(Showing: 1 - 10 of 262)
(Showing: 1 - 262 of 262)
Agullo, Emmanuel and Augonnet, C{\'e}dric and Dongarra, Jack and Ltaief, Hatem and Namyst, Raymond and Thibault, Samuel and Tomov, Stanimire and others
"Faster, cheaper, better--a hybridization methodology to develop linear algebra software for GPUs"
GPU Computing Gems
, v.2
, 2010
Ahmed, Lucky and Rasulev, Bakhtiyor and Turabekova, Malakhat and Leszczynska, Danuta and Leszczynski, Jerzy
"Receptor- and ligand-based study of fullerene analogues: comprehensive computational approach including quantum-chemical, QSAR and molecular docking simulations"
Organic & Biomolecular Chemistry
, v.11
, 2013
, p.5798
10.1039/c3ob40878g
Amaro, Rommie E and Bansal, Manju
"Editorial overview: Theory and simulation: Tools for solving the insolvable"
Current Opinion in Structural Biology
, v.25
, 2014
, p.iv--v
10.1016/j.sbi.2014.04.004
Anthony Danalis;Gabriel Marin;Collin McCurdy;Jeremy S. Meredith;Philip C. Roth;Kyle Spafford;Vinod Tipparaju;Jeffrey S. Vetter;
"The Scalable Heterogeneous Computing (SHOC) benchmark suite"
3rd Workshop on General-Purpose Computation on Graphics Processing Units
, 2010
, p.63-74
Anzt, Hartwig and Tomov, Stanimire and Dongarra, Jack and Heuveline, Vincent
"A block-asynchronous relaxation method for graphics processing units"
Journal of Parallel and Distributed Computing
, v.73
, 2013
, p.1613--162
Anzt, Hartwig and Tomov, Stanimire and Gates, Mark and Dongarra, Jack and Heuveline, Vincent
"Block-asynchronous multigrid smoothers for GPU-accelerated systems"
Procedia Computer Science
, v.9
, 2012
, p.7--16
Baboulin, Marc and Donfack, Simplice and Dongarra, Jack and Grigori, Laura and R{\'e}my, Adrien and Tomov, Stanimire
"A class of communication-avoiding algorithms for solving general dense linear systems on CPU/GPU parallel machines"
Procedia Computer Science
, v.9
, 2012
, p.17--26
Bailey, Jon A. and Bazavov, A. and Bernard, C. and Bouchard, C. M. and DeTar, C. and Du, Daping and El-Khadra, A. X. and Foley, J. and Freeland, E. D. and G{\'a}miz, E. and et al.
"B_{s}?D_{s}/B?D semileptonic form-factor ratios and their application to BR(B_{s}^{0}??^{+}?^{-})"
Physical Review D
, v.85
, 2012
10.1103/PhysRevD.85.114502
Chen, Eric and Swift, Robert V. and Alderson, Nazilla and Feher, Victoria A. and Feng, Gen-Sheng and Amaro, Rommie E.
"Computation-Guided Discovery of Influenza Endonuclease Inhibitors"
ACS Medicinal Chemistry Letters
, v.5
, 2014
, p.61--64
10.1021/ml4003474
Bailey, Jon A. and Bazavov, A. and Bernard, C. and Bouchard, C. M. and DeTar, C. and Du, Daping and El-Khadra, A. X. and Foley, J. and Freeland, E. D. and G{\'a}miz, E. and et al.
"Refining New-Physics Searches in B?D?? with Lattice QCD"
Physical Review Letters
, v.109
, 2012
10.1103/PhysRevLett.109.071802
Bailey, Jon A. and Bazavov, A. and Bernard, C. and Bouchard, C. M. and DeTar, C. and Du, Daping and El-Khadra, A. X. and Foley, J. and Freeland, E. D. and G{\~A}{!'}miz, E. and et al.
"Update of from the form factor at zero recoil with three-flavor lattice QCD"
Phys. Rev. D
, v.89
, 2014
10.1103/physrevd.89.114504
Bailey, Jon A and Bazavov, A and El-Khadra, AX and Gottlieb, Steven and Jain, RD and Kronfeld, AS and Van de Water, RS and Zhou, R and others
"D semileptonic form factors and| V\_cs (d)| from 2+ 1 flavor lattice QCD"
arXiv preprint arXiv:1111.5471
, 2011
Barausse, Enrico and Buonanno, Alessandra and Hughes, Scott A and Khanna, Gaurav and O'Sullivan, Stephen and Pan, Yi
"Modeling multipolar gravitational-wave emission from small mass-ratio mergers"
Physical Review D
, v.85
, 2012
, p.024046
Barausse, Enrico and Cardoso, Vitor and Khanna, Gaurav
"Testing the Cosmic Censorship Conjecture with point particles: the effect of radiation reaction and the self-force"
Physical Review D
, v.84
, 2011
, p.104006
Baron, Riccardo and Molinero, Valeria
"Water-Driven Cavity--Ligand Binding: Comparison of Thermodynamic Signatures from Coarse-Grained and Atomic-Level Simulations"
Journal of Chemical Theory and Computation
, v.8
, 2012
, p.3696--370
10.1021/ct300121r
Baron, Riccardo and Setny, Piotr and Paesani, Francesco
"Water Structure, Dynamics, and Spectral Signatures: Changes Upon Model Cavity--Ligand Recognition"
The Journal of Physical Chemistry B
, v.116
, 2012
, p.13774--13
10.1021/jp309373q
Baron, Riccardo and Vellore, Nadeem A
"LSD1/CoREST is an allosteric nanoscale clamp regulated by H3-histone-tail molecular recognition"
Proceedings of the National Academy of Sciences
, v.109
, 2012
, p.12509--12
Barr, Daniel and Oashi, Taiji and Burkhard, Kimberly and Lucius, Sarah and Samadani, Ramin and Zhang, Jun and Shapiro, Paul and MacKerell, Alexander D. and van der Vaart, Arjan
"Importance of Domain Closure for the Autoactivation of ERK2"
Biochemistry
, v.50
, 2011
, p.8038-8048
10.1021/bi200503a
Basak, S and Bazavov, A and Bernard, C and DeTar, C and Freeland, E and Foley, J and Gottlieb, Steven and Heller, UM and Komijani, J and Laiho, J and others
"Finite-volume effects and the electromagnetic contributions to kaon and pion masses"
arXiv preprint arXiv:1409.7139
, 2014
Basak, S and Bazavov, A and Bernard, C and DeTar, C and Freeland, E and Freeman, W and Foley, J and Gottlieb, Steven and Heller, UM and Hetrick, JE and others
"Electromagnetic contributions to pseudoscalar masses"
arXiv preprint arXiv:1301.7137
, 2013
Basak, S and Bazavov, A and Bernard, C and DeTar, C and Freeland, E and Freeman, W and Foley, J and Gottlieb, Steven and Heller, UM and Hetrick, JE and others
"Status of the MILC calculation of electromagnetic contributions to pseudoscalar masses"
arXiv preprint arXiv:1210.8157
, 2012
Bazavov, A and Bernard, C and Bouchard, C and DeTar, C and Du, D and El-Khadra, AX and Foley, J and Freeland, ED and G{\'a}miz, E and Gottlieb, Steven and others
"The $ D\_s $, $ D\^{}+ $, $ B\_s $ and $ B $ decay constants from $2+ 1$ flavor lattice QCD"
arXiv preprint arXiv:1403.6796
, 2014
Bazavov, A and Bernard, C and Bouchard, C and DeTar, C and Du, D and El-Khadra, AX and Foley, J and Freeland, ED and Gamiz, E and Gottlieb, Steven and others
"Charmed and strange pseudoscalar meson decay constants from HISQ simulations"
arXiv preprint arXiv:1312.0149
, 2013
Bazavov, A and Bernard, C and Bouchard, C and DeTar, C and Du, D and El-Khadra, AX and Foley, J and Freeland, ED and Gamiz, E and Gottlieb, Steven and others
"Pseudoscalar meson physics with four dynamical quarks"
arXiv preprint arXiv:1210.8431
, 2012
Bazavov, A and Bernard, C and Bouchard, C and DeTar, C and Du, D and El-Khadra, AX and Foley, J and Freeland, ED and Gamiz, E and Gottlieb, Steven and others
"Two-point correlator fits on HISQ ensembles"
arXiv preprint arXiv:1212.0613
, 2012
Bazavov, A. and Bernard, C. and Bouchard, C. M. and DeTar, C. and Di Pierro, M. and El-Khadra, A. X. and Evans, R. T. and Freeland, E. D. and G{\'a}miz, E. and Gottlieb, Steven and et al.
"Neutral B-meson mixing from three-flavor lattice quantum chromodynamics: Determination of the SU(3)-breaking ratio ?"
Physical Review D
, v.86
, 2012
10.1103/PhysRevD.86.034503
Bazavov, A and Bernard, C and Bouchard, CM and DeTar, C and Di Pierro, M and El-Khadra, AX and Evans, RT and Freeland, ED and G{\'a}miz, E and Gottlieb, Steven and others
"B-and D-meson decay constants from three-flavor lattice QCD"
Physical Review D
, v.85
, 2012
, p.114506
Bazavov, A. and Bernard, C. and Bouchard, C. M. and DeTar, C. and Du, Daping and El-Khadra, A. X. and Foley, J. and Freeland, E. D. and G{\'a}miz, E. and Gottlieb, Steven and et al.
"Kaon semileptonic vector form factor and determination of |V_{us}| using staggered fermions"
Physical Review D
, v.87
, 2013
10.1103/PhysRevD.87.073012
Bazavov, A. and Bernard, C. and Bouchard, C. M. and DeTar, C. and Du, Daping and El-Khadra, A. X. and Foley, J. and Freeland, E. D. and G{\~A}{!'}miz, E. and Gottlieb, Steven and et al.
"Determination of from a Lattice QCD Calculation of the Semileptonic Form Factor with Physical Quark Masses"
Physical Review Letters
, v.112
, 2014
10.1103/physrevlett.112.112001
Bazavov, A and Bernard, C and Brown, N and DeTar, C and Foley, J and Gottlieb, Steven and Heller, UM and Hetrick, JE and Laiho, J and Levkova, L and others
"Symanzik flow on HISQ ensembles"
arXiv preprint arXiv:1311.1474
, 2013
Bazavov, A. and Bernard, C. and DeTar, C. and Foley, J. and Freeman, W. and Gottlieb, Steven and Heller, U. M. and Hetrick, J. E. and Kim, J. and Laiho, J. and et al.
"Leptonic-Decay-Constant Ratio f_{K^{+}}/f_{?^{+}} from Lattice QCD with Physical Light Quarks"
Physical Review Letters
, v.110
, 2013
10.1103/PhysRevLett.110.172003
Bazavov, A and Bernard, C and DeTar, C and Foley, J and Gottlieb, Steven and Heller, UM and Hetrick, JE and Laiho, J and Levkova, L and Osborn, J and others
"Update on the 2+ 1+ 1 flavor QCD equation of state with HISQ"
arXiv preprint arXiv:1312.5011
, 2013
Bazavov, A and Bernard, C and DeTar, C and Freeman, W and Gottlieb, Steven and Heller, UM and Hetrick, JE and Kim, J and Laiho, J and Levkova, L and others
"Properties of light pseudoscalars from lattice QCD with HISQ ensembles"
arXiv preprint arXiv:1111.4314
, 2011
Bazavov, A and Bernard, C and Komijani, J and Bouchard, CM and DeTar, C and Foley, J and Levkova, L and Du, D and Laiho, J and El-Khadra, AX and others
"Charmed and light pseudoscalar meson decay constants from four-flavor lattice QCD with physical light quarks"
Physical Review D
, v.90
, 2014
, p.074509
Bazavov, A. and Bernard, C. and Komijani, J. and DeTar, C. and Levkova, L. and Freeman, W. and Gottlieb, Steven and Zhou, Ran and Heller, U. M. and Hetrick, J. E. and et al.
"Lattice QCD ensembles with four flavors of highly improved staggered quarks"
Physical Review D
, v.87
, 2013
10.1103/PhysRevD.87.054505
Bazavov, A. and Bhattacharya, T. and Cheng, M. and DeTar, C. and Ding, H.-T. and Gottlieb, Steven and Gupta, R. and Hegde, P. and Heller, U. M. and Karsch, F. and et al.
"Chiral and deconfinement aspects of the QCD transition"
Physical Review D
, v.85
, 2012
10.1103/PhysRevD.85.054503
Bazavov, A. and Bhattacharya, Tanmoy and DeTar, C. E. and Ding, H.-T. and Gottlieb, Steven and Gupta, Rajan and Hegde, P. and Heller, Urs M. and Karsch, F. and Laermann, E. and et al.
"Fluctuations and correlations of net baryon number, electric charge, and strangeness: A comparison of lattice QCD results with the hadron resonance gas model"
Physical Review D
, v.86
, 2012
10.1103/PhysRevD.86.034509
Beckvermit, Jacqueline and Peterson, Joseph and Harman, Todd and Bardenhagen, Scott and Wight, Charles and Meng, Qingyu and Berzins, Martin
"Multiscale Modeling of Accidental Explosions and Detonations"
Comput. Sci. Eng.
, v.15
, 2013
, p.76--86
10.1109/mcse.2013.89
Bergonzo, Christina and Henriksen, Niel M. and Roe, Daniel R. and Swails, Jason M. and Roitberg, Adrian E. and Cheatham, Thomas E.
"Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide"
Journal of Chemical Theory and Computation
, v.10
, 2014
, p.492--499
10.1021/ct400862k
Bernard, C.
"Neutral B mixing in staggered chiral perturbation theory"
Physical Review D
, v.87
, 2013
10.1103/PhysRevD.87.114503
Bernard, C. and Bijnens, J. and G{\~A}{!'}miz, E.
"Semileptonic kaon decay in staggered chiral perturbation theory"
Phys. Rev. D
, v.89
, 2014
10.1103/physrevd.89.054510
Bernard, C and Bouchard, CM and El-Khadra, AX and Freeland, ED and G{\'a}miz, E and Kronfeld, AS and Laiho, J and Van de Water, RS and others
"B Mixing in the Standard Model and Beyond: Lattice QCD"
arXiv preprint arXiv:1111.2968
, 2011
Bernard, C. and DeTar, C. and Di Pierro, M. and El-Khadra, A. X. and Evans, R. T. and Freeland, E. D. and G{\'a}miz, E. and Gottlieb, Steven and Heller, U. M. and Hetrick, J. E. and et al.
"Tuning Fermilab heavy quarks in 2+1 flavor lattice QCD with application to hyperfine splittings"
Physical Review D
, v.83
, 2011
10.1103/PhysRevD.83.034503
Bernard, Claude and Golterman, Maarten
"On the foundations of partially quenched chiral perturbation theory"
Physical Review D
, v.88
, 2013
10.1103/PhysRevD.88.014004
Bernard, Claude and Komijani, Javad
"Chiral perturbation theory for all-staggered heavy-light mesons"
Phys. Rev. D
, v.88
, 2013
10.1103/physrevd.88.094017
Bernard, Peter S.
"Vortex Dynamics in Transitional and Turbulent Boundary Layers"
AIAA Journal
, v.51
, 2013
, p.1828--184
10.2514/1.j051811
Bielak, Jacobo and Karaoglu, Haydar and Taborda, Ricardo
"Memory-efficient displacement-based internal friction for wave propagation simulation"
Geophysics
, v.76
, 2011
, p.T131--T14
Blum, T and Van de Water, RS and Holmgren, D and Brower, R and Catterall, S and Christ, N and Kronfeld, A and Kuti, J and Mackenzie, P and Neil, ET and others
"Report of the Snowmass 2013 Computing Frontier working group on Lattice Field Theory--Lattice field theory for the energy and intensity frontiers: Scientific goals and computing needs"
arXiv preprint arXiv:1310.6087
, 2013
Bollig, Evan F and Flyer, Natasha and Erlebacher, Gordon
"Solution to PDEs using radial basis function finite-differences (RBF-FD) on multiple GPUs"
Journal of Computational Physics
, v.231
, 2012
, p.7133--715
Bouchard, CM and Freeland, ED and Bernard, C and El-Khadra, AX and Gamiz, E and Kronfeld, AS and Laiho, J and Van de Water, RS
"Neutral $ B $ mixing from 2+ 1 flavor lattice-QCD: the Standard Model and beyond"
arXiv preprint arXiv:1112.5642
, 2011
Braiterman, L. T. and Murthy, A. and Jayakanthan, S. and Nyasae, L. and Tzeng, E. and Gromadzka, G. and Woolf, T. B. and Lutsenko, S. and Hubbard, A. L.
"Distinct phenotype of a Wilson disease mutation reveals a novel trafficking determinant in the copper transporter ATP7B"
Proceedings of the National Academy of Sciences
, v.111
, 2014
, p.E1364--E1
10.1073/pnas.1314161111
Browne, James C. and Furlani, Thomas R. and McLay, Robert T. and DeLeon, Robert L. and Lu, Charng-Da and Jones, Matthew D. and Gallo, Steven M. and Ghadersohi, Amin and Patra, Abani K. and Barth, William L. and et al.
"Enabling comprehensive data-driven system management for large computational facilities"
Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis on - SC13
, 2013
10.1145/2503210.2503230
Bundick, Brent and Rhee, Noah and Zeng, Yong
"Bayes estimation via filtering equation through implicit recursive algorithms for financial ultra-high frequency data"
Statistical Inference and Interface
, v.6
, 2013
Burko, Lior M and Khanna, Gaurav
"Self-force gravitational waveforms for extreme and intermediate mass ratio inspirals. II. Importance of the second-order dissipative effect"
Physical Review D
, v.88
, 2013
, p.024002
Buttner, Michael and Choudhury, Pabitra and Karl Johnson, J. and Yates, John T.
"Vacancy clusters as entry ports for cesium intercalation in graphite"
Carbon
, v.49
, 2011
, p.3937-3952
10.1016/j.carbon.2011.05.032
Callaghan, Scott and Maechling, Philip and Small, Patrick and Milner, Kevin and Juve, Gideon and Jordan, Thomas H and Deelman, Ewa and Mehta, Gaurang and Vahi, Karan and Gunter, Dan and others
"Metrics for heterogeneous scientific workflows: A case study of an earthquake science application"
International Journal of High Performance Computing Applications
, 2011
, p.109434201
Caplan, Ronald M
"NLSEmagic: Nonlinear Schr{\"o}dinger equation multi-dimensional Matlab-based GPU-accelerated integrators using compact high-order schemes"
Computer Physics Communications
, v.184
, 2013
, p.1250--127
Cawkwell, MJ and Sanville, EJ and Mniszewski, SM and Niklasson, Anders MN
"Computing the density matrix in electronic structure theory on graphics processing units"
Journal of Chemical Theory and Computation
, v.8
, 2012
, p.4094--410
Chelakkot, R. and Gopinath, A. and Mahadevan, L. and Hagan, M. F.
"Flagellar dynamics of a connected chain of active, polar, Brownian particles"
Journal of The Royal Society Interface
, v.11
, 2013
, p.20130884-
10.1098/rsif.2013.0884
Chen, Chuanying and Pettitt, B. Montgomery
"The Binding Process of a Nonspecific Enzyme with DNA"
Biophysical Journal
, v.101
, 2011
, p.1139-1147
10.1016/j.bpj.2011.07.016
Huang, He and Wang, Liqiang and Lee, En-Jui and Chen, Po
"An MPI-CUDA implementation and optimization for parallel sparse equations and least squares (LSQR)"
Procedia Computer Science
, v.9
, 2012
, p.76--85
Chen, Yong S. and Choi, Woosong and Papanikolaou, Stefanos and Bierbaum, Matthew and Sethna, James P.
"Scaling theory of continuum dislocation dynamics in three dimensions: Self-organized fractal pattern formation"
International Journal of Plasticity
, v.46
, 2013
, p.94--129
10.1016/j.ijplas.2013.02.011
Choi, Dong Ju and Lockwood, Glenn K. and Sinkovits, Robert S. and Tatineni, Mahidhar
"Performance of Applications using Dual-Rail InfiniBand 3D Torus network on the Gordon Supercomputer"
Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE 14
, 2014
10.1145/2616498.2616541
Choi, Young Joon and Vedula, Vijay and Mittal, Rajat
"Computational Study of the Dynamics of a Bileaflet Mechanical Heart Valve in the Mitral Position"
Annals of Biomedical Engineering
, v.42
, 2014
, p.1668--168
10.1007/s10439-014-1018-4
Choudhury, Pabitra and Johnson, J. Karl
"Methyl Chloride Reactions on Lithiated Carbon Nanotubes: Lithium as Both Reactant and Catalyst"
The Journal of Physical Chemistry C
, v.115
, 2011
, p.11694--11
10.1021/jp202688k
Cioce, Christian R. and McLaughlin, Keith and Belof, Jonathan L. and Space, Brian
"A Polarizable and Transferable PHAST N 2 Potential for Use in Materials Simulation"
Journal of Chemical Theory and Computation
, v.9
, 2013
, p.5550--555
10.1021/ct400526a
Cloutier, B and Muite, BK and Rigge, P
"Performance of FORTRAN and C GPU Extensions for a Benchmark Suite of Fourier Pseudospectral Algorithms"
arXiv preprint arXiv:1206.3215
, 2012
Collins, David C. and Kritsuk, Alexei G. and Padoan, Paolo and Li, Hui and Xu, Hao and Ustyugov, Sergey D. and Norman, Michael L.
"THE TWO STATES OF STAR-FORMING CLOUDS"
The Astrophysical Journal
, v.750
, 2012
, p.13
10.1088/0004-637X/750/1/13
D'Alberto, Paolo
"A Heterogeneous Accelerated Matrix Multiplication: OpenCL+ APU+ GPU+ Fast Matrix Multiply"
arXiv preprint arXiv:1205.2927
, 2012
Daniel S. Katz and Sou{-}Cheng T. Choi and Hilmar Lapp and Ketan Maheshwari and Frank L{\{o}}ffler and Matthew Turk and Marcus D. Hanwell and Nancy Wilkins{-}Diehr and James Hetherington and James Howison and Shel Swenson and Gabrielle Allen and Anne C. E
"Summary of the First Workshop on Sustainable Software for Science: Practice and Experiences {(WSSSPE1)}"
CoRR
, v.abs/140
, 2014
Demir, Azlem and Amaro, Rommie E.
"Designing Novel Inhibitors of Trypanosoma brucei"
In Silico Models for Drug Discovery
, 2013
, p.231--243
10.1007/978-1-62703-342-8_15
Demir, Azlem and Labaied, Mehdi and Merritt, Chris and Stuart, Ken and Amaro, Rommie E.
"Computer-Aided Discovery of Trypanosoma brucei RNA-Editing Terminal Uridylyl Transferase 2 Inhibitors"
Chem Biol Drug Des
, v.84
, 2014
, p.131--139
10.1111/cbdd.12302
DeTar, Carleton and Kronfeld, AS and Lee, Song-Haeng and Levkova, L and Mohler, D and Simone, JN
"Charmonium mass splittings at the physical point"
arXiv preprint arXiv:1211.2253
, 2012
Du, Daping and DeTar, Carleton and Kronfeld, Andreas and Laiho, Jack and Meurice, Yannick and Qiu, Si-wei
"Semileptonic form factor ratio B\_s-> D\_s/B-> D and its application to BR (B\^{} 0\_s->$\backslash$ mu\^{}+$\backslash$ mu\^{}-)"
arXiv preprint arXiv:1111.1796
, 2011
Du, Peng and Luszczek, Piotr and Tomov, Stan and Dongarra, Jack
"Soft error resilient QR factorization for hybrid system with GPGPU"
Journal of Computational Science
, v.4
, 2013
, p.457--464
Du, Peng and Tomov, Stanimire and Dongarra, Jack
"Providing GPU capability to LU and QR within the ScaLAPACK framework"
LAPACK Working Note, Tech. Rep
, v.272
, 2012
Du, Peng and Weber, Rick and Luszczek, Piotr and Tomov, Stanimire and Peterson, Gregory and Dongarra, Jack
"From CUDA to OpenCL: Towards a performance-portable solution for multi-platform GPU programming"
Parallel Computing
, v.38
, 2012
, p.391--407
Durrant, Jacob D and Amaro, Rommie E
"De Novo Design by Fragment Growing and Docking"
De novo Molecular Design
, 2013
, p.125--142
Durrant, Jacob D and Amaro, Rommie E
"WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets"
BMC Bioinformatics
, v.15
, 2014
, p.159
10.1186/1471-2105-15-159
Durrant, Jacob D. and Amaro, Rommie E.
"LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry"
PLoS Comput Biol
, v.10
, 2014
, p.e1003720
10.1371/journal.pcbi.1003720
Durrant, Jacob D and Votapka, Lane Andrew and S{\~A}¸rensen, Jesper and Amaro, Rommie E.
"POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics"
Journal of Chemical Theory and Computation
, 2014
, p.140929123
10.1021/ct500381c
Eiring, A M and Page, B D G and Kraft, I L and Mason, C C and Vellore, N A and Resetca, D and Zabriskie, M S and Zhang, T Y and Khorashad, J S and Engar, A J and et al.
"Combined STAT3 and BCR-ABL1 inhibition induces synthetic lethality in therapy-resistant chronic myeloid leukemia"
Leukemia
, 2014
10.1038/leu.2014.245
Elsaidi, Sameh K. and Mohamed, Mona H. and Wojtas, Lukasz and Chanthapally, Anjana and Pham, Tony and Space, Brian and Vittal, Jagadese J. and Zaworotko, Michael J.
"Putting the Squeeze on CH 4 and CO 2 through Control over Interpenetration in Diamondoid Nets"
Journal of the American Chemical Society
, v.136
, 2014
, p.5072--507
10.1021/ja500005k
Feher, Victoria A and Durrant, Jacob D and Van Wart, Adam T and Amaro, Rommie E
"Computational approaches to mapping allosteric pathways"
Current Opinion in Structural Biology
, v.25
, 2014
, p.98--103
10.1016/j.sbi.2014.02.004
Fily, Yaouen and Baskaran, Aparna and Hagan, Michael F.
"Dynamics of self-propelled particles under strong confinement"
Soft Matter
, 2014
10.1039/c4sm00975d
Forrest, Katherine A. and Pham, Tony and Hogan, Adam and McLaughlin, Keith and Tudor, Brant and Nugent, Patrick and Burd, Stephen D. and Mullen, Ashley and Cioce, Christian R. and Wojtas, Lukasz and et al.
"Computational Studies of CO 2 Sorption and Separation in an Ultramicroporous Metal-Organic Material"
The Journal of Physical Chemistry C
, v.117
, 2013
, p.17687--17
10.1021/jp405781c
Forrest, Katherine A. and Pham, Tony and McLaughlin, Keith and Belof, Jonathan L. and Stern, Abraham C. and Zaworotko, Michael J. and Space, Brian
"Simulation of the Mechanism of Gas Sorption in a Metal--Organic Framework with Open Metal Sites: Molecular Hydrogen in PCN-61"
The Journal of Physical Chemistry C
, v.116
, 2012
, p.15538--15
10.1021/jp306084t
Forrest, Katherine A. and Pham, Tony and McLaughlin, Keith and Hogan, Adam and Space, Brian
"Insights into an intriguing gas sorption mechanism in a polar metal-organic framework with open-metal sites and narrow channels"
Chemical Communications
, v.50
, 2014
, p.7283
10.1039/c4cc03070b
Meredith, J. S.;Roth, P. C.;Spafford, K. L.;Vetter, J. S.;
"Performance Implications of Nonuniform Device Topologies in Scalable Heterogeneous Architectures"
IEEE Micro
, v.31
, 2011
, p.66-75
Furlani, Thomas R and Jones, Matthew D and Gallo, Steven M and Bruno, Andrew E and Lu, Charng-Da and Ghadersohi, Amin and Gentner, Ryan J and Patra, Abani and DeLeon, Robert L and Laszewski, Gregor and others
"Performance metrics and auditing framework using application kernels for high-performance computer systems"
Concurrency and Computation: Practice and Experience
, v.25
, 2013
, p.918--931
Galindo-Murillo, Rodrigo and Cheatham, Thomas E.
"DNA Binding Dynamics and Energetics of Cobalt, Nickel, and Copper Metallopeptides"
ChemMedChem
, v.9
, 2014
, p.1252--125
10.1002/cmdc.201402020
Galindo-Murillo, Rodrigo and Roe, Daniel R and Cheatham III, Thomas E
"On the absence of intrahelical DNA dynamics on the $\mu$s to ms timescale"
Nature communications
, v.5
, 2014
Galindo-Murillo, Rodrigo and Roe, Daniel R. and Cheatham, Thomas E.
"Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)"
Biochimica et Biophysica Acta (BBA) - General Subjects
, 2014
10.1016/j.bbagen.2014.09.007
G{\'a}miz, E and Bazavov, A and Bernard, C and Bouchard, C and DeTar, C and Du, D and El-Khadra, AX and Foley, J and Freeland, ED and Gottlieb, Steven and others
"K semileptonic form factor with HISQ fermions at the physical point"
arXiv preprint arXiv:1311.7264
, 2013
Gamiz, E and DeTar, C and El-Khadra, AX and Kronfeld, AS and Mackenzie, PB and Simone, J
"K-> pi l nu form factors with staggered quarks"
arXiv preprint arXiv:1111.2021
, 2011
Ganewatta, Mitra S. and Chen, Yung Pin and Wang, Jifu and Zhou, Jihua and Ebalunode, Jerry and Nagarkatti, Mitzi and Decho, Alan W. and Tang, Chuanbing
"Bio-inspired resin acid-derived materials as anti-bacterial resistance agents with unexpected activities"
Chemical Science
, v.5
, 2014
, p.2011
10.1039/c4sc00034j
Gao, Shuang and Peterson, Gregory D
"GASPRNG: GPU accelerated scalable parallel random number generator library"
Computer Physics Communications
, v.184
, 2013
, p.1241--124
Gatz, Andreas W. and Bucher, Denis and Lindert, Steffen and McCammon, J. Andrew
"Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields"
Journal of Chemical Theory and Computation
, v.10
, 2014
, p.1631--163
10.1021/ct401049q
Glaser, Jens and Medapuram, Pavani and Beardsley, Thomas M. and Matsen, Mark W. and Morse, David C.
"Universality of Block Copolymer Melts"
Phys. Rev. Lett.
, v.113
, 2014
, p.068302
10.1103/PhysRevLett.113.068302
Glaser, Jens and Qin, Jian and Medapuram, Pavani and Morse, David C.
"Collective and Single-Chain Correlations in Disordered Melts of Symmetric Diblock Copolymers: Quantitative Comparison of Simulations and Theory"
Macromolecules
, v.47
, 2014
, p.851--869
10.1021/ma401694u
Glaser, Jens and Qin, Jian and Medapuram, Pavani and M{\"u}ller, Marcus and Morse, David C.
"Test of a scaling hypothesis for the structure factor of disordered diblock copolymer melts"
Soft Matter
, v.8
, 2012
, p.11310
10.1039/c2sm26536b
Godet, O and Lombardi, James C and Antonini, F and Barret, D and Webb, NA and Vingless, Jacob and Thomas, Morgan
"Implications of the Delayed 2013 Outburst of ESO 243-49 HLX-1"
The Astrophysical Journal
, v.793
, 2014
, p.105
Graves, Robert and Jordan, Thomas H and Callaghan, Scott and Deelman, Ewa and Field, Edward and Juve, Gideon and Kesselman, Carl and Maechling, Philip and Mehta, Gaurang and Milner, Kevin and others
"CyberShake: A physics-based seismic hazard model for southern California"
Pure and Applied Geophysics
, v.168
, 2011
, p.367--381
Graziano, Giuseppe
"Molecular driving forces of the pocket--ligand hydrophobic association"
Chemical Physics Letters
, v.533
, 2012
, p.95--99
Gu, Zheng and Small, Matthew and Yuan, Xin and Marathe, Aniruddha and Lowenthal, David K.
"Protocol Customization for Improving MPI Performance on RDMA-Enabled Clusters"
International Journal of Parallel Programming
, v.41
, 2013
, p.682--703
10.1007/s10766-013-0242-0
Gygi, Fran{\~A}{\S}ois and Duchemin, Ivan
"Efficient Computation of Hartree-Fock Exchange Using Recursive Subspace Bisection"
Journal of Chemical Theory and Computation
, v.9
, 2013
, p.582--587
10.1021/ct3007088
HAGAN, Michael F.
"Modeling Viral Capsid Assembly"
Advances in Chemical Physics: Volume 155
, 2014
, p.1--68
10.1002/9781118755815.ch01
Hagan, Michael F. and Elrad, Oren M. and Jack, Robert L.
"Mechanisms of kinetic trapping in self-assembly and phase transformation"
The Journal of Chemical Physics
, v.135
, 2011
, p.104115
10.1063/1.3635775
Hagy, Matthew C. and Hernandez, Rigoberto
"Dynamical simulation of dipolar Janus colloids: Dynamical properties"
The Journal of Chemical Physics
, v.138
, 2013
, p.184903
10.1063/1.4803864
Hagy, Matthew C. and Hernandez, Rigoberto
"Dynamical simulation of dipolar Janus colloids: Equilibrium structure and thermodynamics"
The Journal of Chemical Physics
, v.137
, 2012
, p.044505
10.1063/1.4737432
Hagy, Matthew C. and Hernandez, Rigoberto
"Dynamical simulation of electrostatic striped colloidal particles"
The Journal of Chemical Physics
, v.140
, 2014
, p.034701
10.1063/1.4859855
Hall, Clifford and Ji, Weixiao and Blaisten-Barojas, Estela
"The Metropolis Monte Carlo method with CUDA enabled Graphic Processing Units"
Journal of Computational Physics
, v.258
, 2014
, p.871--879
Hall, Monica and Beckvermit, Jacqueline C. and Wight, Charles A. and Harman, Todd and Berzins, Martin
"The influence of an applied heat flux on the violence of reaction of an explosive device"
Proceedings of the Conference on Extreme Science and Engineering Discovery Environment Gateway to Discovery - XSEDE 13
, 2013
10.1145/2484762.2484786
Hallock, Michael J. and Stone, John E. and Roberts, Elijah and Fry, Corey and Luthey-Schulten, Zaida
"Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations"
Parallel Computing
, v.40
, 2014
, p.86--99
10.1016/j.parco.2014.03.009
Henriksen, Niel M. and Hayatshahi, Hamed S. and Davis, Darrell R. and Cheatham, Thomas E.
"Structural and Energetic Analysis of 2-Aminobenzimidazole Inhibitors in Complex with the Hepatitis C Virus IRES RNA Using Molecular Dynamics Simulations"
J. Chem. Inf. Model.
, v.54
, 2014
, p.1758--177
10.1021/ci500132c
Henriksen, Niel M and Roe, Daniel R and Cheatham III, Thomas E
"Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations"
The Journal of Physical Chemistry B
, v.117
, 2013
, p.4014--402
Holl, Sonja and Memon, Shahbaz and Schuller, Bernd and Riedel, Morris and Mohammed, Yassene and Palmblad, Magnus and Grimshaw, Andrew
"Enhanced Resource Management Enabling Standard Parameter Sweep Jobs for Scientific Applications"
2013 42nd International Conference on Parallel Processing
, 2013
10.1109/icpp.2013.92
Hu, Fang and Kocaogul, Ibrahim and Li, Xiaodong
"On the adjoint problem in duct acoustics and its solution by the Time Domain Wave Packet method"
18th AIAA/CEAS Aeroacoustics Conference (33rd AIAA Aeroacoustics Conference)
, 2012
10.2514/6.2012-2247
Hu, Fang Q.
"An efficient solution of time domain boundary integral equations for acoustic scattering and its acceleration by Graphics Processing Units"
19th AIAA/CEAS Aeroacoustics Conference
, 2013
10.2514/6.2013-2018
Hu, Fang Q.
"Further development of a time domain boundary integral equation method for aeroacoustic scattering computations"
20th AIAA/CEAS Aeroacoustics Conference
, 2014
10.2514/6.2014-3194
Hu, Fang Q. and Li, X. D. and Li, X. Y. and Jiang, M.
"Time Domain Wave Packet Method and Suppression of Instability Waves in Aeroacoustic Computations"
Journal of Fluids Engineering
, v.136
, 2014
, p.061203
10.1115/1.4025866
Hu, Han and Ji, Hai-Feng and Sun, Ying
"The effect of oxygen vacancies on water wettability of a ZnO surface"
Physical Chemistry Chemical Physics
, v.15
, 2013
, p.16557
10.1039/c3cp51848e
Hu, Han and Sun, Ying
"Effect of nanopatterns on Kapitza resistance at a water-gold interface during boiling: A molecular dynamics study"
Journal of Applied Physics
, v.112
, 2012
, p.053508
10.1063/1.4749393
Hu, H. and Sun, Y.
"Molecular dynamics simulations of disjoining pressure effect in ultra-thin water film on a metal surface"
Appl. Phys. Lett.
, v.103
, 2013
, p.263110
10.1063/1.4858469
Iacovella, Christopher R and French, William R and Cook, Brandon G and Kent, Paul RC and Cummings, Peter T
"Role of Polytetrahedral Structures in the Elongation and Rupture of Gold Nanowires"
ACS nano
, v.5
, 2011
, p.10065--10
Ieong, Pek U. and S{\~A}¸rensen, Jesper and Vemu, Prasantha L. and Wong, Celia W. and Demir, Azlem and Williams, Nadya P. and Wang, Jianwu and Crawl, Daniel and Swift, Robert V. and Malmstrom, Robert D. and et al.
"Progress towards Automated Kepler Scientific Workflows for Computer-aided Drug Discovery and Molecular Simulations"
Procedia Computer Science
, v.29
, 2014
, p.1745--175
10.1016/j.procs.2014.05.159
Isbiliroglu, Yigit and Taborda, Ricardo and Bielak, Jacobo
"Coupled Soil-Structure Interaction Effects of Building Clusters During Earthquakes"
Earthquake Spectra
, 2013
, p.131030142
10.1193/102412EQS315M
Ivanova, N. and Justham, S. and Nandez, J. L. A. and Lombardi, J. C.
"Identification of the Long-Sought Common-Envelope Events"
Science
, v.339
, 2013
, p.433--435
10.1126/science.1225540
Karp, Jerome M and Erylimaz, Ertan and Cowburn, David
"Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins"
Journal of biomolecular NMR
, 2014
, p.1--11
Kerr, A. and Diamos, G. and Yalamanchili, S.
"{GPU Application Development, Debugging, and Performance Tuning with GPU Ocelot}"
GPU Computing Gems
, v.2
, 2011
Khajeh-Saeed, Ali and Blair Perot, J
"Direct numerical simulation of turbulence using GPU accelerated supercomputers"
Journal of Computational Physics
, v.235
, 2013
, p.241--257
Khajeh-Saeed, Ali and Perot, J Blair
"Computational fluid dynamics simulations using many graphics processors"
Computing in Science \& Engineering
, v.14
, 2012
, p.10--19
Khanna, Gaurav
"High-precision numerical simulations on a CUDA GPU: kerr black hole tails"
Journal of Scientific Computing
, v.56
, 2013
, p.366--380
Kim, RyangGuk and Corona, Rosario I and Hong, Bo and Guo, Jun-tao
"Benchmarks for flexible and rigid transcription factor-DNA docking"
BMC structural biology
, v.11
, 2011
, p.45
Kokubo, Hironori and Hu, Char Y. and Pettitt, B. Montgomery
"Peptide Conformational Preferences in Osmolyte Solutions: Transfer Free Energies of Decaalanine"
Journal of the American Chemical Society
, v.133
, 2011
, p.1849-1858
10.1021/ja1078128
Kraft, Ira L and Page, Brent DG and Zhang, Tian Y and Khorashad, Jamshid S and Vellore, Nadeem A and Reynolds, Kimberly R and Pomicter, Anthony D and Senina, Anna V and Zabriskie, Matthew S and Ahmad, Shazia and others
"BP5-087, a Novel STAT3 Inhibitor, Combines With BCR-ABL1 Inhibition To Overcome Kinase-Independent Resistance In Chronic Myeloid Leukemia"
Blood
, v.122
, 2013
, p.854--854
Kritsuk, A. G. and Lee, C. T. and Norman, M. L.
"A supersonic turbulence origin of Larsons laws"
Monthly Notices of the Royal Astronomical Society
, v.436
, 2013
, p.3247-3261
10.1093/mnras/stt1805
Kritsuk, Alexei G and Nordlund, {\AA}ke and Collins, David and Padoan, Paolo and Norman, Michael L and Abel, Tom and Banerjee, Robi and Federrath, Christoph and Flock, Mario and Lee, Dongwook and others
"Comparing numerical methods for isothermal magnetized supersonic turbulence"
The Astrophysical Journal
, v.737
, 2011
, p.13
Kritsuk, Alexei G. and Norman, Michael L. and Wagner, Rick
"ON THE DENSITY DISTRIBUTION IN STAR-FORMING INTERSTELLAR CLOUDS"
The Astrophysical Journal
, v.727
, 2011
, p.L20
10.1088/2041-8205/727/1/L20
Kritsuk,Alexei G. and Wagner,Rick and Norman,Michael L.
"Energy cascade and scaling in supersonic isothermal turbulence"
Journal of Fluid Mechanics
, v.729
, 2013
10.1017/jfm.2013.342
Kulkarni, Rhushikesh A. and Stanford, Stephanie M. and Vellore, Nadeem A. and Krishnamurthy, Divya and Bliss, Matthew R. and Baron, Riccardo and Bottini, Nunzio and Barrios, Amy M.
"Thiuram Disulfides as Pseudo-irreversible Inhibitors of Lymphoid Tyrosine Phosphatase"
ChemMedChem
, v.8
, 2013
, p.1561--156
10.1002/cmdc.201300215
Kurzak, Jakub and Dongarra, Jack
"Linear Algebra Libraries for High-Performance Computing: Scientific Computing with Multicore and Accelerators"
SC12
, 2012
Kurzak, Jakub and Luszczek, Piotr and Faverge, Mathieu and Dongarra, Jack
"LU factorization with partial pivoting for a multicore system with accelerators"
Parallel and Distributed Systems, IEEE Transactions on
, v.24
, 2013
, p.1613--162
Kurzak, Jakub and Tomov, Stanimire and Dongarra, Jack
"Autotuning GEMM kernels for the Fermi GPU"
Parallel and Distributed Systems, IEEE Transactions on
, v.23
, 2012
, p.2045--205
Lai, Jonathan and Chen, Ke and Luthey-Schulten, Zaida
"Structural Intermediates and Folding Events in the Early Assembly of the Ribosomal Small Subunit"
The Journal of Physical Chemistry B
, v.117
, 2013
, p.13335--13
10.1021/jp404106r
Larsson, Per and Kasson, Peter M.
"Lipid Tail Protrusion in Simulations Predicts Fusogenic Activity of Influenza Fusion Peptide Mutants and Conformational Models"
PLoS Computational Biology
, v.9
, 2013
, p.e1002950
10.1371/journal.pcbi.1002950
Lee, Tai-Sung and Radak, Brian K and Pabis, Anna and York, Darrin M
"A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations"
Journal of chemical theory and computation
, v.9
, 2012
, p.153--164
Le Grand, Scott and G{\"o}tz, Andreas W and Walker, Ross C
"SPFP: Speed without compromise---A mixed precision model for GPU accelerated molecular dynamics simulations"
Computer Physics Communications
, v.184
, 2013
, p.374--380
Levkova, L. and DeTar, C.
"Charm annihilation effects on the hyperfine splitting in charmonium"
Physical Review D
, v.83
, 2011
10.1103/PhysRevD.83.074504
Levkova, L. and DeTar, C.
"Quark-Gluon Plasma in an External Magnetic Field"
Physical Review Letters
, v.112
, 2014
10.1103/physrevlett.112.012002
Li, Li and Martinis, Susan A. and Luthey-Schulten, Zaida
"Capture and Quality Control Mechanisms for Adenosine-5-triphosphate Binding"
Journal of the American Chemical Society
, v.135
, 2013
, p.6047--605
10.1021/ja308044w
Lin, Zhenjian and Koch, Michael and Abdel Aziz, May Hamdy and Galindo-Murillo, Rodrigo and Tianero, Ma. Diarey and Cheatham, Thomas E. and Barrows, Louis R. and Reilly, Chris A. and Schmidt, Eric W.
"Oxazinin A, a Pseudodimeric Natural Product of Mixed Biosynthetic Origin from a Filamentous Fungus"
Org. Lett.
, v.16
, 2014
, p.4774--477
10.1021/ol502227x
Liu, Yang and Bai, Rong and Wang, Lin and Zhang, Cuntai and Zhao, Ruifu and Wan, Deli and Chen, Xinshan and Caceres, Gabriel and Barr, Daniel and Barajas-Martinez, Hector and Antzelevitch, Charles and Hu, Dan
"Identification of a Novel De Novo Mutation Associated with {PRKAG}2 Cardiac Syndrome and Early Onset of Heart Failure"
{PLoS} {ONE}
, v.8
, 2013
, p.e64603
Liu, Yuzhi and Zhou, Ran and Bailey, Jon A and Bazavov, A and Bernard, C and Bouchard, CM and DeTar, C and Du, Daping and El-Khadra, AX and Foley, J and others
"Heavy-meson semileptonic decays for the Standard Model and beyond"
arXiv preprint arXiv:1312.3197
, 2013
Lombardi, James C and McInally, William G and Faber, Joshua A
"An efficient radiative cooling approximation for use in hydrodynamic simulations"
Monthly Notices of the Royal Astronomical Society
, v.447
, 2015
, p.25--35
Ltaief, Hatem and Tomov, Stanimire and Nath, Rajib and Dongarra, Jack
"Hybrid multicore cholesky factorization with multiple gpu accelerators"
IEEE Transaction on Parallel and Distributed Systems
, 2010
Lu, Gui and Hu, Han and Duan, Yuanyuan and Sun, Ying
"Wetting kinetics of water nano-droplet containing non-surfactant nanoparticles: A molecular dynamics study"
Appl. Phys. Lett.
, v.103
, 2013
, p.253104
10.1063/1.4837717
Luo, Miao and Lu, Xiaoyi and Hamidouche, Khaled and Kandalla, Krishna and Panda, Dhabaleswar K.
"Initial study of multi-endpoint runtime for MPI+OpenMP hybrid programming model on multi-core systems"
Proceedings of the 19th ACM SIGPLAN symposium on Principles and practice of parallel programming - PPoPP 14
, 2014
10.1145/2555243.2555287
Mallya, G. and Zhao, L. and Song, X. C. and Niyogi, D. and Govindaraju, R. S.
"2012 Midwest Drought in the United States"
Journal of Hydrologic Engineering
, v.18
, 2013
, p.737-745
10.1061/(ASCE)HE.1943-5584.0000786
Malmstrom, Robert D. and Lee, Christopher T. and Van Wart, Adam T. and Amaro, Rommie E.
"Application of Molecular-Dynamics Based Markov State Models to Functional Proteins"
Journal of Chemical Theory and Computation
, v.10
, 2014
, p.2648--265
10.1021/ct5002363
Mandeltort, Lynn and Choudhury, Pabitra and Johnson, J. Karl and Yates, John T.
"Methyl Radical Reactivity on the Basal Plane of Graphite"
The Journal of Physical Chemistry C
, v.116
, 2012
, p.18347--18
10.1021/jp3063367
Mandeltort, Lynn and Choudhury, Pabitra and Johnson, J Karl and Yates Jr, John T
"Reaction of the basal plane of graphite with the methyl radical"
The Journal of Physical Chemistry Letters
, v.3
, 2012
, p.1680--168
Masta, Philipp and Mundim, Bruno C and Faber, Joshua A and Haas, Roland and Noble, Scott C and Bode, Tanja and L{\~A}¶ffler, Frank and Ott, Christian D and Reisswig, Christian and Schnetter, Erik
"GRHydro: a new open-source general-relativistic magnetohydrodynamics code for the Einstein toolkit"
Class. Quantum Grav.
, v.31
, 2013
, p.015005
10.1088/0264-9381/31/1/015005
McHarris, Danielle M. and Barr, Daniel A.
"Truncated Variants of the {GCN}4 Transcription Activator Protein Bind {DNA} with Dramatically Different Dynamical Motifs"
Journal of Chemical Information and Modeling
, v.54
, 2014
, p.2869--287
McLaughlin, Keith and Cioce, Christian R. and Belof, Jonathan L. and Space, Brian
"A molecular H2 potential for heterogeneous simulations including polarization and many-body van der Waals interactions"
The Journal of Chemical Physics
, v.136
, 2012
, p.194302
10.1063/1.4717705
McLaughlin, Keith and Cioce, Christian R. and Pham, Tony and Belof, Jonathan L. and Space, Brian
"Efficient calculation of many-body induced electrostatics in molecular systems"
The Journal of Chemical Physics
, v.139
, 2013
, p.184112
10.1063/1.4829144
Memon, Shahbaz and Demeler, Borries and Singh, Raminder and Riedel, Morris and Attig, Norbert and Gorbet, Gary and Gunathilake, Lahiru and Riedel, Morris and Lippert, Thomas and Marru, Suresh and et al.
"Improvements of the UltraScan scientific gateway to enable computational jobs on large-scale and open-standards based cyberinfrastructures"
Proceedings of the Conference on Extreme Science and Engineering Discovery Environment Gateway to Discovery - XSEDE 13
, 2013
10.1145/2484762.2484800
Memon, Shahbaz and Riedel, Morris and Holl, Sonja and Riedel, Morris and Schuller, Bernd and Grimshaw, Andrew
"Enhancing the performance of scientific workflow execution in e-science environments by harnessing the standards based parameter sweep model"
Proceedings of the Conference on Extreme Science and Engineering Discovery Environment Gateway to Discovery - XSEDE 13
, 2013
10.1145/2484762.2484820
Memon, Shahbaz and Riedel, Morris and Janetzko, Florian and Demeler, Borries and Gorbet, Gary and Marru, Suresh and Grimshaw, Andrew and Gunathilake, Lahiru and Singh, Raminder and Attig, Norbert and et al.
"Advancements of the UltraScan scientific gateway for open standards-based cyberinfrastructures"
Concurrency and Computation: Practice and Experience
, 2014
10.1002/cpe.3251
Meng, Qingyu and Humphrey, Alan and Schmidt, John and Berzins, Martin
"Preliminary experiences with the uintah framework on Intel Xeon Phi and stampede"
Proceedings of the Conference on Extreme Science and Engineering Discovery Environment Gateway to Discovery - XSEDE 13
, 2013
10.1145/2484762.2484779
Meredith, Jeremy S and Roth, Philip C and Spafford, Kyle L and Vetter, Jeffrey S
"Performance implications of nonuniform device topologies in scalable heterogeneous architectures"
Micro, IEEE
, v.31
, 2011
, p.66--75
Meredith, JS; Alvarez, G; Maier, TA; Schulthess, TC; Vetter, JS
"Accuracy and performance of graphics processors: A Quantum Monte Carlo application case study"
PARALLEL COMPUTING
, v.35
, 2009
, p.151
View record at
Web of Science
10.1016/j.parco.2008.12.00
Mittal, Rajat and Erath, Byron D. and Plesniak, Michael W.
"Fluid Dynamics of Human Phonation and Speech"
Annual Review of Fluid Mechanics
, v.45
, 2013
, p.437--467
10.1146/annurev-fluid-011212-140636
Mohamed, Mona H. and Elsaidi, Sameh K. and Pham, Tony and Forrest, Katherine A. and Tudor, Brant and Wojtas, Lukasz and Space, Brian and Zaworotko, Michael J.
"Pillar substitution modulates CO2 affinity in mmo topology networks"
Chemical Communications
, v.49
, 2013
, p.9809
10.1039/c3cc44745f
Mohamed, Mona H. and Elsaidi, Sameh K. and Wojtas, Lukasz and Pham, Tony and Forrest, Katherine A. and Tudor, Brant and Space, Brian and Zaworotko, Michael J.
"Highly Selective CO2 Uptake in Uninodal 6-Connected mmo Nets Based upon MO4 2-- (M = Cr, Mo) Pillars"
Journal of the American Chemical Society
, v.134
, 2012
, p.19556--19
10.1021/ja309452y
Mullen, Ashley L. and Pham, Tony and Forrest, Katherine A. and Cioce, Christian R. and McLaughlin, Keith and Space, Brian
"A Polarizable and Transferable PHAST CO 2 Potential for Materials Simulation"
Journal of Chemical Theory and Computation
, v.9
, 2013
, p.5421--542
10.1021/ct400549q
Myers, Christopher G. and Pettitt, B. Montgomery
"Communication: Origin of the contributions to DNA structure in phages"
The Journal of Chemical Physics
, v.138
, 2013
, p.071103
10.1063/1.4791708
Nandez, Jose LA and Ivanova, Natalia and Lombardi Jr, JC
"V1309 Sco?Understanding a Merger"
The Astrophysical Journal
, v.786
, 2014
, p.39
Neil, ET and Bailey, Jon A and Bazavov, A and Bernard, C and Bouchard, CM and DeTar, C and Di Pierro, M and El-Khadra, AX and Evans, RT and Freeland, E and others
"B and D meson decay constants from 2+ 1 flavor improved staggered simulations"
arXiv preprint arXiv:1112.3978
, 2011
Nugent, Patrick and Pham, Tony and McLaughlin, Keith and Georgiev, Peter A. and Lohstroh, Wiebke and Embs, Jan Peter and Zaworotko, Michael J. and Space, Brian and Eckert, Juergen
"Dramatic effect of pore size reduction on the dynamics of hydrogen adsorbed in metal-organic materials"
J. Mater. Chem. A
, v.2
, 2014
, p.13884
10.1039/c4ta02171a
Okal, Abood and Cornillie, Sean and Matissek, Stephan J. and Matissek, Karina J. and Cheatham, Thomas E. and Lim, Carol S.
"Re-Engineered p53 Chimera with Enhanced Homo-Oligomerization That Maintains Tumor Suppressor Activity"
Mol. Pharmaceutics
, v.11
, 2014
, p.2442--245
10.1021/mp500202p
Ozer, Gungor and Quirk, Stephen and Hernandez, Rigoberto
"Thermodynamics of Decaalanine Stretching in Water Obtained by Adaptive Steered Molecular Dynamics Simulations"
Journal of Chemical Theory and Computation
, v.8
, 2012
, p.4837--484
10.1021/ct300709u
Pan, Liubin and Padoan, Paolo and Scalo, John and Kritsuk, Alexei G and Norman, Michael L
"Turbulent clustering of protoplanetary dust and planetesimal formation"
The Astrophysical Journal
, v.740
, 2011
, p.6
Park, Jun Hong and Choudhury, Pabitra and Kummel, Andrew C.
"NO Adsorption on Copper Phthalocyanine Functionalized Graphite"
The Journal of Physical Chemistry C
, v.118
, 2014
, p.10076--10
10.1021/jp5002258
Pasi, M. and Maddocks, J. H. and Beveridge, D. and Bishop, T. C. and Case, D. A. and Cheatham, T. and Dans, P. D. and Jayaram, B. and Lankas, F. and Laughton, C. and et al.
"ABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA"
Nucleic Acids Research
, 2014
10.1093/nar/gku855
Perkett, Matthew R. and Hagan, Michael F.
"Using Markov state models to study self-assembly"
The Journal of Chemical Physics
, v.140
, 2014
, p.214101
10.1063/1.4878494
Perlmutter, Jason D and Perkett, Matthew R and Hagan, Michael F
"Pathways for virus assembly around nucleic acids"
arXiv preprint arXiv:1405.3310
, 2014
Perlmutter, J. D. and Qiao, C. and Hagan, M. F.
"Viral genome structures are optimal for capsid assembly"
eLife
, v.2
, 2013
, p.e00632-e0
10.7554/eLife.00632
Peterson, Joseph R. and Wight, Charles A.
"An Eulerian--Lagrangian computational model for deflagration and detonation of high explosives"
Combustion and Flame
, v.159
, 2012
, p.2491--249
10.1016/j.combustflame.2012.02.006
Peterson, Joseph R and Wight, Charles A and Berzins, Martin
"Applying high-performance computing to petascale explosive simulations"
Procedia Computer Science
, v.18
, 2013
, p.2259--226
Pham, Tony and Forrest, Katherine A. and Eckert, Juergen and Georgiev, Peter A. and Mullen, Ashley and Luebke, Ryan and Cairns, Amy J. and Belmabkhout, Youssef and Eubank, Jarrod F. and McLaughlin, Keith and et al.
"Investigating the Gas Sorption Mechanism in an rht -Metal-Organic Framework through Computational Studies"
The Journal of Physical Chemistry C
, v.118
, 2014
, p.439--456
10.1021/jp409950r
Pham, Tony and Forrest, Katherine A. and Hogan, Adam and McLaughlin, Keith and Belof, Jonathan L. and Eckert, Juergen and Space, Brian
"Simulations of hydrogen sorption in rht-MOF-1: identifying the binding sites through explicit polarization and quantum rotation calculations"
J. Mater. Chem. A
, v.2
, 2014
, p.2088
10.1039/c3ta14591c
Pham, Tony and Forrest, Katherine A. and McLaughlin, Keith and Tudor, Brant and Nugent, Patrick and Hogan, Adam and Mullen, Ashley and Cioce, Christian R. and Zaworotko, Michael J. and Space, Brian
"Theoretical Investigations of CO 2 and H 2 Sorption in an Interpenetrated Square-Pillared Metal-Organic Material"
The Journal of Physical Chemistry C
, v.117
, 2013
, p.9970--998
10.1021/jp402764s
Pham, Tony and Forrest, Katherine A. and Tudor, Brant and Elsaidi, Sameh K. and Mohamed, Mona H. and McLaughlin, Keith and Cioce, Christian R. and Zaworotko, Michael J. and Space, Brian
"Theoretical Investigations of CO 2 and CH 4 Sorption in an Interpenetrated Diamondoid Metal-Organic Material"
Langmuir
, v.30
, 2014
, p.6454--646
10.1021/la500967w
Qiu, Gang and Dennison, C.R. and Knehr, K.W. and Kumbur, E.C. and Sun, Ying
"Pore-scale analysis of effects of electrode morphology and electrolyte flow conditions on performance of vanadium redox flow batteries"
Journal of Power Sources
, v.219
, 2012
, p.223--234
10.1016/j.jpowsour.2012.07.042
Qiu, Gang and Joshi, Abhijit S. and Dennison, C.R. and Knehr, K.W. and Kumbur, E.C. and Sun, Ying
"3-D pore-scale resolved model for coupled species/charge/fluid transport in a vanadium redox flow battery"
Electrochimica Acta
, v.64
, 2012
, p.46--64
10.1016/j.electacta.2011.12.065
Qiu, Si-Wei and DeTar, Carleton and Du, Daping and Kronfeld, Andreas S and Laiho, Jack and Van de Water, Ruth
"Semileptonic B to D decays at nonzero recoil with 2+ 1 flavors of improved staggered quarks. An update"
arXiv preprint arXiv:1211.2247
, 2012
Rajachandrasekar, Raghunath and Perkins, Jonathan and Hamidouche, Khaled and Arnold, Mark and Panda, Dhabaleswar K.(DK)
"Understanding the Memory-Utilization of MPI Libraries"
Proceedings of the 21st European MPI Users Group Meeting on - EuroMPI/ASIA 14
, 2014
10.1145/2642769.2642782
Rathore, Anurag and Carpenter, Michael A. and Demir, Azlem and Ikeda, Terumasa and Li, Ming and Shaban, Nadine M. and Law, Emily K. and Anokhin, Dmitry and Brown, William L. and Amaro, Rommie E. and et al.
"The Local Dinucleotide Preference of APOBEC3G Can Be Altered from 5-CC to 5-TC by a Single Amino Acid Substitution"
Journal of Molecular Biology
, v.425
, 2013
, p.4442--445
10.1016/j.jmb.2013.07.040
Redner, Gabriel S. and Baskaran, Aparna and Hagan, Michael F.
"Reentrant phase behavior in active colloids with attraction"
Phys. Rev. E
, v.88
, 2013
10.1103/physreve.88.012305
Robertson, James C. and Hurley, Nate C. and Tortorici, Marcello and Ciossani, Giuseppe and Borrello, Maria Teresa and Vellore, Nadeem A. and Ganesan, A. and Mattevi, Andrea and Baron, Riccardo
"Expanding the Druggable Space of the LSD1/CoREST Epigenetic Target: New Potential Binding Regions for Drug-Like Molecules, Peptides, Protein Partners, and Chromatin"
PLoS Computational Biology
, v.9
, 2013
, p.e1003158
10.1371/journal.pcbi.1003158
Roe, Daniel R. and Bergonzo, Christina and Cheatham, Thomas E.
"Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods"
The Journal of Physical Chemistry B
, v.118
, 2014
, p.3543--355
10.1021/jp4125099
Ruiz-Herrero, Teresa and Hagan, Michael F
"Virus Assembly on a Membrane is Facilitated by Membrane Microdomains"
arXiv preprint arXiv:1403.2269
, 2014
Ruiz-Herrero, Teresa and Velasco, Enrique and Hagan, Michael F
"Mechanisms of budding of nanoscale particles through lipid bilayers"
The Journal of Physical Chemistry B
, v.116
, 2012
, p.9595--960
Rusu, Victor H and Horta, Vitor AC and Horta, Bruno AC and Lins, Roberto D and Baron, Riccardo
"MDWiZ: A platform for the automated translation of molecular dynamics simulations"
Journal of Molecular Graphics and Modelling
, v.48
, 2014
, p.80--86
Saltz, Joel H and Teodoro, George and Pan, Tony and Cooper, Lee AD and Kong, Jun and Klasky, Scott and Kurc, Tahsin M
"Feature-based analysis of large-scale spatio-temporal sensor data on hybrid architectures"
International Journal of High Performance Computing Applications
, 2013
, p.109434201
Samuel, Tabitha K. and Memon, Shahbaz and Scheuller, Bernd and Smallen, Shava
"UNICORE in XSEDE"
Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE 14
, 2014
10.1145/2616498.2616554
Schmidt, W and Collins, DC and Kritsuk, AG
"Local support against gravity in magnetoturbulent fluids"
Monthly Notices of the Royal Astronomical Society
, 2013
, p.stt399
Seo, Jung Hee and Mittal, Rajat
"A coupled flow-acoustic computational study of bruits from a modeled stenosed artery"
Med Biol Eng Comput
, v.50
, 2012
, p.1025--103
10.1007/s11517-012-0917-5
Seo, Jung Hee and Mittal, Rajat
"Effect of diastolic flow patterns on the function of the left ventricle"
Physics of Fluids
, v.25
, 2013
, p.110801
10.1063/1.4819067
Seo, Jung Hee and Vedula, Vijay and Abraham, Theodore and Mittal, Rajat
"Multiphysics computational models for cardiac flow and virtual cardiography"
Int. J. Numer. Meth. Biomed. Engng.
, v.29
, 2013
, p.850--869
10.1002/cnm.2556
Setny, P. and Baron, R. and Michael Kekenes-Huskey, P. and McCammon, J. A. and Dzubiella, J.
"Solvent fluctuations in hydrophobic cavity-ligand binding kinetics"
Proceedings of the National Academy of Sciences
, v.110
, 2013
, p.1197-1202
10.1073/pnas.1221231110
Setny, Piotr and Baron, Riccardo and McCammon, J. Andrew
"Comment on `Molecular driving forces of the pocket-ligand hydrophobic association' by G. Graziano, Chem. Phys. Lett. 533 (2012) 95"
Chemical Physics Letters
, v.555
, 2013
, p.306-309
10.1016/j.cplett.2012.11.004
Shi, Zheqiang and Day, Steven M.
"Rupture dynamics and ground motion from 3-D rough-fault simulations"
Journal of Geophysical Research: Solid Earth
, v.118
, 2013
, p.1122-1141
10.1002/jgrb.50094
Sivak, David A and Chodera, John D and Crooks, Gavin E
"Using nonequilibrium fluctuation theorems to understand and correct errors in equilibrium and nonequilibrium discrete Langevin dynamics simulations"
arXiv preprint arXiv:1107.2967
, 2011
Smith, Warren and Smallen, Shava
"Building an Information System for a Distributed Testbed"
Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment - XSEDE 14
, 2014
10.1145/2616498.2616543
Stoilova-McPhie, Svetla and Lynch, Gillian C. and Ludtke, Steven and Pettitt, B. Montgomery
"Domain organization of membrane-bound factor VIII"
Biopolymers
, 2013
, p.n/a-n/a
10.1002/bip.22199
Swails, Jason M and Roitberg, Adrian E
"Enhancing conformation and protonation state sampling of hen egg white lysozyme using pH replica exchange molecular dynamics"
Journal of Chemical Theory and Computation
, v.8
, 2012
, p.4393--440
Taborda, R. and Bielak, J.
"Ground-Motion Simulation and Validation of the 2008 Chino Hills, California, Earthquake"
Bulletin of the Seismological Society of America
, v.103
, 2013
, p.131-156
10.1785/0120110325
Taborda, R. and Bielak, J. and Restrepo, D.
"Earthquake Ground-Motion Simulation including Nonlinear Soil Effects under Idealized Conditions with Application to Two Case Studies"
Seismological Research Letters
, v.83
, 2012
, p.1047--106
10.1785/0220120079
Taborda, Ricardo and Bielak, Jacobo
"Large-scale earthquake simulation: computational seismology and complex engineering systems"
Computing in Science \& Engineering
, v.13
, 2011
, p.14--27
Tang, Wenwu
"Parallel construction of large circular cartograms using graphics processing units"
International Journal of Geographical Information Science
, v.27
, 2013
, p.2182--220
Teodoro, George and Pan, Tony and Kurc, Tahsin M and Kong, Jun and Cooper, Lee AD and Saltz, Joel H
"Efficient irregular wavefront propagation algorithms on hybrid CPU--GPU machines"
Parallel computing
, v.39
, 2013
, p.189--211
Teodoro, George and Pan, Tony and Kurc, Tahsin M and Kong, Jun and Cooper, Lee AD and Saltz, Joel H
"High-throughput execution of hierarchical analysis pipelines on hybrid cluster platforms"
arXiv preprint arXiv:1209.3332
, 2012
Thibault, Julien C. and Cheatham, Thomas E. and Facelli, Julio C.
"iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings"
J. Chem. Inf. Model.
, v.54
, 2014
, p.1810--181
10.1021/ci500173w
Thibault, Julien C and Roe, Daniel R and Facelli, Julio C and Cheatham, Thomas E
"Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing"
J Cheminf
, v.6
, 2014
, p.4
10.1186/1758-2946-6-4
Tian, Zhiting and Hu, Han and Sun, Ying
"A molecular dynamics study of effective thermal conductivity in nanocomposites"
International Journal of Heat and Mass Transfer
, v.61
, 2013
, p.577--582
10.1016/j.ijheatmasstransfer.2013.02.023
Tomov, Stanimire and Nath, Rajib and Dongarra, Jack
"Accelerating the reduction to upper Hessenberg, tridiagonal, and bidiagonal forms through hybrid GPU-based computing"
Parallel Computing
, v.36
, 2010
, p.645--654
Tortorici, Marcello and Borrello, Maria Teresa and Tardugno, Maria and Chiarelli, Laurent R. and Pilotto, Simona and Ciossani, Giuseppe and Vellore, Nadeem A. and Bailey, Sarah G. and Cowan, Jonathan and O'Connell, Maria and et al.
"Protein Recognition by Short Peptide Reversible Inhibitors of the Chromatin-Modifying LSD1/CoREST Lysine Demethylase"
ACS Chemical Biology
, 2013
, p.130611105
10.1021/cb4001926
Turabekova, M. and Rasulev, B. and Theodore, M. and Jackman, J. and Leszczynska, D. and Leszczynski, J.
"Immunotoxicity of nanoparticles: a computational study suggests that CNTs and C60 fullerenes might be recognized as pathogens by Toll-like receptors"
Nanoscale
, v.6
, 2014
, p.3488
10.1039/c3nr05772k
Ulusoy, Inga S. and Hernandez, Rigoberto
"Revisiting roaming trajectories in ketene isomerization at higher dimensionality"
Theor Chem Acc
, v.133
, 2014
10.1007/s00214-014-1528-z
Van Wart, Adam T. and Durrant, Jacob and Votapka, Lane and Amaro, Rommie E.
"Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis"
Journal of Chemical Theory and Computation
, v.10
, 2014
, p.511--517
10.1021/ct4008603
Vellore, Nadeem A and Baron, Riccardo
"Molecular dynamics simulations indicate an induced-fit mechanism for LSD1/CoREST-H3-histone molecular recognition"
BMC Biophys
, v.6
, 2013
, p.15
10.1186/2046-1682-6-15
Vellore, Nadeem A. and Baron, Riccardo
"Epigenetic Molecular Recognition: A Biomolecular Modeling Perspective"
ChemMedChem
, v.9
, 2014
, p.484--494
10.1002/cmdc.201300510
Venkatesh, Akshay and Potluri, Sreeram and Rajachandrasekar, Raghunath and Luo, Miao and Hamidouche, Khaled and Panda, Dhabaleswar K.
"High Performance Alltoall and Allgather Designs for InfiniBand MIC Clusters"
2014 IEEE 28th International Parallel and Distributed Processing Symposium
, 2014
10.1109/ipdps.2014.72
Vetter, Jeffrey S and Glassbrook, Richard and Dongarra, Jack and Schwan, Karsten and Loftis, Bruce and McNally, Stephen and Meredith, Jeremy and Rogers, James and Roth, Philip and Spafford, Kyle and others
"Keeneland: Bringing heterogeneous gpu computing to the computational science community"
Computing in Science and Engineering
, v.13
, 2011
, p.90--95
Vetter, Jeffrey S and Glassbrook, Richard and Schwan, Karsten and Yalamanchili, Sudha and Horton, Mitch and Gavrilovska, Ada and Slawinska, Magda and Dongarra, Jack and Meredith, Jeremy and Roth, Philip C and others
"Keeneland: Computational Science Using Heterogeneous GPU Computing"
Contemporary High Performance Computing: From Petascale Toward Exascale
, v.1
, 2014
, p.900
Vetter, J. S.;Glassbrook, R.;Dongarra, J.;Schwan, K.;Loftis, B.;McNally, S.;Meredith, J.;Rogers, J.;Roth, P.;Spafford, K.;Yalamanchili, S.;
"Keeneland: Bringing heterogeneous GPU computing to the computational science community"
IEEE Computing in Science and Engineering
, v.13
, 2011
, p.90-95
Villali, Janice and Pontiggia, Francesco and Clarkson, Michael W. and Hagan, Michael F. and Kern, Dorothee
"Evidence Against the YT Coupling Mechanism of Activation in the Response Regulator NtrC"
Journal of Molecular Biology
, v.426
, 2014
, p.1554--156
10.1016/j.jmb.2013.12.027
Votapka, L. and Amaro, R. E.
"Multistructural hot spot characterization with FTProd"
Bioinformatics
, v.29
, 2012
, p.393--394
10.1093/bioinformatics/bts689
{\v S}poner, Ji{\v r}{\'\i} and Ml{\'a}dek, Arno{\v s}t and {\v S}pa{\v c}kov{\'a}, Na{\v d}a and Cang, Xiaohui and Cheatham, Thomas E. and Grimme, Stefan
"Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations"
Journal of the American Chemical Society
, v.135
, 2013
, p.9785-9796
10.1021/ja402525c
Wagner, R. and Falkovich, G. and Kritsuk, A. G. and Norman, M. L.
"Flux correlations in supersonic isothermal turbulence"
Journal of Fluid Mechanics
, v.713
, 2012
, p.482--490
10.1017/jfm.2012.470
Wang, Kai and Chodera, John D and Yang, Yanzhi and Shirts, Michael R
"Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics"
Journal of computer-aided molecular design
, v.27
, 2013
, p.989--1007
Wan, Li and Iacovella, Christopher R and Nguyen, Trung D and Docherty, Hugh and Cummings, Peter T
"Confined fluid and the fluid-solid transition: Evidence from absolute free energy calculations"
Physical Review B
, v.86
, 2012
, p.214105
Wan, Quan and Spanu, Leonardo and Galli, Giulia A. and Gygi, Fran{\~A}{\S}ois
"Raman Spectra of Liquid Water from Ab Initio Molecular Dynamics: Vibrational Signatures of Charge Fluctuations in the Hydrogen Bond Network"
Journal of Chemical Theory and Computation
, v.9
, 2013
, p.4124--413
10.1021/ct4005307
Wan, Quan and Spanu, Leonardo and Gygi, Francois and Galli, Giulia
"Electronic Structure of Aqueous Sulfuric Acid from First-Principles Simulations with Hybrid Functionals"
The Journal of Physical Chemistry Letters
, v.5
, 2014
, p.2562--256
10.1021/jz501168p
Wassman, Christopher D. and Baronio, Roberta and Demir, Azlem and Wallentine, Brad D. and Chen, Chiung-Kuang and Hall, Linda V. and Salehi, Faezeh and Lin, Da-Wei and Chung, Benjamin P. and Wesley Hatfield, G. and et al.
"Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53"
Nature Communications
, v.4
, 2013
, p.1407
10.1038/ncomms2361
Wu, Jiadong and Chen, Chunlei and Hong, Bo
"A GPU-Based Approach to Accelerate Computational Protein-DNA Docking"
Computing in Science \& Engineering
, v.14
, 2012
, p.20--29
Wu, Jiadong and Hong, Bo and Takeda, Takako and Guo, Jun-tao
"High performance transcription factor-DNA docking with GPU computing"
Proteome Sci
, v.10
, 2012
, p.S17
Yamazaki, Ichitaro and Tomov, Stanimire and Dongarra, Jack
"One-sided Dense Matrix Factorizations on a Multicore with Multiple GPU Accelerators< sup>*"
Procedia Computer Science
, v.9
, 2012
, p.37--46
Yang, Xin and Li, Christopher Y and Sun, Ying
"From multi-ring to spider web and radial spoke: competition between the receding contact line and particle deposition in a drying colloidal drop"
Soft matter
, v.10
, 2014
, p.4458--446
Yang, Xiyang I.A. and Mittal, Rajat
"Acceleration of the Jacobi iterative method by factors exceeding 100 using scheduled relaxation"
Journal of Computational Physics
, v.274
, 2014
, p.695--708
10.1016/j.jcp.2014.06.010
Yan, Jun and Hummelsh{\o}j, Jens S. and N{\o}rskov, Jens K.
"Formation energies of group I and II metal oxides using random phase approximation"
Physical Review B
, v.87
, 2013
10.1103/PhysRevB.87.075207
Yan, Jun and Li, Lin and O'Grady, Christopher
"Graphics Processing Unit acceleration of the Random Phase Approximation in the projector augmented wave method"
Computer Physics Communications
, v.184
, 2013
, p.2728--273
Yu, Naiyin and Hagan, Michael F.
"Simulations of HIV Capsid Protein Dimerization Reveal the Effect of Chemistry and Topography on the Mechanism of Hydrophobic Protein Association"
Biophysical Journal
, v.103
, 2012
, p.1363--136
10.1016/j.bpj.2012.08.016
Zabriskie, Matthew{\^A} S. and Eide, Christopher{\^A} A. and Tantravahi, Srinivas{\^A} K. and Vellore, Nadeem{\^A} A. and Estrada, Johanna and Nicolini, Franck{\^A} E. and Khoury, Hanna{\^A} J. and Larson, Richard{\^A} A. and Konopleva, Marina and Cortes,
"BCR-ABL1 Compound Mutations Combining Key Kinase Domain Positions Confer Clinical Resistance to Ponatinib in Ph Chromosome-Positive Leukemia"
Cancer Cell
, v.26
, 2014
, p.428--442
10.1016/j.ccr.2014.07.006
Zhang, Cheng and Pettitt, B Montgomery
"Computation of high-order virial coefficients in high-dimensional hard-sphere fluids by Mayer sampling"
Molecular Physics
, 2014
, p.1--21
Zhao, Yanli and Padmanabhan, Anand and Wang, Shaowen
"A parallel computing approach to viewshed analysis of large terrain data using graphics processing units"
International Journal of Geographical Information Science
, v.27
, 2013
, p.363-384
10.1080/13658816.2012.692372
Zhou, Jun and Cui, Yifeng and Poyraz, Efecan and Choi, Dong Ju and Guest, Clark C
"Multi-GPU implementation of a 3D finite difference time domain earthquake code on heterogeneous supercomputers"
Procedia Computer Science
, v.18
, 2013
, p.1255--126
Zhou, Jun and Unat, Didem and Choi, Dong Ju and Guest, Clark C and Cui, Yifeng
"Hands-on performance tuning of 3D finite difference earthquake simulation on GPU fermi chipset"
Procedia Computer Science
, v.9
, 2012
, p.976--985
Zhou, Ran and Bailey, Jon A and Bazavov, Alexei and El-Khadra, Aida X and Gottlieb, Steven and Jain, Rajendra D and Kronfeld, Andreas S and Van de Water, Ruth S and Lattice, Fermilab
"Form factors for $ B $ to $ Kll $ semileptonic decay from three-flavor lattice QCD"
arXiv preprint arXiv:1111.0981
, 2011
Zhu, Tian and Lee, Hyun and Lei, Hao and Jones, Christopher and Patel, Kavankumar and Johnson, Michael E. and Hevener, Kirk E.
"Fragment-Based Drug Discovery Using a Multidomain, Parallel MD-MM/PBSA Screening Protocol"
Journal of Chemical Information and Modeling
, v.53
, 2013
, p.560-572
10.1021/ci300502h
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