results on searches for point-like sources of neutrinos using four years of IceCube data, including the first year of data from the completed 86 string detector. The total livetime of the combined data set is 1373 days. For an E-2 spectrum, the observed 90% C. L. flux upper limits are similar to 10(-12) TeV-1 cm(-2) s(-1) for energies between 1 TeV and 1 PeV in the northern sky and similar to 10(-11) TeV-1 cm(-2) s(-1) for energies between 100 TeV and 100 PeV in the southern sky. This represents a 40% improvement compared to previous publications, resulting from both the additional year of data and the introduction of improved reconstructions. In addition, we present the first results from an all-sky search for extended sources of neutrinos. We update the results of searches for neutrino emission from stacked catalogs of sources and test five new catalogs; two of Galactic supernova remnants and three of active galactic nuclei. In all cases, the data are compatible with the background-only hypothesis, and upper limits on the flux of muon neutrinos are reported for the sources considered. C1 [Aartsen, M. G.; Hill, G. C.; Robertson, S.; Whelan, B. J.] Univ Adelaide, Sch Chem & Phys, Adelaide, SA 5005, Australia. [Ackermann, M.; Berghaus, P.; Bernardini, E.; Bretz, H. -P.; Silva, A. H. Cruz; Gluesenkamp, T.; Gora, D.; Jacobi, E.; Kaminsky, B.; Karg, T.; Middell, E.; Mohrmann, L.; Nahnhauer, R.; Schoenwald, A.; Shanidze, R.; Spiering, C.; Stoessl, A.; Terliuk, A.; Yanez, J. P.] DESY, D-15735 Zeuthen, Germany. [Adams, J.; Hickford, S.; Macias, O.] Univ Canterbury, Dept Phys & Astron, Christchurch 1, New Zealand. [Aguilar, J. A.; Christov, A.; Montaruli, T.; Rameez, M.; Vallecorsa, S.] Univ Geneva, Dept Phys Nucl & Corpusculaire, CH-1211 Geneva, Switzerland. [Ahlers, M.; Arguelles, C.; BenZvi, S.; Chirkin, D.; Day, M.; Desiati, P.; Diaz-Velez, J. C.; Eisch, J.; Fadiran, O.; Feintzeig, J.; Gladstone, L.; Halzen, F.; Hoshina, K.; Jacobsen, J.; Jero, K.; Karle, A.; Kauer, M.; Kelley, J. L.; Kheirandish, A.; Kopper, C.; Kurahashi, N.; Larsen, D. T.; Maruyama, R.; McNally, F.; Middlemas, E.; Morse, R.; Rees, I.; Riedel, B.; Rodrigues, J. P.; Santander, M.; Tobin, M. N.; Tosi, D.; Vandenbroucke, J.; van Santen, J.; Weaver, Ch.; Wellons, M.; Wendt, C.; Westerhoff, S.; Whitehorn, N.] Univ Wisconsin, Dept Phys, Madison, WI 53706 USA. [Ahlers, M.; Arguelles, C.; BenZvi, S.; Chirkin, D.; Day, M.; Desiati, P.; Diaz-Velez, J. C.; Eisch, J.; Fadiran, O.; Feintzeig, J.; Gladstone, L.; Halzen, F.; Hoshina, K.; Jacobsen, J.; Jero, K.; Karle, A.; Kauer, M.; Kelley, J. L.; Kheirandish, A.; Kopper, C.; Kurahashi, N.; Larsen, D. T.; Maruyama, R.; McNally, F.; Middlemas, E.; Morse, R.; Rees, I.; Riedel, B.; Rodrigues, J. P.; Santander, M.; Tobin, M. N.; Tosi, D.; Vandenbroucke, J.; van Santen, J.; Weaver, Ch.; Wellons, M.; Wendt, C.; Westerhoff, S.; Whitehorn, N.] Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA. [Ahrens, M.; Bohm, C.; Danninger, M.; Finley, C.; Flis, S.; Hulth, P. O.; Hultqvist, K.; Walck, C.; Wolf, M.; Zoll, M.] Stockholm Univ, Oskar Klein Ctr, SE-10691 Stockholm, Sweden. [Ahrens, M.; Bohm, C.; Danninger, M.; Finley, C.; Flis, S.; Hulth, P. O.; Hultqvist, K.; Walck, C.; Wolf, M.; Zoll, M.] Stockholm Univ, Dept Phys, SE-10691 Stockholm, Sweden. [Altmann, D.; Classen, L.; Kappes, A.; Tselengidou, M.] Univ Erlangen Nurnberg, Erlangen Ctr Astroparticle Phys, D-91058 Erlangen, Germany. [Anderson, T.; Arlen, T. C.; Cowen, D. F.; de Andre, J. P. A. M.; DeYoung, T.; Dunkman, M.; Eagan, R.; Huang, F.; Quinnan, M.; Smith, M. W. E.; Stanisha, N. A.; Tesic, G.] Penn State Univ, Dept Phys, University Pk, PA 16802 USA. [Auffenberg, J.; Bissok, M.; Blumenthal, J.; Gier, D.; Gretskov, P.; Haack, C.; Hallen, P.; Heinen, D.; Hellwig, D.; Jagielski, K.; Koob, A.; Kriesten, A.; Krings, K.; Leuermann, M.; Paul, L.; Penek, O.; Puetz, J.; Reimann, R.; Riedel, B.; Rongen, M.; Schoenen, S.; Schukraft, A.; Vehring, M.; Wallraff, M.; Wichary, C.; Wiebusch, C. H.; Zierke, S.] Rhein Westfal TH Aachen, Inst Phys 3, D-52056 Aachen, Germany. [Bai, X.] South Dakota Sch Mines & Technol, Dept Phys, Rapid City, SD 57701 USA. [Barwick, S. W.; Yodh, G.] Univ Calif Irvine, Dept Phys & Astron, Irvine, CA 92697 USA. [Baum, V.; Eberhardt, B.; Koepke, L.; Luenemann, J.; Schatto, K.; Wiebe, K.] Johannes Gutenberg Univ Mainz, Inst Phys, D-55099 Mainz, Germany. [Beatty, J. J.; Davis, J. C.; Pfendner, C.; Stamatikos, M.] Ohio State Univ, Dept Phys, Columbus, OH 43210 USA. [Beatty, J. J.; Davis, J. C.; Pfendner, 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. [Tjus, J. Becker; Bos, F.; Eichmann, B.; Fedynitch, A.; Kroll, M.; Saba, S. M.; Schoeneberg, S.; Unger, E.] Ruhr Univ Bochum, Fak Phys & Astron, D-44780 Bochum, Germany. [Becker, K. -H.; Bindig, D.; Fischer-Wasels, T.; Helbing, K.; Hoffmann, R.; Klaes, J.; Kopper, S.; Naumann, U.; Obertacke, A.; Omairat, A.; Posselt, J.; Soldin, D.; Tepe, A.] Univ Wuppertal, Dept Phys, D-42119 Wuppertal, Germany. [Berley, D.; Blaufuss, E.; Cheung, E.; Christy, B.; Felde, J.; Goodman, J. A.; Hellauer, R.; Hoffman, K. D.; Maunu, R.; Meagher, K.; Olivas, A.; Redl, P.; Richman, M.; Schmidt, T.; Sullivan, G. W.; Wissing, H.] Univ Maryland, Dept Phys, College Pk, MD 20742 USA. [Bernhard, A.; Coenders, S.; Gross, A.; Jurkovic, M.; Leute, J.; Resconi, E.; Schulz, O.; Sestayo, Y.] Tech Univ Munich, D-85748 Garching, Germany. [Besson, D. Z.] Univ Kansas, Dept Phys & Astron, Lawrence, KS 66045 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.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. [Binder, G.; Filimonov, K.; Gerhardt, L.; Ha, C.; Klein, S. R.; Miarecki, S.; Price, P. B.; Woschnagg, K.] Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA. [Boersma, D. J.; Botner, O.; Euler, S.; Hallgren, A.; Heros, C. Perez De Los; Strom, R.; Taavola, H.] Uppsala Univ, Dept Phys & Astron, S-75120 Uppsala, Sweden. [Bose, D.; Rott, C.] Sungkyunkwan Univ, Dept Phys, Suwon 440746, South Korea. [Boeser, S.; Franckowiak, A.; Hebecker, D.; Homeier, A.; Kowalski, M.; Schulte, L.; Stasik, A.; Strotjohann, N. L.; Usner, M.; Voge, M.] Univ Bonn, Inst Phys, D-53115 Bonn, Germany. [Brayeur, L.; Casier, M.; De Clercq, C.; de Vries, K. D.; Golup, G.; Kunnen, J.; Maggi, G.; Miller, J.; Strahler, E. A.; van Eijndhoven, N.] Vrije Univ Brussel, Dienst ELEM, B-1050 Brussels, Belgium. [Casey, J.; Daughhetee, J.; Taboada, I.] Georgia Inst Technol, Sch Phys, Atlanta, GA 30332 USA. [Daughhetee, J.; Taboada, I.] Georgia Inst Technol, Ctr Relativist Astrophys, Atlanta, GA 30332 USA. [Clark, K.] Univ Toronto, Dept Phys, Toronto, ON M5S 1A7, Canada. [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, Dept Phys, D-44221 Dortmund, Germany. [Cowen, D. F.] Penn State Univ, Dept Astron & Astrophys, University Pk, PA 16802 USA. [De Ridder, S.; Feusels, T.; Ismail, A. Haj; Jlelati, O.; Labare, M.; Meli, A.; Ryckbosch, D.; Vraeghe, M.] Univ Ghent, Dept Phys & Astron, B-9000 Ghent, Belgium. [de With, M.; Kolanoski, H.] Humboldt Univ, Inst Phys, D-12489 Berlin, Germany. [Evenson, P. A.; Gaisser, T. K.; Gonzalez, J. G.; Hussain, S.; Kuwabara, T.; Ruzybayev, B.; Seckel, D.; Stanev, T.; Tamburro, A.; Tilav, S.] Univ Delaware, Bartol Res Inst, Newark, DE 19716 USA. [Evenson, P. A.; Gaisser, T. K.; Gonzalez, J. G.; Hussain, S.; Kuwabara, T.; Ruzybayev, B.; Seckel, D.; Stanev, T.; Tamburro, A.; Tilav, S.] Univ Delaware, Dept Phys & Astron, Newark, DE 19716 USA. [Fazely, A. R.; Ter-Antonyan, S.; Xu, X. W.] Southern Univ, Dept Phys, Baton Rouge, LA 70813 USA. [Gallagher, J.] Univ Wisconsin, Dept Astron, Madison, WI 53706 USA. [Grandmont, D. T.; Grant, D.; Nowicki, S. C.; Odrowski, S.; Sheremata, C.; Wood, T. R.] Univ Alberta, Dept Phys, Edmonton, AB T6G 2E1, Canada. [Hanson, K.; Heereman, D.; Meures, T.; O'Murchadha, A.; Pinat, E.] Univ Libre Bruxelles, Fac Sci, B-1050 Brussels, Belgium. [Hoshina, K.] Univ Tokyo, Earthquake Res Inst, Bunkyo Ku, Tokyo 1130032, Japan. [Ishihara, A.; Mase, K.; Yoshida, S.] Chiba Univ, Dept Phys, Chiba 2638522, Japan. [Japaridze, G. S.] Clark Atlanta Univ, CTSPS, Atlanta, GA 30314 USA. [Kiryluk, J.; Lesiak-Bzdak, M.; Niederhausen, H.] SUNY Stony Brook, Dept Phys & Astron, Stony Brook, NY 11794 USA. [Kohnen, G.] Univ Mons, B-7000 Mons, Belgium. [Koskinen, D. J.; Larson, M. J.; Medici, M.; Sandroos, J.; Sarkar, S.] Univ Copenhagen, Niels Bohr Inst, DK-2100 Copenhagen, Denmark. [Madsen, J.; Seunarine, S.; Spiczak, G. M.] Univ Wisconsin, Dept Phys, River Falls, WI 54022 USA. [Palczewski, T.; Pepper, J. A.; Toale, P. A.; Williams, D. R.; Xu, D. L.; Zarzhitsky, P.] Univ Alabama, Dept Phys & Astron, Tuscaloosa, AL 35487 USA. [Rawlins, K.] Univ Alaska Anchorage, Dept Phys & Astron, Anchorage, AK 99508 USA. [Sarkar, S.] Univ Oxford, Dept Phys, Oxford OX1 3NP, England. [Stamatikos, M.] NASA, Goddard Space Flight Ctr, Greenbelt, MD 20771 USA. RP Aartsen, MG (reprint author), Univ Adelaide, Sch Chem & Phys, Adelaide, SA 5005, Australia. RI Koskinen, David/G-3236-2014; Auffenberg, Jan/D-3954-2014; Maruyama, Reina/A-1064-2013; Aguilar Sanchez, Juan Antonio/H-4467-2015; Tjus, Julia/G-8145-2012; Sarkar, Subir/G-5978-2011; Beatty, James/D-9310-2011; Wiebusch, Christopher/G-6490-2012; Taavola, Henric/B-4497-2011; OI Koskinen, David/0000-0002-0514-5917; Auffenberg, Jan/0000-0002-1185-9094; Maruyama, Reina/0000-0003-2794-512X; Aguilar Sanchez, Juan Antonio/0000-0003-2252-9514; Ter-Antonyan, Samvel/0000-0002-5788-1369; Schukraft, Anne/0000-0002-9112-5479; Larsen, Dag Toppe/0000-0002-9898-2174; Sarkar, Subir/0000-0002-3542-858X; Beatty, James/0000-0003-0481-4952; Wiebusch, Christopher/0000-0002-6418-3008; Rott, Carsten/0000-0002-6958-6033; Groh, John/0000-0001-9880-3634; Taavola, Henric/0000-0002-2604-2810; Perez de los Heros, Carlos/0000-0002-2084-5866; Strotjohann, Nora Linn/0000-0002-4667-6730; Arguelles Delgado, Carlos/0000-0003-4186-4182 FU U. S. National Science Foundation-Office of Polar Programs; U. S. National Science Foundation-Physics Division; University of Wisconsin Alumni Research Foundation; Grid Laboratory of Wisconsin (GLOW); University of Wisconsin-Madison; Open Science Grid (OSG); U.S. Department of Energy; National Energy Research Scientific Computing Center; Louisiana Optical Network Initiative (LONI); Natural Sciences and Engineering Research Council of Canada; West-Grid and Compute/Calcul Canada; 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, United Kingdom; Marsden Fund, New Zealand; Australian Research Council; Japan Society for Promotion of Science (JSPS); Swiss National Science Foundation (SNSF), Switzerland; National Research Foundation of Korea (NRF); Danish National Research Foundation, Denmark (DNRF) FX We acknowledge the support from the following agencies: U. S. National Science Foundation-Office of Polar Programs, U.S. National Science Foundation-Physics Division, University of Wisconsin Alumni Research Foundation, the Grid Laboratory of Wisconsin (GLOW) grid infrastructure at the University of Wisconsin-Madison, the Open Science Grid (OSG) grid infrastructure; U.S. Department of Energy, and National Energy Research Scientific Computing Center, the Louisiana Optical Network Initiative (LONI) grid computing resources; Natural Sciences and Engineering Research Council of Canada, West-Grid and Compute/Calcul Canada; Swedish Research Council, Swedish Polar Research Secretariat, Swedish National Infrastructure for Computing (SNIC), and 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, United Kingdom; Marsden Fund, New Zealand; Australian Research Council; Japan Society for Promotion of Science (JSPS); the Swiss National Science Foundation (SNSF), Switzerland; National Research Foundation of Korea (NRF); Danish National Research Foundation, Denmark (DNRF). NR 70 TC 49 Z9 50 U1 1 U2 15 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0004-637X EI 1538-4357 J9 ASTROPHYS J JI Astrophys. J. PD DEC 1 PY 2014 VL 796 IS 2 AR 109 DI 10.1088/0004-637X/796/2/109 PG 14 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA AT4AI UT WOS:000344878900038 ER PT J AU Abeysekara, AU Alfaro, R Alvarez, C Alvarez, JD Arceo, R Arteaga-Velazquez, JC Solares, HAA Barber, AS Baughman, BM Bautista-Elivar, N Belmont, E BenZvi, SY Berley, D Rosales, MB Braun, J Caballero-Mora, KS Carraminana, A Castillo, M Cotti, U Cotzomi, J De La Fuente, E De Leon, C DeYoung, T Hernandez, RD Diaz-Velez, JC Dingus, BL DuVernois, MA Ellsworth, RW Fiorino, DW Fraija, N Galindo, A Garfias, F Gonzalez, MM Goodman, JA Gussert, M Hampel-Arias, Z Harding, JP Huntemeyer, P Hui, CM Imran, A Iriarte, A Karn, P Kieda, D Kunde, GJ Lara, A Lauer, RJ Lee, WH Lennarz, D Vargas, HL Linnemann, JT Longo, M Luna-Garcia, R Malone, K Marinelli, A Marinelli, SS Martinez, H Martinez, O Martinez-Castro, J Matthews, JAJ McEnery, J Torres, EM Miranda-Romagnoli, P Moreno, E Mostafa, M Nellen, L Newbold, M Noriega-Papaqui, R Oceguera-Becerra, T Patricelli, B Pelayo, R Perez-Perez, EG Pretz, J Riviere, C Rosa-Gonzalez, D Ruiz-Velasco, E Ryan, J Salazar, H Greus, FS Sandoval, A Schneider, M Sinnis, G Smith, AJ Woodle, KS Springer, RW Taboada, I Toale, PA Tollefson, K Torres, I Ukwatta, TN Villasenor, L Weisgarber, T Westerhoff, S Wisher, IG Wood, J Yodh, GB Younk, PW Zaborov, D Zepeda, A Zhou, H AF Abeysekara, A. U. Alfaro, R. Alvarez, C. Alvarez, J. D. Arceo, R. Arteaga-Velazquez, J. C. Solares, H. A. Ayala Barber, A. S. Baughman, B. M. Bautista-Elivar, N. Belmont, E. BenZvi, S. Y. Berley, D. Bonilla Rosales, M. Braun, J. Caballero-Mora, K. S. Carraminana, A. Castillo, M. Cotti, U. Cotzomi, J. De La Fuente, E. De Leon, C. DeYoung, T. Diaz Hernandez, R. Diaz-Velez, J. C. Dingus, B. L. DuVernois, M. A. Ellsworth, R. W. Fiorino, D. W. Fraija, N. Galindo, A. Garfias, F. Gonzalez, M. M. Goodman, J. A. Gussert, M. Hampel-Arias, Z. Harding, J. P. Huentemeyer, P. Hui, C. M. Imran, A. Iriarte, A. Karn, P. Kieda, D. Kunde, G. J. Lara, A. Lauer, R. J. Lee, W. H. Lennarz, D. Leon Vargas, H. Linnemann, J. T. Longo, M. Luna-Garcia, R. Malone, K. Marinelli, A. Marinelli, S. S. Martinez, H. Martinez, O. Martinez-Castro, J. Matthews, J. A. J. McEnery, J. Mendoza Torres, E. Miranda-Romagnoli, P. Moreno, E. Mostafa, M. Nellen, L. Newbold, M. Noriega-Papaqui, R. Oceguera-Becerra, T. Patricelli, B. Pelayo, R. Perez-Perez, E. G. Pretz, J. Riviere, C. Rosa-Gonzalez, D. Ruiz-Velasco, E. Ryan, J. Salazar, H. Greus, F. Salesa Sandoval, A. Schneider, M. Sinnis, G. Smith, A. J. Woodle, K. Sparks Springer, R. W. Taboada, I. Toale, P. A. Tollefson, K. Torres, I. Ukwatta, T. N. Villasenor, L. Weisgarber, T. Westerhoff, S. Wisher, I. G. Wood, J. Yodh, G. B. Younk, P. W. Zaborov, D. Zepeda, A. Zhou, H. CA HAWC Collaboration TI OBSERVATION OF SMALL-SCALE ANISOTROPY IN THE ARRIVAL DIRECTION DISTRIBUTION OF TeV COSMIC RAYS WITH HAWC SO ASTROPHYSICAL JOURNAL LA English DT Article DE astroparticle physics; cosmic rays ID AIR-SHOWER ARRAY; POWER SPECTRA; GAMMA-RAYS; ICECUBE; MILAGRO AB The High-Altitude Water Cherenkov ( HAWC) Observatory is sensitive to gamma rays and charged cosmic rays at TeV energies. The detector is still under construction, but data acquisition with the partially deployed detector started in 2013. An analysis of the cosmic- ray arrival direction distribution based on 4.9 x 10(10) events recorded between 2013 June and 2014 February shows anisotropy at the 10(-4) level on angular scales of about 10 degrees.. The HAWC cosmic- ray sky map exhibits three regions of significantly enhanced cosmic- ray flux; two of these regions were first reported by the Milagro experiment. A third region coincides with an excess recently reported by the ARGO-YBJ experiment. An angular power spectrum analysis of the sky shows that all terms up to l = 15 contribute significantly to the excesses. C1 [Abeysekara, A. U.; DeYoung, T.; Linnemann, J. T.; Marinelli, S. S.; Tollefson, K.; Ukwatta, T. N.] Michigan State Univ, Dept Phys & Astron, E Lansing, MI 48824 USA. [Abeysekara, A. U.; Barber, A. S.; Kieda, D.; Newbold, M.; Springer, R. W.] Univ Utah, Dept Phys & Astron, Salt Lake City, UT USA. [Alfaro, R.; Belmont, E.; Leon Vargas, H.; Marinelli, A.; Oceguera-Becerra, T.; Ruiz-Velasco, E.; Sandoval, A.] Univ Nacl Autonoma Mexico, Inst Fis, Mexico City 01000, DF, Mexico. [Alvarez, C.; Arceo, R.] Univ Autonoma Chiapas, CEFyMAP, Tuxtla Gutierrez, Chiapas, Mexico. [Alvarez, J. D.; Arteaga-Velazquez, J. C.; Cotti, U.; De Leon, C.; Villasenor, L.] Univ Michoacana, Morelia, Michoacan, Mexico. [Solares, H. A. Ayala; Huentemeyer, P.; Hui, C. M.; Zhou, H.] Michigan Technol Univ, Dept Phys, Houghton, MI 49931 USA. [Baughman, B. M.; Berley, D.; Braun, J.; Ellsworth, R. W.; Goodman, J. A.; Riviere, C.; Smith, A. J.; Wood, J.] Univ Maryland, Dept Phys, College Pk, MD 20742 USA. [Bautista-Elivar, N.; Perez-Perez, E. G.] Univ Politecn Pachuca, Pachuca, Hidalgo, Mexico. [BenZvi, S. Y.] Univ Rochester, Dept Phys & Astron, Rochester, NY 14627 USA. [BenZvi, S. Y.; Braun, J.; Diaz-Velez, J. C.; DuVernois, M. A.; Fiorino, D. W.; Hampel-Arias, Z.; Imran, A.; Karn, P.; Weisgarber, T.; Westerhoff, S.; Wisher, I. G.] Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI USA. [BenZvi, S. Y.; Diaz-Velez, J. C.; DuVernois, M. A.; Fiorino, D. W.; Hampel-Arias, Z.; Imran, A.; Karn, P.; Weisgarber, T.; Westerhoff, S.; Wisher, I. G.] Univ Wisconsin, Dept Phys, Madison, WI 53706 USA. [Bonilla Rosales, M.; Carraminana, A.; Diaz Hernandez, R.; Galindo, A.; Mendoza Torres, E.; Rosa-Gonzalez, D.; Torres, I.] Inst Nacl Astrofis Opt & Electr, Puebla, Mexico. [Caballero-Mora, K. S.; Martinez, H.; Zepeda, A.] Inst Politecn Nacl, Ctr Invest & Estudios Avanzados, Mexico City, DF, Mexico. [Castillo, M.; Cotzomi, J.; Martinez, O.; Moreno, E.; Salazar, H.] Benemerita Univ Autonoma Puebla, Fac Ciencias Fis, Puebla 72570, Mexico. [De La Fuente, E.; Oceguera-Becerra, T.] Univ Guadalajara, IAM Dept Fis, Guadalajara, Jalisco, Mexico. [De La Fuente, E.; Oceguera-Becerra, T.] Univ Guadalajara, Dept Elect CUCEI, IT Phd CUCEA, Phys Mat Phd CUVALLES, Guadalajara, Jalisco, Mexico. [Dingus, B. L.; Harding, J. P.; Imran, A.; Kunde, G. J.; Sinnis, G.; Ukwatta, T. N.; Younk, P. W.] Los Alamos Natl Lab, Div Phys, Los Alamos, NM 87545 USA. [Ellsworth, R. W.] George Mason Univ, Sch Phys Astron & Computat Sci, Fairfax, VA 22030 USA. [Fraija, N.; Garfias, F.; Gonzalez, M. M.; Iriarte, A.; Lee, W. H.; Patricelli, B.; Riviere, C.] Univ Nacl Autonoma Mexico, Inst Astron, Mexico City 04510, DF, Mexico. [Gussert, M.; Longo, M.] Colorado State Univ, Dept Phys, Ft Collins, CO 80523 USA. [Karn, P.; Yodh, G. B.] Univ Calif Irvine, Dept Phys & Astron, Irvine, CA USA. [Lara, A.] Univ Nacl Autonoma Mexico, Inst Geofis, Mexico City 04510, DF, Mexico. [Lauer, R. J.; Matthews, J. A. J.] Univ New Mexico, Dept Phys & Astron, Albuquerque, NM 87131 USA. [Lennarz, D.; Taboada, I.] Georgia Inst Technol, Sch Phys, Atlanta, GA 30332 USA. [Lennarz, D.; Taboada, I.] Georgia Inst Technol, Ctr Relativist Astrophys, Atlanta, GA 30332 USA. [Luna-Garcia, R.; Martinez-Castro, J.; Pelayo, R.] Inst Politecn Nacl, Ctr Invest Computac, Mexico City, DF, Mexico. [Malone, K.; Mostafa, M.; Pretz, J.; Greus, F. Salesa; Woodle, K. Sparks; Zaborov, D.] Penn State Univ, Dept Phys, University Pk, PA 16802 USA. [McEnery, J.] NASA, Goddard Space Flight Ctr, Greenbelt, MD 20771 USA. [Miranda-Romagnoli, P.; Noriega-Papaqui, R.] Univ Autonoma Estado Hidalgo, Pachuca, Hidalgo, Mexico. [Nellen, L.] Univ Nacl Autonoma Mexico, Inst Ciencias Nucl, Mexico City 04510, DF, Mexico. [Pelayo, R.] Inst Politecn Nacl, Unidad Profes Interdisciplinaria Ingn & Tecnol Av, Mexico City, DF, Mexico. [Ryan, J.] Univ New Hampshire, Ctr Space Sci, Durham, NH 03824 USA. [Schneider, M.] Univ Calif Santa Cruz, Santa Cruz Inst Particle Phys, Santa Cruz, CA 95064 USA. [Toale, P. A.] Univ Alabama, Dept Phys & Astron, Tuscaloosa, AL 35487 USA. RP Abeysekara, AU (reprint author), Michigan State Univ, Dept Phys & Astron, E Lansing, MI 48824 USA. EM dan.fiorino@wipac.wisc.edu OI Lara, Alejandro/0000-0001-6336-5291 FU US National Science Foundation (NSF); US Department of Energy Office of High- Energy Physics; Laboratory Directed Research and Development (LDRD) program of Los Alamos National Laboratory; Consejo Nacional de Ciencia y Tecnologia (CONACyT), Mexico [55155, 105666, 122331, 132197]; Red de Fisica de Altas Energias, Mexico, DGAPAUNAM [IG100414- 3, IN108713, IN121309, IN115409, IN113612]; VIEP-BUAP [161-EXC-2011]; University of Wisconsin Alumni Research Foundation; Institute of Geophysics, Planetary Physics, and Signatures at Los Alamos National Laboratory; Luc Binette Foundation UNAM FX We gratefully acknowledge Scott DeLay for his dedicated efforts in the construction and maintenance of the HAWC experiment. This work has been supported by the US National Science Foundation (NSF), the US Department of Energy Office of High- Energy Physics, the Laboratory Directed Research and Development (LDRD) program of Los Alamos National Laboratory, Consejo Nacional de Ciencia y Tecnologia (CONACyT), Mexico (grants 55155, 105666, 122331, and 132197), Red de Fisica de Altas Energias, Mexico, DGAPAUNAM (grants IG100414- 3, IN108713, and IN121309, IN115409, IN113612), VIEP-BUAP (grant 161-EXC-2011), the University of Wisconsin Alumni Research Foundation, the Institute of Geophysics, Planetary Physics, and Signatures at Los Alamos National Laboratory, and the Luc Binette Foundation UNAM Postdoctoral Fellowship program. NR 34 TC 19 Z9 19 U1 0 U2 6 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0004-637X EI 1538-4357 J9 ASTROPHYS J JI Astrophys. J. PD DEC 1 PY 2014 VL 796 IS 2 AR 108 DI 10.1088/0004-637X/796/2/108 PG 11 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA AT4AI UT WOS:000344878900037 ER PT J AU Fan, ZS Neff, JC Waldrop, MP Ballantyne, AP Turetsky, MR AF Fan, Zhaosheng Neff, Jason C. Waldrop, Mark P. Ballantyne, Ashley P. Turetsky, Merritt R. TI Transport of oxygen in soil pore-water systems: implications for modeling emissions of carbon dioxide and methane from peatlands SO BIOGEOCHEMISTRY LA English DT Article DE Water table; Model; Oxygen; Microbial; Habitat; Warming; Aerobic; Anaerobic ID HYDRAULIC CONDUCTIVITY; NORTHERN PEATLANDS; ECOSYSTEM MODEL; CLIMATE-CHANGE; POROUS SOLIDS; DIFFUSION; FEN; DENITRIFICATION; GAS; DECOMPOSITION AB Peatlands store vast amounts of soil carbon and are significant sources of greenhouse gases, including carbon dioxide (CO2) andmethane (CH4) emissions. The traditional approach in biogeochemical model simulations of peatland emissions is to simply divide the soil domain into an aerobic zone above and an anaerobic zone below the water table (WT) and then calculate CO2 and CH4 emissions based on the assumed properties of these two discrete zones. However, there are major potential drawbacks associated with the traditional WT-based approach, because aerobic or anaerobic environments are ultimately determined by oxygen (O-2) concentration rather than water content directly. Variations in O2 content above and below the WT can be large and thus may play an important role in partitioning of carbon fluxes between CO2 and CH4. In this paper, we propose an oxygen-based approach, which simulates the vertical and radial components of O-2 movement and consumption through the soil aerobic and anaerobic environments. We then use both our oxygen-based and the traditional WT-based approaches to simulate CO2 and CH4 emissions from an Alaskan fen peatland. The results of model calibration and validation suggest that our physically realistic approach (i.e., oxygen-based approach) cause less biases on the simulated flux of CO2 and CH4. The results of model simulations also suggest that the traditional WT-based approach might substantially under-estimate CH4 emissions and over-estimate CO2 emissions from the fen due to the presence of anaerobic zones in unsaturated soil. Our oxygen-based approach can be easily incorporated into existing ecosystem or earth system models but will require additional validation with more extensive field observations to be implemented within biogeochemical models to improve simulations of soil C fluxes at regional or global scale. C1 [Fan, Zhaosheng] Argonne Natl Lab, Biosci Div, Argonne, IL 60439 USA. [Neff, Jason C.] Univ Colorado, Dept Geol Sci, Boulder, CO 80309 USA. [Waldrop, Mark P.] USGS, Menlo Pk, CA 94025 USA. [Ballantyne, Ashley P.] Univ Montana, Dept Ecosyst & Conservat Sci, Missoula, MT 59812 USA. [Turetsky, Merritt R.] Univ Guelph, Dept Integrat Biol, Guelph, ON N1G 1G2, Canada. RP Fan, ZS (reprint author), Argonne Natl Lab, Biosci Div, 9700 S Cass Ave, Argonne, IL 60439 USA. EM zfan@anl.gov OI Waldrop, Mark/0000-0003-1829-7140 FU U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Climate and Environmental Science Division [DE-AC02-06CH11357]; National Science Foundation (NSF) [DEB-0425328, DEB-0724514, DEB-0830997]; USGS Climate Research & Development Program; Bonanza Creek LTER Program - NSF [DEB-1026415]; Bonanza Creek LTER Program - USDA Forest Service, Pacific Northwest Research Station [PNW01-JV112619320-16] FX This work was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Climate and Environmental Science Division under contract DE-AC02-06CH11357, by the National Science Foundation (NSF) for the APEX project (DEB-0425328, DEB-0724514, DEB-0830997), and by the USGS Climate Research & Development Program. Additional funding and considerable logistic support were provided by the Bonanza Creek LTER Program, which is jointly funded by NSF (DEB-1026415) and the USDA Forest Service, Pacific Northwest Research Station (PNW01-JV112619320-16). NR 65 TC 6 Z9 6 U1 4 U2 51 PU SPRINGER PI DORDRECHT PA VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS SN 0168-2563 EI 1573-515X J9 BIOGEOCHEMISTRY JI Biogeochemistry PD DEC PY 2014 VL 121 IS 3 BP 455 EP 470 DI 10.1007/s10533-014-0012-0 PG 16 WC Environmental Sciences; Geosciences, Multidisciplinary SC Environmental Sciences & Ecology; Geology GA AU0NS UT WOS:000345320700001 ER PT J AU Yang, ZX Sarkar, M Kumar, A Tumuluru, JS Huhnke, RL AF Yang, Zixu Sarkar, Madhura Kumar, Ajay Tumuluru, Jaya Shankar Huhnke, Raymond L. TI Effects of torrefaction and densification on switchgrass pyrolysis products SO BIORESOURCE TECHNOLOGY LA English DT Article DE Torrefaction; Densification; Switchgrass; Pyrolysis; Py-GC/MS ID BIO-OIL; CORN STOVER; BIOMASS; CELLULOSE; HEMICELLULOSE; TEMPERATURE; LIGNIN; WOOD; PRETREATMENT; KINETICS AB The pyrolysis behaviors of four types of pretreated switchgrass (torrefied at 230 and 270 degrees C, densification, and torrefaction at 270 degrees C followed by densification) were studied at three temperatures (500, 600, 700 degrees C) using a pyroprobe attached to a gas chromatogram mass spectroscopy (Py-GC/MS). The torrefaction of switchgrass improved its oxygen to carbon ratio and energy content. Contents of anhydrous sugars and phenols in pyrolysis products of torrefied switchgrass were higher than those in pyrolysis products of raw switchgrass. As the torrefaction temperature increased from 230 to 270 degrees C, the contents of anhydrous sugars and phenols in pyrolysis products increased whereas content of guaiacols decreased. High pyrolysis temperature (600 and 700 degrees C as compared to 500 degrees C) enhanced decomposition of lignin and anhydrous sugars, leading to increase in phenols, aromatics and furans. Densification enhanced depolymerization of cellulose and hemicellulose during pyrolysis. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Yang, Zixu; Sarkar, Madhura; Kumar, Ajay; Huhnke, Raymond L.] Oklahoma State Univ, Dept Biosyst & Agr Engn, Stillwater, OK 74078 USA. [Tumuluru, Jaya Shankar] Idaho Natl Lab, Biofuels & Renewable Energy Technol Dept, Idaho Falls, ID USA. RP Kumar, A (reprint author), 228 Agr Hall, Stillwater, OK 74078 USA. EM ajay.kumar@okstate.edu FU South Central Sungrant Initiative - U.S. Department of Transportation (DOT); Oklahoma Agricultural Experiment Station; U.S. National Science Foundation [EPS-0814361] FX This project was funded, in part, by the South Central Sungrant Initiative - U.S. Department of Transportation (DOT), Oklahoma Agricultural Experiment Station, and U.S. National Science Foundation under Grant No. EPS-0814361. NR 35 TC 18 Z9 19 U1 5 U2 55 PU ELSEVIER SCI LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND SN 0960-8524 EI 1873-2976 J9 BIORESOURCE TECHNOL JI Bioresour. Technol. PD DEC PY 2014 VL 174 BP 266 EP 273 DI 10.1016/j.biortech.2014.10.032 PG 8 WC Agricultural Engineering; Biotechnology & Applied Microbiology; Energy & Fuels SC Agriculture; Biotechnology & Applied Microbiology; Energy & Fuels GA AT5YD UT WOS:000345014900033 PM 25463807 ER PT J AU Newton, MA Di Michiel, M Ferri, D Fernandez-Garcia, M Beale, AM Jacques, SDM Chupas, PJ Chapman, KW AF Newton, Mark A. Di Michiel, Marco Ferri, Davide Fernandez-Garcia, Marcos Beale, Andrew M. Jacques, Simon D. M. Chupas, Peter J. Chapman, Karena W. TI Catalytic Adventures in Space and Time Using High Energy X-rays SO CATALYSIS SURVEYS FROM ASIA LA English DT Article DE Operando studies; High energy X-rays; Diffraction; Pair distribution function methods; Tomography; Combined techniques ID PAIR-DISTRIBUTION-FUNCTION; MODULATION EXCITATION SPECTROSCOPY; REFLECTION INFRARED-SPECTROSCOPY; IN-SITU; HETEROGENEOUS CATALYSTS; SCATTERING EXPERIMENTS; COMPUTED-TOMOGRAPHY; OXYGEN STORAGE; DIFFRACTION; DETECTOR AB Very high energy X-rays (ca. > 40 keV) have long offered great promise in providing great insight into the inner workings of catalysts; insights that may complement the battery of techniques available to researchers in catalysis either in the laboratory or at more conventional X-ray wavelengths. This contribution aims to critically assess the diverse possibilities now available in the high energy domain as a result of the maturation of third generation synchrotron facilities and to look forward to the potential that forthcoming developments in synchrotron source technology may offer the world of catalysis in the near future. C1 [Newton, Mark A.; Di Michiel, Marco] ESRF European Synchrotron, CS40220, F-38043 Grenoble 9, France. [Ferri, Davide] Paul Scherrer Inst, CH-5232 Villigen, Switzerland. [Fernandez-Garcia, Marcos] CSIC, Inst Catalisis & Petroleoquim, E-28049 Madrid, Spain. [Beale, Andrew M.] UCL, Dept Chem, London WC1H 0AJ, England. [Beale, Andrew M.] Rutherford Appleton Lab, UK Catalysis Hub, Didcot OX11 0FA, Oxon, England. [Jacques, Simon D. M.] Rutherford Appleton Lab, MXIF, Didcot OX11 0FA, Oxon, England. [Jacques, Simon D. M.] Univ Manchester, Sch Mat, Manchester M13 9PL, Lancs, England. [Chupas, Peter J.; Chapman, Karena W.] Argonne Natl Lab, Xray Sci Div, Adv Photon Source, Argonne, IL 60439 USA. RP Newton, MA (reprint author), ESRF European Synchrotron, CS40220, F-38043 Grenoble 9, France. EM manewton68@gmail.com RI Fernandez-Garcia, Marcos/A-8122-2014; Jacques, Simon/C-6960-2009; OI Jacques, Simon/0000-0002-7275-5272; Ferri, Davide/0000-0002-9354-5231; Beale, Andrew/0000-0002-0923-1433 FU Royal Society of Chemistry [09 01 639]; NWO (NL); EPSRC (UK) FX We should like to thank the ESRF and the APS for access to the facilities required to make the measurements reported in this review. MAN would like to thank the Royal Society of Chemistry for a journals Grant (09 01 639) that permitted the work PDF work reported here to be undertaken and the APS for a visiting scientist position that permitted the collaborative development of a combined PDF/DRIFTS experiment to be achieved. He should also like to thank all the other authors for putting up with him as long as they have. SDMJ and AMB would like to thank both NWO (NL) and EPSRC (UK) for funding to perform the high energy scattering experiments. NR 64 TC 2 Z9 2 U1 4 U2 31 PU SPRINGER/PLENUM PUBLISHERS PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1571-1013 EI 1574-9266 J9 CATAL SURV ASIA JI Catal. Surv. Asia PD DEC PY 2014 VL 18 IS 4 SI SI BP 134 EP 148 DI 10.1007/s10563-014-9173-z PG 15 WC Chemistry, Physical SC Chemistry GA AT7BL UT WOS:000345091100004 ER PT J AU Seehra, MS Popp, BV Goulay, F Pyapalli, SK Gullion, T Poston, J AF Seehra, M. S. Popp, B. V. Goulay, F. Pyapalli, S. K. Gullion, T. Poston, J. TI Hydrothermal treatment of microcrystalline cellulose under mild conditions: characterization of solid and liquid-phase products SO CELLULOSE LA English DT Article DE Cellulose; Hydrothermal treatment; X-ray diffraction; Phase transformations; NMR spectroscopy ID HOT-COMPRESSED WATER; C-13 NMR-SPECTRA; SUPERCRITICAL WATER; CONVERSION; BIOMASS; CRYSTALLINITY; HYDROLYSIS; LIQUEFACTION; KINETICS AB Microcrystalline cellulose (MCC) particles were subjected to hydrothermal treatment using an autoclave with temperatures ranging from 200 to 250 A degrees C and reaction times ranging from 20 to 100 min. The structure and chemical composition of the reacted solid phase was analyzed by X-ray diffraction, thermo-gravimetric analysis, FTIR spectroscopy and C-13-NMR spectroscopy. The relative composition of the water-soluble products was determined by one-dimensional H-1-NMR and two-dimensional homo and hetero-nuclear NMR spectroscopy. Within the experimental temperature and treatment time ranges, the crystallinity of the reacted solid phase was found to be mostly dependent on the treatment temperature while the aqueous solution was found to change with both temperature and treatment time. At the maximum temperature employed in this study (250 A degrees C), the solid products are similar to amorphous oxidized carbon with glucose as the main water-soluble product. At lower temperatures the particles are unconverted MCC and the liquid products are primarily levulinic acid, formic acid and acetic acid with smaller quantities of 5-hydroxymethyl-furfural and glucose. Heterogeneous and liquid phase reaction-schemes are proposed to explain the observed solid and water-soluble products as a function of temperature and treatment time. C1 [Seehra, M. S.; Pyapalli, S. K.] W Virginia Univ, Dept Phys & Astron, Morgantown, WV 26506 USA. [Popp, B. V.; Goulay, F.; Gullion, T.] W Virginia Univ, C Eugene Bennett Dept Chem, Morgantown, WV 26506 USA. [Poston, J.] US DOE, Natl Energy Technol Labs, Morgantown, WV 26505 USA. RP Seehra, MS (reprint author), W Virginia Univ, Dept Phys & Astron, Morgantown, WV 26506 USA. EM mseehra@wvu.edu; Fabien.Goulay@mail.wvu.edu RI Popp, Brian/D-8577-2011 OI Popp, Brian/0000-0001-6367-1168 FU West Virginia University; U.S. Department of Energy [DE-FC26-05NT42456]; National Science Foundation [CHE-1228336] FX We gratefully acknowledge financial support from West Virginia University. MSS also acknowledges financial support from the U.S. Department of Energy (Contract # DE-FC26-05NT42456) during the initial stages of the project. Funding for solution NMR instrumentation was provided by the National Science Foundation (CHE-1228336). NR 34 TC 4 Z9 4 U1 3 U2 52 PU SPRINGER PI DORDRECHT PA VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS SN 0969-0239 EI 1572-882X J9 CELLULOSE JI Cellulose PD DEC PY 2014 VL 21 IS 6 BP 4483 EP 4495 DI 10.1007/s10570-014-0424-y PG 13 WC Materials Science, Paper & Wood; Materials Science, Textiles; Polymer Science SC Materials Science; Polymer Science GA AT2ZF UT WOS:000344802700052 ER PT J AU Zhang, L Lee, SC Zhao, H Wu, F AF Zhang, L. Lee, S. C. Zhao, H. Wu, F. TI Response to "Erlotinib and Gastric Acid-Reducing Agents: A Combination to Avoid or to Support?" SO CLINICAL PHARMACOLOGY & THERAPEUTICS LA English DT Letter C1 [Zhang, L.; Lee, S. C.; Zhao, H.; Wu, F.] US FDA, Off Clin Pharmacol, Off Translat Sci, Ctr Drug Evaluat & Res, Silver Spring, MD 20993 USA. [Wu, F.] Oak Ridge Inst Sci & Educ, Oak Ridge, TN USA. RP Zhang, L (reprint author), US FDA, Off Clin Pharmacol, Off Translat Sci, Ctr Drug Evaluat & Res, Silver Spring, MD 20993 USA. EM leik.zhang@fda.hhs.gov NR 4 TC 2 Z9 2 U1 0 U2 1 PU NATURE PUBLISHING GROUP PI NEW YORK PA 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA SN 0009-9236 EI 1532-6535 J9 CLIN PHARMACOL THER JI Clin. Pharmacol. Ther. PD DEC PY 2014 VL 96 IS 6 BP 659 EP 659 DI 10.1038/clpt.2014.192 PG 1 WC Pharmacology & Pharmacy SC Pharmacology & Pharmacy GA AT8RS UT WOS:000345200400023 PM 25247623 ER PT J AU Su, Y Agrawal, G Woodring, J Myers, K Wendelberger, J Ahrens, J AF Su, Yu Agrawal, Gagan Woodring, Jonathan Myers, Kary Wendelberger, Joanne Ahrens, James TI Effective and efficient data sampling using bitmap indices SO CLUSTER COMPUTING-THE JOURNAL OF NETWORKS SOFTWARE TOOLS AND APPLICATIONS LA English DT Article DE Big data; Bitmap indexing; Data sampling; Multi-resolution; Parallel processing ID VOLUME VISUALIZATION AB With growing computational capabilities of parallel machines, scientific simulations are being performed at finer spatial and temporal scales, leading to a data explosion. The growing sizes are making it extremely hard to store, manage, disseminate, analyze, and visualize these datasets, especially as neither the memory capacity of parallel machines, memory access speeds, nor disk bandwidths are increasing at the same rate as the computing power. Sampling can be an effective technique to address the above challenges, but it is extremely important to ensure that dataset characteristics are preserved, and the loss of accuracy is within acceptable levels. In this paper, we address the data explosion problems by developing a novel sampling approach, and implementing it in a flexible system that supports server-side sampling and data subsetting. We observe that to allow subsetting over scientific datasets, data repositories are likely to use an indexing technique. Among these techniques, we see that bitmap indexing can not only effectively support subsetting over scientific datasets, but can also help create samples that preserve both value and spatial distributions over scientific datasets. We have developed algorithms for using bitmap indices to sample datasets. We have also shown how only a small amount of additional metadata stored with bitvectors can help assess loss of accuracy with a particular subsampling level. Some of the other properties of this novel approach include: (1) sampling can be flexibly applied to a subset of the original dataset, which may be specified using a value-based and/or a dimension-based subsetting predicate, and (2) no data reorganization is needed, once bitmap indices have been generated. We have extensively evaluated our method with different types of datasets and applications, and demonstrated the effectiveness of our approach. C1 [Su, Yu; Agrawal, Gagan] Ohio State Univ, Columbus, OH 43210 USA. [Woodring, Jonathan; Myers, Kary; Wendelberger, Joanne; Ahrens, James] Los Alamos Natl Lab, Los Alamos, NM 87544 USA. RP Su, Y (reprint author), Ohio State Univ, Columbus, OH 43210 USA. EM su1@cse.ohio-state.edu; agrawal@cse.ohio-state.edu; woodring@lanl.gov; kary@lanl.gov; joanne@lanl.gov; ahrens@lanl.gov OI Myers, Kary/0000-0002-5642-959X; Wendelberger, Joanne/0000-0001-5879-3945 FU Department of Energy (DOE) Office of Science (OSC) Advanced Scientific Computing Research (ASCR); NSF [IIS-0916196] FX This work was supported by the Department of Energy (DOE) Office of Science (OSC) Advanced Scientific Computing Research (ASCR) and NSF award IIS-0916196 to the Ohio State University. NR 51 TC 2 Z9 2 U1 0 U2 8 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1386-7857 EI 1573-7543 J9 CLUSTER COMPUT JI Cluster Comput. PD DEC PY 2014 VL 17 IS 4 BP 1081 EP 1100 DI 10.1007/s10586-014-0360-5 PG 20 WC Computer Science, Information Systems; Computer Science, Theory & Methods SC Computer Science GA AT6WL UT WOS:000345077400001 ER PT J AU Lakshminarasimhan, S Zou, XC Boyuka, DA Pendse, SV Jenkins, J Vishwanath, V Papka, ME Klasky, S Samatova, NF AF Lakshminarasimhan, Sriram Zou, Xiaocheng Boyuka, David A., II Pendse, Saurabh V. Jenkins, John Vishwanath, Venkatram Papka, Michael E. Klasky, Scott Samatova, Nagiza F. TI DIRAQ: scalable in situ data- and resource-aware indexing for optimized query performance SO CLUSTER COMPUTING-THE JOURNAL OF NETWORKS SOFTWARE TOOLS AND APPLICATIONS LA English DT Article DE Exascale computing; Indexing; Query processing; Compression AB Scientific data analytics in high-performance computing environments has been evolving along with the advancement of computing capabilities. With the onset of exascale computing, the increasing gap between compute performance and I/O bandwidth has rendered the traditional post-simulation processing a tedious process. Despite the challenges due to increased data production, there exists an opportunity to benefit from "cheap" computing power to perform query-driven exploration and visualization during simulation time. To accelerate such analyses, applications traditionally augment, post-simulation, raw data with large indexes, which are then repeatedly utilized for data exploration. However, the generation of current state-of-the-art indexes involves a compute- and memory-intensive processing, thus rendering them inapplicable in an in situ context. In this paper we propose DIRAQ, a parallel in situ, in network data encoding and reorganization technique that enables the transformation of simulation output into a query-efficient form, with negligible runtime overhead to the simulation run. DIRAQ's effective core-local, precision-based encoding approach incorporates an embedded compressed index that is 3-6 smaller than current state-of-the-art indexing schemes. Its data-aware index adjustmentation improves performance of group-level index layout creation by up to 35 % and reduces the size of the generated index by up to 27 %. Moreover, DIRAQ's in network index merging strategy enables the creation of aggregated indexes that speed up spatial-context query responses by up to versus alternative techniques. DIRAQ's topology-, data-, and memory-aware aggregation strategy results in efficient I/O and yields overall end-to-end encoding and I/O time that is less than that required to write the raw data with MPI collective I/O. C1 [Lakshminarasimhan, Sriram] IBM India Res Lab, Bangalore 560045, Karnataka, India. [Lakshminarasimhan, Sriram; Zou, Xiaocheng; Boyuka, David A., II; Pendse, Saurabh V.; Jenkins, John; Samatova, Nagiza F.] N Carolina State Univ, Raleigh, NC 27695 USA. [Lakshminarasimhan, Sriram; Zou, Xiaocheng; Boyuka, David A., II; Pendse, Saurabh V.; Jenkins, John; Klasky, Scott; Samatova, Nagiza F.] Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. [Lakshminarasimhan, Sriram; Vishwanath, Venkatram; Papka, Michael E.] Argonne Natl Lab, Argonne, IL 60439 USA. [Papka, Michael E.] Univ Illinois, De Kalb, IL 60115 USA. RP Samatova, NF (reprint author), N Carolina State Univ, Raleigh, NC 27695 USA. EM samatova@csc.ncsu.edu FU LLC U.S. D.O.E. [DEAC05-00OR22725]; U.S. Department of Energy, Office of Science, Advanced Scientific Computing Research (SDAVI Institute); U.S. Department of Energy, Office of Science, Advanced Scientific Computing Research (RSVP Project); U.S. National Science Foundation; DOE [DE-AC02-06CH11357] FX We would like to thank the FLASH Center for Computational Science at the University of Chicago for providing access to the FLASH simulation code and both the FLASH and S3D teams for providing access to the related datasets. We would like to acknowledge the use of resources at the Leadership Computing Facilities at Argonne National Laboratory and Oak Ridge National Laboratory, ALCF and OLCF respectively. Oak Ridge National Laboratory is managed by UT-Battelle for the LLC U.S. D.O.E. under Contract DEAC05-00OR22725. This work was supported in part by the U.S. Department of Energy, Office of Science, Advanced Scientific Computing Research (SDAVI Institute and RSVP Project) and the U.S. National Science Foundation (Expeditions in Computing and EAGER programs). The work of MEP and VV was supported by the DOE Contract DE-AC02-06CH11357. NR 36 TC 1 Z9 1 U1 0 U2 3 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1386-7857 EI 1573-7543 J9 CLUSTER COMPUT JI Cluster Comput. PD DEC PY 2014 VL 17 IS 4 BP 1101 EP 1119 DI 10.1007/s10586-014-0358-z PG 19 WC Computer Science, Information Systems; Computer Science, Theory & Methods SC Computer Science GA AT6WL UT WOS:000345077400002 ER PT J AU Li, SG Hoefler, T Hu, CJ Snir, M AF Li, Shigang Hoefler, Torsten Hu, Chungjin Snir, Marc TI Improved MPI collectives for MPI processes in shared address spaces SO CLUSTER COMPUTING-THE JOURNAL OF NETWORKS SOFTWARE TOOLS AND APPLICATIONS LA English DT Article DE MPI; Multithreading; MPI_Allreduce; Collective communication; NUMA ID COMMUNICATION OPERATIONS; PERFORMANCE; SYNCHRONIZATION; OPTIMIZATION; SUPPORT AB As the number of cores per node keeps increasing, it becomes increasingly important for MPI to leverage shared memory for intranode communication. This paper investigates the design and optimization of MPI collectives for clusters of NUMA nodes. We develop performance models for collective communication using shared memory and we demonstrate several algorithms for various collectives. Experiments are conducted on both Xeon X5650 and Opteron 6100 InfiniBand clusters. The measurements agree with the model and indicate that different algorithms dominate for short vectors and long vectors. We compare our shared-memory allreduce with several MPI implementations-Open MPI, MPICH2, and MVAPICH2-that utilize system shared memory to facilitate interprocess communication. On a 16-node Xeon cluster and 8-node Opteron cluster, our implementation achieves on geometric average 2.3X and 2.1X speedup over the best MPI implementation, respectively. Our techniques enable an efficient implementation of collective operations on future multi- and manycore systems. C1 [Li, Shigang; Hu, Chungjin] Univ Sci & Technol Beijing, Sch Comp & Commun Engn, Beijing 100083, Peoples R China. [Hoefler, Torsten] ETH, Dept Comp Sci, Zurich, Switzerland. [Snir, Marc] Univ Illinois, Dept Comp Sci, Champaign, IL USA. [Snir, Marc] Argonne Natl Lab, Champaign, IL USA. RP Li, SG (reprint author), Univ Sci & Technol Beijing, Sch Comp & Commun Engn, Beijing 100083, Peoples R China. EM shigangli.cs@gmail.com; htor@inf.ethz.ch; huchj.cs@gmail.com; snir@illinois.edu FU DOE Office of Science, Advanced Scientific Computing Research [DE-FC02-10ER26011, DE-AC02-06CH11357]; National Key Basic Research and Development Program of China [2013CB329605, 2013CB329606]; Key Project of the National 25th Year Research Program of China [2011BAK08B04] FX The work is supported in part by the DOE Office of Science, Advanced Scientific Computing Research, under Award number DE-FC02-10ER26011 and DOE Office of Science, Advanced Scientific Computing Research, under Award number DE-AC02-06CH11357. Li is supported in part by National Key Basic Research and Development Program of China under No. 2013CB329605 and No. 2013CB329606, and Key Project of the National 25th Year Research Program of China under No. 2011BAK08B04. This work was supported in part by the DOE Office of Science, Advanced Scientific Computing Research, under Award number DE-FC02-10ER26011, program manager Lucy Nowell. NR 30 TC 4 Z9 4 U1 0 U2 3 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1386-7857 EI 1573-7543 J9 CLUSTER COMPUT JI Cluster Comput. PD DEC PY 2014 VL 17 IS 4 BP 1139 EP 1155 DI 10.1007/s10586-014-0361-4 PG 17 WC Computer Science, Information Systems; Computer Science, Theory & Methods SC Computer Science GA AT6WL UT WOS:000345077400004 ER PT J AU Lubin, M Hall, J Petra, C Anitescu, M AF Lubin, Miles Hall, Julian Petra, Cosmin Anitescu, Mihai TI COAP 2013 Best Paper Prize SO COMPUTATIONAL OPTIMIZATION AND APPLICATIONS LA English DT News Item C1 [Hall, Julian] Univ Edinburgh, Sch Math, Edinburgh EH8 9YL, Midlothian, Scotland. [Petra, Cosmin] Argonne Natl Lab, Math & Comp Sci Div, Argonne, IL 60439 USA. [Anitescu, Mihai] Argonne Natl Lab, Math & Comp Sci Div, Argonne, IL 60439 USA. [Anitescu, Mihai] Univ Chicago, Dept Stat, Chicago, IL 60637 USA. RP Lubin, M (reprint author), MIT, Cambridge, MA 02139 USA. NR 13 TC 0 Z9 0 U1 0 U2 5 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 0926-6003 EI 1573-2894 J9 COMPUT OPTIM APPL JI Comput. Optim. Appl. PD DEC PY 2014 VL 59 IS 3 BP 399 EP 403 DI 10.1007/s10589-014-9707-3 PG 5 WC Operations Research & Management Science; Mathematics, Applied SC Operations Research & Management Science; Mathematics GA AT2ZI UT WOS:000344803000001 ER PT J AU Starinshak, DP Owen, JM Johnson, JN AF Starinshak, D. P. Owen, J. M. Johnson, J. N. TI A new parallel algorithm for constructing Voronoi tessellations from distributed input data SO COMPUTER PHYSICS COMMUNICATIONS LA English DT Article DE Voronoi; Parallel computing; Astrophysical flows; Geophysical flows ID DIAGRAM AB We present a new parallel algorithm for generating consistent Voronoi diagrams from distributed input data for the purposes of simulation and visualization. The algorithm functions by building upon any serial Voronoi tessellation algorithm. The output of such a serial tessellator is used to determine the connectivity of the distributed domains without any assumptions about how points are distributed across those domains, and then in turn to build the portion of the global tessellation local to each domain using information from that domains neighbors. The result is a generalized methodology for adding distributed capabilities to serial tessellation packages. Results from several two-dimensional tests are presented, including strong and weak scaling of its current implementation. (c) 2014 Elsevier B.V. All rights reserved. C1 [Starinshak, D. P.; Owen, J. M.] Lawrence Livermore Natl Lab, AX Div, Livermore, CA 94550 USA. [Johnson, J. N.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA. RP Starinshak, DP (reprint author), Lawrence Livermore Natl Lab, AX Div, M-S L-38,POB 808, Livermore, CA 94550 USA. EM starinshak1@llnl.gov FU US Department of Energy by Lawrence Livermore National Laboratory [DE-AC52-07NA27344] FX Our thanks to Misha Shashkov for many productive discussions on Voronoi mesh generation. This work was performed under the auspices of the US Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. NR 32 TC 3 Z9 4 U1 1 U2 6 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0010-4655 EI 1879-2944 J9 COMPUT PHYS COMMUN JI Comput. Phys. Commun. PD DEC PY 2014 VL 185 IS 12 BP 3204 EP 3214 DI 10.1016/j.cpc.2014.08.020 PG 11 WC Computer Science, Interdisciplinary Applications; Physics, Mathematical SC Computer Science; Physics GA AT3GX UT WOS:000344824900015 ER PT J AU Karasiev, VV Sjostrom, T Trickey, SB AF Karasiev, Valentin V. Sjostrom, Travis Trickey, S. B. TI Finite-temperature orbital-free DFT molecular dynamics: Coupling PROFESS and QUANTUM ESPRESSO SO COMPUTER PHYSICS COMMUNICATIONS LA English DT Article DE Finite-temperature orbital-free density functional theory; Electronic structure; Ab-initio molecular dynamics; Non-interacting free energy; Exchange-correlation free energy ID DENSITY-FUNCTIONAL THEORY; KINETIC-ENERGY; CORRELATION POTENTIALS; ELECTRON LIQUID; EXCHANGE; SYSTEMS; METALS; SIMULATIONS; APPROXIMATION; FORCES AB Implementation of orbital-free free-energy functionals in the PROFESS code and the coupling of PROFESS with the QUANTUM ESPRESSO code are described. The combination enables orbital-free DFT to drive ab initio molecular dynamics simulations on the same footing (algorithms, thermostats, convergence parameters, etc.) as for Kohn Sham (KS) DFT. All the non-interacting free-energy functionals implemented are single-point: the local density approximation (LDA; also known as finite-T Thomas Fermi, ftTF), the second-order gradient approximation (SGA or finite-T gradient-corrected TF), and our recently introduced finite-T generalized gradient approximations (ftGGA). Elimination of the KS orbital bottleneck via orbital-free methodology enables high-T simulations on ordinary computers, whereas those simulations would be costly or even prohibitively time-consuming for KS molecular dynamics (MD) on very high-performance computer systems. Example MD simulations on H over a temperature range 2000 K <= T <= 4,000,000 K are reported, with timings on small clusters (16-128 cores) and even laptops. With respect to KS-driven calculations, the orbital-free calculations are between a few times through a few hundreds of times faster. (c) 2014 Elsevier B.V. All rights reserved. C1 [Karasiev, Valentin V.; Trickey, S. B.] Univ Florida, Dept Phys, Quantum Theory Project, Gainesville, FL 32611 USA. [Karasiev, Valentin V.; Trickey, S. B.] Univ Florida, Dept Chem, Quantum Theory Project, Gainesville, FL 32611 USA. [Sjostrom, Travis] Los Alamos Natl Lab, Div Theoret, Los Alamos, NM 87545 USA. RP Karasiev, VV (reprint author), Univ Florida, Dept Phys, Quantum Theory Project, POB 118435, Gainesville, FL 32611 USA. EM vkarasev@gmail.com RI Karasiev, Valentin/J-2519-2012 OI Karasiev, Valentin/0000-0003-3445-6797 FU US Dept. of Energy TMS program [DE-SC0002139]; DOE Office of Fusion Energy Sciences (FES); NNSA of the US DOE at Los Alamos National Laboratory [DE-AC52-06NA25396] FX VVK and SBT were supported by the US Dept. of Energy TMS program, grant DE-SC0002139, as was the initial part of the effort by TS. The latter part of his work was supported by the DOE Office of Fusion Energy Sciences (FES), and by the NNSA of the US DOE at Los Alamos National Laboratory under Contract No. DE-AC52-06NA25396. We acknowledge with thanks the provision of computational resources and technical support by the University of Florida High-Performance Computing Center. NR 56 TC 10 Z9 10 U1 4 U2 21 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0010-4655 EI 1879-2944 J9 COMPUT PHYS COMMUN JI Comput. Phys. Commun. PD DEC PY 2014 VL 185 IS 12 BP 3240 EP 3249 DI 10.1016/j.cpc.2014.08.023 PG 10 WC Computer Science, Interdisciplinary Applications; Physics, Mathematical SC Computer Science; Physics GA AT3GX UT WOS:000344824900018 ER PT J AU Chen, T Nutter, J Hawk, J Liu, XB AF Chen, Ting Nutter, Jared Hawk, Jeffrey Liu, Xingbo TI Corrosion fatigue crack growth behavior of oil-grade nickel-base alloy 718. Part 1: Effect of corrosive environment SO CORROSION SCIENCE LA English DT Article DE Superalloys; Polarization; SEM; Pitting corrosion; Corrosion fatigue ID ELEVATED-TEMPERATURE; PROPAGATION BEHAVIOR; NACL SOLUTION; WAVE-FORM; SUPERALLOY; ELECTROCHEMISTRY; 650-DEGREES-C; FREQUENCY; VARIABLES; CHEMISTRY AB The effect of corrosive environment on corrosion fatigue crack growth (CFCG) behavior of oil-grade nickel-base alloy 718 is studied. The results demonstrate that there is no obvious effect of 3.5 wt.% NaCl solution at RT, 50 degrees C and 80 degrees C on CGCG rates while 21 wt.% NaCl solution at 80 degrees C produces a deleterious effect on CFCG rates compared to the ones tested in air. Potentiodynamic polarization results show that alloy 718 exhibits passive behavior in 3.5 wt.% NaCl solution, while pitting corrosion resistance decreases with increasing solution temperature. Nevertheless, alloy 718 shows active corrosion behavior in 21 wt.% NaCl solution at 80 degrees C. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Chen, Ting; Nutter, Jared; Hawk, Jeffrey; Liu, Xingbo] Natl Energy Technol Lab, Albany, OR 97321 USA. [Chen, Ting; Nutter, Jared; Liu, Xingbo] W Virginia Univ, Dept Mech & Aerosp Engn, Morgantown, WV 26506 USA. [Chen, Ting] SET Labs Inc, Stafford, TX 77477 USA. RP Liu, XB (reprint author), W Virginia Univ, Dept Mech & Aerosp Engn, Morgantown, WV 26506 USA. EM xingbo.liu@mail.wvu.edu FU National Energy Technology Laboratory's ongoing research in materials for ultra-deep drilling under the RES [DE-FE000400] FX This technical effort was performed in support of the National Energy Technology Laboratory's ongoing research in materials for ultra-deep drilling under the RES contract DE-FE000400. The authors appreciate Dr. Hendrik John and Mr. John Stevens from Baker Hughes for providing the specimens used in this study. We acknowledge use of the WVU Shared Research Facilities. NR 36 TC 4 Z9 4 U1 1 U2 14 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0010-938X EI 1879-0496 J9 CORROS SCI JI Corrosion Sci. PD DEC PY 2014 VL 89 BP 146 EP 153 DI 10.1016/j.corsci.2014.08.022 PG 8 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering SC Materials Science; Metallurgy & Metallurgical Engineering GA AT6OT UT WOS:000345059400017 ER PT J AU Salam, S Hou, PY Zhang, YD Lan, H Wang, HF Zhang, C Yang, ZG AF Salam, S. Hou, P. Y. Zhang, Y-D. Lan, H. Wang, H-F. Zhang, C. Yang, Z-G TI Element accumulation beneath the scale/alloy interface of a CoNiCrAlReY alloy SO CORROSION SCIENCE LA English DT Article DE Alloy; Modelling studies; Oxidation ID FERRITIC STAINLESS-STEELS; ALUMINA SCALE GROWTH; SIGMA-PHASE; OXIDATION BEHAVIOR; CR ALLOYS; CHROMIUM; OXIDE; DEPLETION; COATINGS AB In the present study, two types of subscale Cr and Re accumulation found at scale/alloy interface of two batches of Co32Ni21Cr10Al3.5ReY alloys are described. During oxidation, one alloy developed a supersaturated Cr-Re rich layer and another formed Cr-Re precipitates beneath the oxide in the subscale region. Diffusional and thermodynamic modelling showed the accumulation is a result of decreasing Cr and Re chemical potentials with Al depletion. The observed difference in accumulation forms is caused by the different phases in two alloys, with the former being gamma, beta, alpha, sigma and gamma, beta and the latter having only gamma, beta and sigma. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Salam, S.; Zhang, Y-D.; Wang, H-F.; Zhang, C.; Yang, Z-G] Tsinghua Univ, Sch Mat Sci & Engn, Minist Educ, Key Lab Adv Mat, Beijing 100084, Peoples R China. [Hou, P. Y.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Mat Sci, Berkeley, CA 94720 USA. [Lan, H.] Chinese Acad Sci, Inst Proc Engn, State Key Lab Multiphase Complex Syst, Beijing 100190, Peoples R China. RP Yang, ZG (reprint author), Tsinghua Univ, Sch Mat Sci & Engn, Minist Educ, Key Lab Adv Mat, Beijing 100084, Peoples R China. EM zgyang@tsinghua.edu.cn OI Salam, Shahzad/0000-0002-6710-2947 FU National Basic Research Program of China [2010CB731600]; National Natural Science Foundation of China (NSFC) [51101091] FX The authors are grateful for the financial support by both the National Basic Research Program of China (2010CB731600) and National Natural Science Foundation of China (NSFC No. 51101091). NR 30 TC 3 Z9 3 U1 2 U2 5 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0010-938X EI 1879-0496 J9 CORROS SCI JI Corrosion Sci. PD DEC PY 2014 VL 89 BP 318 EP 325 DI 10.1016/j.corsci.2014.09.015 PG 8 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering SC Materials Science; Metallurgy & Metallurgical Engineering GA AT6OT UT WOS:000345059400035 ER PT J AU Paolini, R Zinzi, M Poli, T Carnielo, E Mainini, AG AF Paolini, Riccardo Zinzi, Michele Poli, Tiziana Carnielo, Emiliano Mainini, Andrea Giovanni TI Effect of ageing on solar spectral reflectance of roofing membranes: Natural exposure in Roma and Milano and the impact on the energy needs of commercial buildings SO ENERGY AND BUILDINGS LA English DT Article DE Solar reflectance; Ageing; Soiling; Cool roof; Building energy need; UV-Vis-NIR; Natural exposure; Building envelope ID URBAN HEAT-ISLAND; RESIDENTIAL BUILDINGS; ENVELOPE SURFACES; COOL; MITIGATION; COATINGS; CONSUMPTION; STRATEGIES; COMFORT; CLIMATE AB Highly reflective roofs, widely known as cool roofs, can reduce peak surface temperatures and the energy required to cool buildings, mitigate urban microclimates, and offset CO2. However, weathering, soiling, and biological growth affect their solar reflectance. In this study, the solar spectral reflectances of 12 roofing membranes were measured before the exposure and after 3, 6, 12, 18, and 24 months of natural ageing in Roma and Milano, Italy. The membranes with an initial solar reflectance greater than 0.80, for example, decreased in reflectance by 0.14 in Roma and 0.22 in Milano after two years. Then, for a typical highly insulated commercial building, the annual cooling load savings were calculated to be reduced by 4.1-7.1 MJ m(-2) y(-1) per 0.1 loss in reflectance. When the buildings are non-insulated, the savings reduction is 58-71 MJ m(-2) y(-1) in Milano and 70-84 MJ m(-2) y(-1) in Roma. Ageing yielded a reduction of the cooling load savings that could be achieved with a new white membrane of 14-23% in Roma and of 20-34% in Milano. Moreover, in Milano, an aged, white, highly insulated roof, which has a solar reflectance of 0.56, may reach a surface temperature 16 degrees C higher than a new roof, which has a solar reflectance of 0.80. (C) 2014 Elsevier B.V. All rights reserved. C1 [Paolini, Riccardo; Poli, Tiziana; Mainini, Andrea Giovanni] Politecn Milan, Dept Architecture Built Environm & Construct Engn, I-20133 Milan, MI, Italy. [Paolini, Riccardo] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Environm Energy Technol Div, Heat Isl Grp, Berkeley, CA 94720 USA. [Zinzi, Michele] Italian Natl Agcy New Technol Energy & Sustainabl, ENEA UTEE ERT, Rome, Italy. [Carnielo, Emiliano] Univ Roma Tre, Rome, Italy. RP Paolini, R (reprint author), Politecn Milan, Dept Architecture Built Environm & Construct Engn, Via Ponzio 31, I-20133 Milan, MI, Italy. EM riccardo.paolini@polimi.it RI Paolini, Riccardo/I-6937-2015; MAININI, Andrea Giovanni/D-7767-2017; Poli, Tiziana/A-3576-2016 OI Paolini, Riccardo/0000-0001-8365-6811; MAININI, Andrea Giovanni/0000-0002-8548-9014; Poli, Tiziana/0000-0001-8558-783X FU Ministero dello Sviluppo Economico (Italian Ministry for Economic Development); Politecnico di Milano & Agenzia delle Entrate (Italian Revenue Agency) FX This work was funded by Ministero dello Sviluppo Economico (Italian Ministry for Economic Development) with the projects "Valutazione delle prestazioni di cool materials esposti all'ambiente urbano" and "Sviluppo di materiali e tecnologie per la riduzione degli effetti della radiazione solare"; and by Politecnico di Milano & Agenzia delle Entrate (Italian Revenue Agency) with the project "Cinque per mule junior-Rivestimenti fluorurati avanzati per superfici edilizie ad alte prestazioni". The authors wish to thank Florian Antretter and Daniel Zirkelbach (Fraunhofer Institut fur Bauphysik) for precious suggestions about hygrothermal simulations; and Hugo Destaillats, Ronnen Levinson, and Mohamad Sleiman (Lawrence Berkeley National Laboratory) for valuable exchanges about the analysis of UV-Vis-NIR spectral data. The authors gratefully acknowledge anonymous reviewers, who provided relevant and helpful suggestions to improve the presentation of results. NR 43 TC 20 Z9 21 U1 1 U2 13 PU ELSEVIER SCIENCE SA PI LAUSANNE PA PO BOX 564, 1001 LAUSANNE, SWITZERLAND SN 0378-7788 EI 1872-6178 J9 ENERG BUILDINGS JI Energy Build. PD DEC PY 2014 VL 84 BP 333 EP 343 DI 10.1016/j.enbuild.2014.08.008 PG 11 WC Construction & Building Technology; Energy & Fuels; Engineering, Civil SC Construction & Building Technology; Energy & Fuels; Engineering GA AT8KJ UT WOS:000345182000033 ER PT J AU Bassamzadeh, N Ghanem, R Lu, S Kazemitabar, SJ AF Bassamzadeh, Nastaran Ghanem, Roger Lu, Shuai Kazemitabar, Seyed Jalal TI Robust scheduling of smart appliances with uncertain electricity prices in a heterogeneous population SO ENERGY AND BUILDINGS LA English DT Article DE Demand response; Heterogeneous population; Optimal scheduling; Robust optimization; Smart grids; Smart homes; Uncertain prices ID ENERGY MANAGEMENT-SYSTEM; OPTIMIZATION; CONSUMPTION AB Majority of the research conducted in the field of optimal scheduling of smart appliances does not consider the inherent uncertainties in this problem. Besides, the ones that count for the uncertainty usually assume full knowledge about the exact form of the probability distribution of the uncertain parameters. This assumption is hardly fulfilled in reality. In this paper, we seek to find solutions that are robust with respect to the probability distribution of the uncertain parameters while making no explicit assumptions about their exact forms. Accordingly, we define a chance-constrained model to find the optimal schedule and use robust optimization to characterize its solution and the associated uncertain parameters. We also consider the effect of heterogeneous populations on the optimal solution while simultaneously determining the most appropriate classification for accurate predictions. In the process, we investigate the effect of delays in information sharing on computed optimal conditions and we develop a new classification for in-house appliances. We explore features of our model using price data from the "Olympic Peninsula" project. We anticipate that by pursuing optimal options, a typical customer can save up to 33% in her electricity bills while sacrificing 19% of her comfort level. Moreover, in a heterogeneous population, while the results suggest no direct dependency between savings and income level, a meaningful correlation is detected between savings and employment status. (C) 2014 Elsevier B.V. All rights reserved. C1 [Bassamzadeh, Nastaran] Univ So Calif, Dept Civil Engn, Los Angeles, CA 90089 USA. [Ghanem, Roger] Univ So Calif, Viterbi Sch Engn, Los Angeles, CA 90089 USA. [Lu, Shuai] Pacific NW Natl Lab, Adv Power & Energy Syst, Richland, WA 99345 USA. [Kazemitabar, Seyed Jalal] Univ So Calif, Dept Comp Sci, Los Angeles, CA 90089 USA. RP Bassamzadeh, N (reprint author), Univ So Calif, Dept Civil Engn, Los Angeles, CA 90089 USA. EM Bassamza@usc.edu; Ghanem@usc.edu; Shuai.lu@pnnl.gov; Kazemita@usc.edu RI Ghanem, Roger/B-8570-2008 OI Ghanem, Roger/0000-0002-1890-920X FU National Science Foundation [EFRI-1025043] FX This work was supported in part by National Science Foundation under Grant EFRI-1025043. NR 27 TC 6 Z9 6 U1 4 U2 19 PU ELSEVIER SCIENCE SA PI LAUSANNE PA PO BOX 564, 1001 LAUSANNE, SWITZERLAND SN 0378-7788 EI 1872-6178 J9 ENERG BUILDINGS JI Energy Build. PD DEC PY 2014 VL 84 BP 537 EP 547 DI 10.1016/j.enbuild.2014.08.035 PG 11 WC Construction & Building Technology; Energy & Fuels; Engineering, Civil SC Construction & Building Technology; Energy & Fuels; Engineering GA AT8KJ UT WOS:000345182000053 ER PT J AU Cetin, KS Tabares-Velasco, PC Novoselac, A AF Cetin, K. S. Tabares-Velasco, P. C. Novoselac, A. TI Appliance daily energy use in new residential buildings: Use profiles and variation in time-of-use SO ENERGY AND BUILDINGS LA English DT Article ID DOMESTIC APPLIANCES; END-USE; CONSUMPTION; HOMES AB One of the largest user of electricity in the average U.S. household is appliances, which when aggregated, account for approximately 30% of electricity used in the residential building sector. As influencing the time-of-use of energy becomes increasingly important to control the stress on today's electrical grid infrastructure, understanding when appliances use energy and what causes variation in their use are of great importance. However, there is limited appliance-specific data available to understand their use patterns. This study provides daily energy use profiles of four major household appliances: refrigerator, clothes washer, clothes dryer, and dishwasher, through analyzing disaggregated energy use data collected for 40 single family homes in Austin, TX. The results show that when compared to those assumed in current energy simulation software for residential buildings, the averaged appliance load profiles have similar daily distributions. Refrigerators showed the most constant and consistent use. However, the three user-dependent appliances, appliances which depend on users to initiate use, varied more greatly between houses and by time-of-day. During peak use times, on weekends, and in homes with household members working at home, the daily use profiles of appliances were less consistent. (C) 2014 Elsevier B.V. All rights reserved. C1 [Cetin, K. S.; Novoselac, A.] Univ Texas Austin, Dept Civil Environm & Architectural Engn, Austin, TX 78712 USA. [Tabares-Velasco, P. C.] Natl Renewable Energy Lab, Elect Resources & Bldg Syst Integrat, Golden, CO USA. RP Novoselac, A (reprint author), Univ Texas Austin, Dept Civil Environm & Architectural Engn, Austin, TX 78712 USA. EM atila@mail.utexas.edu FU National Science Foundation Graduate Research Fellowship [DGE-1110007] FX This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1110007. Any opinion, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. NR 31 TC 9 Z9 10 U1 1 U2 10 PU ELSEVIER SCIENCE SA PI LAUSANNE PA PO BOX 564, 1001 LAUSANNE, SWITZERLAND SN 0378-7788 EI 1872-6178 J9 ENERG BUILDINGS JI Energy Build. PD DEC PY 2014 VL 84 BP 716 EP 726 DI 10.1016/j.enbuild.2014.07.045 PG 11 WC Construction & Building Technology; Energy & Fuels; Engineering, Civil SC Construction & Building Technology; Energy & Fuels; Engineering GA AT8KJ UT WOS:000345182000071 ER PT J AU Bryan, AL Snodgrass, JW Brant, HA Romanek, CS Jagoe, CH Mills, GL Brisbin, IL AF Bryan, Albert L., Jr. Snodgrass, Joel W. Brant, Heather A. Romanek, Christopher S. Jagoe, Charles H. Mills, Gary L. Brisbin, I. Lehr, Jr. TI PRECIPITATION INFLUENCES ON UPTAKE OF A GLOBAL POLLUTANT BY A COASTAL AVIAN SPECIES SO ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY LA English DT Article DE Climate; Rainfall; Mercury; Wetlands; Wood storks ID STORKS MYCTERIA-AMERICANA; BREEDING WOOD STORKS; FORAGING HABITAT USE; MERCURY CONCENTRATIONS; CLIMATE-CHANGE; GEORGIA; BIRDS; FISH; USA; PHENOLOGY AB Climatic variation, including precipitation amounts and timing, has been linked to abundance and breeding success of many avian species. Less studied, but also of significance, is the consequence of climatic variability on the exposure and uptake of nutrients and contaminants by wildlife. The authors examined mercury (Hg) concentrations in nestling wood stork feathers in a coastal setting over a 16-yr period to understand the influence of rainfall amounts on Hg transfer by parental provisioning relative to habitat use, assuming differential bioavailability of Hg within freshwater and saltwater habitat types. Coastal Hg uptake by stork nestlings was linked to freshwater habitat use, as indicated by stable carbon isotope (C-13) analyses. Cumulative rainfall amounts exceeding 220cm in the 23 mo preceding the breeding seasons resulted in greater use of freshwater wetlands as foraging habitat and greater Hg accumulation by nestling storks. Environ Toxicol Chem 2014;33:2711-2715. (c) 2014 SETAC C1 [Bryan, Albert L., Jr.; Brant, Heather A.; Romanek, Christopher S.; Jagoe, Charles H.; Mills, Gary L.; Brisbin, I. Lehr, Jr.] Univ Georgia, Savannah River Ecol Lab, Aiken, SC USA. [Snodgrass, Joel W.] Towson Univ, Dept Biol Sci, Towson, MD USA. RP Bryan, AL (reprint author), Univ Georgia, Savannah River Ecol Lab, Aiken, SC USA. EM lbryan@srel.uga.edu RI Snodgrass, Joel/C-5288-2016 FU US Department of Energy [DE-FC09-96SR18546]; US Fish and Wildlife Service; Georgia Department of Natural Resources FX Numerous personnel from Harris Neck National Wildlife Refuge, including J. Robinette and K. Hayes, assisted with field collections. A. Lindell, J. Gariboldi, N. Garvin, and L. Paddock of SREL assisted with laboratory analyses. J. Brandes of the Skidaway Institute Marine Sciences Center analyzed recent feather samples for stable isotopes. This study received funding from the US Department of Energy, through Financial Assistance Award No. DE-FC09-96SR18546 to the University of Georgia Research Foundation, as well as from the US Fish and Wildlife Service and the Georgia Department of Natural Resources. NR 40 TC 0 Z9 0 U1 3 U2 20 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 0730-7268 EI 1552-8618 J9 ENVIRON TOXICOL CHEM JI Environ. Toxicol. Chem. PD DEC PY 2014 VL 33 IS 12 BP 2711 EP 2715 DI 10.1002/etc.2752 PG 5 WC Environmental Sciences; Toxicology SC Environmental Sciences & Ecology; Toxicology GA AU0NE UT WOS:000345319100009 PM 25242147 ER PT J AU Segovia, J Cloet, IC Roberts, CD Schmidt, SM AF Segovia, Jorge Cloet, Ian C. Roberts, Craig D. Schmidt, Sebastian M. TI Nucleon and Elastic and Transition Form Factors SO FEW-BODY SYSTEMS LA English DT Article ID QUARK-DIQUARK MODEL; GREEN-TAKAHASHI IDENTITIES; DYSON-SCHWINGER EQUATIONS; ANOMALOUS MAGNETIC-MOMENT; PION LOOP CONTRIBUTION; ELECTROMAGNETIC-INTERACTIONS; DECUPLET BARYONS; HADRON PHYSICS; SPIN STRUCTURE; VECTOR-MESONS AB We present a unified study of nucleon and elastic and transition form factors, and compare predictions made using a framework built upon a Faddeev equation kernel and interaction vertices that possess QCD-like momentum dependence with results obtained using a symmetry-preserving treatment of a vector vector contact-interaction. The comparison emphasises that experiments are sensitive to the momentum dependence of the running couplings and masses in the strong interaction sector of the Standard Model and highlights that the key to describing hadron properties is a veracious expression of dynamical chiral symmetry breaking in the bound-state problem. Amongst the results we describe, the following are of particular interest: possesses a zero at Q (2) = 9.5 GeV2; any change in the interaction which shifts a zero in the proton ratio to larger Q (2) relocates a zero in to smaller Q (2); there is likely a value of momentum transfer above which ; and the presence of strong diquark correlations within the nucleon is sufficient to understand empirical extractions of the flavour-separated form factors. Regarding the -baryon, we find that, inter alia: the electric monopole form factor exhibits a zero; the electric quadrupole form factor is negative, large in magnitude, and sensitive to the nature and strength of correlations in the Faddeev amplitude; and the magnetic octupole form factor is negative so long as rest-frame P- and D-wave correlations are included. In connection with the transition, the momentum-dependence of the magnetic transition form factor, , matches that of once the momentum transfer is high enough to pierce the meson-cloud; and the electric quadrupole ratio is a keen measure of diquark and orbital angular momentum correlations, the zero in which is obscured by meson-cloud effects on the domain currently accessible to experiment. Importantly, within each framework, identical propagators and vertices are sufficient to describe all properties discussed herein. Our analysis and predictions should therefore serve as motivation for measurement of elastic and transition form factors involving the nucleon and its resonances at high photon virtualities using modern electron-beam facilities. C1 [Segovia, Jorge; Cloet, Ian C.; Roberts, Craig D.] Argonne Natl Lab, Div Phys, Argonne, IL 60439 USA. [Schmidt, Sebastian M.] Forschungszentrum Julich, Inst Adv Simulat, D-52425 Julich, Germany. [Schmidt, Sebastian M.] JARA, D-52425 Julich, Germany. RP Roberts, CD (reprint author), Argonne Natl Lab, Div Phys, Argonne, IL 60439 USA. EM cdroberts@anl.gov RI Segovia, Jorge/C-7202-2015 OI Segovia, Jorge/0000-0001-5838-7103 FU Helmholtz Association; U.S. Department of Energy, Office of Science, Office of Nuclear Physics [DE-AC02-06CH11357]; GAUSTEQ (Germany) [DE-SC0006758]; GAUSTEQ (U.S. Nuclear Theory Exchange Program for QCD Studies of Hadrons and Nuclei) [DE-SC0006758]; Forschungszentrum Julich GmbH FX JS thanks G. Eichmann for informative discussions and invaluable help when requested. We also thank the following people for useful input: M. Diehl, R. Gothe and V. Mokeev. JS, ICC and CDR are grateful for the opportunity to participate in the workshops "Many Manifestations of Nonperturbative QCD under the Southern Cross", Ubatuba, and the "2nd Workshop on Perspectives in Nonperturbative QCD" at IFT-UNESP, Sao Paulo, during both of which substantial fractions of this work were completed. CDR acknowledges support from an International Fellow Award from the Helmholtz Association. Work otherwise supported by: U.S. Department of Energy, Office of Science, Office of Nuclear Physics, under contract no. DE-AC02-06CH11357; GAUSTEQ (Germany and U.S. Nuclear Theory Exchange Program for QCD Studies of Hadrons and Nuclei) under contract number DE-SC0006758; and Forschungszentrum Julich GmbH. NR 168 TC 24 Z9 24 U1 1 U2 8 PU SPRINGER WIEN PI WIEN PA SACHSENPLATZ 4-6, PO BOX 89, A-1201 WIEN, AUSTRIA SN 0177-7963 EI 1432-5411 J9 FEW-BODY SYST JI Few-Body Syst. PD DEC PY 2014 VL 55 IS 12 BP 1185 EP 1222 DI 10.1007/s00601-014-0907-2 PG 38 WC Physics, Multidisciplinary SC Physics GA AT7TT UT WOS:000345140800001 ER PT J AU Chen, L Kang, QJ Deng, HL Carey, JW Tao, WQ AF Chen, Li Kang, Qinjun Deng, Hailin Carey, J. William Tao, WenQuan TI Mesoscopic study of the formation of pseudomorphs with presence of chemical fluids SO GEOSCIENCES JOURNAL LA English DT Article DE pseudomorph; precipitation; dissolution; reactive transport; lattice Boltzmann method ID MINERAL REPLACEMENT REACTIONS; FINITE-VOLUME; PRECIPITATION; MECHANISM; EXCHANGE; DISSOLUTION; KINETICS; ISOTOPE AB A numerical approach is developed to simulate the formation of pseudomorphs with presence of chemical fluids at the mesoscopic scale. This approach consists of the lattice Boltzmann method (LBM) for transport of chemical species in the pore space, a chemical reaction model including basic kinetics of the coupled dissolution and precipitation reactions, and a mesoscopic model for nucleation and crystal growth. Our study confirms the mechanism of the solution chemistry-driven interface-coupled dissolution-precipitation for the formation of pseudomorphs and identifies several sources for the generation of porosity in the pseudomorphs. We demonstrate that epitaxial precipitation is not necessary and random crystal growth may be more favorable for pseudomorphs. We show that the difference of precipitation barrier on the surface of the primary and secondary minerals should not be too large. Otherwise only the rim of the primary phase is roughly preserved. C1 [Chen, Li; Tao, WenQuan] Xi An Jiao Tong Univ, Sch Energy & Power Engn, Key Lab Thermofluid Sci & Engn MOE, Xian 710049, Shaanxi, Peoples R China. [Kang, Qinjun] Los Alamos Natl Lab, Computat Earth Sci Grp EES 16, Los Alamos, NM 87544 USA. [Deng, Hailin] CSIRO Land & Water, Wembley, WA 6913, Australia. [Carey, J. William] Los Alamos Natl Lab, Earth Syst Observat Grp EES 14, Los Alamos, NM 87544 USA. RP Kang, QJ (reprint author), Los Alamos Natl Lab, Computat Earth Sci Grp EES 16, POB 1663, Los Alamos, NM 87544 USA. EM qkang@lanl.gov RI Chen, Li/P-4886-2014; Kang, Qinjun/A-2585-2010 OI Chen, Li/0000-0001-7956-3532; Kang, Qinjun/0000-0002-4754-2240 FU key project of NNSFC [51136004]; LDRD Program of Los Alamos National Laboratory FX This work was supported by the key project of NNSFC (51136004), and the LDRD Program of Los Alamos National Laboratory. NR 29 TC 0 Z9 0 U1 2 U2 18 PU GEOLOGICAL SOCIETY KOREA PI SEOUL PA NEW BLD RM 813, KSTC, 835-4, YEOKSAM-DONG, KANGNAM-GU, SEOUL, 135-703, SOUTH KOREA SN 1226-4806 EI 1598-7477 J9 GEOSCI J JI Geosci. J. PD DEC PY 2014 VL 18 IS 4 BP 469 EP 475 DI 10.1007/s12303-014-0009-7 PG 7 WC Geosciences, Multidisciplinary SC Geology GA AT9YQ UT WOS:000345280300009 ER PT J AU Smerdon, BD Smith, LA Harrington, GA Gardner, WP Delle Piane, C Sarout, J AF Smerdon, Brian D. Smith, Laura A. Harrington, Glenn A. Gardner, W. Payton Delle Piane, Claudio Sarout, Joel TI Estimating the hydraulic properties of an aquitard from in situ pore pressure measurements SO HYDROGEOLOGY JOURNAL LA English DT Article DE Aquitard; Hydraulic properties; Sedimentary rocks; Pore pressure; Australia ID NATURAL TRACER PROFILES; GREAT ARTESIAN BASIN; GROUNDWATER-FLOW; SOIL-MOISTURE; CONDUCTIVITY; PERMEABILITY; PIEZOMETERS; SCALE; AUSTRALIA; MUDSTONES AB A workflow is described to estimate specific storage (S (s)) and hydraulic conductivity (K) from a profile of vibrating wire piezometers embedded into a regional aquitard in Australia. The loading efficiency, compressibility and S (s) were estimated from pore pressure response to atmospheric pressure changes, and K was estimated from the earliest part of the measurement record following grouting. Results indicate that S (s) and K were, respectively, 8.8 x 10(-6) to 1.2 x 10(-5) m(-1) and 2 x 10(-12) m s(-1) for a claystone/siltstone, and 4.3 x 10(-6) to 9.6 x 10(-6) m(-1) and 1 x 10(-12) to 5 x 10(-12) m s(-1) for a thick mudstone. K estimates from the pore pressure response are within one order of magnitude when compared to direct measurement in a laboratory and inverse modelled flux rates determined from natural tracer profiles. Further analysis of the evolution and longevity of the properties of borehole grout (e.g. thermal and chemical effects) may help refine the estimation of formation hydraulic properties using this workflow. However, the convergence of K values illustrates the benefit of multiple lines of evidence to support aquitard characterization. An additional benefit of in situ pore pressure measurement is the generation of long-term data to constrain groundwater flow models, which provides a link between laboratory scale data and the formation scale. C1 [Smerdon, Brian D.] CSIRO Land & Water, CSIRO Water Hlth Country Res Flagship, Glen Osmond, SA 5064, Australia. [Smith, Laura A.] Univ Saskatchewan, Dept Geol Sci, Saskatoon, SK S7N 0W0, Canada. [Harrington, Glenn A.] Innovat Groundwater Solut Pty Ltd, Blackwood, SA, Australia. [Gardner, W. Payton] Sandia Natl Labs, Albuquerque, NM 87185 USA. [Delle Piane, Claudio; Sarout, Joel] Australian Resources Res Ctr, CSIRO Earth Sci & Resource Engn, Perth, WA 6151, Australia. RP Smerdon, BD (reprint author), Alberta Geol Survey, 402 Twin Atria Bldg,4999-98 Ave, Edmonton, AB T6B 2X3, Canada. EM brian.smerdon@gmail.com RI Sarout, Joel/B-5094-2009 OI Sarout, Joel/0000-0003-3217-7102 FU Australian Government National Water Commission's Groundwater Action Plan; CSIRO Water for a Healthy Country National Research Flagship; NSERC-IRC FX The authors are thankful for the field and laboratory assistance provided by Andrew Taylor (CSIRO), Virginia Chostner (University of Saskatchewan), and Andrew Love (Flinders University of South Australia), as well as Norm Sims (Anna Creek Station manager) and the landowners of pastoral leases on which drilling was completed. This study was funded in part by the Australian Government National Water Commission's Groundwater Action Plan, administered through the South Australian Arid Lands Natural Resources Management Board and Flinders University, and in part by CSIRO Water for a Healthy Country National Research Flagship. Funding was also provided to M. Jim Hendry (University of Saskatchewan) by NSERC-IRC to support Laura Smith and Virginia Chostner. The authors also thank Garth van der Kamp, David Hart, an anonymous reviewer, and the associate editor for constructive comments on an earlier version of this manuscript. NR 57 TC 5 Z9 5 U1 0 U2 17 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1431-2174 EI 1435-0157 J9 HYDROGEOL J JI Hydrogeol. J. PD DEC PY 2014 VL 22 IS 8 BP 1875 EP 1887 DI 10.1007/s10040-014-1161-x PG 13 WC Geosciences, Multidisciplinary; Water Resources SC Geology; Water Resources GA AU0AN UT WOS:000345285600011 ER PT J AU Brown, ET Ottley, A Zhao, H Lin, Q Souvenir, R Endert, A Chang, R AF Brown, Eli T. Ottley, Alvitta Zhao, Helen Lin, Quan Souvenir, Richard Endert, Alex Chang, Remco TI Finding Waldo: Learning about Users from their Interactions SO IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS LA English DT Article DE User Interactions; Analytic Provenance; Visualization; Applied Machine Learning ID INDIVIDUAL-DIFFERENCES; VISUAL ANALYTICS; PERSONALITY; DESIGN AB Visual analytics is inherently a collaboration between human and computer. However, in current visual analytics systems, the computer has limited means of knowing about its users and their analysis processes. While existing research has shown that a user's interactions with a system reflect a large amount of the user's reasoning process, there has been limited advancement in developing automated, real-time techniques that mine interactions to learn about the user. In this paper, we demonstrate that we can accurately predict a user's task performance and infer some user personality traits by using machine learning techniques to analyze interaction data. Specifically, we conduct an experiment in which participants perform a visual search task, and apply well-known machine learning algorithms to three encodings of the users' interaction data. We achieve, depending on algorithm and encoding, between 62% and 83% accuracy at predicting whether each user will be fast or slow at completing the task. Beyond predicting performance, we demonstrate that using the same techniques, we can infer aspects of the user's personality factors, including locus of control, extraversion, and neuroticism. Further analyses show that strong results can be attained with limited observation time: in one case 95% of the final accuracy is gained after a quarter of the average task completion time. Overall, our findings show that interactions can provide information to the computer about its human collaborator, and establish a foundation for realizing mixed-initiative visual analytics systems. C1 [Brown, Eli T.; Ottley, Alvitta; Zhao, Helen; Lin, Quan; Chang, Remco] Tufts U, Medford, MA 02155 USA. [Endert, Alex] Pacific NW Natl Lab, Richland, WA 99352 USA. [Souvenir, Richard] UNC Charlotte, Charlotte, NC USA. RP Brown, ET (reprint author), Tufts U, Medford, MA 02155 USA. EM ebrown@cs.tufts.edu; alvitta.ottley@tufts.edu; jieqiongzhao@purdue.edu; linquan0201@gmail.com; souvenir@uncc.edu; alex.endert@pnnl.gov; remco@cs.tufts.edu NR 47 TC 11 Z9 11 U1 1 U2 13 PU IEEE COMPUTER SOC PI LOS ALAMITOS PA 10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA 90720-1314 USA SN 1077-2626 EI 1941-0506 J9 IEEE T VIS COMPUT GR JI IEEE Trans. Vis. Comput. Graph. PD DEC PY 2014 VL 20 IS 12 BP 1663 EP 1672 DI 10.1109/TVCG.2014.2346575 PG 10 WC Computer Science, Software Engineering SC Computer Science GA AT5OI UT WOS:000344991700011 PM 26356880 ER PT J AU Poco, J Dasgupta, A Wei, YX Hargrove, W Schwalm, CR Huntzinger, DN Cook, R Bertini, E Silva, CT AF Poco, Jorge Dasgupta, Aritra Wei, Yaxing Hargrove, William Schwalm, Christopher R. Huntzinger, Deborah N. Cook, Robert Bertini, Enrico Silva, Claudio T. TI Visual Reconciliation of Alternative Similarity Spaces in Climate Modeling SO IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS LA English DT Article DE Similarity; clustering; matrix; optimization; climate model ID VISUALIZATION; EXPLORATION; CLUSTERINGS; GENERATION AB Visual data analysis often requires grouping of data objects based on their similarity. In many application domains researchers use algorithms and techniques like clustering and multidimensional scaling to extract groupings from data. While extracting these groups using a single similarity criteria is relatively straightforward, comparing alternative criteria poses additional challenges. In this paper we define visual reconciliation as the problem of reconciling multiple alternative similarity spaces through visualization and interaction. We derive this problem from our work on model comparison in climate science where climate modelers are faced with the challenge of making sense of alternative ways to describe their models: one through the output they generate, another through the large set of properties that describe them. Ideally, they want to understand whether groups of models with similar spatio-temporal behaviors share similar sets of criteria or, conversely, whether similar criteria lead to similar behaviors. We propose a visual analytics solution based on linked views, that addresses this problem by allowing the user to dynamically create, modify and observe the interaction among groupings, thereby making the potential explanations apparent. We present case studies that demonstrate the usefulness of our technique in the area of climate science. C1 [Poco, Jorge; Dasgupta, Aritra; Bertini, Enrico; Silva, Claudio T.] NYU, New York, NY 10003 USA. [Wei, Yaxing; Cook, Robert] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Hargrove, William] US Forest Serv, USDA, Washington, DC USA. [Schwalm, Christopher R.; Huntzinger, Deborah N.] No Arizona Univ, Flagstaff, AZ 86011 USA. RP Poco, J (reprint author), NYU, New York, NY 10003 USA. EM jpocom@nyu.edu; adasgupt@nyu.edu; weiy@ornl.gov; hnw@geobabble.org; Christopher.Schwalm@nau.edu; deborah.huntzinger@nau.edu; cookrb@ornl.gov; enrico.bertini@nyu.edu; csilva@nyu.edu OI Cook, Robert/0000-0001-7393-7302; Poco, Jorge/0000-0001-9096-6287 FU DataONE project (NSF) [OCI-0830944]; NSF [CNS-1229185]; NASA ROSES [10-BIOCLIM10-0067]; DOE Office of Science Biological and Environmental Research (BER); NASA [NNH10AN68I] FX This work was supported by: the DataONE project (NSF Grant number OCI-0830944), NSF CNS-1229185, NASA ROSES 10-BIOCLIM10-0067, and DOE Office of Science Biological and Environmental Research (BER). The data was acquired through the MAST-DC (NASA Grant NNH10AN68I) and MsTMIP (NASA Grant NNH10AN68I) projects funded by NASA's Terrestrial Ecology Program. We extend our gratitude to members of the Scientific Exploration, Visualization, and Analysis working group (EVA) for their feedback and support. NR 40 TC 3 Z9 3 U1 0 U2 4 PU IEEE COMPUTER SOC PI LOS ALAMITOS PA 10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA 90720-1314 USA SN 1077-2626 EI 1941-0506 J9 IEEE T VIS COMPUT GR JI IEEE Trans. Vis. Comput. Graph. PD DEC PY 2014 VL 20 IS 12 BP 1923 EP 1932 DI 10.1109/TVCG.2014.2346755 PG 10 WC Computer Science, Software Engineering SC Computer Science GA AT5OI UT WOS:000344991700037 PM 26356906 ER PT J AU Isaacs, KE Bremer, PT Jusufi, I Gamblin, T Bhatele, A Schulz, M Hamann, B AF Isaacs, Katherine E. Bremer, Peer-Timo Jusufi, Ilir Gamblin, Todd Bhatele, Abhinav Schulz, Martin Hamann, Bernd TI Combing the Communication Hairball: Visualizing Parallel Execution Traces using Logical Time SO IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS LA English DT Article DE Information visualization; software visualization. timelines; traces; performance analysis ID PERFORMANCE AB With the continuous rise in complexity of modern supercomputers, optimizing the performance of large-scale parallel programs is becoming increasingly challenging. Simultaneously, the growth in scale magnifies the impact of even minor inefficiencies - potentially millions of compute hours and megawatts in power consumption can be wasted on avoidable mistakes or sub-optimal algorithms. This makes performance analysis and optimization critical elements in the software development process. One of the most common forms of performance analysis is to study execution traces, which record a history of per-process events and inter-process messages in a parallel application. Trace visualizations allow users to browse this event history and search for insights into the observed performance behavior. However, current visualizations are difficult to understand even for small process counts and do not scale gracefully beyond a few hundred processes. Organizing events in time leads to a virtually unintelligible conglomerate of interleaved events and moderately high process counts overtax even the largest display. As an alternative, we present a new trace visualization approach based on transforming the event history into logical time inferred directly from happened-before relationships. This emphasizes the code's structural behavior, which is much more familiar to the application developer. The original timing data, or other information, is then encoded through color, leading to a more intuitive visualization. Furthermore, we use the discrete nature of logical timelines to cluster processes according to their local behavior leading to a scalable visualization of even long traces on large process counts. We demonstrate our system using two case studies on large-scale parallel codes. C1 [Isaacs, Katherine E.; Jusufi, Ilir; Hamann, Bernd] Univ Calif Davis, Davis, CA 95616 USA. [Bremer, Peer-Timo; Gamblin, Todd; Bhatele, Abhinav; Schulz, Martin] Lawrence Livermore Natl Lab, Livermore, CA USA. RP Isaacs, KE (reprint author), Univ Calif Davis, Davis, CA 95616 USA. EM keisaacs@ucdavis.edu; ptbremer@llnl.gov; jusufi@ucdavis.edu; tgamblin@llnl.gov; bhatele@llnl.gov; schulzm@llnl.gov; bhamann@ucdavis.edu RI Jusufi, Ilir/G-2932-2014 OI Jusufi, Ilir/0000-0001-6745-4398 FU U.S. Department of Energy by Lawrence Livermore National Laboratory [DE-AC52-07NA27344, LLNL-JRNL-657418]; Department of Energy Office of Science Graduate Fellowship Program [DE-AC05-06OR23100] 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-657418. This research is supported in part by the Department of Energy Office of Science Graduate Fellowship Program, administered by ORISE-ORAU under contract no. DE-AC05-06OR23100. NR 43 TC 5 Z9 5 U1 4 U2 8 PU IEEE COMPUTER SOC PI LOS ALAMITOS PA 10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA 90720-1314 USA SN 1077-2626 EI 1941-0506 J9 IEEE T VIS COMPUT GR JI IEEE Trans. Vis. Comput. Graph. PD DEC PY 2014 VL 20 IS 12 BP 2349 EP 2358 DI 10.1109/TVCG.2014.2346456 PG 10 WC Computer Science, Software Engineering SC Computer Science GA AT5OI UT WOS:000344991700080 PM 26356949 ER PT J AU Lindstrom, P AF Lindstrom, Peter TI Fixed-Rate Compressed Floating-Point Arrays SO IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS LA English DT Article DE Data compression; floating-point arrays; orthogonal block transform; embedded coding ID LOSSLESS COMPRESSION; VOLUME DATA; IMAGE COMPRESSION; TRANSFORMS; GEOMETRY AB Current compression schemes for floating-point data commonly take fixed-precision values and compress them to a variable-length bit stream, complicating memory management and random access. We present a fixed-rate, near-lossless compression scheme that maps small blocks of 4(d) values in d dimensions to a fixed, user-specified number of bits per block, thereby allowing read and write random access to compressed floating-point data at block granularity. Our approach is inspired by fixed-rate texture compression methods widely adopted in graphics hardware, but has been tailored to the high dynamic range and precision demands of scientific applications. Our compressor is based on a new, lifted, orthogonal block transform and embedded coding, allowing each per-block bit stream to be truncated at any point if desired, thus facilitating bit rate selection using a single compression scheme. To avoid compression or decompression upon every data access, we employ a software write-back cache of uncompressed blocks. Our compressor has been designed with computational simplicity and speed in mind to allow for the possibility of a hardware implementation, and uses only a small number of fixed-point arithmetic operations per compressed value. We demonstrate the viability and benefits of lossy compression in several applications, including visualization, quantitative data analysis, and numerical simulation. C1 Lawrence Livermore Natl Lab, Ctr Appl Sci Comp, Livermore, CA 94550 USA. RP Lindstrom, P (reprint author), Lawrence Livermore Natl Lab, Ctr Appl Sci Comp, Livermore, CA 94550 USA. EM pl@llnl.gov OI Lindstrom, Peter/0000-0003-3817-4199 NR 50 TC 7 Z9 7 U1 0 U2 13 PU IEEE COMPUTER SOC PI LOS ALAMITOS PA 10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA 90720-1314 USA SN 1077-2626 EI 1941-0506 J9 IEEE T VIS COMPUT GR JI IEEE Trans. Vis. Comput. Graph. PD DEC PY 2014 VL 20 IS 12 BP 2674 EP 2683 DI 10.1109/TVCG.2014.2346458 PG 10 WC Computer Science, Software Engineering SC Computer Science GA AT5OI UT WOS:000344991700113 PM 26356981 ER PT J AU Lee, H Lee, KO AF Lee, Hoon Lee, Kyeong O. TI Multi-layered mesh generation and user subroutine development based on an Eulerian-Eulerian approach for soot filtration visualization in a three-dimensional particulate filter model SO INTERNATIONAL JOURNAL OF ENGINE RESEARCH LA English DT Article DE Particulate filter; soot filtration modeling; Eulerian-Eulerian approach; structured mesh; user subroutine ID NUMERICAL-SIMULATION; REGENERATION; FLOW AB A three-dimensional model is developed for computational fluid dynamics analysis of soot filtration processes in a wall flow-type particulate filter based on an Eulerian-Eulerian numerical approach. The primary objective of this study is to accurately capture the local values of filtration parameters, such as volume porosity, collection efficiency, and soot mass deposited, through isotropically discretized computational grids within the multi-layered porous wall regions. Most commercial computational fluid dynamics codes do not have the ability to generate structured mesh with ordered cell index or allow expressing mathematical recursive operation or handling time array through defined user field functions. For these reasons, it is difficult to utilize the code in situations where complex algorithms and mathematical treatments are required. Therefore, custom-build user subroutines, written with C++ programming language, are developed and integrated with the model to calculate localized soot mass distributions in each layer of porous wall. New recursive and computationally efficient algorithms are developed utilizing the functional attributes of the computational fluid dynamics code and coupled with the modified unit collector mechanism in order to obtain temporal and local filtration efficiency. Simulations enabled quantitative visualization of the detailed filtration processes along the filter wall and channel, including the time evolution of filtration parameters, which is difficult to detect experimentally. The model revealed correlations between wall flow pattern and rearrangement behaviors of filtration parameters and provided insights into the soot cake layer profiles with respect to both the length and the width of the channel. C1 [Lee, Hoon; Lee, Kyeong O.] Argonne Natl Lab, Ctr Transportat Res, Argonne, IL 60439 USA. [Lee, Hoon] Adv Inst Convergence Technol, Intelligent Vehicle Platform Ctr, Vehicle Energy Res Lab, Suwon 443270, Gyeonggi Do, South Korea. RP Lee, H (reprint author), Adv Inst Convergence Technol, Intelligent Vehicle Platform Ctr, Vehicle Energy Res Lab, 145 Gwanggyo Ro, Suwon 443270, Gyeonggi Do, South Korea. EM hoonlee@snu.ac.kr FU US Department of Energy, Office of Vehicle Technologies Program FX This research was partially supported by the US Department of Energy, Office of Vehicle Technologies Program. NR 26 TC 1 Z9 1 U1 0 U2 8 PU SAGE PUBLICATIONS LTD PI LONDON PA 1 OLIVERS YARD, 55 CITY ROAD, LONDON EC1Y 1SP, ENGLAND SN 1468-0874 EI 2041-3149 J9 INT J ENGINE RES JI Int. J. Engine Res. PD DEC PY 2014 VL 15 IS 8 SI SI BP 980 EP 992 DI 10.1177/1468087414543707 PG 13 WC Thermodynamics; Engineering, Mechanical; Transportation Science & Technology SC Thermodynamics; Engineering; Transportation GA AU0FY UT WOS:000345300200010 ER PT J AU Damit, B Bischoff, BL Phelps, TJ Wu, CY Cheng, MD AF Damit, Brian Bischoff, Brian L. Phelps, Tommy J. Wu, Chang-Yu Cheng, Meng-Dawn TI Filtration of Bioaerosols Using a Granular Metallic Filter with Micrometer-Sized Collectors SO JOURNAL OF ENVIRONMENTAL ENGINEERING LA English DT Article DE Filters; Filtration; Microbes; Pathogens; Granular media; Viruses; Bacteria AB Experimental studies with granular bed filters composed of sized metallic granules have demonstrated their use in aerosol filtration. However, the effectiveness of metallic membrane filters against bioaerosols has not been established. In this work, the filtration efficiency and filter quality of these filters against airborne B. subtilis endospore and MS2 virus were determined as a function of face velocity and loading time. In experiments, a physical removal efficiency greater than 99.9% and a viable removal efficiency greater than 99.999% were observed for both bacterial spore and viral aerosols. A lower face velocity produced both higher collection efficiency and filter quality for virus but was not a statistically significant factor for spore filtration. Although the filter had high filtration efficiency of the test bioaerosols, its high pressure drop resulted in a low filter quality (0.25-0.75kPa-1). Overall, filters with micrometer-sized collectors capture bioaerosols effectively but their applications in aerosol filtration may be limited by their high pressure drop. C1 [Damit, Brian] Johns Hopkins Univ, Appl Phys Lab, Laurel, MD 20723 USA. [Damit, Brian] Univ Florida, Dept Environm Engn Sci, Gainesville, FL 32611 USA. [Bischoff, Brian L.] Oak Ridge Natl Lab, Mat Sci & Technol Div, Oak Ridge, TN 37831 USA. [Phelps, Tommy J.] Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USA. [Wu, Chang-Yu] Univ Florida, Dept Environm Engn Sci, Gainesville, FL 32611 USA. EM Brian.Damit@jhuapl.edu; bischoffbl@ornl.gov; phelpstj@ornl.gov; cywu@ufl.edu; chengmd@ornl.gov OI Cheng, Meng-Dawn/0000-0003-1407-9576; Bischoff, Brian/0000-0002-3021-7898 FU National Science Foundation Graduate Research Fellowship (NSF GRF) [DGE-0802270]; SERDP [WP 1627]; U.S. Department of Energy [DE-AC05-00OR22725]; U.S. Government [DE-AC05-00OR22725] FX Brian Damit is thankful for the National Science Foundation Graduate Research Fellowship (NSF GRF) under Grant No. DGE-0802270. Meng-Dawn Cheng acknowledges the support from SERDP WP 1627 for membrane separation research. This research was performed at ORNL, which is managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725. The submitted manuscript has been authored by a contractor of the U.S. Government under contract DE-AC05-00OR22725. Accordingly, 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. NR 20 TC 0 Z9 0 U1 2 U2 17 PU ASCE-AMER SOC CIVIL ENGINEERS PI RESTON PA 1801 ALEXANDER BELL DR, RESTON, VA 20191-4400 USA SN 0733-9372 EI 1943-7870 J9 J ENVIRON ENG JI J. Environ. Eng.-ASCE PD DEC PY 2014 VL 140 IS 12 AR 06014007 DI 10.1061/(ASCE)EE.1943-7870.0000848 PG 5 WC Engineering, Environmental; Engineering, Civil; Environmental Sciences SC Engineering; Environmental Sciences & Ecology GA AU0QL UT WOS:000345328600007 ER PT J AU Jung, HK Jo, H Park, G Mascarenas, DL Farrar, CR AF Jung, Hwee Kwon Jo, HyeJin Park, Gyuhae Mascarenas, David L. Farrar, Charles R. TI Relative baseline features for impedance-based structural health monitoring SO JOURNAL OF INTELLIGENT MATERIAL SYSTEMS AND STRUCTURES LA English DT Article; Proceedings Paper CT 7th International Conference on Biomimetics, Artificial Muscles and Nano-Bio (BAMN) CY AUG 26-30, 2013 CL Jeju, SOUTH KOREA DE Structural health monitoring; piezoelectric; electromechanical impedance ID PIEZOELECTRIC ACTIVE-SENSORS; IDENTIFICATION; TRANSDUCERS; DIAGNOSTICS; VALIDATION; CONCRETE; ACTUATOR; SYSTEM AB Various experimental studies have demonstrated that an impedance-based method is an effective means of structural damage detection. Using the self-sensing and active-sensing capabilities of piezoelectric materials, the electromechanical impedance response can be monitored to provide a qualitative indication of the overall health of a structure. In this article, two new signal processing tools for the impedance method are described in order to improve the damage detection capability and to reduce the amount of data to process for structural health assessment. The first approach is to instantaneously correlate the impedance data between different sensor sets, as opposed to be correlated to pre-stored baseline data. Another approach is to use the pre-defined parameter of impedance data to establish a generalized baseline for bolted joint monitoring. These approaches could reduce the number of data sets and could be efficiently used for low-power impedance devices. The proposed signal processing techniques are applied to several experimental structures, and the efficiency in damage detection is demonstrated. C1 [Jung, Hwee Kwon; Jo, HyeJin; Park, Gyuhae] Chonnam Natl Univ, Sch Mech Engn, Kwangju 500757, South Korea. [Mascarenas, David L.; Farrar, Charles R.] Los Alamos Natl Lab, Engn Inst, Los Alamos, NM USA. RP Park, G (reprint author), Chonnam Natl Univ, Sch Mech Engn, YongBong 77, Kwangju 500757, South Korea. EM gpark@jnu.ac.kr OI Farrar, Charles/0000-0001-6533-6996 FU National Research Foundation of Korea - Ministry of Education, Science and Technology [2011-0030065]; Defense Acquisition Program Administration and Agency for Defense Development [UD130058JD]; Chonnam National University FX The research was funded by the Department of Energy through the Laboratory Directed Research and Development Program at Los Alamos National Laboratory. This research was partially supported by the Leading Foreign Research Institute Recruitment Program through the National Research Foundation of Korea funded by the Ministry of Education, Science and Technology (2011-0030065). This research was also partially supported by the financial support provided by Defense Acquisition Program Administration and Agency for Defense Development under the contract UD130058JD. G.P. received the financial support from Chonnam National University (2013). NR 31 TC 1 Z9 1 U1 0 U2 5 PU SAGE PUBLICATIONS LTD PI LONDON PA 1 OLIVERS YARD, 55 CITY ROAD, LONDON EC1Y 1SP, ENGLAND SN 1045-389X EI 1530-8138 J9 J INTEL MAT SYST STR JI J. Intell. Mater. Syst. Struct. PD DEC PY 2014 VL 25 IS 18 SI SI BP 2294 EP 2304 DI 10.1177/1045389X14551435 PG 11 WC Materials Science, Multidisciplinary SC Materials Science GA AU0SX UT WOS:000345335900010 ER PT J AU Kim, J Paliwal, M Zhou, SH Choi, H Jung, IH AF Kim, Junghwan Paliwal, Manas Zhou, Shihuai Choi, Hanshin Jung, In-Ho TI Critical Systematic Evaluation and Thermodynamic Optimization of the Mn-RE System (RE = Tb, Dy, Ho, Er, Tm and Lu) with Key Experiments for the Mn-Dy System SO JOURNAL OF PHASE EQUILIBRIA AND DIFFUSION LA English DT Article DE Mg-RE alloy; Mn-RE system; phase diagrams; thermodynamic modeling; thermodynamic properties ID QUASI-CHEMICAL MODEL; TRANSITION-METAL SYSTEMS; INTERMETALLIC COMPOUNDS; PHASE-DIAGRAMS; SM SYSTEMS; MG; MANGANESE; ALLOYS; ND; CE AB Critical evaluation and optimization of all available phase diagrams and thermodynamic data for the Mn-RE (RE = Tb, Dy, Ho, Er, Tm, and Lu) systems has been conducted to obtain reliable thermodynamic functions of all the phases in the systems. Key experiments for the Mn-Dy system were performed using DSC and solution calorimeter. In the thermodynamic modeling, it is found that the Mn-RE systems show systematic changes in the phase diagrams and thermodynamic properties such as enthalpy of mixing in liquid state in the order of periodic number in the lanthanide series. The systematic thermodynamic modeling approach for RE elements allow to resolve inconsistencies in the experimental data and estimate unknown thermodynamic properties and phase equilibria of Mn-RE system. C1 [Kim, Junghwan; Paliwal, Manas; Jung, In-Ho] McGill Univ, Dept Min & Mat Engn, Montreal, PQ H3A 2B2, Canada. [Zhou, Shihuai] US DOE, Ames Lab, Ames, IA 50011 USA. [Choi, Hanshin] Korea Inst Ind Technol, Inchon 406840, South Korea. RP Jung, IH (reprint author), McGill Univ, Dept Min & Mat Engn, 3610 Univ St, Montreal, PQ H3A 2B2, Canada. EM in-ho.jung@mcgill.ca FU National Sciences and Engineering Research Council of Canada (NSERC) Collaborative Research and Development grant; General Motors of Canada FX This project was supported by the National Sciences and Engineering Research Council of Canada (NSERC) Collaborative Research and Development grant and General Motors of Canada. We would like to thank to Dr. I. Beta and Mr. D. Shepard from Netzsch for DSC experiments. NR 63 TC 4 Z9 4 U1 0 U2 10 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1547-7037 EI 1863-7345 J9 J PHASE EQUILIB DIFF JI J. Phase Equilib. Diffus. PD DEC PY 2014 VL 35 IS 6 BP 670 EP 694 DI 10.1007/s11669-014-0345-3 PG 25 WC Chemistry, Physical; Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering SC Chemistry; Materials Science; Metallurgy & Metallurgical Engineering GA AT9ZB UT WOS:000345281500004 ER PT J AU Kulkarni, NS Warmack, RJB Radhakrishnan, B Hunter, JL Sohn, Y Coffey, KR Murch, GE Belova, IV AF Kulkarni, Nagraj S. Warmack, Robert J. Bruce Radhakrishnan, Bala Hunter, Jerry L. Sohn, Yongho Coffey, Kevin R. Murch, Graeme E. Belova, Irina V. TI Overview of SIMS-Based Experimental Studies of Tracer Diffusion in Solids and Application to Mg Self-Diffusion SO JOURNAL OF PHASE EQUILIBRIA AND DIFFUSION LA English DT Article DE database; diffusion; isotope; magnesium; self diffusivity; SIMS; tracer diffusivity ID GRAIN-BOUNDARY DIFFUSION; ION MASS-SPECTROMETRY; ALLOYS; MAGNESIUM; KINETICS; SIMULATION; MECHANISM; LATTICE; DICTRA AB Tracer diffusivities provide the most fundamental information on diffusion in materials, and are the foundation of robust diffusion databases that enable the use of the Onsager phenomenological formalism with no major assumptions. Compared to traditional radiotracer techniques that utilize radioactive isotopes, the secondary ion mass spectrometry (SIMS)-based thin-film technique for tracer diffusion is based on the use of enriched stable isotopes that can be accurately profiled using SIMS. An overview of the thin-film method for tracer diffusion studies using stable isotopes is provided. Experimental procedures and techniques for the measurement of tracer diffusion coefficients are presented for pure magnesium, which presents some unique challenges due to the ease of oxidation. The development of a modified Shewmon-Rhines diffusion capsule for annealing Mg and an ultra-high vacuum system for sputter deposition of Mg isotopes are discussed. Optimized conditions for accurate SIMS depth profiling in polycrystalline Mg are provided. An automated procedure for correction of heat-up and cool-down times during tracer diffusion annealing is discussed. The non-linear fitting of a SIMS depth profile data using the thin-film Gaussian solution to obtain the tracer diffusivity along with the background tracer concentration and tracer film thickness is demonstrated. An Arrhenius fit of the Mg self-diffusion data obtained using the low-temperature SIMS measurements from this study and the high-temperature radiotracer measurements of Shewmon and Rhines (Trans. AIME 250:1021-1025, 1954) was found to be a good representation of both types of diffusion data over a broad range of temperatures between 250 and 627 A degrees C (523 and 900 K). C1 [Warmack, Robert J. Bruce; Radhakrishnan, Bala] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Hunter, Jerry L.] Virginia Polytech Inst & State Univ, Blacksburg, VA 24061 USA. [Sohn, Yongho; Coffey, Kevin R.] Univ Cent Florida, Orlando, FL 32816 USA. [Murch, Graeme E.; Belova, Irina V.] Univ Newcastle, Callaghan, NSW 2308, Australia. EM Nagraj@alumni.ufl.edu RI Sohn, Yongho/A-8517-2010 OI Sohn, Yongho/0000-0003-3723-4743 FU U.S. Department of Energy (DOE), Assistant Secretary for Energy Efficiency and Renewable Energy (EERE), Office of Vehicle Technologies as part of the Automotive Lightweight Materials Program [DE-AC05-00OR22725]; UT-Battelle, LLC FX The authors are grateful for the support provided by the U.S. Department of Energy (DOE), Assistant Secretary for Energy Efficiency and Renewable Energy (EERE), Office of Vehicle Technologies as part of the Automotive Lightweight Materials Program under contract DE-AC05-00OR22725 with UT-Battelle, LLC. The authors thank the ORNL isotope processing facility, including Scott Aaron and Lee Zevenbergen for providing the enriched 25Mg isotopic foils used in this work and for helpful discussions. The technical expertise provided by Edward Kenik (EBSD analysis) and Harry Meyer (XPS analysis) at the High Temperature Materials Laboratory (HTML) is recognized. The authors acknowledge Edward Dein at the Advanced Materials Processing and Analysis Center (AMPAC) clean room facility, University of Central Florida (UCF) for his assistance with the UHV PVD system and the isotopic deposition experiments. The assistance of Jay Tuggle and the students of one of the authors, J. Hunter, at Virginia Tech during the course of this project are appreciated. The authors thank Sarah Brennan and the graduate students of one of the authors, Y. Sohn, and Mikhail Klimov (SIMS specialist) at UCF for their assistance during various stages of this work. The authors appreciate the many fruitful discussions related to SIMS with Peter Todd, formerly at ORNL and now at Nebulytics, Inc. in Oak Ridge. The authors thank John Allison, Robert McCune and the staff associated with the Mg-ICME initiative for their support and encouragement. The support of Carol Schutte, William Joost and Joe Carpenter with the DOE Vehicle Technologies Program, and Phil Sklad and David Warren at ORNL are gratefully acknowledged. NR 54 TC 3 Z9 3 U1 6 U2 19 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1547-7037 EI 1863-7345 J9 J PHASE EQUILIB DIFF JI J. Phase Equilib. Diffus. PD DEC PY 2014 VL 35 IS 6 BP 762 EP 778 DI 10.1007/s11669-014-0344-4 PG 17 WC Chemistry, Physical; Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering SC Chemistry; Materials Science; Metallurgy & Metallurgical Engineering GA AT9ZB UT WOS:000345281500011 ER PT J AU Kulkarni, NS Warmack, RJB Radhakrishnan, B Hunter, JL Sohn, Y Coffey, KR Murch, GE Belova, IV AF Kulkarni, Nagraj S. Warmack, Robert J. Bruce Radhakrishnan, Bala Hunter, Jerry L. Sohn, Yongho Coffey, Kevin R. Murch, Graeme E. Belova, Irina V. TI Overview of SIMS-Based Experimental Studies of Tracer Diffusion in Solids and Application to Mg Self-Diffusion (vol 35, pg 762, 2014) SO JOURNAL OF PHASE EQUILIBRIA AND DIFFUSION LA English DT Correction C1 [Warmack, Robert J. Bruce; Radhakrishnan, Bala] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Hunter, Jerry L.] Virginia Polytech Inst & State Univ, Blacksburg, VA 24061 USA. [Sohn, Yongho; Coffey, Kevin R.] Univ Cent Florida, Orlando, FL 32816 USA. [Murch, Graeme E.; Belova, Irina V.] Univ Newcastle, Callaghan, NSW 2308, Australia. EM Nagraj@alumni.ufl.edu NR 1 TC 0 Z9 0 U1 2 U2 4 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 1547-7037 EI 1863-7345 J9 J PHASE EQUILIB DIFF JI J. Phase Equilib. Diffus. PD DEC PY 2014 VL 35 IS 6 BP 779 EP 779 DI 10.1007/s11669-014-0352-4 PG 1 WC Chemistry, Physical; Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering SC Chemistry; Materials Science; Metallurgy & Metallurgical Engineering GA AT9ZB UT WOS:000345281500012 ER PT J AU Knapp, FF Pillai, MRA Osso, JA Dash, A AF Knapp, F. F., Jr. Pillai, M. R. A. Osso, J. A., Jr. Dash, Ashutosh TI Re-emergence of the important role of radionuclide generators to provide diagnostic and therapeutic radionuclides to meet future research and clinical demands SO JOURNAL OF RADIOANALYTICAL AND NUCLEAR CHEMISTRY LA English DT Article DE Approved pharmaceutical ingredient (API); Current Good Radiopharmacy Practice (cGRPP); Parent/daughter radionuclide; Radionuclide generators; Positron emission tomography (PET); Radiochemical separation ID TARGETED ALPHA-THERAPY; ZINC-62 COPPER-62 GENERATOR; PROSTATE-CANCER; NUCLEAR-MEDICINE; TUNGSTEN-188/RHENIUM-188 GENERATOR; PET-RADIOPHARMACEUTICALS; AC-225/BI-213 GENERATOR; RADIOISOTOPE GENERATOR; SOLVENT-EXTRACTION; PARTICLE THERAPY AB Radionuclide generators have been the main stay of diagnostic nuclear medicine and it is no exaggeration to state that the growth of nuclear medicine would not have happened to the present levels but for the availability of Mo-99/Tc-99m generator. This article provides a brief account of the various radionuclide generators currently in clinical use or which have made substantial progress or likely to be materialized in the foreseeable future to bring evolutional progress in nuclear medicine. Further, a brief outline on the regulatory challenges and impact on radionuclide generator technology with the emergence of professionally run central radiopharmacies have been provided. C1 [Knapp, F. F., Jr.] Oak Ridge Natl Lab ORNL, Med Radioisotope Program, Oak Ridge, TN 37831 USA. [Pillai, M. R. A.] Mol Grp Co, Kochi 680001, Kerala, India. [Osso, J. A., Jr.] Vienna Int Ctr, Div Phys & Chem Sci, Dept Nucl Sci & Applicat, Int Atom Energy Agcy IAEA, A-1400 Vienna, Austria. [Dash, Ashutosh] Bhabha Atom Res Ctr BARC, Isotope Prod & Applicat Div, Mumbai 400085, Maharashtra, India. RP Dash, A (reprint author), Bhabha Atom Res Ctr BARC, Isotope Prod & Applicat Div, Mumbai 400085, Maharashtra, India. EM adash@barc.gov.in OI Dash, Ashutosh/0000-0001-7541-7298 NR 109 TC 3 Z9 3 U1 5 U2 15 PU SPRINGER PI DORDRECHT PA VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS SN 0236-5731 EI 1588-2780 J9 J RADIOANAL NUCL CH JI J. Radioanal. Nucl. Chem. PD DEC PY 2014 VL 302 IS 3 BP 1053 EP 1068 DI 10.1007/s10967-014-3642-8 PG 16 WC Chemistry, Analytical; Chemistry, Inorganic & Nuclear; Nuclear Science & Technology SC Chemistry; Nuclear Science & Technology GA AT7AQ UT WOS:000345088700001 ER PT J AU Hong-Hermesdorf, A Miethke, M Gallaher, SD Kropat, J Dodani, SC Chan, J Barupala, D Domaille, DW Shirasaki, DI Loo, JA Weber, PK Pett-Ridge, J Stemmler, TL Chang, CJ Merchant, SS AF Hong-Hermesdorf, Anne Miethke, Marcus Gallaher, Sean D. Kropat, Janette Dodani, Sheel C. Chan, Jefferson Barupala, Dulmini Domaille, Dylan W. Shirasaki, Dyna I. Loo, Joseph A. Weber, Peter K. Pett-Ridge, Jennifer Stemmler, Timothy L. Chang, Christopher J. Merchant, Sabeeha S. TI Subcellular metal imaging identifies dynamic sites of Cu accumulation in Chlamydomonas SO NATURE CHEMICAL BIOLOGY LA English DT Article ID SACCHAROMYCES-CEREVISIAE; ZINC STORAGE; COPPER SENSOR; REINHARDTII; CELLS; ACIDOCALCISOMES; METALLOPROTEINS; TRANSPORTERS; PLASTOCYANIN; ASSIMILATION AB We identified a Cu-accumulating structure with a dynamic role in intracellular Cu homeostasis. During Zn limitation, Chlamydomonas reinhardtii hyperaccumulates Cu, a process dependent on the nutritional Cu sensor CRR1, but it is functionally Cu deficient. Visualization of intracellular Cu revealed major Cu accumulation sites coincident with electron-dense structures that stained positive for low pH and polyphosphate, suggesting that they are lysosome-related organelles. Nano-secondary ion MS showed colocalization of Ca and Cu, and X-ray absorption spectroscopy was consistent with Cu+ accumulation in an ordered structure. Zn resupply restored Cu homeostasis concomitant with reduced abundance of these structures. Cu isotope labeling demonstrated that sequestered Cu+ became bioavailable for the synthesis of plastocyanin, and transcriptome profiling indicated that mobilized Cu became visible to CRR1. Cu trafficking to intracellular accumulation sites may be a strategy for preventing protein mismetallation during Zn deficiency and enabling efficient cuproprotein metallation or remetallation upon Zn resupply. C1 [Hong-Hermesdorf, Anne; Miethke, Marcus; Gallaher, Sean D.; Kropat, Janette; Merchant, Sabeeha S.] Univ Calif Los Angeles, Dept Chem & Biochem, Los Angeles, CA 90024 USA. [Dodani, Sheel C.; Chan, Jefferson; Domaille, Dylan W.; Chang, Christopher J.] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. [Dodani, Sheel C.; Chan, Jefferson; Domaille, Dylan W.; Chang, Christopher J.] Univ Calif Berkeley, Howard Hughes Med Inst, Berkeley, CA 94720 USA. [Barupala, Dulmini; Stemmler, Timothy L.] Wayne State Univ, Dept Pharmaceut Sci, Detroit, MI USA. [Shirasaki, Dyna I.; Loo, Joseph A.] Univ Calif Los Angeles, Dept Biol Chem, Los Angeles, CA 90024 USA. [Loo, Joseph A.; Merchant, Sabeeha S.] Univ Calif Los Angeles, Inst Genom & Prote, Los Angeles, CA USA. [Weber, Peter K.; Pett-Ridge, Jennifer] Lawrence Livermore Natl Lab, Div Chem Sci, Livermore, CA USA. RP Merchant, SS (reprint author), Univ Calif Los Angeles, Dept Chem & Biochem, 405 Hilgard Ave, Los Angeles, CA 90024 USA. EM merchant@chem.ucla.edu OI Gallaher, Sean/0000-0002-9773-6051 FU US National Institutes of Health (NIH) [GM42143, GM092473, GM079465]; United States Department of Energy Cooperative Agreement [DE-FC0202ER63421]; German Academic Exchange Service DAAD [D0847579, D1242134]; US Department of Energy at LLNL [DE-AC52-07NA27344]; US Department of Energy Genomic Science Program [SCW1039]; Department of Energy-Office of Biological and Environmental Research; NIH-National Center for Research Resources Biomedical Technology Program; NIH [T32HL120822] FX This work is supported, in part, by grants from the US National Institutes of Health (NIH; GM42143 and GM092473 to S.S.M., DK068139 to T.L.S.and GM079465 to C.J.C.), the United States Department of Energy Cooperative Agreement (DE-FC0202ER63421 to D. Eisenberg for support of J.A.L.) and the German Academic Exchange Service DAAD (D0847579 to A.H.-H. and D1242134 to M.M.). Work at Lawrence Livermore National Laboratory (LLNL) was performed under the auspices of the US Department of Energy at LLNL under contract DE-AC52-07NA27344, with funding provided by the US Department of Energy Genomic Science Program under contract SCW1039. Portions of this research were carried out at the Stanford Synchrotron Radiation Lightsource (SSRL). SSRL is a national user facility operated by Stanford University, and the SSRL Structural Molecular Biology Program is supported by the Department of Energy-Office of Biological and Environmental Research and by the NIH-National Center for Research Resources Biomedical Technology Program. D.B. is supported by the NIH (T32HL120822), and C.J.C. is an investigator with the Howard Hughes Medical Institute. Electron microscopy was performed at the Electron Microscopy Services Center of the University of California-Los Angeles Brain Research Institute. We thank A. Aron and K.M. Ramos-Torres for their help with resynthesis and optical spectroscopy of fresh CS3 and Ctrl-CS3 for control experiments. NR 55 TC 34 Z9 34 U1 10 U2 61 PU NATURE PUBLISHING GROUP PI NEW YORK PA 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA SN 1552-4450 EI 1552-4469 J9 NAT CHEM BIOL JI Nat. Chem. Biol. PD DEC PY 2014 VL 10 IS 12 BP 1034 EP + DI 10.1038/nchembio.1662 PG 11 WC Biochemistry & Molecular Biology SC Biochemistry & Molecular Biology GA AT7MT UT WOS:000345122300011 PM 25344811 ER PT J AU Widgren, K Skar, H Berglund, T Kling, AM Tegnell, A Albert, J AF Widgren, Katarina Skar, Helena Berglund, Torsten Kling, Anna-Maria Tegnell, Anders Albert, Jan TI Delayed HIV diagnosis common in Sweden, 2003-2010 SO SCANDINAVIAN JOURNAL OF INFECTIOUS DISEASES LA English DT Article DE HIV; delayed diagnosis; immunoassay; trends; risk factors ID ANTIRETROVIRAL THERAPY; INFECTION; CHALLENGES; PREVENTION; ENGLAND; ASSAYS; WALES AB Background: Early diagnosis of HIV is important for the prognosis of individual patients, because antiretroviral treatment can be started at the appropriate time, and for public health, because transmission can be prevented. Methods: Data were collected from 767 HIV patients who were diagnosed in Sweden during 2003-2010 and were infected in Sweden or born in Sweden and infected abroad. A recent infection testing algorithm (RITA) was applied to BED-EIA test results (OD-n < 0.8), CD4 counts (>= 200 cells/mu l), and clinical information. A recent infection classification was used as indicator for early diagnosis. Time trends in early diagnosis were investigated to detect population changes in HIV testing behavior. Patients with early diagnosis were compared to patients with delayed diagnosis with respect to age, gender, transmission route, and country of infection (Sweden or abroad). Results: Early diagnosis was observed in 271 patients (35%). There was no statistically significant time trend in the yearly percentage of patients with early diagnosis in the entire study group (p = 0.836) or in subgroups. Early diagnosis was significantly more common in men who have sex men (MSM) (45%) than in heterosexuals (21%) and injecting drug users (27%) (p < 0.001 and p = 0.001, respectively) in both univariate and multivariable analyses. The only other factor that remained associated with early diagnosis in multivariable analysis was young age group. Conclusion: Approximately one-third of the study patients were diagnosed early with no significant change over time. Delayed HIV diagnosis is a considerable problem in Sweden, which does not appear to diminish. C1 [Widgren, Katarina; Berglund, Torsten; Kling, Anna-Maria; Tegnell, Anders] Publ Hlth Agcy Sweden, Dept Monitoring & Evaluat, Solna, Sweden. [Widgren, Katarina] Karolinska Inst, Dept Med, Stockholm, Sweden. [Skar, Helena; Albert, Jan] Karolinska Inst, Dept Microbiol Tumor & Cell Biol, Stockholm, Sweden. [Skar, Helena] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. [Skar, Helena; Albert, Jan] Karolinska Univ Hosp, Dept Clin Microbiol, Stockholm, Sweden. [Skar, Helena] Linkoping Univ, Dept Sci & Technol, Linkoping, Sweden. RP Widgren, K (reprint author), Folkhalsomyndigheten, S-17182 Solna, Sweden. EM Widgren.katarina@gmail.com FU Swedish Research Council [K2008-56X-09935-17-3, K2001-35 56X-0095-20-6, 623-2011-1100, 623-2013-8905]; Swedish International Development Cooperation Agency [SWE-2006-018]; EU project: SPREAD [QLK2-CT-2001-37 01344]; EU project: EHR [LSHP-CT-2006-518211]; EU project: CHAIN; 'Collaborative HIV and Anti-HIV Drug Resistance Network' [223131, 260694] FX Thanks to Rigmor Thorstensson, Hans Gaines, Monica Idestrom, Kajsa Aperia, Frida Hansdotter, Maria Axelsson, Gunilla Rado, and Susanne Karregard at the Public Health Agency of Sweden and Eva C. Eriksson at Karolinska University Hospital. The research leading to these results has received funding from the Swedish Research Council (grant nos K2008-56X-09935-17-3 and K2001-35 56X-0095-20-6); from the Swedish International Development Cooperation Agency (grant no. SWE-2006-018); and the EU projects: SPREAD (QLK2-CT-2001-37 01344); EHR (LSHP-CT-2006-518211); CHAIN (FP7/2007-2013). 'Collaborative HIV and Anti-HIV Drug Resistance Network,' and FP7 grant agreement no. 223131 under EuroCoord grant agreement no. 260694. H.S. was supported by a postdoctoral fellowship from the Swedish Research Council (623-2011-1100, 623-2013-8905). NR 26 TC 1 Z9 1 U1 1 U2 1 PU INFORMA HEALTHCARE PI LONDON PA TELEPHONE HOUSE, 69-77 PAUL STREET, LONDON EC2A 4LQ, ENGLAND SN 0036-5548 EI 1651-1980 J9 SCAND J INFECT DIS JI Scand. J. Infect. Dis. PD DEC PY 2014 VL 46 IS 12 BP 862 EP 867 DI 10.3109/00365548.2014.953575 PG 6 WC Infectious Diseases SC Infectious Diseases GA AT9HF UT WOS:000345238100008 PM 25290584 ER PT J AU Song, B Nelson, K Lipinski, R Bignell, J Ulrich, G George, EP AF Song, B. Nelson, K. Lipinski, R. Bignell, J. Ulrich, G. George, E. P. TI Dynamic High-temperature Testing of an Iridium Alloy in Compression at High-strain Rates SO STRAIN LA English DT Article DE high-strain rate; high temperature; iridium alloy; Kolsky bar (split Hopkinson bar); stress-strain response ID IMPACT DUCTILITY; BEHAVIOR; SHPB; SPECIMENS; ADDITIONS; FRACTURE; DOP-26 AB Iridium alloys have superior strength and ductility at elevated temperatures, making them useful as structural materials for certain high-temperature applications. However, experimental data on their high-strain -rate performance are needed for understanding high-speed impacts in severe environments. Kolsky bars (also called split Hopkinson bars) have been extensively employed for high-strain -rate characterization of materials at room temperature, but it has been challenging to adapt them for the measurement of dynamic properties at high temperatures. In this study, we analyzed the difficulties encountered in high-temperature Kolsky bar testing of thin iridium alloy specimens in compression. Appropriate modifications were then made to the current high-temperature Kolsky bar technique to obtain reliable compressive stress-strain response of an iridium alloy at high-strain rates (300-10000s(-1)) and temperatures (750 and 1030 degrees C). The compressive stress-strain response of the iridium alloy showed significant sensitivity to both strain rate and temperature. C1 [Song, B.; Lipinski, R.; Bignell, J.] Sandia Natl Labs, Albuquerque, NM 87185 USA. [Nelson, K.] Sandia Natl Labs, Livermore, CA 94550 USA. [Ulrich, G.; George, E. P.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. RP Song, B (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87185 USA. RI Ulrich, George/J-7276-2015 OI Ulrich, George/0000-0002-8282-6994 FU United States Department of Energy (DOE) Office of Space and Defense Power Systems [NE-75]; US Department of Energy's National Nuclear Security Administration [DE-AC04-94AL85000]; US DOE [DE-AC05-00OR22725] FX This work was sponsored by the United States Department of Energy (DOE) Office of Space and Defense Power Systems (NE-75). The authors gratefully acknowledge the support and guidance of Ryan D. Bechtel of the US Department of Energy.; Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the US Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.; Oak Ridge National Laboratory is a multi-program research laboratory managed by UT-Battelle, LLC, for the US DOE under contract DE-AC05-00OR22725. NR 22 TC 2 Z9 2 U1 0 U2 6 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 1475-1305 J9 STRAIN JI Strain PD DEC PY 2014 VL 50 IS 6 SI SI BP 539 EP 546 DI 10.1111/str.12100 PG 8 WC Materials Science, Characterization & Testing SC Materials Science GA AT3YT UT WOS:000344872600006 ER PT J AU Dieterich, JM Krisiloff, DB Gaenko, A Libisch, F Windus, TL Gordon, MS Carter, EA AF Dieterich, Johannes M. Krisiloff, David B. Gaenko, Alexander Libisch, Florian Windus, Theresa L. Gordon, Mark S. Carter, Emily A. TI Shared-memory parallelization of a local correlation multi-reference CI program SO COMPUTER PHYSICS COMMUNICATIONS LA English DT Article DE Local correlation; Parallelization; Shared memory; Multi reference; Dioxirane; Multi-reference configuration interaction ID DOUBLES CONFIGURATION-INTERACTION; ELECTRON CORRELATION METHODS; MOLECULAR-ORBITAL METHODS; GROUP GRAPHICAL APPROACH; GAUSSIAN-TYPE BASIS; ORGANIC-MOLECULES; BASIS SETS; SINGLES; REACTIVITY; DIOXIRANE AB We present a shared-memory parallelization of our open-source, local correlation multi-reference framework, TigerCl. Benchmarks of the total parallel speedup show a reasonable scaling for typical modern computing system setups. The efficient use of available computing resources will extend simulations on this high level of theory into a new size regime. We demonstrate our framework using local-correlation multireference computations of alkyl-substituted dioxirane and solvated methyl nitrene as examples. (c) 2014 Elsevier B.V. All rights reserved. C1 [Dieterich, Johannes M.; Libisch, Florian; Carter, Emily A.] Princeton Univ, Dept Mech & Aerosp Engn, Princeton, NJ 08544 USA. [Krisiloff, David B.] Princeton Univ, Dept Chem, Princeton, NJ 08544 USA. [Gaenko, Alexander; Windus, Theresa L.; Gordon, Mark S.] Iowa State Univ, Dept Chem, Ames, IA 50011 USA. [Gaenko, Alexander; Windus, Theresa L.; Gordon, Mark S.] Ames Lab, Ames, IA 50011 USA. [Carter, Emily A.] Princeton Univ, Program Appl & Computat Math, Princeton, NJ 08544 USA. [Carter, Emily A.] Princeton Univ, Andlinger Ctr Energy & Environm, Princeton, NJ 08544 USA. RP Carter, EA (reprint author), Princeton Univ, Dept Mech & Aerosp Engn, Princeton, NJ 08544 USA. EM eac@princeton.edu RI Carter, Emily/P-4075-2014; OI Carter, Emily/0000-0001-7330-7554; Libisch, Florian/0000-0001-5641-9458 FU US National Science Foundation [CHE-1265700]; US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences through the Ames Laboratory PCTC, Chemical Physics, and Homogeneous and Interfacial Catalysis project; Iowa State University [DE-AC02-07CH11358] FX JMD acknowledges a German academic exchange service (DAAD) fellowship. EAC thanks the US National Science Foundation (Grant No. CHE-1265700) for support of this work. All calculations presented in the performance assessment section were carried out using Princeton's TIGRESS High Performance Computing resources.; MSG, TLW and AG were supported by a grant from the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences through the Ames Laboratory PCTC, Chemical Physics, and Homogeneous and Interfacial Catalysis project. The Ames Laboratory is operated for the US Department of Energy by Iowa State University under contract No. DE-AC02-07CH11358. The calculations presented in the applications section were performed on a Linux cluster that was provided by a Department of Defense DURIP grant. NR 65 TC 7 Z9 7 U1 1 U2 5 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0010-4655 EI 1879-2944 J9 COMPUT PHYS COMMUN JI Comput. Phys. Commun. PD DEC PY 2014 VL 185 IS 12 BP 3175 EP 3188 DI 10.1016/j.cpc.2014.08.016 PG 14 WC Computer Science, Interdisciplinary Applications; Physics, Mathematical SC Computer Science; Physics GA AT3GX UT WOS:000344824900013 ER PT J AU Estlack, LE Roth, CC Thompson, GL Lambert, WA Ibey, BL AF Estlack, Larry E. Roth, Caleb C. Thompson, Gary L., III Lambert, William A., III Ibey, Bennett L. TI Nanosecond pulsed electric fields modulate the expression of Fas/CD95 death receptor pathway regulators in U937 and Jurkat Cells SO APOPTOSIS LA English DT Article DE Apoptosis; FasL; CD95; Jurkat; Nanosecond pulsed electric fields; cFLIP; U937 ID MEMBRANE PERMEABILIZATION; HIGH-INTENSITY; PHOSPHOLIPID TRANSLOCATION; INDUCE APOPTOSIS; CARCINOMA-CELLS; PLASMA-MEMBRANE; C-FLIP; ELECTROPORATION; NECROPTOSIS; INHIBITION AB In this publication, we demonstrate that exposure of Jurkat and U937 cells to nanosecond pulsed electrical fields (nsPEF) can modulate the extrinsic-mediated apoptotic pathway via the Fas/CD95 death receptor. An inherent difference in survival between these two cell lines in response to 10 ns exposures has been previously reported (Jurkat being more sensitive to nsPEF than U937), but the reason for this sensitivity difference remains unknown. We found that exposure of each cell line to 100, 10 ns pulses at 50 kV/cm caused a marked increase in expression of cFLIP (extrinsic apoptosis inhibitor) in U937 and FasL (extrinsic apoptosis activator) in Jurkat, respectively. Measurement of basal expression levels revealed an inherent difference between U937 cells, having a higher expression of cFLIP, and Jurkat cells, having a higher expression of FasL. From these data, we hypothesize that the sensitivity difference between the cells to nsPEF exposure may be directly related to expression of extrinsic apoptotic regulators. To validate this hypothesis, we used siRNA to knockdown cFLAR (coding for cFLIP protein) expression in U937, and FasL expression in Jurkat and challenged them to 100, 10 ns pulses at 150 kV/cm, a typical lethal dose. We observed that U937 survival was reduced nearly 60 % in the knockdown population while Jurkat survival improved similar to 40 %. These findings support the hypothesis that cell survival following 10 ns pulse exposures depends on extrinsic apoptotic regulators. Interestingly, pretreatment of U937 with a 100-pulse, 50 kV/cm exposure (to amplify cFLAR expression) significantly reduced the lethality of a 150 kV/cm, 100-pulse exposure applied 24 h later. From these data, we conclude that the observed survival differences between cells, exposed to 10 ns pulsed electric fields, is due to inherent cell biochemistry rather than the biophysics of the exposure itself. Understanding cell sensitivity to nsPEF may provide researchers/clinicians with a predicable way to control or avoid unintended cell death during nsPEF exposure. C1 [Estlack, Larry E.] Gen Dynam Informat Technol, Jbsa Ft Sam Houston, TX USA. [Roth, Caleb C.] Univ Texas Hlth Sci Ctr San Antonio, Dept Radiol, San Antonio, TX 78229 USA. [Thompson, Gary L., III] ORISE, Jbsa Ft Sam Houston, TX USA. [Lambert, William A., III; Ibey, Bennett L.] Air Force Res Lab, Human Effectiveness Directorate, Bioeffects Div, Radio Frequency Bioeffects Branch, Ft Sam Houston, TX 78234 USA. RP Ibey, BL (reprint author), Air Force Res Lab, Human Effectiveness Directorate, Bioeffects Div, Radio Frequency Bioeffects Branch, 711th Human Performance Wing, Ft Sam Houston, TX 78234 USA. EM larry.e.estlack.ctr@mail.mil; Bennettibey@gmail.com FU Air Force Surgeon General's Office, Medical Research Program; Air Force Office of Scientific Research LRIR [13RH08COR]; SMART Program (OSD-T&E (Office of Secretary Defense-Test and Evaluation) [N002440910081]; National Defense Education Program (NDEP)/BA-1, Basic Research) [Defense-Wide/PE0601120D8Z] FX This research was supported by intramural funds from the Air Force Surgeon General's Office, Medical Research Program and the Air Force Office of Scientific Research LRIR 13RH08COR. Mr. Roth would like to thank the SMART Program grant # N002440910081 (OSD-T&E (Office of Secretary Defense-Test and Evaluation), Defense-Wide/PE0601120D8Z National Defense Education Program (NDEP)/BA-1, Basic Research). NR 49 TC 8 Z9 8 U1 0 U2 9 PU SPRINGER PI DORDRECHT PA VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS SN 1360-8185 EI 1573-675X J9 APOPTOSIS JI Apoptosis PD DEC PY 2014 VL 19 IS 12 BP 1755 EP 1768 DI 10.1007/s10495-014-1041-9 PG 14 WC Biochemistry & Molecular Biology; Cell Biology SC Biochemistry & Molecular Biology; Cell Biology GA AT5TC UT WOS:000345003800008 PM 25331537 ER PT J AU Munoz-Esparza, D Kosovic, B Mirocha, J van Beeck, J AF Munoz-Esparza, Domingo Kosovic, Branko Mirocha, Jeff van Beeck, Jeroen TI Bridging the Transition from Mesoscale to Microscale Turbulence in Numerical Weather Prediction Models SO BOUNDARY-LAYER METEOROLOGY LA English DT Article DE Boundary-layer turbulence; Inflow turbulence generation; Large-eddy simulation; Multiscale modelling; Nested mesoscale to large-eddy simulations; Weather Research and Forecasting model ID LARGE-EDDY-SIMULATION; ATMOSPHERIC BOUNDARY-LAYER; VERTICAL VELOCITY; FORECASTING-MODEL; INFLOW CONDITIONS; REYNOLDS-NUMBER; SURFACE-LAYER; FAIR-WEATHER; HEAT-FLUX; WRF MODEL AB With a focus towards developing multiscale capabilities in numerical weather prediction models, the specific problem of the transition from the mesoscale to the microscale is investigated. For that purpose, idealized one-way nested mesoscale to large-eddy simulation (LES) experiments were carried out using the Weather Research and Forecasting model framework. It is demonstrated that switching from one-dimensional turbulent diffusion in the mesoscale model to three-dimensional LES mixing does not necessarily result in an instantaneous development of turbulence in the LES domain. On the contrary, very large fetches are needed for the natural transition to turbulence to occur. The computational burden imposed by these long fetches necessitates the development of methods to accelerate the generation of turbulence on a nested LES domain forced by a smooth mesoscale inflow. To that end, four new methods based upon finite amplitude perturbations of the potential temperature field along the LES inflow boundaries are developed, and investigated under convective conditions. Each method accelerated the development of turbulence within the LES domain, with two of the methods resulting in a rapid generation of production and inertial range energy content associated to microscales that is consistent with non-nested simulations using periodic boundary conditions. The cell perturbation approach, the simplest and most efficient of the best performing methods, was investigated further under neutral and stable conditions. Successful results were obtained in all the regimes, where satisfactory agreement of mean velocity, variances and turbulent fluxes, as well as velocity and temperature spectra, was achieved with reference non-nested simulations. In contrast, the non-perturbed LES solution exhibited important energy deficits associated to a delayed establishment of fully-developed turbulence. The cell perturbation method has negligible computational cost, significantly accelerates the generation of realistic turbulence, and requires minimal parameter tuning, with the necessary information relatable to mean inflow conditions provided by the mesoscale solution. C1 [Munoz-Esparza, Domingo; van Beeck, Jeroen] von Karman Inst Fluid Dynam, Rhode St Genese, Belgium. [Kosovic, Branko] Natl Ctr Atmospher Res, Boulder, CO 80307 USA. [Mirocha, Jeff] Lawrence Livermore Natl Lab, Livermore, CA USA. RP Munoz-Esparza, D (reprint author), Los Alamos Natl Lab, Div Earth & Environm Sci, Los Alamos, NM 87545 USA. EM dmunozes@lanl.com FU U.S. Department of Energy by Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; US DOE Office of Energy Efficiency and Renewable Energy (EERE); National Science Foundation FX DME wants to thank NCAR staff members for their hospitality during his stay within the Research Applications Laboratory Division. Work by JDM was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344, and was supported by the US DOE Office of Energy Efficiency and Renewable Energy (EERE). The authors would like to acknowledge high-performance computing support from Yellowstone (ark:/85065/d7wd3xhc) provided by NCAR's Computational and Information Systems Laboratory, sponsored by the National Science Foundation, as well as the use of supercomputing facilities of the von Karman Institute for Fluid Dynamics. NR 88 TC 21 Z9 21 U1 2 U2 27 PU SPRINGER PI DORDRECHT PA VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS SN 0006-8314 EI 1573-1472 J9 BOUND-LAY METEOROL JI Bound.-Layer Meteor. PD DEC PY 2014 VL 153 IS 3 BP 409 EP 440 DI 10.1007/s10546-014-9956-9 PG 32 WC Meteorology & Atmospheric Sciences SC Meteorology & Atmospheric Sciences GA AT2YT UT WOS:000344801400003 ER PT J AU Sperber, KR Annamalai, H AF Sperber, Kenneth R. Annamalai, H. TI The use of fractional accumulated precipitation for the evaluation of the annual cycle of monsoons SO CLIMATE DYNAMICS LA English DT Article DE Summer monsoon rainfall; Annual cycle; Climate model intercomparison; Systematic error; Metrics ID MODEL INTERCOMPARISON PROJECT; GENERAL-CIRCULATION MODEL; SUMMER MONSOON; INTERANNUAL VARIABILITY; GLOBAL PRECIPITATION; GAUGE OBSERVATIONS; RAINY-SEASON; EL-NINO; RAINFALL; ONSET AB Using pentad rainfall data we demonstrate the benefits of using accumulated rainfall and fractional accumulated rainfall for the evaluation of the annual cycle of rainfall over various monsoon domains. Our approach circumvents issues related to using threshold-based analysis techniques for investigating the life-cycle of monsoon rainfall. In the Coupled Model Intercomparison Project-5 models we find systematic errors in the phase of the annual cycle of rainfall. The models are delayed in the onset of summer rainfall over India, the Gulf of Guinea, and the South American Monsoon, with early onset prevalent for the Sahel and the North American Monsoon. This, in combination with the rapid fractional accumulation rate, impacts the ability of the models to simulate the fractional accumulation observed during summer. The rapid fractional accumulation rate and the time at which the accumulation begins are metrics that indicate how well the models concentrate the monsoon rainfall over the peak rainfall season, and the extent to which there is a phase error in the annual cycle. The lack of consistency in the phase error across all domains suggests that a "global'' approach to the study of monsoons may not be sufficient to rectify the regional differences. Rather, regional process studies are necessary for diagnosing the underlying causes of the regionally-specific systematic model biases over the different monsoon domains. Despite the afore-mentioned biases, most models simulate well the interannual variability in the date of monsoon onset, the exceptions being models with the most pronounced dry biases. Two methods for estimating monsoon duration are presented, one of which includes nonlinear aspects of the fractional accumulation. The summer fractional accumulation of rainfall provides an objective way to estimate the extent of the monsoon domain, even in models with substantial dry biases for which monsoon is not defined using thresholdbased techniques. C1 [Sperber, Kenneth R.] Lawrence Livermore Natl Lab, Program Climate Model Diag & Intercomparison, Livermore, CA 94551 USA. [Annamalai, H.] Univ Hawaii, Int Pacific Res Ctr, Honolulu, HI 96822 USA. RP Sperber, KR (reprint author), Lawrence Livermore Natl Lab, Program Climate Model Diag & Intercomparison, POB 808,L-103, Livermore, CA 94551 USA. EM sperber1@llnl.gov RI Sperber, Kenneth/H-2333-2012 FU Office of Science (BER), U.S. Department of Energy through Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Office of Science (BER) U.S. Department of Energy [DEFG02-07ER6445]; JAMSTEC of the International Pacific Research Center; NOAA of the International Pacific Research Center; NASA of the International Pacific Research Center FX We thank the reviewers for bringing to our attention additional relevant literature, and for suggesting enhancements and clarifications that have improved the paper. We thank Charles Jones for input on the selection of the area-averaged SAM domain. K. R. Sperber was supported by the Office of Science (BER), U.S. Department of Energy through Lawrence Livermore National Laboratory contract DE-AC52-07NA27344. H. Annamalai was supported by the Office of Science (BER) U.S. Department of Energy, Grant DEFG02-07ER6445, and also by three institutional grants (JAMSTEC, NOAA and NASA) of the International Pacific Research Center. We acknowledge the World Climate Research Programme's Working Group on Coupled Modelling, which is responsible for CMIP, and we thank the climate modeling groups (listed in Table 1 of this paper) for producing and making available their model output. For CMIP the U.S. Department of Energy's Program for Climate Model Diagnosis and Intercomparison provides coordinating support and led development of software infrastructure in partnership with the Global Organization for Earth System Science Portals. NR 30 TC 7 Z9 7 U1 0 U2 4 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 0930-7575 EI 1432-0894 J9 CLIM DYNAM JI Clim. Dyn. PD DEC PY 2014 VL 43 IS 12 BP 3219 EP 3244 DI 10.1007/s00382-014-2099-3 PG 26 WC Meteorology & Atmospheric Sciences SC Meteorology & Atmospheric Sciences GA AT3UX UT WOS:000344861900002 ER PT J AU Fairchild, G Hickmann, KS Mniszewski, SM Del Valle, SY Hyman, JM AF Fairchild, Geoffrey Hickmann, Kyle S. Mniszewski, Susan M. Del Valle, Sara Y. Hyman, James M. TI Optimizing human activity patterns using global sensitivity analysis SO COMPUTATIONAL AND MATHEMATICAL ORGANIZATION THEORY LA English DT Article DE Global optimization; Global sensitivity analysis; Sample entropy; Agent-based modeling; Bayesian Gaussian process regression; Harmony search ID HARMONY SEARCH ALGORITHM; TIME-SERIES ANALYSIS; APPROXIMATE ENTROPY; SAMPLE ENTROPY; PANDEMIC INFLUENZA; TRAVEL BEHAVIOR; COMPLEXITY; OPTIMIZATION; VARIABILITY; REGULARITY AB Implementing realistic activity patterns for a population is crucial for modeling, for example, disease spread, supply and demand, and disaster response. Using the dynamic activity simulation engine, DASim, we generate schedules for a population that capture regular (e.g., working, eating, and sleeping) and irregular activities (e.g., shopping or going to the doctor). We use the sample entropy (SampEn) statistic to quantify a schedule's regularity for a population. We show how to tune an activity's regularity by adjusting SampEn, thereby making it possible to realistically design activities when creating a schedule. The tuning process sets up a computationally intractable high-dimensional optimization problem. To reduce the computational demand, we use Bayesian Gaussian process regression to compute global sensitivity indices and identify the parameters that have the greatest effect on the variance of SampEn. We use the harmony search (HS) global optimization algorithm to locate global optima. Our results show that HS combined with global sensitivity analysis can efficiently tune the SampEn statistic with few search iterations. We demonstrate how global sensitivity analysis can guide statistical emulation and global optimization algorithms to efficiently tune activities and generate realistic activity patterns. Though our tuning methods are applied to dynamic activity schedule generation, they are general and represent a significant step in the direction of automated tuning and optimization of high-dimensional computer simulations. C1 [Fairchild, Geoffrey; Del Valle, Sara Y.] Los Alamos Natl Lab, Def Syst & Anal Div, Los Alamos, NM 87545 USA. [Hickmann, Kyle S.; Hyman, James M.] Tulane Univ, Dept Math, Ctr Computat Sci, New Orleans, LA 70118 USA. [Mniszewski, Susan M.] Los Alamos Natl Lab, Comp Computat & Stat Sci Div, Los Alamos, NM USA. RP Fairchild, G (reprint author), Los Alamos Natl Lab, Def Syst & Anal Div, Los Alamos, NM 87545 USA. EM gfairchild@lanl.gov OI Mniszewski, Susan/0000-0002-0077-0537 FU Los Alamos National Laboratory under the Department of Energy [DE-AC52-06NA25396]; NIH/NIGMS in the Models of Infectious Disease Agent Study (MIDAS) program [U01-GM097658-01] FX We would like to acknowledge the Institutional Computing Program at Los Alamos National Laboratory for use of their HPC cluster resources. This research has been supported at Los Alamos National Laboratory under the Department of Energy contract DE-AC52-06NA25396 and a grant from the NIH/NIGMS in the Models of Infectious Disease Agent Study (MIDAS) program U01-GM097658-01. NR 59 TC 1 Z9 1 U1 0 U2 13 PU SPRINGER PI DORDRECHT PA VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS SN 1381-298X EI 1572-9346 J9 COMPUT MATH ORGAN TH JI Comput. Math. Organ. Theory PD DEC PY 2014 VL 20 IS 4 BP 394 EP 416 DI 10.1007/s10588-013-9171-0 PG 23 WC Computer Science, Interdisciplinary Applications; Mathematics, Interdisciplinary Applications; Social Sciences, Mathematical Methods SC Computer Science; Mathematics; Mathematical Methods In Social Sciences GA AT5TP UT WOS:000345005300003 PM 25580080 ER PT J AU Ferrada-Fuentes, S Galleguillos, R Canales-Aguirre, CB Love, CN Jones, KL Lance, SL AF Ferrada-Fuentes, Sandra Galleguillos, Ricardo Canales-Aguirre, Cristian B. Love, Cara N. Jones, Kenneth L. Lance, Stacey L. TI Development and characterization of thirty-three microsatellite markers for the Patagonian sprat, Sprattus fuegensis (Jenyns, 1842), using paired-end Illumina shotgun sequencing SO CONSERVATION GENETICS RESOURCES LA English DT Article DE Sprattus; Illumina; Microsatellite; PAL_FINDER; PCR primers; SSR AB We isolated and characterized a total of 33 microsatellite loci from the Patagonian sprat Sprattus fuegensis, a recent exploited marine resource with a conservation status unknowing. Loci were screened in 24 individuals from the inshore waters of the Aysen Fjord, Chile. The number of alleles per locus ranged from 7 to 24, observed heterozygosity ranged from 0.217 to 0.875, and the probability of identity values ranged from 0.006 to 0.133. These new loci will provide tools for examining population genetic structure, estimating effective population size and provide information to fisheries management and conservation. C1 [Ferrada-Fuentes, Sandra; Galleguillos, Ricardo; Canales-Aguirre, Cristian B.] Univ Concepcion, Lab Genet & Acuicultura, Dept Oceanog, Fac Ciencias Nat & Oceanog, Concepcion, Chile. [Love, Cara N.; Lance, Stacey L.] Univ Georgia, Savannah River Ecol Lab, Aiken, SC 29802 USA. [Jones, Kenneth L.] Univ Colorado, Sch Med, Dept Biochem & Mol Genet, Aurora, CO 80045 USA. RP Ferrada-Fuentes, S (reprint author), Univ Concepcion, Lab Genet & Acuicultura, Dept Oceanog, Fac Ciencias Nat & Oceanog, Casilla 160-C, Concepcion, Chile. EM sferrada@udec.cl RI Lance, Stacey/K-9203-2013 OI Lance, Stacey/0000-0003-2686-1733 FU Doctoral Fellowships for the 'Programa de Doctorado en Sistematica y Biodiversidad', from the graduate school of the Universidad de Concepcion; CONICYT doctoral fellowship; DOE [DE-FC09-07SR22506]; [FIP 2010-17] FX SF and CBCA were supported by Doctoral Fellowships for the 'Programa de Doctorado en Sistematica y Biodiversidad', from the graduate school of the Universidad de Concepcion. SF was supported by a CONICYT doctoral fellowship. This work forms part of the FIP 2010-17 Project. Manuscript preparation was partially supported by the DOE under Award Number DE-FC09-07SR22506 to the University of Georgia Research Foundation. NR 5 TC 0 Z9 0 U1 0 U2 7 PU SPRINGER PI DORDRECHT PA VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS SN 1877-7252 EI 1877-7260 J9 CONSERV GENET RESOUR JI Conserv. Genet. Resour. PD DEC PY 2014 VL 6 IS 4 BP 833 EP 836 DI 10.1007/s12686-014-0281-x PG 4 WC Biodiversity Conservation; Genetics & Heredity SC Biodiversity & Conservation; Genetics & Heredity GA AS8EC UT WOS:000344481900008 ER PT J AU Beasley, R Lance, SL Ruskey, JA Taylor, EB AF Beasley, Rochelle Lance, Stacey L. Ruskey, Jennifer A. Taylor, Eric B. TI Development and characterization of twenty-five microsatellite markers for the longnose dace (Cyprinidae: Rhinichthys) using paired-end Illumina shotgun sequencing SO CONSERVATION GENETICS RESOURCES LA English DT Article DE Rhinichthys; Microsatellite; PAL_FINDER; PCR primers; SSR AB We isolated and characterized a total of 48 microsatellite loci in Rhinichthys cataractae a widely distributed freshwater fish that may contain several cryptic species. Loci were screened in 24 individuals from several areas of British Columbia, Canada. The number of alleles per locus ranged from 5 to 24, observed heterozygosity ranged from 0.250 to 0.940, and the probability of identity ranged from 0.006 to 0.453. These new loci are being used for conducting investigations into the genetic structure, diversity, and speciation in populations of this exceptionally broadly-distributed North American freshwater fish. C1 [Beasley, Rochelle; Lance, Stacey L.] Univ Georgia, Savannah River Ecol Lab, Aiken, SC 29802 USA. [Ruskey, Jennifer A.; Taylor, Eric B.] Univ British Columbia, Biodivers Res Ctr, Dept Zool, Vancouver, BC V6T 1Z4, Canada. [Ruskey, Jennifer A.; Taylor, Eric B.] Univ British Columbia, Beaty Biodivers Museum, Vancouver, BC V6T 1Z4, Canada. RP Taylor, EB (reprint author), Univ British Columbia, Biodivers Res Ctr, Dept Zool, 6270 Univ Blvd, Vancouver, BC V6T 1Z4, Canada. EM etaylor@zoology.ubc.ca RI Lance, Stacey/K-9203-2013; Beasley, Rochelle/M-1396-2015 OI Lance, Stacey/0000-0003-2686-1733; Beasley, Rochelle/0000-0001-7325-4085 FU Natural Sciences and Engineering Research Council of Canada; DOE [DE-FC09-07SR22506] FX Financial support for microsatellite DNA development was provided by grants from the Natural Sciences and Engineering Research Council of Canada awarded to EBT. Manuscript preparation was partially supported by the DOE under Award Number DE-FC09-07SR22506 to the University of Georgia Research Foundation. Bioinformatics support came from Biostatistics/Bioinformatics Shared Resource of the University of Colorado Cancer Center (5P30CA046934). NR 3 TC 1 Z9 1 U1 6 U2 15 PU SPRINGER PI DORDRECHT PA VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS SN 1877-7252 EI 1877-7260 J9 CONSERV GENET RESOUR JI Conserv. Genet. Resour. PD DEC PY 2014 VL 6 IS 4 BP 1011 EP 1013 DI 10.1007/s12686-014-0272-y PG 3 WC Biodiversity Conservation; Genetics & Heredity SC Biodiversity & Conservation; Genetics & Heredity GA AS8EC UT WOS:000344481900052 ER PT J AU DiGiuseppe, N Pouchard, LC Noy, NF AF DiGiuseppe, Nicholas Pouchard, Line C. Noy, Natalya F. TI SWEET ontology coverage for earth system sciences SO EARTH SCIENCE INFORMATICS LA English DT Article DE Ontology; Ontology coverage; Semantic web; Empirical AB Scientists in the Earth and Environmental Sciences (EES) domain increasingly use ontologies to analyze and integrate their data. For example, the NASA's SWEET ontologies (Semantic Web for Earth and Environmental Terminology) have become the de facto standard ontologies to represent the EES domain formally (Raskin 2010). Now we must develop principled ways both to evaluate existing ontologies and to ascertain their quality in a quantitative manner. Existing literature describes many potential quality metrics for ontologies. Among these metrics is the coverage metric, which approximates the relevancy of an ontology to a corpus (Yao et al. (PLoS Comput Biol 7(1):e1001055+, 2011)). This paper has three primary contributions to the EES domain: (1) we present an investigation of the applicability of existing coverage techniques for the EES domain; (2) we present a novel expansion of existing techniques that uses thesauri to generate equivalence and subclass axioms automatically; and (3) we present an experiment to establish an upper-bound coverage expectation for the SWEET ontologies against real-world EES corpora from DataONE (Michener et al. (Ecol Inform 11:5-15, 2012)), and a corpus designed from research articles to specifically match the topics covered by the SWEET ontologies. This initial evaluation suggests that the SWEET ontology can accurately represent real corpora within the EES domain. C1 [DiGiuseppe, Nicholas] Univ Calif Irvine, Irvine, CA 92617 USA. [Pouchard, Line C.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. [Noy, Natalya F.] Stanford Univ, Stanford Ctr Biomed Informat Res, Stanford, CA 94070 USA. RP DiGiuseppe, N (reprint author), Univ Calif Irvine, Irvine, CA 92617 USA. EM nicholas.digiuseppe@gmail.com; pouchardlc@ornl.gov; noy@stanford.edu FU National Science Foundation [CCF-1116943, DGE-0808392] FX This material is based upon work supported by the National Science Foundation, through Award CCF-1116943 and through Graduate Research Fellowship under Grant No. DGE-0808392. Michael Huhns was extremely helpful in directing and crystalizing this research. We would also like to thank Andrey Rzhetsky for providing the seven thesauri used in our experiment. NR 28 TC 3 Z9 3 U1 1 U2 6 PU SPRINGER HEIDELBERG PI HEIDELBERG PA TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY SN 1865-0473 EI 1865-0481 J9 EARTH SCI INFORM JI Earth Sci. Inform. PD DEC PY 2014 VL 7 IS 4 BP 249 EP 264 DI 10.1007/s12145-013-0143-1 PG 16 WC Computer Science, Interdisciplinary Applications; Geosciences, Multidisciplinary SC Computer Science; Geology GA AT9YI UT WOS:000345279300003 ER PT J AU Lin, NH Sayer, AM Wang, SH Loftus, AM Hsiao, TC Sheu, GR Hsu, NC Tsay, SC Chantara, S AF Lin, Neng-Huei Sayer, Andrew M. Wang, Sheng-Hsiang Loftus, Adrian M. Hsiao, Ta-Chih Sheu, Guey-Rong Hsu, N. Christina Tsay, Si-Chee Chantara, Somporn TI Interactions between biomass-burning aerosols and clouds over Southeast Asia: Current status, challenges, and perspectives SO ENVIRONMENTAL POLLUTION LA English DT Article DE Biomass-burning aerosol; Aerosol-cloud interaction; 7-SEAS; Remote sensing; Aerosol chemistry; Southeast Asia ID MARINE BOUNDARY-LAYER; BULK MICROPHYSICS PARAMETERIZATION; LARGE-EDDY SIMULATION; EAST CHINA SEA; OPTICAL DEPTH; STRATOCUMULUS CLOUDS; EFFECTIVE RADIUS; SATELLITE DATA; 7-SEAS/DONGSHA EXPERIMENT; TROPOSPHERIC AEROSOLS AB The interactions between aerosols, clouds, and precipitation remain among the largest sources of uncertainty in the Earth's energy budget. Biomass-burning aerosols are a key feature of the global aerosol system, with significant annually-repeating fires in several parts of the world, including Southeast Asia (SEA). SEA in particular provides a "natural laboratory" for these studies, as smoke travels from source regions downwind in which it is coupled to persistent stratocumulus decks. However, SEA has been under-exploited for these studies. This review summarizes previous related field campaigns in SEA, with a focus on the ongoing Seven South East Asian Studies (7-SEAS) and results from the most recent BASELInE deployment. Progress from remote sensing and modeling studies, along with the challenges faced for these studies, are also discussed. We suggest that improvements to our knowledge of these aerosol/cloud effects require the synergistic use of field measurements with remote sensing and modeling tools. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Lin, Neng-Huei; Wang, Sheng-Hsiang; Sheu, Guey-Rong] Natl Cent Univ, Dept Atmospher Sci, Chungli 32054, Taiwan. [Lin, Neng-Huei; Chantara, Somporn] Chiang Mai Univ, Fac Sci, Chem Dept & Environm Sci Program, Chiang Mai 50200, Thailand. [Sayer, Andrew M.; Loftus, Adrian M.; Hsu, N. Christina; Tsay, Si-Chee] NASA, Goddard Space Flight Ctr, Greenbelt, MD 20771 USA. [Sayer, Andrew M.] Univ Space Res Assoc, Columbia, MD USA. [Loftus, Adrian M.] Oak Ridge Associated Univ, Oak Ridge, TN USA. [Hsiao, Ta-Chih] Natl Cent Univ, Grad Inst Environm Engn, Chungli 32054, Taiwan. RP Lin, NH (reprint author), Natl Cent Univ, Dept Atmospher Sci, Chungli 32054, Taiwan. EM nhlin@cc.ncu.edu.tw RI Sayer, Andrew/H-2314-2012; Wang, Sheng-Hsiang/F-4532-2010 OI Sayer, Andrew/0000-0001-9149-1789; Wang, Sheng-Hsiang/0000-0001-9675-3135 FU Taiwan Environmental Protection Administration [EPA-99-FA11-03-A097, EPA-102-U1L1-02-101]; National Science Council of Taiwan [101-2119-M-008-012] FX The authors thank the continuous support by the Taiwan Environmental Protection Administration under contracts No. EPA-99-FA11-03-A097, EPA-102-U1L1-02-101, and the National Science Council of Taiwan under grant No. 101-2119-M-008-012 for the field operation of 2013 BASELInE. We also thank the Deployments of SMARTLabs and AERONET/MPLNET in Southeast Asia, as part of NASA Radiation Sciences Program managed by Dr. Hal B. Maring. The authors also gratefully acknowledge the team efforts led by Serm Janjai (Silpakorn University, Thailand), Somporn Chantara (Chiang Mai University, Thailand) and Anh X. Nguyen (Institute of Geophysics at Vietnam Academy of Science and Technology, Vietnam) in supporting 7-SEAS/BASELInE over northern Southeast Asia. National Central University, National Museum of Marine Biology and Aquarium, Middle of Central Regional Hydro-Meteorological Observatory, National Hydro-Meteorological Service of Vietnam, and Doi Ang Khang Meteorological Station, facilitated site operations at Lulin, Hengchun, Son La/Yen Bai, and Doi Ang Khang, respectively. Thanks are also given to all assistants and graduate students involving in the site operation, data analysis and technical support for making 2013 BASELInE campaign successful. NR 176 TC 16 Z9 16 U1 5 U2 54 PU ELSEVIER SCI LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND SN 0269-7491 EI 1873-6424 J9 ENVIRON POLLUT JI Environ. Pollut. PD DEC PY 2014 VL 195 BP 292 EP 307 DI 10.1016/j.envpol.2014.06.036 PG 16 WC Environmental Sciences SC Environmental Sciences & Ecology GA AS7LM UT WOS:000344437600037 PM 25085565 ER PT J AU Cregger, MA McDowell, NG Pangle, RE Pockman, WT Classen, AT AF Cregger, Melissa A. McDowell, Nate G. Pangle, Robert E. Pockman, William T. Classen, Aimee T. TI The impact of precipitation change on nitrogen cycling in a semi-arid ecosystem SO FUNCTIONAL ECOLOGY LA English DT Article DE ammonia-oxidizing bacteria; climate change; nitrification; nitrogen availability; nitrogen mineralization; pinon-juniper woodland; precipitation ID PINYON-JUNIPER WOODLAND; CHANGE-TYPE DROUGHT; NUTRIENT DYNAMICS; CLIMATE-CHANGE; TERRESTRIAL ECOSYSTEMS; ELEVATIONAL GRADIENT; GRASSLAND SOILS; SPATIAL-PATTERN; LITTER QUALITY; TREE MORTALITY AB Climatic change is altering ecosystem structure and function, especially in the southwestern United States where trees are near their physiological water stress threshold. In pinon-juniper (Pinus edulis-Juniperus monosperma; PJ) woodlands, increased drought is causing differential mortality of pinon resulting in an ecosystem that is becoming juniper dominated. Using a precipitation manipulation, we assessed how both increased and decreased precipitation altered ecosystem function beneath pinon and juniper. We predicted that changes in precipitation would alter nitrogen (N) availability and mineralization at the site. Further, we predicted that these responses would differ beneath pinon and juniper crowns due to plant-level differences in transpiration and N uptake in response to drought. We found minimal interactions between tree species and the precipitation treatments on N cycling. However, across all years measured, soil nitrate decreased with increasing soil volumetric water content; a pattern that is likely due to reduced turnover in dry plots. In contrast, potential soil net-nitrogen mineralization was reduced in water removal plots relative to water addition plots indicating that nitrogen cycling rates were slower under drought. Tree type also influenced nitrogen dynamics in this woodland. Across all 4years, soil N availability and potential soil net-mineralization rates were higher in soils beneath pinon relative to juniper across all treatments. Interestingly, the observed shifts in N cycling were not reflected in the abundance of N in microbial biomass or in ammonia-oxidizing bacteria, which are responsible for nitrification. The observed patterns may be due to increased N leaching from the soil during periods of increased rainfall or due to decreased microbial activity or plant N uptake when conditions are dry. The effect of precipitation change on N cycling may have long-term consequences on the plant community in this semi-arid ecosystem. Nitrogen concentrations are highest in the soil when water availability is low, thus when N concentrations are high, plants and microbes are relatively inactive and unable to use this resource. 10.1111/(ISSN)1365-2435 100 other bacterial genera indicate a value of 79-80% dDDH as the most promising threshold for delineating subspecies, which in turn suggests the presence of five subspecies within E. coli. C1 [Meier-Kolthoff, Jan P.; Hahnke, Richard L.; Petersen, Joern; Scheuner, Carmen; Michael, Victoria; Fiebig, Anne; Rohde, Christine; Goeker, Markus; Klenk, Hans-Peter] Leibniz Inst DSMZ German Collect Microorganisms &, Inhoffenstr 7B, D-38124 Braunschweig, Germany. [Rohde, Manfred] Helmholtz Ctr Infect Res, D-38124 Braunschweig, Germany. [Fartmann, Berthold] LGC Genom GmbH, D-12459 Berlin, Germany. [Goodwin, Lynne A.; Chertkov, Olga; Reddy, T. B. K.; Pati, Amrita; Ivanova, Natalia N.; Markowitz, Victor; Kyrpides, Nikos C.; Woyke, Tanja] DOE Joint Genome Inst, Walnut Creek, CA USA. [Kyrpides, Nikos C.] King Abdulaziz Univ, Dept Biol Sci, Jeddah, Saudi Arabia. RP Goker, M (reprint author), Leibniz Inst DSMZ German Collect Microorganisms &, Inhoffenstr 7B, D-38124 Braunschweig, Germany. EM markus.goeker@dsmz.de 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 US Department of Energy's Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; University of California, Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; University of California, Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725] FX The authors gratefully acknowledge the help of Bettina Henze, DSMZ, for growing cells of DSM 30083T and of Susanne Schneider, DSMZ, for DNA extraction and quality control. Access to the record card for strain U5/41T provided by Flemming Scheutz of the Danish State Serum Institute is gratefully acknowledged. 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, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725. NR 106 TC 17 Z9 17 U1 0 U2 1 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PD DEC PY 2014 VL 9 IS 1 AR 2 DI 10.1186/1944-3277-9-2 PG 19 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA V45LA UT WOS:000209816900002 PM 24501643 ER PT J AU Reeve, W Sullivan, J Ronson, C Tian, R Brau, L Davenport, K Goodwin, L Chain, P Woyke, T Lobos, E Huntemann, M Pati, A Mavromatis, K Markowitz, V Ivanova, N Kyrpides, N AF Reeve, Wayne Sullivan, John Ronson, Clive Tian, Rui Brau, Lambert Davenport, Karen Goodwin, Lynne Chain, Patrick Woyke, Tanja Lobos, Elizabeth Huntemann, Marcel Pati, Amrita Mavromatis, Konstantinos Markowitz, Victor Ivanova, Natalia Kyrpides, Nikos TI Genome sequence of the Lotus corniculatus microsymbiont Mesorhizobium loti strain R88B SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Root-nodule bacteria; Nitrogen fixation; Symbiosis; Alphaproteobacteria AB Mesorhizobium loti strain R88B was isolated in 1993 in the Rocklands range in Otago, New Zealand from a Lotus corniculatus root nodule. R88B is an aerobic, Gram-negative, non-spore-forming rod. This report reveals the genome of M. loti strain R88B contains a single scaffold of size 7,195,110 bp which encodes 6,950 protein-coding genes and 66 RNA-only encoding genes. This genome does not harbor any plasmids but contains the integrative and conjugative element ICEMlSym(R7A), also known as the R7A symbiosis island, acquired by horizontal gene transfer in the field environment from M. loti strain R7A. It also contains a mobilizable genetic element ICEMladh(R88B), that encodes a likely adhesin gene which has integrated downstream of ICEMlSym(R7A), and three acquired loci that together allow the utilization of the siderophore ferrichrome. 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 (GEBA-RNB) project. C1 [Reeve, Wayne; Tian, Rui] Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. [Sullivan, John; Ronson, Clive] Univ Otago, Dept Microbiol & Immunol, Dunedin, New Zealand. [Brau, Lambert] Deakin Univ, Sch Life & Environm Sci, Geelong, Vic 3217, Australia. [Davenport, Karen; Goodwin, Lynne; Chain, Patrick] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Woyke, Tanja; Lobos, Elizabeth; Huntemann, Marcel; Pati, Amrita; Mavromatis, Konstantinos; Ivanova, Natalia; Kyrpides, Nikos] DOE Joint Genome Inst, Walnut Creek, CA USA. [Markowitz, Victor] Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA USA. [Kyrpides, Nikos] King Abdulaziz Univ, Dept Biol Sci, Jeddah, Saudi Arabia. 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; Fac Sci, KAU, Biol Sci Dept/L-4228-2013; OI Kyrpides, Nikos/0000-0002-6131-0462; Chain, Patrick/0000-0003-3949-3634; Ivanova, Natalia/0000-0002-5802-9485 FU US Department of Energy Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; University of California, Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; University of California, Los Alamos National Laboratory [DE-AC02-06NA25396] FX 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. NR 38 TC 2 Z9 2 U1 0 U2 0 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PD DEC PY 2014 VL 9 IS 1 AR 3 DI 10.1186/1944-3277-9-3 PG 8 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA V45LA UT WOS:000209816900003 PM 25780496 ER PT J AU Scheuner, C Tindall, BJ Lu, M Nolan, M Lapidus, A Cheng, JF Goodwin, L Pitluck, S Huntemann, M Liolios, K Pagani, I Mavromatis, K Ivanova, N Pati, A Chen, A Palaniappan, K Jeffries, CD Hauser, L Land, M Mwirichia, R Rohde, M Abt, B Detter, JC Woyke, T Eisen, JA Markowitz, V Hugenholtz, P Goker, M Kyrpides, NC Klenk, HP AF Scheuner, Carmen Tindall, Brian J. Lu, Megan Nolan, Matt Lapidus, Alla Cheng, Jan-Fang Goodwin, Lynne Pitluck, Sam Huntemann, Marcel Liolios, Konstantinos Pagani, Ioanna Mavromatis, Konstantinos Ivanova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Jeffries, Cynthia D. Hauser, Loren Land, Miriam Mwirichia, Romano Rohde, Manfred Abt, Birte Detter, John C. Woyke, Tanja Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Goeker, Markus Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov and Rubinisphaera gen. nov and emended descriptions of the order Planctomycetales and the family Planctomycetaceae SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Non-peptidoglycan bacteria; Stalked bacteria; Halotolerant; Gram-negative; Taxonomic descriptions; Planctomycetales; Planctomycetes; GEBA AB Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448(T), were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended. C1 [Scheuner, Carmen; Tindall, Brian J.; Abt, Birte; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Lu, Megan; Nolan, Matt; Lapidus, Alla; Cheng, Jan-Fang; Goodwin, Lynne; Pitluck, Sam; Huntemann, Marcel; Liolios, Konstantinos; Pagani, Ioanna; Mavromatis, Konstantinos; Ivanova, Natalia; Pati, Amrita; Jeffries, Cynthia D.; Hauser, Loren; Land, Miriam; Detter, John C.; Woyke, Tanja; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Lu, Megan; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA USA. [Jeffries, Cynthia D.; Hauser, Loren; Land, Miriam] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Mwirichia, Romano] Jomo Kenyatta Univ Agr & Technol, Juja, Kenya. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. [Hugenholtz, Philip] Univ Queensland, Australian Ctr Ecogen, Sch Chem & Mol Biosci, Brisbane, Qld, Australia. [Kyrpides, Nikos C.] King Abdulaziz Univ, Dept Biol Sci, Jeddah, Saudi Arabia. RP Goker, M (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. EM markus.goeker@dsmz.de 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; Lapidus, Alla/0000-0003-0427-8731; Ivanova, Natalia/0000-0002-5802-9485 FU US Department of Energy Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; University of California, Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; University of California, Los Alamos National Laboratory [DE-AC02-06NA25396]; University of California, UT-Battelle; University of California, Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We gratefully acknowledge the help of Helga Pomrenke for growing P. brasiliensis cultures and Evelyne-Marie Brambilla for DNA extraction and quality control (both at DSMZ). We are grateful to Erko Stackebrandt and Christian Jogler (both at DSMZ) for hints regarding Planctomycetes classification and to Edina Weidemann for information regarding the biography of N.I. Gimesi. 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. NR 94 TC 12 Z9 12 U1 1 U2 6 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PD DEC PY 2014 VL 9 IS 1 AR 10 DI 10.1186/1944-3277-9-10 PG 18 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA V45LA UT WOS:000209816900010 PM 25780503 ER PT J AU Westwood, J Burnett, M Spratt, D Ball, M Wilson, DJ Wellsteed, S Cleary, D Green, A Hutley, E Cichowska, A Hopkins, S Wilcox, M Kessel, A Zoubiane, G Bethke, L Crook, DW Walker, J Sutton, M Marsh, P Moore, G Wilson, P Holmes, A Hoffman, P Smith, C Oppenheim, B Parkhill, J Woodford, N Robotham, J Kidgell, C Anyim, M Gilkes, G Field, D Quick, J Pickering, T Kirkup, BC Gilbert, J AF Westwood, Jack Burnett, Matthew Spratt, David Ball, Michael Wilson, Daniel J. Wellsteed, Sally Cleary, David Green, Andy Hutley, Emma Cichowska, Anna Hopkins, Susan Wilcox, Mark Kessel, Anthony Zoubiane, Ghada Bethke, Lara Crook, Derrick W. Walker, Jimmy Sutton, Mark Marsh, Philip Moore, Ginny Wilson, Peter Holmes, Alison Hoffman, Peter Smith, Chris Oppenheim, Beryl Parkhill, Julian Woodford, Neil Robotham, Julie Kidgell, Claire Anyim, Martin Gilkes, Gabriella Field, Dawn Quick, Josh Pickering, Tony Kirkup, Benjamin C. Gilbert, Jack TI The hospital microbiome project: meeting report for the UK science and innovation network UK-USA workshop 'beating the superbugs: hospital microbiome studies for tackling antimicrobial resistance', October 14th 2013 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Antibiotic resistance; Nosocomial infections; Hospital microbiome; Superbugs AB The UK Science and Innovation Network UK-USA workshop 'Beating the Superbugs: Hospital Microbiome Studies for tackling Antimicrobial Resistance' was held on October 14th 2013 at the UK Department of Health, London. The workshop was designed to promote US-UK collaboration on hospital microbiome studies to add a new facet to our collective understanding of antimicrobial resistance. The assembled researchers debated the importance of the hospital microbial community in transmission of disease and as a reservoir for antimicrobial resistance genes, and discussed methodologies, hypotheses, and priorities. A number of complementary approaches were explored, although the importance of the built environment microbiome in disease transmission was not universally accepted. Current whole genome epidemiological methods are being pioneered in the UK and the benefits of moving to community analysis are not necessarily obvious to the pioneers; however, rapid progress in other areas of microbiology suggest to some researchers that hospital microbiome studies will be exceptionally fruitful even in the short term. Collaborative studies will recombine different strengths to tackle the international problems of antimicrobial resistance and hospital and healthcare associated infections. C1 [Westwood, Jack] British Consulate Gen, Chicago, IL 60611 USA. [Burnett, Matthew; Smith, Chris] Univ Cambridge, Dept Pathol, Cambridge, England. [Spratt, David] UCL Eastman Dent Inst, Dept Microbial Dis, London, England. [Ball, Michael] Biotechnol & Biol Sci Res Council, Swindon, Wilts, England. [Wilson, Daniel J.] Univ Oxford, John Radcliffe Hosp, Nuffield Dept Med, Oxford, England. [Wellsteed, Sally] Richmond House, Dept Hlth, London, England. [Cleary, David] Def Sci & Technol Lab, Porton Down, Wilts, England. [Green, Andy; Hutley, Emma] Royal Ctr Def Med, Birmingham, W Midlands, England. [Cichowska, Anna; Hopkins, Susan; Kessel, Anthony] Publ Hlth England, London, England. [Wilcox, Mark] Univ Leeds, Leeds, W Yorkshire, England. [Wilcox, Mark] Leeds Teaching Hosp, Leeds, W Yorkshire, England. [Zoubiane, Ghada] MRC, London, England. [Bethke, Lara] Wellcome Trust Res Labs, London, England. [Crook, Derrick W.] Univ Oxford, John Radcliffe Hosp, Nuffield Dept Med, Oxford OX3 9DU, England. [Walker, Jimmy; Moore, Ginny] Publ Hlth England, Biosafety Unit, Salisbury, Wilts, England. [Sutton, Mark; Marsh, Philip] HPA Microbiol Serv, Salisbury, Wilts, England. [Wilson, Peter] UCLH NHS Fdn Trust, Clin Microbiol & Virol, London, England. [Holmes, Alison] Imperial Coll, London, England. [Hoffman, Peter; Woodford, Neil] Publ Hlth England, Antimicrobial Resistance & Healthcare Associated, London, England. [Smith, Chris] Addenbrookes Hosp, Clin Microbiol & Publ Hlth Lab, Cambridge, England. [Oppenheim, Beryl] Queen Elizabeth Hosp, Birmingham, W Midlands, England. [Parkhill, Julian] Wellcome Trust Genome Campus, Wellcome Trust Sanger Inst, Cambridge, England. [Robotham, Julie] Publ Hlth England, Modeling & Econ Unit, Stat Modeling & Econ Dept, London, England. [Kidgell, Claire] Univ Southampton, Natl Inst Hlth Res, Evaluat Trials & Studies Coordinating Ctr NETSCC, Southampton, Hants, England. [Anyim, Martin] NIHR Invent Innovat Programme, London, England. [Gilkes, Gabriella] Human Micro Biome Project, Eden Project, St Austell PL24 2SG, Cornwall, England. [Field, Dawn] NERC Ctr Ecol & Hydrol, Oxford, England. [Quick, Josh] Univ Birmingham, Inst Microbiol & Infect, Birmingham, W Midlands, England. [Pickering, Tony] Univ South Manchester, North West Lung Res Ctr, Wythenshawe Hosp, Manchester, Lancs, England. [Kirkup, Benjamin C.] Walter Reed Army Inst Res, Dept Wound Infect, Bethesda, MD USA. [Gilbert, Jack] Univ Chicago, Dept Ecol & Evolut, 940 E 57Th St, Chicago, IL 60637 USA. [Gilbert, Jack] Argonne Natl Lab, Inst Genom & Syst Biol, Argonne, IL 60439 USA. RP Gilbert, J (reprint author), Univ Chicago, Dept Ecol & Evolut, 940 E 57Th St, Chicago, IL 60637 USA. EM gilbertjack@uchicago.edu OI Wilson, Daniel/0000-0002-0940-3311; Bethke, Lara/0000-0002-1316-4704; Hopkins, Susan/0000-0001-5179-5702 FU UK Science and Innovation Network; British Consulate-General Chicago; Foreign and Commonwealth Office; APSF; U.S. Dept. of Energy [DE-AC02-06CH11357] FX We acknowledge the UK Science and Innovation Network, British Consulate-General Chicago and Foreign and Commonwealth Office, as well as APSF for funding this workshop. This work was supported in part by the U.S. Dept. of Energy under Contract DE-AC02-06CH11357. The opinions and assertions contained herein are the private views of the authors and are not to be construed as official or as reflecting true views of the Department of Army or the Department of Defense. NR 31 TC 1 Z9 2 U1 0 U2 0 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PD DEC PY 2014 VL 9 IS 1 AR 12 DI 10.1186/1944-3277-9-12 PG 12 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA V45LA UT WOS:000209816900012 ER PT J AU Woo, HL Ballor, NR Hazen, TC Fortney, JL Simmons, B Davenport, KW Goodwin, L Ivanova, N Kyrpides, NC Mavromatis, K Woyke, T Jansson, J Kimbrel, J DeAngelis, KM AF Woo, Hannah L. Ballor, Nicholas R. Hazen, Terry C. Fortney, Julian L. Simmons, Blake Davenport, Karen Walston Goodwin, Lynne Ivanova, Natalia Kyrpides, Nikos C. Mavromatis, Konstantinos Woyke, Tanja Jansson, Janet Kimbrel, Jeff DeAngelis, Kristen M. TI Complete genome sequence of the lignin-degrading bacterium Klebsiella sp strain BRL6-2 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Anaerobic lignin degradation; Tropical forest soil isolate; Facultative anaerobe AB In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated Klebsiella sp. strain BRL6-2 on minimal media with alkali lignin as the sole carbon source. This organism was isolated anaerobically from tropical forest soils collected from the Bisley watershed at the Ridge site in the El Yunque National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research Station. At this site, the soils experience strong fluctuations in redox potential and are characterized by cycles of iron oxidation and reduction. Genome sequencing was targeted because of its ability to grow on lignin anaerobically and lignocellulolytic activity via in vitro enzyme assays. The genome of Klebsiella sp. strain BRL6-2 is 5.80 Mbp with no detected plasmids, and includes a relatively small arsenal of genes encoding lignocellulolytic carbohydrate active enzymes. The genome revealed four putative peroxidases including glutathione and DyP-type peroxidases, and a complete protocatechuate pathway encoded in a single gene cluster. Physiological studies revealed Klebsiella sp. strain BRL6-2 to be relatively stress tolerant to high ionic strength conditions. It grows in increasing concentrations of ionic liquid (1-ethyl-3-methyl-imidazolium acetate) up to 73.44 mM and NaCl up to 1.5 M. C1 [Woo, Hannah L.; Ballor, Nicholas R.; Hazen, Terry C.; Fortney, Julian L.; Simmons, Blake; Kimbrel, Jeff] Joint BioEnergy Inst, Deconstruct Div, Microbial Commun Grp, Emeryville, CA USA. [Woo, Hannah L.] Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA USA. [Woo, Hannah L.; Hazen, Terry C.; Fortney, Julian L.] Univ Tennessee, Dept Civil & Environm Engn, Knoxville, TN USA. [Hazen, Terry C.] Univ Tennessee, Dept Microbiol, Knoxville, TN 37996 USA. [Hazen, Terry C.] Univ Tennessee, Dept Earth & Planetary Sci, Knoxville, TN USA. [Simmons, Blake] Sandia Natl Labs, Livermore, CA USA. [Davenport, Karen Walston; Goodwin, Lynne] Los Alamos Natl Lab, Los Alamos, NM USA. [Ivanova, Natalia; Kyrpides, Nikos C.; Mavromatis, Konstantinos; Woyke, Tanja] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Jansson, Janet] Pacific Northwest Natl Lab, Div Biol Sci, Richland, WA USA. [Kimbrel, Jeff] Lawrence Berkeley Natl Lab, Berkeley, CA USA. [DeAngelis, Kristen M.] Univ Massachusetts, Dept Microbiol, Amherst, MA 01003 USA. RP DeAngelis, KM (reprint author), Univ Massachusetts, Dept Microbiol, Amherst, MA 01003 USA. EM kristen@post.harvard.edu RI Hazen, Terry/C-1076-2012; Kyrpides, Nikos/A-6305-2014; OI Hazen, Terry/0000-0002-2536-9993; Kyrpides, Nikos/0000-0002-6131-0462; Ivanova, Natalia/0000-0002-5802-9485 FU Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231] FX The work conducted in part by the U.S. Department of Energy Joint Genome Institute and in part by the Joint BioEnergy Institute, and is supported by the Office of Science of the U.S. Department of Energy Under Contract No. DE-AC02-05CH11231. NR 41 TC 4 Z9 5 U1 2 U2 8 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PD DEC PY 2014 VL 9 IS 1 AR 19 DI 10.1186/1944-3277-9-19 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA V45LA UT WOS:000209816900019 PM 25566348 ER PT J AU Versino, D Gherlone, M Di Sciuva, M AF Versino, Daniele Gherlone, Marco Di Sciuva, Marco TI Four-node shell element for doubly curved multilayered composites based on the Refined Zigzag Theory SO COMPOSITE STRUCTURES LA English DT Article DE Laminated composites; Refined Zigzag Theory; Doubly curved shell element; Reduced integration; Small deformations ID ONE-POINT QUADRATURE; FREE-VIBRATION ANALYSIS; THICK LAMINATED BEAMS; SANDWICH PLATES; FINITE-ELEMENT; MODEL; STRESS; STABILIZATION; DELAMINATION; ROBUST AB In the present paper a generalization of the Refined Zigzag Theory (RZT) to doubly-curved multilayered structures is proposed. The displacement field characteristic of Naghdi's shell model is enriched with RZT kinematics and a four-node shell finite element is formulated. Assumed Natural Strain (ANS) strategy is employed to overcome shear locking and Enhanced Assumed Strain (EAS) technique is applied to alleviate membrane locking and bending locking. For efficiency purpose, a one-point quadrature rule is used for the in-plane integration and hourglass stabilization is introduced. Finally, several numerical examples, involving static analysis of thick as well as thin shells, are performed to demonstrate the efficiency and accuracy of the proposed shell finite element. Published by Elsevier Ltd. C1 [Versino, Daniele] Los Alamos Natl Lab, Div Theoret, Los Alamos, NM 87545 USA. [Gherlone, Marco; Di Sciuva, Marco] Politecn Torino, Dept Mech & Aerosp Engn, I-10129 Turin, Italy. RP Versino, D (reprint author), Los Alamos Natl Lab, Div Theoret, T-3,MS B216, Los Alamos, NM 87545 USA. EM daniele.versino@lanl.gov OI Gherlone, Marco/0000-0002-5711-0046; versino, daniele/0000-0002-5451-5355 FU Joint DOD/DOE Munitions Technology Development Program (JMP) FX The first author gratefully acknowledges the support of this work by the Joint DOD/DOE Munitions Technology Development Program (JMP). NR 60 TC 9 Z9 9 U1 0 U2 10 PU ELSEVIER SCI LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND SN 0263-8223 EI 1879-1085 J9 COMPOS STRUCT JI Compos. Struct. PD DEC PY 2014 VL 118 BP 392 EP 402 DI 10.1016/j.compstruct.2014.08.018 PG 11 WC Materials Science, Composites SC Materials Science GA AR8QE UT WOS:000343838900040 ER PT J AU Knezevic, M Jahedi, M Korkolis, YP Beyerlein, IJ AF Knezevic, Marko Jahedi, Mohammad Korkolis, Yannis P. Beyerlein, Irene J. TI Material-based design of the extrusion of bimetallic tubes SO COMPUTATIONAL MATERIALS SCIENCE LA English DT Article DE Interface; Tube extrusion; Finite element analysis; Strain gradients; Texture evolution ID CHANNEL ANGULAR EXTRUSION; IMMERSION CORROSION TESTS; PLASTIC PROPERTY CLOSURES; IMPLICIT FINITE-ELEMENTS; ZR-2.5NB PRESSURE TUBES; IN-REACTOR DEFORMATION; UPPER BOUND ANALYSIS; LATENT-HEAT STORAGE; STRAIN-PATH CHANGES; TEXTURE EVOLUTION AB Using finite element and polycrystalline plasticity modeling, we explore the influence of die design and material behavior on the extrusion of bimetallic tubes. Three distinctly different extrusion designs are introduced and evaluated based on a range of macroscopic and microstructural criteria: die and punch stress, interface roughness, peak forming loads, and strain and crystallographic texture heterogeneities across the tube thickness. We find that an extrusion die design proposed here that differs from the conventional one is better for reduction of peak forming load satisfying objectives of the traditional design. However, when the design is more constrained and considerations of strain and microstructural heterogeneities and gradients are made part of the design criteria, we show that one die design promotes such gradients while the other minimizes them. In all three designs, large disparities in flow stress and hardening rate (>3 times) lead to larger interfacial strain gradients. These findings provide basic die designs that can be used to evaluate the degree and locations of strain and texture gradients across the tube thickness. (C) 2014 Elsevier B.V. All rights reserved. C1 [Knezevic, Marko; Jahedi, Mohammad; Korkolis, Yannis P.] Univ New Hampshire, Dept Mech Engn, Durham, NH 03824 USA. [Beyerlein, Irene J.] Los Alamos Natl Lab, Div Theoret, Los Alamos, NM 87545 USA. RP Knezevic, M (reprint author), Univ New Hampshire, Dept Mech Engn, 33 Acad Way,Kingsbury Hall,W119, Durham, NH 03824 USA. EM marko.knezevic@unh.edu RI Beyerlein, Irene/A-4676-2011 FU University of New Hampshire faculty startup funds; Los Alamos National Laboratory Directed Research and Development (LDRD) [ER20140348] FX MK was supported by the University of New Hampshire faculty startup funds. IJB would like to acknowledge support through a Los Alamos National Laboratory Directed Research and Development (LDRD) project ER20140348. NR 70 TC 25 Z9 25 U1 2 U2 11 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0927-0256 EI 1879-0801 J9 COMP MATER SCI JI Comput. Mater. Sci. PD DEC PY 2014 VL 95 BP 63 EP 73 DI 10.1016/j.commatsci.2014.07.021 PG 11 WC Materials Science, Multidisciplinary SC Materials Science GA AR7TC UT WOS:000343781700009 ER PT J AU Yu, YQ Cheng, X AF Yu, Y. Q. Cheng, X. TI Three-dimensional simulation on behavior of water film flow with and without shear stress on water-air interface SO INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER LA English DT Article DE Falling film; Solitary wave; Flat plate; MWR; MLFT ID WAVY LIQUID-FILM; HEAT-TRANSFER; NUMERICAL-SIMULATION; VERTICAL PLATE; FALLING FILMS; MASS-TRANSFER; THIN-FILMS; HYDRODYNAMICS; DYNAMICS; SURFACE AB In this paper, the simulations of falling film behavior on a flat plate with and without interfacial gas-liquid shear stress were carried out. A three-dimensional numerical model was established based on film flow characteristics. A source term was implanted into the numerical model to take into account the interfacial gas-liquid shear stress. The model was validated by the experimental data. Both continuous film flow and film breakup were simulated. The film thickness, velocity distribution and wall shear stress at different Reynolds numbers were presented to understand the film flow behavior comprehensively. The influence of water-air shear stress on film flow behavior was revealed. A reasonable prediction on both MWR (Minimum Wetting Rate: Delta(min)) and MLFT (Minimum Liquid Film Thickness: Gamma(min)) were obtained. The model proposed in this study ought to be profitable for studies on mechanism of film breakup. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Yu, Y. Q.; Cheng, X.] Shanghai Jiao Tong Univ, Sch Nucl Sci & Engn, Shanghai 200240, Peoples R China. [Cheng, X.] Res Ctr Karlsruhe, Inst Nucl & Energy Technol, D-76021 Karlsruhe, Germany. [Yu, Y. Q.] Argonne Natl Lab, Nucl Engn Div, Argonne, IL 60439 USA. RP Yu, YQ (reprint author), Shanghai Jiao Tong Univ, Sch Nucl Sci & Engn, Shanghai 200240, Peoples R China. EM yyu@anl.gov FU National Key Projects [2010ZX06002-005]; U.S. Department of Energy, Basic Energy Sciences, Office of Science [DE-AC02-06CH11357] FX A support from National Key Projects 2010ZX06002-005 is gratefully acknowledged. This work is also supported by the U.S. Department of Energy, Basic Energy Sciences, Office of Science, under contract # DE-AC02-06CH11357. NR 38 TC 1 Z9 2 U1 3 U2 26 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0017-9310 EI 1879-2189 J9 INT J HEAT MASS TRAN JI Int. J. Heat Mass Transf. PD DEC PY 2014 VL 79 BP 561 EP 572 DI 10.1016/j.ijheatmasstransfer.2014.08.035 PG 12 WC Thermodynamics; Engineering, Mechanical; Mechanics SC Thermodynamics; Engineering; Mechanics GA AR7TE UT WOS:000343781900054 ER PT J AU Erikson, WW Cooper, MA Hobbs, ML Kaneshige, MJ Oliver, MS Snedigar, S AF Erikson, W. W. Cooper, M. A. Hobbs, M. L. Kaneshige, M. J. Oliver, M. S. Snedigar, S. TI Determination of thermal diffusivity, conductivity, and energy release from the internal temperature profiles of energetic materials SO INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER LA English DT Article DE Thermal diffusivity; Thermal conductivity; Energetic material AB A novel data processing technique has been developed to obtain thermal diffusivity, conductivity, and reaction heat release for energetic materials from Sandia Instrumented Thermal Ignition (SITI) experiments heated with a linear ramp temperature boundary condition. The method is based on the equivalence of the temperature responses of: (a) ramped temperature boundary condition with no internal heat generation and (b) uniform heat generation (that is, with a negative value) with constant temperature boundary conditions; which is true regardless of the spatial domain. For the specific case analyzed herein (the SITI apparatus), the midplane temperature profile is well represented by a quadratic expression in the radial coordinate for both ramped boundary temperature and uniform heat generation responses. Internal temperature data from temperature ramped SITI experiments with various pyrotechnics, propellants, and explosives were analyzed. Quadratic fits to the temperature profile data were made and the associated fitting coefficients were converted to yield thermal diffusivity directly. Thermal conductivity was then determined from thermal diffusivity, given knowledge of the material's specific heat capacity and density. Finally, because of the equivalence of the cases (a) and (b) above, their individual contributions to a combined temperature profile can be easily separated, thereby yielding internal heat generation as well. This technique allows for measurements of properties for pressed and powdered materials over a range of densities and temperatures. The technique is demonstrated using pyrotechnic materials (KClO4 and Ti/KClO4), a composite solid propellant (herein referred to as "Propellant A", a class 1.3 AP-HTPB-aluminum propellant) and an explosive (PBX 9502). (C) 2014 Elsevier Ltd. All rights reserved. C1 [Erikson, W. W.; Cooper, M. A.; Hobbs, M. L.; Kaneshige, M. J.; Oliver, M. S.; Snedigar, S.] Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Erikson, WW (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87185 USA. FU DOD/DOE Joint Munitions program under Technical Coordination Group - III; Sandia National Laboratories FX This work was supported in part by the DOD/DOE Joint Munitions program under Technical Coordination Group - III as well as internal funding at Sandia National Laboratories. The materials for testing came from a variety of sources and programs (not specifically allocated for this work). The PBX 9502 originated from Los Alamos, the Propellant A material was provided to us by Walt Gill at SNL, and the TKP output powder was manufactured by ATIC. We appreciate the helpful manuscript reviews and comments by Gregg Radtke and Cole Yarrington of SNL. NR 15 TC 3 Z9 3 U1 1 U2 21 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0017-9310 EI 1879-2189 J9 INT J HEAT MASS TRAN JI Int. J. Heat Mass Transf. PD DEC PY 2014 VL 79 BP 676 EP 688 DI 10.1016/j.ijheatmasstransfer.2014.08.059 PG 13 WC Thermodynamics; Engineering, Mechanical; Mechanics SC Thermodynamics; Engineering; Mechanics GA AR7TE UT WOS:000343781900065 ER PT J AU Shaikh, N Valiev, M Lymar, SV AF Shaikh, Nizamuddin Valiev, Marat Lymar, Sergei V. TI Decomposition of amino diazeniumdiolates (NONOates): Molecular mechanisms SO JOURNAL OF INORGANIC BIOCHEMISTRY LA English DT Article DE Diazeniumdiolates; NONOates; NO donor; Mechanism; Tautomerization; Ab initio calculations ID NITRIC-OXIDE RELEASE; DENSITY-FUNCTIONAL THEORY; AQUEOUS-SOLUTIONS; S(N)2 REACTION; NO; CHEMISTRY; NITROXYL; HNO; GENERATION; KINETICS AB Although diazeniumdiolates (X[N(O)NO](-)) are extensively used in biochemical, physiological, and pharmacological studies due to their ability to release NO and/or its congeneric nitroxyl, the mechanisms of these processes remain obscure. In this work, we used a combination of spectroscopic, kinetic, and computational techniques to arrive at a quantitatively consistent molecular mechanism for decomposition of amino diazeniumdiolates (amino NONOates: R2N[N(O)NO](-), where R = -N(C2H5)(2) (1), - N(C3H4NH2)(2) (2), or - N(C2H4NH2)(2) (3)). Decomposition of these NONOates is triggered by protonation of their [NN(O)NO](-) group with the apparent pK(a) and decomposition rate constants of 4.6 and 1 s(-1) for 1; 3.5 and 0.083 s(-1) for 2; and 3.8 and 0.0033 s(-1) for 3. Although protonation occurs mainly on the 0 atoms of the functional group, only the minor R2N(H)N(0)NO tautomer (population similar to 10(-7), for 1) undergoes the N-N heterolytic bond cleavage (k(d) - 10(7) s(-1) for 1) leading to amine and NO. Decompositions of protonated amino NONOates are strongly temperature-dependent; activation enthalpies are 20.4 and 19.4 kcal/mol for 1 and 2, respectively, which includes contributions from both the tautomerization and bond cleavage. The bond cleavage rates exhibit exceptional sensitivity to the nature of R substituents which strongly modulate activation entropy. At pH <2, decompositions of all three NONOates that have been investigated are subject to additional acid catalysis that occurs through di-protonation of the [NN(O)NO](-) group. (C) 2014 Elsevier Inc. All rights reserved. C1 [Shaikh, Nizamuddin; Lymar, Sergei V.] Brookhaven Natl Lab, Dept Chem, Upton, NY 11973 USA. [Valiev, Marat] Pacific NW Natl Lab, William R Wiley Environm Mol Sci Lab, Richland, WA 99352 USA. RP Lymar, SV (reprint author), Brookhaven Natl Lab, Dept Chem, Upton, NY 11973 USA. EM Lymar@bnl.gov FU U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences; Brookhaven National Laboratory [DE-AC02-98CH10886] FX We thank Dr. V. Shafirovich (NYU) for valuable discussions. This research was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. Research at Brookhaven National Laboratory was carried out under contract DE-AC02-98CH10886. Research at Pacific Northwest National Laboratory was performed in part using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory. NR 47 TC 2 Z9 2 U1 1 U2 24 PU ELSEVIER SCIENCE INC PI NEW YORK PA 360 PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA SN 0162-0134 EI 1873-3344 J9 J INORG BIOCHEM JI J. Inorg. Biochem. PD DEC PY 2014 VL 141 BP 28 EP 35 DI 10.1016/j.jinorgbio.2014.08.008 PG 8 WC Biochemistry & Molecular Biology; Chemistry, Inorganic & Nuclear SC Biochemistry & Molecular Biology; Chemistry GA AR7XQ UT WOS:000343790700004 PM 25194941 ER PT J AU Starinshak, DP Karni, S Roe, PL AF Starinshak, David P. Karni, Smadar Roe, Philip L. TI A New Level-Set Model for the Representation of Non-Smooth Geometries SO JOURNAL OF SCIENTIFIC COMPUTING LA English DT Article ID FLOW AB In Starinshak et al. (J Comput Phys 262(1):1-16, 2014), we proposed a new level-set model for representing multimaterial flows in multiple space dimensions. Rather than associating each level-set function with the boundary of a material, the new model associates each level-set function with a pair of materials and the interface that separates them. In this paper, we extend the model to represent geometries with non-smooth boundaries. The model uses multiple level-set functions to describe the shape boundary, typically with one level-set function per smooth boundary segment. Sign information is collected from all level-set functions and a voting algorithm is used to determine the interior/exterior of the geometric shape. The model is well suited for representing boundaries with singularities; it offers significant improvement over standard level-set approaches, both in shape preservation and area conservation; and it eliminates the need for costly redistancing of the level-set function. Numerical examples illustrate the superior performance of the proposed model. C1 [Starinshak, David P.] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. [Karni, Smadar] Univ Michigan, Dept Math, Ann Arbor, MI 48109 USA. [Roe, Philip L.] Univ Michigan, Dept Aerosp Engn, Ann Arbor, MI 48109 USA. RP Starinshak, DP (reprint author), Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. EM starinshak1@llnl.gov FU DOE NNSA-ASC Grant [DE-FC52-08NA28616]; NSF [DMS 0609766]; DOE [DE-FG02-88ER25053] FX This work was supported in part by DOE NNSA-ASC Grant DE-FC52-08NA28616 and NSF Award DMS 0609766. Part of this work was done while S. Karni was on sabbatical leave at the Courant Institute, NYU. The hospitality of Professor Marsha Berger and support from DOE Grant DE-FG02-88ER25053 is gratefully acknowledged. NR 9 TC 0 Z9 0 U1 1 U2 5 PU SPRINGER/PLENUM PUBLISHERS PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 0885-7474 EI 1573-7691 J9 J SCI COMPUT JI J. Sci. Comput. PD DEC PY 2014 VL 61 IS 3 BP 649 EP 672 DI 10.1007/s10915-014-9842-0 PG 24 WC Mathematics, Applied SC Mathematics GA AR8JL UT WOS:000343821300009 ER PT J AU Dingreville, R Hallil, A Berbenni, S AF Dingreville, Remi Hallil, Abdelmalek Berbenni, Stephane TI From coherent to incoherent mismatched interfaces: A generalized continuum formulation of surface stresses SO JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS LA English DT Article DE Surface stresses; Interface properties; Mismatch; Grain boundaries; Generalized Shuttleworth relationship ID THIN-FILMS; NANO-INHOMOGENEITIES; METHANOL OXIDATION; ELASTIC PROPERTIES; SOLIDS; ENERGY; EQUILIBRIUM; CONNECTIONS; COMPOSITES; TRANSITION AB The equilibrium of coherent and incoherent mismatched interfaces is reformulated in the context of continuum mechanics based on the Gibbs dividing surface concept. Two surface stresses are introduced: a coherent surface stress and an incoherent surface stress, as well as a transverse excess strain. The coherent surface stress and the transverse excess strain represent the thermodynamic driving forces of stretching the interface while the incoherent surface stress represents the driving force of stretching one crystal while holding the other fixed and thereby altering the structure of the interface. These three quantities fully characterize the elastic behavior of coherent and incoherent interfaces as a function of the in-plane strain, the transverse stress and the mismatch strain. The isotropic case is developed in detail and particular attention is paid to the case of interfacial thermo-elasticity. This exercise provides an insight on the physical significance of the interfacial elastic constants introduced in the formulation and illustrates the obvious coupling between the interface structure and its associated thermodynamics quantities. Finally, an example based on atomistic simulations of Cu/Cu2O interfaces is given to demonstrate the relevance of the generalized interfacial formulation and to emphasize the dependence of the interfacial thermodynamic quantities on the incoherency strain with an actual material system. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Dingreville, Remi] Sandia Natl Labs, Albuquerque, NM 87185 USA. [Hallil, Abdelmalek] Univ La Rochelle, Lab Sci Ingn Environm LaSIE, F-17042 La Rochelle 1, France. [Berbenni, Stephane] Univ Lorraine, UMR CNRS 7239, Lab Etud Microstruct & Mecan Mat, F-57045 Metz, France. RP Dingreville, R (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87185 USA. EM rdingre@sandia.gov OI HALLIL, Abdelmalek/0000-0002-7562-8228; Dingreville, Remi/0000-0003-1613-695X FU European Commission [NMP-2008-214371]; French government through the National Research Agency (ANR) [ANR-11-LABX-0008-01]; United States Department of Energy [DE-AC04-94AL85000]; UMI GTL/CNRS [UMI 2958] FX A.H. would like to thank the UMI GTL/CNRS (UMI 2958) and Pr. M. Cherkaoui for their valuable support for part of this work along with the support from the European Commission for partial funding of this work under the "NanoInterface" project (NMP-2008-214371). S.B. would also like to thank the support of the French government through the National Research Agency (ANR) under the program "Investment in the future" (Labex DAMAS referenced as ANR-11-LABX-0008-01).; Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy, under Contract no. DE-AC04-94AL85000. NR 45 TC 10 Z9 11 U1 5 U2 57 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0022-5096 EI 1873-4782 J9 J MECH PHYS SOLIDS JI J. Mech. Phys. Solids PD DEC PY 2014 VL 72 BP 40 EP 60 DI 10.1016/j.jmps.2014.08.003 PG 21 WC Materials Science, Multidisciplinary; Mechanics; Physics, Condensed Matter SC Materials Science; Mechanics; Physics GA AR8RJ UT WOS:000343841900003 ER PT J AU Cesana, P Porta, M Lookman, T AF Cesana, Pierluigi Porta, Marcel Lookman, Turab TI Asymptotic analysis of hierarchical martensitic microstructure SO JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS LA English DT Article DE Microstructures; Phase transformation; Strain compatibility; Asymptotic analysis; Variational calculus AB We consider a hierarchical nested microstructure, which also contains a point of singularity (disclination) at the origin, observed in lead orthovanadate. We show how to exactly compute the energy cost and associated displacement field within linearized elasticity by enforcing geometric compatibility of strains across interfaces of the three-phase mixture of distortions (variants) in the microstructure. We prove that the mechanical deformation is purely elastic and discuss the behavior of the system close to the origin. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Cesana, Pierluigi; Porta, Marcel; Lookman, Turab] Los Alamos Natl Lab, Div Theoret, Los Alamos, NM 87545 USA. RP Cesana, P (reprint author), Math Inst, Woodstock Rd, Oxford OX2 6GG, England. EM cesana@maths.ox.ac.uk OI Porta Tena, Marcel/0000-0001-7582-9671 FU Department of Energy National Nuclear Security Administration [DE-FC52-08NA28613]; European Research Council under the European Union's Seventh Framework Programme (FP7) - ERC grant [291053] FX We acknowledge support from the Department of Energy National Nuclear Security Administration under Award Number DE-FC52-08NA28613. P.C. is grateful to Los Alamos National Laboratory for its kind hospitality. P.C. was partially supported by the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013) - ERC grant agreement No. 291053. Part of this work has been written when P.C. was a postdoctoral student at California Institute of Technology. The authors are grateful with Kaushik Bhattacharya, Richard James and Angkana Ruland for several discussions at various stages of the work. NR 11 TC 1 Z9 1 U1 1 U2 6 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0022-5096 EI 1873-4782 J9 J MECH PHYS SOLIDS JI J. Mech. Phys. Solids PD DEC PY 2014 VL 72 BP 174 EP 192 DI 10.1016/j.jmps.2014.08.001 PG 19 WC Materials Science, Multidisciplinary; Mechanics; Physics, Condensed Matter SC Materials Science; Mechanics; Physics GA AR8RJ UT WOS:000343841900011 ER PT J AU Nenoff, TM Rodriguez, MA Soelberg, NR Chapman, KW AF Nenoff, Tina M. Rodriguez, Mark A. Soelberg, Nick R. Chapman, Karena W. TI Silver-mordenite for radiologic gas capture from complex streams: Dual catalytic CH3I decomposition and I confinement SO MICROPOROUS AND MESOPOROUS MATERIALS LA English DT Article DE Mordenite; Methyl iodide; Synchrotron; Pair distribution function (PDF); Fission gas capture ID METAL-ORGANIC FRAMEWORKS; CHALCOGEN-BASED AEROGELS; RADIOACTIVE IODINE; WASTE FORMS; X-RAY; ZEOLITES; REMEDIATION; CONDUCTION; CONVERSION; MECHANISM AB The selective capture of radiological iodine (I-129) is a persistent concern for safe nuclear energy. In nuclear fuel reprocessing scenarios, the gas streams to be treated are extremely complex, containing several distinct iodine-containing molecules amongst a large variety of other species. Silver-containing mordenite (MOR) is a longstanding benchmark for radioiodine capture, reacting with molecular iodine (I-2) to form AgI. However the mechanisms for organoiodine capture is not well understood. Here we investigate the capture of methyl iodide from complex mixed gas streams by combining chemical analysis of the effluent gas stream with in depth characterization of the recovered sorbent. Tools applied include infrared spectroscopy, thermogravimetric analysis with mass spectrometry, micro X-ray fluorescence, powder X-ray diffraction analysis, and pair distribution function analysis. The MOR zeolite catalyzes decomposition of the methyl iodide through formation of surface methoxy species (SMS), which subsequently reacts with water in the mixed gas stream to form methanol, and with methanol to form dimethyl ether, which are both detected downstream in the effluent. The liberated iodine reacts with Ag in the MOR pore to the form subnanometer AgI clusters, smaller than the MOR pores, suggesting that the iodine is both physically and chemically confined within the zeolite. (C) 2014 Elsevier Inc. All rights reserved. C1 [Nenoff, Tina M.] Sandia Natl Labs, Nanoscale Sci Dept, Albuquerque, NM 87185 USA. [Soelberg, Nick R.] Idaho Natl Lab, Idaho Falls, ID 83402 USA. [Rodriguez, Mark A.] Sandia Natl Labs, Mat Characterizat & Performance Dept, Albuquerque, NM 87185 USA. [Chapman, Karena W.] Argonne Natl Lab, Adv Photon Source, Xray Sci Div, Argonne, IL 60439 USA. RP Nenoff, TM (reprint author), Sandia Natl Labs, POB 5800,MS,1415, Albuquerque, NM 87185 USA. EM tmnenof@sandia.gov; chapmank@aps.anl.gov FU U.S. DOE/NE/FCRD-SWG; U.S. DOE's NNSA [DE-AC04-94AL85000]; USDOE [DE-AC02-06CH11357]; U.S. Department of Energy, Office of Nuclear Energy, under DOE Idaho Operations Office [DE-AC07-05ID14517] FX The authors thank Dr. James L. Krumhansl and David X. Rademacher (SNL) for materials characterization work, and Dr. R.T. Jubin and S. Bruffey (ORNL) for providing the Ag degrees-MOR and AgI-MOR samples. This research was supported by the U.S. DOE/NE/FCRD-SWG. Sandia National Laboratories is a multiprogram laboratory managed and operated by Sandia Corp., a wholly owned subsidiary of Lockheed Martin Corp., for the U.S. DOE's NNSA, under Contract No. DE-AC04-94AL85000. Work done at Argonne and use of the Advanced Photon Source, an Office of Science User Facility operated for the U.S. DOE/Office of Science by Argonne National Laboratory, was supported by the USDOE, Contract No. DE-AC02-06CH11357. The Idaho National Laboratory is a U.S. Department of Energy National Laboratory operated by Battelle Energy Alliance, for the U.S. Department of Energy, Office of Nuclear Energy, under DOE Idaho Operations Office Contract DE-AC07-05ID14517. NR 47 TC 15 Z9 15 U1 10 U2 53 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 1387-1811 EI 1873-3093 J9 MICROPOR MESOPOR MAT JI Microporous Mesoporous Mat. PD DEC PY 2014 VL 200 BP 297 EP 303 DI 10.1016/j.micromeso.2014.04.041 PG 7 WC Chemistry, Applied; Chemistry, Physical; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary SC Chemistry; Science & Technology - Other Topics; Materials Science GA AR5NB UT WOS:000343630100038 ER PT J AU Bosland, L Dickinson, S Glowa, GA Herranz, LE Kim, HC Powers, DA Salay, M Tietze, S AF Bosland, L. Dickinson, S. Glowa, G. A. Herranz, L. E. Kim, H. C. Powers, D. A. Salay, M. Tietze, S. TI Iodine-paint interactions during nuclear reactor severe accidents SO ANNALS OF NUCLEAR ENERGY LA English DT Article; Proceedings Paper CT ERMSAR Conference of the SARNET-Network CY OCT 02-04, 2013 CL Avignon, FRANCE DE Severe accident; Accident analysis; Iodine behaviour; Containment paint ID CURED EPOXY-RESINS; CHARGE-TRANSFER COMPLEXES; THERMAL-DEGRADATION; GAMMA-IRRADIATION; MOLECULAR-IODINE; RADIO-OXIDATION; WATER DIFFUSION; FTIR; SPECTROSCOPY; TEMPERATURE AB To assess the radiological consequences of a severe reactor accident, it is important to be able to predict the behaviour of iodine in containment. Some interactions between iodine and containment paint (e.g., adsorption) have been well known for a long time. However, in recent years, new phenomena have been identified that can affect the gas phase iodine concentration in the longer term (e.g., the release of molecular iodine and organic iodides from irradiated painted surfaces). Several international collaborations and organizations around the world are currently addressing different aspects of this topic, including laboratory experiments and theoretical studies (ab initio) designed to improve the mechanistic understanding of the phenomena. Knowledge of the underlying mechanisms will provide explanations for behavioural differences observed between paint types, and will support the extrapolation of laboratory results to the safety analyses of nuclear reactors. The purpose of this paper is to present a selection of recent work performed by Severe Accident Research Network (SARNET) members regarding iodine-paint interactions and paint aging in order to improve the common understanding and better define what has still to be done in this area. The Severe Accident Research Network (SARNET) provides a framework within which members can share and discuss results. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Bosland, L.] Ctr Cadarache, Inst Radioprotect & Surete Nucl, PSN SAG LETR, F-13115 St Paul Les Durance, France. [Dickinson, S.] Harwell Oxford Business Ctr, Natl Nucl Lab, Didcot OX11 0QT, Oxon, England. [Glowa, G. A.] Atom Energy Canada Ltd, Chalk River Labs, Chalk River, ON K0J 1J0, Canada. [Herranz, L. E.] CIEMAT, Madrid 28040, Spain. [Kim, H. C.] Korea Inst Nucl Safety, Taejon 305338, South Korea. [Powers, D. A.] Sandia Natl Labs, Albuquerque, NM 87185 USA. [Salay, M.] US Nucl Regulatory Commiss, Washington, DC 20555 USA. [Tietze, S.] Chalmers, SE-41296 Gothenburg, Sweden. RP Glowa, GA (reprint author), Atom Energy Canada Ltd, Chalk River Labs, Chalk River, ON K0J 1J0, Canada. EM glowag@aecl.ca RI BOSLAND, Loic/J-5858-2016 OI BOSLAND, Loic/0000-0002-5235-2740 FU European Commission [237147] FX The authors wish to acknowledge the support of the SARNET2 project (Contract 237147) within the European Commission 7th Framework Program of Research and Development. NR 85 TC 8 Z9 8 U1 1 U2 14 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0306-4549 J9 ANN NUCL ENERGY JI Ann. Nucl. Energy PD DEC PY 2014 VL 74 SI SI BP 184 EP 199 DI 10.1016/j.anucene.2014.07.016 PG 16 WC Nuclear Science & Technology SC Nuclear Science & Technology GA AR1IB UT WOS:000343337800018 ER PT J AU Dickinson, S Auvinen, A Ammar, Y Bosland, L Clement, B Funke, F Glowa, G Karkela, T Powers, DA Tietze, S Weber, G Zhang, S AF Dickinson, S. Auvinen, A. Ammar, Y. Bosland, L. Clement, B. Funke, F. Glowa, G. Karkela, T. Powers, D. A. Tietze, S. Weber, G. Zhang, S. TI Experimental and modelling studies of iodine oxide formation and aerosol behaviour relevant to nuclear reactor accidents SO ANNALS OF NUCLEAR ENERGY LA English DT Article; Proceedings Paper CT ERMSAR Conference of the SARNET-Network CY OCT 02-04, 2013 CL Avignon, FRANCE DE Iodine; Severe accident; Radiation; Methyl iodine; Iodine oxide; Aerosol ID PROJECT RADIOLYTIC OXIDATION; PARTICLE FORMATION; MOLECULAR-IODINE; CONTAINMENT; DESTRUCTION; GROWTH; IODATE; OZONE; I2O5; AIR AB Plant assessments have shown that iodine contributes significantly to the source term for a range of accident scenarios. Iodine has a complex chemistry that determines its chemical form and, consequently, its volatility in the containment. If volatile iodine species are formed by reactions in the containment, they will be subject to radiolytic reactions in the atmosphere, resulting in the conversion of the gaseous species into involatile iodine oxides, which may deposit on surfaces or re-dissolve in water pools. The concentration of airborne iodine in the containment will, therefore, be determined by the balance between the reactions contributing to the formation and destruction of volatile species, as well as by the physicochemical properties of the iodine oxide aerosols which will influence their longevity in the atmosphere. This paper summarises the work that has been done in the framework of the EC SARNET (Severe Accident Research Network) to develop a greater understanding of the reactions of gaseous iodine species in irradiated air/steam atmospheres, and the nature and behaviour of the reaction products. This work has mainly been focussed on investigating the nature and behaviour of iodine oxide aerosols, but earlier work by members of the SARNET group on gaseous reaction rates is also discussed to place the more recent work into context. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Dickinson, S.] Natl Nucl Lab, Didcot OX11 0QT, Oxon, England. [Auvinen, A.; Karkela, T.] VTT Tech Res Ctr Finland, FI-02044 Espoo, Finland. [Ammar, Y.] Newcastle Univ, Sch Mech & Syst Engn, Newcastle Upon Tyne NE1 7RU, Tyne & Wear, England. [Clement, B.] IRSN, Cadarache, F-13115 St Paul Les Durance, France. [Funke, F.] AREVA GmbH, Dept Radiat Protect, D-91001 Erlangen, Germany. [Glowa, G.] Chalk River Labs, AECL, Chalk River, ON K0J 1J0, Canada. [Powers, D. A.] Sandia Natl Labs, Adv Nucl Energy Programs, Albuquerque, NM 87185 USA. [Tietze, S.] Chalmers, Dept Chem & Biol Engn, S-41296 Gothenburg, Sweden. [Weber, G.] Gesell Anlagen & Reaktorsicherheit GRS mbH, Forschungszentrum, D-85748 Garching, Germany. RP Dickinson, S (reprint author), Natl Nucl Lab, Bldg 168,Harwell Oxford Sci Campus, Didcot OX11 0QT, Oxon, England. EM shirley.dickinson@nnl.co.uk RI BOSLAND, Loic/J-5858-2016 OI BOSLAND, Loic/0000-0002-5235-2740 FU EC [237147] FX This work was carried out under the EC SARNET 2 program, no 237147 within the 7th Framework Program of Research and Development. NR 36 TC 9 Z9 9 U1 2 U2 23 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0306-4549 J9 ANN NUCL ENERGY JI Ann. Nucl. Energy PD DEC PY 2014 VL 74 SI SI BP 200 EP 207 DI 10.1016/j.anucene.2014.05.012 PG 8 WC Nuclear Science & Technology SC Nuclear Science & Technology GA AR1IB UT WOS:000343337800019 ER PT J AU Ghiasi, B Kumar, L Furubayashi, T Lim, CJ Bi, XT Kim, CS Sokhansanj, S AF Ghiasi, Bahman Kumar, Linoj Furubayashi, Takaaki Lim, C. Jim Bi, Xiaotao Kim, Chang Soo Sokhansanj, Shahab TI Densified biocoal from woodchips: Is it better to do torrefaction before or after densification? SO APPLIED ENERGY LA English DT Article DE Biomass; Torrefaction Densification; Torrefied pellet; Densified biocoal ID BIO-OIL; LIGNOCELLULOSIC BIOMASS; PELLETIZING PROPERTIES; STEAM PRETREATMENT; TORREFIED BIOMASS; WOOD PELLETS; GRINDABILITY; QUALITY; COAL; RESOURCES AB Torrefied biomass represents a high quality renewable energy commodity that can be used to substitute fossil fuels such as coal. However, densification processes such as pelletisation is necessary to improve the tradability of "low-dense" torrefied biomass. In this work, two process pathways were assessed for energy and mass balance in making torrefied pellets from softwood chips and qualities of the resulting torrefied pellets were compared. Pathway I involve drying the wood chips, torrefaction, grinding followed by densification. In pathway II, wood chips were dried, ground, densified and finally torrefied. The results showed that it was difficult to bind the torrefied biomass particles and a binding agent was necessary to enable their effective pelletisation with reasonable energy consumption. In contrary, pelletization of raw materials was possible without using binding agents and when the "raw wood pellets" were torrefied, the pellets surprisingly stayed intact and had several promising properties such as higher energy/carbon value, reduced moisture content and higher stability in water. In addition, the pathway II was more efficient in terms of overall energy and material balance. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Ghiasi, Bahman; Kumar, Linoj; Lim, C. Jim; Bi, Xiaotao; Sokhansanj, Shahab] Univ British Columbia, Dept Chem & Biol Engn, Biomass & Bioenergy Res Grp, Vancouver, BC V5Z 1M9, Canada. [Furubayashi, Takaaki] Tohoku Univ, Grad Sch Engn, Dept Management Sci & Technol, Sendai, Miyagi 980, Japan. [Kim, Chang Soo] Korea Inst Sci & Technol, Seoul, South Korea. [Sokhansanj, Shahab] Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA. RP Ghiasi, B (reprint author), Univ British Columbia, Dept Chem & Biol Engn, Biomass & Bioenergy Res Grp, Vancouver, BC V5Z 1M9, Canada. EM bghiasi@chbe.ubc.ca; linojkumar@gmail.com FU Natural Sciences and Engineering Research Council of Canada (NSERC); BioFuelNet, Canada FX Authors gratefully acknowledge the research support from Natural Sciences and Engineering Research Council of Canada (NSERC) and BioFuelNet, Canada. NR 44 TC 5 Z9 5 U1 3 U2 47 PU ELSEVIER SCI LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND SN 0306-2619 EI 1872-9118 J9 APPL ENERG JI Appl. Energy PD DEC 1 PY 2014 VL 134 BP 133 EP 142 DI 10.1016/j.apenergy.2014.07.076 PG 10 WC Energy & Fuels; Engineering, Chemical SC Energy & Fuels; Engineering GA AR1HP UT WOS:000343336600013 ER PT J AU Bradman, A Castorina, R Gaspar, F Nishioka, M Colon, M Weathers, W Egeghy, PP Maddalena, R Williams, J Jenkins, PL McKone, TE AF Bradman, Asa Castorina, Rosemary Gaspar, Fraser Nishioka, Marcia Colon, Maribel Weathers, Walter Egeghy, Peter P. Maddalena, Randy Williams, Jeffery Jenkins, Peggy L. McKone, Thomas E. TI Flame retardant exposures in California early childhood education environments SO CHEMOSPHERE LA English DT Article DE Child care; Children; Exposure; Flame retardant; PBDEs ID POLYBROMINATED DIPHENYL ETHERS; IN-HOUSE DUST; SERUM CONCENTRATIONS; HORMONE DISRUPTION; THYROID-HORMONE; PHASE-OUT; PBDES; ASSOCIATIONS; PRODUCTS; SAMPLES AB Infants and young children spend as much as 50 h per week in child care and preschool. Although approximately 13 million children, or 65% of all U.S. children, spend some time each day in early childhood education (ECE) facilities, little information is available about environmental exposures in these environments. We measured flame retardants in air and dust collected from 40 California ECE facilities between May 2010 and May 2011. Low levels of six polybrominated diphenyl ether (PBDE) congeners and four non-PBDE flame retardants were present in air, including two constituents of Firemaster 550 and two tris phosphate compounds [tris (2-chloroethyl) phosphate (TCEP) and tris (1,3-dichloroisopropyl) phosphate (TDCIPP)]. Tris phosphate, Firemaster 550 and PBDE compounds were detected in 100% of the dust samples. BDE47, BDE99, and BDE209 comprised the majority of the PBDE mass measured in dust. The median concentrations of TCEP (319 ng g(-1)) and TDCIPP (2265 ng g(-1)) were similar to or higher than any PBDE congener. Levels of TCEP and TDCIPP in dust were significantly higher in facilities with napping equipment made out of foam (Mann Whitney p-values < 0.05). Child BDE99 dose estimates exceeded the RID in one facility for children < 3 years old. In 51% of facilities, TDCIPP dose estimates for children < 6 years old exceeded age-specific "No Significant Risk Levels (NSRLs)" based on California Proposition 65 guidelines for carcinogens. Given the overriding interest in providing safe and healthy environments for young children, additional research is needed to identify strategies to reduce indoor sources of flame retardant chemicals. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Bradman, Asa; Castorina, Rosemary; Gaspar, Fraser; McKone, Thomas E.] Univ Calif Berkeley, Sch Publ Hlth, Ctr Environm Res & Childrens Hlth, Berkeley, CA 94704 USA. [Nishioka, Marcia] Battelle Mem Inst, Columbus, OH 43201 USA. [Colon, Maribel; Weathers, Walter; Egeghy, Peter P.] US EPA, Res Triangle Pk, NC 27711 USA. [Maddalena, Randy; McKone, Thomas E.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. [Williams, Jeffery; Jenkins, Peggy L.] Calif Air Resources Board, Sacramento, CA USA. RP Bradman, A (reprint author), Univ Calif Berkeley, Sch Publ Hlth, Ctr Environm Res & Childrens Hlth, 1995 Univ Ave,Suite 265, Berkeley, CA 94704 USA. EM abradman@berkeley.edu OI Gaspar, Fraser/0000-0002-0782-5721 FU California Air Resources Board (ARB) [08-305] FX This research was funded by the California Air Resources Board (ARB Contract No. 08-305). This work does not necessarily reflect the opinion or official policy of the ARB. Although this work was reviewed by U.S. EPA and approved for publication, it does not necessarily reflect the opinion or official policy of the U.S. EPA. Co-author Walter Weathers has recently retired from the U.S. EPA. NR 44 TC 18 Z9 18 U1 4 U2 61 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0045-6535 EI 1879-1298 J9 CHEMOSPHERE JI Chemosphere PD DEC PY 2014 VL 116 SI SI BP 61 EP 66 DI 10.1016/j.chemosphere.2014.02.072 PG 6 WC Environmental Sciences SC Environmental Sciences & Ecology GA AR5KH UT WOS:000343623200010 PM 24835158 ER PT J AU Ballard, GM Baxley, JV AF Ballard, Grey M. Baxley, John V. TI ASYMPTOTIC BEHAVIOR OF THE EIGENVALUES OF TOEPLITZ INTEGRAL OPERATORS ASSOCIATED WITH THE HANKEL TRANSFORM SO DYNAMIC SYSTEMS AND APPLICATIONS LA English DT Article ID EXTREME EIGENVALUES AB We prove results concerning the asymptotic behavior of eigenvalues of finite section Toeplitz integral operators associated with the Hankel transform. We also make conjectures about the corresponding problem for the Jacobi transform. C1 [Ballard, Grey M.; Baxley, John V.] Wake Forest Univ, Dept Math, Winston Salem, NC 27109 USA. RP Ballard, GM (reprint author), Sandia Natl Labs, Livermore, CA 94551 USA. NR 15 TC 0 Z9 0 U1 0 U2 7 PU DYNAMIC PUBLISHERS, INC PI ATLANTA PA PO BOX 48654, ATLANTA, GA 30362-0654 USA SN 1056-2176 J9 DYNAM SYST APPL JI Dyn. Syst. Appl. PD DEC PY 2014 VL 23 IS 4 BP 505 EP 529 PG 25 WC Mathematics, Applied; Mathematics SC Mathematics GA AR1GH UT WOS:000343333200001 ER PT J AU Christensen, E McCormick, RL AF Christensen, Earl McCormick, Robert L. TI Long-term storage stability of biodiesel and biodiesel blends SO FUEL PROCESSING TECHNOLOGY LA English DT Article DE Biodiesel; Oxidation stability; Biofuels ID OXIDATION STABILITY; DIESEL/BIODIESEL BLENDS; COMMERCIAL ADDITIVES; PURIFICATION STEP; ANTIOXIDANTS; DIESEL; METHYL; OIL AB Longer-term storage stability of biodiesel and blends was studied in experiments simulating up to one year for 100% biodiesel (B100) and three years for blends. Aging was simulated by holding samples at 43 degrees C to accelerate oxidation (ASTM D4625). Biodiesels were treated with antioxidants before and after aging, with continued aging after antioxidant treatment. Treating aged biodiesel was effective at restoring stability; however, antioxidant effectiveness was decreased relative to fresh biodiesel. Blends were prepared at B5 (5 vol.%) and B20 (20 vol.%) with biodiesel having either 3- or 6-hour Rancimat induction time and low or high polyunsaturated ester content with two diesels produced from hydrocracked or hydrotreated feedstocks. All B5s were stable for the entire storage time regardless of B100 induction time. B20s were unstable if prepared from high polyunsaturated ester biodiesel with a 3-hour induction time. Base diesel stability had considerable effect on blend stability. All but the lowest-stability B20s remained within specification, indicating that long-term storage of biodiesel blends is possible if the biodiesel has high oxidative stability and storage conditions are clean. Induction time decreases indicated loss of stability (consumption of antioxidant) prior to blend degradation; therefore, induction time monitoring is recommended for predicting quality changes during storage. (C) 2014 The Authors. Published by Elsevier B.V. C1 [Christensen, Earl; McCormick, Robert L.] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Christensen, E (reprint author), Natl Renewable Energy Lab, 15013 Denver West Pkwy, Golden, CO 80401 USA. EM earl.christensen@nrel.gov RI McCormick, Robert/B-7928-2011 FU U.S. Department of Energy [DE347AC36-99GO10337]; National Renewable Energy Laboratory; National Biodiesel Board FX This work was supported by the U.S. Department of Energy under Contract No. DE347AC36-99GO10337 with the National Renewable Energy Laboratory. Additional support was provided by the National Biodiesel Board. The authors gratefully acknowledge the assistance of Lisa Fouts for chemical analysis of samples. NR 31 TC 14 Z9 15 U1 2 U2 33 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0378-3820 EI 1873-7188 J9 FUEL PROCESS TECHNOL JI Fuel Process. Technol. PD DEC PY 2014 VL 128 BP 339 EP 348 DI 10.1016/j.fuproc.2014.07.045 PG 10 WC Chemistry, Applied; Energy & Fuels; Engineering, Chemical SC Chemistry; Energy & Fuels; Engineering GA AR2BZ UT WOS:000343389900039 ER PT J AU Garcia, S Liu, Q Bacon, DH Maroto-Valer, MM AF Garcia, S. Liu, Q. Bacon, D. H. Maroto-Valer, M. M. TI An investigation of reaction parameters on geochemical storage of non-pure CO2 streams in iron oxide-bearing formations SO FUEL PROCESSING TECHNOLOGY LA English DT Article DE CO2 storage; Mineral trapping; Hematite; Kaolinite; SO2; Kinetic modelling ID CARBON-DIOXIDE; THERMAL-DECOMPOSITION; MINERAL TRAP; FERRIC IRON; SEQUESTRATION; AQUIFERS; XPS; SIMULATION; DAWSONITE; SEDIMENTS AB Hematite deposit that is the main Fern-bearing mineral in sedimentary red beds was proposed as a potential host repository for converting CO2 into carbonate minerals such as siderite (FeCO3), when CO2 -SO2 gas mixtures are co-injected. This work investigated CO2 mineral trapping using hematite and sensitivity of the reactive systems to different parameters, including particle size, gas composition, temperature, pressure, and solid-to-liquid ratio. Experimental and modelling studies of hydrothermal experiments were conducted, which emulated a CO2 sequestration scenario by injecting CO2-SO2 gas streams into a NaCI-NaOH brine hosted in iron oxide-containing aquifer. This study provides novel information on the mineralogical changes and fluid chemistry derived from the co-injection of CO2-SO2 gas mixtures in hematite deposit. It can be concluded that the amount of siderite precipitate depends primarily on the SO2 content of the gas stream. Increasing SO2 content in the system could promote the reduction of Fe3+ from the hematite sample to Fe2+, which will be further available for its precipitation as siderite. Moreover, siderite precipitation is enhanced at low temperatures and high pressures. The influence of the solid to liquid ratio on the overall carbonation reaction suggests that the conversion increases if the system becomes more diluted. (C) 2014 Elsevier B.V. All rights reserved. C1 [Garcia, S.] CSIC, Inst Nacl Carbon, INCAR, E-33080 Oviedo, Spain. [Liu, Q.; Maroto-Valer, M. M.] Heriot Watt Univ, Sch Engn & Phys Sci, Ctr Innovat Carbon Capture & Storage, Edinburgh EH14 4AS, Midlothian, Scotland. [Bacon, D. H.] Pacific NW Natl Lab, Richland, WA 99352 USA. [Maroto-Valer, M. M.] Heriot Watt Univ, Inst Petr Engn, Edinburgh EH14 4AS, Midlothian, Scotland. RP Liu, Q (reprint author), Heriot Watt Univ, Sch Engn & Phys Sci, Ctr Innovat Carbon Capture & Storage, Edinburgh EH14 4AS, Midlothian, Scotland. EM q.liu@hw.ac.uk RI Maroto-Valer, Mercedes/F-5016-2014; OI Maroto-Valer, Mercedes/0000-0003-1643-2863; Liu, Qi/0000-0001-9074-0077 FU Centre for Innovation in Carbon Capture and Storage (CICCS) through the Engineering and Physical Sciences Research Council, EPSRC [EP/F012098/1, EP/F012098/2] FX The financial support of the Centre for Innovation in Carbon Capture and Storage (CICCS) through the Engineering and Physical Sciences Research Council, EPSRC (EP/F012098/1 and EP/F012098/2) is gratefully acknowledged. The authors would like to thank Ignacio Villar for his great help and assistance with XPS analyses. NR 34 TC 2 Z9 2 U1 3 U2 24 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0378-3820 EI 1873-7188 J9 FUEL PROCESS TECHNOL JI Fuel Process. Technol. PD DEC PY 2014 VL 128 BP 402 EP 411 DI 10.1016/j.fuproc.2014.07.027 PG 10 WC Chemistry, Applied; Energy & Fuels; Engineering, Chemical SC Chemistry; Energy & Fuels; Engineering GA AR2BZ UT WOS:000343389900047 ER PT J AU Gascon, M Samulon, EC Gundiah, G Yan, Z Khodyuk, IV Derenzo, SE Bizarri, GA Bourret-Courchesne, ED AF Gascon, M. Samulon, E. C. Gundiah, G. Yan, Z. Khodyuk, I. V. Derenzo, S. E. Bizarri, G. A. Bourret-Courchesne, E. D. TI Scintillation properties of CsBa2I5 activated with monovalent ions Tl+, Na+ and In+ SO JOURNAL OF LUMINESCENCE LA English DT Article DE Crystals; Gamma-ray detection; Activators; Cesium; Barium; Iodine ID ENERGY-RESOLUTION; INORGANIC SCINTILLATORS; NON-PROPORTIONALITY; LIGHT YIELD; CRYSTALS; EMISSION; CSI(T1) AB We have previously reported the scintillation properties of CsBa2I5 activated with Eu2+, which exhibits excellent behavior [1,2]. The presence of Cs in the lattice makes CsBa2I5 a good candidate for activation with monovalent ions. We grew single crystals of CsBa(2)l(5) with monovalent ions Tl, Na and In as activators. We performed a series of luminescence and scintillation measurements, including pulse height measurements using two different photosensors, on these crystals. We show not only that the monovalent ions are suitable activators in the chosen host lattice but also that the system has light yields between 33,000 and 40,000 ph/MeV, lower self-absorption than observed in Eu doped samples and excellent proportionality. The measured energy resolution on our initial samples of 7.1% FWHM for 662 key gamma rays using avalanche photodiodes is very promising. (C) 2014 Elsevier B.V. All rights reserved. C1 [Gascon, M.; Samulon, E. C.; Gundiah, G.; Yan, Z.; Khodyuk, I. V.; Derenzo, S. E.; Bizarri, G. A.; Bourret-Courchesne, E. D.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Gascon, M (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Cyclotron Rd, Berkeley, CA 94720 USA. EM mmgascon@lbl.gov RI Gascon, Martin/C-9440-2011 OI Gascon, Martin/0000-0002-2065-009X FU US Department of Homeland Security; Domestic Nuclear Detection Office, under competitively awarded [IAA HSHQDC-09-X-00075]; U.S. Department of Energy/ NNSA/NA22; Lawrence Berkeley National Laboratory [ACO2-05CH11231] FX The authors would like to thank Kathleen Brennan, Stephen Hanrahan, Christopher Ramsey, David Wilson and James Powell for their technical and engineering expertise. This work has been supported by the US Department of Homeland Security, Domestic Nuclear Detection Office, under competitively awarded contract/ IAA HSHQDC-09-X-00075 and by the U.S. Department of Energy/ NNSA/NA22 and carried out at Lawrence Berkeley National Laboratory under Contract no. ACO2-05CH11231. This support does not constitute an express or implied endorsement on the part of the Government. NR 27 TC 6 Z9 6 U1 4 U2 23 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0022-2313 EI 1872-7883 J9 J LUMIN JI J. Lumines. PD DEC PY 2014 VL 156 BP 63 EP 68 DI 10.1016/j.jlumin.2014.07.017 PG 6 WC Optics SC Optics GA AR1PW UT WOS:000343358100010 ER PT J AU Nguyen, SD Ryan, K Chai, P Shatruk, M Xin, Y Chapman, KW Chupas, PJ Fronczek, FR Macaluso, RT AF Nguyen, Sau Doan Ryan, Kevin Chai, Ping Shatruk, Michael Xin, Yan Chapman, Karena W. Chupas, Peter J. Fronczek, Frank R. Macaluso, Robin T. TI Pr1.33Pt4Ga10: Superstructure and magnetism SO JOURNAL OF SOLID STATE CHEMISTRY LA English DT Article DE Pr1.33Pt4Ga10; Superstructure; Intermetallic; Pair distribution function; Transmission electron microscopy; Magnetism ID CRYSTAL-STRUCTURE; GD; SUPERCONDUCTIVITY; DIFFRACTION; PHASES; RE; ALUMINIDES; TRIANGLES; BEHAVIOR; TB AB Pr1.33Pt4Ga10 crystals were prepared by Ga-flux method. The superstructure of this compound was studied by single-crystal X-ray diffraction (XRD), transmission electron microscopy (TEM), and diffuse X-ray scattering. Pr133Pt4Ga10 adopts the P6(3)/mmc space group with a = b = 4.3227(5) angstrom, c = 16.485(3) angstrom: the structure features Pr2Ga3 layers alternating with Pt2Ga4 layers along the c-axis. TEM studies and pair distribution function (PDF) analysis of X-ray total scattering data show that Pr2Ga3 layers possess an ordered superstructure (of dimension a' = a root 3) in which Pr vacancies and Ga atoms are ordered within the ab-plane but disordered along the c-direction. PDF analysis also shows temperature-dependent structural features local to the Pr3+ ion. Magnetic measurements reveal that Pr3+ ions order ferrimagnetically below 12.5(2) K. (C) 2014 Elsevier Inc. All rights reserved. C1 [Nguyen, Sau Doan; Ryan, Kevin; Macaluso, Robin T.] Univ No Colorado, Dept Chem & Biochem, Greeley, CO 80639 USA. [Chai, Ping; Shatruk, Michael] Florida State Univ, Dept Chem & Biochem, Tallahassee, FL 32306 USA. [Shatruk, Michael; Xin, Yan] Florida State Univ, Natl High Magnet Field Lab, Tallahassee, FL 32306 USA. [Chapman, Karena W.; Chupas, Peter J.] Argonne Natl Lab, XRay Sci Div, Lemont, IL 60439 USA. [Fronczek, Frank R.] Louisiana State Univ, Dept Chem, Baton Rouge, LA 70803 USA. RP Macaluso, RT (reprint author), Univ No Colorado, Dept Chem & Biochem, Greeley, CO 80639 USA. EM robin.macaluso@unco.edu FU National Science Foundation CAREER Award [DMR-1056515, DMR-0955353]; ANL [20130011]; U.S. DOE [DE-ACO2-06CH11357]; Florida State University Research Foundation; National High Magnetic Field Laboratory; National Science Foundation Cooperative Agreement [DMR-1157490]; State of Florida; U.S. Department of Energy; Florida State University FX Support of this research via the National Science Foundation CAREER Award (DMR-1056515 to R.M. and DMR-0955353 to M.S.) and ANL Project #20130011 are gratefully acknowledged. RTM and SDN also thank R. Osborn, O. J. Borkiewicz and K. A. Beyer for assistance and useful discussions. Work done at Argonne National Laboratory and the use of the Advanced Photon Source (APS) was supported by the U.S. DOE under Contract no. DE-ACO2-06CH11357. The TEM work was carried out at FSU TEM facility, which is funded and supported by the Florida State University Research Foundation, and the National High Magnetic Field Laboratory, which was supported in part by the National Science Foundation Cooperative Agreement DMR-1157490, the State of Florida, the U.S. Department of Energy, and Florida State University. NR 32 TC 1 Z9 1 U1 2 U2 20 PU ACADEMIC PRESS INC ELSEVIER SCIENCE PI SAN DIEGO PA 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA SN 0022-4596 EI 1095-726X J9 J SOLID STATE CHEM JI J. Solid State Chem. PD DEC PY 2014 VL 220 BP 9 EP 16 DI 10.1016/j.jssc.2014.07.033 PG 8 WC Chemistry, Inorganic & Nuclear; Chemistry, Physical SC Chemistry GA AR1LG UT WOS:000343346100002 ER PT J AU Aitkaliyeva, A Madden, JW Miller, BD Cole, JI AF Aitkaliyeva, A. Madden, J. W. Miller, B. D. Cole, J. I. TI Implementation of focused ion beam (FIB) system in characterization of nuclear fuels and materials SO MICRON LA English DT Article DE Focused ion beam (FIB); Nuclear materials; Contamination; Radioactivity ID TRANSMISSION ELECTRON-MICROSCOPY; TEM SPECIMEN PREPARATION; TRISO COATED PARTICLES; MIXED-OXIDE FUEL; SAMPLE PREPARATION; AGR-1 EXPERIMENT; GRAIN-GROWTH; IDENTIFICATION; DAMAGE AB Beginning in 2007, a program was established at the Idaho National Laboratory to update key capabilities enabling microstructural and micro-chemical characterization of highly irradiated and/or radiologically contaminated nuclear fuels and materials at scales that previously had not been achieved for these types of materials. Such materials typically cannot be contact handled and pose unique hazards to instrument operators, facilities, and associated personnel. Over the ensuing years, techniques have been developed and operational experience gained that has enabled significant advancement in the ability to characterize a variety of fuel types including metallic, ceramic, and coated particle fuels, obtaining insights into in-reactor degradation phenomena not achievable by any other means. The following article describes insights gained, challenges encountered, and provides examples of unique results obtained in adapting dual beam FIB technology to nuclear fuels characterization. Published by Elsevier Ltd. C1 [Aitkaliyeva, A.; Madden, J. W.; Miller, B. D.; Cole, J. I.] Idaho Natl Lab, Idaho Falls, ID 83415 USA. RP Aitkaliyeva, A (reprint author), Idaho Natl Lab, POB 1625,MS 6188, Idaho Falls, ID 83415 USA. EM assel.aitkaliyeva@inl.gov OI Aitkaliyeva, Assel/0000-0003-1481-6804; Cole, James/0000-0003-1178-5846 FU U.S. Department of Energy, under DOE Idaho Operations Office [DE-AC07-05ID14517] FX This work is supported by the U.S. Department of Energy, under DOE Idaho Operations Office Contract DE-AC07-05ID14517. Accordingly, 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. NR 25 TC 2 Z9 2 U1 4 U2 29 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0968-4328 J9 MICRON JI Micron PD DEC PY 2014 VL 67 BP 65 EP 73 DI 10.1016/j.micron.2014.06.010 PG 9 WC Microscopy SC Microscopy GA AR5RN UT WOS:000343641300007 PM 25051120 ER PT J AU Hernandez-Rivera, E Tikare, V Noirot, L Wang, LM AF Hernandez-Rivera, Efrain Tikare, Veena Noirot, Laurence Wang, Lumin TI Direct handling of sharp interfacial energy for microstructural evolution SO SCRIPTA MATERIALIA LA English DT Article DE Cahn-Hilliard; Ostwald ripening; Sharp interface; Potts Monte Carlo ID NONUNIFORM SYSTEM AB We introduce a simplification to the previously demonstrated hybrid Potts phase field (hPPF), which relates interfacial energies to microstructural sharp interfaces. The model defines interfacial energy by a Potts-like discrete interface approach of counting unlike neighbors, which we use to compute local curvature. The model is compared to the hPPF by studying interfacial characteristics and grain growth behavior. The two models give virtually identical results, while the new model allows the simulator more direct control of interfacial energy. Published by Elsevier Ltd. on behalf of Acta Materialia Inc. C1 [Hernandez-Rivera, Efrain; Wang, Lumin] Univ Michigan, Dept Nucl Engn & Radiol Sci, Ann Arbor, MI 48109 USA. [Hernandez-Rivera, Efrain; Tikare, Veena] Sandia Natl Labs, Adv Nucl Energy Programs Dept, Albuquerque, NM 87185 USA. [Noirot, Laurence] CEA, DEN, DEC, F-13108 St Paul Les Durance, France. RP Tikare, V (reprint author), Sandia Natl Labs, Adv Nucl Energy Programs Dept, POB 5800, Albuquerque, NM 87185 USA. EM vtikare@sandia.gov FU U.S. Department of Energy's National Nuclear Security Administration [DE-AC04-94AL85000] FX Sandia National Laboratories is a multi-rogram 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 11 TC 0 Z9 0 U1 0 U2 4 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 1359-6462 J9 SCRIPTA MATER JI Scr. Mater. PD DEC 1 PY 2014 VL 92 BP 11 EP 14 DI 10.1016/j.scriptamat.2014.07.018 PG 4 WC Nanoscience & Nanotechnology; Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering SC Science & Technology - Other Topics; Materials Science; Metallurgy & Metallurgical Engineering GA AR5KQ UT WOS:000343624100004 ER PT J AU Wang, L Lind, J Phukan, H Kenesei, P Park, JS Suter, RM Beaudoin, AJ Bider, TR AF Wang, L. Lind, J. Phukan, H. Kenesei, P. Park, J. -S. Suter, R. M. Beaudoin, A. J. Bider, T. R. TI Mechanical twinning and detwinning in pure Ti during loading and unloading - An in situ high-energy X-ray diffraction microscopy study SO SCRIPTA MATERIALIA LA English DT Article DE High-energy X-ray diffraction microscopy; Titanium; In situ mechanical testing; Twinning; Detwinning ID INDIVIDUAL GRAINS; STRAIN TENSOR; SINGLE-GRAIN; DEFORMATION; NUCLEATION; MAGNESIUM; METALS; ALLOY AB Far-field high-energy X-ray diffraction microscopy (HEDM) was used to study {10 (1) over bar2} ((1) over bar 011) twinning in Ti. Twin nucleation within a bulk parent grain is observed at a resolved shear stress (RSS) of 225 MPa. During unloading, the RSS on the twin plane reversed sign, providing a driving force for detwinning. Formation of the twin, however, prevented the parent grain from returning to its original stress state even after complete unloading. The twin morphology and surrounding environment were examined using near-field HEDM. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved. C1 [Wang, L.] Helmholtz Zentrum Geesthacht, Inst Mat Res, D-21502 Geesthacht, Germany. [Lind, J.; Suter, R. M.] Carnegie Mellon Univ, Dept Phys, Pittsburgh, PA 15213 USA. [Phukan, H.; Bider, T. R.] Michigan State Univ, E Lansing, MI 48824 USA. [Kenesei, P.; Park, J. -S.] Argonne Natl Lab, Adv Photon Source, Argonne, IL 60439 USA. [Beaudoin, A. J.] Univ Illinois, Dept Mech Sci & Engn, Urbana, IL USA. [Lind, J.] Lawrence Livermore Natl Lab, Livermore, CA USA. [Wang, L.] Argonne Natl Lab, Nucl Engn Div, Argonne, IL 60439 USA. RP Wang, L (reprint author), Helmholtz Zentrum Geesthacht, Inst Mat Res, Max Planck Str 1, D-21502 Geesthacht, Germany. EM wly857@gmail.com RI Suter, Robert/P-2541-2014 OI Suter, Robert/0000-0002-0651-0437 FU NSF at Michigan State University [DMR-1108211, DMR-0710570]; U.S. Department of Energy [DESC0002001]; [DE-AC02-06CH11357] FX This work was supported by NSF grants DMR-1108211 and DMR-0710570 at Michigan State University. Work at Carnegie Mellon University was supported by U.S. Department of Energy grant DESC0002001. Use of the APS was made possible under contract number DE-AC02-06CH11357. NR 31 TC 10 Z9 10 U1 6 U2 38 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 1359-6462 J9 SCRIPTA MATER JI Scr. Mater. PD DEC 1 PY 2014 VL 92 BP 35 EP 38 DI 10.1016/j.scriptamat.2014.08.008 PG 4 WC Nanoscience & Nanotechnology; Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering SC Science & Technology - Other Topics; Materials Science; Metallurgy & Metallurgical Engineering GA AR5KQ UT WOS:000343624100010 ER PT J AU Wang, JW Zhang, FX Zhang, JM Ewing, RC Becker, U Cai, ZH AF Wang, Jianwei Zhang, Fuxiang Zhang, Jiaming Ewing, Rodney C. Becker, Udo Cai, Zhonghou TI Carbonate orientational order and superlattice structure in vaterite SO JOURNAL OF CRYSTAL GROWTH LA English DT Article DE Order and disorder; X-ray diffraction; Transmission electron microscopy; Vaterite; Calcium carbonate ID AMORPHOUS CALCIUM-CARBONATE; RAMAN-SPECTROSCOPY; CRYSTALLIZATION; ARAGONITE; PEARLS; CACO3; DISORDER; SPECTRA AB Vaterite is considered to play an important role as a precursor phase in the formation of calcium carbonate phases, including those related to biomineralization. An accurate description of vaterite's structure associated with the order of carbonate groups is essential to understanding the formation, stabilization, and functionality of vaterite in organisms. Molecular dynamics simulations, synchrotron X-ray diffraction, and transmission electron microscopy have been combined in order to investigate the structure of vaterite. The electrostatic interactions between Ca and neighboring CO3 groups promote local and long-range ordering of CO3 groups, which may result in a superstructure of vaterite. Molecular dynamics simulations show that the superstructure (06(5)22) with ordered carbonate ions has a relatively lower energy than the disordered structure. The kinetics of the disorder-to-order transition suggests that the transition is rapid and that the superstructure is expected to form. X-ray diffraction data confirm the presence of the P6(5)22 superstructure. The measured diffraction peaks are consistent with the calculated diffraction peaks, especially those weak peaks predicted as a result of the superstructure. Transmission electron microscopy also reveals minor satellite electron diffraction peaks with the more intense peaks of the primary pattern, suggesting a superlattice structure resulted from ordering in both crystallographic oh plan and c direction, which is consistent with the proposed superstructure. (C) 2014 Elsevier B.V. All rights reserved. C1 [Wang, Jianwei] Louisiana State Univ, Dept Geol & Geophys, Ctr Computat & Technol, Baton Rouge, LA 70803 USA. [Zhang, Fuxiang; Becker, Udo] Univ Michigan, Dept Earth & Environm Sci, Ann Arbor, MI 48109 USA. [Zhang, Jiaming; Ewing, Rodney C.] Stanford Univ, Dept Geol & Environm Sci, Stanford, CA 94305 USA. [Cai, Zhonghou] Argonne Natl Lab, Adv Photon Source, Argonne, IL 60439 USA. RP Wang, JW (reprint author), Louisiana State Univ, Dept Geol & Geophys, E235 Howe Russell Bldg, Baton Rouge, LA 70803 USA. EM jianwei@lsu.edu RI Becker, Udo /F-7339-2011; Zhang, Fuxiang/P-7365-2015 OI Becker, Udo /0000-0002-1550-0484; Zhang, Fuxiang/0000-0003-1298-9795 FU National Energy Research Scientific Computing Center (NERSC); XSEDE resources [TG-DMR080047N, TG-DMR100034]; U.S. Department of Energy, Office of Science, Basic Energy Sciences [DE-AC02-06CH11357] FX The computational simulations were supported by the National Energy Research Scientific Computing Center (NERSC) and XSEDE resources under grant TG-DMR080047N and TG-DMR100034. Use of the Advanced Photon Source was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. Data were collected on the X-ray Operations and Research beamline 2-ID-D at the Advanced Photon Source, Argonne National Laboratory. NR 37 TC 4 Z9 4 U1 5 U2 52 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0022-0248 EI 1873-5002 J9 J CRYST GROWTH JI J. Cryst. Growth PD DEC 1 PY 2014 VL 407 BP 78 EP 86 DI 10.1016/j.jcrysgro.2014.08.028 PG 9 WC Crystallography; Materials Science, Multidisciplinary; Physics, Applied SC Crystallography; Materials Science; Physics GA AQ8QG UT WOS:000343093500015 ER PT J AU Dumbser, M Zanotti, O Loubere, R Diot, S AF Dumbser, Michael Zanotti, Olindo Loubere, Raphael Diot, Steven TI A posteriori subcell limiting of the discontinuous Galerkin finite element method for hyperbolic conservation laws SO JOURNAL OF COMPUTATIONAL PHYSICS LA English DT Article DE Arbitrary high-order discontinuous Galerkin schemes; A posteriori subcell finite volume limiter; MOOD paradigm; ADER-DG; ADER-WENO; High performance computing (HPC); Hyperbolic conservation laws ID HERMITE WENO SCHEMES; ESSENTIALLY NONOSCILLATORY SCHEMES; ADAPTIVE MESH REFINEMENT; SHOCK-CAPTURING SCHEMES; TIME-DEPENDENT DOMAINS; HLLC RIEMANN SOLVER; DYNAMIC GRID MOTION; HIGH-ORDER SCHEMES; UNSTRUCTURED MESHES; VOLUME SCHEMES AB The purpose of this work is to propose a novel a posteriori finite volume subcell limiter technique for the Discontinuous Galerkin finite element method for nonlinear systems of hyperbolic conservation laws in multiple space dimensions that works well for arbitrary high order of accuracy in space and time and that does not destroy the natural subcell resolution properties of the DG method. High order time discretization is achieved via a one-step ADER approach that uses a local space-time discontinuous Galerkin predictor method to evolve the data locally in time within each cell. Our new limiting strategy is based on the so-called MOOD paradigm, which a posteriori verifies the validity of a discrete candidate solution against physical and numerical detection criteria after each time step. Here, we employ a relaxed discrete maximum principle in the sense of piecewise polynomials and the positivity of the numerical solution as detection criteria. Within the DG scheme on the main grid, the discrete solution is represented by piecewise polynomials of degree N. For those troubled cells that need limiting, our new limiter approach recomputes the discrete solution by scattering the DG polynomials at the previous time step onto a set of N-s = 2N + 1 finite volume subcells per space dimension. A robust but accurate ADER-WENO finite volume scheme then updates the subcell averages of the conservative variables within the detected troubled cells. The recomputed subcell averages are subsequently gathered back into high order cell-centered DG polynomials on the main grid via a subgrid reconstruction operator. The choice of N-s = 2N + 1 subcells is optimal since it allows to match the maximum admissible time step of the finite volume scheme on the subgrid with the maximum admissible time step of the DG scheme on the main grid, minimizing at the same time also the local truncation error of the subcell finite volume scheme. It furthermore provides an excellent subcell resolution of discontinuities. Our new approach is therefore radically different from classical DG limiters, where the limiter is using TVB or (H)WENO reconstruction based on the discrete solution of the DG scheme on the main grid at the new time level. In our case, the discrete solution is recomputed within the troubled cells from the old time level using a different and more robust numerical scheme on a subgrid level. We illustrate the performance of the new a posteriori subcell ADER-WENO finite volume limiter approach for very high order DG methods via the simulation of numerous test cases run on Cartesian grids in two and three space dimensions, using DG schemes of up to tenth order of accuracy in space and time (N = 9). The method is also able to run on massively parallel large scale supercomputing infrastructure, which is shown via one 3D test problem that uses 10 billion space-time degrees of freedom per time step. (C) 2014 Elsevier Inc. All rights reserved. C1 [Dumbser, Michael; Zanotti, Olindo] Univ Trento, Dept Civil Environm & Mech Engn, I-38123 Trento, Italy. [Loubere, Raphael] Univ Toulouse 3, CNRS, F-31062 Toulouse, France. [Loubere, Raphael] Univ Toulouse 3, IMT, F-31062 Toulouse, France. [Diot, Steven] Los Alamos Natl Lab, Fluid Dynam & Solid Mech T 3, Los Alamos, NM 87545 USA. RP Dumbser, M (reprint author), Univ Trento, Dept Civil Environm & Mech Engn, Via Mesiano 77, I-38123 Trento, Italy. EM michael.dumbser@unitn.it; olindo.zanotti@unitn.it; raphael.loubere@math.univ-toulouse.fr; diot@lanl.gov RI Dumbser, Michael/F-2740-2010; OI Dumbser, Michael/0000-0002-8201-8372 FU European Research Council (ERC) under the European Union [278267]; ANR under the JCJC project "ALE INC(ubator) 3D" [ANR-JS01-012-01] FX M.D. and O.Z. have been financed by the European Research Council (ERC) under the European Union's Seventh Framework Programme (FP7/2007-2013) with the research project STiMulUs, ERC Grant agreement no. 278267. R. L. has been partially funded by the ANR under the JCJC project "ALE INC(ubator) 3D", Grand no. ANR-JS01-012-01. This work has been authorized for publication under the reference LA-UR-14-24778. NR 117 TC 41 Z9 41 U1 7 U2 23 PU ACADEMIC PRESS INC ELSEVIER SCIENCE PI SAN DIEGO PA 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA SN 0021-9991 EI 1090-2716 J9 J COMPUT PHYS JI J. Comput. Phys. PD DEC 1 PY 2014 VL 278 BP 47 EP 75 DI 10.1016/j.jcp.2014.08.009 PG 29 WC Computer Science, Interdisciplinary Applications; Physics, Mathematical SC Computer Science; Physics GA AQ4FS UT WOS:000342749300003 ER PT J AU Mlynczak, J Sawicz-Kryniger, K Fry, AR Glownia, JM Leemans, S AF Mlynczak, J. Sawicz-Kryniger, K. Fry, A. R. Glownia, J. M. Leemans, S. TI Practical application of cross correlation technique to measure jitter of master-oscillator-power-amplifier (MOPA) laser system SO OPTO-ELECTRONICS REVIEW LA English DT Article DE jitter; cross-correlation; laser amplifier; pump-and-probe technique ID PROBE TECHNIQUE; WAVELENGTH AB The Linac coherent light source (LCLS) at the SLAC National Accelerator Laboratory (SLAC) is the world's first hard X-ray free electron laser (XFEL) and is capable of producing high-energy, femtosecond duration X-ray pulses. A common technique to study fast timescale physical phenomena, various "pump/probe" techniques are used. In these techniques there are two lasers, one optical and one X-ray, that work as a pump and as a probe to study dynamic processes in atoms and molecules. In order to resolve phenomena that occur on femtosecond timescales, it is imperative to have very precise timing between the optical lasers and X-rays (on the order of similar to 20 fs or better). The lasers are synchronized to the same RF source that drives the accelerator and produces the X-ray laser. However, elements in the lasers cause some drift and time jitter, thereby de-synchronizing the system. This paper considers cross-correlation technique as a way to quantify the drift and jitter caused by the regenerative amplifier of the ultrafast optical laser. C1 [Mlynczak, J.] Mil Univ Technol, Inst Optoelect, PL-00908 Warsaw, Poland. [Sawicz-Kryniger, K.] Univ Technol, Dept Chem Engn & Technol, PL-31155 Krakow, Poland. [Fry, A. R.; Glownia, J. M.] Natl Accelerator Lab, Stanford Linear Accelerator Ctr, Menlo Pk, CA 94025 USA. [Leemans, S.] Univ Calif Santa Cruz, Santa Cruz, CA 95064 USA. RP Mlynczak, J (reprint author), Mil Univ Technol, Inst Optoelect, 2 Kaliskiego Str, PL-00908 Warsaw, Poland. EM jmlynczak@wat.edu.pl RI Mlynczak, Jaroslaw/E-1725-2013; OI Mlynczak, Jaroslaw/0000-0002-0823-9302 FU Polish Ministry of Science and Higher Education; European Union FX The work was made possible by the program "Top 500 Innovators" sponsored by the Polish Ministry of Science and Higher Education and by the European Union. NR 16 TC 0 Z9 0 U1 0 U2 9 PU WALTER DE GRUYTER GMBH PI BERLIN PA GENTHINER STRASSE 13, D-10785 BERLIN, GERMANY SN 1230-3402 EI 1896-3757 J9 OPTO-ELECTRON REV JI Opto-Electron. Rev. PD DEC PY 2014 VL 22 IS 4 BP 218 EP 223 DI 10.2478/s11772-014-0200-4 PG 6 WC Engineering, Electrical & Electronic; Optics; Physics, Applied SC Engineering; Optics; Physics GA AQ1PX UT WOS:000342554400003 ER PT J AU Kesler, M Kisacikoglu, MC Tolbert, LM AF Kesler, Metin Kisacikoglu, Mithat C. Tolbert, Leon M. TI Vehicle-to-Grid Reactive Power Operation Using Plug-In Electric Vehicle Bidirectional Offboard Charger SO IEEE TRANSACTIONS ON INDUSTRIAL ELECTRONICS LA English DT Article DE Battery charger; electric vehicle (EV); reactive power; vehicle to grid (V2G) ID BATTERY CHARGER AB The number of offboard fast charging stations is increasing as plug-in electric vehicles (PEVs) are more widespread in the world. Additional features on the operation of chargers will result in more benefits for investors, utility companies, and PEV owners. This paper investigates reactive power support operation using offboard PEV charging stations while charging a PEV battery. The topology consists of a three-phase ac-dc boost rectifier that is capable of operating in all four quadrants. The operation modes that are of interest are power-factor-corrected charging operation, and charging and capacitive/inductive reactive power operation. This paper also presents a control system for the PQ command following of a bidirectional offboard charger. The controller only receives the charging power command from a user and the reactive power command (when needed) from a utility, and it adjusts the line current and the battery charging current correspondingly. The vehicle's battery is not affected during the reactive power operation. A simulation study is developed utilizing PSIM, and the control system is experimentally tested using a 12.5-kVA charging station design. C1 [Kesler, Metin] Bilecik Seyh Edebali Univ, Dept Comp Engn, TR-11210 Bilecik, Turkey. [Kisacikoglu, Mithat C.] Hacettepe Univ, Coll Engn, Dept Elect & Elect Engn, TR-06800 Ankara, Turkey. [Tolbert, Leon M.] Univ Tennessee, Coll Engn, Dept Elect Engn & Comp Sci, Knoxville, TN 37996 USA. [Tolbert, Leon M.] Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. RP Kesler, M (reprint author), Bilecik Seyh Edebali Univ, Dept Comp Engn, TR-11210 Bilecik, Turkey. EM metin.kesler@bilecik.edu.tr; mkisacik@hacettepe.edu.tr; tolbert@utk.edu OI Tolbert, Leon/0000-0002-7285-609X FU Engineering Research Center Program of the National Science Foundation (NSF); Department of Energy under NSF Award [EEC-1041877]; Center for Ultra-Wide-Area Resilient Electric Energy Transmission Networks (CURENT) Industry Partnership Program; Scientific and Technological Research Council of Turkey (TUBITAK) [BIDEB 2219, BIDEB 2232] FX This work was supported in part by the Engineering Research Center Program of the National Science Foundation (NSF) and the Department of Energy under NSF Award EEC-1041877, in part by the Center for Ultra-Wide-Area Resilient Electric Energy Transmission Networks (CURENT) Industry Partnership Program, and in part by the Scientific and Technological Research Council of Turkey (TUBITAK) under Award Program BIDEB 2219 and Award Program BIDEB 2232. NR 29 TC 26 Z9 26 U1 3 U2 33 PU IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC PI PISCATAWAY PA 445 HOES LANE, PISCATAWAY, NJ 08855-4141 USA SN 0278-0046 EI 1557-9948 J9 IEEE T IND ELECTRON JI IEEE Trans. Ind. Electron. PD DEC PY 2014 VL 61 IS 12 BP 6778 EP 6784 DI 10.1109/TIE.2014.2314065 PG 7 WC Automation & Control Systems; Engineering, Electrical & Electronic; Instruments & Instrumentation SC Automation & Control Systems; Engineering; Instruments & Instrumentation GA AP7UQ UT WOS:000342282900031 ER PT J AU Ramasamy, KK Zhang, H Sun, JM Wang, Y AF Ramasamy, Karthikeyan K. Zhang, He Sun, Junming Wang, Yong TI Conversion of ethanol to hydrocarbons on hierarchical HZSM-5 zeolites SO CATALYSIS TODAY LA English DT Article; Proceedings Paper CT 7th World Congress on Oxidation Catalysis, with the theme From Fundamentals to Applications CY JUN 09-13, 2013 CL Washington Univ, St Louis, MO SP Clariant, BASF, shell, BP, Langmuir Res Inst, UoP, Agilent Technol, Mettler Toledo, Anonymous Donor, Sabic HO Washington Univ DE HZSM-5; Hierarchical zeolite; Ethanol to hydrocarbon; Coke deposition; Improved catalyst life-time ID COKE FORMATION; METHANOL; CATALYST; MFI; TRANSFORMATION; MESOPOROSITY; DEACTIVATION; NANOZEOLITES AB This study reports synthesis, characterization, and catalytic activity of the nano-size hierarchical HZSM-5 zeolite with high mesoporosity produced via a solvent evaporation procedure. Further, this study compares hierarchical zeolites with conventional HZSM-5 zeolite with similar Si/Al ratios for the ethanol-to-hydrocarbon conversion process. The catalytic performance of the hierarchical and conventional zeolites was evaluated using a fixed-bed reactor at 360 degrees C, 300 psig, and a weight hourly space velocity of 7.9 h(-1). For the low Si/Al ratio zeolite (similar to 40), the catalytic life-time for the hierarchical HZSM-5 was approximately 2 times greater than the conventional HZSM-5 despite its coking amount deposited 1.6 times higher than conventional HZSM-5. For the high Si/Al ratio zeolite (similar to 140), the catalytic life-time for the hierarchical zeolite was approximately 5 times greater than the conventional zeolite and the amount of coking deposited was 2.1 times higher. Correlation was observed between catalyst life time, porosity, and the crystal size of the zeolite. The nano-size hierarchical HZSM-5 zeolites containing mesoporosity demonstrated improved catalyst life-time compared to the conventional catalyst due to faster removal of products, shorter diffusion path length, and the migration of the coke deposits to the external surface from the pore structure. (C) 2014 Elsevier B.V. All rights reserved. C1 [Ramasamy, Karthikeyan K.; Wang, Yong] Pacific NW Natl Lab, Inst Integrated Catalysis, Richland, WA 99354 USA. [Ramasamy, Karthikeyan K.; Zhang, He; Sun, Junming; Wang, Yong] Washington State Univ, Voiland Sch Chem Engn & Bioengn, Pullman, WA 99163 USA. EM karthi@pnnl.gov RI Sun, Junming/B-3019-2011; Ramasamy, karthikeyan/H-9981-2014 OI Sun, Junming/0000-0002-0071-9635; FU Pacific Northwest National Laboratory's Laboratory Directed Research and Development Funding; U.S. Department of Energy [DE-AC05 - 76RL01830] FX This work was supported by the Pacific Northwest National Laboratory's Laboratory Directed Research and Development Funding. Pacific Northwest National Laboratory is operated by Battelle Memorial Institute for the U.S. Department of Energy under Contract No. DE-AC05 - 76RL01830. NR 37 TC 21 Z9 22 U1 6 U2 77 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0920-5861 EI 1873-4308 J9 CATAL TODAY JI Catal. Today PD DEC PY 2014 VL 238 BP 103 EP 110 DI 10.1016/j.cattod.2014.01.037 PG 8 WC Chemistry, Applied; Chemistry, Physical; Engineering, Chemical SC Chemistry; Engineering GA AP2BY UT WOS:000341878600015 ER PT J AU King, WE Barth, HD Castillo, VM Gallegos, GF Gibbs, JW Hahn, DE Kamath, C Rubenchik, AM AF King, Wayne E. Barth, Holly D. Castillo, Victor M. Gallegos, Gilbert F. Gibbs, John W. Hahn, Douglas E. Kamath, Chandrika Rubenchik, Alexander M. TI Observation of keyhole-mode laser melting in laser powder-bed fusion additive manufacturing SO JOURNAL OF MATERIALS PROCESSING TECHNOLOGY LA English DT Article DE Keyhole-mode laser melting; Additive manufacturing; Powder-bed fusion; Selective laser sintering; Selective laser melting; Direct metal laser sintering ID STAINLESS-STEEL AB Laser powder-bed fusion additive manufacturing of metals employs high-power focused laser beams. Typically, the depth of the molten pool is controlled by conduction of heat in the underlying solid material. But, under certain conditions, the mechanism of melting can change from conduction to so-called "keyhole-mode" laser melting. In this mode, the depth of the molten pool is controlled by evaporation of the metal. Keyhole-mode laser melting results in melt pool depths that can be much deeper than observed in conduction mode. In addition, the collapse of the vapor cavity that is formed by the evaporation of the metal can result in a trail of voids in the wake of the laser beam. In this paper, the experimental observation of keyhole-mode laser melting in a laser powder-bed fusion additive manufacturing setting for 316L stainless steel is presented. The conditions required to transition from conduction controlled melting to keyhole-mode melting are identified. (c) 2014 Elsevier B.V. All rights reserved. C1 [King, Wayne E.; Gibbs, John W.] Lawrence Livermore Natl Lab, Phys & Life Sci Directorate, Livermore, CA 94550 USA. [Barth, Holly D.; Castillo, Victor M.; Gallegos, Gilbert F.; Hahn, Douglas E.] Lawrence Livermore Natl Lab, Engn Directorate, Livermore, CA 94550 USA. [Gibbs, John W.] Northwestern Univ, Dept Mat Sci & Engn, Evanston, IL 60208 USA. [Kamath, Chandrika] Lawrence Livermore Natl Lab, Computat Directorate, Livermore, CA 94550 USA. [Rubenchik, Alexander M.] Lawrence Livermore Natl Lab, NIF, Livermore, CA 94550 USA. [Rubenchik, Alexander M.] Lawrence Livermore Natl Lab, Photon Sci Directorate, Livermore, CA 94550 USA. RP King, WE (reprint author), Lawrence Livermore Natl Lab, Phys & Life Sci Directorate, Livermore, CA 94550 USA. EM weking@llnl.gov OI King, Wayne/0000-0002-5060-5484; Gibbs, John/0000-0002-0231-1318 FU Stewardship Science Graduate Fellowship - DOE/NNSA [DE-FC52-08NA28752]; U.S. Department of Energy by Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Laboratory Directed Research and Development Program at LLNL [13-SI-002]; Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy [DE-AC02-05CH11231] FX JWG would like to thank the Stewardship Science Graduate Fellowship, funded by DOE/NNSA under grant number DE-FC52-08NA28752.; This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. This work was funded by the Laboratory Directed Research and Development Program at LLNL under project tracking code 13-SI-002. 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 19 TC 40 Z9 40 U1 26 U2 142 PU ELSEVIER SCIENCE SA PI LAUSANNE PA PO BOX 564, 1001 LAUSANNE, SWITZERLAND SN 0924-0136 J9 J MATER PROCESS TECH JI J. Mater. Process. Technol. PD DEC PY 2014 VL 214 IS 12 BP 2915 EP 2925 DI 10.1016/j.jmatprotec.2014.06.005 PG 11 WC Engineering, Industrial; Engineering, Manufacturing; Materials Science, Multidisciplinary SC Engineering; Materials Science GA AP7GJ UT WOS:000342245500011 ER PT J AU Sudasinghe, N Cort, JR Hallen, R Olarte, M Schmidt, A Schaub, T AF Sudasinghe, Nilusha Cort, John R. Hallen, Richard Olarte, Mariefel Schmidt, Andrew Schaub, Tanner TI Hydrothermal liquefaction oil and hydrotreated product from pine feedstock characterized by heteronuclear two-dimensional NMR spectroscopy and FT-ICR mass spectrometry SO FUEL LA English DT Article DE FT-ICR MS; Pine; Hydrothermal liquefaction; Hydrotreatment; NMR ID ION-CYCLOTRON-RESONANCE; COMPOSITIONALLY DISTINCT COMPONENTS; FIELD DESORPTION IONIZATION; FAST PYROLYSIS OIL; ELECTROSPRAY-IONIZATION; NEGATIVE-ION; BIO-OIL; FULVIC-ACIDS; CRUDE-OIL; ELEMENTAL COMPOSITIONS AB Hydrothermal liquefaction (HTL) oil and hydrotreated product from pine tree farm waste (forest product residual, FPR) have been analyzed by direct infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) in both positive-and negative-ionization modes and high-resolution two-dimensional heteronuclear H-1-C-13 NMR spectroscopy. FT-ICR MS resolves thousands of compounds in complex oils and provides unparalleled compositional details for individual molecules for identification of compound class (heteroatom content), type (number of rings plus double bonds to carbon or double bond equivalents (DBE) and carbon number (degree of alkylation). Heteronuclear H-1-C-13 NMR spectroscopy provides one-bond and multiple-bond correlations between pairs of H-1 and C-13 chemical shifts that are characteristic of different organic functional groups. Taken together this information provides a picture of the chemical composition of these oils. Pyrolysis crude oil product from pine wood was characterized for comparison. Generally, pyrolysis oil is comprised of a more diverse distribution of heteroatom classes with higher oxygen number relative to HTL oil as shown by both positive-and negative-ion ESI FT-ICR MS. A total of 300 N-1, 594 O-1 and 267 O-2 compounds were observed as products of hydrotreatment. The relative abundance of N1O1, N1O2, N1O3, N-2, N2O1, N2O2 and O-3 compounds are reduced to different degrees after hydrotreatment and other higher heteroatom containing species (O-4-O-10, N1O4, N1O5 and N2O3) are completely removed by hydrotreatment. (C) 2014 Elsevier Ltd. All rights reserved. C1 [Sudasinghe, Nilusha; Schaub, Tanner] New Mexico State Univ, Coll Agr Consumer & Environm Sci, Chem Anal & Instrumentat Lab, Las Cruces, NM 88003 USA. [Cort, John R.] Pacific NW Natl Lab, Div Biol Sci, Richland, WA 99352 USA. [Hallen, Richard; Olarte, Mariefel; Schmidt, Andrew] Pacific NW Natl Lab, Chem & Biol Proc Dev Grp, Richland, WA 99352 USA. RP Schaub, T (reprint author), New Mexico State Univ, Coll Agr Consumer & Environm Sci, Chem Anal & Instrumentat Lab, 945 Coll Ave, Las Cruces, NM 88003 USA. EM tschaub@nmsu.edu RI Olarte, Mariefel/D-3217-2013 OI Olarte, Mariefel/0000-0003-2989-1110 FU U.S. Department of Energy's Office of Energy Efficiency and Renewable Energy (Bioenergy Technologies Office); United States National Science Foundation [IIA-1301346]; Center for Animal Health and Food Safety at New Mexico State University FX This work was supported by the U.S. Department of Energy's Office of Energy Efficiency and Renewable Energy (Bioenergy Technologies Office), the United States National Science Foundation (IIA-1301346) and the Center for Animal Health and Food Safety at New Mexico State University. NR 44 TC 13 Z9 14 U1 5 U2 58 PU ELSEVIER SCI LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND SN 0016-2361 EI 1873-7153 J9 FUEL JI Fuel PD DEC 1 PY 2014 VL 137 BP 60 EP 69 DI 10.1016/j.fuel.2014.07.069 PG 10 WC Energy & Fuels; Engineering, Chemical SC Energy & Fuels; Engineering GA AO4JL UT WOS:000341303300008 ER PT J AU Liang, L Schwartz, MD Wang, ZS Gao, F Schaaf, CB Tan, B Morisette, JT Zhang, XY AF Liang, Liang Schwartz, Mark D. Wang, Zhuosen Gao, Feng Schaaf, Crystal B. Tan, Bin Morisette, Jeffrey T. Zhang, Xiaoyang TI A Cross Comparison of Spatiotemporally Enhanced Springtime Phenological Measurements From Satellites and Ground in a Northern U.S. Mixed Forest SO IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING LA English DT Article DE Daily Moderate Resolution Imaging Spectroradiometer (MODIS); Earth Observing System (EOS) land validation core sites; landscape phenology (LP); land surface phenology (LSP); phenology; Spatial and Temporal Adaptive Reflectance Fusion Model (STARFM) ID DECIDUOUS BROADLEAF FOREST; LAND-SURFACE PHENOLOGY; IMAGING SPECTRORADIOMETER MODIS; REFLECTANCE FUSION MODEL; LEAF-AREA INDEX; VEGETATION PHENOLOGY; CANOPY PHENOLOGY; TEMPORAL RESOLUTION; NEAR-SURFACE; DYNAMICS AB Cross comparison of satellite-derived land surface phenology (LSP) and ground measurements is useful to ensure the relevance of detected seasonal vegetation change to the underlying biophysical processes. While standard 16-day and 250-m Moderate Resolution Imaging Spectroradiometer (MODIS) vegetation index (VI)-based springtime LSP has been evaluated in previous studies, it remains unclear whether LSP with enhanced temporal and spatial resolutions can capture additional details of ground phenology. In this paper, we compared LSP derived from 500-m daily MODIS and 30-m MODIS-Landsat fused VI data with landscape phenology (LP) in a northern U. S. mixed forest. LP was previously developed from intensively observed deciduous and coniferous tree phenology using an upscaling approach. Results showed that daily MODIS-based LSP consistently estimated greenup onset dates at the study area (625 m x 625 m) level with 4.48 days of mean absolute error (MAE), slightly better than that of using 16-day standard VI (4.63 days MAE). For the observed study areas, the time series with increased number of observations confirmed that post-bud burst deciduous tree phenology contributes the most to vegetation reflectance change. Moreover, fused VI time series demonstrated closer correspondences with LP at the community level (0.1-20 ha) than using MODIS alone at the study area level (390 ha). The fused LSP captured greenup onset dates for respective forest communities of varied sizes and compositions with four days of the overall MAE. This study supports further use of spatiotemporally enhanced LSP for more precise phenological monitoring. C1 [Liang, Liang] Univ Kentucky, Dept Geog, Lexington, KY 40506 USA. [Schwartz, Mark D.] Univ Wisconsin, Dept Geog, Milwaukee, WI 53201 USA. [Wang, Zhuosen; Schaaf, Crystal B.] Univ Massachusetts, Sch Environm, Boston, MA 02125 USA. [Wang, Zhuosen] NASA, Terr Informat Syst Lab, Goddard Space Flight Ctr, Greenbelt, MD 20771 USA. [Wang, Zhuosen] Oak Ridge Associated Univ, NASA, Postdoctoral Program, Oak Ridge, TN 37831 USA. [Gao, Feng] ARS, Hydrol & Remote Sensing Lab, USDA, Beltsville, MD 20705 USA. [Tan, Bin] NASA, Goddard Space Flight Ctr, Sigma Space Corp, Greenbelt, MD 20771 USA. [Morisette, Jeffrey T.] Colorado State Univ, North Cent Climate Sci Ctr, US Geol Survey, Ft Collins, CO 80525 USA. [Zhang, Xiaoyang] S Dakota State Univ, Geospatial Sci Ctr Excellence, Brookings, SD 57007 USA. RP Liang, L (reprint author), Univ Kentucky, Dept Geog, Lexington, KY 40506 USA. EM liang.liang@uky.edu FU National Science Foundation [BCS-0649380, BCS-0703360]; National Aeronautics and Space Administration [NNX12AL38G] FX This work was supported in part by the National Science Foundation under Grant BCS-0649380 and Grant BCS-0703360 and in part by the National Aeronautics and Space Administration under Grant NNX12AL38G. NR 70 TC 8 Z9 8 U1 8 U2 58 PU IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC PI PISCATAWAY PA 445 HOES LANE, PISCATAWAY, NJ 08855-4141 USA SN 0196-2892 EI 1558-0644 J9 IEEE T GEOSCI REMOTE JI IEEE Trans. Geosci. Remote Sensing PD DEC PY 2014 VL 52 IS 12 BP 7513 EP 7526 DI 10.1109/TGRS.2014.2313558 PG 14 WC Geochemistry & Geophysics; Engineering, Electrical & Electronic; Remote Sensing; Imaging Science & Photographic Technology SC Geochemistry & Geophysics; Engineering; Remote Sensing; Imaging Science & Photographic Technology GA AO7KM UT WOS:000341532100004 ER PT J AU Galletti, M Zrnic, DS Gekat, F Goelz, P AF Galletti, Michele Zrnic, Dusan S. Gekat, Frank Goelz, Peter TI Eigenvalue Signal Processing for Weather Radar Polarimetry: Removing the Bias Induced by Antenna Coherent Cross-Channel Coupling SO IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING LA English DT Article DE Antenna radiation pattern; coherency matrix; copolar radiation pattern; covariance matrix; cross-channel coupling; cross-polar correlation coefficient; cross-polar radiation pattern; degree of polarization at horizontal transmit; eigenvalues; linear depolarization ratio; polarimetric phased array weather radar ID SCATTERING MATRIX; POLARIZATION; RADIATION AB We present a novel digital signal processing procedure, named eigenvalue signal pocessing (henceforth ESP), patented by the first author with Brookhaven Science Associates in 2013. The method enables the removal of the bias due to antenna coherent cross-channel coupling and is applicable in the LDR mode, the ATSR mode and the STSR orthogonal mode of weather radar measurements. In this paper, we focus on the LDR mode and consider copolar reflectivity at horizontal transmit (Z(HH)), cross-polar reflectivity at horizontal transmit (Z(VH)), linear depolarization ratio at horizontal transmit (LDRH) and degree of polarization at horizontal transmit (DOPH). The ESP (ESP) method is substantiated by an experiment carried out in November 2012 using C-band weather radar with a parabolic reflector located at the Selex ES-Gematronik facilities in Neuss, Germany. The experiment involved comparison of weather radar measurements taken 1.5 minutes apart in two hardware configurations, namely with cross-coupling on (cc-on) and cross-coupling off (cc-off). It is experimentally demonstrated that eigenvalue-derived variables are invariant with respect to antenna coherent cross-channel coupling. This property had to be expected, since the eigenvalues of the Coherency matrix are SU(2) invariant. C1 [Galletti, Michele] Brookhaven Natl Lab, US Dept Energy, Environm & Climate Sci Dept, Upton, NY 11973 USA. [Zrnic, Dusan S.] NOAA, Natl Severe Storms Lab, Norman, OK 73072 USA. [Gekat, Frank; Goelz, Peter] Selex ES GmbH, D-41470 Neuss, Germany. RP Galletti, M (reprint author), Brookhaven Natl Lab, US Dept Energy, Environm & Climate Sci Dept, Upton, NY 11973 USA. EM mgalletti@bnl.gov NR 32 TC 6 Z9 6 U1 1 U2 36 PU IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC PI PISCATAWAY PA 445 HOES LANE, PISCATAWAY, NJ 08855-4141 USA SN 0196-2892 EI 1558-0644 J9 IEEE T GEOSCI REMOTE JI IEEE Trans. Geosci. Remote Sensing PD DEC PY 2014 VL 52 IS 12 BP 7695 EP 7707 DI 10.1109/TGRS.2014.2316821 PG 13 WC Geochemistry & Geophysics; Engineering, Electrical & Electronic; Remote Sensing; Imaging Science & Photographic Technology SC Geochemistry & Geophysics; Engineering; Remote Sensing; Imaging Science & Photographic Technology GA AO7KM UT WOS:000341532100019 ER PT J AU Vanhille, C Campos-Pozuelo, C Sinha, DN AF Vanhille, Christian Campos-Pozuelo, Cleofe Sinha, Dipen N. TI Nonlinear frequency mixing in a resonant cavity: Numerical simulations in a bubbly liquid SO ULTRASONICS LA English DT Article DE Nonlinear frequency mixing; Bubbly liquids; Standing waves; Numerical simulations; Nonlinear acoustics ID PARAMETRIC ACOUSTIC ARRAY; GENERATION; WAVES AB The study of nonlinear frequency mixing for acoustic standing waves in a resonator cavity is presented. Two high frequencies are mixed in a highly nonlinear bubbly liquid filled cavity that is resonant at the difference frequency. The analysis is carried out through numerical experiments, and both linear and nonlinear regimes are compared. The results show highly efficient generation of the difference frequency at high excitation amplitude. The large acoustic nonlinearity of the bubbly liquid that is responsible for the strong difference-frequency resonance also induces significant enhancement of the parametric frequency mixing effect to generate second harmonic of the difference frequency. (C) 2014 Elsevier B.V. All rights reserved. C1 [Vanhille, Christian] Univ Rey Juan Carlos, Madrid 28933, Spain. [Campos-Pozuelo, Cleofe] CSIC, E-28006 Madrid, Spain. [Sinha, Dipen N.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Vanhille, C (reprint author), Univ Rey Juan Carlos, Tulipan S-N, Madrid 28933, Spain. EM christian.vanhille@urjc.es; ccampos@ia.cetef.csic.es; sinha@lanl.gov FU Los Alamos National Laboratory; [DPI2012-34613] FX This work is funded by the research project DPI2012-34613 (Spain) and also supported by the Los Alamos National Laboratory. NR 19 TC 3 Z9 3 U1 1 U2 24 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0041-624X EI 1874-9968 J9 ULTRASONICS JI Ultrasonics PD DEC PY 2014 VL 54 IS 8 BP 2051 EP 2054 DI 10.1016/j.ultras.2014.07.004 PG 4 WC Acoustics; Radiology, Nuclear Medicine & Medical Imaging SC Acoustics; Radiology, Nuclear Medicine & Medical Imaging GA AO2GT UT WOS:000341136700001 PM 25064635 ER PT J AU Eroglu, D Ha, S Gallagher, KG AF Eroglu, Damla Ha, Seungbum Gallagher, Kevin G. TI Fraction of the theoretical specific energy achieved on pack level for hypothetical battery chemistries SO JOURNAL OF POWER SOURCES LA English DT Article DE Beyond lithium-ion; Lithium-ion; Battery design; System analysis; Specific energy; Energy density ID LITHIUM-SULFUR BATTERIES; AIR; ELECTROLYTE; PROMISE; STORAGE AB In valuing new active materials chemistries for advanced batteries, the theoretical specific energy is commonly used to motivate research and development. A packaging factor is then used to relate the theoretical specific energy to the pack-level specific energy. As this factor is typically assumed constant, higher theoretical specific energies are judged to result in higher pack-level specific energies. To test this implicit assumption, we calculated the fraction of the theoretical specific energy achieved on the pack level for hypothetical cell chemistries with various open-circuit voltages and theoretical specific energies using a peer-review bottom-up battery design model. The pack-level specific energy shows significant dependence on the open-circuit voltage and electrochemical impedance due to changes in the quantity of inactive materials required. At low-valued average open-circuit voltages, systems with dramatically different theoretical specific energies may result in battery packs similar in mass and volume. The fraction of the theoretical specific energy achieved on the pack level is higher for the lower theoretical specific energy systems mainly because the active materials mass dominates the pack mass. Finally, low-valued area-specific impedance is shown to be critical for chemistries of high theoretical specific energy and low open-circuit voltage to achieve higher pack-level specific energies. (C) 2014 Elsevier B.V. All rights reserved. C1 [Eroglu, Damla; Ha, Seungbum; Gallagher, Kevin G.] Argonne Natl Lab, Joint Ctr Energy Storage Res, Argonne, IL 60439 USA. [Eroglu, Damla; Ha, Seungbum; Gallagher, Kevin G.] Argonne Natl Lab, Chem Sci & Engn Div, Argonne, IL 60439 USA. RP Eroglu, D (reprint author), Argonne Natl Lab, Chem Sci & Engn Div, 9700 S Cass Ave,Bldg 200, Argonne, IL 60439 USA. EM eroglud@anl.gov FU Joint Center for Energy Storage Research, an Energy Innovation Hub - U.S. Department of Energy, Office of Science, Basic Energy Sciences; U.S. Department of Energy Office of Science laboratory [DE-AC02-06CH11357] FX This work was supported as part of the Joint Center for Energy Storage Research, an Energy Innovation Hub funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences. The submitted manuscript has been created by UChicago Argonne, LLC, Operator of Argonne National Laboratory ("Argonne"). Argonne, an U.S. Department of Energy Office of Science laboratory, is operated under Contract No. DE-AC02-06CH11357. NR 25 TC 6 Z9 6 U1 5 U2 115 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0378-7753 EI 1873-2755 J9 J POWER SOURCES JI J. Power Sources PD DEC 1 PY 2014 VL 267 BP 14 EP 19 DI 10.1016/j.jpowsour.2014.05.071 PG 6 WC Chemistry, Physical; Electrochemistry; Energy & Fuels; Materials Science, Multidisciplinary SC Chemistry; Electrochemistry; Energy & Fuels; Materials Science GA AM1JI UT WOS:000339601800003 ER PT J AU Baggetto, L Hah, HY Jumas, JC Johnson, CE Johnson, JA Keum, JK Bridges, CA Veith, GM AF Baggetto, Loic Hah, Hien-Yoong Jumas, Jean-Claude Johnson, Charles E. Johnson, Jacqueline A. Keum, Jong K. Bridges, Craig A. Veith, Gabriel M. TI The reaction mechanism of SnSb and Sb thin film anodes for Na-ion batteries studied by X-ray diffraction, Sn-119 and Sb-121 Mossbauer spectroscopies SO JOURNAL OF POWER SOURCES LA English DT Article DE Sodium ion anode; Tin antimony (SnSb); Antimony (Sb); X-ray diffraction (XRD); Sn-119 Mossbauer spectroscopy; Sb-121 Mossbauer spectroscopy ID LI-ION; ELECTRODE MATERIALS; SODIUM; INSERTION; TIN; SPECTRA; SYSTEM AB The electrochemical reaction of Sb and SnSb anodes with Na results in the formation of amorphous materials. To understand the resulting phases and electrochemical capacities we studied the local order using Sn-119 and Sb-121 Mossbauer spectroscopies in conjunction with measurements performed on model powder compounds of Na-Sn and Na Sb to further clarify the reactions steps. For pure Sb the sodiation starts with the formation of an amorphous phase composed of atomic environments similar to those found in NaSb, and proceeds further by the formation of crystalline Na3Sb. The reversible reaction takes place during a large portion of the charge process. At full charge the anode material still contains a substantial fraction of Na, explaining the lack of recrystallization into crystalline Sb. The reaction of SnSb yields Na3Sb at full discharge at higher temperatures (65 and 95 degrees C) while the RT reaction yields amorphous compounds. The electrochemically-driven, solid-state amorphization reaction occurring at RI is governed by the simultaneous formation of Na-coordinated Sn and Sb environments, as monitored by the decrease (increase) of the (119)sn No) Mossbauer isomer shifts. Overall, the monitoring of the hyperfine parameters enables to correlate changes in Na content to the local chemical environments. (C) 2014 Elsevier B.V. All rights reserved. C1 [Baggetto, Loic; Veith, Gabriel M.] Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. [Hah, Hien-Yoong; Johnson, Charles E.] Univ Tennessee, Inst Space, Ctr Laser Applicat, Tullahoma, TN 37388 USA. [Hah, Hien-Yoong; Johnson, Jacqueline A.] Univ Tennessee, Inst Space, Dept Mech Aeronaut & Biomed Engn, Tullahoma, TN 37388 USA. [Jumas, Jean-Claude] Univ Montpellier 2, Inst Charles Gerhardt, F-34095 Montpellier 5, France. [Keum, Jong K.] Oak Ridge Natl Lab, Spallat Neutron Source, Neutron Sci Directorate, Oak Ridge, TN 37831 USA. [Bridges, Craig A.] Oak Ridge Natl Lab, Div Chem Sci, Oak Ridge, TN 37831 USA. RP Baggetto, L (reprint author), Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. EM loic_baggetto@yahoo.fr; veithgm@ornl.gov RI Johnson, Jacqueline/P-4844-2014; Baggetto, Loic/D-5542-2017; Keum, Jong/N-4412-2015 OI Johnson, Jacqueline/0000-0003-0830-9275; Baggetto, Loic/0000-0002-9029-2363; Keum, Jong/0000-0002-5529-1373 FU U.S. Department of Energy (DOE); Basic Energy Sciences (BES; Materials Sciences and Engineering Division; ORNL's Shared Research Equipment (ShaRE) User Program; Center for Laser Applications; University of Tennessee Space Institute in relation FX This work was supported by the U.S. Department of Energy (DOE), Basic Energy Sciences (BES), Materials Sciences and Engineering Division (LB, GMV). Microscopy research was supported via a user project supported by ORNL's Shared Research Equipment (ShaRE) User Program, which is also supported by DOE-BES. HYH, CEJ, JAJ would like to acknowledge the support of the Center for Laser Applications and the University of Tennessee Space Institute in relation with 121Sb Mossbauer spectroscopy measurements. Xi. gratefully acknowledges Region Languedoc-Roussillon (France) for the financial support to the "X-rays and gamma-rays platform" of Universite Montpellier II in relation with 119Sn Mossbauer spectroscopy experiments. NR 25 TC 32 Z9 32 U1 26 U2 231 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0378-7753 EI 1873-2755 J9 J POWER SOURCES JI J. Power Sources PD DEC 1 PY 2014 VL 267 BP 329 EP 336 DI 10.1016/j.jpowsour.2014.05.083 PG 8 WC Chemistry, Physical; Electrochemistry; Energy & Fuels; Materials Science, Multidisciplinary SC Chemistry; Electrochemistry; Energy & Fuels; Materials Science GA AM1JI UT WOS:000339601800041 ER PT J AU Dufek, EJ Stone, ML Jamison, DK Stewart, FF Gering, KL Petkovic, LM Wilson, AD Harrup, MK Rollins, HW AF Dufek, Eric J. Stone, Mark L. Jamison, David K. Stewart, Frederick F. Gering, Kevin L. Petkovic, Lucia M. Wilson, Aaron D. Harrup, Mason K. Rollins, Harry W. TI Hybrid phosphazene anodes for energy storage applications SO JOURNAL OF POWER SOURCES LA English DT Article DE Phosphazene; Anode; Battery; Hybrid system; Lithium ion battery ID SOLID POLYMER ELECTROLYTES; LITHIUM-ION BATTERIES; ACCELERATING RATE CALORIMETRY; TRIPHENYL PHOSPHATE; INTERCALATED GRAPHITE; INORGANIC POLYMER; THERMAL-STABILITY; CATHODE MATERIAL; ELECTRODES; CELLS AB The use of hybrid cyclic phosphazene polymer/graphite anodes, where the phosphazene serves as distributed loci for Li deposition, has been investigated. Capacity within the hybrid system was found to occur reversibly in distinct regions. At the most positive voltages, above 0.06 V vs Li/Li+, the capacity was associated mostly with Li+ intercalation into graphite. In the most negative region, deposition of Li within the polymer was the predominate mechanism. A transitional region is inferred by the data whereby bulk aggregation or clustering of Li atoms occurs in proximity to the phosphazene sites that then serve as a template for more widespread population of Li within the anode at higher voltages, akin to a nucleation process. In full cells with a mixed oxide cathode, controlling the extent of Li deposition by limiting the charging voltage to 4.45 V enabled repeated cycling with no loss in capacity. Capacities as high as 183 mAh g(-1) have been achieved for systems containing as little as 10% graphite while retaining coulombic efficiencies of 98% over 50 cycles. This level of cycling equates to the deposition of 7.4 Li per cyclic phosphazene. (C) 2014 Elsevier B.V. All rights reserved. C1 [Dufek, Eric J.; Stone, Mark L.; Jamison, David K.; Stewart, Frederick F.; Gering, Kevin L.; Petkovic, Lucia M.; Wilson, Aaron D.; Harrup, Mason K.; Rollins, Harry W.] Idaho Natl Lab, Idaho Falls, ID 83415 USA. RP Dufek, EJ (reprint author), Idaho Natl Lab, POB 1625, Idaho Falls, ID 83415 USA. EM eric.dufek@inl.gov RI Wilson, Aaron/C-4364-2008; Rollins, Harry/B-6327-2017; Dufek, Eric/B-8847-2017 OI Wilson, Aaron/0000-0001-5865-6537; Rollins, Harry/0000-0002-3926-7445; Dufek, Eric/0000-0003-4802-1997 FU Vehicle Technologies Office of the Energy Efficiency and Renewable Energy Office of the U.S. Department of Energy; Battelle Energy Alliance, LLC [DE-AC07-05ID14517]; U.S. Department of Energy FX The authors would like to thank Dr. Sergiy Sazhin for helpful discussion during the preparation of this manuscript. Funding was provided from Vehicle Technologies Office of the Energy Efficiency and Renewable Energy Office of the U.S. Department of Energy under the guidance of the Advanced Battery Research (ABR) program. 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 39 TC 3 Z9 3 U1 6 U2 65 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0378-7753 EI 1873-2755 J9 J POWER SOURCES JI J. Power Sources PD DEC 1 PY 2014 VL 267 BP 347 EP 355 DI 10.1016/j.jpowsour.2014.05.105 PG 9 WC Chemistry, Physical; Electrochemistry; Energy & Fuels; Materials Science, Multidisciplinary SC Chemistry; Electrochemistry; Energy & Fuels; Materials Science GA AM1JI UT WOS:000339601800043 ER PT J AU Kamp, SD Morrison, SJ AF Kamp, Susan D. Morrison, Stan J. TI Use of Chemical and Isotopic Signatures to Distinguish Between Uranium Mill-Related and Naturally Occurring Groundwater Constituents SO GROUND WATER MONITORING AND REMEDIATION LA English DT Article ID WATER AB Chemical and isotopic signatures were determined in groundwater samples to aid in distinguishing the source of contamination in three desert arroyos and a buried channel (the swale) near Shiprock, New Mexico. The contamination in the swale and one of the arroyos, Many Devils Wash, was previously attributed to a former uranium mill site because of the similar suite of contaminants (nitrate, selenium, sulfate, and uranium) and the close (0.8 km) proximity. The other two arroyos are far removed from the mill site and could not have received contamination from it. Principal component and cluster analysis indicated similarities in groundwater chemistry among the swale and the three arroyos that contrasted with groundwater chemistry at the disposal cell. Disposal cell groundwater is characterized by high uranium and bicarbonate concentrations, whereas that in remaining study areas is characterized by high sodium and sulfate, but lower uranium concentrations. Mancos Shale forms the bedrock in the region and contains elevated concentrations of the same chemical constituents that appear in the swale and arroyo groundwater. Dissolved sulfate in arroyo groundwater was depleted in sulfur-34, in contrast to mill-derived sulfate with more enriched sulfur-34. Uranium-234 to uranium-238 activity ratios (ARs) were near the secular equilibrium value of 1 in mill site groundwater, whereas ARs in all arroyo groundwater samples exceeded 2. Elevated tritium activities present in mill site groundwater (49 to 142 pCi/L) are attributed to the mill being operated during atomic bomb testing in the 1950s and 1960s. The combined chemical and isotopic results indicate that groundwater in Many Devils Wash and the swale was likely derived from the Mancos Shale and not from the milling operation. C1 [Kamp, Susan D.; Morrison, Stan J.] US DOE, Off Legacy Management, Grand Junction, CO 81503 USA. RP Kamp, SD (reprint author), US DOE, Off Legacy Management, Grand Junction, CO 81503 USA. EM Susan.Kamp@lm.doe.gov FU U.S. Department of Energy (DOE) Office of Legacy Management FX The study was funded by the U.S. Department of Energy (DOE) Office of Legacy Management; we thank Richard P. Bush, Program Manager, for his continued support of these efforts. We also thank Aaron Tigar and Craig Goodknight (both at S. M. Stoller) for field assistance, and Dave Peterson (S. M. Stoller) for his review and insights into Mancos hydrology and chemistry. We acknowledge Steve Austin of the Navajo Nation Environmental Protection Agency for providing information and insight on several of the seeps and discussions of regional groundwater conditions. Finally, the manuscript was greatly improved by the efforts of two anonymous reviewers. NR 26 TC 1 Z9 1 U1 2 U2 163 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 1069-3629 EI 1745-6592 J9 GROUND WATER MONIT R JI Ground Water Monit. Remediat. PD WIN PY 2014 VL 34 IS 1 BP 68 EP 78 DI 10.1111/gwmr.12042 PG 11 WC Water Resources SC Water Resources GA AB2IU UT WOS:000331617200023 ER PT J AU Bartholomay, RC Twining, BV Rose, PE AF Bartholomay, Roy C. Twining, Brian V. Rose, Peter E. TI Ambient Changes in Tracer Concentrations from a Multilevel Monitoring System in Basalt SO GROUND WATER MONITORING AND REMEDIATION LA English DT Article ID FRACTURED ROCK; TRANSPORT AB Starting in 2008, a 4-year tracer study was conducted to evaluate ambient changes in groundwater concentrations of a 1,3,6-naphthalene trisulfonate tracer that was added to drill water. Samples were collected under open borehole conditions and after installing a multilevel groundwater monitoring system completed with 11 discrete monitoring zones within dense and fractured basalt and sediment layers in the eastern Snake River aquifer. The study was done in cooperation with the U.S. Department of Energy to test whether ambient fracture flow conditions were sufficient to remove the effects of injected drill water prior to sample collection. Results from thief samples indicated that the tracer was present in minor concentrations 28 days after coring, but was not present 6 months after coring or 7 days after reaming the borehole. Results from sampling the multilevel monitoring system indicated that small concentrations of the tracer remained in 5 of 10 zones during some period after installation. All concentrations were several orders of magnitude lower than the initial concentrations in the drill water. The ports that had remnant concentrations of the tracer were either located near sediment layers or were located in dense basalt, which suggests limited groundwater flow near these ports. The ports completed in well-fractured and vesicular basalt had no detectable concentrations. C1 [Bartholomay, Roy C.; Twining, Brian V.] US Geol Survey, Idaho Natl Lab, Project Off, Idaho Falls, ID 83415 USA. [Rose, Peter E.] Univ Utah, Energy & Geosci Inst, Salt Lake City, UT 84108 USA. RP Bartholomay, RC (reprint author), US Geol Survey, Idaho Natl Lab, Project Off, 1955 N Fremont Ave, Idaho Falls, ID 83415 USA. EM rcbarth@usgs.gov; btwining@usgs.gov; prose@egi.utah.edu FU U.S. Department of Energy FX This study was supported by funding provided by the U.S. Department of Energy. Appreciation is extended to Jayson Blom, Betty Tucker, and Neil Maimer of the USGS for their assistance with sampling. The authors also thank the reviewers of the paper for their comments and suggestions to improve the manuscript. NR 25 TC 0 Z9 0 U1 0 U2 63 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 1069-3629 EI 1745-6592 J9 GROUND WATER MONIT R JI Ground Water Monit. Remediat. PD WIN PY 2014 VL 34 IS 1 BP 79 EP 88 DI 10.1111/gwmr.12038 PG 10 WC Water Resources SC Water Resources GA AB2IU UT WOS:000331617200024 ER PT J AU Seref, O Fan, YJ Chaovalitwongse, WA AF Seref, Onur Fan, Ya-Ju Chaovalitwongse, Wanpracha Art TI Mathematical Programming Formulations and Algorithms for Discrete k-Median Clustering of Time-Series Data SO INFORMS JOURNAL ON COMPUTING LA English DT Article DE clustering; optimization; discrete k-median; mixed-integer programming; uncoupled bilinear program algorithm; sequential optimization; time series ID ABNORMAL BRAIN ACTIVITY; LOCATION-PROBLEMS; HUB LOCATION; CLASSIFICATION AB Discrete k-median (DKM) clustering problems arise in many real-life applications that involve time-series data sets, in which nondiscrete clustering methods may not represent the problem domain adequately. In this study, we propose mathematical programming formulations and solution methods to efficiently solve the DKM clustering problem. We develop approximation algorithms from a bilinear formulation of the discrete k-median problem using an uncoupled bilinear program algorithm. This approximation algorithm, which we refer to as DKM-L, is composed of two alternating linear programs, where one can be solved in linear time and the other is a minimum cost assignment problem. We then modify this algorithm by replacing the assignment problem with an efficient sequential algorithm for a faster approximation, which we call DKM-S. We also propose a compact exact integer formulation, DKM-I, and a more efficient network design-based exact mixed-integer formulation, DKM-M. All of our methods use arbitrary pairwise distance matrices as input. We apply our methods to simulated single-variate and multivariate random walk time-series data. We report comparative clustering performances using normalized mutual information (NMI) and solution speeds among the DKM methods we propose. We also compare our methods to other clustering algorithms that can operate with distance matrices, such as hierarchical cluster trees (HCT) and partition around medoids (PAM). We present NMI scores and classification accuracies of our DKM algorithms compared to HCT and PAM using five different distance measures on simluated data, as well as public benchmark and real-life neural time-series data sets. We show that DKM-S is much faster than HCT, PAM, and all other DKM methods and produces consistently good clustering results on all data sets. C1 [Seref, Onur] Virginia Polytech Inst & State Univ, Dept Business Informat Technol, Blacksburg, VA 24061 USA. [Fan, Ya-Ju] Lawrence Livermore Natl Lab, Livermore, CA 94551 USA. [Chaovalitwongse, Wanpracha Art] Univ Washington, Dept Ind & Syst Engn, Seattle, WA 98195 USA. [Chaovalitwongse, Wanpracha Art] Univ Washington, Dept Radiol, Seattle, WA 98195 USA. RP Seref, O (reprint author), Virginia Polytech Inst & State Univ, Dept Business Informat Technol, Blacksburg, VA 24061 USA. EM seref@vt.edu; fan4@llnl.gov; artchao@uw.edu FU National Science Foundation under CAREER [0546574] FX This work was supported by the National Science Foundation under CAREER [Grant 0546574]. NR 31 TC 4 Z9 4 U1 3 U2 122 PU INFORMS PI CATONSVILLE PA 5521 RESEARCH PARK DR, SUITE 200, CATONSVILLE, MD 21228 USA SN 1091-9856 EI 1526-5528 J9 INFORMS J COMPUT JI INFORMS J. Comput. PD WIN PY 2014 VL 26 IS 1 BP 160 EP 172 DI 10.1287/ijoc.2013.0554 PG 13 WC Computer Science, Interdisciplinary Applications; Operations Research & Management Science SC Computer Science; Operations Research & Management Science GA AA4SJ UT WOS:000331086100012 ER PT J AU Larson, JK Carvan, MJ Teeguarden, JG Watanabe, G Taya, K Krystofiak, E Hutz, RJ AF Larson, Jeremy K. Carvan, Michael J., III Teeguarden, Justin G. Watanabe, Gen Taya, Kazuyoshi Krystofiak, Evan Hutz, Reinhold J. TI Low-dose gold nanoparticles exert subtle endocrine-modulating effects on the ovarian steroidogenic pathway ex vivo independent of oxidative stress SO NANOTOXICOLOGY LA English DT Article DE nanotoxicology; genomics ID IN-VITRO; DISRUPTING CHEMICALS; GRANULOSA-CELLS; TOXICITY; INHIBIN; MODEL; GENERATION; APOPTOSIS; EXPOSURE; MICE AB Gold nanoparticles (GNPs) have gained considerable attention for application in science and industry. However, the untoward effects of such particles on female fertility remain unclear. The objectives of this study were to (1) examine the effects of 10-nm GNPs on progesterone and estradiol-17 beta accumulation by rat ovaries ex vivo and (2) to identify the locus/loci whereby GNPs modulate steroidogenesis via multiple-reference gene quantitative real-time RT-PCR. Regression analyses indicated a positive relationship between both Star (p < 0.05, r(2) = 0.278) and Cyp11a1 (p < 0.001, r(2) = 0.366) expression and P4 accumulation upon exposure to 1.43 x 10(6) GNPs/mL. Additional analyses showed that E2 accumulation was positively associated with Hsd3b1 (p < 0.05, r(2) = 0.181) and Cyp17a1 (p < 0.01, r(2) = 0.301) expression upon exposure to 1.43 x 1(3) and 1.43 x 10(9) GNPs/mL, respectively. These results suggest a subtle treatment-dependent impact of low-dose GNPs on the relationship between progesterone or estradiol-17 beta and specific steroidogenic target genes, independent of oxidative stress or inhibin. C1 [Larson, Jeremy K.; Carvan, Michael J., III; Krystofiak, Evan; Hutz, Reinhold J.] Univ Wisconsin, Milwaukee, WI 53211 USA. [Larson, Jeremy K.; Carvan, Michael J., III; Hutz, Reinhold J.] NIEHS Childrens Environm Hlth Sci Core Ctr, Childrens Res Inst, Milwaukee, WI 53211 USA. [Carvan, Michael J., III] Univ Wisconsin, Sch Freshwater Sci, Milwaukee, WI 53211 USA. [Teeguarden, Justin G.] Pacific NW Natl Lab, Richland, WA 99352 USA. [Watanabe, Gen; Taya, Kazuyoshi] Tokyo Univ Agr & Technol, Vet Physiol Lab, Tokyo, Japan. RP Hutz, RJ (reprint author), Univ Wisconsin, 1921 E Hartford Ave, Milwaukee, WI 53211 USA. EM rjhutz@uwm.edu RI Geracitano, Laura/E-6926-2013; Watanabe, Gen/G-1134-2013; OI Watanabe, Gen/0000-0001-7611-4678; Teeguarden, Justin/0000-0003-3817-4391; Carvan, Michael/0000-0002-9190-9417 FU Children's Environmental Health Sciences Core Center at the University of Wisconsin-Milwaukee and Children's Research Institute [NIEHS P30 ES004184 PRJ32IR] FX We thank R. Klaper for allowing our use of the Malvern Zetasizer Nano Z, Q. Liu for his assistance with molecular techniques, and D. Arndt for acquisition of the SEM micrographs. We express sincere gratitude to J. Ghorai and P. Dunn for their advice on statistical analyses. We thank H. Owen for his advice on imaging strategies. We thank M. Gajdardziska-Josifovska, M. Schofield and D. Robertson for their collaborative acquisition of high-resolution TEM micrographs. We also thank M. Engelhard of the Environmental Molecular Sciences Laboratory (EMSL) at Pacific Northwest National Laboratory, for characterizing our GNPs via X-ray photoelectron spectroscopy. This research was supported by the Children's Environmental Health Sciences Core Center at the University of Wisconsin-Milwaukee and Children's Research Institute (NIEHS P30 ES004184 PRJ32IR). NR 44 TC 2 Z9 2 U1 2 U2 359 PU INFORMA HEALTHCARE PI NEW YORK PA 52 VANDERBILT AVE, NEW YORK, NY 10017 USA SN 1743-5390 EI 1743-5404 J9 NANOTOXICOLOGY JI Nanotoxicology PD DEC PY 2014 VL 8 IS 8 BP 856 EP 866 DI 10.3109/17435390.2013.837208 PG 11 WC Nanoscience & Nanotechnology; Toxicology SC Science & Technology - Other Topics; Toxicology GA 267XF UT WOS:000328131000005 PM 23992423 ER PT J AU Rider, WJ AF Rider, William J. TI Reconsidering remap methods SO INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS LA English DT Article DE polynomial reconstruction; stability analysis; dissipation; dispersion; limiters ID FLUX-CORRECTED TRANSPORT; CONSERVATIVE DIFFERENCE SCHEME; PIECEWISE PARABOLIC METHOD; ESSENTIALLY NONOSCILLATORY SCHEMES; HIGH-RESOLUTION SCHEMES; HIGH-ORDER; UNSTRUCTURED MESHES; FINITE-VOLUME; LOCAL STENCIL; LAWS AB Methods for discretizing remap are often based on algorithms developed for hyperbolic conservation laws. Because its introduction in 1977 Van Leer's monotonicity-preserving piecewise linear method and its extensions have been ubiquitous in remap Van Leer's fourth paper in his series Towards the Ultimate. In that 1977 paper, Van Leer introduced another five algorithms, which largely have not been used for remap despite the observation that the piecewise linear method had the least favorable theoretical properties. This adoption parallels the algorithmic choices in other related fields. Two factors have led to the lack of attraction to the five algorithms: the simplicity and effectiveness of the piecewise linear method and complications in practical implementation of the other methods. Plainly stated, Van Leer's piecewise linear method enabled ALE methods to move forward by providing a high-resolution, monotonicity-preserving remap. As a cell-centered scheme, the extension to remap was straightforward. Several factors may be conspiring to reconsider these methods anew: computing architectures are more favorable toward more floating point intensive methods, methods lacking data movement, and 30years of experience in devising nonlinear stability mechanisms (i.e., limiters). In particular, one of the methods blends characteristics of finite volume and finite difference methods together in an ingenious manner that has exceptional numerical properties and should be considered as a viable alternative to the ubiquitous piecewise linear method. Published 2014. This article is a U.S. Government work and is in the public domain in the USA. C1 [Rider, William J.] Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Rider, WJ (reprint author), Sandia Natl Labs, Dept 1446, Mail Stop 1323, Albuquerque, NM 87185 USA. EM wjrider@sandia.gov FU Army Research Laboratory; LDRD/ESRF FX This work was supported by the Army Research Laboratory and LDRD/ESRF. NR 61 TC 0 Z9 0 U1 0 U2 4 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 0271-2091 EI 1097-0363 J9 INT J NUMER METH FL JI Int. J. Numer. Methods Fluids PD NOV 30 PY 2014 VL 76 IS 9 BP 587 EP 610 DI 10.1002/fld.3950 PG 24 WC Computer Science, Interdisciplinary Applications; Mathematics, Interdisciplinary Applications; Mechanics; Physics, Fluids & Plasmas SC Computer Science; Mathematics; Mechanics; Physics GA AQ8BM UT WOS:000343046600003 ER PT J AU Schwender, J Konig, C Klapperstuck, M Heinzel, N Munz, E Hebbelmann, I Hay, JO Denolf, P De Bodt, S Redestig, H Caestecker, E Jakob, PM Borisjuk, L Rolletschek, H AF Schwender, Joerg Koenig, Christina Klapperstueck, Matthias Heinzel, Nicolas Munz, Eberhard Hebbelmann, Inga Hay, Jordan O. Denolf, Peter De Bodt, Stefanie Redestig, Henning Caestecker, Evelyne Jakob, Peter M. Borisjuk, Ljudmilla Rolletschek, Hardy TI Transcript abundance on its own cannot be used to infer fluxes in central metabolism SO FRONTIERS IN PLANT SCIENCE LA English DT Article DE Brassica napus; C-13-metabolic flux analysis; flux balance analysis; central metabolism; targeted metabolite profiling; lipid biosynthesis; oilseeds ID HETEROTROPHIC ARABIDOPSIS CELLS; CENTRAL CARBON METABOLISM; GENE-EXPRESSION DATA; BRASSICA-NAPUS; RNA-SEQ; SACCHAROMYCES-CEREVISIAE; DEVELOPING OILSEEDS; MAIZE KERNELS; EMBRYOS; SEED AB An attempt has been made to define the extent to which metabolic flux in central plant metabolism is reflected by changes in the transcriptome and metabolome, based on an analysis of in vitro cultured immature embryos of two oilseed rape (Brassica napus) accessions which contrast for seed lipid accumulation. Metabolic flux analysis (MFA) was used to constrain a flux balance metabolic model which included 671 biochemical and transport reactions within the central metabolism. This highly confident flux information was eventually used for comparative analysis of flux vs. transcript (metabolite). Metabolite profiling succeeded in identifying 79 intermediates within the central metabolism, some of which differed quantitatively between the two accessions and displayed a significant shift corresponding to flux. An RNA-Seq based transcriptome analysis revealed a large number of genes which were differentially transcribed in the two accessions, including some enzymes/proteins active in major metabolic pathways. With a few exceptions, differential activity in the major pathways (glycolysis, TCA cycle, amino acid, and fatty acid synthesis) was not reflected in contrasting abundances of the relevant transcripts. The conclusion was that transcript abundance on its own cannot be used to infer metabolic activity/fluxes in central plant metabolism. This limitation needs to be borne in mind in evaluating transcriptome data and designing metabolic engineering experiments. C1 [Schwender, Joerg; Hebbelmann, Inga; Hay, Jordan O.] Brookhaven Natl Lab, Dept Environm & Climate Sci, Upton, NY 11973 USA. [Koenig, Christina; Klapperstueck, Matthias; Heinzel, Nicolas; Munz, Eberhard; Borisjuk, Ljudmilla; Rolletschek, Hardy] Leibniz Inst Pflanzengenet & Kulturpflanzenforch, D-06466 Gatersleben, Germany. [Munz, Eberhard; Jakob, Peter M.] Univ Wurzburg, Inst Expt Phys 5, D-97070 Wurzburg, Germany. [Denolf, Peter; De Bodt, Stefanie; Redestig, Henning; Caestecker, Evelyne] Bayer Crop Sci NV, Trait Res, Zwijnaarde, Belgium. RP Rolletschek, H (reprint author), Leibniz Inst Pflanzengenet & Kulturpflanzenforch, Corrensstr 3, D-06466 Gatersleben, Germany. EM rollet@ipk-gatersleben.de RI Schwender, Jorg/P-2282-2014; OI Schwender, Jorg/0000-0003-1350-4171; Redestig, Henning/0000-0003-2130-9288; Jakob, Peter/0000-0002-3481-5545; Munz, Eberhard/0000-0002-4994-3304 FU Bayer Crop Science NV; Deutsche Forschungsgemeinschaft [BO-1917/4-1]; U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division [DEACO298CH10886] FX We thank Steffen Wagner and Sabine Herrmann for excellent technical assistance. This research was financially supported by the Bayer Crop Science NV and the Deutsche Forschungsgemeinschaft (BO-1917/4-1). This material (plant culture, in vitro embryo culture, biochemical analysis, 13C-Metabolic Flux Analysis, computational modeling of metabolism, data analysis and interpretation that was performed by Jorg Schwender, Jordan 0. Hay and Inga Hebbelmann) is based on work supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division under contract number DEACO298CH10886. NR 51 TC 13 Z9 13 U1 0 U2 27 PU FRONTIERS RESEARCH FOUNDATION PI LAUSANNE PA PO BOX 110, LAUSANNE, 1015, SWITZERLAND SN 1664-462X J9 FRONT PLANT SCI JI Front. Plant Sci. PD NOV 28 PY 2014 VL 5 AR 668 DI 10.3389/fpls.2014.00668 PG 16 WC Plant Sciences SC Plant Sciences GA AY0ZZ UT WOS:000347324500001 PM 25506350 ER PT J AU Ridley, DA Solomon, S Barnes, JE Burlakov, VD Deshler, T Dolgii, SI Herber, AB Nagai, T Neely, RR Nevzorov, AV Ritter, C Sakai, T Santer, BD Sato, M Schmidt, A Uchino, O Vernier, JP AF Ridley, D. A. Solomon, S. Barnes, J. E. Burlakov, V. D. Deshler, T. Dolgii, S. I. Herber, A. B. Nagai, T. Neely, R. R., III Nevzorov, A. V. Ritter, C. Sakai, T. Santer, B. D. Sato, M. Schmidt, A. Uchino, O. Vernier, J. P. TI Total volcanic stratospheric aerosol optical depths and implications for global climate change SO GEOPHYSICAL RESEARCH LETTERS LA English DT Article DE volcanic aerosol; forcing uncertainty; warming hiatus; AERONET retrieval; lower stratospheric AOD; stratospheric aerosol ID SIZE DISTRIBUTION MEASUREMENTS AB Understanding the cooling effect of recent volcanoes is of particular interest in the context of the post-2000 slowing of the rate of global warming. Satellite observations of aerosol optical depth above 15km have demonstrated that small-magnitude volcanic eruptions substantially perturb incoming solar radiation. Here we use lidar, Aerosol Robotic Network, and balloon-borne observations to provide evidence that currently available satellite databases neglect substantial amounts of volcanic aerosol between the tropopause and 15km at middle to high latitudes and therefore underestimate total radiative forcing resulting from the recent eruptions. Incorporating these estimates into a simple climate model, we determine the global volcanic aerosol forcing since 2000 to be -0.190.09Wm(-2). This translates into an estimated global cooling of 0.05 to 0.12 degrees C. We conclude that recent volcanic events are responsible for more post-2000 cooling than is implied by satellite databases that neglect volcanic aerosol effects below 15km. C1 [Ridley, D. A.] MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA. [Solomon, S.] MIT, Dept Earth Atmospher & Planetary Sci, Cambridge, MA USA. [Barnes, J. E.] NOAA, Mauna Loa Observ, Hilo, HI USA. [Burlakov, V. D.; Dolgii, S. I.; Nevzorov, A. V.] Russian Acad Sci, Siberian Branch, VE Zuev Inst Atmospher Opt, Tomsk, Russia. [Deshler, T.] Univ Wyoming, Dept Atmospher Sci, Laramie, WY 82071 USA. [Herber, A. B.] Helmholtz Ctr Polar & Marine Res, Alfred Wegener Inst, Bremerhaven, Germany. [Nagai, T.; Sakai, T.; Uchino, O.] Meteorol Res Inst, Tsukuba, Ibaraki 305, Japan. [Neely, R. R., III] Natl Ctr Atmospher Res, Adv Study Program, Boulder, CO 80307 USA. [Ritter, C.] Helmholtz Ctr Polar & Marine Res, Alfred Wegener Inst, Potsdam, Germany. [Santer, B. D.] Lawrence Livermore Natl Lab, Program Climate Model Diag & Intercomparison, Livermore, CA USA. [Sato, M.] Columbia Univ, Earth Inst, New York, NY USA. [Schmidt, A.] Univ Leeds, Sch Earth & Environm, Leeds, W Yorkshire, England. [Vernier, J. P.] Sci Syst & Applicat Inc, Hampton, VA USA. [Vernier, J. P.] NASA, Langley Res Ctr, Hampton, VA 23665 USA. RP Ridley, DA (reprint author), MIT, Dept Civil & Environm Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA. EM daridley@mit.edu RI Santer, Benjamin/F-9781-2011; Schmidt, Anja/C-9617-2012; Neely, Ryan/F-8702-2010; OI Neely, Ryan/0000-0003-4560-4812; Nevzorov, Aleksey/0000-0002-5493-8657; Schmidt, Anja/0000-0001-8759-2843 FU National Science Foundation [1011827]; Ministry of Science and Education of the Russian Federation [14.604.21.0046, 14.604.21.0100]; Russian Science Foundation [14-27-00022] FX The Laramie in situ aerosol measurements have been supported primarily by the National Science Foundation, with the current measurements funded under grant 1011827. Measurements at Tomsk were supported in part by the Ministry of Science and Education of the Russian Federation (agreements 14.604.21.0046 and 14.604.21.0100) and the Russian Science Foundation (agreement 14-27-00022). The authors would like to thank the PIs of AERONET stations used in this study, the data from which can be obtained at http://aeronet.gsfc.nasa.gov/. NR 21 TC 41 Z9 44 U1 8 U2 79 PU AMER GEOPHYSICAL UNION PI WASHINGTON PA 2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA SN 0094-8276 EI 1944-8007 J9 GEOPHYS RES LETT JI Geophys. Res. Lett. PD NOV 28 PY 2014 VL 41 IS 22 BP 7763 EP 7769 DI 10.1002/2014GL061541 PG 7 WC Geosciences, Multidisciplinary SC Geology GA AX0LT UT WOS:000346644600001 ER PT J AU He, CL Li, QB Liou, KN Takano, Y Gu, Y Qi, L Mao, YH Leung, LR AF He, Cenlin Li, Qinbin Liou, Kuo-Nan Takano, Yoshi Gu, Yu Qi, Ling Mao, Yuhao Leung, L. Ruby TI Black carbon radiative forcing over the Tibetan Plateau SO GEOPHYSICAL RESEARCH LETTERS LA English DT Article DE black carbon; snow albedo forcing; direct radiative forcing; Tibetan Plateau ID LIGHT-ABSORPTION; SNOW GRAINS; ATMOSPHERIC AEROSOLS; CLIMATE; GLACIERS; ALBEDO; DEPOSITION; SCATTERING; SOOT AB We estimate the snow albedo forcing and direct radiative forcing (DRF) of black carbon (BC) in the Tibetan Plateau using a global chemical transport model in conjunction with a stochastic snow model and a radiative transfer model. The annual mean BC snow albedo forcing is 2.9Wm(-2) averaged over snow-covered plateau regions, which is a factor of 3 larger than the value over global land snowpack. BC-snow internal mixing increases the albedo forcing by 40-60% compared with external mixing, and coated BC increases the forcing by 30-50% compared with uncoated BC aggregates, whereas Koch snowflakes reduce the forcing by 20-40% relative to spherical snow grains. The annual BC DRF at the top of the atmosphere is 2.3Wm(-2) with uncertainties of -70-85% in the plateau after scaling the modeled BC absorption optical depth to Aerosol Robotic Network observations. The BC forcings are attributed to emissions from different regions. C1 [He, Cenlin; Li, Qinbin; Liou, Kuo-Nan; Takano, Yoshi; Gu, Yu; Qi, Ling] Univ Calif Los Angeles, Joint Inst Reg Earth Syst Sci & Engn, Los Angeles, CA 90095 USA. [He, Cenlin; Li, Qinbin; Liou, Kuo-Nan; Takano, Yoshi; Gu, Yu; Qi, Ling] Univ Calif Los Angeles, Dept Atmospher & Ocean Sci, Los Angeles, CA USA. [Mao, Yuhao] Chinese Acad Sci, Inst Atmospher Phys, Beijing, Peoples R China. [Leung, L. Ruby] Pacific NW Natl Lab, Richland, WA 99352 USA. RP He, CL (reprint author), Univ Calif Los Angeles, Joint Inst Reg Earth Syst Sci & Engn, Los Angeles, CA 90095 USA. EM cenlinhe@atmos.ucla.edu OI He, Cenlin/0000-0002-7367-2815 FU NASA from the Atmospheric Chemistry Modeling and Analysis Program [NNX09AF07G, NNX08AF64G]; DOE [DESC0006742] FX This study was funded by NASA grants NNX09AF07G and NNX08AF64G from the Atmospheric Chemistry Modeling and Analysis Program and by DOE grant DESC0006742. We thank J. Zhang and M. Gao for their help in this work. Users can access the data from this paper via the authors without any restrictions. NR 45 TC 8 Z9 9 U1 8 U2 39 PU AMER GEOPHYSICAL UNION PI WASHINGTON PA 2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA SN 0094-8276 EI 1944-8007 J9 GEOPHYS RES LETT JI Geophys. Res. Lett. PD NOV 28 PY 2014 VL 41 IS 22 BP 7806 EP 7813 DI 10.1002/2014GL062191 PG 8 WC Geosciences, Multidisciplinary SC Geology GA AX0LT UT WOS:000346644600007 ER PT J AU Porazik, P Johnson, JR Kaganovich, I Sanchez, E AF Porazik, Peter Johnson, Jay R. Kaganovich, Igor Sanchez, Ennio TI Modification of the loss cone for energetic particles SO GEOPHYSICAL RESEARCH LETTERS LA English DT Article DE loss cone; magnetic moment invariant; energetic particles; beam injection from space; energetic particle precipitation; magnetic mirror ID ADIABATIC INVARIANTS AB The optimal pitch angle which maximizes the penetration distance, along the magnetic field, of relativistic charged particles injected from the midplane of an axisymmetric field is investigated analytically and numerically. Higher-order terms of the magnetic moment invariant are necessary to correctly determine the mirror point of trapped energetic particles, and therefore the loss cone. The modified loss cone resulting from the inclusion of higher-order terms is no longer entirely defined by the pitch angle but also by the phase angle of the particle at the point of injection. The optimal orientation of the injection has a nonzero component perpendicular to the magnetic field line, and is in the plane tangential to the flux surface. Numerical integration of particle orbits were carried out for a relativistic electron in a dipole field, showing agreement with analytic expressions. The results are relevant to experiments, which are concerned with injection of relativistic beams into the atmosphere from aboard a spacecraft in the magnetosphere. C1 [Porazik, Peter; Johnson, Jay R.; Kaganovich, Igor] Princeton Univ, Plasma Phys Lab, Princeton Ctr Heliophys, Princeton, NJ 08544 USA. [Sanchez, Ennio] SRI Int, Ctr Geospace Sci, Menlo Pk, CA 94025 USA. RP Johnson, JR (reprint author), Princeton Univ, Plasma Phys Lab, Princeton Ctr Heliophys, Princeton, NJ 08544 USA. EM jrj@pppl.gov FU NSF [AGS-1344303, ATM-0902730, AGS-1203299]; NASA [NNH09AM531, NNH09AK631, NNH11AR071]; U.S. Department of Energy [DE-AC02-09CH11466] FX The data for this paper may be obtained by contacting the corresponding author. The authors acknowledge support from NSF grants AGS-1344303, ATM-0902730, and AGS-1203299 and NASA grants NNH09AM531, NNH09AK631, and NNH11AR071. This manuscript was authored by Princeton University under contract DE-AC02-09CH11466 with the U.S. Department of Energy. This work was facilitated by the Max-Planck/Princeton Center for Plasma Physics. 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, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. NR 18 TC 1 Z9 1 U1 2 U2 10 PU AMER GEOPHYSICAL UNION PI WASHINGTON PA 2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA SN 0094-8276 EI 1944-8007 J9 GEOPHYS RES LETT JI Geophys. Res. Lett. PD NOV 28 PY 2014 VL 41 IS 22 BP 8107 EP 8113 DI 10.1002/2014GL061869 PG 7 WC Geosciences, Multidisciplinary SC Geology GA AX0LT UT WOS:000346644600045 ER PT J AU Narula, CK Allard, LF Stocks, GM Moses-DeBusk, M AF Narula, Chaitanya K. Allard, Lawrence F. Stocks, G. M. Moses-DeBusk, Melanie TI Remarkable NO oxidation on single supported platinum atoms SO SCIENTIFIC REPORTS LA English DT Article ID AUGMENTED-WAVE METHOD; CATALYTIC-REACTION; NITROGEN-DIOXIDE; PT(111); SURFACE; OXYGEN; ADSORPTION; PT/AL2O3; O-2; ENVIRONMENT AB Our first-principles density functional theoretical modeling suggests that NO oxidation is feasible on fully oxidized single theta-Al2O3 supported platinum atoms via a modified Langmuir-Hinshelwood pathway. This is in contrast to the known decrease in NO oxidation activity of supported platinum with decreasing Pt particle size believed to be due to increased platinum oxidation. In order to validate our theoretical study, we evaluated single theta-Al2O3 supported platinum atoms and found them to exhibit remarkable NO oxidation activity. A comparison of turnover frequencies (TOF) of single supported Pt atoms with those of platinum particles for NO oxidation shows that single supported Pt atoms are as active as fully formed platinum particles. Thus, the overall picture of NO oxidation on supported Pt is that NO oxidation activity decreases with decreasing Pt particle size but accelerates when Pt is present only as single atoms. C1 [Narula, Chaitanya K.; Allard, Lawrence F.; Stocks, G. M.] Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. [Moses-DeBusk, Melanie] Oak Ridge Natl Lab, Energy & Transportat Sci Div, Oak Ridge, TN 37831 USA. RP Narula, CK (reprint author), Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. EM narulack@ornl.gov RI Stocks, George Malcollm/Q-1251-2016; OI Stocks, George Malcollm/0000-0002-9013-260X; Moses-DeBusk, Melanie/0000-0003-0382-0824 FU U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Office, Propulsion Materials Program; Division of Materials Sciences and Engineering, Office of Basic Energy Sciences [DE-AC05-ooOR22725]; UT-Battelle, LLC.; Oak Ridge National Laboratory by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy FX The research was sponsored by the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Office, Propulsion Materials Program (C.K.N., M.M.D.L.F.A.) and Division of Materials Sciences and Engineering, Office of Basic Energy Sciences (G.M.S.) under contract DE-AC05-ooOR22725 with UT-Battelle, LLC. The DRIFTS studies were conducted at the Center for Nanophase Materials Sciences, which is sponsored at Oak Ridge National Laboratory by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy. NR 40 TC 10 Z9 10 U1 6 U2 53 PU NATURE PUBLISHING GROUP PI LONDON PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND SN 2045-2322 J9 SCI REP-UK JI Sci Rep PD NOV 28 PY 2014 VL 4 AR 7238 DI 10.1038/srep07238 PG 6 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA AW4MI UT WOS:000346254800003 PM 25429995 ER PT J AU Santala, MK Raoux, S Topuria, T Reed, BW LaGrange, T Campbell, GH AF Santala, M. K. Raoux, S. Topuria, T. Reed, B. W. LaGrange, T. Campbell, G. H. TI Distinguishing mechanisms of morphological instabilities in phase change materials during switching SO THIN SOLID FILMS LA English DT Article DE Thin film instabilities; Phase change materials; In situ transmission electron microscopy; Dynamic transmission electron microscopy ID THIN LIQUID-FILMS; TRANSMISSION ELECTRON-MICROSCOPY; OPTICAL-DATA STORAGE; AMORPHOUS GETE; NUCLEATION; CRYSTALLIZATION; GROWTH; TRANSITIONS; EVOLUTION; CRYSTAL AB The process of dewetting of a thin film from a solid substrate is important for its scientific and technological relevance, but can be difficult to observe experimentally. We report on an experimental method that may be used to investigate morphological changes, including dewetting, during laser heat treatment of alloys used for phase change memory devices. We have used nanosecond-scale time-resolved imaging to differentiate between competing thin film instabilities in GeTe, a chalcogenide-based phase change material. It is shown that in the absence of nucleated dewetting, thin films of phase change alloys may be unstable, but that nucleated dewetting can lead to a more disrupted final state of the thin film. (C) 2014 Elsevier B.V. All rights reserved. C1 [Santala, M. K.; Reed, B. W.; LaGrange, T.; Campbell, G. H.] Lawrence Livermore Natl Lab, Condensed Matter & Mat Div, Livermore, CA 94551 USA. [Raoux, S.] IBM Corp, TJ Watson Res Ctr, Yorktown Hts, NY 10598 USA. [Topuria, T.] IBM Res Almaden, San Jose, CA 95120 USA. RP Santala, MK (reprint author), Lawrence Livermore Natl Lab, Condensed Matter & Mat Div, Livermore, CA 94551 USA. EM santala1@llnl.gov RI Raoux, Simone/G-3920-2016; OI Santala, Melissa/0000-0002-5189-5153 FU U.S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering, Lawrence Livermore National Laboratory [DE-AC52-07NA27344] FX This work performed under the auspices of the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. We thank P. Tchoulfian for performing ex situ laser experiments and E.A. Delenia for the preparation of the FIB cross section. NR 38 TC 2 Z9 2 U1 4 U2 32 PU ELSEVIER SCIENCE SA PI LAUSANNE PA PO BOX 564, 1001 LAUSANNE, SWITZERLAND SN 0040-6090 J9 THIN SOLID FILMS JI Thin Solid Films PD NOV 28 PY 2014 VL 571 BP 39 EP 44 DI 10.1016/j.tsf.2014.09.063 PN 1 PG 6 WC Materials Science, Multidisciplinary; Materials Science, Coatings & Films; Physics, Applied; Physics, Condensed Matter SC Materials Science; Physics GA AW1MQ UT WOS:000346053900007 ER PT J AU Lotfian, S Mayer, C Chawla, N Llorca, J Misra, A Baldwin, JK Molina-Aldareguia, JM AF Lotfian, S. Mayer, C. Chawla, N. Llorca, J. Misra, A. Baldwin, J. K. Molina-Aldareguia, J. M. TI Effect of layer thickness on the high temperature mechanical properties of Al/SiC nanolaminates SO THIN SOLID FILMS LA English DT Article DE Metal-ceramic composite; Multilayers; Layer thickness; Nanolaminate; High temperature nanomechanics; Nanoindentation ID METAL-CERAMIC COMPOSITES; NANOINDENTATION BEHAVIOR; MULTILAYERED COMPOSITES; MICROPILLAR COMPRESSION; DEFORMATION; COATINGS; HARDNESS AB Composite laminates on the nanoscale have shown superior hardness and toughness, but little is known about their high temperature behavior. The mechanical properties (elastic modulus and hardness) were measured as a function of temperature by means of nanoindentation in Al/SiC nanolaminates, a model metal-ceramic nanolaminate fabricated by physical vapor deposition. The influence of the Al and SiC volume fraction and layer thicknesses was determined between room temperature and 150 degrees C and, the deformation modes were analyzed by transmission electron microscopy, using a focused ion beam to prepare cross-sections through selected indents. It was found that ambient temperature deformation was controlled by the plastic flow of the Al layers, constrained by the SiC, and the elastic bending of the SiC layers. The reduction in hardness with temperature showed evidence of the development of interface-mediated deformation mechanisms, which led to a clear influence of layer thickness on the hardness. (C) 2014 Elsevier B.V. All rights reserved. C1 [Lotfian, S.; Llorca, J.; Molina-Aldareguia, J. M.] IMDEA Mat Inst, Madrid 28906, Spain. [Mayer, C.; Chawla, N.] Arizona State Univ, Tempe, AZ 85287 USA. [Llorca, J.] Univ Politecn Madrid, Dept Mat Sci, ETS Ingenieros Caminos, E-28040 Madrid, Spain. [Misra, A.; Baldwin, J. K.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Molina-Aldareguia, JM (reprint author), IMDEA Mat Inst, C Eric Kandel 2, Madrid 28906, Spain. EM jon.molina@imdea.org RI LLorca, Javier/C-1140-2013; Molina-Aldareguia, Jon/G-6413-2014; Misra, Amit/H-1087-2012 OI LLorca, Javier/0000-0002-3122-7879; Molina-Aldareguia, Jon/0000-0003-3508-6003; FU National Science Foundation of the US; Spanish Ministry of Economy and Competitiveness under the Materials World Network Program through the project "High temperature mechanical behavior of metal/ceramic nanolaminate composites" [NSF-DMR-1209988, PCIN-2013-029]; US DOE, Office of Basic Energy Sciences; Spanish Ministry of Economy and Competitiveness [MAT2012-31889]; European Commission through the project RADINTERFACES [263273] FX This investigation was supported by the National Science Foundation of the US and the Spanish Ministry of Economy and Competitiveness under the Materials World Network Program through the project "High temperature mechanical behavior of metal/ceramic nanolaminate composites" (NSF-DMR-1209988 and PCIN-2013-029). The multilayer deposition work at LANL was supported by US DOE, Office of Basic Energy Sciences. Additional support from the Spanish Ministry of Economy and Competitiveness (MAT2012-31889) and the European Commission through the project RADINTERFACES (Grant Agreement Number 263273) is also gratefully acknowledged. NR 39 TC 7 Z9 7 U1 3 U2 25 PU ELSEVIER SCIENCE SA PI LAUSANNE PA PO BOX 564, 1001 LAUSANNE, SWITZERLAND SN 0040-6090 J9 THIN SOLID FILMS JI Thin Solid Films PD NOV 28 PY 2014 VL 571 BP 260 EP 267 DI 10.1016/j.tsf.2014.06.022 PN 2 PG 8 WC Materials Science, Multidisciplinary; Materials Science, Coatings & Films; Physics, Applied; Physics, Condensed Matter SC Materials Science; Physics GA AW1MX UT WOS:000346054600004 ER PT J AU Aspnes, DE Choi, SG AF Aspnes, D. E. Choi, S. G. TI Combined direct- and reciprocal-space approach for converting spectra to energy scales with negligible loss of information SO THIN SOLID FILMS LA English DT Article; Proceedings Paper CT 6th International Conference on Spectroscopic Ellipsometry (ICSE) CY MAY 26-31, 2013 CL Kyoto, JAPAN DE Ellipsometry; Interpolation; Optical spectra; Wavelength; Fourier analysis ID LEAST-SQUARES AB Extracting information from spectra is best done in reciprocal space, provided that baseline effects, information, and noise can be localized in low-, intermediate-, and high-index coefficients, respectively. In optical spectroscopy this occurs if data are equally spaced in energy E. We develop and quantify a procedure to generate such spectra from any initial distribution of wavelengths lambda. Reciprocal-space analysis shows that this transformation can be accomplished with negligible loss of information. The procedure can be applied to any system where the Fourier coefficients of the result can be separated as noted above. (C) 2013 Elsevier B.V. All rights reserved. C1 [Aspnes, D. E.] Kyung Hee Univ, Dept Phys, Seoul 130701, South Korea. [Aspnes, D. E.] N Carolina State Univ, Dept Phys, Raleigh, NC 27695 USA. [Choi, S. G.] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Aspnes, DE (reprint author), Kyung Hee Univ, Dept Phys, Seoul 130701, South Korea. EM aspnes@unity.ncsu.edu NR 8 TC 0 Z9 0 U1 3 U2 5 PU ELSEVIER SCIENCE SA PI LAUSANNE PA PO BOX 564, 1001 LAUSANNE, SWITZERLAND SN 0040-6090 J9 THIN SOLID FILMS JI Thin Solid Films PD NOV 28 PY 2014 VL 571 BP 506 EP 508 DI 10.1016/j.tsf.2013.11.028 PN 3 PG 3 WC Materials Science, Multidisciplinary; Materials Science, Coatings & Films; Physics, Applied; Physics, Condensed Matter SC Materials Science; Physics GA AW1ND UT WOS:000346055200030 ER PT J AU Zollner, CJ Willett-Gies, TI Zollner, S Choi, S AF Zollner, Christian J. Willett-Gies, Travis I. Zollner, Stefan Choi, Sukgeun TI Infrared to vacuum-ultraviolet ellipsometry studies of spinel (MgAl2O4) SO THIN SOLID FILMS LA English DT Article; Proceedings Paper CT 6th International Conference on Spectroscopic Ellipsometry (ICSE) CY MAY 26-31, 2013 CL Kyoto, JAPAN DE Spectroscopic ellipsometry; Magnesium aluminate; Spinel; Lattice dynamics; Dielectric function; Phonon ID MODES; ANHARMONICITY; TRANSVERSE; QUARTZ; AL2O3 AB The dielectric function and the loss function for spinel (MgAl2O4) were determined using Fourier-transform infrared ellipsometry from 250 to 1000 cm(-1). We fit our data using two different dispersion models: (1) The Lorentz oscillator model describes the lattice optical response using a sum of independent classical harmonic oscillators with constant damping. (2) We also use a factorized oscillator model with independent broadening parameters for the transverse and longitudinal optical phonons. By fitting our data to these models, we determine the transverse and longitudinal optical phonon energies, their broadenings, and their amplitudes. The factorized model provides a better description of the data at high energies. The agreement is not so good for the lower-energy phonons, presumably due to broadenings caused by cation disorder. We also studied the Raman-active phonons by Raman spectroscopy. Using spectroscopic ellipsometry, we also determine the dispersion of the refractive index from 0.76 to 9.0 eV. Combining both data sets we find the high-and low-frequency dielectric constant. In the visible and ultraviolet region, the data are dominated by a Lorentz oscillator peak at 8.1 eV masked by surface roughness (13-16 angstrom). (C) 2013 Elsevier B.V. All rights reserved. C1 [Zollner, Christian J.] Cornell Univ, Sch Appl & Engn Phys, Ithaca, NY 14853 USA. [Willett-Gies, Travis I.; Zollner, Stefan] New Mexico State Univ, Dept Phys, Las Cruces, NM 88003 USA. [Choi, Sukgeun] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Zollner, S (reprint author), New Mexico State Univ, Dept Phys, MSC 3D,POB 30001, Las Cruces, NM 88003 USA. EM zollner@nmsu.edu RI Zollner, Stefan/B-4858-2012 OI Zollner, Stefan/0000-0001-7752-7941 NR 22 TC 5 Z9 5 U1 1 U2 4 PU ELSEVIER SCIENCE SA PI LAUSANNE PA PO BOX 564, 1001 LAUSANNE, SWITZERLAND SN 0040-6090 J9 THIN SOLID FILMS JI Thin Solid Films PD NOV 28 PY 2014 VL 571 BP 689 EP 694 DI 10.1016/j.tsf.2013.11.141 PN 3 PG 6 WC Materials Science, Multidisciplinary; Materials Science, Coatings & Films; Physics, Applied; Physics, Condensed Matter SC Materials Science; Physics GA AW1ND UT WOS:000346055200067 ER PT J AU Sippel, KH Vyas, NK Zhang, W Sankaran, B Quiocho, FA AF Sippel, Katherine H. Vyas, Nand K. Zhang, Wei Sankaran, Banumathi Quiocho, Florante A. TI Crystal Structure of the Human Fatty Acid Synthase Enoyl-Acyl Carrier Protein-Reductase Domain Complexed with Triclosan Reveals Allosteric Protein-Protein Interface Inhibition SO JOURNAL OF BIOLOGICAL CHEMISTRY LA English DT Article ID BREAST-CANCER CELLS; THIOESTERASE DOMAIN; IN-VITRO; PROSTATE-CANCER; OVARIAN-CANCER; DATA QUALITY; OVEREXPRESSION; APOPTOSIS; MILK; CHEMOPREVENTION AB Human fatty acid synthase (FAS) is a large, multidomain protein that synthesizes long chain fatty acids. Because these fatty acids are primarily provided by diet, FAS is normally expressed at low levels; however, it is highly up-regulated in many cancers. Human enoyl-acyl carrier protein-reductase (hER) is one of the FAS catalytic domains, and its inhibition by drugs like triclosan (TCL) can increase cytotoxicity and decrease drug resistance in cancer cells. We have determined the structure of hER in the presence and absence of TCL. TCL was not bound in the active site, as predicted, but rather at the protein-protein interface (PPI). TCL binding induces a dimer orientation change that causes downstream structural rearrangement in critical active site residues. Kinetics studies indicate that TCL is capable of inhibiting the isolated hER domain with an IC50 of similar to 55 mu M. Given the hER-TCL structure and the inhibition observed in the hER domain, it seems likely that TCL is observed in the physiologically relevant binding site and that it acts as an allosteric PPI inhibitor. TCL may be a viable scaffold for the development of anti-cancer PPI FAS inhibitors. C1 [Sippel, Katherine H.; Vyas, Nand K.; Zhang, Wei; Quiocho, Florante A.] Baylor Coll Med, Verna & Marrs McLean Dept Biochem & Mol Biol, Houston, TX 77030 USA. [Sankaran, Banumathi] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley Ctr Struct Biol, Berkeley, CA 94720 USA. RP Quiocho, FA (reprint author), Baylor Coll Med, Verna & Marrs McLean Dept Biochem & Mol Biol, Houston, TX 77030 USA. EM faq@bcm.edu FU NIGMS, National Institutes of Health; Welch Foundation [Q-0581]; Howard Hughes Medical Institute; U.S. Department of Energy [DE-AC02-05CH11231] FX This work was supported, in whole or in part, by a NIGMS, National Institutes of Health grant. This work was also supported by Welch Foundation Grant Q-0581, by the Howard Hughes Medical Institute, and by the U.S. Department of Energy under Contract DE-AC02-05CH11231. NR 68 TC 3 Z9 4 U1 2 U2 8 PU AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC PI BETHESDA PA 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3996 USA SN 0021-9258 EI 1083-351X J9 J BIOL CHEM JI J. Biol. Chem. PD NOV 28 PY 2014 VL 289 IS 48 BP 33287 EP 33295 DI 10.1074/jbc.M114.608547 PG 9 WC Biochemistry & Molecular Biology SC Biochemistry & Molecular Biology GA AU5HC UT WOS:000345636600020 PM 25301948 ER PT J AU Doudna, JA Charpentier, E AF Doudna, Jennifer A. Charpentier, Emmanuelle TI The new frontier of genome engineering with CRISPR-Cas9 SO SCIENCE LA English DT Review ID TRIPLE-HELIX FORMATION; RNA-GUIDED CAS9; CRISPR/CAS9-MEDIATED TARGETED MUTAGENESIS; PLURIPOTENT STEM-CELLS; SITE-SPECIFIC CLEAVAGE; ZINC-FINGER NUCLEASES; DOUBLE-STRAND BREAKS; DNA-REPAIR SYSTEM; HOMOLOGOUS RECOMBINATION; STREPTOCOCCUS-THERMOPHILUS AB The advent of facile genome engineering using the bacterial RNA-guided CRISPR-Cas9 system in animals and plants is transforming biology. We review the history of CRISPR (clustered regularly interspaced palindromic repeat) biology from its initial discovery through the elucidation of the CRISPR-Cas9 enzyme mechanism, which has set the stage for remarkable developments using this technology to modify, regulate, or mark genomic loci in a wide variety of cells and organisms from all three domains of life. These results highlight a new era in which genomic manipulation is no longer a bottleneck to experiments, paving the way toward fundamental discoveries in biology, with applications in all branches of biotechnology, as well as strategies for human therapeutics. C1 [Doudna, Jennifer A.] Univ Calif Berkeley, Dept Mol & Cell Biol, Howard Hughes Med Inst, Berkeley, CA 94720 USA. [Doudna, Jennifer A.] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. [Doudna, Jennifer A.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA. [Charpentier, Emmanuelle] Helmholtz Ctr Infect Res, Dept Regulat Infect Biol, D-38124 Braunschweig, Germany. [Charpentier, Emmanuelle] Umea Univ, Lab Mol Infect Med Sweden, Umea Ctr Microbial Res, Dept Mol Biol, S-90187 Umea, Sweden. [Charpentier, Emmanuelle] Hannover Med Sch, D-30625 Hannover, Germany. RP Doudna, JA (reprint author), Univ Calif Berkeley, Dept Mol & Cell Biol, Howard Hughes Med Inst, 229 Stanley Hall, Berkeley, CA 94720 USA. EM doudna@berkeley.edu; emmanuelle.charpentier@helmholtz-hzi.de FU Alexander von Humboldt Foundation; German Federal Ministry for Education and Research; Helmholtz Association; German Research Foundation; Goran Gustafsson Foundation; Swedish Research Council; Kempe Foundation; Umea University; Howard Hughes Medical Institute; NSF; Gates Foundation; Li Ka Shing Foundation; NIH FX J.A.D. is a co-founder of Caribou Biosciences Inc. and Editas Medicine and is on the scientific advisory board of Caribou Biosciences Inc. E. C. is a cofounder of CRISPR Therapeutics and is on the scientific advisory board of CRISPR Therapeutics and Horizon Discovery. E. C. is supported by the Alexander von Humboldt Foundation, the German Federal Ministry for Education and Research, the Helmholtz Association, the German Research Foundation, the Goran Gustafsson Foundation, the Swedish Research Council, the Kempe Foundation, and Umea University. J.A.D. acknowledges financial support from the Howard Hughes Medical Institute, NSF, the Gates Foundation, the Li Ka Shing Foundation, and NIH; J.A.D. is a Howard Hughes Medical Institute Investigator and a member of the Center for RNA Systems Biology at UC Berkeley (J. Cate, P.I.). NR 153 TC 644 Z9 685 U1 322 U2 1315 PU AMER ASSOC ADVANCEMENT SCIENCE PI WASHINGTON PA 1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA SN 0036-8075 EI 1095-9203 J9 SCIENCE JI Science PD NOV 28 PY 2014 VL 346 IS 6213 BP 1077 EP + AR 1258096 DI 10.1126/science.1258096 PG 10 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA AU7EK UT WOS:000345763400031 PM 25430774 ER PT J AU Davis, JP Brown, JL Knudson, MD Lemke, RW AF Davis, Jean-Paul Brown, Justin L. Knudson, Marcus D. Lemke, Raymond W. TI Analysis of shockless dynamic compression data on solids to multi-megabar pressures: Application to tantalum SO JOURNAL OF APPLIED PHYSICS LA English DT Article ID EQUATION-OF-STATE; ISENTROPIC COMPRESSION; GPA; ALUMINUM; METALS; COPPER; MODEL; WAVES; MBAR; TA AB Magnetically-driven, planar shockless-compression experiments to multi-megabar pressures were performed on tantalum samples using a stripline target geometry. Free-surface velocity waveforms were measured in 15 cases; nine of these in a dual-sample configuration with two samples of different thicknesses on opposing electrodes, and six in a single-sample configuration with a bare electrode opposite the sample. Details are given on the application of inverse Lagrangian analysis (ILA) to these data, including potential sources of error. The most significant source of systematic error, particularly for single-sample experiments, was found to arise from the pulse-shape dependent free-surface reflected wave interactions with the deviatoric-stress response of tantalum. This could cause local, possibly temporary, unloading of material from a ramp compressed state, and thus multi-value response in wave speed that invalidates the free-surface to in-material velocity mapping step of ILA. By averaging all 15 data sets, a final result for the principal quasi-isentrope of tantalum in stress-strain was obtained to a peak longitudinal stress of 330 GPa with conservative uncertainty bounds of 64.5% in stress. The result agrees well with a tabular equation of state developed at Los Alamos National Laboratory. (C) 2014 AIP Publishing LLC. C1 [Davis, Jean-Paul; Brown, Justin L.; Knudson, Marcus D.; Lemke, Raymond W.] Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Davis, JP (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87185 USA. FU U.S. Department of Energy's National Nuclear Security Administration [DE-AC04-94AL85000] FX The authors wish to acknowledge the support of the large inter-disciplinary team it takes to design, fabricate, and execute experiments on the Z machine. Thanks are due to James R. Asay and Matthew R. Martin for discussions around relevant topics, to G. T. "Rusty" Gray for providing some of the tantalum samples as well as work to specify the Starck material, and to Dawn G. Flicker for reviewing the manuscript. 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-AC04-94AL85000. NR 69 TC 11 Z9 12 U1 5 U2 22 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0021-8979 EI 1089-7550 J9 J APPL PHYS JI J. Appl. Phys. PD NOV 28 PY 2014 VL 116 IS 20 AR 204903 DI 10.1063/1.4902863 PG 17 WC Physics, Applied SC Physics GA AU5IM UT WOS:000345640200030 ER PT J AU Lorbeer, C Behrends, F Cybinska, J Eckert, H Mudring, AV AF Lorbeer, C. Behrends, F. Cybinska, J. Eckert, H. Mudring, A. -V. TI Charge compensation in RE3+ (RE = Eu, Gd) and M+ (M = Li, Na, K) co-doped alkaline earth nanofluorides obtained by microwave reaction with reactive ionic liquids leading to improved optical properties SO JOURNAL OF MATERIALS CHEMISTRY C LA English DT Article ID SELECTIVE LASER SPECTROSCOPY; LUMINESCENCE SPECTROSCOPY; SYNCHROTRON-RADIATION; DEFECT PROPERTIES; FLUORIDES; SCATTERING; BAF2; SRF2; NMR AB Alkaline earth fluorides are extraordinarily promising host matrices for phosphor materials with regard to rare earth doping. In particular, quantum cutting materials, which might considerably enhance the efficiency of mercury-free fluorescent lamps or SC solar cells, are often based on rare earth containing crystalline fluorides such as NaGdF4, GdF3 or LaF3. Substituting most of the precious rare earth ions and simultaneously retaining the efficiency of the phosphor is a major goal. Alkaline earth fluoride nanoparticles doped with trivalent lanthanide ions (which are required for the quantum cutting phenomenon) were prepared via a microwave assisted method in ionic liquids. As doping trivalent ions into a host with divalent cations requires charge compensation, this effect was thoroughly studied by powder X-ray and electron diffraction, luminescence spectroscopy and Na-23, La-139 and F-19 solid state NMR spectroscopy. Monovalent alkali ions were codoped with the trivalent lanthanide ions to relieve stress and achieve a better crystallinity and higher quantum cutting abilities of the prepared material. F-19-magic angle spinning (MAS)-NMR-spectra, assisted by F-19{Na-23} rotational echo double resonance (REDOR) studies, reveal distinct local fluoride environments, the populations of which are discussed in relation to spatial distribution and clustering models. In the co-doped samples, fluoride species having both Na+ and La3+ ions within their coordination sphere can be identified and quantified. This interplay of mono- and trivalent ions in the CaF2 lattice appears to be an efficient charge compensation mechanism that allows for improved performance characteristics of such co-doped phosphor materials. C1 [Lorbeer, C.; Cybinska, J.; Mudring, A. -V.] Ruhr Univ Bochum, D-44780 Bochum, Germany. [Behrends, F.; Eckert, H.] Univ Munster, Inst Phys Chem, D-48149 Munster, Germany. [Cybinska, J.] Univ Wroclaw, Fac Chem, PL-50383 Wroclaw, Poland. [Eckert, H.] Univ Sao Paulo, Inst Phys, Sao Carlos, SP, Brazil. [Mudring, A. -V.] Iowa State Univ, Dept Mat Sci & Engn, Ames, IA 50011 USA. [Mudring, A. -V.] Ames Lab, Crit Mat Inst, Ames, IA 50011 USA. RP Mudring, AV (reprint author), Ruhr Univ Bochum, Univ Str 150, D-44780 Bochum, Germany. EM mudring@iastate.edu RI FAPESP, CeRTEV/J-6817-2015; Sao Carlos Institute of Physics, IFSC/USP/M-2664-2016 FU Critical Materials Institute, an Energy Innovation Hub - U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Advanced Manufacturing Office; European Research Council with an ERC starting grant ("EMIL") [200475]; Fonds der Chemischen Industrie; FAPESP (CERTEV - Center for Research, Technology and Education in Vitreous Materials) [2013/07793-6] FX This work was supported in part by the Critical Materials Institute, an Energy Innovation Hub funded by the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Advanced Manufacturing Office and the European Research Council with an ERC starting grant ("EMIL", contract no. 200475). A.-V. M. thanks the Fonds der Chemischen Industrie for a Dozentenstipendium, C. L. and F. B. thank the Fonds der Chemischen Industrie for doctoral scholarships. DESY (proposal no. II-20090181) is acknowledged for access to synchrotron facilities. H. E. is grateful for funding by FAPESP, grant number 2013/07793-6 (CERTEV - Center for Research, Technology and Education in Vitreous Materials). NR 37 TC 12 Z9 12 U1 14 U2 101 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 2050-7526 EI 2050-7534 J9 J MATER CHEM C JI J. Mater. Chem. C PD NOV 28 PY 2014 VL 2 IS 44 BP 9439 EP 9450 DI 10.1039/c4tc01214c PG 12 WC Materials Science, Multidisciplinary; Physics, Applied SC Materials Science; Physics GA AS5SU UT WOS:000344330700014 ER PT J AU Kelly, SJ Kim, Y Eliseev, E Morozovska, A Jesse, S Biegalski, MD Mitchell, JF Zheng, H Aarts, J Hwang, I Oh, S Choi, JS Choi, T Park, BH Kalinin, SV Maksymovych, P AF Kelly, Simon J. Kim, Yunseok Eliseev, Eugene Morozovska, Anna Jesse, Stephen Biegalski, Michael D. Mitchell, J. F. Zheng, H. Aarts, J. Hwang, Inrok Oh, Sungtaek Choi, Jin Sik Choi, Taekjib Park, Bae Ho Kalinin, Sergei V. Maksymovych, Peter TI Controlled mechnical modification of manganite surface with nanoscale resolution SO NANOTECHNOLOGY LA English DT Article DE manganite; pressure; patterning; vacancy; Vegard ID DOPED MANGANITES; POLARIZATION; TRANSITIONS; FILMS AB We investigated the surfaces of magnetoresistive manganites, La1-xCaxMnO3 and La2-2xSr1+2xMn2O7, using a combination of ultrahigh vacuum conductive, electrostatic and magnetic force microscopy methods. Scanning as-grown film with a metal tip, even with zero applied bias, was found to modify the surface electronic properties such that in subsequent scans, the conductivity is reduced below the noise level of conductive probe microscopy. Scanned areas also reveal a reduced contact potential difference relative to the pristine surface by similar to 0.3 eV. We propose that contact-pressure of the tip modifies the electrochemical potential of oxygen vacancies via the Vegard effect, causing vacancy motion and concomitant changes of the electronic properties. C1 [Kelly, Simon J.; Kim, Yunseok; Jesse, Stephen; Biegalski, Michael D.; Kalinin, Sergei V.; Maksymovych, Peter] Oak Ridge Natl Lab, Ctr Nanophase Mat Sci, Oak Ridge, TN 37831 USA. [Kelly, Simon J.; Aarts, J.] Leiden Univ, Leiden Inst Phys, NL-2333 CA Leiden, Netherlands. [Eliseev, Eugene] Natl Acad Sci Ukraine, Inst Problems Mat Sci, UA-03142 Kiev, Ukraine. [Morozovska, Anna] Natl Acad Sci Ukraine, Inst Phys, UA-03028 Kiev, Ukraine. [Mitchell, J. F.; Zheng, H.] Argonne Natl Lab, Div Mat Sci, Argonne, IL 60439 USA. [Hwang, Inrok; Oh, Sungtaek; Choi, Jin Sik; Park, Bae Ho] Konkuk Univ, Dept Phys, Div Quantum Phases & Devices, Seoul