FN Thomson Reuters Web of Science™ VR 1.0 PT J AU Zdeborova, L Krzakala, F AF Zdeborova, Lenka Krzakala, Florent TI QUIET PLANTING IN THE LOCKED CONSTRAINT SATISFACTION PROBLEMS SO SIAM JOURNAL ON DISCRETE MATHEMATICS LA English DT Article DE constraint satisfaction problems; planted random ensemble; belief propagation; reconstruction on trees; instances with a unique satisfying assignment ID SATISFIABILITY PROBLEMS; GLASS-TRANSITION; TREES; RECONSTRUCTION; ALGORITHM; GRAPHS; CODES; MODEL AB We study the planted ensemble of locked constraint satisfaction problems. We describe the connection between the random and planted ensembles. The use of the cavity method is combined with arguments from reconstruction on trees and the first and second moment considerations. Our main result is the location of the hard region in the planted ensemble. In a part of that hard region, instances have with high probability a single satisfying assignment. C1 [Zdeborova, Lenka; Krzakala, Florent] Los Alamos Natl Lab, Div Theoret, Los Alamos, NM 87545 USA. [Zdeborova, Lenka; Krzakala, Florent] Los Alamos Natl Lab, Ctr Nonlinear Studies, Los Alamos, NM 87545 USA. RP Zdeborova, L (reprint author), Los Alamos Natl Lab, Div Theoret, Los Alamos, NM 87545 USA. EM lenka.zdeborova@cea.fr; fk@espci.fr RI Krzakala, Florent/D-8846-2012; Zdeborova, Lenka/B-9999-2014 NR 43 TC 8 Z9 8 U1 0 U2 0 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 0895-4801 EI 1095-7146 J9 SIAM J DISCRETE MATH JI SIAM Discret. Math. PY 2011 VL 25 IS 2 BP 750 EP 770 DI 10.1137/090750755 PG 21 WC Mathematics, Applied SC Mathematics GA 786JH UT WOS:000292302000023 ER PT J AU Kudekar, S Macris, N AF Kudekar, Shrinivas Macris, Nicolas TI DECAY OF CORRELATIONS FOR SPARSE GRAPH ERROR CORRECTING CODES SO SIAM JOURNAL ON DISCRETE MATHEMATICS LA English DT Article DE graphical codes; decay of correlations; belief propagation; cluster expansions; channel communication ID BOUNDS; MODEL AB The subject of this paper is transmission over a general class of binary-input memoryless symmetric channels using error correcting codes based on sparse graphs, namely, low-density generator-matrix and low-density parity-check codes. The optimal (or ideal) decoder based on the posterior measure over the code-bits and its relationship to the suboptimal belief propagation decoder are investigated. We consider the correlation (or covariance) between two code-bits, averaged over the noise realizations, as a function of the graph distance for the optimal decoder. Our main result is that this correlation decays exponentially fast for given low-density generator-matrix codes and a high enough noise parameter and also for given low-density parity-check codes and a low enough noise parameter. This has many consequences. Appropriate performance curves-called generalized extrinsic information transfer (GEXIT) functions-of the belief propagation and optimal decoders match in high/low noise regimes. This means that in high/low noise regimes the performance curves of the optimal decoder can be computed by density evolution. Another interpretation is that the replica predictions of spin-glass theory are exact. Our methods are rather general and use cluster expansions first developed in the context of mathematical statistical mechanics. C1 [Kudekar, Shrinivas] Los Alamos Natl Lab, New Mexico Consortium, Los Alamos, NM 87545 USA. [Kudekar, Shrinivas] Los Alamos Natl Lab, Ctr Nonlinear Studies, Los Alamos, NM 87545 USA. [Macris, Nicolas] Ecole Polytech Fed Lausanne, Commun Theory Lab, Sch Comp & Commun Sci, CH-1015 Lausanne, Switzerland. RP Kudekar, S (reprint author), Los Alamos Natl Lab, New Mexico Consortium, Los Alamos, NM 87545 USA. EM skudekar@lanl.gov; nicolas.macris@epfl.ch FU Swiss National Foundation [200020-113412] FX New Mexico Consortium and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM (skudekar@lanl.gov). This author's work has been supported by a grant of the Swiss National Foundation 200020-113412. NR 31 TC 5 Z9 5 U1 0 U2 1 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 0895-4801 J9 SIAM J DISCRETE MATH JI SIAM Discret. Math. PY 2011 VL 25 IS 2 BP 956 EP 988 DI 10.1137/090751827 PG 33 WC Mathematics, Applied SC Mathematics GA 786JH UT WOS:000292302000032 ER PT J AU Chandrasekaran, V Chertkov, M Gamarnik, D Shah, D Shin, J AF Chandrasekaran, Venkat Chertkov, Misha Gamarnik, David Shah, Devavrat Shin, Jinwoo TI COUNTING INDEPENDENT SETS USING THE BETHE APPROXIMATION SO SIAM JOURNAL ON DISCRETE MATHEMATICS LA English DT Article DE Bethe free energy; independent set; belief propagation; loop series ID RANDOM REGULAR GRAPHS; ASYMPTOTIC-DISTRIBUTION; MARKOV-CHAINS; CYCLES AB We consider the #P-complete problem of counting the number of independent sets in a given graph. Our interest is in understanding the effectiveness of the popular belief propagation (BP) heuristic. BP is a simple iterative algorithm that is known to have at least one fixed point, where each fixed point corresponds to a stationary point of the Bethe free energy (introduced by Yedidia, Freeman, and Weiss [IEEE Trans. Inform. Theory, 51 (2004), pp. 2282-2312] in recognition of Bethe's earlier work in 1935). The evaluation of the Bethe free energy at such a stationary point (or BP fixed point) leads to the Bethe approximation for the number of independent sets of the given graph. BP is not known to converge in general, nor is an efficient, convergent procedure for finding stationary points of the Bethe free energy known. Furthermore, the effectiveness of the Bethe approximation is not well understood. As the first result of this paper we propose a BP-like algorithm that always converges to a stationary point of the Bethe free energy for any graph for the independent set problem. This procedure finds an e-approximate stationary point in O(n(2)d(4)2(d)epsilon(-4)log(3)(n epsilon(-1))) iterations for a graph of n nodes with max-degree d. We study the quality of the resulting Bethe approximation using the recently developed "loop series" framework of Chertkov and Chernyak [J. Stat. Mech. Theory Exp., 6 (2006), P06009]. As this characterization is applicable only for exact stationary points of the Bethe free energy, we provide a slightly modified characterization that holds for e-approximate stationary points. We establish that for any graph on n nodes with max-degree d and girth larger than 8d log(2) n, the multiplicative error between the number of independent sets and the Bethe approximation decays as 1 + O(n(-gamma)) for some gamma > 0. This provides a deterministic counting algorithm that leads to strictly different results compared to a recent result of Weitz [in Proceedings of the Thirty-Eighth Annual ACM Symposium on Theory of Computing, ACM Press, New York, 2006, pp. 140-149]. Finally, as a consequence of our analysis we prove that the Bethe approximation is exceedingly good for a random 3-regular graph conditioned on the shortest cycle cover conjecture of Alon and Tarsi [SIAM J. Algebr. Discrete Methods, 6 (1985), pp. 345-350] being true. C1 [Chandrasekaran, Venkat; Shah, Devavrat] MIT, Lab Informat & Decis Syst, Dept EECS, Cambridge, MA 02139 USA. [Chertkov, Misha] Los Alamos Natl Lab, Ctr Nonlinear Studies, Los Alamos, NM 87545 USA. [Chertkov, Misha] Los Alamos Natl Lab, Div Theoret, Los Alamos, NM 87545 USA. [Chertkov, Misha] New Mexico Consortium, Los Alamos, NM 87544 USA. [Gamarnik, David] MIT, Ctr Operat Res, Cambridge, MA 02139 USA. [Gamarnik, David] MIT, Alfred P Sloan Sch Management, Cambridge, MA 02139 USA. [Shin, Jinwoo] Georgia Inst Technol, Algorithms & Randomness Ctr, Atlanta, GA 30332 USA. RP Chandrasekaran, V (reprint author), MIT, Lab Informat & Decis Syst, Dept EECS, 77 Massachusetts Ave, Cambridge, MA 02139 USA. EM venkatc@mit.edu; chertkov@lanl.gov; gamarnik@mit.edu; devavrat@mit.edu; jshin72@cc.gatech.edu RI Shin, Jinwoo/M-5389-2013; Chertkov, Michael/O-8828-2015; OI Chertkov, Michael/0000-0002-6758-515X FU NSF EMT/MISC [0829893] FX Received by the editors August 10, 2009; accepted for publication (in revised form) July 16, 2010; published electronically July 1, 2011. This work was supported in part by NSF EMT/MISC collaborative project 0829893. NR 21 TC 8 Z9 8 U1 0 U2 2 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 0895-4801 EI 1095-7146 J9 SIAM J DISCRETE MATH JI SIAM Discret. Math. PY 2011 VL 25 IS 2 BP 1012 EP 1034 DI 10.1137/090767145 PG 23 WC Mathematics, Applied SC Mathematics GA 786JH UT WOS:000292302000034 ER PT J AU Kolda, TG Mayo, JR AF Kolda, Tamara G. Mayo, Jackson R. TI SHIFTED POWER METHOD FOR COMPUTING TENSOR EIGENPAIRS SO SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS LA English DT Article DE tensor eigenvalues; E-eigenpairs; Z-eigenpairs; l(2)-eigenpairs; rank-1 approximation; symmetric higher-order power method (S-HOPM); shifted symmetric higher-order power method (SS-HOPM) ID NONNEGATIVE TENSOR; LARGEST EIGENVALUE; SYMMETRIC TENSOR; APPROXIMATION; RANK-1 AB Recent work on eigenvalues and eigenvectors for tensors of order m >= 3 has been motivated by applications in blind source separation, magnetic resonance imaging, molecular conformation, and more. In this paper, we consider methods for computing real symmetric-tensor eigenpairs of the form Ax(m-1) = lambda x subject to parallel to x parallel to = 1, which is closely related to optimal rank-1 approximation of a symmetric tensor. Our contribution is a shifted symmetric higher-order power method (SS-HOPM), which we show is guaranteed to converge to a tensor eigenpair. SS-HOPM can be viewed as a generalization of the power iteration method for matrices or of the symmetric higher-order power method. Additionally, using fixed point analysis, we can characterize exactly which eigenpairs can and cannot be found by the method. Numerical examples are presented, including examples from an extension of the method to finding complex eigenpairs. C1 [Kolda, Tamara G.; Mayo, Jackson R.] Sandia Natl Labs, Livermore, CA 94551 USA. RP Kolda, TG (reprint author), Sandia Natl Labs, Livermore, CA 94551 USA. EM tgkolda@sandia.gov; jmayo@sandia.gov RI Kolda, Tamara/B-1628-2009 OI Kolda, Tamara/0000-0003-4176-2493 FU U.S. Department of Energy; Laboratory Directed Research & Development (LDRD) at Sandia National Laboratories; U.S. Department of Energy's National Nuclear Security Administration [DE-AC04-94AL85000] FX This work was funded by the applied mathematics program at the U.S. Department of Energy and by an Excellence Award from the Laboratory Directed Research & Development (LDRD) program at Sandia National Laboratories. Sandia National Laboratories is a multiprogram laboratory 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. The U.S. Government retains a nonexclusive, royalty-free license to publish or reproduce the published form of this contribution, or allow others to do so, for U.S. Government purposes. Copyright is owned by SIAM to the extent not limited by these rights. NR 27 TC 70 Z9 77 U1 0 U2 7 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 0895-4798 J9 SIAM J MATRIX ANAL A JI SIAM J. Matrix Anal. Appl. PY 2011 VL 32 IS 4 BP 1095 EP 1124 DI 10.1137/100801482 PG 30 WC Mathematics, Applied SC Mathematics GA 866IG UT WOS:000298373400002 ER PT J AU Chen, J Anitescu, M Saad, Y AF Chen, Jie Anitescu, Mihai Saad, Yousef TI COMPUTING f(A)b VIA LEAST SQUARES POLYNOMIAL APPROXIMATIONS SO SIAM JOURNAL ON SCIENTIFIC COMPUTING LA English DT Article DE matrix function; least squares polynomials; Gaussian process; sampling ID KRYLOV SUBSPACE METHOD; MATRIX EXPONENTIAL OPERATOR; ITERATIVE SOLUTION; COMPUTATION; EQUATIONS; SYSTEMS AB Given a certain function f, various methods have been proposed in the past for addressing the important problem of computing the matrix-vector product f(A)b without explicitly computing the matrix f(A). Such methods were typically developed for a specific function f, a common case being that of the exponential. This paper discusses a procedure based on least squares polynomials that can, in principle, be applied to any (continuous) function f. The idea is to start by approximating the function by a spline of a desired accuracy. Then a particular definition of the function inner product is invoked that facilitates the computation of the least squares polynomial to this spline function. Since the function is approximated by a polynomial, the matrix A is referenced only through a matrix-vector multiplication. In addition, the choice of the inner product makes it possible to avoid numerical integration. As an important application, we consider the case when f(t) = root t and A is a sparse, symmetric positive-definite matrix, which arises in sampling from a Gaussian process distribution. The covariance matrix of the distribution is defined by using a covariance function that has a compact support, at a very large number of sites that are on a regular or irregular grid. We derive error bounds and show extensive numerical results to illustrate the effectiveness of the proposed technique. C1 [Chen, Jie; Saad, Yousef] Univ Minnesota Twin Cities, Dept Comp Sci & Engn, Minneapolis, MN 55455 USA. [Anitescu, Mihai] Argonne Natl Lab, Div Math & Comp Sci, Argonne, IL 60439 USA. RP Chen, J (reprint author), Univ Minnesota Twin Cities, Dept Comp Sci & Engn, Minneapolis, MN 55455 USA. EM jchen@cs.umn.edu; anitescu@mcs.anl.gov; saad@cs.umn.edu FU NSF [DMS-0810938]; DOE [DE-FG-08ER25841]; University of Minnesota; U.S. Department of Energy [DE-AC02-06CH11357] FX The work of these authors was supported by NSF grant DMS-0810938 and DOE grant DE-FG-08ER25841. The first author was supported in part by a University of Minnesota Doctoral Dissertation Fellowship.; The work of this author was supported by the U.S. Department of Energy through contract DE-AC02-06CH11357. NR 48 TC 12 Z9 12 U1 0 U2 4 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 1064-8275 EI 1095-7197 J9 SIAM J SCI COMPUT JI SIAM J. Sci. Comput. PY 2011 VL 33 IS 1 BP 195 EP 222 DI 10.1137/090778250 PG 28 WC Mathematics, Applied SC Mathematics GA 726DA UT WOS:000287697800009 ER PT J AU Olson, LN Schroder, JB Tuminaro, RS AF Olson, Luke N. Schroder, Jacob B. Tuminaro, Raymond S. TI A GENERAL INTERPOLATION STRATEGY FOR ALGEBRAIC MULTIGRID USING ENERGY MINIMIZATION SO SIAM JOURNAL ON SCIENTIFIC COMPUTING LA English DT Article DE algebraic multigrid; interpolation; nonsymmetric; non-Hermitian; smoothed aggregation ID AGGREGATION ALPHA-SA; SMOOTHED AGGREGATION; NONSYMMETRIC PROBLEMS; PRECONDITIONER; AMG AB Algebraic multigrid methods solve sparse linear systems Ax - b by automatic construction of a multilevel hierarchy. This hierarchy is defined by grid transfer operators that must accurately capture algebraically smooth error relative to the relaxation method. We propose a methodology to improve grid transfers through energy minimization. The proposed strategy is applicable to Hermitian, non-Hermitian, definite, and indefinite problems. Each column of the grid transfer operator P is minimized in an energy-based norm while enforcing two types of constraints: a defined sparsity pattern and preservation of specified modes in the range of P. A Krylov-based strategy is used to minimize energy, which is equivalent to solving AP(j) = 0 for each column j of P, with the constraints ensuring a nontrivial solution. For the Hermitian positive definite case, a conjugate gradient (CG-)based method is utilized to construct grid transfers, while methods based on generalized minimum residual (GMRES) and CG on the normal equations (CGNR) are explored for the general case. The approach is flexible, allowing for arbitrary coarsenings, unrestricted sparsity patterns, straightforward long-distance interpolation, and general use of constraints, either user-defined or auto-generated. We conclude with numerical evidence in support of the proposed framework. C1 [Olson, Luke N.] Univ Illinois, Siebel Ctr Comp Sci, Urbana, IL 61801 USA. [Schroder, Jacob B.] Univ Colorado, Dept Appl Math, Boulder, CO 80309 USA. [Tuminaro, Raymond S.] Sandia Natl Labs, Livermore, CA 94551 USA. RP Olson, LN (reprint author), Univ Illinois, Siebel Ctr Comp Sci, 201 N Goodwin Ave, Urbana, IL 61801 USA. EM lukeo@illinois.edu; jacob.schroder@colorado.edu; rstumin@sandia.gov FU NSF [DMS-0612448]; U.S. Department of Energy [DE-AC04-94-AL85000]; DOE Office of Science FX This work was partially supported by the NSF under award DMS-0612448. The U.S. Government retains a nonexclusive, royalty-free license to publish or reproduce the published form of this contribution, or allow others to do so, for U.S. Government purposes. Copyright is owned by SIAM to the extent not limited by these rights.; Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the U.S. Department of Energy under contract DE-AC04-94-AL85000. The work of this author was partially supported by the DOE Office of Science ASCR Program and by the ASC Program at Sandia National Laboratories. NR 32 TC 13 Z9 14 U1 0 U2 8 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 1064-8275 J9 SIAM J SCI COMPUT JI SIAM J. Sci. Comput. PY 2011 VL 33 IS 2 BP 966 EP 991 DI 10.1137/100803031 PG 26 WC Mathematics, Applied SC Mathematics GA 755XL UT WOS:000289973500023 ER PT J AU Sonday, BE Berry, RD Najm, HN Debusschere, BJ AF Sonday, Benjamin E. Berry, Robert D. Najm, Habib N. Debusschere, Bert J. TI EIGENVALUES OF THE JACOBIAN OF A GALERKIN-PROJECTED UNCERTAIN ODE SYSTEM SO SIAM JOURNAL ON SCIENTIFIC COMPUTING LA English DT Article DE ordinary differential equation; uncertainty quantification; polynomial chaos; stochastic Jacobian; eigenvalue ID POLYNOMIAL CHAOS; DIFFERENTIAL-EQUATIONS; ORTHOGONAL POLYNOMIALS; TOEPLITZ MATRICES; FINITE-ELEMENTS; CSP; MODELS; REPRESENTATIONS; PROPAGATION; MANIFOLDS AB Projection onto polynomial chaos (PC) basis functions is often used to reformulate a system of ordinary differential equations (ODEs) with uncertain parameters and initial conditions as a deterministic ODE system that describes the evolution of the PC modes. The deterministic Jacobian of this projected system is different and typically much larger than the random Jacobian of the original ODE system. This paper shows that the location of the eigenvalues of the projected Jacobian is largely determined by the eigenvalues of the original Jacobian, regardless of PC order or choice of orthogonal polynomials. Specifically, the eigenvalues of the projected Jacobian always lie in the convex hull of the numerical range of the Jacobian of the original system. C1 [Sonday, Benjamin E.] Princeton Univ, Program Appl & Computat Math, Princeton, NJ 08544 USA. [Berry, Robert D.; Najm, Habib N.; Debusschere, Bert J.] Sandia Natl Labs, Combust Res Facil, Livermore, CA 94551 USA. RP Sonday, BE (reprint author), Princeton Univ, Program Appl & Computat Math, Fine Hall,Washington Rd, Princeton, NJ 08544 USA. EM bsonday@math.princeton.edu; rdberry@sandia.gov; hnnajm@sandia.gov; bjdebus@sandia.gov FU DOE [DE-FG02-97ER25308]; Sandia Corporation, a Lockheed Martin Company [DE-AC04-94-AL85000]; U.S. Department of Energy (DOE), Office of Advanced Scientific Computing Research (ASCR); DOE Office of Basic Energy Sciences (BES) Division of Chemical Sciences, Geosciences, and Biosciences FX The Program in Applied and Computational Mathematics, Princeton University, Fine Hall, Washington Road, Princeton, NJ 08544-1000 (bsonday@math.princeton.edu). This author was supported by DOE Computational Science Graduate Fellowship, provided under grant DE-FG02-97ER25308.; Combustion Research Facility, Sandia National Laboratories, 7011 East Avenue, Livermore, CA 94551-9610 (rdberry@sandia.gov, hnnajm@sandia.gov, bjdebus@sandia.gov). Sandia National Laboratories is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the U.S. Department of Energy under contract DE-AC04-94-AL85000. These authors were supported by the U.S. Department of Energy (DOE), Office of Advanced Scientific Computing Research (ASCR), Applied Mathematics program, 2009 American Recovery and Reinvestment Act, and by the DOE Office of Basic Energy Sciences (BES) Division of Chemical Sciences, Geosciences, and Biosciences. NR 37 TC 9 Z9 9 U1 0 U2 2 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 1064-8275 J9 SIAM J SCI COMPUT JI SIAM J. Sci. Comput. PY 2011 VL 33 IS 3 BP 1212 EP 1233 DI 10.1137/100785922 PG 22 WC Mathematics, Applied SC Mathematics GA 782RN UT WOS:000292027900008 ER PT J AU Butler, T Dawson, C Wildey, T AF Butler, T. Dawson, C. Wildey, T. TI A POSTERIORI ERROR ANALYSIS OF STOCHASTIC DIFFERENTIAL EQUATIONS USING POLYNOMIAL CHAOS EXPANSIONS SO SIAM JOURNAL ON SCIENTIFIC COMPUTING LA English DT Article DE a posteriori error analysis; adjoint problem; polynomial chaos; stochastic spectral methods ID PROPAGATION; UNCERTAINTY; SCHEMES AB We develop computable a posteriori error estimates for linear functionals of a solution to a general nonlinear stochastic differential equation with random model/source parameters. These error estimates are based on a variational analysis applied to stochastic Galerkin methods for forward and adjoint problems. The result is a representation for the error estimate as a polynomial in the random model/source parameter. The advantage of this method is that we use polynomial chaos representations for the forward and adjoint systems to cheaply produce error estimates by simple evaluation of a polynomial. By comparison, the typical method of producing such estimates requires repeated forward/adjoint solves for each new choice of random parameter. We present numerical examples showing that there is excellent agreement between these methods. C1 [Butler, T.; Dawson, C.] Univ Texas Austin, ICES, Austin, TX 78712 USA. [Wildey, T.] Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Butler, T (reprint author), Univ Texas Austin, ICES, Austin, TX 78712 USA. EM tbutler@ices.utexas.edu; clint@ices.utexas.edu; tmwilde@sandia.gov RI Butler, Troy/K-8307-2015 FU King Abdullah University of Science and Technology (KAUST); Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation [DE-AC04-94-AL85000]; NSF [DMS 0618679] FX Submitted to the journal's Methods and Algorithms for Scientific Computing section May 18, 2010; accepted for publication (in revised form) March 2, 2011; published electronically June 7, 2011. This work was made possible with funding from the King Abdullah University of Science and Technology (KAUST).; Sandia National Labs, Albuquerque, NM 87185 (tmwilde@sandia.gov). Sandia is a multiprogram laboratory operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94-AL85000. This author's work was partially supported by NSF grant DMS 0618679. NR 31 TC 10 Z9 10 U1 0 U2 2 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 1064-8275 J9 SIAM J SCI COMPUT JI SIAM J. Sci. Comput. PY 2011 VL 33 IS 3 BP 1267 EP 1291 DI 10.1137/100795760 PG 25 WC Mathematics, Applied SC Mathematics GA 782RN UT WOS:000292027900011 ER PT J AU More, JJ Wild, SM AF More, Jorge J. Wild, Stefan M. TI ESTIMATING COMPUTATIONAL NOISE SO SIAM JOURNAL ON SCIENTIFIC COMPUTING LA English DT Article DE computational noise; deterministic simulations; iterative solvers AB Computational noise in deterministic simulations is as ill-defined a concept as can be found in scientific computing. When coupled with adaptive strategies, the effects of finite precision destroy smoothness of the simulation output and complicate subsequent analysis. Following the work of Hamming on roundoff errors, we present a new algorithm, ECnoise, for quantifying the noise level of a computed function. Our theoretical framework is based on stochastic noise but does not assume a specific distribution for the noise. For the deterministic simulations considered, ECnoise produces reliable results in a few function evaluations and offers new insights into building blocks of large scale simulations. C1 [More, Jorge J.; Wild, Stefan M.] Argonne Natl Lab, Div Math & Comp Sci, Argonne, IL 60439 USA. RP More, JJ (reprint author), Argonne Natl Lab, Div Math & Comp Sci, 9700 S Cass Ave, Argonne, IL 60439 USA. EM more@mcs.anl.gov; wild@mcs.anl.gov RI Wild, Stefan/P-4907-2016 OI Wild, Stefan/0000-0002-6099-2772 FU Office of Advanced Scientific Computing Research, Office of Science, U.S. Department of Energy; U.S. Department of Energy; U.S. Department of Energy Office of Science laboratory [DE-AC02-06CH11357] FX Submitted to the journal's Methods and Algorithms for Scientific Computing section February 17, 2010; accepted for publication (in revised form) March 11, 2011; published electronically June 7, 2011. This work was supported by the Office of Advanced Scientific Computing Research, Office of Science, U.S. Department of Energy. This paper has been created by UChicago Argonne, LLC, Operator of Argonne National Laboratory ("Argonne"). Argonne, a U.S. Department of Energy Office of Science laboratory, is operated under contract DE-AC02-06CH11357. The U.S. Government retains a nonexclusive, royalty-free license to publish or reproduce the published form of this contribution, or allow others to do so, for U.S. Government purposes. Copyright is owned by SIAM to the extent not limited by these rights. NR 23 TC 9 Z9 9 U1 0 U2 1 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 1064-8275 EI 1095-7197 J9 SIAM J SCI COMPUT JI SIAM J. Sci. Comput. PY 2011 VL 33 IS 3 BP 1292 EP 1314 DI 10.1137/100786125 PG 23 WC Mathematics, Applied SC Mathematics GA 782RN UT WOS:000292027900012 ER PT J AU Lin, L Yang, C Lu, JF Ying, LX E, WN AF Lin, Lin Yang, Chao Lu, Jianfeng Ying, Lexing E, Weinan TI A FAST PARALLEL ALGORITHM FOR SELECTED INVERSION OF STRUCTURED SPARSE MATRICES WITH APPLICATION TO 2D ELECTRONIC STRUCTURE CALCULATIONS SO SIAM JOURNAL ON SCIENTIFIC COMPUTING LA English DT Article DE selected inversion; parallel algorithm; electronic structure calculation ID CHOLESKY FACTORIZATION; LINEAR-EQUATIONS; SYSTEMS; SOLVER; TOOL AB An efficient parallel algorithm is presented for computing selected components of A(-1) where A is a structured symmetric sparse matrix. Calculations of this type are useful for several applications, including electronic structure analysis of materials in which the diagonal elements of the Green's functions are needed. The algorithm proposed here is a direct method based on a block LDLT factorization. The selected elements of A(-1) we compute lie in the nonzero positions of L+L-T. We use the elimination tree associated with the block LDLT factorization to organize the parallel algorithm, and reduce the synchronization overhead by passing the data level by level along this tree using the technique of local buffers and relative indices. We demonstrate the efficiency of our parallel implementation by applying it to a discretized two dimensional Hamiltonian matrix. We analyze the performance of the parallel algorithm by examining its load balance and communication overhead, and show that our parallel implementation exhibits an excellent weak scaling on a large-scale high performance distributed-memory parallel machine. C1 [Lin, Lin] Princeton Univ, Program Appl & Computat Math, Princeton, NJ 08544 USA. [Yang, Chao] Univ Calif Berkeley, Lawrence Berkeley Lab, Computat Res Div, Berkeley, CA 94720 USA. [Lu, Jianfeng] Courant Inst Math Sci, Dept Math, New York, NY 10012 USA. [Ying, Lexing] Univ Texas Austin, Dept Math, Austin, TX 78712 USA. [Ying, Lexing] Univ Texas Austin, ICES, Austin, TX 78712 USA. [E, Weinan] Princeton Univ, Dept Math, Princeton, NJ 08544 USA. [E, Weinan] Princeton Univ, PACM, Princeton, NJ 08544 USA. RP Lin, L (reprint author), Princeton Univ, Program Appl & Computat Math, Princeton, NJ 08544 USA. EM linlin@math.princeton.edu; cyang@lbl.gov; jianfeng@cims.nyu.edu; lexing@math.utexas.edu; weinan@math.princeton.edu RI Lin, Lin/I-2726-2012; OI Lin, Lin/0000-0001-7738-5947; Lu, Jianfeng/0000-0001-6255-5165 FU Office of Advanced Scientific Computing Research of the U.S. DOE [DE-AC02-05CH11232]; DOE [DE-FG02-03ER25587]; ONR [N00014-01-1-0674]; Office of Science, Division of Mathematical, Information, and Computational Sciences of the U.S. DOE [DE-AC02-05CH11231]; Alfred P. Sloan fellowship; NSF [DMS-0846501] FX Submitted to the journal's Methods and Algorithms for Scientific Computing section October 20, 2009; accepted for publication (in revised form) March 29, 2011; published electronically June 7, 2011. The computational results presented were obtained at the National Energy Research Scientific Computing Center (NERSC), which is supported by the Director, Office of Advanced Scientific Computing Research of the U.S. DOE under contract number DE-AC02-05CH11232.; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (cyang@lbl.gov). This author was supported by the Director, Office of Science, Division of Mathematical, Information, and Computational Sciences of the U.S. DOE under contract number DE-AC02-05CH11231.; Department of Mathematics and ICES, University of Texas at Austin, 1 University Station/C1200, Austin, TX 78712 (lexing@math.utexas.edu). This author was supported by an Alfred P. Sloan fellowship and NSF CAREER grant DMS-0846501. NR 45 TC 22 Z9 22 U1 0 U2 3 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 1064-8275 EI 1095-7197 J9 SIAM J SCI COMPUT JI SIAM J. Sci. Comput. PY 2011 VL 33 IS 3 BP 1329 EP 1351 DI 10.1137/09077432X PG 23 WC Mathematics, Applied SC Mathematics GA 782RN UT WOS:000292027900014 ER PT J AU d'Avezac, M Botts, R Mohlenkamp, MJ Zunger, A AF d'Avezac, Mayeul Botts, Ryan Mohlenkamp, Martin J. Zunger, Alex TI LEARNING TO PREDICT PHYSICAL PROPERTIES USING SUMS OF SEPARABLE FUNCTIONS SO SIAM JOURNAL ON SCIENTIFIC COMPUTING LA English DT Article DE separated representation; multivariate regression; optimized materials ID DIMENSIONS AB We present an algorithm for learning the function that maps a material structure to its value on some property, given the value of this function on several structures. We pose this problem as one of learning (regressing) a function of many variables from scattered data. Each structure is first converted to a weighted set of points by a process that removes irrelevant translations and rotations but otherwise retains full information about the structure. Then, incorporating a weighted average for each structure, we construct the multivariate regression function as a sum of separable functions, following the paradigm of separated representations. The algorithm can treat all finite and periodic structures within a common framework, and in particular does not require all structures to lie on a common lattice. We show how the algorithm simplifies when the structures do lie on a common lattice, and we present numerical results for that case. C1 [d'Avezac, Mayeul] Natl Renewable Energy Lab, Golden, CO 80401 USA. [Botts, Ryan; Mohlenkamp, Martin J.] 1 Ohio Univ, Dept Math, Athens, OH 45701 USA. [Zunger, Alex] Univ Colorado, Boulder, CO 80309 USA. RP d'Avezac, M (reprint author), Natl Renewable Energy Lab, 1617 Cole Blvd, Golden, CO 80401 USA. EM mayeul.davezac@nrel.gov; rb110503@ohio.edu; mohlenka@ohio.edu; Alex.Zunger@colorado.edu RI Zunger, Alex/A-6733-2013; OI d'Avezac, Mayeul/0000-0002-2615-8397 FU U.S. department of Energy, Office of Basic Energy Science and Engineering [DE-AC36-08GO28308]; Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division of the U.S. Department of Energy; National Science Foundation [DMS-0545895] FX This author's work was supported by the U.S. department of Energy, Office of Basic Energy Science and Engineering, under Award DE-AC36-08GO28308, and by the Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division of the U.S. Department of Energy.; The work of these authors was supported by the National Science Foundation under grant DMS-0545895. NR 12 TC 4 Z9 4 U1 1 U2 4 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 1064-8275 J9 SIAM J SCI COMPUT JI SIAM J. Sci. Comput. PY 2011 VL 33 IS 6 BP 3381 EP 3401 DI 10.1137/100805959 PG 21 WC Mathematics, Applied SC Mathematics GA 866HB UT WOS:000298370000014 ER PT J AU Lunacek, M Nag, A Alber, DM Gruchalla, K Chang, CH Graf, PA AF Lunacek, Monte Nag, Ambarish Alber, David M. Gruchalla, Kenny Chang, Christopher H. Graf, Peter A. TI SIMULATION, CHARACTERIZATION, AND OPTIMIZATION OF METABOLIC MODELS WITH THE HIGH PERFORMANCE SYSTEMS BIOLOGY TOOLKIT SO SIAM JOURNAL ON SCIENTIFIC COMPUTING LA English DT Article DE systems biology; parameter identification; metabolic modeling; ordinary differential equations; simulation optimization ID ADAPTATION; SBML AB The High Performance Systems Biology Toolkit (HiPer SBTK) is a collection of simulation and optimization components for metabolic modeling and the means to assemble these components into large parallel processing hierarchies suiting a particular simulation and optimization need. The components come in a variety of different categories: model translation, model simulation, parameter sampling, sensitivity analysis, parameter estimation, and optimization. They can be configured at runtime into hierarchically parallel arrangements to perform nested combinations of simulation characterization tasks with excellent parallel scaling to thousands of processors. We describe the observations that led to the system, the components, and how one can arrange them. We show nearly 90% efficient scaling to over 13,000 processors, and we demonstrate three complex yet typical examples that have run on similar to 1000 processors and accomplished billions of stiff ordinary differential equation simulations. This work opens the door for the systems biology metabolic modeling community to take effective advantage of large scale high performance computing resources for the first time. C1 [Lunacek, Monte; Nag, Ambarish; Alber, David M.; Gruchalla, Kenny; Chang, Christopher H.; Graf, Peter A.] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Lunacek, M (reprint author), Natl Renewable Energy Lab, 1617 Cole Blvd, Golden, CO 80401 USA. EM monte.lunacek@nrel.gov; ambarish.nag@nrel.gov; kenny.gruchalla@nrel.gov; christopher.chang@nrel.gov; peter.graf@nrel.gov FU U.S. Department of Energy; ASCR and BER Offices within the Office of Science [DE-AC36-99GO10337]; Office of Energy Efficiency and Renewable Energy of the U.S. Department of Energy [DE-AC36-08GO28308] FX This work was supported by the U.S. Department of Energy through the SciDAC and GTL programs by the ASCR and BER Offices within the Office of Science (contract DE-AC36-99GO10337). This research used capabilities of the National Renewable Energy Laboratory Computational Sciences Center, which is supported by the Office of Energy Efficiency and Renewable Energy of the U.S. Department of Energy under contract DE-AC36-08GO28308. NR 26 TC 0 Z9 0 U1 1 U2 1 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 1064-8275 J9 SIAM J SCI COMPUT JI SIAM J. Sci. Comput. PY 2011 VL 33 IS 6 BP 3402 EP 3424 DI 10.1137/110822402 PG 23 WC Mathematics, Applied SC Mathematics GA 866HB UT WOS:000298370000015 ER PT J AU Chen, J Safro, I AF Chen, Jie Safro, Ilya TI ALGEBRAIC DISTANCE ON GRAPHS SO SIAM JOURNAL ON SCIENTIFIC COMPUTING LA English DT Article DE graph connectivity measure; combinatorial scientific computing; stationary iterative process ID ALGORITHM AB Measuring the connection strength between a pair of vertices in a graph is one of the most important concerns in many graph applications. Simple measures such as edge weights may not be sufficient for capturing the effects associated with short paths of lengths greater than one. In this paper, we consider an iterative process that smooths an associated value for nearby vertices, and we present a measure of the local connection strength (called the algebraic distance; see [D. Ron, I. Safro, and A. Brandt, Multiscale Model. Simul., 9 (2011), pp. 407-423]) based on this process. The proposed measure is attractive in that the process is simple, linear, and easily parallelized. An analysis of the convergence property of the process reveals that the local neighborhoods play an important role in determining the connectivity between vertices. We demonstrate the practical effectiveness of the proposed measure through several combinatorial optimization problems on graphs and hypergraphs. C1 [Safro, Ilya] Argonne Natl Lab, Div Math & Comp Sci, Argonne, IL 60439 USA. [Chen, Jie] Univ Minnesota Twin Cities, Dept Comp Sci & Engn, Minneapolis, MN 55455 USA. RP Chen, J (reprint author), Argonne Natl Lab, Div Math & Comp Sci, 9700 S Cass Ave, Argonne, IL 60439 USA. EM jiechen@mcs.anl.gov; safro@mcs.anl.gov RI Safro, Ilya/D-9383-2012 FU U.S. Department of Energy Office of Science laboratory [DE-AC02-06CH11357]; NSF [DMS-0810938]; University of Minnesota; CSCAPES Institute, a U.S. Department of Energy; U.S. Department of Energy [DE-AC02-06CH11357] FX The submitted manuscript has been created in part 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 DE-AC02-06CH11357. The U.S. Government retains for itself, and others acting on its behalf, a paid-up nonexclusive, irrevocable worldwide license in said article to reproduce, prepare derivative works, distribute copies to the public, and perform publicly and display publicly, by or on behalf of the U.S. Government. Copyright is owned by SIAM to the extent not limited by these rights.; The work of this author was supported by NSF grant DMS-0810938, a University of Minnesota Doctoral Dissertation Fellowship, and the CSCAPES Institute, a U.S. Department of Energy project.; The work of this author was funded by the CSCAPES Institute, a U.S. Department of Energy project, and in part by U.S. Department of Energy contract DE-AC02-06CH11357. NR 30 TC 8 Z9 8 U1 2 U2 4 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 1064-8275 EI 1095-7197 J9 SIAM J SCI COMPUT JI SIAM J. Sci. Comput. PY 2011 VL 33 IS 6 BP 3468 EP 3490 DI 10.1137/090775087 PG 23 WC Mathematics, Applied SC Mathematics GA 866HB UT WOS:000298370000018 ER PT J AU Wang, B Miller, GH Colella, P AF Wang, B. Miller, G. H. Colella, P. TI A PARTICLE-IN-CELL METHOD WITH ADAPTIVE PHASE-SPACE REMAPPING FOR KINETIC PLASMAS SO SIAM JOURNAL ON SCIENTIFIC COMPUTING LA English DT Article DE particle methods; adaptive mesh refinement; remapping; Vlasov-Poisson equation ID VLASOV-POISSON EQUATION; VORTEX METHODS; NUMERICAL-METHOD; 3 DIMENSIONS; CONVERGENCE; SIMULATION; SCHEMES; HYDRODYNAMICS; SYSTEMS AB We present a new accurate and efficient particle-in-cell (PIC) method for computing the dynamics of one-dimensional kinetic plasmas. The method overcomes the numerical noise inherent in particle-based methods by periodically remapping the distribution function on a hierarchy of locally refined grids in phase space. Remapping on phase-space grids also provides an opportunity to integrate a collisional model and an associated grid-based solver. The positivity of the distribution function is enforced by redistributing excess phase-space density in a local neighborhood. We demonstrate the method on a number of standard plasma physics problems. It is shown that remapping significantly reduces the numerical noise and results in a more consistent second-order method than the standard PIC method. An error analysis is presented which is based on prior results of Cottet and Raviart's work [SIAM J. Numer. Anal., 21 (1984), pp. 52-76]. C1 [Wang, B.] Univ Calif Davis, Dept Appl Sci, Davis, CA 95616 USA. [Miller, G. H.] Univ Calif Davis, Dept Chem Engn & Mat Sci, Davis, CA 95616 USA. [Colella, P.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Appl Numer Algorithms Grp, Berkeley, CA 94720 USA. RP Wang, B (reprint author), Univ Calif Davis, Dept Appl Sci, 1 Shields Ave, Davis, CA 95616 USA. EM beiwang@ucdavis.edu; grgmiller@ucdavis.edu; colella@hpcrdm.lbl.gov RI Wang, Bei/G-4605-2014 OI Wang, Bei/0000-0003-4942-9652 FU U.S. Department of Energy Office of Advanced Scientific Computing Research at the Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; DOE [DE-SC0001981] FX This work was supported by the U.S. Department of Energy Office of Advanced Scientific Computing Research under contract DE-AC02-05CH11231 at the Lawrence Berkeley National Laboratory.; The research of this author was supported by DOE grant DE-SC0001981. NR 45 TC 8 Z9 9 U1 1 U2 4 PU SIAM PUBLICATIONS PI PHILADELPHIA PA 3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USA SN 1064-8275 EI 1095-7197 J9 SIAM J SCI COMPUT JI SIAM J. Sci. Comput. PY 2011 VL 33 IS 6 BP 3509 EP 3537 DI 10.1137/100811805 PG 29 WC Mathematics, Applied SC Mathematics GA 866HB UT WOS:000298370000020 ER PT S AU Yan, F Espenlaub, A Devaty, RP Ohshima, T Choyke, WJ AF Yan, F. Espenlaub, A. Devaty, R. P. Ohshima, T. Choyke, W. J. BE Monakhov, EV Hornos, T Svensson, BG TI Using Intrinsic Defect Spectra in 4H SiC as Imbedded Thermometers in the Temperature Range from 100 degrees C to 1500 degrees C SO SILICON CARBIDE AND RELATED MATERIALS 2010 SE Materials Science Forum LA English DT Proceedings Paper CT 8th European Conference on Silicon Carbide and Related Materials CY AUG 29-SEP 02, 2010 CL Sundvolden Conf Ctr, Oslo, NORWAY SP Aixtron, Dow Corning, Birkeland Innovation, Centrotherm, CREE Inc, Gen Elect, LPE, Norden NordForsk, SiCED, SiCrystal AG, Res Council Norway, Univ Oslo HO Sundvolden Conf Ctr DE Interface Temperature; Intrinsic Defect Spectra; Electron Irradiation; Thin Films; Graphene AB Low doped epitaxial films of 4H SiC irradiated at 1 MeV and electron fluences of 1 x 10(15) cm(-2), 3 x 10(15) cm(-2) and 1 x 10(16) cm(-2) have been used to measure temperatures in two temperature intervals: 580 degrees C to 640 degrees C and 1220 degrees C to 1320 degrees C. Possible accuracy of the temperature measurements is judged to be better than 10 degrees Centigrade. Similar measurements should be possible from 100 degrees C to 1500 degrees C. C1 [Yan, F.] Natl Renewable Energy Lab, Golden, CO 80401 USA. [Espenlaub, A.; Devaty, R. P.; Choyke, W. J.] Univ Pittsburgh, Dept Phys, Pittsburgh, PA 15260 USA. [Ohshima, T.] Japan Atom Energy Agcy, Gunma 3701292, Japan. RP Yan, F (reprint author), Natl Renewable Energy Lab, Golden, CO 80401 USA. EM choyke@pitt.edu FU II-VI Foundation FX The University of Pittsburgh group thanks the II-VI Foundation for the support of this research. We are very grateful to Dr. Al Burk and his group at Cree, Inc. for much assistance with the thick, low doped epitaxial 4H SiC. We thank Kent Berthoud of the University of Pittsburgh for help in taking data and data reduction. NR 1 TC 0 Z9 0 U1 1 U2 1 PU TRANS TECH PUBLICATIONS LTD PI DURNTEN-ZURICH PA KREUZSTRASSE 10, 8635 DURNTEN-ZURICH, SWITZERLAND SN 0255-5476 J9 MATER SCI FORUM PY 2011 VL 679-680 BP 237 EP + DI 10.4028/www.scientific.net/MSF.679-680.237 PG 2 WC Engineering, Multidisciplinary; Materials Science, Multidisciplinary; Physics, Applied SC Engineering; Materials Science; Physics GA BVJ83 UT WOS:000291673500056 ER PT B AU Keiter, ER Thornquist, HK Hoekstra, RJ Russo, TV Schiek, RL Rankin, EL AF Keiter, Eric R. Thornquist, Heidi K. Hoekstra, Robert J. Russo, Thomas V. Schiek, Richard L. Rankin, Eric L. BE Li, P Silveira, LM Feldmann, P TI Parallel Transistor-Level Circuit Simulation SO SIMULATION AND VERIFICATION OF ELECTRONIC AND BIOLOGICAL SYSTEMS LA English DT Proceedings Paper CT Circuit and Multi-Domain Simulation Workshop CY NOV 05, 2009 CL San Jose, CA SP Synopsys Inc, ACM SIGDA Phys Design Techn Comm ID DOMAIN DECOMPOSITION; ALGORITHM; SOLVER AB With the advent of multi-core technology, inexpensive large-scale parallel platforms are now widely available. While this presents new opportunities for the EDA community, traditional transistor-level, SPICE-style circuit simulation has unique parallel simulation challenges. Here the Xyce Parallel Circuit Simulator is described, which has been designed from the "from-the-ground-up" to be distributed memory-parallel. Xyce has demonstrated scalable circuit simulation on hundreds of processors, but doing so required a comprehensive parallel strategy. This included the development of new solver technologies, including novel preconditioned iterative solvers, as well as attention to other aspects of the simulation such as parallel file I/O, and efficient load balancing of device evaluations and linear systems. Xyce relies primarily upon a message-passing (MPI-based) implementation, but optimal scalability on multi-core platforms can require a combination of message-passing and threading. To accommodate future parallel platforms, software abstractions allowing adaptation to other parallel paradigms are part of the Xyce design. C1 [Keiter, Eric R.; Thornquist, Heidi K.; Russo, Thomas V.; Schiek, Richard L.; Rankin, Eric L.] Sandia Natl Labs, Elect & Microsyst Modeling Dept, POB 5800, Albuquerque, NM 87185 USA. [Hoekstra, Robert J.] Sandia Natl Labs, Appl Math & Applicat Dept, Albuquerque, NM 87185 USA. RP Keiter, ER (reprint author), Sandia Natl Labs, Elect & Microsyst Modeling Dept, POB 5800, Albuquerque, NM 87185 USA. EM erkeite@sandia.gov; hkthorn@sandia.gov; rjhoeks@sandia.gov; tvrusso@sandia.gov; rlschiek@sandia.gov; elranki@sandia.gov NR 30 TC 4 Z9 4 U1 0 U2 0 PU SPRINGER PI DORDRECHT PA PO BOX 17, 3300 AA DORDRECHT, NETHERLANDS BN 978-94-007-0148-9 PY 2011 BP 1 EP + DI 10.1007/978-94-007-0149-6_1 PG 3 WC Engineering, Electrical & Electronic SC Engineering GA BEO36 UT WOS:000317550800001 ER PT B AU May, EE AF May, Elebeoba E. BE Li, P Silveira, LM Feldmann, P TI Circuit-Based Models of Biomolecular System Dynamics SO SIMULATION AND VERIFICATION OF ELECTRONIC AND BIOLOGICAL SYSTEMS LA English DT Proceedings Paper CT Circuit and Multi-Domain Simulation Workshop CY NOV 05, 2009 CL San Jose, CA SP Synopsys Inc, ACM SIGDA Phys Design Techn Comm ID SOFTWARE ENVIRONMENT; SIMULATION; PATHWAY; CELL; MECHANISM; NETWORKS AB Methods from the field of electrical engineering have been used for the modeling and analysis of biological systems. In this work we exploit parallels between electrical and biological circuits for simulation of bimolecular processes and systems. We review the development of BioXyce, an electrical circuit-based systems biology simulation platform, and demonstrate its use in simulating intracellular biochemical pathways. We present simulation results for metabolic pathways and eukaryotic signal transduction pathways important in host immune response. C1 Sandia Natl Labs, Albuquerque, NM 87185 USA. RP May, EE (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87185 USA. EM eemay@sandia.gov NR 26 TC 3 Z9 3 U1 0 U2 2 PU SPRINGER PI DORDRECHT PA PO BOX 17, 3300 AA DORDRECHT, NETHERLANDS BN 978-94-007-0148-9 PY 2011 BP 137 EP 156 DI 10.1007/978-94-007-0149-6_7 PG 20 WC Engineering, Electrical & Electronic SC Engineering GA BEO36 UT WOS:000317550800007 ER PT B AU Ahn, TH Dechev, D Lin, HS Adalsteinsson, H Janssen, C AF Ahn, Tae-Hyuk Dechev, Damian Lin, Heshan Adalsteinsson, Helgi Janssen, Curtis BE Kacprzyk, J Pina, N Filipe, J TI EVALUATING PERFORMANCE OPTIMIZATIONS OF LARGE-SCALE GENOMIC SEQUENCE SEARCH APPLICATIONS USING SST/MACRO SO SIMULTECH 2011: PROCEEDINGS OF THE 1ST INTERNATIONAL CONFERENCE ON SIMULATION AND MODELING METHODOLOGIES, TECHNOLOGIES AND APPLICATIONS LA English DT Proceedings Paper CT 1st International Conference on Simulation and Modeling Methodologies, Technologies and Applications (SIMULTECH 2011) CY JUL 29-31, 2011 CL Noordwijkerhout, NETHERLANDS SP Inst Syst & Technol Informat, Control & Commun, Soc Model & Simulat Int, Informat Interact Intelligence, Liophant Simulat, Simulat Team DE Exascale architecture simulator; mpiBLAST; Performance and scalability modeling ID SIMULATION; BLAST; PROGRAMS AB The next decade will see a rapid evolution of HPC node architectures as power and cooling constraints are limiting increases in microprocessor clock speeds and constraining data movement. Future and current HPC applications will have to change and adapt as node architectures evolve. The application of advanced cycle accurate node architecture simulators will play a crucial role for the design and optimization of future data intensive applications. In this paper, we present our simulation-based framework for analyzing the scalability and performance of a number of critical optimizations of a massively parallel genomic search application, mpiBLAST, using an advanced macroscale simulator (SST/macro). In this paper we report the use of our framework for the evaluation of three potential improvements of mpiBLAST: enabling high-performance parallel output, an approach for caching database fragments in memory, and a methodology for pre-distributing database segments. In our experimental setup, we performed query sequence matching on the genome of the yellow fever mosquito, Aedes aegypti. C1 [Ahn, Tae-Hyuk; Lin, Heshan] Virginia Tech, Dept Comp Sci, Blacksburg, VA 24061 USA. [Dechev, Damian] Univ Cent Florida, Dept Elect Engn & Comp Sci, Orlando, FL 32816 USA. [Dechev, Damian; Adalsteinsson, Helgi; Janssen, Curtis] Sandia Natl Labs, Scalable Comp R&D Dept, Livermore, CA 94551 USA. RP Ahn, TH (reprint author), Virginia Tech, Dept Comp Sci, Blacksburg, VA 24061 USA. EM thahn@cs.vt.edu; ddechev@sandia.gov; hlin2@cs.vt.edu; hadalst@sandia.gov; cljanss@sandia.gov NR 29 TC 0 Z9 0 U1 0 U2 0 PU INSTICC-INST SYST TECHNOLOGIES INFORMATION CONTROL & COMMUNICATION PI SETUBAL PA AVENIDA D MANUEL L, 27A 2 ESQUERDO, SETUBAL, 2910-595, PORTUGAL BN 978-989-8425-78-2 PY 2011 BP 65 EP 73 PG 9 WC Computer Science, Interdisciplinary Applications SC Computer Science GA BG9SB UT WOS:000393719200009 ER PT S AU Dagel, DJ Liu, YS Zhong, L Luo, Y Zeng, Y Himmel, M Ding, SY Smith, S AF Dagel, D. J. Liu, Y. -S. Zhong, L. Luo, Y. Zeng, Y. Himmel, M. Ding, S. -Y. Smith, S. BE Enderlein, J Gryczynski, ZK Erdmann, R TI DOPI and PALM Imaging of Single Carbohydrate Binding Modules Bound to Cellulose Nanocrystals SO SINGLE MOLECULE SPECTROSCOPY AND IMAGING IV SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on Single Molecule Spectroscopy and Imaging IV CY JAN 22-23, 2011 CL San Francisco, CA SP SPIE DE Single Molecule; PALM; DOPI; GFP; TIRF; Cellulose; Carbohydrate Binding Module; Bioenergy; Biomass ID ORIENTATION; MICROSCOPY AB We use single molecule imaging methods to study the binding characteristics of carbohydrate-binding modules (CBMs) to cellulose crystals. The CBMs are carbohydrate specific binding proteins, and a functional component of most cellulase enzymes, which in turn hydrolyze cellulose, releasing simple sugars suitable for fermentation to biofuels. The CBM plays the important role of locating the crystalline face of cellulose, a critical step in cellulase action. A biophysical understanding of the CBM action aids in developing a mechanistic picture of the cellulase enzyme, important for selection and potential modification. Towards this end, we have genetically modified cellulose-binding CBM derived from bacterial source with green fluorescent protein (GFP), and photo-activated fluorescence protein PAmCherry tags, respectively. Using the single molecule method known as Defocused Orientation and Position Imaging (DOPI), we observe a preferred orientation of the CBM-GFP complex relative to the Valonia cellulose nanocrystals. Subsequent analysis showed the CBMs bind to the opposite hydrophobic < 110 > faces of the cellulose nanocrystals with a well-defined cross-orientation of about similar to 70 degrees. Photo Activated Localization Microscopy (PALM) is used to localize CBM-PAmCherry with a localization accuracy of similar to 10nm. Analysis of the nearest neighbor distributions along and perpendicular to the cellulose nanocrystal axes are consistent with single-file CBM binding along the fiber axis, and microfibril bundles consisting of close packed similar to 20nm or smaller cellulose microfibrils. C1 [Dagel, D. J.; Zhong, L.; Smith, S.] S Dakota Sch Mines & Technol, Rapid City, SD 57701 USA. RP Ding, SY (reprint author), Natl Renewable Energy Lab, Biosci Ctr, Golden, CO 80401 USA. EM Shi.You.Ding@nrel.gov; Steve.Smith@sdsmt.edu RI Ding, Shi-You/O-1209-2013 NR 14 TC 2 Z9 2 U1 3 U2 6 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-8442-0 J9 PROC SPIE PY 2011 VL 7905 AR 79050P DI 10.1117/12.875285 PG 6 WC Optics; Radiology, Nuclear Medicine & Medical Imaging; Spectroscopy SC Optics; Radiology, Nuclear Medicine & Medical Imaging; Spectroscopy GA BXZ25 UT WOS:000297674400013 ER PT S AU Gaiotto, T Nguyena, HB Jung, J Gnanakaran, GS Schmidt, JG Waldo, GS Bradbury, AM Goodwin, PM AF Gaiotto, Tiziano Nguyena, Hau B. Jung, Jaemyeong Gnanakaran, Gnana S. Schmidt, Jurgen G. Waldo, Geoffrey S. Bradbury, Andrew M. Goodwin, Peter M. BE Enderlein, J Gryczynski, ZK Erdmann, R TI A photophysical study of two fluorogen-activating proteins bound to their cognate fluorogens SO SINGLE MOLECULE SPECTROSCOPY AND IMAGING IV SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on Single Molecule Spectroscopy and Imaging IV CY JAN 22-23, 2011 CL San Francisco, CA SP SPIE DE fluorogen-activating protein; fluorescence correlation spectroscopy; single-molecule; imaging; spectroscopy; fluorogen; thiazole orange; malachite green ID FLUORESCENCE CORRELATION SPECTROSCOPY; SINGLE-CHAIN ANTIBODIES; DIFFUSION-COEFFICIENTS; QUANTUM DOTS; MOLECULES; BIOLOGY AB We are exploring the use of fluorogen-activating proteins (FAPs) as reporters for single-molecule imaging. FAPs are single-chain antibodies selected to specifically bind small chromophoric molecules termed fluorogens. Upon binding to its cognate FAP the fluorescence quantum yield of the fluorogen increases giving rise to a fluorescent complex. Based on the seminal work of Szent-Gyorgyi et al. (Nature Biotechnology, Volume 26, Number 2, pp 235-240, 2008) we have chosen to study two fluorogen-activating single-chain antibodies, HL1.0.1-TO1 and H6-MG, bound to their cognate fluorogens, thiazole orange and malachite green derivatives, respectively. Here we use fluorescence correlation spectroscopy to study the photophysics of these fluorescent complexes. C1 [Gaiotto, Tiziano; Nguyena, Hau B.; Waldo, Geoffrey S.; Bradbury, Andrew M.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Gaiotto, T (reprint author), Los Alamos Natl Lab, Los Alamos, NM 87545 USA. EM tiziano@lanl.gov; pmg@lanl.gov OI Schmidt, Jurgen/0000-0002-8192-9940; Gnanakaran, S/0000-0002-9368-3044; Bradbury, Andrew/0000-0002-5567-8172 NR 23 TC 0 Z9 0 U1 0 U2 3 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-8442-0 J9 PROC SPIE PY 2011 VL 7905 AR 79050O DI 10.1117/12.875418 PG 10 WC Optics; Radiology, Nuclear Medicine & Medical Imaging; Spectroscopy SC Optics; Radiology, Nuclear Medicine & Medical Imaging; Spectroscopy GA BXZ25 UT WOS:000297674400012 ER PT J AU Anafi, R Sato, TK Kim, J Hogenesch, JB AF Anafi, R. Sato, T. K. Kim, J. Hogenesch, J. B. TI IDENTIFICATION OF NOVEL CORE CLOCK GENES BY BAYESIAN INTEGRATION SO SLEEP LA English DT Meeting Abstract CT 25th Anniversary Meeting of the Associated-Professional-Sleep-Societies (APSS) CY JUN 11-15, 2011 CL Minneapolis, MN SP Associated Profess Sleep Soc (APSS) C1 [Anafi, R.] Univ Penn, Div Sleep Med, Philadelphia, PA 19104 USA. [Hogenesch, J. B.] Univ Penn, Dept Pharmacol, Philadelphia, PA 19104 USA. [Hogenesch, J. B.] Univ Penn, Inst Translat Med & Therapeut, Philadelphia, PA 19104 USA. [Kim, J.] Univ Penn, Dept Biol, Philadelphia, PA 19104 USA. [Kim, J.] Univ Penn, Penn Genome Frontiers Inst, Philadelphia, PA 19104 USA. [Sato, T. K.] Univ Wisconsin, Great Lakes Bioenergy Res Ctr, Madison, WI USA. NR 0 TC 0 Z9 0 U1 0 U2 0 PU AMER ACAD SLEEP MEDICINE PI WESTCHESTER PA ONE WESTBROOK CORPORATE CTR, STE 920, WESTCHESTER, IL 60154 USA SN 0161-8105 J9 SLEEP JI Sleep PY 2011 VL 34 SU S MA 0026 BP A12 EP A12 PG 1 WC Clinical Neurology; Neurosciences SC Neurosciences & Neurology GA 886EG UT WOS:000299834400028 ER PT J AU Presley, AD Chang, JJ Xu, T AF Presley, Andrew D. Chang, Joseph J. Xu, Ting TI Directed co-assembly of heme proteins with amphiphilic block copolymers toward functional biomolecular materials SO SOFT MATTER LA English DT Article ID DE-NOVO DESIGN; 4-HELIX BUNDLE PEPTIDES; THIN-FILMS; DIRECT ELECTROCHEMISTRY; EXTENDED CHROMOPHORES; ELECTRON-TRANSFER; HELIX BUNDLE; TEMPLATES; HEMOGLOBIN; MAQUETTES AB Directed co-assembly of block copolymers and proteins/peptides may lead to hierarchically structured functional biomolecular materials. However, this requires one to synergistically direct multiple self-assembly processes. Retaining proper cofactor binding is essential to utilize many bio-motifs for catalytic reactions and sensing. Here, by using a heme-binding helix bundle peptide-polymer conjugate and a holo myoglobin-polymer conjugate as examples, we show that the simultaneous, macroscopic assembly of heme-binding proteins and diblock copolymers can be achieved in thin films without compromising protein structures, cofactor binding and enzymatic activities. To our knowledge, this is the first example of a protein/cofactor complex formed upon being co-assembled with an amphiphilic block copolymer in thin films. Molecular assembly via a combination of biomolecular recognition and polymer phase separation in this fashion will lead to hybrid materials combining properties of both synthetic and biological building blocks. C1 [Presley, Andrew D.; Chang, Joseph J.; Xu, Ting] Univ Calif Berkeley, Dept Mat Sci & Engn, Berkeley, CA 94720 USA. [Xu, Ting] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. [Xu, Ting] Lawrence Berkeley Natl Lab, Mat Sci Div, Berkeley, CA 94720 USA. RP Xu, T (reprint author), Univ Calif Berkeley, Dept Mat Sci & Engn, Berkeley, CA 94720 USA. EM tingxu@berkeley.edu FU U.S. Department of Energy at Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy [DE-AC02-05CH11231, DE-AC02-06CH11357] FX This work is supported by the U.S. Department of Energy through the Hybrid Biomaterials Scattering Program at Lawrence Berkeley National Laboratory under Contract DE-AC02-05CH11231. Use of 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. Use of the Advanced Photon Source was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. We acknowledge helpful discussions with Jessica Y. Shu and Yu-Ja Huang regarding spectroscopic characterization of peptide/BCP thin films. NR 54 TC 20 Z9 20 U1 9 U2 52 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1744-683X J9 SOFT MATTER JI Soft Matter PY 2011 VL 7 IS 1 BP 172 EP 179 DI 10.1039/c0sm00817f PG 8 WC Chemistry, Physical; Materials Science, Multidisciplinary; Physics, Multidisciplinary; Polymer Science SC Chemistry; Materials Science; Physics; Polymer Science GA 695HC UT WOS:000285360200024 ER PT J AU Li, X Zamponi, M Hong, KL Porcar, L Shew, CY Jenkins, T Liu, E Smith, GS Herwig, KW Liu, Y Chen, WR AF Li, Xin Zamponi, Michaela Hong, Kunlun Porcar, Lionel Shew, Chwen-Yang Jenkins, Timothy Liu, Emily Smith, Gregory S. Herwig, Kenneth W. Liu, Yun Chen, Wei-Ren TI pH Responsiveness of polyelectrolyte dendrimers: a dynamical perspective SO SOFT MATTER LA English DT Article ID ANGLE NEUTRON-SCATTERING; PAMAM DENDRIMERS; MOLECULAR-DYNAMICS; AQUEOUS-SOLUTIONS; POLY(AMIDOAMINE) DENDRIMERS; CONFORMATIONAL-CHANGES; INTERNAL DYNAMICS; FIELD GRADIENT; SPIN ECHOES; DIFFUSION AB A combined quasi-elastic neutron scattering (QENS) and high-resolution solution NMR spectroscopy study was conducted to investigate the internal dynamics of aqueous (D(2)O) G5 PAMAM dendrimer solutions as a function of molecular protonation at room temperature. Localized motion of the dendrimer segments was clearly exhibited in the QENS data analysis while the global, center-of-mass translational diffusion was measured by NMR. Our results unambiguously demonstrate an increased rapidity in local scale (similar to 3 angstrom) motion upon increasing the molecular protonation. This is contrary to an intuitive picture that increased charge stiffens the dendrimer segments thereby inhibiting local motion. These charge-induced changes may be a result of interactions with the surrounding counterions and water molecules as the segments explore additional intra-dendrimer volume made available by slight electrostatic swelling and redistribution of mass in the dendrimer interior. This observation is relevant to development of a microscopic picture of dendrimer-based packages as guest-molecule delivery vehicles because reorganization of the confining dendrimer segments must be a precursor to guest-molecule release. C1 [Li, Xin; Zamponi, Michaela; Smith, Gregory S.; Herwig, Kenneth W.; Chen, Wei-Ren] Oak Ridge Natl Lab, Neutron Scattering Sci Div, Oak Ridge, TN 37831 USA. [Li, Xin; Liu, Emily] Rensselaer Polytech Inst, Dept Mech Aerosp & Nucl Engn, Troy, NY 12180 USA. [Zamponi, Michaela] Forschungszentrum Julich, Julich Ctr Neutron Sci, D-52425 Julich, Germany. [Hong, Kunlun] Oak Ridge Natl Lab, Ctr Nanophase Mat Sci, Oak Ridge, TN 37831 USA. [Porcar, Lionel] Inst Laue Langevin, F-38042 Grenoble 9, France. [Shew, Chwen-Yang] CUNY, Dept Chem, Coll Staten Isl, Staten Isl, NY 10314 USA. [Jenkins, Timothy; Liu, Yun] Natl Inst Stand & Technol, NIST Ctr Neutron Res, Gaithersburg, MD 20899 USA. [Liu, Yun] Univ Delaware, Dept Chem Engn, Newark, DE 19716 USA. [Chen, Wei-Ren] Oak Ridge Natl Lab, Joint Inst Neutron Sci, Oak Ridge, TN 37831 USA. [Chen, Wei-Ren] Univ Tennessee, Dept Chem & Biomol Engn, Knoxville, TN 37996 USA. RP Herwig, KW (reprint author), Oak Ridge Natl Lab, Neutron Scattering Sci Div, Oak Ridge, TN 37831 USA. EM herwigkw@ornl.gov; yunliu@nist.gov; chenw@ornl.gov RI Herwig, Kenneth/F-4787-2011; Sanders, Susan/G-1957-2011; Liu, Yun/F-6516-2012; Li, Xin/K-9646-2013; Smith, Gregory/D-1659-2016; Hong, Kunlun/E-9787-2015 OI Liu, Yun/0000-0002-0944-3153; Li, Xin/0000-0003-0606-434X; Smith, Gregory/0000-0001-5659-1805; Hong, Kunlun/0000-0002-2852-5111 FU Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy; ORNL by the Division of Scientific User Facilities, U.S. Department of Energy FX This research at Oak Ridge National Laboratory's SNS was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy. CNMS is sponsored at ORNL by the Division of Scientific User Facilities, U.S. Department of Energy. NR 33 TC 19 Z9 19 U1 2 U2 39 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1744-683X J9 SOFT MATTER JI Soft Matter PY 2011 VL 7 IS 2 BP 618 EP 622 DI 10.1039/c0sm00671h PG 5 WC Chemistry, Physical; Materials Science, Multidisciplinary; Physics, Multidisciplinary; Polymer Science SC Chemistry; Materials Science; Physics; Polymer Science GA 705EE UT WOS:000286110900038 ER PT J AU Kewalramani, S Wang, ST Lin, YA Huong, GN Wang, QA Fukuto, M Yang, L AF Kewalramani, Sumit Wang, Suntao Lin, Yuan Huong Giang Nguyen Wang, Qian Fukuto, Masafumi Yang, Lin TI Systematic approach to electrostatically induced 2D crystallization of nanoparticles at liquid interfaces SO SOFT MATTER LA English DT Article ID COWPEA MOSAIC-VIRUS; CHARGED LIPID LAYERS; PROTEIN CRYSTALLIZATION; PHOSPHOLIPID MONOLAYERS; COLLOIDAL CRYSTALS; ARRAYS; CRYSTALLOGRAPHY; SURFACES; POINT AB We report an experimental demonstration of a strategy for inducing two-dimensional (2D) crystallization of charged nanoparticles on oppositely charged fluid interfaces. This strategy aims to maximize the interfacial adsorption of nanoparticles, and hence their lateral packing density, by utilizing a combination of weakly charged particles and a high surface charge density on the planar interface. In order to test this approach, we investigated the assembly of cowpea mosaic virus (CPMV) on positively charged lipid monolayers at the aqueous solution surface, by means of in situ X-ray scattering measurements at the liquid-vapor interface. The assembly was studied as a function of the solution pH, which was used to vary the charge on CPMV, and of the mole fraction of the cationic lipid in the binary lipid monolayer, which set the interface charge density. The 2D crystallization of CPMV occurred in a narrow pH range just above the particle's isoelectric point, where the particle charge was weakly negative, and only when the cationic-lipid fraction in the monolayer exceeded a threshold. The observed 2D crystals exhibited nearly the same packing density as the densest lattice plane within the known 3D crystals of CPMV. The above electrostatic approach of maximizing interfacial adsorption may provide an efficient route to the crystallization of nanoparticles at aqueous interfaces. C1 [Kewalramani, Sumit; Fukuto, Masafumi] Brookhaven Natl Lab, Condensed Matter Phys & Mat Sci Dept, Upton, NY 11973 USA. [Wang, Suntao; Yang, Lin] Brookhaven Natl Lab, Natl Synchrotron Light Source, Upton, NY 11973 USA. [Lin, Yuan; Huong Giang Nguyen; Wang, Qian] Univ S Carolina, Dept Chem & Biochem, Columbia, SC 29208 USA. [Lin, Yuan; Huong Giang Nguyen; Wang, Qian] Univ S Carolina, Nanoctr, Columbia, SC 29208 USA. RP Fukuto, M (reprint author), Brookhaven Natl Lab, Condensed Matter Phys & Mat Sci Dept, Upton, NY 11973 USA. EM fukuto@bnl.gov; lyang@bnl.gov RI Yang, Lin/D-5872-2013; OI Yang, Lin/0000-0003-1057-9194; Wang, Qian/0000-0002-2149-384X FU US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering [DE-AC02-98CH10886]; National Science Foundation [CHE-0748690]; Department of Defense [WN11NF-09-1-236]; Department of Energy, Office of Basic Energy Sciences [DE-SC0001477]; W. M. Keck Foundation FX We thank H. Hlaing for assistance with sample preparation. The BNL contribution to this work, including use of the National Synchrotron Light Source, was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering, under contract no. DE-AC02-98CH10886. QW acknowledges the financial support from National Science Foundation under contract no. CHE-0748690, Department of Defense under contract no. WN11NF-09-1-236, Department of Energy, Office of Basic Energy Sciences, under contract no. DE-SC0001477, and the W. M. Keck Foundation. NR 44 TC 14 Z9 14 U1 3 U2 32 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1744-683X J9 SOFT MATTER JI Soft Matter PY 2011 VL 7 IS 3 BP 939 EP 945 DI 10.1039/c0sm00956c PG 7 WC Chemistry, Physical; Materials Science, Multidisciplinary; Physics, Multidisciplinary; Polymer Science SC Chemistry; Materials Science; Physics; Polymer Science GA 711TY UT WOS:000286615500021 ER PT J AU Sadakane, K Iguchi, N Nagao, M Endo, H Melnichenko, YB Seto, H AF Sadakane, Koichiro Iguchi, Natsuki Nagao, Michihiro Endo, Hitoshi Melnichenko, Yuri B. Seto, Hideki TI 2D-Ising-like critical behavior in mixtures of water and 3-methylpyridine including antagonistic salt or ionic surfactant SO SOFT MATTER LA English DT Article ID AQUEOUS-ELECTROLYTE SOLUTION; ANGLE NEUTRON-SCATTERING; X-RAY-SCATTERING; PHASE-SEPARATION; 3RD COMPONENTS; CRITICAL-POINT; CROSSOVER; SYSTEM; RENORMALIZATION; DENSITY AB The effect of an antagonistic salt on the phase behavior and nanoscale structure of a mixture of D(2)O and 3-methylpyridine was investigated by visual inspection and small-angle neutron scattering (SANS). The addition of the antagonistic salt, namely sodium tetraphenylborate (NaBPh(4)), induces the shrinking of the two-phase region in contrast to the case in which a normal (hydrophilic) salt is added. Below the phase separation point, the SANS profiles cannot be described by the Ornstein-Zernike function owing to the existence of a long-range periodic structure. With increasing salt concentration, the critical exponents change from the values of 3D-Ising and approach those of 2D-Ising. These results suggest that the concentration fluctuation of the mixture of solvents is limited to a quasi two-dimensional space by the periodic structure induced by the adding the salt. The same behaviors were also observed in mixtures composed of water, 3-methylpyridine, and ionic surfactant. C1 [Sadakane, Koichiro; Seto, Hideki] High Energy Accelerator Res Org, KENS, Tsukuba, Ibaraki 3050801, Japan. [Sadakane, Koichiro; Seto, Hideki] High Energy Accelerator Res Org, Inst Mat Struct Sci, CMRC, Tsukuba, Ibaraki 3050801, Japan. [Iguchi, Natsuki] Kyoto Univ, Dept Phys, Kyoto 6068502, Japan. [Nagao, Michihiro] Natl Inst Stand & Technol, NCNR, Gaithersburg, MD 20899 USA. [Endo, Hitoshi] Univ Tokyo, Inst Solid State Phys, NSL, Tokai, Ibaraki 3191106, Japan. [Melnichenko, Yuri B.] Oak Ridge Natl Lab, NSSD, Oak Ridge, TN 37831 USA. [Nagao, Michihiro] Indiana Univ, CEEM, Bloomington, IN 47408 USA. RP Seto, H (reprint author), High Energy Accelerator Res Org, KENS, Tsukuba, Ibaraki 3050801, Japan. EM hideki.seto@kek.jp RI Sanders, Susan/G-1957-2011; OI Seto, Hideki/0000-0002-1658-3576 FU Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan; Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy FX The authors acknowledge Prof. A. Onuki at Kyoto University for valuable discussions. This work was supported by a Grant-in-Aid for Scientific Research on Priority Area "Soft Matter Physics'' from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan. The SANS experiments in JAEA were performed under the approval of the Neutron Scattering Program Advisory Committee (Proposal No. 8616). The Research at Oak Ridge National Laboratory's High Flux Isotope Reactor was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy, and approved by the steering committee of the US-Japan Collaborative Program on Neutron Scattering (2008-14). NR 27 TC 18 Z9 18 U1 0 U2 9 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1744-683X J9 SOFT MATTER JI Soft Matter PY 2011 VL 7 IS 4 BP 1334 EP 1340 DI 10.1039/c0sm00598c PG 7 WC Chemistry, Physical; Materials Science, Multidisciplinary; Physics, Multidisciplinary; Polymer Science SC Chemistry; Materials Science; Physics; Polymer Science GA 718AM UT WOS:000287091600012 ER PT J AU Kalb, J Dukes, D Kumar, SK Hoy, RS Grest, GS AF Kalb, Joshua Dukes, Douglas Kumar, Sanat K. Hoy, Robert S. Grest, Gary S. TI End grafted polymer nanoparticles in a polymeric matrix: Effect of coverage and curvature SO SOFT MATTER LA English DT Article ID LINEAR FLEXIBLE MACROMOLECULES; MOLECULAR-DYNAMICS SIMULATION; DISPERSING NANOPARTICLES; COMPUTER-SIMULATIONS; SURFACE; BRUSHES; DENSITY; MELTS; CHAINS; LAYERS AB It has recently been proposed that the miscibility of nanoparticles with a polymer matrix can be controlled by grafting polymer chains to the nanoparticle surface. We examine this hypothesis using molecular dynamics simulations on a single nanoparticle of radius R (4 sigma <= R <= 16 sigma, where sigma is the diameter of a polymer monomer) grafted with chains of length 500 in a polymer melt of chains of length 1000. The grafting density Sigma is varied between 0.04-0.32 chains/sigma(2). To facilitate equilibration a Monte Carlo double-bridging algorithm is applied - new bonds are formed across a pair of chains, creating two new chains each substantially different from the original. For the long brush chains studied here, the structure of the brush assumes its large particle limit even for R as small as 8 sigma, which is consistent with recent experimental findings and the small chain lattice simulations of Klos and Pakula. We study autophobic dewetting of the melt from the brush as a function of increasing Sigma. Even these long brush and matrix chains of lengths 6 and 12 N(e), respectively, (the entanglement length is N(e) similar to 85) give somewhat ambiguous results for the interfacial width, showing that studies of two or more nanoparticles are necessary to properly understand these miscibility issues. Entanglement between the brush and melt chains is identified using path analysis. We find that the number of entanglements between the brush and melt chains scale simply with the product of the local monomer densities of brush and melt chains. C1 [Kalb, Joshua; Kumar, Sanat K.] Columbia Univ, Dept Chem Engn, New York, NY 10027 USA. [Dukes, Douglas] Rensselaer Polytech Inst, Dept Mat Sci & Engn, Troy, NY USA. [Hoy, Robert S.] Yale Univ, Dept Mech Engn & Mat Sci, New Haven, CT USA. [Grest, Gary S.] Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Kumar, SK (reprint author), Columbia Univ, Dept Chem Engn, New York, NY 10027 USA. EM sk2794@columbia.edu RI Hoy, Robert/B-1169-2009 FU National Science Foundation [DMR05-20415, DMR-0835742]; Sandia National Laboratories; United States Department of Energy [DEAC04-94AL85000]; New York State Office of Science, Technology & Academic Research [C070119] FX We thank the New Mexico Computing Application Center NMCAC for a generous allocation of computer time. Funding for this research at Columbia was provided by the National Science Foundation through a NIRT grant. Support from NSF Award Nos. DMR05-20415, DMR-0835742 is gratefully acknowledged. This work was performed, in part, at the Center for Integrated Nanotechnologies, a U.S. Department of Energy, Office of Basic Energy Sciences user facility. Supported, in part, by the Laboratory Directed Research and Development program at Sandia National Laboratories. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy under Contract No. DEAC04-94AL85000. This material is based upon work supported, in part, by the New York State Office of Science, Technology & Academic Research under contract no. C070119. NR 46 TC 57 Z9 57 U1 5 U2 65 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1744-683X J9 SOFT MATTER JI Soft Matter PY 2011 VL 7 IS 4 BP 1418 EP 1425 DI 10.1039/c0sm00725k PG 8 WC Chemistry, Physical; Materials Science, Multidisciplinary; Physics, Multidisciplinary; Polymer Science SC Chemistry; Materials Science; Physics; Polymer Science GA 718AM UT WOS:000287091600022 ER PT J AU Yoo, SY Merzlyak, A Lee, SW AF Yoo, So Young Merzlyak, Anna Lee, Seung-Wuk TI Facile growth factor immobilization platform based on engineered phage matrices SO SOFT MATTER LA English DT Article ID SCANNING ELECTRON-MICROSCOPY; ARTIFICIAL JUXTACRINE STIMULATION; EXTRACELLULAR-MATRIX; CELL-ADHESION; BASEMENT-MEMBRANE; FILAMENTOUS PHAGE; PEPTIDE LIGANDS; HPQ SEQUENCE; STEM-CELLS; DISPLAY AB Immobilized growth factors on tissue matrices play a critical role in controlling cell growth processes and cell morphology. We report a strategy for immobilizing growth factors on genetically engineered phage matrices for tissue regeneration. We modified M13 phages to express biotin-like peptides (HPQ) and/or integrin binding peptides (RGD) on their major and minor coat proteins. The resulting phages formed nanofibrous matrices that could easily immobilize growth factors FGFb and NGF. We demonstrated the synergistic roles of the growth factors and integrin binding peptides in controlling cell morphologies and growth. Our phage matrices, which can be easily functionalized with various ligands and growth factors, can be used as a convenient test bed for investigating the functions of various biochemical stimulants of numerous cell types. C1 [Yoo, So Young; Merzlyak, Anna; Lee, Seung-Wuk] Univ Calif Berkeley, Lawrence Berkeley Lab, Phys Biosci Div, Berkeley Nanosci & Nanoengn Inst,Donner Lab 1 220, Berkeley, CA 94720 USA. RP Lee, SW (reprint author), Univ Calif Berkeley, Lawrence Berkeley Lab, Phys Biosci Div, Berkeley Nanosci & Nanoengn Inst,Donner Lab 1 220, Berkeley, CA 94720 USA. EM leesw@berkeley.edu FU Hellman Family Faculty Fund; Berkeley Nanoscience and Nanoengineering Institute at the University of California, Berkeley; Lawrence Berkeley National Laboratory FX We thank Professor David Schaffer for generously donating the neural progenitor cells. This work was supported by the Hellman Family Faculty Fund (SWL); start-up funds from the Berkeley Nanoscience and Nanoengineering Institute at the University of California, Berkeley (SWL); and the Laboratory Directed Research and Development fund from the Lawrence Berkeley National Laboratory. NR 60 TC 16 Z9 18 U1 0 U2 12 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1744-683X EI 1744-6848 J9 SOFT MATTER JI Soft Matter PY 2011 VL 7 IS 5 BP 1660 EP 1666 DI 10.1039/c0sm01220c PG 7 WC Chemistry, Physical; Materials Science, Multidisciplinary; Physics, Multidisciplinary; Polymer Science SC Chemistry; Materials Science; Physics; Polymer Science GA 724PN UT WOS:000287588800015 ER PT J AU McEwan, ME Egorov, SA Ilavsky, J Green, DL Yang, Y AF McEwan, Maura E. Egorov, Sergei A. Ilavsky, Jan Green, David L. Yang, Yang TI Mechanical reinforcement of polymer nanocomposites: theory and ultra-small angle X-ray scattering (USAXS) studies SO SOFT MATTER LA English DT Article ID ORDER PHASE-TRANSITIONS; PARTICLES; HARD; EQUATION; SPHERES; MICROSTRUCTURE; SUSPENSIONS; FLUIDS; STATE; NANOPARTICLES AB The microstructure of polymer-grafted nanoparticles in polymer melts that are chemically identical to the brush was investigated using ultra-small angle X-ray scattering (USAXS). The dispersions were thermodynamically stable. Particle size and melt molecular weight were varied such that the particle softness, L*, or the ratio of the brush thickness to the particle radius ranged from L* = 0.02-0.29. The experimentally extracted structure factors and radial distribution functions from USAXS show stronger particle interactions in lower molecular weight melts due to brush stretching corresponding to an enhancement in bulk properties at particle concentrations above the jamming transition. Good agreement was found between the measured structure factors and those predicted using the Percus-Yevick closure. Further, enhancement in the storage modulus, previously observed with rheology, was predicted through the Zwanzig-Mountain relation and Monte Carlo simulations. Overall, the use of USAXS and rheology enables the connection between experiment and theory to predict, and ultimately control the interactions of polymer-grafted nanoparticles in polymer melts. C1 [McEwan, Maura E.; Green, David L.; Yang, Yang] Univ Virginia, Dept Chem Engn, Charlottesville, VA 22904 USA. [Egorov, Sergei A.] Univ Virginia, Dept Chem, Charlottesville, VA 22904 USA. [Ilavsky, Jan] Argonne Natl Lab, Adv Photon Source, Argonne, IL 60439 USA. RP Green, DL (reprint author), Univ Virginia, Dept Chem Engn, 102 Engineers Way, Charlottesville, VA 22904 USA. EM dlgreen@virginia.edu RI Egorov, Sergei/E-6061-2012; Ilavsky, Jan/D-4521-2013; USAXS, APS/D-4198-2013 OI Ilavsky, Jan/0000-0003-1982-8900; FU US Department of Energy, Office of Science, Office of Basic Energy Sciences [DE-AC02-06CH11357]; National Science Foundation Division of Chemical, Bioengineering, Environment and Transport Systems [CBET-0644890]; Old Dominion University Research Foundation; Alexander von Humboldt Foundation FX Use of the Advanced Photon Source was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. This research was supported by the National Science Foundation Division of Chemical, Bioengineering, Environment and Transport Systems (CBET-0644890) and the Old Dominion University Research Foundation. S. A. E. acknowledges Alexander von Humboldt Foundation for financial support. NR 47 TC 13 Z9 13 U1 1 U2 20 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1744-683X EI 1744-6848 J9 SOFT MATTER JI Soft Matter PY 2011 VL 7 IS 6 BP 2725 EP 2733 DI 10.1039/c0sm00393j PG 9 WC Chemistry, Physical; Materials Science, Multidisciplinary; Physics, Multidisciplinary; Polymer Science SC Chemistry; Materials Science; Physics; Polymer Science GA 732CX UT WOS:000288162500063 ER PT J AU Liu, HQ Bachand, GD AF Liu, Haiqing Bachand, George D. TI Understanding energy dissipation and thermodynamics in biomotor-driven nanocomposite assemblies SO SOFT MATTER LA English DT Article ID FLEXURAL RIGIDITY; KINESIN; MICROTUBULES; TRANSPORT; DYNAMICS; MOTORS; STEP AB We report a bimolecular motor-driven, dynamic self-assembly system in which the thermodynamic (biotin-streptavidin bond formation) and energy dissipative (ATP catalysis) components can systematically be varied to achieve several morphologically distinct nanocomposite structures consisting of microtubules and semiconductor nanocrystals. C1 [Bachand, George D.] Sandia Natl Labs, Ctr Integrated Nanotechnol, Albuquerque, NM 87185 USA. [Liu, Haiqing] Sandia Natl Labs, Surface & Interface Sci Dept, Albuquerque, NM 87185 USA. RP Bachand, GD (reprint author), Sandia Natl Labs, Ctr Integrated Nanotechnol, POB 5800, Albuquerque, NM 87185 USA. EM gdbacha@sandia.gov FU US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering [KC0203010]; US Department of Energy's National Nuclear Security Administration [DE-AC04-94AL85000] FX We thank Andy Boal, Bruce Bunker, Darryl Sasaki, and Marlene Bachand for helpful discussion and comments on this manuscript, and Dr Joe Howard for generously providing the Drosophila kinesin expression clone. This research was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering, Project KC0203010. Sandia National Laboratories is a multi-program laboratory operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Company, for the US Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. NR 33 TC 9 Z9 9 U1 5 U2 12 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1744-683X J9 SOFT MATTER JI Soft Matter PY 2011 VL 7 IS 7 BP 3087 EP 3091 DI 10.1039/c0sm01106a PG 5 WC Chemistry, Physical; Materials Science, Multidisciplinary; Physics, Multidisciplinary; Polymer Science SC Chemistry; Materials Science; Physics; Polymer Science GA 738XZ UT WOS:000288677200007 ER PT J AU Xu, J Russell, TP Ocko, BM Checco, A AF Xu, Ji Russell, Thomas P. Ocko, Benjamin M. Checco, Antonio TI Block copolymer self-assembly in chemically patterned squares SO SOFT MATTER LA English DT Article ID SINGLE-LAYER FILMS; DIBLOCK COPOLYMER; NANOPATTERNED SURFACES; THIN-FILMS; ARRAYS; LITHOGRAPHY; CYLINDERS; NANOSTRUCTURES; GRAPHOEPITAXY; TEMPLATES AB The self-assembly of block copolymers thin films laterally confined within square geometries that are incompatible with the bulk packing symmetry of the block copolymer microdomains is investigated. The lateral confinement is provided by chemical patterns made by oxidation nanolithography of octadecyltrichlorosilane-coated silicon surfaces. We find that the size and shape of the confinement affect the order of the block copolymer microdomains and their packing symmetries. Specifically, if the size of the square pattern is smaller than the characteristic grain size the hexagonally packed microdomains form a single-crystal oriented along the edges of the pattern and with "edge-boundaries" located preferentially at the perimeter of the pattern. If the size of the pattern is comparable with the natural bulk period of the copolymer, the packing symmetry changes from hexagonal to square. In this case the ordering induced by the pattern edges becomes dominant allowing the square lattice to be more stable than the hexagonal one. C1 [Xu, Ji; Russell, Thomas P.] Univ Massachusetts, Dept Polymer Sci & Engn, Amherst, MA 01003 USA. [Ocko, Benjamin M.; Checco, Antonio] Brookhaven Natl Lab, Condensed Matter Phys & Mat Sci Dept, Upton, NY 11973 USA. RP Russell, TP (reprint author), Univ Massachusetts, Dept Polymer Sci & Engn, Amherst, MA 01003 USA. EM russell@mail.pse.umass.edu; checco@bnl.gov FU U.S. Department of Energy, Basic Energy Sciences, Materials Sciences and Engineering Division; Materials Research Science and Engineering Center; Center on Functional Engineered Nano Architectonics FX Research supported by the U.S. Department of Energy, Basic Energy Sciences, Materials Sciences and Engineering Division (A.C., B.M.O., T.P.R.), by the Materials Research Science and Engineering Center (J.X.), and by the Center on Functional Engineered Nano Architectonics (J.X.). NR 32 TC 28 Z9 28 U1 1 U2 28 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1744-683X J9 SOFT MATTER JI Soft Matter PY 2011 VL 7 IS 8 BP 3915 EP 3919 DI 10.1039/c0sm01066a PG 5 WC Chemistry, Physical; Materials Science, Multidisciplinary; Physics, Multidisciplinary; Polymer Science SC Chemistry; Materials Science; Physics; Polymer Science GA 745NZ UT WOS:000289173500035 ER PT J AU Wang, X Beers, KM Kerr, JB Balsara, NP AF Wang, Xin Beers, Keith M. Kerr, John B. Balsara, Nitash P. TI Conductivity and water uptake in block copolymers containing protonated polystyrene sulfonate and their imidazolium salts SO SOFT MATTER LA English DT Article ID POLYMER ELECTROLYTE MEMBRANES; FUEL-CELL MEMBRANES; MICROPHASE SEPARATION; MOLECULAR-WEIGHT; HUMID AIR; NAFION; TRANSPORT; EXCHANGE; NANOCHANNELS; TEMPERATURE AB There is considerable interest in the properties of polymer electrolyte membranes due to their presence in fuel cells. In this paper, we report on the ionic conductivity and degree of hydration, l, of model membranes composed of polystyrene sulfonate-b-polymethylbutylene (PSS-PMB) copolymers and their imidazolium salts (PSI-PMB). The membranes were in intimate contact with humid air, and their properties were studied as a function of temperature and relative humidity of the air (RH 50 and 98%). All of the samples have a lamellar structure in the dry state, and lambda = 14 +/- 2 for PSS-PMB and PSI-PMB at RH 98%. However, the conductivity behaviors of PSS-PMB and PSI-PMB are very different. The normalized conductivity, sigma(n) (the normalization accounts for small differences in the ion concentrations in the different samples), of PSS-PMB is highly history-dependent and equilibrated behavior is only seen when the samples are annealed at high temperature (80 degrees C) for long times (about 24 h). In contrast, the equilibrated behavior is obtained rapidly in PSI-PMB samples over the entire temperature window (25-90 degrees C). At RH 98%, the equilibrated conductivities of the PSI-PMB samples at RH 98% were independent of sample molecular weight and within the experimental error of that obtained from the high molecular weight PSS-PMB sample. The low molecular weight PSS-PMB sample exhibited higher conductivity than the three samples described above. At RH = 50% both PSS-PMB and PSI-PMB samples were relatively dry with lambda < 5 over the accessible temperature window. In the dry state (1) PSS-PMB samples exhibited slow kinetics while PSI-PMB samples equilibrated rapidly, (2) molecular weight had no effect on conductivity in both PSS-PMB and PSI-PMB samples, and (3) the conductivities of PSI-PMB were significantly lower than those of PSS-PMB. C1 [Beers, Keith M.; Kerr, John B.; Balsara, Nitash P.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Mat Sci, Berkeley, CA 94720 USA. [Wang, Xin; Balsara, Nitash P.] Univ Calif Berkeley, Lawrence Berkeley Lab, Environm Energy Technol Div, Berkeley, CA 94720 USA. [Wang, Xin; Beers, Keith M.; Balsara, Nitash P.] Univ Calif Berkeley, Dept Chem & Biomol Engn, Berkeley, CA 94720 USA. RP Kerr, JB (reprint author), Univ Calif Berkeley, Lawrence Berkeley Lab, Div Mat Sci, Berkeley, CA 94720 USA. EM nbalsara@berkeley.edu FU Office of Science of the U.S. Department of Energy through both the Office of Basic Energy Sciences, Materials Sciences and Engineering Division [DE-AC02-05CH11231]; Energy Efficiency and Renewable Energy Division; Department of Energy, Office of Basic Energy Sciences, User Facilities Division FX This work was supported by the Director, Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 through both the Office of Basic Energy Sciences, Materials Sciences and Engineering Division (XW, KB, NB) and the Fuel Cell Technologies Program, Energy Efficiency and Renewable Energy Division (XW, JK). The SAXS experiments were performed at the Advanced Light Source, Lawrence Berkeley National Laboratory, a DOE national user facility supported by the Department of Energy, Office of Basic Energy Sciences, User Facilities Division, under the same contract. NR 41 TC 4 Z9 4 U1 3 U2 21 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1744-683X EI 1744-6848 J9 SOFT MATTER JI Soft Matter PY 2011 VL 7 IS 9 BP 4446 EP 4452 DI 10.1039/c0sm01520b PG 7 WC Chemistry, Physical; Materials Science, Multidisciplinary; Physics, Multidisciplinary; Polymer Science SC Chemistry; Materials Science; Physics; Polymer Science GA 751QZ UT WOS:000289634000048 ER PT J AU Wang, XJ Hong, KL Baskaran, D Goswami, M Sumpter, B Mays, J AF Wang, Xiaojun Hong, Kunlun Baskaran, Durairaj Goswami, Monojoy Sumpter, Bobby Mays, Jimmy TI Asymmetrical self-assembly from fluorinated and sulfonated block copolymers in aqueous media SO SOFT MATTER LA English DT Article ID DIBLOCK COPOLYMERS; MULTICOMPARTMENT MICELLES; MORPHOLOGICAL-CHANGES; SEGREGATION REGIME; DILUTE-SOLUTION; PHASE-BEHAVIOR; SINGLE-CHAIN; POLYSTYRENE; POLYMERS; WATER AB Block copolymers of fluorinated isoprene and partially sulfonated styrene form novel tapered rods and ribbon-like micelles in aqueous media due to a distribution of sulfonation sites and a large Flory-Huggins interaction parameter. A combination of microscopy, light scattering, and simulation demonstrates the presence of these unique nanostructures. This study sheds light on the micellization behavior of amphiphilic block polymers by revealing a new mechanism of self-assembly. C1 [Wang, Xiaojun; Baskaran, Durairaj; Mays, Jimmy] Univ Tennessee, Dept Chem, Knoxville, TN 37996 USA. [Hong, Kunlun; Sumpter, Bobby; Mays, Jimmy] Oak Ridge Natl Lab, Ctr Nanophase Mat Sci, Oak Ridge, TN 37831 USA. [Goswami, Monojoy; Sumpter, Bobby] Oak Ridge Natl Lab, Comp Sci & Math Div, Oak Ridge, TN 37831 USA. RP Mays, J (reprint author), Univ Tennessee, Dept Chem, Knoxville, TN 37996 USA. EM jimmymays@utk.edu RI Wang, Xiaojun/E-5510-2012; Goswami, Monojoy/G-7943-2012; Sumpter, Bobby/C-9459-2013; Durairaj, Baskaran/C-3692-2009; Hong, Kunlun/E-9787-2015 OI Goswami, Monojoy/0000-0002-4473-4888; Sumpter, Bobby/0000-0001-6341-0355; Durairaj, Baskaran/0000-0002-6886-5604; Hong, Kunlun/0000-0002-2852-5111 FU U.S. Department of Energy Basic Energy Sciences, MSE Division; ORNL by BSE/DOE FX We appreciate help from Tom Malmgren and John Dunlap at the University of Tennessee. This research was supported by the U.S. Department of Energy Basic Energy Sciences, MSE Division and performed in part at the Center for Nanophase Materials Sciences CKHI, sponsored at ORNL by BSE/DOE. NR 47 TC 8 Z9 8 U1 0 U2 18 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1744-683X J9 SOFT MATTER JI Soft Matter PY 2011 VL 7 IS 18 BP 7960 EP 7964 DI 10.1039/c1sm06040f PG 5 WC Chemistry, Physical; Materials Science, Multidisciplinary; Physics, Multidisciplinary; Polymer Science SC Chemistry; Materials Science; Physics; Polymer Science GA 814JW UT WOS:000294447600009 ER PT J AU Hur, SM Frischknecht, AL Huber, DL Fredrickson, GH AF Hur, Su-Mi Frischknecht, Amalie L. Huber, Dale L. Fredrickson, Glenn H. TI Self-consistent field simulations of self- and directed-assembly in a mixed polymer brush SO SOFT MATTER LA English DT Article ID COPOLYMER THIN-FILMS; STRONG-STRETCHING THEORY; BLOCK-COPOLYMER; DIBLOCK COPOLYMER; MICROPHASE SEPARATION; MATERIALS SCIENCE; MEMORY; PATTERNS; DENSITY; LAYER AB While self-assembling block copolymer thin films have attracted attention as a promising high resolution lithographic tool, the self assembly of mixed polymer brushes for lithography is relatively unexplored. Here we study the directed self-assembly of a mixed polymer brush using self-consistent field theory (SCFT) simulations. Using the model equations and numerical methods introduced and verified in our previous study, the bulk phase behavior of a mixed melt brush is studied in depth through full three dimensional calculations. We assume that the mixed A/B polymer chains, which are of the same length, are exposed to a neutral top surface and are uniformly grafted at a high density. We identify phase-separated morphologies and calculate a phase diagram for the mixed brush under melt conditions as a function of the segregation force and composition. The observed lateral microphase separation is similar to that in block copolymer thin films, but the phase separation occurs at a smaller segregation force and the transition between cylindrical and spherical morphologies are quite different than the first-order phase transition in block copolymers. We demonstrate that lateral confinement can induce long-range, in-plane order in mixed brushes and suggest promising directed self-assembly methods for the application of self-assembled mixed polymer brushes in next-generation information storage and electronic devices. C1 [Hur, Su-Mi; Fredrickson, Glenn H.] Univ Calif Santa Barbara, Dept Chem Engn, Santa Barbara, CA 93106 USA. [Frischknecht, Amalie L.; Huber, Dale L.] Sandia Natl Labs, Ctr Integrated Nanotechnol, Albuquerque, NM 87185 USA. [Fredrickson, Glenn H.] Univ Calif Santa Barbara, Dept Mat, Santa Barbara, CA 93106 USA. [Hur, Su-Mi; Fredrickson, Glenn H.] Univ Calif Santa Barbara, Mat Res Lab, Santa Barbara, CA 93106 USA. RP Hur, SM (reprint author), Univ Calif Santa Barbara, Dept Chem Engn, Santa Barbara, CA 93106 USA. RI Frischknecht, Amalie/N-1020-2014; Huber, Dale/A-6006-2008 OI Frischknecht, Amalie/0000-0003-2112-2587; Huber, Dale/0000-0001-6872-8469 FU U.S. Department of Energy [DE-AC04-94AL85000]; Sandia LDRD program; MARCO Center on Functional Engineered Nano Architectonics (FENA) FX SH would like to thank T. L. Chantawansri and K. Delaney for useful discussions. This work was performed, in part, at the Center for Integrated Nanotechnologies, a U.S. Department of Energy, Office of Basic Energy Sciences user facility. Sandia National Laboratories is a multi-program laboratory operated by Sandia Corporation, a Lockheed-Martin Company, for the U.S. Department of Energy under Contract No. DE-AC04-94AL85000. Partial support was also provided from the Sandia LDRD program and from the MARCO Center on Functional Engineered Nano Architectonics (FENA). NR 48 TC 19 Z9 19 U1 0 U2 28 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1744-683X J9 SOFT MATTER JI Soft Matter PY 2011 VL 7 IS 19 BP 8776 EP 8788 DI 10.1039/c1sm05747b PG 13 WC Chemistry, Physical; Materials Science, Multidisciplinary; Physics, Multidisciplinary; Polymer Science SC Chemistry; Materials Science; Physics; Polymer Science GA 822YE UT WOS:000295085700014 ER PT J AU Li, MD Chu, XQ Fratini, E Baglioni, P Alatas, A Alp, EE Chen, SH AF Li, Mingda Chu, Xiang-qiang Fratini, Emiliano Baglioni, Piero Alatas, Ahmet Alp, E. Ercan Chen, Sow-Hsin TI Phonon-like excitation in secondary and tertiary structure of hydrated protein powders SO SOFT MATTER LA English DT Article ID X-RAY-SCATTERING; COLLECTIVE DYNAMICS; NEUTRON-SCATTERING; ENERGY RESOLUTION; WATER; CASEIN; TRANSITION; SOFT AB Existence of sub-thermal collective excitations in proteins is of great interest due to its possible close coupling with the onset of their biological functions. We use high-energy resolution inelastic X-ray scattering to directly measure phonon dispersion relations and their damping in two hydrated proteins, alpha-chymotrypsinogen A and casein, differing in their secondary and tertiary structures. We observe that specific phonons in the Q range 28-30 nm(-1) are markedly softened only above T-D = 220 K, the observed protein dynamic transition temperature. This might indicate that only phonon modes within the wavelengths in the length scale comparable to the secondary structure dimension could be linked to the onset of protein biological activity. We also infer that the presence of tertiary structure contributes little to the population of phonons, while the alpha-helix seems to be the major contributor to phonons propagation. C1 [Li, Mingda; Chu, Xiang-qiang; Chen, Sow-Hsin] MIT, Dept Nucl Sci & Engn, Cambridge, MA 02139 USA. [Fratini, Emiliano; Baglioni, Piero] Univ Florence, Dept Chem, I-50019 Florence, Italy. [Fratini, Emiliano; Baglioni, Piero] Univ Florence, CSGI, I-50019 Florence, Italy. [Alatas, Ahmet; Alp, E. Ercan] Argonne Natl Lab, Adv Photon Source, Argonne, IL 60439 USA. RP Chen, SH (reprint author), MIT, Dept Nucl Sci & Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA. EM sowhsin@mit.edu RI Baglioni, Piero/B-1208-2011; Fratini, Emiliano/C-9983-2010; Chu, Xiangqiang/A-1572-2011; OI Baglioni, Piero/0000-0003-1312-8700; Fratini, Emiliano/0000-0001-7104-6530; Chu, Xiang-qiang/0000-0003-4320-5316 FU Basic Energy Sciences Division of US DOE [DE-FG02-90ER45429]; U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences [DE-AC02-06CH11357]; Ministero dell'Istruzione, Universita e della Ricerca Scientifica (MIUR) [prot. 20087K9A2J, FIRB-RBPR05JH2P007 Italnanonet]; Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI) FX This research at MIT is supported by a grant from Basic Energy Sciences Division of US DOE DE-FG02-90ER45429. The work at the Advanced Photon Source was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. Emiliano Fratini and Piero Baglioni acknowledge the financial support from Ministero dell'Istruzione, Universita e della Ricerca Scientifica (MIUR, grant PRIN-2008, prot. 20087K9A2J, and FIRB-RBPR05JH2P007 Italnanonet) and Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI). NR 31 TC 7 Z9 7 U1 0 U2 10 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND SN 1744-683X J9 SOFT MATTER JI Soft Matter PY 2011 VL 7 IS 21 BP 9848 EP 9853 DI 10.1039/c1sm05954h PG 6 WC Chemistry, Physical; Materials Science, Multidisciplinary; Physics, Multidisciplinary; Polymer Science SC Chemistry; Materials Science; Physics; Polymer Science GA 835HH UT WOS:000296026700005 ER PT S AU Corley, CD Mihalcea, R Mikler, AR Sanfilippo, AP AF Corley, Courtney D. Mihalcea, Rada Mikler, Armin R. Sanfilippo, Antonio P. BE Arabnia, HR Tran, QN TI Predicting Individual Affect of Health Interventions to Reduce HPV Prevalence SO SOFTWARE TOOLS AND ALGORITHMS FOR BIOLOGICAL SYSTEMS SE Advances in Experimental Medicine and Biology LA English DT Article; Book Chapter DE Computational epidemiology; Data mining; Epidemic models; Health informatics; Public health; Sentiment analysis ID HUMAN-PAPILLOMAVIRUS; COST-EFFECTIVENESS; VACCINE; BEHAVIOR; IMPACT; MODEL; POPULATION; INFECTIONS; CANCER AB Recently, human papilloma virus (HPV) has been implicated to cause several throat and oral cancers and HPV is established to cause most cervical cancers. A human papilloma virus vaccine has been proven successful to reduce infection incidence in FDA clinical trials, and it is currently available in the USA. Current intervention policy targets adolescent females for vaccination; however, the expansion of suggested guidelines may extend to other age groups and males as well. This research takes a first step towards automatically predicting personal beliefs, regarding health intervention, on the spread of disease. Using linguistic or statistical approaches, sentiment analysis determines a text's affective content. Self-reported HPV vaccination beliefs published in web and social media are analyzed for affect polarity and leveraged as knowledge inputs to epidemic models. With this in mind, we have developed a discrete-time model to facilitate predicting impact on the reduction of HPV prevalence due to arbitrary age- and gender-targeted vaccination schemes. C1 [Corley, Courtney D.; Sanfilippo, Antonio P.] Pacific NW Natl Lab, Richland, WA 99352 USA. [Mihalcea, Rada; Mikler, Armin R.] Univ N Texas, Dept Comp Sci & Engn, Denton, TX 76203 USA. RP Corley, CD (reprint author), Pacific NW Natl Lab, Richland, WA 99352 USA. EM court@pnl.gov; rada@cs.unt.edu; mikler@unt.edu; antonio.sanfilippo@pnl.gov RI Sanfilippo, Antonio/B-6743-2016 OI Sanfilippo, Antonio/0000-0001-7097-4562 NR 19 TC 2 Z9 2 U1 1 U2 7 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 0065-2598 BN 978-1-4419-7045-9 J9 ADV EXP MED BIOL JI Adv.Exp.Med.Biol. PY 2011 VL 696 BP 181 EP 190 DI 10.1007/978-1-4419-7046-6_18 D2 10.1007/978-1-4419-7046-6 PG 10 WC Biology; Mathematical & Computational Biology; Medicine, Research & Experimental SC Life Sciences & Biomedicine - Other Topics; Mathematical & Computational Biology; Research & Experimental Medicine GA BUK92 UT WOS:000289694000018 PM 21431558 ER PT J AU Haddix, ML Plante, AF Conant, RT Six, J Steinweg, JM Magrini-Bair, K Drijber, RA Morris, SJ Paul, EA AF Haddix, Michelle L. Plante, Alain F. Conant, Richard T. Six, Johan Steinweg, J. Megan Magrini-Bair, Kim Drijber, Rhae A. Morris, Sherri J. Paul, Eldor A. TI The Role of Soil Characteristics on Temperature Sensitivity of Soil Organic Matter SO SOIL SCIENCE SOCIETY OF AMERICA JOURNAL LA English DT Article ID IONIZATION MASS-SPECTROMETRY; ARCTIC TUNDRA SOILS; NITROGEN MINERALIZATION; CARBON MINERALIZATION; MICROBIAL RESPIRATION; HIGHLAND SOILS; CLIMATE-CHANGE; CO2 EMISSIONS; FOREST SOILS; PY-MBMS AB The uncertainty associated with how projected climate change will affect global C cycling could have a large impact on predictions of soil C stocks. The purpose of our study was to determine how various soil decomposition and chemistry characteristics relate to soil organic matter (SOM) temperature sensitivity. We accomplished this objective using long-term soil incubations at three temperatures (15, 25, and 35 degrees C) and pyrolysis molecular beam mass spectrometry (py-MBMS) on 12 soils from 6 sites along a mean annual temperature (MAT) gradient (2-25.6 degrees C). The Q(10) values calculated from the CO(2) respired during a long-term incubation using the Q(10-q) method showed decomposition of the more resistant fraction to be more temperature sensitive with a Q(10-q) of 1.95 +/- 0.08 for the labile fraction and a Q(10-q) of 3.33 +/- 0.04 for the more resistant fraction. We compared the fit of soil respiration data using a two-pool model (active and slow) with first-order kinetics with a three-pool model and found that the two and three-pool models statistically fit the data equally well. The three-pool model changed the size and rate constant for the more resistant pool. The size of the active pool in these soils, calculated using the two-pool model, increased with incubation temperature and ranged from 0.1 to 14.0% of initial soil organic C. Sites with an intermediate MAT and lowest C/N ratio had the largest active pool. Pyrolysis molecular beam mass spectrometry showed declines in carbohydrates with conversion from grassland to wheat cultivation and a greater amount of protected carbohydrates in allophanic soils which may have lead to differences found between the total amount of CO(2) respired, the size of the active pool, and the Q(10-q) values of the soils. C1 [Haddix, Michelle L.; Steinweg, J. Megan] Colorado State Univ, Nat Resource Ecol Lab, Grad Degree Program Ecol, Ft Collins, CO 80523 USA. [Plante, Alain F.] Univ Penn, Dep Earth & Environm Sci, Philadelphia, PA 19104 USA. [Six, Johan] Univ Calif Davis, Dep Plant Sci, Davis, CA 95616 USA. [Magrini-Bair, Kim] Natl Renewable Energy Lab, Golden, CO 80401 USA. [Drijber, Rhae A.] Univ Nebraska, Dep Agron & Hort, Lincoln, NE 68583 USA. [Morris, Sherri J.] Bradley Univ, Dept Biol, Peoria, IL 61625 USA. [Paul, Eldor A.] Colorado State Univ, Nat Resource Ecol Lab, Dep Soil & Crop Sci, Ft Collins, CO 80523 USA. RP Haddix, ML (reprint author), Colorado State Univ, Nat Resource Ecol Lab, Grad Degree Program Ecol, 200 W Lake St, Ft Collins, CO 80523 USA. EM mlhaddix@nrel.colostate.edu RI Plante, Alain/C-3498-2008; Conant, Richard/B-7586-2013; OI Plante, Alain/0000-0003-0124-6187; Conant, Richard/0000-0001-7315-2476; Haddix, Michelle/0000-0003-0984-0404 FU Office of Science (BER); U.S. Department of Energy; National Science Foundation [DEB-0444880] FX M. Vigil, R. Teague, D. Tanaka, C. C. Cerri, and C. E. P Cerri assisted with site selection and sampling. Rebecca Greenwood, Jenny Carlson, Matt Carpenter, and Jeremy Schulman assisted in laboratory measurements. This research was supported by the Office of Science (BER), U.S. Department of Energy and a National Science Foundation grant DEB-0444880. NR 60 TC 39 Z9 39 U1 4 U2 77 PU SOIL SCI SOC AMER PI MADISON PA 677 SOUTH SEGOE ROAD, MADISON, WI 53711 USA SN 0361-5995 J9 SOIL SCI SOC AM J JI Soil Sci. Soc. Am. J. PD JAN PY 2011 VL 75 IS 1 BP 56 EP 68 DI 10.2136/sssaj2010.0118 PG 13 WC Soil Science SC Agriculture GA 698VG UT WOS:000285620700009 ER PT S AU Bower, W AF Bower, Ward BE Tachibana, Y TI Solar Energy Grid Integration Systems (SEGIS) Adding functionality while maintaining reliability and economics SO SOLAR HYDROGEN AND NANOTECHNOLOGY VI SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on Solar Hydrogen and Nanotechnology VI CY AUG 23-25, 2011 CL San Diego, CA SP SPIE, RMIT Univ, Platform Technol Res Inst DE SEGIS; inverter; PV systems; smart grid; interconnect; VAr support; communications; energy management AB An overview of the activities and progress made during the US DOE Solar Energy Grid Integration Systems (SEGIS) solicitation, while maintaining reliability and economics is provided. The SEGIS R&D opened pathways for interconnecting PV systems to intelligent utility grids and micro-grids of the future. In addition to new capabilities are "value added" features. The new hardware designs resulted in smaller, less material-intensive products that are being viewed by utilities as enabling dispatchable generation and not just unpredictable negative loads. The technical solutions enable "advanced integrated system" concepts and "smart grid" processes to move forward in a faster and focused manner. The advanced integrated inverters/controllers can now incorporate energy management functionality, intelligent electrical grid support features and a multiplicity of communication technologies. Portals for energy flow and two-way communications have been implemented. SEGIS hardware was developed for the utility grid of today, which was designed for one-way power flow, for intermediate grid scenarios, AND for the grid of tomorrow, which will seamlessly accommodate managed two-way power flows as required by large-scale deployment of solar and other distributed generation. The SEGIS hardware and control developed for today meets existing standards and codes AND provides for future connections to a "smart grid" mode that enables utility control and optimized performance. C1 Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Bower, W (reprint author), Sandia Natl Labs, MS0734, Albuquerque, NM 87185 USA. EM wibower@sandia.gov NR 8 TC 0 Z9 0 U1 0 U2 3 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-81948-719-3 J9 PROC SPIE PY 2011 VL 8109 BP IX EP XIV AR 811202 DI 10.1117/12.915598 PG 6 WC Chemistry, Applied; Nanoscience & Nanotechnology; Optics SC Chemistry; Science & Technology - Other Topics; Optics GA BXY05 UT WOS:000297588100001 ER PT S AU Vasseur, R Lookman, T AF Vasseur, Romain Lookman, Turab BE Brechet, Y Clouet, E Deschamps, A Finel, A Soisson, F TI Spin Models for Ferroelastics: Towards a Spin Glass Description of Strain Glass SO SOLID-SOLID PHASE TRANSFORMATIONS IN INORGANIC MATERIALS, PTS 1-2 SE Solid State Phenomena LA English DT Proceedings Paper CT International Conference on Solid-Solid Phase Transformations in Inorganic Materials (PTM 2010) CY JUN 06-11, 2010 CL Avignon, FRANCE SP Mat & Process Sci & Engn Lab, CEA, Tranverse Programme Adv Mat, French Aerospace Lab, Inst Chem, Natl Ctr Sci Res, French Phase Field Network, Lab Etude Microstructures DE Ferroelastic Transitions; Strain Glass; Spin Glass Models ID CRYSTAL-FIELD AB We review the description of ferroelastic transitions in terms of spin models. We show how one can systematically obtain a pseudo-spin Hamiltonian from the Landau energy describing the first order transition between Austenite/Martensite phases. It is shown that a Local Mean-field approximation predicts the same microstructure as the continuous Landau model in terms of strain variables. This method can be applied to a wide range of two and three dimensional transitions. We then demonstrate how quenched disorder in such pseudo-spin models yields the existence of a glass phase, characterized by the Edwards-Anderson order parameter. Our approach uses Mean-field approximation and Monte-Carlo simulations (using Zero Field Cooling/Field Cooling experiments) to study the influence of the long-range interactions. Although our model captures the salient features of a ferroelastic material in the presence of disorder, the influence of the disorder on the high symmetry austenite phase is not quite consistent with expected behavior. We examine different means of introducing disorder that can improve upon the results. C1 [Vasseur, Romain] CEA Saclay, Inst Phys Theor, F-91191 Gif Sur Yvette, France. [Vasseur, Romain] Ecole Normale Super, LPTENS, F-75231 Paris, France. [Lookman, Turab] Los Alamos Natl Lab, Theoret Div, Los Alamos, NM 87454 USA. RP Vasseur, R (reprint author), CEA Saclay, Inst Phys Theor, F-91191 Gif Sur Yvette, France. EM romain.vasseur@lpt.ens.fr; txl@lanl.gov OI Lookman, Turab/0000-0001-8122-5671 FU Department of Energy [DE-AC52-06NA25396] FX We are grateful to the Center for Nonlinear Science at Los Alamos National Laboratory for summer student support for RV during 2009 and the Department of Energy under Contract No. DE-AC52-06NA25396. Discussions with M. Porta, A. Saxena and S.R. Shenoy are also acknowledged. NR 15 TC 0 Z9 0 U1 0 U2 5 PU TRANS TECH PUBLICATIONS LTD PI DURNTEN-ZURICH PA KREUZSTRASSE 10, 8635 DURNTEN-ZURICH, SWITZERLAND SN 1012-0394 J9 SOLID STATE PHENOMEN PY 2011 VL 172-174 BP 1078 EP + DI 10.4028/www.scientific.net/SSP.172-174.1078 PN 1 PG 2 WC Materials Science, Multidisciplinary; Physics, Condensed Matter SC Materials Science; Physics GA BZY35 UT WOS:000303359700167 ER PT S AU Souza, SWD Rai, A Nayak, J Maniraj, M Dhaka, RS Barman, SR Schlagel, DL Lograsso, TA AF Souza, S. W. D' Rai, Abhishek Nayak, J. Maniraj, M. Dhaka, R. S. Barman, S. R. Schlagel, D. L. Lograsso, T. A. BE Garg, AB Mittal, R Mukhopadhyay, R TI Modulation on Ni2MnGa(001) surface SO SOLID STATE PHYSICS: PROCEEDINGS OF THE 55TH DAE SOLID STATE PHYSICS SYMPOSIUM 2010, PTS A AND B SE AIP Conference Proceedings LA English DT Proceedings Paper CT 55th Symposium on DAE Solid State Physics (SSPS) CY DEC 26-30, 2010 CL Manipal Univ, Manipal, INDIA SP Govt India, Dept Atom Energy (DAE), Board Res Nucl Sci (BRNS) HO Manipal Univ DE Low-energy electron diffraction; Commensurate-incommensurate transformations AB We report periodic modulation on (001) surface of Ni2MnGa ferromagnetic shape memory alloy. For the stoichiometric surface, analysis of the low energy electron diffraction (LEED) spot profiles shows that the modulation is incommensurate. The modulation appears at 200K, concomitant with the first order structural transition to the martensitic phase. C1 [Souza, S. W. D'; Rai, Abhishek; Nayak, J.; Maniraj, M.; Dhaka, R. S.; Barman, S. R.] UGC DAE Consortium Sci Res, Khandwa Rd, Indore 452001, Madhya Pradesh, India. [Schlagel, D. L.; Lograsso, T. A.] Lowa State Univ, US DOE, Ames Lab, Ames, IA 50011 USA. RP Souza, SWD (reprint author), UGC DAE Consortium Sci Res, Khandwa Rd, Indore 452001, Madhya Pradesh, India. EM sunilwilfred@gmail.com RI Dhaka, Rajendra/C-2486-2013; Roy Barman, Sudipta/B-2026-2010 NR 4 TC 0 Z9 0 U1 0 U2 1 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0905-7 J9 AIP CONF PROC PY 2011 VL 1349 BP 767 EP + DI 10.1063/1.3606084 PG 2 WC Physics, Condensed Matter SC Physics GA BZT87 UT WOS:000302939900362 ER PT J AU Swancutt, KL Mezyk, SP Tillotson, RD Pailloux, S Chakravarty, M Paine, RT Martin, LR AF Swancutt, Katy L. Mezyk, Stephen P. Tillotson, Richard D. Pailloux, Sylvie Chakravarty, Manab Paine, Robert T. Martin, Leigh R. TI Radiolytic Degradation in Lanthanide/Actinide Separation Ligands-NOPOPO: Radical Kinetics and Efficiencies Determinations SO SOLVENT EXTRACTION AND ION EXCHANGE LA English DT Article DE Solvent extraction; radiolysis; actinide lanthanide separation ID SOLVENT-EXTRACTION; RADIATION-CHEMISTRY; TRIVALENT ACTINIDES; LACTIC-ACID; F-ELEMENTS; AMERICIUM(III); ARTICLE; TRIBUTYLPHOSPHATE; N,P,P'-TRIOXIDE; COMPLEXES AB Trivalent lanthanide/actinide separations from used nuclear fuel occurs in the presence radiation fields that degrades the extraction ligands and solvents. Here we have investigated the stability of a new ligand for lanthanide/actinide separation; 2,6-bis[(di(2-ethylhexyl)phosphino)methyl] pyridine N,P,P-trioxide, TEH(NOPOPO). The impact of gamma-radiolysis on the distribution ratios for actinide (Am) and Lanthanide (Eu) extraction both in the presence and absence of an acidic aqueous phase by TEH(NOPOPO) was determined. Corresponding reaction rate constants for the two major radicals, hydroxyl and nitrate, were determined for TEH(NOPOPO) in the aqueous phase, with room temperature values of (3.49 +/- 0.10) x 10(9) and (1.95 +/- 0.15) x 10(8) M-1 s(-1), respectively. The activation energy for this reaction was found to be 30.2 +/- 4.1 kJ mol(-1). Rate constants for two analogues (2-methylphosphonic acid pyridine N, P-dioxide and 2,6-bis(methylphosphonic acid) pyridine N, P, P-trioxide) were also determined to assist in determining the major reaction pathways. C1 [Swancutt, Katy L.; Mezyk, Stephen P.] Calif State Univ Long Beach, Dept Chem & Biochem, Long Beach, CA 90840 USA. [Tillotson, Richard D.; Martin, Leigh R.] Idaho Natl Lab, Aqueous Separat & Radiochem Dept, Idaho Falls, ID 83415 USA. [Pailloux, Sylvie; Chakravarty, Manab; Paine, Robert T.] Univ New Mexico, Dept Chem, Albuquerque, NM 87131 USA. RP Mezyk, SP (reprint author), Calif State Univ Long Beach, Dept Chem & Biochem, 1250 Bellflower Blvd, Long Beach, CA 90840 USA. EM smezyk@csulb.edu; leigh.martin@inl.gov RI Martin, Leigh/P-3167-2016; OI Martin, Leigh/0000-0001-7241-7110; Pailloux, Sylvie/0000-0001-7318-7089 FU Office of Basic Energy Sciences, U.S. Department of Energy; University Nuclear Energy Research Initiative (UNERI) U.S. Department of Energy, Office of Nuclear Energy, under DOE Idaho Operations Office [DE-AC07-05ID14517]; DOE [DE-FC07-06ID14730] FX The kinetics measurements described here were performed at the Radiation Laboratory, University of Notre Dame, which is supported by the Office of Basic Energy Sciences, U.S. Department of Energy. Steady-state irradiations were performed at Idaho National Laboratories. Support for this work was provided by the University Nuclear Energy Research Initiative (UNERI) U.S. Department of Energy, Office of Nuclear Energy, under DOE Idaho Operations Office Contract DE-AC07-05ID14517. UNM efforts were sponsored under DOE contract DE-FC07-06ID14730. NR 32 TC 1 Z9 1 U1 1 U2 10 PU TAYLOR & FRANCIS INC PI PHILADELPHIA PA 325 CHESTNUT ST, SUITE 800, PHILADELPHIA, PA 19106 USA SN 0736-6299 J9 SOLVENT EXTR ION EXC JI Solvent Extr. Ion Exch. PY 2011 VL 29 IS 4 BP 637 EP 654 DI 10.1080/07366299.2011.581051 PG 18 WC Chemistry, Multidisciplinary SC Chemistry GA 883CX UT WOS:000299611500007 ER PT S AU Brockman, RA Kramer, DP Barklay, CD Cairns-Gallimore, D Brown, JL Huling, JC Van Pelt, CE AF Brockman, R. A. Kramer, D. P. Barklay, C. D. Cairns-Gallimore, D. Brown, J. L. Huling, J. C. Van Pelt, C. E. BE Robertson, GA TI Modeling of Selected Ceramic Processing Parameters Employed in the Fabrication of (PuO2)-Pu-238 Fuel Pellets SO SPACE, PROPULSION AND ENERGY SCIENCES INTERNATIONAL FORUM SE Physics Procedia LA English DT Proceedings Paper CT Space, Propulsion and Energy Sciences International Forum CY MAR 15-17, 2011 CL Univ Maryland, Coll Pk, MD SP Inst Adv Studies Space, Prop & Energy Sci (IASSPES), Integr Res Inst (IRI), Amer Astronaut Soc, Astrosociol Res Inst, Nucl Plasma Soc HO Univ Maryland DE Sintering; Modeling; Plutonium-238 Dioxide; (PuO2)-Pu-238; RTG; GPHS AB Recent deep space missions utilize the thermal output of the radioisotope plutonium-238 as the fuel in the thermal to electrical power system. Since the application of plutonium in its elemental state has several disadvantages, the fuel employed in these deep space power systems is typically in the oxide form such as plutonium-238 dioxide ((PuO2)-Pu-238). As an oxide, the processing of the plutonium dioxide into fuel pellets is performed via "classical" ceramic processing unit operations such as sieving of the powder, pressing, sintering, etc. Modeling of these unit operations can be beneficial in the understanding and control of processing parameters with the goal of further enhancing the desired characteristics of the (PuO2)-Pu-238 fuel pellets. A finite element model has been used to help identify the time-temperature-stress profile within a pellet during a furnace operation taking into account that (PuO2)-Pu-238 itself has a significant thermal output. Results of the modeling efforts will be discussed. (C) 2011 Published by Elsevier B.V. Selection and/or peer-review under responsibility of Institute for Advanced studies in Space, Propulsion and Energy Sciences C1 [Brockman, R. A.; Kramer, D. P.; Barklay, C. D.] Univ Dayton, Dayton, OH 45469 USA. [Van Pelt, C. E.] US DOE, Germantown, MD 20874 USA. [Brown, J. L.; Huling, J. C.; Van Pelt, C. E.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Kramer, DP (reprint author), Univ Dayton, Dayton, OH 45469 USA. EM daniel.kramer@udri.udayton.edu NR 2 TC 0 Z9 0 U1 0 U2 2 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA SARA BURGERHARTSTRAAT 25, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 1875-3892 J9 PHYSCS PROC PY 2011 VL 20 DI 10.1016/j.phpro.2011.08.035 PG 7 WC Engineering, Aerospace; Astronomy & Astrophysics SC Engineering; Astronomy & Astrophysics GA BYP01 UT WOS:000299526500034 ER PT J AU Dyar, MD Tucker, JM Humphries, S Clegg, SM Wiens, RC Lane, MD AF Dyar, M. Darby Tucker, Jonathan M. Humphries, Seth Clegg, Samuel M. Wiens, Roger C. Lane, Melissa D. TI Strategies for Mars remote Laser-Induced Breakdown Spectroscopy analysis of sulfur in geological samples SO SPECTROCHIMICA ACTA PART B-ATOMIC SPECTROSCOPY LA English DT Article DE LIBS; Sulfate; Sulfide; Sulfur; ChemCam ID X-RAY SPECTROMETER; MERIDIANI-PLANUM; CHASSIGNY METEORITE; MARTIAN METEORITES; OMEGA/MARS EXPRESS; VACUUM-ULTRAVIOLET; SNC METEORITES; CHEMICAL-COMPOSITION; NAKHLA METEORITE; SULFATE MINERALS AB The key to understanding the sulfur history on Mars is to identify and determine sulfate and sulfide compositions and then to draw from them geologic clues about their environments of formation. To lay a foundation for use of remote LIBS to sulfur analysis in planetary exploration, we have undertaken a focused study of sulfur LIBS in geological samples in a simulated Mars atmosphere, with experimental parameters replicating the ChemCam LIBS instrument. A suite of twelve samples was selected, including rocks rich in minerals representative of sulfates and sulfides that might be encountered on Mars. Univariate analysis of sulfur emission lines did not provide quantitative information. Partial least squares (PLS) analysis was successful at modeling sulfur concentrations for a subset of samples with similar matrices. Sulfide minerals were identified on the basis of other siderophile or chalcophile peaks, such as those arising from Zn and Cu. Because the S lines are very weak compared to those of other elements, optimal PIS results were obtained by restricting the wavelength range to channels close to the most intense sulfur lines similar to 540-570 nm. Principal components analysis was attempted on the dataset, but did not differentiate the samples into meaningful groups because the sulfur lines are not strong enough. However, areas of the relatively weak S, H, and 0 peaks may be used to correctly classify all samples. Based on these outcomes, a flowchart that outlines a possible decision tree for identification and quantification of sulfur in remote LIBS analysis was constructed. Results suggest that LIBS data acquired under Mars conditions can meet the science requirements for the ChemCam instrument. (C) 2010 Elsevier B.V. All rights reserved. C1 [Dyar, M. Darby; Tucker, Jonathan M.] Mt Holyoke Coll, Dept Astron, S Hadley, MA 01075 USA. [Humphries, Seth; Clegg, Samuel M.; Wiens, Roger C.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. [Lane, Melissa D.] Planetary Sci Inst, Tucson, AZ 85719 USA. RP Dyar, MD (reprint author), Mt Holyoke Coll, Dept Astron, 50 Coll St, S Hadley, MA 01075 USA. EM mdyar@mtholyoke.edu; jtucker@mtholyoke.edu; sethdh@lanl.gov; sclegg@lanl.gov; rwiens@lanl.gov; lane@psi.edu OI Clegg, Sam/0000-0002-0338-0948 FU NASA [NNG06GH35G, NNX09AL21G, NNX06AB62G] FX We are grateful for support from NASA grants NNG06GH35G, NNX09AL21G, and NNX06AB62G. NR 149 TC 61 Z9 68 U1 6 U2 44 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0584-8547 J9 SPECTROCHIM ACTA B JI Spectroc. Acta Pt. B-Atom. Spectr. PD JAN PY 2011 VL 66 IS 1 BP 39 EP 56 DI 10.1016/j.sab.2010.11.016 PG 18 WC Spectroscopy SC Spectroscopy GA 732MM UT WOS:000288189400005 ER PT J AU Pan, YX Liu, GK AF Pan, Y. X. Liu, G. K. TI Enhancement of Eu2+ Luminescence in BaO-SiO2 Compounds Through Composition Modification SO SPECTROSCOPY LETTERS LA English DT Article DE luminescence enhancement; phosphors; silicates; white LEDs ID HOST LATTICE; WHITE LEDS; PHOSPHOR; EMISSION; IONS; EFFICIENCY; PHOTOLUMINESCENCE; CONVERSION; GREEN; B3+ AB Phosphors of Eu2+-doped BaO-SiO2 compounds composed of a major BaSiO3 phase and a minor Ba2SiO4 phase were synthesized by a solid-state method at 1200 degrees C under CO atmosphere. An enhancement of the photoluminescence of Eu2+ up to 18 times has been achieved by mixing ZnO into the composition. The composition-optimized phosphor emits bright yellow-green luminescence with excitation between 380 and 420 nm, indicating potential of application in AlGaN-based UV-LEDs. Under the similar synthesis and measurement conditions, the emission band of the optimized phosphor is more intense and has stronger red component than that of Ba2SiO4:Eu2+. Our experimental results suggest that the addition of ZnO may retain and stabilize Eu2+ in BaSiO3 crystalline lattice and thus may enhance the 5d-4f luminescence and eliminate Eu3+ 4f-4f transition. C1 [Pan, Y. X.; Liu, G. K.] Argonne Natl Lab, Chem Sci & Engn Div, Argonne, IL 60439 USA. RP Liu, GK (reprint author), Argonne Natl Lab, Chem Sci & Engn Div, 9700 S Cass Ave, Argonne, IL 60439 USA. EM gkliu@anl.gov FU U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences [DE-AC02-06CH11357] FX Work performed at Argonne National Laboratory was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences, under contract DE-AC02-06CH11357. NR 25 TC 7 Z9 7 U1 2 U2 12 PU TAYLOR & FRANCIS INC PI PHILADELPHIA PA 325 CHESTNUT ST, SUITE 800, PHILADELPHIA, PA 19106 USA SN 0038-7010 J9 SPECTROSC LETT JI Spectr. Lett. PY 2011 VL 44 IS 1 BP 1 EP 7 DI 10.1080/00387010.2010.547388 PG 7 WC Spectroscopy SC Spectroscopy GA 729CL UT WOS:000287925600001 ER PT S AU Chen, WNW Song, B AF Chen, Weinong W. Song, Bo TI Split Hopkinson (Kolsky) Bar: Design, Testing and Applications SO SPLIT HOPKINSON (KOLSKY) BAR: DESIGN, TESTING AND APPLICATIONS SE Mechanical Engineering Series LA English DT Article; Book ID HIGH-STRAIN-RATE; EPOXY SYNTACTIC FOAM; DYNAMIC COMPRESSIVE RESPONSE; PULSE-SHAPING TECHNIQUES; PRESSURE BAR; FRACTURE-TOUGHNESS; SOFT MATERIALS; ELEVATED-TEMPERATURES; EPDM RUBBER; MECHANICAL RESPONSE C1 [Chen, Weinong W.] Purdue Univ, Sch Aeronaut & Astronaut, Sch Mat Engn, W Lafayette, IN 47907 USA. [Song, Bo] Sandia Natl Labs, Dept Mech Mat, Livermore, CA 94551 USA. RP Chen, WNW (reprint author), Purdue Univ, Sch Aeronaut & Astronaut, Sch Mat Engn, 701 W Stadium Ave, W Lafayette, IN 47907 USA. EM wchen@purdue.edu; bsong@sandia.gov NR 193 TC 122 Z9 122 U1 0 U2 10 PU SPRINGER PI NEW YORK PA 233 SPRING STREET, NEW YORK, NY 10013, UNITED STATES SN 0941-5122 BN 978-1-4419-7981-0 J9 MECH ENG SER PY 2011 BP 1 EP + DI 10.1007/978-1-4419-7982-7 PG 354 WC Engineering, Mechanical SC Engineering GA BSO41 UT WOS:000285117100001 ER PT B AU Morgan, K Stegner, G AF Morgan, Kenneth Stegner, Gary BE Burger, J TI How Clean Is Clean? Stakeholders and Consensus-Building at the Fernald Uranium Plant SO STAKEHOLDERS AND SCIENTISTS: ACHIEVING IMPLEMENTABLE SOLUTIONS TO ENERGY AND ENVIRONMENTAL ISSUES LA English DT Article; Book Chapter AB This is an account of the Fernald Uranium plant, the pollution from the plant, and its impact on the community. The Fernald Feed Materials Plant provided uranium metal to the United States nuclear weapons program from 1951 to 1989. In 1984, public awareness and concern over environmental releases began to grow, culminating in a lawsuit against the operators of the plant. Public reaction to the site was so negative that it became difficult, if not impossible, to operate or remediate the site. Systematic application of a program of public participation restored institutional credibility. Stakeholder input dramatically improved the quality of decision making, resulting in reduced costs and an accelerated environmental restoration. C1 [Morgan, Kenneth; Stegner, Gary] US DOE, Ohio Field Off, Miamisburg, OH 45342 USA. RP Morgan, K (reprint author), US DOE, Ohio Field Off, Miamisburg, OH 45342 USA. EM morgan.ken@mac.com; Gary.Stegner@lm.doe.gov NR 6 TC 1 Z9 1 U1 1 U2 3 PU SPRINGER PI NEW YORK PA 233 SPRING STREET, NEW YORK, NY 10013, UNITED STATES BN 978-1-4419-8812-6 PY 2011 BP 63 EP 87 DI 10.1007/978-1-4419-8813-3_4 D2 10.1007/978-1-4419-8813-3 PG 25 WC Environmental Sciences SC Environmental Sciences & Ecology GA BYL56 UT WOS:000299249000004 ER PT J AU Anderson, I Wirth, R Lucas, S Copeland, A Lapidus, A Cheng, JF Goodwin, L Pitluck, S Davenport, K Detter, JC Han, C Tapia, R Land, M Hauser, L Pati, A Mikhailova, N Woyke, T Klenk, HP Kyrpides, N Ivanova, N AF Anderson, Iain Wirth, Reinhard Lucas, Susan Copeland, Alex Lapidus, Alla Cheng, Jan-Fang Goodwin, Lynne Pitluck, Samuel Davenport, Karen Detter, John C. Han, Cliff Tapia, Roxanne Land, Miriam Hauser, Loren Pati, Amrita Mikhailova, Natalia Woyke, Tanja Klenk, Hans-Peter Kyrpides, Nikos Ivanova, Natalia TI Complete genome sequence of Staphylothermus hellenicus P8(T) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Archaea; Crenarchaeota; Desulfurococcaceae; hyperthermophile; hydrothermal vent; anaerobe ID PYROCOCCUS-FURIOSUS; SP-NOV; SULFUR; METABOLISM; ARCHAEA; SYSTEM; GRAPHS; GENUS; TOOL AB Staphylothermus hellenicus belongs to the order Desulfurococcales within the archaeal phylum Crenarchaeota. Strain P8(T) is the type strain of the species and was isolated from a shallow hydrothermal vent system at Palaeochori Bay, Milos, Greece. It is a hyperthermophilic, anaerobic heterotroph. Here we describe the features of this organism together with the complete genome sequence and annotation. The 1,580,347 bp genome with its 1,668 protein-coding and 48 RNA genes was sequenced as part of a DOE Joint Genome Institute (JGI) Laboratory Sequencing Program (LSP) project. C1 [Anderson, Iain; Lucas, Susan; Copeland, Alex; Lapidus, Alla; Cheng, Jan-Fang; Goodwin, Lynne; Pitluck, Samuel; Davenport, Karen; Detter, John C.; Han, Cliff; Tapia, Roxanne; Pati, Amrita; Mikhailova, Natalia; Woyke, Tanja; Kyrpides, Nikos; Ivanova, Natalia] DOE Joint Genome Inst, Walnut Creek, CA USA. [Wirth, Reinhard] Univ Regensburg, Microbiol Archaeenzentrum, Regensburg, Germany. [Goodwin, Lynne; Davenport, Karen; Detter, John C.; Han, Cliff; Tapia, Roxanne] Los Alamos Natl Lab, Los Alamos, NM USA. [Land, Miriam; Hauser, Loren] Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA. [Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RP Anderson, I (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. EM IJAnderson@lbl.gov RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Ivanova, Natalia/0000-0002-5802-9485 NR 36 TC 5 Z9 5 U1 1 U2 2 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 5 IS 1 BP 12 EP 20 DI 10.4056/sigs.2054696 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GU UT WOS:000298944200002 PM 22180806 ER PT J AU Woyke, T Chertkov, O Lapidus, A Nolan, M Lucas, S Del Rio, TG Tice, H Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Pagani, I Ivanova, N Huntemann, M Mavromatis, K Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Hauser, L Brambilla, EM Rohde, M Mwirichia, R Sikorski, J Tindall, BJ Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Klenk, HP Kyrpides, NC AF Woyke, Tanja Chertkov, Olga Lapidus, Alla Nolan, Matt Lucas, Susan Del Rio, Tijana Glavina Tice, Hope Cheng, Jan-Fang Tapia, Roxanne Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Ivanova, Natalia Huntemann, Marcel Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Brambilla, Evelyne-Marie Rohde, Manfred Mwirichia, Romano Sikorski, Johannes Tindall, Brian J. Goeker, Markus Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Klenk, Hans-Peter Kyrpides, Nikos C. TI Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE strictly aerobic; motile by gliding; Gram-negative; flexirubin-synthesizing; mesophilic; chemoorganotrophic; Cryomorphaceae; GEBA ID GEN. NOV.; MARINE BACTERIUM; FAMILY CRYOMORPHACEAE; ARCHAEA; FLAVOBACTERIA; ALGORITHM; DATABASE; SYSTEM; GRAPHS; TOOL AB Fluviicola taffensis O'Sullivan et al. 2005 belongs to the monotypic genus Fluviicola within the family Cryomorphaceae. The species is of interest because of its isolated phylogenetic location in the genome-sequenced fraction of the tree of life. Strain RW262(T) forms a monophyletic lineage with uncultivated bacteria represented in freshwater 16S rRNA gene libraries. A similar phylogenetic differentiation occurs between freshwater and marine bacteria in the family Flavobacteriaceae, a sister family to Cryomorphaceae. Most remarkable is the inability of this freshwater bacterium to grow in the presence of Na+ ions. All other genera in the family Cryomorphaceae are from marine habitats and have an absolute requirement for Na+ ions or natural sea water. F. taffensis is the first member of the family Cryomorphaceae with a completely sequenced and publicly available genome. The 4,633,577 bp long genome with its 4,082 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Woyke, Tanja; Chertkov, Olga; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Huntemann, Marcel; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Tapia, Roxanne; Han, Cliff; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Markowitz, Victor] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Brambilla, Evelyne-Marie; Sikorski, Johannes; Tindall, Brian J.; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. [Hugenholtz, Philip] Univ Queensland, Australian Ctr Ecogen, Sch Chem & Mol Biosci, Brisbane, Qld, Australia. RP Kyrpides, NC (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. RI Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Helga Pomrenke (DSMZ) for growing F. taffensis cultures. 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 38 TC 8 Z9 9 U1 2 U2 9 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 5 IS 1 BP 21 EP 29 DI 10.4056/sigs.2124912 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GU UT WOS:000298944200003 PM 22180807 ER PT J AU Liolios, K Sikorski, J Lu, MG Nolan, M Lapidus, A Lucas, S Hammon, N Deshpande, S Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Huntemann, M Ivanova, N Pagani, I Mavromatis, K Ovchinikova, G Pati, A Chen, A Palaniappan, K Land, M Hauser, L Brambilla, EM Kotsyurbenko, O Rohde, M Tindall, BJ Abt, B Goker, M Detter, JC Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Klenk, HP Kyrpides, NC AF Liolios, Konstantinos Sikorski, Johannes Lu, Meagan Nolan, Matt Lapidus, Alla Lucas, Susan Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Tapia, Roxanne Han, Cliff Goodwin, Lynne Pitluck, Sam Huntemann, Marcel Ivanova, Natalia Pagani, Ioanna Mavromatis, Konstantinos Ovchinikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Brambilla, Evelyne-Marie Kotsyurbenko, Oleg Rohde, Manfred Tindall, Brian J. Abt, Birte Goeker, Markus Detter, John C. Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Klenk, Hans-Peter Kyrpides, Nikos C. TI Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE strictly aerobic; gliding motility; Gram-negative; heparinolytic; mesophilic; chemoorganotrophic; Sphingobacteriaceae; GEBA ID SP-NOV.; FAMILY SPHINGOBACTERIACEAE; EMENDED DESCRIPTION; GENUS PEDOBACTER; SP. NOV.; BACTERIA; PROPOSAL; ARCHAEA; SOIL; CLASSIFICATION AB Pedobacter saltans Steyn et al. 1998 is one of currently 32 species in the genus Pedobacter within the family Sphingobacteriaceae. The species is of interest for its isolated location in the tree of life. Like other members of the genus P. saltans is heparinolytic. Cells of P. saltans show a peculiar gliding, dancing motility and can be distinguished from other Pedobacter strains by their ability to utilize glycerol and the inability to assimilate D-cellobiose. The genome presented here is only the second completed genome sequence of a type strain from a member of the family Sphingobacteriaceae to be published. The 4,635,236 bp long genome with its 3,854 protein-coding and 67 RNA genes consists of one chromosome, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Liolios, Konstantinos; Nolan, Matt; Lapidus, Alla; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Huntemann, Marcel; Ivanova, Natalia; Pagani, Ioanna; Mavromatis, Konstantinos; Ovchinikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Sikorski, Johannes; Brambilla, Evelyne-Marie; Tindall, Brian J.; Abt, Birte; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Lu, Meagan; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Kotsyurbenko, Oleg] Tech Univ Carolo Wilhelmina Braunschweig, Inst Microbiol, D-38106 Braunschweig, Germany. [Kotsyurbenko, Oleg] Lomonosov Moscow State Univ, Dept Biol, Moscow, Russia. [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. RP Kyrpides, NC (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. RI Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013 OI Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Helga Pomrenke (DSMZ) for growing P. saltans cultures. 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 52 TC 7 Z9 7 U1 1 U2 4 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 5 IS 1 BP 30 EP 40 DI 10.4056/sigs.2154937 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GU UT WOS:000298944200004 PM 22180808 ER PT J AU Pati, A Gronow, S Lu, MG Lapidus, A Nolan, M Lucas, S Hammon, N Deshpande, S Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Pagani, I Mavromatis, K Mikhailova, N Huntemann, M Chen, A Palaniappan, K Land, M Hauser, L Detter, JC Brambilla, EM Rohde, M Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Ivanova, N AF Pati, Amrita Gronow, Sabine Lu, Megan Lapidus, Alla Nolan, Matt Lucas, Susan Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Tapia, Roxanne Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Mavromatis, Konstantinos Mikhailova, Natalia Huntemann, Marcel Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Detter, John C. Brambilla, Evelyne-Marie Rohde, Manfred Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Ivanova, Natalia TI Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE obligately anaerobic; non-motile; Gram-negative; mesophilic; chemoorganotrophic; opportunistic pathogen; Prevotellaceae; GEBA ID BACTERIA; ARCHAEA; DATABASE; SYSTEM; GRAPHS; GENUS; TOOL AB Prevotella multisaccharivorax Sakamoto et al. 2005 is a species of the large genus Prevotella, which belongs to the family Prevotellaceae. The species is of medical interest because its members are able to cause diseases in the human oral cavity such as periodontitis, root caries and others. Although 77 Prevotella genomes have already been sequenced or are targeted for sequencing, this is only the second completed genome sequence of a type strain of a species within the genus Prevotella to be published. The 3,388,644 bp long genome is assembled in three non-contiguous contigs, harbors 2,876 protein-coding and 75 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Gronow, Sabine; Brambilla, Evelyne-Marie; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Pati, Amrita; Lu, Megan; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Mavromatis, Konstantinos; Mikhailova, Natalia; Huntemann, Marcel; Land, Miriam; Hauser, Loren; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Ivanova, Natalia] DOE Joint Genome Inst, Walnut Creek, CA USA. [Lu, Megan; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren] Oak Ridge Natl Lab, Oak Ridge, TN USA. [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. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Sabine Welnitz (DSMZ) for growing P. multisaccharivorax cultures. 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 35 TC 1 Z9 1 U1 2 U2 4 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 5 IS 1 BP 41 EP 49 DI 10.4056/sigs.2164949 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GU UT WOS:000298944200005 PM 22180809 ER PT J AU Anderson, I Risso, C Holmes, D Lucas, S Copeland, A Lapidus, A Cheng, JF Bruce, D Goodwin, L Pitluck, S Saunders, E Brettin, T Detter, JC Han, C Tapia, R Larimer, F Land, M Hauser, L Woyke, T Lovley, D Kyrpides, N Ivanova, N AF Anderson, Iain Risso, Carla Holmes, Dawn Lucas, Susan Copeland, Alex Lapidus, Alla Cheng, Jan-Fang Bruce, David Goodwin, Lynne Pitluck, Samuel Saunders, Elizabeth Brettin, Thomas Detter, John C. Han, Cliff Tapia, Roxanne Larimer, Frank Land, Miriam Hauser, Loren Woyke, Tanja Lovley, Derek Kyrpides, Nikos Ivanova, Natalia TI Complete genome sequence of Ferroglobus placidus AEDII12DO SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Archaea; Euryarchaeota; Archaeoglobales; hydrothermal vent; hyperthermophile; anaerobe ID FE(III) REDUCTION; METABOLISM; OXIDATION; SYSTEM; PREDICTION; ACONITASE; PATHWAY; ARCHAEA; TOOL AB Ferroglobus placidus belongs to the order Archaeoglobales within the archaeal phylum Euryarchaeota. Strain AEDII12DO is the type strain of the species and was isolated from a shallow marine hydrothermal system at Vulcano, Italy. It is a hyperthermophilic, anaerobic chemolithoautotroph, but it can also use a variety of aromatic compounds as electron donors. Here we describe the features of this organism together with the complete genome sequence and annotation. The 2,196,266 bp genome with its 2,567 protein-coding and 55 RNA genes was sequenced as part of a DOE Joint Genome Institute Laboratory Sequencing Program (LSP) project. C1 [Anderson, Iain; Lucas, Susan; Copeland, Alex; Lapidus, Alla; Cheng, Jan-Fang; Bruce, David; Goodwin, Lynne; Pitluck, Samuel; Saunders, Elizabeth; Brettin, Thomas; Detter, John C.; Han, Cliff; Tapia, Roxanne; Woyke, Tanja; Kyrpides, Nikos; Ivanova, Natalia] DOE Joint Genome Inst, Walnut Creek, CA USA. [Risso, Carla; Holmes, Dawn; Lovley, Derek] Univ Massachusetts, Dept Microbiol, Amherst, MA 01003 USA. [Bruce, David; Goodwin, Lynne; Saunders, Elizabeth; Brettin, Thomas; Detter, John C.; Han, Cliff; Tapia, Roxanne] Los Alamos Natl Lab, Los Alamos, NM USA. [Larimer, Frank; Land, Miriam; Hauser, Loren] Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA. RP Anderson, I (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. EM IJAnderson@lbl.gov RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Ivanova, Natalia/0000-0002-5802-9485; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231] FX The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. NR 42 TC 9 Z9 9 U1 2 U2 6 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 5 IS 1 BP 50 EP 60 DI 10.4056/sigs.2225018 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GU UT WOS:000298944200006 PM 22180810 ER PT J AU DeAngelis, KM D'Haeseleer, P Chivian, D Fortney, JL Khudyakov, J Simmons, B Woo, H Arkin, AP Davenport, KW Goodwin, L Chen, A Ivanova, N Kyrpides, NC Mavromatis, K Woyke, T Hazen, TC AF DeAngelis, Kristen M. D'Haeseleer, Patrik Chivian, Dylan Fortney, Julian L. Khudyakov, Jane Simmons, Blake Woo, Hannah Arkin, Adam P. Davenport, Karen Walston Goodwin, Lynne Chen, Amy Ivanova, Natalia Kyrpides, Nikos C. Mavromatis, Konstantinos Woyke, Tanja Hazen, Terry C. TI Complete genome sequence of "Enterobacter lignolyticus" SCF1 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Anaerobic lignin degradation; tropical forest soil isolate; facultative anaerobe ID AROMATIC-COMPOUNDS; RNA GENES; ANNOTATION; DECOMPOSITION; ACCURACY; BACTERIA; LIGNIN; SYSTEM; SOIL; TOOL AB In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated "Enterobacter lignolyticus" SCF1 on minimal media with alkali lignin as the sole source of carbon. This organism was isolated anaerobically from tropical forest soils collected from the Short Cloud Forest 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 net methane producers. Because of its ability to grow on lignin anaerobically, we sequenced the genome. The genome of "E. lignolyticus" SCF1 is 4.81 Mbp with no detected plasmids, and includes a relatively small arsenal of lignocellulolytic carbohydrate active enzymes. Lignin degradation was observed in culture, and the genome revealed two putative laccases, a putative peroxidase, and a complete 4-hydroxyphenylacetate degradation pathway encoded in a single gene cluster. C1 [DeAngelis, Kristen M.; D'Haeseleer, Patrik; Fortney, Julian L.; Woo, Hannah; Hazen, Terry C.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Dept Ecol, Berkeley, CA 94720 USA. [DeAngelis, Kristen M.; Khudyakov, Jane; Simmons, Blake; Woo, Hannah; Hazen, Terry C.] Joint BioEnergy Inst, Deconstruct Div, Microbial Communities Grp, Emeryville, CA USA. [D'Haeseleer, Patrik; Khudyakov, Jane] Lawrence Livermore Natl Lab, Livermore, CA USA. [Chivian, Dylan; Arkin, Adam P.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA. [Chivian, Dylan; Arkin, Adam P.] Joint BioEnergy Inst, Technol Div, Emeryville, CA USA. [Simmons, Blake] Sandia Natl Labs, Livermore, CA USA. [Davenport, Karen Walston; Goodwin, Lynne] Los Alamos Natl Lab, Los Alamos, NM USA. [Chen, Amy; Ivanova, Natalia; Kyrpides, Nikos C.; Mavromatis, Konstantinos; Woyke, Tanja] US DOE, Joint Genome Inst, Walnut Creek, CA USA. RP DeAngelis, KM (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Dept Ecol, Berkeley, CA 94720 USA. EM kristen@post.harvard.edu RI Khudyakov, Jane/C-1213-2014; Arkin, Adam/A-6751-2008; Hazen, Terry/C-1076-2012; Kyrpides, Nikos/A-6305-2014; OI Khudyakov, Jane/0000-0001-7038-102X; Woo, Hannah/0000-0002-9342-6072; Ivanova, Natalia/0000-0002-5802-9485; DeAngelis, Kristen/0000-0002-5585-4551; Arkin, Adam/0000-0002-4999-2931; Hazen, Terry/0000-0002-2536-9993; Kyrpides, Nikos/0000-0002-6131-0462; D'haeseleer, Patrik/0000-0003-0007-8150; Simmons, Blake/0000-0002-1332-1810 FU U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research [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 (http://www.jbei.org) supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, under Contract No. DE-AC02-05CH11231. NR 49 TC 23 Z9 24 U1 2 U2 19 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 5 IS 1 BP 69 EP 85 DI 10.4056/sigs.2104875 PG 17 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GU UT WOS:000298944200008 PM 22180812 ER PT J AU Lapidus, A Chertkov, O Nolan, M Lucas, S Hammon, N Deshpande, S Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Pagani, I Ivanova, N Huntemann, M Mavromatis, K Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Hauser, L Brambilla, EM Rohde, M Abt, B Spring, S Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Woyke, T AF Lapidus, Alla Chertkov, Olga Nolan, Matt Lucas, Susan Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Tapia, Roxanne Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Ivanova, Natalia Huntemann, Marcel Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Brambilla, Evelyne-Marie Rohde, Manfred Abt, Birte Spring, Stefan Goeker, Markus Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Woyke, Tanja TI Genome sequence of the moderately thermophilic halophile Flexistipes sinusarabici strain (MAS10(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE strictly anaerobic; Gram-negative; non-motile; heterotrophic; moderately thermophilic; marine; brine; Deferribacteraceae; GEBA ID BACTERIA; ARCHAEA; DATABASE; SYSTEM; GRAPHS; TOOL; SEA AB Flexistipes sinusarabici Fiala et al. 2000 is the type species of the genus Flexistipes in the family Deferribacteraceae. The species is of interest because of its isolated phylogenetic location in a genomically under-characterized region of the tree of life, and because of its origin from a multiply extreme environment; the Atlantis Deep brines of the Red Sea, where it had to struggle with high temperatures, high salinity, and a high concentrations of heavy metals. This is the fourth completed genome sequence to be published of a type strain of the family Deferribacteraceae. The 2,526,590 bp long genome with its 2,346 protein-coding and 53 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Brambilla, Evelyne-Marie; Abt, Birte; Spring, Stefan; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Lapidus, Alla; Chertkov, Olga; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Huntemann, Marcel; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Woyke, Tanja] DOE Joint Genome Inst, Walnut Creek, CA USA. [Chertkov, Olga; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Markowitz, Victor] Oak Ridge Natl Lab, Oak Ridge, TN USA. [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. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013; Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938; FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Maren Schroder (DSMZ) for growing F. sinusarabici cultures. 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, as well as German Research Foundation (DFG) INST 599/1-2. NR 38 TC 4 Z9 5 U1 2 U2 9 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 5 IS 1 BP 86 EP 96 DI 10.4056/sigs.2235024 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GU UT WOS:000298944200009 PM 22180813 ER PT J AU Chang, YJ Land, M Hauser, L Chertkov, O Del Rio, TG Nolan, M Copeland, A Tice, H Cheng, JF Lucas, S Han, C Goodwin, L Pitluck, S Ivanova, N Ovchinikova, G Pati, A Chen, A Palaniappan, K Mavromatis, K Liolios, K Brettin, T Fiebig, A Rohde, M Abt, B Goker, M Detter, JC Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Lapidus, A AF Chang, Yun-juan Land, Miriam Hauser, Loren Chertkov, Olga Del Rio, Tijana Glavina Nolan, Matt Copeland, Alex Tice, Hope Cheng, Jan-Fang Lucas, Susan Han, Cliff Goodwin, Lynne Pitluck, Sam Ivanova, Natalia Ovchinikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Mavromatis, Konstantinos Liolios, Konstantinos Brettin, Thomas Fiebig, Anne Rohde, Manfred Abt, Birte Goeker, Markus Detter, John C. Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Lapidus, Alla TI Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE aerobic; heterotrophic; filamentous; non-motile; Gram-positive; moderately acidophilic; sporulating; transposon; broken-stick distribution; entropy; Ktedonobacteraceae; Chloroflexi; GEBA ID GROUP-II INTRONS; SPHAEROBACTER-THERMOPHILUS; EMENDED DESCRIPTION; ARCHAEA; ALGORITHM; SYSTEM; ROSEUM; TOOL; NOV AB Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobacter, which in turn is the type genus of the family Ktedonobacteraceae, the type family of the order Ktedonobacterales within the class Ktedonobacteria in the phylum 'Chloroflexi'. Although K. racemifer shares some morphological features with the actinobacteria, it is of special interest because it was the first cultivated representative of a deep branching unclassified lineage of otherwise uncultivated environmental phylotypes tentatively located within the phylum 'Chloroflexi'. The aerobic, filamentous, non-motile, spore-forming Gram-positive heterotroph was isolated from soil in Italy. The 13,661,586 bp long non-contiguous finished genome consists of ten contigs and is the first reported genome sequence from a member of the class Ktedonobacteria. With its 11,453 protein-coding and 87 RNA genes, it is the largest prokaryotic genome reported so far. It comprises a large number of over-represented COGs, particularly genes associated with transposons, causing the genetic redundancy within the genome being considerably larger than expected by chance. This work is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Fiebig, Anne; Abt, Birte; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Chang, Yun-juan; Land, Miriam; Hauser, Loren] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Chang, Yun-juan; Land, Miriam; Hauser, Loren; Chertkov, Olga; Del Rio, Tijana Glavina; Nolan, Matt; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Ovchinikova, Galina; Pati, Amrita; Mavromatis, Konstantinos; Liolios, Konstantinos; Brettin, Thomas; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Lapidus, Alla] DOE Joint Genome Inst, Walnut Creek, CA USA. [Chertkov, Olga; Han, Cliff; Goodwin, Lynne; Brettin, Thomas; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [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. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1] FX We would like to gratefully acknowledge the help of Marlen Jando for growing K. racemifer cultures and Susanne Schneider for DNA extraction and quality control (both at DSMZ). 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, as well as German Research Foundation (DFG) INST 599/1-1. NR 48 TC 28 Z9 28 U1 1 U2 15 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 5 IS 1 BP 97 EP 111 DI 10.4056/sigs.2114901 PG 15 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GU UT WOS:000298944200010 PM 22180814 ER PT J AU Chertkov, O Copeland, A Lucas, S Lapidus, A Berry, KW Detter, JC Del Rio, TG Hammon, N Dalin, E Tice, H Pitluck, S Richardson, P Bruce, D Goodwin, L Han, C Tapia, R Saunders, E Schmutz, J Brettin, T Larimer, F Land, M Hauser, L Spring, S Rohde, M Kyrpides, NC Ivanova, N Goker, M Beller, HR Klenk, HP Woyke, T AF Chertkov, Olga Copeland, Alex Lucas, Susan Lapidus, Alla Berry, Kerrie W. Detter, John C. Del Rio, Tijana Glavina Hammon, Nancy Dalin, Eileen Tice, Hope Pitluck, Sam Richardson, Paul Bruce, David Goodwin, Lynne Han, Cliff Tapia, Roxanne Saunders, Elizabeth Schmutz, Jeremy Brettin, Thomas Larimer, Frank Land, Miriam Hauser, Loren Spring, Stefan Rohde, Manfred Kyrpides, Nikos C. Ivanova, Natalia Goeker, Markus Beller, Harry R. Klenk, Hans-Peter Woyke, Tanja TI Complete genome sequence of Tolumonas auensis type strain (TA 4(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE facultatively anaerobic; chemoorganotrophic; Gram-negative; non-motile; toluene producer; Aeromonadaceae; Gammaproteobacteria; JBEI 2008 ID RNA GENES; DATABASE; PREDICTION; ALGORITHM; PROPOSAL; TOOL; NOV AB Tolumonas auensis Fischer-Romero et al. 1996 is currently the only validly named species of the genus Tolumonas in the family Aeromonadaceae. The strain is of interest because of its ability to produce toluene from phenylalanine and other phenyl precursors, as well as phenol from tyrosine. This is of interest because toluene is normally considered to be a tracer of anthropogenic pollution in lakes, but T. auensis represents a biogenic source of toluene. Other than Aeromonas hydrophila subsp. hydrophila, T. auensis strain TA 4(T) is the only other member in the family Aeromonadaceae with a completely sequenced type-strain genome. The 3,471,292 bp chromosome with a total of 3,288 protein-coding and 116 RNA genes was sequenced as part of the DOE Joint Genome Institute Program JBEI 2008. C1 [Beller, Harry R.] Joint BioEnergy Inst JBEI, Emeryville, CA USA. [Chertkov, Olga; Copeland, Alex; Lucas, Susan; Lapidus, Alla; Berry, Kerrie W.; Detter, John C.; Del Rio, Tijana Glavina; Hammon, Nancy; Dalin, Eileen; Tice, Hope; Pitluck, Sam; Richardson, Paul; Bruce, David; Goodwin, Lynne; Han, Cliff; Tapia, Roxanne; Saunders, Elizabeth; Brettin, Thomas; Larimer, Frank; Land, Miriam; Hauser, Loren; Kyrpides, Nikos C.; Ivanova, Natalia; Woyke, Tanja] DOE Joint Genome Inst, Walnut Creek, CA USA. [Chertkov, Olga; Detter, John C.; Bruce, David; Goodwin, Lynne; Han, Cliff; Tapia, Roxanne; Saunders, Elizabeth; Schmutz, Jeremy] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Brettin, Thomas; Larimer, Frank; Land, Miriam; Hauser, Loren] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Spring, Stefan; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Beller, Harry R.] Lawrence Berkeley Natl Lab, Emeryville, CA USA. RP Beller, HR (reprint author), Joint BioEnergy Inst JBEI, Emeryville, CA USA. RI Spring, Stefan/N-6933-2013; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Schmutz, Jeremy/N-3173-2013; Beller, Harry/H-6973-2014; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Spring, Stefan/0000-0001-6247-0938; Lapidus, Alla/0000-0003-0427-8731; Schmutz, Jeremy/0000-0001-8062-9172; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]; Office of Science, Office of Biological and Environmental Research, of the U.S. Department of Energy [DE-AC02-05CH11231] FX The work conducted by the U.S. Department of Energy Joint Genome Institute was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231, and work conducted by the Joint BioEnergy Institute (H. R. B.) 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 32 TC 1 Z9 1 U1 0 U2 4 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 5 IS 1 BP 112 EP 120 DI 10.4056/sigs.2184986 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GU UT WOS:000298944200011 PM 22180815 ER PT J AU Klenk, HP Lapidus, A Chertkov, O Copeland, A Del Rio, TG Nolan, M Lucas, S Chen, F Tice, H Cheng, JF Han, C Bruce, D Goodwin, L Pitluck, S Pati, A Ivanova, N Mavromatis, K Daum, C Chen, A Palaniappan, K Chang, YJ Land, M Hauser, L Jeffries, CD Detter, JC Rohde, M Abt, B Pukall, R Goker, M Bristow, J Markowitz, V Hugenholtz, P Eisen, JA AF Klenk, Hans-Peter Lapidus, Alla Chertkov, Olga Copeland, Alex Del Rio, Tijana Glavina Nolan, Matt Lucas, Susan Chen, Feng Tice, Hope Cheng, Jan-Fang Han, Cliff Bruce, David Goodwin, Lynne Pitluck, Sam Pati, Amrita Ivanova, Natalia Mavromatis, Konstantinos Daum, Chris Chen, Amy Palaniappan, Krishna Chang, Yun-juan Land, Miriam Hauser, Loren Jeffries, Cynthia D. Detter, John C. Rohde, Manfred Abt, Birte Pukall, Ruediger Goeker, Markus Bristow, James Markowitz, Victor Hugenholtz, Philip Eisen, Jonathan A. TI Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2(T)) and reclassification in the new genus, Kyrpidia gen. nov as Kyrpidia tusciae comb. nov and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE hydrogen-oxidizing; aerobe; facultative chemolithoautotroph; thermoacidophile; free-living; solfatara; spore-forming; Bacillaceae; GEBA ID BACTERIA; ACIDOCALDARIUS; ARCHAEA; TOOL; IDENTIFICATION; DATABASE; PROPOSAL; SYSTEM; RDNA AB Bacillus tusciae Bonjour & Aragno 1994 is a hydrogen-oxidizing, thermoacidophilic spore former that lives as a facultative chemolithoautotroph in solfataras. Although 16S rRNA gene sequencing was well established at the time of the initial description of the organism, 16S sequence data were not available and the strain was placed into the genus Bacillus based on limited chemotaxonomic information. Despite the now obvious misplacement of strain T2(T) as a member of the genus Bacillus in 16S rRNA-based phylogenetic trees, the misclassification remained uncorrected for many years, which was likely due to the extremely difficult, analysis-hampering cultivation conditions and poor growth rate of the strain. Here we provide a taxonomic re-evaluation of strain T2(T) (= DSM 2912 = NBRC 15312) and propose its reclassification as the type strain of a new species, Kyrpidia tusciae, and the type species of the new genus Kyrpidia, which is a sister-group of Alicyclobacillus. The family Alicyclobacillaceae da Costa and Rainey, 2010 is emended. The 3,384,766 bp genome with its 3,323 protein-coding and 78 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Klenk, Hans-Peter; Abt, Birte; Pukall, Ruediger; Goeker, Markus] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Lapidus, Alla; Chertkov, Olga; Copeland, Alex; Del Rio, Tijana Glavina; Nolan, Matt; Lucas, Susan; Chen, Feng; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Pati, Amrita; Ivanova, Natalia; Mavromatis, Konstantinos; Daum, Chris; Chang, Yun-juan; Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.; Detter, John C.; Bristow, James; Hugenholtz, Philip; Eisen, Jonathan A.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Chertkov, Olga; Han, Cliff; Bruce, David; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Chang, Yun-juan; Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Hugenholtz, Philip] Univ Queensland, Australian Ctr Ecogen, Sch Chem & Mol Biosci, Brisbane, Qld, Australia. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; German Research Foundation (DFG) [INST 599/1-1] FX We would like to gratefully acknowledge the help of Claudia Wahrenburg for growing the B. tusciae cells, and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, as well as German Research Foundation (DFG) INST 599/1-1. NR 49 TC 13 Z9 14 U1 3 U2 12 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 5 IS 1 BP 121 EP 134 DI 10.4056/sigs.2144922 PG 14 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GU UT WOS:000298944200012 PM 22180816 ER PT J AU Kallimanis, A Karabika, E Mavromatis, K Lapidus, A LaButti, KM Liolios, K Ivanova, N Goodwin, L Woyke, T Velentzas, AD Perisynakis, A Ouzounis, CC Kyrpides, NC Koukkou, AI Drainas, C AF Kallimanis, Aristeidis Karabika, Eugenia Mavromatis, Kostantinos Lapidus, Alla LaButti, Kurt M. Liolios, Konstantinos Ivanova, Natalia Goodwin, Lynne Woyke, Tanja Velentzas, Athanasios D. Perisynakis, Angelos Ouzounis, Christos C. Kyrpides, Nikos C. Koukkou, Anna I. Drainas, Constantin TI Complete genome sequence of Mycobacterium sp strain (Spyr1) and reclassification to Mycobacterium gilvum Spyr1 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Mycobacterium gilvum; PAH biodegradation; pyrene degradation ID POLYCYCLIC AROMATIC-HYDROCARBONS; CLASSIFICATION; PROPOSAL; PYRENE; SYSTEM; ACTINOBACTERIA; IDENTIFICATION; DEGRADATION; DEFINITION; BACTERIA AB Mycobacterium sp. Spyr1 is a newly isolated strain that occurs in a creosote contaminated site in Greece. It was isolated by an enrichment method using pyrene as sole carbon and energy source and is capable of degrading a wide range of PAH substrates including pyrene, fluoranthene, fluorene, anthracene and acenapthene. Here we describe the genomic features of this organism, together with the complete sequence and annotation. The genome consists of a 5,547,747 bp chromosome and two plasmids, a larger and a smaller one with sizes of 211,864 and 23,681 bp, respectively. In total, 5,588 genes were predicted and annotated. C1 [Kallimanis, Aristeidis; Karabika, Eugenia; Perisynakis, Angelos; Koukkou, Anna I.; Drainas, Constantin] Univ Ioannina, Sect Organ Chem & Biochem, GR-45110 Ioannina, Greece. [Mavromatis, Kostantinos; Lapidus, Alla; LaButti, Kurt M.; Liolios, Konstantinos; Ivanova, Natalia; Goodwin, Lynne; Woyke, Tanja; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Velentzas, Athanasios D.] Univ Athens, Fac Biol, Dept Cell Biol & Biophys, Athens 15701, Greece. [Ouzounis, Christos C.] Kings Coll London, Ctr Bioinformat, Dept Informat, Sch Nat & Math Sci, London WC2R 2LS, England. RP Koukkou, AI (reprint author), Univ Ioannina, Sect Organ Chem & Biochem, GR-45110 Ioannina, Greece. EM akukku@cc.uoi.gr RI Lapidus, Alla/I-4348-2013; Ouzounis, Christos/G-2302-2010; Kyrpides, Nikos/A-6305-2014; OI Lapidus, Alla/0000-0003-0427-8731; Kyrpides, Nikos/0000-0002-6131-0462; Velentzas, Athanasios D./0000-0002-9755-395X; Ivanova, Natalia/0000-0002-5802-9485 FU National Funds; European Social Funds (ESF); European Commission [222886-2]; MICROME [222886-2]; US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396] FX This work was funded by the program "Pythagoras II" of EPEAEK with 25% National Funds and 75% European Social Funds (ESF) and partly supported by the European Commission FP7 Collaborative Project MICROME (grant agreement number 222886-2). Sequencing and annotation was supported by 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 24 TC 9 Z9 9 U1 1 U2 8 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 5 IS 1 BP 144 EP 153 DI 10.4056/sigs.2265047 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GU UT WOS:000298944200014 PM 22180818 ER PT J AU Pati, A Heath, LS Kyrpides, NC Ivanova, N AF Pati, Amrita Heath, Lenwood S. Kyrpides, Nikos C. Ivanova, Natalia TI ClaMS: A Classifier for Metagenomic Sequences SO STANDARDS IN GENOMIC SCIENCES LA English DT Article ID PHYLOGENETIC CLASSIFICATION AB ClaMS - "Classifier for Metagenomic Sequences" - is a Java application for binning assembled contigs in metagenomes using user-specified training sets and initial parameters. Since ClaMS trains on sequence composition-based genomic signatures, it is much faster than binning tools that rely on alignments to homologs; ClaMS can bin similar to 20,000 sequences in 3 minutes on a laptop with a 2.4 GHx Intel Core 2 Duo processor and 2 GB RAM. ClaMS is meant to be a desktop application for biologists and can be run on any machine under any Operating System on which the Java Runtime Environment can be installed. C1 [Pati, Amrita; Kyrpides, Nikos C.; Ivanova, Natalia] DOE Joint Genome Inst, Genome Biol Program, Walnut Creek, CA 94598 USA. [Heath, Lenwood S.] Virginia Tech, Dept Comp Sci, Blacksburg, VA 24061 USA. RP Pati, A (reprint author), DOE Joint Genome Inst, Genome Biol Program, Walnut Creek, CA 94598 USA. EM apati@lbl.gov RI Kyrpides, Nikos/A-6305-2014; OI Kyrpides, Nikos/0000-0002-6131-0462; Ivanova, Natalia/0000-0002-5802-9485 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396] FX ClaMS was developed 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 DE-AC02-05CH11231, Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344 and Los Alamos National Laboratory under contract DE-AC02-06NA25396. NR 9 TC 20 Z9 20 U1 1 U2 7 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 5 IS 2 BP 248 EP 253 DI 10.4056/sigs.2075298 PG 6 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GV UT WOS:000298944300006 PM 22180827 ER PT J AU Abt, B Teshima, H Lucas, S Lapidus, A Del Rio, TG Nolan, M Tice, H Cheng, JF Pitluck, S Liolios, K Pagani, I Ivanova, N Mavromatis, K Pati, A Tapia, R Han, C Goodwin, L Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Rohde, M Goker, M Tindall, BJ Detter, JC Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Klenk, HP Kyrpides, NC AF Abt, Birte Teshima, Hazuki Lucas, Susan Lapidus, Alla Del Rio, Tijana Glavina Nolan, Matt Tice, Hope Cheng, Jan-Fang Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Ivanova, Natalia Mavromatis, Konstantinos Pati, Amrita Tapia, Roxane Han, Cliff Goodwin, Lynne Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Rohde, Manfred Goeker, Markus Tindall, Brian J. Detter, John C. Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Klenk, Hans-Peter Kyrpides, Nikos C. TI Complete genome sequence of Leadbetterella byssophila type strain (4M15(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE non-motile; non-sporulating; aerobic; mesophile; Gram-negative; flexirubin; Cytophagaceae; GEBA ID SP-NOV.; GEN.-NOV.; FAMILY FLEXIBACTERACEAE; PHYLOGENETIC ANALYSIS; BACTERIA; ARCHAEA; IDENTIFICATION; ALGORITHM; DATABASE; SYSTEM AB Leadbetterella byssophila Weon et al. 2005 is the type species of the genus Leadbetterella of the family Cytophagaceae in the phylum Bacteroidetes. Members of the phylum Bacteroidetes are widely distributed in nature, especially in aquatic environments. They are of special interest for their ability to degrade complex biopolymers. L. byssophila occupies a rather isolated position in the tree of life and is characterized by its ability to hydrolyze starch and gelatine, but not agar, cellulose or chitin. Here we describe the features of this organism, together with the complete genome sequence, and annotation. L. byssophila is already the 16(th) member of the family Cytophagaceae whose genome has been sequenced. The 4,059,653 bp long single replicon genome with its 3,613 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Teshima, Hazuki; Lucas, Susan; Lapidus, Alla; Del Rio, Tijana Glavina; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Pati, Amrita; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA. [Abt, Birte; Goeker, Markus; Tindall, Brian J.; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Teshima, Hazuki; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Lawrence Livermore Natl Lab, Livermore, CA USA. [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, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Kyrpides, NC (reprint author), US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA. RI Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; German Research Foundation (DFG) [INST 599/1-2]; Oak Ridge National Laboratory [DE-AC05-00OR22725] FX We would like to gratefully acknowledge the help of Helga Pomrenke for growing L. byssophila cultures, Susanne Schneider for DNA extraction and quality analysis and Jennifer Gregor for substrate assays (all at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2. NR 43 TC 8 Z9 9 U1 1 U2 10 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 4 IS 1 BP 2 EP 12 DI 10.4056/sigs.1413518 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EL UT WOS:000290223400001 PM 21475582 ER PT J AU Chertkov, O Sikorski, J Nolan, M Lapidus, A Lucas, S Del Rio, TG Tice, H Cheng, JF Goodwin, L Pitluck, S Liolios, K Ivanova, N Mavromatis, K Mikhailova, N Ovchinnikova, G Pati, A Chen, A Palaniappan, K Djao, ODN Land, M Hauser, L Chang, YJ Jeffries, CD Brettin, T Han, C Detter, JC Rohde, M Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Klenk, HP Kyrpides, NC AF Chertkov, Olga Sikorski, Johannes Nolan, Matt Lapidus, Alla Lucas, Susan Del Rio, Tijana Glavina Tice, Hope Cheng, Jan-Fang Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Ovchinnikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Djao, Olivier D. Ngatchou Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Brettin, Thomas Han, Cliff Detter, John C. Rohde, Manfred Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Klenk, Hans-Peter Kyrpides, Nikos C. TI Complete genome sequence of Thermomonospora curvata type strain (B9(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE chemoorganotroph; facultative aerobe; eurythermal thermophile; mycelium; Gram-positive; cellulose degradation; Thermomonosporaceae; GEBA ID CELLULOLYTIC ACTIVITY; CELLULASE BIOSYNTHESIS; BACTERIA; CLASSIFICATION; PROPOSAL; ARCHAEA; SYSTEM; ACTINOBACTERIA; IDENTIFICATION; PURIFICATION AB Thermomonospora curvata Henssen 1957 is the type species of the genus Thermomonospora. This genus is of interest because members of this clade are sources of new antibiotics, enzymes, and products with pharmacological activity. In addition, members of this genus participate in the active degradation of cellulose. This is the first complete genome sequence of a member of the family Thermomonosporaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,639,016 bp long genome with its 4,985 protein-coding and 76 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Chertkov, Olga; Nolan, Matt; Lapidus, Alla; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Ovchinnikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Brettin, Thomas; Han, Cliff; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA. [Chertkov, Olga; Goodwin, Lynne; Han, Cliff; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Sikorski, Johannes; Goeker, Markus] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Djao, Olivier D. Ngatchou; Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Brettin, Thomas] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. [Hugenholtz, Philip] Univ Queensland, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Kyrpides, NC (reprint author), US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA. RI Kyrpides, Nikos/A-6305-2014; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011 OI Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; German Research Foundation (DFG) [INST 599/1-1]; Oak Ridge National Laboratory [DE-AC05-00OR22725] FX We would like to gratefully acknowledge the help of Marlen Jando for growing T. curvata cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1. NR 53 TC 12 Z9 22 U1 2 U2 5 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. PY 2011 VL 4 IS 1 BP 13 EP 22 DI 10.4056/sigs.1453580 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EL UT WOS:000290223400002 PM 21475583 ER PT J AU Muyzer, G Sorokin, DY Mavromatis, K Lapidus, A Clum, A Ivanova, N Pati, A d'Haeseleer, P Woyke, T Kyrpides, NC AF Muyzer, Gerard Sorokin, Dimitry Yu Mavromatis, Konstantinos Lapidus, Alla Clum, Alicia Ivanova, Natalia Pati, Amrita d'Haeseleer, Patrick Woyke, Tanja Kyrpides, Nikos C. TI Complete genome sequence of "Thioalkalivibrio sulfidophilus" HL-EbGr7 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE haloalkaliphilic; sulfide; thiosulfate; sulfur-oxidizing bacteria (SOB) ID SULFUR-OXIDIZING BACTERIA; SODA LAKES; GLYCINE BETAINE; RIBOSOMAL-RNA; ALKALINE PH; SP-NOV; SYSTEM; DENITRIFICATION; CARBOXYSOMES; THIOCYANATE AB "Thioalkalivibrio sulfidophilus" HL-EbGr7 is an obligately chemolithoautotrophic, haloalkaliphilic sulfur-oxidizing bacterium (SOB) belonging to the Gammaproteobacteria. The strain was found to predominate a full-scale bioreactor, removing sulfide from biogas. Here we report the complete genome sequence of strain HL-EbGr7 and its annotation. The genome was sequenced within the Joint Genome Institute Community Sequencing Program, because of its relevance to the sustainable removal of sulfide from bio- and industrial waste gases. C1 [Muyzer, Gerard; Sorokin, Dimitry Yu] Delft Univ Technol, Dept Biotechnol, Delft, Netherlands. [Sorokin, Dimitry Yu] Russian Acad Sci, Winogradsky Inst Microbiol, Moscow, Russia. [Mavromatis, Konstantinos; Lapidus, Alla; Clum, Alicia; Ivanova, Natalia; Pati, Amrita; Woyke, Tanja; Kyrpides, Nikos C.] Joint Genome Inst, Walnut Creek, CA USA. [d'Haeseleer, Patrick] Joint Bioenergy Inst, Berkeley, CA 94720 USA. RP Muyzer, G (reprint author), Delft Univ Technol, Dept Biotechnol, Delft, Netherlands. RI Muyzer, Gerard/A-3161-2013; Lapidus, Alla/I-4348-2013; Kyrpides, Nikos/A-6305-2014; OI Ivanova, Natalia/0000-0002-5802-9485; Lapidus, Alla/0000-0003-0427-8731; Kyrpides, Nikos/0000-0002-6131-0462; Muyzer, Gerard/0000-0002-2422-0732 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; RFBR [10-04-00152]; Oak Ridge National Laboratory [DE-AC05-00OR22725] 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, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725. DS was supported financially by RFBR grant 10-04-00152. NR 45 TC 21 Z9 280 U1 5 U2 24 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 4 IS 1 BP 23 EP 35 DI 10.4056/sigs.1483693 PG 13 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EL UT WOS:000290223400003 PM 21475584 ER PT J AU Gronow, S Munk, C Lapidus, A Nolan, M Lucas, S Hammon, N Deshpande, S Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Ivanova, N Mavromatis, K Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Brambilla, E Rohde, M Goker, M Detter, JC Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Gronow, Sabine Munk, Christine Lapidus, Alla Nolan, Matt Lucas, Susan Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Tapia, Roxane Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Brambilla, Evelyne Rohde, Manfred Goeker, Markus Detter, John C. Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Paludibacter propionicigenes type strain (WB4(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE strictly anaerobic; nonmotile; Gram-negative; anoxic rice-field soil; mesophilic; chemoorganotrophic; Porphyromonadaceae; GEBA ID PLANT RESIDUE; FIELD SOIL; BACTERIA; ARCHAEA; PHYLOGENY; ALGORITHM; DATABASE; SYSTEM; GRAPHS AB Paludibacter propionicigenes Ueki et al. 2006 is the type species of the genus Paludibacter, which belongs to the family Porphyromonadaceae. The species is of interest because of the position it occupies in the tree of life where it can be found in close proximity to members of the genus Dysgonomonas. This is the first completed genome sequence of a member of the genus Paludibacter and the third sequence from the family Porphyromonadaceae. The 3,685,504 bp long genome with its 3,054 protein-coding and 64 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Gronow, Sabine; Brambilla, Evelyne; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Munk, Christine; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Munk, Christine; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [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, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; German Research Foundation (DFG) [INST 599/1-2]; Oak Ridge National Laboratory [DE-AC05-00OR22725] FX We would like to gratefully acknowledge the help of Sabine Welnitz (DSMZ) for growing P. propionicigenes cultures. 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 28 TC 13 Z9 14 U1 1 U2 11 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. PY 2011 VL 4 IS 1 BP 36 EP 44 DI 10.4056/sigs.1503846 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EL UT WOS:000290223400004 PM 21475585 ER PT J AU Pati, A Gronow, S Zeytun, A Lapidus, A Nolan, M Hammon, N Deshpande, S Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Pagani, I Ivanova, N Mavromatis, K Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Detter, JC Brambilla, E Rohde, M Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Lucas, S AF Pati, Amrita Gronow, Sabine Zeytun, Ahmet Lapidus, Alla Nolan, Matt Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Tapia, Roxane Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Ivanova, Natalia Mavromatis, Konstantinos Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Detter, John C. Brambilla, Evelyne Rohde, Manfred Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Lucas, Susan TI Complete genome sequence of Bacteroides helcogenes type strain (P 36-108(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE strictly anaerobic; mesophilic; nonmotile; Gram-negative; chemoorganotrophic; pig abscess; animal pathogen; Bacteroidaceae; GEBA ID BACTERIA; ARCHAEA; ALGORITHM; FRAGILIS; DATABASE; PROPOSAL; SYSTEM; GRAPHS; NOV AB Bacteroides helcogenes Benno et al. 1983 is of interest because of its isolated phylogenetic location and, although it has been found in pig feces and is known to be pathogenic for pigs, occurrence of this bacterium is rare and it does not cause significant damage in intensive animal husbandry. The genome of B. helcogenes P 36-108(T) is already the fifth completed and published type strain genome from the genus Bacteroides in the family Bacteroidaceae. The 3,998,906 bp long genome with its 3,353 protein-coding and 83 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Gronow, Sabine; Brambilla, Evelyne; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Pati, Amrita; Zeytun, Ahmet; Lapidus, Alla; Nolan, Matt; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Lucas, Susan] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Zeytun, Ahmet; Tapia, Roxane; Han, Cliff; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [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, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; German Research Foundation (DFG) [INST 599/1-2]; Oak Ridge National Laboratory [DE-AC05-00OR22725] FX We would like to gratefully acknowledge the help of Sabine Welnitz (DSMZ) for growing B. helcogenes cultures. 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 36 TC 6 Z9 8 U1 1 U2 5 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. PY 2011 VL 4 IS 1 BP 45 EP 53 DI 10.4056/sigs.1513795 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EL UT WOS:000290223400005 PM 21475586 ER PT J AU Pitluck, S Sikorski, J Zeytun, A Lapidus, A Nolan, M Lucas, S Hammon, N Deshpande, S Cheng, JF Tapia, R Han, C Goodwin, L Liolios, K Pagani, I Ivanova, N Mavromatis, K Pati, A Chen, A Palaniappan, K Hauser, L Chang, YJ Jeffries, CD Detter, JC Brambilla, E Djao, ODN Rohde, M Spring, S Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Land, M AF Pitluck, Sam Sikorski, Johannes Zeytun, Ahmet Lapidus, Alla Nolan, Matt Lucas, Susan Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Tapia, Roxane Han, Cliff Goodwin, Lynne Liolios, Konstantinos Pagani, Ioanna Ivanova, Natalia Mavromatis, Konstantinos Pati, Amrita Chen, Amy Palaniappan, Krishna Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Detter, John C. Brambilla, Evelyne Djao, Oliver D. Ngatchou Rohde, Manfred Spring, Stefan Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Land, Miriam TI Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE moderately thermophilic; strictly anaerobic; motile; Gram-negative; chemoorganoheterotroph; hot spring; Deferribacteraceae; GEBA ID DENITROVIBRIO-ACETIPHILUS; BACTERIUM; ARCHAEA; ALGORITHM; RESERVOIR; DATABASE; SYSTEM; GRAPHS; GENUS; NOV AB Calditerrivibrio nitroreducens Iino et al. 2008 is the type species of the genus Calditerrivibrio. The species is of interest because of its important role in the nitrate cycle as nitrate reducer and for its isolated phylogenetic position in the Tree of Life. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the third complete genome sequence of a member of the family Deferribacteraceae. The 2,216,552 bp long genome with its 2,128 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Sikorski, Johannes; Brambilla, Evelyne; Spring, Stefan; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Pitluck, Sam; Zeytun, Ahmet; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Pati, Amrita; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Land, Miriam] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Zeytun, Ahmet; Tapia, Roxane; Han, Cliff; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Land, Miriam] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Djao, Oliver D. Ngatchou; 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, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Spring, Stefan/N-6933-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Spring, Stefan/0000-0001-6247-0938; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; German Research Foundation (DFG) [INST 599/1-1]; Oak Ridge National Laboratory [DE-AC05-00OR22725] FX We would like to gratefully acknowledge the help of Maren Schroder (DSMZ) for the growth of C. nitroreducens cultures. 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 599/1-1. NR 33 TC 6 Z9 9 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. PY 2011 VL 4 IS 1 BP 54 EP 62 DI 10.4056/sigs.1523807 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EL UT WOS:000290223400006 PM 21475587 ER PT J AU Goker, M Cleland, D Saunders, E Lapidus, A Nolan, M Lucas, S Hammon, N Deshpande, S Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Pagani, I Ivanova, N Mavromatis, K Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Detter, JC Beck, B Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Goeker, Markus Cleland, David Saunders, Elizabeth Lapidus, Alla Nolan, Matt Lucas, Susan Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Tapia, Roxane Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Ivanova, Natalia Mavromatis, Konstantinos Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Detter, John C. Beck, Brian Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Isosphaera pallida type strain (IS1B(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE thermophilic; aerobic; filamentous; budding; gliding motility; Gram-negative; phototactic comets; gas vesicles; chemoheterotrophic; hot spring; Planctomycetaceae; GEBA ID BUDDING EUBACTERIUM; HOT-SPRINGS; BACTERIA; ARCHAEA; PLANCTOMYCES; ALGORITHM; DATABASE; SYSTEM; GRAPHS; NOV AB Isosphaera pallida (ex Woronichin 1927) Giovannoni et al. 1995 is the type species of the genus Isosphaera. The species is of interest because it was the first heterotrophic bacterium known to be phototactic, and it occupies an isolated phylogenetic position within the Planctomycetaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the genus Isosphaera and the third of a member of the family Planctomycetaceae. The 5,472,964 bp long chromosome and the 56,340 bp long plasmid with a total of 3,763 protein-coding and 60 RNA genes are part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Cleland, David; Beck, Brian] ATCC Amer Type Culture Collect, Manassas, VA USA. [Saunders, Elizabeth; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Saunders, Elizabeth; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. [Hugenholtz, Philip] Univ Queensland, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725] 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, UT-Battelle, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725. NR 33 TC 22 Z9 23 U1 3 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. PY 2011 VL 4 IS 1 BP 63 EP 71 DI 10.4056/sigs.1533840 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EL UT WOS:000290223400007 PM 21475588 ER PT J AU Abt, B Lu, M Misra, M Han, C Nolan, M Lucas, S Hammon, N Deshpande, S Cheng, JF Tapia, R Goodwin, L Pitluck, S Liolios, K Pagani, I Ivanova, N Mavromatis, K Ovchinikova, G Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Detter, JC Brambilla, E Rohde, M Tindall, BJ Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Lapidus, A AF Abt, Birte Lu, Megan Misra, Monica Han, Cliff Nolan, Matt Lucas, Susan Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Tapia, Roxane Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Ivanova, Natalia Mavromatis, Konstantinos Ovchinikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Detter, John C. Brambilla, Evelyne Rohde, Manfred Tindall, Brian J. Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Lapidus, Alla TI Complete genome sequence of Cellulophaga algicola type strain (IC166(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE aerobic; motile by gliding; Gram-negative; agarolytic; chemoorganotrophic; cold adapted enzymes; Flavobacteriaceae; GEBA ID EMENDED DESCRIPTION; COMB. NOV; BACTERIA; ARCHAEA; FLAVOBACTERIACEAE; RECLASSIFICATION; CLASSIFICATION; ALGORITHM; DATABASE; PROPOSAL AB Cellulophaga algicola Bowman 2000 belongs to the family Flavobacteriaceae within the phylum 'Bacteroidetes' and was isolated from Melosira collected from the Eastern Antarctic coastal zone. The species is of interest because its members produce a wide range of extracellular enzymes capable of degrading proteins and polysaccharides with temperature optima of 20-30 degrees C. This is the first completed genome sequence of a member of the genus Cellulophaga. The 4,888,353 bp long genome with its 4,285 protein-coding and 62 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Lu, Megan; Misra, Monica; Han, Cliff; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxane; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Lapidus, Alla] US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA. [Abt, Birte; Brambilla, Evelyne; Tindall, Brian J.; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Lu, Megan; Misra, Monica; Han, Cliff; Tapia, Roxane; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [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, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Lapidus, A (reprint author), US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA. RI Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; German Research Foundation (DFG) [INST 599/1-2]; Oak Ridge National Laboratory [DE-AC05-00OR22725] FX We would like to gratefully acknowledge the help of Regine Fahnrich (DSMZ) for growing C. algicola cultures. 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 36 TC 8 Z9 8 U1 3 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. PY 2011 VL 4 IS 1 BP 72 EP 80 DI 10.4056/sigs.1543845 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EL UT WOS:000290223400008 PM 21475589 ER PT J AU Lang, E Teshima, H Lucas, S Lapidus, A Hammon, N Deshpande, S Nolan, M Cheng, JF Pitluck, S Liolios, K Pagani, I Mikhailova, N Ivanova, N Mavromatis, K Pati, A Tapia, R Han, C Goodwin, L Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Brambilla, EM Kopitz, M Rohde, M Goker, M Tindall, BJ Detter, JC Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Klenk, HP Kyrpides, NC AF Lang, Elke Teshima, Hazuki Lucas, Susan Lapidus, Alla Hammon, Nancy Deshpande, Shweta Nolan, Matt Cheng, Jan-Fang Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Mikhailova, Natalia Ivanova, Natalia Mavromatis, Konstantinos Pati, Amrita Tapia, Roxane Han, Cliff Goodwin, Lynne Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Brambilla, Evelyne-Marie Kopitz, Markus Rohde, Manfred Goeker, Markus Tindall, Brian J. Detter, John C. Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Klenk, Hans-Peter Kyrpides, Nikos C. TI Complete genome sequence of Weeksella virosa type strain (9751(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE strictly aerobic; slimy; Gram-negative; lyses proteins; inhabitant of mucosa; Flavobacteriaceae; GEBA ID FORMERLY GROUP-IIF; SP NOV.; FAMILY FLAVOBACTERIACEAE; EMENDED DESCRIPTION; CLINICAL SPECIMENS; GEN.-NOV.; BACTERIA; CHRYSEOBACTERIUM; CLASSIFICATION; ARCHAEA AB Weeksella virosa Holmes et al. 1987 is the sole member and type species of the genus Weeksella which belongs to the family Flavobacteriaceae of the phylum Bacteroidetes. Twenty-nine isolates, collected from clinical specimens provided the basis for the taxon description. While the species seems to be a saprophyte of the mucous membranes of healthy man and warm-blooded animals a causal relationship with disease has been reported in a few instances. Except for the ability to produce indole and to hydrolyze Tween and proteins such as casein and gelatin, this aerobic, non-motile, non-pigmented bacterial species is metabolically inert in most traditional biochemical tests. The 2,272,954 bp long genome with its 2,105 protein-coding and 76 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Teshima, Hazuki; Lucas, Susan; Lapidus, Alla; Hammon, Nancy; Deshpande, Shweta; Nolan, Matt; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Mikhailova, Natalia; Ivanova, Natalia; Mavromatis, Konstantinos; Pati, Amrita; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA. [Lang, Elke; Brambilla, Evelyne-Marie; Kopitz, Markus; Goeker, Markus; Tindall, Brian J.; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Teshima, Hazuki; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Lawrence Livermore Natl Lab, Livermore, CA USA. [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, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Kyrpides, NC (reprint author), US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA. RI Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; German Research Foundation (DFG) [INST 599/1-2]; Oak Ridge National Laboratory [DE-AC05-00OR22725] 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, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2. NR 50 TC 5 Z9 5 U1 1 U2 5 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. PY 2011 VL 4 IS 1 BP 81 EP 90 DI 10.4056/sigs.1603927 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EL UT WOS:000290223400009 PM 21475590 ER PT J AU Ivanova, N Rohde, C Munk, C Nolan, M Lucas, S Del Rio, TG Tice, H Deshpande, S Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Mavromatis, K Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Brambilla, E Rohde, M Goker, M Tindall, BJ Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Lapidus, A AF Ivanova, Natalia Rohde, Christine Munk, Christine Nolan, Matt Lucas, Susan Del Rio, Tijana Glavina Tice, Hope Deshpande, Shweta Cheng, Jan-Fang Tapia, Roxane Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Brambilla, Evelyne Rohde, Manfred Goeker, Markus Tindall, Brian J. Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Lapidus, Alla TI Complete genome sequence of Truepera radiovictrix type strain (RQ-24(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE aerobic; chemoorganotrophic; non-motile; thermophilic; facultatively halophilic; alkaliphilic; radiation resistant; Gram-indeterminate; spherical-shaped; Trueperaceae; GEBA ID RADIATION-RESISTANCE; BACTERIA; ARCHAEA; ALGORITHM; DATABASE; PROPOSAL; SYSTEM; GRAPHS AB Truepera radiovictrix Albuquerque et al. 2005 is the type species of the genus Truepera within the phylum "Deinococcus/Thermus". T. radiovictrix is of special interest not only because of its isolated phylogenetic location in the order Deinococcales, but also because of its ability to grow under multiple extreme conditions in alkaline, moderately saline, and high temperature habitats. Of particular interest is the fact that, T. radiovictrix is also remarkably resistant to ionizing radiation, a feature it shares with members of the genus Deinococcus. This is the first completed genome sequence of a member of the family Trueperaceae and the fourth type strain genome sequence from a member of the order Deinococcales. The 3,260,398 bp long genome with its 2,994 protein-coding and 52 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Ivanova, Natalia; Munk, Christine; Nolan, Matt; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Lapidus, Alla] US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA. [Rohde, Christine; Brambilla, Evelyne; Goeker, Markus; Tindall, Brian J.; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Munk, Christine; Tapia, Roxane; Han, Cliff; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [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, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Lapidus, A (reprint author), US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; German Research Foundation (DFG) [INST 599/1-2]; Oak Ridge National Laboratory [DE-AC05-00OR22725] FX We would like to gratefully acknowledge the help of Helga Pomrenke (DSMZ) for growing T. radiovictrix cultures. 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 35 TC 12 Z9 12 U1 2 U2 11 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. PY 2011 VL 4 IS 1 BP 91 EP 99 DI 10.4056/sigs.1563919 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EL UT WOS:000290223400010 PM 21475591 ER PT J AU Pagani, I Lapidus, A Nolan, M Lucas, S Hammon, N Deshpande, S Cheng, JF Chertkov, O Davenport, K Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Mavromatis, K Ivanova, N Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Detter, JC Brambilla, E Kannan, KP Djao, ODN Rohde, M Pukall, R Spring, S Goker, M Sikorski, J Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Pagani, Ioanna Lapidus, Alla Nolan, Matt Lucas, Susan Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Chertkov, Olga Davenport, Karen Tapia, Roxane Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Mavromatis, Konstantinos Ivanova, Natalia Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Detter, John C. Brambilla, Evelyne Kannan, K. Palani Djao, Olivier D. Ngatchou Rohde, Manfred Pukall, Ruediger Spring, Stefan Goeker, Markus Sikorski, Johannes Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Desulfobulbus propionicus type strain (1pr3(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE anaerobic; non-motile; Gram-negative; chemoorganotroph; ellipsoidal to lemon-shaped; non spore-forming; mesophilic; Desulfobulbaceae; GEBA ID SULFATE-REDUCING BACTERIA; CELLULAR FATTY-ACIDS; ELEMENTAL SULFUR; OXIDATION; SEDIMENTS; ARCHAEA; ABSENCE; DESULFOBACTER; ALGORITHM; DATABASE AB Desulfobulbus propionicus Widdel 1981 is the type species of the genus Desulfobulbus, which belongs to the family Desulfobulbaceae. The species is of interest because of its great implication in the sulfur cycle in aquatic sediments, its large substrate spectrum and a broad versatility in using various fermentation pathways. The species was the first example of a pure culture known to disproportionate elemental sulfur to sulfate and sulfide. This is the first completed genome sequence of a member of the genus Desulfobulbus and the third published genome sequence from a member of the family Desulfobulbaceae. The 3,851,869 bp long genome with its 3,351 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Brambilla, Evelyne; Kannan, K. Palani; Pukall, Ruediger; Spring, Stefan; Goeker, Markus; Sikorski, Johannes; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Pagani, Ioanna; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Chertkov, Olga; Davenport, Karen; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, Konstantinos; Ivanova, Natalia; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Chertkov, Olga; Davenport, Karen; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Djao, Olivier D. Ngatchou; 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, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Spring, Stefan/N-6933-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013 OI Spring, Stefan/0000-0001-6247-0938; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; German Research Foundation (DFG) [INST 599/1-2]; Oak Ridge National Laboratory [DE-AC05-00OR22725] FX We would like to gratefully acknowledge the help of Katja Steenblock (DSMZ) for growing D. propionicus cultures. 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 45 TC 15 Z9 15 U1 1 U2 24 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. PY 2011 VL 4 IS 1 BP 100 EP 110 DI 10.4056/sigs.1613929 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EL UT WOS:000290223400011 PM 21475592 ER PT J AU Kallimanis, A LaButti, KM Lapidus, A Clum, A Lykidis, A Mavromatis, K Pagani, I Liolios, K Ivanova, N Goodwin, L Pitluck, S Chen, A Palaniappan, K Markowitz, V Bristow, J Velentzas, AD Perisynakis, A Ouzounis, CC Kyrpides, NC Koukkou, AI Drainas, C AF Kallimanis, Aristeidis LaButti, Kurt M. Lapidus, Alla Clum, Alicia Lykidis, Athanasios Mavromatis, Kostantinos Pagani, Ioanna Liolios, Konstantinos Ivanova, Natalia Goodwin, Lynne Pitluck, Sam Chen, Amy Palaniappan, Krishna Markowitz, Victor Bristow, Jim Velentzas, Athanasios D. Perisynakis, Angelos Ouzounis, Christos C. Kyrpides, Nikos C. Koukkou, Anna I. Drainas, Constantin TI Complete genome sequence of Arthrobacter phenanthrenivorans type strain (Sphe3) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Arthrobacter; dioxygenases; PAH biodegradation; phenanthrene degradation ID DEGRADING BACTERIUM; IDENTIFICATION; CLASSIFICATION; PROPOSAL; SYSTEM; ACTINOBACTERIA; DEGRADATION; NOV AB Arthrobacter phenanthrenivorans is the type species of the genus, and is able to metabolize phenanthrene as a sole source of carbon and energy. A. phenanthrenivorans is an aerobic, non-motile, and Gram-positive bacterium, exhibiting a rod-coccus growth cycle which was originally isolated from a creosote polluted site in Epirus, Greece. Here we describe the features of this organism, together with the complete genome sequence, and annotation. C1 [Kallimanis, Aristeidis; Perisynakis, Angelos; Koukkou, Anna I.; Drainas, Constantin] Univ Ioannina, Sector Organ Chem & Biochem, GR-45110 Ioannina, Greece. [LaButti, Kurt M.; Lapidus, Alla; Clum, Alicia; Lykidis, Athanasios; Mavromatis, Kostantinos; Pagani, Ioanna; Liolios, Konstantinos; Ivanova, Natalia; Goodwin, Lynne; Pitluck, Sam; Bristow, Jim; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Velentzas, Athanasios D.] Univ Athens, Fac Biol, Dept Cell Biol & Biophys, Athens, Greece. [Ouzounis, Christos C.] Kings Coll London, Dept Informat, Ctr Bioinformat, Sch Nat & Math Sci, London WC2R 2LS, England. RP Koukkou, AI (reprint author), Univ Ioannina, Sector Organ Chem & Biochem, GR-45110 Ioannina, Greece. EM akukku@cc.uoi.gr RI Lapidus, Alla/I-4348-2013; Ouzounis, Christos/G-2302-2010; Kyrpides, Nikos/A-6305-2014; Pagani, Ioanna/E-7390-2012 OI Lapidus, Alla/0000-0003-0427-8731; Kyrpides, Nikos/0000-0002-6131-0462; Velentzas, Athanasios D./0000-0002-9755-395X; Ivanova, Natalia/0000-0002-5802-9485; FU EPEAEK; European Social Funds (ESF); US Department of Energy Office of Science; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396] FX This work was supported by the program "Pythagoras II" of EPEAEK with 25% National Funds and 75% European Social Funds (ESF). NCK is supported by 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 21 TC 9 Z9 10 U1 4 U2 15 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 4 IS 2 BP 123 EP 130 DI 10.4056/sigs.1393494 PG 8 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 786XD UT WOS:000292340300002 PM 21677849 ER PT J AU Zeytun, A Sikorski, J Nolan, M Lapidus, A Lucas, S Han, J Tice, H Cheng, JF Tapia, R Goodwin, L Pitluck, S Liolios, K Ivanova, N Mavromatis, K Mikhailova, N Ovchinnikova, G Pati, A Chen, A Palaniappan, K Ngatchou-Djao, OD Land, M Hauser, L Jeffries, CD Han, C Detter, JC Ubler, S Rohde, M Tindall, BJ Goker, M Wirth, R Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Klenk, HP Kyrpides, NC AF Zeytun, Ahmet Sikorski, Johannes Nolan, Matt Lapidus, Alla Lucas, Susan Han, James Tice, Hope Cheng, Jan-Fang Tapia, Roxanne Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Ovchinnikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Ngatchou-Djao, Olivier D. Land, Miriam Hauser, Loren Jeffries, Cynthia D. Han, Cliff Detter, John C. Uebler, Susanne Rohde, Manfred Tindall, Brian J. Goeker, Markus Wirth, Reinhard Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Klenk, Hans-Peter Kyrpides, Nikos C. TI Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE strictly thermophilic; obligately chemolithoautotrophic; Gram-negative; aerobic; hydrogen-oxidizing; nonmotile; non sporeforming; rod shaped; Aquificaceae; Aquificae; GE-BA ID TRICARBOXYLIC-ACID CYCLE; OXIDIZING BACTERIUM; SP-NOV; GENUS HYDROGENOBACTER; ELEMENTAL SULFUR; AQUIFICALES; ARCHAEA; GROWTH; 2-METHYLTHIO-1,4-NAPHTHOQUINONE; PURIFICATION AB Hydrogenobacter thermophilus Kawasumi et al. 1984 is the type species of the genus Hydrogenobacter. H. thermophilus was the first obligate autotrophic organism reported among aerobic hydrogen-oxidizing bacteria. Strain TK-6(T) is of interest because of the unusually efficient hydrogen-oxidizing ability of this strain, which results in a faster generation time compared to other autotrophs. It is also able to grow anaerobically using nitrate as an electron acceptor when molecular hydrogen is used as the energy source, and able to aerobically fix CO2 via the reductive tricarboxylic acid cycle. This is the fifth completed genome sequence in the family Aquificaceae, and the second genome sequence determined from a strain derived from the original isolate. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,742,932 bp long genome with its 1,899 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Zeytun, Ahmet; Nolan, Matt; Lapidus, Alla; Lucas, Susan; Han, James; Tice, Hope; Cheng, Jan-Fang; Tapia, Roxanne; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Ovchinnikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.; Han, Cliff; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Sikorski, Johannes; Tindall, Brian J.; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Zeytun, Ahmet; Tapia, Roxanne; Goodwin, Lynne; Han, Cliff; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Ngatchou-Djao, Olivier D.; Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Uebler, Susanne; Wirth, Reinhard] Univ Regensburg, Archaea Ctr, Regensburg, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. [Hugenholtz, Philip] Univ Queensland, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Kyrpides, NC (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1] FX We would like to gratefully acknowledge the help of Susanne Schneider (DSMZ) for DNA extraction and quality analysis. 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 599/1-1. NR 59 TC 4 Z9 14 U1 2 U2 6 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 4 IS 2 BP 131 EP 143 DI 10.4056/sigs.1463589 PG 13 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 786XD UT WOS:000292340300003 PM 21677850 ER PT J AU Mavromatis, K Lu, M Misra, M Lapidus, A Nolan, M Lucas, S Hammon, N Deshpande, S Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Pagani, I Ivanova, N Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Hauser, L Jeffries, CD Detter, JC Brambilla, EM Rohde, M Goker, M Gronow, S Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Klenk, HP Kyrpides, NC AF Mavromatis, Konstantinos Lu, Megan Misra, Monica Lapidus, Alla Nolan, Matt Lucas, Susan Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Tapia, Roxane Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Ivanova, Natalia Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Jeffries, Cynthia D. Detter, John C. Brambilla, Evelyne-Marie Rohde, Manfred Goeker, Markus Gronow, Sabine Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Klenk, Hans-Peter Kyrpides, Nikos C. TI Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE capnophilic; non-motile; Gram-negative; poultry pathogen; mesophilic; chemoorganotrophic; Flavobacteriaceae; GEBA ID EMENDED DESCRIPTION; FLAVOBACTERIUM; ORGANISMS; BACTERIA; ARCHAEA; FAMILY; NOV; CLASSIFICATION; PASTEURELLA; ALGORITHM AB Riemerella anatipestifer (Hendrickson and Hilbert 1932) Segers et al. 1993 is the type species of the genus Riemerella, which belongs to the family Flavobacteriaceae. The species is of interest because of the position of the genus in the phylogenetic tree and because of its role as a pathogen of commercially important avian species worldwide. This is the first completed genome sequence of a member of the genus Riemerella. The 2,155,121 bp long genome with its 2,001 protein-coding and 51 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Mavromatis, Konstantinos; Lu, Megan; Misra, Monica; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Lu, Megan; Misra, Monica; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Brambilla, Evelyne-Marie; Goeker, Markus; Gronow, Sabine; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [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, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Kyrpides, NC (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. RI Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013 OI Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Sabine Welnitz (DSMZ) for growing R. anatipestifer cultures. 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 49 TC 17 Z9 21 U1 1 U2 5 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 4 IS 2 BP 144 EP 153 DI 10.4056/sigs.1553862 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 786XD UT WOS:000292340300004 PM 21677851 ER PT J AU Pagani, I Chertkov, O Lapidus, A Lucas, S Del Rio, TG Tice, H Copeland, A Cheng, JF Nolan, M Saunders, E Pitluck, S Held, B Goodwin, L Liolios, K Ovchinikova, G Ivanova, N Mavromatis, K Pati, A Chen, A Palaniappan, K Land, M Hauser, L Jeffries, CD Detter, JC Han, C Tapia, R Ngatchou-Djao, OD Rohde, M Goker, M Spring, S Sikorski, J Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Klenk, HP Kyrpides, NC AF Pagani, Ioanna Chertkov, Olga Lapidus, Alla Lucas, Susan Del Rio, Tijana Glavina Tice, Hope Copeland, Alex Cheng, Jan-Fang Nolan, Matt Saunders, Elizabeth Pitluck, Sam Held, Brittany Goodwin, Lynne Liolios, Konstantinos Ovchinikova, Galina Ivanova, Natalia Mavromatis, Konstantinos Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Jeffries, Cynthia D. Detter, John C. Han, Cliff Tapia, Roxanne Ngatchou-Djao, Olivier D. Rohde, Manfred Goeker, Markus Spring, Stefan Sikorski, Johannes Woyke, Tanja Bristow, Jim Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Klenk, Hans-Peter Kyrpides, Nikos C. TI Complete genome sequence of Marivirga tractuosa type strain (H-43(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE mesophilic; chemoorganotrophic; strictly aerobic; Gram-negative; slender and flexible rod-shaped; non-sporeforming; motile by gliding; Flammeovirgaceae; GEBA ID BACTERIA; ARCHAEA; CLASSIFICATION; FLEXIBACTERIA; ALGORITHM; DATABASE; SYSTEM; GRAPHS AB Marivirga tractuosa (Lewin 1969) Nedashkovskaya et al. 2010 is the type species of the genus Marivirga, which belongs to the family Flammeovirgaceae. Members of this genus are of interest because of their gliding motility. The species is of interest because representative strains show resistance to several antibiotics, including gentamicin, kanamycin, neomycin, polymixin and streptomycin. This is the first complete genome sequence of a member of the family Flammeovirgaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,511,574 bp long chromosome and the 4,916 bp plasmid with their 3,808 protein-coding and 49 RNA genes are a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Pagani, Ioanna; Chertkov, Olga; Lapidus, Alla; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Nolan, Matt; Saunders, Elizabeth; Pitluck, Sam; Held, Brittany; Goodwin, Lynne; Liolios, Konstantinos; Ovchinikova, Galina; Ivanova, Natalia; Mavromatis, Konstantinos; Pati, Amrita; Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.; Detter, John C.; Han, Cliff; Tapia, Roxanne; Woyke, Tanja; Bristow, Jim; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Chertkov, Olga; Saunders, Elizabeth; Held, Brittany; Goodwin, Lynne; Han, Cliff; Tapia, Roxanne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.; Detter, John C.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Ngatchou-Djao, Olivier D.; Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Goeker, Markus; Spring, Stefan; Sikorski, Johannes; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. [Hugenholtz, Philip] Univ Queensland, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Kyrpides, NC (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. RI Pagani, Ioanna/E-7390-2012; Kyrpides, Nikos/A-6305-2014; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Spring, Stefan/N-6933-2013; Land, Miriam/A-6200-2011 OI Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731; Spring, Stefan/0000-0001-6247-0938; Land, Miriam/0000-0001-7102-0031 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Maren Schroder for growing M. tractuosa cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2. NR 31 TC 5 Z9 5 U1 1 U2 4 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. PY 2011 VL 4 IS 2 BP 154 EP 162 DI 10.4056/sigs.1623941 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 786XD UT WOS:000292340300005 PM 21677852 ER PT J AU Pukall, R Zeytun, A Lucas, S Lapidus, A Hammon, N Deshpande, S Nolan, M Cheng, JF Pitluck, S Liolios, K Pagani, I Mikhailova, N Ivanova, N Mavromatis, K Pati, A Tapia, R Han, C Goodwin, L Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Brambilla, EM Rohde, M Goker, M Detter, JC Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Pukall, Rudeiger Zeytun, Ahmet Lucas, Susan Lapidus, Alla Hammon, Nancy Deshpande, Shweta Nolan, Matt Cheng, Jan-Fang Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Mikhailova, Natalia Ivanova, Natalia Mavromatis, Konstantinos Pati, Amrita Tapia, Roxane Han, Cliff Goodwin, Lynne Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Brambilla, Evelyne-Marie Rohde, Manfred Goeker, Markus Detter, J. Chris Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Deinococcus maricopensis type strain (LB-34(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE aerobic; non-motile; Gram-positive; radiation-resistant; mesophilic; chemoorganotrophic; Deinococcaceae; GEBA ID RADIATION-RESISTANT BACTERIUM; SP-NOV.; GENUS DEINOCOCCUS; RADIOACTIVE SITE; DESERT SOIL; SP. NOV.; ARCHAEA; GEOTHERMALIS; RADIODURANS; DIVERSITY AB Deinococcus maricopensis (Rainey and da Costa 2005) is a member of the genus Deinococcus, which is comprised of 44 validly named species and is located within the deeply branching bacterial phylum Deinococcus-Thermus. Strain LB-34(T) was isolated from a soil sample from the Sonoran Desert in Arizona. Various species of the genus Deinococcus are characterized by extreme radiation resistance, with D. maricopensis being resistant in excess of 10 kGy. Even though the genomes of three Deinococcus species, D. radiodurans, D. geothermalis and D. deserti, have already been published, no special physiological characteristic is currently known that is unique to this group. It is therefore of special interest to analyze the genomes of additional species of the genus Deinococcus to better understand how these species adapted to gamma- or UV ionizing-radiation. The 3,498,530 bp long genome of D. maricopensis with its 3,301 protein-coding and 66 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Pukall, Rudeiger; Brambilla, Evelyne-Marie; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Zeytun, Ahmet; Lucas, Susan; Lapidus, Alla; Hammon, Nancy; Deshpande, Shweta; Nolan, Matt; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Mikhailova, Natalia; Ivanova, Natalia; Mavromatis, Konstantinos; Pati, Amrita; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Detter, J. Chris] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Lawrence Livermore Natl Lab, Livermore, CA USA. [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, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; 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 and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Gabriele Gehrich-Schroter (DSMZ) for growing D. maricopensis cultures. 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 55 TC 7 Z9 7 U1 3 U2 7 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 4 IS 2 BP 163 EP 172 DI 10.4056/sigs.1633949 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 786XD UT WOS:000292340300006 PM 21677853 ER PT J AU Wirth, R Chertkov, O Held, B Lapidus, A Nolan, M Lucas, S Hammon, N Deshpande, S Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Ioanna, P Ivanova, N Mavromatis, K Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Bilek, Y Hader, T Rohde, M Spring, S Sikorski, J Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Wirth, Reinhard Chertkov, Olga Held, Brittany Lapidus, Alla Nolan, Matt Lucas, Susan Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Tapia, Roxane Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Ioanna, Pagani Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Bilek, Yvonne Hader, Thomas Rohde, Manfred Spring, Stefan Sikorski, Johannes Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Desulfurococcus mucosus type strain (O7/1(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE hyperthermophile; anaerobic; organotroph; sulfur respiration; spheroid-shaped; non-motile; extracellular enzymes; Desulfurococcaceae; GEBA ID ARCHAEBACTERIA; BACTERIA; ARCHAEA; HYBRIDIZATION; ALGORITHM; MOBILIS; SYSTEM; GRAPHS AB Desulfurococcus mucosus Zillig and Stetter 1983 is the type species of the genus Desulfurococcus, which belongs to the crenarchaeal family Desulfurococcaceae. The species is of interest because of its position in the tree of life, its ability for sulfur respiration, and several bio-technologically relevant thermostable and thermoactive extracellular enzymes. This is the third completed genome sequence of a member of the genus Desulfurococcus and already the 8(th) sequence from a member the family Desulfurococcaceae. The 1,314,639 bp long genome with its 1,371 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Spring, Stefan; Sikorski, Johannes; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Chertkov, Olga; Held, Brittany; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ioanna, Pagani; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Wirth, Reinhard; Bilek, Yvonne; Hader, Thomas] Univ Regensburg, Archaeenzentrum, Regensburg, Germany. [Chertkov, Olga; Held, Brittany; Tapia, Roxane; Han, Cliff; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [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, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Spring, Stefan/N-6933-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Spring, Stefan/0000-0001-6247-0938; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC0206NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Olivier D. Ngatchou-Djao (HZI) in preparing the manuscript. 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-AC0206NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2. NR 47 TC 5 Z9 5 U1 1 U2 5 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 4 IS 2 BP 173 EP 182 DI 10.4056/sigs.1644004 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 786XD UT WOS:000292340300007 PM 21677854 ER PT J AU Temperton, B Thomas, S Tait, K Parry, H Emery, M Allen, M Quinn, J MacGrath, J Gilbert, J AF Temperton, Ben Thomas, Simon Tait, Karen Parry, Helen Emery, Matt Allen, Mike Quinn, John MacGrath, John Gilbert, Jack TI Permanent draft genome sequence of Vibrio tubiashii strain NCIMB 1337 (ATCC19106) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article ID BIVALVE MOLLUSKS; BACTERIA; PATHOGEN; SYSTEM; RNA AB Vibrio tubiashii NCIMB 1337 is a major and increasingly prevalent pathogen of bivalve mollusks, and shares a close phylogenetic relationship with both V. orientalis and V. coralliilyticus. It is a Gram-negative, curved rod-shaped bacterium, originally isolated from a moribund juvenile oyster, and is both oxidase and catalase positive. It is capable of growth under both aerobic and anaerobic conditions. Here we describe the features of this organism, together with the draft genome and annotation. The genome is 5,353,266 bp long, consisting of two chromosomes, and contains 4,864 protein-coding and 86 RNA genes. C1 [Temperton, Ben; Thomas, Simon; Tait, Karen; Parry, Helen; Allen, Mike; Gilbert, Jack] Plymouth Marine Lab, Plymouth, Devon, England. [Temperton, Ben; Thomas, Simon; Quinn, John; MacGrath, John] Queens Univ Belfast, Sch Biol Sci, Ctr Med Biol, Belfast, Antrim, North Ireland. [Emery, Matt] Univ Plymouth, Dept Microbiol, Plymouth PL4 8AA, Devon, England. [Gilbert, Jack] Argonne Natl Lab, Argonne, IL 60439 USA. [Gilbert, Jack] Univ Chicago, Dept Ecol & Evolut, Chicago, IL 60637 USA. RP Temperton, B (reprint author), Plymouth Marine Lab, Prospect Pl, Plymouth, Devon, England. RI Allen, Michael (Mike)/C-1248-2011; GenePool, The/D-8812-2012; OI Allen, Michael (Mike)/0000-0001-8504-7171; Temperton, Ben/0000-0002-3667-8302 FU i-G Peninsula (Prospect Place, the Hoe, Plymouth, Devon, UK) FX We wish to thank i-G Peninsula (Prospect Place, the Hoe, Plymouth, Devon, UK) for providing funding for this project, and NBAF Edinburgh for performing the sequencing. NR 25 TC 11 Z9 11 U1 0 U2 2 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 4 IS 2 BP 183 EP 190 DI 10.4056/sigs.1654066 PG 8 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 786XD UT WOS:000292340300008 PM 21677855 ER PT J AU Gronow, S Held, B Lucas, S Lapidus, A Del Rio, TG Nolan, M Tice, H Deshpande, S Cheng, JF Pitluck, S Liolios, K Pagani, I Ivanova, N Mavromatis, K Pati, A Tapia, R Han, C Goodwin, L Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Brambilla, EM Rohde, M Goker, M Detter, JC Woyke, T Bristow, J Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Eisen, JA AF Gronow, Sabine Held, Brittany Lucas, Susan Lapidus, Alla Del Rio, Tijana Glavina Nolan, Matt Tice, Hope Deshpande, Shweta Cheng, Jan-Fang Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Ivanova, Natalia Mavromatis, Konstantinos Pati, Amrita Tapia, Roxane Han, Cliff Goodwin, Lynne Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Brambilla, Evelyne-Marie Rohde, Manfred Goeker, Markus Detter, John C. Woyke, Tanja Bristow, James Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Eisen, Jonathan A. TI Complete genome sequence of Bacteroides salanitronis type strain (BL78(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE strictly anaerobic; non-motile; rod-shaped; Gram-negative; mesophilic; cecum; poultry; chemoorganotrophic; Bacteroidaceae; GEBA ID BACTERIA; ARCHAEA; ALGORITHM; INTESTINE; MUTUALISM; FRAGILIS; DATABASE; PROPOSAL; SYSTEM; GRAPHS AB Bacteroides salanitronis Lan et al. 2006 is a species of the genus Bacteroides, which belongs to the family Bacteroidaceae. The species is of interest because it was isolated from the gut of a chicken and the growing awareness that the anaerobic microflora of the cecum is of benefit for the host and may impact poultry farming. The 4,308,663 bp long genome consists of a 4.24 Mbp chromosome and three plasmids (6 kbp, 19 kbp, 40 kbp) containing 3,737 protein-coding and 101 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Held, Brittany; Lucas, Susan; Lapidus, Alla; Del Rio, Tijana Glavina; Nolan, Matt; Tice, Hope; Deshpande, Shweta; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Pati, Amrita; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Woyke, Tanja; Bristow, James; Hugenholtz, Philip; Kyrpides, Nikos C.; Eisen, Jonathan A.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Gronow, Sabine; Brambilla, Evelyne-Marie; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Held, Brittany; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Lawrence Livermore Natl Lab, Livermore, CA USA. [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, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Eisen, JA (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. RI Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Sabine Welnitz (DSMZ) for growing cultures of B. salanitronis. 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 39 TC 5 Z9 6 U1 2 U2 5 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. PY 2011 VL 4 IS 2 BP 191 EP 199 DI 10.4056/sigs.1704212 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 786XD UT WOS:000292340300009 PM 21677856 ER PT J AU Goker, M Gronow, S Zeytun, A Nolan, M Lucas, S Lapidus, A Hammon, N Deshpande, S Cheng, JF Pitluck, S Liolios, K Pagani, I Ivanova, N Mavromatis, K Ovchinikova, G Pati, A Tapia, R Han, C Goodwin, L Chen, A Palaniappan, K Land, M Hauser, L Jeffries, CD Brambilla, EM Rohde, M Detter, JC Woyke, T Bristow, J Markowitz, V Hugenholtz, P Eisen, JA Kyrpides, NC Klenk, HP AF Goeker, Markus Gronow, Sabine Zeytun, Ahmet Nolan, Matt Lucas, Susan Lapidus, Alla Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Ivanova, Natalia Mavromatis, Konstantinos Ovchinikova, Galina Pati, Amrita Tapia, Roxane Han, Cliff Goodwin, Lynne Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Jeffries, Cynthia D. Brambilla, Evelyne-Marie Rohde, Manfred Detter, John C. Woyke, Tanja Bristow, James Markowitz, Victor Hugenholtz, Philip Eisen, Jonathan A. Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Odoribacter splanchnicus type strain (1651/6(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE strictly anaerobic; non-motile; Gram-negative; opportunistic pathogen; mesophilic; chemoorganotrophic; Porphyromonadaceae; GEBA ID BACTEROIDES-SPLANCHNICUS; GENUS BACTEROIDES; BACTERIA; ARCHAEA; PORPHYROMONAS; PHYLOGENY; ALGORITHM; DATABASE; SYSTEM; GRAPHS AB Odoribacter splanchnicus (Werner et al. 1975) Hardham et al. 2008 is the type species of the genus Odoribacter, which belongs to the family Porphyromonadaceae in the order 'Bacteroidales'. The species is of interest because members of the Odoribacter form an isolated cluster within the Porphyromonadaceae. This is the first completed genome sequence of a member of the genus Odoribacter and the fourth sequence from the family Porphyromonadaceae. The 4,392,288 bp long genome with its 3,672 protein-coding and 74 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Goeker, Markus; Gronow, Sabine; Brambilla, Evelyne-Marie; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Zeytun, Ahmet; Nolan, Matt; Lucas, Susan; Lapidus, Alla; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinikova, Galina; Pati, Amrita; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.; Detter, John C.; Woyke, Tanja; Bristow, James; Hugenholtz, Philip; Eisen, Jonathan A.; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Zeytun, Ahmet; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Hugenholtz, Philip] Univ Queensland, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Sabine Welnitz (DSMZ) for growing O. splanchnicus cultures. 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 43 TC 14 Z9 14 U1 2 U2 9 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. PY 2011 VL 4 IS 2 BP 200 EP 209 DI 10.4056/sigs.1714269 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 786XD UT WOS:000292340300010 PM 21677857 ER PT J AU Pati, A Zhang, XJ Lapidus, A Nolan, M Lucas, S Del Rio, TG Tice, H Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Pagani, I Ivanova, N Mavromatis, K Chen, A Palaniappan, K Hauser, L Jeffries, CD Brambilla, EM Rohl, A Mwirichia, R Rohde, M Tindall, BJ Sikorski, J Wirth, R Goker, M Woyke, T Detter, JC Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Land, M AF Pati, Amrita Zhang, Xiaojing Lapidus, Alla Nolan, Matt Lucas, Susan Del Rio, Tijana Glavina Tice, Hope Cheng, Jan-Fang Tapia, Roxane Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Ivanova, Natalia Mavromatis, Konstantinos Chen, Amy Palaniappan, Krishna Hauser, Loren Jeffries, Cynthia D. Brambilla, Evelyne-Marie Roehl, Alina Mwirichia, Romano Rohde, Manfred Tindall, Brian J. Sikorski, Johannes Wirth, Reinhard Goeker, Markus Woyke, Tanja Detter, John C. Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Land, Miriam TI Complete genome sequence of Oceanithermus profundus type strain (506(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE microaerophilic; non-motile; Gram-negative; nitrate-reducing; moderate thermophilic; neutrophilic; chemolithoheterotrophic; hydrothermal vent; Thermaceae; GEBA ID EXTREMELY RADIATION-RESISTANT; FATTY-ACID-COMPOSITION; SEA HYDROTHERMAL VENT; GEN. NOV.; SP. NOV.; THERMOPHILIC BACTERIUM; THERMUS-AQUATICUS; MEIOTHERMUS; DEINOCOCCUS; ARCHAEA AB Oceanithermus profundus Miroshnichenko et al. 2003 is the type species of the genus Oceanithermus, which belongs to the family Thermaceae. The genus currently comprises two species whose members are thermophilic and are able to reduce sulfur compounds and nitrite. The organism is adapted to the salinity of sea water, is able to utilize a broad range of carbohydrates, some proteinaceous substrates, organic acids and alcohols. This is the first completed genome sequence of a member of the genus Oceanithermus and the fourth sequence from the family Thermaceae. The 2,439,291 bp long genome with its 2,391 protein-coding and 54 RNA genes consists of one chromosome and a 135,351 bp long plasmid, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Brambilla, Evelyne-Marie; Tindall, Brian J.; Sikorski, Johannes; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Pati, Amrita; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Hauser, Loren; Jeffries, Cynthia D.; Woyke, Tanja; Detter, John C.; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Land, Miriam] DOE Joint Genome Inst, Walnut Creek, CA USA. [Zhang, Xiaojing; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Hauser, Loren; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Roehl, Alina; Wirth, Reinhard] Univ Regensburg, Microbiol Archaeenzentrum, Regensburg, Germany. [Mwirichia, Romano] Jomo Kenyatta Univ Agr & Technol, Nairobi, 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, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] 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, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2. NR 47 TC 3 Z9 3 U1 2 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. PY 2011 VL 4 IS 2 BP 210 EP 220 DI 10.4056/sigs.1734292 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 786XD UT WOS:000292340300011 PM 21677858 ER PT J AU Pati, A Abt, B Teshima, H Nolan, M Lapidus, A Lucas, S Hammon, N Deshpande, S Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Pagani, I Mavromatis, K Ovchinikova, G Chen, A Palaniappan, K Land, M Hauser, L Jeffries, CD Detter, JC Brambilla, EM Kannan, KP Rohde, M Spring, S Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Ivanova, N AF Pati, Amrita Abt, Birte Teshima, Hazuki Nolan, Matt Lapidus, Alla Lucas, Susan Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Tapia, Roxane Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Mavromatis, Konstantinos Ovchinikova, Galina Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Jeffries, Cynthia D. Detter, John C. Brambilla, Evelyne-Marie Kannan, K. Palani Rohde, Manfred Spring, Stefan Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Ivanova, Natalia TI Complete genome sequence of Cellulophaga lytica type strain (LIM-21(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE aerobic; motile by gliding; Gram-negative; agarolytic; chemoorganotrophic; Flavobacteriaceae; GEBA ID EMENDED DESCRIPTION; BACTERIAL NAMES; COMB. NOV; CLASSIFICATION; ARCHAEA; FLAVOBACTERIACEAE; RECLASSIFICATION; FLEXIBACTERIA; ALGORITHM; DATABASE AB Cellulophaga lytica (Lewin 1969) Johansen et al. 1999 is the type species of the genus Cellulophaga, which belongs to the family Flavobacteriaceae within the phylum 'Bacteroidetes' and was isolated from marine beach mud in Limon, Costa Rica. The species is of biotechnological interest because its members produce a wide range of extracellular enzymes capable of degrading proteins and polysaccharides. After the genome sequence of Cellulophaga algicola this is the second completed genome sequence of a member of the genus Cellulophaga. The 3,765,936 bp long genome with its 3,303 protein-coding and 55 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Abt, Birte; Brambilla, Evelyne-Marie; Kannan, K. Palani; Spring, Stefan; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Pati, Amrita; Teshima, Hazuki; Nolan, Matt; Lapidus, Alla; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Mavromatis, Konstantinos; Ovchinikova, Galina; Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Ivanova, Natalia] DOE Joint Genome Inst, Walnut Creek, CA USA. [Teshima, Hazuki; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [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, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Kyrpides, Nikos/A-6305-2014; Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Spring, Stefan/N-6933-2013; Land, Miriam/A-6200-2011 OI Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731; Spring, Stefan/0000-0001-6247-0938; Land, Miriam/0000-0001-7102-0031 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Maren Schroder (DSMZ) for growing C. lytica cultures. 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, as well as German Research Foundation (DFG) INST 599/1-2. NR 46 TC 12 Z9 12 U1 1 U2 5 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. PY 2011 VL 4 IS 2 BP 221 EP 232 DI 10.4056/sigs.1774329 PG 12 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 786XD UT WOS:000292340300012 PM 21677859 ER PT J AU Land, M Held, B Gronow, S Abt, B Lucas, S Del Rio, TG Nolan, M Tice, H Cheng, JF Pitluck, S Liolios, K Pagani, I Ivanova, N Mavromatis, K Mikhailova, N Pati, A Tapia, R Han, C Goodwin, L Chen, A Palaniappan, K Hauser, L Brambilla, EM Rohde, M Goker, M Detter, JC Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Lapidus, A AF Land, Miriam Held, Brittany Gronow, Sabine Abt, Birte Lucas, Susan Del Rio, Tijana Glavina Nolan, Matt Tice, Hope Cheng, Jan-Fang Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Tapia, Roxane Han, Cliff Goodwin, Lynne Chen, Amy Palaniappan, Krishna Hauser, Loren Brambilla, Evelyne-Marie Rohde, Manfred Goeker, Markus Detter, John C. Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Lapidus, Alla TI Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE strictly anaerobic; non-motile; Gram-negative; mesophilic; chemoorganotrophic; Bacteroidaceae; GEBA ID BACTERIA; ARCHAEA; ALGORITHM; INTESTINE; MUTUALISM; FRAGILIS; DATABASE; PROPOSAL; SYSTEM; GRAPHS AB Bacteroides coprosuis Whitehead et al. 2005 belongs to the genus Bacteroides, which is a member of the family Bacteroidaceae. Members of the genus Bacteroides in general are known as beneficial protectors of animal guts against pathogenic microorganisms, and as contributors to the degradation of complex molecules such as polysaccharides. B. coprosuis itself was isolated from a manure storage pit of a swine facility, but has not yet been found in an animal host. The species is of interest solely because of its isolated phylogenetic location. The genome of B. coprosuis is already the 5(th) sequenced type strain genome from the genus Bacteroides. The 2,991,798 bp long genome with its 2,461 protein-coding and 78 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Land, Miriam; Held, Brittany; Lucas, Susan; Del Rio, Tijana Glavina; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Chen, Amy; Palaniappan, Krishna; Hauser, Loren; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Lapidus, Alla] DOE Joint Genome Inst, Walnut Creek, CA USA. [Land, Miriam; Hauser, Loren] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Held, Brittany; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Gronow, Sabine; Abt, Birte; Brambilla, Evelyne-Marie; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [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, Sch Chem & Mol Biosci, Australian Ctr Ecogenom, Brisbane, Qld, Australia. RP Lapidus, A (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. RI Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013 OI Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Sabine Welnitz (DSMZ) for growing B. coprosuis cultures. 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 43 TC 1 Z9 1 U1 0 U2 3 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. PY 2011 VL 4 IS 2 BP 233 EP 243 DI 10.4056/sigs.1784330 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 786XD UT WOS:000292340300013 PM 21677860 ER PT J AU Morrison, N Hancock, D Hirschman, L Dawyndt, P Verslyppe, B Kyrpides, N Kottmann, R Yilmaz, P Glockner, FO Grethe, J Booth, T Sterk, P Nenadic, G Field, D AF Morrison, Norman Hancock, David Hirschman, Lynette Dawyndt, Peter Verslyppe, Bert Kyrpides, Nikos Kottmann, Renzo Yilmaz, Pelin Gloeckner, Frank Oliver Grethe, Jeff Booth, Tim Sterk, Peter Nenadic, Goran Field, Dawn TI Data shopping in an open marketplace: Introducing the Ontogrator web application for marking up data using ontologies and browsing using facets SO STANDARDS IN GENOMIC SCIENCES LA English DT Article ID INTEGRATION; INFORMATION; COMMUNITY; RESOURCE AB In the future, we hope to see an open and thriving data market in which users can find and select data from a wide range of data providers. In such an open access market, data are products that must be packaged accordingly. Increasingly, eCommerce sellers present heterogeneous product lines to buyers using faceted browsing. Using this approach we have developed the Ontogrator platform, which allows for rapid retrieval of data in a way that would be familiar to any online shopper. Using Knowledge Organization Systems (KOS), especially ontologies, Ontogrator uses text mining to mark up data and faceted browsing to help users navigate, query and retrieve data. Ontogrator offers the potential to impact scientific research in two major ways: 1) by significantly improving the retrieval of relevant information; and 2) by significantly reducing the time required to compose standard database queries and assemble information for further research. Here we present a pilot implementation developed in collaboration with the Genomic Standards Consortium (GSC) that includes content from the StrainInfo, GOLD, CAMERA, Silva and Pubmed databases. This implementation demonstrates the power of ontogration and highlights that the usefulness of this approach is fully dependent on both the quality of data and the KOS (ontologies) used. Ideally, the use and further expansion of this collaborative system will help to surface issues associated with the underlying quality of annotation and could lead to a systematic means for accessing integrated data resources. C1 [Morrison, Norman; Hancock, David; Nenadic, Goran] Univ Manchester, Sch Comp Sci, Manchester, Lancs, England. [Morrison, Norman; Hancock, David; Booth, Tim; Field, Dawn] NERC Ctr Ecol & Hydrol, Nat Environm Res Council Environm Bioinformat Ctr, Wallingford, Oxon, England. [Hirschman, Lynette] Mitre Corp, Bedford, MA 01730 USA. [Dawyndt, Peter; Verslyppe, Bert] Univ Ghent, Dept Appl Math & Comp Sci, B-9000 Ghent, Belgium. [Kyrpides, Nikos] DOE Joint Genome Inst, Walnut Creek, CA USA. [Kottmann, Renzo; Yilmaz, Pelin; Gloeckner, Frank Oliver] Max Planck Inst Marine Microbiol, Microbial Genom Grp, Bremen, Germany. [Yilmaz, Pelin] Jacobs Univ Bremen GmbH, Bremen, Germany. [Grethe, Jeff] Univ Calif San Diego, La Jolla, CA 92093 USA. [Sterk, Peter; Field, Dawn] NERC Ctr Ecol & Hydrol, Mol Evolut & Bioinformat Grp, Wallingford, Oxon, England. RP Morrison, N (reprint author), Univ Manchester, Sch Comp Sci, Manchester, Lancs, England. RI Dawyndt, Peter/A-1566-2013; Kyrpides, Nikos/A-6305-2014; OI Kyrpides, Nikos/0000-0002-6131-0462; Yilmaz, Pelin/0000-0003-4724-323X; Sterk, Peter/0000-0003-1668-7778; Grethe, Jeffrey/0000-0001-5212-7052; Dawyndt, Peter/0000-0002-1623-9070; Nenadic, Goran/0000-0003-0795-5363 FU NERC Environmental Bioinformatics Centre (NEBC), UK FX The work on the Ontogrator Platform presented here was funded by the NERC Environmental Bioinformatics Centre (NEBC), UK. NR 18 TC 1 Z9 1 U1 4 U2 9 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. PY 2011 VL 4 IS 2 BP 286 EP 292 DI 10.4056/sigs.1344279 PG 7 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 786XD UT WOS:000292340300017 PM 21677865 ER PT J AU Munk, AC Copeland, A Lucas, S Lapidus, A Del Rio, TG Barry, K Detter, JC Hammon, N Israni, S Pitluck, S Brettin, T Bruce, D Han, C Tapia, R Gilna, P Schmutz, J Larimer, F Land, M Kyrpides, NC Mavromatis, K Richardson, P Rohde, M Goker, M Klenk, HP Zhang, YP Roberts, GP Reslewic, S Schwartz, DC AF Munk, A. Christine Copeland, Alex Lucas, Susan Lapidus, Alla Del Rio, Tijana Glavina Barry, Kerrie Detter, John C. Hammon, Nancy Israni, Sanjay Pitluck, Sam Brettin, Thomas Bruce, David Han, Cliff Tapia, Roxanne Gilna, Paul Schmutz, Jeremy Larimer, Frank Land, Miriam Kyrpides, Nikos C. Mavromatis, Konstantinos Richardson, Paul Rohde, Manfred Goeker, Markus Klenk, Hans-Peter Zhang, Yaoping Roberts, Gary P. Reslewic, Susan Schwartz, David C. TI Complete genome sequence of Rhodospirillum rubrum type strain (S1(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE facultatively anaerobic; photolithotrophic; mesophile; Gram-negative; motile; Rhodospirillaceae; Alphaproteobacteria; DOEM 2002 ID PURPLE NONSULFUR BACTERIA; SYSTEM; GENES; PROTEINS; TOOL; IDENTIFICATION; NITROGENASE; ALGORITHM; DATABASE; 16S AB Rhodospirillum rubrum (Esmarch 1887) Molisch 1907 is the type species of the genus Rhodospirillum, which is the type genus of the family Rhodospirillaceae in the class Alphaproteobacteria. The species is of special interest because it is an anoxygenic phototroph that produces extracellular elemental sulfur (instead of oxygen) while harvesting light. It contains one of the most simple photosynthetic systems currently known, lacking light harvesting complex 2. Strain S1(T) can grow on carbon monoxide as sole energy source. With currently over 1,750 PubMed entries, R. rubrum is one of the most intensively studied microbial species, in particular for physiological and genetic studies. Next to R. centenum strain SW, the genome sequence of strain S1(T) is only the second genome of a member of the genus Rhodospirillum to be published, but the first type strain genome from the genus. The 4,352,825 bp long chromosome and 53,732 bp plasmid with a total of 3,850 protein-coding and 83 RNA genes were sequenced as part of the DOE Joint Genome Institute Program DOEM 2002. C1 [Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Munk, A. Christine; Detter, John C.; Israni, Sanjay; Han, Cliff; Tapia, Roxanne; Schmutz, Jeremy; Larimer, Frank] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Copeland, Alex; Lucas, Susan; Lapidus, Alla; Del Rio, Tijana Glavina; Barry, Kerrie; Detter, John C.; Hammon, Nancy; Pitluck, Sam; Brettin, Thomas; Bruce, David; Han, Cliff; Tapia, Roxanne; Land, Miriam; Kyrpides, Nikos C.; Mavromatis, Konstantinos; Richardson, Paul] DOE Joint Genome Inst, Walnut Creek, CA USA. [Gilna, Paul] Univ Calif San Diego, La Jolla, CA 92093 USA. [Land, Miriam] Lawrence Livermore Natl Lab, Livermore, CA USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Zhang, Yaoping; Roberts, Gary P.; Reslewic, Susan; Schwartz, David C.] Univ Wisconsin, Madison, WI USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Lapidus, Alla/I-4348-2013; Schmutz, Jeremy/N-3173-2013; Land, Miriam/A-6200-2011; Gilna, Paul/I-3608-2016; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Schmutz, Jeremy/0000-0001-8062-9172; Land, Miriam/0000-0001-7102-0031; Gilna, Paul/0000-0002-6542-0191; Kyrpides, Nikos/0000-0002-6131-0462 FU Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]; NIGMS [GM65891] FX We would like to gratefully acknowledge the help of Brian J. Tindall and his team (DSMZ) for growing a R. rubrum culture for the EM image. The work conducted by the U.S. Department of Energy Joint Genome Institute was supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231, and was also supported by NIGMS grant GM65891 to G. P. R. NR 45 TC 11 Z9 11 U1 7 U2 17 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 4 IS 3 BP 293 EP 302 DI 10.4056/sigs.1804360 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GP UT WOS:000298943700001 PM 21886856 ER PT J AU Huntemann, M Lu, MG Nolan, M Lapidus, A Lucas, S Hammon, N Deshpande, S Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Pagani, I Ivanova, N Ovchinikova, G Pati, A Chen, A Palaniappan, K Land, M Hauser, L Jeffries, CD Detter, JC Brambilla, EM Rohde, M Spring, S Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Mavromatis, K AF Huntemann, Marcel Lu, Megan Nolan, Matt Lapidus, Alla Lucas, Susan Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Tapia, Roxanne Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Ivanova, Natalia Ovchinikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Jeffries, Cynthia D. Detter, John C. Brambilla, Evelyne-Marie Rohde, Manfred Spring, Stefan Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Mavromatis, Konstantinos TI Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH2T) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE anaerobic; motile; rod-shaped; Gram-negative; marine; moderately thermophilic; sulfur-reducer; Desulfurellaceae; GEBA ID SUBMARINE HOT VENTS; ARCHAEA; BACTERIA; ALGORITHM; DATABASE; SYSTEM; GRAPHS; NOV. AB Hippea maritima (Miroshnichenko et al. 1999) is the type species of the genus Hippea, which belongs to the family Desulfurellaceae within the class Deltaproteobacteria. The anaerobic, moderately thermophilic marine sulfur-reducer was first isolated from shallow-water hot vents in Matipur Harbor, Papua New Guinea. H. maritima was of interest for genome sequencing because of its isolated phylogenetic location, as a distant next neighbor of the genus Desulfurella. Strain MH2T is the first type strain from the order Desulfurellales with a completely sequenced genome. The 1,694,430 bp long linear genome with its 1,723 protein-coding and 57 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Brambilla, Evelyne-Marie; Spring, Stefan; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Huntemann, Marcel; Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Lu, Megan; Nolan, Matt; Lapidus, Alla; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Ovchinikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Mavromatis, Konstantinos] DOE Joint Genome Inst, Walnut Creek, CA USA. [Lu, Megan; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [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. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013; Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011 OI Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031 FU US Department of Energy Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Maren Schroder (DSMZ) for growing H. maritima cultures. 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 28 TC 4 Z9 4 U1 2 U2 5 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 4 IS 3 BP 303 EP 311 DI 10.4056/sigs.1814460 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GP UT WOS:000298943700002 PM 21886857 ER PT J AU Ivanova, N Sikorski, J Chertkov, O Nolan, M Lucas, S Hammon, N Deshpande, S Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Huntemann, M Liolios, K Pagani, I Mavromatis, K Ovchinikova, G Pati, A Chen, A Palaniappan, K Land, M Hauser, L Brambilla, EM Kannan, KP Rohde, M Tindall, BJ Goker, M Detter, JC Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Lapidus, A AF Ivanova, Natalia Sikorski, Johannes Chertkov, Olga Nolan, Matt Lucas, Susan Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Tapia, Roxanne Han, Cliff Goodwin, Lynne Pitluck, Sam Huntemann, Marcel Liolios, Konstantinos Pagani, Ioanna Mavromatis, Konstantinos Ovchinikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Brambilla, Evelyne-Marie Kannan, K. Palani Rohde, Manfred Tindall, Brian J. Goeker, Markus Detter, John C. Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Lapidus, Alla TI Complete genome sequence of the extremely halophilic Halanaerobium praevalens type strain (GSL(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE strictly anaerobic; non-motile; Gram-negative; straight rod-shaped; halophilic; moderate alkaliphile; mesophilic; chemoorganotroph; Halanaerobiaceae; GEBA ID GREAT-SALT-LAKE; HALOANAEROBIUM-PRAEVALENS; SP-NOV; ANAEROBIC BACTERIUM; SEDIMENTS; ARCHAEA; EUBACTERIA; ALGORITHM; DATABASE; PROTEIN AB Halanaerobium praevalens Zeikus et al. 1984 is the type species of the genus Halanaerobium, which in turn is the type genus of the family Halanaerobiaceae. The species is of interest because it is able to reduce a variety of nitro-substituted aromatic compounds at a high rate, and because of its ability to degrade organic pollutants. The strain is also of interest because it functions as a hydrolytic bacterium, fermenting complex organic matter and producing intermediary metabolites for other trophic groups such as sulfate-reducing and methanogenic bacteria. It is further reported as being involved in carbon removal in the Great Salt Lake, its source of isolation. This is the first completed genome sequence of a representative of the genus Halanaerobium and the second genome sequence from a type strain of the family Halanaerobiaceae. The 2,309,262 bp long genome with its 2,110 protein-coding and 70 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Ivanova, Natalia; Chertkov, Olga; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Huntemann, Marcel; Liolios, Konstantinos; Pagani, Ioanna; Mavromatis, Konstantinos; Ovchinikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Lapidus, Alla] DOE Joint Genome Inst, Walnut Creek, CA USA. [Sikorski, Johannes; Brambilla, Evelyne-Marie; Kannan, K. Palani; Tindall, Brian J.; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Chertkov, Olga; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren] Oak Ridge Natl Lab, Oak Ridge, TN USA. [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. RP Lapidus, A (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. RI Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013 OI Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731 FU US Department of Energy Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Olivier D. Ngatchou-Djao (HZI) for drafting the manuscript, and Helga Pomrenke (DSMZ) for growing H. praevalens cultures. 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 48 TC 12 Z9 12 U1 2 U2 13 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 4 IS 3 BP 312 EP 321 DI 10.4056/sigs.1824509 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GP UT WOS:000298943700003 PM 21886858 ER PT J AU Anderson, I Sikorski, J Zeytun, A Nolan, M Lapidus, A Lucas, S Hammon, N Deshpande, S Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Pagani, I Ivanova, N Huntemann, M Mavromatis, K Ovchinikova, G Pati, A Chen, A Palaniappan, K Land, M Hauser, L Brambilla, EM Ngatchou-Djao, OD Rohde, M Tindall, BJ Goker, M Detter, JC Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Klenk, HP Kyrpides, NC AF Anderson, Iain Sikorski, Johannes Zeytun, Ahmet Nolan, Matt Lapidus, Alla Lucas, Susan Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Tapia, Roxanne Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Ivanova, Natalia Huntemann, Marcel Mavromatis, Konstantinos Ovchinikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Brambilla, Evelyne-Marie Ngatchou-Djao, Olivier D. Rohde, Manfred Tindall, Brian J. Goeker, Markus Detter, John C. Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Klenk, Hans-Peter Kyrpides, Nikos C. TI Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE anaerobic; microaerobic; non-motile; Gram-negative; mesophilic; strictly chemolithoautotroph; Nautiliaceae; GEBA ID EPSILON-PROTEOBACTERIA; SP-NOV.; BACTERIA; ARCHAEA; SYSTEM; EPSILONPROTEOBACTERIA; DIVERSITY; ALGORITHM; GRAPHS; 16S AB Nitratifractor salsuginis Nakagawa et al. 2005 is the type species of the genus Nitratifractor, a member of the family Nautiliaceae. The species is of interest because of its high capacity for nitrate reduction via conversion to N-2 through respiration, which is a key compound in plant nutrition. The strain is also of interest because it represents the first mesophilic and facultatively anaerobic member of the Epsilonproteobacteria reported to grow on molecular hydrogen. This is the first completed genome sequence of a member of the genus Nitratifractor and the second sequence from the family Nautiliaceae. The 2,101,285 bp long genome with its 2,121 protein-coding and 54 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Anderson, Iain; Zeytun, Ahmet; Nolan, Matt; Lapidus, Alla; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Huntemann, Marcel; Mavromatis, Konstantinos; Ovchinikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Sikorski, Johannes; Brambilla, Evelyne-Marie; Tindall, Brian J.; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Zeytun, Ahmet; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Ngatchou-Djao, Olivier D.; 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. RP Kyrpides, NC (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. RI Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Andrea Schutze (DSMZ) for growing N. salsuginis cultures. 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 31 TC 4 Z9 4 U1 1 U2 4 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 4 IS 3 BP 322 EP 330 DI 10.4056/sigs.1844518 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GP UT WOS:000298943700004 PM 21886859 ER PT J AU Sikorski, J Teshima, H Nolan, M Lucas, S Hammon, N Deshpande, S Cheng, JF Pitluck, S Liolios, K Pagani, I Ivanova, N Huntemann, M Mavromatis, K Ovchinikova, G Pati, A Tapia, R Han, C Goodwin, L Chen, A Palaniappan, K Land, M Hauser, L Ngatchou-Djao, OD Rohde, M Pukall, R Spring, S Abt, B Goker, M Detter, JC Woyke, T Bristow, J Markowitz, V Hugenholtz, P Eisen, JA Kyrpides, NC Klenk, HP Lapidus, A AF Sikorski, Johannes Teshima, Hazuki Nolan, Matt Lucas, Susan Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Ivanova, Natalia Huntemann, Marcel Mavromatis, Konstantinos Ovchinikova, Galina Pati, Amrita Tapia, Roxanne Han, Cliff Goodwin, Lynne Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Ngatchou-Djao, Olivier D. Rohde, Manfred Pukall, Ruediger Spring, Stefan Abt, Birte Goeker, Markus Detter, John C. Woyke, Tanja Bristow, James Markowitz, Victor Hugenholtz, Philip Eisen, Jonathan A. Kyrpides, Nikos C. Klenk, Hans-Peter Lapidus, Alla TI Complete genome sequence of Mahella australiensis type strain (50-1 BONT) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE strictly anaerobic; motile; spore-forming; Gram-positive; moderately thermophilic; chemoorganotrophic; Thermoanaerobacteraceae; GEBA ID BACTERIA; ARCHAEA; ALGORITHM; SYSTEM; GRAPHS; 16S AB Mahella australiensis Bonilla Salinas et al. 2004 is the type species of the genus Mahella, which belongs to the family Thermoanaerobacteraceae. The species is of interest because it differs from other known anaerobic spore-forming bacteria in its G+C content, and in certain phenotypic traits, such as carbon source utilization and relationship to temperature. Moreover, it has been discussed that this species might be an indigenous member of petroleum and oil reservoirs. This is the first completed genome sequence of a member of the genus Mahella and the ninth completed type strain genome sequence from the family Thermoanaerobacteraceae. The 3,135,972 bp long genome with its 2,974 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Teshima, Hazuki; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Huntemann, Marcel; Mavromatis, Konstantinos; Ovchinikova, Galina; Pati, Amrita; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Land, Miriam; Hauser, Loren; Pukall, Ruediger; Detter, John C.; Woyke, Tanja; Bristow, James; Hugenholtz, Philip; Eisen, Jonathan A.; Kyrpides, Nikos C.; Lapidus, Alla] DOE Joint Genome Inst, Walnut Creek, CA USA. [Sikorski, Johannes; Pukall, Ruediger; Spring, Stefan; Abt, Birte; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Teshima, Hazuki; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Ngatchou-Djao, Olivier D.; Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Hugenholtz, Philip] Univ Queensland, Australian Ctr Ecogen, Sch Chem & Mol Biosci, Brisbane, Qld, Australia. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Lapidus, A (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. RI Spring, Stefan/N-6933-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013 OI Spring, Stefan/0000-0001-6247-0938; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731 FU US Department of Energy Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Katja Steenblock for growing M. australiensis cultures, and Susanne Schneider for DNA extractions and quality control (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2. NR 37 TC 4 Z9 4 U1 1 U2 3 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 4 IS 3 BP 331 EP 341 DI 10.4056/sigs.1864526 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GP UT WOS:000298943700005 PM 21886860 ER PT J AU Munk, AC Lapidus, A Lucas, S Nolan, M Tice, H Cheng, JF Del Rio, TG Goodwin, L Pitluck, S Liolios, K Huntemann, M Ivanova, N Mavromatis, K Mikhailova, N Pati, A Chen, A Palaniappan, K Tapia, R Han, C Land, M Hauser, L Chang, YJ Jeffries, CD Brettin, T Yasawong, M Brambilla, EM Rohde, M Sikorski, J Goker, M Detter, JC Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Munk, A. Christine Lapidus, Alla Lucas, Susan Nolan, Matt Tice, Hope Cheng, Jan-Fang Del Rio, Tijana Glavina Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Huntemann, Marcel Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Tapia, Roxanne Han, Cliff Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Brettin, Thomas Yasawong, Montri Brambilla, Evelyne-Marie Rohde, Manfred Sikorski, Johannes Goeker, Markus Detter, John C. Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Tsukamurella paurometabola type strain (no. 33(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE obligately aerobic; non-motile; mesophilic; chemoorganotrophic; Gram-positive; metachromatic granules; opportunistic pathogen; Tsukamurellaceae; GEBA ID CATHETER-RELATED BACTEREMIA; RHODOCOCCUS-AURANTIACUS; BACTERIAL NAMES; CLASSIFICATION; NOMENCLATURE; PROPOSAL; ARCHAEA; SYSTEM; ACTINOBACTERIA; INFECTIONS AB Tsukamurella paurometabola corrig. (Steinhaus 1941) Collins et al. 1988 is the type species of the genus Tsukamurella, which is the type genus to the family Tsukamurellaceae. The species is not only of interest because of its isolated phylogenetic location, but also because it is a human opportunistic pathogen with some strains of the species reported to cause lung infection, lethal meningitis, and necrotizing tenosynovitis. This is the first completed genome sequence of a member of the genus Tsukamurella and the first genome sequence of a member of the family Tsukamurellaceae. The 4,479,724 bp long genome contains a 99,806 bp long plasmid and a total of 4,335 protein-coding and 56 RNA genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Brambilla, Evelyne-Marie; Sikorski, Johannes; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Munk, A. Christine; Lapidus, Alla; Lucas, Susan; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Del Rio, Tijana Glavina; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Huntemann, Marcel; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Tapia, Roxanne; Han, Cliff; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Brettin, Thomas; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Munk, A. Christine; Goodwin, Lynne; Tapia, Roxanne; Han, Cliff; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Brettin, Thomas] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Yasawong, Montri; 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. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Kyrpides, Nikos/A-6305-2014; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011 OI Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031 FU US Department of Energy Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1]; Thailand Research Fund Royal Golden Jubilee Ph.D. Program [PHD/0019/2548] FX We would like to gratefully acknowledge the help of Marlen Jando (DSMZ) for growing cultures of T. paurometabola. 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 Con-tract 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 599/1-1 and Thailand Research Fund Royal Golden Jubilee Ph.D. Program No. PHD/0019/2548 for MY. NR 41 TC 3 Z9 3 U1 1 U2 7 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 4 IS 3 BP 342 EP 351 DI 10.4056/sigs.1894556 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GP UT WOS:000298943700006 PM 21886861 ER PT J AU Daligault, H Lapidus, A Zeytun, A Nolan, M Lucas, S Del Rio, TG Tice, H Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Pagani, I Ivanova, N Huntemann, M Mavromatis, K Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Hauser, L Brambilla, EM Rohde, M Verbarg, S Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Woyke, T AF Daligault, Hajnalka Lapidus, Alla Zeytun, Ahmet Nolan, Matt Lucas, Susan Del Rio, Tijana Glavina Tice, Hope Cheng, Jan-Fang Tapia, Roxanne Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Ivanova, Natalia Huntemann, Marcel Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Brambilla, Evelyne-Marie Rohde, Manfred Verbarg, Susanne Goeker, Markus Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Woyke, Tanja TI Complete genome sequence of Haliscomenobacter hydrossis type strain (O-T) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE strictly aerobic; non-motile; Gram-negative; branching; sheathed; mesophilic; chemoorganotrophic; "Saprospiraceae"; GEBA ID FILAMENTOUS BACTERIA; ACTIVATED-SLUDGE; BULKING; ARCHAEA; SYSTEM; ALGORITHM; DATABASE; GRAPHS; NAMES; TOOL AB Haliscomenobacter hydrossis van Veen et al. 1973 is the type species of the genus Haliscomenobacter, which belongs to order "Sphingobacteriales". The species is of interest because of its isolated phylogenetic location in the tree of life, especially the so far genomically uncharted part of it, and because the organism grows in a thin, hardly visible hyaline sheath. Members of the species were isolated from fresh water of lakes and from ditch water. The genome of H. hydrossis is the first completed genome sequence reported from a member of the family "Saprospiraceae". The 8,771,651 bp long genome with its three plasmids of 92 kbp, 144 kbp and 164 kbp length contains 6,848 protein-coding and 60 RNA genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Brambilla, Evelyne-Marie; Verbarg, Susanne; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Daligault, Hajnalka; Lapidus, Alla; Zeytun, Ahmet; Nolan, Matt; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Huntemann, Marcel; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Woyke, Tanja] DOE Joint Genome Inst, Walnut Creek, CA USA. [Daligault, Hajnalka; Zeytun, Ahmet; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Markowitz, Victor] Oak Ridge Natl Lab, Oak Ridge, TN USA. [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. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1] FX We would like to gratefully acknowledge the help of Anja Fruhling (DSMZ) for growing H. hydrossis cultures. 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 599/1-1. NR 35 TC 12 Z9 12 U1 1 U2 14 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 4 IS 3 BP 352 EP 360 DI 10.4056/sigs.1964579 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GP UT WOS:000298943700007 PM 21886862 ER PT J AU Han, C Gronow, S Teshima, H Lapidus, A Nolan, M Lucas, S Hammon, N Deshpande, S Cheng, JF Zeytun, A Tapia, R Goodwin, L Pitluck, S Liolios, K Pagani, I Ivanova, N Mavromatis, K Mikhailova, N Huntemann, M Pati, A Chen, A Palaniappan, K Land, M Hauser, L Brambilla, EM Rohde, M Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Detter, JC AF Han, Cliff Gronow, Sabine Teshima, Hazuki Lapidus, Alla Nolan, Matt Lucas, Susan Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Zeytun, Ahmed Tapia, Roxanne Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Pagani, Ioanna Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Huntemann, Marcel Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Brambilla, Evelyne-Marie Rohde, Manfred Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Detter, John C. TI Complete genome sequence of Treponema succinifaciens type strain (6091(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE anaerobic; motile; Gram-negative; mesophilic; chemoorganotrophic; Spirochaetaceae; GEBA ID BACTERIA; ARCHAEA; CLASSIFICATION; ALGORITHM; DATABASE; SYSTEM; GRAPHS; TOOL AB Treponema succinifaciens Cwyk and Canale-Parola 1981 is of interest because this strictly anaerobic, apathogenic member of the genus Treponema oxidizes carbohydrates and couples the Embden-Meyerhof pathway via activity of a pyruvate-formate lyase to the production of acetyl-coenzyme A and formate. This feature separates this species from most other anaerobic spirochetes. The genome of T. succinifaciens 6091(T) is only the second completed and published type strain genome from the genus Treponema in the family Spirochaetaceae. The 2,897,425 bp long genome with one plasmid harbors 2,723 protein-coding and 63 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Gronow, Sabine; Brambilla, Evelyne-Marie; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Han, Cliff; Teshima, Hazuki; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Zeytun, Ahmed; Tapia, Roxanne; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Huntemann, Marcel; Pati, Amrita; Land, Miriam; Hauser, Loren; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Han, Cliff; Teshima, Hazuki; Zeytun, Ahmed; Tapia, Roxanne; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren] Oak Ridge Natl Lab, Oak Ridge, TN USA. [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. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Sabine Welnitz (DSMZ) for growing T. succinifaciens cultures. 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 40 TC 12 Z9 12 U1 1 U2 4 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 4 IS 3 BP 361 EP 370 DI 10.4056/sigs.1984594 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GP UT WOS:000298943700008 PM 21886863 ER PT J AU Han, C Mwirichia, R Chertkov, O Held, B Lapidus, A Nolan, M Lucas, S Hammon, N Deshpande, S Cheng, JF Tapia, R Goodwin, L Pitluck, S Huntemann, M Liolios, K Ivanova, N Pagani, I Mavromatis, K Ovchinikova, G Pati, A Chen, A Palaniappan, K Land, M Hauser, L Brambilla, EM Rohde, M Spring, S Sikorski, J Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Detter, JC AF Han, Cliff Mwirichia, Romano Chertkov, Olga Held, Brittany Lapidus, Alla Nolan, Matt Lucas, Susan Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Tapia, Roxanne Goodwin, Lynne Pitluck, Sam Huntemann, Marcel Liolios, Konstantinos Ivanova, Natalia Pagani, Ioanna Mavromatis, Konstantinos Ovchinikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Brambilla, Evelyne-Marie Rohde, Manfred Spring, Stefan Sikorski, Johannes Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Detter, John C. TI Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE glycolate-oxidizing; Gram-negative with Gram-positive cell wall structure; strictly anaerobic; chemotrophic; mesophilic; non-motile; rod-shaped; spore-forming; Peptococcaceae; Clostridiales; GEBA ID ELECTRON-TRANSPORT; MEMBRANE-VESICLES; BACTERIAL NAMES; GLYCOLLATE; ARCHAEA; DRIVEN; ALGORITHM; EXCRETION; HYDROGEN; DATABASE AB Syntrophobotulus glycolicus Friedrich et al. 1996 is currently the only member of the genus Syntrophobotulus within the family Peptococcaceae. The species is of interest because of its isolated phylogenetic location in the genome-sequenced fraction of tree of life. When grown in pure culture with glyoxylate as carbon source the organism utilizes glyoxylate through fermentative oxidation, whereas, when grown in syntrophic co-culture with homoacetogenic or methanogenic bacteria, it is able to oxidize glycolate to carbon dioxide and hydrogen. No other organic or inorganic carbon source is utilized by S. glycolicus. The subdivision of the family Peptococcaceae into genera does not reflect the natural relationships, particularly regarding the genera most closely related to Syntrophobotulus. Both Desulfotomaculum and Pelotomaculum are paraphyletic assemblages, and the taxonomic classification is in significant conflict with the 16S rRNA data. S. glycolicus is already the ninth member of the family Peptococcaceae with a completely sequenced and publicly available genome. The 3,406,739 bp long genome with its 3,370 protein-coding and 69 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Brambilla, Evelyne-Marie; Spring, Stefan; Sikorski, Johannes; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Han, Cliff; Chertkov, Olga; Held, Brittany; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Goodwin, Lynne; Pitluck, Sam; Huntemann, Marcel; Liolios, Konstantinos; Ivanova, Natalia; Pagani, Ioanna; Mavromatis, Konstantinos; Ovchinikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Detter, John C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Han, Cliff; Chertkov, Olga; Held, Brittany; Tapia, Roxanne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren] Oak Ridge Natl Lab, Oak Ridge, TN USA. [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. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Spring, Stefan/N-6933-2013; Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Spring, Stefan/0000-0001-6247-0938; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Maren Schroder (DSMZ) for growing S. glycolicus cultures. 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 46 TC 1 Z9 2 U1 1 U2 3 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 4 IS 3 BP 371 EP 380 DI 10.4056/sigs.2004684 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GP UT WOS:000298943700009 PM 21886864 ER PT J AU Anderson, I Goker, M Nolan, M Lucas, S Hammon, N Deshpande, S Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Huntemann, M Liolios, K Ivanova, N Pagani, I Mavromatis, K Ovchinikova, G Pati, A Chen, A Palaniappan, K Land, M Hauser, L Brambilla, EM Huber, H Yasawong, M Rohde, M Spring, S Abt, B Sikorski, J Wirth, R Detter, JC Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Lapidus, A AF Anderson, Iain Goeker, Markus Nolan, Matt Lucas, Susan Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Tapia, Roxanne Han, Cliff Goodwin, Lynne Pitluck, Sam Huntemann, Marcel Liolios, Konstantinos Ivanova, Natalia Pagani, Ioanna Mavromatis, Konstantinos Ovchinikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Brambilla, Evelyne-Marie Huber, Harald Yasawong, Montri Rohde, Manfred Spring, Stefan Abt, Birte Sikorski, Johannes Wirth, Reinhard Detter, John C. Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Lapidus, Alla TI Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE hyperthermophile; chemolithoautotroph; facultative microaerophilic; non-motile; hydrothermal solfataric vents; black smoker; Pyrodictiaceae; GEBA ID UPPER TEMPERATURE LIMIT; TRANSFER-RNA; IN-VITRO; ARCHAEA; BACTERIA; ALGORITHM; DATABASE; SYSTEM; GRAPHS; LIFE AB Pyrolobus fumarii Blochl et al. 1997 is the type species of the genus Pyrolobus, which belongs to the crenarchaeal family Pyrodictiaceae. The species is a facultatively microaerophilic non-motile crenarchaeon. It is of interest because of its isolated phylogenetic location in the tree of life and because it is a hyperthermophilic chemolithoautotroph known as the primary producer of organic matter at deep-sea hydrothermal vents. P. fumarii exhibits currently the highest optimal growth temperature of all life forms on earth (106 degrees C). This is the first completed genome sequence of a member of the genus Pyrolobus to be published and only the second genome sequence from a member of the family Pyrodictiaceae. Although Diversa Corporation announced the completion of sequencing of the P. fumarii genome on September 25, 2001, this sequence was never released to the public. The 1,843,267 bp long genome with its 1,986 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Anderson, Iain; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Huntemann, Marcel; Liolios, Konstantinos; Ivanova, Natalia; Pagani, Ioanna; Mavromatis, Konstantinos; Ovchinikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Lapidus, Alla] DOE Joint Genome Inst, Walnut Creek, CA USA. [Goeker, Markus; Brambilla, Evelyne-Marie; Spring, Stefan; Abt, Birte; Sikorski, Johannes; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Huber, Harald; Wirth, Reinhard] Univ Regensburg, Microbiol Archaeenzentrum, Regensburg, Germany. [Yasawong, Montri; 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. RP Lapidus, A (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. RI Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013; Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013 OI Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938; Lapidus, Alla/0000-0003-0427-8731 FU US Department of Energy Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle, and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1, SI 1352/1-2]; Thailand Research Fund Royal Golden Jubilee Ph.D. Program [PHD/0019/2548'] 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, UT-Battelle, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1 and SI 1352/1-2 and Thailand Research Fund Royal Golden Jubilee Ph.D. Program No. PHD/0019/2548' for MY. NR 52 TC 6 Z9 6 U1 8 U2 27 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 4 IS 3 BP 381 EP 392 DI 10.4056/sigs.2014648 PG 12 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GP UT WOS:000298943700010 PM 21886865 ER PT J AU Goker, M Teshima, H Lapidus, A Nolan, M Lucas, S Hammon, N Deshpande, S Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Huntemann, M Liolios, K Ivanova, N Pagani, I Mavromatis, K Ovchinikova, G Pati, A Chen, A Palaniappan, K Land, M Hauser, L Brambilla, EM Rohde, M Spring, S Detter, JC Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Goeker, Markus Teshima, Hazuki Lapidus, Alla Nolan, Matt Lucas, Susan Hammon, Nancy Deshpande, Shweta Cheng, Jan-Fang Tapia, Roxanne Han, Cliff Goodwin, Lynne Pitluck, Sam Huntemann, Marcel Liolios, Konstantinos Ivanova, Natalia Pagani, Ioanna Mavromatis, Konstantinos Ovchinikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Brambilla, Evelyne-Marie Rohde, Manfred Spring, Stefan Detter, John C. Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE anaerobic; mesophile; organoheterotroph; non-motile; sulfate-reducing; sludge bed reactor; Syntrophaceae; GEBA ID BACTERIA; ARCHAEA; ALGORITHM; DATABASE; SYSTEM; GRAPHS; TOOL AB Desulfobacca acetoxidans Elferink et al. 1999 is the type species of the genus Desulfobacca, which belongs to the family Syntrophaceae in the class Deltaproteobacteria. The species was first observed in a study on the competition of sulfate-reducers and acetoclastic methanogens for acetate in sludge. D. acetoxidans is considered to be the most abundant acetate-degrading sulfate reducer in sludge. It is of interest due to its isolated phylogenetic location in the 16S rRNA-based tree of life. This is the second completed genome sequence of a member of the family Syntrophaceae to be published and only the third genome sequence from a member of the order Syntrophobacterales. The 3,282,536 bp long genome with its 2,969 protein-coding and 54 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Goeker, Markus; Brambilla, Evelyne-Marie; Spring, Stefan; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Teshima, Hazuki; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Huntemann, Marcel; Liolios, Konstantinos; Ivanova, Natalia; Pagani, Ioanna; Mavromatis, Konstantinos; Ovchinikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Teshima, Hazuki; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren] Oak Ridge Natl Lab, Oak Ridge, TN USA. [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. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Kyrpides, Nikos/A-6305-2014; Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Spring, Stefan/N-6933-2013 OI Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Spring, Stefan/0000-0001-6247-0938 FU US Department of Energy Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle, and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Esther Schuler (DSMZ) for growing D. acetoxidans cultures. 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 36 TC 6 Z9 6 U1 1 U2 4 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2011 VL 4 IS 3 BP 393 EP 401 DI 10.4056/sigs.2064705 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 874GP UT WOS:000298943700011 PM 21886866 ER PT S AU Valyaev, AN Passell, HD Solodukhin, VP Stepanets, OV Aleksanyan, GM Petrov, VA Valyaeva, AA AF Valyaev, A. N. Passell, H. D. Solodukhin, V. P. Stepanets, O. V. Aleksanyan, G. M. Petrov, V. A. Valyaeva, A. A. BE Avagyan, A Barry, DL Coldewey, WG Reimer, DWG TI Geochemical and Radiological Risks in the Most Dangerous Regions of Central Asia and Caucasus SO STIMULUS FOR HUMAN AND SOCIETAL DYNAMICS IN THE PREVENTION OF CATASTROPHES SE Nato Science for Peace and Security Series E-Human and Societal Dynamics LA English DT Proceedings Paper CT NATO Advanced Research Workshop on Stimulus for Human and Social Dynamics in the Prevention of Catastrophes CY OCT 05-08, 2010 CL Yerevan, ARMENIA SP NATO DE Water bodies; mountainous areas; pollution; risk; monitoring; prediction; prevention; safety AB Many regions of Central Asia and Caucasus are characterised as zones of great global geochemical and radiological risks. This is connected with intense natural and man-made impacts, as well as the political and economic situation. For the first group of impacts we address mountainous areas with high seismic levels, large lakes and rivers with powerful hydroelectric stations, sizeable reservoirs and large high dams, high degrees of industrial activity that increases probabilities for man-induced and natural catastrophes with irreversible high levels of radioactive, toxic and other pollutants of large areas such as the Black, Caspian and Kara Seas, and their river basins. The second group of impacts relate to the disbanding of the USSR and the creation of new independent states with additional international frictions, which results in inadequate or totally absent environmental monitoring of, especially, trans-boundary areas. The proximity of these regions to zones of dormant or active conflicts promote situations with great opportunities for performing deliberate acts of terrorism using explosives, and area also able to cause man-induced catastrophes and stimulate natural calamities. Presented here is our approach to resolving the noted actual problems, and its implementation will promote the realization of the concept of substantial development and decreasing political stress for all countries located on the continent. C1 [Valyaev, A. N.] Russian Acad Sci, Nucl Safety Inst, Moscow, Russia. [Passell, H. D.] Sandia Natl Labs, Cooperat Monitoring Ctr, Geosci & Environm Ctr, Livermore, CA 94550 USA. [Solodukhin, V. P.] Natl Acad Sci, Inst Nucl Phys, Alma Ata, Kazakhstan. [Stepanets, O. V.] Vernadsky Inst Geochem & Analyt Chem RAS, Moscow, Russia. [Aleksanyan, G. M.] Yerevan State Univ, Yerevan 375049, Armenia. [Petrov, V. A.] Tech Univ, Ust Kamenogorsk, Kazakhstan. [Valyaeva, A. A.] Tambov State Univ, Tambov, Russia. RP Valyaev, AN (reprint author), Russian Acad Sci, Nucl Safety Inst, 52 B-6 Tulskaya Str, Moscow, Russia. NR 12 TC 0 Z9 0 U1 2 U2 2 PU IOS PRESS PI AMSTERDAM PA NIEUWE HEMWEG 6B, 1013 BG AMSTERDAM, NETHERLANDS SN 1879-8268 BN 978-1-60750-738-3; 978-1-60750-737-6 J9 NATO SCI PEACE SEC PY 2011 VL 80 BP 194 EP 209 DI 10.3233/978-1-60750-738-3-194 PG 16 WC Environmental Studies; Political Science; Social Sciences, Interdisciplinary SC Environmental Sciences & Ecology; Government & Law; Social Sciences - Other Topics GA BC2UG UT WOS:000351352000020 ER PT B AU Brodsky, SJ de Teramond, G Deur, A AF Brodsky, Stanley J. de Teramond, Guy Deur, Alexandre BE Fukaya, H Harada, M Tanabashi, M Yamawaki, K TI AdS/QCD, Light-Front Holography, and the Nonperturbative Running Coupling SO STRONG COUPLING GAUGE THEORIES IN LHC ERA LA English DT Proceedings Paper CT International Workshop on Strong Coupling Gauge Theories in the LHC Era (SCGT 09) CY DEC 08-11, 2009 CL Nagoya Univ, Nagoya, JAPAN HO Nagoya Univ DE AdS/CFT correspondence; AdS/QCD; light-front QCD; light-front quantization; nonperturbative QCD coupling ID DEEP-INELASTIC SCATTERING; QUANTUM CHROMODYNAMICS; SPIN ASYMMETRIES; MAGNETIC-MOMENTS; SUM-RULE; QCD; NUCLEON; BARYONS; DISTRIBUTIONS; CONSTANT AB The combination of Anti-de Sitter space (AdS) methods with light-front (LF) holography provides a remarkably accurate first approximation for the spectra and wavefunctions of meson and baryon light-quark bound states. The resulting bound-state Hamiltonian equation of motion in QCD leads to relativistic light-front wave equations in terms of an invariant impact variable zeta which measures the separation of the quark and gluonic constituents within the hadron at equal light-front time. These equations of motion in physical space-time are equivalent to the equations of motion which describe the propagation of spin-J modes in anti de Sitter (AdS) space. The eigenvalues give the hadronic spectrum, and the eigenmodes represent the probability distributions of the hadronic constituents at a given scale. A positive-sign confining dilaton background modifying AdS space gives a very good account of meson and baryon spectroscopy and form factors. The light-front holographic mapping of this model also leads to a non-perturbative effective coupling alpha(S) (ADS)(Q(2)) which agrees with the effective charge defined by the Bjorken sum rule and lattice simulations. It displays a transition from perturbative to nonperturbative conformal regimes at a momentum scale similar to 1 GeV. The resulting beta-function appears to capture the essential characteristics of the full beta-function of QCD, thus giving further support to the application of the gauge/gravity duality to the confining dynamics of strongly coupled QCD. C1 [Brodsky, Stanley J.] Stanford Univ, SLAC Natl Accelerator Lab, Stanford, CA 94309 USA. [de Teramond, Guy] Univ Costa Rica, San Jose, Costa Rica. [Deur, Alexandre] Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. RP Brodsky, SJ (reprint author), Stanford Univ, SLAC Natl Accelerator Lab, Stanford, CA 94309 USA. EM sjbth@slac.stanford.edu; gdt@asterix.crnet.cr; deurpam@jlab.org FU Department of Energy [DE ACO2-76SF00515, DE-AC05-84ER40150, SLAC-PUB-13998, JLAB-PHY10-1130] FX Presented by SJB at SCGT09, 2009 International Workshop on Strong Coupling Gauge Theories in the LHC Era, Nagoya, December 8-11, 2009. We thank Volker Burkert, John Cornwall, Sadataka Furui, Philipp Hagler, Wolfgang Korsch, G. Peter Lepage, Takemichi Okui, Joannis Papavassiliou and Anatoly Radyushkin for helpful comments. This research was supported by the Department of Energy contracts DE ACO2-76SF00515 and DE-AC05-84ER40150. SLAC-PUB-13998. JLAB-PHY10-1130. NR 73 TC 0 Z9 0 U1 0 U2 0 PU WORLD SCIENTIFIC PUBL CO PTE LTD PI SINGAPORE PA PO BOX 128 FARRER RD, SINGAPORE 9128, SINGAPORE BN 978-981-4329-51-4 PY 2011 BP 1 EP 16 PG 16 WC Physics, Particles & Fields SC Physics GA BH0BL UT WOS:000394555200001 ER PT B AU Sinclair, DK Kogut, JB AF Sinclair, D. K. Kogut, J. B. BE Fukaya, H Harada, M Tanabashi, M Yamawaki, K TI Lattice Gauge Theory and (Quasi)-Conformal Technicolor SO STRONG COUPLING GAUGE THEORIES IN LHC ERA LA English DT Proceedings Paper CT International Workshop on Strong Coupling Gauge Theories in the LHC Era (SCGT 09) CY DEC 08-11, 2009 CL Nagoya Univ, Nagoya, JAPAN HO Nagoya Univ DE Lattice gauge theory; Walking Technicolor ID SYMMETRY-BREAKING; QUARK FLAVORS; QCD; HYPERCOLOR; FERMIONS; NUMBER; SCALE AB QCD with 2 flavours of massless colour-sextet quarks is studied as a theory which might exhibit a range of scales over which the running coupling constant evolves very slowly (walks). We simulate lattice QCD with 2 flavours of sextet staggered quarks to determine whether walks, or if it has an infrared fixed point, making it a conformal field theory. Our initial simulations are performed at finite temperatures T = 1/N(t)a (N-t = 4 and N-t = 6), which allows us to identify the scales of confinement and chiral-symmetry breaking from the deconfinement and chiral-symmetry restoring transitions. Unlike QCD with fundamental quarks, these two transitions appear to be well-separated. The change in coupling constants at these transitions between the two different temporal extents N-t, is consistent with these being finite temperature transitions for an asymptotically free theory, which favours walking behaviour. In the deconfined phase, the Wilson Line shows a 3-state signal. Between the confinement and chiral transitions, there is an additional transition where the states with Wilson Lines oriented in the directions of the complex cube roots of unity disorder into a state with a negative Wilson Line. C1 [Sinclair, D. K.] Argonne Natl Lab, HEP Div, 9700 South Cass Ave, Argonne, IL 60439 USA. [Kogut, J. B.] US DOE, Div High Energy Phys, Washington, DC 20585 USA. [Kogut, J. B.] Univ Maryland, Dept Phys TQHN, College Pk, MD 20742 USA. RP Sinclair, DK (reprint author), Argonne Natl Lab, HEP Div, 9700 South Cass Ave, Argonne, IL 60439 USA. EM dks@hep.anl.gov; jbkogut@umd.edu FU U.S. Department of Energy, Division of High Energy Physics [DE-AC02-06CH11357]; Argonne/University of Chicago Joint Theory Institute; NSF [PHY03-04252] FX DKS is supported in part by the U.S. Department of Energy, Division of High Energy Physics, Contract DE-AC02-06CH11357, and in part by the Argonne/University of Chicago Joint Theory Institute. JBK is supported in part by NSF grant NSF PHY03-04252. These simulations were performed on the Cray XT4, Franklin at NERSC under an ERCAP allocation, and on the Cray XT5, Kraken at NICS under an LRAC/TRAC allocation. NR 39 TC 0 Z9 0 U1 0 U2 0 PU WORLD SCIENTIFIC PUBL CO PTE LTD PI SINGAPORE PA PO BOX 128 FARRER RD, SINGAPORE 9128, SINGAPORE BN 978-981-4329-51-4 PY 2011 BP 283 EP 289 PG 7 WC Physics, Particles & Fields SC Physics GA BH0BL UT WOS:000394555200030 ER PT B AU Graesser, ML Kitano, R Kurachi, M AF Graesser, Michael L. Kitano, Ryuichiro Kurachi, Masafumi BE Fukaya, H Harada, M Tanabashi, M Yamawaki, K TI Higgsinoless Supersymmetry and Hidden Gravity SO STRONG COUPLING GAUGE THEORIES IN LHC ERA LA English DT Proceedings Paper CT International Workshop on Strong Coupling Gauge Theories in the LHC Era (SCGT 09) CY DEC 08-11, 2009 CL Nagoya Univ, Nagoya, JAPAN HO Nagoya Univ ID ELECTROWEAK SYMMETRY-BREAKING; NON-LINEAR REALIZATIONS; LOCAL SYMMETRY; NONLINEAR REALIZATION; BROKEN SUPERSYMMETRY; GAUGE BOSON; DIMENSIONS; PHENOMENOLOGY; SUPERGRAVITY; LAGRANGIANS AB We present a simple formulation of non-linear supersymmetry where superfields and partnerless fields can coexist. Using this formalism, we propose a supersymmetric Standard Model without the Higgsino as an effective model for the TeV-scale supersymmetry breaking scenario. We also consider an application of the Hidden Local Symmetry in non-linear supersymmetry, where we can naturally incorporate a spin-two resonance into the theory in a manifestly supersymmetric way. Possible signatures at the LHC experiments are discussed. C1 [Graesser, Michael L.] Los Alamos Natl Lab, Theoret Div T2, Los Alamos, NM 87545 USA. [Kitano, Ryuichiro; Kurachi, Masafumi] Tohoku Univ, Dept Phys, Sendai, Miyagi 9808578, Japan. RP Graesser, ML (reprint author), Los Alamos Natl Lab, Theoret Div T2, Los Alamos, NM 87545 USA. FU U.S. Department of Energy at Los Alamos National Laboratory [DE-AC52-06NA25396]; JSPS [21840006] FX RK thanks the organizers of the SCGT 2009 workshop. He especially thanks Prof. Koichi Yamawaki for his hospitality in Nagoya. The work of MG is supported by the U.S. Department of Energy at Los Alamos National Laboratory under Contract No. DE-AC52-06NA25396. The work of RK is supported in part by the Grant-in-Aid for Scientific Research 21840006 of JSPS. NR 58 TC 0 Z9 0 U1 0 U2 0 PU WORLD SCIENTIFIC PUBL CO PTE LTD PI SINGAPORE PA PO BOX 128 FARRER RD, SINGAPORE 9128, SINGAPORE BN 978-981-4329-51-4 PY 2011 BP 311 EP 323 PG 13 WC Physics, Particles & Fields SC Physics GA BH0BL UT WOS:000394555200034 ER PT J AU Stull, CJ Taylor, SG Wren, J Mascarenus, DL Farrar, CR AF Stull, C. J. Taylor, S. G. Wren, J. Mascarenus, D. L. Farrar, C. R. BE Chang, FK TI Real-Time Condition Assessment of RAPTOR Telescope Systems SO STRUCTURAL HEALTH MONITORING 2011: CONDITION-BASED MAINTENANCE AND INTELLIGENT STRUCTURES, VOL 1 SE Structural Health Monitoring LA English DT Proceedings Paper CT 8th International Workshop on Structural Health Monitoring CY SEP 13-15, 2011 CL Stanford Univ, Stanford, CA SP AF Off Sci Res, Army Res Off, Natl Sci Fdn, Off Naval Res HO Stanford Univ ID SKY AB The RAPid Telescopes for Optical Response (RAPTOR) observatory network consists of several astronomical telescopes designed to search for astrophysical transients called gamma-ray bursts (GRBs). Although intrinsically bright, GRBs are difficult to detect due to their short durations, and as such, the RAPTOR telescopes must operate autonomously, at high duty-cycles and in peak operating condition. To facilitate more efficient planning of maintenance schedules, a recent research effort at Los Alamos National Laboratory (LANL) has focused on developing a structural health monitoring (SHM) system for these telescopes. This paper summarizes the results from this effort. The damage scenario of concern, namely damage to the telescope drive mechanism, is first presented. Next, a damage detection algorithm is developed with LANL's new publically available software package, SHMTools and the results of this process are discussed in detail. The paper then concludes with a summary of future planned refinements of the RAPTOR SHM system. C1 [Stull, C. J.; Taylor, S. G.; Wren, J.; Mascarenus, D. L.; Farrar, C. R.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Stull, CJ (reprint author), Los Alamos Natl Lab, POB 1663, Los Alamos, NM 87545 USA. RI Farrar, Charles/C-6954-2012; Taylor, Stuart/B-1347-2013 NR 13 TC 0 Z9 0 U1 0 U2 1 PU DESTECH PUBLICATIONS, INC PI LANCASTER PA 439 DUKE STREET, LANCASTER, PA 17602-4967 USA BN 978-1-60595-053-2 J9 STRUCT HLTH MONIT PY 2011 BP 501 EP 508 PG 8 WC Endocrinology & Metabolism; Instruments & Instrumentation SC Endocrinology & Metabolism; Instruments & Instrumentation GA BXY69 UT WOS:000297634100060 ER PT J AU Mascarenas, D Hush, D Theiler, J Farrar, C AF Mascarenas, D. Hush, D. Theiler, J. Farrar, C. BE Chang, FK TI The Application of Compressed Sensing to Detecting Damage in Structures SO STRUCTURAL HEALTH MONITORING 2011: CONDITION-BASED MAINTENANCE AND INTELLIGENT STRUCTURES, VOL 1 SE Structural Health Monitoring LA English DT Proceedings Paper CT 8th International Workshop on Structural Health Monitoring CY SEP 13-15, 2011 CL Stanford Univ, Stanford, CA SP AF Off Sci Res, Army Res Off, Natl Sci Fdn, Off Naval Res HO Stanford Univ AB One of the principal challenges facing the structural health monitoring (SHM) community is taking large, heterogeneous sets of data collected from sensors, and extracting information that allows the estimation of the remaining service life of a structure. Another important challenge is to collect relevant data from a structure in a manner that is cost effective, and respects the size, weight, cost, energy consumption, and bandwidth limitations placed on the system. In this work we explore the suitability of compressed sensing to address both challenges. In this work a digital version of a compressed sensor is implemented on-board a microcontroller similar to those used in embedded SHM sensor nodes. The sensor node is tested in a surrogate SHM application requiring acceleration measurements. Currently the prototype compressed sensor is capable of collecting compressed coefficients from measurements and sending them to an off-board processor for reconstruction using L1 norm minimization. A compressed version of the matched filter known as the smashed filter, has also been implemented on-board the sensor node, and its suitability for detecting structural damage will be discussed. C1 [Mascarenas, D.; Hush, D.; Theiler, J.; Farrar, C.] Los Alamos Natl Lab, Los Alamos, NM 87544 USA. RP Mascarenas, D (reprint author), Los Alamos Natl Lab, POB 1663,MS T001, Los Alamos, NM 87544 USA. RI Farrar, Charles/C-6954-2012 NR 7 TC 0 Z9 0 U1 0 U2 1 PU DESTECH PUBLICATIONS, INC PI LANCASTER PA 439 DUKE STREET, LANCASTER, PA 17602-4967 USA BN 978-1-60595-053-2 J9 STRUCT HLTH MONIT PY 2011 BP 1013 EP 1020 PG 8 WC Endocrinology & Metabolism; Instruments & Instrumentation SC Endocrinology & Metabolism; Instruments & Instrumentation GA BXY69 UT WOS:000297634100123 ER PT J AU Dalton, A Asal, V AF Dalton, Angela Asal, Victor TI Is It Ideology or Desperation: Why Do Organizations Deploy Women in Violent Terrorist Attacks? SO STUDIES IN CONFLICT & TERRORISM LA English DT Article ID MILITARY; GENDER AB Why do some terrorist organizations deploy women on the front lines and in violent attacks? This study explores the social conditions, economic factors, and organizational characteristics that might explain women's participation in violent terrorist activity. With a new data set of 395 terrorist organizations, women's participation in terrorist attacks was quantified and coded. The logistic regression analysis results suggest that women's educational attainment, social rights, terrorist organization's age and size, and the level of a country's economic development are important predictors of the deployment of women in terrorist violence while a terrorist group's ideological or religious orientation and the level of democracy do not significantly influence the likelihood of women's participation. C1 [Dalton, Angela] Pacific NW Natl Lab, Fundamental & Computat Sci Directorate, Richland, WA 99352 USA. [Asal, Victor] SUNY Albany, Dept Polit Sci, Nelson A Rockefeller Coll Publ Affairs & Policy, Albany, NY 12222 USA. RP Dalton, A (reprint author), Pacific NW Natl Lab, Fundamental & Computat Sci Directorate, 902 Battelle Blvd,MSIN K7-90, Richland, WA 99352 USA. EM angela.dalton@pnnl.gov NR 58 TC 3 Z9 3 U1 3 U2 10 PU TAYLOR & FRANCIS INC PI PHILADELPHIA PA 325 CHESTNUT ST, SUITE 800, PHILADELPHIA, PA 19106 USA SN 1057-610X J9 STUD CONFL TERROR JI Stud. Confl. Terror. PY 2011 VL 34 IS 10 BP 802 EP 819 DI 10.1080/1057610X.2011.604833 PG 18 WC International Relations; Political Science SC International Relations; Government & Law GA 887XB UT WOS:000299964000004 ER PT J AU Yurgens, A Bulaevskii, LN AF Yurgens, A. Bulaevskii, L. N. TI Temperature distribution in a stack of intrinsic Josephson junctions with their CuO-plane electrodes oriented perpendicular to supporting substrate SO SUPERCONDUCTOR SCIENCE & TECHNOLOGY LA English DT Article ID THERMAL-CONDUCTIVITY; SINGLE-CRYSTALS; PLASMA EMISSION; COOPER PAIRS; BI2SR2CACU2O8+DELTA; SUPERCONDUCTORS; RADIATION; TRANSPORT; WAVES AB We numerically study Joule heating in a THz emitter made of Bi2Sr2CaCu2O8+delta (Bi2212) single crystal with its CuO planes oriented perpendicular to supporting substrate. The single crystal is glued to the substrate by a layer of PMMA. The electrical current is applied in the c-axis direction across many intrinsic Josephson junctions (IJJ's) in Bi2212. The calculations show that the internal temperature increases to an acceptable 10-20 K only above the bath temperature for a Joule power density of similar to 10(5) W cm(-3) typical for experiments on THz emission from IJJ's. This makes the suggested geometry promising for boosting the output power of the emitter. C1 [Yurgens, A.] Chalmers, Dept Microtechnol & Nanosci MC2, SE-41296 Gothenburg, Sweden. [Bulaevskii, L. N.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Yurgens, A (reprint author), Chalmers, Dept Microtechnol & Nanosci MC2, SE-41296 Gothenburg, Sweden. EM yurgens@chalmers.se RI Yurgens, August/C-6319-2012 OI Yurgens, August/0000-0002-3038-1911 FU Swedish Research Council through the Linnaeus Centrum; National Nuclear Security Administration of the US Department of Energy FX AY acknowledges support from the Swedish Research Council through the Linnaeus Centrum 'Engineering quantum systems'. The work of LNB was carried out under the auspices of the National Nuclear Security Administration of the US Department of Energy by the LANL/LDRD Program. NR 27 TC 10 Z9 10 U1 0 U2 4 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0953-2048 EI 1361-6668 J9 SUPERCOND SCI TECH JI Supercond. Sci. Technol. PD JAN PY 2011 VL 24 IS 1 AR 015003 DI 10.1088/0953-2048/24/1/015003 PG 5 WC Physics, Applied; Physics, Condensed Matter SC Physics GA 695BA UT WOS:000285344400004 ER PT J AU Zhu, ZH Shutthanandan, V Nachimuthu, P AF Zhu, Zihua Shutthanandan, Vaithiyalingam Nachimuthu, Ponnusamy TI Using C-60(+) sputtering to improve detection limit of nitrogen in zinc oxide SO SURFACE AND INTERFACE ANALYSIS LA English DT Article; Proceedings Paper CT SIMS XVII Conference CY SEP, 2009 CL Toronto, CANADA DE depth profiling; ToF-SIMS; zinc oxide; nitrogen; C-60(+); Cs+ ID BOMBARDMENT; DEPOSITION; FILMS AB C-60(+) sputtering was firstly used to determine depth profile of nitrogen in zinc oxide materials by time-of-flight (ToF) SIMS. Compared to traditional Cs+ sputtering depth profiling, the C-60(+) sputtering provides increase in signal intensity by a factor of over 200 and improves the detection limit by a factor of about 10. In addition, our XPS results show that sputtering zinc oxide materials by 10 keV C-60(+) to very little carbon deposition at the bottom of the sputter crater. Copyright (C) 2010 John Wiley & Sons, Ltd. C1 [Zhu, Zihua; Shutthanandan, Vaithiyalingam; Nachimuthu, Ponnusamy] Pacific NW Natl Lab, Environm Mol Sci Lab, Richland, WA 99352 USA. RP Zhu, ZH (reprint author), Pacific NW Natl Lab, Environm Mol Sci Lab, Richland, WA 99352 USA. EM zihua.zhu@pnl.gov RI Zhu, Zihua/K-7652-2012 FU Department of Energy's Office of Biological and Environmental Research at Pacific Northwest National Laboratory (PNNL); Battelle for the US Department of Energy [DE-AC05-76RL01830] FX This research was performed using Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research located at Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for the US Department of Energy under Contract No. DE-AC05-76RL01830. The ZnO thin-film samples were obtained from Dr Scott A. Chambers in PNNL. The authors would also like to acknowledge writing suggestions from Dr Anil Shukla in PNNL. NR 13 TC 3 Z9 3 U1 0 U2 2 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 0142-2421 EI 1096-9918 J9 SURF INTERFACE ANAL JI Surf. Interface Anal. PD JAN-FEB PY 2011 VL 43 IS 1-2 BP 661 EP 663 DI 10.1002/sia.3414 PG 3 WC Chemistry, Physical SC Chemistry GA 725TR UT WOS:000287669500163 ER PT J AU Cummings, M Gliga, S Lukanov, B Altman, EI Bode, M Barrera, EV AF Cummings, Marvin Gliga, Sebastian Lukanov, Boris Altman, Eric I. Bode, Matthias Barrera, Enrique V. TI Surface interactions of molecular C-60 and impact on Ni(100) and Co(0001) film growth: A scanning tunneling microscopy study SO SURFACE SCIENCE LA English DT Article DE C-60; Mobility; Ni(100); Co(0001); Moire; Epitaxy ID THIN-FILMS; NI(110) SURFACES; METAL-SURFACES; ADSORPTION; ORIENTATION; TRANSITION; MORPHOLOGY AB Here, the interactions of C-60 at the surface of pseudomorphic Ni/Cu(100) and Co/Ru(0001) thin films and its effect on film growth and morphology were determined using in-situ scanning tunneling microscopy (STM) and Auger electron spectroscopy (AES). The novel development of C-60-metallic based nanosystems, such as C-60 molecular junction transistors, hinges on our ability to understand the factors governing structural stability in these nanosystems and the nature of the bond interactions at the C-60-metal interface. In this study. C-60 deposited onto the Ni(100) film surface is observed to be fairly immobile and uniformly distributed across the Ni surface. On the Co(0001) film surface however, C-60 mobility is observed to be severely limited in some regions and highly mobile in others dependent upon Co film surface reconstruction, resulting in a non-uniform distribution of C-60 across the Co film surface. Despite the presence of C-60 on the Ni surface, there is no obvious influence of the C-60 on further Ni film growth. In contrast, during Co film growth, islands only nucleate and grow from step edges or locally around C-60 molecules. The strength of the Co-C-60 bond interaction appears stronger than the Co-Co bond on Co film terrace. Generally, the Ni and Co films both continue epitaxial film growth in the presence of molecular C-60. AES results indicate the C-60 molecules maintain their chemical integrity during growth. (C) 2010 Elsevier B.V. All rights reserved. C1 [Cummings, Marvin; Barrera, Enrique V.] Rice Univ, Dept Mech Engn & Mat Sci, Houston, TX 77005 USA. [Lukanov, Boris; Altman, Eric I.] Yale Univ, Dept Chem & Environm Engn, New Haven, CT 06511 USA. [Gliga, Sebastian; Bode, Matthias] Argonne Natl Lab, Ctr Nanoscale Mat, Argonne, IL 60439 USA. RP Cummings, M (reprint author), Rice Univ, Dept Mech Engn & Mat Sci, 6100 Main St MS-321, Houston, TX 77005 USA. EM marvinc@rice.edu; ebarrera@rice.edu RI Gliga, Sebastian/K-4019-2015; Bode, Matthias/S-3249-2016 OI Gliga, Sebastian/0000-0003-1729-1070; Bode, Matthias/0000-0001-7514-5560 FU National Science Foundation (NSF) [HRD-0450363, DMR-0520495]; Welch Foundation [C-1494]; U. S. Department of Energy, Office of Science, Office of Basic Energy Sciences [DE-AC02-06CH11357] FX We acknowledge the National Science Foundation (NSF Cooperative Agreement Number HRD-0450363) for their financial support, the Welch Foundation (grant no. C-1494), and the use of the Yale Center for Research on Interface Structures and Phenomena facilities (NSF grant number DMR-0520495). Use of the Center for Nanoscale Materials was supported by the U. S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. NR 34 TC 4 Z9 4 U1 1 U2 18 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0039-6028 J9 SURF SCI JI Surf. Sci. PD JAN PY 2011 VL 605 IS 1-2 BP 72 EP 80 DI 10.1016/j.susc.2010.10.002 PG 9 WC Chemistry, Physical; Physics, Condensed Matter SC Chemistry; Physics GA 703ZQ UT WOS:000286021000011 ER PT J AU Newberg, JT Starr, DE Yamamoto, S Kaya, S Kendelewicz, T Mysak, ER Porsgaard, S Salmeron, MB Brown, GE Nilsson, A Bluhm, H AF Newberg, John T. Starr, David E. Yamamoto, Susumu Kaya, Sarp Kendelewicz, Tom Mysak, Erin R. Porsgaard, Soeren Salmeron, Miquel B. Brown, Gordon E., Jr. Nilsson, Anders Bluhm, Hendrik TI Formation of hydroxyl and water layers on MgO films studied with ambient pressure XPS SO SURFACE SCIENCE LA English DT Article DE Magnesium oxide; Surface chemistry; Geochemistry; Catalysis ID RAY PHOTOELECTRON-SPECTROSCOPY; MEAN FREE PATHS; OXIDE SURFACES; ELECTRONIC-STRUCTURE; ATTENUATION LENGTHS; MGO(100) SURFACES; CROSS-SECTIONS; THIN-FILMS; ADSORPTION; MODEL AB To understand the interaction of water with MgO(100), a detailed quantitative assessment of the interfacial chemistry is necessary. We have used ambient pressure X-ray photoelectron spectroscopy (XPS) to measure molecular (H2O) and dissociative (OH) water adsorption on a 4 monolayer (ML) thick MgO(100)/Ag(100) film under ambient conditions. Since the entire 4 ML metal oxide (Ox) film is probed by XPS, the reaction of the MgO film with water can be quantitatively studied. Using a multilayer model (Model 1) that measures changes in Ox thickness from O is (film) and Ag 3d (substrate) spectra, it is shown that the oxide portion of the MgO film becomes thinner upon hydroxylation. A reaction mechanism is postulated in which the topmost layer of MgO converts to Mg(OH)(2) upon dissociation of water. Based on this mechanism a second model (Model 2) is developed to calculate Ox and OH thickness changes based on OH/Ox intensity ratios from O is spectra measured in situ, with the known initial Ox thickness prior to hydroxylation. Models 1 and 2 are applied to a 0.15 Torr isobar experiment, yielding similar results for H2O. OH and Ox thickness changes as a function of relative humidity. Published by Elsevier B.V. C1 [Newberg, John T.; Mysak, Erin R.; Bluhm, Hendrik] Lawrence Berkeley Natl Lab, Div Chem Sci, Berkeley, CA 94720 USA. [Starr, David E.] Brookhaven Natl Lab, Ctr Funct Nanomat, Upton, NY 11973 USA. [Yamamoto, Susumu; Kaya, Sarp; Brown, Gordon E., Jr.; Nilsson, Anders] SLAC Natl Accelerator Lab, Dept Photon Sci & Stanford Synchrotron Radiat Lig, Menlo Pk, CA 94025 USA. [Kendelewicz, Tom; Brown, Gordon E., Jr.] Stanford Univ, Dept Geol & Environm Sci, Stanford, CA 94305 USA. [Porsgaard, Soeren; Salmeron, Miquel B.] Lawrence Berkeley Natl Lab, Div Mat Sci, Berkeley, CA 94720 USA. [Porsgaard, Soeren] Aarhus Univ, iNANO, Interdisciplinary Nanosci Ctr, DK-8000 Aarhus C, Denmark. RP Bluhm, H (reprint author), Lawrence Berkeley Natl Lab, Div Chem Sci, Berkeley, CA 94720 USA. EM hbluhm@lbl.gov RI Nilsson, Anders/E-1943-2011; Yamamoto, Susumu/C-1584-2008; Newberg, John/E-8961-2010; Kaya, Sarp/C-4001-2008 OI Nilsson, Anders/0000-0003-1968-8696; Yamamoto, Susumu/0000-0002-6116-7993; Kaya, Sarp/0000-0002-2591-5843 FU Office of Science, Biological and Environmental Research, Environmental Remediation Sciences Division (ERSD), U.S. Department of Energy [DE-AC02-05CH11231]; National Science Foundation under (Stanford Environmental Molecular Science Institute) [CHE-0431425]; Director, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences of the U.S. Department of Energy [DE-AC02-05CH11231] FX This work was supported by the Office of Science, Biological and Environmental Research, Environmental Remediation Sciences Division (ERSD), U.S. Department of Energy under Contract No. DE-AC02-05CH11231, and by the National Science Foundation under Contract No. CHE-0431425 (Stanford Environmental Molecular Science Institute). The ALS, and the ALS-MES beamline 11.0.2 are supported by the Director, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences of the U.S. Department of Energy at the Lawrence Berkeley National Laboratory under Contract No. DE-AC02-05CH11231. NR 57 TC 45 Z9 45 U1 6 U2 93 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0039-6028 J9 SURF SCI JI Surf. Sci. PD JAN PY 2011 VL 605 IS 1-2 BP 89 EP 94 DI 10.1016/j.susc.2010.10.004 PG 6 WC Chemistry, Physical; Physics, Condensed Matter SC Chemistry; Physics GA 703ZQ UT WOS:000286021000013 ER PT S AU Zhang, YHP AF Zhang, Y. -H. Percival BE Zhu, JJY Zhang, X Pan, XJ TI Hydrogen Production from Carbohydrates: A Mini-Review SO SUSTAINABLE PRODUCTION OF FUELS, CHEMICALS, AND FIBERS FROM FOREST BIOMASS SE ACS Symposium Series LA English DT Article; Book Chapter ID SYNTHETIC ENZYMATIC PATHWAY; CLOSTRIDIUM-THERMOCELLUM; BIOMASS GASIFICATION; BIOHYDROGEN PRODUCTION; CELLULOSE UTILIZATION; AFFINITY ADSORPTION; RENEWABLE HYDROGEN; SOLID-WASTES; HYDROLYSIS; WATER AB The hydrogen economy promises a clean energy future featuring higher energy utilization efficiency and fewer pollutants compared to liquid fuel/internal combustion engines. Hydrogen production from the enriched low-cost biomass carbohydrates would achieve nearly zero carbon emissions in a whole life cycle. In this book chapter, we present latest advances of hydrogen generation from biomass carbohydrates by chemical catalysis (e.g., gasification, pyrolysis, gasification in supercritical water, and aqueous phase reforming), biocatalysis (e.g., anaerobic fermentation, electrohydrogenesis, photo-fermentation, and cell-free synthetic pathway biotransformation - SyPaB), and their combinations. Since hydrogen yield or energy efficiency is the most critical economic factor for hydrogen generation, SyPaB that can produce 12 H-2 per glucose equivalent seems to be an ultimate winner. When more stable enzyme building blocks with total turn-over number (TTN) values of more than 3 x 10(7) mol of product per mol of enzyme and engineered redox enzymes that can use low-cost stable biomimetic cofactor are available, cell-free SyPaB would produce hydrogen at the overall costs of less than $2 kg of hydrogen. C1 [Zhang, Y. -H. Percival] Virginia Tech, Dept Biol Syst Engn, Blacksburg, VA 24061 USA. [Zhang, Y. -H. Percival] Virginia Tech, ICTAS, Blacksburg, VA 24061 USA. [Zhang, Y. -H. Percival] DOE BioEnergy Sci Ctr BESC, Oak Ridge, TN 37831 USA. RP Zhang, YHP (reprint author), Virginia Tech, Dept Biol Syst Engn, 210-A Seitz Hall, Blacksburg, VA 24061 USA. EM ypzhang@vt.edu NR 69 TC 5 Z9 5 U1 0 U2 6 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 SIXTEENTH ST NW, WASHINGTON, DC 20036 USA SN 0097-6156 BN 978-0-8412-2643-2 J9 ACS SYM SER JI ACS Symp. Ser. PY 2011 VL 1067 BP 203 EP 216 D2 10.1021/bk-2011-1067 PG 14 WC Energy & Fuels; Engineering, Chemical SC Energy & Fuels; Engineering GA BDD12 UT WOS:000312747400008 ER PT S AU Xia, B Bhatia, S Bubenheim, B Dadgar, M Densmore, D Anderson, JC AF Xia, Bing Bhatia, Swapnil Bubenheim, Ben Dadgar, Maisam Densmore, Douglas Anderson, J. Christopher BE Voigt, C TI DEVELOPER'S AND USER'S GUIDE TO CLOTHO v2.0: A SOFTWARE PLATFORM FOR THE CREATION OF SYNTHETIC BIOLOGICAL SYSTEMS SO SYNTHETIC BIOLOGY, PT B: COMPUTER AIDED DESIGN AND DNA ASSEMBLY SE Methods in Enzymology LA English DT Review; Book Chapter AB To design the complex systems that synthetic biologists propose to create, software tools must be developed. Critical to success is the enablement of collaboration across our community such that individual tools that perform specific tasks combine with other tools to provide multiplicative benefits. This will require standardization of the form of the data that exists within the field (Parts, Strains, measurements, etc.), a software environment that enables communication between tools, and a sharing mechanism for distributing the tools. Additionally, this data model must describe the data in a sufficiently rigorous and validated form such that meaningful layers of abstraction can be built upon the base. Herein, we describe a software platform called "Clotho" which provides such a data model, and the plugin and sharing mechanisms needed for a rich tool environment. This document provides a tutorial for users of Clotho and information for software developers who wish to contribute new tools (known as "Apps") to it. C1 [Xia, Bing; Bubenheim, Ben; Anderson, J. Christopher] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. [Bhatia, Swapnil; Densmore, Douglas] Boston Univ, Dept Elect & Comp Engn, Boston, MA 02215 USA. [Dadgar, Maisam; Densmore, Douglas] Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA. [Anderson, J. Christopher] Univ Calif, SynBERC Synthet Biol Engn Res Ctr, Emeryville, CA USA. [Anderson, J. Christopher] Univ Calif, Calif Inst Quantitat Biol Res QB3, Emeryville, CA USA. [Anderson, J. Christopher] Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA USA. RP Xia, B (reprint author), Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. OI Bhatia, Swapnil /0000-0003-1079-7570 FU SynBERC NSF ERG; Autodesk; Quintara Biosciences FX The authors would like to thank the members of the UC Berkeley 2008 iGEM team (Anne Van Devender, Matthew Johnson, Nade Sritanyaratana); the UC Berkeley 2009 iGEM team (Lesia Bilitchenko, Joanna Chen, Adam Liu, Richard Mar, Thien Nguyen, Nina Revko); Josh Kittleson, Michal Galdzicki, Tim Hsiau, Tim Ham, Carlos Olguin, and Cesar Rodriguez for their help in support for getting Clotho development, infrastructure, and publicity to the point at which it is today. Financial support was provided by SynBERC NSF ERG, Autodesk, and Quintara Biosciences. NR 7 TC 35 Z9 35 U1 0 U2 8 PU ELSEVIER ACADEMIC PRESS INC PI SAN DIEGO PA 525 B STREET, SUITE 1900, SAN DIEGO, CA 92101-4495 USA SN 0076-6879 BN 978-0-12-385120-8 J9 METHOD ENZYMOL JI Methods Enzymol. PY 2011 VL 498 BP 97 EP 135 DI 10.1016/B978-0-12-385120-8.00005-X PG 39 WC Biochemical Research Methods; Biochemistry & Molecular Biology SC Biochemistry & Molecular Biology GA BVN83 UT WOS:000292007500005 PM 21601675 ER PT S AU Leguia, M Brophy, J Densmore, D Anderson, JC AF Leguia, Mariana Brophy, Jennifer Densmore, Douglas Anderson, J. Christopher BE Voigt, C TI AUTOMATED ASSEMBLY OF STANDARD BIOLOGICAL PARTS SO SYNTHETIC BIOLOGY, PT B: COMPUTER AIDED DESIGN AND DNA ASSEMBLY SE Methods in Enzymology LA English DT Review; Book Chapter AB The primary bottleneck in synthetic biology research today is the construction of physical DNAs, a process that is often expensive, time-consuming, and riddled with cloning difficulties associated with the uniqueness of each DNA sequence. We have developed a series of biological and computational tools that lower existing barriers to automation and scaling to enable affordable, fast, and accurate construction of large DNA sets. Here we provide detailed protocols for high-throughput, automated assembly of BglBrick standard biological parts using iterative 2ab reactions. We have implemented these protocols on a minimal hardware platform consisting of a Biomek 3000 liquid handling robot, a benchtop centrifuge and a plate thermocycler, with additional support from a software tool called AssemblyManager. This methodology enables parallel assembly of several hundred large error-free DNAs with a 96+% success rate. C1 [Leguia, Mariana; Brophy, Jennifer; Anderson, J. Christopher] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. [Leguia, Mariana; Anderson, J. Christopher] Univ Calif Berkeley, Calif Inst Quantitat Biol Res QB3, Berkeley, CA 94720 USA. [Leguia, Mariana; Anderson, J. Christopher] Synthet Biol Engn Res Ctr, Berkeley, CA USA. [Densmore, Douglas] Boston Univ, Dept Elect & Comp Engn, Boston, MA 02215 USA. [Anderson, J. Christopher] Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA USA. RP Leguia, M (reprint author), Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. FU SynBERC FX We thank Martin Pollard of the Joint Genome Institute (www.jgi.doe.gov) for helpful discussions on assembly line automation design. We also thank Nina Reyko and the 2009 Berkeley computational iGEM team for early work on the automated assembly software. This work was funded by SynBERC (www.synberc.org). NR 4 TC 17 Z9 18 U1 0 U2 11 PU ELSEVIER ACADEMIC PRESS INC PI SAN DIEGO PA 525 B STREET, SUITE 1900, SAN DIEGO, CA 92101-4495 USA SN 0076-6879 BN 978-0-12-385120-8 J9 METHOD ENZYMOL JI Methods Enzymol. PY 2011 VL 498 BP 363 EP 397 DI 10.1016/B978-0-12-385120-8.00016-4 PG 35 WC Biochemical Research Methods; Biochemistry & Molecular Biology SC Biochemistry & Molecular Biology GA BVN83 UT WOS:000292007500016 PM 21601686 ER PT S AU King, DL de Klerk, A AF King, David L. de Klerk, Arno BE DeKlerk, A King, DL TI Overview of Feed-to-Liquid (XTL) Conversion SO SYNTHETIC LIQUIDS PRODUCTION AND REFINING SE ACS Symposium Series LA English DT Proceedings Paper CT Symposium on Coal, Gas, Biomass and Waste-to-Liquids Conversion CY AUG, 2010 CL Boston, MA SP ACS, Div Fuel Chem ID FISCHER-TROPSCH; POLYETHYLENE; METHANOL; DEGRADATION; PYROLYSIS; CATALYSTS AB The overview addresses some important questions related to the future relevance of XTL technology, sustainability, non-carbon based carriers and carbon (CO2) footprint. The difference between XTL conversion technologies are explained, which covers topics such as direct liquefaction, pyrolysis and indirect liquefaction (methanol and Fischer-Tropsch). The present status of XTL technology is discussed. C1 [King, David L.] Pacific Northwest Natl Lab, Hydrocarbon Proc, POB 999, Richland, WA 99352 USA. [de Klerk, Arno] Univ Alberta, Dept Chem & Mat Engn, Edmonton, AB T6G 2V4, Canada. RP King, DL (reprint author), Pacific Northwest Natl Lab, Hydrocarbon Proc, POB 999, Richland, WA 99352 USA. EM david.king@pnl.gov; deklerk@ualberta.ca OI de Klerk, Arno/0000-0002-8146-9024 NR 56 TC 2 Z9 2 U1 0 U2 2 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 SIXTEENTH ST NW, WASHINGTON, DC 20036 USA SN 0097-6156 BN 978-0-8412-2681-4 J9 ACS SYM SER JI ACS Symp. Ser. PY 2011 VL 1084 BP 1 EP + PG 4 WC Energy & Fuels SC Energy & Fuels GA BDE77 UT WOS:000312966300001 ER PT S AU Bolin, TB AF Bolin, Trudy B. BE DeKlerk, A King, DL TI The Use of S-XANES To Track Thermal Transformations of Metal Sulfides in Argonne Premium Coals SO SYNTHETIC LIQUIDS PRODUCTION AND REFINING SE ACS Symposium Series LA English DT Proceedings Paper CT Symposium on Coal, Gas, Biomass and Waste-to-Liquids Conversion CY AUG, 2010 CL Boston, MA SP ACS, Div Fuel Chem ID RAY-ABSORPTION-SPECTROSCOPY; X-RAY; SULFUR; FORMS; MODEL AB Argonne Premium Coal Samples are used by researchers world-wide as standards in coal research. They consist of a suite of eight samples of varying rank from the United States. The Sulfur X-ray Near-Edge Absorption Spectroscopy (S-XANES) third-derivative analysis method utilizes a well-defined library of model compounds to curve fit each sample spectrum and enables sulfur speciation to within about 10% for materials such as coals and kerogens. This direct non-destructive characterization technique, used in conjunction with other techniques such as X-ray photoelectron spectroscopy (XPS), can provide valuable information about chemical and thermal sulfur transformations. The S-XANES third-derivative analysis method provides quantitative results for organic sulfur species in coal but has not been used to quantify pyritic sulfur until recently. In general, the direct determination of the pyrite content, a metal sulfide, has been problematic. It is known through wet chemical methods that several of the Argonne premium coal samples exceed 50 mole% pyrite but only show a weak pyrite feature in the S-XANES absorbance and third-derivative spectrum. It has been shown that particle size effects are responsible for attenuating the pyrite signal for high-pyrite-containing Argonne Premium coals. In this study, iron sulfide transformations at two stages of pyrolysis for an Illinois # 6 Argonne Premium coal and an isolated pyrite sample are quantified using S-XANES. C1 Argonne Natl Lab, Argonne, IL 60439 USA. RP Bolin, TB (reprint author), Argonne Natl Lab, 9700 S Cass Ave, Argonne, IL 60439 USA. EM bolitru@aps.anl.gov NR 9 TC 1 Z9 1 U1 0 U2 0 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 SIXTEENTH ST NW, WASHINGTON, DC 20036 USA SN 0097-6156 BN 978-0-8412-2681-4 J9 ACS SYM SER JI ACS Symp. Ser. PY 2011 VL 1084 BP 103 EP 108 PG 6 WC Energy & Fuels SC Energy & Fuels GA BDE77 UT WOS:000312966300004 ER PT B AU Wiedlea, A AF Wiedlea, Andrew BE Johnson, SB Gormley, TJ Kessler, SS Mott, CD PattersonHine, A Reichard, KM Scandura, PA TI Highly Reliable Organizations SO SYSTEM HEALTH MANAGEMENT: WITH AEROSPACE APPLICATIONS LA English DT Article; Book Chapter ID HIGH-RELIABILITY; SYSTEMS; RISK; MANAGEMENT C1 Los Alamos Natl Lab, Los Alamos, NM 87544 USA. RP Wiedlea, A (reprint author), Los Alamos Natl Lab, Los Alamos, NM 87544 USA. NR 62 TC 0 Z9 0 U1 0 U2 0 PU BLACKWELL SCIENCE PUBL PI OXFORD PA OSNEY MEAD, OXFORD OX2 0EL, ENGLAND BN 978-1-119-99404-6; 978-0-470-74133-7 PY 2011 BP 49 EP 63 D2 10.1002/9781119994053 PG 15 WC Engineering, Aerospace; Operations Research & Management Science SC Engineering; Operations Research & Management Science GA BA6FH UT WOS:000337126800006 ER PT S AU Wu, ZR Ng, WR Gehm, M Xin, H AF Wu, Ziran Ng, Wei-Ren Gehm, Michael Xin, Hao BE Sadwick, LP OSullivan, CMM TI Electromagnetic Crystal (EMXT) based THz Components SO TERAHERTZ TECHNOLOGY AND APPLICATIONS IV SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on Terahertz Technology and Applications IV CY JAN 26-27, 2011 CL San Francisco, CA SP SPIE DE Terahertz; electromagnetic crystal; rapid prototyping; integrated system AB Various all-dielectric electromagnetic crystal (EMXT) based THz components, including filter/reflector, waveguide, antenna, and transition structure to planar circuits are proposed and simulated. Several of them have been fabricated via a THz rapid prototyping technique, and the measurements show very good consistency with the simulations. Potential integrated THz micro-systems could be constructed using these components. The layer-by-layer printing virtue of the rapid prototyping technique may enable the integration and packaging of various THz components in a systematic manner. C1 [Wu, Ziran] Stanford Linear Accelerator Ctr, Menlo Pk, CA 94025 USA. RP Wu, ZR (reprint author), Stanford Linear Accelerator Ctr, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA. RI Wu, Ziran/G-2308-2014 OI Wu, Ziran/0000-0003-2009-991X NR 5 TC 0 Z9 0 U1 0 U2 0 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-81948-475-8 J9 PROC SPIE PY 2011 VL 7938 AR 79380I DI 10.1117/12.874213 PG 7 WC Optics; Physics, Applied SC Optics; Physics GA BYD22 UT WOS:000298083400016 ER PT J AU Li, ZB Jin, QL Huang, CW Dasa, S Chen, LH Yap, LP Liu, SL Cai, HC Park, R Conti, PS AF Li, Zibo Jin, Qiaoling Huang, Chiunwei Dasa, Siva Chen, Liaohai Yap, Li-peng Liu, Shuanglong Cai, Hancheng Park, Ryan Conti, Peter S. TI Trackable and Targeted Phage as Positron Emission Tomography (PET) Agent for Cancer Imaging SO THERANOSTICS LA English DT Article DE phage particle; positron emission tomography; integrin alpha(v)beta(3); RGD; Cu-64 ID INTEGRIN ALPHA(V)BETA(3) EXPRESSION; RGD PEPTIDES; BACTERIOPHAGES; NANOPARTICLES; NANOMATERIALS; CHEMISTRY; TOXICITY; MELANOMA AB The recent advancement of nanotechnology has provided unprecedented opportunities for the development of nanoparticle enabled technologies for detecting and treating cancer. Here, we reported the construction of a PET trackable organic nanoplatform based on phage particle for targeted tumor imaging. Method: The integrin alpha(v)beta(3) targeted phage nanoparticle was constructed by expressing RGD peptides on its surface. The target binding affinity of this engineered phage particle was evaluated in vitro. A bifunctional chelator (BFC) 1,4,7,10-tetraazadodecane-N,N',N '',N"'-tetraacetic acid (DOTA) or 4-((8-amino-3,6,10,13,16,19-hexaazabicyclo [6.6.6] icosane-1-ylamino) methyl) benzoic acid (AmBaSar) was then conjugated to the phage surface for (64)Cu(2+) chelation. After (64)Cu radiolabeling, microPET imaging was performed in U87MG tumor model and the receptor specificity was confirmed by blocking experiments. Results: The phage-RGD demonstrated target specificity based on ELISA experiment. According to the TEM images, the morphology of the phage was unchanged after the modification with BFCs. The labeling yield was 25 +/- 4% for (64)Cu-DOTA-phage-RGD and 46 +/- 5% for (64)Cu-AmBaSar-phage-RGD, respectively. At 1 h time point, (64)Cu-DOTA-phage-RGD and (64)Cu-AmBaSar-phage-RGD have comparable tumor uptake (similar to 8%ID/g). However, (64)Cu-AmBaSar-phage-RGD showed significantly higher tumor uptake (13.2 +/- 1.5 %ID/g, P<0.05) at late time points compared with (64)Cu-DOTA-phage-RGD (10 +/- 1.2 %ID/g). (64)Cu-AmBaSar-phage-RGD also demonstrated significantly lower liver uptake, which could be attributed to the stability difference between these chelators. There is no significant difference between two tracers regarding the uptake in kidney and muscle at all time points tested. In order to confirm the receptor specificity, blocking experiment was performed. In the RGD blocking experiment, the cold RGD peptide was injected 2 min before the administration of (64)Cu-AmBaSar-phage-RGD. Tumor uptake was partially blocked at 1 h time point. Phage-RGD particle was also used as the competitive ligand. In this case, the tumor uptake was significantly reduced and the value was kept at low level consistently. Conclusion: In this report, we constructed a PET trackable nanoplatform based on phage particle and demonstrated the imaging capability of these targeted agents. We also demonstrated that the choice of chelator could have significant impact on imaging results of nano-agents. The method established in this research may be applicable to other receptor/ligand systems for theranostic agent construction, which could have an immediate and profound impact on the field of imaging/therapy and lay the foundation for the construction of next generation cancer specific theranostic agents. C1 [Li, Zibo; Huang, Chiunwei; Yap, Li-peng; Liu, Shuanglong; Cai, Hancheng; Park, Ryan; Conti, Peter S.] Univ So Calif, Mol Imaging Ctr, Dept Radiol, Los Angeles, CA 90033 USA. [Jin, Qiaoling; Dasa, Siva; Chen, Liaohai] Argonne Natl Lab, Biosci Div, Argonne, IL 60439 USA. RP Li, ZB (reprint author), Univ So Calif, Mol Imaging Ctr, Dept Radiol, Los Angeles, CA 90033 USA. EM ziboli@usc.edu; lhchen@anl.gov RI Cai, Hancheng/B-4299-2012 FU USC Department of Radiology; Department of Energy [DE-SC0002353]; National Cancer Institute [P30A014089]; USC Biomedical Imaging Science Initiative FX This work was supported by the USC Department of Radiology, the Department of Energy (DE-SC0002353), the National Cancer Institute (P30A014089), and the USC Biomedical Imaging Science Initiative. NR 38 TC 18 Z9 18 U1 1 U2 28 PU IVYSPRING INT PUBL PI LAKE HAVEN PA PO BOX 4546, LAKE HAVEN, NSW 2263, AUSTRALIA SN 1838-7640 J9 THERANOSTICS JI Theranostics PY 2011 VL 1 BP 371 EP 380 DI 10.7150/thno/v01p0371 PG 10 WC Medicine, Research & Experimental SC Research & Experimental Medicine GA 876PX UT WOS:000299121000031 PM 22211143 ER PT B AU Wang, DB Kodali, VK Curtis, JE Riedo, E AF Wang, Debin Kodali, Vamsi K. Curtis, Jennifer E. Riedo, Elisa BA Tseng, AA BF Tseng, AA TI Nanofabrication of Functional Nanostructures by Thermochemical Nanolithography SO TIP-BASED NANOFABRICATION: FUNDAMENTALS AND APPLICATIONS LA English DT Article; Book Chapter DE Atomic force microscopy (AFM); Scanning probe microscopy (SPM); Nanofabrication; Nanomanufacturing; Nanolithography; Nanopatterning; Thermochemical nanolithography (TCNL); Thermomechanical nanolithography; Thermal dip-pen nanolithography (tDPN); Millipede; Wettability; Conjugated polymer; Graphene; Graphene oxide ID DIP-PEN NANOLITHOGRAPHY; ATOMIC-FORCE MICROSCOPE; SILICON MICROCANTILEVER HEATERS; REDUCED GRAPHENE OXIDE; SCANNING TUNNELING MICROSCOPE; BLOCK-COPOLYMER FILMS; DATA-STORAGE; NANOMETER-SCALE; PROBE ARRAYS; POLYMER NANOSTRUCTURES AB Nanofabrication is the process of building functional structures with nanoscale dimensions, which can be used as components, devices, or systems with high density, in large quantities, and at low cost. Since the invention of scanning tunneling microscopy (STM) and atomic force microscopy (AFM) in 1980s, the application of scanning probe based lithography (SPL) techniques for modification of substrates and creation of functional nanoscale structures and nanostructured materials has been widespread, resulting in the emergence of a large variety of methodologies. In this chapter, we review the recent development of a thermal probe based nanofabrication technique called thermochemical nanolithography (TCNL). We start with a brief review of the evolution of the thermal AFM probes integrated with resistive heaters. We then provide an overview of some established nanofabrication techniques in which thermal probes are used, namely thermomechanical nanolithography, the Millipede project, and thermal dip-pen nanolithography. We discuss the heat transfer mechanisms of the thermal probes in the thermal writing process of TCNL. The remainder of the chapter focuses on the use of TCNL on a variety of systems and thermochemical reactions. TCNL has been successfully used for fabrication of functional nanostructures that are appealing for various applications in nanofluidics, nanoelectronics, nanophotonics, and biosensing devices. Finally, we close this chapter by discussing some future research directions where the capabilities and robustness of TCNL can be further extended. C1 [Kodali, Vamsi K.; Riedo, Elisa] Univ Heidelberg, Sch Phys, Dept Biophys Chem, Georgia Inst Technol, Atlanta, GA 30332 USA. [Curtis, Jennifer E.] Georgia Inst Technol, Sch Phys, Petit Inst Bioengn & Biosci, Atlanta, GA 30332 USA. [Wang, Debin] Univ Calif Berkeley, Lawrence Berkeley Lab, Mol Foundry, Berkeley, CA 94720 USA. RP Riedo, E (reprint author), Univ Heidelberg, Sch Phys, Dept Biophys Chem, Georgia Inst Technol, Atlanta, GA 30332 USA. EM debinwang@lbl.gov; vamsi.kodali@physics.gatech.edu; jennifer.curtis@physics.gatech.edu; elisa.riedo@physics.gatech.edu RI Wang, Debin/H-2713-2012; OI Wang, Debin/0000-0001-8052-731X; Kodali, Vamsi/0000-0001-6177-0568 NR 106 TC 2 Z9 2 U1 1 U2 4 PU SPRINGER PI NEW YORK PA 233 SPRING STREET, NEW YORK, NY 10013, UNITED STATES BN 978-1-4419-9898-9 PY 2011 BP 265 EP 297 DI 10.1007/978-1-4419-9899-6_7 D2 10.1007/978-1-4419-9899-6 PG 33 WC Nanoscience & Nanotechnology SC Science & Technology - Other Topics GA BWK23 UT WOS:000294134800007 ER PT J AU Sullivan, JL Gaines, L Burnham, A AF Sullivan, J. L. Gaines, L. Burnham, A. GP TMS TI ROLE OF RECYCLING IN THE LIFE CYCLE OF BATTERIES SO TMS2011 SUPPLEMENTAL PROCEEDINGS, VOL 1: MATERIALS PROCESSING AND ENERGY MATERIALS LA English DT Proceedings Paper CT TMS 140th Annual Meeting and Exhibition CY FEB 27-MAR 03, 2011 CL San Diego, CA SP TMS DE battery; materials; recycling; energy AB Over the last few decades, rechargeable battery production has increased substantially. Applications including phones, computers, power tools, power storage, and electric-drive vehicles are either commonplace or will be in the next decade or so. Because advanced rechargeable batteries, like those using nickel metal hydride or lithium-ion chemistries, consist of less-plentiful and comparatively expensive materials (e. g., nickel, cobalt, cadmium, mischmetal) that often require considerable energy to be formed into battery components, battery recycling has the potential to significantly reduce the burdens associated with the life cycle of batteries. Therefore, the key issue is to determine the most practical type of recycling. Is it feasible to recover such components as anodes, cathodes, and electrolytes, or should the elements be recovered? Estimates of the impacts of battery recycling are given. C1 [Sullivan, J. L.; Gaines, L.; Burnham, A.] Argonne Natl Lab, Div Energy Syst, Argonne, IL 60439 USA. RP Sullivan, JL (reprint author), Argonne Natl Lab, Div Energy Syst, Argonne, IL 60439 USA. NR 10 TC 2 Z9 2 U1 0 U2 2 PU JOHN WILEY & SONS PI CHICHESTER PA THE ATRIUM, SOUTHERN GATE, CHICHESTER, W SUSSEX PO 19 8SQ, ENGLAND BN 978-1-11802-945-9 PY 2011 BP 25 EP 32 PG 8 WC Materials Science, Multidisciplinary SC Materials Science GA BHY24 UT WOS:000327008200003 ER PT J AU Shet, S Chen, L Tang, HW Deutsch, T Wang, HL Ravindra, N Yan, YF Turner, J Al-Jassim, M AF Shet, Sudhakar Chen, Le Tang, Houwen Deutsch, Todd Wang, Heli Ravindra, Nuggehalli Yan, Yanfa Turner, John Al-Jassim, Mowafak GP TMS TI Effect of gas ambient on the synthesis of Al and N co-doped ZnO:(Al,N) films and their influence on PEC response for photoelectrochemical water splitting application SO TMS2011 SUPPLEMENTAL PROCEEDINGS, VOL 1: MATERIALS PROCESSING AND ENERGY MATERIALS LA English DT Proceedings Paper CT TMS 140th Annual Meeting and Exhibition CY FEB 27-MAR 03, 2011 CL San Diego, CA SP TMS DE ZnO; RF power; sputter; ZnO:(Al,N); substrate temperature; co-doping; gas ambient; photoelectrochemical; crystallinity; N concentration; band gap ID ZNO THIN-FILMS; P-TYPE ZNO; ALIGNED NANORODS; TIO2 AB Al and N co-doped ZnO thin films, ZnO:(Al, N), are synthesized by radio-frequency magnetron sputtering in mixed Ar and N-2 and mixed O-2 and N-2 gas ambient at 100 degrees C. The ZnO:(Al, N) films deposited in mixed Ar and N-2 gas ambient did not incorporate N, whereas ZnO:(Al, N) films deposited in mixed O-2 and N-2 gas ambient showed enhanced N incorporation and crystallinity as compared to ZnO: N thin films deposited in the same gas ambient. As a result, ZnO:(Al, N) films deposited in mixed O-2 and N-2 gas ambient showed higher photocurrents than the ZnO:(Al, N) thin films deposited in mixed Ar and N-2 gas ambient. Our results indicate that the gas ambient plays an important role in N incorporation and crystallinity control in Al and N co-doped ZnO thin films. C1 [Shet, Sudhakar; Chen, Le; Tang, Houwen; Deutsch, Todd; Wang, Heli; Yan, Yanfa; Turner, John; Al-Jassim, Mowafak] Natl Renewable Energy Lab, Golden, CO 80401 USA. [Ravindra, Nuggehalli] New Jersey Inst Technol, Newark, NJ 07102 USA. RP Shet, S (reprint author), Natl Renewable Energy Lab, Golden, CO 80401 USA. OI Deutsch, Todd/0000-0001-6577-1226 FU U.S. Department of Energy [DE-AC36-08GO28308] FX This work was supported by the U.S. Department of Energy under Contract # DE-AC36-08GO28308. NR 29 TC 0 Z9 0 U1 4 U2 6 PU JOHN WILEY & SONS PI CHICHESTER PA THE ATRIUM, SOUTHERN GATE, CHICHESTER, W SUSSEX PO 19 8SQ, ENGLAND BN 978-1-11802-945-9 PY 2011 BP 135 EP 142 PG 8 WC Materials Science, Multidisciplinary SC Materials Science GA BHY24 UT WOS:000327008200014 ER PT J AU Shet, S Wang, HL Ravindra, N Yan, YF Turner, J Al-Jassim, M AF Shet, Sudhakar Wang, Heli Ravindra, Nuggehalli Yan, Yanfa Turner, John Al-Jassim, Mowafak GP TMS TI Influence of substrate temperature on the photoelectrochcmical responses of Ga and N co-doped ZnO films SO TMS2011 SUPPLEMENTAL PROCEEDINGS, VOL 1: MATERIALS PROCESSING AND ENERGY MATERIALS LA English DT Proceedings Paper CT TMS 140th Annual Meeting and Exhibition CY FEB 27-MAR 03, 2011 CL San Diego, CA SP TMS DE ZnO; RF power; sputter; substrate temperature; co-doping; gas ambient; photoelectrochemical; crystallinity; N concentration; bandgap ID THIN-FILMS; HYDROGEN-PRODUCTION; ALIGNED NANORODS; ZNO(AL,N) FILMS; WATER; PHOTOCATALYSIS; PERFORMANCE; TIO2 AB Ga-N co-doped ZnO thin films with reduced bandgaps were deposited on F-doped tin-oxide-coated glass by radio-frequency magnetron sputtering at different substrate temperatures in mixed N-2 and O-2 gas ambient. We found that Ga-N co-doped ZnO films exhibited enhanced crystallinity compared to undoped ZnO films grown under the same conditions. Furthermore, Ga-N co-doping ensured enhanced N-incorporation in ZnO thin films as the substrate temperature is increased. As a result, Ga-N co-doped ZnO thin films exhibited much improved photoelectrochemical (PEC) response, compared to ZnO thin films. Our results therefore suggest that the passive co-doping approach could be a means to improve PEC response for bandgap-reduced wide-bandgap oxides through impurity incorporation. C1 [Shet, Sudhakar; Wang, Heli; Yan, Yanfa; Turner, John; Al-Jassim, Mowafak] Natl Renewable Energy Lab, Golden, CO 80401 USA. [Shet, Sudhakar; Ravindra, Nuggehalli] New Jersey Inst Technol, Newark, NJ 07102 USA. RP Shet, S (reprint author), Natl Renewable Energy Lab, Golden, CO 80401 USA. FU U.S. Department of Energy [DE-AC36-08GO28308] FX This work was supported by the U.S. Department of Energy under Contract # DE-AC36-08GO28308. NR 35 TC 0 Z9 0 U1 1 U2 2 PU JOHN WILEY & SONS PI CHICHESTER PA THE ATRIUM, SOUTHERN GATE, CHICHESTER, W SUSSEX PO 19 8SQ, ENGLAND BN 978-1-11802-945-9 PY 2011 BP 183 EP 190 PG 8 WC Materials Science, Multidisciplinary SC Materials Science GA BHY24 UT WOS:000327008200019 ER PT J AU Gorti, SB Sabau, AS Peter, WH Nunn, SD Yamamoto, Y Chen, W AF Gorti, Sarma B. Sabau, Adrian S. Peter, William H. Nunn, Stephen D. Yamamoto, Yukinori Chen, Wei GP TMS TI Process Simulation of Cold Pressing and Sintering of Armstrong CP-Ti Powders SO TMS2011 SUPPLEMENTAL PROCEEDINGS, VOL 1: MATERIALS PROCESSING AND ENERGY MATERIALS LA English DT Proceedings Paper CT TMS 140th Annual Meeting and Exhibition CY FEB 27-MAR 03, 2011 CL San Diego, CA SP TMS ID RETURN MAPPING ALGORITHM; LOW-COST TITANIUM; DENSIFICATION BEHAVIOR; ALLOY POWDER; METAL; PLASTICITY; COMPACTION; MODELS AB A computational methodology is presented for the process simulation of cold pressing and sintering of Armstrong CP-Ti powders. Since the powder consolidation is governed by specific pressure-dependent constitutive equations, solution algorithms were developed for the ABAQUS user material subroutine, UMAT, for computing the plastic strain increments based on an implicit integration of the nonlinear yield function, flow rule, and hardening equations. Sintering was simulated using a model based on diffusional creep using the user subroutine CREEP. The initial mesh, stress, and density for the simulation of sintering were obtained from the results of the cold pressing simulation, minimizing the errors from decoupling the cold pressing and sintering simulations. Numerical simulation results are presented for the cold compaction followed by a sintering step of the Ti powders. The numerical simulation results for the relative density were compared to those measured from experiments before and after sintering, showing that the relative density can be accurately predicted. C1 [Gorti, Sarma B.; Sabau, Adrian S.; Peter, William H.; Nunn, Stephen D.; Yamamoto, Yukinori; Chen, Wei] Oak Ridge Natl Lab, Mat Sci & Technol Div, Oak Ridge, TN 37831 USA. RP Gorti, SB (reprint author), Oak Ridge Natl Lab, Mat Sci & Technol Div, 1 Bethel Valley Rd, Oak Ridge, TN 37831 USA. OI Sabau, Adrian/0000-0003-3088-6474 NR 26 TC 0 Z9 0 U1 0 U2 1 PU JOHN WILEY & SONS PI CHICHESTER PA THE ATRIUM, SOUTHERN GATE, CHICHESTER, W SUSSEX PO 19 8SQ, ENGLAND BN 978-1-11802-945-9 PY 2011 BP 483 EP 490 PG 8 WC Materials Science, Multidisciplinary SC Materials Science GA BHY24 UT WOS:000327008200054 ER PT J AU Sediako, D Kasprzak, W Swainson, I Garlea, O AF Sediako, D. Kasprzak, W. Swainson, I. Garlea, O. GP TMS TI SOLIDIFICATION ANALYSIS OF Al-Si ALLOYS MODIFIED WITH ADDITION OF Cu USING IN-SITU NEUTRON DIFFRACTION SO TMS2011 SUPPLEMENTAL PROCEEDINGS, VOL 2: MATERIALS FABRICATION, PROPERTIES, CHARACTERIZATION, AND MODELING LA English DT Proceedings Paper CT TMS 140th Annual Meeting and Exhibition CY FEB 27-MAR 03, 2011 CL San Diego, CA SP TMS DE hypereutectic aluminum alloy; solidification; neutron diffraction; phase evolution; thermal analysis ID MONOLITHIC CYLINDER BLOCKS; DIE-CASTING ALLOY; ALUMINUM-ALLOYS; MICROSTRUCTURE AB The potential of application of in-situ neutron diffraction for studies of solidification of Al alloys have been previously reported by the authors for the binary hypereutectic A-Si system. This illustrated the potential of neutron diffraction for high resolution melt analysis at near-liquidus temperatures required for advanced studies of grain refining, eutectic modification, etc. The solid and liquid volume fractions were determined based on the change of intensity of neutron diffraction peaks over the solidification interval. The path of non-equilibrium solidification for the alloy modified with addition of copper and magnesium is very complex. Phase diagrams and FactSage-based computations give only approximate kinetics of solid phase(s) evolution during cooling and solidification. On the other hand, in-situ neutron diffraction, coupled with the results of thermal analysis, provides non-biased experimental data on phase evolution; for example, on formation of FCC Al-Cu-Si and diamond silicon during solidification of hypereutectic Al-Si-Cu alloy. C1 [Sediako, D.; Swainson, I.] CNR, Canadian Neutron Beam Ctr, Chalk River, ON, Canada. [Kasprzak, W.] Natl Res Ctr, Canmet MTL, Ottawa, ON, Canada. [Garlea, O.] Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. RP Sediako, D (reprint author), CNR, Canadian Neutron Beam Ctr, Chalk River, ON, Canada. RI Garlea, Vasile/A-4994-2016 OI Garlea, Vasile/0000-0002-5322-7271 FU Advanced Structural Materials for Next Generation Vehicles (ASM-NGV) Program of Natural Resources Canada; Natural Sciences and Engineering Research Council of Canada; Scientific User Facilities Division; Office of Basic Energy Sciences, U. S. Department of Energy FX The authors would like to acknowledge the support of the Advanced Structural Materials for Next Generation Vehicles (ASM-NGV) Program of Natural Resources Canada. Studies completed at the Canadian Neutron Beam Center were partially sponsored by grant from Natural Sciences and Engineering Research Council of Canada. A portion of this research at Oak Ridge National Laboratory's High Flux Isotope Reactor was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U. S. Department of Energy. The authors would like to thank Ms. Marta Aniolek M. Se. Eng., CANMET-MTL, for assistance with for cooling curve analysis and Mr. Denis Shishin of University of Montreal for assistance in conducting the FactSage analysis. NR 12 TC 3 Z9 3 U1 1 U2 4 PU JOHN WILEY & SONS PI CHICHESTER PA THE ATRIUM, SOUTHERN GATE, CHICHESTER, W SUSSEX PO 19 8SQ, ENGLAND BN 978-1-11802-946-6 PY 2011 BP 279 EP 289 PG 11 WC Materials Science, Multidisciplinary SC Materials Science GA BHY36 UT WOS:000327013200035 ER PT J AU Sediako, D D'Elia, F Lombardi, A Machin, A Ravindran, C Hubbard, C Mackay, R AF Sediako, D. D'Elia, F. Lombardi, A. Machin, A. Ravindran, C. Hubbard, C. Mackay, R. GP TMS TI APPLICATION OF NEUTRON DIFFRACTION IN ANALYSIS OF RESIDUAL STRESS PROFILES IN THE CYLINDER WEB REGION OF AN AS-CAST V6 Al ENGINE BLOCK WITH CAST-IN Fe LINERS SO TMS2011 SUPPLEMENTAL PROCEEDINGS, VOL 2: MATERIALS FABRICATION, PROPERTIES, CHARACTERIZATION, AND MODELING LA English DT Proceedings Paper CT TMS 140th Annual Meeting and Exhibition CY FEB 27-MAR 03, 2011 CL San Diego, CA SP TMS DE 319 aluminum alloy; engine block; sand casting; neutron diffraction; residual stresses; microstructure; hardness AB Continuous efforts to develop a lightweight alloy suitable for the most demanding applications in automotive industry resulted in a number of advanced aluminum (Al) and magnesium alloys and manufacturing routes. One example of this is the application of 319 Al alloy for production of 3.6L V6 gasoline engine blocks. Aluminum is sand cast around Fe-liner cylinder inserts, prior to undergoing the T7 heat treatment process. One of the critical factors determining the quality of the final product is the type, level, and profile of residual stresses along the Fe liners (or extent of liner distortion) that are always present in a cast component. In this study, neutron diffraction was used to characterize residual stresses along the Al and the Fe liners in the web region of the cast engine block. The strains were measured both in Al and Fe in hoop, radial, and axial orientations. The stresses were subsequently determined using generalized Hooke's law. Further, optical microscopy and hardness measurements were performed from top to bottom along the interbore region of each cylinder. The results indicate that a variation in cooling rate along the cylinder caused a refinement of dendrites at the bottom of the cylinder, resulting in increased hardness. This study gives invaluable insight on anticipated service properties of the engine block and demonstrates that neutron strain mapping is an efficient tool for optimization of manufacturing technologies. C1 [Sediako, D.] Natl Res Council Canada, Canadian Neutron Beam Ctr, Chalk River Labs, Chalk River, ON K0J 1J0, Canada. [D'Elia, F.; Lombardi, A.; Machin, A.; Ravindran, C.] Ryerson Univ, Ctr Near Net Shape Proc Mat, Toronto, ON M5B 2K3, Canada. [Hubbard, C.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. [Mackay, R.] Nemak Canada, Windsor, ON N9C 4G8, Canada. RP Sediako, D (reprint author), Natl Res Council Canada, Canadian Neutron Beam Ctr, Chalk River Labs, Chalk River, ON K0J 1J0, Canada. RI D'Elia, Francesco/K-2229-2016 FU AUT021 Network of Centres of Excellence; Natural Sciences and Research Council of Canada (NSERC); Department of Energy, Office of Energy Efficiency and Renewable Energy; Scientific User Facilities Division; Office of Basic Energy Sciences, U.S. Department of Energy; CNBC; NRC Canada, under NSERC FX The authors are grateful to AUT021 Network of Centres of Excellence and the Natural Sciences and Research Council of Canada (NSERC) for their financial support. Studies at the 2nd Generation Neutron Residual Stress Mapping Facility at the High Flux Isotope Reactor was partially sponsored by the Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Program, through the Oak Ridge National Laboratory's High Temperature Materials Laboratory User Program and by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy. Neutron stress analysis was completed at CNBC, NRC Canada, under the grant of NSERC. Further, the authors are thankful to Nemak Canada and the members of the Centre for Near-Net-Shape Processing of Materials at Ryerson University. NR 11 TC 0 Z9 0 U1 1 U2 3 PU JOHN WILEY & SONS PI CHICHESTER PA THE ATRIUM, SOUTHERN GATE, CHICHESTER, W SUSSEX PO 19 8SQ, ENGLAND BN 978-1-11802-946-6 PY 2011 BP 299 EP 308 PG 10 WC Materials Science, Multidisciplinary SC Materials Science GA BHY36 UT WOS:000327013200037 ER PT J AU Biner, SB Kubin, LP AF Biner, S. B. Kubin, L. P. GP TMS TI TRUNCATED DISLOCATION SOURCES IN NANOMETRIC ALUMINUM CRYSTALS: A MOLECULAR DYNAMICS STUDY SO TMS2011 SUPPLEMENTAL PROCEEDINGS, VOL 2: MATERIALS FABRICATION, PROPERTIES, CHARACTERIZATION, AND MODELING LA English DT Proceedings Paper CT TMS 140th Annual Meeting and Exhibition CY FEB 27-MAR 03, 2011 CL San Diego, CA SP TMS DE Twinning; cross-slip; stacking fault; partial dislocations ID MECHANICAL-PROPERTIES; SINGLE-CRYSTALS; SIZE DEPENDENCE; YIELD STRENGTH; MICRO-PILLARS; PLASTICITY; SCALE; METALS; GOLD; COMPRESSION AB In this study, the evolution of dislocation loops truncated by free surfaces in small finite volumes is investigated in aluminum using molecular dynamics simulations. Three types of truncated dislocation loops, U-shaped, C-shaped and L-shaped, are considered. In the absence of truncated dislocation loops and without applied stress, surface effects induce the formation of very large stress gradients, of the order of several GPa's. Under an applied shear strain, the evolution of the truncated loops reveals the occurrence of several major phenomena. Very large stacking faults were formed during motion of the partial dislocations and the development of full and helix dislocations were observed. In addition, cross-slip behavior by the Fleischer mechanism, twin formation and untwinning were identified. C1 [Biner, S. B.] Idaho Natl Lab, Fuel Modeling & Simulat, POB 1625, Idaho Falls, ID 83415 USA. [Kubin, L. P.] Off Natl Etud & Rech Aerosp, CNRS, LEM, F-92322 Chatillon, France. RP Biner, SB (reprint author), Idaho Natl Lab, Fuel Modeling & Simulat, POB 1625, Idaho Falls, ID 83415 USA. FU DOE-Basic Energy Sciences [DE-AC0207CH11358] FX Part of this work was initiated by one author (S.B.B.) at Ames Laboratory and was supported by DOE-Basic Energy Sciences under Contract No. DE-AC0207CH11358. NR 41 TC 0 Z9 0 U1 0 U2 1 PU JOHN WILEY & SONS PI CHICHESTER PA THE ATRIUM, SOUTHERN GATE, CHICHESTER, W SUSSEX PO 19 8SQ, ENGLAND BN 978-1-11802-946-6 PY 2011 BP 505 EP 512 PG 8 WC Materials Science, Multidisciplinary SC Materials Science GA BHY36 UT WOS:000327013200062 ER PT J AU Xu, D Ritchie, RO AF Xu, David Ritchie, Robert O. GP TMS TI Role of Austenite Plasticity in the Deformation of Superelastic Nitinol SO TMS2011 SUPPLEMENTAL PROCEEDINGS, VOL 2: MATERIALS FABRICATION, PROPERTIES, CHARACTERIZATION, AND MODELING LA English DT Proceedings Paper CT TMS 140th Annual Meeting and Exhibition CY FEB 27-MAR 03, 2011 CL San Diego, CA SP TMS DE Nitinol; superelastic; austenite; martensite; deformation ID TRANSFORMATION; BEHAVIOR; ALLOY AB Nitinol is a Ni-Ti shape-memory alloy which is important for biomedical implant applications due to its mechanical property of superelastically. It derives this property (of up to similar to 10% reversible deformation) from an in situ stress-induced martensitic transformation between its austenite and martensite phases. This transformation is traditionally assumed to be the major source of strain below similar to 8%, and occurs when local strain within the austenite phase exceeds similar to 1.2%. In this work, we used synchrotron x-ray micro-diffraction to examine the grain-by-grain source of the deformation during the in situ phase transformation of NiTi tensile ("dogbone") samples loaded in the x-ray beam. Although most individual austenite grains were observed to transform to martensite at local strains exceeding 1.2%, we found that numerous austenite grains remained untransformed at strains above this level. Although this effect can be due to grain orientation, we believe that it is also associated with specific austenite grains becoming locally plastically deformed instead of transforming, i.e., that the martensite transformation is not the sole contribution to the strain below similar to 8%. We consider this notion of local austenite plasticity to be a feasible explanation for the limits to the reversibility of transformation during the cyclic loading of NiTi. C1 [Xu, David] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Sci Mat, Berkeley, CA 94720 USA. Univ Calif Berkeley, Dept Mat Sci & Engn, Div Sci Mat, Berkeley, CA 94720 USA. RP Xu, D (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Sci Mat, Berkeley, CA 94720 USA. FU U.S. Department of Energy [DE-AC02-05CH11231] FX This work was supported by the Director, Office of Science, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. The authors wish to thank Drs. Scott W. Robertson, and Alan R. Pelton (Nitinol Devices & Components) and Apurva Metha (Stanford Synchrotron Radiation Laboratory), for their role in the synchrotron measurements and for numerous helpful discussions. NR 5 TC 0 Z9 0 U1 0 U2 0 PU JOHN WILEY & SONS PI CHICHESTER PA THE ATRIUM, SOUTHERN GATE, CHICHESTER, W SUSSEX PO 19 8SQ, ENGLAND BN 978-1-11802-946-6 PY 2011 BP 609 EP 616 PG 8 WC Materials Science, Multidisciplinary SC Materials Science GA BHY36 UT WOS:000327013200074 ER PT S AU Dillard, SE Thoma, D Hamann, B AF Dillard, Scott E. Thoma, Dan Hamann, Bernd BE Pascucci, V Tricoche, X Hagen, H Tierny, J TI Reconstructing Cell Complexes From Cross-sections SO TOPOLOGICAL METHODS IN DATA ANALYSIS AND VISUALIZATION: THEORY, ALGORITHMS, AND APPLICATIONS SE Mathematics and Visualization LA English DT Proceedings Paper CT 3rd Workshop on Topological Methods in Data Analysis and Visualization CY FEB 23-24, 2009 CL Snowbird, UT SP Univ Utah, Sci Comp Imag Inst, Tech Univ Kaiserslautern, Enabl Technologies, SciDAC Visualizat Anal Ctr, NVIDIA Corp ID MODELS AB Many interesting segmentations take the form of cell complexes. We present a method to infer a 3D cell complex from of a series of 2D cross-sections. We restrict our attention to the class of complexes whose duals resemble triangulations. This class includes microstructures of polycrystalline materials, as well as other cellular structures found in nature. Given a prescribed matching of 2D cells in adjacent cross-sections we produce a 3D complex spanning these sections such that matched 2-cells are contained in the interior of the same 3-cell. The reconstruction method considers only the topological structure of the input. After an initial 3D complex is recovered, the structure is altered to accommodate geometric properties of the dataset. We evaluate the method using ideal, synthetic datasets as well as serial-sectioned micrographs from a sample of tantalum metal. C1 [Dillard, Scott E.; Thoma, Dan] Los Alamos Natl Lab, Mat Design Inst, Los Alamos, NM 87545 USA. RP Dillard, SE (reprint author), Los Alamos Natl Lab, Mat Design Inst, Los Alamos, NM 87545 USA. NR 6 TC 0 Z9 0 U1 1 U2 1 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 1612-3786 BN 978-3-642-15013-5 J9 MATH VIS PY 2011 BP 43 EP 54 PG 12 WC Mathematics, Applied; Mathematics SC Mathematics GA BGI39 UT WOS:000323090600004 ER PT S AU Mascarenhas, A Grout, RW Bremer, PT Hawkes, ER Pascucci, V Chen, JH AF Mascarenhas, Ajith Grout, Ray W. Bremer, Peer-Timo Hawkes, Evatt R. Pascucci, Valerio Chen, Jacqueline H. BE Pascucci, V Tricoche, X Hagen, H Tierny, J TI Topological Feature Extraction for Comparison of Terascale Combustion Simulation Data SO TOPOLOGICAL METHODS IN DATA ANALYSIS AND VISUALIZATION: THEORY, ALGORITHMS, AND APPLICATIONS SE Mathematics and Visualization LA English DT Proceedings Paper CT 3rd Workshop on Topological Methods in Data Analysis and Visualization CY FEB 23-24, 2009 CL Snowbird, UT SP Univ Utah, Sci Comp Imag Inst, Tech Univ Kaiserslautern, Enabl Technologies, SciDAC Visualizat Anal Ctr, NVIDIA Corp ID 3-DIMENSIONAL SCALAR FUNCTIONS; MORSE-SMALE COMPLEXES; TURBULENT COMBUSTION; JET FLAMES; FIELD AB We describe a combinatorial streaming algorithm to extract features which identify regions of local intense rates of mixing in two terascale turbulent combustion simulations. Our algorithm allows simulation data comprised of scalar fields represented on 728x896x512 or 2025x1600x400 grids to be processed on a single relatively lightweight machine. The turbulence-induced mixing governs the rate of reaction and hence is of principal interest in these combustion simulations. We use our feature extraction algorithm to compare two very different simulations and find that in both the thickness of the extracted features grows with decreasing turbulence intensity. Simultaneous consideration of results of applying the algorithm to the HO2 mass fraction field indicates that autoignition kernels near the base of a lifted flame tend not to overlap with the high mixing rate regions. C1 [Mascarenhas, Ajith; Grout, Ray W.; Chen, Jacqueline H.] Sandia Natl Labs, Livermore, CA 94550 USA. RP Mascarenhas, A (reprint author), Sandia Natl Labs, Livermore, CA 94550 USA. RI Hawkes, Evatt/C-5307-2012 OI Hawkes, Evatt/0000-0003-0539-7951 NR 21 TC 8 Z9 8 U1 0 U2 0 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 1612-3786 BN 978-3-642-15013-5 J9 MATH VIS PY 2011 BP 229 EP 240 PG 12 WC Mathematics, Applied; Mathematics SC Mathematics GA BGI39 UT WOS:000323090600019 ER PT S AU Weber, G Bremer, PT Day, M Bell, J Pascucci, V AF Weber, Gunther Bremer, Peer-Timo Day, Marcus Bell, John Pascucci, Valerio BE Pascucci, V Tricoche, X Hagen, H Tierny, J TI Feature Tracking Using Reeb Graphs SO TOPOLOGICAL METHODS IN DATA ANALYSIS AND VISUALIZATION: THEORY, ALGORITHMS, AND APPLICATIONS SE Mathematics and Visualization LA English DT Proceedings Paper CT 3rd Workshop on Topological Methods in Data Analysis and Visualization CY FEB 23-24, 2009 CL Snowbird, UT SP Univ Utah, Sci Comp Imag Inst, Tech Univ Kaiserslautern, Enabl Technologies, SciDAC Visualizat Anal Ctr, NVIDIA Corp DE Topological data analysis; Feature tracking; Combustion simulation; Reeb graph; Tracking graph; Tracking accuracy AB Tracking features and exploring their temporal dynamics can aid scientists in identifying interesting time intervals in a simulation and serve as basis for performing quantitative analyses of temporal phenomena. In this paper, we develop a novel approach for tracking subsets of isosurfaces, such as burning regions in simulated flames, which are defined as areas of high fuel consumption on a temperature isosurface. Tracking such regions as they merge and split over time can provide important insights into the impact of turbulence on the combustion process. However, the convoluted nature of the temperature isosurface and its rapid movement make this analysis particularly challenging. Our approach tracks burning regions by extracting a temperature isovolume from the four-dimensional space-time temperature field. It then obtains isosurfaces for the original simulation time steps and labels individual connected "burning" regions based on the local fuel consumption value. Based on this information, a boundary surface between burning and non-burning regions is constructed. The Reeb graph of this boundary surface is the tracking graph for burning regions. C1 [Weber, Gunther; Day, Marcus; Bell, John] Lawrence Berkeley Natl Lab, Berkeley, CA USA. RP Weber, G (reprint author), Lawrence Berkeley Natl Lab, Berkeley, CA USA. EM GHWeber@lbl.gov; ptbremer@llnl.gov; MSDay@lbl.gov; JBBell@lbl.gov; pascucci@sci.utah.edu NR 19 TC 9 Z9 9 U1 0 U2 1 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 1612-3786 BN 978-3-642-15013-5 J9 MATH VIS PY 2011 BP 241 EP 253 PG 13 WC Mathematics, Applied; Mathematics SC Mathematics GA BGI39 UT WOS:000323090600020 ER PT J AU Carney, EW Tornesi, B Liberacki, AB Markham, DA Weitz, KK Luders, TM Studniski, KG Blessing, JC Gies, RA Corley, RA AF Carney, Edward W. Tornesi, Belen Liberacki, Ashley B. Markham, Daniel A. Weitz, Karl K. Luders, Teressa M. Studniski, Kristine G. Blessing, John C. Gies, Richard A. Corley, Richard A. TI The Impact of Dose Rate on Ethylene Glycol Developmental Toxicity and Pharmacokinetics in Pregnant CD Rats SO TOXICOLOGICAL SCIENCES LA English DT Article DE toxicokinetics; teratogenicity; human relevance; developmental pharmacokinetics ID WHOLE-EMBRYO CULTURE; SPRAGUE-DAWLEY RATS; IN-VITRO; PLASMA DISPOSITION; WEAK ACIDS; MICE; PENETRATION; METABOLITES; EXPOSURE; AEROSOL AB High-dose bolus exposure of rats to ethylene glycol (EG) causes developmental toxicity mediated by a metabolite, glycolic acid (GA), whose levels increase disproportionately when its metabolism is saturated. However, low-level exposures that do not saturate GA metabolism have a low potential for developmental effects. Toward the goal of developing EG risk assessments based on internal dose metrics, this study examined the differences between fast (bolus) and slow (continuous infusion) dose-rate exposures to EG on developmental outcome and pharmacokinetics. Time-mated female CD rats received sc bolus injections of 0, 1000, or 2000 mg/kg/day of EG on gestation day (GD) 6-15 once daily, whereas three corresponding groups were given the same daily doses as an infusion administered continuously from GD 6-15 via an sc implantable pump. In the sc bolus groups, increases in 11 fetal malformations (major defects) and 12 variations (minor alterations) were seen at the 2000 mg/kg/day dose level, whereas increases in 2 malformations and 2 variations occurred at 1000 mg/kg/day. In contrast, equivalent daily doses of EG given slowly via infusion did not cause any developmental effects. A pharmacokinetics time course was then conducted to compare GD 11-12 kinetics from oral bolus (gavage) exposure versus sc infusion of EG. Although dose rate had a modest impact (8- to 11-fold difference) on peak EG levels, peak levels of GA in maternal blood, kidney, embryo, and exocoelomic fluid were 59, 100, 49, and 56 times higher, respectively, following gavage versus the same dose given by infusion. These data illustrate how high-dose bolus exposure to EG causes a dramatic shift to nonlinear GA kinetics, an event which is highly unlikely to occur following exposures to humans associated with consumer and worker uses. C1 [Carney, Edward W.; Tornesi, Belen; Liberacki, Ashley B.; Markham, Daniel A.] Dow Chem Co USA, Toxicol & Environm Res & Consulting, Midland, MI 48674 USA. [Blessing, John C.] Pacific NW Natl Lab, Mol Biosci Dept, Richland, WA 99352 USA. RP Carney, EW (reprint author), Dow Chem Co USA, Toxicol & Environm Res & Consulting, 1803 Bldg, Midland, MI 48674 USA. EM ecarney@dow.com FU Ethylene Glycol Panel of The American Chemistry Council, Arlington, VA FX Funding for this study was provided by the Ethylene Glycol Panel of The American Chemistry Council, Arlington, VA. NR 35 TC 2 Z9 2 U1 1 U2 9 PU OXFORD UNIV PRESS PI OXFORD PA GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND SN 1096-6080 J9 TOXICOL SCI JI Toxicol. Sci. PD JAN PY 2011 VL 119 IS 1 BP 178 EP 188 DI 10.1093/toxsci/kfq310 PG 11 WC Toxicology SC Toxicology GA 701TD UT WOS:000285845400017 PM 20952502 ER PT J AU Brandizzi, F AF Brandizzi, Federica TI Is There a COPII-Mediated Membrane Traffic in Chloroplasts? SO TRAFFIC LA English DT Article DE chloroplasts; COPII proteins; ER-to-Golgi protein transport; Sar1 ID GTP-BINDING PROTEIN; ENDOPLASMIC-RETICULUM; ESCHERICHIA-COLI; GOLGI-APPARATUS; EXPORT SITES; CELLS; TRANSPORT; COAT; DYNAMICS; TOBACCO AB COPII proteins facilitate membrane transport from the endoplasmic reticulum (ER) to the Golgi. They are highly conserved, although there are variations in their subcellular localization across plant, animal and yeast cells. Such variations may be needed to suit the unique organization of the ER and Golgi in the different cell systems. Earlier bioinformatics analyses have indicated that the Arabidopsis nuclear genome may encode chloroplast isoforms of the cytosolic trafficking protein machineries, including COPI and COPII, for vesicular transport within chloroplasts. These analyses suggest the intriguing possibility that plants may have evolved or adapted COP-like proteins to suit membrane trafficking events within specialized organelles. Here, we discuss recent data on the distribution and activity of the product of the At5g18570 locus, which encodes a putative chloroplast isoform of Sar1, the GTPase that regulates COPII assembly on the surface of the ER. Evidence is accumulating that the protein is targeted to the chloroplasts, that it has GTPase activity and that it may have a role in thylakoid membrane development, supporting the possibility that COPII-like trafficking machinery may be active in chloroplasts. C1 Michigan State Univ, DOE Plant Res Lab, E Lansing, MI 48824 USA. RP Brandizzi, F (reprint author), Michigan State Univ, DOE Plant Res Lab, E Lansing, MI 48824 USA. EM fb@msu.edu FU National Science Foundation [MCB 0948584]; Chemical Sciences, Geosciences and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U.S. Department of Energy [DE-FG02-91ER20021] FX Support by the Chemical Sciences, Geosciences and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U.S. Department of Energy (award number DE-FG02-91ER20021) and National Science Foundation (MCB 0948584) is acknowledged. Ramu Subramanian Saravanan and Sarabjeet Singh are thanked for their technical help in the preparation of Figure 1. NR 24 TC 4 Z9 4 U1 1 U2 6 PU WILEY-BLACKWELL PUBLISHING, INC PI MALDEN PA COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA SN 1398-9219 J9 TRAFFIC JI Traffic PD JAN PY 2011 VL 12 IS 1 BP 9 EP 11 DI 10.1111/j.1600-0854.2010.01129.x PG 3 WC Cell Biology SC Cell Biology GA 693ED UT WOS:000285206500002 PM 21040296 ER PT J AU Geist, DR Deng, ZQ Mueller, RP Cullinan, V Brink, S Chandler, JA AF Geist, David R. Deng, Zhiqun Mueller, Robert P. Cullinan, Valerie Brink, Steven Chandler, James A. TI The Effect of Fluctuating Temperatures and Ration Levels on the Growth of Juvenile Snake River Fall Chinook Salmon SO TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY LA English DT Article ID WATER TEMPERATURE; ONCORHYNCHUS-KISUTCH; PREDATOR AVOIDANCE; STEELHEAD TROUT; SOCKEYE SALMON; GAIRDNERI; FISH; TSHAWYTSCHA; INFECTIONS; CONSTANT AB Determining the fate of juvenile fish that are exposed to elevated temperatures is complicated by the fact that the optimum temperature for the growth and survival of salmonids decreases as the amount of food becomes restricted. In this study, naturally produced juvenile Snake River fall Chinook salmon Oncorhynchus tshawytscha were fed daily ration levels of 1, 4, or 8% of their body weight and exposed to either constant temperatures (10-14 degrees C) or fluctuating temperatures that mimicked the heating rate (1.5 degrees C/h) and maximum daily temperatures (19-23 degrees C) of entrapment pools that form along the shoreline downstream of Hells Canyon Dam when river flows are altered to meet electric power demand. The survival rate for all groups was 99.9%, and there was no evidence that juvenile fall Chinook salmon fed reduced rations and exposed to constant temperatures grew to a greater extent than juvenile fall Chinook salmon exposed to fluctuating temperatures. The only exception was with the 1% ration level in which juvenile fall Chinook salmon that were exposed to a constant 10 degrees C added more weight over the 14-d exposure period (1% of body weight per day [WT/d]) than fish exposed to temperatures that fluctuated from 10 degrees C to 19.0 degrees C (0.3% WT/d) and from 10 degrees C to 22 degrees C daily (0% WT/d). We conclude that the lack of difference in growth rates between the fluctuating and constant temperature regimes at daily ration levels of at least 4% stems from the facts that the rate of temperature change in this study was within the acclimation range for growth, the daily average temperatures were less than thermal optimum values, and the temperature amplitudes were within lethal limits. C1 [Geist, David R.; Deng, Zhiqun; Mueller, Robert P.] Battelle Pacific NW Div, Earth Syst Sci Div, Richland, WA 99352 USA. [Cullinan, Valerie] Battelle Pacific NW Div, Marine Sci Lab, Sequim, WA 98382 USA. [Brink, Steven; Chandler, James A.] Idaho Power Co, Boise, ID 83707 USA. RP Geist, DR (reprint author), Battelle Pacific NW Div, Earth Syst Sci Div, POB 999, Richland, WA 99352 USA. EM david.geist@pnl.gov RI Deng, Daniel/A-9536-2011 OI Deng, Daniel/0000-0002-8300-8766 FU Idaho Power Company [56697A]; Battelle Memorial Institute [DE-AC05-76RL01830] FX The authors thank Phil Groves and Brad Alcorn (Idaho Power Company) for catching the fish used in this study. Greg Gaulke and Chris Vernon (Battelle Memorial Institute) and Jennifer Monroe (Cascade Aquatics) were responsible for fish care. Chuck Coutant provided consultation on the study design and reviewed early versions of the manuscript. Andrea Currie (Battelle) was the technical editor and made substantial improvements to the document. Numerous other Battelle staff assisted on the study; we thank all of them very much for their support. Billy Connor and two anonymous reviewers improved the quality of this paper. This study was funded by Idaho Power Company under contract 56697A. The Pacific Northwest National Laboratory is owned by the U.S. Department of Energy and operated by Battelle Memorial Institute under contract DE-AC05-76RL01830. NR 33 TC 4 Z9 4 U1 2 U2 13 PU TAYLOR & FRANCIS INC PI PHILADELPHIA PA 520 CHESTNUT STREET, STE 850, PHILADELPHIA, PA 19106 USA SN 0002-8487 EI 1548-8659 J9 T AM FISH SOC JI Trans. Am. Fish. Soc. PD JAN PY 2011 VL 140 IS 1 BP 190 EP 200 AR PII 934601844 DI 10.1080/00028487.2011.556997 PG 11 WC Fisheries SC Fisheries GA 733RI UT WOS:000288280100017 ER PT J AU Silin, D Tomutsa, L Benson, SM Patzek, TW AF Silin, Dmitriy Tomutsa, Liviu Benson, Sally M. Patzek, Tad W. TI Microtomography and Pore-Scale Modeling of Two-Phase Fluid Distribution SO TRANSPORT IN POROUS MEDIA LA English DT Article DE Capillary pressure; Microtomography; Pore-scale modeling; Two-phase flow ID X-RAY MICROTOMOGRAPHY; POROUS-MEDIA; NETWORK MODEL; COMPUTED MICROTOMOGRAPHY; CAPILLARY-PRESSURE; DYNAMIC PROPERTIES; MULTIPHASE FLOW; CO2 INJECTION; PERMEABILITY; WETTABILITY AB Synchrotron-based X-ray microtomography (micro CT) at the Advanced Light Source (ALS) line 8.3.2 at the Lawrence Berkeley National Laboratory produces three-dimensional micron-scale-resolution digital images of the pore space of the reservoir rock along with the spacial distribution of the fluids. Pore-scale visualization of carbon dioxide flooding experiments performed at a reservoir pressure demonstrates that the injected gas fills some pores and pore clusters, and entirely bypasses the others. Using 3D digital images of the pore space as input data, the method of maximal inscribed spheres (MIS) predicts two-phase fluid distribution in capillary equilibrium. Verification against the tomography images shows a good agreement between the computed fluid distribution in the pores and the experimental data. The model-predicted capillary pressure curves and tomography-based porosimetry distributions compared favorably with the mercury injection data. Thus, micro CT in combination with modeling based on the MIS is a viable approach to study the pore-scale mechanisms of CO2 injection into an aquifer, as well as more general multi-phase flows. C1 [Silin, Dmitriy; Tomutsa, Liviu] Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. [Benson, Sally M.] Stanford Univ, Energy Resources Engn Dept, Stanford, CA 94305 USA. [Patzek, Tad W.] Univ Texas Austin, Dept Petr & Geosyst Engn, Austin, TX 78712 USA. RP Silin, D (reprint author), Lawrence Berkeley Natl Lab, 1 Cyclotron Rd,MS 90R1116, Berkeley, CA 94720 USA. EM DSilin@lbl.gov FU U.S. Department of Energy's Assistant Secretary for Coal through the Zero Emission Research and Technology under US Department of Energy [DE-AC02-05CH11231]; Office of Science, Office of Basic Energy Sciences, U.S. Department of Energy [DE-AC02-05CH11231] FX This work was partially supported by the U.S. Department of Energy's Assistant Secretary for Coal through the Zero Emission Research and Technology Program under US Department of Energy contract no. DE-AC02-05CH11231 to Lawrence Berkeley National Laboratory. Part of this work has been done while the first author was visiting the Energy Resources Engineering Department at Stanford University. The hospitality of this department and the Global Climate and Energy Project is gratefully appreciated. The first author also acknowledges partial support from the Research Partnership to Secure Energy for America. Portions of this work were performed at the ALS, Lawrence Berkeley National Laboratory, which is supported by the Office of Science, Office of Basic Energy Sciences, U.S. Department of Energy, under Contract No. DE-AC02-05CH11231. Special Core Analysis Laboratories, Inc. conducted the mercury injection experiments mentioned in this study. NR 57 TC 58 Z9 59 U1 4 U2 53 PU SPRINGER PI NEW YORK PA 233 SPRING ST, NEW YORK, NY 10013 USA SN 0169-3913 EI 1573-1634 J9 TRANSPORT POROUS MED JI Transp. Porous Media PD JAN PY 2011 VL 86 IS 2 BP 525 EP 545 DI 10.1007/s11242-010-9636-2 PG 21 WC Engineering, Chemical SC Engineering GA 715VT UT WOS:000286918900012 ER PT J AU Benisti, D Morice, O Gremillet, L Strozzi, DJ AF Benisti, Didier Morice, Olivier Gremillet, Laurent Strozzi, David J. TI NONLINEAR ENVELOPE EQUATION AND NONLINEAR LANDAU DAMPING RATE FOR A DRIVEN ELECTRON PLASMA WAVE SO TRANSPORT THEORY AND STATISTICAL PHYSICS LA English DT Article ID OSCILLATIONS AB In this article, we provide a theoretical description and calculate the nonlinear frequency shift, group velocity, and collionless damping rate, nu, of a driven electron plasma wave (EPW). All these quantities, whose physical content will be discussed, are identified as terms of an envelope equation allowing one to predict how efficiently an EPW may be externally driven. This envelope equation is derived directly from Gauss' law and from the investigation of the nonlinear electron motion, provided that the time and space rates of variation of the EPW amplitude, E-p, are small compared to the plasma frequency or the inverse of the Debye length. nu arises within the EPW envelope equation as a more complicated operator than a plain damping rate and may only be viewed as such because [nu(E-p)]/E-p remains nearly constant before abruptly dropping to zero. We provide a practical analytic formula for nu and show, without resorting to complex contour deformation, that in the limit E-p -> 0, nu is nothing but the Landau damping rate. We then term. the "nonlinear Landau damping rate" of the driven plasma wave. As for the nonlinear frequency shift of the driven EPW, it is also derived theoretically and found to assume values significantly different from previously published ones, which were obtained by assuming that the wave was freely propagating. Moreover, we find no limitation in k lambda(D), k being the plasma wavenumber and lambda(D) the Debye length, for a solution to the dispertion relation to exist, and want to stress here the importance of specifying how an EPW is generated to discuss its properties. Our theoretical predictions are in excellent agreement with results inferred from Vlasov simulations of stimulated Raman scattering (SRS), and an application of our theory to the study of SRS is presented. C1 [Benisti, Didier; Morice, Olivier; Gremillet, Laurent] CEA, DAM, DIF, F-91297 Arpajon, France. [Strozzi, David J.] Lawrence Livermore Natl Lab, AX Div, Livermore, CA USA. RP Benisti, D (reprint author), CEA, DAM, DIF, F-91297 Arpajon, France. EM didier.benisti@cea.fr OI Strozzi, David/0000-0001-8814-3791 NR 25 TC 4 Z9 4 U1 0 U2 2 PU TAYLOR & FRANCIS INC PI PHILADELPHIA PA 325 CHESTNUT ST, SUITE 800, PHILADELPHIA, PA 19106 USA SN 0041-1450 J9 TRANSPORT THEOR STAT JI Transport. Theor. Statist. Phys. PY 2011 VL 40 IS 4 BP 185 EP 224 DI 10.1080/00411450.2011.604568 PG 40 WC Mathematics, Applied; Physics, Mathematical SC Mathematics; Physics GA 885NJ UT WOS:000299785400002 ER PT J AU Henson, KM Goulias, KG AF Henson, Kriste M. Goulias, Konstadinos G. TI Travel Determinants and Multiscale Transferability of National Activity Patterns to Local Populations SO TRANSPORTATION RESEARCH RECORD LA English DT Article ID BEHAVIOR AB The ability to transfer national travel patterns to a local population is of interest for modeling either large areas that exceed the boundaries of a metropolitan planning organization or small regions with no available travel survey data. At the core of this research are questions about the connection between travel behavior and land use, urban form, and accessibility. To explore this relationship, the researchers selected a group of land use variables to define activity and travel patterns for individuals and households. The 2001 National Household Travel Survey (NHTS) participants were divided into categories consisting of a set of latent cluster models representing persons, travel, and land use. This set was compared with two sets of cluster models constructed for two local travel surveys. Mean statistical tests were compared to assess differences among socio-demographic groups residing in localities with similar land uses. The results showed that the NHTS and the local surveys shared mean population activity and travel characteristics. However, these similarities masked behavioral heterogeneity, which was seen when distributions of activity and travel behavior were examined. Therefore, data from a national household travel survey in combination with land use data cannot be used to model local population travel characteristics if the goal is to model the behavioral distributions and not just mean travel behavior characteristics. C1 [Henson, Kriste M.] Los Alamos Natl Lab, Decis Applicat Div, Los Alamos, NM 87545 USA. [Goulias, Konstadinos G.] Univ Calif Santa Barbara, Dept Geog, Santa Barbara, CA 93106 USA. RP Henson, KM (reprint author), Los Alamos Natl Lab, Decis Applicat Div, POB 1663,MS F609, Los Alamos, NM 87545 USA. EM kriste@lanl.gov FU University of California; National Highway Institute of the Federal Highway Administration; University of California Transportation Center; National Science Foundation FX This research was supported by the University of California Lab Fees Research Program, the National Highway Institute of the Federal Highway Administration's Dwight David Eisenhower Graduate Transportation Fellowship, the University of California Transportation Center's Doctoral Dissertation Research Grant, and the National Science Foundation's Doctoral Dissertation Research Grant in Geography and Regional Science. NR 23 TC 0 Z9 0 U1 0 U2 0 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0361-1981 J9 TRANSPORT RES REC JI Transp. Res. Record PY 2011 IS 2231 BP 35 EP 43 DI 10.3141/2231-05 PG 9 WC Engineering, Civil; Transportation; Transportation Science & Technology SC Engineering; Transportation GA 865LR UT WOS:000298312900006 ER PT J AU Lee, JD McGehee, DV Brown, JL Richard, CM Ahmad, O Ward, NJ Hallmark, S Lee, J AF Lee, John D. McGehee, Daniel V. Brown, James L. Richard, Christian M. Ahmad, Omar Ward, Nicholas J. Hallmark, Shauna Lee, Joonbum TI Matching Simulator Characteristics to Highway Design Problems SO TRANSPORTATION RESEARCH RECORD LA English DT Article ID DRIVING SIMULATOR; ROAD AB Driving simulators hold much promise for addressing roadway design issues. However, although simulators have demonstrated their value in experimental research addressing driver performance, their ability to support road design projects has not been as clearly established. This paper describes a design-centered framework to make simulators valuable for traffic engineers and geometric designers. This framework includes several steps: (a) identification of design issues that would benefit from driving simulators, (h) identification of simulator characteristics to match them to design issues, and (c) translation of driver performance data from the simulator to traffic behavior on the road. Several critical obstacles inhibit application of simulators to highway design. First, driving safety researchers and engineers comprise separate communities and their perspectives on how simulators can be applied to address road design issues often diverge. This paper seeks to reduce this divergence and make simulators useful to highway engineers. Interviews with engineers revealed important issues that simulators could address, such as intersection and interchange design. Second, driving simulators are often broadly defined as high fidelity, which provides little value in matching simulators to design issues. A survey of simulators and simulator characteristics clarifies the meaning of simulator fidelity and links it to road design issues. Third, simulators often produce data that do not correspond to data collected by traffic engineers. This mismatch can result from inadequate simulator fidelity, but can also arise from more fundamental sources traffic engineers focus on traffic behavior and driving simulator researchers focus on driver behavior. Obstacles in using simulators for highway design reflect both technical and communication challenges. C1 [Lee, John D.; Lee, Joonbum] Univ Wisconsin, Dept Ind & Syst Engn, Madison, WI 53706 USA. [McGehee, Daniel V.] Univ Iowa, Human Factors & Vehicle Safety Res Div, Publ Policy Ctr, Iowa City, IA 52242 USA. [Brown, James L.; Richard, Christian M.] Battelle Seattle Res Ctr, Ctr Human Performance & Safety, Seattle, WA 98109 USA. [Ward, Nicholas J.] Montana State Univ, Western Transportat Inst, Bozeman, MT 59717 USA. [Hallmark, Shauna] Iowa State Univ, Ctr Transportat Res & Educ, Ames, IA 50011 USA. RP Lee, JD (reprint author), Univ Wisconsin, Dept Ind & Syst Engn, 1513 Univ Ave, Madison, WI 53706 USA. EM jdlee@engr.wisc.edu OI Lee, John/0000-0001-9808-2160 FU FHWA FX This paper was made possible by funding from FHWA. Tom Granda, Chris Monk, John Molino, and Paul Tremont provided valuable contributions to the paper, particularly in soliciting information on design issues facing highway engineers. NR 21 TC 4 Z9 4 U1 1 U2 8 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0361-1981 J9 TRANSPORT RES REC JI Transp. Res. Record PY 2011 IS 2248 BP 53 EP 60 DI 10.3141/2248-07 PG 8 WC Engineering, Civil; Transportation; Transportation Science & Technology SC Engineering; Transportation GA 875IL UT WOS:000299023500007 ER PT J AU Peters, NE Bohlke, JK Brooks, PD Burt, TP Gooseff, MN Hamilton, DP Mulholland, PJ Roulet, NT Turner, JV AF Peters, N. E. Boehlke, J. K. Brooks, P. D. Burt, T. P. Gooseff, M. N. Hamilton, D. P. Mulholland, P. J. Roulet, N. T. Turner, J. V. BE Wilderer, P TI Hydrology and Biogeochemistry Linkages SO TREATISE ON WATER SCIENCE, VOL 2: THE SCIENCE OF HYDROLOGY LA English DT Article; Book Chapter ID DISSOLVED ORGANIC-CARBON; ATMOSPHERIC NITROGEN DEPOSITION; TEMPERATE FOREST ECOSYSTEMS; CALIFORNIA REDWOOD FOREST; NORTHERN HARDWOOD FOREST; WATER-TABLE FLUCTUATIONS; EUROPEAN SURFACE WATERS; ATLANTIC COASTAL-PLAIN; GRADIENT TRACER TESTS; SOUTH-CENTRAL ONTARIO C1 [Peters, N. E.] US Geol Survey, Atlanta, GA 30360 USA. [Boehlke, J. K.] US Geol Survey, Reston, VA 22092 USA. [Brooks, P. D.] Univ Arizona, Tucson, AZ USA. [Burt, T. P.] Univ Durham, Durham, England. [Gooseff, M. N.] Penn State Univ, University Pk, PA 16802 USA. [Hamilton, D. P.] Univ Waikato, Hamilton, New Zealand. [Mulholland, P. J.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Roulet, N. T.] McGill Univ, Montreal, PQ, Canada. [Turner, J. V.] CSIRO Land & Water, Wembley, WA, Australia. RP Peters, NE (reprint author), US Geol Survey, Atlanta, GA 30360 USA. RI Gooseff, Michael/N-6087-2015 OI Gooseff, Michael/0000-0003-4322-8315 NR 429 TC 5 Z9 5 U1 3 U2 6 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA SARA BURGERHARTSTRAAT 25, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS BN 978-0-444-53199-5 PY 2011 BP 271 EP 304 PG 34 WC Geosciences, Multidisciplinary; Water Resources SC Geology; Water Resources GA BA2FH UT WOS:000333356000012 ER PT J AU Hubbard, SS Linde, N AF Hubbard, S. S. Linde, N. BE Wilderer, P TI Hydrogeophysics SO TREATISE ON WATER SCIENCE, VOL 2: THE SCIENCE OF HYDROLOGY LA English DT Article; Book Chapter ID GROUND-PENETRATING-RADAR; ELECTRICAL-RESISTIVITY TOMOGRAPHY; BACTERIAL TRANSPORT SITE; WAVE-FORM INVERSION; SOIL-WATER CONTENT; HYDRAULIC CONDUCTIVITY; FIELD-SCALE; POROUS-MEDIA; DC RESISTIVITY; INDUCED POLARIZATION C1 [Hubbard, S. S.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. [Linde, N.] Univ Lausanne, Lausanne, Switzerland. RP Hubbard, SS (reprint author), Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RI Linde, Niklas/A-9440-2008; Hubbard, Susan/E-9508-2010 OI Linde, Niklas/0000-0003-1613-353X; NR 200 TC 20 Z9 20 U1 0 U2 5 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA SARA BURGERHARTSTRAAT 25, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS BN 978-0-444-53199-5 PY 2011 BP 401 EP 434 PG 34 WC Geosciences, Multidisciplinary; Water Resources SC Geology; Water Resources GA BA2FH UT WOS:000333356000016 ER PT J AU Grimaldi, S Kao, SC Castellarin, A Papalexiou, SM Viglione, A Laio, F Aksoy, H Gedikli, A AF Grimaldi, S. Kao, S-C Castellarin, A. Papalexiou, S-M Viglione, A. Laio, F. Aksoy, H. Gedikli, A. BE Wilderer, P TI Statistical Hydrology SO TREATISE ON WATER SCIENCE, VOL 2: THE SCIENCE OF HYDROLOGY LA English DT Article; Book Chapter ID FLOOD FREQUENCY-ANALYSIS; GOODNESS-OF-FIT; PARTIAL-DURATION SERIES; ANNUAL MAXIMUM SERIES; PEARSON TYPE-3 DISTRIBUTION; HYDROMETEOROLOGICAL TIME-SERIES; PRECIPITATION ANNUAL MAXIMA; GUMBEL-HOUGAARD COPULA; RAINFALL INTENSITY; PROBABILITY-DISTRIBUTION C1 [Grimaldi, S.] Univ Tuscia, Viterbo, Italy. [Kao, S-C] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Castellarin, A.] Univ Bologna, Bologna, Italy. [Papalexiou, S-M] Natl Tech Univ Athens, Zografos, Greece. [Viglione, A.] Vienna Univ Technol, A-1060 Vienna, Austria. [Laio, F.] Politecn Torino, Turin, Italy. [Aksoy, H.; Gedikli, A.] Istanbul Tech Univ, TR-80626 Istanbul, Turkey. RP Grimaldi, S (reprint author), Univ Tuscia, Viterbo, Italy. NR 250 TC 6 Z9 6 U1 0 U2 3 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA SARA BURGERHARTSTRAAT 25, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS BN 978-0-444-53199-5 PY 2011 BP 479 EP 517 PG 39 WC Geosciences, Multidisciplinary; Water Resources SC Geology; Water Resources GA BA2FH UT WOS:000333356000019 ER PT J AU Volkow, ND Wang, GJ Baler, RD AF Volkow, Nora D. Wang, Gene-Jack Baler, Ruben D. TI Reward, dopamine and the control of food intake: implications for obesity SO TRENDS IN COGNITIVE SCIENCES LA English DT Review ID BODY-MASS INDEX; ORBITOFRONTAL-CORTEX; ENDOCANNABINOID SYSTEM; EATING BEHAVIOR; ENERGY-BALANCE; PROBABILISTIC REINFORCEMENT; NUCLEUS-ACCUMBENS; FEEDING-BEHAVIOR; DORSAL STRIATUM; BRAIN STRUCTURE AB The ability to resist the urge to eat requires the proper functioning of neuronal circuits involved in top-down control to oppose the conditioned responses that predict reward from eating the food and the desire to eat the food. Imaging studies show that obese subjects might have impairments in dopaminergic pathways that regulate neuronal systems associated with reward sensitivity, conditioning and control. It is known that the neuropeptides that regulate energy balance (homeostatic processes) through the hypothalamus also modulate the activity of dopamine cells and their projections into regions involved in the rewarding processes underlying food intake. It is postulated that this could also be a mechanism by which overeating and the resultant resistance to homoeostatic signals impairs the function of circuits involved in reward sensitivity, conditioning and cognitive control. C1 [Volkow, Nora D.; Baler, Ruben D.] Natl Inst Drug Abuse, NIH, Bethesda, MD 20892 USA. [Wang, Gene-Jack] Brookhaven Natl Lab, Dept Med, Upton, NY 11973 USA. RP Volkow, ND (reprint author), Natl Inst Drug Abuse, NIH, Bethesda, MD 20892 USA. EM nvolkow@nida.nih.gov FU Intramural NIH HHS [ZIA AA000550-07] NR 106 TC 298 Z9 305 U1 16 U2 100 PU ELSEVIER SCIENCE LONDON PI LONDON PA 84 THEOBALDS RD, LONDON WC1X 8RR, ENGLAND SN 1364-6613 J9 TRENDS COGN SCI JI TRENDS COGN. SCI. PD JAN PY 2011 VL 15 IS 1 BP 37 EP 46 DI 10.1016/j.tics.2010.11.001 PG 10 WC Behavioral Sciences; Neurosciences; Psychology, Experimental SC Behavioral Sciences; Neurosciences & Neurology; Psychology GA 715FH UT WOS:000286865500006 PM 21109477 ER PT B AU Menon, S Kerstein, AR AF Menon, Suresh Kerstein, Alan R. BE Echekki, T Mastorakos, E TI The Linear-Eddy Model SO TURBULENT COMBUSTION MODELING: ADVANCES, NEW TRENDS AND PERSPECTIVES SE Fluid Mechanics and Its Applications LA English DT Article; Book Chapter ID ARTIFICIAL NEURAL-NETWORKS; DIFFERENTIAL MOLECULAR-DIFFUSION; DIRECT NUMERICAL SIMULATIONS; HOMOGENEOUS TURBULENT-FLOW; DIRECT-INJECTION COMBUSTOR; NON-PREMIXED COMBUSTION; REACTION-ZONES REGIME; PLANE JET FLAMES; CHEMICAL-KINETICS; SCALAR STATISTICS AB Regime-independent modeling is important for accurate simulation of the complex combustor designs needed to meet increasingly stringent performance requirements. One strategy for achieving robust yet affordable predictive capability is to resolve, in space and time, the relevant advection-diffusion-reaction couplings using a low-dimensional representation of turbulent advection. In the linear-eddy model (LEM), this is accomplished in one spatial dimension by introducing an instantaneous map, the 'triplet map,' that emulates the effect of an eddy turnover on property profiles along a notional line of sight. The map preserves the continuity of these profiles and obeys applicable conservation laws. Details and representative applications of the model are presented for passive and reactive scalar mixing, with emphasis on its use as a mixing-reaction closure for large-eddy simulation (LES) based on the embedding of an LEM domain in each LES control volume. C1 [Menon, Suresh] Georgia Inst Technol, Sch Aerosp Engn, Atlanta, GA 30332 USA. [Kerstein, Alan R.] Sandia Natl Labs, Combust Res Facil, Livermore, CA USA. RP Menon, S (reprint author), Georgia Inst Technol, Sch Aerosp Engn, Atlanta, GA 30332 USA. EM suresh.menon@aerospace.gatech.edu; arkerst@sandia.gov NR 79 TC 13 Z9 13 U1 0 U2 2 PU SPRINGER PI DORDRECHT PA PO BOX 17, 3300 AA DORDRECHT, NETHERLANDS BN 978-94-007-0411-4 J9 FLUID MECH APPL PY 2011 VL 95 BP 221 EP 247 DI 10.1007/978-94-007-0412-1_10 D2 10.1007/978-94-007-0412-1 PG 27 WC Computer Science, Theory & Methods; Engineering, Mechanical; Mathematics, Applied SC Computer Science; Engineering; Mathematics GA BSY44 UT WOS:000286131200010 ER PT S AU Prasankumar, RP Shenoi, RV Urayama, J Chow, WW Krishna, S Taylor, AJ AF Prasankumar, R. P. Shenoi, R. V. Urayama, J. Chow, W. W. Krishna, S. Taylor, A. J. BE Tsen, KT Song, JJ Betz, M Elezzabi, AY TI Ultrafast density-and-temperature-dependent carrier dynamics in a quantum dots-in-a-well heterostructure SO ULTRAFAST PHENOMENA IN SEMICONDUCTORS AND NANOSTRUCTURE MATERIALS XV SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on Ultrafast Phenomena in Semiconductors and Nanostructure Materials XV CY JAN 23-26, 2011 CL San Francisco, CA SP SPIE DE Ultrafast dynamics; quantum dots; dots-in-a-well; ultrafast phenomena; semiconductor heterostructures ID SEMICONDUCTOR NANOCRYSTALS; PHONON BOTTLENECK; RELAXATION; PERFORMANCE; DETECTOR; CAPTURE; DEVICES; LASERS; STATES AB The incorporation of semiconductor quantum dots into different heterostructures for applications in nanoscale photodetection, lasing and amplification has been an active area of research in recent years. Here, we use ultrafast differential transmission spectroscopy to temporally and spectrally resolve density-and-temperature-dependent carrier dynamics in an InAs/InGaAs quantum dots-in-a-well (DWELL) heterostructure. In our experiments, electron-hole pairs are optically injected into the three dimensional GaAs barriers, after which we monitor carrier relaxation into the two dimensional InGaAs quantum wells and the zero dimensional InAs quantum dots by tuning the probe photon energy. We find that for low photoinjected carrier densities, carrier capture and relaxation are dominated by Auger carrier-carrier scattering at low temperatures, with thermal emission playing an increasing role with temperature. At low temperatures we also observe excitation-dependent shifts of the quantum dot energy levels. In contrast, high density measurements reveal an anomalous induced absorption at the quantum dot excited state that is correlated with quantum well population dynamics. Our experiments provide essential insight into carrier relaxation across multiple spatial dimensions and reveal unique Coulomb interaction-induced phenomena, with important implications for DWELL-based lasers and amplifiers. C1 [Prasankumar, R. P.; Taylor, A. J.] Los Alamos Natl Lab, Ctr Integrated Nanotechnol, Los Alamos, NM 87545 USA. RP Prasankumar, RP (reprint author), Los Alamos Natl Lab, Ctr Integrated Nanotechnol, POB 1663, Los Alamos, NM 87545 USA. EM rpprasan@lanl.gov NR 45 TC 0 Z9 0 U1 1 U2 2 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-8474-1 J9 PROC SPIE PY 2011 VL 7937 AR 793707 DI 10.1117/12.872887 PG 12 WC Engineering, Electrical & Electronic; Nanoscience & Nanotechnology; Optics SC Engineering; Science & Technology - Other Topics; Optics GA BWD60 UT WOS:000293630900004 ER PT J AU Glaeser, RM McMullan, G Faruqi, AR Henderson, R AF Glaeser, R. M. McMullan, G. Faruqi, A. R. Henderson, R. TI Images of paraffin monolayer crystals with perfect contrast: Minimization of beam-induced specimen motion SO ULTRAMICROSCOPY LA English DT Article DE Tetratetracontane; 2D crystals; Beam-induced specimen motion; Radiation damage; Image contrast; Carbon support films; Medipix detector ID TRANSMISSION ELECTRON-MICROSCOPY; RADIATION-DAMAGE; PHASE-CONTRAST; CRYOELECTRON MICROSCOPY; HIGH-RESOLUTION; CRYOMICROSCOPY; FILMS; TEMPERATURES; MICROGRAPHS; SUBSTRATE AB Quantitative analysis of electron microscope images of organic and biological two-dimensional crystals has previously shown that the absolute contrast reached only a fraction of that expected theoretically from the electron diffraction amplitudes. The accepted explanation for this is that irradiation of the specimen causes beam-induced charging or movement, which in turn causes blurring of the image due to image or specimen movement. In this paper, we used three different approaches to try to overcome this image-blurring problem in monolayer crystals of paraffin. Our first approach was to use an extreme form of spotscan imaging, in which a single image was assembled on film by the successive illumination of up to 50,000 spots, each of a diameter of around 7 nm. The second approach was to use the Medipix II detector with its zero-noise readout to assemble a time-sliced series of images of the same area in which each frame from a movie with up to 400 frames had an exposure of only 500 electrons. In the third approach, we simply used a much thicker carbon support film to increase the physical strength and conductivity of the support. Surprisingly, the first two methods involving dose fractionation in space or time produced only partial improvements in contrast whereas the third approach produced many virtually perfect images, where the absolute contrast predicted from the electron diffraction amplitudes was observed in the images. We conclude that it is possible to obtain consistently almost perfect images of beam-sensitive specimens if they are attached to an appropriately strong and conductive support: however great care is needed in practice and the problem remains of how to best image ice-embedded biological structures in the absence of a strong, conductive support film. (C) 2010 Elsevier B.V. All rights reserved. C1 [McMullan, G.; Faruqi, A. R.; Henderson, R.] MRC Lab Mol Biol, Cambridge CB2 0QH, England. [Glaeser, R. M.] Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA. RP Henderson, R (reprint author), MRC Lab Mol Biol, Hills Road, Cambridge CB2 0QH, England. EM rh15@mrc-lmb.cam.ac.uk FU Medical Research Council, UK; US Department of Energy [DE-AC02-05CH11231] FX We thank Shaoxia Chen for help with detector installation and electron microscope operation. This work was supported by funding from the Medical Research Council, UK and by the US Department of Energy under Contract DE-AC02-05CH11231, neither of whom influenced the design nor interpretation of the experiments. RMG prepared all the specimens and devised appropriate electron-optical conditions. RMG and RH carried out the electron microscopy. GM and RH carried out the data analysis. ARF installed the Medipix detector and developed it as a tool for electron microscopy. NR 35 TC 30 Z9 30 U1 2 U2 17 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0304-3991 J9 ULTRAMICROSCOPY JI Ultramicroscopy PD JAN PY 2011 VL 111 IS 2 BP 90 EP 100 DI 10.1016/j.ultramic.2010.10.010 PG 11 WC Microscopy SC Microscopy GA 710YF UT WOS:000286552200002 PM 21185452 ER PT B AU Rugh, JP Bennion, K Brooker, A Langewisch, J Smith, K Meyer, J AF Rugh, J. P. Bennion, K. Brooker, A. Langewisch, J. Smith, K. Meyer, J. GP IMechE TI PHEV/EV integrated vehicle thermal management - development of a KULI model to assess combined cooling loops SO VEHICLE THERMAL MANAGEMENT SYSTEMS CONFERENCE AND EXHIBITION (VTMS 10) LA English DT Proceedings Paper CT Conference on Vehicle Thermal Management Systems (VTMS) CY MAY 15-19, 2011 CL Gaydon, ENGLAND SP Inst Mech Engineers, Automobile Div, Inst Mech Engineers, Combust Engines & Fuels Grp, SAE Int AB Electric drive vehicles (EDVs) must incorporate thermal management systems for powertrain-related subsystems, including the power electronics, electric motors, and energy storage system (ESS) as well as the passenger compartment. Multiple independent heating and cooling loops reduce the effectiveness of fuel-saving control strategies, increase weight and volume, and reduce all-electric range. Building on the National Renewable Energy Laboratory's (NREL's) extensive experience, integrated thermal management concepts in an overall vehicle context are being investigated. The initial results of the air conditioning (A/C), passenger compartment, and power electronics KULI models of an electric vehicle (EV) are described. Various concepts for combining the systems will be assessed and the performance compared to a baseline system. C1 [Rugh, J. P.; Bennion, K.; Brooker, A.; Langewisch, J.; Smith, K.] Natl Renewable Energy Lab, Golden, CO 80401 USA. [Meyer, J.] Visteon, Grove City, OH USA. RP Rugh, JP (reprint author), Natl Renewable Energy Lab, Golden, CO 80401 USA. FU Vehicle Technologies Program of the U. S. Department of Energy's Office of Energy Efficiency and Renewable Energy FX The authors gratefully acknowledge the support for this work provided by Lee Slezak, David Anderson, Susan Rogers, David Howell, and Patrick Davis in the Vehicle Technologies Program of the U. S. Department of Energy's Office of Energy Efficiency and Renewable Energy. NR 13 TC 1 Z9 1 U1 0 U2 3 PU WOODHEAD PUBL LTD PI CAMBRIDGE PA ABINGTON HALL ABINGTON, CAMBRIDGE CB1 6AH, CAMBS, ENGLAND BN 978-1-78063-048-9; 978-0-85709-172-7 PY 2011 BP 649 EP 660 PG 12 WC Engineering, Mechanical; Transportation Science & Technology SC Engineering; Transportation GA BB2XH UT WOS:000342453400056 ER PT J AU Piccone, ME Segundo, FDS Kramer, E Rodriguez, LL de los Santos, T AF Piccone, Maria E. Segundo, Fayna Diaz-San Kramer, Edward Rodriguez, Luis L. de los Santos, Teresa TI Introduction of tag epitopes in the inter-AUG region of foot and mouth disease virus: Effect on the L protein SO VIRUS RESEARCH LA English DT Article DE Foot-and-mouth disease; Viral translation; Leader protein ID TRANSLATION INITIATION SITES; LEADER PROTEINASE; PICORNAVIRUS IRESES; A VIRUS; RNA; GENE; CELLS; IDENTIFICATION; PURIFICATION; PARAMETERS AB Foot-and-mouth disease virus (FMDV) initiates translation from two in-frame AUG codons producing two forms of the leader (L) proteinase, Lab (starting at the first AUG) and Lb (starting at second AUG). In a previous study, we have demonstrated that a cDNA-derived mutant FMDV (A24-L1123) containing a 57-nucleotide transposon (tn) insertion between the two AUG initiation codons (inter-AUG region) was completely attenuated in cattle, suggesting that this region is involved in viral pathogenesis. To investigate the potential role of the Lab protein in attenuation, we have introduced two epitope tags (Flag: DYKDDDK and HA: YPYDVPDYA) or a small tetracysteine motif (tc: CCGPCC) into the pA24-L1123 infectious DNA clone. Mutant viruses with a small plaque phenotype similar to the parental A24-L1123 were recovered after transfection of constructs encoding the Flag tag and the tc motif. However, expression of the Flag- or tc-tagged Lab protein was abolished or greatly diminished in these viruses. Interestingly, the A24-L1123/Flag virus acquired an extra base in the inter-AUG region that resulted in new AUG codons in-frame with the second AUG, and produced a larger Lb protein. This N terminal extension of the Lb protein in mutant A24-L1123/Flag did not affect virus viability or L functions in cell culture. (C) 2010 Elsevier B.V. All rights reserved. C1 [Piccone, Maria E.; Segundo, Fayna Diaz-San; Kramer, Edward; Rodriguez, Luis L.; de los Santos, Teresa] ARS, Plum Isl Anim Dis Ctr, USDA, Greenport, NY 11944 USA. [Piccone, Maria E.] Univ Connecticut, Dept Pathobiol & Vet Sci, Storrs, CT USA. [Segundo, Fayna Diaz-San] PIADC Res Program, Oak Ridge Inst Sci & Educ, Oak Ridge, TN USA. RP Piccone, ME (reprint author), ARS, Plum Isl Anim Dis Ctr, USDA, POB 848, Greenport, NY 11944 USA. EM maria.piccone@ars.usda.gov NR 44 TC 9 Z9 13 U1 1 U2 3 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0168-1702 J9 VIRUS RES JI Virus Res. PD JAN PY 2011 VL 155 IS 1 BP 91 EP 97 DI 10.1016/j.virusres.2010.09.004 PG 7 WC Virology SC Virology GA 716YV UT WOS:000287010300013 PM 20849893 ER PT B AU Greenbaum, E Evans, BR AF Greenbaum, Elias Evans, Barbara R. BE Dagnelie, G TI Synthetic Chromophores and Neural Stimulation of the Visual System SO VISUAL PROSTHETICS: PHYSIOLOGY, BIOENGINEERING, REHABILITATION LA English DT Article; Book Chapter ID PHOTOSYNTHETIC REACTION CENTERS; OPTICAL CONTROL; PHOTOSYSTEM-I; GREEN-ALGAE; MAMMALIAN-CELLS; EXCITABLE CELLS; REMOTE-CONTROL; ION CHANNELS; DRAGON FISH; LIGHT AB This chapter presents an overview of optical stimulation of neural cells by synthetic chromophores and their potential use in the field of artificial sight. The chromophores and techniques that are discussed include azo chromophores, photo release of caged neurotransmitters, pore blockers and photoisomerization, the channelrhodopsins, melanopsin, and the Photosystem I reaction center of green plants. C1 [Greenbaum, Elias; Evans, Barbara R.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. RP Greenbaum, E (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. EM greenbaum@ornl.gov; evansb@ornl.gov NR 42 TC 1 Z9 1 U1 0 U2 0 PU SPRINGER PI NEW YORK PA 233 SPRING STREET, NEW YORK, NY 10013, UNITED STATES BN 978-1-4419-0753-0 PY 2011 BP 193 EP 206 DI 10.1007/978-1-4419-0754-7_10 D2 10.1007/978-1-4419-0754-7 PG 14 WC Engineering, Biomedical; Neurosciences; Ophthalmology SC Engineering; Neurosciences & Neurology; Ophthalmology GA BTZ08 UT WOS:000288483800010 ER PT J AU Marra, JE Palmer, RA AF Marra, John E. Palmer, Ronald A. BE Letcher, TM Vallero, DA TI Radioactive Waste Management SO WASTE: A HANDBOOK FOR MANAGEMENT LA English DT Article; Book Chapter C1 [Marra, John E.] Savannah River Natl Lab, Aiken, SC 29802 USA. [Palmer, Ronald A.] Mississippi State Univ, Inst Clean Energy Technol, Starkville, MS 39762 USA. RP Marra, JE (reprint author), Savannah River Natl Lab, Aiken, SC 29802 USA. NR 13 TC 1 Z9 1 U1 0 U2 0 PU ELSEVIER ACADEMIC PRESS INC PI SAN DIEGO PA 525 B STREET, SUITE 1900, SAN DIEGO, CA 92101-4495 USA BN 978-0-12-381476-0 PY 2011 BP 101 EP 108 DI 10.1016/B978-0-12-381475-3.10007-5 PG 8 WC Engineering, Environmental SC Engineering GA BET35 UT WOS:000318016300009 ER PT J AU Levenson, M Ewing, R AF Levenson, Milt Ewing, Rod GP Natl Res Council TI Waste Forms Technology and Performance FINAL REPORT Executive Summary SO WASTE FORMS TECHNOLOGY AND PERFORMANCE: FINAL REPORT LA English DT Editorial Material; Book Chapter C1 [Levenson, Milt] Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. [Levenson, Milt] Argonne Natl Lab, Argonne, IL 60439 USA. [Levenson, Milt] Elect Power Res Inst, Palo Alto, CA USA. [Levenson, Milt] Bechtel, San Francisco, CA USA. [Levenson, Milt] Amer Nucl Soc, La Grange Pk, IL USA. [Levenson, Milt] Amer Inst Chem Engineers, New York, NY USA. [Levenson, Milt] Natl Acad Studies, Washington, DC USA. [Ewing, Rod] Univ Michigan, Dept Nucl Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Radiol Sci, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Mat Sci & Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ New Mexico, Dept Earth & Planetary Sci, Albuquerque, NM 87131 USA. [Ewing, Rod] Amer Assoc Advancement Sci, Washington, DC USA. [Ewing, Rod] Geol Soc Amer, New York, NY USA. [Ewing, Rod] Mineral Soc Amer, New York, NY USA. [Ewing, Rod] Int Union Mat Res Soc, McKeesport, PA USA. RP Levenson, M (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. NR 0 TC 0 Z9 0 U1 0 U2 0 PU NATL ACADEMIES PRESS PI WASHINGTON PA 2101 CONSTITUTION AVE, WASHINGTON, DC 20418 USA BN 978-0-309-18733-6 PY 2011 BP 1 EP 2 PG 2 WC Energy & Fuels; Nuclear Science & Technology SC Energy & Fuels; Nuclear Science & Technology GA BC7IS UT WOS:000354900900002 ER PT J AU Levenson, M Ewing, R AF Levenson, Milt Ewing, Rod GP Natl Res Council TI Waste Forms Technology and Performance FINAL REPORT Findings and Recommendations SO WASTE FORMS TECHNOLOGY AND PERFORMANCE: FINAL REPORT LA English DT Article; Book Chapter C1 [Levenson, Milt] Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. [Levenson, Milt] Argonne Natl Lab, Argonne, IL 60439 USA. [Levenson, Milt] Elect Power Res Inst, Palo Alto, CA USA. [Levenson, Milt] Bechtel, San Francisco, CA USA. [Levenson, Milt] Amer Nucl Soc, La Grange Pk, IL USA. [Levenson, Milt] Amer Inst Chem Engineers, New York, NY USA. [Levenson, Milt] Natl Acad Studies, Washington, DC USA. [Ewing, Rod] Univ Michigan, Dept Nucl Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Radiol Sci, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Mat Sci & Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ New Mexico, Dept Earth & Planetary Sci, Albuquerque, NM 87131 USA. [Ewing, Rod] Amer Assoc Advancement Sci, Washington, DC USA. [Ewing, Rod] Geol Soc Amer, New York, NY USA. [Ewing, Rod] Mineral Soc Amer, New York, NY USA. [Ewing, Rod] Int Union Mat Res Soc, McKeesport, PA USA. RP Levenson, M (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. NR 0 TC 0 Z9 0 U1 1 U2 1 PU NATL ACADEMIES PRESS PI WASHINGTON PA 2101 CONSTITUTION AVE, WASHINGTON, DC 20418 USA BN 978-0-309-18733-6 PY 2011 BP 3 EP 14 PG 12 WC Energy & Fuels; Nuclear Science & Technology SC Energy & Fuels; Nuclear Science & Technology GA BC7IS UT WOS:000354900900003 ER PT J AU Levenson, M Ewing, R AF Levenson, Milt Ewing, Rod GP Natl Res Council TI Waste Forms Technology and Performance FINAL REPORT Preface SO WASTE FORMS TECHNOLOGY AND PERFORMANCE: FINAL REPORT LA English DT Editorial Material; Book Chapter C1 [Levenson, Milt] Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. [Levenson, Milt] Argonne Natl Lab, Argonne, IL 60439 USA. [Levenson, Milt] Elect Power Res Inst, Palo Alto, CA USA. [Levenson, Milt] Bechtel, San Francisco, CA USA. [Levenson, Milt] Amer Nucl Soc, La Grange Pk, IL USA. [Levenson, Milt] Amer Inst Chem Engineers, New York, NY USA. [Levenson, Milt] Natl Acad Studies, Washington, DC USA. [Ewing, Rod] Univ Michigan, Dept Nucl Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Radiol Sci, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Mat Sci & Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ New Mexico, Dept Earth & Planetary Sci, Albuquerque, NM 87131 USA. [Ewing, Rod] Amer Assoc Advancement Sci, Washington, DC USA. [Ewing, Rod] Geol Soc Amer, New York, NY USA. [Ewing, Rod] Mineral Soc Amer, New York, NY USA. [Ewing, Rod] Int Union Mat Res Soc, McKeesport, PA USA. RP Levenson, M (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. NR 0 TC 0 Z9 0 U1 0 U2 0 PU NATL ACADEMIES PRESS PI WASHINGTON PA 2101 CONSTITUTION AVE, WASHINGTON, DC 20418 USA BN 978-0-309-18733-6 PY 2011 BP VII EP VIII PG 2 WC Energy & Fuels; Nuclear Science & Technology SC Energy & Fuels; Nuclear Science & Technology GA BC7IS UT WOS:000354900900001 ER PT J AU Levenson, M Ewing, R AF Levenson, Milt Ewing, Rod GP Natl Res Council TI Waste Forms Technology and Performance FINAL REPORT Background and Study Task SO WASTE FORMS TECHNOLOGY AND PERFORMANCE: FINAL REPORT LA English DT Editorial Material; Book Chapter C1 [Levenson, Milt] Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. [Levenson, Milt] Argonne Natl Lab, Argonne, IL 60439 USA. [Levenson, Milt] Elect Power Res Inst, Palo Alto, CA USA. [Levenson, Milt] Bechtel, San Francisco, CA USA. [Levenson, Milt] Amer Nucl Soc, La Grange Pk, IL USA. [Levenson, Milt] Amer Inst Chem Engineers, New York, NY USA. [Levenson, Milt] Natl Acad Studies, Washington, DC USA. [Ewing, Rod] Univ Michigan, Dept Nucl Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Radiol Sci, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Mat Sci & Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ New Mexico, Dept Earth & Planetary Sci, Albuquerque, NM 87131 USA. [Ewing, Rod] Amer Assoc Advancement Sci, Washington, DC USA. [Ewing, Rod] Geol Soc Amer, New York, NY USA. [Ewing, Rod] Mineral Soc Amer, New York, NY USA. [Ewing, Rod] Int Union Mat Res Soc, McKeesport, PA USA. RP Levenson, M (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. NR 23 TC 0 Z9 0 U1 1 U2 1 PU NATL ACADEMIES PRESS PI WASHINGTON PA 2101 CONSTITUTION AVE, WASHINGTON, DC 20418 USA BN 978-0-309-18733-6 PY 2011 BP 15 EP 28 PG 14 WC Energy & Fuels; Nuclear Science & Technology SC Energy & Fuels; Nuclear Science & Technology GA BC7IS UT WOS:000354900900004 ER PT J AU Levenson, M Ewing, R AF Levenson, Milt Ewing, Rod GP Natl Res Council TI Waste Forms SO WASTE FORMS TECHNOLOGY AND PERFORMANCE: FINAL REPORT LA English DT Article; Book Chapter ID IRON PHOSPHATE-GLASSES; LEVEL NUCLEAR-WASTE; DECAY-INDUCED AMORPHIZATION; SEPARATED PLUTONIUM STOCKS; MURATAITE-BASED CERAMICS; RICH TITANATE CERAMICS; X-RAY PHOTOELECTRON; RADIOACTIVE-WASTES; WEAPONS PLUTONIUM; TOXIC METALS C1 [Levenson, Milt] Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. [Levenson, Milt] Argonne Natl Lab, Argonne, IL 60439 USA. [Levenson, Milt] Elect Power Res Inst, Palo Alto, CA USA. [Levenson, Milt] Bechtel, San Francisco, CA USA. [Levenson, Milt] Amer Nucl Soc, La Grange Pk, IL USA. [Levenson, Milt] Amer Inst Chem Engineers, New York, NY USA. [Levenson, Milt] Natl Acad Studies, Washington, DC USA. [Ewing, Rod] Univ Michigan, Dept Nucl Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Radiol Sci, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Mat Sci & Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ New Mexico, Dept Earth & Planetary Sci, Albuquerque, NM 87131 USA. [Ewing, Rod] Amer Assoc Advancement Sci, Washington, DC USA. [Ewing, Rod] Geol Soc Amer, New York, NY USA. [Ewing, Rod] Mineral Soc Amer, New York, NY USA. [Ewing, Rod] Int Union Mat Res Soc, McKeesport, PA USA. RP Levenson, M (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. NR 298 TC 0 Z9 0 U1 1 U2 4 PU NATL ACADEMIES PRESS PI WASHINGTON PA 2101 CONSTITUTION AVE, WASHINGTON, DC 20418 USA BN 978-0-309-18733-6 PY 2011 BP 29 EP 85 PG 57 WC Energy & Fuels; Nuclear Science & Technology SC Energy & Fuels; Nuclear Science & Technology GA BC7IS UT WOS:000354900900005 ER PT J AU Levenson, M Ewing, R AF Levenson, Milt Ewing, Rod GP Natl Res Council TI Waste Processing and Waste Form Production SO WASTE FORMS TECHNOLOGY AND PERFORMANCE: FINAL REPORT LA English DT Article; Book Chapter ID NUCLEAR-WASTE; IMMOBILIZATION; DISSOLUTION; FILMS C1 [Levenson, Milt] Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. [Levenson, Milt] Argonne Natl Lab, Argonne, IL 60439 USA. [Levenson, Milt] Elect Power Res Inst, Palo Alto, CA USA. [Levenson, Milt] Bechtel, San Francisco, CA USA. [Levenson, Milt] Amer Nucl Soc, La Grange Pk, IL USA. [Levenson, Milt] Amer Inst Chem Engineers, New York, NY USA. [Levenson, Milt] Natl Acad Studies, Washington, DC USA. [Ewing, Rod] Univ Michigan, Dept Nucl Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Radiol Sci, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Mat Sci & Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ New Mexico, Dept Earth & Planetary Sci, Albuquerque, NM 87131 USA. [Ewing, Rod] Amer Assoc Advancement Sci, Washington, DC USA. [Ewing, Rod] Geol Soc Amer, New York, NY USA. [Ewing, Rod] Mineral Soc Amer, New York, NY USA. [Ewing, Rod] Int Union Mat Res Soc, McKeesport, PA USA. RP Levenson, M (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. NR 60 TC 0 Z9 0 U1 0 U2 0 PU NATL ACADEMIES PRESS PI WASHINGTON PA 2101 CONSTITUTION AVE, WASHINGTON, DC 20418 USA BN 978-0-309-18733-6 PY 2011 BP 87 EP 118 PG 32 WC Energy & Fuels; Nuclear Science & Technology SC Energy & Fuels; Nuclear Science & Technology GA BC7IS UT WOS:000354900900006 ER PT J AU Levenson, M Ewing, R AF Levenson, Milt Ewing, Rod GP Natl Res Council TI Waste Form Testing SO WASTE FORMS TECHNOLOGY AND PERFORMANCE: FINAL REPORT LA English DT Article; Book Chapter ID KINETIC CONSTRAINTS; GLASS DISSOLUTION; AQUEOUS-SOLUTIONS; REACTION-RATES; RATE LAW; MINERALS C1 [Levenson, Milt] Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. [Levenson, Milt] Argonne Natl Lab, Argonne, IL 60439 USA. [Levenson, Milt] Elect Power Res Inst, Palo Alto, CA USA. [Levenson, Milt] Bechtel, San Francisco, CA USA. [Levenson, Milt] Amer Nucl Soc, La Grange Pk, IL USA. [Levenson, Milt] Amer Inst Chem Engineers, New York, NY USA. [Levenson, Milt] Natl Acad Studies, Washington, DC USA. [Ewing, Rod] Univ Michigan, Dept Nucl Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Radiol Sci, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Mat Sci & Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ New Mexico, Dept Earth & Planetary Sci, Albuquerque, NM 87131 USA. [Ewing, Rod] Amer Assoc Advancement Sci, Washington, DC USA. [Ewing, Rod] Geol Soc Amer, New York, NY USA. [Ewing, Rod] Mineral Soc Amer, New York, NY USA. [Ewing, Rod] Int Union Mat Res Soc, McKeesport, PA USA. RP Levenson, M (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. NR 58 TC 0 Z9 0 U1 0 U2 0 PU NATL ACADEMIES PRESS PI WASHINGTON PA 2101 CONSTITUTION AVE, WASHINGTON, DC 20418 USA BN 978-0-309-18733-6 PY 2011 BP 119 EP 152 PG 34 WC Energy & Fuels; Nuclear Science & Technology SC Energy & Fuels; Nuclear Science & Technology GA BC7IS UT WOS:000354900900007 ER PT J AU Levenson, M Ewing, R AF Levenson, Milt Ewing, Rod GP Natl Res Council TI Waste Forms and Disposal Environments SO WASTE FORMS TECHNOLOGY AND PERFORMANCE: FINAL REPORT LA English DT Article; Book Chapter ID NUCLEAR-FUEL; PLUTONIUM; WATER; FIELD; REPOSITORY; MIGRATION; TRANSPORT; BEHAVIOR; FATE; SOIL C1 [Levenson, Milt] Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. [Levenson, Milt] Argonne Natl Lab, Argonne, IL 60439 USA. [Levenson, Milt] Elect Power Res Inst, Palo Alto, CA USA. [Levenson, Milt] Bechtel, San Francisco, CA USA. [Levenson, Milt] Amer Nucl Soc, La Grange Pk, IL USA. [Levenson, Milt] Amer Inst Chem Engineers, New York, NY USA. [Levenson, Milt] Natl Acad Studies, Washington, DC USA. [Ewing, Rod] Univ Michigan, Dept Nucl Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Radiol Sci, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Mat Sci & Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ New Mexico, Dept Earth & Planetary Sci, Albuquerque, NM 87131 USA. [Ewing, Rod] Amer Assoc Advancement Sci, Washington, DC USA. [Ewing, Rod] Geol Soc Amer, New York, NY USA. [Ewing, Rod] Mineral Soc Amer, New York, NY USA. [Ewing, Rod] Int Union Mat Res Soc, McKeesport, PA USA. RP Levenson, M (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. NR 35 TC 0 Z9 0 U1 0 U2 0 PU NATL ACADEMIES PRESS PI WASHINGTON PA 2101 CONSTITUTION AVE, WASHINGTON, DC 20418 USA BN 978-0-309-18733-6 PY 2011 BP 153 EP 174 PG 22 WC Energy & Fuels; Nuclear Science & Technology SC Energy & Fuels; Nuclear Science & Technology GA BC7IS UT WOS:000354900900008 ER PT J AU Levenson, M Ewing, R AF Levenson, Milt Ewing, Rod GP Natl Res Council TI Waste Form Performance in Disposal Systems SO WASTE FORMS TECHNOLOGY AND PERFORMANCE: FINAL REPORT LA English DT Article; Book Chapter C1 [Levenson, Milt] Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. [Levenson, Milt] Argonne Natl Lab, Argonne, IL 60439 USA. [Levenson, Milt] Elect Power Res Inst, Palo Alto, CA USA. [Levenson, Milt] Bechtel, San Francisco, CA USA. [Levenson, Milt] Amer Nucl Soc, La Grange Pk, IL USA. [Levenson, Milt] Amer Inst Chem Engineers, New York, NY USA. [Levenson, Milt] Natl Acad Studies, Washington, DC USA. [Ewing, Rod] Univ Michigan, Dept Nucl Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Radiol Sci, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Mat Sci & Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ New Mexico, Dept Earth & Planetary Sci, Albuquerque, NM 87131 USA. [Ewing, Rod] Amer Assoc Advancement Sci, Washington, DC USA. [Ewing, Rod] Geol Soc Amer, New York, NY USA. [Ewing, Rod] Mineral Soc Amer, New York, NY USA. [Ewing, Rod] Int Union Mat Res Soc, McKeesport, PA USA. RP Levenson, M (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. NR 36 TC 0 Z9 0 U1 0 U2 0 PU NATL ACADEMIES PRESS PI WASHINGTON PA 2101 CONSTITUTION AVE, WASHINGTON, DC 20418 USA BN 978-0-309-18733-6 PY 2011 BP 175 EP 195 PG 21 WC Energy & Fuels; Nuclear Science & Technology SC Energy & Fuels; Nuclear Science & Technology GA BC7IS UT WOS:000354900900009 ER PT J AU Levenson, M Ewing, R AF Levenson, Milt Ewing, Rod GP Natl Res Council TI Legal and Regulatory Factors for Waste Form Performance SO WASTE FORMS TECHNOLOGY AND PERFORMANCE: FINAL REPORT LA English DT Article; Book Chapter C1 [Levenson, Milt] Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. [Levenson, Milt] Argonne Natl Lab, Argonne, IL 60439 USA. [Levenson, Milt] Elect Power Res Inst, Palo Alto, CA USA. [Levenson, Milt] Bechtel, San Francisco, CA USA. [Levenson, Milt] Amer Nucl Soc, La Grange Pk, IL USA. [Levenson, Milt] Amer Inst Chem Engineers, New York, NY USA. [Levenson, Milt] Natl Acad Studies, Washington, DC USA. [Ewing, Rod] Univ Michigan, Dept Nucl Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Radiol Sci, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Mat Sci & Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ New Mexico, Dept Earth & Planetary Sci, Albuquerque, NM 87131 USA. [Ewing, Rod] Amer Assoc Advancement Sci, Washington, DC USA. [Ewing, Rod] Geol Soc Amer, New York, NY USA. [Ewing, Rod] Mineral Soc Amer, New York, NY USA. [Ewing, Rod] Int Union Mat Res Soc, McKeesport, PA USA. RP Levenson, M (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. NR 23 TC 0 Z9 0 U1 0 U2 0 PU NATL ACADEMIES PRESS PI WASHINGTON PA 2101 CONSTITUTION AVE, WASHINGTON, DC 20418 USA BN 978-0-309-18733-6 PY 2011 BP 197 EP 217 PG 21 WC Energy & Fuels; Nuclear Science & Technology SC Energy & Fuels; Nuclear Science & Technology GA BC7IS UT WOS:000354900900010 ER PT J AU Levenson, M Ewing, R AF Levenson, Milt Ewing, Rod GP Natl Res Council TI Possible Opportunities in Waste Form Science and Technology SO WASTE FORMS TECHNOLOGY AND PERFORMANCE: FINAL REPORT LA English DT Article; Book Chapter ID MESOPOROUS MOLECULAR-SIEVES; SELF-ASSEMBLED MONOLAYERS; NUCLEAR-WASTE; FULLERENE TOPOLOGIES; SILICATE MELTS; IMMOBILIZATION; DESIGN; SIMULATIONS; FRAMEWORKS; GLASSES C1 [Levenson, Milt] Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. [Levenson, Milt] Argonne Natl Lab, Argonne, IL 60439 USA. [Levenson, Milt] Elect Power Res Inst, Palo Alto, CA USA. [Levenson, Milt] Bechtel, San Francisco, CA USA. [Levenson, Milt] Amer Nucl Soc, La Grange Pk, IL USA. [Levenson, Milt] Amer Inst Chem Engineers, New York, NY USA. [Levenson, Milt] Natl Acad Studies, Washington, DC USA. [Ewing, Rod] Univ Michigan, Dept Nucl Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Radiol Sci, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ Michigan, Dept Mat Sci & Engn, Geol Sci, Ann Arbor, MI 48109 USA. [Ewing, Rod] Univ New Mexico, Dept Earth & Planetary Sci, Albuquerque, NM 87131 USA. [Ewing, Rod] Amer Assoc Advancement Sci, Washington, DC USA. [Ewing, Rod] Geol Soc Amer, New York, NY USA. [Ewing, Rod] Mineral Soc Amer, New York, NY USA. [Ewing, Rod] Int Union Mat Res Soc, McKeesport, PA USA. RP Levenson, M (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. NR 67 TC 0 Z9 0 U1 0 U2 0 PU NATL ACADEMIES PRESS PI WASHINGTON PA 2101 CONSTITUTION AVE, WASHINGTON, DC 20418 USA BN 978-0-309-18733-6 PY 2011 BP 219 EP 240 PG 22 WC Energy & Fuels; Nuclear Science & Technology SC Energy & Fuels; Nuclear Science & Technology GA BC7IS UT WOS:000354900900011 ER PT J AU Wakelin, S Page, D Dillon, P Pavelic, P Abell, GCJ Gregg, AL Brodie, E DeSantis, TZ Goldfarb, KC Anderson, G AF Wakelin, S. Page, D. Dillon, P. Pavelic, P. Abell, G. C. J. Gregg, A. L. Brodie, E. DeSantis, T. Z. Goldfarb, K. C. Anderson, G. TI Microbial community structure of a slow sand filter schmutzdecke: a phylogenetic snapshot based on rRNA sequence analysis SO WATER SCIENCE AND TECHNOLOGY-WATER SUPPLY LA English DT Article DE Archaea; bacteria; Eukarya; PhyloChip; schmutzdecke; slow sand filter; SSU rRNA AB Slow sand filters (SSF) are widely used to treat water for potable use. The process is dependent on the activities of complex microbial communities in the biofilm (schmutzdecke) layer. In this study, we generated a comprehensive view of three-domain microbiological complexity within a model SSF. DNA was analysed using a high-density microarray (PhyloChip) and rRNA library analysis. The Eukaryotic community was dominated by Cercozoa (Ebridd-type protists); these are likely to be involved in predation of other organisms in the schmutzdecke layer, thus proving opportunity for successional development. Ciliate protozoa, green microalgae, stramenopiles, amoeboid protozoa and fungi in the Phylum Ascomycota and the deep-branching Chytridiomycota were also detected. The Archaeal community was dominated by Euryarchaeota, and most were Halobacteriales. These organisms may contribute to filter function through removal of dissolved organic carbon, a primary treatment goal of these filters. Given that the Eukaryotic and Archaeal communities were examined using clone libraries, the expected richness of taxa present is expected to be greater than detected here and dependent on sampling effort (library size). The bacterial community was rich in taxa (21 Phyla) but was not dominated by any phylogenetic group. The successful function of SSF's relies on interactions between taxa (e. g. grazing of Cercozoa protists on bacteria), and removal of dissolved organic matter from the influent. Understanding the taxa and functions in these systems will aid in monitoring and managing SSF for optimal water quality. C1 [Wakelin, S.] AgResearch Ltd, Lincoln Res Ctr, Christchurch 8140, New Zealand. [Wakelin, S.; Page, D.; Dillon, P.; Pavelic, P.; Gregg, A. L.] CSIRO, Water Hlth Country Flagship, Glen Osmond, SA, Australia. [Pavelic, P.] Int Crops Res Inst Semi Arid Trop, IWMI, Patancheru 502324, Andhra Pradesh, India. [Abell, G. C. J.] CSIRO, Marine & Atmospher Sci, Hobart, Tas 7001, Australia. [Brodie, E.; DeSantis, T. Z.; Goldfarb, K. C.; Anderson, G.] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Dept Ecol, Div Earth Sci, Berkeley, CA 94720 USA. RP Wakelin, S (reprint author), AgResearch Ltd, Lincoln Res Ctr, Private Bag 4749, Christchurch 8140, New Zealand. EM steve.wakelin@agresearch.co.nz RI Page, Declan/F-2566-2011; Abell, Guy/A-1767-2010; Brodie, Eoin/A-7853-2008; OI Page, Declan/0000-0002-4902-3911; Brodie, Eoin/0000-0002-8453-8435; Wakelin, Steve/0000-0002-1167-8699 FU CSIRO Water for a Healthy Country Programme; ACIAR [LWR/2003/006]; CSIRO Julius Award; US DOE Berkeley labs FX The authors thank Mr Antoine Chassange, Ms Karren Barry and Dr Hartmut Hollander for help with experimental work at the Urrbrae wetlands. This work was supported by CSIRO Water for a Healthy Country Programme and ACIAR project LWR/2003/006 'Enhancing production in the Philippines by sustainable use of shallow groundwater'. S.A. Wakelin was supported by a CSIRO Julius Award (funding for travel to US DOE Berkeley labs for PhyloChip analysis). NR 44 TC 8 Z9 8 U1 1 U2 13 PU IWA PUBLISHING PI LONDON PA ALLIANCE HOUSE, 12 CAXTON ST, LONDON SW1H0QS, ENGLAND SN 1606-9749 J9 WATER SCI TECH-W SUP JI Water Sci. Technol.-Water Supply PY 2011 VL 11 IS 4 BP 426 EP 436 DI 10.2166/ws.2011.063 PG 11 WC Engineering, Environmental; Environmental Sciences; Water Resources SC Engineering; Environmental Sciences & Ecology; Water Resources GA V33UH UT WOS:000209043200006 ER PT S AU Moody, DI Brumby, SP Myers, KL Pawley, NH AF Moody, Daniela I. Brumby, Steven P. Myers, Kary L. Pawley, Norma H. BE Papadakis, M VanDeVille, D Goyal, VK TI Radio Frequency (RF) Transient Classification using Sparse Representations over Learned Dictionaries SO WAVELETS AND SPARSITY XIV SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on Wavelets and Sparsity XIV CY AUG 21-24, 2011 CL San Diego, CA SP SPIE DE RF classification; sparse representation; dictionary learning; K-SVD algorithm; Hebbian learning algorithm ID PURSUIT AB Automatic classification of transitory or pulsed radio frequency (RF) signals is of particular interest in persistent surveillance and remote sensing applications. Such transients are often acquired in noisy, cluttered environments, and may be characterized by complex or unknown analytical models, making feature extraction and classification difficult. We propose a fast, adaptive classification approach based on non-analytical dictionaries learned from data. We compare two dictionary learning methods from the image analysis literature, the K-SVD algorithm and Hebbian learning, and extend them for use with RF data. Both methods allow us to learn discriminative RF dictionaries directly from data without relying on analytical constraints or additional knowledge about the expected signal characteristics. We then use a pursuit search over the learned dictionaries to generate sparse classification features in order to identify time windows that contain a target pulse. In this paper we compare the two dictionary learning methods and discuss how their performance changes as a function of dictionary training parameters. We demonstrate that learned dictionary techniques are suitable for pulsed RF analysis and present results with varying background clutter and noise levels. C1 [Moody, Daniela I.; Brumby, Steven P.; Myers, Kary L.; Pawley, Norma H.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Moody, DI (reprint author), Los Alamos Natl Lab, POB 1663, Los Alamos, NM 87545 USA. EM brumby@lanl.gov OI Moody, Daniela/0000-0002-4452-8208; Myers, Kary/0000-0002-5642-959X NR 11 TC 0 Z9 0 U1 1 U2 4 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-81948-748-3 J9 PROC SPIE PY 2011 VL 8138 AR 81381S DI 10.1117/12.898894 PG 8 WC Engineering, Electrical & Electronic; Optics; Physics, Applied SC Engineering; Optics; Physics GA BXX99 UT WOS:000297583100047 ER PT S AU Qiao, HA Anheier, NC Musgraves, JD Richardson, K Hewak, DW AF Qiao, Hong A. Anheier, Norm C. Musgraves, J. David Richardson, Kathleen Hewak, Daniel W. BE Tustison, RW TI Measurement of Chalcogenide Glass Optical Dispersion Using a Mid-Infrared Prism Coupler SO WINDOW AND DOME TECHNOLOGIES AND MATERIALS XII SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on Window and Dome Technologies and Materials XII CY APR 27-28, 2011 CL Orlando, FL SP SPIE DE mid-infrared; optical index; prism coupling; chalcogenide glass; dn/dT ID INDEX AB Physical properties of chalcogenide glass, including broadband infrared transparency, high refractive index, low glass transition temperature, and nonlinear properties, make them attractive candidates for advanced mid-infrared (3 to 12 mu m) optical designs. Efforts focused at developing new chalcogenide glass formulations and processing methods require rapid quantitative evaluation of their optical constants to guide the materials research. However, characterization of important optical parameters such as optical dispersion and thermal coefficient remains a slow and costly process, generally with limited accuracy. The recent development of a prism coupler at the Pacific Northwest National Laboratory (PNNL) now enables rapid, high precision measurement of refractive indices at discrete wavelengths from the visible to the mid-infrared. Optical dispersion data of several chalcogenide glass families were collected using this method. Variations in the optical dispersion were correlated to glass composition and compared against measurements using other methods. While this work has been focused on facilitating chalcogenide glass synthesis, mid-infrared prism coupler analysis has broader applications to other mid-infrared optical material development efforts, including oxide glasses and crystalline materials. C1 [Qiao, Hong A.; Anheier, Norm C.] Pacific NW Natl Lab, Richland, WA 99352 USA. RP Qiao, HA (reprint author), Pacific NW Natl Lab, Richland, WA 99352 USA. EM amy.qiao@pnnl.gov RI Richardson, Kathleen/A-6012-2011 NR 16 TC 2 Z9 2 U1 0 U2 3 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-81948-590-8 J9 PROC SPIE PY 2011 VL 8016 AR 80160F DI 10.1117/12.884320 PG 10 WC Optics; Physics, Condensed Matter SC Optics; Physics GA BWW03 UT WOS:000295118800013 ER PT J AU Lichty, MG Janowitz, IL Rempel, DM AF Lichty, Monica G. Janowitz, Ira L. Rempel, David M. TI Ergonomic evaluation of ten single-channel pipettes SO WORK-A JOURNAL OF PREVENTION ASSESSMENT & REHABILITATION LA English DT Article DE Laboratory; usability testing; tool design; biotechnology ID HAND AB Repetitive pipetting is a task that is associated with work-related musculoskeletal disorders of the hand and arm. Objective: The purpose of this study was to evaluate the usability and ergonomic performance of commercially available pipettes as determined by user ratings and objective measurements. Participants: Participants were laboratory technicians and scientists at the Lawrence Berkeley National Laboratory with experience performing pipetting tasks. Methods: Twenty-one experienced pipette users completed a standardized pipetting task with 5 manual and 5 electronic pipettes. After using each pipette, the user rated it for attributes of comfort and usability. Results: Although no single pipette was rated significantly better than all of the others for every attribute tested, some significant differences were found between pipettes. The Rainin Pipet-Lite received the highest overall quality score among manual pipettes, while the Thermo Scientific Finnpipette Novus was the top-ranked electronic pipette. Features correlated with greater hand and arm comfort were lower tip ejection force, lower blowout force, and pipette balance in the hand. Conclusions: The findings, when considered with participant comments, provide insights into desirable pipette features and emphasize the value of user testing and the importance of the interactions between task, workplace layout, and pipette design. C1 [Lichty, Monica G.] Battelle Ctr Human Performance & Safety, Seattle, WA 98109 USA. [Janowitz, Ira L.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Environm Hlth & Safety, Berkeley, CA 94720 USA. [Rempel, David M.] Univ Calif Berkeley, Ergon Program, Berkeley, CA 94720 USA. [Rempel, David M.] Univ Calif San Francisco, Div Occupat & Environm Med, Richmond, CA USA. RP Lichty, MG (reprint author), Battelle Ctr Human Performance & Safety, 1100 Dexter Ave N,Ste 400, Seattle, WA 98109 USA. EM lichtym@battelle.org RI Rempel, David/E-8424-2013 NR 6 TC 3 Z9 3 U1 0 U2 6 PU IOS PRESS PI AMSTERDAM PA NIEUWE HEMWEG 6B, 1013 BG AMSTERDAM, NETHERLANDS SN 1051-9815 J9 WORK JI Work PY 2011 VL 39 IS 2 SI SI BP 177 EP 185 DI 10.3233/WOR-2011-1164 PG 9 WC Public, Environmental & Occupational Health SC Public, Environmental & Occupational Health GA 789PD UT WOS:000292526900011 PM 21673445 ER PT J AU Rempel, P Janowitz, I Alexandre, M Lee, DL Rempel, D AF Rempel, Paul Janowitz, Ira Alexandre, Melanie Lee, David L. Rempel, David TI The effect of two alternative arm supports on shoulder and upper back muscle loading during pipetting SO WORK-A JOURNAL OF PREVENTION ASSESSMENT & REHABILITATION LA English DT Article DE Electromyography (EMG); musculoskeletal disorders (MSD); ergonomics ID FOREARM SUPPORT; DISCOMFORT; DISORDERS; WORK AB Objective: Pipetting involves static upper arm positions with the pipette held away from the body for sustained periods of time, putting increased musculoskeletal load on the shoulder and upper back. This study explores the effect of using two alternative arm supports while pipetting on muscle loading in the shoulder/neck region. Participants: 15 experienced pipette users participated in this study. Methods: In a repeated-measures design, participants performed simulated pipetting in a laboratory setting under three arm support conditions: (1) a gel pad on the work surface, (2) a freely-moving counter-balanced forearm support, and (3) no support (control). Surface electromyography (EMG) of the anterior deltoid and upper trapezius muscles were recorded, as well as productivity and subjective usability. Results: Both arm support conditions resulted in significantly lower mean muscle activity of the anterior deltoid and upper trapezius muscles (p < 0.001) and significantly higher subjective comfort ratings (p < 0.001) compared to the control condition. The freely moving forearm support resulted in significantly lower peak muscle activity in the anterior deltoid compared to the control condition (p < 0.001). Productivity was not affected by the arm supports. These findings suggest that arm support may be beneficial in reducing muscle loading and improving comfort in the shoulder and upper back during pipetting. Future studies are needed to measure the impact of these arm supports in the workplace. C1 [Rempel, Paul] Univ Calif Berkeley, Berkeley, CA 94720 USA. [Alexandre, Melanie] Univ Calif Berkeley, Lawrence Berkeley Lab, Joint Genome Inst, Berkeley, CA 94720 USA. [Lee, David L.; Rempel, David] Univ Calif San Francisco, Dept Med, San Francisco, CA USA. RP Rempel, D (reprint author), Univ Calif San Francisco, Dept Med, 1301 S 46th St,UC RFS Bldg 163, Richmond, CA 94804 USA. EM david.rempel@ucsf.edu RI Rempel, David/E-8424-2013 NR 9 TC 5 Z9 5 U1 0 U2 2 PU IOS PRESS PI AMSTERDAM PA NIEUWE HEMWEG 6B, 1013 BG AMSTERDAM, NETHERLANDS SN 1051-9815 J9 WORK JI Work PY 2011 VL 39 IS 2 SI SI BP 195 EP 200 DI 10.3233/WOR-2011-1166 PG 6 WC Public, Environmental & Occupational Health SC Public, Environmental & Occupational Health GA 789PD UT WOS:000292526900013 PM 21673447 ER PT S AU Clementson, J AF Clementson, Joel BE Dunn, J Klisnick, A TI Spectral modeling of Fe XVII pumped by a free-electron x-ray laser SO X-RAY LASERS AND COHERENT X-RAY SOURCES: DEVELOPMENT AND APPLICATIONS IX SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on X-ray Lasers and Coherent X-ray Sources - Development and Applications IX CY AUG 23-25, 2011 CL San Diego, CA SP SPIE DE atomic spectra; x-ray pumping; laboratory astrophysics; free-electron laser ID BEAM ION-TRAP; LABORATORY MEASUREMENTS; ATOMIC DATA; RELATIVE INTENSITY; IRON; LINES; PHOTOIONIZATION; TRANSITIONS; SOLAR; RECOMBINATION AB The atomic structure and x-ray pumping of neonlike Fe XVII have been calculated and modeled under free-electron laser excitation conditions using the Flexible Atomic Code. Specifically, pumping of the (2p(3/2)3s(1/2))(2,1), (2p(1/2)3s(1/2))(1), (2p(3/2)3d(5/2))(1), and (2p(1/2)3d(3/2))(1) levels that connect with the ground state (2s(2)2p(6))(0) by the so-called M2, 3G, 3F, 3D, and 3C transitions have been studied. In addition, the spectrum of sodiumlike Fe XVI has been modeled to account for possible line coincidences with the neonlike spectrum. The calculations include oscillator strengths, radiative lifetimes, autoionization rates, non-resonant photoionization cross sections, and line emissivities. C1 Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. RP Clementson, J (reprint author), Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. EM clementson@llnl.gov NR 50 TC 0 Z9 0 U1 0 U2 1 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-8750-6 J9 PROC SPIE PY 2011 VL 8140 AR 81401C DI 10.1117/12.896956 PG 11 WC Engineering, Electrical & Electronic; Optics; Physics, Applied SC Engineering; Optics; Physics GA BXY65 UT WOS:000297632800034 ER PT S AU Dunn, J Shepherd, R Graf, A Steel, A Park, J Moon, SJ Lee, RW Audebert, P Levy, A Gauthier, M Fuchs, J Fritz, DM Cammarata, M Milathianaki, D Lee, HJ Nagler, B Fourment, C Deneuville, F Williams, G Fajardo, M Gaudin, J Vinko, S Ciricosta, O Wark, J Chung, HK AF Dunn, J. Shepherd, R. Graf, A. Steel, A. Park, J. Moon, S. J. Lee, R. W. Audebert, P. Levy, A. Gauthier, M. Fuchs, J. Fritz, D. M. Cammarata, M. Milathianaki, D. Lee, H. J. Nagler, B. Fourment, C. Deneuville, F. Williams, G. Fajardo, M. Gaudin, J. Vinko, S. Ciricosta, O. Wark, J. Chung, H. K. BE Dunn, J Klisnick, A TI Spectroscopic studies of hard x-ray free-electron laser-heated foils at 10(16) Wcm(-2) irradiances SO X-RAY LASERS AND COHERENT X-RAY SOURCES: DEVELOPMENT AND APPLICATIONS IX SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on X-ray Lasers and Coherent X-ray Sources - Development and Applications IX CY AUG 23-25, 2011 CL San Diego, CA SP SPIE DE Free electron laser; hard x-ray; x-ray crystal spectroscopy; warm dense matter; high energy density; plasmas ID OPERATION; SPECTRUM AB We report a recent experiment where the first hard x-ray beam line, X-ray Pump Probe (XPP) instrument using the SLAC National Accelerator Laboratory's Linac Coherent Light Source (LCLS) free electron laser, was used to heat thin foils to high energy densities similar to 10(7) J/cm(3). An intense 9 keV, 60 fs (FWHM) duration beam with energy of 2 - 4 mJ at the XPP beam line was focused using beryllium lenses to an irradiance approaching 10(16) Wcm(-2). Targets of 0.5 - 3.5 mu m thick foils of Ag and Cu were studied using a suite of diagnostics including Fourier Domain Interferometry, energy calorimetry and grating and crystal spectrometers. The experimental details and spectroscopic results from the campaign will be described. Preliminary results indicate that the target is heated relatively uniformly to a temperature lower than 20 eV. C1 [Dunn, J.; Shepherd, R.; Graf, A.; Steel, A.; Park, J.; Moon, S. J.; Lee, R. W.] Lawrence Livermore Natl Lab, Livermore, CA 94551 USA. RP Dunn, J (reprint author), Lawrence Livermore Natl Lab, Livermore, CA 94551 USA. RI Vinko, Sam/I-4845-2013; gauthier, Maxence/K-2578-2014; Fajardo, Marta/A-4608-2012 OI Vinko, Sam/0000-0003-1016-0975; gauthier, Maxence/0000-0001-6608-9325; Fajardo, Marta/0000-0003-2133-2365 NR 10 TC 1 Z9 1 U1 1 U2 6 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-8750-6 J9 PROC SPIE PY 2011 VL 8140 AR 81400O DI 10.1117/12.895264 PG 8 WC Engineering, Electrical & Electronic; Optics; Physics, Applied SC Engineering; Optics; Physics GA BXY65 UT WOS:000297632800018 ER PT S AU Nilsen, J Rohringer, N AF Nilsen, Joseph Rohringer, Nina BE Dunn, J Klisnick, A TI Using the X-FEL to photo-pump X-ray laser transitions in He-like Ne SO X-RAY LASERS AND COHERENT X-RAY SOURCES: DEVELOPMENT AND APPLICATIONS IX SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on X-ray Lasers and Coherent X-ray Sources - Development and Applications IX CY AUG 23-25, 2011 CL San Diego, CA SP SPIE DE X-ray laser; X-FEL; Photo-pumping AB Nearly four decades ago H-like and He-like resonantly photo-pumped laser schemes were proposed for producing X-ray lasers. However, demonstrating these schemes in the laboratory has proved to be elusive because of the difficulty of finding a strong resonant pump line. With the advent of the X-ray free electron laser (X-FEL) at the SLAC Linac Coherent Light Source (LCLS) we now have a tunable X-ray laser source that can be used to replace the pump line in previously proposed laser schemes and allow researchers to study the physics and feasibility of resonantly photo-pumped laser schemes. In this paper we use the X-FEL at 1174 eV to photo-pump the singly excited 1s2p state of He-like Ne to the doubly excited 2p3p state and model gain on the 2p3p-2p2s transition at 175 eV and the 2p3p-1s3p transition at 1017 eV. One motivation for studying this scheme is to explore possible quenching of the gain due to strong non-linear coupling effects from the intense X-FEL beam. We compare this scheme with photo-pumping the He-like Ne ground state to the 1s3p singly excited state followed by lasing on the 3p-2s and 3d-2p transitions at 158 and 151 eV. Experiments are being planned at LCLS to study these laser processes and coherent quantum effects. C1 [Nilsen, Joseph] Lawrence Livermore Natl Lab, Livermore, CA 94551 USA. RP Nilsen, J (reprint author), Lawrence Livermore Natl Lab, Livermore, CA 94551 USA. RI Rohringer, Nina/N-3238-2014 OI Rohringer, Nina/0000-0001-7905-3567 NR 5 TC 0 Z9 0 U1 0 U2 5 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-8750-6 J9 PROC SPIE PY 2011 VL 8140 AR 814003 DI 10.1117/12.893589 PG 8 WC Engineering, Electrical & Electronic; Optics; Physics, Applied SC Engineering; Optics; Physics GA BXY65 UT WOS:000297632800003 ER PT S AU de Teramond, GF Brodsky, SJ AF de Teramond, Guy F. Brodsky, Stanley J. GP IOP TI Light-Front Quantization and AdS/QCD: An overview SO XIV MEXICAN SCHOOL ON PARTICLES AND FIELDS SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 14th Mexican School on Particles and Fields (MSPF) CY NOV 04-12, 2010 CL Morelia, MEXICO SP Mexican Phys Soc, Div Particles & Fields, Estado Michoacan, Consejo Estatal Ciencia & Tecnologico (COECyT), Univ Michoacana San Nicolas Hidalgo, Univ Sonora, Univ Nacl Autonoma Mexico, Univ Guanajuato, Univ Sinaloa, Centro Investigaciones Estudios Avanzados IPN (CINVESTAV), Consejo Nacl Ciencia & Tecnologia (CONACyT), Acad Mexicana Ciencias, Red Nacl Fisica Altas Energias ID GAUGE/GRAVITY DUALITY; FORM-FACTORS; SPIN FIELDS; QCD; HOLOGRAPHY; SPECTROSCOPY; SUPERGRAVITY; THRESHOLD; MASSLESS; BARYONS AB We give an overview of the light front holographic approach to strongly coupled QCD, whereby a confining gauge theory quantized on the light front is mapped to a higher-dimensional anti de Sitter (AdS) space incorporating the AdS/CFT correspondence as a useful guide. One can start from the Hamiltonian equation of motion in physical space time by studying the off-shell dynamics of the bound state wavefunctions as a function of the invariant mass of the constituents. To a first semiclassical approximation, where quantum loops and quark masses are not included, this leads to a light-front Hamiltonian equation which describes the bound state dynamics of light hadrons in terms of an invariant impact variable zeta, which measures the separation of the partons within the hadron at equal light-front time. Alternatively, one can start from the gravity side by studying the propagation of hadronic modes in a fixed effective gravitational background which encodes salient properties of the QCD dual theory, such as the ultraviolet conformal limit at the AdS boundary at z -> 0,as well as modifications of the background geometry in the large z infrared region to describe confinement. In the semi classical approximation both approaches are equivalent. This allows us to identify the holographic variable z in AdS space with the impact variable zeta. Light-front holography also allows a precise mapping of transition amplitudes from AdS to physical space-time. In contrast with the usual AdS/QCD framework, in light front holography the internal structure of hadrons is explicitly introduced and the angular momentum of the constituents plays a key role. C1 [de Teramond, Guy F.] Univ Costa Rica, San Jose, Costa Rica. [Brodsky, Stanley J.] Stanford Univ, SLAC, Natl Accelerator Lab, Stanford, CA 94305 USA. RP de Teramond, GF (reprint author), Univ Costa Rica, San Jose, Costa Rica. FU Department of Energy [DE-AC02-76SF00515]; [SLAC-PUB-14393] FX This research was supported by the Department of Energy contract DE-AC02-76SF00515. yySLAC-PUB-14393. NR 60 TC 6 Z9 6 U1 0 U2 1 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2011 VL 287 AR 012007 DI 10.1088/1742-6596/287/1/012007 PG 12 WC Physics, Particles & Fields SC Physics GA BDC24 UT WOS:000312559800007 ER PT S AU Hernandez-Garcia, C Napsuciale, M AF Hernandez-Garcia, C. Napsuciale, M. GP IOP TI Prospects for an Accelerator Program in Mexico Focused on Photon Science SO XIV MEXICAN SCHOOL ON PARTICLES AND FIELDS SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 14th Mexican School on Particles and Fields (MSPF) CY NOV 04-12, 2010 CL Morelia, MEXICO SP Mexican Phys Soc, Div Particles & Fields, Estado Michoacan, Consejo Estatal Ciencia & Tecnologico (COECyT), Univ Michoacana San Nicolas Hidalgo, Univ Sonora, Univ Nacl Autonoma Mexico, Univ Guanajuato, Univ Sinaloa, Centro Investigaciones Estudios Avanzados IPN (CINVESTAV), Consejo Nacl Ciencia & Tecnologia (CONACyT), Acad Mexicana Ciencias, Red Nacl Fisica Altas Energias AB Recent interest in developing Mexican expertise in Accelerator Science and Technology has resulted in several actions by the Division of Particles and Fields in Mexico, and by the electron accelerator community in the United States. We report on the very encouraging activities over the past two years which were aimed at developing a light source as the most effective starting point. We present a number of possibilities to initiate and grow an accelerator science program and present a path that would lead to building, commissioning and operating a third or fourth generation light source in Mexico. C1 [Hernandez-Garcia, C.] Jefferson Lab, 12000 Jefferson Ave,Suite 19, Newport News, VA 23606 USA. [Napsuciale, M.] Univ Guanajuato Campus Leon, Dept Fis, Guanajuato 37150, Mexico. RP Hernandez-Garcia, C (reprint author), Jefferson Lab, 12000 Jefferson Ave,Suite 19, Newport News, VA 23606 USA. EM chgarcia@jlab.org NR 2 TC 0 Z9 0 U1 0 U2 0 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2011 VL 287 AR 012008 DI 10.1088/1742-6596/287/1/012008 PG 8 WC Physics, Particles & Fields SC Physics GA BDC24 UT WOS:000312559800008 ER PT S AU Escher, JE Burke, JT Dietrich, FS Scielzo, ND Ressler, JJ AF Escher, J. E. Burke, J. T. Dietrich, F. S. Scielzo, N. D. Ressler, J. J. BE BarronPalos, L Bijker, R TI Nuclear reactions for astrophysics and other applications SO XXXIV SYMPOSIUM ON NUCLEAR PHYSICS SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 34th Symposium on Nuclear Physics CY JAN 04-07, 2011 CL Cocoyoc, MEXICO SP Instituto de Ciencias Nucleares, UNAM, Instituto de Fisica, UNAM, Instituto Nacional de Investigaciones Nucleares, Division de Fisica Nuclear de la SMF, Centro Latinoamericano de Fisica ID FISSION CROSS-SECTIONS; NEUTRON; ELEMENTS; PROGRESS; STARS AB Cross sections for compound-nuclear reactions are required for many applications. The surrogate nuclear reactions method provides an indirect approach for determining cross sections for reactions on unstable isotopes, which are difficult or impossible to measure otherwise. Current implementations of the method provide useful cross sections for (n,f) reactions, but need to be improved upon for applications to capture reactions. C1 [Escher, J. E.; Burke, J. T.; Dietrich, F. S.; Scielzo, N. D.; Ressler, J. J.] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. RP Escher, JE (reprint author), Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. EM escher1@llnl.gov RI Escher, Jutta/E-1965-2013; Burke, Jason/I-4580-2012 NR 29 TC 0 Z9 0 U1 0 U2 4 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2011 VL 322 AR 012006 DI 10.1088/1742-6596/322/1/012006 PG 8 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA BYJ87 UT WOS:000299059000006 ER PT J AU Bokov, AA Rodriguez, BJ Zhao, XH Ko, JH Jesse, S Long, XF Qu, WG Kim, TH Budai, JD Morozovska, AN Kojima, S Tan, XL Kalinin, SV Ye, ZG AF Bokov, Alexei A. Rodriguez, Brian J. Zhao, Xiaohui Ko, Jae-Hyeon Jesse, Stephen Long, Xifa Qu, Weiguo Kim, Tae Hyun Budai, John D. Morozovska, Anna N. Kojima, Seiji Tan, Xiaoli Kalinin, Sergei V. Ye, Zuo-Guang TI Compositional disorder, polar nanoregions and dipole dynamics in Pb(Mg1/3Nb2/3)O-3-based relaxor ferroelectrics SO ZEITSCHRIFT FUR KRISTALLOGRAPHIE LA English DT Article DE Relaxor ferroelectrics; Compositional disorder; Lead magnesium niobate; Dielectric relaxation; Domain structure ID SINGLE-CRYSTALS; PBMG1/3NB2/3O3; PEROVSKITES; TRANSITION; CLUSTERS; DOMAINS; OXIDES; ORDER AB The complex structure of relaxor ferroelectrics comprises polar nanoregions (PNRs) which appear upon cooling below the Burns temperature and quenched compositional (chemical) disorder. The relation between the polar nanostructure and compositionally ordered regions (CORs) often observed in relaxors has been the subject of extensive theoretical investigations; however, the experimental data, especially concerning Pb(B'B-1/3 ''(2/3))O-3-type complex perovskite relaxors, are rather limited. In this paper, we analyse and discuss the results of our recent investigations of the morphology of CORs and the dynamics of PNRs in Pb(Mg1/3Nb2/3)O-3-based solid solutions in which the degree of compositional disorder was varied by means of changing the composition and/or by means of high-temperature annealing. The samples were characterised using X-ray diffraction, transmission electron microscopy, piezoresponse force microscopy, Brillouin light scattering, dielectric spectroscopy, as well as by measuring pyroelectric effect and ferroelectric hysteresis loops. No influence of the size of CORs on the PNRs relaxation in the ergodic relaxor phase is found. Instead, the CORs size influences significantly the diffuseness of the transition from the field-induced ferroelectric phase to the ergodic relaxor state. The results are interpreted in the framework of a model suggesting the coexistence of static and dynamic PNRs in the ergodic relaxor phase. C1 [Bokov, Alexei A.; Long, Xifa; Ye, Zuo-Guang] Simon Fraser Univ, Dept Chem, Burnaby, BC V5A 1A6, Canada. [Bokov, Alexei A.; Long, Xifa; Ye, Zuo-Guang] Simon Fraser Univ, LABS 4D, Burnaby, BC V5A 1A6, Canada. [Rodriguez, Brian J.] Univ Coll Dublin, Dublin 4, Ireland. [Zhao, Xiaohui; Qu, Weiguo; Tan, Xiaoli] Iowa State Univ, Dept Mat Sci & Engn, Ames, IA 50011 USA. [Ko, Jae-Hyeon; Kim, Tae Hyun] Hallym Univ, Dept Phys, Chunchon 200702, Gangwondo, South Korea. [Jesse, Stephen; Budai, John D.; Kalinin, Sergei V.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. [Morozovska, Anna N.] Natl Acad Sci Ukraine, V Lashkaryov Inst Semicond Phys, UA-03028 Kiev, Ukraine. [Kojima, Seiji] Univ Tsukuba, Inst Mat Sci, Tsukuba, Ibaraki 3058573, Japan. RP Bokov, AA (reprint author), Simon Fraser Univ, Dept Chem, Burnaby, BC V5A 1A6, Canada. EM abokov@sfu.ca; zye@sfu.ca RI Bokov, Alexei/C-6924-2008; Kalinin, Sergei/I-9096-2012; Tan, Xiaoli/C-3376-2013; Qu, Weiguo/D-9875-2013; Rodriguez, Brian/A-6253-2009; Jesse, Stephen/D-3975-2016; Kojima, Seiji/L-9006-2016; Budai, John/R-9276-2016 OI Bokov, Alexei/0000-0003-1126-3378; Kalinin, Sergei/0000-0001-5354-6152; Tan, Xiaoli/0000-0002-4182-663X; Qu, Weiguo/0000-0001-7925-7340; Rodriguez, Brian/0000-0001-9419-2717; Jesse, Stephen/0000-0002-1168-8483; Kojima, Seiji/0000-0003-1933-9269; Budai, John/0000-0002-7444-1306 FU U.S. Office of Naval Research; Natural Science & Engineering Research Council of Canada; National Science Foundation [DMR-0346819]; National Research Foundation of Korea [2010-0010497]; Division of Scientific User Facilities, US DOE, through the Center for Nanophase Materials Sciences at ORNL FX The work was supported by the U.S. Office of Naval Research and the Natural Science & Engineering Research Council of Canada (AAB, ZGY), National Science Foundation (DMR-0346819, XT), the National Research Foundation of Korea (2010-0010497, JHK) and Division of Scientific User Facilities, US DOE, through the Center for Nanophase Materials Sciences at ORNL (BJR, SJ, SVK). NR 39 TC 19 Z9 19 U1 2 U2 48 PU WALTER DE GRUYTER GMBH PI BERLIN PA GENTHINER STRASSE 13, D-10785 BERLIN, GERMANY SN 0044-2968 J9 Z KRISTALLOGR JI Z. Kristall. PY 2011 VL 226 IS 2 BP 99 EP 107 DI 10.1524/zkri.2011.1299 PG 9 WC Crystallography SC Crystallography GA 731JS UT WOS:000288102900002 ER PT J AU Thimmaiah, S Han, MK Miller, GJ AF Thimmaiah, Srinivasa Han, Mi-Kyung Miller, Gordon J. TI Zn-13(CrxAl1-x)(27) (x=0.34-0.37): a new intermetallic phase containing icosahedra as building units SO ZEITSCHRIFT FUR KRISTALLOGRAPHIE LA English DT Article DE Intermetallic compound; I3 cluster; Single crystal structure analysis; Powder diffraction analysis; X-ray diffraction; Complex ID CR-ZN SYSTEM; QUASI-CRYSTAL; THERMODYNAMIC ASSESSMENT; METALLIC PHASE; APPROXIMANT; ALLOY; 460-DEGREES-C; MAGNETISM; AL-4(CR; CLUSTER AB The title compounds Zn-13(CrxAl1 (-) (x))(27) (x = 0.34-0.37) were obtained by melting the pure elements at 923 K, and followed by a heat treatment at 723 K in a tantalum container. According to single crystal structural analysis, the title compounds crystallize in the rhombohedral system, adopting a new structure type (R (3) over barm, a = 7.5971(8), c = 36.816(6), for crystal I). Single crystal X-ray structural analysis reveals a statistical mixing of Cr/Al in their crystallographic positions. Single crystal and powder X-ray diffraction as well as energy dispersive X-ray analyses suggested the title phase to have a narrow homogeneity range. The substructure of Zn-13(CrxAl1 (-) (x))(27) shows close resemblance with the Mn3Al10 structure type. A bonding analysis, through crystal orbital Hamiltonian populations (COHPs), of "Cr9Al18Zn13" as a representative composition indicated that both homo- and heteronuclear interactions are important for the stability of this new phase. C1 [Thimmaiah, Srinivasa] Iowa State Univ, Ames, IA 50011 USA. US DOE, Ames Lab, Ames, IA 50011 USA. RP Thimmaiah, S (reprint author), Iowa State Univ, Ames, IA 50011 USA. EM srini@iastate.edu RI Thimmaiah, Srinivasa/H-1049-2012 FU Iowa State University [DE-AC02-07CH11358]; Materials Sciences Division of the Office of Basic Energy Sciences of the U.S. Department of Energy FX This work was carried out at the Ames Laboratory, which is operated for the U.S. Department of Energy by Iowa State University under Contract No. DE-AC02-07CH11358. This work was supported by the Materials Sciences Division of the Office of Basic Energy Sciences of the U.S. Department of Energy. NR 55 TC 3 Z9 3 U1 0 U2 0 PU WALTER DE GRUYTER GMBH PI BERLIN PA GENTHINER STRASSE 13, D-10785 BERLIN, GERMANY SN 0044-2968 J9 Z KRISTALLOGR JI Z. Kristall. PY 2011 VL 226 IS 7 BP 557 EP 567 DI 10.1524/zkri.2011.1376 PG 11 WC Crystallography SC Crystallography GA 789PE UT WOS:000292527000003 ER PT J AU Lake, CH Toby, BH AF Lake, Charles H. Toby, Brian H. TI Recent developments targeting new and experienced users in EXPGUI, an open source Rietveld analysis interface SO ZEITSCHRIFT FUR KRISTALLOGRAPHIE LA English DT Article DE EXPGUI; Rietveld refinement; GSAS ID POWDER DIFFRACTION; CHEMICAL REASONABLENESS; CIF APPLICATIONS; CRYSTALLOGRAPHY; PDCIF AB EXPGUI is an open source interface that supplements the GSAS program package, which together provide a powerful set of tools for structure refinement, especially Rietveld Analysis. The combined GSAS-EXPGUI packages are freely distributed and are ideal for both new and experienced users. The latest EXPGUI version includes many new intuitive features including methods of implementing distance restraints, fixing coordinates, advanced searching and viewing of interatomic distances and angles as well as improved user friendliness and much more. C1 [Lake, Charles H.] Indiana Univ Penn, Indiana, PA 15705 USA. [Toby, Brian H.] Argonne Natl Lab, Adv Photon Source, Argonne, IL 60439 USA. RP Lake, CH (reprint author), Indiana Univ Penn, Indiana, PA 15705 USA. EM lake@iup.edu RI Toby, Brian/F-3176-2013 OI Toby, Brian/0000-0001-8793-8285 FU U.S. DOE [DE-AC02-06CH11357]; APS FX Use of the Advanced Photon Source, an Office of Science User Facility operated for the U.S. Department of Energy (DOE) Office of Science by Argonne National Laboratory, was supported by the U.S. DOE under Contract No. DE-AC02-06CH11357. The APS Visitor Program provided partial funds to support CHL's sabbatical at the APS. NR 18 TC 0 Z9 0 U1 1 U2 18 PU OLDENBOURG VERLAG PI MUNICH PA LEKTORAT MINT, POSTFACH 80 13 60, D-81613 MUNICH, GERMANY SN 0044-2968 J9 Z KRISTALLOGR JI Z. Kristall. PY 2011 VL 226 IS 12 BP 892 EP 897 DI 10.1524/zkri.2011.1378 PG 6 WC Crystallography SC Crystallography GA 866ER UT WOS:000298363800005 ER PT J AU Tian, P Billinge, SJL AF Tian, Peng Billinge, Simon J. L. TI Testing different methods for estimating uncertainties on Rietveld refined parameters using SrRietveld SO ZEITSCHRIFT FUR KRISTALLOGRAPHIE LA English DT Article DE Rietveld refinement; Error estimation; Monte Carlo; Subset sampling ID NEUTRON POWDER-DIFFRACTION; PROFILE AB The advent of fast computing allows more computationally expensive, though possibly more accurate, approaches for estimating uncertainties on Rietveld refined parameters. Here we compare three such methods, using two different refinement programs, FullProf and GSAS. This is facilitated by the use of a new Rietveld refinement package, SrRietveld, that provides Python wrappers for FullProf and GSAS. The refined values on the parameters from two different refinement engines match each other very well. The uncertainty estimates determined using the different methods are also consistent, though FullProf and GSAS estimate the parameter uncertainties slightly differently from each other, which is discussed. More importantly, we find that the refined results are very sensitive to the statistical weights used in the least squares equation. Different weights, for example from uncertain or incorrectly propagated random errors on the data, lead to significantly different refined values. This means that uncertainty estimates on refined parameters should be increased when the random errors on the data are not well known, as for example in many cases where area detectors are used, and care should be taken to propagate errors correctly in any data preprocessing such as normalization by a smoothed spectrum. The computationally expensive bootstrap error estimation methods are facilitated by the use of SrRietveld, but are not required in most cases though may be useful in some cases, for example if the random errors on the data are not well known. C1 [Billinge, Simon J. L.] Columbia Univ, Dept Appl Phys & Appl Math, New York, NY 10027 USA. [Tian, Peng] Michigan State Univ, Dept Phys & Astron, E Lansing, MI 48824 USA. [Billinge, Simon J. L.] Brookhaven Natl Lab, Condensed Matter Phys & Mat Sci Dept, Upton, NY 11973 USA. RP Billinge, SJL (reprint author), Columbia Univ, Dept Appl Phys & Appl Math, 500 W 120th St, New York, NY 10027 USA. EM sb2896@columbia.edu FU NSF [DMR-0520547, DMR 0703940]; DOE [W-7405-ENG-36] FX We thank Robert B. Von Dreele and Juan Rodriguez-Carvajal for their helpful discussions. We also thank Thomas Proffen for providing standard data from NPDF that is used in this study. SrRietveld was developed under NSF award DMR-0520547. PT acknowledges support from the NSF through grant DMR 0703940. This work has benefited from the use of NPDF at the Lujan Center at Los Alamos Neutron Science Center, funded by DOE through Contract No. W-7405-ENG-36. NR 16 TC 4 Z9 4 U1 2 U2 9 PU OLDENBOURG VERLAG PI MUNICH PA LEKTORAT MINT, POSTFACH 80 13 60, D-81613 MUNICH, GERMANY SN 0044-2968 J9 Z KRISTALLOGR JI Z. Kristall. PY 2011 VL 226 IS 12 BP 898 EP 904 DI 10.1524/zkri.2011.1421 PG 7 WC Crystallography SC Crystallography GA 866ER UT WOS:000298363800006 ER PT J AU Ge, MH Corbett, JD AF Ge, Ming-Hui Corbett, John D. TI Crystal structure of triytterbium pentastannide, Sn5Yb3 SO ZEITSCHRIFT FUR KRISTALLOGRAPHIE-NEW CRYSTAL STRUCTURES LA English DT Article ID ZINTL PHASE; SOLID-STATE; ANIONS; CLUSTERS; BA3PB5; LA3IN5; TIN AB Sn5Yb3, orthorhombic, Cmcm (no. 63), a = 10.193(2) angstrom, b = 8.168(2) angstrom, c = 10.375(2) angstrom, V = 863.7 angstrom(3), Z = 4, R-gt(F) = 0.032, wR(ref)(F-2) = 0.081, T = 293 K. C1 [Ge, Ming-Hui] Beijing Inst Petrochem Technol, Coll Chem Engn, Beijing 102617, Peoples R China. [Corbett, John D.] Iowa State Univ, Ames Lab, DOE & Dept Chem, Ames, IA 50010 USA. RP Ge, MH (reprint author), Beijing Inst Petrochem Technol, Coll Chem Engn, Beijing 102617, Peoples R China. EM mhge@bipt.edu.en FU DOE by Iowa State University [DE-AC02-07CH11358]; Beijing Institute of Petrochemical Engineering FX This research was supported by the Ames Laboratory operated for DOE by Iowa State University (contract no. DE-AC02-07CH11358) and the fund for Young Scholars from Beijing Institute of Petrochemical Engineering. NR 13 TC 2 Z9 2 U1 2 U2 3 PU OLDENBOURG VERLAG PI MUNICH PA LEKTORAT MINT, POSTFACH 80 13 60, D-81613 MUNICH, GERMANY SN 1433-7266 J9 Z KRIST-NEW CRYST ST JI Z. Krist.-New Cryst. Struct. PY 2011 VL 226 IS 4 BP 445 EP 446 DI 10.1524/ncrs.2011.0199 PG 2 WC Crystallography SC Crystallography GA 882TV UT WOS:000299587700006 ER PT J AU Kasper, T Lucassen, A Jasper, AW Li, WJ Westmoreland, PR Kohse-Hoinghaus, K Yang, B Wang, J Cool, TA Hansen, N AF Kasper, Tina Lucassen, Arnas Jasper, Ahren W. Li, Wenjun Westmoreland, Phillip R. Kohse-Hoeinghaus, Katharina Yang, Bin Wang, Juan Cool, Terrill A. Hansen, Nils TI Identification of Tetrahydrofuran Reaction Pathways in Premixed Flames SO ZEITSCHRIFT FUR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS LA English DT Article DE Combustion Chemistry; Laminar Flames; Molecular Beam Mass Spectrometry; Tetrahydrofuran; Biofuel ID PHOTOIONIZATION MASS-SPECTROMETRY; DIMETHYL ETHER FLAMES; GAS-PHASE OXIDATION; LOW-PRESSURE FLAMES; FUEL-RICH FLAMES; THERMAL-REACTIONS; HIGH-TEMPERATURES; REFLECTED SHOCKS; CYCLIC ETHERS; COMBUSTION CHEMISTRY AB Premixed low-pressure tetrahydrofuran/oxygen/argon flames are investigated by photoionization molecular-beam mass spectrometry using vacuum-ultraviolet synchrotron radiation. For two equivalence ratios (phi = 1.00 and 1.75), mole fractions are measured as a function of distance from the burner for almost 60 intermediates with molar masses ranging from 2 (H(2)) to 88 (C(4)H(6)O(2)), providing a broad database for flame modeling studies. The isomeric composition is resolved by comparisons between experimental photoionization efficiency data and theoretical simulations, based on calculated ionization energies and Franck-Condon factors. Special emphasis is put on the resolution of the first reaction steps in the fuel destruction. The photoionization experiments are complemented by electron-ionization molecular-beam mass-spectrometry measurements that provide data with high mass resolution. For three additional flames with intermediate equivalence ratios (phi = 1.20, 1.40 and 1.60), mole fractions of major species and photoionization efficiency spectra of intermediate species are reported, extending the database for the development of chemical kinetic models. C1 [Kasper, Tina; Jasper, Ahren W.; Hansen, Nils] Sandia Natl Labs, Combust Res Facil, Livermore, CA 94551 USA. [Lucassen, Arnas; Kohse-Hoeinghaus, Katharina] Univ Bielefeld, Dept Chem, D-33615 Bielefeld, Germany. [Li, Wenjun; Westmoreland, Phillip R.] N Carolina State Univ, Dept Chem & Biomol Engn, Raleigh, NC 27695 USA. [Yang, Bin; Wang, Juan; Cool, Terrill A.] Cornell Univ, Sch Appl & Engn Phys, Ithaca, NY 14853 USA. RP Kasper, T (reprint author), Univ Duisburg Essen, Fac Engn, Inst Combust & Gasdynam, Duisburg, Germany. EM tina.kasper@uni-due.de RI Kohse-Hoinghaus, Katharina/A-3867-2012; Hansen, Nils/G-3572-2012; Lucassen, Arnas/G-3803-2013; Yang, Bin/A-7158-2008; Jasper, Ahren/A-5292-2011; Kasper, Tina/A-2975-2017 OI Lucassen, Arnas/0000-0003-2967-2030; Yang, Bin/0000-0001-7333-0017; Kasper, Tina/0000-0003-3993-5316 FU Office of Basic Energy Sciences (BES), U.S. Department of Energy (DOE) [DE-FG02-01ER1518 (TAC), DE-FG02-91ER14192 (PRW)]; DFG [KO 1363/18-3]; MIWF of the state of North Rhine Westphalia, Germany; U.S. DOE, Office of Basic Energy Sciences under the Energy Frontier Research Center for Combustion Science [DE-SC0001198]; NNSA [DE-AC04-94-AL85000]; DOE/BES [DE-AC02-05CH11231] FX We thank Paul Fugazzi and Sarah Ferrell for technical assistance. This work was supported by the Office of Basic Energy Sciences (BES), U.S. Department of Energy (DOE), under grants DE-FG02-01ER1518 (TAC) and DE-FG02-91ER14192 (PRW) and by the DFG under KO 1363/18-3 (KKH). TK is supported by MIWF of the state of North Rhine Westphalia, Germany. NH and BY are supported by the U.S. DOE, Office of Basic Energy Sciences under the Energy Frontier Research Center for Combustion Science (Grant No. DE-SC0001198). Sandia is a multi-program laboratory operated by Sandia Corporation for NNSA under contract DE-AC04-94-AL85000. The Advanced Light Source is supported by DOE/BES under DE-AC02-05CH11231. NR 52 TC 24 Z9 24 U1 7 U2 50 PU OLDENBOURG VERLAG PI MUNICH PA LEKTORAT MINT, POSTFACH 80 13 60, D-81613 MUNICH, GERMANY SN 0942-9352 J9 Z PHYS CHEM JI Z. Phys. Chemie-Int. J. Res. Phys. Chem. Chem. Phys. PY 2011 VL 225 IS 11-12 SI SI BP 1237 EP 1270 DI 10.1524/zpch.2011.0163 PG 34 WC Chemistry, Physical SC Chemistry GA 880GQ UT WOS:000299393700007 ER PT J AU Kappler, C Zador, J Welz, O Fernandes, RX Olzmann, M Taatjes, CA AF Kappler, Claudia Zador, Judit Welz, Oliver Fernandes, Ravi X. Olzmann, Matthias Taatjes, Craig A. TI Competing Channels in the Propene plus OH Reaction: Experiment and Validated Modeling over a Broad Temperature and Pressure Range SO ZEITSCHRIFT FUR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS LA English DT Article DE Reaction Kinetics; Combustion Chemistry; Unimolecular Dissociation; Laser Induced Fluorescence; High Pressure ID HYDROXYL RADICAL REACTIONS; KINETIC-DATA EVALUATION; REACTION-PATH DYNAMICS; GAS-PHASE KINETICS; RATE CONSTANTS; ATMOSPHERIC CHEMISTRY; LASER FLUORESCENCE; IUPAC SUBCOMMITTEE; REACTION-RATES; C3H6 AB Although the propene + OH reaction has been in the center of interest of numerous experimental and theoretical studies, rate coefficients have never been determined experimentally between similar to 600 and similar to 750 K, where the reaction is governed by the complex interaction of addition, back-dissociation and abstraction. In this work OH time-profiles are measured in two independent laboratories over a wide temperature region (200-950 K) and are analyzed incorporating recent theoretical results. The datasets are consistent both with each other and with the calculated rate coefficients. We present a simplified set of reactions validated over a broad temperature and pressure range, that can be used in smaller combustion models for propene + OH. In addition, the experimentally observed kinetic isotope effect for the abstraction is rationalized using ab initio calculations and variational transition-state theory. We recommend the following approximate description of the OH + C(3)H(6) reaction: C(3)H(6) + OH reversible arrow C(3)H(6)OH (R1a,R-1a) C(3)H(6) + OH -> C(3)H(5) + H(2)O (R1b) k(1a)(200 K <= T <= 950 K; 1 bar <= P) = 1.45 x 10(-11) (T/K)(-0.18)e(460 K/T) cm(3) molecule(-1) s(-1) k(-1a)(200 K <= T <= 950 K; 1 bar <= P) = 5.74 x 10(12) e(-12690 K/T) s(-1) k(1b)(200 K <= T <= 950 K) = 1.63 x 10(-18) (T/K)(2.36)e(-725 K/T) cm(3) molecule(-1) s(-1) C1 [Zador, Judit; Welz, Oliver; Fernandes, Ravi X.; Taatjes, Craig A.] Sandia Natl Labs, Combust Res Facil, Livermore, CA 94551 USA. [Kappler, Claudia; Olzmann, Matthias] Karlsruher Inst Technol KIT, Inst Phys Chem, D-76131 Karlsruhe, Germany. RP Zador, J (reprint author), Sandia Natl Labs, Combust Res Facil, Mail Stop 9055, Livermore, CA 94551 USA. EM jzador@sandia.gov; matthias.olzmann@kit.edu RI Welz, Oliver/C-1165-2013; Olzmann, Matthias/A-3718-2017 OI Welz, Oliver/0000-0003-1978-2412; Olzmann, Matthias/0000-0002-9932-4261 FU Division of Chemical Sciences, Geosciences, and Biosciences, the Office of Basic Energy Sciences, the U.S. Department of Energy; Sandia National Laboratories; Lockheed Martin Company; United States Department of Energy [DE-AC04-94AL85000]; Cluster of Excellence "Tailor-Made Fuels from Biomass"; Excellence Initiative of the German federal and state governments to promote science and research at German universities; Argonne-Sandia Consortium on High-Pressure Combustion Chemistry [2009 ANL 59044]; Deutsche Forschungsgemeinschaft [SFB 606] FX Work at Sandia by R. X. F., J. Z., and C. A. T. was supported by the Division of Chemical Sciences, Geosciences, and Biosciences, the Office of Basic Energy Sciences, the U.S. Department of Energy and by the Laboratory Directed Research and Development program at Sandia National Laboratories, a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy, under contract DE-AC04-94AL85000. R. X. F. also acknowledges support at RWTH Aachen from Cluster of Excellence "Tailor-Made Fuels from Biomass", which is funded by the Excellence Initiative of the German federal and state governments to promote science and research at German universities. O. W. was supported as part of the Argonne-Sandia Consortium on High-Pressure Combustion Chemistry (FWP# 2009 ANL 59044). C. K. and M. O. thank the Deutsche Forschungsgemeinschaft for financial support within SFB 606, "Non-stationary Combustion: Transport Phenomena, Chemical Reactions, Technical Systems". NR 44 TC 8 Z9 8 U1 0 U2 33 PU OLDENBOURG VERLAG PI MUNICH PA LEKTORAT MINT, POSTFACH 80 13 60, D-81613 MUNICH, GERMANY SN 0942-9352 J9 Z PHYS CHEM JI Z. Phys. Chemie-Int. J. Res. Phys. Chem. Chem. Phys. PY 2011 VL 225 IS 11-12 SI SI BP 1271 EP 1291 DI 10.1524/zpch.2011.0165 PG 21 WC Chemistry, Physical SC Chemistry GA 880GQ UT WOS:000299393700008 ER PT J AU Yang, B Westbrook, CK Cool, TA Hansen, N Kohse-Hoinghaus, K AF Yang, Bin Westbrook, Charles K. Cool, Terrill A. Hansen, Nils Kohse-Hoeinghaus, Katharina TI The Effect of Carbon-Carbon Double Bonds on the Combustion Chemistry of Small Fatty Acid Esters SO ZEITSCHRIFT FUR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS LA English DT Article DE Unsaturated Esters; C4H6O2; Combustion; Molecular Beam Mass Spectrometry; Modeling ID PHOTOIONIZATION CROSS-SECTIONS; LOW-PRESSURE FLAMES; METHYL BUTANOATE; PREMIXED FLAMES; BIODIESEL FUELS; MASS-SPECTROMETRY; ETHYL PROPANOATE; DIESEL-ENGINES; ALKYL ESTERS; DECOMPOSITION AB Environmentally friendly biodiesel is a mixture of saturated and unsaturated methyl (or ethyl) esters of long-chain fatty acids. To experimentally examine the effect of C=C double bonds on the combustion chemistry of fatty acid esters, low-pressure premixed laminar flames of four small esters have been studied using flame-sampling molecular-beam mass spectrometry. Mole fraction profiles of reactants, products, and well-identified stable and reactive combustion intermediates in flames of the saturated species methyl propanoate (CH3CH3COOCH3) and its isomer ethyl acetate (CH3COOCH2CH3) have been compared with results from flames of the unsaturated fuels methyl propenoate (CH2CHCOOCH3) and vinyl acetate (CH3COOCHCH2) flames. A total of eight flames have been studied, with two fuel-rich flame conditions investigated (fuel-equivalence ratios phi = 1.2 and 1.56) for each fuel. In addition, the underlying oxidation chemistry at these premixed flame conditions has been investigated using a detailed chemical kinetic reaction mechanism, which is largely based on a previously proposed model for saturated esters [B. Yang et al., Phys. Chem. Chem. Phys. 13 (2011) 7205]. The combined results provide a detailed understanding of the similarities and differences between the combustion of saturated vs. unsaturated esters. Meanwhile, the isomeric and stoichiometric effects on their combustion chemistry are also addressed. In this paper, experimental and modeling details are discussed with a special focus on the different reaction pathways. C1 [Westbrook, Charles K.] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. [Yang, Bin; Cool, Terrill A.] Cornell Univ, Sch Appl & Engn Phys, Ithaca, NY 14853 USA. [Hansen, Nils] Sandia Natl Labs, Combust Res Facil, Livermore, CA 94551 USA. [Kohse-Hoeinghaus, Katharina] Univ Bielefeld, Dept Chem, D-33615 Bielefeld, Germany. RP Westbrook, CK (reprint author), Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. EM westbrook1@llnl.gov; tac13@cornell.edu RI Kohse-Hoinghaus, Katharina/A-3867-2012; Hansen, Nils/G-3572-2012; Yang, Bin/A-7158-2008 OI Yang, Bin/0000-0001-7333-0017 FU Office of Basic Energy Sciences (BES), U. S. Department of Energy (USDOE) at Cornell University (TAC) [DE-FG02-01ER1518]; Office of Basic Energy Sciences (BES), U. S. Department of Energy (USDOE) at the Lawrence Livermore National Laboratory (CKW) [DE-AC52-07NA27344]; Deutsche Forschungsgemeinschaft [KO 1363/18-3]; Sandia Corporation for NNSA [DE-AC04-94-AL85000]; USDOE, Office of Basic Energy Sciences under the Energy Frontier Research Center for Combustion Science [DE-SC0001198]; Office of Science, BES/USDOE [DE-AC02-05CH11231] FX We thank Paul Fugazzi and Sarah Ferrell for expert technical assistance and Juan Wang, Tina Kasper, Patrick Osswald and Wenjun Li for experimental assistance. This work is supported by the Office of Basic Energy Sciences (BES), U. S. Department of Energy (USDOE), under grant DE-FG02-01ER1518 at Cornell University (TAC), under contract DE-AC52-07NA27344 at the Lawrence Livermore National Laboratory (CKW), by the Deutsche Forschungsgemeinschaft under KO 1363/18-3 (KKH) and by the Sandia Corporation for NNSA under contract DE-AC04-94-AL85000. BY and NH are also supported by the USDOE, Office of Basic Energy Sciences under the Energy Frontier Research Center for Combustion Science (Grant No. DE-SC0001198). The Advanced Light Source is supported by the Director, Office of Science, BES/USDOE under Contract No. DE-AC02-05CH11231. NR 47 TC 13 Z9 13 U1 7 U2 36 PU OLDENBOURG VERLAG PI MUNICH PA LEKTORAT MINT, POSTFACH 80 13 60, D-81613 MUNICH, GERMANY SN 0942-9352 J9 Z PHYS CHEM JI Z. Phys. Chemie-Int. J. Res. Phys. Chem. Chem. Phys. PY 2011 VL 225 IS 11-12 SI SI BP 1293 EP 1314 DI 10.1524/zpch.2011.0167 PG 22 WC Chemistry, Physical SC Chemistry GA 880GQ UT WOS:000299393700009 ER PT J AU Li, N Carter, JJ Misra, A Shao, L Wang, H Zhang, X AF Li, Nan Carter, J. J. Misra, A. Shao, L. Wang, H. Zhang, X. TI The influence of interfaces on the formation of bubbles in He-ion-irradiated Cu/Mo nanolayers SO PHILOSOPHICAL MAGAZINE LETTERS LA English DT Article DE ion irradiation; Cu; Mo multilayers; He bubbles; interfaces ID HELIUM IMPLANTED COPPER; GRAIN-BOUNDARIES; PURE METALS; DAMAGE; COMPOSITES; NUCLEATION; ACCUMULATION; MECHANISMS; EVOLUTION; LANSCE AB The role of immiscible Cu/Mo interfaces on the formation of helium (He) bubbles in ion-irradiated Cu/Mo 5 nm multilayers is examined. Interfaces significantly enhance the critical He concentration above which bubbles, approximately 1 nm in diameter, are detected via through-focus imaging in a transmission electron microscope. He-to-vacancy ratio affects the formation and distribution of He bubbles. The diameter of He bubbles in Cu appears to be slightly larger than that in Mo. C1 [Li, Nan; Zhang, X.] Texas A&M Univ, Dept Mech Engn, College Stn, TX 77843 USA. [Li, Nan; Zhang, X.] Texas A&M Univ, Mat Sci & Engn Program, College Stn, TX 77843 USA. [Carter, J. J.; Shao, L.] Texas A&M Univ, Dept Nucl Engn, College Stn, TX 77843 USA. [Li, Nan; Misra, A.] Los Alamos Natl Lab, Mat Phys & Applicat Div, Los Alamos, NM 87545 USA. [Wang, H.] Texas A&M Univ, Dept Elect & Comp Engn, College Stn, TX 77843 USA. RP Zhang, X (reprint author), Texas A&M Univ, Dept Mech Engn, College Stn, TX 77843 USA. EM zhangx@tamu.edu RI Li, Nan /F-8459-2010; Misra, Amit/H-1087-2012; Wang, Haiyan/P-3550-2014 OI Li, Nan /0000-0002-8248-9027; Wang, Haiyan/0000-0002-7397-1209 FU US Army Research Office - Materials Science Division [W911NF-09-1-0223]; LANL Lab Directed RD (LDRD); DOE, Office of Basic Energy Sciences, Energy Frontier Research Center FX The authors at TAMU acknowledge funding by the US Army Research Office - Materials Science Division, under contract no. W911NF-09-1-0223. NL and AM at LANL acknowledge support from LANL Lab Directed R&D (LDRD) and DOE, Office of Basic Energy Sciences, Energy Frontier Research Center. The authors are grateful for discussions with M.J. Demkowicz (MIT) and Q.M. Wei (at LANL). NR 40 TC 25 Z9 25 U1 4 U2 32 PU TAYLOR & FRANCIS LTD PI ABINGDON PA 4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND SN 0950-0839 EI 1362-3036 J9 PHIL MAG LETT JI Philos. Mag. Lett. PY 2011 VL 91 IS 1 BP 19 EP 29 AR PII 927461278 DI 10.1080/09500839.2010.522210 PG 11 WC Materials Science, Multidisciplinary; Metallurgy & Metallurgical Engineering; Physics, Applied; Physics, Condensed Matter SC Materials Science; Metallurgy & Metallurgical Engineering; Physics GA 678XH UT WOS:000284116300002 ER PT J AU Bozzolo, G Mosca, HO Yacout, AM Hofman, GL AF Bozzolo, G. Mosca, H. O. Yacout, A. M. Hofman, G. L. TI Lanthanides migration in U-Zr based nuclear fuels SO JOURNAL OF NUCLEAR MATERIALS LA English DT Article AB Atomistic modeling using the BFS method for alloys is performed to study the formation of lanthanide-rich precipitates in U-Zr fuel and the segregation patterns of all constituents to the surface. Surface energies for all elements were computed and, together with the underlying concepts of the BFS method, the migration of lanthanides to the surface region in U-Zr fuels is explained. (C) 2010 Elsevier B.V. All rights reserved. C1 [Bozzolo, G.; Yacout, A. M.; Hofman, G. L.] Argonne Natl Lab, Argonne, IL 60439 USA. [Mosca, H. O.] CNEA, Buenos Aires, DF, Argentina. RP Bozzolo, G (reprint author), Argonne Natl Lab, 9700 S Cass Av, Argonne, IL 60439 USA. EM guille_bozzolo@yahoo.com FU US Department of Energy [DE-AC02-06CH11357] FX Fruitful discussions with N. Bozzolo are gratefully acknowledged. This work was supported under US Department of Energy Contract DE-AC02-06CH11357. NR 5 TC 7 Z9 7 U1 0 U2 21 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0022-3115 J9 J NUCL MATER JI J. Nucl. Mater. PD DEC 31 PY 2010 VL 407 IS 3 BP 228 EP 231 DI 10.1016/j.jnucmat.2010.10.001 PG 4 WC Materials Science, Multidisciplinary; Nuclear Science & Technology SC Materials Science; Nuclear Science & Technology GA 701XT UT WOS:000285859200014 ER PT J AU Jian, LK Russell, CT Luhmann, JG Anderson, BJ Boardsen, SA Strangeway, RJ Cowee, MM Wennmacher, A AF Jian, L. K. Russell, C. T. Luhmann, J. G. Anderson, B. J. Boardsen, S. A. Strangeway, R. J. Cowee, M. M. Wennmacher, A. TI Observations of ion cyclotron waves in the solar wind near 0.3 AU SO JOURNAL OF GEOPHYSICAL RESEARCH-SPACE PHYSICS LA English DT Article ID PICK-UP; INTERSTELLAR HYDROGEN; HELIUM AB Using 2 Hz magnetic field data from the MESSENGER mission, we have investigated more than 300 strong narrowband ion cyclotron wave (ICW) events at a heliocentric distance of about 0.3 AU during 31 May to 9 June 2008. These nearly circularly polarized transverse waves are observed extensively and discretely in the solar wind, with a median duration of 21 s. They are preferentially observed when the magnetic field is more radial than the ambient solar wind. The waves appear both left-handed and right-handed in the spacecraft frame. Their wave frequencies in the spacecraft frame are generally larger than the local proton cyclotron frequency (f(pc)), with a median of 1.44 f(pc). The wave power spectra do not cutoff at the local f(pc). On the basis of their wave characteristics, we conclude that they are intrinsically left-handed in the solar wind frame and they are generated closer to the Sun and carried out to the spacecraft by the super Alfvenic solar wind. After removing the Doppler shift, the wave frequencies in the solar wind frame are all below the local f(pc), with a median of 0.35 f(pc). The ICWs propagate nearly parallel to the magnetic field, and the median wave amplitude is about 0.73 nT, 3% of the background magnetic field. We compare these observations with earlier Helios observations at 0.3 AU in 1976 and contemporary 1 AU observations. C1 [Jian, L. K.; Russell, C. T.; Strangeway, R. J.] Univ Calif Los Angeles, Inst Geophys & Planetary Phys, Los Angeles, CA 90095 USA. [Luhmann, J. G.] Univ Calif Berkeley, Space Sci Lab, Berkeley, CA 94720 USA. [Anderson, B. J.] Johns Hopkins Univ, Appl Phys Lab, Baltimore, MD 20723 USA. [Boardsen, S. A.] NASA, Goddard Space Flight Ctr, Heliophys Sci Div, Greenbelt, MD 20771 USA. [Boardsen, S. A.] Univ Maryland, Goddard Earth Sci & Technol Ctr, Baltimore, MD 21201 USA. [Cowee, M. M.] Los Alamos Natl Lab, Space Sci & Applicat ISR 1, Los Alamos, NM 87545 USA. [Wennmacher, A.] Univ Cologne, Inst Geophys & Meteorol, D-50923 Cologne, Germany. RP Jian, LK (reprint author), Univ Calif Los Angeles, Inst Geophys & Planetary Phys, Los Angeles, CA 90095 USA. EM jlan@igpp.ucla.edu RI Anderson, Brian/I-8615-2012; Russell, Christopher/E-7745-2012; Jian, Lan/B-4053-2010 OI Russell, Christopher/0000-0003-1639-8298; Jian, Lan/0000-0002-6849-5527 FU NASA [NAS5-03131] FX This work is supported by NASA's STEREO program through grant NAS5-03131 administered by University of California-Berkeley. We thank all the PIs for making the data available. We appreciate Fritz Neubauer, Peter Gary, and Philip Isenberg for their useful discussions. NR 30 TC 25 Z9 25 U1 0 U2 4 PU AMER GEOPHYSICAL UNION PI WASHINGTON PA 2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA SN 0148-0227 J9 J GEOPHYS RES-SPACE JI J. Geophys. Res-Space Phys. PD DEC 31 PY 2010 VL 115 AR A12115 DI 10.1029/2010JA015737 PG 11 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA 701RJ UT WOS:000285839900003 ER PT J AU Kim, JH Byun, TS Hoelzer, DT AF Kim, Jeoung Han Byun, Thak Sang Hoelzer, D. T. TI Tensile fracture characteristics of nanostructured ferritic alloy 14YWT SO JOURNAL OF NUCLEAR MATERIALS LA English DT Article ID MECHANICAL-PROPERTIES; STEELS; DEFORMATION AB High temperature tensile fracture behavior has been characterized for the nanostructured ferritic alloy 14YWT (SM10 heat). Uniaxial tensile tests were performed at temperatures ranging from room temperature to 1000 degrees C in vacuum at a nominal strain rate of 10(-3) s(-1). Comparing with the existing oxide dispersion strengthened (ODS) steels such as Eurofer 97 and PM2000, the nanostructured alloy showed much higher yield and tensile strength, but with lower elongation. Microstructural characterization for the tested specimens was focused on the details of fracture morphology and mechanism to provide a feedback for process improvement. Below 600 degrees C, the fracture surfaces exhibited a quasi-brittle behavior presented by a mixture of dimples and cleavage facets. At or above 600 degrees C, however, the fracture surfaces were fully covered with fine dimples. Above 700 degrees C dimple formation occurred by sliding and decohesion of grain boundaries. It was notable that numerous microcracks were observed on the side surface of broken specimens. Formation of these microcracks is believed to be the main origin of the poor ductility of 14YWT alloy. It is suggested that a grain boundary strengthening measure is essential to improve the fracture property of the alloy. Published by Elsevier B.V. C1 [Byun, Thak Sang; Hoelzer, D. T.] Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37830 USA. [Kim, Jeoung Han] Korea Inst Mat Sci, Special Alloys Grp, Chang Won, South Korea. RP Byun, TS (reprint author), Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37830 USA. EM byunts@ornl.gov RI Hoelzer, David/L-1558-2016 FU Korea Ministry of Knowledge with the US Department of Energy [IAN: 168642601]; US Department of Energy, Office of Nuclear Energy with UT-Battelle, LLC [DE-AC05-00OR22725] FX This research was performed at the Oak Ridge National Laboratory, Materials Science and Technology Division and sponsored by the Korea Ministry of Knowledge, Visiting Scientists Program, under IAN: 168642601, with the US Department of Energy. This research was also sponsored by US Department of Energy, Office of Nuclear Energy under Contract DE-AC05-00OR22725 with UT-Battelle, LLC. The authors would like to express special thanks to Drs. J.T. Busby and L. Tan for their technical reviews and thoughtful comments. NR 21 TC 28 Z9 28 U1 3 U2 16 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0022-3115 J9 J NUCL MATER JI J. Nucl. Mater. PD DEC 31 PY 2010 VL 407 IS 3 BP 143 EP 150 DI 10.1016/j.jnucmat.2010.09.054 PG 8 WC Materials Science, Multidisciplinary; Nuclear Science & Technology SC Materials Science; Nuclear Science & Technology GA 701XT UT WOS:000285859200002 ER PT J AU Fu, EG Misra, A Wang, H Shao, L Zhang, X AF Fu, E. G. Misra, A. Wang, H. Shao, Lin Zhang, X. TI Interface enabled defects reduction in helium ion irradiated Cu/V nanolayers SO JOURNAL OF NUCLEAR MATERIALS LA English DT Article ID AUSTENITIC STAINLESS-STEELS; RADIATION-DAMAGE PRODUCTION; STACKING-FAULT TETRAHEDRA; RESEARCH-AND-DEVELOPMENT; ENERGETIC HEAVY-IONS; EQUATION-OF-STATE; MECHANICAL-PROPERTIES; GRAIN-SIZE; FCC METALS; FERRITIC/MARTENSITIC STEELS AB Sputter-deposited Cu/V nanolayer films with individual layer thickness, h, varying from 1 to 200 nm were subjected to helium (He) ion irradiation at room temperature. At a peak dose level of 6 displacements per atom (dpa), the average helium bubble density and lattice expansion decrease significantly with decreasing h. The magnitude of radiation hardening decreases with decreasing individual layer thickness, and becomes negligible when h is 2.5 nm or less. This study indicates that nearly immiscible Cu/V interfaces spaced a few nm apart can effectively reduce the concentration of radiation induced point defects. Consequently, Cu/V nanolayers possess enhanced radiation tolerance, i.e., reduction of swelling and suppression of radiation hardening, compared to monolithic Cu or V. (C) 2010 Elsevier B.V. All rights reserved. C1 [Fu, E. G.; Zhang, X.] Texas A&M Univ, Dept Mech Engn, Mat Sci & Engn Program, College Stn, TX 77843 USA. [Fu, E. G.; Misra, A.] Los Alamos Natl Lab, Mat Phys & Applicat Div, Los Alamos, NM 87545 USA. [Wang, H.] Texas A&M Univ, Dept Elect & Comp Engn, College Stn, TX 77843 USA. [Shao, Lin] Texas A&M Univ, Dept Nucl Engn, College Stn, TX 77843 USA. RP Zhang, X (reprint author), Texas A&M Univ, Dept Mech Engn, Mat Sci & Engn Program, College Stn, TX 77843 USA. EM zhangx@tamu.edu RI Misra, Amit/H-1087-2012; Zhang, Xinghang/H-6764-2013; Wang, Haiyan/P-3550-2014 OI Zhang, Xinghang/0000-0002-8380-8667; Wang, Haiyan/0000-0002-7397-1209 FU US Army Research Office - Materials Science Division [W911NF-09-1-0223]; US DOE, Office of Science, Office of Basic Energy Sciences; Center for Integrated Nanotechnologies (CINT); Consortium for Nanomaterials for Aerospace Commerce and Technology (CONTACT) program from Texas; Air Force FX XZ acknowledges financial support by US Army Research Office - Materials Science Division, under Contract No. W911NF-09-1-0223. AM acknowledges support by the US DOE, Office of Science, Office of Basic Energy Sciences. The authors also acknowledge discussions with Drs. J.P. Hirth and R.G. Hoagland. Support by Center for Integrated Nanotechnologies (CINT) under user agreement at Los Alamos National Laboratory is also acknowledged. The authors thank Dr. J. Carter and Drs. J.G. Swadener and Y.Q. Wang for conducting the He ion irradiation experiments at Texas A&M University and Los Alamos National Laboratory for reproducibility studies. E.G. Fu acknowledges the support from Consortium for Nanomaterials for Aerospace Commerce and Technology (CONTACT) program from Texas and the Air Force. We also acknowledge the usage of microscopes at the Microscopy and Imaging Center at Texas A&M University, and Mr. K. Baldwin and O. Anderoglu for their assistance in sputter-deposition of nanolayers. NR 90 TC 71 Z9 74 U1 4 U2 44 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0022-3115 EI 1873-4820 J9 J NUCL MATER JI J. Nucl. Mater. PD DEC 31 PY 2010 VL 407 IS 3 BP 178 EP 188 DI 10.1016/j.jnucmat.2010.10.011 PG 11 WC Materials Science, Multidisciplinary; Nuclear Science & Technology SC Materials Science; Nuclear Science & Technology GA 701XT UT WOS:000285859200007 ER PT J AU Bock, J Fukuyo, Y Kang, S Phipps, ML Alexandrov, LB Rasmussen, KO Bishop, AR Rosen, ED Martinez, JS Chen, HT Rodriguez, G Alexandrov, BS Usheva, A AF Bock, Jonathan Fukuyo, Yayoi Kang, Sona Phipps, M. Lisa Alexandrov, Ludmil B. Rasmussen, Kim O. Bishop, Alan R. Rosen, Evan D. Martinez, Jennifer S. Chen, Hou-Tong Rodriguez, George Alexandrov, Boian S. Usheva, Anny TI Mammalian Stem Cells Reprogramming in Response to Terahertz Radiation SO PLOS ONE LA English DT Article ID GENE-EXPRESSION; TRANSCRIPTION INITIATION; NUCLEAR RECEPTOR; BINDING-PROTEIN; DNA; ADIPOGENESIS; SPECTROSCOPY; ACTIVATION; DYNAMICS; MODEL AB We report that extended exposure to broad-spectrum terahertz radiation results in specific changes in cellular functions that are closely related to DNA-directed gene transcription. Our gene chip survey of gene expression shows that whereas 89% of the protein coding genes in mouse stem cells do not respond to the applied terahertz radiation, certain genes are activated, while other are repressed. RT-PCR experiments with selected gene probes corresponding to transcripts in the three groups of genes detail the gene specific effect. The response was not only gene specific but also irradiation conditions dependent. Our findings suggest that the applied terahertz irradiation accelerates cell differentiation toward adipose phenotype by activating the transcription factor peroxisome proliferator-activated receptor gamma (PPARG). Finally, our molecular dynamics computer simulations indicate that the local breathing dynamics of the PPARG promoter DNA coincides with the gene specific response to the THz radiation. We propose that THz radiation is a potential tool for cellular reprogramming. C1 [Bock, Jonathan; Fukuyo, Yayoi; Kang, Sona; Alexandrov, Ludmil B.; Rosen, Evan D.; Usheva, Anny] Harvard Univ, Beth Israel Deaconess Med Ctr, Sch Med, Dept Med, Boston, MA 02215 USA. [Phipps, M. Lisa; Martinez, Jennifer S.; Chen, Hou-Tong; Rodriguez, George] Los Alamos Natl Lab, Ctr Integrated Nanotechnol, Los Alamos, NM USA. [Rasmussen, Kim O.; Bishop, Alan R.; Alexandrov, Boian S.] Los Alamos Natl Lab, Div Theoret, Los Alamos, NM USA. RP Bock, J (reprint author), Harvard Univ, Beth Israel Deaconess Med Ctr, Sch Med, Dept Med, Boston, MA 02215 USA. EM ausheva@bidmc.harvard.edu RI Rasmussen, Kim/B-5464-2009; Chen, Hou-Tong/C-6860-2009; Alexandrov, Boian/D-2488-2010; Alexandrov, Ludmil/B-6582-2014; Rodriguez, George/G-7571-2012 OI Rasmussen, Kim/0000-0002-4029-4723; Chen, Hou-Tong/0000-0003-2014-7571; Alexandrov, Boian/0000-0001-8636-4603; Alexandrov, Ludmil/0000-0003-3596-4515; Rodriguez, George/0000-0002-6044-9462 FU U.S. Department of Energy, Office of Basic Energy Sciences [DE- AC52-06NA25396]; Sandia National Laboratories [DE- AC04-94AL85000]; NIH [R01GM73911]; Richard and Susan Smith Family Foundation [ADA 1-08-PPG-02]; NIH ARRA supplement [3R01GM73911-4S1] FX This work was performed, in part, at the Center for Integrated Nanotechnologies, U.S. Department of Energy, Office of Basic Energy Sciences user facility at Los Alamos National Laboratory (Contract DE- AC52-06NA25396) and Sandia National Laboratories (Contract DE- AC04-94AL85000); NIH grants R01GM73911; NIH ARRA supplement (3R01GM73911-4S1); Richard and Susan Smith Family Foundation Pinnacle Award ADA 1-08-PPG-02. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. NR 35 TC 40 Z9 43 U1 1 U2 31 PU PUBLIC LIBRARY SCIENCE PI SAN FRANCISCO PA 185 BERRY ST, STE 1300, SAN FRANCISCO, CA 94107 USA SN 1932-6203 J9 PLOS ONE JI PLoS One PD DEC 31 PY 2010 VL 5 IS 12 AR e15806 DI 10.1371/journal.pone.0015806 PG 6 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 701RA UT WOS:000285838900036 PM 21209821 ER PT J AU Liu, KJ Gary, SP Winske, D AF Liu, Kaijun Gary, S. Peter Winske, Dan TI Heliosheath fluctuations near the perpendicular termination shock: Two-dimensional hybrid simulations SO JOURNAL OF GEOPHYSICAL RESEARCH-SPACE PHYSICS LA English DT Article ID CYCLOTRON ANISOTROPY INSTABILITIES; NUMBER PLASMA INTERACTIONS; INTERSTELLAR PICKUP IONS; BOUNDARY EXPLORER IBEX; SOLAR-WIND; COLLISIONLESS SHOCKS; MAGNETIC-FIELDS; MAGNETOSHEATH; ACCELERATION; DOWNSTREAM AB The two-dimensional Los Alamos hybrid simulation code is used to study the excitation of fluctuations and the associated ion dynamics at the high Alfven-Mach heliospheric termination shock and in the near-shock heliosheath. This simulation represents the electrons as a zero-mass fluid, addresses only a perpendicular shock, and considers the upstream ions to consist of a cool solar wind component and a more energetic pickup component. The shock yields two strongly heated downstream components: the more dense thermals and the more tenuous suprathermals, each with strong T(perpendicular to) > T(parallel to) anisotropies. In the downstream, relatively homogeneous sheath plasma, linear dispersion theory predicts that each component anisotropy drives both the Alfven-cyclotron instability and the proton mirror instability. The simulation demonstrates that Alfven-cyclotron modes dominate mirror-like modes in the downstream, in contrast to earlier two-dimensional hybrid simulations of high-Mach quasi-perpendicular shocks without pickup ions, in which the Alfven-cyclotron and mirror modes were excited to comparable intensities. A hypothesis is presented that the presence of pickup ions implies a relatively low magnetosonic Mach number at termination shocks, thereby favoring the excitation of the Alfven-cyclotron instability. The primary consequence of wave-particle interactions from this instability is pitch angle scattering, so the energetic part of the ion perpendicular velocity distribution in the heliosheath is depleted by comparison with the distribution computed from a comparable one-dimensional hybrid simulation. C1 [Liu, Kaijun; Gary, S. Peter; Winske, Dan] Los Alamos Natl Lab, Grp ISR 1, Los Alamos, NM 87545 USA. RP Liu, KJ (reprint author), Los Alamos Natl Lab, Grp ISR 1, Mail Stop D466, Los Alamos, NM 87545 USA. EM kaijun@lanl.gov; pgary@lanl.gov; winske@lanl.gov RI Dong, Li/F-4931-2010 FU U.S. Department of Energy (DOE); National Aeronautics and Space Administration FX This work was performed under the auspices of the U.S. Department of Energy (DOE). It was supported by the Solar and Heliospheric Physics SR&T Program of the National Aeronautics and Space Administration. NR 50 TC 2 Z9 2 U1 1 U2 4 PU AMER GEOPHYSICAL UNION PI WASHINGTON PA 2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA SN 0148-0227 J9 J GEOPHYS RES-SPACE JI J. Geophys. Res-Space Phys. PD DEC 30 PY 2010 VL 115 AR A12114 DI 10.1029/2010JA015694 PG 12 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA 701RF UT WOS:000285839400002 ER PT J AU McLerran, L AF McLerran, Larry TI STRONGLY INTERACTING MATTER AT HIGH ENERGY DENSITY SO INTERNATIONAL JOURNAL OF MODERN PHYSICS A LA English DT Review ID GAUGE VECTOR-MESONS; GLUON DISTRIBUTION-FUNCTIONS; HEAVY-ION COLLISIONS; GROUND-STATE ENERGY; FINITE TEMPERATURE; NUCLEAR COLLISIONS; QUARK LIBERATION; MONTE-CARLO; TRANSVERSE-MOMENTUM; SMALL-X AB This lecture concerns the properties of strongly interacting matter (which is described by Quantum Chromodynamics) at very high energy density. I review the properties of matter at high temperature, discussing the deconfinement phase transition. At high baryon density and low temperature, large N(c) arguments are developed which suggest that high baryonic density matter is a third form of matter, Quarkyonic Matter, that is distinct from confined hadronic matter and deconfined matter. I finally discuss the Color Glass Condensate which controls the high energy limit of QCD, and forms the low x part of a hadron wave function. The Glasma is introduced as matter formed by the Color Glass Condensate which eventually thermalizes into a Quark Gluon Plasma. C1 [McLerran, Larry] Brookhaven Natl Lab, Riken Brookhaven Ctr, Upton, NY 11973 USA. [McLerran, Larry] Brookhaven Natl Lab, Dept Phys, Upton, NY 11973 USA. RP McLerran, L (reprint author), Brookhaven Natl Lab, Riken Brookhaven Ctr, Upton, NY 11973 USA. FU US Department of Energy [DE-AC02-98CH0886] FX This manuscript has been authorized under Contract No. DE-AC02-98CH0886 with the US Department of Energy. NR 73 TC 6 Z9 6 U1 0 U2 2 PU WORLD SCIENTIFIC PUBL CO PTE LTD PI SINGAPORE PA 5 TOH TUCK LINK, SINGAPORE 596224, SINGAPORE SN 0217-751X J9 INT J MOD PHYS A JI Int. J. Mod. Phys. A PD DEC 30 PY 2010 VL 25 IS 32 BP 5847 EP 5864 DI 10.1142/S0217751X10051335 PG 18 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA 735PL UT WOS:000288429300003 ER PT J AU Kimball, DFJ Boyd, A Budker, D AF Kimball, D. F. Jackson Boyd, Alec Budker, D. TI Constraints on anomalous spin-spin interactions from spin-exchange collisions SO PHYSICAL REVIEW A LA English DT Article ID FOREIGN GAS NUCLEI; ENERGY CURVES; CP INVARIANCE; TORSION; SEARCH; HE; POTENTIALS; PARTICLE; GRAVITY; SYSTEMS AB A comparison between existing measurements and calculated cross sections for spin exchange between alkali-metal atoms and noble gases (specifically sodium and helium) is used to constrain anomalous spin-dependent forces between nuclei at the atomic scale (similar to 10(-8) cm). Combined with existing stringent limits on anomalous short-range, spin-dependent couplings of the proton, the dimensionless coupling constant for an axial vector interaction of the neutron arising from exchange of a boson of mass less than or similar to 100 eV is constrained to be g(A)(n)/root 4 pi(h) over barc < 2 x 10(-3). Constraints are established for a velocity-and spin-dependent interaction alpha (I . v)(K . v), where I and K are the nuclear spins of He and Na, respectively, and v is the relative velocity of the atoms. Constraints on torsion gravity are also considered. C1 [Kimball, D. F. Jackson] Calif State Univ E Bay, Dept Phys, Hayward, CA 94542 USA. [Boyd, Alec] Pomona Coll, Dept Phys & Astron, Claremont, CA 91711 USA. [Budker, D.] Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA. [Budker, D.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Nucl Sci, Berkeley, CA 94720 USA. RP Kimball, DFJ (reprint author), Calif State Univ E Bay, Dept Phys, Hayward, CA 94542 USA. EM derek.jacksonkimball@csueastbay.edu RI Budker, Dmitry/F-7580-2016 OI Budker, Dmitry/0000-0002-7356-4814 FU National Science Foundation [PHY-0652824, PHY-0969666]; California State University-East Bay FX The authors are grateful for enlightening conversations with Thad Walker, Micah Ledbetter, and Timur Tscherbul. This work has been supported by Grants PHY-0652824 and PHY-0969666 from the National Science Foundation and Faculty Support Grants from California State University-East Bay. NR 50 TC 8 Z9 8 U1 0 U2 6 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 2469-9926 EI 2469-9934 J9 PHYS REV A JI Phys. Rev. A PD DEC 30 PY 2010 VL 82 IS 6 AR 062714 DI 10.1103/PhysRevA.82.062714 PG 5 WC Optics; Physics, Atomic, Molecular & Chemical SC Optics; Physics GA 713OP UT WOS:000286747600004 ER PT J AU Deng, SHM Vane, CR Bannister, ME Fogle, M AF Deng, S. H. M. Vane, C. R. Bannister, M. E. Fogle, M. TI Electron-impact dissociation of ozone cations O-3(+) SO PHYSICAL REVIEW A LA English DT Article ID CROSS-SECTIONS; PHOTOELECTRON-SPECTROSCOPY; IONS; IONIZATION; PHOTOIONIZATION; COLLISIONS; ENERGY; STATES; O3+ AB Absolute cross sections for electron-impact dissociation of O-3(+) ions yielding O+ and O-2(+) fragment ions have been measured using a crossed electron-ion beams method for energies from about 3 eV to 100 eV. While the O-2(+) channel dominates the dissociation cross section over the measured energy range, a strong enhancement is observed in the O+ channel at low energy. C1 [Deng, S. H. M.; Vane, C. R.; Bannister, M. E.] Oak Ridge Natl Lab, Div Phys, Oak Ridge, TN 37831 USA. [Fogle, M.] Auburn Univ, Dept Phys, Auburn, AL 36849 USA. RP Deng, SHM (reprint author), Oak Ridge Natl Lab, Div Phys, Oak Ridge, TN 37831 USA. RI Deng, Shihu/H-8053-2012; OI Bannister, Mark E./0000-0002-9572-8154 FU Office of Fusion Energy Sciences; Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the US Department of Energy; Auburn University Office of the Vice President for Research, College of Science and Mathematics and Department of Physics; ORNL FX This research was supported in part by the Office of Fusion Energy Sciences and the Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the US Department of Energy. One of the authors (S.D.) gratefully acknowledges support from the ORNL Postdoctoral Research Associates Program administered jointly by the Oak Ridge Institute for Science and Education and Oak Ridge National Laboratory. M. F. would like to acknowledge support from the Auburn University Office of the Vice President for Research, College of Science and Mathematics and Department of Physics. NR 31 TC 3 Z9 3 U1 2 U2 11 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 1050-2947 J9 PHYS REV A JI Phys. Rev. A PD DEC 30 PY 2010 VL 82 IS 6 AR 062715 DI 10.1103/PhysRevA.82.062715 PG 4 WC Optics; Physics, Atomic, Molecular & Chemical SC Optics; Physics GA 713OP UT WOS:000286747600005 ER PT J AU Wang, LJ Exarhos, GJ AF Wang, Lisa J. Exarhos, Gregory J. TI Persistent conductivity in post-growth doped ZnO films following pulsed UV laser irradiation SO THIN SOLID FILMS LA English DT Article; Proceedings Paper CT 37th International Conference on Metallurgical Coatings and Thin Films CY APR 26-30, 2010 CL San Diego, CA SP Amer Vacuum Soc, Adv Surface Engn Div DE Laser irradiation; ZnO; TCO film; Conductivity; Raman spectroscopy ID ZINC-OXIDE; THIN-FILMS; TRANSPARENT; SINGLE; LAYER; RAMAN AB Solution and rf sputter deposited doped ZnO films were subjected to cumulative 4-ns pulses of 355 nm light from a pulsed Nd:YAG laser at fluences between 5 and 150 mJ/cm(2). Film densification, change in refractive index, and an increase in conductivity were observed following room temperature irradiation in air, a carbon monoxide reducing environment, or under vacuum. At fluences between 20 and 80 mJ/cm(2), the films did not damage catastrophically under irradiation and high visible transparency persisted. The increase in conductivity is attributed to creation of oxygen vacancies and subsequent promotion of free carriers into the conduction band. Effects were most pronounced for films treated in vacuum. All treated films became insulating again upon equilibration in air at room temperature after several days. Films were characterized by means of UV-VIS-NIR transmission spectroscopy, Raman spectroscopy, and Hall measurements. Analysis of interference fringes in measured transmission spectra allowed evaluation of optical properties. Raman measurements showed an increase of LO mode intensity with respect to TO mode intensity as the films became more conducting in accord with previous work. Results of this study are not only important for continued development of transparent conducting oxides, but also provide compelling evidence for the role of free carriers as initiators of laser damage in wide bandgap metal oxide films. (C) 2010 Elsevier B.V. All rights reserved. C1 [Exarhos, Gregory J.] Pacific NW Natl Lab, Chem & Mat Sci Div, Richland, WA 99352 USA. [Wang, Lisa J.] Carleton Coll, Dept Chem, Northfield, MN 55057 USA. RP Exarhos, GJ (reprint author), Pacific NW Natl Lab, Chem & Mat Sci Div, Richland, WA 99352 USA. EM greg.exarhos@pnl.gov NR 41 TC 3 Z9 3 U1 2 U2 12 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 DEC 30 PY 2010 VL 519 IS 5 SI SI BP 1495 EP 1500 DI 10.1016/j.tsf.2010.04.118 PG 6 WC Materials Science, Multidisciplinary; Materials Science, Coatings & Films; Physics, Applied; Physics, Condensed Matter SC Materials Science; Physics GA 707SA UT WOS:000286305100003 ER PT J AU Deng, XY Lee, J Wang, CJ Matranga, C Aksoy, F Liu, Z AF Deng, Xingyi Lee, Junseok Wang, Congjun Matranga, Christopher Aksoy, Funda Liu, Zhi TI Reactivity Differences of Nanocrystals and Continuous Films of alpha-Fe2O3 on Au(111) Studied with In Situ X-ray Photoelectron Spectroscopy SO JOURNAL OF PHYSICAL CHEMISTRY C LA English DT Article ID WATER-GAS-SHIFT; REACTION-MECHANISM; SURFACE-CHEMISTRY; CATALYSTS; ADSORPTION; CO; NANOPARTICLES; GROWTH; OXIDATION; REACTANT AB The interaction of CO with nanocrystals and continuous films of alpha-Fe2O3 grown on Au(111) was investigated using in situ X-ray photoelectron spectroscopy (XPS) at near ambient pressure (200 mTorr) and scanning tunneling microscopy (STM). Adsorbed CO was detected by XPS when alpha-Fe2O3 nanocrystals (6-7 nm) grown on Au( Ill) were exposed to 200 mTorr of the gas at room temperature. Under a low H2O background, surface bound hydroxyl groups (adsorbed OH) were also noted on these alpha-Fe2O3 nanocrystals as a result of H2O dissociation on the edges of the particles. Adsorbed formate (HCOO-) was detected during heating to 373 K and believed to originate from the reaction of adsorbed CO with the OH groups. The adsorbed formate desorbed or decomposed above 473 K. Continuous alpha-Fe2O3 thin films on Au(111) were inert under the same conditions studied for nanocrystalline alpha-Fe2O3. Specifically, neither adsorbed CO nor OH groups were observed for the continuous films of alpha-Fe2O3. This reactivity difference can be explained by the presence of alpha-Fe2O3 crystal edges and the interface which exists between the alpha-Fe2O3 nanocrystals and the Au(111) substrate. These edges and interfaces are present for the nanocrystalline alpha-Fe2O3/Au(111) system but are not present in significant amounts for the continuous films of alpha-Fe2O3. The implications of these experimental results for the water-gas shift reaction will be also discussed. C1 [Deng, Xingyi; Lee, Junseok; Wang, Congjun; Matranga, Christopher] US DOE, Natl Energy Technol Lab, Pittsburgh, PA 15236 USA. [Deng, Xingyi; Lee, Junseok; Wang, Congjun] URS, South Pk, PA 15129 USA. [Aksoy, Funda; Liu, Zhi] Univ Calif Berkeley, Lawrence Berkeley Lab, Adv Light Source, Berkeley, CA 94720 USA. [Aksoy, Funda] Cukurova Univ, Dept Phys, TR-01330 Adana, Turkey. RP Deng, XY (reprint author), US DOE, Natl Energy Technol Lab, POB 10940, Pittsburgh, PA 15236 USA. EM Xingyi.Deng@netl.doe.gov RI Wang, Congjun/A-9608-2010; Liu, Zhi/B-3642-2009; Matranga, Christopher/E-4741-2015; OI Liu, Zhi/0000-0002-8973-6561; Matranga, Christopher/0000-0001-7082-5938; Deng, Xingyi/0000-0001-9109-1443 FU National Energy Technology Laboratory under RES [DE-FE0000400]; Office of Science, Office of Basic Energy Sciences, of the US Department of Energy [DE-AC02-05CH11231] FX This technical effort was performed in support of the National Energy Technology Laboratory's ongoing research under the RES contract DE-FE0000400. 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. Reference in this work to any specific commercial product is to facilitate understanding and does not necessarily imply endorsement by the US Department of Energy. NR 34 TC 18 Z9 19 U1 2 U2 35 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1932-7447 J9 J PHYS CHEM C JI J. Phys. Chem. C PD DEC 30 PY 2010 VL 114 IS 51 BP 22619 EP 22623 DI 10.1021/jp1085697 PG 5 WC Chemistry, Physical; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary SC Chemistry; Science & Technology - Other Topics; Materials Science GA 696NB UT WOS:000285447000035 ER PT J AU Tang, M Carter, WC Belak, JF Chiang, YM AF Tang, Ming Carter, W. Craig Belak, James F. Chiang, Yet-Ming TI Modeling the competing phase transition pathways in nanoscale olivine electrodes SO ELECTROCHIMICA ACTA LA English DT Article DE Lithium-ion battery cathodes; Olivines; Amorphization; Overpotential; Diffuse-interface model ID RECHARGEABLE LITHIUM BATTERIES; MISCIBILITY GAP; TRANSFORMATION; TEMPERATURE; SIZE; LIXFEPO4; CATHODES; STORAGE; ALLOYS; ENERGY AB Recent experimental developments reveal that nanoscale lithium iron phosphate (LiFePO4) olivine particles exhibit very different phase transition behavior from the bulk olivine phase. A crystalline-to-amorphous phase transition has been observed in nanosized particles in competition with the equilibrium phase transition between the lithium-rich and lithium-poor olivine phases. Here we apply a diffuse-interface (phase-field) model to study the kinetics of the different phase transition pathways in nanosized LiFePO4 particles upon delithiation. We find that the nucleation and growth kinetics of the crystalline-to-crystalline and crystalline-to-amorphous phase transformations are sensitive to the applied electrical overpotential and particle size, which collectively determine the preferred phase transition pathway. While the crystalline-to-crystalline phase transition is favored by either faster nucleation or growth kinetics at low or high overpotentials, particle amorphization dominates at intermediate overpotentials. Decreasing particle size expands the overpotential region in which amorphization is preferred. The asymmetry in the nucleation energy barriers for amorphization and recrystallization results in a phase transition hysteresis that should promote the accumulation of the amorphous phase in electrodes after repeated electrochemical cycling. The predicted overpotential- and size-dependent phase transition behavior of nanoscale LiFePO4 particles is consistent with experimental observations. Published by Elsevier Ltd. C1 [Tang, Ming; Belak, James F.] Lawrence Livermore Natl Lab, Condensed Matter & Mat Div, Livermore, CA 94550 USA. [Carter, W. Craig; Chiang, Yet-Ming] MIT, Dept Mat Sci & Engn, Cambridge, MA 02139 USA. RP Tang, M (reprint author), Lawrence Livermore Natl Lab, Condensed Matter & Mat Div, Livermore, CA 94550 USA. EM tang25@llnl.gov RI Carter, W/K-2406-2012 FU U.S. Department of Energy by Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Lawrence Postdoctoral Fellowship; U.S. Department of Energy [DE-SC0002626] FX The research work of MT and JFB was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344. MT is grateful for the financial support by the Lawrence Postdoctoral Fellowship. WCC and YMC acknowledge the financial support of U.S. Department of Energy Grant No. DE-SC0002626. We thank Nonglak Meethong and Yu-Hua Kao for many helpful discussions. We also acknowledge helpful comments from the anonymous reviewers. NR 40 TC 26 Z9 26 U1 2 U2 56 PU PERGAMON-ELSEVIER SCIENCE LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND SN 0013-4686 EI 1873-3859 J9 ELECTROCHIM ACTA JI Electrochim. Acta PD DEC 30 PY 2010 VL 56 IS 2 BP 969 EP 976 DI 10.1016/j.electacta.2010.09.027 PG 8 WC Electrochemistry SC Electrochemistry GA 692TL UT WOS:000285177900047 ER PT J AU Scovazzi, G Love, E AF Scovazzi, G. Love, E. TI A generalized view on Galilean invariance in stabilized compressible flow computations SO INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS LA English DT Article; Proceedings Paper CT 15th International Conference on Finite Elements in Flow Problems CY APR 01-03, 2009 CL Tokyo, JAPAN DE variational multi-scale methods; stabilized methods; SUPG methods; Galilean transformations; invariance ID FINITE-ELEMENT FORMULATION; NAVIER-STOKES EQUATIONS; VARIATIONAL MULTISCALE METHOD; LARGE-EDDY SIMULATION; INCOMPRESSIBLE FLOWS; FLUID-DYNAMICS; CONSERVATION VARIABLES; WAVE-EQUATION; GALERKIN; EULER AB This article presents a generalized analysis on the significance of Galilean invariance in compressible flow computations with stabilized and variational multi-scale methods. The understanding of the key issues and the development of general approaches to Galilean-invariant stabilization are facilitated by the use of a matrix-operator description of Galilean transformations. The analysis of invariance for discontinuity capturing operators is also included. Published in 2010 by John Wiley & Sons, Ltd. C1 [Scovazzi, G.; Love, E.] Sandia Natl Labs, Computat Shock & Multiphys Dept 1431, Albuquerque, NM 87185 USA. RP Scovazzi, G (reprint author), Sandia Natl Labs, Computat Shock & Multiphys Dept 1431, POB 5800,MS 1319, Albuquerque, NM 87185 USA. EM gscovaz@sandia.gov NR 35 TC 11 Z9 11 U1 0 U2 5 PU WILEY-BLACKWELL PI HOBOKEN PA 111 RIVER ST, HOBOKEN 07030-5774, NJ USA SN 0271-2091 J9 INT J NUMER METH FL JI Int. J. Numer. Methods Fluids PD DEC 30 PY 2010 VL 64 IS 10-12 BP 1065 EP 1083 DI 10.1002/fld.2417 PG 19 WC Computer Science, Interdisciplinary Applications; Mathematics, Interdisciplinary Applications; Mechanics; Physics, Fluids & Plasmas SC Computer Science; Mathematics; Mechanics; Physics GA 693YN UT WOS:000285261400002 ER PT J AU Lin, PT Shadid, JN Tuminaro, RS Sala, M Hennigan, GL Pawlowski, RP AF Lin, Paul T. Shadid, John N. Tuminaro, Raymond S. Sala, Marzio Hennigan, Gary L. Pawlowski, Roger P. TI A parallel fully coupled algebraic multilevel preconditioner applied to multiphysics PDE applications: Drift-diffusion, flow/transport/reaction, resistive MHD SO INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS LA English DT Article; Proceedings Paper CT 15th International Conference on Finite Elements in Flow Problems CY APR 01-03, 2009 CL Tokyo, JAPAN DE multilevel preconditioners; algebraic multigrid; finite element methods; Newton-Krylov; Schwarz domain decomposition preconditioners; graph partitioning ID DOMAIN DECOMPOSITION PRECONDITIONERS; NEWTON-KRYLOV METHODS; STABILIZATION PARAMETERS; SMOOTHED AGGREGATION; INCOMPRESSIBLE-FLOW; SYSTEMS; PERFORMANCE; FORMULATION; EQUATIONS; COMPUTATIONS AB This study considers the performance of a fully coupled algebraic multilevel preconditioner for Newton-Krylov solution methods. The performance of the preconditioner is demonstrated on a set of challenging multiphysics partial differential equation (PDE) applications: a drift-diffusion approximation for semiconductor devices; a low Mach number formulation for the simulation of coupled flow, transport and non-equilibrium chemical reactions; and a low Mach number formulation for visco-resistive magnetohydrodynamics (MHD) systems. These systems contain multiple physical mechanisms that are strongly coupled, highly nonlinear, non-symmetric and produce solutions with multiple length-and time-scales. In the context of this study the governing PDEs for these systems are discretized in space by a stabilized finite element (FE) method that collocates all unknowns at each node of the FE mesh. The algebraic multilevel preconditioner is based on an aggressive-coarsening graph-partitioning of the non-zero block structure of the Jacobian matrix. The performance of the algebraic multilevel preconditioner is compared with a standard variable overlap additive Schwarz domain decomposition preconditioner. Representative performance and parallel scaling results are presented for a set of direct-to-steady-state and fully implicit transient solutions. The performance studies include parallel weak scaling studies on up to 4096 cores and also includes the solution of systems as large as two billion unknowns carried out on 24 000 cores of a Cray XT3/4. In general, the results of this study indicate that on this reasonably diverse set of challenging multiphysics applications the algebraic multilevel preconditioner performs very well. Copyright (C) 2010 John Wiley & Sons, Ltd. C1 [Lin, Paul T.; Shadid, John N.; Hennigan, Gary L.; Pawlowski, Roger P.] Sandia Natl Labs, Albuquerque, NM 87185 USA. [Tuminaro, Raymond S.] Sandia Natl Labs, Livermore, CA 94551 USA. [Sala, Marzio] BMW Sauber, Hinwil, Switzerland. RP Lin, PT (reprint author), Sandia Natl Labs, POB 5800,MS 0316, Albuquerque, NM 87185 USA. EM ptlin@sandia.gov NR 69 TC 12 Z9 12 U1 0 U2 11 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 DEC 30 PY 2010 VL 64 IS 10-12 BP 1148 EP 1179 DI 10.1002/fld.2402 PG 32 WC Computer Science, Interdisciplinary Applications; Mathematics, Interdisciplinary Applications; Mechanics; Physics, Fluids & Plasmas SC Computer Science; Mathematics; Mechanics; Physics GA 693YN UT WOS:000285261400006 ER PT J AU Li, FY Ramaswamy, V Ginoux, P Broccoli, AJ Delworth, T Zeng, FR AF Li, Fuyu Ramaswamy, V. Ginoux, Paul Broccoli, Anthony J. Delworth, Thomas Zeng, Fanrong TI Toward understanding the dust deposition in Antarctica during the Last Glacial Maximum: Sensitivity studies on plausible causes SO JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES LA English DT Article ID C ICE-CORE; EAST ANTARCTICA; DOME-C; ATMOSPHERIC CO2; CLIMATE-CHANGE; MODEL; CIRCULATION; SIMULATION; VOSTOK; RECORD AB Understanding the plausible causes for the observed high dust concentrations in Antarctic ice cores during the Last Glacial Maximum (LGM) is crucial for interpreting the Antarctic dust records in the past climates and could provide insights into dust variability in future climates. Using the Geophysical Fluid Dynamics Laboratory (GFDL) General Circulation Models, we conduct an investigation into the various factors modulating dust emission, transport, and deposition, with a view toward an improved quantification of the LGM dust enhancements in the Antarctic ice cores. The model simulations show that the expansion of source areas and changes in the Antarctic ice accumulation rates together can account for most of the observed increase of dust concentrations in the Vostok, Dome C, and Taylor Dome cores, but there is an overestimate of the LGM/present ratio in the case of the Byrd core. The source expansion due to the lowering of sea level yields a factor of 2-3 higher contribution than that due to the reduction of continental vegetation. The changes in other climate parameters (e.g., SH precipitation change) are estimated to be relatively less important within the context of this sensitivity study, while the model-simulated LGM surface winds yield a 20%-30% reduction rather than an increase in dust deposition in Antarctica. This research yields insights toward a fundamental understanding of the causes for the significant enhancement of the dust deposition in the Antarctic ice cores during the LGM. C1 [Li, Fuyu] Princeton Univ, Program Atmospher & Ocean Sci, Princeton, NJ 08544 USA. [Ramaswamy, V.; Ginoux, Paul; Delworth, Thomas] NOAA, Geophys Fluid Dynam Lab, Princeton, NJ 08452 USA. [Broccoli, Anthony J.] Rutgers State Univ, Ctr Environm Predict, New Brunswick, NJ 08901 USA. [Broccoli, Anthony J.] Rutgers State Univ, Dept Environm Sci, New Brunswick, NJ 08901 USA. RP Li, FY (reprint author), Univ Calif Berkeley, Lawrence Berkeley Lab, 1 Cyclotron Rd,Mail Stop 90R1116, Berkeley, CA 94720 USA. EM fli@lbl.gov RI Ginoux, Paul/C-2326-2008; Li, Fuyu/B-9055-2013; Delworth, Thomas/C-5191-2014; Broccoli, Anthony/D-9186-2014 OI Ginoux, Paul/0000-0003-3642-2988; Broccoli, Anthony/0000-0003-2619-1434 FU NASA Headquarters [NESSF07] FX This work was supported by NASA Headquarters under the Earth and Space Science Fellowship Program (NESSF07). NR 49 TC 6 Z9 6 U1 0 U2 14 PU AMER GEOPHYSICAL UNION PI WASHINGTON PA 2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA SN 2169-897X EI 2169-8996 J9 J GEOPHYS RES-ATMOS JI J. Geophys. Res.-Atmos. PD DEC 30 PY 2010 VL 115 AR D24120 DI 10.1029/2010JD014791 PG 14 WC Meteorology & Atmospheric Sciences SC Meteorology & Atmospheric Sciences GA 701QO UT WOS:000285837500004 ER PT J AU Juodagalvis, A Langanke, K Hix, WR Martinez-Pinedo, G Sampaio, JM AF Juodagalvis, A. Langanke, K. Hix, W. R. Martinez-Pinedo, G. Sampaio, J. M. TI Improved estimate of electron capture rates on nuclei during stellar core collapse SO NUCLEAR PHYSICS A LA English DT Article DE Electron capture rates; Supernova simulations ID WEAK-INTERACTION RATES; BOLTZMANN NEUTRINO TRANSPORT; RANDOM-PHASE-APPROXIMATION; INTERMEDIATE-MASS NUCLEI; SD-SHELL NUCLEI; SHOCK SUPERNOVA MECHANISM; EQUATION-OF-STATE; RATE TABLES; STATISTICAL EQUILIBRIUM; POSTBOUNCE EVOLUTION AB Electron captures on nuclei play an important role in the dynamics of the collapsing core of a massive star that leads to a supernova explosion. Recent calculations of these capture rates were based on microscopic models which account for relevant degrees of freedom. Due to computational restrictions such calculations were limited to a modest number of nuclei, mainly in the mass range A = 45-110. Recent supernova simulations show that this pool of nuclei, however, omits the very neutron-rich and heavy nuclei which dominate the nuclear composition during the last phase of the collapse before neutrino trapping. Assuming that the composition is given by Nuclear Statistical Equilibrium we present here electron capture rates for collapse conditions derived from individual rates for roughly 2700 individual nuclei. For those nuclei which dominate in the early stage of the collapse, the individual rates are derived within the framework of microscopic models, while for the nuclei which dominate at high densities we have derived the rates based on the Random Phase Approximation with a global parametrization of the single particle occupation numbers. In addition, we have improved previous rate evaluations by properly including screening corrections to the reaction rates into account. (C) 2010 Elsevier B.V. All rights reserved. C1 [Juodagalvis, A.] VU ITPA, LT-01108 Vilnius, Lithuania. [Langanke, K.; Martinez-Pinedo, G.] GSI Helmholtzzentrum Schwerionenforsch, D-64291 Darmstadt, Germany. [Langanke, K.] Tech Univ Darmstadt, Inst Kernphys, D-64291 Darmstadt, Germany. [Langanke, K.] Frankfurt Inst Adv Studies, D-60438 Frankfurt, Germany. [Hix, W. R.] Oak Ridge Natl Lab, Div Phys, Oak Ridge, TN 37831 USA. [Sampaio, J. M.] CFNUL, P-1649003 Lisbon, Portugal. RP Juodagalvis, A (reprint author), VU ITPA, A Gostauto St 12, LT-01108 Vilnius, Lithuania. EM andrius.juodagalvis@tfai.vu.lt RI Hix, William/E-7896-2011; Martinez-Pinedo, Gabriel/A-1915-2013; Sampaio, Jorge/M-4750-2013 OI Hix, William/0000-0002-9481-9126; Martinez-Pinedo, Gabriel/0000-0002-3825-0131; Sampaio, Jorge/0000-0003-4359-493X FU US DOE; EU [FP6-FP7]; Deutsche Forschungsgemeinschaft [SFB 634]; ExtreMe Matter Institute EMMI; Helmholtz International Center for FAIR; Office of Nuclear Physics, US Department of Energy FX At the early stage of the project A.J.'s work was partly supported by the US DOE through the SciDAC programme "Terascale Supernova Initiative" during his stay at GSI, Germany, hospitality of which is appreciated. A.J. acknowledges support from the EU FP6-FP7 project "BalticGrid". G.M.P. and K.L. acknowledge support by the Deutsche Forschungsgemeinschaft through contract SFB 634, by the ExtreMe Matter Institute EMMI and by the Helmholtz International Center for FAIR. W.R.H. acknowledges support from the Office of Nuclear Physics, US Department of Energy. Discussions with Eduardo Bravo about the treatment of screening corrections are acknowledged. The computer-net BalticGrid infrastructure was used to calculate this huge number of rates and spectra. NR 66 TC 55 Z9 55 U1 0 U2 10 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0375-9474 EI 1873-1554 J9 NUCL PHYS A JI Nucl. Phys. A PD DEC 30 PY 2010 VL 848 IS 3-4 BP 454 EP 478 DI 10.1016/j.nuclphysa.2010.09.012 PG 25 WC Physics, Nuclear SC Physics GA 696HK UT WOS:000285432300012 ER PT J AU Adare, A Afanasiev, S Aidala, C Ajitanand, NN Akiba, Y Al-Bataineh, H Alexander, J Al-Ta'ani, H Angerami, A Aoki, K Apadula, N Aphecetche, L Aramaki, Y Asai, J Atomssa, ET Averbeck, R Awes, TC Azmoun, B Babintsev, V Bai, M Baksay, G Baksay, L Baldisseri, A Barish, KN Barnes, PD Bassalleck, B Basye, AT Bathe, S Batsouli, S Baublis, V Baumann, C Bazilevsky, A Belikov, S Belmont, R Bennett, R Berdnikov, A Berdnikov, Y Bhom, JH Bickley, AA Blau, DS Boissevain, JG Bok, JS Borel, H Borggren, N Boyle, K Brooks, ML Buesching, H Bumazhnov, V Bunce, G Butsyk, S Camacho, CM Campbell, S Caringi, A Chang, BS Chang, WC Charvet, JL Chen, CH Chernichenko, S Chi, CY Chiu, M Choi, IJ Choi, JB Choudhury, RK Christiansen, P Chujo, T Chung, P Churyn, A Chvala, O Cianciolo, V Citron, Z Cole, BA del Valle, ZC Connors, M Constantin, P Csanad, M Csorgo, T Dahms, T Dairaku, S Danchev, I Das, K Datta, A David, G Dayananda, MK Denisov, A d'Enterria, D Deshpande, A Desmond, EJ Dharmawardane, KV Dietzsch, O Dion, A Donadelli, M D'Orazio, L Drapier, O Drees, A Drees, KA Dubey, AK Durham, JM Durum, A Dutta, D Dzhordzhadze, V Edwards, S Efremenko, YV Ellinghaus, F Engelmore, T Enokizono, A En'yo, H Esumi, S Eyser, KO Fadem, B Fields, DE Finger, M Finger, M Fleuret, F Fokin, SL Fraenkel, Z Frantz, JE Franz, A Frawley, AD Fujiwara, K Fukao, Y Fusayasu, T Garishvili, I Glenn, A Gong, H Gonin, M Gosset, J Goto, Y de Cassagnac, RG Grau, N Greene, SV Grim, G Perdekamp, MG Gunji, T Gustafsson, HA Henni, AH Haggerty, JS Hahn, KI Hamagaki, H Hamblen, J Hanks, J Han, R Hartouni, EP Haruna, K Haslum, E Hayano, R Heffner, M Hemmick, TK Hester, T He, X Hill, JC Hohlmann, M Holzmann, W Homma, K Hong, B Horaguchi, T Hornback, D Huang, S Ichihara, T Ichimiya, R Iinuma, H Ikeda, Y Imai, K Imrek, J Inaba, M Isenhower, D Ishihara, M Isobe, T Issah, M Isupov, A Ivanischev, D Iwanaga, Y Jacak, BV Jia, J Jiang, X Jin, J Johnson, BM Jones, T Joo, KS Jouan, D Jumper, DS Kajihara, F Kametani, S Kamihara, N Kamin, J Kang, JH Kapustinsky, J Karatsu, K Kasai, M Kawall, D Kawashima, M Kazantsev, AV Kempel, T Khanzadeev, A Kijima, KM Kikuchi, J Kim, A Kim, BI Kim, DH Kim, DJ Kim, EJ Kim, E Kim, SH Kim, YJ Kinney, E Kiriluk, K Kiss, A Kistenev, E Klay, J Klein-Boesing, C Kochenda, L Komkov, B Konno, M Koster, J Kozlov, A Kral, A Kravitz, A Kunde, GJ Kurita, K Kurosawa, M Kweon, MJ Kwon, Y Kyle, GS Lacey, R Lai, YS Lajoie, JG Layton, D Lebedev, A Lee, DM Lee, J Lee, KB Lee, KS Lee, T Leitch, MJ Leite, MAL Lenzi, B Lichtenwalner, P Liebing, P Levy, LAL Liska, T Litvinenko, A Liu, H Liu, MX Li, X Love, B Lynch, D Maguire, CF Makdisi, YI Malakhov, A Malik, MD Manko, VI Mannel, E Mao, Y Masek, L Masui, H Matathias, F McCumber, M McGaughey, PL Means, N Meredith, B Miake, Y Mibe, T Mignerey, AC Mikes, P Miki, K Milov, A Mishra, M Mitchell, JT Mohanty, AK Moon, HJ Morino, Y Morreale, A Morrison, DP Moukhanova, TV Mukhopadhyay, D Murakami, T Murata, J Nagamiya, S Nagle, JL Naglis, M Nagy, MI Nakagawa, I Nakamiya, Y Nakamura, KR Nakamura, T Nakano, K Nam, S Newby, J Nguyen, M Nihashi, M Niita, T Nouicer, R Nyanin, AS Oakley, C O'Brien, E Oda, SX Ogilvie, CA Okada, K Oka, M Onuki, Y Oskarsson, A Ouchida, M Ozawa, K Pak, R Palounek, APT Pantuev, V Papavassiliou, V Park, IH Park, J Park, SK Park, WJ Pate, SF Pei, H Peng, JC Pereira, H Peresedov, V Peressounko, DY Petti, R Pinkenburg, C Pisani, RP Proissl, M Purschke, ML Purwar, AK Qu, H Rak, J Rakotozafindrabe, A Ravinovich, I Read, KF Rembeczki, S Reygers, K Riabov, V Riabov, Y Richardson, E Roach, D Roche, G Rolnick, SD Rosati, M Rosen, CA Rosendahl, SSE Rosnet, P Rukoyatkin, P Ruzicka, P Rykov, VL Sahlmueller, B Saito, N Sakaguchi, T Sakai, S Sakashita, K Samsonov, V Sano, S Sato, T Sawada, S Sedgwick, K Seele, J Seidl, R Semenov, AY Semenov, V Seto, R Sharma, D Shein, I Shibata, TA Shigaki, K Shimomura, M Shoji, K Shukla, P Sickles, A Silva, CL Silvermyr, D Silvestre, C Sim, KS Singh, BK Singh, CP Singh, V Slunecka, M Soldatov, A Soltz, RA Sondheim, WE Sorensen, SP Sourikova, IV Staley, F Stankus, PW Stenlund, E Stepanov, M Ster, A Stoll, SP Sugitate, T Suire, C Sukhanov, A Sziklai, J Takagui, EM Taketani, A Tanabe, R Tanaka, Y Taneja, S Tanida, K Tannenbaum, MJ Tarafdar, S Taranenko, A Tarjan, P Themann, H Thomas, D Thomas, TL Togawa, M Toia, A Tomasek, L Tomita, Y Torii, H Towell, RS Tram, VN Tserruya, I Tsuchimoto, Y Vale, C Valle, H van Hecke, HW Vazquez-Zambrano, E Veicht, A Velkovska, J Vertesi, R Vinogradov, AA Virius, M Vrba, V Vznuzdaev, E Wang, XR Watanabe, D Watanabe, K Watanabe, Y Wei, F Wessels, J White, SN Winter, D Woody, CL Wright, RM Wysocki, M Xie, W Yamaguchi, YL Yamaura, K Yang, R Yanovich, A Ying, J Yokkaichi, S Young, GR Younus, I You, Z Yushmanov, IE Zajc, WA Zaudtke, O Zhang, C Zhou, S Zolin, L AF Adare, A. Afanasiev, S. Aidala, C. Ajitanand, N. N. Akiba, Y. Al-Bataineh, H. Alexander, J. Al-Ta'ani, H. Angerami, A. Aoki, K. Apadula, N. Aphecetche, L. Aramaki, Y. Asai, J. Atomssa, E. T. Averbeck, R. Awes, T. C. Azmoun, B. Babintsev, V. Bai, M. Baksay, G. Baksay, L. Baldisseri, A. Barish, K. N. Barnes, P. D. Bassalleck, B. Basye, A. T. Bathe, S. Batsouli, S. Baublis, V. Baumann, C. Bazilevsky, A. Belikov, S. Belmont, R. Bennett, R. Berdnikov, A. Berdnikov, Y. Bhom, J. H. Bickley, A. A. Blau, D. S. Boissevain, J. G. Bok, J. S. Borel, H. Borggren, N. Boyle, K. Brooks, M. L. Buesching, H. Bumazhnov, V. Bunce, G. Butsyk, S. Camacho, C. M. Campbell, S. Caringi, A. Chang, B. S. Chang, W. C. Charvet, J. -L. Chen, C. -H. Chernichenko, S. Chi, C. Y. Chiu, M. Choi, I. J. Choi, J. B. Choudhury, R. K. Christiansen, P. Chujo, T. Chung, P. Churyn, A. Chvala, O. Cianciolo, V. Citron, Z. Cole, B. A. del Valle, Z. Conesa Connors, M. Constantin, P. Csanad, M. Csoergo, T. Dahms, T. Dairaku, S. Danchev, I. Das, K. Datta, A. David, G. Dayananda, M. K. Denisov, A. d'Enterria, D. Deshpande, A. Desmond, E. J. Dharmawardane, K. V. Dietzsch, O. Dion, A. Donadelli, M. D'Orazio, L. Drapier, O. Drees, A. Drees, K. A. Dubey, A. K. Durham, J. M. Durum, A. Dutta, D. Dzhordzhadze, V. Edwards, S. Efremenko, Y. V. Ellinghaus, F. Engelmore, T. Enokizono, A. En'yo, H. Esumi, S. Eyser, K. O. Fadem, B. Fields, D. E. Finger, M., Jr. Finger, M. Fleuret, F. Fokin, S. L. Fraenkel, Z. Frantz, J. E. Franz, A. Frawley, A. D. Fujiwara, K. Fukao, Y. Fusayasu, T. Garishvili, I. Glenn, A. Gong, H. Gonin, M. Gosset, J. Goto, Y. de Cassagnac, R. Granier Grau, N. Greene, S. V. Grim, G. Perdekamp, M. Grosse Gunji, T. Gustafsson, H. -A Henni, A. Hadj Haggerty, J. S. Hahn, K. I. Hamagaki, H. Hamblen, J. Hanks, J. Han, R. Hartouni, E. P. Haruna, K. Haslum, E. Hayano, R. Heffner, M. Hemmick, T. K. Hester, T. He, X. Hill, J. C. Hohlmann, M. Holzmann, W. Homma, K. Hong, B. Horaguchi, T. Hornback, D. Huang, S. Ichihara, T. 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CA PHENIX Collaboration TI Measurement of transverse single-spin asymmetries for J/psi production in polarized p plus p collisions at root s=200 GeV SO PHYSICAL REVIEW D LA English DT Article ID QUANTUM CHROMODYNAMICS; PION-PRODUCTION; ANALYZING POWER; SCATTERING; MOMENTUM; NUCLEON; TARGET AB We report the first measurement of transverse single-spin asymmetries in J/psi production from transversely polarized p + p collisions at root s = 200 GeV with data taken by the PHENIX experiment in 2006 and 2008. The measurement was performed over the rapidity ranges 1.2 < vertical bar y vertical bar < 2.2 and vertical bar y vertical bar < 0.35 for transverse momenta up to 6 GeV/c. J/psi production at the Relativistic Heavy Ion Collider is dominated by processes involving initial-state gluons, and transverse single-spin asymmetries of the J/psi can provide access to gluon dynamics within the nucleon. Such asymmetries may also shed light on the long-standing question in QCD of the J/psi production mechanism. Asymmetries were obtained as a function of J/psi transverse momentum and Feynman-x, with a value of -0.086 +/- 0.026(stat) +/- 0.003(syst) in the forward region. This result suggests possible nonzero trigluon correlation functions in transversely polarized protons and, if well defined in this reaction, a nonzero gluon Sivers distribution function. C1 [Adare, A.; Bickley, A. A.; Ellinghaus, F.; Glenn, A.; Kinney, E.; Kiriluk, K.; Levy, L. A. Linden; Nagle, J. L.; Rosen, C. A.; Seele, J.; Wysocki, M.] Univ Colorado, Boulder, CO 80309 USA. [Basye, A. T.; Isenhower, D.; Jones, T.; Jumper, D. S.; Thomas, D.; Towell, R. S.; Wright, R. M.] Abilene Christian Univ, Abilene, TX 79699 USA. [Chang, W. C.] Acad Sinica, Inst Phys, Taipei 11529, Taiwan. [Mishra, M.; Singh, B. K.; Singh, C. P.; Singh, V.; Tarafdar, S.] Banaras Hindu Univ, Dept Phys, Varanasi 221005, Uttar Pradesh, India. 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EM jacak@skipper.physics.sunysb.edu RI Sorensen, Soren /K-1195-2016; Yokkaichi, Satoshi/C-6215-2017; Mignerey, Alice/D-6623-2011; seto, richard/G-8467-2011; Csanad, Mate/D-5960-2012; Wei, Feng/F-6808-2012; Csorgo, Tamas/I-4183-2012; Tomasek, Lukas/G-6370-2014; Blau, Dmitry/H-4523-2012; En'yo, Hideto/B-2440-2015; Hayano, Ryugo/F-7889-2012; HAMAGAKI, HIDEKI/G-4899-2014; Durum, Artur/C-3027-2014; Taketani, Atsushi/E-1803-2017; Semenov, Vitaliy/E-9584-2017 OI Sorensen, Soren /0000-0002-5595-5643; Tomasek, Lukas/0000-0002-5224-1936; Hayano, Ryugo/0000-0002-1214-7806; Taketani, Atsushi/0000-0002-4776-2315; FU Office of Nuclear Physics in the Office of Science of the Department of Energy; National Science Foundation; Renaissance Technologies LLC; Abilene Christian University Research Council; Research Foundation of SUNY; College of Arts and Sciences; Vanderbilt University (USA); Ministry of Education, Culture, Sports, Science, and Technology; Japan Society for the Promotion of Science (Japan); Conselho Nacional de Desenvolvimento Cientifico e Tecnologico; Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (Brazil); Natural Science Foundation of China (People's Republic of China); Ministry of Education, Youth and Sports (Czech Republic); Centre National de la Recherche Scientifique; Commissariat a l'Energie Atomique; Institut National de Physique Nucleaire et de Physique des Particules (France); Ministry of Industry, Science and Tekhnologies; Bundesministerium fur Bildung und Forschung; Deutscher Akademischer Austausch Dienst; Alexander von Humboldt Stiftung (Germany); Hungarian National Science Fund; OTKA (Hungary); Department of Atomic Energy (India); Israel Science Foundation (Israel); National Research Foundation; Ministry Education Science and Technology (Korea); Ministry of Education and Science; Russia Academy of Sciences; Federal Agency of Atomic Energy (Russia); VR; Wallenberg Foundation (Sweden); U.S. Civilian Research and Development Foundation for the Independent States of the Former Soviet Union; US-Hungarian Fulbright Foundation for Educational Exchange; US-Israel Binational Science Foundation FX We thank the staff of the Collider-Accelerator and Physics Departments at Brookhaven National Laboratory and the staff of the other PHENIX participating institutions for their vital contributions. We also thank Feng Yuan, Jianwei Qiu, Zhongbo Kang, Yuji Koike, Kazuhiro Tanaka, and Jian Zhou for helpful discussions. We acknowledge support from the Office of Nuclear Physics in the Office of Science of the Department of Energy, the National Science Foundation, a sponsored research grant from Renaissance Technologies LLC, Abilene Christian University Research Council, Research Foundation of SUNY, and Dean of the College of Arts and Sciences, Vanderbilt University (USA); Ministry of Education, Culture, Sports, Science, and Technology and the Japan Society for the Promotion of Science (Japan); Conselho Nacional de Desenvolvimento Cientifico e Tecnologico and Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (Brazil), Natural Science Foundation of China (People's Republic of China); Ministry of Education, Youth and Sports (Czech Republic); Centre National de la Recherche Scientifique, Commissariat a l'Energie Atomique, and Institut National de Physique Nucleaire et de Physique des Particules (France); Ministry of Industry, Science and Tekhnologies, Bundesministerium fur Bildung und Forschung, Deutscher Akademischer Austausch Dienst, and Alexander von Humboldt Stiftung (Germany); Hungarian National Science Fund, OTKA (Hungary); Department of Atomic Energy (India); Israel Science Foundation (Israel); National Research Foundation and WCU Program of the Ministry Education Science and Technology (Korea); Ministry of Education and Science, Russia Academy of Sciences, and Federal Agency of Atomic Energy (Russia); VR and the Wallenberg Foundation (Sweden); the U.S. Civilian Research and Development Foundation for the Independent States of the Former Soviet Union; the US-Hungarian Fulbright Foundation for Educational Exchange; and the US-Israel Binational Science Foundation. NR 47 TC 17 Z9 17 U1 6 U2 29 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 1550-7998 J9 PHYS REV D JI Phys. Rev. D PD DEC 30 PY 2010 VL 82 IS 11 AR 112008 DI 10.1103/PhysRevD.82.112008 PG 13 WC Astronomy & Astrophysics; Physics, Particles & Fields SC Astronomy & Astrophysics; Physics GA 711HP UT WOS:000286578000002 ER PT J AU Riordan, S Abrahamyan, S Craver, B Kelleher, A Kolarkar, A Miller, J Cates, GD Liyanage, N Wojtsekhowski, B Acha, A Allada, K Anderson, B Aniol, KA Annand, JRM Arrington, J Averett, T Beck, A Bellis, M Boeglin, W Breuer, H Calarco, JR Camsonne, A Chen, JP Chudakov, E Coman, L Crowe, B Cusanno, F Day, D Degtyarenko, P Dolph, PAM Dutta, C Ferdi, C Fernandez-Ramirez, C Feuerbach, R Fraile, LM Franklin, G Frullani, S Fuchs, S Garibaldi, F Gevorgyan, N Gilman, R Glamazdin, A Gomez, J Grimm, K Hansen, JO Herraiz, JL Higinbotham, DW Holmes, R Holmstrom, T Howell, D de Jager, CW Jiang, X Jones, MK Katich, J Kaufman, LJ Khandaker, M Kelly, JJ Kiselev, D Korsch, W LeRose, J Lindgren, R Markowitz, P Margaziotis, DJ Beck, SMT Mayilyan, S McCormick, K Meziani, ZE Michaels, R Moffit, B Nanda, S Nelyubin, V Ngo, T Nikolenko, DM Norum, B Pentchev, L Perdrisat, CF Piasetzky, E Pomatsalyuk, R Protopopescu, D Puckett, AJR Punjabi, VA Qian, X Qiang, Y Quinn, B Rachek, I Ransome, RD Reimer, PE Reitz, B Roche, J Ron, G Rondon, O Rosner, G Saha, A Sargsian, MM Sawatzky, B Segal, J Shabestari, M Shahinyan, A Shestakov, Y Singh, J Sirca, S Souder, P Stepanyan, S Stibunov, V Sulkosky, V Tajima, S Tobias, WA Udias, JM Urciuoli, GM Vlahovic, B Voskanyan, H Wang, K Wesselmann, FR Vignote, JR Wood, SA Wright, J Yao, H Zhu, X AF Riordan, S. Abrahamyan, S. Craver, B. Kelleher, A. Kolarkar, A. Miller, J. Cates, G. D. Liyanage, N. Wojtsekhowski, B. Acha, A. Allada, K. Anderson, B. Aniol, K. A. Annand, J. R. M. Arrington, J. Averett, T. Beck, A. Bellis, M. Boeglin, W. Breuer, H. Calarco, J. R. Camsonne, A. Chen, J. P. Chudakov, E. Coman, L. Crowe, B. Cusanno, F. Day, D. Degtyarenko, P. Dolph, P. A. M. Dutta, C. Ferdi, C. Fernandez-Ramirez, C. Feuerbach, R. Fraile, L. M. Franklin, G. Frullani, S. Fuchs, S. Garibaldi, F. Gevorgyan, N. Gilman, R. Glamazdin, A. Gomez, J. Grimm, K. Hansen, J-O Herraiz, J. L. Higinbotham, D. W. Holmes, R. Holmstrom, T. Howell, D. de Jager, C. W. Jiang, X. Jones, M. K. Katich, J. Kaufman, L. J. Khandaker, M. Kelly, J. J. Kiselev, D. Korsch, W. LeRose, J. Lindgren, R. Markowitz, P. Margaziotis, D. J. Beck, S. May-Tal Mayilyan, S. McCormick, K. Meziani, Z-E Michaels, R. Moffit, B. Nanda, S. Nelyubin, V. Ngo, T. Nikolenko, D. M. Norum, B. Pentchev, L. Perdrisat, C. F. Piasetzky, E. Pomatsalyuk, R. Protopopescu, D. Puckett, A. J. R. Punjabi, V. A. Qian, X. Qiang, Y. Quinn, B. Rachek, I. Ransome, R. D. Reimer, P. E. Reitz, B. Roche, J. Ron, G. Rondon, O. Rosner, G. Saha, A. Sargsian, M. M. Sawatzky, B. Segal, J. Shabestari, M. Shahinyan, A. Shestakov, Yu. Singh, J. Sirca, S. Souder, P. Stepanyan, S. Stibunov, V. Sulkosky, V. Tajima, S. Tobias, W. A. Udias, J. M. Urciuoli, G. M. Vlahovic, B. Voskanyan, H. Wang, K. Wesselmann, F. R. Vignote, J. R. Wood, S. A. Wright, J. Yao, H. Zhu, X. TI Measurements of the Electric Form Factor of the Neutron up to Q(2)=3.4 GeV2 Using the Reaction (3)(He)over-right-arrowe((e)over-right-arrow, e ' n)pp SO PHYSICAL REVIEW LETTERS LA English DT Article ID GENERALIZED PARTON DISTRIBUTIONS; POLARIZATION TRANSFER; SCATTERING; NUCLEON; (GEV/C)(2); HE-3 AB The electric form factor of the neutron was determined from studies of the reaction (3)(He) over right arrowe((e) over right arrow, e ' n)pp in quasielastic kinematics in Hall A at Jefferson Lab. Longitudinally polarized electrons were scattered off a polarized target in which the nuclear polarization was oriented perpendicular to the momentum transfer. The scattered electrons were detected in a magnetic spectrometer in coincidence with neutrons that were registered in a large-solid-angle detector. More than doubling the Q(2) range over which it is known, we find G(E)(n) = 0.0236 +/- 0.0017(stat) +/- 0.0026(syst), 0.0208 +/- 0. 0024 +/- 0.0019, and 0.0147 +/- 0.0020 +/- 0.0014 for Q(2) = 1.72, 2.48, and 3.41 GeV2, respectively. C1 [Wojtsekhowski, B.; Beck, A.; Camsonne, A.; Chen, J. P.; Chudakov, E.; Degtyarenko, P.; Feuerbach, R.; Gilman, R.; Gomez, J.; Hansen, J-O; Higinbotham, D. W.; de Jager, C. W.; Jones, M. K.; LeRose, J.; Beck, S. May-Tal; Michaels, R.; Nanda, S.; Reitz, B.; Roche, J.; Saha, A.; Segal, J.; Wood, S. A.] Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. [Riordan, S.; Bellis, M.; Franklin, G.; Quinn, B.] Carnegie Mellon Univ, Pittsburgh, PA 15213 USA. [Riordan, S.; Craver, B.; Cates, G. D.; Liyanage, N.; Day, D.; Dolph, P. A. M.; Lindgren, R.; Nelyubin, V.; Norum, B.; Rondon, O.; Shabestari, M.; Singh, J.; Tajima, S.; Tobias, W. A.; Wang, K.] Univ Virginia, Charlottesville, VA 22903 USA. [Riordan, S.; Kaufman, L. J.] Univ Massachusetts, Amherst, MA 01003 USA. [Abrahamyan, S.; Gevorgyan, N.; Mayilyan, S.; Shahinyan, A.; Voskanyan, H.] Yerevan Phys Inst, Yerevan 375036, Armenia. [Kelleher, A.; Averett, T.; Feuerbach, R.; Fuchs, S.; Grimm, K.; Holmstrom, T.; Katich, J.; Moffit, B.; Pentchev, L.; Perdrisat, C. F.; Sulkosky, V.] Coll William & Mary, Williamsburg, VA 23187 USA. [Kolarkar, A.; Allada, K.; Dutta, C.; Korsch, W.] Univ Kentucky, Lexington, KY 40506 USA. [Miller, J.; Breuer, H.; Kelly, J. J.] Univ Maryland, College Pk, MD 20742 USA. [Acha, A.; Boeglin, W.; Coman, L.; Markowitz, P.; Sargsian, M. M.] Florida Int Univ, Miami, FL 33199 USA. [Anderson, B.] Kent State Univ, Kent, OH 44242 USA. [Aniol, K. A.; Margaziotis, D. J.; Ngo, T.] Calif State Univ Los Angeles, Los Angeles, CA 90032 USA. [Annand, J. R. M.; Protopopescu, D.; Rosner, G.] Univ Glasgow, Glasgow G12 8QQ, Lanark, Scotland. [Arrington, J.; Reimer, P. E.] Argonne Natl Lab, Div Phys, Argonne, IL 60439 USA. [Beck, A.; Beck, S. May-Tal; Puckett, A. J. R.; Qiang, Y.; Sirca, S.; Zhu, X.] MIT, Cambridge, MA 02139 USA. [Calarco, J. R.] Univ New Hampshire, Durham, NH 03824 USA. [Crowe, B.; Vlahovic, B.] N Carolina Cent Univ, Durham, NC 27707 USA. [Cusanno, F.; Frullani, S.; Garibaldi, F.; Urciuoli, G. M.] Ist Nazl Fis Nucl, Grp Sanita Coll, Sez Roma, Rome, Italy. [Cusanno, F.; Frullani, S.; Garibaldi, F.; Urciuoli, G. M.] Ist Super Sanita, I-00161 Rome, Italy. [Ferdi, C.] Univ Clermont Ferrand, IN2P3, F-63177 Clermont Ferrand, France. [Fernandez-Ramirez, C.; Fraile, L. M.; Herraiz, J. L.; Udias, J. M.] Univ Complutense Madrid, Madrid, Spain. [Gilman, R.; Jiang, X.; Ransome, R. D.] Rutgers State Univ, Piscataway, NJ 08854 USA. [Glamazdin, A.; Pomatsalyuk, R.] Kharkov Phys & Technol Inst, UA-61108 Kharkov, Ukraine. [Holmes, R.; Souder, P.] Syracuse Univ, Syracuse, NY 13244 USA. [Howell, D.] Univ Illinois, Urbana, IL 61801 USA. [Khandaker, M.; Punjabi, V. A.; Wesselmann, F. R.] Norfolk State Univ, Norfolk, VA 23504 USA. [Kiselev, D.] Univ Basel, CH-4056 Basel, Switzerland. [McCormick, K.; Wright, J.] Old Dominion Univ, Norfolk, VA 23529 USA. [Meziani, Z-E; Sawatzky, B.; Yao, H.] Temple Univ, Philadelphia, PA 19122 USA. [Nikolenko, D. M.; Rachek, I.; Shestakov, Yu.] Budker Inst Nucl Phys, Novosibirsk 630090, Russia. [Piasetzky, E.; Ron, G.] Tel Aviv Univ, IL-69978 Tel Aviv, Israel. [Qian, X.] Duke Univ, Durham, NC 27708 USA. [Qian, X.] TUNL, Durham, NC 27708 USA. [Stepanyan, S.] Kyungpook Natl Univ, Taegu 702701, South Korea. [Stibunov, V.] Inst Nucl Phys, Tomsk 634050, Russia. [Vignote, J. R.] Inst Estruct Mat, E-28006 Madrid, Spain. RP Wojtsekhowski, B (reprint author), Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. EM bogdanw@jlab.org RI Day, Donal/C-5020-2015; LOPEZ HERRAIZ, JOAQUIN/E-9234-2010; Quinn, Brian/N-7343-2014; Singh, Jaideep/H-2346-2013; Higinbotham, Douglas/J-9394-2014; Franklin, Gregg/N-7743-2014; Fernandez Ramirez, Cesar/E-9213-2010; Fraile, Luis/B-8668-2011; Udias, Jose/A-7523-2010; Arrington, John/D-1116-2012; Protopopescu, Dan/D-5645-2012; Rondon Aramayo, Oscar/B-5880-2013; Reimer, Paul/E-2223-2013 OI Day, Donal/0000-0001-7126-8934; LOPEZ HERRAIZ, JOAQUIN/0000-0001-7208-8863; Quinn, Brian/0000-0003-2800-986X; Singh, Jaideep/0000-0002-4810-4824; Higinbotham, Douglas/0000-0003-2758-6526; Franklin, Gregg/0000-0003-4176-1378; Fernandez Ramirez, Cesar/0000-0001-8979-5660; Fraile, Luis/0000-0002-6281-3635; Udias, Jose/0000-0003-3714-764X; Arrington, John/0000-0002-0702-1328; FU National Science Foundation; U.S. Department of Energy; United Kingdom Engineering and Physical Science Research Council; U.S. DOE [DE-AC05-060R23177] FX We thank the Jefferson Lab Hall A technical staff for their outstanding support. This work was supported in part by the National Science Foundation, the U.S. Department of Energy and the United Kingdom Engineering and Physical Science Research Council. Jefferson Science Associates, LLC, operates Jefferson Lab for the U.S. DOE under U.S. DOE Contract No. DE-AC05-060R23177. NR 47 TC 75 Z9 75 U1 1 U2 12 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 0031-9007 J9 PHYS REV LETT JI Phys. Rev. Lett. PD DEC 30 PY 2010 VL 105 IS 26 AR 262302 DI 10.1103/PhysRevLett.105.262302 PG 5 WC Physics, Multidisciplinary SC Physics GA 713VZ UT WOS:000286766800001 PM 21231649 ER PT J AU Fehl, DL Chandler, GA Stygar, WA Olson, RE Ruiz, CL Hohlfelder, JJ Mix, LP Biggs, F Berninger, M Frederickson, PO Frederickson, R AF Fehl, D. L. Chandler, G. A. Stygar, W. A. Olson, R. E. Ruiz, C. L. Hohlfelder, J. J. Mix, L. P. Biggs, F. Berninger, M. Frederickson, P. O. Frederickson, R. TI Characterization and error analysis of an N X N unfolding procedure applied to filtered, photoelectric x-ray detector arrays. II. Error analysis and generalization SO PHYSICAL REVIEW SPECIAL TOPICS-ACCELERATORS AND BEAMS LA English DT Article ID LINEAR INVERSE PROBLEMS; GROSS EARTH DATA; DISCRETE-DATA; PLASMAS; SPECTROMETER; POWER AB A five-channel, filtered-x-ray-detector (XRD) array has been used to measure time-dependent, soft-x-ray flux emitted by z-pinch plasmas at the Z pulsed-power accelerator (Sandia National Laboratories, Albuquerque, New Mexico, USA). The preceding, companion paper [D. L. Fehl et al., Phys. Rev. ST Accel. Beams 13, 120402 (2010)] describes an algorithm for spectral reconstructions (unfolds) and spectrally integrated flux estimates from data obtained by this instrument. The unfolded spectrum S-unfold(E, t) is based on (N = 5) first-order B-splines (histograms) in contiguous unfold bins j = 1, ... ,N; the recovered x-ray flux F-unfold(t) is estimated as integral S-unfold(E, t)dE, where E is x-ray energy and t is time. This paper adds two major improvements to the preceding unfold analysis: (a) Error analysis.-Both data noise and response-function uncertainties are propagated into S-unfold(E, t) and F-unfold(t). Noise factors nu are derived from simulations to quantify algorithm-induced changes in the noise-to-signal ratio (NSR) for S-unfold in each unfold bin j and for F-unfold (nu equivalent to NSRoutput/NSRinput): for S-unfold, 1 less than or similar to nu(j) less than or similar to 30, an outcome that is strongly spectrally dependent; for F-unfold, 0.6 less than or similar to nu(F) less than or similar to 1, a result that is less spectrally sensitive and corroborated independently. For nominal z-pinch experiments, the combined uncertainty (noise and calibrations) in F-unfold(t) at peak is estimated to be similar to 15%. (b) Generalization of the unfold method.-Spectral sensitivities (called here passband functions) are constructed for Sunfold and Funfold. Predicting how the unfold algorithm reconstructs arbitrary spectra is thereby reduced to quadratures. These tools allow one to understand and quantitatively predict algorithmic distortions (including negative artifacts), to identify potentially troublesome spectra, and to design more useful response functions. C1 [Fehl, D. L.; Chandler, G. A.; Stygar, W. A.; Olson, R. E.; Ruiz, C. L.; Hohlfelder, J. J.; Mix, L. P.; Biggs, F.] Sandia Natl Labs, Albuquerque, NM 87185 USA. [Berninger, M.; Frederickson, P. O.; Frederickson, R.] Natl Secur Technol LLC, Los Alamos, NM 87544 USA. RP Fehl, DL (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87185 USA. FU United States Department of Energy [DE-AC04-94AL85000] FX This work was performed by Sandia National Laboratories. 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. We also wish to thank the reviewers of this article for their patience, insights, and helpful suggestions. NR 55 TC 1 Z9 1 U1 0 U2 2 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 1098-4402 J9 PHYS REV SPEC TOP-AC JI Phys. Rev. Spec. Top.-Accel. Beams PD DEC 30 PY 2010 VL 13 IS 12 AR 120403 DI 10.1103/PhysRevSTAB.13.120403 PG 20 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA 701DB UT WOS:000285793400002 ER PT J AU Fehl, DL Chandler, GA Stygar, WA Olson, RE Ruiz, CL Hohlfelder, JJ Mix, LP Biggs, F Berninger, M Frederickson, PO Frederickson, R AF Fehl, D. L. Chandler, G. A. Stygar, W. A. Olson, R. E. Ruiz, C. L. Hohlfelder, J. J. Mix, L. P. Biggs, F. Berninger, M. Frederickson, P. O. Frederickson, R. TI Characterization and error analysis of an N X N unfolding procedure applied to filtered, photoelectric x-ray detector arrays. I. Formulation and testing SO PHYSICAL REVIEW SPECIAL TOPICS-ACCELERATORS AND BEAMS LA English DT Article ID FREDHOLM INTEGRAL-EQUATIONS; INERTIAL CONFINEMENT FUSION; LINEAR INVERSE PROBLEMS; LASER-PRODUCED PLASMAS; Z-PINCH EXPERIMENTS; GROSS EARTH DATA; DISCRETE-DATA; RADIATION; SPECTROMETER; TEMPERATURES AB An algorithm for spectral reconstructions (unfolds) and spectrally integrated flux estimates from data obtained by a five-channel, filtered x-ray-detector array (XRD) is described in detail and characterized. This diagnostic is a broad-channel spectrometer, used primarily to measure time-dependent soft x-ray flux emitted by z-pinch plasmas at the Z pulsed-power accelerator (Sandia National Laboratories, Albuquerque, New Mexico, USA), and serves as both a plasma probe and a gauge of accelerator performance. The unfold method, suitable for online analysis, arises naturally from general assumptions about the x-ray source and spectral properties of the channel responses; a priori constraints control the ill-posed nature of the inversion. The unfolded spectrum is not assumed to be Planckian. This study is divided into two consecutive papers. This paper considers three major issues: (a) Formulation of the unfold method.-The mathematical background, assumptions, and procedures leading to the algorithm are described: the spectral reconstruction S-unfold(E,t)-five histogram x-ray bins j over the x-ray interval, 137 <= E <= 2300 eV at each time step t-depends on the shape and overlap of the calibrated channel responses and on the maximum electrical power delivered to the plasma. The x-ray flux F-unfold is estimated as integral S-unfold(E, t)dE. (b) Validation with simulations.-Tests of the unfold algorithm with known static and time-varying spectra are described. These spectra included-but were not limited to-Planckian spectra S-bb(E, T) (25 <= T <= 250 eV), from which noise-free channel data were simulated and unfolded. For Planckian simulations with 125 <= T <= 250 eV and typical responses, the binwise unfold values S-j and the corresponding binwise averages < S-bb >(j) agreed to similar to 20%, except where S-bb << max{S-bb}. Occasionally, unfold values S-j less than or similar to 0 (artifacts) were encountered. The algorithm recovered greater than or similar to 90% of the x-ray flux over the wider range, 75 <= T <= 250 eV. For lower T, the test and unfolded spectra increasingly diverged as larger fractions of S-bb(E, T) fell below the detection threshold (similar to 137 eV) of the diagnostic. (c) Comparison with other analyses and diagnostics.-The results of the histogram algorithm are compared with other analyses, including a test with data acquired by the DANTE filtered-XRD array at the NOVA laser facility. Overall, the histogram algorithm is found to be most useful for x-ray flux estimates, as opposed to spectral details. The following companion paper [D. L. Fehl et al., Phys. Rev. ST Accel. Beams 13, 120403 (2010)] considers (a) uncertainties in S-unfold and F-unfold induced by both data noise and calibrational errors in the response functions; and (b) generalization of the algorithm to arbitrary spectra. These techniques apply to other diagnostics with analogous channel responses and supported by unfold algorithms of invertible matrix form. C1 [Fehl, D. L.; Chandler, G. A.; Stygar, W. A.; Olson, R. E.; Ruiz, C. L.; Hohlfelder, J. J.; Mix, L. P.; Biggs, F.] Sandia Natl Labs, Albuquerque, NM 87185 USA. [Berninger, M.; Frederickson, P. O.; Frederickson, R.] Natl Secur Technol LLC, Los Alamos, NM 87544 USA. RP Fehl, DL (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87185 USA. FU United States Department of Energy [DE-AC04-94AL85000] FX It is a pleasure to note the contributions of Harry Kornblum (Lawrence Livermore Laboratories), Tom Tunnel (NSTech), Ray Dukart, Jim Bailey, and especially Ray Leeper. We are also grateful to our reviewers for their comments and for additional references. This work was performed by Sandia National Laboratories. 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 122 TC 4 Z9 4 U1 0 U2 4 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 1098-4402 J9 PHYS REV SPEC TOP-AC JI Phys. Rev. Spec. Top.-Accel. Beams PD DEC 30 PY 2010 VL 13 IS 12 AR 120402 DI 10.1103/PhysRevSTAB.13.120402 PG 26 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA 701DB UT WOS:000285793400001 ER PT J AU Zhao, X Geng, RL Tyagi, PV Hayano, H Kato, S Nishiwaki, M Saeki, T Sawabe, M AF Zhao, Xin Geng, Rong-Li Tyagi, P. V. Hayano, Hitoshi Kato, Shigeki Nishiwaki, Michiru Saeki, Takayuki Sawabe, Motoaki TI Surface characterization of Nb samples electropolished with real superconducting rf accelerator cavities SO PHYSICAL REVIEW SPECIAL TOPICS-ACCELERATORS AND BEAMS LA English DT Article ID FIELD-EMISSION; NIOBIUM AB We report the results of surface characterizations of niobium (Nb) samples electropolished together with a single cell superconducting radio-frequency accelerator cavity. These witness samples were located in three regions of the cavity, namely at the equator, the iris, and the beam pipe. Auger electron spectroscopy was utilized to probe the chemical composition of the topmost four atomic layers. Scanning electron microscopy with energy dispersive x ray for elemental analysis was used to observe the surface topography and chemical composition at the micrometer scale. A few atomic layers of sulfur (S) were found covering the samples nonuniformly. Niobium oxide granules with a sharp geometry were observed on every sample. Some Nb-O granules appeared to also contain sulfur. C1 [Zhao, Xin; Geng, Rong-Li] Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. [Tyagi, P. V.; Kato, Shigeki] Grad Univ Adv Studies, Sch Adv Sci GUAS AS, Ibaraki, Japan. [Hayano, Hitoshi; Kato, Shigeki; Nishiwaki, Michiru; Saeki, Takayuki; Sawabe, Motoaki] High Energy Accelerator Res Org KEK, Ibaraki, Japan. RP Zhao, X (reprint author), Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. EM xinzhao@jlab.org FU U.S. DOE [DE-AC05-06OR23177] FX We acknowledge Dr. Seo Kang of Norfolk State University for his support on AES experiments. We thank the College of William & Mary for the support on SEM experiments. This manuscript has been sponsored by Jefferson Science Associates, LLC under U.S. DOE Contract No. DE-AC05-06OR23177. NR 11 TC 4 Z9 4 U1 0 U2 5 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 1098-4402 J9 PHYS REV SPEC TOP-AC JI Phys. Rev. Spec. Top.-Accel. Beams PD DEC 30 PY 2010 VL 13 IS 12 AR 124702 DI 10.1103/PhysRevSTAB.13.124702 PG 7 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA 701DB UT WOS:000285793400003 ER PT J AU Trabert, E Clementson, J Beiersdorfer, P Santana, JA Ishikawa, Y AF Traebert, Elmar Clementson, Joel Beiersdorfer, Peter Santana, Juan A. Ishikawa, Yasuyuki TI Extreme-ultraviolet spectra of highly charged Pt ions with several valence-shell electrons: Observation and accurate calculations SO PHYSICAL REVIEW A LA English DT Article ID ZN-LIKE IONS; X-RAY-SPECTRA; CU-LIKE IONS; ENERGY-LEVELS; NA-LIKE; LI-LIKE; TRANSITION-PROBABILITIES; 2S(1/2)-2P(3/2) LEVELS; LAMB SHIFT; EBIT DATA AB Previous observations of Cu- through Ge-like high-Z ions have demonstrated that accurate measurements and theory agree well for ions with a single valence electron but that additional electrons in the valence shell cause progressively worsening computational problems. We have obtained highly resolved euv spectra of Pt (Z = 78) ions in an electron-beam ion trap. The measured wavelengths are compared to the results of a number of recent large-scale calculations, including our own multireference Moller-Plesset computations. The latter calculations match the best for Cu- and Zn-like ions and represent an order-of-magnitude improvement in predictive accuracy for Ga- and Ge-like ions. C1 [Traebert, Elmar; Clementson, Joel; Beiersdorfer, Peter] Lawrence Livermore Natl Lab, Div Phys, Livermore, CA 94550 USA. [Traebert, Elmar] Ruhr Univ Bochum, Fak Phys & Astron, Astron Inst, D-44780 Bochum, Germany. [Santana, Juan A.; Ishikawa, Yasuyuki] Univ Puerto Rico, Dept Chem, San Juan, PR 00931 USA. [Santana, Juan A.; Ishikawa, Yasuyuki] Univ Puerto Rico, Chem Phys Program, San Juan, PR 00931 USA. RP Trabert, E (reprint author), Lawrence Livermore Natl Lab, Div Phys, Livermore, CA 94550 USA. EM traebert@astro.rub.de RI Santana, Juan A./G-4329-2011 OI Santana, Juan A./0000-0003-2349-6312 FU Deutsche Forschungsgemeinschaft (DFG); US Department of Energy by Lawrence Livermore National Laboratory [DE-AC52-07NA27344] FX E. T. acknowledges support by the Deutsche Forschungsgemeinschaft (DFG). Some of this work was performed under the auspices of the US Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344. NR 58 TC 7 Z9 7 U1 0 U2 3 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 1050-2947 J9 PHYS REV A JI Phys. Rev. A PD DEC 29 PY 2010 VL 82 IS 6 AR 062519 DI 10.1103/PhysRevA.82.062519 PG 6 WC Optics; Physics, Atomic, Molecular & Chemical SC Optics; Physics GA 713OI UT WOS:000286746900005 ER PT J AU Zou, RQ Zhong, RQ Han, SB Xu, HW Burrell, AK Henson, N Cape, JL Hickmott, DD Timofeeva, TV Larson, TE Zhao, YS AF Zou, Ruqiang Zhong, Ruiqin Han, Songbai Xu, Hongwu Burrell, Anthony K. Henson, Neil Cape, Jonathan L. Hickmott, Donald D. Timofeeva, Tatiana V. Larson, Toti E. Zhao, Yusheng TI A Porous Metal-Organic Replica of alpha-PbO2 for Capture of Nerve Agent Surrogate SO JOURNAL OF THE AMERICAN CHEMICAL SOCIETY LA English DT Article ID ZEOLITIC IMIDAZOLATE FRAMEWORKS; SPACE GAUSSIAN PSEUDOPOTENTIALS; COORDINATION POLYMERS; SURFACE-AREAS; ADSORPTION; TOPOLOGIES; STRATEGY; DESIGN; SITES; ACID AB A novel metal-organic replica of alpha-PbO2 exhibits high capacity for capture of nerve agent surrogate. C1 [Zou, Ruqiang] Peking Univ, Dept Adv Mat & Nanotechnol, Dept Energy & Resources Engn, Coll Engn, Beijing 100871, Peoples R China. [Zou, Ruqiang; Zhong, Ruiqin; Xu, Hongwu; Burrell, Anthony K.; Henson, Neil; Cape, Jonathan L.; Hickmott, Donald D.; Larson, Toti E.; Zhao, Yusheng] Los Alamos Natl Lab, Div Earth & Environm Sci, Los Alamos Neutron Sci Ctr, Mat Phys & Applicat Div, Los Alamos, NM 87545 USA. [Zou, Ruqiang; Zhong, Ruiqin; Xu, Hongwu; Burrell, Anthony K.; Henson, Neil; Cape, Jonathan L.; Hickmott, Donald D.; Larson, Toti E.; Zhao, Yusheng] Los Alamos Natl Lab, Div Theoret, Los Alamos, NM USA. [Han, Songbai] China Inst Atom Energy, Neutron Scattering Lab, Beijing 102413, Peoples R China. [Timofeeva, Tatiana V.] New Mexico Highlands Univ, Dept Chem, Las Vegas, NM 87701 USA. RP Zou, RQ (reprint author), Peking Univ, Dept Adv Mat & Nanotechnol, Dept Energy & Resources Engn, Coll Engn, Beijing 100871, Peoples R China. EM rzou@pku.edu.cn; tlarson@lanl.gov; yzhao@lanl.gov RI Hickmott, Donald/C-2886-2011; Lujan Center, LANL/G-4896-2012; zou, ruqiang/N-8803-2013; OI Larson, Toti/0000-0002-2291-5979; Xu, Hongwu/0000-0002-0793-6923; Henson, Neil/0000-0002-1842-7884; Zou, Ruqiang/0000-0003-0456-4615 FU National Basic Research Program of China [2009CB939902]; LANL [20080780PRD2] FX This work was financially supported by the National Basic Research Program of China (No. 2009CB939902) and LANL Director's funded postdoctoral LDRD Project # 20080780PRD2. We also would like to express our sincere thanks to the reviewers for their comments and constructive suggestions. NR 34 TC 39 Z9 39 U1 7 U2 52 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0002-7863 J9 J AM CHEM SOC JI J. Am. Chem. Soc. PD DEC 29 PY 2010 VL 132 IS 51 BP 17996 EP 17999 DI 10.1021/ja101440z PG 4 WC Chemistry, Multidisciplinary SC Chemistry GA 701LF UT WOS:000285818700007 PM 21138256 ER PT J AU Campbell, PG Abbey, ER Neiner, D Grant, DJ Dixon, DA Liu, SY AF Campbell, Patrick G. Abbey, Eric R. Neiner, Doinita Grant, Daniel J. Dixon, David A. Liu, Shih-Yuan TI Resonance Stabilization Energy of 1,2-Azaborines: A Quantitative Experimental Study by Reaction Calorimetry SO JOURNAL OF THE AMERICAN CHEMICAL SOCIETY LA English DT Article ID HOMOGENEOUS HYDROGENATION; SUBSTITUTED 1,2-DIHYDRO-1,2-AZABORINES; ELECTRON DELOCALIZATION; C-C; B-N; AROMATICITY; OLEFINS; ACETYLENES; BENZENE; SYSTEMS AB Aromatic and single-olefin six-membered BN heterocycles were synthesized, and the heats of hydrogenation were measured calorimetrically. A comparison of the hydrogenation enthalpies of these compounds revealed that 1,2-azaborines have a resonance stabilization energy of 16.6 +/- 1.3 kcal/mol, in good agreement with calculated values. C1 [Campbell, Patrick G.; Abbey, Eric R.; Liu, Shih-Yuan] Univ Oregon, Dept Chem, Eugene, OR 97403 USA. [Neiner, Doinita] Pacific NW Natl Lab, Fundamental Sci Div, Richland, WA 99352 USA. [Grant, Daniel J.; Dixon, David A.] Univ Alabama, Dept Chem, Tuscaloosa, AL 35487 USA. RP Liu, SY (reprint author), Univ Oregon, Dept Chem, Eugene, OR 97403 USA. EM lsy@uoregon.edu RI Liu, Shih-Yuan/J-7813-2012; OI Liu, Shih-Yuan/0000-0003-3148-9147; Campbell, Patrick/0000-0003-0167-4624 FU U.S. Department of Energy [DE-FG36-08GO18143]; Department of Energy, Office of Energy Efficiency and Renewable Energy [DE-PS36-03GO93013] FX The calorimetric measurements were made at Pacific Northwest National Laboratory (PNNL). We thank Dr. Tom Autrey, Dr. John Linehan, Dr. Abhi Karkamkar, and Dr. Kshitij Parab at PNNL for their help with the calorimetric measurements. Support for this work was provided by the U.S. Department of Energy (DE-FG36-08GO18143). Funding was provided in part by the Department of Energy, Office of Energy Efficiency and Renewable Energy, under the Hydrogen Storage Grand Challenge (Solicitation DE-PS36-03GO93013). This work was done as part of the Chemical Hydrogen Storage Center. D.A.D. is indebted to the Robert Ramsay Endowment of the University of Alabama. Dr. Monica Valiliu is thanked for computational data collection. NR 40 TC 46 Z9 47 U1 3 U2 17 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0002-7863 J9 J AM CHEM SOC JI J. Am. Chem. Soc. PD DEC 29 PY 2010 VL 132 IS 51 BP 18048 EP 18050 DI 10.1021/ja109596m PG 3 WC Chemistry, Multidisciplinary SC Chemistry GA 701LF UT WOS:000285818700022 PM 21141893 ER PT J AU Harman, WH Harris, TD Freedman, DE Fong, H Chang, A Rinehart, JD Ozarowski, A Sougrati, MT Grandjean, F Long, GJ Long, JR Chang, CJ AF Harman, W. Hill Harris, T. David Freedman, Danna E. Fong, Henry Chang, Alicia Rinehart, Jeffrey D. Ozarowski, Andrew Sougrati, Moulay T. Grandjean, Fernande Long, Gary J. Long, Jeffrey R. Chang, Christopher J. TI Slow Magnetic Relaxation in a Family of Trigonal Pyramidal Iron(II) Pyrrolide Complexes SO JOURNAL OF THE AMERICAN CHEMICAL SOCIETY LA English DT Article ID SINGLE-MOLECULE MAGNETS; ELECTRON-PARAMAGNETIC-RESONANCE; ORBITAL ANGULAR-MOMENTUM; TRANSITION-METAL IONS; HIGH-SPIN MOLECULES; HIGH-VALENT IRON; SPECTROSCOPIC CHARACTERIZATION; 3-COORDINATE NICKEL; IMIDO COMPLEXES; NITRIDO COMPLEX AB We present a family of trigonal pyramidal iron(II) complexes supported by tris(pyrrolyl-alpha-methyl)amine ligands of the general formula [M(solv)(n)][(tpa(R))Fe] (M = Na, R = tert-butyl (1), phenyl (4); M = K, R = mesityl (2), 2,4,6-triisopropylphenyl (3), 2,6-difluorophenyl (5)) and their characterization by X-ray crystallography, Mossbauer spectroscopy, and high-field EPR spectroscopy. Expanding on the discovery of slow magnetic relaxation in the recently reported mesityl derivative 2, this homologous series of high-spin iron(II) complexes enables an initial probe of how the ligand field influences the static and dynamic magnetic behavior. Magnetization experiments reveal large, uniaxial zero-field splitting parameters of D = -48, -44, -30, -26, and -6.2 cm(-1) for 1-5, respectively, demonstrating that the strength of axial magnetic anisotropy scales with increasing ligand field strength at the iron(II) center. In the case of 2,6-difluorophenyl substituted 5, high-field EPR experiments provide an independent determination of the zero-field splitting parameter (D = -4.397(9) cm(-1)) that is in reasonable agreement with that obtained from fits to magnetization data. Ac magnetic susceptibility measurements indicate field-dependent, thermally activated spin reversal barriers in complexes 1, 2, and 4 of U-eff = 65, 42, and 25 cm(-1), respectively, with the barrier of 1 constituting the highest relaxation barrier yet observed for a mononuclear transition metal complex. In addition, in the case of 1, the large range of temperatures in which slow relaxation is observed has enabled us to fit the entire Arrhenius curve simultaneously to three distinct relaxation processes. Finally, zero-field Mossbauer spectra collected for 1 and 4 also reveal the presence of slow magnetic relaxation, with two independent relaxation barriers in 4 corresponding to the barrier obtained from ac susceptibility data and to the 3D energy gap between the M-S = +/- 2 and +/- 1 levels, respectively. C1 [Long, Gary J.] Univ Missouri, Missouri Univ Sci & Technol, Dept Chem, Rolla, MO 65409 USA. [Harman, W. Hill; Harris, T. David; Freedman, Danna E.; Fong, Henry; Chang, Alicia; Rinehart, Jeffrey D.; Long, Jeffrey R.; Chang, Christopher J.] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. [Chang, Christopher J.] Univ Calif Berkeley, Howard Hughes Med Inst, Berkeley, CA 94720 USA. [Harman, W. Hill; Chang, Christopher J.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Chem Sci, Berkeley, CA 94720 USA. [Sougrati, Moulay T.; Grandjean, Fernande] Univ Liege, Dept Phys, B-4000 Sart Tilman Par Liege, Belgium. [Ozarowski, Andrew] Florida State Univ, Natl High Magnet Field Lab, Tallahassee, FL 32310 USA. RP Long, GJ (reprint author), Univ Missouri, Missouri Univ Sci & Technol, Dept Chem, Rolla, MO 65409 USA. EM glong@mst.edu; jrlong@berkeley.edu; chrischang@berkeley.edu RI Harris, David/M-9204-2014; Sougrati, Moulay Tahar/B-6283-2011; OI Harris, David/0000-0003-4144-900X; Sougrati, Moulay Tahar/0000-0003-3740-2807; Freedman, Danna/0000-0002-2579-8835 FU Packard foundation; DOE/LBNL [403801]; NSF [CHE-0617063, DMR-0654118]; FNRS-Belgium [9.456595, 1.5.064.05]; Arkema; Tyco Electronics; State of Florida; DOE FX We thank the Packard foundation (C.J.C.), DOE/LBNL (403801 to C.J.C.), the NSF (CHE-0617063 to J.R.L.), and the FNRS-Belgium (9.456595 and 1.5.064.05 to F.G.) for funding this work. We also thank Arkema (W.H.H.) as well as Tyco Electronics (T.D.H. and D.E.F.) for graduate fellowship support. C.J.C. is an Investigator with the Howard Hughes Medical Institute. The NHMFL is funded by the NSF through the Cooperative Agreement No. DMR-0654118, the State of Florida, and the DOE. F.G. thanks Prof. R. Cloots for the use of his controlled atmosphere glove box. NR 102 TC 180 Z9 181 U1 10 U2 94 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0002-7863 J9 J AM CHEM SOC JI J. Am. Chem. Soc. PD DEC 29 PY 2010 VL 132 IS 51 BP 18115 EP 18126 DI 10.1021/ja105291x PG 12 WC Chemistry, Multidisciplinary SC Chemistry GA 701LF UT WOS:000285818700030 PM 21141856 ER PT J AU Tinberg, CE Tonzetich, ZJ Wang, HX Do, LH Yoda, Y Cramer, SP Lippard, SJ AF Tinberg, Christine E. Tonzetich, Zachary J. Wang, Hongxin Do, Loi H. Yoda, Yoshitaka Cramer, Stephen P. Lippard, Stephen J. TI Characterization of Iron Dinitrosyl Species Formed in the Reaction of Nitric Oxide with a Biological Rieske Center SO JOURNAL OF THE AMERICAN CHEMICAL SOCIETY LA English DT Article ID THIOL-CONTAINING LIGANDS; RESONANCE VIBRATIONAL SPECTROSCOPY; ELECTRON-SPIN RESONANCE; DNA-REPAIR RESPONSE; ESCHERICHIA-COLI; NITROSYL COMPLEXES; 2FE-2S CLUSTERS; MITOCHONDRIAL ACONITASES; ACTIVATED MACROPHAGES; SULFUR CLUSTERS AB Reactions of nitric oxide with cysteine-ligated iron-sulfur cluster proteins typically result in disassembly of the iron-sulfur core and formation of dinitrosyl iron complexes (DNICs). Here we report the first evidence that DNICs also form in the reaction of NO with Rieske-type [2Fe-2S] clusters. Upon treatment of a Rieske protein, component C of toluene/o-xylene monooxygenase from Pseudomonas sp. OX1, with an excess of NO(g) or NO-generators S-nitroso-N-acetyl-D,L-pencillamine and diethylamine NONOate, the absorbance bands of the [2Fe-2S] cluster are extinguished and replaced by a new feature that slowly grows in at 367 nm. Analysis of the reaction products by electron paramagnetic resonance, Mossbauer, and nuclear resonance vibrational spectroscopy reveals that the primary product of the reaction is a thiolate-bridged diiron tetranitrosyl species, [Fe(2)(mu-SCys)(2)(NO)(4)], having a Roussin's red ester (RRE) formula, and that mononuclear DNICs account for only a minor fraction of nitrosylated iron. Reduction of this RRE reaction product with sodium dithionite produces the one-electron-reduced ARE, having absorptions at 640 and 960 nm. These results demonstrate that NO reacts readily with a Rieske center in a protein and suggest that dinuclear RRE species, not mononuclear DNICs, may be the primary iron dinitrosyl species responsible for the pathological and physiological effects of nitric oxide in such systems in biology. C1 [Tinberg, Christine E.; Tonzetich, Zachary J.; Do, Loi H.; Lippard, Stephen J.] MIT, Dept Chem, Cambridge, MA 02139 USA. [Wang, Hongxin; Cramer, Stephen P.] Univ Calif Berkeley, Lawrence Berkeley Lab, Phys Biosci Div, Berkeley, CA 94720 USA. [Yoda, Yoshitaka] Japan Synchrotron Radiat Res Inst, Sayo, Hyogo 6795198, Japan. [Cramer, Stephen P.] Univ Calif Davis, Dept Appl Sci, Davis, CA 95616 USA. RP Lippard, SJ (reprint author), MIT, Dept Chem, Cambridge, MA 02139 USA. EM lippard@mit.edu OI Tonzetich, Zachary/0000-0001-7010-8007 FU National Science Foundation; National Institute of General Medical Sciences (NIGMS) [GM032134, GM065440, T32 GM08334, 1 F32 GM082031-03]; Department of Energy (DOE OBER); JST (CREST) FX This work was funded by the National Science Foundation and grant GM032134 from the National Institute of General Medical Sciences (NIGMS). S.P.C. thanks the Department of Energy (DOE OBER) and the NIGMS (GM065440) for financial support. C.E.T. received partial support from the NIGMS under Interdepartmental Biotechnology Training Grant T32 GM08334. Z.J.T. thanks the NIGMS for a postdoctoral fellowship (1 F32 GM082031-03). The high-resolution monochromator at SPring-8 was upgraded with funding from JST (CREST). NR 71 TC 62 Z9 63 U1 0 U2 39 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0002-7863 J9 J AM CHEM SOC JI J. Am. Chem. Soc. PD DEC 29 PY 2010 VL 132 IS 51 BP 18168 EP 18176 DI 10.1021/ja106290p PG 9 WC Chemistry, Multidisciplinary SC Chemistry GA 701LF UT WOS:000285818700035 PM 21133361 ER PT J AU Owen, JS Chan, EM Liu, HT Alivisatos, AP AF Owen, Jonathan S. Chan, Emory M. Liu, Haitao Alivisatos, A. Paul TI Precursor Conversion Kinetics and the Nucleation of Cadmium Selenide Nanocrystals SO JOURNAL OF THE AMERICAN CHEMICAL SOCIETY LA English DT Article ID SILVER-HALIDE PARTICLES; CDSE QUANTUM DOTS; SEMICONDUCTOR NANOCRYSTALS; II-VI; EXTINCTION COEFFICIENT; LIQUID PARAFFIN; GROWTH-KINETICS; IDENTIFICATION; CHEMISTRY; RODS AB The kinetics of cadmium selenide (CdSe) nanocrystal formation was studied using UV-visible absorption spectroscopy integrated with an automated, high-throughput synthesis platform. Reaction of anhydrous cadmium octadecylphosphonate (Cd-ODPA) with alkylphosphine selenides (1, tri-n-octylphosphine selenide; 2, di-n-butylphenylphosphine selenide; 3, n-butyldiphenylphosphine selenide) in recrystallized tri-n-octylphosphine oxide was monitored by following the absorbance of CdSe at lambda = 350 nm, where the extinction coefficient is independent of size, and the disappearance of the selenium precursor using {(1)H}(31)P NMR spectroscopy. Our results indicate that precursor conversion limits the rate of nanocrystal nucleation and growth. The initial precursor conversion rate (Q(o)) depends linearly on [1] (Q(0)(1) = 3.0-36 mu M/s) and decreases as the number of aryl groups bound to phosphorus increases (1 > 2 > 3). Changes to Q(o) influence the final number of nanocrystals and thus control particle size. Using similar methods, we show that changing [ODPA] has a negligible influence on precursor reactivity while increasing the growth rate of nuclei, thereby decreasing the final number of nanocrystals. These results are interpreted in light of a mechanism where the precursors react in an irreversible step that supplies the reaction medium with a solute form of the semiconductor. C1 [Alivisatos, A. Paul] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Mat Sci, Berkeley, CA 94720 USA. Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. RP Alivisatos, AP (reprint author), Univ Calif Berkeley, Lawrence Berkeley Lab, Div Mat Sci, Berkeley, CA 94720 USA. EM alivis@berkeley.edu RI Alivisatos , Paul /N-8863-2015; OI Alivisatos , Paul /0000-0001-6895-9048; Owen, Jonathan/0000-0001-5502-3267 FU American Chemical Society; Office of Science, Office of Basic Energy Sciences of the U.S. Department of Energy [DE-AC02-78105CH11231]; Physical Chemistry of Semiconductor Nanocrystals Program; Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division of the U.S. Department of Energy [DE-AC02-05CH11231] FX We are grateful to Symyx Technologies, now Freeslate Inc., for the design and construction of the high-throughput reactor used in this work. J.S.O. thanks William Buhro, Dmitri Talapin, Michael Clark, and Sanat Kumar for helpful discussions. E.M.C. thanks Delia Milliron for helpful discussions. J.S.O. acknowledges the donors of the American Chemical Society Petroleum Research Fund for their partial support of this research. High-throughput kinetics measurements were performed by J.S.O. and E.M.C. at the Molecular Foundry, supported by the Office of Science, Office of Basic Energy Sciences of the U.S. Department of Energy, under Contract No. DE-AC02-78105CH11231. All other kinetics studies were performed by J.S.O. and H.L. and funded by the Physical Chemistry of Semiconductor Nanocrystals Program, supported by the Director, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division of the U.S. Department of Energy, under Contract No. DE-AC02-05CH11231. NR 62 TC 104 Z9 105 U1 11 U2 112 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0002-7863 J9 J AM CHEM SOC JI J. Am. Chem. Soc. PD DEC 29 PY 2010 VL 132 IS 51 BP 18206 EP 18213 DI 10.1021/ja106777j PG 8 WC Chemistry, Multidisciplinary SC Chemistry GA 701LF UT WOS:000285818700039 PM 21128655 ER PT J AU Kang, J Wei, SH Kim, YH AF Kang, Joongoo Wei, Su-Huai Kim, Yong-Hyun TI Origin of the Diverse Melting Behaviors of Intermediate-Size Nanoclusters: Theoretical Study of Al-N (N=51-58, 64) SO JOURNAL OF THE AMERICAN CHEMICAL SOCIETY LA English DT Article ID AUGMENTED-WAVE METHOD; GLOBAL OPTIMIZATION; ATOMIC CLUSTERS; FINITE SYSTEMS; METAL-CLUSTERS; ARGON CLUSTERS; COEXISTENCE; NANOPARTICLES; REACTIVITY AB Microscopic understanding of thermal behaviors of metal nanoparticles is important for nanoscale catalysis and thermal energy storage applications. However, it is a challenge to obtain a structural interpretation at the atomic level from measured thermodynamic quantities such as heat capacity. Using first-principles molecular dynamics simulations, we reproduce the size-sensitive heat capacities of Al-N clusters with N around 55, which exhibit several distinctive shapes associated with diverse melting behaviors of the clusters. We reveal a clear correlation of the diverse melting behaviors with cluster core symmetries. For the Al-N clusters with N = 51-58 and 64, we identify several competing structures with widely different degree of symmetry. The conceptual link between the degree of symmetry (e.g., T-d, D-2d, and C-s) and solidity of atomic clusters is quantitatively demonstrated through the analysis of the configuration entropy. The size-dependent, diverse melting behaviors of Al clusters originate from the reduced symmetry (T-d -> D-2d -> C-s) with increasing the cluster size. In particular, the sudden drop of the melting temperature and appearance of the dip at N = 56 are due to the T-d-to-D-2d symmetry change, triggered by the surface saturation of the tetrahedral Al-55 with the T-d symmetry. C1 [Kang, Joongoo; Wei, Su-Huai] Natl Renewable Energy Lab, Golden, CO 80401 USA. [Kim, Yong-Hyun] Korea Adv Inst Sci & Technol, Grad Sch Nanosci & Technol WCU, Taejon 305701, South Korea. RP Kang, J (reprint author), Natl Renewable Energy Lab, Golden, CO 80401 USA. EM Joongoo.Kang@nrel.gov; Yong.Hyun.Kim@kaist.ac.kr RI Kim, Yong-Hyun/C-2045-2011 OI Kim, Yong-Hyun/0000-0003-4255-2068 FU U.S. DOE [DE-AC36-08GO28308]; Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]; Office of Energy Efficiency and Renewable Energy of the U.S. Department of Energy [DE-AC36-08GO28308]; Ministry of Education, Science and Technology [R31-2008-000-10071-0] FX This work was funded by the U.S. DOE EERE CSP and NREL LDRD programs under Contract No. DE-AC36-08GO28308. This research used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. This research also used capabilities of the National Renewable Energy Laboratory Computational Sciences Center, which is supported by the Office of Energy Efficiency and Renewable Energy of the U.S. Department of Energy under Contact No. DE-AC36-08GO28308. Y.-H. Kim was also supported by WCU (World Class University) program through the National Research Foundation of Korea funded by the Ministry of Education, Science and Technology (R31-2008-000-10071-0). We thank A. K. Starace for discussions and for reading the manuscript. NR 35 TC 17 Z9 17 U1 1 U2 15 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0002-7863 J9 J AM CHEM SOC JI J. Am. Chem. Soc. PD DEC 29 PY 2010 VL 132 IS 51 BP 18287 EP 18291 DI 10.1021/ja107683m PG 5 WC Chemistry, Multidisciplinary SC Chemistry GA 701LF UT WOS:000285818700048 PM 21141857 ER PT J AU Yazyev, OV Moore, JE Louie, SG AF Yazyev, Oleg V. Moore, Joel E. Louie, Steven G. TI Spin Polarization and Transport of Surface States in the Topological Insulators Bi2Se3 and Bi2Te3 from First Principles SO PHYSICAL REVIEW LETTERS LA English DT Article ID SELF-CONSISTENT THEORY; SINGLE DIRAC CONE; DIELECTRIC RESPONSE; ELECTRONIC STATES; ORBIT INTERACTION; SEMICONDUCTORS; NANORIBBONS; MAGNETISM; GRAPHENE; LIMIT AB We investigate the band dispersion and the spin texture of topologically protected surface states in the bulk topological insulators Bi2Se3 and Bi2Te3 by first-principles methods. Strong spin-orbit entanglement in these materials reduces the spin polarization of the surface states to similar to 50% in both cases; this reduction is absent in simple models but of important implications to essentially any spintronic application. We propose a way of controlling the magnitude of spin polarization associated with a charge current in thin films of topological insulators by means of an external electric field. The proposed dual-gate device configuration provides new possibilities for electrical control of spin. C1 [Yazyev, Oleg V.] Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA. Univ Calif Berkeley, Lawrence Berkeley Lab, Div Mat Sci, Berkeley, CA 94720 USA. RP Yazyev, OV (reprint author), Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA. RI Yazyev, Oleg/A-4073-2008; li, yuan/B-4627-2011; Moore, Joel/O-4959-2016 OI Yazyev, Oleg/0000-0001-7281-3199; Moore, Joel/0000-0002-4294-5761 FU NSF [DMR07-05941, DMR08-04413]; Office of Science, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering Division, U.S. Department of Energy [DE-AC02-05CH11231]; Swiss NSF [PBELP2-123086] FX We would like to thank E. Kioupakis, J. Orenstein, and C. Jozwiak for discussions. This work was supported by NSF Grants No. DMR07-05941 (S. G. L.) and No. DMR08-04413 (J. E. M.) and by the Director, Office of Science, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering Division, U.S. Department of Energy under Contract No. DE-AC02-05CH11231 (O. V. Y.). O. V. Y. received partial support from the Swiss NSF (Grant No. PBELP2-123086). Computational resources have been provided by TeraGrid. NR 43 TC 253 Z9 255 U1 18 U2 148 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 0031-9007 EI 1079-7114 J9 PHYS REV LETT JI Phys. Rev. Lett. PD DEC 29 PY 2010 VL 105 IS 26 AR 266806 DI 10.1103/PhysRevLett.105.266806 PG 4 WC Physics, Multidisciplinary SC Physics GA 713VT UT WOS:000286766200008 PM 21231702 ER PT J AU Kim, SH Yeon, J Sefat, AS Mandrus, DG Halasyamani, PS AF Kim, Sang-Hwan Yeon, Jeongho Sefat, Athena S. Mandrus, David G. Halasyamani, P. Shiv TI Stereo-Active Lone-Pair Control on the Ferromagnetic Behavior in VO(SeO2OH)(2): A New Acentric Ferromagnetic Material SO CHEMISTRY OF MATERIALS LA English DT Article ID SPIN-EXCHANGE INTERACTIONS; BOND-VALENCE PARAMETERS; CRYSTAL-STRUCTURE; MAGNETIC-PROPERTIES; DIMER; STEREOCHEMISTRY; SEMICONDUCTORS; INSULATORS; DISTORTION; VOSE2O5 AB A new acentric ferromagnetic material, VO(SeO2OH)(2), has been synthesized and characterized by single crystal X-ray diffraction, second harmonic generation (SHG), and magnetization measurements. The crystal structure of VO(SeO2OH)(2) consists of linear chains of corner-shared V4+O6 octahedra that are connected by SeO2OH groups. The material exhibits a weak SHG efficiency, comparable to alpha-SiO2, and a ferromagnetic transition (T-C) at similar to 2.5 K with a saturated magnetic moment of l.09.0 mu(B) per formula unit (mu(B)/FU). The origin of the ferromagnetism is explained by the suppression of the antiferromagnetic superexchange (SE) and supersuper-exchange (SSE) interactions in the intro-chain and inter-chain magnetic interactions, respectively. In addition, using first principles density functional theory (DFT) calculations, we show that the SSE interactions depend on the O(2)-Se4+-O(3) angle. As we demonstrate, the stereoactive lone-pair on See(4+) is the driving force for the inter-chain ferromagnetic interactions. C1 [Kim, Sang-Hwan; Yeon, Jeongho; Halasyamani, P. Shiv] Univ Houston, Dept Chem, Houston, TX 77204 USA. [Sefat, Athena S.] Oak Ridge Natl Lab, Mat Sci & Technol Div, Oak Ridge, TN 37831 USA. [Mandrus, David G.] Univ Tennessee, Dept Mat Sci & Engn, Knoxville, TN 37996 USA. RP Halasyamani, PS (reprint author), Univ Houston, Dept Chem, 136 Fleming Bldg, Houston, TX 77204 USA. EM psh@uh.edu RI Halasyamani, P. Shiv/A-8620-2009; Mandrus, David/H-3090-2014; Halasyamani, Shiv/J-3438-2014; Sefat, Athena/R-5457-2016 OI Halasyamani, Shiv/0000-0003-1787-1040; Sefat, Athena/0000-0002-5596-3504 FU Robert A. Welch Foundation [E-1457]; ACS [PRF 47345-AC10]; NSF [DMR-0652150]; Division of Materials Sciences and Engineering, Office of Basic Energy Sciences, U.S. Department of Energy FX We thank the Robert A. Welch Foundation (Grant E-1457), the ACS PRF 47345-AC10, and the NSF (DMR-0652150) for support. Research is partly sponsored by the Division of Materials Sciences and Engineering, Office of Basic Energy Sciences, U.S. Department of Energy. NR 52 TC 8 Z9 8 U1 0 U2 5 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0897-4756 EI 1520-5002 J9 CHEM MATER JI Chem. Mat. PD DEC 28 PY 2010 VL 22 IS 24 BP 6665 EP 6672 DI 10.1021/cm102659w PG 8 WC Chemistry, Physical; Materials Science, Multidisciplinary SC Chemistry; Materials Science GA 696GD UT WOS:000285429000019 ER PT J AU Leventis, N Sotiriou-Leventis, C Chandrasekaran, N Mulik, S Larimore, ZJ Lu, HB Churu, G Mang, JT AF Leventis, Nicholas Sotiriou-Leventis, Chariklia Chandrasekaran, Naveen Mulik, Sudhir Larimore, Zachary J. Lu, Hongbing Churu, Gitogo Mang, Joseph T. TI Multifunctional Polyurea Aerogels from Isocyanates and Water. A Structure-Property Case Study SO CHEMISTRY OF MATERIALS LA English DT Article ID SMALL-ANGLE SCATTERING; DYNAMIC COMPRESSIVE RESPONSE; MECHANICALLY STRONG AEROGELS; CORE-SHELL SUPERSTRUCTURES; OPEN-PORE POLYURETHANE; ORGANIC AEROGELS; FORMALDEHYDE AEROGELS; NEUTRON-SCATTERING; SILICA AEROGELS; CARBON AB It is well-known that isocyanates and water yield polyureas; however, that reaction is not generally associated with the synthesis of the latter, being used instead for environmental curing of films baring free NCO groups or for foaming polyurethanes. Here we report that careful control of the relative isocyanate/water/catalyst (Et3N) ratio in acetone, acetonitrile, or DMSO prevents precipitation, yielding instead polyurea (PUA) gels convertible to highly porous (up to 98.6% v/v) aerogels over a very wide density range (0.016-0.55 g cm(-3)). The method has been implemented successfully with several aliphatic and aromatic di and triisocyanates. PUA aerogels have been studied at the molecular level (C-13 NM R, IR, XRD), the elementary nanoparticle level (SANS/USANS), and the microscopic level (SEM). Their porous structure has been probed with N-2-sorption porosimetry. Despite that the nanomorphology varies with density from fibrous at the low density end to particulate at the high density end, all samples consist of similarly sized primary particles assembled differently, probably via a reaction-limited cluster cluster aggregation mechanism at the low density end, which changes into diffusion-limited aggregation as the isocyanate concentration increases. Higher density PUA aerogels (>0.3 g cm(-3)) are mechanically strong enough to tolerate the capillary forces of evaporating low surface tension solvents (e.g., pentane) and can be dried under ambient pressure; under compression, they can absorb energy (up to 90 J g(-1) at 0.55 g cm(-3)) at levels observed only with polyurea-cross-linked silica and vanadia aerogels (50-190 J g(-1) at similar densities). At cryogenic temperatures (-173 degrees C) PUA aerogels remain relatively ductile, a fact attributed to sintering effects and their entangled fibrous nanomorphology. Upon pyrolysis (>500 degrees C, Ar), PUA aerogels from aromatic isocyanates are converted to carbon aerogels in high yields (similar to 60% w/w). Those properties, considered together with the simple synthetic protocol, render PUA aerogels attractive multifunctional materials. C1 [Leventis, Nicholas; Sotiriou-Leventis, Chariklia; Chandrasekaran, Naveen; Mulik, Sudhir] Missouri Univ Sci & Technol, Dept Chem, Rolla, MO 65409 USA. [Larimore, Zachary J.] Missouri Univ Sci & Technol, Dept Mech Engn, Rolla, MO 65409 USA. [Lu, Hongbing; Churu, Gitogo] Univ Texas Dallas, Dept Mech Engn, Richardson, TX 75080 USA. [Mang, Joseph T.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Leventis, N (reprint author), Missouri Univ Sci & Technol, Dept Chem, Rolla, MO 65409 USA. RI Lu, Hongbing/A-1312-2011 FU National Science Foundation [CHE-0809562, DMR-0907291, CMMI-0653970, CMMI-0653919, DMR-0454672]; Army Research Office [W911NF-10-1-0476]; DOE office of Basic Energy Sciences; National Institute of Standards and Technology, U.S. Department of Commerce FX For financial support we thank the National Science Foundation under Agreement Nos. CHE-0809562 (N.L., C.S.-L.), DMR-0907291 (N.L., H.L.), CMMI-0653970 (N.L., C.S.-L.), and CMMI-0653919 (H.L.) and the Army Research Office under Award No. W911NF-10-1-0476 (N.L., C.S.-L.). We also acknowledge the Materials Research Center of Missouri S&T for support in sample characterization (SEM, XRD). Solids NMR work was conducted at the University of Missouri Columbia by Dr. Wei Wycoff. This work benefited tremendously from the use of the SANS instrument, LQD at the Manuel Lujan, Jr. Neutron Scattering Center of the Los Alamos National Laboratory, supported by the DOE office of Basic Energy Sciences and utilized facilities supported in part by the National Science Foundation under Agreement No. DMR-0454672. We also acknowledge the support of the National Institute of Standards and Technology, U.S. Department of Commerce, in providing additional neutron research facilities used in this work. Finally, we thank Bayer Corporation USA for their generous supply of isocyanates. NR 70 TC 53 Z9 54 U1 6 U2 101 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0897-4756 J9 CHEM MATER JI Chem. Mat. PD DEC 28 PY 2010 VL 22 IS 24 BP 6692 EP 6710 DI 10.1021/cm102891d PG 19 WC Chemistry, Physical; Materials Science, Multidisciplinary SC Chemistry; Materials Science GA 696GD UT WOS:000285429000022 ER PT J AU Wang, QF Keffer, DJ Nicholson, DM Thomas, JB AF Wang, Qifei Keffer, David J. Nicholson, Donald M. Thomas, J. Brock TI Coarse-Grained Molecular Dynamics Simulation of Polyethylene Terephthalate (PET) SO MACROMOLECULES LA English DT Article ID AMORPHOUS POLY(ETHYLENE-TEREPHTHALATE); POLYMER MELTS; POLY(ETHYLENE ISOPHTHALATE); POLYSTYRENE; EQUATION; BEHAVIOR; CHAINS; ENTANGLEMENT; RELAXATION; DIMENSIONS AB A coarse grained (CG) model of poly(ethylene terephthalate) (PET) was developed and implemented in CG molecular dynamics (MD) simulations of PET chains with degree of polymerization up to 50 The CG potential is parametrized to structural distribution functions obtained from atomistic simulations [J Phys Chem B 2010, 114, 786] using an inversion procedure based on the Ornstein-Zernike equation with the Percus-Yevick approximation (OZPY) [ Phys Rev E2010, 81,061204] The CGMD simulation of PET chains satisfactorily reproduces the structural and dynamic properties from atomistic MD simulation of the same systems We report the average chain end-to end distance and radius of gyration, relaxation time, self diffusivity, and zero shear-rate viscosity s dependence on degree of polymerization For the longest chains, we find the scaling exponents of 0 51 0 50, and -2 00 for average chain end-to end distance, radius of gyration and self-diffusivity, respectively The exponents are very close to the theoretical values of entangled polymer melt systems (0 50, 0 50 and -2 0) The study of entanglement in the longer chains shows that the tube diameter, number of monomers between entanglement points and interentanglement strand length are in close agreement with the reported values for an entangled PET melt C1 [Wang, Qifei; Keffer, David J.] Univ Tennessee, Dept Chem & Biomol Engn, Knoxville, TN 37996 USA. [Nicholson, Donald M.] Oak Ridge Natl Lab, Comp Sci & Math Div, Oak Ridge, TN 37830 USA. [Thomas, J. Brock] Eastman Chem Co, Kingsport, TN 37662 USA. RP Keffer, DJ (reprint author), Univ Tennessee, Dept Chem & Biomol Engn, Knoxville, TN 37996 USA. RI Keffer, David/C-5133-2014 OI Keffer, David/0000-0002-6246-0286 FU Eastman Chemical Company; National Science Foundation [DGE 0801470, OCI 07-11134 5]; U S Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering FX This research was supported by the Eastman Chemical Company and by a grant from the National Science Foundation (DGE 0801470) and by the U S Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering This research project used resources of the National Institute for Computational Sciences (NICS) supported by NSF under agreement number OCI 07-11134 5 NR 68 TC 19 Z9 19 U1 4 U2 41 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0024-9297 EI 1520-5835 J9 MACROMOLECULES JI Macromolecules PD DEC 28 PY 2010 VL 43 IS 24 BP 10722 EP 10734 DI 10.1021/ma102084a PG 13 WC Polymer Science SC Polymer Science GA 696GH UT WOS:000285429400071 ER PT J AU Bai, Y Nelson, AE AF Bai, Yang Nelson, Ann E. TI CP violating contribution to Delta Gamma in the B-s system from mixing with a hidden pseudoscalar SO PHYSICAL REVIEW D LA English DT Article AB Recent evidence for a CP violating asymmetry in the semileptonic decays of B-s mesons cannot be accommodated within the standard model. Such an asymmetry can be explained by new physics contributions to Delta B 2 components of either the mass matrix or the decay matrix. We show that mixing with a hidden pseudoscalar meson with a mass around 5 GeV can result in a new CP violating contribution to the mixing and can resolve several anomalies in this system including the width difference, the average width and the charge asymmetry. We also discuss the effects of the hidden meson on other b physics observables, and present viable decay modes for the hidden meson. We make predictions for new decay channels of B hadrons, which can be tested at the Tevatron, the LHC and B-factories. C1 [Bai, Yang] Fermilab Natl Accelerator Lab, Dept Theoret Phys, Batavia, IL 60510 USA. [Nelson, Ann E.] Univ Washington, Dept Phys, Seattle, WA 98195 USA. RP Bai, Y (reprint author), Fermilab Natl Accelerator Lab, Dept Theoret Phys, Batavia, IL 60510 USA. FU DOE [DE-FGO3-96-ER40956]; United States Department of Energy [DE-AC02-07CH11359] FX We would like to thank Bogdan Dobrescu, Patrick Fox, Elvira Gamiz, Yuval Grossman, Roni Harnik, Alex Kagan, Adam Martin, Michele Papucci and Andrew Wagner for useful discussions. We also thank the Aspen Center of Physics where part of this work was finished. This work (A. N.) was partially supported by the DOE under Contract No. DE-FGO3-96-ER40956. Fermilab is operated by Fermi Research Alliance, LLC, under Contract No. DE-AC02-07CH11359 with the United States Department of Energy. NR 33 TC 22 Z9 22 U1 0 U2 2 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 1550-7998 J9 PHYS REV D JI Phys. Rev. D PD DEC 28 PY 2010 VL 82 IS 11 AR 114027 DI 10.1103/PhysRevD.82.114027 PG 10 WC Astronomy & Astrophysics; Physics, Particles & Fields SC Astronomy & Astrophysics; Physics GA 711HM UT WOS:000286577700002 ER PT J AU Davoudiasl, H McElmurry, T Soni, A AF Davoudiasl, Hooman McElmurry, Thomas Soni, Amarjit TI Promising diphoton signals of the little radion at hadron colliders SO PHYSICAL REVIEW D LA English DT Article ID RANDALL-SUNDRUM MODEL; PHOTON PAIR PRODUCTION; BULK FIELDS; MODULUS; SECTOR AB In little Randall-Sundrum models, the bulk couplings of the radion to massless gauge fields can yield a greatly enhanced diphoton signal at hadron colliders. We examine the implications of the Tevatron data for the little radion and also show that the 7 TeV run at the Large Hadron Collider will have an impressive reach in this channel. The diphoton signal is crucial in the search for a light radion, or the dual dilaton, and can potentially probe the ultraviolet scale of the theory. C1 [Davoudiasl, Hooman; McElmurry, Thomas; Soni, Amarjit] Brookhaven Natl Lab, Dept Phys, Upton, NY 11973 USA. RP Davoudiasl, H (reprint author), Brookhaven Natl Lab, Dept Phys, Upton, NY 11973 USA. FU U.S. DOE [DE-AC02-98CH10886] FX We thank Y. Bai for conversations on dilaton couplings, S. Dawson, J. Hubisz, and M. Toharia for discussions, and J.-P. Guillet for assistance with DIPHOX. This work is supported in part by the U.S. DOE Grant No. DE-AC02-98CH10886. NR 43 TC 21 Z9 21 U1 0 U2 2 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 1550-7998 J9 PHYS REV D JI Phys. Rev. D PD DEC 28 PY 2010 VL 82 IS 11 AR 115028 DI 10.1103/PhysRevD.82.115028 PG 5 WC Astronomy & Astrophysics; Physics, Particles & Fields SC Astronomy & Astrophysics; Physics GA 711HM UT WOS:000286577700004 ER PT J AU Kondo, T Khasanov, R Karpinski, J Kazakov, SM Zhigadlo, ND Bukowski, Z Shi, M Bendounan, A Sassa, Y Chang, J Pailhes, S Mesot, J Schmalian, J Keller, H Kaminski, A AF Kondo, Takeshi Khasanov, R. Karpinski, J. Kazakov, S. M. Zhigadlo, N. D. Bukowski, Z. Shi, M. Bendounan, A. Sassa, Y. Chang, J. Pailhes, S. Mesot, J. Schmalian, J. Keller, H. Kaminski, A. TI Anomalies in the Fermi Surface and Band Dispersion of Quasi-One-Dimensional CuO Chains in the High-Temperature Superconductor YBa2Cu4O8 SO PHYSICAL REVIEW LETTERS LA English DT Article ID COPPER-OXIDE SUPERCONDUCTORS; MAGNETIC EXCITATIONS; T-C; CROSSOVER; BI2SR2CACU2O8+DELTA; LUTTINGER; PRESSURE; LIQUIDS AB We have investigated the electronic states in quasi-one-dimensional CuO chains by microprobe angle resolved photoemission spectroscopy. We find that the quasiparticle Fermi surface consists of six disconnected segments, consistent with recent theoretical calculations that predict the formation of narrow, elongated Fermi surface pockets for coupled CuO chains. In addition, we find a strong renormalization effect with a significant kink structure in the band dispersion. The properties of this latter effect [energy scale (similar to 40 meV), temperature dependence, and behavior with Zn-doping] are identical to those of the bosonic mode observed in CuO2 planes of high-temperature superconductors, indicating they have a common origin. C1 [Kondo, Takeshi; Schmalian, J.; Kaminski, A.] Iowa State Univ, Ames Lab, Ames, IA 50011 USA. [Kondo, Takeshi; Schmalian, J.; Kaminski, A.] Iowa State Univ, Dept Phys & Astron, Ames, IA 50011 USA. [Khasanov, R.] Paul Scherrer Inst, Lab Muon Spin Spect, CH-5232 Villigen, Switzerland. [Karpinski, J.; Kazakov, S. M.; Zhigadlo, N. D.; Bukowski, Z.] ETH, Solid State Phys Lab, CH-8093 Zurich, Switzerland. [Shi, M.] Paul Scherrer Inst, Swiss Light Source, CH-5232 Villigen, Switzerland. [Bendounan, A.; Sassa, Y.; Chang, J.; Pailhes, S.; Mesot, J.] Swiss Fed Inst Technol, Neutron Scattering Lab, CH-5232 Villigen, Switzerland. [Keller, H.] Univ Zurich, Inst Phys, CH-8057 Zurich, Switzerland. RP Kondo, T (reprint author), Iowa State Univ, Ames Lab, Ames, IA 50011 USA. RI Schmalian, Joerg/H-2313-2011; Kazakov, Sergey/A-4139-2014; Chang, Johan/F-1506-2014; Kondo, Takeshi/H-2680-2016; Sassa, Yasmine/F-3362-2017 OI Kazakov, Sergey/0000-0002-0553-7881; Chang, Johan/0000-0002-4655-1516; FU Director's Office for Basic Energy Sciences, US DOE; Swiss NCCR MaNEP; Iowa State University [W-7405-ENG-82]; NSF [DMR 9212658]; Swiss National Science Foundation; K. Alex Muller Foundation FX We thank C. Berthod and T. Giamarchi for discussions and Fig. 1(e). This work was supported by the Director's Office for Basic Energy Sciences, US DOE and the Swiss NCCR MaNEP. The Ames Laboratory is operated for the US DOE by Iowa State University under Contract No. W-7405-ENG-82. The Synchrotron Radiation Center is supported by NSF DMR 9212658. R. K. gratefully acknowledges the support of the Swiss National Science Foundation and the K. Alex Muller Foundation. NR 32 TC 10 Z9 10 U1 2 U2 23 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 0031-9007 J9 PHYS REV LETT JI Phys. Rev. Lett. PD DEC 28 PY 2010 VL 105 IS 26 AR 267003 DI 10.1103/PhysRevLett.105.267003 PG 4 WC Physics, Multidisciplinary SC Physics GA 713VJ UT WOS:000286765200009 PM 21231707 ER PT J AU Steffen, JH Upadhye, A Baumbaugh, A Chou, AS Mazur, PO Tomlin, R Weltman, A Wester, W AF Steffen, J. H. Upadhye, A. Baumbaugh, A. Chou, A. S. Mazur, P. O. Tomlin, R. Weltman, A. Wester, W. TI Laboratory Constraints on Chameleon Dark Energy and Power-Law Fields SO PHYSICAL REVIEW LETTERS LA English DT Article AB We report results from a search for chameleon particles created via photon-chameleon oscillations within a magnetic field. This experiment is sensitive to a wide class of unexplored chameleon power-law and dark energy models. These results exclude 5 orders of magnitude in the coupling of chameleons to photons covering a range of 4 orders of magnitude in chameleon effective mass and, for individual models, exclude between 4 and 12 orders of magnitude in chameleon couplings to matter. C1 [Steffen, J. H.; Baumbaugh, A.; Chou, A. S.; Mazur, P. O.; Tomlin, R.; Wester, W.] Fermilab Natl Accelerator Lab, Batavia, IL 60510 USA. [Upadhye, A.] Univ Chicago, Kavli Inst Cosmol Phys, Chicago, IL 60637 USA. [Weltman, A.] Univ Cape Town, Astrophys Cosmol & Grav Ctr, ZA-7700 Rondebosch, South Africa. RP Steffen, JH (reprint author), Fermilab Natl Accelerator Lab, POB 500, Batavia, IL 60510 USA. FU U.S. Department of Energy [DE-AC02-07CH11359]; Kavli Institute for Cosmological Physics (NSF) [PHY-0114422] FX We thank the staff at Fermilab in the Technical Division Test and Instrumentation Department, the Particle Physics Division mechanical design and electrical engineering groups, the Accelerator Division vacuum experts, the U.S. Department of Energy (Contract No. DE-AC02-07CH11359) and the Kavli Institute for Cosmological Physics (NSF Contract PHY-0114422). NR 20 TC 33 Z9 35 U1 1 U2 1 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 0031-9007 EI 1079-7114 J9 PHYS REV LETT JI Phys. Rev. Lett. PD DEC 28 PY 2010 VL 105 IS 26 AR 261803 DI 10.1103/PhysRevLett.105.261803 PG 4 WC Physics, Multidisciplinary SC Physics GA 713VJ UT WOS:000286765200004 PM 21231645 ER PT J AU Gao, HC Wang, XH Yang, ZMK Chen, JR Liang, YL Chen, HJ Palzkill, T Zhou, JZ AF Gao, Haichun Wang, Xiaohu Yang, Zamin K. Chen, Jingrong Liang, Yili Chen, Haijiang Palzkill, Timothy Zhou, Jizhong TI Physiological Roles of ArcA, Crp, and EtrA and Their Interactive Control on Aerobic and Anaerobic Respiration in Shewanella oneidensis SO PLOS ONE LA English DT Article ID GLOBAL TRANSCRIPTOME ANALYSIS; ESCHERICHIA-COLI; PUTREFACIENS MR-1; REGULATORY NETWORKS; PROTEIN-PHOSPHORYLATION; ELECTRON-TRANSPORT; CARBON METABOLISM; RECEPTOR PROTEIN; GENE-EXPRESSION; SHOCK RESPONSE AB In the genome of Shewanella oneidensis, genes encoding the global regulators ArcA, Crp, and EtrA have been identified. All these proteins deviate from their counterparts in E. coli significantly in terms of functionality and regulon. It is worth investigating the involvement and relationship of these global regulators in aerobic and anaerobic respiration in S. oneidensis. In this study, the impact of the transcriptional factors ArcA, Crp, and EtrA on aerobic and anaerobic respiration in S. oneidensis were assessed. While all these proteins appeared to be functional in vivo, the importance of individual proteins in these two major biological processes differed. The ArcA transcriptional factor was critical in aerobic respiration while the Crp protein was indispensible in anaerobic respiration. Using a newly developed reporter system, it was found that expression of arcA and etrA was not influenced by growth conditions but transcription of crp was induced by removal of oxygen. An analysis of the impact of each protein on transcription of the others revealed that Crp expression was independent of the other factors whereas ArcA repressed both etrA and its own transcription while EtrA also repressed arcA transcription. Transcriptional levels of arcA in the wild type, crp, and etrA strains under either aerobic or anaerobic conditions were further validated by quantitative immunoblotting with a polyclonal antibody against ArcA. This extensive survey demonstrated that all these three global regulators are functional in S. oneidensis. In addition, the reporter system constructed in this study will facilitate in vivo transcriptional analysis of targeted promoters. C1 [Gao, Haichun; Chen, Haijiang] Zhejiang Univ, Inst Microbiol, Hangzhou 310003, Zhejiang, Peoples R China. [Gao, Haichun; Chen, Haijiang] Zhejiang Univ, Coll Life Sci, Hangzhou 310003, Zhejiang, Peoples R China. [Gao, Haichun; Chen, Jingrong; Liang, Yili; Zhou, Jizhong] Univ Oklahoma, Dept Bot & Microbiol, Norman, OK 73019 USA. [Gao, Haichun; Chen, Jingrong; Liang, Yili; Zhou, Jizhong] Univ Oklahoma, Inst Environm Genom, Norman, OK 73019 USA. [Wang, Xiaohu; Palzkill, Timothy] Baylor Coll Med, Dept Pharmacol, Houston, TX 77030 USA. [Wang, Xiaohu; Palzkill, Timothy] Baylor Coll Med, Dept Mol Virol & Microbiol, Houston, TX 77030 USA. [Yang, Zamin K.] Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA. RP Gao, HC (reprint author), Zhejiang Univ, Inst Microbiol, Hangzhou 310003, Zhejiang, Peoples R China. EM haichung@zju.edu.cn; jzhou@rccc.ou.edu RI Gao, Haichun/A-2160-2014; Chen, Haijiang/D-1893-2009 FU Major State Basic Research Development Program (973 Program) [2010CB833803]; National Natural Science Foundation of China [30870032]; U.S. Department of Energy through Shewanella Federation, Office of Biological and Environmental Research, Office of Science FX This research was supported by Major State Basic Research Development Program (973 Program: 2010CB833803) and National Natural Science Foundation of China (30870032) to HG. This research was also supported by The U.S. Department of Energy under the Genomics: GTL Program through Shewanella Federation, Office of Biological and Environmental Research, Office of Science. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. NR 49 TC 35 Z9 36 U1 2 U2 22 PU PUBLIC LIBRARY SCIENCE PI SAN FRANCISCO PA 185 BERRY ST, STE 1300, SAN FRANCISCO, CA 94107 USA SN 1932-6203 J9 PLOS ONE JI PLoS One PD DEC 28 PY 2010 VL 5 IS 12 AR e15295 DI 10.1371/journal.pone.0015295 PG 11 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 701CS UT WOS:000285792500028 PM 21203399 ER PT J AU Liu, LV Bell, CB Wong, SD Wilson, SA Kwak, Y Chow, MS Zhao, JY Hodgson, KO Hedman, B Solomon, EI AF Liu, Lei V. Bell, Caleb B., III Wong, Shaun D. Wilson, Samuel A. Kwak, Yeonju Chow, Marina S. Zhao, Jiyong Hodgson, Keith O. Hedman, Britt Solomon, Edward I. TI Definition of the intermediates and mechanism of the anticancer drug bleomycin using nuclear resonance vibrational spectroscopy and related methods SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA LA English DT Article DE nonheme iron; structure/reactivity ID ACTIVATED BLEOMYCIN; NONHEME IRON; ELECTRONIC-STRUCTURE; CRYSTAL-STRUCTURE; FERRIC BLEOMYCIN; CESIUM ALUMS; Q-BAND; DNA; COMPLEX; OXYGEN AB Bleomycin (BLM) is a glycopeptide anticancer drug capable of effecting single- and double-strand DNA cleavage. The last detectable intermediate prior to DNA cleavage is a low spin Fe-III peroxy level species, termed activated bleomycin (ABLM). DNA strand scission is initiated through the abstraction of the C-4' hydrogen atom of the deoxyribose sugar unit. Nuclear resonance vibrational spectroscopy (NRVS) aided by extended X-ray absorption fine structure spectroscopy and density functional theory (DFT) calculations are applied to define the natures of (FeBLM)-B-III and ABLM as (BLM)Fe-III-OH and (BLM)Fe-III-(eta(1)-OOH) species, respectively. The NRVS spectra of (FeBLM)-B-III and ABLM are strikingly different because in ABLM the delta Fe-O-O bending mode mixes with, and energetically splits, the doubly degenerate, intense O-Fe-N-ax transaxial bends. DFT calculations of the reaction of ABLM with DNA, based on the species defined by the NRVS data, show that the direct H-atom abstraction by ABLM is thermodynamically favored over other proposed reaction pathways. C1 [Liu, Lei V.; Bell, Caleb B., III; Wong, Shaun D.; Wilson, Samuel A.; Kwak, Yeonju; Chow, Marina S.; Hodgson, Keith O.; Solomon, Edward I.] Stanford Univ, Dept Chem, Stanford, CA 94305 USA. [Zhao, Jiyong] Argonne Natl Lab, Adv Photon Source, Argonne, IL 60439 USA. [Hodgson, Keith O.; Hedman, Britt; Solomon, Edward I.] Stanford Univ, SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA. RP Solomon, EI (reprint author), Stanford Univ, Dept Chem, Stanford, CA 94305 USA. EM edward.solomon@stanford.edu RI Liu, Lei/H-4942-2011 FU National Institutes of Health (NIH) [GM 40392, RR-001209]; National Science Foundation [MCB 0919027]; Department of Energy (Office of Basic Energy Science); NIH; National Center for Research Resources; Department of Energy (DOE), Office of Biological and Environmental Research; DOE, Office of Science, Office of Basic Energy Sciences [DE-AC02-06CH11357]; DOE, Office of Basic Energy Sciences [DE-AC02-76SF00515]; Environmental Protection Agency [SU833912]; Larry Yung Stanford Graduate Fellowship FX Financial support was provided by the National Institutes of Health (NIH) (Grants GM 40392 to E. I. S., and RR-001209 to K.O.H.) and National Science Foundation (Grant MCB 0919027 to E. I. S.). SSRL operations are funded by the Department of Energy (Office of Basic Energy Science). The Structural Molecular Biology program at SSRL is funded by the NIH, National Center for Research Resources, Biomedical Technology Program and the Department of Energy (DOE), Office of Biological and Environmental Research. Use of the Advanced Photon Source at Argonne National Laboratory was supported by the DOE, Office of Science, Office of Basic Energy Sciences, under Contract DE-AC02-06CH11357. This work was made possible [in part] by the computational resources of the Stanford Institute for Materials and Energy Science supported by the DOE, Office of Basic Energy Sciences under contract DE-AC02-76SF00515. Travel funds were provided by Environmental Protection Agency (Grant SU833912). L. V. L. is supported by a Larry Yung Stanford Graduate Fellowship. NR 43 TC 28 Z9 28 U1 1 U2 15 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0027-8424 J9 P NATL ACAD SCI USA JI Proc. Natl. Acad. Sci. U. S. A. PD DEC 28 PY 2010 VL 107 IS 52 BP 22419 EP 22424 DI 10.1073/pnas.1016323107 PG 6 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 699SX UT WOS:000285684200017 PM 21149675 ER PT J AU Hu, YY Rawal, A Schmidt-Rohr, K AF Hu, Y. -Y. Rawal, A. Schmidt-Rohr, K. TI Strongly bound citrate stabilizes the apatite nanocrystals in bone SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA LA English DT Article DE nanocrystal stabilization; nanocomposite; organic-inorganic interface; bone composition; solid-state NMR ID SOLID-STATE NMR; CITRIC-ACID; MINERAL INTERFACE; CALCIUM-CARBONATE; HYDROXYAPATITE; SPECTROSCOPY; PRECIPITATION; BIOMOLECULES; COMPOSITES; DYNAMICS AB Nanocrystals of apatitic calcium phosphate impart the organic-inorganic nanocomposite in bone with favorable mechanical properties. So far, the factors preventing crystal growth beyond the favorable thickness of ca. 3 nm have not been identified. Here we show that the apatite surfaces are studded with strongly bound citrate molecules, whose signals have been identified unambiguously by multinuclear magnetic resonance (NMR) analysis. NMR reveals that bound citrate accounts for 5.5 wt% of the organic matter in bone and covers apatite at a density of about 1 molecule per (2 nm)(2), with its three carboxylate groups at distances of 0.3 to 0.45 nm from the apatite surface. Bound citrate is highly conserved, being found in fish, avian, and mammalian bone, which indicates its critical role in interfering with crystal thickening and stabilizing the apatite nanocrystals in bone. C1 [Schmidt-Rohr, K.] Iowa State Univ, Ames Lab, Ames, IA 50011 USA. Iowa State Univ, Dept Chem, Ames, IA 50011 USA. RP Schmidt-Rohr, K (reprint author), Iowa State Univ, Ames Lab, Ames, IA 50011 USA. EM srohr@iastate.edu RI Hu, Yan-Yan/A-1795-2015 OI Hu, Yan-Yan/0000-0003-0677-5897 FU Department of Energy, Office of Basic Energy Science, Division of Materials Sciences and Engineering, at the Ames Laboratory [DE-AC02-07CH11358] FX This work was supported by the Department of Energy, Office of Basic Energy Science, Division of Materials Sciences and Engineering, at the Ames Laboratory, under Contract No. DE-AC02-07CH11358. NR 42 TC 142 Z9 143 U1 5 U2 75 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0027-8424 J9 P NATL ACAD SCI USA JI Proc. Natl. Acad. Sci. U. S. A. PD DEC 28 PY 2010 VL 107 IS 52 BP 22425 EP 22429 DI 10.1073/pnas.1009219107 PG 5 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 699SX UT WOS:000285684200018 PM 21127269 ER PT J AU Miao, YC Liu, CJ AF Miao, Yu-Chen Liu, Chang-Jun TI ATP-binding cassette-like transporters are involved in the transport of lignin precursors across plasma and vacuolar membranes SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA LA English DT Article ID INSIDE-OUT; SECONDARY METABOLITES; ARABIDOPSIS-THALIANA; SEED COAT; BIOSYNTHESIS; VESICLES; DIFFERENTIATION; RESISTANCE; MUTANT; XYLEM AB Lignin is a complex biopolymer derived primarily from the condensation of three monomeric precursors, the monolignols. The synthesis of monolignols occurs in the cytoplasm. To reach the cell wall where they are oxidized and polymerized, they must be transported across the cell membrane. However, the molecular mechanisms underlying the transport process are unclear. There are conflicting views about whether the transport of these precursors occurs by passive diffusion or is an energized active process; further, we know little about what chemical forms are required. Using isolated plasma and vacuolar membrane vesicles prepared from Arabidopsis, together with applying different transporter inhibitors in the assays, we examined the uptake of monolignols and their derivatives by these native membrane vesicles. We demonstrate that the transport of lignin precursors across plasmalemma and their sequestration into vacuoles are ATP-dependent primary-transport processes, involving ATP-binding cassette-like transporters. Moreover, we show that both plasma and vacuolar membrane vesicles selectively transport different forms of lignin precursors. In the presence of ATP, the inverted plasma membrane vesicles preferentially take up monolignol aglycones, whereas the vacuolar vesicles are more specific for glucoconjugates, suggesting that the different ATP-binding cassette-like transporters recognize different chemical forms in conveying them to distinct sites, and that glucosylation of monolignols is necessary for their vacuolar storage but not required for direct transport into the cell wall in Arabidopsis. C1 [Miao, Yu-Chen; Liu, Chang-Jun] Brookhaven Natl Lab, Dept Biol, Upton, NY 11973 USA. RP Liu, CJ (reprint author), Brookhaven Natl Lab, Dept Biol, Upton, NY 11973 USA. EM cliu@bnl.gov FU Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the US Department of Energy (DOE) [DEAC0298CH10886]; Office of Biological and Environmental Research of DOE [BO148] FX This work was supported by the Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the US Department of Energy (DOE) through Grant DEAC0298CH10886 to C.-J. L. Initially, this work was also partially supported by the Office of Biological and Environmental Research of DOE through the pilot project of biofuel Scientific Focus Area program (BO148). NR 43 TC 69 Z9 72 U1 3 U2 52 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0027-8424 J9 P NATL ACAD SCI USA JI Proc. Natl. Acad. Sci. U. S. A. PD DEC 28 PY 2010 VL 107 IS 52 BP 22728 EP 22733 DI 10.1073/pnas.1007747108 PG 6 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 699SX UT WOS:000285684200070 PM 21149736 ER PT J AU Schauer, MM Danielson, JR Feldbaum, D Rahaman, MS Wang, LB Zhang, J Zhao, X Torgerson, JR AF Schauer, M. M. Danielson, J. R. Feldbaum, D. Rahaman, M. S. Wang, L. -B. Zhang, J. Zhao, X. Torgerson, J. R. TI Isotope-selective trapping of doubly charged Yb ions SO PHYSICAL REVIEW A LA English DT Article ID ULTRAVIOLET; EXCITATION; LIFETIMES; SPACE; GAS AB We report isotope-selective loading and trapping of doubly ionized ytterbium into an rf quadrupole trap. Isotopically pure clouds of Yb-174(+) ions were first loaded into the rf trap via a multistage photoionization process. The Yb2+ ions were then produced by electron impact ionization of the trapped Yb+ ions. The Yb2+ ions were subsequently detected by rf excitation of their secular motion in the trap, which led to sympathetic heating and changes in the fluorescence of the laser-cooled Yb+ ions. The presence of doubly charged Yb ions was further verified by the appearance of a dark band in the center of Yb+ ion cloud after electron impact ionization. We discuss the possible formation of Yb2+ H and similar compounds and the schemes for the direct optical detection of the Yb2+ ions. C1 [Schauer, M. M.; Danielson, J. R.; Feldbaum, D.; Rahaman, M. S.; Wang, L. -B.; Zhang, J.; Zhao, X.; Torgerson, J. R.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Schauer, MM (reprint author), Los Alamos Natl Lab, POB 1663, Los Alamos, NM 87545 USA. OI Zhao, Xinxin/0000-0001-8128-2561 FU NNSA US Department of Energy [DE-AC52-06NA25396] FX This work was supported by the Laboratory Directed Research and Development program at Los Alamos National Laboratory, operated by Los Alamos National Security, LLC, for the NNSA US Department of Energy under Contract No. DE-AC52-06NA25396. NR 24 TC 6 Z9 6 U1 0 U2 4 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 1050-2947 J9 PHYS REV A JI Phys. Rev. A PD DEC 27 PY 2010 VL 82 IS 6 AR 062518 DI 10.1103/PhysRevA.82.062518 PG 6 WC Optics; Physics, Atomic, Molecular & Chemical SC Optics; Physics GA 713NR UT WOS:000286745200007 ER PT J AU Fu, H Zou, M Singh, NK AF Fu, H. Zou, M. Singh, Niraj K. TI Modification of magnetic and magnetocaloric properties of Dy-Co-Al bulk metallic glass introduced by hydrogen SO APPLIED PHYSICS LETTERS LA English DT Article ID ENTROPY CHANGE; TEMPERATURE; ANISOTROPY; TB AB Dy(53.8)Co(17.3)Al(28.9) bulk metallic glass with a diameter of 3 mm exhibits spin-glass behavior and large coercivity and remanence. Hydrogenation of Dy(53.8)Co(17.3)Al(28.9) suppresses the magnetic transition temperature and removes coercivity and remanence because of the expansion of average interatomic distance. The advantage of large magnetic entropy changes (17.5 and 9.5 J/kg K for the field changes from 0 to 50, and from 0 to 20 kOe, respectively) without any hysteresis loss makes Dy(53.8)Co(17.3)Al(28.9) H(170.6) alloy a promising magnetic refrigerant. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3534794] C1 [Fu, H.] Univ Elect Sci & Technol China, Dept Appl Phys, Chengdu 610054, Peoples R China. [Fu, H.; Zou, M.; Singh, Niraj K.] Iowa State Univ, Ames Lab, US DOE, Ames, IA 50011 USA. RP Fu, H (reprint author), Univ Elect Sci & Technol China, Dept Appl Phys, Chengdu 610054, Peoples R China. EM fuhao@uestc.edu.cn FU U.S. Department of Energy [DE-AC02-07CH11358]; China Scholarship Council; National Natural Science Foundation of China [50901013] FX The Ames Laboratory is operated by Iowa State University of Science and Technology for the U.S. Department of Energy under Contract No. DE-AC02-07CH11358. H. Fu's work at the Ames Laboratory was also supported by the China Scholarship Council and the National Natural Science Foundation of China (Grant No. 50901013). We acknowledge Dr. K. A. Gshneidner, Jr. and Dr. V. K. Pecharsky for their support in sample preparation and characterization. NR 12 TC 5 Z9 5 U1 3 U2 13 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0003-6951 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 27 PY 2010 VL 97 IS 26 AR 262509 DI 10.1063/1.3534794 PG 3 WC Physics, Applied SC Physics GA 700TV UT WOS:000285768100054 ER PT J AU Gao, P Chen, HY Tyson, TA Liu, ZX Bai, JM Wang, LP Choi, YJ Cheong, SW AF Gao, P. Chen, H. Y. Tyson, T. A. Liu, Z. X. Bai, J. M. Wang, L. P. Choi, Y. J. Cheong, S. -W. TI Observation of anomalous phonons in orthorhombic rare-earth manganites SO APPLIED PHYSICS LETTERS LA English DT Article ID PHASE; POLARIZATION AB We observe the appearance of a phonon near the lock-in temperature in orthorhombic REMnO3 (RE denotes rare earth) (RE: Lu and Ho) and anomalous phonon hardening in orthorhombic LuMnO3. The anomalous phonon occurs at the onset of spontaneous polarization. No such changes were found in incommensurate orthorhombic DyMnO3. These observations directly reveal different electric polarization mechanisms in the E-type and incommensurate-type orthorhombic REMnO3. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3533022] C1 [Gao, P.; Chen, H. Y.; Tyson, T. A.] New Jersey Inst Technol, Dept Phys, Newark, NJ 07102 USA. [Tyson, T. A.; Choi, Y. J.; Cheong, S. -W.] Rutgers State Univ, Dept Phys & Astron, Piscataway, NJ 08854 USA. [Tyson, T. A.; Choi, Y. J.; Cheong, S. -W.] Rutgers State Univ, Rutgers Ctr Emergent Mat, Piscataway, NJ 08854 USA. [Liu, Z. X.] Carnegie Inst Sci, Geophys Lab, Washington, DC 20015 USA. [Bai, J. M.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. [Wang, L. P.] SUNY Stony Brook, Inst Mineral Phys, Stony Brook, NY 11794 USA. RP Gao, P (reprint author), New Jersey Inst Technol, Dept Phys, Newark, NJ 07102 USA. EM pg35@njit.edu; tyson@adm.njit.edu RI Chen, Haiyan/C-8109-2012; Bai, Jianming/O-5005-2015 FU DOE [DE-FG02-07ER46402, DE-FG02-07ER46382]; U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences [DE-AC02-98CH10886]; COMPRES, Consortium for Materials Properties Research in Earth Sciences under NSF [EAR01-35554] FX This research was funded by DOE Grant Nos. DE-FG02-07ER46402 (NJIT) and DE-FG02-07ER46382 (Rutgers). The U2A beam line at the National Synchrotron Light Source is supported by COMPRES, the Consortium for Materials Properties Research in Earth Sciences under NSF Cooperative Agreement No. EAR01-35554, U.S. Department of Energy (DOE-BES and NNSA/CDAC). The use of the NSLS at Brookhaven National Laboratory was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-98CH10886. NR 25 TC 1 Z9 1 U1 3 U2 16 PU AMER INST PHYSICS PI MELVILLE PA 1305 WALT WHITMAN RD, STE 300, MELVILLE, NY 11747-4501 USA SN 0003-6951 EI 1077-3118 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 27 PY 2010 VL 97 IS 26 AR 262905 DI 10.1063/1.3533022 PG 3 WC Physics, Applied SC Physics GA 700TV UT WOS:000285768100059 ER PT J AU Jones, WA Barnes, PN Mullins, MJ Baca, FJ Emergo, RLS Wu, J Haugan, TJ Clem, JR AF Jones, W. A. Barnes, P. N. Mullins, M. J. Baca, F. J. Emergo, R. L. S. Wu, J. Haugan, T. J. Clem, J. R. TI Impact of edge-barrier pinning in superconducting thin films SO APPLIED PHYSICS LETTERS LA English DT Article ID CRITICAL-CURRENT-DENSITY; CRITICAL CURRENTS; YBA2CU3O7-DELTA; FLUX; STRIPS AB It has been suggested that edge-barrier pinning might cause the critical current density (J(c)) in bridged superconducting films to increase. Subsequent work indicated that this edge-barrier effect does not impact bridges larger than 1 mu m. However, we provide a theoretical assessment with supporting experimental data suggesting edge-barrier pinning can significantly enhance J(c) for bridges of a few microns or even tens of microns thus skewing any comparisons among institutions. As such, when reporting flux pinning and superconductor processing improvements for J(c) comparisons, the width of the sample has to be taken into consideration as is currently done with film thickness. (C) 2010 American Institute of Physics. [doi:10.1063/1.3529945] C1 [Jones, W. A.; Mullins, M. J.] Univ Dayton, Dayton, OH 45469 USA. [Jones, W. A.; Barnes, P. N.; Mullins, M. J.; Baca, F. J.; Haugan, T. J.] USAF, Res Lab, Wright Patterson AFB, OH 45433 USA. [Baca, F. J.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. [Emergo, R. L. S.; Wu, J.] Univ Kansas, Dept Phys & Astron, Lawrence, KS 66045 USA. [Clem, J. R.] Iowa State Univ, Dept Phys & Astron, Ames, IA 50011 USA. [Clem, J. R.] Iowa State Univ, Ames Lab, Ames, IA 50011 USA. RP Jones, WA (reprint author), Univ Dayton, Dayton, OH 45469 USA. EM wesley.jones@wpafb.af.mil FU Air Force Office of Scientific Research; U.S. Department of Energy, Office of Basic Energy Science, Division of Materials Sciences and Engineering [DE-AC02-07CH11358] FX The Air Force Office of Scientific Research supported this work. We thank R. L. Dunning and J. A. Connors for their help. The University of Kansas thanks the National Science Foundation and the Department of Energy. Theoretical work at the Ames Laboratory, Iowa State University, was supported by the U.S. Department of Energy, Office of Basic Energy Science, Division of Materials Sciences and Engineering, under Contract No. DE-AC02-07CH11358. NR 25 TC 9 Z9 9 U1 3 U2 14 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0003-6951 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 27 PY 2010 VL 97 IS 26 AR 262503 DI 10.1063/1.3529945 PG 3 WC Physics, Applied SC Physics GA 700TV UT WOS:000285768100048 ER PT J AU Ihlefeld, JF Folkman, CM Baek, SH Brennecka, GL George, MC Carroll, JF Eom, CB AF Ihlefeld, J. F. Folkman, C. M. Baek, S. H. Brennecka, G. L. George, M. C. Carroll, J. F., III Eom, C. B. TI Effect of domain structure on dielectric nonlinearity in epitaxial BiFeO3 films SO APPLIED PHYSICS LETTERS LA English DT Article ID THIN-FILMS; FERROELECTRIC PROPERTIES; PIEZOELECTRIC CERAMICS; PERMITTIVITY AB Rayleigh analysis has been used to investigate dielectric nonlinearity in epitaxial (001)-oriented BiFeO3 films with engineered domain structures from single-to four-variant and stripe domain samples with 71 and 109 domain walls. Single-domain variant films display minimal irreversible contributions, whereas the ratio of irreversible to reversible contributions increases by approximately one order of magnitude as the number of variants increases to two-and four-variants, respectively. These measurements indicate that the density of domain walls and degree of domain wall complexity influence the number and strength of domain wall pinning sites. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3533017] C1 [Ihlefeld, J. F.; Brennecka, G. L.; George, M. C.; Carroll, J. F., III] Sandia Natl Labs, Albuquerque, NM 87185 USA. [Folkman, C. M.; Baek, S. H.; Eom, C. B.] Univ Wisconsin, Dept Mat Sci & Engn, Madison, WI 53706 USA. RP Ihlefeld, JF (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87185 USA. EM jihlefe@sandia.gov RI Ihlefeld, Jon/B-3117-2009; Brennecka, Geoff/J-9367-2012; Baek, Seung-Hyub/B-9189-2013; Eom, Chang-Beom/I-5567-2014 OI Brennecka, Geoff/0000-0002-4476-7655; FU Army Research Office [W911NF-10-1-0362]; National Science Foundation [ECCS-0708759]; David and Lucile Packard Fellowship; United States Department of Energy's National Nuclear Security Administration [DE-AC04-94AL85000] FX The authors gratefully acknowledge the financial support of Army Research Office under Grant No. W911NF-10-1-0362, the National Science Foundation under Grant No. ECCS-0708759, and David and Lucile Packard Fellowship (UW-M). Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Co., for the United States Department of Energy's National Nuclear Security Administration under Contract No. DE-AC04-94AL85000. NR 19 TC 11 Z9 11 U1 0 U2 26 PU AMER INST PHYSICS PI MELVILLE PA 1305 WALT WHITMAN RD, STE 300, MELVILLE, NY 11747-4501 USA SN 0003-6951 EI 1077-3118 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 27 PY 2010 VL 97 IS 26 AR 262904 DI 10.1063/1.3533017 PG 3 WC Physics, Applied SC Physics GA 700TV UT WOS:000285768100058 ER PT J AU Lo, CF Kang, TS Liu, L Chang, CY Pearton, SJ Kravchenko, II Laboutin, O Johnson, JW Ren, F AF Lo, C. F. Kang, T. S. Liu, L. Chang, C. Y. Pearton, S. J. Kravchenko, I. I. Laboutin, O. Johnson, J. W. Ren, F. TI Isolation blocking voltage of nitrogen ion-implanted AlGaN/GaN high electron mobility transistor structure SO APPLIED PHYSICS LETTERS LA English DT Article ID GAN; HEMTS; IRRADIATION; PERFORMANCE; BREAKDOWN; LAYERS; MBE AB Nitrogen ion-implanted AlGaN/GaN high electron mobility transistor structures showed an isolation blocking voltage of 900 V with a leakage current at 1 mu A/mm across an implanted isolation-gap of 10 mu m between two Ohmic pads. The effect of implanted gap distance (1.7, 5, or 10 mu m) between two Ohmic contact pads was evaluated. The isolation current density was determined to be solely dependent on the applied field between the contact pads. A model using a combination of resistive current and Poole-Frenkel current is consistent with the experimental data. The resistance of the isolation implantation region significantly decreased after the sample was annealed at temperatures above 600 degrees C. (C) 2010 American Institute of Physics. [doi:10.1063/1.3533381] C1 [Lo, C. F.; Kang, T. S.; Liu, L.; Ren, F.] Univ Florida, Dept Chem Engn, Gainesville, FL 32611 USA. [Chang, C. Y.; Pearton, S. J.] Univ Florida, Dept Mat Sci & Engn, Gainesville, FL 32611 USA. [Kravchenko, I. I.] Oak Ridge Natl Lab, Ctr Nanophase Mat Sci, Oak Ridge, TN 37830 USA. [Laboutin, O.; Johnson, J. W.] Kopin Corp, Taunton, MA 02780 USA. RP Lo, CF (reprint author), Univ Florida, Dept Chem Engn, Gainesville, FL 32611 USA. EM fren@che.ufl.edu RI LIU, LU/H-2307-2013; Kravchenko, Ivan/K-3022-2015 OI LIU, LU/0000-0001-7256-3775; Kravchenko, Ivan/0000-0003-4999-5822 FU AFOSR MURI; Scientific User Facilities Division, U.S. Department of Energy FX The work performed at UF is supported by an AFOSR MURI monitored by Gregg Jessen and Kitt Reinhardt. Part of the work conducted at the Center for Nanophase Materials Science in Oak Ridge National Laboratory was sponsored by the Scientific User Facilities Division, U.S. Department of Energy. NR 20 TC 23 Z9 23 U1 2 U2 17 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0003-6951 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 27 PY 2010 VL 97 IS 26 AR 262116 DI 10.1063/1.3533381 PG 3 WC Physics, Applied SC Physics GA 700TV UT WOS:000285768100042 ER PT J AU Vergniory, MG Granadino-Roldan, JM Garcia-Lekue, A Wang, LW AF Vergniory, M. G. Granadino-Roldan, J. M. Garcia-Lekue, A. Wang, Lin-Wang TI Molecular conductivity switching of two benzene rings under electric field SO APPLIED PHYSICS LETTERS LA English DT Article ID TRANSPORT; DENSITY AB A molecular transistor based on torsion-angle conformation change driven by gate electric field is designed and studied using ab initio calculations. This transistor consists of a SH-C(6)H(2)F(CH(3))C(6)H(2)(CH(3))F-SH molecule sandwiched between two Au(111) electrodes, where the interaction between the molecular dipole and a gate voltage induced electric field will cause the molecule to twist along its c-axis, changing the quantum conductivity of the molecule. The effect of thermal fluctuation on the molecular conformation is studied, so is the ability of the transistor to shut off its current. The advantages and challenges of using such molecular conformation change as a mechanism for transistor gating are discussed. (C) 2010 American Institute of Physics. [doi:10.1063/1.3533383] C1 [Vergniory, M. G.; Garcia-Lekue, A.] DIPC, Basque Country 20018, Spain. [Vergniory, M. G.; Wang, Lin-Wang] Univ Calif Berkeley, Lawrence Berkeley Lab, Computat Res Div, Berkeley, CA 94720 USA. [Granadino-Roldan, J. M.] Univ Jaen, Dept Phys & Analyt Chem, E-23071 Jaen, Spain. RP Vergniory, MG (reprint author), DIPC, Basque Country 20018, Spain. EM maiagv@gmail.com RI Granadino-Roldan, Jose M./A-6557-2011; DONOSTIA INTERNATIONAL PHYSICS CTR., DIPC/C-3171-2014 OI Granadino-Roldan, Jose M./0000-0002-9527-1158; FU U.S. Department of Energy BES/SC [DE-AC02-05CH11231]; Consejeria de Innovacion Ciencia y Empresa, Junta de Andalucia [PAI-FQM 337, FQM-P06-01864]; Basque Departamento de Educacion; UPV/EHU; Diputacion Foral de Guipuzcoa; Spanish MICINN [FIS2010-19609-C02-02] FX This work has been supported partially by the U.S. Department of Energy BES/SC under Contract No. DE-AC02-05CH11231, Consejeria de Innovacion Ciencia y Empresa, Junta de Andalucia (Contract Nos. PAI-FQM 337 and FQM-P06-01864), Basque Departamento de Educacion, UPV/EHU, the Diputacion Foral de Guipuzcoa, and the Spanish MICINN (Grant No. FIS2010-19609-C02-02). This research used the resource of the National Energy Research Scientific Computing Center (NERSC). NR 21 TC 13 Z9 13 U1 2 U2 10 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0003-6951 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 27 PY 2010 VL 97 IS 26 AR 262114 DI 10.1063/1.3533383 PG 3 WC Physics, Applied SC Physics GA 700TV UT WOS:000285768100040 ER PT J AU Kato, Y Martin, I Batista, CD AF Kato, Yasuyuki Martin, Ivar Batista, C. D. TI Stability of the Spontaneous Quantum Hall State in the Triangular Kondo-Lattice Model SO PHYSICAL REVIEW LETTERS LA English DT Article ID PHASE-TRANSITION; BERRY PHASE; MAGNETORESISTANCE; ANTIFERROMAGNET; FERROMAGNET AB We study the behavior of the quarter-filled Kondo-lattice model on a triangular lattice by combining a zero-temperature variational approach and finite-temperature Monte Carlo simulations. For intermediate coupling between itinerant electrons and classical moments S(j), we find a thermodynamic phase transition into an exotic spin ordering with uniform scalar spin chirality and < S(j)> = 0. The state exhibits a spontaneous quantum Hall effect. We also study how its properties are affected by the application of an external magnetic field. C1 [Kato, Yasuyuki; Martin, Ivar; Batista, C. D.] Los Alamos Natl Lab, Div Theoret, Los Alamos, NM 87545 USA. RP Kato, Y (reprint author), Los Alamos Natl Lab, Div Theoret, Los Alamos, NM 87545 USA. RI Batista, Cristian/J-8008-2016 FU NNSA of the U.S. DOE at LANL [DE-AC52-06NA25396]; LANL/LDRD Program FX We thank S. Nakatsuji and Y. Motome for useful discussions. This work was carried out under the auspices of the NNSA of the U.S. DOE at LANL under Contract No. DE-AC52-06NA25396 and supported by the LANL/LDRD Program. This research used resources of the NERSC Center. NR 26 TC 36 Z9 36 U1 4 U2 16 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 0031-9007 J9 PHYS REV LETT JI Phys. Rev. Lett. PD DEC 27 PY 2010 VL 105 IS 26 AR 266405 DI 10.1103/PhysRevLett.105.266405 PG 4 WC Physics, Multidisciplinary SC Physics GA 713UQ UT WOS:000286763300005 PM 21231691 ER PT J AU McBride, RD Jennings, CA Vesey, RA Rochau, GA Savage, ME Stygar, WA Cuneo, ME Sinars, DB Jones, M LeChien, KR Lopez, MR Moore, JK Struve, KW Wagoner, TC Waisman, EM AF McBride, R. D. Jennings, C. A. Vesey, R. A. Rochau, G. A. Savage, M. E. Stygar, W. A. Cuneo, M. E. Sinars, D. B. Jones, M. LeChien, K. R. Lopez, M. R. Moore, J. K. Struve, K. W. Wagoner, T. C. Waisman, E. M. TI Displacement current phenomena in the magnetically insulated transmission lines of the refurbished Z accelerator SO PHYSICAL REVIEW SPECIAL TOPICS-ACCELERATORS AND BEAMS LA English DT Article ID Z-PINCHES; SIMULATIONS; GENERATION; IMPEDANCE; FLOW AB Experimental data is presented that illustrates important displacement current phenomena in the magnetically insulated transmission lines (MITLs) of the refurbished Z accelerator [D. V. Rose et al., Phys. Rev. ST Accel. Beams 13, 010402 (2010)]. Specifically, we show how displacement current in the MITLs causes significant differences between the accelerator current measured at the vacuum-insulator stack (at a radial position of about 1.6 m from the Z axis of symmetry) and the accelerator current measured at the load (at a radial position of about 6 cm from the Z axis of symmetry). The importance of accounting for these differences was first emphasized by Jennings et al. [C. A. Jennings et al., IEEE Trans. Plasma Sci. 38, 529 (2010)], who calculated them using a full transmission-line-equivalent model of the four-level MITL system. However, in the data presented by Jennings et al., many of the interesting displacement current phenomena were obscured by parasitic current losses that occurred between the vacuum-insulator stack and the load (e.g., electron flow across the anode-cathode gap). By contrast, the data presented herein contain very little parasitic current loss, and thus for these low-loss experiments we are able to demonstrate that the differences between the current measured at the stack and the current measured at the load are due primarily to the displacement current that results from the shunt capacitance of the MITLs (about 8.41 nF total). Demonstrating this is important because displacement current is an energy storage mechanism, where energy is stored in the MITL electric fields and can later be used by the system. Thus, even for higher-loss experiments, the differences between the current measured at the stack and the current measured at the load are often largely due to energy storage and subsequent release, as opposed to being due solely to some combination of measurement error and current loss in the MITLs and/or double post-hole convolute. Displacement current also explains why the current measured downstream of the MITLs (i.e., the load current) often exceeds the current measured upstream of the MITLs (i.e., the stack current) at various times in the power pulse (this particular phenomenon was initially thought to be due to timing and/or calibration errors). To facilitate a better understanding of these phenomena, we also introduce and analyze a simple LC circuit model of the MITLs. This model is easily implemented as a simple drive circuit in simulation codes, which has now been done for the LASNEX code [G. B. Zimmerman and W. L. Kruer, Comments Plasma Phys. Controlled Fusion 2, 51 (1975)] at Sandia, as well as for simpler MATLAB (R)-based codes at Sandia. An example of this LC model used as a drive circuit will also be presented. C1 [McBride, R. D.; Jennings, C. A.; Vesey, R. A.; Rochau, G. A.; Savage, M. E.; Stygar, W. A.; Cuneo, M. E.; Sinars, D. B.; Jones, M.; LeChien, K. R.; Lopez, M. R.; Struve, K. W.; Waisman, E. M.] Sandia Natl Labs, Albuquerque, NM 87185 USA. [Moore, J. K.; Wagoner, T. C.] Ktech Corp Inc, Albuquerque, NM 87123 USA. RP McBride, RD (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87185 USA. FU United States Department of Energy's National Nuclear Security Administration [DE-AC04-94AL85000] FX The authors would like to thank M. K. Matzen, M. C. Herrmann, and J. L. Porter for programmatic support, and the Z operations, diagnostics, engineering, load hardware, and target teams for their technical assistance. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed-Martin company, for the United States Department of Energy's National Nuclear Security Administration, under Contract No. DE-AC04-94AL85000. NR 40 TC 8 Z9 9 U1 0 U2 6 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 1098-4402 J9 PHYS REV SPEC TOP-AC JI Phys. Rev. Spec. Top.-Accel. Beams PD DEC 27 PY 2010 VL 13 IS 12 AR 120401 DI 10.1103/PhysRevSTAB.13.120401 PG 9 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA 701DA UT WOS:000285793300001 ER PT J AU Cook, BA Harringa, JL Anderegg, J Russell, AM Qu, J Blau, PJ Higdon, C Elmoursi, AA AF Cook, Bruce A. Harringa, Joel L. Anderegg, James Russell, Alan M. Qu, Jun Blau, Peter J. Higdon, Clifton Elmoursi, Alaa A. TI Analysis of wear mechanisms in low-friction AlMgB14-TiB2 coatings SO SURFACE & COATINGS TECHNOLOGY LA English DT Article DE Tribology; Boride; Coating; Auger spectroscopy; XPS; Wear ID DIAMOND-LIKE CARBON; INDUCED PHASE-TRANSFORMATION; FILMS AB Recent developments in coating science and technology offer new opportunities to enhance the energy-efficiency and performance of industrial machinery such as hydraulic fluid pumps and motors. The lubricated friction and wear characteristics of two wear-resistant coatings, diamond-like carbon and a nanocomposite material based on AlMgB14-50 vol.% TiB2, were compared in pin-on-disk tribotests using Mobil DTE-24 (TM) oil as the lubricant. In each case, the pins were fixed 9.53 mm diameter spheres of AISI 52100 steel, the load was 10 N, and the speed 0.5 m/s in all tests. Average steady-state friction coefficient values of 0.10 and 0.08 were measured for the DLC and nanocomposite, respectively. The coatings and their 52100 steel counterfaces were analyzed after the tests by X-ray photoelectron and Auger spectroscopy for evidence of material transfer or tribo-chemical reactions. The low-friction behavior of the boride nanocomposite coating is due to the formation of lubricative boric acid, B(OH)(3). In contrast, the low-friction behavior of the DLC coating is related to the relatively low dielectric constant of the oil-based lubricant, leading to desorption of surface hydrogen from the coating. (C) 2010 Elsevier B.V. All rights reserved. C1 [Cook, Bruce A.; Harringa, Joel L.; Anderegg, James] Iowa State Univ, Div Mat Sci & Engn, Ames Lab, Ames, IA 50011 USA. [Qu, Jun; Blau, Peter J.] Oak Ridge Natl Lab, Mat Sci & Technol Div, Oak Ridge, TN 37830 USA. [Higdon, Clifton; Elmoursi, Alaa A.] Eaton Corp, Innovat Ctr, Southfield, MI 48076 USA. RP Cook, BA (reprint author), Iowa State Univ, Div Mat Sci & Engn, Ames Lab, Ames, IA 50011 USA. EM cook@ameslab.gov OI Qu, Jun/0000-0001-9466-3179; Russell, Alan/0000-0001-5264-0104 FU Iowa State University [DE-AC02-07CH11358]; U.S. Department of Energy; [DE-AC05-00OR22725] FX The Ames Laboratory is operated for the U.S. Department of Energy by Iowa State University under contract DE-AC02-07CH11358. Oak Ridge National Laboratory is operated under contract to UT-Battelle LLC under contract DE-AC05-00OR22725. This work was supported by the U.S. Department of Energy, EERE Industrial Technologies Program. NR 19 TC 18 Z9 19 U1 1 U2 22 PU ELSEVIER SCIENCE SA PI LAUSANNE PA PO BOX 564, 1001 LAUSANNE, SWITZERLAND SN 0257-8972 J9 SURF COAT TECH JI Surf. Coat. Technol. PD DEC 25 PY 2010 VL 205 IS 7 BP 2296 EP 2301 DI 10.1016/j.surfcoat.2010.09.007 PG 6 WC Materials Science, Coatings & Films; Physics, Applied SC Materials Science; Physics GA 708DY UT WOS:000286343100068 ER PT J AU Jones, MK Zhang, L Catte, A Li, L Oda, MN Ren, G Segrest, JP AF Jones, Martin K. Zhang, Lei Catte, Andrea Li, Ling Oda, Michael N. Ren, Gang Segrest, Jere P. TI Assessment of the Validity of the Double Superhelix Model for Reconstituted High Density Lipoproteins A COMBINED COMPUTATIONAL-EXPERIMENTAL APPROACH SO JOURNAL OF BIOLOGICAL CHEMISTRY LA English DT Article ID GRADIENT GEL-ELECTROPHORESIS; MOLECULAR-DYNAMICS; ELECTRON-MICROSCOPY; PLASMA-LIPOPROTEINS; NEUTRON-SCATTERING; FORCE-FIELD; APOA-I; HDL; CHOLESTEROL; PHOSPHATIDYLCHOLINE AB For several decades, the standard model for high density lipoprotein (HDL) particles reconstituted from apolipoprotein A-I (apoA-I) and phospholipid (apoA-I/HDL) has been a discoidal particle similar to 100 angstrom in diameter and the thickness of a phospholipid bilayer. Recently, Wu et al. (Wu, Z., Gogonea, V., Lee, X., Wagner, M. A., Li, X. M., Huang, Y., Undurti, A., May, R. P., Haertlein, M., Moulin, M., Gutsche, I., Zaccai, G., Didonato, J. A., and Hazen, S. L. (2009) J. Biol. Chem. 284, 3660536619) used small angle neutron scattering to develop a new model they termed double superhelix (DSH) apoA-I that is dramatically different from the standard model. Their model possesses an open helical shape that wraps around a prolate ellipsoidal type I hexagonal lyotropic liquid crystalline phase. Here, we used three independent approaches, molecular dynamics, EM tomography, and fluorescence resonance energy transfer spectroscopy (FRET) to assess the validity of the DSH model. (i) By using molecular dynamics, two different approaches, all-atom simulated annealing and coarse-grained simulation, show that initial ellipsoidal DSH particles rapidly collapse to discoidal bilayer structures. These results suggest that, compatible with current knowledge of lipid phase diagrams, apoA-I cannot stabilize hexagonal I phase particles of phospholipid. (ii) By using EM, two different approaches, negative stain and cryo-EM tomography, show that reconstituted apoA-I/HDL particles are discoidal in shape. (iii) By using FRET, reconstituted apoA-I/HDL particles show a 28 -34-angstrom intermolecular separation between terminal domain residues 40 and 240, a distance that is incompatible with the dimensions of the DSH model. Therefore, we suggest that, although novel, the DSH model is energetically unfavorable and not likely to be correct. Rather, we conclude that all evidence supports the likelihood that reconstituted apoA-I/HDL particles, in general, are discoidal in shape. C1 [Jones, Martin K.; Catte, Andrea; Li, Ling; Segrest, Jere P.] Univ Alabama Birmingham, Dept Med, Birmingham, AL 35294 USA. [Jones, Martin K.; Catte, Andrea; Li, Ling; Segrest, Jere P.] Univ Alabama Birmingham, Atherosclerosis Res Unit, Birmingham, AL 35294 USA. [Jones, Martin K.; Catte, Andrea; Segrest, Jere P.] Univ Alabama Birmingham, Ctr Computat & Struct Dynam, Birmingham, AL 35294 USA. [Zhang, Lei; Ren, Gang] Univ Calif Berkeley, Lawrence Berkeley Lab, Mol Foundry, Berkeley, CA 94720 USA. [Zhang, Lei; Ren, Gang] Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94158 USA. [Oda, Michael N.] Childrens Hosp Oakland Res Inst, Oakland, CA 94609 USA. RP Segrest, JP (reprint author), 1808 7th Ave S,BDB 630, Birmingham, AL 35294 USA. EM segrest@uab.edu RI Zhang, Lei/G-6427-2012 OI Zhang, Lei/0000-0002-4880-824X FU National Institutes of Health [P01 HL-34343]; W. M. Keck Foundation [011808] FX This work was supported, in whole or in part, by National Institutes of Health Grant P01 HL-34343 (to J. P. S.). This work was also supported by W. M. Keck Foundation (No. 011808, to G. R.). NR 48 TC 32 Z9 32 U1 0 U2 10 PU AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC PI BETHESDA PA 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3996 USA SN 0021-9258 J9 J BIOL CHEM JI J. Biol. Chem. PD DEC 24 PY 2010 VL 285 IS 52 BP 41161 EP 41171 DI 10.1074/jbc.M110.187799 PG 11 WC Biochemistry & Molecular Biology SC Biochemistry & Molecular Biology GA 696AN UT WOS:000285414400078 PM 20974855 ER PT J AU Sirinupong, N Brunzelle, J Ye, J Pirzada, A Nico, L Yang, Z AF Sirinupong, Nualpun Brunzelle, Joseph Ye, Jun Pirzada, Ali Nico, Lindsey Yang, Zhe TI Crystal Structure of Cardiac-specific Histone Methyltransferase SmyD1 Reveals Unusual Active Site Architecture SO JOURNAL OF BIOLOGICAL CHEMISTRY LA English DT Article ID TRANSCRIPTION FACTOR; FUNCTIONAL-ANALYSIS; ZEBRAFISH EMBRYOS; CANCER-CELLS; MYND DOMAIN; METHYLATION; PROTEIN; SET7/9; MECHANISM; SOFTWARE AB SmyD1 is a cardiac-and muscle-specific histone methyltransferase that methylates histone H3 at lysine 4 and regulates gene transcription in early heart development. The unique domain structure characterized by a "split" SET domain, a conserved MYND zinc finger, and a novel C-terminal domain (CTD) distinguishes SmyD1 from other SET domain containing methyltransferases. Here we report the crystal structure of full-length SmyD1 in complex with the cofactor analog sinefungin at 2.3 angstrom. The structure reveals that SmyD1 folds into a wrench-shaped structure with two thick "grips" separated by a large, deep concave opening. Importantly, our structural and functional analysis suggests that SmyD1 appears to be regulated by an autoinhibition mechanism, and that unusually spacious target lysine-access channel and the presence of the CTD domain both negatively contribute to the regulation of this cardiovascularly relevant methyltransferase. Furthermore, our structure also provides a structural basis for the interaction between SmyD1 and cardiac transcription factor skNAC, and suggests that the MYND domain may primarily serve as a protein interaction module and cooperate SmyD1 with skNAC to regulate cardiomyocyte growth and maturation. Overall, our data provide novel insights into the mechanism of SmyD1 regulation, which would be helpful in further understanding the role of this protein in heart development and cardiovascular diseases. C1 [Sirinupong, Nualpun; Ye, Jun; Pirzada, Ali; Nico, Lindsey; Yang, Zhe] Wayne State Univ, Dept Biochem & Mol Biol, Sch Med, Detroit, MI USA. [Brunzelle, Joseph] Argonne Natl Lab, Adv Photon Source, Argonne, IL 60439 USA. RP Yang, Z (reprint author), 540 E Canfield St, Detroit, MI 48201 USA. EM zyang@med.wayne.edu FU American Heart Association FX This work was supported by the American Heart Association. NR 31 TC 39 Z9 41 U1 1 U2 8 PU AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC PI BETHESDA PA 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3996 USA SN 0021-9258 J9 J BIOL CHEM JI J. Biol. Chem. PD DEC 24 PY 2010 VL 285 IS 52 DI 10.1074/jbc.M110.168187 PG 10 WC Biochemistry & Molecular Biology SC Biochemistry & Molecular Biology GA 696AN UT WOS:000285414400026 PM 20943667 ER PT J AU Urban, J Svec, F Frechet, JMJ AF Urban, Jiri Svec, Frantisek Frechet, Jean M. J. TI Hypercrosslinking: New approach to porous polymer monolithic capillary columns with large surface area for the highly efficient separation of small molecules SO JOURNAL OF CHROMATOGRAPHY A LA English DT Article DE Hypercrosslinked polymer monolith; Poly(styrene-co-vinylbenzyl chloride-co-divinylbenzene); Reversed phase chromatography; Size-exclusion chromatography; Small molecules ID PERFORMANCE LIQUID-CHROMATOGRAPHY; SIZE-EXCLUSION CHROMATOGRAPHY; REVERSED-PHASE CHROMATOGRAPHY; STABLE FREE-RADICALS; STATIONARY PHASES; MACROPOROUS POLY(STYRENE-CO-DIVINYLBENZENE); ORGANIC MONOLITHS; HYDROGEN STORAGE; PACKING MATERIAL; HPLC COLUMN AB Monolithic polymers with an unprecedented surface area of over 600 m(2)/g have been prepared from a poly(styrene-co-vinylbenzyl chloride-co-divinylbenzene) precursor monolith that was swollen in 1,2-dichloroethane and hypercrosslinked via Friedel-Crafts reaction catalyzed by ferric chloride. Both the composition of the reaction mixture used for the preparation of the precursor monolith and the conditions of the hypercrosslinking reaction have been varied using mathematical design of experiments and the optimized system validated. Hypercrosslinked monolithic capillary columns contain an array of small pores that make the column ideally suited for the high efficiency isocratic separations of small molecules such as uracil and alkylbenzenes with column efficiencies reproducibly exceeding 80,000 plates/m for retained compounds. The separation process could be accelerated while also improving peak shape through the use of higher temperatures and a ternary mobile phase consisting of acetonitrile, tetrahydrofuran, and water. As a result, seven compounds were well separated in less than 2 min. These columns also facilitate separations of peptide mixtures such as a tryptic digest of cytochrome c using a gradient elution mode which affords a sequence coverage of 93%. A 65 cm long hypercrosslinked capillary column used in size exclusion mode with tetrahydrofuran as the mobile phase afforded almost baseline separation of toluene and five polystyrene standards. (C) 2010 Elsevier B.V. All rights reserved. C1 [Urban, Jiri; Frechet, Jean M. J.] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. [Svec, Frantisek; Frechet, Jean M. J.] EO Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Frechet, JMJ (reprint author), Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. EM frechet1@gmail.com RI Urban, Jiri/D-1133-2014; OI Frechet, Jean /0000-0001-6419-0163 FU National Institute of Health [GM48364]; Office of Science, Office of Basic Energy Sciences, U.S. Department of Energy [DE-AC02-05CH11231] FX Financial support of this research by a grant of the National Institute of Health (GM48364) is gratefully acknowledged. Analytical work performed at the Molecular Foundry, Lawrence Berkeley National Laboratory and F.S. were supported by the Office of Science, Office of Basic Energy Sciences, U.S. Department of Energy, under Contract No. DE-AC02-05CH11231. NR 76 TC 97 Z9 98 U1 12 U2 121 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0021-9673 EI 1873-3778 J9 J CHROMATOGR A JI J. Chromatogr. A PD DEC 24 PY 2010 VL 1217 IS 52 BP 8212 EP 8221 DI 10.1016/j.chroma.2010.10.100 PG 10 WC Biochemical Research Methods; Chemistry, Analytical SC Biochemistry & Molecular Biology; Chemistry GA 702MS UT WOS:000285899400017 PM 21092973 ER PT J AU Padgett, S Madurga, M Grzywacz, R Darby, IG Liddick, SN Paulauskas, SV Cartegni, L Bingham, CR Gross, CJ Rykaczewski, K Shapira, D Stracener, DW Mendez, AJ Winger, JA Ilyushkin, SV Korgul, A Krolas, W Zganjar, E Mazzocchi, C Liu, S Hamilton, JH Batchelder, JC Rajabali, MM AF Padgett, S. Madurga, M. Grzywacz, R. Darby, I. G. Liddick, S. N. Paulauskas, S. V. Cartegni, L. Bingham, C. R. Gross, C. J. Rykaczewski, K. Shapira, D. Stracener, D. W. Mendez H, A. J. Winger, J. A. Ilyushkin, S. V. Korgul, A. Krolas, W. Zganjar, E. Mazzocchi, C. Liu, S. Hamilton, J. H. Batchelder, J. C. Rajabali, M. M. TI beta decay of Zn-81 and migrations of states observed near the N=50 closed shell SO PHYSICAL REVIEW C LA English DT Article ID NEUTRON-RICH ISOTOPES; STABILITY AB The beta decay of the N = 51 nucleus Zn-81 was studied by means of beta-gamma spectroscopy and from isotopically pure beams produced at the Holifield Radioactive Ion Beam Facility (HRIBF). We observe several competing beta transitions populating Ga-81 that are interpreted as allowed Gamow-Teller decays to positive parity, core excited states, and first-forbidden decays to negative parity states. The measured beta-decay pattern suggests an assignment of I-pi = 5/2(+) for the Zn-81 ground state. The systematics of core excited states in N = 50 isotones indicate a strengthening of the N = 40 subshell gap near Ni-78. C1 [Padgett, S.; Madurga, M.; Grzywacz, R.; Darby, I. G.; Liddick, S. N.; Paulauskas, S. V.; Cartegni, L.; Bingham, C. R.; Rajabali, M. M.] Univ Tennessee, Dept Phys & Astron, Knoxville, TN 37996 USA. [Gross, C. J.; Rykaczewski, K.; Shapira, D.; Stracener, D. W.; Mendez H, A. J.] Oak Ridge Natl Lab, Div Phys, Oak Ridge, TN 37830 USA. [Winger, J. A.; Ilyushkin, S. V.] Mississippi State Univ, Dept Phys & Astron, Mississippi State, MS 39762 USA. [Korgul, A.; Mazzocchi, C.] Univ Warsaw, Fac Phys, PL-00681 Warsaw, Poland. [Krolas, W.] Polish Acad Sci, Inst Nucl Phys, PL-31342 Krakow, Poland. [Zganjar, E.] Louisiana State Univ, Dept Phys & Astron, Baton Rouge, LA 70803 USA. [Mazzocchi, C.] Univ Milan, I-20133 I Milano, Italy. [Mazzocchi, C.] Ist Nazl Fis Nucl, Sez Milano, I-20133 I Milano, Italy. [Liu, S.; Hamilton, J. H.] Vanderbilt Univ, Dept Phys & Astron, Nashville, TN 37235 USA. [Batchelder, J. C.] Oak Ridge Associated Univ, UNIRIB, Oak Ridge, TN 37831 USA. RP Padgett, S (reprint author), Univ Tennessee, Dept Phys & Astron, Knoxville, TN 37996 USA. RI Krolas, Wojciech/N-9391-2013 FU Office of Science, US Department of Energy [DE-AC05-00OR22725, DE-FG02-96ER40983] FX We thank the HRIBF operations staff for providing the excellent quality radioactive ion beams necessary for this work. We thank M. Hjorth-Jensen for supplying his N3LO nucleon-nucleon interactions and for the use of his shell-model calculation code. This research is sponsored by the Office of Science, US Department of Energy under Contract Nos. DE-AC05-00OR22725 (ORNL) and DE-FG02-96ER40983 (UTK). NR 29 TC 18 Z9 18 U1 0 U2 7 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 2469-9985 EI 2469-9993 J9 PHYS REV C JI Phys. Rev. C PD DEC 23 PY 2010 VL 82 IS 6 AR 064314 DI 10.1103/PhysRevC.82.064314 PG 9 WC Physics, Nuclear SC Physics GA 713MK UT WOS:000286741900002 ER PT J AU Barone, V Melis, S Prokudin, A AF Barone, Vincenzo Melis, Stefano Prokudin, Alexei TI Azimuthal asymmetries in unpolarized Drell-Yan processes and the Boer-Mulders distributions of antiquarks SO PHYSICAL REVIEW D LA English DT Article ID DEEP-INELASTIC SCATTERING; FINAL-STATE INTERACTIONS; SINGLE-SPIN ASYMMETRIES; ANGULAR-DISTRIBUTIONS; PARTON DISTRIBUTIONS; TRANSVERSE-MOMENTUM; ODD DISTRIBUTION; NEGATIVE PIONS; PAIRS; LEPTOPRODUCTION AB Using a previous extraction of the quark Boer-Mulders distributions from semi-inclusive deep inelastic scattering data, we fit the unpolarized Drell-Yan data on the cos2 phi asymmetry, determining the antiquark Boer-Mulders distributions. A good agreement with the data is found in the region of low q(T), where the transverse-momentum factorization approach applies. C1 [Barone, Vincenzo; Melis, Stefano] Univ Piemonte Orientale, DiSTA, I-15121 Alessandria, Italy. [Barone, Vincenzo; Melis, Stefano] Ist Nazl Fis Nucl, Grp Coll Alessandria, I-15121 Alessandria, Italy. [Prokudin, Alexei] Jefferson Lab, Newport News, VA 23606 USA. RP Barone, V (reprint author), Univ Piemonte Orientale, DiSTA, I-15121 Alessandria, Italy. OI Melis, Stefano/0000-0001-7316-4346 FU European Community [RII3-CT-2004-506078]; Italian Ministry of Education, University and Research; Helmholtz Association [VH-VI-231]; Regione Piemonte; DOE [DE-AC05-06OR23177] FX We acknowledge support by the European Community-Research Infrastructure Activity under the FP6 Program "Structuring the European Research Area'' (Hadron Physics, Contract No. RII3-CT-2004-506078), by the Italian Ministry of Education, University and Research (PRIN 2008) and by the Helmholtz Association through funds provided to the virtual institute "Spin and Strong QCD'' (VH-VI-231). The work of one of us (S. M.) is also supported by Regione Piemonte. This work was supported by DOE Contract No. DE-AC05-06OR23177, under which Jefferson Science Associates, LLC, operates Jefferson Laboratory. NR 52 TC 20 Z9 20 U1 0 U2 1 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 1550-7998 J9 PHYS REV D JI Phys. Rev. D PD DEC 23 PY 2010 VL 82 IS 11 AR 114025 DI 10.1103/PhysRevD.82.114025 PG 5 WC Astronomy & Astrophysics; Physics, Particles & Fields SC Astronomy & Astrophysics; Physics GA 711HI UT WOS:000286577300003 ER PT J AU Boers, R de Haij, MJ Wauben, WMF Baltink, HK van Ulft, LH Savenije, M Long, CN AF Boers, R. de Haij, M. J. Wauben, W. M. F. Baltink, H. Klein van Ulft, L. H. Savenije, M. Long, C. N. TI Optimized fractional cloudiness determination from five ground-based remote sensing techniques SO JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES LA English DT Article ID SKY COVER AB A 1 year record of fractional cloudiness at 10 min intervals was generated for the Cabauw Experimental Site for Atmospheric Research (CESAR) (51 degrees 58'N, 4 degrees 55'E) using an integrated assessment of five different observational methods. The five methods are based on active as well as passive systems and use either a hemispheric or column remote sensing technique. The 1 year instrumental cloudiness data were compared against a 30 year climatology of Observer data in the vicinity of CESAR (1971-2000). In the intermediate 2-6 octa range, most instruments, but especially the column methods, report lower frequency of occurrence of cloudiness than the absolute minimum values from the 30 year Observer climatology. At night, the Observer records fewer clouds in the 1-2 octa range than during the day, while the instrumental techniques registered more clouds. During daytime the Observer also records much more 7 octa cloudiness than the instruments. A reference algorithm was designed to derive a continuous and optimized record of fractional cloudiness. Output from individual instruments were weighted according to the cloud base height reported at the observation time; the larger the height, the lower the weight. The algorithm was able to provide fractional cloudiness observations every 10 min for 99.92% of the total period of 12 months (15 May 2008 to 14 May 2009). C1 [Boers, R.; de Haij, M. J.; Wauben, W. M. F.; Baltink, H. Klein; van Ulft, L. H.; Savenije, M.] Royal Netherlands Meteorol Inst, NL-3730 AE De Bilt, Netherlands. [Long, C. N.] US DOE, Pacific NW Natl Lab, Richland, WA 99352 USA. RP Boers, R (reprint author), Royal Netherlands Meteorol Inst, POB 201, NL-3730 AE De Bilt, Netherlands. EM reinout.boers@knmi.nl FU Climate Change Research Division of the U.S. Department of Energy FX The Raman lidar data were kindly provided to us by A. Apituley from RIVM, Netherlands, who operates this system at CESAR. C.N. Long acknowledges the support of the Climate Change Research Division of the U.S. Department of Energy as part of the Atmospheric System Research (ASR) Program. NR 23 TC 16 Z9 16 U1 0 U2 2 PU AMER GEOPHYSICAL UNION PI WASHINGTON PA 2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA SN 2169-897X EI 2169-8996 J9 J GEOPHYS RES-ATMOS JI J. Geophys. Res.-Atmos. PD DEC 23 PY 2010 VL 115 AR D24116 DI 10.1029/2010JD014661 PG 16 WC Meteorology & Atmospheric Sciences SC Meteorology & Atmospheric Sciences GA 699CT UT WOS:000285642200007 ER PT J AU Stevens, WR Ruscic, B Baer, T AF Stevens, William R. Ruscic, Branko Baer, Tomas TI Heats of Formation of C6H5 center dot, C6H5+, and C6H5NO by Threshold Photoelectron Photoion Coincidence and Active Thermochemical Tables Analysis SO JOURNAL OF PHYSICAL CHEMISTRY A LA English DT Article ID BOND-DISSOCIATION ENERGIES; LOWER ELECTRONIC STATES; SET MODEL CHEMISTRY; DENSITY-FUNCTIONAL GEOMETRIES; UNIMOLECULAR DECAY-RATES; HIGH-PRESSURE PYROLYSIS; DEPENDENT MASS-SPECTRA; ZERO-POINT ENERGIES; DER-WAALS COMPLEXES; IONIZATION-POTENTIALS AB Threshold photoelectron photoion coincidence has been used to prepare selected internal energy distributions of nitrosobenzene ions [C6H5NO+]. Dissociation to C6H5+ + NO products was measured over a range of internal energies and rate constants from 10(3) to 10(7) s(-1) and fitted with the statistical theory of unimolecular decay. A 0 K dissociative photoionization onset energy of 10.607 +/- 0.020 eV was derived by using the simplified statistical adiabatic channel model. The thermochemical network of Active Thermochemical Tables (ATcT) was expanded to include phenyl and phenylium, as well as nitrosobenzene. The current ATcT heats of formation of these three species at 0 K (298.15 K) are 350.6 (337.3) +/- 0.6, 1148.7 (1136.8) +/- 1.0, and 215.6 (198.6) +/- 1.5 kJ mol(-1), respectively. The resulting adiabatic ionization energy of phenyl is 8.272 +/- 0.010 eV. The new ATcT thermochemistry for phenyl entails a 0 K (298.15 K) C-H bond dissociation enthalpy of benzene of 465.9 (472.1) +/- 0.6 kJ mol(-1). Several related thermochemical quantities from ATcT, including the current enthalpies of formation of benzene, monohalobenzenes, and their ions, as well as interim ATcT values for the constituent atoms, are also given. C1 [Ruscic, Branko] Argonne Natl Lab, Chem Sci & Engn Div, Argonne, IL 60439 USA. [Stevens, William R.; Baer, Tomas] Univ N Carolina, Dept Chem, Chapel Hill, NC 27517 USA. [Ruscic, Branko] Univ Chicago, Computat Inst, Chicago, IL 60637 USA. RP Ruscic, B (reprint author), Argonne Natl Lab, Chem Sci & Engn Div, 9700 S Cass Ave, Argonne, IL 60439 USA. EM ruscic@anl.gov; baer@unc.edu RI Ruscic, Branko/A-8716-2008 OI Ruscic, Branko/0000-0002-4372-6990 FU U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences [DE-ACO2-06CH11357, DE-FG02-97ER14776] FX This work was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences under Contract No. DE-ACO2-06CH11357 (at Argonne National Laboratory) and DE-FG02-97ER14776 (at UNC-Chapel Hill). We thank Andras Bodi of the Swiss Light Source for help in running the nitrosobenzene TPES. Portions of this research are related to the effort of the Task Group of the International Union of Pure and Applied Chemistry, "Selected Free Radicals and Critical Intermediates: Thermodynamic Properties from Theory and Experiment" (IUPAC Project 2003-024-1-100). NR 141 TC 53 Z9 53 U1 0 U2 16 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1089-5639 J9 J PHYS CHEM A JI J. Phys. Chem. A PD DEC 23 PY 2010 VL 114 IS 50 BP 13134 EP 13145 DI 10.1021/jp107561s PG 12 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 693PR UT WOS:000285236500024 PM 21128587 ER PT J AU Cunsolo, A Orecchini, A Petrillo, C Sacchetti, F AF Cunsolo, Alessandro Orecchini, Andrea Petrillo, Caterina Sacchetti, Francesco TI Interplay between Microscopic Diffusion and Local Structure of Liquid Water SO JOURNAL OF PHYSICAL CHEMISTRY B LA English DT Article ID ELASTIC NEUTRON-SCATTERING; SUPERCOOLED WATER; LOW-TEMPERATURES; RELAXATIONAL DYNAMICS; DENSITY-FLUCTUATIONS; VISCOSITY; PRESSURE; BEHAVIOR; GLASS; TRANSITION AB We present a quasielastic neutron scattering (QENS) study of single-particle dynamics in pure water, measured at temperatures between 256 and 293 K along an isobaric path at 200 MPa. A thorough analysis of the spectral line shapes reveals a departure from simple models of continuous or jump diffusion, with such an effect becoming stronger at lower temperatures. We show that such a diverging trend of dynamical quantities upon cooling closely resembles the divergent (anomalous) compressibility observed in water by small-angle diffraction. Such an analogy suggests an interesting interplay between single-particle diffusion and structural arrangements in liquid water, both bearing witness of the well-known water anomalies. In particular, a fit of dynamical parameters by a Vogel-Tammann-Fulcher law provides a critical temperature of about 220K, interestingly close to the hypothesized position of the second critical point of water and to the so-called Widom line. C1 [Cunsolo, Alessandro] Brookhaven Natl Lab, Natl Synchrotron Light Source 2, Upton, NY 11973 USA. [Orecchini, Andrea] Inst Max Von Laue Paul Langevin, F-38042 Grenoble 9, France. [Orecchini, Andrea; Petrillo, Caterina; Sacchetti, Francesco] Ctr Ric & Sviluppo SOFT, CNR INFM, I-00185 Rome, Italy. [Orecchini, Andrea; Petrillo, Caterina; Sacchetti, Francesco] Univ Perugia, Dipartimento Fis, I-06123 Perugia, Italy. RP Cunsolo, A (reprint author), Brookhaven Natl Lab, Natl Synchrotron Light Source 2, POB 5000, Upton, NY 11973 USA. RI Cunsolo, Alessandro/C-7617-2013 NR 41 TC 6 Z9 6 U1 0 U2 15 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1520-6106 J9 J PHYS CHEM B JI J. Phys. Chem. B PD DEC 23 PY 2010 VL 114 IS 50 BP 16713 EP 16717 DI 10.1021/jp1073768 PG 5 WC Chemistry, Physical SC Chemistry GA 693PT UT WOS:000285236700005 PM 21114328 ER PT J AU Mamontov, E Faraone, A Hagaman, EW Han, KS Fratini, E AF Mamontov, E. Faraone, A. Hagaman, E. W. Han, K. S. Fratini, E. TI A Low-Temperature Crossover in Water Dynamics in an Aqueous LiCl Solution: Diffusion Probed by Neutron Spin-Echo and Nuclear Magnetic Resonance SO JOURNAL OF PHYSICAL CHEMISTRY B LA English DT Article ID STOKES-EINSTEIN RELATION; CONFINED WATER; SUPERCOOLED WATER; MOLECULAR-DYNAMICS; SILICA MATRICES; HYDRATION WATER; LIQUID WATER; SCATTERING; TRANSITION; SPECTROSCOPY AB Aqueous solutions of lithium chloride are an excellent model system for studying the dynamics of water molecules down to low temperatures without freezing. The apparent dynamic crossover observed in an aqueous solution of LiCl at about 220 to 225 K [Mamontov, JPCB 2009, 113, 14073] is located practically at the same temperature as the crossover found for pure water confined in small hydrophilic pores. This finding suggests a strong similarity of water behavior in these two types of systems. At the same time, studies of solutions allow more effective explorations of the long-range diffusion dynamics, because the water molecules are not confined inside an impenetrable matrix. In contrast to the earlier incoherent quasielastic neutron scattering results obtained for the scattering momentum transfers of 0.3 angstrom(-1) <= Q <= 0.9 angstrom(-1), our present incoherent neutron spin-echo measurements at a lower Q of 0.1 angstrom(-1) exhibit no apparent crossover in the relaxation times down to 200 K. At the same time, our present nuclear magnetic resonance measurements of the diffusion coefficients clearly show a deviation at the lower temperatures from the non-Arrhenius law obtained at the higher temperatures. Our results are consistent with a scenario in which more than one relaxational component may exist below the temperature of the dynamic crossover in water. C1 [Mamontov, E.] Oak Ridge Natl Lab, Neutron Scattering Sci Div, Oak Ridge, TN 37831 USA. [Faraone, A.] Natl Inst Stand & Technol, Ctr Neutron Res, Gaithersburg, MD 20899 USA. [Faraone, A.] Univ Maryland, Dept Mat Sci & Engn, College Pk, MD 20742 USA. [Hagaman, E. W.; Han, K. S.] Oak Ridge Natl Lab, Div Chem Sci, Oak Ridge, TN 37831 USA. [Fratini, E.] Univ Florence, Dept Chem, I-50019 Florence, Italy. [Fratini, E.] Univ Florence, CSGI, I-50019 Florence, Italy. RP Mamontov, E (reprint author), Oak Ridge Natl Lab, Neutron Scattering Sci Div, Oak Ridge, TN 37831 USA. EM mamontove@ornl.gov RI Fratini, Emiliano/C-9983-2010; Mamontov, Eugene/Q-1003-2015; OI Fratini, Emiliano/0000-0001-7104-6530; Mamontov, Eugene/0000-0002-5684-2675; Han, Kee Sung/0000-0002-3535-1818 FU U.S. Department of Energy; Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences, U.S. Department of Energy; National Science Foundation [DMR-0454672]; CSGI; MIUR FX A part of this research performed at the Oak Ridge National Laboratory was supported by the U.S. Department of Energy. The work at the Chemical Sciences Division of the ORNL was sponsored by the Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences, U.S. Department of Energy. We are thankful to A. P. Sokolov for valuable discussion. This work utilized facilities supported in part by the National Science Foundation under Agreement No. DMR-0454672. E. Fratini kindly acknowledges financial support from CSGI and MIUR. NR 56 TC 19 Z9 19 U1 2 U2 18 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1520-6106 J9 J PHYS CHEM B JI J. Phys. Chem. B PD DEC 23 PY 2010 VL 114 IS 50 BP 16737 EP 16743 DI 10.1021/jp108497b PG 7 WC Chemistry, Physical SC Chemistry GA 693PT UT WOS:000285236700009 PM 21117619 ER PT J AU Gilbert, B Katz, JE Denlinger, JD Yin, YD Falcone, R Waychunas, GA AF Gilbert, Benjamin Katz, Jordan E. Denlinger, Jonathan D. Yin, Yadong Falcone, Roger Waychunas, Glenn A. TI Soft X-ray Spectroscopy Study of the Electronic Structure of Oxidized and Partially Oxidized Magnetite Nanoparticles SO JOURNAL OF PHYSICAL CHEMISTRY C LA English DT Article ID OXYGEN K-EDGE; IRON-OXIDES; ABSORPTION SPECTROSCOPY; VERWEY TRANSITION; NANOCRYSTALS; OXIDATION; GAMMA-FE2O3; SCATTERING; NANOSCALE; MINERALS AB The crystal structure of magnetite nanoparticles may be transformed to maghemite by complete oxidation, but under many relevant conditions the oxidation is partial, creating a mixed-valence material with structural and electronic properties that are poorly characterized. We used X-ray diffraction, Fe K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy, and soft X-ray absorption and emission spectroscopy to characterize the products of oxidizing uncoated and oleic acid-coated magnetite nanoparticles in air. The oxidization of uncoated magnetite nanoparticles creates a material that is structurally and electronically indistinguishable from maghemite. By contrast, while oxidized oleic acid-coated nanoparticles are also structurally indistinguishable from maghemite, Fe L-edge spectroscopy revealed the presence of interior reduced iron sites even after a 2-year period. We used X-ray emission spectroscopy at the O K-edge to study the valence bands (VB) of the iron oxide nanoparticles, using resonant excitation to remove the contributions from oxygen atoms in the ligands and from low-energy excitations that obscured the VB edge. The bonding in all nanoparticles was typical of maghemite, with no detectable VB states introduced by the long-lived, reduced-iron sites in the oleic acid-coated sample. However, O K-edge absorption spectroscopy observed a similar to 0.2 eV shift in the position of the lowest unoccupied states in the coated sample, indicating an increase in the semiconductor band gap relative to bulk stoichiometric maghemite that was also observed by optical absorption spectroscopy. The results show that the ferrous iron sites within ferric iron oxide nanoparticles coated by an organic ligand can persist under ambient conditions with no evidence of a distinct interior phase and can exert an effect on the global electronic and optical properties of the material. This phenomenon resembles the band gap enlargement caused by electron accumulation in the conduction band of TiO(2). C1 [Gilbert, Benjamin; Katz, Jordan E.; Waychunas, Glenn A.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Earth Sci, Berkeley, CA 94720 USA. [Denlinger, Jonathan D.; Falcone, Roger] Univ Calif Berkeley, Lawrence Berkeley Lab, Adv Light Source, Berkeley, CA 94720 USA. [Yin, Yadong] Univ Calif Riverside, Dept Chem, Riverside, CA 92521 USA. RP Gilbert, B (reprint author), Univ Calif Berkeley, Lawrence Berkeley Lab, Div Earth Sci, Berkeley, CA 94720 USA. EM BGilbert@lbl.gov RI Yin, Yadong/D-5987-2011; Gilbert, Benjamin/E-3182-2010; Katz, Jordan/J-5599-2016 OI Yin, Yadong/0000-0003-0218-3042; Katz, Jordan/0000-0002-6242-2124 FU Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy (DOE) [DE-AC02-05CH11231]; Office of Science, of the U.S. Department of Energy [DE-AC02-05CH11231] FX Soft X-ray spectroscopy was performed on beamlines 7 and 8 at the Advanced Light Source (ALS), and we thank Pers-Anders Glans and Jinghua Guo. X-ray diffraction was performed on beamline 11.3.3 at the ALS, and we thank Simon Teat. The ALS is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy (DOE) under Contract DE-AC02-05CH11231. Iron K-edge absorption spectroscopy was performed at beamline 10-2 at the Stanford Synchrotron Radiation Lightsource (SSRL), a national user facility operated by Stanford University on behalf of the DOE Office of Basic Energy Sciences, and we thank Matthew Lattimer and Allyson Aranda. We thank Rebecca Mezler, Pupa Gilbert, and Jinghua Guo for the opportunity to acquire Fe L-edge data and Klaus Attenkofer and David Sherman for valuable discussions. This work was supported by the Director, Office of Science, of the U.S. Department of Energy under Contract DE-AC02-05CH11231. NR 57 TC 23 Z9 23 U1 1 U2 51 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1932-7447 J9 J PHYS CHEM C JI J. Phys. Chem. C PD DEC 23 PY 2010 VL 114 IS 50 BP 21994 EP 22001 DI 10.1021/jp106919a PG 8 WC Chemistry, Physical; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary SC Chemistry; Science & Technology - Other Topics; Materials Science GA 693PU UT WOS:000285236800016 ER PT J AU Caldwell, MA Haynor, B Aloni, S Ogletree, DF Wong, HSP Urban, JJ Milliron, DJ AF Caldwell, Marissa A. Haynor, Ben Aloni, Shaul Ogletree, D. Frank Wong, H-S. Philip Urban, Jeffrey J. Milliron, Delia J. TI Spectroscopic Evidence for Exceptional Thermal Contribution to Electron Beam-Induced Fragmentation SO JOURNAL OF PHYSICAL CHEMISTRY C LA English DT Article ID TEMPERATURE-DEPENDENCE; NANOWIRE GROWTH; BAND-GAPS; CATHODOLUMINESCENCE; NANOCRYSTALS; MICROSCOPY; TRANSFORMATION; NANOPARTICLES; IRRADIATION; DYNAMICS AB While electron beam-induced fragmentation (EBIF) has been reported to result in the formation of nanocrystals of various compositions, the physical forces driving this phenomenon are still poorly understood. We report EBIF to be a much more general phenomenon than previously appreciated, operative across a wide variety of metals, semiconductors, and insulators. In addition, we leverage the temperature dependent bandgap of several semiconductors, using in situ cathodoluminescence spectroscopy, to quantify the thermal contribution to EBIF and find extreme temperature rises upward of 1000 K. C1 [Haynor, Ben; Aloni, Shaul; Ogletree, D. Frank; Urban, Jeffrey J.; Milliron, Delia J.] Univ Calif Berkeley, Lawrence Berkeley Lab, Mol Foundry, Berkeley, CA 94720 USA. [Caldwell, Marissa A.; Wong, H-S. Philip] Stanford Univ, Dept Chem, Stanford, CA 94305 USA. [Caldwell, Marissa A.; Wong, H-S. Philip] Stanford Univ, Dept Elect Engn, Stanford, CA 94305 USA. [Caldwell, Marissa A.; Wong, H-S. Philip] Stanford Univ, Ctr Integrated Syst, Stanford, CA 94305 USA. RP Urban, JJ (reprint author), Univ Calif Berkeley, Lawrence Berkeley Lab, Mol Foundry, Berkeley, CA 94720 USA. EM jjurban@lbl.gov; dmilliron@lbl.gov RI Milliron, Delia/D-6002-2012; Ogletree, D Frank/D-9833-2016 OI Ogletree, D Frank/0000-0002-8159-0182 FU IBM; Non-Volatile Memory Technology Research Initiative (NMTRI) at Stanford University; Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy [DE-AC02-05CH11231] FX We thank R. Y. Wang for critical discussions. M.A.C. is supported in part by the IBM Ph.D. Fellowship. This work was supported in part by the member companies of the Non-Volatile Memory Technology Research Initiative (NMTRI) at Stanford University. 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 34 TC 3 Z9 3 U1 1 U2 3 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1932-7447 J9 J PHYS CHEM C JI J. Phys. Chem. C PD DEC 23 PY 2010 VL 114 IS 50 BP 22064 EP 22068 DI 10.1021/jp1078086 PG 5 WC Chemistry, Physical; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary SC Chemistry; Science & Technology - Other Topics; Materials Science GA 693PU UT WOS:000285236800025 ER PT J AU Xu, P Jeon, SH Chen, HT Luo, HM Zou, GF Jia, QX Anghel, M Teuscher, C Williams, DJ Zhang, B Han, XJ Wang, HL AF Xu, Ping Jeon, Sea-Ho Chen, Hou-Tong Luo, Hongmei Zou, Guifu Jia, Quanxi Anghel, Marian Teuscher, Christof Williams, Darrick J. Zhang, Bin Han, Xijiang Wang, Hsing-Lin TI Facile Synthesis and Electrical Properties of Silver Wires through Chemical Reduction by Polyaniline SO JOURNAL OF PHYSICAL CHEMISTRY C LA English DT Article ID ENHANCED RAMAN-SCATTERING; CATALYTIC-PROPERTIES; METAL NANOPARTICLES; NONVOLATILE MEMORY; GROWTH-MECHANISM; NANOWIRES; DEPOSITION; SPECTROSCOPY; GOLD; DEFORMATION AB We demonstrate here for the first time a facile fabrication of silver wire (SW) structures with a wide range of sizes and morphologies through direct chemical reduction by polyaniline (PANT). The synthesis of SW is mostly determined by the nature of the PANI dopant and silver nitrate concentration. Time-resolved optical microscopy allows monitoring the growth of SWs in real time and reveals the possible growth mechanism. Temperature-dependent resistance of a SW with 150 nm diameter by a four-probe method shows typical resistance behavior of silver metal, and the electrical conductivity is 2.1 x 10(5) S/cm at room temperature. The morphology-dependent electrical properties of these SWs are measured using a two-probe method. The wires comprised of self-assembled silver nanoparticles usually have lower electrical conductivities than those with smooth surfaces, due to the presence of growth defects and enhanced surface scattering. Current voltage (I-V) curve measurements in a wide potential range either break down or cause surface transformation of the SWs by a synergism of electromigration and surface diffusion. A SW network that shows surface transformation after I-V curve measurement displays a higher resistance. The study of the electrical stability of the SWs opens up a new view of the applicable feasibility of metal nanowires in nanoelectronic devices. C1 [Xu, Ping; Jeon, Sea-Ho; Chen, Hou-Tong; Zou, Guifu; Jia, Quanxi; Anghel, Marian; Williams, Darrick J.; Wang, Hsing-Lin] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. [Xu, Ping; Zhang, Bin; Han, Xijiang] Harbin Inst Technol, Dept Chem, Harbin 150001, Peoples R China. [Luo, Hongmei] New Mexico State Univ, Dept Chem Engn, Las Cruces, NM 88003 USA. [Teuscher, Christof] Portland State Univ, Dept Elect & Comp Engn, Portland, OR 97201 USA. RP Xu, P (reprint author), Los Alamos Natl Lab, POB 1663, Los Alamos, NM 87545 USA. EM pxu@hit.edu.cn; hwang@lanl.gov RI Chen, Hou-Tong/C-6860-2009; ZOU, GUIFU/C-8498-2011; Xu, Ping/I-1910-2013; Jia, Q. X./C-5194-2008 OI Chen, Hou-Tong/0000-0003-2014-7571; Xu, Ping/0000-0002-1516-4986; FU DOE; BES Office of Science; National Nanotechnology Enterprise Development Center (NNEDC); U.S. Department of Energy, Center for Integrated Nanotechnologies, at Los Alamos National Laboratory [DE-AC52-06NA25396]; Sandia National Laboratories [DE-AC04-94AL85000]; Chinese Scholarship Council (CSC), NSF of China [20776032, 21071037]; Harbin Technological Innovation [2010RFXXG012] FX H.-L.W. acknowledges the financial support from Laboratory Directed Research and Development (LDRD) fund under the auspices of DOE, BES Office of Science, and the National Nanotechnology Enterprise Development Center (NNEDC). This work was performed in part at the U.S. Department of Energy, Center for Integrated Nanotechnologies, at Los Alamos National Laboratory (Contract DE-AC52-06NA25396) and Sandia National Laboratories (Contract DE-AC04-94AL85000). P.X. is thankful for the support from the Joint Educational Ph.D. Program of Chinese Scholarship Council (CSC), NSF of China (No. 20776032, 21071037), and Special Fund of Harbin Technological Innovation (2010RFXXG012). NR 49 TC 25 Z9 26 U1 1 U2 34 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1932-7447 EI 1932-7455 J9 J PHYS CHEM C JI J. Phys. Chem. C PD DEC 23 PY 2010 VL 114 IS 50 BP 22147 EP 22154 DI 10.1021/jp109207d PG 8 WC Chemistry, Physical; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary SC Chemistry; Science & Technology - Other Topics; Materials Science GA 693PU UT WOS:000285236800036 ER PT J AU Rance, WL Rupert, BL Mitchell, WJ Kose, ME Ginley, DS Shaheen, SE Rumbles, G Kopidakis, N AF Rance, William L. Rupert, Benjamin L. Mitchell, William J. Koese, Muhammet E. Ginley, David S. Shaheen, Sean E. Rumbles, Garry Kopidakis, Nikos TI Conjugated Thiophene Dendrimer with an Electron-Withdrawing Core and Electron-Rich Dendrons: How the Molecular Structure Affects the Morphology and Performance of Dendrimer:Fullerene Photovoltaic Devices SO JOURNAL OF PHYSICAL CHEMISTRY C LA English DT Article ID HETEROJUNCTION SOLAR-CELLS; CONVERSION EFFICIENCY; CHARGE-CARRIERS; POLY(3-HEXYLTHIOPHENE); MOBILITY; POLYMER; FILMS; OLIGOTHIOPHENES; SEPARATION; KINETICS AB The combination of electron-rich and electron-poor moieties in conjugated molecules is frequently utilized in order to red shift the absorption spectrum and improve photon harvesting in bulk heterojunction photovoltaic devices. In this study we characterize a conjugated thiophene dendrimer that has an electron-withdrawing core and electron-rich dendrons in order to investigate the effects of this design approach on the salient properties that influence the performance of photovoltaic devices with this dendrimer donor. Beside the absorption onset, these properties are the morphology of dendrimer:fullerene films and the dynamics of photoinduced carrier generation and loss. For comparison we also characterize a control dendrimer with the same structure but without the electron-withdrawing core. In addition to lowering the band gap by ca. 0.5 eV, the electron-withdrawing core also planarizes the dendrimer resulting in enhanced order in bulk heterojunction films. We observe longer photocarrier lifetimes in this ordered structure compared to the films of the predominantly amorphous control. The characterization of dendrimer:fullerene bulk heterojunction photovoltaic devices shows no voltage loss despite the decreased absorption onset. The properties of the device are consistent with the improved photocarrier lifetimes, but they are limited by a low short-circuit photocurrent density. We attribute this to electron confinement in the core that hinders transfer to the fullerene acceptor. C1 [Rance, William L.] Colorado Sch Mines, Dept Phys, Golden, CO 80401 USA. [Rupert, Benjamin L.; Mitchell, William J.; Ginley, David S.; Rumbles, Garry; Kopidakis, Nikos] Natl Renewable Energy Lab, Golden, CO 80401 USA. [Koese, Muhammet E.] N Dakota State Univ, Dept Chem & Biochem, Fargo, ND 58108 USA. [Shaheen, Sean E.] Univ Denver, Dept Phys & Astron, Denver, CO 80208 USA. RP Rance, WL (reprint author), Colorado Sch Mines, Dept Phys, 1500 Illinois St, Golden, CO 80401 USA. EM wrance@mines.edu; nikos.kopidakis@nrel.gov RI Rupert, Benjamin/E-1694-2011; Kose, Muhammet/C-7167-2012; Shaheen, Sean/M-7893-2013; Rumbles, Garry/A-3045-2014; Kopidakis, Nikos/N-4777-2015; OI Rumbles, Garry/0000-0003-0776-1462 FU U.S. Department of Energy [DE-AC36-08GO28308]; NREL; Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the U.S. Department of Energ FX This work was supported by the U.S. Department of Energy's Solar Energy Technologies Program under Contract No. DE-AC36-08GO28308 with NREL. G.R. gratefully acknowledges the Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the U.S. Department of Energy for funding the development of the transient microwave conductivity measurement. NR 34 TC 21 Z9 21 U1 1 U2 33 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1932-7447 J9 J PHYS CHEM C JI J. Phys. Chem. C PD DEC 23 PY 2010 VL 114 IS 50 BP 22269 EP 22276 DI 10.1021/jp106850f PG 8 WC Chemistry, Physical; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary SC Chemistry; Science & Technology - Other Topics; Materials Science GA 693PU UT WOS:000285236800052 ER PT J AU Marois, C Zuckerman, B Konopacky, QM Macintosh, B Barman, T AF Marois, Christian Zuckerman, B. Konopacky, Quinn M. Macintosh, Bruce Barman, Travis TI Images of a fourth planet orbiting HR 8799 SO NATURE LA English DT Article ID EXTRASOLAR GIANT PLANETS; DEBRIS DISK; BROWN DWARFS; SYSTEM; SPECTROSCOPY; STARS; LUMINOSITY AB High-contrast near-infrared imaging of the nearby star HR 8799 has shown three giant planets(1). Such images were possible because of the wide orbits (>25 astronomical units, where 1 AU is the Earth-Sun distance) and youth (<100 Myr) of the imaged planets, which are still hot and bright as they radiate away gravitational energy acquired during their formation. An important area of contention in the exoplanet community is whether outer planets (>10 AU) more massive than Jupiter form by way of one-step gravitational instabilities(2) or, rather, through a two-step process involving accretion of a core followed by accumulation of a massive outer envelope composed primarily of hydrogen and helium(3). Here we report the presence of a fourth planet, interior to and of about the same mass as the other three. The system, with this additional planet, represents a challenge for current planet formation models as none of them can explain the in situ formation of all four planets. With its four young giant planets and known cold/warm debris belts(4), the HR 8799 planetary system is a unique laboratory in which to study the formation and evolution of giant planets at wide (>10 AU) separations. C1 [Marois, Christian] Natl Res Council Canada, Herzberg Inst Astrophys, Victoria, BC V9E 2E7, Canada. [Zuckerman, B.] Univ Calif Los Angeles, Dept Phys & Astron, Los Angeles, CA 90095 USA. [Konopacky, Quinn M.; Macintosh, Bruce] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. [Barman, Travis] Lowell Observ, Flagstaff, AZ 86001 USA. RP Marois, C (reprint author), Natl Res Council Canada, Herzberg Inst Astrophys, 5071 W Saanich Rd, Victoria, BC V9E 2E7, Canada. EM christian.marois@nrc-cnrc.gc.ca FU US Department of Energy by LLNL; NSF Center for Adaptive Optics; NASA FX We thank the Keck staff, particularly H. Lewis, B. Goodrich and J. Lyke, for support with the follow-up observations. We thank G. Laughlin and D. C. Fabrycky for discussions. Portions of this research were performed under the auspices of the US Department of Energy by LLNL and also supported in part by the NSF Center for Adaptive Optics. We acknowledge support by NASA grants to UCLA, LLNL and Lowell Observatory. The data were obtained at the W. M. Keck Observatory. This publication makes use of data products from the Two Micron All Sky Survey and the SIMBAD database. NR 30 TC 368 Z9 368 U1 3 U2 22 PU NATURE PUBLISHING GROUP PI LONDON PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND SN 0028-0836 J9 NATURE JI Nature PD DEC 23 PY 2010 VL 468 IS 7327 BP 1080 EP 1083 DI 10.1038/nature09684 PG 4 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 697XT UT WOS:000285553800053 PM 21150902 ER PT J AU Pelka, A Gregori, G Gericke, DO Vorberger, J Glenzer, SH Gunther, MM Harres, K Heathcote, R Kritcher, AL Kugland, NL Li, B Makita, M Mithen, J Neely, D Niemann, C Otten, A Riley, D Schaumann, G Schollmeier, M Tauschwitz, A Roth, M AF Pelka, A. Gregori, G. Gericke, D. O. Vorberger, J. Glenzer, S. H. Guenther, M. M. Harres, K. Heathcote, R. Kritcher, A. L. Kugland, N. L. Li, B. Makita, M. Mithen, J. Neely, D. Niemann, C. Otten, A. Riley, D. Schaumann, G. Schollmeier, M. Tauschwitz, An. Roth, M. TI Ultrafast Melting of Carbon Induced by Intense Proton Beams SO PHYSICAL REVIEW LETTERS LA English DT Article ID RAY THOMSON SCATTERING; LIQUID-PHASE; PLASMAS; SOLIDS; URANUS AB Laser-produced proton beams have been used to achieve ultrafast volumetric heating of carbon samples at solid density. The isochoric melting of carbon was probed by a scattering of x rays from a secondary laser-produced plasma. From the scattering signal, we have deduced the fraction of the material that was melted by the inhomogeneous heating. The results are compared to different theoretical approaches for the equation of state which suggests modifications from standard models. C1 [Pelka, A.; Guenther, M. M.; Harres, K.; Otten, A.; Schaumann, G.; Schollmeier, M.; Roth, M.] Tech Univ Darmstadt, IKP, D-64289 Darmstadt, Germany. [Gregori, G.; Mithen, J.] Univ Oxford, Dept Phys, Oxford OX1 3PU, England. [Gregori, G.; Heathcote, R.; Li, B.; Neely, D.] Rutherford Appleton Lab, Cent Laser Facil, Didcot OX11 0QX, Oxon, England. [Gericke, D. O.; Vorberger, J.] Univ Warwick, Dept Phys, Ctr Fus Space & Astrophys, Coventry CV4 7AL, W Midlands, England. [Glenzer, S. H.; Kritcher, A. L.; Kugland, N. L.; Niemann, C.] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. [Kugland, N. L.; Niemann, C.] Univ Calif Los Angeles, Dept Phys, Los Angeles, CA 94550 USA. [Makita, M.; Riley, D.] Queens Univ Belfast, Dept Phys & Astron, Belfast BT7 1NN, Antrim, North Ireland. [Schollmeier, M.] Sandia Natl Labs, Albuquerque, NM 87185 USA. [Tauschwitz, An.] Goethe Univ Frankfurt, D-60438 Frankfurt, Germany. RP Pelka, A (reprint author), Tech Univ Darmstadt, IKP, Schlossgartenstr 9, D-64289 Darmstadt, Germany. RI Schollmeier, Marius/H-1056-2012; Vorberger, Jan/D-9162-2015 OI Schollmeier, Marius/0000-0002-0683-022X; FU BMBF [06DA9043I, 06DA9044I, 05KS7SJ1]; STFC; John Fell Fund; EPSRC [EP/G007187/1, EP/D062837, EP/C001869/1]; LDRD [08-ERI-002]; U.S. Department of Energy by the Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; U.S. DOE [DE-AC04-94AL85000] FX We thank the CLF staff at RAL for their assistance. The work of A. P., M. M. G., K. H., A. O., M. S., and M. R. was supported by the BMBF, support codes 06DA9043I, 06DA9044I, and 05KS7SJ1. The work of G. G., and B. L. was partially supported by the STFC. The work of J. M. was supported by the John Fell Fund. Support from EPSRC grants is acknowledged by G. G. (EP/G007187/1), D. G., J. V. (EP/D062837), and D. R., M. M. (EP/C001869/1). The work of N. L. K., A. L. K., and S. H. G. was supported by LDRD Grant No. 08-ERI-002 and was performed under the auspices of the U.S. Department of Energy by the Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344. We also acknowledge support from the LLNL Lawrence Scholar Program. Sandia is operated by Lockheed Martin Corp. for the U.S. DOE (Contract No. DE-AC04-94AL85000). NR 32 TC 51 Z9 51 U1 0 U2 17 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 0031-9007 J9 PHYS REV LETT JI Phys. Rev. Lett. PD DEC 23 PY 2010 VL 105 IS 26 AR 265701 DI 10.1103/PhysRevLett.105.265701 PG 4 WC Physics, Multidisciplinary SC Physics GA 713UC UT WOS:000286761900007 PM 21231678 ER PT J AU Gerstein, MB Lu, ZJ Van Nostrand, EL Cheng, C Arshinoff, BI Liu, T Yip, KY Robilotto, R Rechtsteiner, A Ikegami, K Alves, P Chateigner, A Perry, M Morris, M Auerbach, RK Feng, X Leng, J Vielle, A Niu, W Rhrissorrakrai, K Agarwal, A Alexander, RP Barber, G Brdlik, CM Brennan, J Brouillet, JJ Carr, A Cheung, MS Clawson, H Contrino, S Dannenberg, LO Dernburg, AF Desai, A Dick, L Dose, AC Du, JA Egelhofer, T Ercan, S Euskirchen, G Ewing, B Feingold, EA Gassmann, R Good, PJ Green, P Gullier, F Gutwein, M Guyer, MS Habegger, L Han, T Henikoff, JG Henz, SR Hinrichs, A Holster, H Hyman, T Iniguez, AL Janette, J Jensen, M Kato, M Kent, WJ Kephart, E Khivansara, V Khurana, E Kim, JK Kolasinska-Zwierz, P Lai, EC Latorre, I Leahey, A Lewis, S Lloyd, P Lochovsky, L Lowdon, RF Lubling, Y Lyne, R MacCoss, M Mackowiak, SD Mangone, M Mckay, S Mecenas, D Merrihew, G Miller, DM Muroyama, A Murray, JI Ooi, SL Pham, H Phippen, T Preston, EA Rajewsky, N Ratsch, G Rosenbaum, H Rozowsky, J Rutherford, K Ruzanov, P Sarov, M Sasidharan, R Sboner, A Scheid, P Segal, E Shin, HJ Shou, C Slack, FJ Slightam, C Smith, R Spencer, WC Stinson, EO Taing, S Takasaki, T Vafeados, D Voronina, K Wang, GL Washington, NL Whittle, CM Wu, BJ Yan, KK Zeller, G Zha, Z Zhong, M Zhou, XL Ahringer, J Strome, S Gunsalus, KC Micklem, G Liu, XS Reinke, V Kim, SK Hillier, LW Henikoff, S Piano, F Snyder, M Stein, L Lieb, JD Waterston, RH AF Gerstein, Mark B. Lu, Zhi John Van Nostrand, Eric L. Cheng, Chao Arshinoff, Bradley I. Liu, Tao Yip, Kevin Y. Robilotto, Rebecca Rechtsteiner, Andreas Ikegami, Kohta Alves, Pedro Chateigner, Aurelien Perry, Marc Morris, Mitzi Auerbach, Raymond K. Feng, Xin Leng, Jing Vielle, Anne Niu, Wei Rhrissorrakrai, Kahn Agarwal, Ashish Alexander, Roger P. Barber, Galt Brdlik, Cathleen M. Brennan, Jennifer Brouillet, Jeremy Jean Carr, Adrian Cheung, Ming-Sin Clawson, Hiram Contrino, Sergio Dannenberg, Luke O. Dernburg, Abby F. Desai, Arshad Dick, Lindsay Dose, Andrea C. Du, Jiang Egelhofer, Thea Ercan, Sevinc Euskirchen, Ghia Ewing, Brent Feingold, Elise A. Gassmann, Reto Good, Peter J. Green, Phil Gullier, Francois Gutwein, Michelle Guyer, Mark S. Habegger, Lukas Han, Ting Henikoff, Jorja G. Henz, Stefan R. Hinrichs, Angie Holster, Heather Hyman, Tony Iniguez, A. Leo Janette, Judith Jensen, Morten Kato, Masaomi Kent, W. James Kephart, Ellen Khivansara, Vishal Khurana, Ekta Kim, John K. Kolasinska-Zwierz, Paulina Lai, Eric C. Latorre, Isabel Leahey, Amber Lewis, Suzanna Lloyd, Paul Lochovsky, Lucas Lowdon, Rebecca F. Lubling, Yaniv Lyne, Rachel MacCoss, Michael Mackowiak, Sebastian D. Mangone, Marco Mckay, Sheldon Mecenas, Desirea Merrihew, Gennifer Miller, David M., III Muroyama, Andrew Murray, John I. Ooi, Siew-Loon Pham, Hoang Phippen, Taryn Preston, Elicia A. Rajewsky, Nikolaus Raetsch, Gunnar Rosenbaum, Heidi Rozowsky, Joel Rutherford, Kim Ruzanov, Peter Sarov, Mihail Sasidharan, Rajkumar Sboner, Andrea Scheid, Paul Segal, Eran Shin, Hyunjin Shou, Chong Slack, Frank J. Slightam, Cindie Smith, Richard Spencer, William C. Stinson, E. O. Taing, Scott Takasaki, Teruaki Vafeados, Dionne Voronina, Ksenia Wang, Guilin Washington, Nicole L. Whittle, Christina M. Wu, Beijing Yan, Koon-Kiu Zeller, Georg Zha, Zheng Zhong, Mei Zhou, Xingliang Ahringer, Julie Strome, Susan Gunsalus, Kristin C. Micklem, Gos Liu, X. Shirley Reinke, Valerie Kim, Stuart K. Hillier, LaDeana W. Henikoff, Steven Piano, Fabio Snyder, Michael Stein, Lincoln Lieb, Jason D. Waterston, Robert H. CA modENCODE Consortium TI Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project SO SCIENCE LA English DT Article ID C. ELEGANS; NUCLEOSOME ORGANIZATION; TRANSCRIPTION FACTORS; RNA-SEQ; REVEALS; EXPRESSION; EMBRYOS; NETWORK; DNA; CHROMATIN AB We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor-binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome. C1 [Gerstein, Mark B.; Lu, Zhi John; Cheng, Chao; Yip, Kevin Y.; Robilotto, Rebecca; Alves, Pedro; Auerbach, Raymond K.; Leng, Jing; Alexander, Roger P.; Habegger, Lukas; Lochovsky, Lucas; Rozowsky, Joel; Sboner, Andrea; Shou, Chong; Yan, Koon-Kiu] Yale Univ, Program Computat Biol & Bioinformat, New Haven, CT 06520 USA. [Gerstein, Mark B.; Lu, Zhi John; Cheng, Chao; Yip, Kevin Y.; Agarwal, Ashish; Alexander, Roger P.; Rozowsky, Joel; Sasidharan, Rajkumar; Sboner, Andrea; Yan, Koon-Kiu] Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT 06520 USA. [Gerstein, Mark B.; Agarwal, Ashish; Du, Jiang] Yale Univ, Dept Comp Sci, New Haven, CT 06511 USA. [Van Nostrand, Eric L.; Brdlik, Cathleen M.; Brouillet, Jeremy Jean; Kim, Stuart K.; Snyder, Michael] Stanford Univ, Med Ctr, Dept Genet, Stanford, CA 94305 USA. [Arshinoff, Bradley I.; Perry, Marc; Feng, Xin; Kephart, Ellen; Lloyd, Paul; Ruzanov, Peter; Zha, Zheng; Stein, Lincoln] Ontario Inst Canc Res, Toronto, ON M5G 0A3, Canada. [Arshinoff, Bradley I.; Stein, Lincoln] Univ Toronto, Dept Mol Genet, Toronto, ON M5S 1A1, Canada. [Liu, Tao; Shin, Hyunjin; Taing, Scott; Liu, X. Shirley] Dana Farber Canc Inst, Dept Biostat & Computat Biol, Boston, MA 02115 USA. [Liu, Tao; Shin, Hyunjin; Liu, X. Shirley] Harvard Univ, Sch Publ Hlth, Dept Biostat, Boston, MA 02115 USA. [Ikegami, Kohta; Brennan, Jennifer; Ercan, Sevinc; Jensen, Morten; Whittle, Christina M.; Zhou, Xingliang; Lieb, Jason D.] Univ N Carolina, Dept Biol, Chapel Hill, NC 27599 USA. [Ikegami, Kohta; Brennan, Jennifer; Ercan, Sevinc; Jensen, Morten; Whittle, Christina M.; Zhou, Xingliang; Lieb, Jason D.] Univ N Carolina, Carolina Ctr Genome Sci, Chapel Hill, NC 27599 USA. [Chateigner, Aurelien; Carr, Adrian; Contrino, Sergio; Gullier, Francois; Lyne, Rachel; Rutherford, Kim; Smith, Richard; Micklem, Gos] Univ Cambridge, Dept Genet, Cambridge CB2 3EH, England. [Chateigner, Aurelien; Carr, Adrian; Contrino, Sergio; Gullier, Francois; Lyne, Rachel; Rutherford, Kim; Smith, Richard; Micklem, Gos] Cambridge Syst Biol Ctr, Cambridge CB2 1QR, England. [Morris, Mitzi; Rhrissorrakrai, Kahn; Gutwein, Michelle; Khurana, Ekta; Mangone, Marco; Mecenas, Desirea; Scheid, Paul; Gunsalus, Kristin C.; Piano, Fabio] NYU, Dept Biol, Ctr Genom & Syst Biol, New York, NY 10003 USA. [Vielle, Anne; Cheung, Ming-Sin; Kolasinska-Zwierz, Paulina; Latorre, Isabel; Ahringer, Julie] Univ Cambridge, Wellcome Trust Canc Res UK Gurdon Inst, Cambridge CB2 1QN, England. [Niu, Wei; Euskirchen, Ghia; Zhong, Mei; Snyder, Michael] Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT 06824 USA. [Niu, Wei; Janette, Judith; Wang, Guilin; Reinke, Valerie] Yale Univ, Sch Med, Dept Genet, New Haven, CT 06520 USA. Univ Calif Santa Cruz, Dept Biomol Engn, Santa Cruz, CA 95064 USA. [Dannenberg, Luke O.; Holster, Heather; Iniguez, A. Leo; Rosenbaum, Heidi] Roche NimbleGen, Madison, WI 53719 USA. [Dernburg, Abby F.; Dose, Andrea C.; Pham, Hoang] Univ Calif Berkeley, Howard Hughes Med Inst, Dept Mol & Cell Biol, Berkeley, CA 94720 USA. [Dernburg, Abby F.; Dose, Andrea C.; Pham, Hoang] Lawrence Berkeley Natl Lab, Div Life Sci, Berkeley, CA 94720 USA. [Desai, Arshad; Gassmann, Reto; Muroyama, Andrew; Voronina, Ksenia] Univ Calif San Diego, Ludwig Inst Canc Res, Dept Cellular & Mol Med, San Diego, CA 92093 USA. [Ewing, Brent; Green, Phil; Leahey, Amber; MacCoss, Michael; Merrihew, Gennifer; Murray, John I.; Preston, Elicia A.; Vafeados, Dionne; Hillier, LaDeana W.; Waterston, Robert H.] Univ Washington, Sch Med, Dept Genome Sci, Seattle, WA 98195 USA. [Feingold, Elise A.; Good, Peter J.; Guyer, Mark S.; Lowdon, Rebecca F.] NHGRI, Div Extramural Res, NIH, Bethesda, MD 20892 USA. [Feng, Xin] SUNY Stony Brook, Dept Biomed Engn, Stony Brook, NY 11794 USA. [Han, Ting; Khivansara, Vishal; Kim, John K.] Univ Michigan, Inst Life Sci, Dept Human Genet, Ann Arbor, MI 48109 USA. [Henikoff, Jorja G.; Ooi, Siew-Loon; Henikoff, Steven] Fred Hutchinson Canc Res Ctr, Div Basic Sci, Seattle, WA 98109 USA. [Raetsch, Gunnar; Zeller, Georg] Max Planck Gesell, Friedrich Miescher Lab, D-72076 Tubingen, Germany. [Hyman, Tony; Sarov, Mihail] Max Planck Inst Mol Cell Biol & Genet, D-01307 Dresden, Germany. [Miller, David M., III; Spencer, William C.] Vanderbilt Univ, Dept Cell & Dev Biol, Nashville, TN 37232 USA. [Kato, Masaomi; Slack, Frank J.] Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT 06520 USA. [Henz, Stefan R.] Max Planck Inst Dev Biol, D-72076 Tubingen, Germany. [Lai, Eric C.] Sloan Kettering Inst, New York, NY 10065 USA. [Lewis, Suzanna; Stinson, E. O.; Washington, Nicole L.] Lawrence Berkeley Natl Lab, Genom Div, Berkeley, CA 94720 USA. [Lubling, Yaniv; Segal, Eran] Weizmann Inst Sci, Dept Comp Sci & Appl Math, IL-76100 Rehovot, Israel. [Mackowiak, Sebastian D.; Rajewsky, Nikolaus] Max Delbruck Ctr Mol Med, Div Syst Biol, D-13125 Berlin, Germany. [Mckay, Sheldon; Stein, Lincoln] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11542 USA. [Slightam, Cindie; Wu, Beijing; Kim, Stuart K.] Stanford Univ, Med Ctr, Dept Dev Biol, Stanford, CA 94305 USA. [Zeller, Georg] European Mol Biol Lab, D-69117 Heidelberg, Germany. [Gunsalus, Kristin C.; Piano, Fabio] NYU, Abu Dhabi, U Arab Emirates. [Dick, Lindsay] Rockefeller Univ, David Rockefeller Grad Program, New York, NY 10065 USA. RP Gerstein, MB (reprint author), Yale Univ, Program Computat Biol & Bioinformat, Bass 432,266 Whitney Ave, New Haven, CT 06520 USA. EM modencode.worm.pi@gersteinlab.org RI Alexander, Roger/A-8643-2008; NUI, WEI/B-8300-2011; Gassmann, Reto/M-6488-2013; Liu, Tao/G-3585-2010; Zeller, Georg/M-6484-2013; Hyman, Anthony/B-3917-2017; Sboner, Andrea/C-6487-2008; Spencer, William/E-8529-2010; yu, yan/C-2322-2012; Khurana, Ekta/C-4933-2013; Yan, Koon-Kiu/A-5940-2009; OI Alexander, Roger/0000-0002-2967-7395; Gassmann, Reto/0000-0002-0360-2977; Liu, Tao/0000-0002-8818-8313; Zeller, Georg/0000-0003-1429-7485; Hyman, Anthony/0000-0003-3664-154X; McKay, Sheldon/0000-0002-4011-3160; Sboner, Andrea/0000-0001-6915-3070; Rutherford, Kim/0000-0001-6277-726X; Micklem, Gos/0000-0002-6883-6168; Lewis, Suzanna/0000-0002-8343-612X; Liu, Tao/0000-0003-0446-9001; Lloyd, Paul/0000-0003-3508-5553; Segal, Eran/0000-0002-6859-1164; Hinrichs, Angie/0000-0002-1697-1130; Slack, Frank/0000-0001-8263-0409; Rozowsky, Joel/0000-0002-3565-0762; Dernburg, Abby/0000-0001-8037-1079; Mangone, Marco/0000-0001-7551-8793; Latorre, Isabel/0000-0003-0638-1783 FU NHGRI of the NIH [R01GM088565]; Muscular Dystrophy Association; Pew Charitable Trusts; Helmholtz-Alliance on Systems Biology (Max Delbruck Centrum Systems Biology Network); Wellcome Trust; William H. Gates III Endowed Chair of Biomedical Sciences FX Funding for this work came from the NHGRI of the NIH as part of the modENCODE project, NIH (grant R01GM088565), Muscular Dystrophy Association, and the Pew Charitable Trusts (J.K.K.); the Helmholtz-Alliance on Systems Biology (Max Delbruck Centrum Systems Biology Network) (S.D.M.); the Wellcome Trust (J.A.); the William H. Gates III Endowed Chair of Biomedical Sciences (R.H.W.); and the A. L. Williams Professorship (M.B.G.). M. Snyder has an advisory role with DNANexus, a DNA sequence storage and analysis company. Transfer of GFP-tagged fosmids requires a Materials Transfer Agreement with the Max Planck Institute of Molecular Cell Biology and Genetics. Raw microarray data are available from the Gene Expression Omnibus archive, and raw sequencing data are available from the SRA archive (accessions are in table S18). We appreciate help from S. Anthony, K. Bell, C. Davis, C. Dieterich, Y. Field, A. S. Hammonds, J. Jo, N. Kaplan, A. Manrai, B. Mathey-Prevot, R. McWhirter, S. Mohr, S. Von Stetina, J. Watson, K. Watkins, C. Xue, and Y. Zhang, and B. Carpenter. We thank C. Jan and D. Bartel for sharing data on poly(A) sites before publication, WormBase curator G. Williams for assistance in quality checking and preparing the transcriptomics data sets for publication, as well as his fellow curator P. Davis for reviewing and hand-checking the list of pseudogenes. NR 76 TC 458 Z9 462 U1 6 U2 90 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 DEC 23 PY 2010 VL 330 IS 6012 BP 1775 EP 1787 DI 10.1126/science.1196914 PG 13 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 698OS UT WOS:000285603700031 PM 21177976 ER PT J AU Roy, S Ernst, J Kharchenko, PV Kheradpour, P Negre, N Eaton, ML Landolin, JM Bristow, CA Ma, LJ Lin, MF Washietl, S Arshinoff, BI Ay, F Meyer, PE Robine, N Washington, NL Di Stefano, L Berezikov, E Brown, CD Candeias, R Carlson, JW Carr, A Jungreis, I Marbach, D Sealfon, R Tolstorukov, MY Will, S Alekseyenko, AA Artieri, C Booth, BW Brooks, AN Dai, Q Davis, CA Duff, MO Feng, X Gorchakov, AA Gu, TT Henikoff, JG Kapranov, P Li, RH MacAlpine, HK Malone, J Minoda, A Nordman, J Okamura, K Perry, M Powell, SK Riddle, NC Sakai, A Samsonova, A Sandler, JE Schwartz, YB Sher, N Spokony, R Sturgill, D van Baren, M Wan, KH Yang, L Yu, C Feingold, E Good, P Guyer, M Lowdon, R Ahmad, K Andrews, J Berger, B Brenner, SE Brent, MR Cherbas, L Elgin, SCR Gingeras, TR Grossman, R Hoskins, RA Kaufman, TC Kent, W Kuroda, MI Orr-Weaver, T Perrimon, N Pirrotta, V Posakony, JW Ren, B Russell, S Cherbas, P Graveley, BR Lewis, S Micklem, G Oliver, B Park, PJ Celniker, SE Henikoff, S Karpen, GH Lai, EC MacAlpine, DM Stein, LD White, KP Kellis, M AF Roy, Sushmita Ernst, Jason Kharchenko, Peter V. Kheradpour, Pouya Negre, Nicolas Eaton, Matthew L. Landolin, Jane M. Bristow, Christopher A. Ma, Lijia Lin, Michael F. Washietl, Stefan Arshinoff, Bradley I. Ay, Ferhat Meyer, Patrick E. Robine, Nicolas Washington, Nicole L. Di Stefano, Luisa Berezikov, Eugene Brown, Christopher D. Candeias, Rogerio Carlson, Joseph W. Carr, Adrian Jungreis, Irwin Marbach, Daniel Sealfon, Rachel Tolstorukov, Michael Y. Will, Sebastian Alekseyenko, Artyom A. Artieri, Carlo Booth, Benjamin W. Brooks, Angela N. Dai, Qi Davis, Carrie A. Duff, Michael O. Feng, Xin Gorchakov, Andrey A. Gu, Tingting Henikoff, Jorja G. Kapranov, Philipp Li, Renhua MacAlpine, Heather K. Malone, John Minoda, Aki Nordman, Jared Okamura, Katsutomo Perry, Marc Powell, Sara K. Riddle, Nicole C. Sakai, Akiko Samsonova, Anastasia Sandler, Jeremy E. Schwartz, Yuri B. Sher, Noa Spokony, Rebecca Sturgill, David van Baren, Marijke Wan, Kenneth H. Yang, Li Yu, Charles Feingold, Elise Good, Peter Guyer, Mark Lowdon, Rebecca Ahmad, Kami Andrews, Justen Berger, Bonnie Brenner, Steven E. Brent, Michael R. Cherbas, Lucy Elgin, Sarah C. R. Gingeras, Thomas R. Grossman, Robert Hoskins, Roger A. Kaufman, Thomas C. Kent, William Kuroda, Mitzi I. Orr-Weaver, Terry Perrimon, Norbert Pirrotta, Vincenzo Posakony, James W. Ren, Bing Russell, Steven Cherbas, Peter Graveley, Brenton R. Lewis, Suzanna Micklem, Gos Oliver, Brian Park, Peter J. Celniker, Susan E. Henikoff, Steven Karpen, Gary H. Lai, Eric C. MacAlpine, David M. Stein, Lincoln D. White, Kevin P. Kellis, Manolis CA modENCODE Consortium TI Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE SO SCIENCE LA English DT Article ID PREDICTIVE CHROMATIN SIGNATURES; TRANSCRIPTION FACTORS; SOMATIC-CELLS; HUMAN GENOME; DNA-BINDING; RNA PATHWAY; MELANOGASTER; SEQUENCE; REGIONS; NETWORK AB To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage-and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation. C1 [Roy, Sushmita; Ernst, Jason; Kheradpour, Pouya; Bristow, Christopher A.; Lin, Michael F.; Washietl, Stefan; Ay, Ferhat; Meyer, Patrick E.; Di Stefano, Luisa; Candeias, Rogerio; Jungreis, Irwin; Marbach, Daniel; Sealfon, Rachel; Will, Sebastian; Berger, Bonnie; Kellis, Manolis] MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA. [Roy, Sushmita; Ernst, Jason; Kheradpour, Pouya; Bristow, Christopher A.; Lin, Michael F.; Jungreis, Irwin; Marbach, Daniel; Sealfon, Rachel; Berger, Bonnie; Kellis, Manolis] MIT, Broad Inst, Cambridge, MA 02140 USA. [Roy, Sushmita; Ernst, Jason; Kheradpour, Pouya; Bristow, Christopher A.; Lin, Michael F.; Jungreis, Irwin; Marbach, Daniel; Sealfon, Rachel; Berger, Bonnie; Kellis, Manolis] Harvard Univ, Cambridge, MA 02140 USA. [Kharchenko, Peter V.; Tolstorukov, Michael Y.; Schwartz, Yuri B.; Park, Peter J.] Harvard Univ, Sch Med, Ctr Biomed Informat, Boston, MA 02115 USA. [Negre, Nicolas; Ma, Lijia; Brown, Christopher D.; Spokony, Rebecca; Grossman, Robert; White, Kevin P.] Univ Chicago, Inst Genom & Syst Biol, Dept Human Genet, Chicago, IL 60637 USA. [Eaton, Matthew L.; MacAlpine, Heather K.; Powell, Sara K.; MacAlpine, David M.] Duke Univ, Med Ctr, Dept Pharmacol & Canc Biol, Durham, NC 27710 USA. [Landolin, Jane M.; Carlson, Joseph W.; Booth, Benjamin W.; Minoda, Aki; Sandler, Jeremy E.; Wan, Kenneth H.; Yu, Charles; Hoskins, Roger A.; Celniker, Susan E.; Karpen, Gary H.] Lawrence Berkeley Natl Lab, Dept Genome Dynam, Berkeley, CA 94720 USA. [Arshinoff, Bradley I.] Univ Toronto, Dept Mol Genet, Toronto, ON M5S 1A1, Canada. [Robine, Nicolas; Dai, Qi; Henikoff, Jorja G.; Okamura, Katsutomo; Lai, Eric C.] Sloan Kettering Inst, New York, NY 10065 USA. [Washington, Nicole L.; Lewis, Suzanna] LBNL, Genome Sci Div, Berkeley, CA 94720 USA. [Carr, Adrian; Russell, Steven; Micklem, Gos] Univ Cambridge, Dept Genet, Cambridge CB2 3EH, England. [Carr, Adrian; Russell, Steven; Micklem, Gos] Univ Cambridge, Cambridge Syst Biol Ctr, Cambridge CB2 3EH, England. [Alekseyenko, Artyom A.; Gorchakov, Andrey A.; Kuroda, Mitzi I.] Harvard Univ, Brigham & Womens Hosp, Sch Med, Dept Med, Boston, MA 02115 USA. [Alekseyenko, Artyom A.; Gorchakov, Andrey A.; Kuroda, Mitzi I.] Harvard Univ, Brigham & Womens Hosp, Sch Med, Dept Genet, Boston, MA 02115 USA. [Artieri, Carlo; Malone, John; Sturgill, David; Oliver, Brian] NIDDK, Sect Dev Genom, Cellular & Dev Biol Lab, NIH, Bethesda, MD 20892 USA. [Davis, Carrie A.; Feng, Xin; Gingeras, Thomas R.] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA. [Duff, Michael O.; Yang, Li; Graveley, Brenton R.] Univ Connecticut, Stem Cell Inst, Dept Genet & Dev Biol, Farmington, CT 06030 USA. [Gu, Tingting; Riddle, Nicole C.; Elgin, Sarah C. R.] Washington Univ, Dept Biol, St Louis, MO 63130 USA. [Kapranov, Philipp; Gingeras, Thomas R.] Affymetrix, Santa Clara, CA 95051 USA. [Li, Renhua; Feingold, Elise; Good, Peter; Guyer, Mark; Lowdon, Rebecca] NHGRI, Div Extramural Res, NIH, Bethesda, MD 20892 USA. [Arshinoff, Bradley I.; Feng, Xin; Perry, Marc; Stein, Lincoln D.] Ontario Inst Canc Res, Toronto, ON M5G 0A3, Canada. [Samsonova, Anastasia; Perrimon, Norbert] Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA. [Samsonova, Anastasia; Perrimon, Norbert] Harvard Univ, Sch Med, Drosophila RNAi Screening Ctr, Boston, MA 02115 USA. [van Baren, Marijke; Brent, Michael R.] Washington Univ, Ctr Genome Sci, St Louis, MO 63108 USA. [Andrews, Justen; Cherbas, Lucy; Kaufman, Thomas C.; Cherbas, Peter] Indiana Univ, Dept Biol, Bloomington, IN 47405 USA. [Nordman, Jared; Sher, Noa; Orr-Weaver, Terry] Whitehead Inst, Cambridge, MA 02142 USA. [Berezikov, Eugene] Royal Netherlands Acad Arts & Sci, Hubrecht Inst, Utrecht, Netherlands. [Berezikov, Eugene] Univ Med Ctr Utrecht, Utrecht, Netherlands. [Cherbas, Lucy; Cherbas, Peter] Indiana Univ, Ctr Genom & Bioinformat, Bloomington, IN 47405 USA. [Henikoff, Steven] Fred Hutchinson Canc Res Ctr, Div Basic Sci, Seattle, WA 98109 USA. [Posakony, James W.; Ren, Bing] Univ Calif San Diego, Sect Cell & Dev Biol, Div Biol Sci, La Jolla, CA 92093 USA. [Pirrotta, Vincenzo] Rutgers State Univ, Dept Mol Biol & Biochem, Piscataway, NJ 08854 USA. [Brooks, Angela N.; Brenner, Steven E.; Karpen, Gary H.] Univ Calif Berkeley, Dept Mol & Cell Biol, Berkeley, CA 94720 USA. [Sakai, Akiko; Ahmad, Kami] Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA. [Meyer, Patrick E.] Univ Libre Brussels, Machine Learning Grp, B-1050 Brussels, Belgium. [Di Stefano, Luisa] Harvard Univ, Sch Med, Massachusetts Gen Hosp, Ctr Canc, Charlestown, MA 02129 USA. [Brenner, Steven E.] Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA. [Ay, Ferhat] Univ Florida, Gainesville, FL 32611 USA. [Kent, William] Univ Calif Santa Cruz, Sch Engn, Ctr Biomol Sci & Engn, Santa Cruz, CA 95064 USA. [Kent, William] Univ Calif Santa Cruz, Howard Hughes Med Inst, Santa Cruz, CA 95064 USA. [Feng, Xin] SUNY Stony Brook, Dept Biomed Engn, Stony Brook, NY 11794 USA. RP Kellis, M (reprint author), MIT, Comp Sci & Artificial Intelligence Lab, 77 Massachusetts Ave, Cambridge, MA 02139 USA. EM celniker@fruitfly.org; steveh@fhcrc.org; karpen@fruitfly.org; laie@mskcc.org; david.macalpine@duke.edu; lincoln.stein@gmail.com; kpwhite@uchicago.edu; manoli@mit.edu RI Samsonova, Anastasia/Q-7591-2016; Minoda, Aki/D-5335-2017; Sakai, Akiko/A-8929-2010; Eaton, Matthew/C-4408-2011; jiang, lichun/F-3776-2012; White, Rob/G-4835-2012; Russell, Steve/A-4072-2011; Brooks, Angela/B-6173-2011; Graveley, Brenton/C-3108-2013; Hansen, Kasper/E-6094-2011; Berezikov, Eugene/D-3363-2013; Brenner, Steven/A-8729-2008; Venken, Koen/B-9909-2013; Gorchakov, Andrey/N-5840-2015 OI Samsonova, Anastasia/0000-0002-9353-9173; Minoda, Aki/0000-0002-2927-5791; Gingeras, Thomas/0000-0001-9106-3573; Washington, Nicole/0000-0001-8936-9143; Grossman, Robert/0000-0003-3741-5739; Graveley, Brenton/0000-0001-5777-5892; Rutherford, Kim/0000-0001-6277-726X; McKay, Sheldon/0000-0002-4011-3160; Micklem, Gos/0000-0002-6883-6168; Lewis, Suzanna/0000-0002-8343-612X; Meyer, Folker/0000-0003-1112-2284; Lloyd, Paul/0000-0003-3508-5553; Bellen, Hugo/0000-0001-5992-5989; Hinrichs, Angie/0000-0002-1697-1130; Negre, Nicolas/0000-0001-9727-3416; Robine, Nicolas/0000-0001-5698-8183; Brown, Christopher/0000-0002-3785-5008; jiang, lichun/0000-0003-2462-7636; Russell, Steve/0000-0003-0546-3031; Hansen, Kasper/0000-0003-0086-0687; Berezikov, Eugene/0000-0002-1145-2884; Brenner, Steven/0000-0001-7559-6185; Venken, Koen/0000-0003-0741-4698; Gorchakov, Andrey/0000-0003-2830-4236 FU National Human Genome Research Institute [RC2HG005639, U01HG004271, U01HG004258, U01HG004264, U01HG004279, U01HG004261, U01HG004274, U41HG004269]; LBNL [DE-AC02-05CH11231]; NSF [0937060, 0905968, 0644282]; Natural Sciences and Engineering Research Council of Canada (NSERC); Japan Society for the Promotion of Science; Swedish Research Council; NIH National Research Service; National Defense Science and Engineering; Austrian Fonds zur Forderung der wissenschaftlichen Forschung; Leukemia and Lymphoma Society; Lilly-Life Sciences Research Foundation; Affymetrix; Swiss National Science Foundation; German Research Foundation [WI 3628/1-1]; HHMI; Indiana Genomics Initiative; NIDDK genomics core laboratory; NIH [R01HG004037]; Sloan Foundation FX This work was supported by the National Human Genome Research Institute as part of the modENCODE project under RC2HG005639 (M.K.), U01HG004271 (S.E.C.), U01HG004258 (G.H.K.), U01HG004264 (K.P.W.), U01HG004279 (D.M.M.), U01HG004261 (E.L.), U01HG004274 (S.H.), and U41HG004269 (L.S.). Awards to S.E.C. and G.H.K. were carried out at LBNL under contract no. DE-AC02-05CH11231. Additional support was provided by the NSF under grant 0937060 to the Computing Research Association for the CIFellows Project (S.R.) and under award no. 0905968 (J.E.), a Natural Sciences and Engineering Research Council of Canada (NSERC) fellowship (B.A.), T. Kahveci (F.A.), the Japan Society for the Promotion of Science (K.O.), the Swedish Research Council (Q.D.), a NIH National Research Service Award postdoctoral fellowship (C.A.B.), a National Defense Science and Engineering Graduate Fellowship (R.S.), an Erwin Schrodinger Fellowship of the Austrian Fonds zur Forderung der wissenschaftlichen Forschung (S.W.), a Leukemia and Lymphoma Society fellowship (S.W.), a Lilly-Life Sciences Research Foundation fellowship (C.D.B.), a NSERC postdoctoral fellowship (C. G. A.), Affymetrix (T.G.R.), a fellowship from the Swiss National Science Foundation (D.M.), a German Research Foundation grant WI 3628/1-1 (S.W.), a HHMI Damon Runyon Cancer Research fellowship (J.T.N.), the Indiana Genomics Initiative (T.C.K.), H. Smith and the NIDDK genomics core laboratory (B.O.), NIH R01HG004037, NSF CAREER award 0644282, and the Sloan Foundation (M.K.). A full list of author contributions is available in the SOM. NR 69 TC 524 Z9 531 U1 17 U2 82 PU AMER ASSOC ADVANCEMENT SCIENCE PI WASHINGTON PA 1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA SN 0036-8075 J9 SCIENCE JI Science PD DEC 23 PY 2010 VL 330 IS 6012 BP 1787 EP 1797 DI 10.1126/science.1198374 PG 11 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 698OS UT WOS:000285603700032 ER PT J AU Teolis, BD Jones, GH Miles, PF Tokar, RL Magee, BA Waite, JH Roussos, E Young, DT Crary, FJ Coates, AJ Johnson, RE Tseng, WL Baragiola, RA AF Teolis, B. D. Jones, G. H. Miles, P. F. Tokar, R. L. Magee, B. A. Waite, J. H. Roussos, E. Young, D. T. Crary, F. J. Coates, A. J. Johnson, R. E. Tseng, W-L Baragiola, R. A. TI Cassini Finds an Oxygen-Carbon Dioxide Atmosphere at Saturn's Icy Moon Rhea SO SCIENCE LA English DT Article ID CONDENSED O-2; SATELLITES; GANYMEDE; OZONE; CALLISTO; EUROPA; DIONE AB The flyby measurements of the Cassini spacecraft at Saturn's moon Rhea reveal a tenuous oxygen (O(2))-carbon dioxide (CO(2)) atmosphere. The atmosphere appears to be sustained by chemical decomposition of the surface water ice under irradiation from Saturn's magnetospheric plasma. This in situ detection of an oxidizing atmosphere is consistent with remote observations of other icy bodies, such as Jupiter's moons Europa and Ganymede, and suggestive of a reservoir of radiolytic O(2) locked within Rhea's ice. The presence of CO(2) suggests radiolysis reactions between surface oxidants and organics or sputtering and/or outgassing of CO(2) endogenic to Rhea's ice. Observations of outflowing positive and negative ions give evidence for pickup ionization as a major atmospheric loss mechanism. C1 [Teolis, B. D.; Miles, P. F.; Magee, B. A.; Waite, J. H.; Young, D. T.; Crary, F. J.] SW Res Inst, Space Sci & Engn Div, San Antonio, TX 78238 USA. [Jones, G. H.; Coates, A. J.] Univ Coll London, Mullard Space Sci Lab, Dept Space & Climate Phys, Dorking RH5 6NT, Surrey, England. [Jones, G. H.; Coates, A. J.] UCL Birkbeck, Ctr Planetary Sci, London WC1E 6BT, England. [Tokar, R. L.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. [Roussos, E.] Max Planck Inst Sonnensyst Forsch, D-37191 Katlenburg Lindau, Germany. [Johnson, R. E.; Tseng, W-L; Baragiola, R. A.] Univ Virginia, Dept Mat Sci & Engn, Charlottesville, VA 22903 USA. RP Teolis, BD (reprint author), SW Res Inst, Space Sci & Engn Div, 6220 Culebra Rd, San Antonio, TX 78238 USA. EM ben.teolis@swri.org RI Roussos, Elias/H-2249-2011; Coates, Andrew/C-2396-2008; Jones, Geraint/C-1682-2008; OI Coates, Andrew/0000-0002-6185-3125; Jones, Geraint/0000-0002-5859-1136; Roussos, Elias/0000-0002-5699-0678 FU NASA under SwRI [1283095]; Jet Propulsion Laboratory under SwRI [1356497]; UK Science and Technology Facilities Council; NSF [AST0807830] FX We thank E. Roussos, D. Mitchell, and the Cassini MIMI team for providing the MIMI data used in figs. S1 and S4 and N. G. Petrik, A. G. Kavetsky, and G. A. Kimmel at Pacific Northwest National Laboratory, Richland, Washington, USA, for contributing the O2 electron-stimulated desorption measurements in fig. S9. The INMS and CAPS teams acknowledge support from NASA and the Jet Propulsion Laboratory under SwRI subcontracts 1283095 and 1356497, respectively. G.H.J. and A.J.C. acknowledge support for CAPS-ELS operations and analysis by the United Kingdom Space Agency, and G.H.J. was supported by a UK Science and Technology Facilities Council Advanced Fellowship. B.D.T. and R.A.B. acknowledge support by the NSF Astronomy and Astrophysics Program through grant AST0807830. NR 23 TC 59 Z9 59 U1 5 U2 19 PU AMER ASSOC ADVANCEMENT SCIENCE PI WASHINGTON PA 1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA SN 0036-8075 J9 SCIENCE JI Science PD DEC 23 PY 2010 VL 330 IS 6012 BP 1813 EP 1815 DI 10.1126/science.1198366 PG 3 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 698OS UT WOS:000285603700038 PM 21109635 ER PT J AU Helm, RF Jervis, J Ray, WK Willoughby, N Irvin, B Hastie, J Schell, DJ Nagle, N AF Helm, Richard F. Jervis, Judith Ray, W. Keith Willoughby, Nicholas Irvin, Benjamin Hastie, Jessica Schell, Daniel J. Nagle, Nick TI Mass Spectral Analyses of Corn Stover Prehydrolysates To Assess Conditioning Processes SO JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY LA English DT Article DE Conditioning; corn stover; malate; mass spectrometry; oligosaccharides; limit xylodextrins ID DILUTE-SULFURIC-ACID; STRAW LIGNIN POLYMER; FERMENTATION INHIBITORS; SACCHAROMYCES-CEREVISIAE; ALKALINE DETOXIFICATION; D-XYLOSE; SPECTROMETRY; PRETREATMENT; ETHANOL; ELUCIDATION AB Flow injection electrospray (FIE) and LC-tandem mass spectrometry techniques were used to characterize corn stover acid hydrolysates before and after overliming and ammonia conditioning steps. Analyses were performed on samples without fractionation (dilution only) in an effort provide an inventory of ionizable substances. Statistical evaluation of the results indicates that the ammonia-treated and crude hydrolysates were more similar to one another than any other pairing, with conditioning leading to a decrease in malate levels. LC-tandem mass spectrometry studies were also developed to characterize the oligosaccharides present in each hydrolysate utilizing a hydrophilic interaction chromatographic separation method. Neutral and acidic pentose-based oligosaccharides (xylodextrins) with degrees of polymerization between 2 and 5 were quantified with 4-O-methyl glucuronic acid-containing dimer and trimers predominating. Conditioning had little effect on the quantified oligosaccharide pool. C1 [Helm, Richard F.; Jervis, Judith; Ray, W. Keith; Willoughby, Nicholas; Irvin, Benjamin; Hastie, Jessica] Virginia Tech, Dept Biochem, Blacksburg, VA 24061 USA. [Schell, Daniel J.; Nagle, Nick] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Helm, RF (reprint author), Virginia Tech, Dept Biochem, Blacksburg, VA 24061 USA. EM helmrf@vt.edu OI Helm, Richard/0000-0001-5317-0925 FU US Department of Energy through NREL [NDJ-7-77600] FX This work was funded by the Biomass Program of the US Department of Energy through NREL Subcontract NDJ-7-77600 to Virginia Tech. NR 39 TC 6 Z9 6 U1 2 U2 11 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0021-8561 J9 J AGR FOOD CHEM JI J. Agric. Food Chem. PD DEC 22 PY 2010 VL 58 IS 24 BP 12642 EP 12649 DI 10.1021/jf1031197 PG 8 WC Agriculture, Multidisciplinary; Chemistry, Applied; Food Science & Technology SC Agriculture; Chemistry; Food Science & Technology GA 693PQ UT WOS:000285236400010 PM 21080713 ER PT J AU Hakala, JA Chin, YP AF Hakala, Jacqueline Alexandra Chin, Yu-Ping TI Abiotic Reduction of Pendimethalin and Trifluralin in Controlled and Natural Systems Containing Fe(II) and Dissolved Organic Matter SO JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY LA English DT Article DE Trifluralin; pendimethalin; dinitroaniline; Fe(II); dissolved organic matter; pore water; reduction; iron; pesticide; Pony Lake fulvic acid; Suwannee River fulvic acid; Old Woman Creek fulvic acid ID NITROAROMATIC COMPOUNDS; DEGRADATION; IRON; PENTACHLORONITROBENZENE; TRANSFORMATION; PESTICIDES; COMPLEXES; WATERS; CARBON AB The environmental fate of dinitroaniline herbicides is poorly understood, despite their classification as Persistent Bioaccumulative Toxins by the U.S. Environmental Protection Agency. This study investigated the abiotic reduction of pendimethalin and trifluralin in controlled laboratory systems in the presence of Fe(II) and fulvic acids isolated from various surface waters and in sediment pore waters containing naturally abundant levels of dissolved Fe(II) and dissolved organic matter (DOM). It was found that Fe(II) was necessary for pendimethalin and trifluralin reduction to occur in controlled systems and that higher concentrations of DOM slowed Fe(II)-mediated reactions. Pendimethalin and trifluralin reduction in natural pore waters was roughly an order of magnitude slower compared to controlled Fe(II) DOM solutions, indicating that the reactive Fe(II) species responsible for reduction are concentration-limited in natural pore waters relative to controlled systems. The results show that caution must be exercised when extrapolating results from controlled system reactions to natural systems and that abiotic reduction of both trifluralin and pendimethalin is observed within 3-7 days in anaerobic sedimentary pore waters containing high concentrations of both dissolved Fe(II) and DOM. C1 [Hakala, Jacqueline Alexandra] Natl Energy Technol Lab, Geosci Div, Pittsburgh, PA 15236 USA. [Chin, Yu-Ping] Ohio State Univ, Sch Earth Sci, Mendenhall Lab 275, Columbus, OH 43210 USA. RP Hakala, JA (reprint author), Natl Energy Technol Lab, Geosci Div, POB 10940, Pittsburgh, PA 15236 USA. EM Jacqueline.Hakala@netl.doe.gov NR 34 TC 9 Z9 9 U1 2 U2 26 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0021-8561 J9 J AGR FOOD CHEM JI J. Agric. Food Chem. PD DEC 22 PY 2010 VL 58 IS 24 BP 12840 EP 12846 DI 10.1021/jf102814b PG 7 WC Agriculture, Multidisciplinary; Chemistry, Applied; Food Science & Technology SC Agriculture; Chemistry; Food Science & Technology GA 693PQ UT WOS:000285236400038 PM 21087048 ER PT J AU Halford, AJ Fraser, BJ Morley, SK AF Halford, A. J. Fraser, B. J. Morley, S. K. TI EMIC wave activity during geomagnetic storm and nonstorm periods: CRRES results SO JOURNAL OF GEOPHYSICAL RESEARCH-SPACE PHYSICS LA English DT Article ID ION-CYCLOTRON WAVES; PITCH-ANGLE SCATTERING; RING CURRENT; MAGNETIC STORMS; RADIATION-BELT; GEOSYNCHRONOUS ORBIT; MAGNETOSPHERE; PLASMA; DYNAMICS; TIME AB Electromagnetic ion cyclotron (EMIC) waves have been observed during geomagnetic storms and are thought to contribute to ring current and radiation belt particle loss during the main phase. Ground-based storm time studies alternatively observe the majority of storm time Pc1-2 pulsations during the recovery phase. In this study we look at the occurrences of EMIC waves during 119 storms occurring throughout the CRRES mission. The storms were defined using the Sym-H index. The storm was divided into three phases: pre-onset, main, and recovery (80% of minimum Sym-H value). The majority, 56.25%, of storm time EMIC waves were found to occur during the main phase, while 35.57% were observed in the recovery phase. The recovery phase definition was then extended to 6 days after the minimum in order to compare with past ground studies. Although more EMIC waves were observed during this extended recovery phase, the maximum occurrence rate of EMIC waves remains in the main phase. A slight increase does appear in the 4-6 days after the minimum Sym-H value. The mean occurrence location of EMIC waves was at L = 6.07, MLT = 15.12. This suggests that EMIC waves may have been generated when the ring current and plasmasphere or plasma plume particle populations overlap, often observed during the main phase due to storm dynamics. The rise in the occurrence rate in the extended recovery phase potentially is dominated by the process of plasmaspheric expansion after the end of the storm. C1 [Halford, A. J.; Fraser, B. J.] Univ Newcastle, Ctr Space Phys, Callaghan, NSW 2308, Australia. [Morley, S. K.] Los Alamos Natl Lab, Space Sci & Applicat ISR 1, Los Alamos, NM 87545 USA. RP Halford, AJ (reprint author), Univ Newcastle, Ctr Space Phys, Callaghan, NSW 2308, Australia. EM alexa.halford@gmail.com; brian.fraser@newcastle.edu.au; smorley@lanl.gov RI Morley, Steven/A-8321-2008; OI Morley, Steven/0000-0001-8520-0199; Halford, Alexa/0000-0002-5383-4602 FU Australian Research Council [DP0772504, LX0882515]; University of Newcastle FX This research was supported by Australian Research Council Project grant DP0772504 and Linkage International grant LX0882515. We would like to thank WDC for Geomagnetism, Kyoto for providing the Sym-H and Kp indices. A.J. Halford was supported by a University of Newcastle Postgraduate Research Scholarship. NR 69 TC 56 Z9 56 U1 0 U2 5 PU AMER GEOPHYSICAL UNION PI WASHINGTON PA 2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA SN 2169-9380 EI 2169-9402 J9 J GEOPHYS RES-SPACE JI J. Geophys. Res-Space Phys. PD DEC 22 PY 2010 VL 115 AR A12248 DI 10.1029/2010JA015716 PG 15 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA 699BS UT WOS:000285639500003 ER PT J AU Beeler, B Good, B Rashkeev, S Deo, C Baskes, M Okuniewski, M AF Beeler, B. Good, B. Rashkeev, S. Deo, C. Baskes, M. Okuniewski, M. TI First principles calculations for defects in U SO JOURNAL OF PHYSICS-CONDENSED MATTER LA English DT Article ID TOTAL-ENERGY CALCULATIONS; AUGMENTED-WAVE METHOD; ELECTRON-GAS; URANIUM; METALS; TEMPERATURES; STABILITY; PLUTONIUM; PHASE; MODEL AB Uranium (U) exhibits a high temperature body-centered cubic (bcc) allotrope that is often stabilized by alloying with transition metals such as Zr, Mo, and Nb for technological applications. One such application involves U-Zr as nuclear fuel, where radiation damage and diffusion (processes heavily dependent on point defects) are of vital importance. Several systems of U are examined within a density functional theory framework utilizing projector augmented wave pseudopotentials. Two separate generalized gradient approximations of the exchange-correlation are used to calculate defect properties and are compared. The bulk modulus, the lattice constant, and the Birch-Murnaghan equation of state for the defect free bcc uranium allotrope are calculated. Defect parameters calculated include energies of formation of vacancies in the alpha and gamma allotropes, as well as self-interstitials, Zr interstitials, and Zr substitutional defects for the gamma allotrope. The results for vacancies agree very well with experimental and previous computational studies. The most probable self-interstitial site in gamma-U is the < 110 > dumbbell, and the most probable defect location for dilute Zr in. gamma-U is the substitutional site. This is the first detailed study of self-defects in the bcc allotrope of U and also the first comprehensive study of dilute Zr defects in. gamma-U. C1 [Beeler, B.; Good, B.; Deo, C.] Georgia Inst Technol, Atlanta, GA 30318 USA. [Rashkeev, S.; Okuniewski, M.] Idaho Natl Lab, Idaho Falls, ID 83415 USA. [Baskes, M.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. [Baskes, M.] Univ Calif San Diego, La Jolla, CA 92093 USA. RP Beeler, B (reprint author), Georgia Inst Technol, 770 State St, Atlanta, GA 30318 USA. EM benbeeler@gatech.edu FU DOE NERI-C [DEFG0714891]; INL [DE-AC07-05ID14517]; Office of Nuclear Energy of the US Department of Energy [DE-AC07-05ID14517] FX We acknowledge support from DOE NERI-C Grant No. DEFG0714891 and INL subcontract DE-AC07-05ID14517. BB acknowledges computing resources provided by Idaho National Laboratory, which is supported by the Office of Nuclear Energy of the US Department of Energy under contract DE-AC07-05ID14517. NR 28 TC 27 Z9 27 U1 4 U2 33 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0953-8984 J9 J PHYS-CONDENS MAT JI J. Phys.-Condes. Matter PD DEC 22 PY 2010 VL 22 IS 50 AR 505703 DI 10.1088/0953-8984/22/50/505703 PG 7 WC Physics, Condensed Matter SC Physics GA 690ZK UT WOS:000285049200016 PM 21406806 ER PT J AU Dunne, JF Fulton, DB Ellern, A Sadow, AD AF Dunne, James F. Fulton, D. Bruce Ellern, Arkady Sadow, Aaron D. TI Concerted C-N and C-H Bond Formation in a Magnesium-Catalyzed Hydroamination SO JOURNAL OF THE AMERICAN CHEMICAL SOCIETY LA English DT Article ID UNPROTECTED AMINO OLEFINS; INTRAMOLECULAR HYDROAMINATION; ALKYL DERIVATIVES; INTERNAL ALKYNES; AMIDO BOND; COMPLEXES; INSERTION; MECHANISM; ALKENES; AMINOALKENES AB Coordinatively saturated To(M)MgMe (1; To(M) = tris(4,4-dimethyl-2-oxazolinyl)phenylborate) is an active precatalyst for intramolecular hydroamination/cyclization at 50 degrees C. The empirical rate law of -d[substrate]/dt = K-obs[Mg](1)[substrate](1) and Michaelis-Menten-type kinetics are consistent with a mechanism involving reversible catalyst-substrate association prior to cyclization. The resting state of the catalyst, To(M)MgNHCH(2)CR(2)CH(2)CH=CH2 [R = Ph, Me, -(CH2)(5)-], is isolable, but isolated magnesium amidoalkene does not undergo unimolecular cyclization at 50 degrees C. However, addition of trace amounts of substrate allows cyclization to occur. Therefore, we propose a two-substrate, six-center transition state involving concerted C-N bond formation and N-H bond cleavage as the turnover-limiting step of the catalytic cycle. C1 [Sadow, Aaron D.] Iowa State Univ, Dept Chem, Ames Lab, Ames, IA 50011 USA. Iowa State Univ, US DOE, Ames Lab, Ames, IA 50011 USA. RP Sadow, AD (reprint author), Iowa State Univ, Dept Chem, Ames Lab, Ames, IA 50011 USA. EM sadow@iastate.edu FU U.S. DOE Office of Basic Energy Science [DE-AC02-07CH11358]; ACS Green Chemistry Institute-PRF; GAANN FX We thank Dr. A. Bakac and Dr. K. Kristian for valuable mechanistic discussions. Mr. J. Engelkemier is thanked for preparation of 3-d2. The U.S. DOE Office of Basic Energy Science (DE-AC02-07CH11358) and the ACS Green Chemistry Institute-PRF provided financial support. James F. Dunne is supported by a GAANN Fellowship. Aaron D. Sadow is an Alfred P. Sloan Fellow. NR 38 TC 73 Z9 73 U1 2 U2 21 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0002-7863 J9 J AM CHEM SOC JI J. Am. Chem. Soc. PD DEC 22 PY 2010 VL 132 IS 50 BP 17680 EP 17683 DI 10.1021/ja108881s PG 4 WC Chemistry, Multidisciplinary SC Chemistry GA 696GL UT WOS:000285429800013 PM 21117645 ER PT J AU Wang, LY Wang, X Luo, J Wanjala, BN Wang, CM Chernova, NA Engelhard, MH Liu, Y Bae, IT Zhong, CJ AF Wang, Lingyan Wang, Xin Luo, Jin Wanjala, Bridgid N. Wang, Chongmin Chernova, Natasha A. Engelhard, Mark H. Liu, Yao Bae, In-Tae Zhong, Chuan-Jian TI Core-Shell-Structured Magnetic Ternary Nanocubes SO JOURNAL OF THE AMERICAN CHEMICAL SOCIETY LA English DT Article ID MNZN-FERRITE NANOPARTICLES; AU NANOPARTICLES; OXIDE; FE; NANOCRYSTALS; MICROEMULSIONS AB We report a novel core-shell-structured ternary nanocube of MnZn ferrite synthesized by controlling the reaction temperature and composition in the absence of conventionally used reducing agents. The highly monodispersed core-shell structure consists of an Fe(3)O(4) core and an MnZn Ferrite shell. The observation of a Moire pattern indicates that the core and the shell are two highly crystalline materials with slightly different lattice constants that are rotated relative to each other by a small angle. The ternary core-shell nanocubes display magnetic properties regulated by a combination of the core-shell composition and exhibit an increased coercivity and field-cooled/zero-field-cooled characteristics drastically different from those of regular MnZn ferrite nanoparticles. The ability to engineer the spatial nanostructures of ternary magnetic nanoparticles in terms of shape and composition offers atomic-level versatility in fine-tuning the nanoscale magnetic properties. C1 [Wang, Lingyan; Wang, Xin; Luo, Jin; Wanjala, Bridgid N.; Chernova, Natasha A.; Liu, Yao; Bae, In-Tae; Zhong, Chuan-Jian] SUNY Binghamton, Dept Chem, Binghamton, NY 13902 USA. [Wang, Chongmin; Engelhard, Mark H.] Pacific NW Natl Lab, EMSL, Richland, WA 99352 USA. RP Zhong, CJ (reprint author), SUNY Binghamton, Dept Chem, Binghamton, NY 13902 USA. EM cjzhong@binghamton.edu RI Engelhard, Mark/F-1317-2010; Zhong, Chuan-Jian/D-3394-2013; OI Engelhard, Mark/0000-0002-5543-0812 FU NSF [CHE 0848701, CBET 0709113] FX This work was supported by NSF (CHE 0848701, CBET 0709113). The XPS and some HRTEM were performed using the EMSL User Facility of the DOE at PNNL. NR 39 TC 29 Z9 30 U1 3 U2 46 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0002-7863 J9 J AM CHEM SOC JI J. Am. Chem. Soc. PD DEC 22 PY 2010 VL 132 IS 50 BP 17686 EP 17689 DI 10.1021/ja1091084 PG 4 WC Chemistry, Multidisciplinary SC Chemistry GA 696GL UT WOS:000285429800015 PM 21121606 ER PT J AU Hanson, SK Baker, RT Gordon, JC Scott, BL Silks, LA Thorn, DL AF Hanson, Susan K. Baker, R. Tom Gordon, John C. Scott, Brian L. Silks, L. A. Pete Thorn, David L. TI Mechanism of Alcohol Oxidation by Dipicolinate Vanadium(V): Unexpected Role of Pyridine SO JOURNAL OF THE AMERICAN CHEMICAL SOCIETY LA English DT Article ID ENANTIOSELECTIVE AEROBIC OXIDATION; ALPHA-HYDROXY ESTERS; QUINQUEVALENT VANADIUM; ORGANIC COMPOUNDS; MOLECULAR-OXYGEN; CATALYZED OXIDATION; BOND-CLEAVAGE; 2-ELECTRON OXIDATIONS; PROPARGYLIC ALCOHOLS; SELECTIVE OXIDATION AB Dipicolinate vanadium(V) alkoxide complexes (dipic)V-v(O)(OR) (OR = isopropoxide (1), n-butanoxide (2), cyclobutanoxide (3), and alpha-tert-butylbenzylalkoxide (4)) react with pyridine to afford vanadium(IV) and 0.5 equiv of an aldehyde or ketone product. The role of pyridine in the reaction has been investigated. Both NMR and X-ray crystallography experiments indicate that pyridine coordinates to 1, which is in equilibrium with (dipic)V-v(O)((OPr)-Pr-i)(pyr) (1-Pyr). Kinetic studies of the alcohol oxidation suggest a pathway where the rate-limiting step is bimolecular and involves attack of pyridine on the C-H bond of the isopropoxide ligand of 1 or 1-Pyr. The oxidations of mechanistic probes cyclobutanol and alpha-tert-butylbenzylalcohol support a two-electron pathway proceeding through a vanadium(III) intermediate. The alcohol oxidation reaction is promoted by more basic pyridines and facilitated by electron-withdrawing substituents on the dipicolinate ligand. The involvement of base in the elementary alcohol oxidation step observed for the dipicolinate system is an unprecedented mechanism for vanadium-mediated alcohol oxidation and suggests new ways to tune reactivity and selectivity of vanadium catalysts. C1 [Hanson, Susan K.] Los Alamos Natl Lab, Div Chem, Los Alamos, NM 87544 USA. Los Alamos Natl Lab, Biosci Div, Los Alamos, NM 87544 USA. Los Alamos Natl Lab, Mat Phys Applicat Div, Los Alamos, NM 87544 USA. RP Hanson, SK (reprint author), Los Alamos Natl Lab, Div Chem, POB 1663, Los Alamos, NM 87544 USA. EM skhanson@lanl.gov RI Scott, Brian/D-8995-2017; OI Scott, Brian/0000-0003-0468-5396; Silks, Pete/0000-0002-2993-5630 FU Los Alamos National Laboratory LDRD [ER 20100160]; NSF via the Center for Enabling New Technologies through Catalysis (CENTC) FX This work was supported by Los Alamos National Laboratory LDRD (ER 20100160 and Director's PD Fellowship to S.K.H.) and NSF via the Center for Enabling New Technologies through Catalysis (CENTC). We thank Professors W. T. Borden (UNT), D. Hrovat (UNT), S. L. Scott (UCSB), and P. C. Ford (UCSB) for helpful discussions and collaborations, and Dr. P. C. Stark (LANL) for help with instrumentation. NR 76 TC 41 Z9 41 U1 7 U2 50 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0002-7863 J9 J AM CHEM SOC JI J. Am. Chem. Soc. PD DEC 22 PY 2010 VL 132 IS 50 BP 17804 EP 17816 DI 10.1021/ja105739k PG 13 WC Chemistry, Multidisciplinary SC Chemistry GA 696GL UT WOS:000285429800033 PM 21121665 ER PT J AU Akerib, DS Attisha, MJ Baudis, L Bauer, DA Bolozdynya, AI Brink, PL Bunker, R Cabrera, B Caldwell, DO Chang, CL Clarke, RM Cooley, J Crisler, MB Cushman, P DeJongh, F Dixon, R Driscoll, DD Filippini, J Funkhouser, S Gaitskell, RJ Golwala, SR Holmgren, D Hsu, L Huber, ME Kamat, S Mahapatra, R Mandic, V Meunier, P Mirabolfathi, N Moore, D Nam, SW Nelson, H Ogburn, RW Qiu, X Rau, W Reisetter, A Saab, T Sadoulet, B Sander, J Savage, C Schnee, RW Seitz, DN Shutt, TA Wang, G Yellin, S Yoo, J Young, BA AF Akerib, D. S. Attisha, M. J. Baudis, L. Bauer, D. A. Bolozdynya, A. I. Brink, P. L. Bunker, R. Cabrera, B. Caldwell, D. O. Chang, C. L. Clarke, R. M. Cooley, J. Crisler, M. B. Cushman, P. DeJongh, F. Dixon, R. Driscoll, D. D. Filippini, J. Funkhouser, S. Gaitskell, R. J. Golwala, S. R. Holmgren, D. Hsu, L. Huber, M. E. Kamat, S. Mahapatra, R. Mandic, V. Meunier, P. Mirabolfathi, N. Moore, D. Nam, S. W. Nelson, H. Ogburn, R. W. Qiu, X. Rau, W. Reisetter, A. Saab, T. Sadoulet, B. Sander, J. Savage, C. Schnee, R. W. Seitz, D. N. Shutt, T. A. Wang, G. Yellin, S. Yoo, J. Young, B. A. CA CDMS Collaboration TI Low-threshold analysis of CDMS shallow-site data SO PHYSICAL REVIEW D LA English DT Article ID LARGE-SCALE STRUCTURE; DARK-MATTER; CONSTRAINTS; DAMA/LIBRA; EFFICIENCY; DETECTORS; UNIVERSE; CRYSTAL; RAVE AB Data taken during the final shallow-site run of the first tower of the Cryogenic Dark Matter Search (CDMS II) detectors have been reanalyzed with improved sensitivity to small energy depositions. Four similar to 224 g germanium and two similar to 105 g silicon detectors were operated at the Stanford Underground Facility (SUF) between December 2001 and June 2002, yielding 118 live days of raw exposure. Three of the germanium and both silicon detectors were analyzed with a new low-threshold technique, making it possible to lower the germanium and silicon analysis thresholds down to the actual trigger thresholds of similar to 1 and similar to 2 keV, respectively. Limits on the spin-independent cross section for weakly interacting massive particles (WIMPs) to elastically scatter from nuclei based on these data exclude interesting parameter space for WIMPs with masses below 9 GeV/c(2). Under standard halo assumptions, these data partially exclude parameter space favored by interpretations of the DAMA/LIBRA and CoGeNT experiments' data as WIMP signals, and exclude new parameter space for WIMP masses between 3 and 4 GeV/c(2). C1 [Bunker, R.; Caldwell, D. O.; Nelson, H.; Savage, C.; Yellin, S.] Univ Calif Santa Barbara, Dept Phys, Santa Barbara, CA 93106 USA. [Attisha, M. J.; Gaitskell, R. J.] Brown Univ, Dept Phys, Providence, RI 02912 USA. [Filippini, J.; Golwala, S. R.; Moore, D.] CALTECH, Div Phys Math & Astron, Pasadena, CA 91125 USA. [Akerib, D. S.; Bolozdynya, A. I.; Driscoll, D. D.; Kamat, S.; Wang, G.] Case Western Reserve Univ, Dept Phys, Cleveland, OH 44106 USA. [Bauer, D. A.; Crisler, M. B.; DeJongh, F.; Dixon, R.; Holmgren, D.; Hsu, L.; Yoo, J.] Fermilab Natl Accelerator Lab, Batavia, IL 60510 USA. [Sadoulet, B.] Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA. [Reisetter, A.] St Olaf Coll, Dept Phys, Northfield, MN 55057 USA. [Shutt, T. A.] Princeton Univ, Dept Phys, Princeton, NJ 08544 USA. [Rau, W.] Queens Univ, Dept Phys, Kingston, ON K7L 3N6, Canada. [Young, B. A.] Santa Clara Univ, Dept Phys, Santa Clara, CA 95053 USA. [Brink, P. L.] SLAC Natl Accelerator Lab KIPAC, Menlo Pk, CA 94025 USA. [Cooley, J.] So Methodist Univ, Dept Phys, Dallas, TX 75275 USA. [Cabrera, B.; Chang, C. L.; Clarke, R. M.; Nam, S. W.; Ogburn, R. W.; Yellin, S.] Stanford Univ, Dept Phys, Stanford, CA 94305 USA. [Schnee, R. W.] Syracuse Univ, Dept Phys, Syracuse, NY 13244 USA. [Mahapatra, R.; Sander, J.] Texas A&M Univ, Dept Phys, College Stn, TX 77843 USA. [Funkhouser, S.; Meunier, P.; Mirabolfathi, N.; Sadoulet, B.; Seitz, D. N.] Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA. [Huber, M. E.] Univ Colorado, Dept Phys, Denver, CO 80217 USA. [Huber, M. E.] Univ Colorado, Dept Elect Engn, Denver, CO 80217 USA. [Saab, T.] Univ Florida, Dept Phys, Gainesville, FL 32611 USA. [Cushman, P.; Mandic, V.; Qiu, X.; Reisetter, A.] Univ Minnesota, Sch Phys & Astron, Minneapolis, MN 55455 USA. [Baudis, L.] Univ Zurich, Inst Phys, CH-8057 Zurich, Switzerland. RP Bunker, R (reprint author), Univ Calif Santa Barbara, Dept Phys, Santa Barbara, CA 93106 USA. EM bunker@hep.ucsb.edu RI Huber, Martin/B-3354-2011; Qiu, Xinjie/C-6164-2012; Yoo, Jonghee/K-8394-2016 FU National Science Foundation [AST-9978911, PHY-0542066, PHY-0503729, PHY-0503629, PHY-0503641, PHY-0504224, PHY-0705052, PHY-0801708, PHY-0801712, PHY-0802575, PHY-0855525, PHY-9722414]; Department of Energy [DE-AC03-76SF00098, DE-FG02-91ER40688, DE-FG02-92ER40701, DE-FG03-90ER40569, DE-FG03-91ER40618]; Swiss National Foundation (SNF) [20-118119]; NSERC Canada [SAPIN 341314-07] FX The CDMS Collaboration gratefully acknowledges the contributions of numerous engineers and technicians. We would like to especially thank Judith Alvaro-Dean, Jim Beaty, Sam Burke, Daniel Callahan, Pat Castle, John Emes, Merle Haldeman, David Hale, Michael Hennessey, Wayne Johnson, Jim Perales, Garth Smith, and Astrid Tomada. Additionally, we would like to thank former CDMS collaborators for their contributions to the successful completion of this work, including Long Duong, Jochen Hellmig, Al Lu, John Martinis, Thushara Perera, Maria Perillo Isaac, Ron Ross, Tony Spadafora, and John-Paul Thompson. This work is supported in part by the National Science Foundation (Grants No. AST-9978911, No. PHY-0542066, No. PHY-0503729, No. PHY-0503629, No. PHY-0503641, No. PHY-0504224, No. PHY-0705052, No. PHY-0801708, No. PHY-0801712, No. PHY-0802575, No. PHY-0855525, and No. PHY-9722414), by the Department of Energy (Contracts No. DE-AC03-76SF00098, No. DE-FG02-91ER40688, No. DE-FG02-92ER40701, No. DE-FG03-90ER40569, and No. DE-FG03-91ER40618), by the Swiss National Foundation (SNF Grant No. 20-118119), and by NSERC Canada (Grant No. SAPIN 341314-07). NR 57 TC 86 Z9 87 U1 1 U2 3 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 1550-7998 J9 PHYS REV D JI Phys. Rev. D PD DEC 22 PY 2010 VL 82 IS 12 AR 122004 DI 10.1103/PhysRevD.82.122004 PG 18 WC Astronomy & Astrophysics; Physics, Particles & Fields SC Astronomy & Astrophysics; Physics GA 713NN UT WOS:000286744800001 ER PT J AU Berger, EL Guzzi, M Lai, HL Nadolsky, PM Olness, FI AF Berger, Edmond L. Guzzi, Marco Lai, Hung-Liang Nadolsky, Pavel M. Olness, Fredrick I. TI Constraints on color-octet fermions from a global parton distribution analysis SO PHYSICAL REVIEW D LA English DT Article ID MISSING TRANSVERSE ENERGY; GLUINO PRODUCTION; PARTICLE PHYSICS; ROOT-S=1.96 TEV; CROSS-SECTION; SEARCH; SUPERSYMMETRY; COLLISIONS; SQUARKS; EVENTS AB We report a parton distribution function analysis of a complete set of hadron scattering data, in which a color-octet fermion (such as a gluino of supersymmetry) is incorporated as an extra parton constituent along with the usual standard model constituents. The data set includes the most up-to-date results from deep inelastic scattering and from jet production in hadron collisions. Another feature is the inclusion in the fit of data from determinations of the strong coupling alpha(s)(Q) at large and small values of the hard scale Q. Our motivation is to determine the extent to which the global parton distribution function analysis may provide constraints on the new fermion, as a function of its mass and alpha(s)(M-Z), independent of assumptions such as the mechanism of gluino decays. Based on this analysis, we find that gluino masses as low as 30 to 50 GeV may be compatible with the current hadronic data. Gluino masses below 15 GeV (25 GeV) are excluded if alpha(s)(M-Z) varies freely (is equal to 0.118). At the outset, stronger constraints had been anticipated from jet production cross sections, but experimental systematic uncertainties, particularly in normalization, reduce the discriminating power of these data. C1 [Berger, Edmond L.] Argonne Natl Lab, Div High Energy Phys, Argonne, IL 60439 USA. [Guzzi, Marco; Nadolsky, Pavel M.; Olness, Fredrick I.] So Methodist Univ, Dept Phys, Dallas, TX 75275 USA. [Lai, Hung-Liang] Taipei Municipal Univ Educ, Taipei, Taiwan. RP Berger, EL (reprint author), Argonne Natl Lab, Div High Energy Phys, Argonne, IL 60439 USA. OI Guzzi, Marco/0000-0003-3430-2691 FU U.S. Department of Energy [DE-AC02-06CH11357, DE-FG02-04ER41299, DE-SC0003870]; U.S. National Science Foundation [PHY-0705862, PHY-0855561]; Lightner-Sams Foundation; National Science Council of Taiwan [NSC-98-2112-M-133-002-MY3, NSC-99-2918-I-133-001] FX We thank Tom Rizzo for discussions regarding searches for new physics and bounds on gluino masses, and Mike Whalley and Andy Buckley for extending the LHAPDF library [55,56] to incorporate PDFs with light gluinos. The authors also thank CTEQ members for helpful discussions. E. L. B. is supported by the U.S. Department of Energy under Contract No. DE-AC02-06CH11357. The work at SMU is supported in part by U.S. D.O.E. Contract No. DE-FG02-04ER41299; the U.S. D.O.E. Early Career Research Grant No. DE-SC0003870; the U.S. National Science Foundation Grant No. PHY-0705862; and by Lightner-Sams Foundation. H.-L.L. is supported by the U.S. National Science Foundation under Grant No. PHY-0855561 and by National Science Council of Taiwan under Grants No. NSC-98-2112-M-133-002-MY3 and No. NSC-99-2918-I-133-001. E. L. B. and P. M. N. thank the Aspen Center for Physics for hospitality during the summer of 2010 when part of this work was done. F. I. O thanks CERN for hospitality during his work on this study. NR 55 TC 4 Z9 4 U1 0 U2 2 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 2470-0010 EI 2470-0029 J9 PHYS REV D JI Phys. Rev. D PD DEC 22 PY 2010 VL 82 IS 11 AR 114023 DI 10.1103/PhysRevD.82.114023 PG 16 WC Astronomy & Astrophysics; Physics, Particles & Fields SC Astronomy & Astrophysics; Physics GA 711HH UT WOS:000286577200006 ER PT J AU Bousso, R Freivogel, B Leichenauer, S Rosenhaus, V AF Bousso, Raphael Freivogel, Ben Leichenauer, Stefan Rosenhaus, Vladimir TI Boundary definition of a multiverse measure SO PHYSICAL REVIEW D LA English DT Article ID STATIONARY UNIVERSE; SCALAR CURVATURE; YAMABE PROBLEM; COSMOLOGY; CONSTANT; SPACE; TIME AB We propose to regulate the infinities of eternal inflation by relating a late time cutoff in the bulk to a short-distance cutoff on the future boundary. The light-cone time of an event is defined in terms of the volume of its future light cone on the boundary. We seek an intrinsic definition of boundary volumes that makes no reference to bulk structures. This requires taming the fractal geometry of the future boundary and lifting the ambiguity of the conformal factor. We propose to work in the conformal frame in which the boundary Ricci scalar is constant. We explore this proposal in the Friedmann-Robertson-Walker approximation for bubble universes. Remarkably, we find that the future boundary becomes a round three-sphere, with smooth metric on all scales. Our cutoff yields the same relative probabilities as a previous proposal that defined boundary volumes by projection into the bulk along timelike geodesics. Moreover, it is equivalent to an ensemble of causal patches defined without reference to bulk geodesics. It thus yields a holographically motivated and phenomenologically successful measure for eternal inflation. C1 [Bousso, Raphael; Freivogel, Ben; Leichenauer, Stefan; Rosenhaus, Vladimir] Univ Calif Berkeley, Dept Phys, Ctr Theoret Phys, Berkeley, CA 94720 USA. [Bousso, Raphael; Freivogel, Ben; Leichenauer, Stefan; Rosenhaus, Vladimir] Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA. [Bousso, Raphael] Univ Tokyo, Inst Phys & Math Universe, Kashiwa, Chiba 2778568, Japan. RP Bousso, R (reprint author), Univ Calif Berkeley, Dept Phys, Ctr Theoret Phys, Berkeley, CA 94720 USA. FU Berkeley Center for Theoretical Physics; National Science Foundation [0855653]; Institute for the Physics and Mathematics of the Universe; fqxi Grant [RFP2-08-06]; U.S. Department of Energy [DE-AC02-05CH11231] FX We thank David Berenstein, Petr Horava, Gary Horowitz, Shamit Kachru, Steve Shenker, Eva Silverstein, Lenny Susskind, and Edward Witten for discussions. This work was supported by the Berkeley Center for Theoretical Physics, by the National Science Foundation (Grant No. 0855653), by the Institute for the Physics and Mathematics of the Universe, by fqxi Grant No. RFP2-08-06, and by the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. NR 61 TC 22 Z9 22 U1 0 U2 1 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 2470-0010 EI 2470-0029 J9 PHYS REV D JI Phys. Rev. D PD DEC 22 PY 2010 VL 82 IS 12 AR 125032 DI 10.1103/PhysRevD.82.125032 PG 18 WC Astronomy & Astrophysics; Physics, Particles & Fields SC Astronomy & Astrophysics; Physics GA 713NN UT WOS:000286744800017 ER PT J AU Sanchez, PD Lees, JP Poireau, V Prencipe, E Tisserand, V Tico, JG Grauges, E Martinelli, M Palano, A Pappagallo, M Eigen, G Stugu, B Sun, L Battaglia, M Brown, DN Hooberman, B Kerth, LT Kolomensky, YG Lynch, G Osipenkov, IL Tanabe, T Hawkes, CM Watson, AT Koch, H Schroeder, T Asgeirsson, DJ Hearty, C Mattison, TS McKenna, JA Khan, A Randle-Conde, A Blinov, VE Buzykaev, AR Druzhinin, VP Golubev, VB Onuchin, AP Serednyakov, SI Skovpen, YI Solodov, EP Todyshev, KY Yushkov, AN Bondioli, M Curry, S Kirkby, D Lankford, AJ Mandelkern, M Martin, EC Stoker, DP Atmacan, H Gary, JW Liu, F Long, O Vitug, GM Campagnari, C Hong, TM Kovalskyi, D Richman, JD Eisner, AM Heusch, CA Kroseberg, J Lockman, WS Martinez, AJ Schalk, T Schumm, BA Seiden, A Winstrom, LO Cheng, CH Doll, DA Echenard, B Hitlin, DG Ongmongkolkul, P Porter, FC Rakitin, AY Andreassen, R Dubrovin, MS Mancinelli, G Meadows, BT Sokoloff, MD Bloom, PC Ford, WT Gaz, A Hirschauer, JF Nagel, M Nauenberg, U Smith, JG Wagner, SR Ayad, R Toki, WH Karbach, TM Merkel, J Petzold, A Spaan, B Wacker, K Kobel, MJ Schubert, KR Schwierz, R Bernard, D Verderi, M Clark, PJ Playfer, S Watson, JE Andreotti, M Bettoni, D Bozzi, C Calabrese, R Cecchi, A Cibinetto, G Fioravanti, E Franchini, P Luppi, E Munerato, M Negrini, M Petrella, A Piemontese, L Baldini-Ferroli, R Calcaterra, A de Sangro, R Finocchiaro, G Nicolaci, M Pacetti, S Patteri, P Peruzzi, IM Piccolo, M Rama, M Zallo, A Contri, R Guido, E Lo Vetere, M Monge, MR Passaggio, S Patrignani, C Robutti, E Tosi, S Bhuyan, B Morii, M Adametz, A Marks, J Schenk, S Uwer, U Bernlochner, FU Lacker, HM Lueck, T Volk, A Dauncey, PD Tibbetts, M Behera, PK Mallik, U Chen, C Cochran, J Crawley, HB Dong, L Meyer, WT Prell, S Rosenberg, EI Rubin, AE Gao, YY Gritsan, AV Guo, ZJ Arnaud, N Davier, M Derkach, D da Costa, JF Grosdidier, G Le Diberder, F Lutz, AM Malaescu, B Perez, A Roudeau, P Schune, MH Serrano, J Sordini, V Stocchi, A Wang, L Wormser, G Lange, DJ Wright, DM Bingham, I Burke, JP Chavez, CA Coleman, JP Fry, JR Gabathuler, E Gamet, R Hutchcroft, DE Payne, DJ Touramanis, C Bevan, AJ Di Lodovico, F Sacco, R Sigamani, M Cowan, G Paramesvaran, S Wren, AC Brown, DN Davis, CL Denig, AG Fritsch, M Gradl, W Hafner, A Alwyn, KE Bailey, D Barlow, RJ Jackson, G Lafferty, GD West, TJ Anderson, J Cenci, R Jawahery, A Roberts, DA Simi, G Tuggle, JM Dallapiccola, C Salvati, E Cowan, R Dujmic, D Fisher, PH Sciolla, G Zhao, M Lindemann, D Patel, PM Robertson, SH Schram, M Biassoni, P Lazzaro, A Lombardo, V Palombo, F Stracka, S Cremaldi, L Godang, R Kroeger, R Sonnek, P Summers, DJ Zhao, HW Nguyen, X Simard, M Taras, P De Nardo, G Monorchio, D Onorato, G Sciacca, C Raven, G Snoek, HL Jessop, CP Knoepfel, KJ LoSecco, JM Wang, WF Corwin, LA Honscheid, K Kass, R Morris, JP 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TI Observation of the Y(1(3)D(J)) bottomonium state through decays to pi(+)pi Y-(1S) SO PHYSICAL REVIEW D LA English DT Article ID D-WAVE QUARKONIUM; HADRONIC TRANSITIONS AB Based on 122 X 10(6)Y(3S) events collected with the BABAR detector, we have observed the Y(1(3)D(J)) bottomonium state through the Y(3S) -> gamma gamma Y(1(3)D(J)) -> gamma gamma pi(+)pi Y-(1S) decay chain. The significance for the J = 2 member of the Y(1(3)D(J)) triplet is 5.8 standard deviations including systematic uncertainties. The mass of the J = 2 state is determined to be 10 164.5 +/- 0.8(stat) +/- 0.5(syst) MeV/c(2). We use the pi(+)pi(-) invariant mass distribution to confirm the consistency of the observed state with the orbital angular momentum assignment of the Y(1(3)D(J)). C1 [Sanchez, P. del Amo; Lees, J. P.; Poireau, V.; Prencipe, E.; Tisserand, V.] Univ Savoie, LAPP, CNRS, IN2P3, F-74941 Annecy Le Vieux, France. [Tico, J. Garra; Grauges, E.] Univ Barcelona, Fac Fis, Dept ECM, E-08028 Barcelona, Spain. [Martinelli, M.; Palano, A.; Pappagallo, M.] INFN, Sez Bari, I-70126 Bari, Italy. [Martinelli, M.; Palano, A.; Pappagallo, M.] Univ Bari, Dipartimento Fis, I-70126 Bari, Italy. [Eigen, G.; Stugu, B.; Sun, L.] Univ Bergen, Inst Phys, N-5007 Bergen, Norway. [Battaglia, M.; Brown, D. N.; Hooberman, B.; Kerth, L. T.; Kolomensky, Yu. G.; Lynch, G.; Osipenkov, I. L.; Tanabe, T.] Univ Calif Berkeley, Berkeley, CA 94720 USA. [Battaglia, M.; Brown, D. N.; Hooberman, B.; Kerth, L. T.; Kolomensky, Yu. G.; Lynch, G.; Osipenkov, I. L.; Tanabe, T.] Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. [Hawkes, C. M.; Watson, A. T.] Univ Birmingham, Birmingham B15 2TT, W Midlands, England. [Koch, H.; Schroeder, T.] Ruhr Univ Bochum, Inst Expt Phys 1, D-44780 Bochum, Germany. [Asgeirsson, D. J.; Hearty, C.; Mattison, T. S.; McKenna, J. A.] Univ British Columbia, Vancouver, BC V6T 1Z1, Canada. 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R.; Briand, H.; Calderini, G.; Chauveau, J.; Hamon, O.; Leruste, Ph.; Marchiori, G.; Ocariz, J.; Prendki, J.; Sitt, S.] Univ Paris 07, Univ Paris 06, CNRS, Lab Phys Nucl & Hautes Energies,IN2P3, F-75252 Paris, France. [Biasini, M.; Manoni, E.] INFN, Sez Perugia, I-06100 Perugia, Italy. [Peruzzi, I. M.; Biasini, M.; Manoni, E.] Univ Perugia, Dipartimento Fis, I-06100 Perugia, Italy. [Angelini, C.; Batignani, G.; Bettarini, S.; Carpinelli, M.; Casarosa, G.; Cervelli, A.; Forti, F.; Giorgi, M. A.; Lusiani, A.; Neri, N.; Paoloni, E.; Rizzo, G.; Walsh, J. J.] INFN, Sez Pisa, I-56127 Pisa, Italy. [Angelini, C.; Batignani, G.; Bettarini, S.; Carpinelli, M.; Casarosa, G.; Cervelli, A.; Forti, F.; Giorgi, M. A.; Neri, N.; Paoloni, E.; Rizzo, G.] Univ Pisa, Dipartimento Fis, I-56127 Pisa, Italy. [Lusiani, A.] Scuola Normale Super Pisa, I-56127 Pisa, Italy. [Pegna, D. Lopes; Lu, C.; Olsen, J.; Smith, A. J. S.; Telnov, A. V.] Princeton Univ, Princeton, NJ 08544 USA. [Anulli, F.; Baracchini, E.; Cavoto, G.; Faccini, R.; Ferrarotto, F.; Ferroni, F.; Gaspero, M.; Gioi, L. Li; Mazzoni, M. A.; Piredda, G.; Renga, F.] INFN, Sez Roma, I-00185 Rome, Italy. [Baracchini, E.; Faccini, R.; Ferroni, F.; Gaspero, M.; Renga, F.] Univ Roma La Sapienza, Dipartimento Fis, I-00185 Rome, Italy. [Ebert, M.; Hartmann, T.; Leddig, T.; Schroeder, H.; Waldi, R.] Univ Rostock, D-18051 Rostock, Germany. [Adye, T.; Franek, B.; Olaiya, E. O.; Wilson, F. F.] Rutherford Appleton Lab, Didcot OX11 0QX, Oxon, England. [Emery, S.; de Monchenault, G. Hamel; Vasseur, G.; Yeche, Ch.; Zito, M.] CEA, SPP, Ctr Saclay, F-91191 Gif Sur Yvette, France. [Allen, M. T.; Aston, D.; Bard, D. J.; Bartoldus, R.; Benitez, J. F.; Cartaro, C.; Convery, M. R.; Dorfan, J.; Dubois-Felsmann, G. P.; Dunwoodie, W.; Field, R. C.; Sevilla, M. Franco; Fulsom, B. G.; Gabareen, A. M.; Graham, M. T.; Grenier, P.; Hast, C.; Innes, W. R.; Kelsey, M. H.; Kim, H.; Kim, P.; Kocian, M. L.; Leith, D. W. G. S.; Li, S.; Lindquist, B.; Luitz, S.; Luth, V.; Lynch, H. L.; MacFarlane, D. B.; Marsiske, H.; Muller, D. R.; Neal, H.; Nelson, S.; O'Grady, C. P.; Ofte, I.; Perl, M.; Pulliam, T.; Ratcliff, B. N.; Roodman, A.; Salnikov, A. A.; Santoro, V.; Schindler, R. H.; Schwiening, J.; Snyder, A.; Su, D.; Sullivan, M. K.; Sun, S.; Suzuki, K.; Thompson, J. M.; Va'vra, J.; Wagner, A. P.; Weaver, M.; West, C. A.; Wisniewski, W. J.; Wittgen, M.; Wright, D. H.; Wulsin, H. W.; Yarritu, A. K.; Young, C. C.; Ziegler, V.] SLAC Natl Accelerator Lab, Stanford, CA 94309 USA. [Chen, X. R.; Park, W.; Purohit, M. V.; White, R. M.; Wilson, J. R.] Univ S Carolina, Columbia, SC 29208 USA. [Sekula, S. J.] So Methodist Univ, Dallas, TX 75275 USA. [Bellis, M.; Burchat, P. R.; Edwards, A. J.; Miyashita, T. S.] Stanford Univ, Stanford, CA 94305 USA. [Ahmed, S.; Alam, M. S.; Ernst, J. A.; Pan, B.; Saeed, M. A.; Zain, S. B.] SUNY Albany, Albany, NY 12222 USA. [Guttman, N.; Soffer, A.] Tel Aviv Univ, Sch Phys & Astron, IL-69978 Tel Aviv, Israel. [Lund, P.; Spanier, S. M.] Univ Tennessee, Knoxville, TN 37996 USA. [Eckmann, R.; Ritchie, J. L.; Ruland, A. M.; Schilling, C. J.; Schwitters, R. F.; Wray, B. C.] Univ Texas Austin, Austin, TX 78712 USA. [Izen, J. M.; Lou, X. C.] Univ Texas Dallas, Richardson, TX 75083 USA. [Bianchi, F.; Gamba, D.; Pelliccioni, M.] INFN, Sez Torino, I-10125 Turin, Italy. [Bianchi, F.; Gamba, D.; Pelliccioni, M.] Univ Turin, Dipartimento Fis Sperimentale, I-10125 Turin, Italy. [Bomben, M.; Lanceri, L.; Vitale, L.] INFN, Sez Trieste, I-34127 Trieste, Italy. [Bomben, M.; Lanceri, L.; Vitale, L.] Univ Trieste, Dipartimento Fis, I-34127 Trieste, Italy. [Lopez-March, N.; Martinez-Vidal, F.; Milanes, D. A.; Oyanguren, A.] Univ Valencia, CSIC, IFIC, E-46071 Valencia, Spain. [Albert, J.; Banerjee, Sw.; Choi, H. H. F.; Hamano, K.; King, G. J.; Kowalewski, R.; Lewczuk, M. J.; Nugent, I. M.; Roney, J. M.; Sobie, R. J.] Univ Victoria, Victoria, BC V8W 3P6, Canada. [Gershon, T. J.; Harrison, P. F.; Ilic, J.; Latham, T. E.; Puccio, E. M. T.] Univ Warwick, Dept Phys, Coventry CV4 7AL, W Midlands, England. [Band, H. R.; Chen, X.; Dasu, S.; Flood, K. T.; Pan, Y.; Prepost, R.; Vuosalo, C. O.; Wu, S. L.] Univ Wisconsin, Madison, WI 53706 USA. [Carpinelli, M.] Univ Sassari, I-07100 Sassari, Italy. RP Sanchez, PD (reprint author), Univ Savoie, LAPP, CNRS, IN2P3, F-74941 Annecy Le Vieux, France. RI Neri, Nicola/G-3991-2012; Calabrese, Roberto/G-4405-2015; Forti, Francesco/H-3035-2011; Rotondo, Marcello/I-6043-2012; de Sangro, Riccardo/J-2901-2012; Saeed, Mohammad Alam/J-7455-2012; Negrini, Matteo/C-8906-2014; Patrignani, Claudia/C-5223-2009; Monge, Maria Roberta/G-9127-2012; Oyanguren, Arantza/K-6454-2014; Luppi, Eleonora/A-4902-2015; White, Ryan/E-2979-2015; Martinez Vidal, F*/L-7563-2014; Kolomensky, Yury/I-3510-2015; Lo Vetere, Maurizio/J-5049-2012; Lusiani, Alberto/N-2976-2015; Morandin, Mauro/A-3308-2016; Lusiani, Alberto/A-3329-2016; Stracka, Simone/M-3931-2015; Di Lodovico, Francesca/L-9109-2016; Pappagallo, Marco/R-3305-2016; Calcaterra, Alessandro/P-5260-2015; Frey, Raymond/E-2830-2016 OI Neri, Nicola/0000-0002-6106-3756; Calabrese, Roberto/0000-0002-1354-5400; Forti, Francesco/0000-0001-6535-7965; Rotondo, Marcello/0000-0001-5704-6163; de Sangro, Riccardo/0000-0002-3808-5455; Saeed, Mohammad Alam/0000-0002-3529-9255; Negrini, Matteo/0000-0003-0101-6963; Patrignani, Claudia/0000-0002-5882-1747; Monge, Maria Roberta/0000-0003-1633-3195; Oyanguren, Arantza/0000-0002-8240-7300; Luppi, Eleonora/0000-0002-1072-5633; White, Ryan/0000-0003-3589-5900; Martinez Vidal, F*/0000-0001-6841-6035; Kolomensky, Yury/0000-0001-8496-9975; Lo Vetere, Maurizio/0000-0002-6520-4480; Lusiani, Alberto/0000-0002-6876-3288; Morandin, Mauro/0000-0003-4708-4240; Lusiani, Alberto/0000-0002-6876-3288; Stracka, Simone/0000-0003-0013-4714; Di Lodovico, Francesca/0000-0003-3952-2175; Pappagallo, Marco/0000-0001-7601-5602; Calcaterra, Alessandro/0000-0003-2670-4826; Frey, Raymond/0000-0003-0341-2636 FU DOE; NSF (USA); NSERC (Canada); CEA; CNRS-IN2P3 (France); BMBF; DFG (Germany); INFN (Italy); FOM (The Netherlands); NFR (Norway); MES (Russia); MEC (Spain); STFC (United Kingdom); Marie Curie EIF (European Union); A. P. Sloan Foundation FX We are grateful for the excellent luminosity and machine conditions provided by our PEP-II colleagues and for the substantial dedicated effort from the computing organizations that support BABAR. The collaborating institutions thank SLAC for its support and kind hospitality. This work is supported by DOE and NSF (USA), NSERC (Canada), CEA and CNRS-IN2P3 (France), BMBF and DFG (Germany), INFN (Italy), FOM (The Netherlands), NFR (Norway), MES (Russia), MEC (Spain), and STFC (United Kingdom). Individuals have received support from the Marie Curie EIF (European Union) and the A. P. Sloan Foundation. NR 24 TC 20 Z9 20 U1 1 U2 11 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 2470-0010 EI 2470-0029 J9 PHYS REV D JI Phys. Rev. D PD DEC 22 PY 2010 VL 82 IS 11 AR 111102 DI 10.1103/PhysRevD.82.111102 PG 7 WC Astronomy & Astrophysics; Physics, Particles & Fields SC Astronomy & Astrophysics; Physics GA 711HH UT WOS:000286577200001 ER PT J AU Avakian, H Bosted, P Burkert, VD Elouadrhiri, L Adhikari, KP Aghasyan, M Amaryan, M Anghinolfi, M Baghdasaryan, H Ball, J Battaglieri, M Bedlinskiy, I Biselli, AS Branford, D Briscoe, WJ Brooks, W Carman, DS Casey, L Cole, PL Collins, P Crabb, D Crede, V D'Angelo, A Daniel, A Dashyan, N De Vita, R De Sanctis, E Deur, A Dey, B Dhamija, S Dickson, R Djalali, C Dodge, G Doughty, D Dupre, R El Alaoui, A Eugenio, P Fegan, S Fersch, R Forest, TA Fradi, A Gabrielyan, MY Gavalian, G Gevorgyan, N Gilfoyle, GP Giovanetti, KL Girod, FX Gohn, W Gothe, RW Griffioen, KA Guidal, M Guler, N Guo, L Hafidi, K Hakobyan, H Hanretty, C Hassall, N Heddle, D Hicks, K Holtrop, M Ilieva, Y Ireland, DG Isupov, EL Jawalkar, SS Jo, HS Joo, K Keller, D Khandaker, M Khetarpal, P Kim, W Klein, A Klein, FJ Konczykowski, P Kubarovsky, V Kuhn, SE Kuleshov, SV Kuznetsov, V Livingston, K Lu, HY Markov, N Mayer, M Martinez, D McAndrew, J McCracken, ME McKinnon, B Meyer, CA Mineeva, T Mirazita, M Mokeev, V Moreno, B Moriya, K Morrison, B Moutarde, H Munevar, E Nadel-Turonski, P Nasseripour, R Niccolai, S Niculescu, G Niculescu, I Niroula, MR Osipenko, M Ostrovidov, AI Paremuzyan, R Park, K Park, S Pasyuk, E Pereira, SA Perrin, Y Pisano, S Pogorelko, O Price, JW Procureur, S Prok, Y Protopopescu, D Raue, BA Ricco, G Ripani, M Rosner, G Rossi, P Sabatic, F Saini, MS Salamanca, J Salgado, C Schumacher, RA Seder, E Seraydaryan, H Sharabian, YG Sober, DI Sokhan, D Stepanyan, SS Stepanyan, S Stoler, P Strauch, S Suleiman, R Taiuti, M Tedeschi, DJ Tkachenko, S Ungaro, M Vernarsky, B Vineyard, MF Voutier, E Watts, DP Weinstein, LB Weygand, DP Wood, MH Zhang, J Zhao, B Zhao, ZW AF Avakian, H. Bosted, P. Burkert, V. D. Elouadrhiri, L. Adhikari, K. P. Aghasyan, M. Amaryan, M. Anghinolfi, M. Baghdasaryan, H. Ball, J. Battaglieri, M. Bedlinskiy, I. Biselli, A. S. Branford, D. Briscoe, W. J. Brooks, W. Carman, D. S. Casey, L. Cole, P. L. Collins, P. Crabb, D. Crede, V. D'Angelo, A. Daniel, A. Dashyan, N. De Vita, R. De Sanctis, E. Deur, A. Dey, B. Dhamija, S. Dickson, R. Djalali, C. Dodge, G. Doughty, D. Dupre, R. El Alaoui, A. Eugenio, P. Fegan, S. Fersch, R. Forest, T. A. Fradi, A. Gabrielyan, M. Y. Gavalian, G. Gevorgyan, N. Gilfoyle, G. P. Giovanetti, K. L. Girod, F. X. Gohn, W. Gothe, R. W. Griffioen, K. A. Guidal, M. Guler, N. Guo, L. Hafidi, K. Hakobyan, H. Hanretty, C. Hassall, N. Heddle, D. Hicks, K. Holtrop, M. Ilieva, Y. Ireland, D. G. Isupov, E. L. Jawalkar, S. S. Jo, H. S. Joo, K. Keller, D. Khandaker, M. Khetarpal, P. Kim, W. Klein, A. Klein, F. J. Konczykowski, P. Kubarovsky, V. Kuhn, S. E. Kuleshov, S. V. Kuznetsov, V. Livingston, K. Lu, H. Y. Markov, N. Mayer, M. Martinez, D. McAndrew, J. McCracken, M. E. McKinnon, B. Meyer, C. A. Mineeva, T. Mirazita, M. Mokeev, V. Moreno, B. Moriya, K. Morrison, B. Moutarde, H. Munevar, E. Nadel-Turonski, P. Nasseripour, R. Niccolai, S. Niculescu, G. Niculescu, I. Niroula, M. R. Osipenko, M. Ostrovidov, A. I. Paremuzyan, R. Park, K. Park, S. Pasyuk, E. Pereira, S. Anefalos Perrin, Y. Pisano, S. Pogorelko, O. Price, J. W. Procureur, S. Prok, Y. Protopopescu, D. Raue, B. A. Ricco, G. Ripani, M. Rosner, G. Rossi, P. Sabatic, F. Saini, M. S. Salamanca, J. Salgado, C. Schumacher, R. A. Seder, E. Seraydaryan, H. Sharabian, Y. G. Sober, D. I. Sokhan, D. Stepanyan, S. S. Stepanyan, S. Stoler, P. Strauch, S. Suleiman, R. Taiuti, M. Tedeschi, D. J. Tkachenko, S. Ungaro, M. Vernarsky, B. Vineyard, M. F. Voutier, E. Watts, D. P. Weinstein, L. B. Weygand, D. P. Wood, M. H. Zhang, J. Zhao, B. Zhao, Z. W. CA CLAS Collaboration TI Measurement of Single- and Double-Spin Asymmetries in Deep Inelastic Pion Electroproduction with a Longitudinally Polarized Target SO PHYSICAL REVIEW LETTERS LA English DT Article ID FINAL-STATE INTERACTIONS; TRANSVERSE-MOMENTUM; AZIMUTHAL ASYMMETRIES; DRELL-YAN; SCATTERING; DISTRIBUTIONS; QUARK; DEPENDENCE; CLAS; QCD AB We report the first measurement of the transverse momentum dependence of double-spin asymmetries in semi-inclusive production of pions in deep-inelastic scattering off the longitudinally polarized proton. Data have been obtained using a polarized electron beam of 5.7 GeV with the CLAS detector at the Jefferson Lab (JLab). Modulations of single spin asymmetries over the azimuthal angle between lepton scattering and hadron production planes phi have been measured over a wide kinematic range in Bjorken x and virtual photon squared four-momentum Q(2). A significant nonzero sin2 phi single spin asymmetry was observed for the first time indicating strong spin-orbit correlations for transversely polarized quarks in the longitudinally polarized proton. C1 [Avakian, H.; Bosted, P.; Burkert, V. D.; Elouadrhiri, L.; Brooks, W.; Carman, D. S.; Cole, P. L.; Deur, A.; Doughty, D.; Guo, L.; Heddle, D.; Joo, K.; Klein, F. J.; Kubarovsky, V.; Mokeev, V.; Nadel-Turonski, P.; Raue, B. A.; Sharabian, Y. G.; Stepanyan, S.; Weygand, D. P.] Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. [Dupre, R.; El Alaoui, A.; Hafidi, K.] Argonne Natl Lab, Argonne, IL 60441 USA. [Collins, P.; Morrison, B.; Pasyuk, E.] Arizona State Univ, Tempe, AZ 85287 USA. [Price, J. W.] Calif State Univ Dominguez Hills, Carson, CA 90747 USA. [Wood, M. H.] Canisius Coll, Buffalo, NY 14208 USA. [Dey, B.; Dickson, R.; McCracken, M. E.; Meyer, C. A.; Moriya, K.; Schumacher, R. A.; Vernarsky, B.] Carnegie Mellon Univ, Pittsburgh, PA 15213 USA. [Casey, L.; Klein, F. J.; Sober, D. I.] Catholic Univ Amer, Washington, DC 20064 USA. [Ball, J.; Girod, F. X.; Konczykowski, P.; Moreno, B.; Moutarde, H.; Procureur, S.; Sabatic, F.] CEA, Ctr Saclay, Irfu Serv Phys Nucl, F-91191 Gif Sur Yvette, France. [Doughty, D.; Heddle, D.; Stepanyan, S.] Christopher Newport Univ, Newport News, VA 23606 USA. [Gohn, W.; Joo, K.; Markov, N.; Mineeva, T.; Seder, E.; Ungaro, M.; Zhao, B.] Univ Connecticut, Storrs, CT 06269 USA. [Branford, D.; McAndrew, J.; Sokhan, D.; Watts, D. P.] Univ Edinburgh, Edinburgh EH9 3JZ, Midlothian, Scotland. [Biselli, A. S.] Fairfield Univ, Fairfield, CT 06824 USA. [Dhamija, S.; Gabrielyan, M. Y.; Raue, B. A.] Florida Int Univ, Miami, FL 33199 USA. [Crede, V.; Eugenio, P.; Hanretty, C.; Ostrovidov, A. I.; Park, S.; Saini, M. S.] Florida State Univ, Tallahassee, FL 32306 USA. [Briscoe, W. J.; Munevar, E.; Niculescu, I.] George Washington Univ, Washington, DC 20052 USA. [Cole, P. L.; Forest, T. A.; Mayer, M.; Martinez, D.; Salamanca, J.] Idaho State Univ, Pocatello, ID 83209 USA. [Aghasyan, M.; De Sanctis, E.; Mirazita, M.; Pereira, S. Anefalos; Rossi, P.] INFN, Lab Nazl Frascati, I-00044 Frascati, Italy. [Anghinolfi, M.; Battaglieri, M.; De Vita, R.; Osipenko, M.; Ricco, G.; Ripani, M.; Taiuti, M.] INFN, Sez Genova, I-16146 Genoa, Italy. [D'Angelo, A.] INFN, Sez Roma Tor Vergata, I-00133 Rome, Italy. [Fradi, A.; Guidal, M.; Jo, H. S.; Niccolai, S.; Pisano, S.] Inst Phys Nucl ORSAY, Orsay, France. [Bedlinskiy, I.; Kuleshov, S. V.; Pogorelko, O.] Inst Theoret & Expt Phys, Moscow 117259, Russia. [Giovanetti, K. L.; Niculescu, G.; Niculescu, I.] James Madison Univ, Harrisonburg, VA 22807 USA. [Kim, W.; Kuznetsov, V.; Park, K.; Stepanyan, S. S.] Kyungpook Natl Univ, Taegu 702701, South Korea. [Perrin, Y.; Voutier, E.] Univ Grenoble 1, CNRS, IN2P3, LPSC,INPG, Grenoble, France. [Suleiman, R.] MIT, Cambridge, MA 02139 USA. [Holtrop, M.] Univ New Hampshire, Durham, NH 03824 USA. [Khandaker, M.; Salgado, C.] Norfolk State Univ, Norfolk, VA 23504 USA. [Daniel, A.; Hicks, K.; Keller, D.; Niculescu, G.] Ohio Univ, Athens, OH 45701 USA. [Adhikari, K. P.; Amaryan, M.; Dodge, G.; Forest, T. A.; Gavalian, G.; Guler, N.; Klein, A.; Kuhn, S. E.; Mayer, M.; Martinez, D.; Niroula, M. R.; Sabatic, F.; Seraydaryan, H.; Tkachenko, S.; Weinstein, L. B.; Zhang, J.] Old Dominion Univ, Norfolk, VA 23529 USA. [Biselli, A. S.; Khetarpal, P.; Stoler, P.] Rensselaer Polytech Inst, Troy, NY 12180 USA. [Gilfoyle, G. P.; Vineyard, M. F.] Univ Richmond, Richmond, VA 23173 USA. [D'Angelo, A.] Univ Roma Tor Vergata, I-00133 Rome, Italy. [Isupov, E. L.; Mokeev, V.] Skobeltsyn Nucl Phys Inst, Moscow 119899, Russia. [Djalali, C.; Gothe, R. W.; Ilieva, Y.; Lu, H. Y.; Nasseripour, R.; Park, K.; Strauch, S.; Tedeschi, D. J.; Zhao, Z. W.] Univ S Carolina, Columbia, SC 29208 USA. [Vineyard, M. F.] Union Coll, Schenectady, NY 12308 USA. [Hakobyan, H.; Joo, K.; Kuleshov, S. V.] Univ Tecn Federico Santa Maria, Valparaiso, Chile. [Fegan, S.; Hassall, N.; Ireland, D. G.; Livingston, K.; McKinnon, B.; Protopopescu, D.; Rosner, G.] Univ Glasgow, Glasgow G12 8QQ, Lanark, Scotland. [Baghdasaryan, H.; Crabb, D.; Prok, Y.] Univ Virginia, Charlottesville, VA 22901 USA. [Fersch, R.; Griffioen, K. A.; Jawalkar, S. S.] Coll William & Mary, Williamsburg, VA 23187 USA. [Dashyan, N.; Gevorgyan, N.; Hakobyan, H.; Paremuzyan, R.; Sharabian, Y. G.; Stepanyan, S.] Yerevan Phys Inst, Yerevan 375036, Armenia. RP Avakian, H (reprint author), Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. RI Osipenko, Mikhail/N-8292-2015; Zhang, Jixie/A-1461-2016; Meyer, Curtis/L-3488-2014; El Alaoui, Ahmed/B-4638-2015; Ireland, David/E-8618-2010; Lu, Haiyun/B-4083-2012; Protopopescu, Dan/D-5645-2012; Isupov, Evgeny/J-2976-2012; Zhao, Bo/J-6819-2012; Brooks, William/C-8636-2013; Sabatie, Franck/K-9066-2015; Kuleshov, Sergey/D-9940-2013; Schumacher, Reinhard/K-6455-2013; D'Angelo, Annalisa/A-2439-2012 OI Osipenko, Mikhail/0000-0001-9618-3013; Meyer, Curtis/0000-0001-7599-3973; Ireland, David/0000-0001-7713-7011; Zhao, Bo/0000-0003-3171-5335; Brooks, William/0000-0001-6161-3570; Sabatie, Franck/0000-0001-7031-3975; Kuleshov, Sergey/0000-0002-3065-326X; Schumacher, Reinhard/0000-0002-3860-1827; D'Angelo, Annalisa/0000-0003-3050-4907 FU U.S. Department of Energy; National Science Foundation; Italian Istituto Nazionale di Fisica Nucleare; French Centre National de la Recherche Scientifique; French Commissariat a l'Energie Atomique; National Research Foundation of Korea; United States Department of Energy [DE-AC05-06OR23177] FX We thank A. Afanasev, S. Brodsky, A. Kotzinian, and P. Schweitzer for stimulating discussions. We would like to acknowledge the outstanding efforts of the staff of the Accelerator and the Physics Divisions at JLab that made this experiment possible. This work was supported in part by the U.S. Department of Energy and the National Science Foundation, the Italian Istituto Nazionale di Fisica Nucleare, the French Centre National de la Recherche Scientifique, the French Commissariat a l'Energie Atomique, and the National Research Foundation of Korea. The Southeastern Universities Research Association (SURA) operates the Thomas Jefferson National Accelerator Facility for the United States Department of Energy under Contract No. DE-AC05-06OR23177. NR 48 TC 49 Z9 49 U1 1 U2 6 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 0031-9007 J9 PHYS REV LETT JI Phys. Rev. Lett. PD DEC 22 PY 2010 VL 105 IS 26 AR 262002 DI 10.1103/PhysRevLett.105.262002 PG 5 WC Physics, Multidisciplinary SC Physics GA 713SD UT WOS:000286756800006 PM 21231647 ER PT J AU Jiang, YH Rudenko, A Herrwerth, O Foucar, L Kurka, M Kuhnel, KU Lezius, M Kling, MF van Tilborg, J Belkacem, A Ueda, K Dusterer, S Treusch, R Schroter, CD Moshammer, R Ullrich, J AF Jiang, Y. H. Rudenko, A. Herrwerth, O. Foucar, L. Kurka, M. Kuehnel, K. U. Lezius, M. Kling, M. F. van Tilborg, J. Belkacem, A. Ueda, K. Duesterer, S. Treusch, R. Schroeter, C. D. Moshammer, R. Ullrich, J. TI Ultrafast Extreme Ultraviolet Induced Isomerization of Acetylene Cations SO PHYSICAL REVIEW LETTERS LA English DT Article ID FREE-ELECTRON LASER; MOLECULAR-IONS; PHOTOIONIZATION; DISSOCIATION; SPECTROSCOPY; VINYLIDENE; DYNAMICS; DICATION; ENERGY; STATES AB Ultrafast isomerization of acetylene cations (inverted right perpendicular HC = CH inverted left perpendicular(+)) in the low-lying excited A(2)Sigma(+)(g) state, populated by the absorption of extreme ultraviolet (XUV) photons (38 eV), has been observed at the Free Electron Laser in Hamburg, (FLASH). Recording coincident fragments C(+) + CH(2)(+) as a function of time between XUV-pump and -probe pulses, generated by a split-mirror device, we find an isomerization time of 52 +/- 15 fs in a kinetic energy release (KER) window of 5.8 < KER < 8 eV, providing clear evidence for the existence of a fast, nonradiative decay channel. C1 [Jiang, Y. H.; Kurka, M.; Kuehnel, K. U.; Schroeter, C. D.; Moshammer, R.; Ullrich, J.] Max Planck Inst Kernphys, D-69117 Heidelberg, Germany. [Rudenko, A.; Foucar, L.; Ullrich, J.] CFEL, Max Planck Adv Study Grp, D-22607 Hamburg, Germany. [Herrwerth, O.; Lezius, M.; Kling, M. F.] Max Planck Inst Quantum Opt, D-85748 Garching, Germany. [van Tilborg, J.; Belkacem, A.] Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA. [Ueda, K.] Tohoku Univ, Inst Multidisciplinary Res Adv Mat, Sendai, Miyagi 9808577, Japan. [Duesterer, S.; Treusch, R.] DESY, D-22607 Hamburg, Germany. RP Jiang, YH (reprint author), Max Planck Inst Kernphys, D-69117 Heidelberg, Germany. RI Rudenko, Artem/C-7412-2009; Kling, Matthias/D-3742-2014; Treusch, Rolf/C-3935-2015; OI Rudenko, Artem/0000-0002-9154-8463; Treusch, Rolf/0000-0001-8479-8862 FU Max-Planck Advanced Study Group at CFEL; DFG [JI 110/2]; Cluster of Excellence: Munich Center for Advanced Photonics FX The authors are greatly indebted to the scientific and technical team at FLASH. Support from the Max-Planck Advanced Study Group at CFEL is gratefully acknowledged. Y.H.J. acknowledges support from DFG Project No. JI 110/2, O. H., M. L., and M. F. K. from the DFG via the Emmy-Noether program and the Cluster of Excellence: Munich Center for Advanced Photonics. NR 26 TC 77 Z9 78 U1 3 U2 50 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 0031-9007 J9 PHYS REV LETT JI Phys. Rev. Lett. PD DEC 22 PY 2010 VL 105 IS 26 AR 263002 DI 10.1103/PhysRevLett.105.263002 PG 4 WC Physics, Multidisciplinary SC Physics GA 713SD UT WOS:000286756800008 PM 21231652 ER PT J AU Close, S Colestock, P Cox, L Kelley, M Lee, N AF Close, S. Colestock, P. Cox, L. Kelley, M. Lee, N. TI Electromagnetic pulses generated by meteoroid impacts on spacecraft SO JOURNAL OF GEOPHYSICAL RESEARCH-SPACE PHYSICS LA English DT Article ID PLASMA; DEBRIS AB Meteoroid impacts on spacecraft are known to cause mechanical damage, but their electrical effect on spacecraft systems are not well characterized. Several reported spacecraft anomalies are suggestive of an electrical failure associated with meteoroid impact. We present a theory to explain plasma production and subsequent electric fields occurring when a meteoroid strikes a spacecraft, ionizing itself and part of the spacecraft. This plasma, with a charge separation commensurate with different specie mobilities, can produce a strong electromagnetic pulse (EMP) at broad frequency spectra, potentially causing catastrophic damage if the impact is relatively near an area with low shielding or an open umbilical. Anomalies such as gyrostability loss can be caused by an EMP without any detectable momentum transfer due to small (<1 mu g) particle mass. Subsequent plasma oscillations can also emit significant power and may be responsible for many reported satellite anomalies. The presented theory discusses both a dust-free plasma expansion with coherent electron oscillation and a dusty plasma expansion with macroscopic charge separation. C1 [Close, S.; Lee, N.] Stanford Univ, Dept Aeronaut & Astronaut, Stanford, CA 94305 USA. [Colestock, P.; Cox, L.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. [Kelley, M.] Cornell Univ, Sch Elect & Comp Engn, Ithaca, NY 14853 USA. RP Close, S (reprint author), Stanford Univ, Dept Aeronaut & Astronaut, 496 Lomita Mall, Stanford, CA 94305 USA. EM sigridc@stanford.edu OI Lee, Nicolas/0000-0001-5500-1324 NR 20 TC 27 Z9 27 U1 1 U2 3 PU AMER GEOPHYSICAL UNION PI WASHINGTON PA 2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA SN 0148-0227 J9 J GEOPHYS RES-SPACE JI J. Geophys. Res-Space Phys. PD DEC 21 PY 2010 VL 115 AR A12328 DI 10.1029/2010JA015921 PG 7 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA 699BQ UT WOS:000285639300013 ER PT J AU Szarko, JM Guo, JC Liang, YY Lee, B Rolczynski, BS Strzalka, J Xu, T Loser, S Marks, TJ Yu, LP Chen, LX AF Szarko, Jodi M. Guo, Jianchang Liang, Yongye Lee, Byeongdu Rolczynski, Brian S. Strzalka, Joseph Xu, Tao Loser, Stephen Marks, Tobin J. Yu, Luping Chen, Lin X. TI When Function Follows Form: Effects of Donor Copolymer Side Chains on Film Morphology and BHJ Solar Cell Performance SO ADVANCED MATERIALS LA English DT Article ID POWER CONVERSION EFFICIENCY; ORGANIC PHOTOVOLTAIC CELLS; INTERFACIAL LAYER; POLYMERS; TRANSPORT; OXIDE AB Detailed structural organization in organic films are investigated using grazing incidence X-ray scattering (GIXS) methods. The key structural features are revealed and the influence of specific side chain positions and shapes are characterized. A correlation between the fill factor (FF) of the corresponding device and the tightness of the polymer chain stacking inspires a new set of structural parameters for design of materials to optimize device efficiency. [GRAPHICS] . C1 [Szarko, Jodi M.; Rolczynski, Brian S.; Loser, Stephen; Marks, Tobin J.; Chen, Lin X.] Northwestern Univ, Dept Chem, Evanston, IL 60208 USA. [Szarko, Jodi M.; Guo, Jianchang; Rolczynski, Brian S.; Chen, Lin X.] Argonne Natl Lab, Chem Sci & Engn Div, Argonne, IL 60439 USA. [Szarko, Jodi M.; Guo, Jianchang; Rolczynski, Brian S.; Loser, Stephen; Marks, Tobin J.; Chen, Lin X.] Northwestern Univ, Argonne NW Solar Energy Res ANSER Ctr, Evanston, IL 60208 USA. [Guo, Jianchang; Liang, Yongye; Xu, Tao; Yu, Luping] Univ Chicago, Dept Chem, Chicago, IL 60637 USA. [Guo, Jianchang; Liang, Yongye; Xu, Tao; Yu, Luping] Univ Chicago, James Franck Inst, Chicago, IL 60637 USA. [Lee, Byeongdu; Strzalka, Joseph] Argonne Natl Lab, Xray Sci Div, Argonne, IL 60439 USA. RP Marks, TJ (reprint author), Northwestern Univ, Dept Chem, 2145 Sheridan Rd, Evanston, IL 60208 USA. EM t-marks@northwestern.edu; lupingyu@uchicago.edu; lchen@anl.gov RI Liang, Yongye/D-1099-2010; Yang, Zengchao/H-3884-2011; Liang, Yongye/D-9275-2012; OI Szarko, Jodi/0000-0002-2181-9408; Lee, Byeongdu/0000-0003-2514-8805 FU U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences [DE-SC0001059]; Division of Chemical Sciences, Office of Basic Energy Sciences, the U.S. Department of Energy [DE-AC02-06CH11357]; National Science Foundation; AFOSR FX This research is supported by the ANSER Center, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Award Number DE-SC0001059, and the Division of Chemical Sciences, Office of Basic Energy Sciences, the U.S. Department of Energy under contract DE-AC02-06CH11357 (for L. X. C.). The synthesis of polymers is also supported by the National Science Foundation, AFOSR, and the NSF MRSEC program at the University of Chicago (L.Y.). The authors would also like to thank Sonke Seifert for help with the X-ray scattering experiments. NR 28 TC 223 Z9 223 U1 8 U2 106 PU WILEY-BLACKWELL PI MALDEN PA COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA SN 0935-9648 J9 ADV MATER JI Adv. Mater. PD DEC 21 PY 2010 VL 22 IS 48 BP 5468 EP 5472 DI 10.1002/adma.201002687 PG 5 WC Chemistry, Multidisciplinary; Chemistry, Physical; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary; Physics, Applied; Physics, Condensed Matter SC Chemistry; Science & Technology - Other Topics; Materials Science; Physics GA 695UF UT WOS:000285397400004 PM 21089063 ER PT J AU Antezana, E Venkatesan, A Mungall, C Mironov, V Kuiper, M AF Antezana, Erick Venkatesan, Aravind Mungall, Chris Mironov, Vladimir Kuiper, Martin TI ONTO-ToolKit: enabling bio-ontology engineering via Galaxy SO BMC BIOINFORMATICS LA English DT Article; Proceedings Paper CT 11th Annual Bioinformatics Open Source Conference (BOSC) CY JUL 09-10, 2010 CL Boston, MA ID DATA INTEGRATION; BIOINFORMATICS; BIOLOGY AB Background: The biosciences increasingly face the challenge of integrating a wide variety of available data, information and knowledge in order to gain an understanding of biological systems. Data integration is supported by a diverse series of tools, but the lack of a consistent terminology to label these data still presents significant hurdles. As a consequence, much of the available biological data remains disconnected or worse: becomes misconnected. The need to address this terminology problem has spawned the building of a large number of bio-ontologies. OBOF, RDF and OWL are among the most used ontology formats to capture terms and relationships in the Life Sciences, opening the potential to use the Semantic Web to support data integration and further exploitation of integrated resources via automated retrieval and reasoning procedures. Methods: We extended the Perl suite ONTO-PERL and functionally integrated it into the Galaxy platform. The resulting ONTO-ToolKit supports the analysis and handling of OBO-formatted ontologies via the Galaxy interface, and we demonstrated its functionality in different use cases that illustrate the flexibility to obtain sets of ontology terms that match specific search criteria. Results: ONTO-ToolKit is available as a tool suite for Galaxy. Galaxy not only provides a user friendly interface allowing the interested biologist to manipulate OBO ontologies, it also opens up the possibility to perform further biological (and ontological) analyses by using other tools available within the Galaxy environment. Moreover, it provides tools to translate OBO-formatted ontologies into Semantic Web formats such as RDF and OWL. Conclusions: ONTO-ToolKit reaches out to researchers in the biosciences, by providing a user-friendly way to analyse and manipulate ontologies. This type of functionality will become increasingly important given the wealth of information that is becoming available based on ontologies. C1 [Antezana, Erick; Venkatesan, Aravind; Mironov, Vladimir; Kuiper, Martin] Norwegian Univ Sci & Technol NTNU, Dept Biol, N-7491 Trondheim, Norway. [Mungall, Chris] Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA. RP Antezana, E (reprint author), Norwegian Univ Sci & Technol NTNU, Dept Biol, Hogskoleringen 5, N-7491 Trondheim, Norway. EM erick.antezana@bio.ntnu.no OI Antezana, Erick/0000-0002-2497-8236; Kuiper, Martin/0000-0002-1171-9876 NR 23 TC 2 Z9 2 U1 1 U2 3 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1471-2105 J9 BMC BIOINFORMATICS JI BMC Bioinformatics PD DEC 21 PY 2010 VL 11 SU 12 AR S8 DI 10.1186/1471-2105-11-S12-S8 PG 9 WC Biochemical Research Methods; Biotechnology & Applied Microbiology; Mathematical & Computational Biology SC Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Mathematical & Computational Biology GA 759DA UT WOS:000290219600008 PM 21210987 ER PT J AU Taylor, RC AF Taylor, Ronald C. TI An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics SO BMC BIOINFORMATICS LA English DT Article; Proceedings Paper CT 11th Annual Bioinformatics Open Source Conference (BOSC) CY JUL 09-10, 2010 CL Boston, MA ID CLOUD; MAPREDUCE AB Background: Bioinformatics researchers are now confronted with analysis of ultra large-scale data sets, a problem that will only increase at an alarming rate in coming years. Recent developments in open source software, that is, the Hadoop project and associated software, provide a foundation for scaling to petabyte scale data warehouses on Linux clusters, providing fault-tolerant parallelized analysis on such data using a programming style named MapReduce. Description: An overview is given of the current usage within the bioinformatics community of Hadoop, a top-level Apache Software Foundation project, and of associated open source software projects. The concepts behind Hadoop and the associated HBase project are defined, and current bioinformatics software that employ Hadoop is described. The focus is on next-generation sequencing, as the leading application area to date. Conclusions: Hadoop and the MapReduce programming paradigm already have a substantial base in the bioinformatics community, especially in the field of next-generation sequencing analysis, and such use is increasing. This is due to the cost-effectiveness of Hadoop-based analysis on commodity Linux clusters, and in the cloud via data upload to cloud vendors who have implemented Hadoop/HBase; and due to the effectiveness and ease-of-use of the MapReduce method in parallelization of many data analysis algorithms. C1 Pacific NW Natl Lab, Computat Biol & Bioinformat Grp, Richland, WA 99352 USA. RP Taylor, RC (reprint author), Pacific NW Natl Lab, Computat Biol & Bioinformat Grp, Richland, WA 99352 USA. EM ronald.taylor@pnl.gov OI Taylor, Ronald/0000-0001-9777-9767 NR 42 TC 112 Z9 122 U1 13 U2 147 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1471-2105 J9 BMC BIOINFORMATICS JI BMC Bioinformatics PD DEC 21 PY 2010 VL 11 SU 12 AR S1 DI 10.1186/1471-2105-11-S12-S1 PG 6 WC Biochemical Research Methods; Biotechnology & Applied Microbiology; Mathematical & Computational Biology SC Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Mathematical & Computational Biology GA 759DA UT WOS:000290219600001 PM 21210976 ER PT J AU Dong, X Horn, B Silverstein, E Torroba, G AF Dong, Xi Horn, Bart Silverstein, Eva Torroba, Gonzalo TI Micromanaging de Sitter holography SO CLASSICAL AND QUANTUM GRAVITY LA English DT Article ID FLUX COMPACTIFICATIONS; STRING THEORY; COSMOLOGICAL CONSTANT AB We develop tools to engineer de Sitter vacua with semi-holographic duals, using elliptic fibrations and orientifolds to uplift Freund-Rubin compactifications with CFT duals. The dual brane construction is compact and constitutes a microscopic realization of the dS/dS correspondence, realizing d-dimensional de Sitter space as a warped compactification down to (d - 1)-dimensional de Sitter gravity coupled to a pair of large-N matter sectors. This provides a parametric microscopic interpretation of the Gibbons-Hawking entropy. We illustrate these ideas with an explicit class of examples in three dimensions, and describe ongoing work on four-dimensional constructions. C1 [Dong, Xi; Horn, Bart; Silverstein, Eva; Torroba, Gonzalo] Univ Calif Santa Barbara, Kavli Inst Theoret Phys, Santa Barbara, CA 93106 USA. [Dong, Xi; Horn, Bart; Silverstein, Eva; Torroba, Gonzalo] Univ Calif Santa Barbara, Dept Phys, Santa Barbara, CA 93106 USA. [Dong, Xi; Horn, Bart; Silverstein, Eva; Torroba, Gonzalo] Stanford Univ, SLAC, Stanford, CA 94305 USA. [Dong, Xi; Horn, Bart; Silverstein, Eva; Torroba, Gonzalo] Stanford Univ, Dept Phys, Stanford, CA 94305 USA. RP Dong, X (reprint author), Univ Calif Santa Barbara, Kavli Inst Theoret Phys, Santa Barbara, CA 93106 USA. EM xidong@stanford.edu; bhorn@stanford.edu; evas@stanford.edu; torrobag@slac.stanford.edu FU National Science Foundation [PHY05-51164]; UCSB Department of Physics; DOE [DE-AC03-76SF00515]; William K Bowes Jr Stanford Graduate Fellowship FX We are grateful to Joe Polchinski for many interesting discussions and comments on a draft. We would also like to thank M Douglas, D Morrison and S Shenker for extensive discussions of various aspects of this work, and R Flauger, B Freivogel, S Kachru, R Kallosh, L Susskind, D Tong and E Witten for useful comments. This work was supported by the National Science Foundation under grant PHY05-51164, the UCSB Department of Physics, the DOE under contract DE-AC03-76SF00515 and by a William K Bowes Jr Stanford Graduate Fellowship. NR 62 TC 37 Z9 37 U1 0 U2 2 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0264-9381 J9 CLASSICAL QUANT GRAV JI Class. Quantum Gravity PD DEC 21 PY 2010 VL 27 IS 24 AR 245020 DI 10.1088/0264-9381/27/24/245020 PG 28 WC Astronomy & Astrophysics; Physics, Multidisciplinary; Physics, Particles & Fields SC Astronomy & Astrophysics; Physics GA 688DG UT WOS:000284829400020 ER PT J AU Cho, J Berbil-Bautista, L Levy, N Poulsen, D Frechet, JMJ Crommie, MF AF Cho, Jongweon Berbil-Bautista, L. Levy, Niv Poulsen, Daniel Frechet, Jean M. J. Crommie, Michael F. TI Functionalization, self-assembly, and photoswitching quenching for azobenzene derivatives adsorbed on Au(111) SO JOURNAL OF CHEMICAL PHYSICS LA English DT Article ID CONTROLLED SIZE; SURFACES; MOLECULE; LIGHT; NANOSTRUCTURES; ISOMERIZATION; SHAPE AB We have used scanning tunneling microscopy to investigate the structure and photoswitching behavior of azobenzene molecules functionalized with bulky spacer groups and adsorbed onto Au(111). We find that positioning tert-butyl "legs" in a canted arrangement on the azobenzene phenyl rings quenches photoisomerizability of the molecule on Au(111). Addition of cyano groups at the para positions changes the molecular self-assembly significantly, but does not alter the quenched photoisomerizability. This behavior likely arises from a combination of molecule-surface interactions, molecule-molecule interactions, and alteration of azobenzene electronic structure resulting from the position-specific addition of tert-butyl groups. (c) 2010 American Institute of Physics. [doi:10.1063/1.3519557] C1 [Cho, Jongweon; Berbil-Bautista, L.; Levy, Niv; Crommie, Michael F.] Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA. [Cho, Jongweon; Crommie, Michael F.] Univ Calif Berkeley, Ctr Integrated Nanomech Syst, Berkeley, CA 94720 USA. [Berbil-Bautista, L.; Levy, Niv; Poulsen, Daniel; Frechet, Jean M. J.; Crommie, Michael F.] Lawrence Berkeley Natl Lab, Div Mat Sci, Berkeley, CA 94720 USA. [Poulsen, Daniel; Frechet, Jean M. J.] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. RP Crommie, MF (reprint author), Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA. EM crommie@socrates.berkeley.edu RI Cho, Jongweon/F-3704-2011; OI Frechet, Jean /0000-0001-6419-0163 FU Office of Science, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering Division, U.S. Department of Energy [DE-AC03-76SF0098]; National Science Foundation within the Center of Integrated Nanomechanical Systems [EEC-0425941] FX We are grateful to M. J. Comstock for helpful discussions. Molecular synthesis and STM measurements were supported by the Director, Office of Science, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering Division, U.S. Department of Energy under Contract No. DE-AC03-76SF0098; STM data analysis was supported by the National Science Foundation within the Center of Integrated Nanomechanical Systems, under Grant No. EEC-0425941. NR 20 TC 9 Z9 9 U1 1 U2 13 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0021-9606 J9 J CHEM PHYS JI J. Chem. Phys. PD DEC 21 PY 2010 VL 133 IS 23 AR 234707 DI 10.1063/1.3519557 PG 4 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 697NG UT WOS:000285519700038 PM 21186884 ER PT J AU Fernandez, CA Nune, SK Motkuri, RK Thallapally, PK Wang, CM Liu, J Exarhos, GJ McGrail, BP AF Fernandez, Carlos A. Nune, Satish K. Motkuri, Radha Kishan Thallapally, Praveen K. Wang, Chongmin Liu, Jun Exarhos, Gregory J. McGrail, B. Peter TI Synthesis, Characterization, and Application of Metal Organic Framework Nanostructures SO LANGMUIR LA English DT Article ID PRUSSIAN BLUE NANOPARTICLES; HYDROGEN STORAGE; ADSORPTION; ANALOGS; CO; IMMOBILIZATION; NANOCRYSTALS; CRYSTALS; SO2; ZN AB The considerable number of important physical properties, including optical, electronic, and magnetic properties, of Prussian blue (PB) analogues have attracted fundamental and industrial interest. Nevertheless, the gas sorption properties of PB coordination compounds were only investigated very recently. In this work, we report the synthesis and gas sorption properties of PB nanocomposites with different size and shape obtained by using poly(vinylpyrrolidone) (PVP), chitosan, and dioctyl sodium sulfosuccinate (AOT) as stabilizers and structure directing agents. All three porous nanocrystals show high and selective CO(2) adsorption over CH(4) or N(2). No distinct relationship was found between the size (or shape) of the nanosorbents and their gas uptake capacities. To our knowledge, this is the first report on the use of PB nanocomposites for CO(2) capture applications. C1 [Fernandez, Carlos A.; Nune, Satish K.; Motkuri, Radha Kishan; Thallapally, Praveen K.; McGrail, B. Peter] Pacific NW Natl Lab, Energy & Environm Directorate, Richland, WA 99352 USA. [Wang, Chongmin] Pacific NW Natl Lab, WR Wiley Environm Mol Sci Lab, Richland, WA 99352 USA. [Liu, Jun; Exarhos, Gregory J.] Pacific NW Natl Lab, Fundamental & Computat Sci Directorate, Richland, WA 99352 USA. RP Thallapally, PK (reprint author), Pacific NW Natl Lab, Energy & Environm Directorate, Richland, WA 99352 USA. EM Praveen.Thallapally@pnl.gov RI Motkuri, Radha/F-1041-2014; thallapally, praveen/I-5026-2014 OI Motkuri, Radha/0000-0002-2079-4798; thallapally, praveen/0000-0001-7814-4467 FU U.S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering [KC020105-FWP12152]; U.S. Department of Energy, Office of Fossil Energy; U.S. Department of Energy [DE-AC05-76RL01830] FX Synthesis and characterization were supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award KC020105-FWP12152. In addition, portions of the work (gas sorption measurements) were supported by the U.S. Department of Energy, Office of Fossil Energy. The Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy under Contract DE-AC05-76RL01830. NR 33 TC 15 Z9 15 U1 5 U2 64 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0743-7463 J9 LANGMUIR JI Langmuir PD DEC 21 PY 2010 VL 26 IS 24 BP 18591 EP 18594 DI 10.1021/la103590t PG 4 WC Chemistry, Multidisciplinary; Chemistry, Physical; Materials Science, Multidisciplinary SC Chemistry; Materials Science GA 693IL UT WOS:000285217700002 PM 20958058 ER PT J AU Ciftlikli, EZ Lee, EYM Lallo, J Rangan, S Senanayake, SD Hinch, BJ AF Ciftlikli, Erkan Z. Lee, Everett Y. M. Lallo, James Rangan, Sylvie Senanayake, Sanjaya D. Hinch, B. J. TI Implementation of New TPD Analysis Techniques in the Evaluation of Second Order Desorption Kinetics of Cyanogen from Cu(001) SO LANGMUIR LA English DT Article ID TEMPERATURE-PROGRAMMED DESORPTION; THERMAL-DESORPTION; METAL-SURFACES; ADSORPTION; CN; CHLORINE; CU(100); PT(111) AB The interactions of cyanide species with a copper (001) surface were studied with temperature programmed desorption (TPD) and X-ray photoelectron spectroscopy (XPS). Adsorbed cyanide species (CN((a))) undergo recombinative desorption evolving molecular cyanogen (C(2)N(2)). As the adsorbed CN species charge upon adsorption, mutually repulsive dipolar interactions lead to a marked desorption energy reduction with increasing CN((a)) coverages. Two new TPD analysis approaches were developed, which used only accurately discernible observables and which do not assume constant desorption energies, E(d), and pre-exponential values, v. These two approaches demonstrated a linear variation of E(d) with instantaneous coverage. The first approach involved an analysis of the variations of desorption peak asymmetry with initial CN coverages. The second quantitative approach utilized only temperatures and intensities of TPD peaks, together with deduced surface coverages at the peak maxima, also as a function of initial surface coverages. Parameters derived from the latter approach were utilized as initial inputs for a comprehensive curve fit analysis technique. Excellent fits for all experimental desorption curves were produced in simulations. The curve fit analysis confirms that the activation energy of desorption of 170-180 kJ/mol at low coverage decreases by up to 14-15 kJ/mol at CN saturation. C1 [Ciftlikli, Erkan Z.; Lee, Everett Y. M.; Lallo, James; Hinch, B. J.] Rutgers State Univ, Dept Chem & Chem Biol, Piscataway, NJ 08854 USA. [Rangan, Sylvie] Rutgers State Univ, Dept Phys & Astron, Piscataway, NJ 08854 USA. [Senanayake, Sanjaya D.] Brookhaven Natl Lab, Dept Chem, Upton, NY 11973 USA. RP Hinch, BJ (reprint author), Rutgers State Univ, Dept Chem & Chem Biol, 610 Taylor Rd, Piscataway, NJ 08854 USA. EM jhinch@rutchem.rutgers.edu RI Rangan, Sylvie/H-6522-2013; Senanayake, Sanjaya/D-4769-2009 OI Senanayake, Sanjaya/0000-0003-3991-4232 FU NSF [CHE-0718055]; Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences, U.S. Department of Energy with Oak Ridge National Laboratory [DE-AC05-00OR22725]; U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences [DE-AC02-98CH10886] FX The work was supported by the NSF, CHE-0718055. The U12a beamline and S.D.S. have been supported by the Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences, U.S. Department of Energy, under Contract DE-AC05-00OR22725 with Oak Ridge National Laboratory. The National Synchrotron Light Source, Brookhaven National Laboratory, was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-98CH10886. NR 26 TC 2 Z9 2 U1 0 U2 9 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0743-7463 J9 LANGMUIR JI Langmuir PD DEC 21 PY 2010 VL 26 IS 24 BP 18742 EP 18749 DI 10.1021/la102304m PG 8 WC Chemistry, Multidisciplinary; Chemistry, Physical; Materials Science, Multidisciplinary SC Chemistry; Materials Science GA 693IL UT WOS:000285217700027 PM 21090656 ER PT J AU Olsson, R Giesler, R Loring, JS Persson, P AF Olsson, Rickard Giesler, Reiner Loring, John S. Persson, Per TI Adsorption, Desorption, and Surface-Promoted Hydrolysis of Glucose-1-Phosphate in Aqueous Goethite (alpha-FeOOH) Suspensions SO LANGMUIR LA English DT Article ID INOSITOL HEXAPHOSPHATE; MYOINOSITOL HEXAPHOSPHATE; ORGANIC PHOSPHORUS; SOIL; INTERFACE; ARSENATE; COMPLEXATION; SPECTROSCOPY; MECHANISMS; PHOSPHATE AB Adsorption, desorption, and precipitation reactions at environmental interfaces govern the fate of phosphorus in terrestrial and aquatic environments. Typically, a substantial part of the total pool of phosphorus consists of organophosphate, and in this study we have focused on the interactions between glucose-I-phosphate (G I P) and goethite (alpha-FeOOH) particles. The adsorption and surface-promoted hydrolysis reactions have been studied at room temperature as a function of pH, time, and total concentration of GIP by means of quantitative batch experiments in combination with infrared spectroscopy. A novel simultaneous infrared and potentiometric titration (SI PT) technique has also been used to study the rates and mechanisms of desorption of the surface complexes. The results have shown that GIP adsorption occurs over a wide pH interval and at pH values above the isoelectric point of goethite (IEP(goethite) = 9.4), indicating a comparatively strong interaction with the particle surfaces. As evidenced by IR spectroscopy, GIP formed pH-dependent surface complexes on goethite, and investigations of both adsorption and desorption processes were consistent with a model including three types of surface complexes. These complexes interact monodentately with surface Fe but differ in hydrogen bonding interactions via the auxiliary oxygens of the phosphate group. The apparent desorption rates were shown to be influenced by reaction pathways that include interconversion of surface species, which highlights the difficulty in determining the intrinsic desorption rates of individual surface complexes. Desorption results have also indicated that the molecular structures of surface complexes and the surface charge are two important determinants of GIP desorption rates. Finally, this study has shown that surface-promoted hydrolysis of GIP by goethite is base-catalyzed but that the extent of hydrolysis was small. C1 [Olsson, Rickard; Loring, John S.; Persson, Per] Umea Univ, Dept Chem, SE-90187 Umea, Sweden. [Giesler, Reiner] Umea Univ, Climate Impacts Res Ctr, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden. [Loring, John S.] Pacific NW Natl Lab, Richland, WA 99352 USA. RP Persson, P (reprint author), Umea Univ, Dept Chem, SE-90187 Umea, Sweden. EM per.persson@chem.umu.se RI Persson, Per/D-7388-2012 OI Persson, Per/0000-0001-9172-3068 FU Swedish Research Council; Kempe foundation FX This work was supported by the Swedish Research Council. The Kempe foundation is acknowledged for providing funding of the infrared spectrometer. The molecular orbital calculations were conducted using the resources of High Performance Computing Center North (HPC2N). NR 45 TC 24 Z9 26 U1 9 U2 49 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0743-7463 J9 LANGMUIR JI Langmuir PD DEC 21 PY 2010 VL 26 IS 24 BP 18760 EP 18770 DI 10.1021/la1026152 PG 11 WC Chemistry, Multidisciplinary; Chemistry, Physical; Materials Science, Multidisciplinary SC Chemistry; Materials Science GA 693IL UT WOS:000285217700029 PM 21087005 ER PT J AU Xu, F Zhang, HY Ilavsky, J Stanciu, L Ho, D Justice, MJ Petrache, HI Xie, JA AF Xu, Fan Zhang, Hang Yu Ilavsky, Jan Stanciu, Lia Ho, Derek Justice, Matthew J. Petrache, Horia I. Xie, Jian TI Investigation of a Catalyst Ink Dispersion Using Both Ultra-Small-Angle X-ray Scattering and Cryogenic TEM SO LANGMUIR LA English DT Article ID ELECTROLYTE FUEL-CELL; PERFLUOROSULFONATED IONOMERS; MEMBRANES; NAFION AB The dispersion of Nation ionomer particles and Pt/C catalyst aggregates in liquid media was studied using both ultra-small-angle X-ray scattering (USAXS) and cryogenic TEM. A systematic approach was taken to study first the dispersion of each component (i.e., ionomer particles and Pt/C aggregates), then the combination of the components, and last the catalyst ink. Multiple-level curve fitting was used to extract the particle size, size distribution, and geometry of the Pt/C aggregates and the Nation particles in liquid media from the scattering data. The results suggest that the particle size, size distribution, and geometry are not uniform throughout the systems but rather vary significantly. It was found that the interaction of each component (i.e., the Nation ionomer particles and the Pt/C aggregates) occurs in the dispersion. Cryogenic TEM was used to observe the size and geometry of the particles in liquid directly and to validate the scattering results. The TEM results showed excellent agreement. C1 [Xu, Fan; Xie, Jian] Indiana Univ Purdue Univ Indianapolis IUPUI, Dept Mech Engn, Indianapolis, IN 46202 USA. [Justice, Matthew J.; Petrache, Horia I.] Indiana Univ Purdue Univ Indianapolis IUPUI, Dept Phys, Indianapolis, IN 46202 USA. [Zhang, Hang Yu; Stanciu, Lia] Purdue Univ, Weldon Sch Biomed Engn, W Lafayette, IN 47907 USA. [Stanciu, Lia] Purdue Univ, Sch Mat Engn, W Lafayette, IN 47907 USA. [Ilavsky, Jan] Argonne Natl Lab, Xray Sci Div, Argonne, IL 60439 USA. [Ho, Derek] NIST, Div Polymer, Gaithersburg, MD 20899 USA. RP Xie, JA (reprint author), Indiana Univ Purdue Univ Indianapolis IUPUI, Dept Mech Engn, Indianapolis, IN 46202 USA. EM jianxie@iupui.edu RI Ilavsky, Jan/D-4521-2013; Xu, Fan/L-1114-2013; USAXS, APS/D-4198-2013 OI Ilavsky, Jan/0000-0003-1982-8900; NR 18 TC 14 Z9 14 U1 2 U2 26 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0743-7463 J9 LANGMUIR JI Langmuir PD DEC 21 PY 2010 VL 26 IS 24 BP 19199 EP 19208 DI 10.1021/la1028228 PG 10 WC Chemistry, Multidisciplinary; Chemistry, Physical; Materials Science, Multidisciplinary SC Chemistry; Materials Science GA 693IL UT WOS:000285217700085 PM 21090580 ER PT J AU Basore, JR Lavrik, NV Baker, LA AF Basore, Joseph R. Lavrik, Nickolay V. Baker, Lane A. TI Electromagnetic Micropores: Fabrication and Operation SO LANGMUIR LA English DT Article ID NANOPOROUS COLLOIDAL FILMS; MICROELECTROMAGNETIC TRAPS; MAGNETIC NANOPARTICLES; MICROFLUIDIC PLATFORM; ION-TRANSPORT; ON-CHIP; MEMBRANES; SEPARATION; DNA; MANIPULATION AB We describe the fabrication and characterization of electromagnetic micropores. These devices consist of a micropore encompassed by a microelectromagnetic trap. Fabrication of the device involves multiple photolithographic steps, combined with deep reactive ion etching and subsequent insulation steps. When immersed in an electrolyte solution, application of a constant potential across the micropore results in an ionic current. Energizing the electromagnetic trap surrounding the micropore produces regions of high magnetic field gradients in the vicinity of the micropore that can direct motion of a ferrofluid onto or off of the micropore. This results in dynamic gating of the ion current through the micropore structure. In this report, we detail fabrication and characterize the electrical and ionic properties of the prepared electromagnetic micropores. C1 [Basore, Joseph R.; Baker, Lane A.] Indiana Univ, Dept Chem, Bloomington, IN 47405 USA. [Lavrik, Nickolay V.] Oak Ridge Natl Lab, Ctr Nanophase Mat Sci, Oak Ridge, TN 37831 USA. RP Baker, LA (reprint author), Indiana Univ, Dept Chem, Bloomington, IN 47405 USA. EM lanbaker@indiana.edu RI Baker, Lane/B-6452-2008; Lavrik, Nickolay/B-5268-2011 OI Lavrik, Nickolay/0000-0002-9543-5634 FU NSF [CHE-0847624]; Division of Scientific User Facilities, U.S. Department of Energy FX Financial support was provided by the NSF (CHE-0847624). Portions of this research were conducted at the Center for Nanophase Materials Sciences, which is sponsored at Oak Ridge National Laboratory by the Division of Scientific User Facilities, U.S. Department of Energy. NR 61 TC 4 Z9 4 U1 2 U2 16 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0743-7463 J9 LANGMUIR JI Langmuir PD DEC 21 PY 2010 VL 26 IS 24 BP 19239 EP 19244 DI 10.1021/la103977e PG 6 WC Chemistry, Multidisciplinary; Chemistry, Physical; Materials Science, Multidisciplinary SC Chemistry; Materials Science GA 693IL UT WOS:000285217700090 PM 21087004 ER PT J AU Descalle, MA Vetter, K Hansen, A Daniel, J Prussin, SG AF Descalle, Marie-Anne Vetter, Kai Hansen, Araina Daniel, Joseph Prussin, Stanley G. TI Detector design for high-resolution MeV photon imaging of cargo containers using spectral information SO NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT LA English DT Article DE Monte Carlo simulations; Container scanning; Bremsstrahlung; Inorganic scintillator; MeV photon imaging; Energy discrimination AB Monte Carlo simulations of a pixelated detector array of inorganic scintillators for high spatial resolution imaging of 1-9 MeV photons are presented The results suggest that a detector array of 05 cm x 0 5 cm x 5 cm pixels of bismuth germanate may provide sufficient efficiency and spatial resolution to permit imaging of an object with uncertainties in dimension of several millimeters The crosstalk between pixels is found to be in the range of a few percent when pixels are shielded by similar to 1 mm of lead or tungsten The contrast at the edge of an object is greatly improved by rejection of events depositing less than similar to 1 MeV Given the relatively short decay time of BGO the simulations suggest that such a detector may prove adequate for the purpose of rapid scanning of highly shielded cargos for possible presence of high atomic number (including clandestine fissionable) materials when used with low current high duty factor X-ray sources (C) 2010 Elsevier B V All rights reserved C1 [Descalle, Marie-Anne] Lawrence Livermore Natl Lab, Phys & Life Sci Directorate L 211, Livermore, CA 94550 USA. [Vetter, Kai; Hansen, Araina; Daniel, Joseph; Prussin, Stanley G.] Univ Calif Berkeley, Dept Nucl Engn, Berkeley, CA 94720 USA. [Vetter, Kai; Hansen, Araina; Daniel, Joseph; Prussin, Stanley G.] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. RP Descalle, MA (reprint author), Lawrence Livermore Natl Lab, Phys & Life Sci Directorate L 211, 7000 East Ave, Livermore, CA 94550 USA. FU US Department of Energy by Lawrence Livermore National Laboratory [AC52-07NA27344]; University Office of the President University of California Berkeley FX This work was performed under the auspices of the US Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 This work was funded by a grant of the University Office of the President University of California Berkeley NR 13 TC 0 Z9 0 U1 0 U2 7 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0168-9002 J9 NUCL INSTRUM METH A JI Nucl. Instrum. Methods Phys. Res. Sect. A-Accel. Spectrom. Dect. Assoc. Equip. PD DEC 21 PY 2010 VL 624 IS 3 BP 635 EP 640 DI 10.1016/j.nima.2010.09.150 PG 6 WC Instruments & Instrumentation; Nuclear Science & Technology; Physics, Nuclear; Physics, Particles & Fields SC Instruments & Instrumentation; Nuclear Science & Technology; Physics GA 695LC UT WOS:000285370600011 ER PT J AU Cross, AS Knauer, JP Mycielski, A Kochanowska, D Wiktowska-Baran, M Jakiela, R Domagala, J Cui, Y James, RB Sobolewski, R AF Cross, A. S. Knauer, J. P. Mycielski, A. Kochanowska, D. Wiktowska-Baran, M. Jakiela, R. Domagala, J. Cui, Y. James, R. B. Sobolewski, Roman TI (Cd,Mn)Te detectors for characterization of X-ray emissions generated during laser-driven fusion experiments SO NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT LA English DT Article DE II-VI compound semiconductor devices; CdMnTe; Photoconductive devices; Semiconductor radiation detectors; X ray detectors; X ray spectroscopy ID PHOTOCONDUCTIVE DEVICES; CRYSTAL; DIAMOND; CD1-XMNXTE; GROWTH; CDMNTE AB We present our measurements of (Cd Mn)Te photoconductive detectors (PCDs) intending to characterize both the temporal and spectral dependence of X-ray emissions from laser-illuminated targets during inertial confinement fusion experiments Our Cd(1-x)Mn(x)Te (x=0 05) single crystals doped with V were grown using a vertical Bridgman method and annealed in Cd vapor for the highest resistivity of similar to 10(10) Omega cm The 1-mm-long and 2 3-mm-long detectors were placed in the same housing as two 1-mm-long diamond PCDs Each device was preceded by a Be X-ray filter with 37% X-ray transmission at the 1 keV cutoff energy Energy of the incident OMEGA laser pulses varied from 2 3 to 28 kJ Using targets of empty plastic shells we observed two X-ray emission events separated by 1 24 ns the first event was caused by heating of the shell that created a hot corona while the second event was an X-ray emission from the fully compressed target Experiments with targets with steel cores enabled us to analyze the time-resolved relaxation dynamics of photo-excited carriers in the (Cd Mn)Te crystals According to our calculations the (Cd Mn)Te material can very effectively absorb X-rays with energies of up to above 100 keV and the (Cd Mn)Te PCDs are likely to complement the diamond detectors currently used in laser-confinement fusion experiments (C) 2010 Elsevier B V All rights reserved C1 [Cross, A. S.; Knauer, J. P.; Sobolewski, Roman] Univ Rochester, Laser Energet Lab, Rochester, NY 14623 USA. [Cross, A. S.; Sobolewski, Roman] Univ Rochester, Dept Elect & Comp Engn, Rochester, NY 14627 USA. [Mycielski, A.; Kochanowska, D.; Wiktowska-Baran, M.; Jakiela, R.; Domagala, J.] Polish Acad Sci, Inst Phys, PL-02668 Warsaw, Poland. [Cui, Y.; James, R. B.] Brookhaven Natl Lab, Upton, NY 11973 USA. RP Cross, AS (reprint author), Univ Rochester, Laser Energet Lab, 250 E River Rd, Rochester, NY 14623 USA. RI Kochanowska, Dominika/P-8978-2016; Sobolewski, Roman/A-1979-2013; Domagala, Jaroslaw/P-1811-2016 OI Domagala, Jaroslaw/0000-0001-5515-9877 FU University of Rochester Laboratory for Laser Energetics; U S Department of Energy Office of Inertial Confinement Fusion [DE-FC52-08NA28302]; University of Rochester; New York State Energy Research and Development Authority; Polish Ministry of Science and Higher Education [3T08A-046-30] FX AS Cross acknowledges support from the Frank Horton Graduate Fellowship Program at the University of Rochester Laboratory for Laser Energetics Work in Rochester was supported in part by the U S Department of Energy Office of Inertial Confinement Fusion under Cooperative Agreement no DE-FC52-08NA28302 the University of Rochester and the New York State Energy Research and Development Authority The support of DOE does not constitute an endorsement by DOE of the views expressed in this article Work in Warsaw was supported by the Polish Ministry of Science and Higher Educationunder Grant no 3T08A-046-30 NR 22 TC 2 Z9 2 U1 1 U2 3 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0168-9002 J9 NUCL INSTRUM METH A JI Nucl. Instrum. Methods Phys. Res. Sect. A-Accel. Spectrom. Dect. Assoc. Equip. PD DEC 21 PY 2010 VL 624 IS 3 BP 649 EP 655 DI 10.1016/j.nima.2010.09.076 PG 7 WC Instruments & Instrumentation; Nuclear Science & Technology; Physics, Nuclear; Physics, Particles & Fields SC Instruments & Instrumentation; Nuclear Science & Technology; Physics GA 695LC UT WOS:000285370600014 ER PT J AU Bleuel, DL Bernstein, LA Burke, JT Gibelin, J Heffner, MD Mintz, J Norman, EB Phair, L Scielzo, ND Sheets, SA Snyderman, NJ Stoyer, MA Wiedeking, M AF Bleuel, D. L. Bernstein, L. A. Burke, J. T. Gibelin, J. Heffner, M. D. Mintz, J. Norman, E. B. Phair, L. Scielzo, N. D. Sheets, S. A. Snyderman, N. J. Stoyer, M. A. Wiedeking, M. TI Gamma-ray multiplicity measurement of the spontaneous fission of Cf-252 in a segmented HPGe/BGO detector array SO NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT LA English DT Article DE Fission; Multiplicity; Gamma ray; Neutron ID DISTRIBUTIONS; INSIGHTS; NUCLEI; CLOVER AB Coincident gamma rays from a Cf-252 source were measured using an array of six segmented high-purity germanium (HPGe) Clover detectors each enclosed by 16 bismuth-germanate (BGO) detectors The detectors were arranged in a cubic pattern around a 1 mu Ci Cf-252 source to cover a large solid angle for gamma-ray measurement with a reasonable reconstruction of the multiplicity Neutron multiplicity was determined in certain cases by identifying the prompt gamma rays from individual fission fragment pairs Multiplicity distributions from previous experiments and theoretical models were convolved with the response function of the array and compared to the present results These results suggest a gamma-ray multiplicity spectrum broader than previous measurements and models and provide no evidence of correlation with neutron multiplicity (C) 2010 Elsevier B V All rights reserved C1 [Bleuel, D. L.; Bernstein, L. A.; Burke, J. T.; Heffner, M. D.; Norman, E. B.; Scielzo, N. D.; Sheets, S. A.; Snyderman, N. J.; Stoyer, M. A.; Wiedeking, M.] Lawrence Livermore Natl Lab, Livermore, CA 94551 USA. [Gibelin, J.; Norman, E. B.; Phair, L.; Wiedeking, M.] Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA. [Mintz, J.; Norman, E. B.] Univ Calif Berkeley, Dept Nucl Engn, Berkeley, CA 94720 USA. RP Bleuel, DL (reprint author), Lawrence Livermore Natl Lab, Livermore, CA 94551 USA. OI GIBELIN, Julien/0000-0001-6751-3714 FU U S Department of Energy by Lawrence Livermore National Laboratory [W-7405-Eng-48, DE-AC52-07NA27344]; U S Department of Energy by Lawrence Berkeley National Laboratory [DE-AC02-05CH11231] FX This work was performed under the auspices of the U S Department of Energy by Lawrence Livermore National Laboratory in part under Contract W-7405-Eng-48 and in part under Contract DE-AC52-07NA27344 and the U S Department of Energy by Lawrence Berkeley National Laboratory under Contract no DE-AC02-05CH11231 NR 30 TC 6 Z9 6 U1 1 U2 4 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0168-9002 J9 NUCL INSTRUM METH A JI Nucl. Instrum. Methods Phys. Res. Sect. A-Accel. Spectrom. Dect. Assoc. Equip. PD DEC 21 PY 2010 VL 624 IS 3 BP 691 EP 698 DI 10.1016/j.nima.2010.09.145 PG 8 WC Instruments & Instrumentation; Nuclear Science & Technology; Physics, Nuclear; Physics, Particles & Fields SC Instruments & Instrumentation; Nuclear Science & Technology; Physics GA 695LC UT WOS:000285370600020 ER PT J AU Weber, JKR Benmore, CJ Jennings, G Wilding, MC Parise, JB AF Weber, J. K. R. Benmore, C. J. Jennings, G. Wilding, M. C. Parise, J. B. TI Instrumentation for fast in-situ X-ray structure measurements on non-equilibrium liquids SO NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT LA English DT Article DE X ray; Structure; Liquids; Glass; Extreme temperature; Supercooled AB Probing the structure of non-equilibrium melts is important to advance the fundamental understanding of liquids and glass formation and development of new materials Combined use of high flux high energy X-rays and fast large area detectors enables in situ probing of liquids suspended and laser beam heated in an aerodynamic levitator High-energy X-rays provide high resolution data and avoid the complications of multiple scattering and absorption within the sample The use of non-contact processing heating and measurement enables deep supercooling and avoids the need for corrections due to scattering by the container The technique provides an extreme temperature sample environment for measurements at rates of 5 spectra per second from superheated and supercooled liquids (C) 2010 Elsevier BV All rights reserved C1 [Weber, J. K. R.] Mat Dev Inc, Arlington Hts, IL 60004 USA. [Weber, J. K. R.; Benmore, C. J.; Jennings, G.] Argonne Natl Lab, Argonne, IL 60439 USA. [Wilding, M. C.] Aberystwyth Univ, Aberystwyth SY23 3BZ, Dyfed, Wales. [Parise, J. B.] SUNY Stony Brook, Stony Brook, NY 11794 USA. RP Weber, JKR (reprint author), Mat Dev Inc, 3090 Daniels Court, Arlington Hts, IL 60004 USA. OI Benmore, Chris/0000-0001-7007-7749 FU DOE [DE-AC05-00OR22725, DE-AC02-06CH11357, DE-FG02-09ER46650]; Aberystwyth University FX Work supported by DOE Contract nos DE-AC05-00OR22725 DE-AC02-06CH11357 and DE-FG02-09ER46650 and the Aberystwyth University Research Fund (CAFMaD) NR 9 TC 11 Z9 12 U1 1 U2 14 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0168-9002 J9 NUCL INSTRUM METH A JI Nucl. Instrum. Methods Phys. Res. Sect. A-Accel. Spectrom. Dect. Assoc. Equip. PD DEC 21 PY 2010 VL 624 IS 3 BP 728 EP 730 DI 10.1016/j.nima.2010.09.125 PG 3 WC Instruments & Instrumentation; Nuclear Science & Technology; Physics, Nuclear; Physics, Particles & Fields SC Instruments & Instrumentation; Nuclear Science & Technology; Physics GA 695LC UT WOS:000285370600024 ER PT J AU Yao, H Lee, DH AF Yao, Hong Lee, Dung-Hai TI Topological insulators and topological nonlinear sigma models SO PHYSICAL REVIEW B LA English DT Article ID ISOTROPIC HEISENBERG CHAIN; HGTE QUANTUM-WELLS; SINGLE DIRAC CONE; ARBITRARY SPINS; EXCITATIONS; SOLITONS; FERMIONS; SURFACE; BI2TE3; PHASE AB In this paper we link the physics of topological nonlinear sigma models with that of Chern-Simons insulators. We show that corresponding to every 2n-dimensional Chern-Simons insulator there is a (n-1)-dimensional topological nonlinear sigma model with the Wess-Zumino-Witten term. Breaking internal symmetry in these nonlinear sigma models leads to nonlinear sigma models with the theta term. [This is analogous to the dimension reduction leading from 2n-dimensional Chern-Simons insulators to (2n-1) and (2n-2)-dimensional topological insulators protected by discrete symmetries.] The correspondence described in this paper allows one to derive the topological term in a theory involving fermions and order parameters (we shall referred to them as "fermion-sigma models") when the conventional gradient-expansion method fails. We also discuss the quantum number of solitons in topological nonlinear sigma model and the electromagnetic action of the (2n-1)-dimensional topological insulators. Throughout the paper we use a simple model to illustrate how things work. C1 [Yao, Hong] Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA. Lawrence Berkeley Natl Lab, Div Mat Sci, Berkeley, CA 94720 USA. RP Yao, H (reprint author), Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA. RI Yao, Hong/D-3202-2011 OI Yao, Hong/0000-0003-2867-6144 FU DOE [DE-AC02-05CH11231] FX We thank Ying Ran, Ashvin Vishwanath, Tao Xiang, and Guang-Ming Zhang for useful discussions. This work is supported by DOE under Grant No. DE-AC02-05CH11231. NR 43 TC 10 Z9 10 U1 0 U2 5 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 1098-0121 J9 PHYS REV B JI Phys. Rev. B PD DEC 21 PY 2010 VL 82 IS 24 AR 245117 DI 10.1103/PhysRevB.82.245117 PG 16 WC Physics, Condensed Matter SC Physics GA 715PZ UT WOS:000286897700001 ER PT J AU Bousso, R Harnik, R AF Bousso, Raphael Harnik, Roni TI Entropic landscape SO PHYSICAL REVIEW D LA English DT Article AB We initiate a quantitative exploration of the entire landscape. Predictions thus far have focused on subsets of landscape vacua that share most properties with our own. Using the entropic principle (the assumption that entropy production traces the formation of complex structures such as observers), we derive six predictions that apply to the whole landscape. Typical observers find themselves in a flat Universe, at the onset of vacuum domination, surrounded by a recently produced bath of relativistic quanta. These quanta are neither very dilute nor condensed, and thus appear as a roughly thermal background. Their characteristic wavelength is of order the inverse fourth root of the vacuum energy. These predictions hold for completely arbitrary observers, in arbitrary vacua with potentially exotic particle physics and cosmology. They agree with observation: We live in a flat Universe at the onset of vacuum domination, whose dominant entropy production process (the glow of galactic dust) has recently produced a radiation bath (the cosmic infrared background). This radiation is marginally dilute, relativistic, and has a wavelength of order 100 microns, as predicted. C1 [Bousso, Raphael] Univ Calif Berkeley, Dept Phys, Ctr Theoret Phys, Berkeley, CA 94720 USA. [Bousso, Raphael] Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. [Bousso, Raphael] Univ Tokyo, Inst Phys & Math Universe, Kashiwa, Chiba 2778568, Japan. [Harnik, Roni] Stanford Univ, Dept Phys, Stanford Inst Theoret Phys, Stanford, CA 94305 USA. RP Bousso, R (reprint author), Univ Calif Berkeley, Dept Phys, Ctr Theoret Phys, Berkeley, CA 94720 USA. FU Berkeley Center for Theoretical Physics; National Science Foundation [08556553]; Institute for the Physics and Mathematics of the Universe; fqxi [RFP2-08-06]; U.S. Department of Energy [DE-AC02-05CH11231] FX We are grateful to M. Arvanitaki, M. Davis, S. Dimopoulos, S. Dubovsky, D. Finkbeiner, B. Freivogel, P. Graham, L. Hall, S. Leichenauer, Y. Nomura, P. Richards, and U. Seljak for discussions. The work of R.B. was supported by the Berkeley Center for Theoretical Physics, by the National Science Foundation under Grant No. 08556553, by the Institute for the Physics and Mathematics of the Universe, by fqxi under Grant No. RFP2-08-06, and by the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. NR 27 TC 16 Z9 16 U1 0 U2 0 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 1550-7998 J9 PHYS REV D JI Phys. Rev. D PD DEC 21 PY 2010 VL 82 IS 12 AR 123523 DI 10.1103/PhysRevD.82.123523 PG 19 WC Astronomy & Astrophysics; Physics, Particles & Fields SC Astronomy & Astrophysics; Physics GA 713NJ UT WOS:000286744400004 ER PT J AU Zeng, GSL Gullberg, GT Kadrmas, DJ AF Zeng, Gengsheng L. Gullberg, Grant T. Kadrmas, Dan J. TI Closed-form kinetic parameter estimation solution to the truncated data problem SO PHYSICS IN MEDICINE AND BIOLOGY LA English DT Article ID POSITRON EMISSION TOMOGRAPHY; COMPUTED-TOMOGRAPHY; INTERIOR PROBLEM; NOISE PROPERTIES; EM ALGORITHM; RECONSTRUCTION; SPECT; TRANSMISSION; MAPS AB In a dedicated cardiac single photon emission computed tomography (SPECT) system, the detectors are focused on the heart and the background is truncated in the projections. Reconstruction using truncated data results in biased images, leading to inaccurate kinetic parameter estimates. This paper has developed a closed-form kinetic parameter estimation solution to the dynamic emission imaging problem. This solution is insensitive to the bias in the reconstructed images that is caused by the projection data truncation. This paper introduces two new ideas: (1) it includes background bias as an additional parameter to estimate, and (2) it presents a closed-form solution for compartment models. The method is based on the following two assumptions: (i) the amount of the bias is directly proportional to the truncated activities in the projection data, and (ii) the background concentration is directly proportional to the concentration in the myocardium. In other words, the method assumes that the image slice contains only the heart and the background, without other organs, that the heart is not truncated, and that the background radioactivity is directly proportional to the radioactivity in the blood pool. As long as the background activity can be modeled, the proposed method is applicable regardless of the number of compartments in the model. For simplicity, the proposed method is presented and verified using a single compartment model with computer simulations using both noiseless and noisy projections. C1 [Zeng, Gengsheng L.; Kadrmas, Dan J.] Univ Utah, Dept Radiol, Utah Ctr Adv Imaging Res, Salt Lake City, UT 84108 USA. [Gullberg, Grant T.] Ernest Orlando Lawrence Berkeley Natl Lab, Dept Radiotracer Dev & Imaging Technol, Berkeley, CA 94720 USA. RP Zeng, GSL (reprint author), Univ Utah, Dept Radiol, Utah Ctr Adv Imaging Res, 729 Arapeen Dr, Salt Lake City, UT 84108 USA. EM larry@ucair.med.utah.edu; gtgullberg@lbl.gov; kadrmas@ucair.med.utha.edu FU Margolis Foundation; NIH [R01 CA135556, R01 HL50663]; Office of Science, Office of Biological and Environmental Research of the US Department of Energy [DE-AC02-05CH11231] FX This work was supported in part by the Margolis Foundation, NIH grants R01 CA135556, R01 HL50663, and by the Director, Office of Science, Office of Biological and Environmental Research of the US Department of Energy under contract DE-AC02-05CH11231. NR 25 TC 5 Z9 6 U1 0 U2 4 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0031-9155 J9 PHYS MED BIOL JI Phys. Med. Biol. PD DEC 21 PY 2010 VL 55 IS 24 BP 7453 EP 7468 DI 10.1088/0031-9155/55/24/005 PG 16 WC Engineering, Biomedical; Radiology, Nuclear Medicine & Medical Imaging SC Engineering; Radiology, Nuclear Medicine & Medical Imaging GA 688BT UT WOS:000284825200005 PM 21098917 ER PT J AU Wang, HZ Avci, U Nakashima, J Hahn, MG Chen, F Dixon, RA AF Wang, Huanzhong Avci, Utku Nakashima, Jin Hahn, Michael G. Chen, Fang Dixon, Richard A. TI Mutation of WRKY transcription factors initiates pith secondary wall formation and increases stem biomass in dicotyledonous plants SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA LA English DT Article DE lignocellulosic bioenergy crops; transcriptional regulation; lignin modification; biomass yield ID LEGUME MEDICAGO-TRUNCATULA; INSERTIONAL MUTAGENESIS; ARABIDOPSIS-THALIANA; ECTOPIC DEPOSITION; DIRECT TARGET; BIOSYNTHESIS; LIGNIN; SND1; GENOMICS; ETHYLENE AB Stems of dicotyledonous plants consist of an outer epidermis, a cortex, a ring of secondarily thickened vascular bundles and interfascicular cells, and inner pith parenchyma cells with thin primary walls. It is unclear how the different cell layers attain and retain their identities. Here, we show that WRKY transcription factors are in part responsible for the parenchymatous nature of the pith cells in dicotyledonous plants. We isolated mutants of Medicago truncatula and Arabidopsis thaliana with secondary cell wall thickening in pith cells associated with ectopic deposition of lignin, xylan, and cellulose, leading to an similar to 50% increase in biomass density in stem tissue of the Arabidopsis mutants. The mutations are caused by disruption of stem-expressed WRKY transcription factor (TF) genes, which consequently up-regulate downstream genes encoding the NAM, ATAF1/2, and CUC2 (NAC) and CCCH type (C3H) zinc finger TFs that activate secondary wall synthesis. Direct binding of WRKY to the NAC gene promoter and repression of three downstream TFs were confirmed by in vitro assays and in planta transgenic experiments. Secondary wall-bearing cells form lignocellulosic biomass that is the source for second generation biofuel production. The discovery of negative regulators of secondary wall formation in pith opens up the possibility of significantly increasing the mass of fermentable cell wall components in bioenergy crops. C1 [Wang, Huanzhong; Nakashima, Jin; Chen, Fang; Dixon, Richard A.] Samuel Roberts Noble Fdn Inc, Div Plant Biol, Ardmore, OK 73401 USA. [Avci, Utku; Hahn, Michael G.] Univ Georgia, Complex Carbohydrate Res Ctr, Athens, GA 30602 USA. [Avci, Utku; Hahn, Michael G.; Chen, Fang; Dixon, Richard A.] Bioenergy Sci Ctr BESC, Oak Ridge, TN 37831 USA. RP Dixon, RA (reprint author), Samuel Roberts Noble Fdn Inc, Div Plant Biol, Ardmore, OK 73401 USA. EM radixon@noble.org RI AVCI, Utku/B-9745-2011; OI Hahn, Michael/0000-0003-2136-5191 FU US Department of Energy [DE-GG02-06ER64303, DEPS02-06ER64304]; Oklahoma Bioenergy Center (OBC); Samuel Roberts Noble Foundation; Office of Biological and Environmental Research in the Department of Energy Office of Science; National Science Foundation [DBI-0421683, 703285] FX We thank Drs. Elison Blancaflor and Richard S. Nelson for critical reading of the manuscript and Dr. Yuhong Tang for assistance with microarray analysis. This work was supported by grants from the US Department of Energy (DE-GG02-06ER64303 and DEPS02-06ER64304), the Oklahoma Bioenergy Center (OBC), and the Samuel Roberts Noble Foundation. The BioEnergy Science Center is supported by the Office of Biological and Environmental Research in the Department of Energy Office of Science. Generation of the Complex Carbohydrate Research Center series of monoclonal antibodies used in this research was supported by Grant DBI-0421683 from the National Science Foundation Plant Genome Program, and the M. truncatula Tnt1 mutants, jointly owned by Centre National de la Recherche Scientifique and the Noble Foundation, were created through research funded in part by Grant 703285 from the National Science Foundation. NR 34 TC 90 Z9 99 U1 4 U2 47 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0027-8424 J9 P NATL ACAD SCI USA JI Proc. Natl. Acad. Sci. U. S. A. PD DEC 21 PY 2010 VL 107 IS 51 BP 22338 EP 22343 DI 10.1073/pnas.1016436107 PG 6 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 697OB UT WOS:000285521800073 PM 21135241 ER PT J AU Rzaca-Urban, T Urban, W Pinston, JA Simpson, GS Smith, AG Smith, JF Ahmad, I AF Rzaca-Urban, T. Urban, W. Pinston, J. A. Simpson, G. S. Smith, A. G. Smith, J. F. Ahmad, I. TI Near-yrast structure of Pr-149 SO PHYSICAL REVIEW C LA English DT Article ID NUCLEAR-DATA SHEETS; MASS PR ISOTOPES; HIGH-SPIN STATES; NEUTRON-RICH; OCTUPOLE CORRELATIONS; FISSION FRAGMENTS; ROTATIONAL BANDS; LEVEL STRUCTURE; EXCITED-LEVELS; LARGE ARRAYS AB The neutron-rich nucleus Pr-149 has been studied by means of prompt and delayed gamma-ray spectroscopy using the EUROGAM2 and Gammasphere arrays of Ge detectors. New spins have been assigned to a previously reported band and it is interpreted as having a h(11/2) proton structure, from a comparison with quasiparticle-rotor model calculations. The strength of octupole correlations in odd-Z nuclei of the region is discussed. C1 [Rzaca-Urban, T.; Urban, W.] Univ Warsaw, Fac Phys, PL-00681 Warsaw, Poland. [Urban, W.] Inst Max Von Laue Paul Langevin, F-38042 Grenoble 9, France. [Pinston, J. A.; Simpson, G. S.] Univ Grenoble 1, LPSC, CNRS, Inst Natl Polytechn Grenoble,IN2P3, F-38026 Grenoble, France. [Smith, A. G.; Smith, J. F.] Univ Manchester, Dept Phys & Astron, Manchester M13 9PL, Lancs, England. [Ahmad, I.] Argonne Natl Lab, Argonne, IL 60439 USA. RP Rzaca-Urban, T (reprint author), Univ Warsaw, Fac Phys, Ul Hoza 69, PL-00681 Warsaw, Poland. FU US Department of Energy, Office of Nuclear Physics [DE-AC02-06CH11357] FX The authors are indebted for the use of 248Cm to the Office of Basic Energy Sciences, US Department of Energy, through the transplutonium element production facilities at the Oak Ridge National Laboratory. This work has been partly supported by the US Department of Energy, Office of Nuclear Physics, under Contract No. DE-AC02-06CH11357. NR 41 TC 5 Z9 5 U1 0 U2 6 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 0556-2813 J9 PHYS REV C JI Phys. Rev. C PD DEC 20 PY 2010 VL 82 IS 6 AR 067304 DI 10.1103/PhysRevC.82.067304 PG 4 WC Physics, Nuclear SC Physics GA 713LV UT WOS:000286740400005 ER PT J AU Cao, Y Sheng, G Zhang, JX Choudhury, S Li, YL Randall, CA Chen, LQ AF Cao, Y. Sheng, G. Zhang, J. X. Choudhury, S. Li, Y. L. Randall, C. A. Chen, L. Q. TI Piezoelectric response of single-crystal PbZr1-xTixO3 near morphotropic phase boundary predicted by phase-field simulation SO APPLIED PHYSICS LETTERS LA English DT Article ID LEAD-ZIRCONATE-TITANATE; THIN-FILMS; HIGH-STRAIN; SYSTEM; FERROELECTRICS; CERAMICS; DOMAIN; GROWTH; PB(ZN1/3NB2/3)O3-PBTIO3; TEMPERATURE AB The piezoelectric property of hypothetic single-crystal PbZr(1-x)TixO(3) (PZT) is studied using phase-field simulations. The dependence of piezoelectric coefficient (d(33)) on PbTiO3 compositions (x) near the morphotropic phase boundary of PZT was obtained. Using the existing thermodynamic description of PZT, it is shown that d(33) reaches a peak value of 720 pC/N at x=0.47 which is more than three times of that for the ceramic counterpart. The relation between the domain structure of the poled PZT single crystals and the enhancement of d(33) near the MPB composition is discussed. (C) 2010 American Institute of Physics. [doi:10.1063/1.3530443] C1 [Cao, Y.; Sheng, G.; Zhang, J. X.; Randall, C. A.; Chen, L. Q.] Penn State Univ, Dept Mat Sci & Engn, University Pk, PA 16802 USA. [Choudhury, S.] Univ Wisconsin, Dept Mat Sci & Engn, Madison, WI 53792 USA. [Li, Y. L.] Pacific NW Natl Lab, Richland, WA 99352 USA. RP Cao, Y (reprint author), Penn State Univ, Dept Mat Sci & Engn, University Pk, PA 16802 USA. EM yxc238@psu.edu RI Sheng, Guang/C-2043-2012; Choudhury, Samrat/B-4115-2009; Chen, LongQing/I-7536-2012; Cao, Ye/L-1271-2016 OI Chen, LongQing/0000-0003-3359-3781; Cao, Ye/0000-0002-7365-7447 FU NSF-IUCRC Center for Dielectric Studies at Penn State; National Science Foundation [ECCS-0708759, DMR-1006541] FX The authors are grateful to the financial support for NSF-IUCRC Center for Dielectric Studies at Penn State and the National Science Foundation under Grant Nos. ECCS-0708759 and DMR-1006541. NR 42 TC 15 Z9 15 U1 4 U2 36 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0003-6951 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 20 PY 2010 VL 97 IS 25 AR 252904 DI 10.1063/1.3530443 PG 3 WC Physics, Applied SC Physics GA 700SJ UT WOS:000285764300058 ER PT J AU Clearfield, R Railsback, JG Pearce, RC Hensley, DK Fowlkes, JD Fuentes-Cabrera, M Simpson, ML Rack, PD Melechko, AV AF Clearfield, Raphael Railsback, Justin G. Pearce, Ryan C. Hensley, Dale K. Fowlkes, Jason D. Fuentes-Cabrera, Miguel Simpson, Michael L. Rack, Philip D. Melechko, Anatoli V. TI Reactive solid-state dewetting of Cu-Ni films on silicon SO APPLIED PHYSICS LETTERS LA English DT Article ID NICKEL SILICIDE; THIN; GROWTH AB The behavior of a 50 nm Cu-Ni alloy film on Si in a process of reactive solid-state dewetting is presented. The films were annealed at a range of temperatures (300-700 degrees C) in 1% H(2) 99% N(2) reducing atmosphere. The resulting alloy and silicide particles formed by film dewetting and film reaction with the substrate were distinguished by selective wet etching and examined by scanning electron microscopy and spectroscopy. After potassium hydroxide etch, regions that etch slower than silicon substrate have distribution statistics similar to the alloy and silicide particles prior to their removal, indicating strong coupling between mass transport across the interface and along the surface. (C) 2010 American Institute of Physics. [doi:10.1063/1.3527078] C1 [Clearfield, Raphael; Railsback, Justin G.; Pearce, Ryan C.; Melechko, Anatoli V.] N Carolina State Univ, Dept Mat Sci & Engn, Raleigh, NC 27695 USA. [Pearce, Ryan C.; Simpson, Michael L.; Rack, Philip D.] Univ Tennessee, Dept Mat Sci & Engn, Knoxville, TN 37996 USA. [Hensley, Dale K.; Fowlkes, Jason D.; Fuentes-Cabrera, Miguel; Simpson, Michael L.; Rack, Philip D.] Oak Ridge Natl Lab, Ctr Nanophase Mat Sci, Oak Ridge, TN 37831 USA. RP Clearfield, R (reprint author), N Carolina State Univ, Dept Mat Sci & Engn, Box 7907, Raleigh, NC 27695 USA. EM rclearf@ncsu.edu RI Melechko, Anatoli/B-8820-2008; Simpson, Michael/A-8410-2011; Fuentes-Cabrera, Miguel/Q-2437-2015; Hensley, Dale/A-6282-2016; OI Simpson, Michael/0000-0002-3933-3457; Fuentes-Cabrera, Miguel/0000-0001-7912-7079; Hensley, Dale/0000-0001-8763-7765; Rack, Philip/0000-0002-9964-3254 FU Materials Sciences and Engineering Division, Office of Basic Energy Sciences, U.S. Department of Energy; Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy FX This research was supported by the Materials Sciences and Engineering Division, Office of Basic Energy Sciences, U.S. Department of Energy (processing, analytical microscopy, and experimental design). Thin film deposition was conducted through a user project at the Center for Nanophase Materials Sciences, Oak Ridge National Laboratory sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy. NR 15 TC 6 Z9 6 U1 0 U2 15 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0003-6951 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 20 PY 2010 VL 97 IS 25 AR 253101 DI 10.1063/1.3527078 PG 3 WC Physics, Applied SC Physics GA 700SJ UT WOS:000285764300060 ER PT J AU Hindmarch, AT Harnchana, V Ciudad, D Negusse, E Arena, DA Brown, AP Brydson, RMD Marrows, CH AF Hindmarch, A. T. Harnchana, V. Ciudad, D. Negusse, E. Arena, D. A. Brown, A. P. Brydson, R. M. D. Marrows, C. H. TI Magnetostructural influences of thin Mg insert layers in crystalline CoFe(B)/MgO/CoFe(B) magnetic tunnel junctions SO APPLIED PHYSICS LETTERS LA English DT Article ID MAGNETORESISTANCE AB It is common to find a thin (similar to 0.5 nm) layer of Mg deposited prior to the MgO tunnel barrier in crystalline CoFe(B)/MgO/CoFe(B) magnetic tunnel junctions, due to the improved device performance that results. However, despite their common usage, the reasons why such layers are effective are unclear. We use structures that model the lower electrode of such devices to show that a suitably thick Mg insert layer enhances the crystal quality of both MgO and CoFe(B), permits interfacial oxides to reduce back to a metallic ferromagnetic state, and hence improves magnetic switching of the CoFe(B) electrode, properties which are inextricably linked to device performance. (C) 2010 American Institute of Physics. [doi:10.1063/1.3527939] C1 [Hindmarch, A. T.; Ciudad, D.; Marrows, C. H.] Univ Leeds, Sch Phys & Astron, Leeds LS2 9JT, W Yorkshire, England. [Harnchana, V.; Brown, A. P.; Brydson, R. M. D.] Univ Leeds, Inst Mat Res, Leeds LS2 9JT, W Yorkshire, England. [Negusse, E.] Montana State Univ, Dept Phys, Bozeman, MT 59717 USA. [Arena, D. A.] Brookhaven Natl Lab, Natl Synchrotron Light Source, Upton, NY 11973 USA. RP Hindmarch, AT (reprint author), Univ Nottingham, Sch Phys & Astron, Nottingham NG7 2RD, England. EM aidan.hindmarch@nottingham.ac.uk; c.h.marrows@leeds.ac.uk RI Marrows, Christopher/D-7980-2011; Hindmarch, Aidan/B-7970-2012; Ciudad, David/C-5787-2017; OI Ciudad, David/0000-0001-8047-6559; Brown, Andy/0000-0001-9692-2154; Marrows, Christopher/0000-0003-4812-6393 FU EPSRC; Thai government; Spanish Ministry of Science and Innovation [2008-0352]; U.S. Army Research Office [W911NF-08-1-0325]; DOE [DE-08NT0004115] FX We acknowledge financial support from EPSRC and are grateful to Brookhaven National Laboratory for NSLS beam-time. V.H. acknowledges sponsorship from the Thai government, D.C. acknowledges support from the Spanish Ministry of Science and Innovation through Postdoctoral Grant Ref. No. 2008-0352, and E.N. acknowledges support from the U.S. Army Research Office under Grant No. W911NF-08-1-0325 and DOE under Grant No. DE-08NT0004115. We appreciate discussions with K. J. Dempsey, G. Burnell, M. Ali, A. K. Suszka, B. J. Hickey, and A. P. Mihai; and the invaluable assistance provided by the NSLS VUV ring technical staff. NR 17 TC 7 Z9 7 U1 0 U2 12 PU AMER INST PHYSICS PI MELVILLE PA 1305 WALT WHITMAN RD, STE 300, MELVILLE, NY 11747-4501 USA SN 0003-6951 EI 1077-3118 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 20 PY 2010 VL 97 IS 25 AR 252502 DI 10.1063/1.3527939 PG 3 WC Physics, Applied SC Physics GA 700SJ UT WOS:000285764300048 ER PT J AU Lee, J Joo, S Kim, T Kim, KH Rhie, K Hong, J Shin, KH AF Lee, Jinseo Joo, Sungjung Kim, Taeyueb Kim, Ki Hyun Rhie, Kungwon Hong, Jinki Shin, Kyung-Ho TI An electrical switching device controlled by a magnetic field-dependent impact ionization process SO APPLIED PHYSICS LETTERS LA English DT Article ID SILICON; LOGIC AB An abrupt change of conductance at a threshold magnetic field was observed in a device consisting of a nonmagnetic narrow-gap semiconductor. The conductance varies more than 25 times as the magnetic field increases. The threshold magnetic field can be tuned using a bias voltage from zero to several hundred Gauss. This large magnetoconductance effect is caused by the magnetic field-dependent impact ionization process. A theoretical model is proposed, and calculations based on this model simulate the experimental results closely. This device may be a good candidate for an electrical switching device controlled by a magnetic field. (C) 2010 American Institute of Physics. [doi:10.1063/1.3532105] C1 [Lee, Jinseo; Joo, Sungjung; Kim, Taeyueb; Rhie, Kungwon; Hong, Jinki] Korea Univ, Dept Phys, Jochiwon 339700, South Korea. [Kim, Ki Hyun] Brookhaven Natl Lab, Upton, NY 11973 USA. [Shin, Kyung-Ho] KIST, Nano Devices Res Ctr, Seoul 130650, South Korea. RP Lee, J (reprint author), Korea Univ, Dept Phys, Jochiwon 339700, South Korea. EM krhie@korea.ac.kr; jkhongjkhong@korea.ac.kr FU MEST [2010-0000506] FX This work was supported by the KIST vision 21 program and the midcareer researcher program through the NRF grant funded by the MEST (Grant No. 2010-0000506). NR 16 TC 6 Z9 6 U1 0 U2 15 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0003-6951 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 20 PY 2010 VL 97 IS 25 AR 253505 DI 10.1063/1.3532105 PG 3 WC Physics, Applied SC Physics GA 700SJ UT WOS:000285764300091 ER PT J AU Kumah, DP Reiner, JW Segal, Y Kolpak, AM Zhang, Z Su, D Zhu, Y Sawicki, MS Broadbridge, CC Ahn, CH Walker, FJ AF Kumah, D. P. Reiner, J. W. Segal, Y. Kolpak, A. M. Zhang, Z. Su, D. Zhu, Y. Sawicki, M. S. Broadbridge, C. C. Ahn, C. H. Walker, F. J. TI The atomic structure and polarization of strained SrTiO3/Si SO APPLIED PHYSICS LETTERS LA English DT Article ID X-RAY-DIFFRACTION; CRYSTALLINE OXIDES; SILICON; INTERFACE AB For thin film devices based on coupling ferroelectric polarization to charge carriers in semiconductors, the role of the interface is critical. To elucidate this role, we use synchrotron x-ray diffraction to determine the interface structure of epitaxial SrTiO3 grown on the (001) surface of Si. The average displacement of the O octahedral sublattice relative to the Sr sublattice determines the film polarization and is measured to be about 0.05 nm toward the Si, with Ti off-center displacements 0.009 nm away from the substrate. Measurements of films with different boundary conditions on the top of the SrTiO3 show that the polarization at the SrTiO3/Si interface is dominated by oxide-Si chemical interactions. (C) 2010 American Institute of Physics. [doi:10.1063/1.3529460] C1 [Kumah, D. P.; Reiner, J. W.; Segal, Y.; Kolpak, A. M.; Ahn, C. H.; Walker, F. J.] Yale Univ, Ctr Res Interface Struct & Phenomena, New Haven, CT 06520 USA. [Zhang, Z.] Argonne Natl Lab, Adv Photon Source, Argonne, IL 60439 USA. [Su, D.; Zhu, Y.] Brookhaven Natl Lab, Ctr Funct Nanomat, Upton, NY 11973 USA. [Sawicki, M. S.; Broadbridge, C. C.] So Connecticut State Univ, Dept Phys, New Haven, CT 06515 USA. RP Kumah, DP (reprint author), Yale Univ, Ctr Res Interface Struct & Phenomena, New Haven, CT 06520 USA. EM divine.kumah@yale.edu RI Kumah, Divine/A-7031-2011; Su, Dong/A-8233-2013; Zhang, Zhan/A-9830-2008; OI Kumah, Divine/0000-0003-0715-1285; Su, Dong/0000-0002-1921-6683; Zhang, Zhan/0000-0002-7618-6134; Walker, Frederick/0000-0002-8094-249X FU NSF [MRSEC DMR 0520495, DMR 100625]; DOE, Office of Science, Office of Basic Energy Sciences [DE-AC02-06CH11357]; U.S. Department of Energy, Office of Basic Energy Science [DE-AC02-98CH10886] FX The authors acknowledge support from the NSF under Grant Nos. MRSEC DMR 0520495 and DMR 100625. Work at the Advanced Photon Source was supported by the DOE, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. Work at Brookhaven was supported by the U.S. Department of Energy, Office of Basic Energy Science, under Contract No. DE-AC02-98CH10886. NR 26 TC 14 Z9 14 U1 3 U2 25 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0003-6951 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 20 PY 2010 VL 97 IS 25 AR 251902 DI 10.1063/1.3529460 PG 3 WC Physics, Applied SC Physics GA 700SJ UT WOS:000285764300020 ER PT J AU Pan, W Howell, SW Ross, AJ Ohta, T Friedmann, TA AF Pan, Wei Howell, Stephen W. Ross, Anthony Joseph, III Ohta, Taisuke Friedmann, Thomas A. TI Observation of the integer quantum Hall effect in high quality, uniform wafer-scale epitaxial graphene films SO APPLIED PHYSICS LETTERS LA English DT Article AB We report the observation of the integer quantum Hall states at Landau level fillings of nu=2, 6, and 10 in a Hall bar device made of a single-layer epitaxial graphene film on the silicon-face of silicon-carbide prepared via argon-assisted graphitization. The two-dimensional electron gas exhibits a low-temperature (at 4 K) carrier mobility of similar to 14 000 cm(2)/V s at the electron density of 6.1 x 10(11) cm(-2). Furthermore, the sheet resistance obtained from four-probe measurements across the whole area (12 x 6 mm(2)) of another specimen grown under similar condition displays roughly uniform values (similar to 1600 Omega/square), suggesting that the macroscopic steps and accompanying multilayer graphene domains play a minor role in the low-temperature electronic transport. (C) 2010 American Institute of Physics. [doi:10.1063/1.3525588] C1 [Pan, Wei; Howell, Stephen W.; Ross, Anthony Joseph, III; Ohta, Taisuke; Friedmann, Thomas A.] Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Pan, W (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87185 USA. EM wpan@sandia.gov FU LDRD at Sandia National Laboratories; U.S. Department of Energy, Office of Basic Energy Sciences user facility at Los Alamos National Laboratory [DE-AC52-06NA25396]; U.S. Department of Energy, Office of Basic Energy Sciences user facility at Sandia National Laboratories [DE-AC04-94AL85000]; U.S. Department of Energy's National Nuclear Security Administration [DE-AC04-94AL85000] FX This work was supported by LDRD at Sandia National Laboratories and was performed, in part, at the Center for Integrated Nanotechnologies, a U.S. Department of Energy, Office of Basic Energy Sciences user facility at Los Alamos National Laboratory (Contract No. DE-AC52-06NA25396) and Sandia National Laboratories (Contract No. DE-AC04-94AL85000). Sandia National Laboratories is a multiprogram laboratory operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin company, for the U.S. Department of Energy's National Nuclear Security Administration under Contract No. DE-AC04-94AL85000. We thank Professor C.-T. Liang of National Taiwan University for the help on WL fitting and Dr. N. Bishop of Sandia National Laboratories for useful discussions. The authors would also like to thank Michael Lilly and Nathaniel Bishop for their help in setting up the cryogenic probe station measurements. NR 19 TC 14 Z9 14 U1 3 U2 13 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0003-6951 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 20 PY 2010 VL 97 IS 25 AR 252101 DI 10.1063/1.3525588 PG 3 WC Physics, Applied SC Physics GA 700SJ UT WOS:000285764300034 ER PT J AU Perna, P Maccariello, D Radovic, M di Uccio, US Pallecchi, I Codda, M Marre, D Cantoni, C Gazquez, J Varela, M Pennycook, SJ Granozio, FM AF Perna, P. Maccariello, D. Radovic, M. di Uccio, U. Scotti Pallecchi, I. Codda, M. Marre, D. Cantoni, C. Gazquez, J. Varela, M. Pennycook, S. J. Granozio, F. Miletto TI Conducting interfaces between band insulating oxides: The LaGaO3/SrTiO3 heterostructure (vol 97, 152111, 2010) SO APPLIED PHYSICS LETTERS LA English DT Correction C1 [Cantoni, C.; Gazquez, J.; Varela, M.; Pennycook, S. J.; Granozio, F. Miletto] Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. [Maccariello, D.; Radovic, M.; di Uccio, U. Scotti; Pallecchi, I.; Codda, M.; Marre, D.] Univ Genoa, Dipartimento Fis, CNR, SPIN, I-16146 Genoa, Italy. [Perna, P.] Univ Naples Federico 2, CNR, SPIN, Dipartimento Sci Fis, I-80126 Naples, Italy. RP Granozio, FM (reprint author), Oak Ridge Natl Lab, Div Mat Sci & Technol, 1 Bethel Valley Rd, Oak Ridge, TN 37831 USA. EM miletto@na.infn.it RI Scotti di Uccio, Umberto/A-4647-2012; Varela, Maria/H-2648-2012; Maccariello, Davide/J-8165-2013; Gazquez, Jaume/C-5334-2012; Varela, Maria/E-2472-2014; PERNA, PAOLO/C-3862-2012; Marre, Daniele/G-5965-2014; Cantoni, Claudia/G-3031-2013 OI Maccariello, Davide/0000-0002-8681-2717; Gazquez, Jaume/0000-0002-2561-328X; Varela, Maria/0000-0002-6582-7004; PERNA, PAOLO/0000-0001-8537-4834; Marre, Daniele/0000-0002-6230-761X; Cantoni, Claudia/0000-0002-9731-2021 NR 1 TC 0 Z9 0 U1 1 U2 10 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0003-6951 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 20 PY 2010 VL 97 IS 25 AR 259901 DI 10.1063/1.3514199 PG 1 WC Physics, Applied SC Physics GA 700SJ UT WOS:000285764300095 ER PT J AU Qian, HJ Murphy, JB Shen, Y Tang, CX Wang, XJ AF Qian, H. J. Murphy, J. B. Shen, Y. Tang, C. X. Wang, X. J. TI Surface photoemission in a high-brightness electron beam radio frequency gun SO APPLIED PHYSICS LETTERS LA English DT Article ID MAGNESIUM; ROUGHNESS AB We report the experimental characterization of high-brightness electron beam generation from a magnesium (Mg) photocathode. Both the quantum efficiency (QE) and the thermal emittance of an Mg cathode are experimentally investigated. The measured QE similar to 0.2% is the highest reported for a metal cathode. We observed no change in the Mg cathode thermal emittance as the QE varies from 0.015% to 0.15%. The upper-limit of the thermal emittance, 0.5 mm mrad, is about 50% lower than the theoretical prediction. Our results demonstrated the feasibility of having a high QE and a low thermal emittance simultaneously for a robust metal photocathode. c 2010 American Institute of Physics. [doi:10.1063/1.3531561] C1 [Qian, H. J.; Murphy, J. B.; Shen, Y.; Wang, X. J.] Brookhaven Natl Lab, Natl Synchrotron Light Source, Upton, NY 11973 USA. [Qian, H. J.; Tang, C. X.] Tsinghua Univ, Dept Engn Phys, Beijing 100084, Peoples R China. RP Wang, XJ (reprint author), Brookhaven Natl Lab, Natl Synchrotron Light Source, Upton, NY 11973 USA. EM xwang@bnl.gov FU U.S. Department of Energy [DE-AC02-98CH1-886]; BNL Laboratory Directed Research and Development [08-037] FX This work was supported in part by U.S. Department of Energy under Contract No. DE-AC02-98CH1-886 and BNL Laboratory Directed Research and Development Contract No. 08-037. NR 15 TC 15 Z9 15 U1 0 U2 8 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0003-6951 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 20 PY 2010 VL 97 IS 25 AR 253504 DI 10.1063/1.3531561 PG 3 WC Physics, Applied SC Physics GA 700SJ UT WOS:000285764300090 ER PT J AU Asano, K Inoue, S Meszaros, P AF Asano, Katsuaki Inoue, Susumu Meszaros, Peter TI PROMPT X-RAY AND OPTICAL EXCESS EMISSION DUE TO HADRONIC CASCADES IN GAMMA-RAY BURSTS SO ASTROPHYSICAL JOURNAL LETTERS LA English DT Article DE cosmic rays; gamma-ray burst: general; gamma-ray burst: individual (090902B, 080319B); radiation mechanisms: non-thermal ID ENERGY COSMIC-RAYS; SPECTRAL COMPONENT; FERMI OBSERVATIONS; BATSE OBSERVATIONS; SUPERNOVA REMNANT; DELAYED EMISSION; GRB 090510; ACCELERATION; BEHAVIOR; PROTONS AB A fraction of gamma-ray bursts (GRBs) exhibit distinct spectral features in their prompt emission below few tens of keV that exceed simple extrapolations of the low-energy power-law portion of the Band spectral model. This is also true for the prompt optical emission observed in several bursts. Through Monte Carlo simulations, we model such low-energy spectral excess components as hadronic cascade emission initiated by photomeson interactions of ultra-high-energy protons accelerated within GRB outflows. Synchrotron radiation from the cascading, secondary electron-positron pairs can naturally reproduce the observed soft spectra in the X-ray band, and in some cases the optical spectra as well. These components can be directly related to the higher energy radiation at GeV energies due to the hadronic cascades. Depending on the spectral shape, the total energy in protons is required to be comparable to or appreciably larger than the observed total photon energy. In particular, we apply our model to the excess X-ray and GeV emission of GRB 090902B, and the bright optical emission of the "naked-eye" GRB 080319B. Besides the hard GeV components detected by Fermi, such X-ray or optical spectral excesses are further potential signatures of ultra-high-energy cosmic ray production in GRBs. C1 [Asano, Katsuaki] Tokyo Inst Technol, Interact Res Ctr Sci, Meguro Ku, Tokyo 1528550, Japan. [Inoue, Susumu] Kyoto Univ, Dept Phys, Sakyo Ku, Kyoto 6068502, Japan. [Meszaros, Peter] Penn State Univ, Dept Astron & Astrophys, University Pk, PA 16802 USA. [Meszaros, Peter] Penn State Univ, Dept Phys, University Pk, PA 16802 USA. [Meszaros, Peter] Penn State Univ, Ctr Particle Astrophys, University Pk, PA 16802 USA. [Meszaros, Peter] Fermilab Natl Accelerator Lab, Batavia, IL 60510 USA. RP Asano, K (reprint author), Tokyo Inst Technol, Interact Res Ctr Sci, Meguro Ku, 2-12-1 Ookayama, Tokyo 1528550, Japan. EM asano@phys.titech.ac.jp; inoue@tap.scphys.kyoto-u.ac.jp; nnp@astro.psu.edu FU Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan [22740117, 22540278, 19047004]; NASA [NNX09AT72G, NNX08AL40G]; NSF [PHY-0757155]; Universality and Emergence at Kyoto University from MEXT FX This study is partially supported by Grants-in-Aid for Scientific Research No. 22740117, No. 22540278, and No. 19047004 from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan, and NASA NNX09AT72G, NASA NNX08AL40G, and NSF PHY-0757155. Also acknowledged are U.R.A. and Grants-in-Aid for the global COE program The Next Generation of Physics, Spun from Universality and Emergence at Kyoto University from MEXT. NR 49 TC 25 Z9 25 U1 0 U2 2 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 2041-8205 J9 ASTROPHYS J LETT JI Astrophys. J. Lett. PD DEC 20 PY 2010 VL 725 IS 2 BP L121 EP L125 DI 10.1088/2041-8205/725/2/L121 PG 5 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA 691AD UT WOS:000285051400003 ER PT J AU Pulliam, RL Savage, C Agundez, M Cernicharo, J Guelin, M Ziurys, LM AF Pulliam, R. L. Savage, C. Agundez, M. Cernicharo, J. Guelin, M. Ziurys, L. M. TI IDENTIFICATION OF KCN IN IRC+10216: EVIDENCE FOR SELECTIVE CYANIDE CHEMISTRY SO ASTROPHYSICAL JOURNAL LETTERS LA English DT Article DE astrochemistry; circumstellar matter; line: identification; stars: AGB and post-AGB; stars: individual (IRC+10216) ID VY CANIS MAJORIS; METAL CHEMISTRY; OXYGEN-RICH; 215-285 GHZ; MGNC; ENVELOPE; NACN; SPECTROSCOPY; MILLIMETER; ALF AB A new interstellar molecule, KCN, has been identified toward the circumstellar envelope of the carbon-rich asymptotic giant branch star, IRC+10216-the fifth metal cyanide species to be detected in space. Fourteen rotational transitions of this T-shaped, asymmetric top were searched for in the frequency range of 83-250 GHz using the Arizona Radio Observatory (ARO) 12 m Kitt Peak antenna, the IRAM 30 m telescope, and the ARO Submillimeter Telescope. Distinct lines were measured for 10 of these transitions, including the K-a = 1 and 2 asymmetry components of the J = 11 -> 10 and J = 10 -> 9 transitions, i.e., the K-ladder structure distinct to an asymmetric top. These data are some of the most sensitive astronomical spectra at lambda similar to 1 and 3 mm obtained to date, with 3 sigma noise levels similar to 0.3 mK, made possible by new ALMA technology. The line profiles from the ARO and IRAM telescopes are consistent with a shell-like distribution for KCN with r(outer) similar to 15 '', but with an inner shell radius that extends into warmer gas. The column density for KCN in IRC+10216 was found to be N-tot approximate to 1.0 x 10(12) cm(-2) with a rotational temperature of T-rot similar to 53 K. The fractional abundance was calculated to be f(KCN/H-2) similar to 6 x 10(-10), comparable to that of KCl. The presence of KCN in IRC+10216, along with MgNC, MgCN, NaCN, and AlNC, suggests that cyanide/isocyanide species are the most common metal-containing molecules in carbon-rich circumstellar gas. C1 [Pulliam, R. L.; Ziurys, L. M.] Univ Arizona, Dept Astron, Dept Chem, Tucson, AZ 85721 USA. [Savage, C.] Univ Arizona, Steward Observ, Tucson, AZ 85721 USA. [Savage, C.] Los Alamos Natl Lab, Appl Electromagnet IAT 2, Los Alamos, NM 87545 USA. [Agundez, M.] Observ Paris, LUTH, F-92190 Meudon, France. [Cernicharo, J.] CSIC INTA, Ctr Astrobiol, Dept Astrofis, Madrid 28850, Spain. [Guelin, M.] Inst Radioastron Millimetr, F-38406 St Martin Dheres, France. [Ziurys, L. M.] Univ Arizona, Arizona Radio Observ, Tucson, AZ 85721 USA. RP Pulliam, RL (reprint author), Univ Arizona, Dept Astron, Dept Chem, 933 N Cherry Ave, Tucson, AZ 85721 USA. RI Agundez, Marcelino/I-5369-2012 OI Agundez, Marcelino/0000-0003-3248-3564 FU NSF [AST-09-06534]; European Community [235753] FX The research is funded by the NSF Grant AST-09-06534. M.A. is supported by a Marie Curie Intra-European Individual Fellowship within the European Community 7th Framework Programme under grant agreement no. 235753. NR 25 TC 25 Z9 25 U1 2 U2 4 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 2041-8205 J9 ASTROPHYS J LETT JI Astrophys. J. Lett. PD DEC 20 PY 2010 VL 725 IS 2 BP L181 EP L185 DI 10.1088/2041-8205/725/2/L181 PG 5 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA 691AD UT WOS:000285051400015 ER PT J AU Thanos, PK Tucci, A Stamos, J Robison, L Wang, GJ Anderson, BJ Volkow, ND AF Thanos, Panayotis K. Tucci, Andrew Stamos, Joshua Robison, Lisa Wang, Gene-Jack Anderson, Brenda J. Volkow, Nora D. TI Chronic forced exercise during adolescence decreases cocaine conditioned place preference in Lewis rats SO BEHAVIOURAL BRAIN RESEARCH LA English DT Article DE Dopamine; Exercise; Cocaine; Conditioned place preference ID DOPAMINE D2 RECEPTOR; DIET-INDUCED OBESITY; SEX-DIFFERENCES; FEMALE RATS; LOCOMOTOR-ACTIVITY; AEROBIC EXERCISE; BIOLOGICAL BASIS; BRAIN DOPAMINE; FIRING RATE; WHEEL AB Chronic physical activity (exercise) may be beneficial in the prevention of substance use disorders; however, the extent to which physical activity can interfere with the reinforcing effects of drugs during the adolescent period, which is one of great vulnerability for drug experimentation, has not been fully evaluated. Here, we assess the effects of chronic forced exercise during adolescence on preference for cocaine using the conditioned place preference (CPP) paradigm in male and female Lewis rats. The group of rats exposed to exercise ran on a treadmill for 6 weeks on a progressive time-increased schedule for up to 1 h of exercise per day, while the groups of sedentary rats remained in their home cage. Following the 6 weeks of exercise exposure, rats were tested for cocaine CPP. Results showed that chronic exercise significantly attenuated cocaine CPP in both males and females compared to a sedentary environment. Furthermore, male exercise rats failed to show significant cocaine CPP. In contrast, female exercise rats still showed cocaine CPP but it was significantly reduced compared to the female sedentary rats. Females also exhibited greater cocaine CPP than males overall. These findings suggest that strategies to promote physical activity during adolescence may be protective against cocaine abuse in both males and females, and these findings merit further investigation. We also corroborate a gender-specific sensitivity to the reinforcing effects of cocaine, highlighting the need to consider gender-tailored exercise interventions for drug abuse prevention. (C) 2010 Published by Elsevier B.V. C1 [Thanos, Panayotis K.; Tucci, Andrew; Stamos, Joshua; Wang, Gene-Jack] Brookhaven Natl Lab, Dept Med, Behav Neuropharmacol & Neuroimaging Lab, Upton, NY 11973 USA. [Thanos, Panayotis K.; Robison, Lisa; Volkow, Nora D.] NIAAA, Lab Neuroimaging, NIH, Bethesda, MD 20892 USA. [Thanos, Panayotis K.; Anderson, Brenda J.] SUNY Stony Brook, Dept Psychol, Stony Brook, NY 11794 USA. RP Thanos, PK (reprint author), Brookhaven Natl Lab, Dept Med, Behav Neuropharmacol & Neuroimaging Lab, Upton, NY 11973 USA. EM thanos@bnl.gov FU NIAAA [AA 11034, AA07574, AA07611]; SULI; IRTA FX This work was supported by the NIAAA (AA 11034 & AA07574, AA07611). We also thank the SULI and IRTA programs for partial support of LSR. We also thank Joe Gatz for technical assistance with the equipment. NR 60 TC 23 Z9 24 U1 0 U2 3 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0166-4328 J9 BEHAV BRAIN RES JI Behav. Brain Res. PD DEC 20 PY 2010 VL 215 IS 1 BP 77 EP 82 DI 10.1016/j.bbr.2010.06.033 PG 6 WC Behavioral Sciences; Neurosciences SC Behavioral Sciences; Neurosciences & Neurology GA 653GG UT WOS:000282076500010 PM 20615434 ER PT J AU Ko, H Gourdon, O Gout, D Mun, ED Thimmaiah, S Miller, GJ AF Ko, Hyunjin Gourdon, Olivier Gout, Delphine Mun, Eun-Deok Thimmaiah, Srinivasa Miller, Gordon J. TI Rhombohedrally Distorted gamma-Brasses Cr1-xFexGa SO INORGANIC CHEMISTRY LA English DT Article ID QUASI-CRYSTAL APPROXIMANTS; PAIR DISTRIBUTION FUNCTION; ELECTRONIC-STRUCTURE; INTERMETALLIC COMPOUNDS; INTERGROWTH COMPOUNDS; MAGNETISM; PHASES; REFINEMENT; STABILITY; SOLIDS AB A series of rhombohedrally distorted gamma-brass structures containing a mixture of magnetically active 3d elements, Cr and Fe, Cr1-xFexGa, is investigated crystallographically. These structures consist of chains of trans-face-sharing Ga-centered transition metal icosahedra. Neutron powder diffraction specifically. on Cr0.5Fe0.5Ga, which could be prepared as a single phase material, gave lattice constants (11 K) a = 12.5172(2) angstrom and c = 7.8325(2) angstrom and a refined composition of Cr0.502(6)Fe0.498Ga = Cr6.523Fe6.477Ga13 and revealed partial ordering of Cr and Fe atoms among three crystallographic sites. Magnetic susceptibility and magnetization studies, of Cr0.5Fe0.5Ga showed the onset of magnetic ordering at ca. 25 K. Theoretical calculations suggested both site-energy and bond-energy factors influencing the Cr/Fe distribution. Heteroatomic interactions significantly affect exchange interactions and create low local magnetic moments. Models created to mimic Cr0.5Fe0.5Ga showed ferromagnet c Fe-Fe and antiferromagnetic Cr-Fe interactions, with an overall ferrimagnetic ordering. C1 [Ko, Hyunjin; Thimmaiah, Srinivasa; Miller, Gordon J.] Iowa State Univ, Dept Chem, Ames, IA 50011 USA. [Ko, Hyunjin; Thimmaiah, Srinivasa; Miller, Gordon J.] Ames Lab, Ames, IA 50011 USA. [Gourdon, Olivier; Gout, Delphine] Oak Ridge Natl Lab, Julich Ctr Neutron Sci Outstn SNS, Oak Ridge, TN 37831 USA. [Mun, Eun-Deok] Iowa State Univ, Dept Phys & Astron, Ames, IA 50011 USA. RP Miller, GJ (reprint author), Iowa State Univ, Dept Chem, Ames, IA 50011 USA. EM gmiller@iastate.edu RI Thimmaiah, Srinivasa/H-1049-2012 FU U.S. Department of Energy [DE-AC02-07CH11358]; Materials Sciences Division of the Office of Basic Energy Sciences of the U.S. Department of Energy FX This work was carried out at the Ames Laboratory, which is operated for the U.S. Department of Energy by Iowa State University under Contract No. DE-AC02-07CH11358. This work was supported by the Materials Sciences Division of the Office of Basic Energy Sciences of the U.S. Department of Energy. NR 53 TC 5 Z9 5 U1 0 U2 8 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0020-1669 J9 INORG CHEM JI Inorg. Chem. PD DEC 20 PY 2010 VL 49 IS 24 BP 11505 EP 11515 DI 10.1021/ic101671k PG 11 WC Chemistry, Inorganic & Nuclear SC Chemistry GA 694AJ UT WOS:000285266800028 PM 21077651 ER PT J AU Naderi, NA Grillot, F Yang, K Wright, JB Gin, A Lester, LF AF Naderi, Nader A. Grillot, Frederic Yang, Kai Wright, Jeremy B. Gin, Aaron Lester, Luke F. TI Two-color multi-section quantum dot distributed feedback laser SO OPTICS EXPRESS LA English DT Article ID LOW-THRESHOLD CURRENT; TERAHERTZ TECHNOLOGY; SEMICONDUCTOR-LASERS; HIGH-SPEED; GENERATION; RADIATION; TEMPERATURE; DIODES; MODE; LINEWIDTH AB A dual-wavelength emission source is realized by asymmetrically pumping a two-section quantum-dot distributed feedback laser. It is found that under asymmetric bias conditions, the powers between the ground-state and excited-state modes of the two-section device can be equalized, which is mainly attributed to the unique carrier dynamics of the quantum-dot gain medium. As a result, a two-color emission with an 8-THz frequency difference is realized that has potential as a compact THz source. It is also shown that the combination of significant inhomogeneous broadening and excited-state coupled mode operation allows the manipulation of the quantum-dot states through external optical stabilization. (C) 2010 Optical Society of America C1 [Naderi, Nader A.; Yang, Kai; Lester, Luke F.] Univ New Mexico, Ctr High Technol Mat, Albuquerque, NM 87106 USA. [Grillot, Frederic] Univ Europeenne Bretagne, INSA, CNRS, Lab FOTON, F-35708 Rennes 7, France. [Wright, Jeremy B.; Gin, Aaron] Sandia Natl Labs, Ctr Integrated Nanotechnol, Albuquerque, NM 87185 USA. RP Naderi, NA (reprint author), Univ New Mexico, Ctr High Technol Mat, 1313 Goddard SE, Albuquerque, NM 87106 USA. EM nader@unm.edu RI Gin, Aaron/E-3647-2010; Wright, Jeremy/G-7149-2011; Grillot, Frederic/N-5613-2014 OI Wright, Jeremy/0000-0001-6861-930X; FU Air Force Research Laboratory and Air Force Office of Scientific Research [FA8750-06-1-0085, FA9550-10-1-0276]; U.S. Department of Energy, Office of Basic Energy Sciences [DE-AC52-06NA25396, DE-AC04-94AL85000] FX This work was performed, in part, at the Center for Integrated Nanotechnologies, a U.S. Department of Energy, Office of Basic Energy Sciences user facility at Los Alamos National Laboratory (Contract DE-AC52-06NA25396) and Sandia National Laboratories (Contract DE-AC04-94AL85000). This work was also supported by the Air Force Research Laboratory and Air Force Office of Scientific Research under Grant Numbers FA8750-06-1-0085 and FA9550-10-1-0276, respectively. The authors wish to thank Dr. Hui Su for valuable discussions on the use of LAPAREX. NR 32 TC 32 Z9 32 U1 0 U2 8 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 20 PY 2010 VL 18 IS 26 BP 27028 EP 27035 DI 10.1364/OE.18.027028 PG 8 WC Optics SC Optics GA 698HF UT WOS:000285584200041 PM 21196979 ER PT J AU Griffith, WC Knappe, S Kitching, J AF Griffith, W. Clark Knappe, Svenja Kitching, John TI Femtotesla atomic magnetometry in a microfabricated vapor cell SO OPTICS EXPRESS LA English DT Article AB We describe an optically pumped Rb-87 magnetometer with 5 fT/Hz(1/2) sensitivity when operated in the spin-exchange relaxation free (SERF) regime. The magnetometer uses a microfabricated vapor cell consisting of a cavity etched in a 1 mm thick silicon wafer with anodically bonded Pyrex windows. The measurement volume of the magnetometer is 1 mm(3), defined by the overlap region of a circularly polarized pump laser and a linearly polarized probe laser, both operated near 795 nm. Sensitivity limitations unique to the use of microfabricated cells are discussed. (C)2010 Optical Society of America C1 [Griffith, W. Clark; Knappe, Svenja; Kitching, John] Natl Inst Stand & Technol, Div Time & Frequency, Boulder, CO 80305 USA. [Knappe, Svenja] Univ Colorado, Boulder, CO 80309 USA. RP Griffith, WC (reprint author), Los Alamos Natl Lab, Subat Phys Grp P 25, POB 1663, Los Alamos, NM 87545 USA. EM wclarkg@gmail.com OI Kitching, John/0000-0002-4540-1954; Griffith, William Clark/0000-0002-0260-1956 FU Defense Advanced Research Projects Agency; NIST FX Thanks to Susan Schima for help with vapor cell fabrication, and to Jan Preusser, Ricardo Jimenez-Martinez, and Rahul Mhaskar for valuable discussions. This work was supported by the Defense Advanced Research Projects Agency and NIST. This work is a partial contribution of NIST, an agency of the U.S. government, and is not subject to copyright. NR 20 TC 36 Z9 39 U1 5 U2 37 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 20 PY 2010 VL 18 IS 26 BP 27167 EP 27172 DI 10.1364/OE.18.027167 PG 6 WC Optics SC Optics GA 698HF UT WOS:000285584200005 PM 21196993 ER PT J AU Bae, T Jang, YC Jung, C Kim, HJ Kim, J Kim, J Kim, K Lee, W Sharpe, SR Yoon, B AF Bae, Taegil Jang, Yong-Chull Jung, Chulwoo Kim, Hyung-Jin Kim, Jangho Kim, Jongjeong Kim, Kwangwoo Lee, Weonjong Sharpe, Stephen R. Yoon, Boram CA SWME Collaboration TI B-K using HYP-smeared staggered fermions in N-f = 2+1 unquenched QCD SO PHYSICAL REVIEW D LA English DT Article ID MATRIX-ELEMENTS; PARAMETER; OPERATORS AB We present results for the kaon mixing parameter B-K calculated using HYP (hypercubic fat link)smeared improved staggered fermions on the asqtad lattices generated by the MILC collaboration. We use three lattice spacings (a approximate to 0.12, 0.09 and 0.06 fm), ten different valence-quark masses (m approximate to m(s)/10 - m(s)), and several light sea-quark masses in order to control the continuum and chiral extrapolations. We derive the next-to-leading order staggered chiral perturbation theory (SChPT) results necessary to fit our data, and use these results to do extrapolations based both on SU(2) and SU(3) SChPT. The SU(2) fitting is particularly straightforward because parameters related to taste breaking and matching errors appear only at next-to-next-to-leading order. We match to the continuum renormalization scheme [naive dimensional regularization (NDR)] using one-loop perturbation theory. Our final result is from the SU(2) analysis, with the SU(3) result providing a (less accurate) cross check. We find B-K(NDR, mu = 2 GeV) = 0.529 +/- 0.009 +/- 0.032 and (B) over cap (K) = B-K(RGI) = 0.724 +/- 0.012 +/- 0.043, where the first error is statistical and the second systematic. The error is dominated by the truncation error in the matching factor. Our results are consistent with those obtained using valence domain-wall fermions on lattices generated with asqtad or domain-wall sea quarks. C1 [Bae, Taegil; Jang, Yong-Chull; Kim, Hyung-Jin; Kim, Jangho; Kim, Jongjeong; Kim, Kwangwoo; Lee, Weonjong; Yoon, Boram] Seoul Natl Univ, Lattice Gauge Theory Res Ctr, FPRD, Seoul 151747, South Korea. [Bae, Taegil; Jang, Yong-Chull; Kim, Hyung-Jin; Kim, Jangho; Kim, Jongjeong; Kim, Kwangwoo; Lee, Weonjong; Yoon, Boram] Seoul Natl Univ, Dept Phys & Astron, CTP, Seoul 151747, South Korea. [Jung, Chulwoo] Brookhaven Natl Lab, Dept Phys, Upton, NY 11973 USA. [Lee, Weonjong; Sharpe, Stephen R.] Univ Washington, Dept Phys, Seattle, WA 98195 USA. RP Bae, T (reprint author), Seoul Natl Univ, Lattice Gauge Theory Res Ctr, FPRD, Seoul 151747, South Korea. EM chulwoo@bnl.gov; wlee@snu.ac.kr; xsharpe@phys.washington.edu FU US DOE [DE-AC02-98CH10886, DE-FG02-96ER40956]; Korean government (MEST) [3348-20090015]; Office of Science of the U.S. Department of Energy FX C. Jung is supported by the US DOE under Grant No. DE-AC02-98CH10886. The research of W. Lee is supported by the Creative Research Initiatives program Grant No. (3348-20090015) of the NRF grant funded by the Korean government (MEST). The work of S. Sharpe is supported in part by the US DOE Grant No. DE-FG02-96ER40956. Computations for this work were carried out in part on QCDOC computers of the USQCD Collaboration at Brookhaven National Laboratory. The USQCD Collaboration are funded by the Office of Science of the U.S. Department of Energy. NR 53 TC 28 Z9 28 U1 0 U2 1 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 1550-7998 J9 PHYS REV D JI Phys. Rev. D PD DEC 20 PY 2010 VL 82 IS 11 AR 114509 DI 10.1103/PhysRevD.82.114509 PG 37 WC Astronomy & Astrophysics; Physics, Particles & Fields SC Astronomy & Astrophysics; Physics GA 711DK UT WOS:000286567100003 ER PT J AU Keung, WY Low, I Shaughnessy, G AF Keung, Wai-Yee Low, Ian Shaughnessy, Gabe TI Confronting the direct search of low mass dark matter from CoGeNT data with antiproton PAMELA data SO PHYSICAL REVIEW D LA English DT Article ID ENERGIES; CDMS AB If the excess events from the CoGeNT experiment arise from elastic scatterings of a light dark matter off the nuclei, crossing symmetry implies nonvanishing annihilation cross sections of the light dark matter into hadronic final states inside the Galactic halo, which we confront with the antiproton spectrum measured by the PAMELA Collaboration. We consider two types of effective interactions between the dark matter and the quarks: (1) contact interactions from integrating out heavy particles and (2) long-range interactions due to the electromagnetic properties of the dark matter. The lack of excess in the antiproton spectrum results in tensions for a scalar and, to a lesser extent, vector dark matter interacting with the quarks through the Higgs portal. C1 [Keung, Wai-Yee] Univ Illinois, Dept Phys, Chicago, IL 60607 USA. [Low, Ian; Shaughnessy, Gabe] Argonne Natl Lab, Div High Energy Phys, Argonne, IL 60439 USA. [Low, Ian; Shaughnessy, Gabe] Northwestern Univ, Dept Phys & Astron, Evanston, IL 60208 USA. RP Keung, WY (reprint author), Univ Illinois, Dept Phys, Chicago, IL 60607 USA. FU U.S. Department of Energy [DE-AC02-06CH11357, DE-FG02-91ER40684, DE-FG02-84ER40173] FX We thank V. Barger and D. Marfatia for helpful comments and Q.-H. Cao and H. Zhang for earlier collaborations. This work is supported in part by the U.S. Department of Energy under Contracts No. DE-AC02-06CH11357, No. DE-FG02-91ER40684, and No. DE-FG02-84ER40173. NR 48 TC 15 Z9 15 U1 0 U2 0 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 2470-0010 EI 2470-0029 J9 PHYS REV D JI Phys. Rev. D PD DEC 20 PY 2010 VL 82 IS 11 AR 115019 DI 10.1103/PhysRevD.82.115019 PG 8 WC Astronomy & Astrophysics; Physics, Particles & Fields SC Astronomy & Astrophysics; Physics GA 711DK UT WOS:000286567100007 ER PT J AU Nicmorus, D Eichmann, G Alkofer, R AF Nicmorus, D. Eichmann, G. Alkofer, R. TI Delta and omega electromagnetic form factors in a Dyson-Schwinger/Bethe-Salpeter approach SO PHYSICAL REVIEW D LA English DT Article ID CHIRAL PERTURBATION-THEORY; RELATIVISTIC QUARK-MODEL; BARYON MAGNETIC-MOMENTS; SYMMETRY-BREAKING; SKYRME MODEL; ELECTRO-EXCITATION; OCTUPOLE MOMENTS; VERTEX FUNCTION; HADRON PHYSICS; DIQUARK MODEL AB We investigate the electromagnetic form factors of the Delta and the Omega baryons within the Poincare-covariant framework of Dyson-Schwinger and Bethe-Salpeter equations. The three-quark core contributions of the form factors are evaluated by employing a quark-diquark approximation. We use a consistent setup for the quark-gluon dressing, the quark-quark bound-state kernel and the quark-photon interaction. Our predictions for the multipole form factors are compatible with available experimental data and quark model estimates. The current-quark mass evolution of the static electromagnetic properties agrees with results provided by lattice calculations. C1 [Nicmorus, D.] Goethe Univ Frankfurt, FIAS, D-60438 Frankfurt, Germany. [Nicmorus, D.] Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. [Eichmann, G.] Tech Univ Darmstadt, Inst Kernphys, D-64289 Darmstadt, Germany. [Alkofer, R.] Karl Franzens Univ Graz, Inst Phys, A-8010 Graz, Austria. RP Nicmorus, D (reprint author), Goethe Univ Frankfurt, FIAS, D-60438 Frankfurt, Germany. EM nicmorus@th.physik.uni-frankfurt.de OI Eichmann, Gernot/0000-0002-0546-2533 FU Austrian Science Fund FWF [P20592-N16]; Erwin-Schrodinger-Stipendium [J3039]; Helmholtz Young Investigator Grant [VH-NG-332]; Helmholtz International Center FX D. N. thanks D. Rischke for his support. We would also like to thank I. C. Cloet, C. S. Fischer, A. Krassnigg, G. Ramalho, and R. Williams for fruitful discussions. This work was supported by the Austrian Science Fund FWF under Project No. P20592-N16 and Erwin-Schrodinger-Stipendium No. J3039, by the Helmholtz Young Investigator Grant No. VH-NG-332, and by the Helmholtz International Center for FAIR within the framework of the LOEWE program launched by the State of Hesse, GSI, BMBF and DESY. NR 89 TC 28 Z9 28 U1 0 U2 1 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 1550-7998 J9 PHYS REV D JI Phys. Rev. D PD DEC 20 PY 2010 VL 82 IS 11 AR 114017 DI 10.1103/PhysRevD.82.114017 PG 16 WC Astronomy & Astrophysics; Physics, Particles & Fields SC Astronomy & Astrophysics; Physics GA 711DK UT WOS:000286567100002 ER PT J AU Chen, YL Liu, ZK Analytis, JG Chu, JH Zhang, HJ Yan, BH Mo, SK Moore, RG Lu, DH Fisher, IR Zhang, SC Hussain, Z Shen, ZX AF Chen, Y. L. Liu, Z. K. Analytis, J. G. Chu, J. -H. Zhang, H. J. Yan, B. H. Mo, S. -K. Moore, R. G. Lu, D. H. Fisher, I. R. Zhang, S. C. Hussain, Z. Shen, Z. -X. TI Single Dirac Cone Topological Surface State and Unusual Thermoelectric Property of Compounds from a New Topological Insulator Family SO PHYSICAL REVIEW LETTERS LA English DT Article ID TLBITE2; BI2TE3 AB Angle resolved photoemission spectroscopy study on TlBiTe2 and TlBiSe2 from a thallium-based ternary chalcogenides family revealed a single surface Dirac cone at the center of the Brillouin zone for both compounds. For TlBiSe2, the large bulk gap (similar to 200 meV) makes it a topological insulator with better mechanical properties than the previous binary 3D topological insualtor family. For TlBiTe2, the observed negative bulk gap indicates it as a semimetal, instead of a narrow-gap semiconductor as conventionally believed; this semimetality naturally explains its mysteriously small thermoelectric figure of merit comparing to other compounds in the family. Finally, the unique band structures of TlBiTe2 also suggest it as a candidate for topological superconductors. C1 [Chen, Y. L.; Liu, Z. K.; Analytis, J. G.; Chu, J. -H.; Zhang, H. J.; Yan, B. H.; Moore, R. G.; Lu, D. H.; Fisher, I. R.; Zhang, S. C.; Shen, Z. -X.] SLAC Natl Accelerator Lab, Stanford Inst Mat & Energy Sci, Menlo Pk, CA 94025 USA. [Chen, Y. L.; Liu, Z. K.; Analytis, J. G.; Chu, J. -H.; Zhang, H. J.; Yan, B. H.; Fisher, I. R.; Zhang, S. C.; Shen, Z. -X.] Stanford Univ, Dept Phys & Appl Phys, Geballe Lab Adv Mat, Stanford, CA 94305 USA. [Chen, Y. L.; Mo, S. -K.; Hussain, Z.] Univ Calif Berkeley, Lawrence Berkeley Lab, Adv Light Source, Berkeley, CA 94720 USA. RP Chen, YL (reprint author), SLAC Natl Accelerator Lab, Stanford Inst Mat & Energy Sci, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA. RI Chen, Yulin/C-1918-2012; Zhang, Shou-Cheng/B-2794-2010; Yan, Binghai /D-2404-2013; Mo, Sung-Kwan/F-3489-2013 OI Yan, Binghai /0000-0003-2164-5839; Mo, Sung-Kwan/0000-0003-0711-8514 FU Department of Energy, Office of Basic Energy Science [DE-AC02-76SF00515] FX We thank X. L. Qi and C. X. Liu for insightful discussions. This work is supported by the Department of Energy, Office of Basic Energy Science under Contract No. DE-AC02-76SF00515. NR 30 TC 120 Z9 120 U1 13 U2 89 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 0031-9007 J9 PHYS REV LETT JI Phys. Rev. Lett. PD DEC 20 PY 2010 VL 105 IS 26 AR 266401 DI 10.1103/PhysRevLett.105.266401 PG 4 WC Physics, Multidisciplinary SC Physics GA 713RI UT WOS:000286754700014 PM 21231687 ER PT J AU Giustino, F Louie, SG Cohen, ML AF Giustino, Feliciano Louie, Steven G. Cohen, Marvin L. TI Electron-Phonon Renormalization of the Direct Band Gap of Diamond SO PHYSICAL REVIEW LETTERS LA English DT Article ID TEMPERATURE-DEPENDENCE; WANNIER FUNCTIONS; SEMICONDUCTORS; SYSTEMS; PSEUDOPOTENTIALS; ISOTOPE; ENERGY AB We calculate from first principles the temperature-dependent renormalization of the direct band gap of diamond arising from electron-phonon interactions. The calculated temperature dependence is in good agreement with spectroscopic ellipsometry measurements, and the zero-point renormalization of the band gap is found to be as large as 0.6 eV. We also calculate the temperature-dependent broadening of the direct absorption edge and find good agreement with experiment. Our work calls for a critical revision of the band structures of other carbon-based materials calculated by neglecting electron-phonon interactions. C1 [Giustino, Feliciano] Univ Oxford, Dept Mat, Oxford OX1 3PH, England. [Giustino, Feliciano; Louie, Steven G.; Cohen, Marvin L.] Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA. [Giustino, Feliciano; Louie, Steven G.; Cohen, Marvin L.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Mat Sci, Berkeley, CA 94720 USA. RP Giustino, F (reprint author), Univ Oxford, Dept Mat, Parks Rd, Oxford OX1 3PH, England. RI Giustino, Feliciano/F-6343-2013; OI Giustino, Feliciano/0000-0001-9293-1176 FU NSF [DMR10-1006184]; Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division; U.S. DOE [DE-AC02-05CH11231]; ERC under European Community [239578] FX The authors are grateful to Manuel Cardona and Philip Allen for fruitful discussions. This work was supported by NSF Grant No. DMR10-1006184 (GW methodology and computation), by the Director, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, and the U.S. DOE under Contract No. DE-AC02-05CH11231 (electron-phonon codes and calculations). This work has also received funding from the ERC under the European Community's 7th Framework Programme Grant No. 239578. Part of the calculations were performed at the Oxford Supercomputing Centre. NR 33 TC 88 Z9 88 U1 0 U2 30 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 0031-9007 J9 PHYS REV LETT JI Phys. Rev. Lett. PD DEC 20 PY 2010 VL 105 IS 26 AR 265501 DI 10.1103/PhysRevLett.105.265501 PG 4 WC Physics, Multidisciplinary SC Physics GA 713RI UT WOS:000286754700010 PM 21231677 ER PT J AU Khachatryan, V Sirunyan, AM Tumasyan, A Adam, W Bergauer, T Dragicevic, M Ero, J Fabjan, C Friedl, M Fruhwirth, R Ghete, VM Hammer, J Hansel, S Hartl, C Hoch, M Horman, N Hrubec, J Jeitler, M Kasieczka, G Kiesenhofer, W Krammer, M Liko, D Mikulec, I Pernicka, M Rohringer, H Schofbeck, R Strauss, J Taurok, A Teischinger, F Waltenberger, W Walzel, G Widl, E Wulz, CE Mossolov, V Shumeiko, N Gonzalez, JS Benucci, L Ceard, L De Wolf, EA Janssen, X Maes, T Mucibello, L Ochesanu, S Roland, B Rougny, R Selvaggi, M Van Haevermaet, H Van Mechelen, P Van Remortel, N Adler, V Beauceron, S Blyweert, S D'Hondt, J Devroede, O Kalogeropoulos, A Maes, J Maes, M Tavernier, S Van Doninck, W Van Mulders, P Van Onsem, GP Villella, I Charaf, O Clerbaux, B De Lentdecker, G Dero, V Gay, APR Hammad, GH Hreus, T Marage, PE Thomas, L Velde, CV Vanlaer, P Wickens, J Costantini, S Grunewald, M Klein, B Marinov, A Ryckbosch, D Thyssen, F Tytgat, M Vanelderen, L Verwilligen, P Walsh, S Zaganidis, N Basegmez, S Bruno, G Caudron, J De Jeneret, JD Delaere, C Demin, P Favart, D Giammanco, A Gregoire, G Hollar, J Lemaitre, V Militaru, O Ovyn, S Pagano, D Pin, A Piotrzkowski, K Quertenmont, L Schul, N Beliy, N Caebergs, T Daubie, E Alves, GA De JesusDamiao, D Pol, ME Souza, MHG Carvalho, W Da Costa, EM Martins, CD De Souza, SF Mundim, L Nogima, H Oguri, V Goicochea, JMO Da Silva, WLP Santoro, A Do Amaral, SMS Sznajder, A De Araujo, FTD Dias, FA Dias, MAF Tomei, TRFP Gregores, EM Marinho, F Novaes, SF Padula, SS Darmenov, N Dimitrov, L Genchev, V Iaydjiev, P Piperov, S Rodozov, M Stoykova, S Sultanov, G Tcholakov, V Trayanov, R Vankov, I Dyulendarova, M Hadjiiska, R Kozhuharov, V Litov, L Marinova, E Mateev, M Pavlov, B Petkov, P Bian, JG Chen, GM Chen, HS Jiang, CH Liang, D Liang, S Wang, J Wang, J Wang, X Wang, Z Yang, M Zang, J Zhang, Z Ban, Y Guo, S Hu, Z Li, W Mao, Y Qian, SJ Teng, H Zhu, B Cabrera, A Moreno, BG Rios, AAO Oliveros, AFO Sanabria, JC Godinovic, N Lelas, D Lelas, K Plestina, R Polic, D Puljak, I Antunovic, Z Dzelalija, M Brigljevic, V Duric, S Kadija, K Morovic, S Attikis, A Fereos, R Galanti, M Mousa, J Nicolaou, C Ptochos, F Razis, PA Rykaczewski, H Abdel-Basit, A Assran, Y Mahmoud, MA Hektor, A Kadastik, M Kannike, K Ntel, MM Raidal, M Rebane, L Azzolini, V Eerola, P Czellar, S Harkonen, J Heikkinen, A Karimaki, V Kinnunen, R Klem, J Kortelainen, MJ Lampen, T Lassila-Perini, K Lehti, S Linden, T Luukka, P Maenpaa, T Tuominen, E Tuominiemi, J Tuovinen, E Ungaro, D Wendland, L Banzuzi, K Korpela, A Tuuva, T Sillou, D Besancon, M Dejardin, M Denegri, D Fabbro, B Faure, JL Ferri, F Ganjour, S Gentit, FX Givernaud, A Gras, P de Monchenault, GH Jarry, P Locci, E Malcles, J Marionneau, M Millischer, L Rander, J Rosowsky, A Titov, M Verrecchia, P Baffioni, S Bianchini, L Bluj, M Broutin, C Busson, P Charlot, C Dobrzynski, L de Cassagnac, RG Haguenauer, M Mine, P Mironov, C Ochando, C Paganini, P Sabes, D Salerno, R Sirois, Y Thiebaux, C Wyslouch, B Zabi, A Agram, JL Andrea, J Besson, A Bloch, D Bodin, D Brom, JM Cardaci, M Chabert, EC Collard, C Conte, E Drouhin, F Ferro, C Fontaine, JC Gele, D Goerlach, U Greder, S Juillot, P Karim, M Le Bihan, AC Mikami, Y Van Hove, P Fassi, F Mercier, D Baty, C Beaupere, N Bedjidian, M Bondu, O Boudoul, G Boumediene, D Brun, H Chanon, N Chierici, R Contardo, D Depasse, P El Mamouni, H Falkiewicz, A Fay, J Gascon, S Ille, B Kurca, T Le Grand, T Lethuillier, M Mirabito, L Perries, S Sordini, V Tosi, S Tschudi, Y Verdier, P Xiao, H Roinishvili, V Anagnostou, G Edelhoff, M Feld, L Heracleous, N Hindrichs, O Jussen, R Klein, K Merz, J Mohr, N Ostapchuk, A Perieanu, A Raupach, F Sammet, J Schael, S Sprenger, D Weber, H Weber, M Wittmer, B Ata, M Bender, W Erdmann, M Frangenheim, J Hebbeker, T Hinzmann, A Hoepfner, K Hof, C Klimkovich, T Klingebiel, D Kreuzer, P Lanske, D Magass, C Masetti, G Merschmeyer, M Meyer, A Papacz, P Pieta, H Reithler, H Schmitz, SA Sonnenschein, L Steggemann, J Teyssier, D Bontenackels, M Davids, M Duda, M Flugge, G Geenen, H Giffels, M Ahmad, WH Heydhausen, D Kress, T Kuessel, Y Linn, A Nowack, A Perchalla, L Pooth, O Rennefeld, J Sauerland, P Stahl, A Thomas, M Tornier, D Zoeller, MH Martin, MA Behrenhoff, W Behrens, U Bergholz, M Borras, K Cakir, A Campbell, A Castro, E Dammann, D Eckerlin, G Eckstein, D Flossdorf, A Flucke, G Geiser, A Glushkov, I Hauk, J Jung, H Kasemann, M Katkov, I Katsas, P Kleinwort, C Kluge, H Knutsson, A Krucker, D Kuznetsova, E Lange, W Lohmann, W Mankel, R Marienfeld, M