Applications > gromacs

Publications

Users of this package associated the following 198 publications with the XSEDE allocation/account under which they were running this software. Thus the publications may have come before or after the runs of this software, but the authors considered them to be related to the same line of research.

  • Walter Freeman (University of Arizona), Douglas Toussaint (University of Arizona), (2010) "Improved method for calculating nucleon strangeness", Lattice 2010 Villasimius, Sardinia Italy , . http://arxiv.org/pdf/1011.5271.pdf
  • Ludmila Levkova (University of Utah), Carleton DeTar (University of Utah), (April2011) "Charm annihilation effects on the hyperfine splitting in charmonium", Physical Review D 83 / 7, . http://dx.doi.org/10.1103/PhysRevD.83.074504
  • Evgeni Penev, Joel Ireta, Joan-Emma Shea, (2008) "Energetics of Infinite Homopolypeptide Chains: A New Look at Commonly Used Force Fields", The Journal of Physical Chemistry B 112 / 22, 6872-6877. http://dx.doi.org/10.1021/jp800058f
  • Sakunchai Khumsubdee, Yubo Fan (University of Houston-Downtown), Kevin Burgess, (September2013) "A Comparison between Oxazoline-imidazolinylidene, -imidazolylidine, -benzimidazolylidene Hydrogenation Catalysts", The Journal of Organic Chemistry 78 / 19, 9969-9974. http://dx.doi.org/10.1021/jo4013783
  • Yuzhuo Chu, Jianzhuang Yao, Hong Guo (University of Tennessee, Knoxville), (2012) "QM/MM MD and Free Energy Simulations of G9a-Like Protein (GLP) and Its Mutants: Understanding the Factors that Determine the Product Specificity", PLoS ONE 7 / 5, e37674. http://dx.doi.org/10.1371/journal.pone.0037674
  • Claude Bernard (Washington University in St. Louis), Maarten Golterman (San Francisco State University), (2013) "On the foundations of partially quenched chiral perturbation theory", Physical Review D 88 / 1, . http://dx.doi.org/10.1103/PhysRevD.88.014004
  • Claude Bernard (Washington University in St. Louis), (March2013) "Neutral B mixing in staggered chiral perturbation theory", Physical Review D 87 / 11, . http://dx.doi.org/10.1103/PhysRevD.87.114503
  • David G Ackerman (Cornell University), Frederick A Heberle (Oak Ridge National Laboratory), Gerald W Feigenson (Cornell University), (April2013) "Limited Perturbation of a DPPC Bilayer by Fluorescent Lipid Probes: A Molecular Dynamics Study", The Journal of Physical Chemistry B 117 / 17, 4844-4852. http://dx.doi.org/10.1021/jp400289d
  • Carleton DeTar (University of Utah), A. Kronfeld (Fermi National Accelerator Laboratory), S.-H. Lee (University of Utah), Ludmila Levkova (University of Utah), D. Mohler (Ferm), James Simone (Fermi National Accelerator Laboratory), (2012) "Charmonium mass splittings at the physical point", Lattice 2012 Cairns, Australia , . http://arxiv.org/pdf/1211.2253.pdf
  • Anand Padmanabhan (University of Illinois at Urbana-Champaign), Shaowen Wang (University of Illinois at Urbana-Champaign), Guofeng Cao (University of Illinois at Urbana-Champaign), Myunghwa Hwang, Yanli Zhao (University of Illinois at Urbana-Champaign), Zhenhua Zhang, Yizhao Gao, (2013) "FluMapper", Proceedings of the Conference on Extreme Science and Engineering Discovery Environment Gateway to Discovery - XSEDE '13 San Diego, CA, USA , . http://dx.doi.org/10.1145/2484762.2484821
  • Jianzhuang Yao, Alexander Wlodawer, Hong Guo (University of Tennessee, Knoxville), (2013) "Understanding the Autocatalytic Process of Pro-kumamolisin Activation from Molecular Dynamics and Quantum Mechanical/Molecular Mechanical (QM/MM) Free-Energy Simulations", Chemistry - A European Journal undefined / undefined, n/a-n/a. http://dx.doi.org/10.1002/chem.201301310
  • Claude Bernard (Washington University in St. Louis), Carleton DeTar (University of Utah), M. Di Pierro (DePaul U.), A. El-Khadra (U. of Illinois), R. Evans (U. of Illinois), E. Freeland (Art Institute of Chicago), E. Gamiz (U. of Illinois), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), A. Kronfeld (Fermi National Accelerator Laboratory), John Laiho (Washington University in St. Louis), Ludmila Levkova (University of Utah), Paul Mackenzie (Fermi National Accelerator Laboratory), M. Okamoto (Fermi National Accelerator Laboratory), James Simone (Fermi National Accelerator Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Fermi National Accelerator Laboratory), (January2009) "B¯→D*ℓν¯ form factor at zero recoil from three-flavor lattice QCD: A model independent determination of |Vcb|", Physical Review D 79 / 1, . http://dx.doi.org/10.1103/PhysRevD.79.014506
  • Apratim Bhattacharya (Lehigh University), Robert B. Best, Jeetain Mittal (Lehigh University), (2012) "Smoothing of the GB1 Hairpin Folding Landscape by Interfacial Confinement", Biophysical Journal 103 / 3, 596-600. http://dx.doi.org/10.1016/j.bpj.2012.07.005
  • Robert B. Best, Jeetain Mittal (Lehigh University), Michael Feig (Michigan State University), Alexander D. MacKerell, Jr. (University of Maryland, Baltimore County), (2012) "Inclusion of Many-Body Effects in the Additive CHARMM Protein CMAP Potential Results in Enhanced Cooperativity of α-Helix and β-Hairpin Formation", Biophysical Journal 103 / 5, 1045-1051. http://dx.doi.org/10.1016/j.bpj.2012.07.042
  • Steven Gottlieb (Indiana University), G. Shi (U. of Illinois), A. Torok (Indiana University), V. Kindratenko (U. of Illinois), (2010) "QUDA Programming for Staggered Quarks", Lattice 2010 Villasimius, Sardinia Italy , . http://pos.sissa.it/archive/conferences/105/026/Lattice 2010_026.pdf
  • R. Babich (Boston U.), m. Clark (Harvard-Smithsonian Center for Astrophysics), Balint Joo (Jefferson Laboratory), G. Shi (U. of Illinois), Richard Brower (Boston University), Steven Gottlieb (Indiana University), (2011) "Scaling Lattice QCD beyond 100 GPUs", 2011 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis (SC11) Seattle, WA , . http://arxiv.org/pdf/1109.2935.pdf
  • Qiangjun Zhou, Jiangmei Li, Hang Yu, Yujia Zhai, Zhen Gao, Yanxin Liu, Xiaoyun Pang, Lunfeng Zhang, Klaus Schulten, Fei Sun, Chang Chen, (March2014) "Molecular insights into the membrane-associated phosphatidylinositol 4-kinase IIα", Nature Communications 5, 3552. http://dx.doi.org/10.1038/ncomms4552
  • Y. Wang, Yanxin Liu, H. A. DeBerg, T. Nomura, M. T. Hoffman, P. R. Rohde, K. Schulten, B. Martinac, P. R. Selvin, (February2014) "Single molecule FRET reveals pore size and opening mechanism of a mechano-sensitive ion channel", eLife 3, e01834-e01834. http://dx.doi.org/10.7554/eLife.01834
  • Yanxin Liu, Maxim B. Prigozhin, Klaus Schulten, Martin Gruebele, (March2014) "Observation of Complete Pressure-Jump Protein Refolding in Molecular Dynamics Simulation and Experiment", Journal of the American Chemical Society 136 / 11, 4265-4272. http://dx.doi.org/10.1021/ja412639u
  • Wei Li Wang, Elton Santos (Stanford University), Bin Jiang, Ekin Cubuk, Colin Ophus, Alba Centeno, Amaia Pesquera, Amaia Zurutuza, Jim Ciston, Robert M Westervelt, Efthimios Kaxiras, (January2014) "Direct Observation of a long-lived single-atom catalyst chiseling atomic structures in graphene", Nano Letters undefined / undefined, 140121142046000. http://dx.doi.org/10.1021/nl403327u
  • Mikalai Budzevich, Vasily Zhakhovsky (University of South Florida), Carter White, Ivan Oleynik, (September2012) "Evolution of Shock-Induced Orientation-Dependent Metastable States in Crystalline Aluminum", Physical Review Letters 109 / 12, 125505. http://dx.doi.org/10.1103/PhysRevLett.109.125505
  • Scott Callaghan (University of Southern California), Philip Maechling (University of Southern California), Patrick Small (University of Southern California), Kevin Milner (University of Southern California), Gideon Juve (University of Southern California), Thomas Jordan (University of Southern California), Ewa Deelman (University of Southern California), Gaurang Mehta (University of Southern California), Karan Vahi (University of Southern California), D. Gunter, K. Beattie, C. Brooks, (August2011) "Metrics for heterogeneous scientific workflows: A case study of an earthquake science application", International Journal of High Performance Computing Applications 25 / 3, 274-285. http://dx.doi.org/10.1177/1094342011414743
  • Scott Callaghan (University of Southern California), Ewa Deelman (University of Southern California), Dan Gunter, Gideon Juve (University of Southern California), Philip Maechling (University of Southern California), Christopher Brooks, Karan Vahi (University of Southern California), Kevin Milner (University of Southern California), Robert Gall (National Oceanic and Atmospheric Administration), Edward Field, David Okaya (University of Southern California), Thomas Jordan (University of Southern California), (September2010) "Scaling up workflow-based applications", Journal of Computer and System Sciences 76 / 6, 428-446. http://dx.doi.org/10.1016/j.jcss.2009.11.005
  • Robert Graves (US Geological Survey), Thomas Jordan (University of Southern California), Scott Callaghan (University of Southern California), Ewa Deelman (University of Southern California), Edward Field, Gideon Juve (University of Southern California), Carl Kesselman, Philip Maechling (University of Southern California), Gaurang Mehta (University of Southern California), Kevin Milner (University of Southern California), David Okaya (University of Southern California), Patrick Small (University of Southern California), Karan Vahi (University of Southern California), (March2011) "CyberShake: A Physics-Based Seismic Hazard Model for Southern California", Pure and Applied Geophysics 168 / 3-4, 367-381. http://dx.doi.org/10.1007/s00024-010-0161-6
  • Mats Rynge (University of Southern California), Scott Callaghan (University of Southern California), Ewa Deelman (University of Southern California), Gideon Juve (University of Southern California), Gaurang Mehta (University of Southern California), Karan Vahi (University of Southern California), Philip Maechling (University of Southern California), (July2012) "Enabling large-scale scientific workflows on petascale resources using MPI master/worker", Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment on Bridging from the eXtreme to the campus and beyond - XSEDE '12 Chicago, Illinois , 1. http://dx.doi.org/10.1145/2335755.2335846
  • Yifeng Cui (University of California-San Diego), Kim Olsen (San Diego State University), Thomas Jordan (University of Southern California), Kwangyoon Lee (San Diego Supercomputer Center), Jun Zhou (University of California-San Diego), Patrick Small (University of Southern California), Daniel Roten (ETH Zurich), Geoffrey Ely (Argonne National Laboratory), Dhabaleswar Panda (Ohio State University), Amit Chourasia (University of California-San Diego), John Levesque, Steven Day (San Diego State University), Philip Maechling (University of Southern California), (November2010) "Scalable Earthquake Simulation on Petascale Supercomputers", 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis New Orleans, Louisiana , 1-20. http://dx.doi.org/10.1109/SC.2010.45
  • Kim Olsen (San Diego State University), Steven Day (San Diego State University), Jean-Bernard Minster (Scripps Institution of Oceanography), Yifeng Cui (University of California-San Diego), Amit Chourasia (University of California-San Diego), David Okaya (University of Southern California), Philip Maechling (University of Southern California), Thomas Jordan (University of Southern California), (June2008) "TeraShake2: Spontaneous Rupture Simulations of Mw 7.7 Earthquakes on the Southern San Andreas Fault", Bulletin of the Seismological Society of America 98 / 3, 1162-1185. http://dx.doi.org/10.1785/0120070148
  • Anand Padmanabhan (University of Illinois at Urbana-Champaign), Choonhan Youn (San Diego Supercomputer Center), Myunghwa Hwang, Yan Liu (University of Illinois at Urbana-Champaign), Shaowen Wang (University of Illinois at Urbana-Champaign), Nancy Wilkins-Diehr (University of California-San Diego), Christopher Crosby, (2013) "Integration of science gateways", Proceedings of the Conference on Extreme Science and Engineering Discovery Environment Gateway to Discovery - XSEDE '13 San Diego, CA, USA , . http://dx.doi.org/10.1145/2484762.2484808
  • J. Douglas Zechar, Danijel Schorlemmer, Maria Liukis, John Yu, Fabian Euchner, Philip Maechling (University of Southern California), Thomas Jordan (University of Southern California), (August2010) "The Collaboratory for the Study of Earthquake Predictability perspective on computational earthquake science", Concurrency and Computation: Practice and Experience 22 / 12, 1836-1847. http://dx.doi.org/10.1002/cpe.1519
  • Jon Bailey (Fermi National Accelerator Laboratory), Claude Bernard (Washington University in St. Louis), Carleton DeTar (University of Utah), M. Di Pierro (DePaul U.), A. El-Khadra (U. of Illinois), R. Evans (U. of Illinois), E. Freeland (Benedictine U.), E. Gamiz (U. de Granada), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), A. Kronfeld (Fermi National Accelerator Laboratory), John Laiho (Washington University in St. Louis), Ludmila Levkova (University of Utah), Paul Mackenzie (Fermi National Accelerator Laboratory), M. Okamoto (Fermi National Accelerator Laboratory), James Simone (Fermi National Accelerator Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Fermi National Accelerator Laboratory), (March2009) "B→πlν semileptonic form factor from three-flavor lattice QCD: A model-independent determination of |Vub|", Physical Review D 79 / 5, . http://dx.doi.org/10.1103/PhysRevD.79.054507
  • Xueqing Zou, Yanxin Liu, Zhongzhou Chen, Gloria Ines Cárdenas-Jirón, Klaus Schulten, (August2010) "Flow-Induced β-Hairpin Folding of the Glycoprotein Ibα β-Switch", Biophysical Journal 99 / 4, 1182-1191. http://dx.doi.org/10.1016/j.bpj.2010.05.035
  • Xiaoming Hu, Petra M. Klein, Ming Xue, Alan Shapiro, Anita Nallapareddy, (2013) "Enhanced vertical mixing associated with a nocturnal cold front passage and its impact on near-surface temperature and ozone concentration", Journal of Geophysical Research: Atmospheres 118 / 7, 2714-2728. http://dx.doi.org/10.1002/jgrd.50309
  • Xiao-Ming Hu, Petra M. Klein, Ming Xue, Julie K. Lundquist, Fuqing Zhang, Youcun Qi, (2013) "Impact of Low-Level Jets on the Nocturnal Urban Heat Island Intensity in Oklahoma City", Journal of Applied Meteorology and Climatology 52 / 8, 1779-1802. http://dx.doi.org/10.1175/JAMC-D-12-0256.1
  • Xiaoming Hu, Petra M. Klein, Ming Xue, (2013) "Evaluation of the updated YSU planetary boundary layer scheme within WRF for wind resource and air quality assessments", Journal of Geophysical Research: Atmospheres 118 / 18, 10,490-10,505. http://dx.doi.org/10.1002/jgrd.50823
  • Petra M. Klein, Xiaoming Hu, Ming Xue, (2014) "Impacts of Mixing Processes in Nocturnal Atmospheric Boundary Layer on Urban Ozone Concentrations", Boundary-Layer Meteorology 150 / 1, 107-130. http://dx.doi.org/10.1007/s10546-013-9864-4
  • Xiao-Ming Hu, Petra M. Klein, Ming Xue, Fuqing Zhang, David C. Doughty, Renate Forkel, Everette Joseph, Jose D. Fuentes, (2013) "Impact of the vertical mixing induced by low-level jets on boundary layer ozone concentration", Atmospheric Environment 70 / undefined, 123-130. http://dx.doi.org/10.1016/j.atmosenv.2012.12.046
  • Rogan Carr (University of Illinois at Urbana-Champaign), Jeffrey Comer (University of Illinois at Urbana-Champaign), Mark D. Ginsberg, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2011) "Modeling Pressure-Driven Transport of Proteins Through a Nanochannel", IEEE Transactions on Nanotechnology 10 / 1, 75-82. http://dx.doi.org/10.1109/TNANO.2010.2062530
  • Jeffrey Comer, Aleksei Aksimentiev, (January2012) "Predicting the DNA Sequence Dependence of Nanopore Ion Current Using Atomic-Resolution Brownian Dynamics", The Journal of Physical Chemistry C 116 / 5, 3376-3393. http://dx.doi.org/10.1021/jp210641j
  • Alexei Bazavov (University of Arizona), Claude Bernard (Washington University in St. Louis), Carleton DeTar (University of Utah), Walter Freeman (University of Arizona), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), John Laiho (Washington University in St. Louis), Ludmila Levkova (University of Utah), James Osborn (Argonne National Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Brookhaven National Laboratory), (2009) "Progress on four flavor QCD with the HISQ action", Lattice 2009 Beijing, China , . http://arxiv.org/pdf/0911.0869.pdf
  • Davoud Ebrahimi, Roland J.-M. Pellenq, Andrew J. Whittle, (2012) "Nanoscale Elastic Properties of Montmorillonite upon Water Adsorption", Langmuir 28 / 49, 16855-16863. http://dx.doi.org/10.1021/la302997g
  • Fangzhou Wei (University of Texas at Austin), Ali Yilmaz (University of Texas at Austin), (July2012) "Parallel truncated multigrid preconditioning of AIM for biolectromagnetics", USNC/URSI Radio Science Meeting Chicago, IL , .
  • Ran Zhou (Indiana University), J. Bailey (Seoul National University), Alexei Bazavov (Brookhaven National Laboratory), A. X. El-Khadra (U. of Illinois), Steven Gottlieb (Indiana University), R. Jain (U. of Illinois), A. Kronfeld (Fermi National Accelerator Laboratory), Ruth Van de Water (Fermi National Accelerator Laboratory), (2011) "Form factors for B to Kll semileptonic decay from three-flavor lattice QCD", Lattice 2011 Squaw Valley, CA , . http://arxiv.org/pdf/1111.0981.pdf
  • Jejoong Yoo, Aleksei Aksimentiev, (2012) "Improved Parametrization of Li+, Na+, K+, and Mg2+Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems", The Journal of Physical Chemistry Letters 3 / 1, 45-50. http://dx.doi.org/10.1021/jz201501a
  • Jianzhuang Yao, Yuzhuo Chu, Ran An, Hong Guo (University of Tennessee, Knoxville), (2012) "Understanding Product Specificity of Protein Lysine Methyltransferases from QM/MM Molecular Dynamics and Free Energy Simulations: The Effects of Mutation on SET7/9 beyond the Tyr/Phe Switch", Journal of Chemical Information and Modeling 52 / 2, 449-456. http://dx.doi.org/10.1021/ci200364m
  • Noa Marom (University of Texas at Austin), Minjung Kim (University of Texas at Austin), James Chelikowsky (University of Texas at Austin), (2012) "Structure Selection Based on High Vertical Electron Affinity for TiO_{2} Clusters", Physical Review Letters 108 / 10, 106801. http://dx.doi.org/10.1103/PhysRevLett.108.106801
  • Thomas Furlani (SUNY at Buffalo), Matthew D. Jones, Steve Gallo (SUNY at Buffalo), Andrew E. Bruno, Charng-Da Lu, Amin Ghadersohi, Ryan J. Gentner, Abani Patra, Robert L. DeLeon, Gregor von Laszewski, Fugang Wang, Ann Zimmerman, (2012) "Performance metrics and auditing framework using application kernels for high-performance computer systems", Concurrency and Computation: Practice and Experience 25 / 7, 918-931. http://dx.doi.org/10.1002/cpe.2871
  • James C. Browne, Thomas Furlani (SUNY at Buffalo), Robert T. McLay, Robert L. DeLeon, Charng-Da Lu, Matthew D. Jones, Steve Gallo (SUNY at Buffalo), Amin Ghadersohi, Abani K. Patra, William Barth (University of Texas at Austin), John Hammond, (November2013) "Enabling comprehensive data-driven system management for large computational facilities", Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis on - SC '13 Denver, CO, USA , 1-11. http://dx.doi.org/10.1145/2503210.2503230
  • Jason Naylor (University of North Dakota), Matthew Gilmore (University of North Dakota), Richard L Thompson (Storm Prediction Center), Roger Edwards (Storm Prediction Center), Robert Wilhelmson (University of Illinois at Urbana-Champaign), (July2012) "Comparison of Objective Supercell Identification Techniques Using an Idealized Cloud Model", Monthly Weather Review 140/7, 2090-2102. http://journals.ametsoc.org/doi/abs/10.1175/MWR-D-11-00209.1
  • Carleton DeTar (University of Utah), Urs Heller (American Physical Society), (2009) "QCD thermodynamics from the lattice", The European Physical Journal A 41 / 3, 405-437. http://dx.doi.org/10.1140/epja/i2009-10825-3
  • Matthew Small, Xin Yuan, (September2013) "A New Design of RDMA-based Small Message Channels for InfiniBand Clusters", International Conference on Cluster Computing Denver , .
  • Zheng Gu, Matthew Small, Xin Yuan, Aniruddha Marathe, David K. Lowenthal, (2013) "Protocol Customization for Improving MPI Performance on RDMA-Enabled Clusters", International Journal of Parallel Programming 41 / 5, 682-703. http://dx.doi.org/10.1007/s10766-013-0242-0
  • Georgios A Tritsaris (Harvard University), Brad D Malone (Harvard University), Efthimios Kaxiras (Harvard University), (2013) "Optoelectronic Properties of Single-layer, Double-layer and Bulk Tin Sulfide: A Theoretical Study", Journal of Applied Physics , .
  • T. Burch (U. of Utah), Carleton DeTar (University of Utah), M. Di Pierro (DePaul U.), A. X. El-Khadra (U. of Illinois), E. D. Freeland (Benedictine U.), Steven Gottlieb (Indiana University), A. S. Kronfeld (Fermi National Accelerator Laboratory), Ludmila Levkova (University of Utah), Paul Mackenzie (Fermi National Accelerator Laboratory), James Simone (Fermi National Accelerator Laboratory), (2010) "Quarkonium mass splittings in three-flavor lattice QCD", Physical Review D 81 / 3, . http://dx.doi.org/10.1103/PhysRevD.81.034508
  • B. Dorvel, G. Sigalov, Q. Zhao, Jeffrey Comer (University of Illinois at Urbana-Champaign), V. Dimitrov, U. Mirsaidov, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), G. Timp, (2009) "Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore", Nucleic Acids Research 37 / 12, 4170-4179. http://dx.doi.org/10.1093/nar/gkp317
  • Jeffrey Comer (University of Illinois at Urbana-Champaign), Valentin Dimitrov, Qian Zhao, Gregory Timp, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2009) "Microscopic Mechanics of Hairpin DNA Translocation through Synthetic Nanopores", Biophysical Journal 96 / 2, 593-608. http://dx.doi.org/10.1016/j.bpj.2008.09.023
  • Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Robert Brunner, Eduardo Cruz-Chu, Jeffrey Comer (University of Illinois at Urbana-Champaign), Klaus Schulten, (2009) "Modeling transport through synthetic nanopores", IEEE Nanotechnology Magazine 3 / 1, 20-28. http://dx.doi.org/10.1109/MNANO.2008.931112
  • Yanli Zhao (University of Illinois at Urbana-Champaign), Anand Padmanabhan (University of Illinois at Urbana-Champaign), Shaowen Wang (University of Illinois at Urbana-Champaign), (2013) "A parallel computing approach to viewshed analysis of large terrain data using graphics processing units", International Journal of Geographical Information Science 27 / 2, 363-384. http://dx.doi.org/10.1080/13658816.2012.692372
  • Kyong Min Yeo (Lawrence Berkeley National Laboratory), David M. Romps, (2012) "Measurement of Convective Entrainment using Lagrangian Particles", Journal of the Atmospheric Sciences undefined / undefined, 120907120245001. http://dx.doi.org/10.1175/JAS-D-12-0144.1
  • Yanxin Liu, Jen Hsin, HyeongJun Kim, Paul R. Selvin, Klaus Schulten, (June2011) "Extension of a Three-Helix Bundle Domain of Myosin VI and Key Role of Calmodulins", Biophysical Journal 100 / 12, 2964-2973. http://dx.doi.org/10.1016/j.bpj.2011.05.010
  • Jason Naylor (University of North Dakota), Matthew Gilmore (University of North Dakota), (October2012) "Environmental factors influential to the duration and intensity of tornadoes in simulated supercells", 26th Conf. on Severe Local Storms Nashville, TN , . https://ams.confex.com/ams/26SLS/webprogram/Paper212409.html
  • Justin K. Weber (University of North Dakota), Matthew S. Gilmore (University of North Dakota), Jason A. Naylor (NorthWest Research Associates), (January2013) "Comparisons of Eulerian Circulation and Circulation Budgets for Numerically Simulated Tornado-Like Vortices in Altered Shear Environments", 12th Annual AMS Student Conference Austin, Texas , . https://ams.confex.com/ams/93Annual/webprogram/Paper224743.html
  • Christopher Maffeo (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2009) "Structure, Dynamics, and Ion Conductance of the Phospholamban Pentamer", Biophysical Journal 96 / 12, 4853-4865. http://dx.doi.org/10.1016/j.bpj.2009.03.053
  • Alexei Bazavov (Brookhaven National Laboratory), Claude Bernard (Washington University in St. Louis), C. Bouchard (Ohio State U.), Carleton DeTar (University of Utah), D. Du (U. of Illinois), A. X. El-Khadra (U. of Illinois), Justin Foley (University of Utah), E. Freeland (Benedictine U.), E. Gamiz (U. de Granada), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), J. Kim (U. of Arizona), A. Kronfeld (Fermi National Accelerator Laboratory), John Laiho (U. of Glasgow), Ludmila Levkova (University of Utah), M. Lightman (Washington U.), Paul Mackenzie (Fermi National Accelerator Laboratory), E. Neil (Fermi National Accelerator Laboratory), M. Oktay (University of Utah), James Simone (Fermi National Accelerator Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Fermi National Accelerator Laboratory), Ran Zhou (Indiana University), (2012) "Pseudoscalar meson physics with four dynamical quarks", Lattice 2012 Cairns, Australia , . http://arxiv.org/pdf/1210.8431.pdf
  • Luca Larini (University of California-Santa Barbara), Megan Murray Gessel, Nichole E. LaPointe, Thanh Do (University of California-Santa Barbara), Michael Bowers (University of California-Santa Barbara), Stuart C. Feinstein, Joan-Emma Shea (University of California-Santa Barbara), (2013) "Initiation of assembly of tau(273-284) and its ΔK280 mutant: an experimental and computational study", Physical Chemistry Chemical Physics 15 / 23, 8916. http://dx.doi.org/10.1039/C3CP00063J
  • Lijiang Yang (Peking University), Yubo Fan (The Methodist Hospital System), Yi Qin Gao (Peking University), (November2011) "Differences of Cations and Anions: Their Hydration, Surface Adsorption, and Impact on Water Dynamics", The Journal of Physical Chemistry B 115 / 43, 12456-12465. http://dx.doi.org/10.1021/jp207652h
  • Binquan Luan, Rogan Carr, Martin Caffrey, Aleksei Aksimentiev, (2010) "The effect of calcium on the conformation of cobalamin transporter BtuB", Proteins: Structure, Function, and Bioinformatics 78 / 5, 1153-1162. http://dx.doi.org/10.1002/prot.22635
  • Y. Lai, J. Diao, Yanxin Liu (University of Illinois at Urbana-Champaign), Y. Ishitsuka, Z. Su, Klaus Schulten (University of Illinois at Urbana-Champaign), T. Ha, Y.-K. Shin, (January2013) "Fusion pore formation and expansion induced by Ca2+ and synaptotagmin 1", Proceedings of the National Academy of Sciences 110 / 4, 1333-1338. http://dx.doi.org/10.1073/pnas.1218818110
  • Liang Gao, Ahmad A. Hammoudi, Fuhai Li, Michael J. Thrall, Philip T. Cagle, Yuanxin Chen, Jian Yang, Xiaofeng Xia, Yubo Fan (The Methodist Hospital System), Yehia Massoud, Zhiyong Wang, Stephen T. C. Wong, (June2012) "Differential diagnosis of lung carcinoma with three-dimensional quantitative molecular vibrational imaging", Journal of Biomedical Optics 17 / 6, 066017. http://dx.doi.org/10.1117/1.JBO.17.6.066017
  • Jesmin Jahan Tithi (SUNY at Stony Brook), (May2013) "Polarization Energy on a Cluster of Multicores", IPDPSW, HICOMB2013 BOSTON, MA , .
  • Daniel Angles-Alcazar (University of Arizona), Feryal Ozel (University of Arizona), Romeel Dave (University of Arizona), (June2013) "BLACK HOLE-GALAXY CORRELATIONS WITHOUT SELF-REGULATION", The Astrophysical Journal 770 / 1, 5. http://dx.doi.org/10.1088/0004-637X/770/1/5
  • Fangzhou Wei (University of Texas at Austin), Ali Yilmaz (University of Texas at Austin), (September2012) "Surface-preconditioned AIM-accelerated surface-volume integral equation solution for bioelectromagnetics", 2012 International Conference on Electromagnetics in Advanced Applications Cape Town, South Africa , 869-872. http://dx.doi.org/10.1109/ICEAA.2012.6328757
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  • Qiang Shao (DDDC), Yubo Fan (The Methodist Hospital System), Lijiang Yang (Peking University), Yi Qin Gao (Peking University), (March2012) "From protein denaturant to protectant: Comparative molecular dynamics study of alcohol∕protein interactions", The Journal of Chemical Physics 136 / 11, 115101. http://dx.doi.org/10.1063/1.3692801
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  • Ricardo Taborda (University of Memphis), Jacobo Bielak (Carnegie Mellon University), (2013) "Ground-Motion Simulation and Validation of the 2008 Chino Hills, California, Earthquake", Bulletin of the Seismological Society of America 103 / 1, 131-156. http://dx.doi.org/10.1785/0120110325
  • Sara Nichols (University of California-San Diego), Carlos Hernandez (Stanford University), Yi Wang (University of California-San Diego), James McCammon (University of California-San Diego), (June2013) "Structure-based network analysis of an evolved G protein-coupled receptor homodimer interface", Protein Science 22 / 6, 745-754. http://dx.doi.org/10.1002/pro.2258
  • Ricardo Taborda (University of Memphis), Jacobo Bielak (Carnegie Mellon University), (2011) "Large-Scale Earthquake Simulation: Computational Seismology and Complex Engineering Systems", Computing in Science & Engineering 13 / 4, 14-27. http://dx.doi.org/10.1109/MCSE.2011.19
  • Ricardo Taborda (University of Memphis), Jacobo Bielak (Carnegie Mellon University), Dorian Restrepo (Carnegie Mellon University), (2012) "Earthquake Ground-Motion Simulation including Nonlinear Soil Effects under Idealized Conditions with Application to Two Case Studies", Seismological Research Letters 83 / 6, 1047-1060. http://dx.doi.org/10.1785/0220120079
  • Alexei Bazavov (Brookhaven National Laboratory), Claude Bernard (Washington University in St. Louis), C. Bouchard (U. of Illinois), Carleton DeTar (University of Utah), D. Du (U. of Illinois), A. X. El-Khadra (U. of Illinois), Justin Foley (University of Utah), E. Freeland (Benedictine U.), E. Gamiz (U. de Granada), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), J. Kim (University of Arizona), A. Kronfeld (Fermi National Accelerator Laboratory), John Laiho (U. of Glasgow), Ludmila Levkova (University of Utah), M. Lightman (Washington U.), Paul Mackenzie (Fermi National Accelerator Laboratory), E. Neil (Fermi National Accelerator Laboratory), M. Oktay (University of Utah), James Simone (Fermi National Accelerator Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Fermi National Accelerator Laboratory), Ran Zhou (Indiana University), (2012) "Two-point Correlator Fits on HISQ Ensembles", Lattice 2012 Cairns, Australia , . http://arxiv.org/pdf/1212.0613.pdf
  • Alexei Bazavov (Brookhaven National Laboratory), Claude Bernard (Washington University in St. Louis), C. M. Bouchard (U. of Illinois), Carleton DeTar (University of Utah), M. Di Pierro (DePaul U.), A. X. El-Khadra (U. of Illinois), R. T. Evans (U. of Illinois), E. D. Freeland (Benedictine U.), E. Gámiz (U. de Granada), Steven Gottlieb (Indiana University), U. M. Heller (American Physics Society), James Hetrick (University of the Pacific), R. Jain (U. of Illinois), A. S. Kronfeld (Fermi National Accelerator Laboratory), J. Laiho (U. of Glasgow), Ludmila Levkova (University of Utah), Paul Mackenzie (Fermi National Accelerator Laboratory), E. T. Neil (Fermi National Accelerator Laboratory), M. B. Oktay (U. of Utah), J. N. Simone (Fermi National Accelerator Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Brookhaven National Laboratory), (June2012) "B- and D-meson decay constants from three-flavor lattice QCD", Physical Review D 85 / 11, . http://dx.doi.org/10.1103/PhysRevD.85.114506
  • Alexei Bazavov (Brookhaven National Laboratory), T. Bhattacharya (Los Alamos National Laboratory), M. Cheng (Lawrence Livermore National Laboratory), Carleton DeTar (University of Utah), H.-T. Ding (Brookhaven National Laboratory), Steven Gottlieb (Indiana University), Rajan Gupta (Los Alamos National Laboratory), P. Hegde (Brookhaven National Laboratory), Urs Heller (American Physical Society), F. Karsch (Brookhaven National Laboratory), E. Laermann (U. Bielefeld), Ludmila Levkova (University of Utah), S. Mukherjee (Brookhaven National Laboratory), P. Petreczky (Brookhaven National Laboratory), C. Schmidt (U. Bielefeld), R. A. Soltz (Lawrence Livermore National Laboratory), W. Soeldner (U. Regensberg), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), W. Unger (ETH Zurich), Pavlos M. Vranas (Lawrence Livermore National Laboratory), (March2012) "Chiral and deconfinement aspects of the QCD transition", Physical Review D 85 / 5, . http://dx.doi.org/10.1103/PhysRevD.85.054503
  • Alexei Bazavov (Brookhaven National Laboratory), Claude Bernard (Washington University in St. Louis), J. Komijani (Washington U.), Carleton DeTar (University of Utah), Ludmila Levkova (University of Utah), Walter Freeman (George Washington University), Steven Gottlieb (Indiana University), Ran Zhou (Indiana U.), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), John Laiho (U. of Glasgow), James Osborn (Argonne National Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Fermi National Accelerator Laboratory), (March2013) "Lattice QCD ensembles with four flavors of highly improved staggered quarks", Physical Review D 87 / 5, . http://dx.doi.org/10.1103/PhysRevD.87.054505
  • Alexei Bazavov (Brookhaven National Laboratory), Claude Bernard (Washington University in St. Louis), C. M. Bouchard (Ohio State U.), Carleton DeTar (University of Utah), Daping Du (U. of Illinois), A. X. El-Khadra (U. of Illinois), Justin Foley (University of Utah), E. D. Freeland (Benedictine U.), E. Gámiz (U. de Granada), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), Jongjeong Kim (U. of Arizona), A. S. Kronfeld (Fermi National Accelerator Laboratory), J. Laiho (U. of Glasgow), Ludmila Levkova (University of Utah), Paul Mackenzie (Fermi National Accelerator Laboratory), E. T. Neil (Fermi National Accelerator Laboratory), M. B. Oktay (U. of Utah), Si-Wei Qiu (U. of Utah), J. N. Simone (Fermi National Accelerator Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Fermi National Accelerator Laboratory), Ran Zhou (Indiana U.), (April2013) "Kaon semileptonic vector form factor and determination of |V_{us}| using staggered fermions", Physical Review D 87 / 7, . http://dx.doi.org/10.1103/PhysRevD.87.073012
  • Alexei Bazavov (Brookhaven National Laboratory), Claude Bernard (Washington University in St. Louis), Carleton DeTar (University of Utah), Justin Foley (University of Utah), Walter Freeman (George Washington University), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), J. Kim (U. of Arizona), John Laiho (Washington University in St. Louis), Ludmila Levkova (University of Utah), M. Lightman (Washington U.), James Osborn (Argonne National Laboratory), S. Qiu (U. of Utah), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Fermi National Accelerator Laboratory), R. Zhou (Indiana U.), (April2013) "Leptonic-Decay-Constant Ratio f_{K^{+}}/f_{π^{+}} from Lattice QCD with Physical Light Quarks", Physical Review Letters 110 / 17, . http://dx.doi.org/10.1103/PhysRevLett.110.172003
  • Jianzhuang Yao, Qin Xu, Hong Guo (University of Tennessee, Knoxville), (2013) "QM/MM and free-energy simulations of deacylation reaction catalysed by sedolisin, a serine-carboxyl peptidase", Molecular Simulation 39 / 3, 206-213. http://dx.doi.org/10.1080/08927022.2012.714467
  • Jon A. Bailey (Seoul National University), Alexei Bazavov (Brookhaven National Laboratory), Claude Bernard (Washington University in St. Louis), C. M. Bouchard (U. of Illinois), Carleton DeTar (University of Utah), Daping Du (U. of Iowa), A. X. El-Khadra (U. of Illinois), J. Foley (U. of Utah), E. D. Freeland (Benedictine U.), E. Gámiz (U. de Granada), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), Jongjeong Kim (U. of Arizona), A. S. Kronfeld (Fermi National Accelerator Laboratory), John Laiho (U. of Glasgow), Ludmila Levkova (University of Utah), Paul Mackenzie (Fermi National Accelerator Laboratory), Y. Meurice (U. of Iowa), E. Neil (Fermi National Accelerator Laboratory), M. B. Oktay (U. of Utah), Si-Wei Qiu (U. of Utah), J. N. Simone (Fermi National Accelerator Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Brookhaven National Laboratory), Ran Zhou (Indiana U.), (June2012) "B_{s}→D_{s}/B→D semileptonic form-factor ratios and their application to BR(B_{s}^{0}→μ^{+}μ^{-})", Physical Review D 85 / 11, . http://dx.doi.org/10.1103/PhysRevD.85.114502
  • Alexei Bazavov (Brookhaven National Laboratory), Tanmoy Bhattacharya (Los Alamos National Laboratory), Carleton DeTar (University of Utah), H.-T. Ding (Brookhaven National Laboratory), Steven Gottlieb (Indiana U.), Rajan Gupta (Los Alamos National Laboratory), P. Hegde (Brookhaven National Laboratory), Urs Heller (American Physical Society), F. Karsch (Brookhaven National Laboratory), E. Laermann (U. Bielefeld), Ludmila Levkova (University of Utah), Swagato Mukherjee (Brookhaven National Laboratory), P. Petreczky (Brookhaven National Laboratory), Christian Schmidt (U. Bielefeld), R. A. Soltz (Lawrence Livermore National Laboratory), W. Soeldner (U. Regensberg), Robert Sugar (University of California-Santa Barbara), Pavlos M. Vranas (Lawrence Livermore National Laboratory), (August2012) "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 86 / 3, . http://dx.doi.org/10.1103/PhysRevD.86.034509
  • Alexei Bazavov (Brookhaven National Laboratory), Claude Bernard (Washington University in St. Louis), C. M. Bouchard (U. of Illinois), Carleton DeTar (University of Utah), M. Di Pierro (DePaul U.), A. X. El-Khadra (U. of Illinois), R. T. Evans (U. of Illinois), E. D. Freeland (Benedictine U.), E. Gámiz (U. de Granada), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), R. Jain (U. of Illinois), A. S. Kronfeld (Fermi National Accelerator Laboratory), John Laiho (U. of Glasgow), Ludmila Levkova (University of Utah), Paul Mackenzie (Fermi National Accelerator Laboratory), E. T. Neil (Fermi National Accelerator Laboratory), M. B. Oktay (U. of Utah), J. N. Simone (Fermi National Accelerator Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Brookhaven National Laboratory), (August2012) "Neutral B-meson mixing from three-flavor lattice quantum chromodynamics: Determination of the SU(3)-breaking ratio ξ", Physical Review D 86 / 3, . http://dx.doi.org/10.1103/PhysRevD.86.034503
  • Jon A. Bailey (Seoul National University), Alexei Bazavov (Brookhaven National Laboratory), Claude Bernard (Washington University in St. Louis), C. M. Bouchard (Ohio State U.), Carleton DeTar (University of Utah), Daping Du (U. of Illinois), A. X. El-Khadra (U. of Illinois), J. Foley (U. of Utah), E. D. Freeland (Benedictine U.), E. Gámiz (U. de Granada), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), Jongjeong Kim (U. of Arizona), A. S. Kronfeld (Fermi National Accelerator Laboratory), John Laiho (U. of Glasgow), Ludmila Levkova (University of Utah), Paul Mackenzie (Fermi National Accelerator Laboratory), Y. Meurice (U. of Iowa), E. T. Neil (Fermi National Accelerator Laboratory), M. B. Oktay (U. of Utah), Si-Wei Qiu (U. of Utah), J. N. Simone (Fermi National Accelerator Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Fermi National Accelerator Laboratory), Ran Zhou (Indiana U.), (August2012) "Refining New-Physics Searches in B→Dτν with Lattice QCD", Physical Review Letters 109 / 7, . http://dx.doi.org/10.1103/PhysRevLett.109.071802
  • Elton Jose Dos Santos (Stanford University), Efthimios Kaxiras, (2013) "Electric-Field Dependence of the Effective Dielectric Constant in Graphene", Nano Letters 13 / 3, 898-902. http://dx.doi.org/10.1021/nl303611v
  • Maria L Kireeva, Kristopher Opron (Michigan State University), Steve A Seibold, C�line Domecq, Robert Cukier (Michigan State University), Benoit Coulombe, Mikhail Kashlev, Zachary Burton (Michigan State University), (June2012) "Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase", BMC Biophysics 5 / 1, 11. http://dx.doi.org/10.1186/2046-1682-5-11
  • Douglas Toussaint (University of Arizona), Walter Freeman (University of Arizona), (2009) "Strange Quark Condensate in the Nucleon in 2+1 Flavor QCD", Physical Review Letters 103 / 12, . http://dx.doi.org/10.1103/PhysRevLett.103.122002
  • Qijun Hong (California Institute of Technology), Axel van de Walle (Brown University), (September2013) "Solid-liquid coexistence in small systems: A statistical method to calculate melting temperatures", The Journal of Chemical Physics 139 / 9, 094114. http://dx.doi.org/10.1063/1.4819792
  • Jacobo Bielak (Carnegie Mellon University), Robert Graves (US Geological Survey), Kim Olsen (San Diego State University), Ricardo Taborda (Carnegie Mellon University), Leonardo Ramirez-Guzman (US Geological Survey), Steven Day (San Diego State University), Geoffrey Ely (Argonne National Laboratory), Daniel Roten (ETH Zurich), Thomas Jordan (University of Southern California), Philip Maechling (University of Southern California), John Urbanic (Pittsburgh Supercomputing Center), Yifeng Cui (University of California-San Diego), Gideon Juve (University of Southern California), (November2009) "The ShakeOut earthquake scenario: Verification of three simulation sets", Geophysical Journal International 180 / 1, 375-404. http://dx.doi.org/10.1111/j.1365-246X.2009.04417.x
  • Yifeng Cui (University of California-San Diego), Reagan Moore (San Diego Supercomputer Center), Kim Olsen (San Diego State University), Amit Chourasia (University of California-San Diego), Philip Maechling (University of Southern California), Jean-Bernard Minster (Scripps Institution of Oceanography), Steven Day (San Diego State University), Yuanfang Hu (San Diego Supercomputer Center), Jing Zhu (San Diego Supercomputer Center), Thomas Jordan (University of Southern California), (July2009) "Toward petascale earthquake simulations", Acta Geotechnica 4 / 2, 79-93. http://dx.doi.org/10.1007/s11440-008-0055-2
  • Luca Larini (University of California-Santa Barbara), Joan-Emma Shea (University of California-Santa Barbara), (August2012) "Role of β-Hairpin Formation in Aggregation: The Self-Assembly of the Amyloid-β(25–35) Peptide", Biophysical Journal 103 / 3, 576-586. http://dx.doi.org/10.1016/j.bpj.2012.06.027
  • Xue Wang, Fengting Xu, Jiasen Liu, Bingquan Gao, Yanxin Liu, Yujia Zhai, Jun Ma, Kai Zhang, Timothy S. Baker, Klaus Schulten, Dong Zheng, Hai Pang, Fei Sun, (January2013) "Atomic Model of Rabbit Hemorrhagic Disease Virus by Cryo-Electron Microscopy and Crystallography", PLoS Pathogens 9 / 1, e1003132. http://dx.doi.org/10.1371/journal.ppat.1003132
  • Yanxin Liu, Johan Strümpfer, Peter L. Freddolino, Martin Gruebele, Klaus Schulten, (May2012) "Structural Characterization of λ-Repressor Folding from All-Atom Molecular Dynamics Simulations", The Journal of Physical Chemistry Letters 3 / 9, 1117-1123. http://dx.doi.org/10.1021/jz300017c
  • Thomas Blum (University of Connecticut), Ruth Van de Water (Fermi National Accelerator Laboratory), Donald Holmgren (Fermi National Accelerator Laboratory), Richard Brower (Boston University), Ethan Neil (University of Colorado), Stephen Sharpe (University of Washington), Robert Sugar (University of California, Santa Barbara), (November2013) "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", Community Summer Study ("Snowmass") 2013 University of Minnesota , . http://arxiv.org/abs/1310.6087
  • Alexei Bazavov (Brookhaven National Laboratory), Claude Bernard (Washington University in St. Louis), C. M. Bouchard (Ohio State University), Carleton DeTar (University of Utah), Daping Du (Syracuse University), A. X. El-Khadra (University of Illinois), Justin Foley (University of Utah), E. D. Freeland (School of the Art Institute, Chicago), E. Gámiz (Universidad de Granada), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), Jongjeong Kim (University of Arizona), A. S. Kronfeld (Fermi National Accelerator Laboratory), John Laiho (Syracuse University), Ludmila Levkova (University of Utah), Paul Mackenzie (Fermi National Accelerator Laboratory), E. T. Neil (University of Colorado), M. B. Oktay (Univerity of Utah), Si-Wei Qiu (University of Utah), James Simone (Fermi National Accelerator Laboratory), Robert Sugar (University of California, Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Fermi National Accelerator Laboratory), Ran Zhou (Indiana University), (March2014) "Determination of |Vus| from a lattice-QCD calculation of the K → πlν semileptonic form factor with physical quark masses", Physical Review Letters 112 / 11, . http://dx.doi.org/10.1103/PhysRevLett.112.112001
  • E. Neil (Fermi National Accelerator Laboratory), J. Bailey (Seoul National University), Alexei Bazavov (Brookhaven National Laboratory), Claude Bernard (Washington University in St. Louis), C. Bouchard (U. of Illinois), Carleton DeTar (University of Utah), M. Di Pierro (DePaul U.), A. X. El-Khadra (U. of Illinois), R. Evans (U. of Illinois), E. Freeland (Benedictine U.), E. Gamiz (U. de Granada), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), R. Jain (U. of Illinois), A. Kronfeld (Fermi National Accelerator Laboratory), John Laiho (U. of Glasgow), Ludmila Levkova (University of Utah), Paul Mackenzie (Fermi National Accelerator Laboratory), M. Oktay (University of Utah), James Simone (Fermi National Accelerator Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Fermi National Accelerator Laboratory), (2011) "B and D meson decay constants from 2+1 flavor improved staggered simulations", Lattice 2011 Squaw Valley, CA , . http://arxiv.org/pdf/1112.3978.pdf
  • Bala Murali Venkatesan, James Polans, Jeffrey Comer (University of Illinois at Urbana-Champaign), Supriya Sridhar, David Wendell, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Rashid Bashir, (2011) "Lipid bilayer coated Al2O3 nanopore sensors: towards a hybrid biological solid-state nanopore", Biomedical Microdevices 13 / 4, 671-682. http://dx.doi.org/10.1007/s10544-011-9537-3
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  • J. Bailey (Fermi National Accelerator Laboratory), Alexei Bazavov (University of Arizona), Claude Bernard (Washington University in St. Louis), C. Bouchard (U. of Illinois), Carleton DeTar (University of Utah), A. X. El-Khadra (U. of Illinois), E. Freeland (Washington U.), Walter Freeman (University of Arizona), E. Gamiz (U. of Illinois), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), A. Kronfeld (Fermi National Accelerator Laboratory), John Laiho (Washington University in St. Louis), Ludmila Levkova (University of Utah), Paul Mackenzie (Fermi National Accelerator Laboratory), M. Oktay (University of Utah), M. Di Pierro (DePaul U.), James Simone (Fermi National Accelerator Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Brookhaven National Laboratory), (2009) "Progress on charm semileptonic form factors from 2+1 flavor lattice QCD", Lattice 2009 Beijing, China , . http://arxiv.org/pdf/0912.0214.pdf
  • Alexei Bazavov (University of Arizona), Claude Bernard (Washington University in St. Louis), Carleton DeTar (University of Utah), X Du (Washington U.), Walter Freeman (University of Arizona), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), John Laiho (Washington University in St. Louis), Ludmila Levkova (University of Utah), M. Oktay (University of Utah), James Osborn (Argonne National Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Brookhaven National Laboratory), (2009) "SU(2) chiral fits to light pseudoscalar masses and decay constants", Lattice 2009 Beijing, China , . http://arxiv.org/pdf/0911.0472.pdf
  • T. Burch (University of Utah), Carleton DeTar (University of Utah), M. Di Pierro (DePaul U.), A. X. El-Khadra (U. of Illinois), Steven Gottlieb (Indiana University), A. Kronfeld (Fermi National Accelerator Laboratory), Ludmila Levkova (University of Utah), Paul Mackenzie (Fermi National Accelerator Laboratory), James Simone (Fermi National Accelerator Laboratory), (2009) "Quarkonium mass splittings with Fermilab heavy quarks and 2+1 flavors of improved staggered sea quarks", Lattice 2009 Beijing, China , . http://arxiv.org/pdf/0911.0361.pdf
  • Alexei Bazavov (University of Arizona), Claude Bernard (Washington University in St. Louis), Carleton DeTar (University of Utah), X. Du (Washington U.), Walter Freeman (University of Arizona), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), John Laiho (Washington University in St. Louis), Ludmila Levkova (University of Utah), M. Oktay (University of Utah), James Osborn (Argonne National Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Brookhaven National Laboratory), (2009) "Results from the MILC collaboration's SU(3) chiral perturbation theory analysis", Lattice 2009 Beijing, China , . http://arxiv.org/pdf/0910.3618.pdf
  • D. Du (U. of Iowa), Carleton DeTar (University of Utah), A. Kronfeld (Fermi National Accelerator Laboratory), John Laiho (U. of Glasgow), Y. Meurice (U. of Iowa), S.-W. Qiu (University of Utah), (2011) "Semileptonic form factor ratio B_s --> D_s/B --> D and its application to BR(B^0_s --> mu^+ mu^-)", Lattice 2011 Squaw Valley, CA , . http://arxiv.org/pdf/1111.1796.pdf
  • C. Bouchard (U. of Illinois), E. Freeland (Benedictine U.), Claude Bernard (Washington University in St. Louis), A. X. El-Khadra (U. of Illinois), E. Gamiz (U. de Granada), A. Kronfeld (Fermi National Accelerator Laboratory), John Laiho (Washington University in St. Louis), Ruth Van de Water (Brookhaven National Laboratory), (2011) "Neutral B mixing from 2+1 flavor lattice-QCD: the Standard Model and beyond", Lattice 2011 Squaw Valley, CA , . http://arxiv.org/pdf/1112.5642.pdf
  • S.-W. Qiu (University of Utah), Carleton DeTar (University of Utah), D. Du (U. of Iowa), A. Kr (Fermi National Accelerator Laboratory), John Laiho (U. of Glasgow), Ruth Van de Water (Brookhaven National Laboratory), (2011) "Semileptonic B to D decays at nonzero recoil with 2+1 flavors of improved staggered quarks", Lattice 2011 Squaw Valley, CA , . http://arxiv.org/pdf/1111.0677.pdf
  • G. Shi (U. of Illinois), Steven Gottlieb (Indiana University), A. Torok (Indiana University), V. Kindratenko (U. of Illinois), (2011) "Design of MILC lattice QCD application for GPU clusters", 25th IEEE International Parallel & Distributed Processing Symposium, (IEEE IPDPS 2011) Anchorage, AK , .
  • A. Torok (Indiana University), S. Basak (Orissa, India), V. Kindratenko (U. of Illinois), G. Shi (U. of Illinois), Alexei Bazavov (Brookhaven National Laboratory), Claude Bernard (Washington University in St. Louis), Carleton DeTar (University of Utah), E. Freeland (U. of Illinois), Walter Freeman (University of Arizona), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), John Laiho (U. of Glasgow), Ludmila Levkova (University of Utah), M. Oktay (University of Utah), James Osborn (Argonne National Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Fermi National Accelerator Laboratory), (2010) "Electromagnetic splitting of charged and neutral mesons", Lattice 2010 Villasimius, Sardinia Italy , . http://pos.sissa.it//archive/conferences/105/127/Lattice%202010_127.pdf
  • Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Robert Brunner, Eduardo Cruz-Chu, Jeffrey Comer (University of Illinois at Urbana-Champaign), Klaus Schulten, (2009) "Modeling transport through synthetic nanopores", IEEE Nanotechnology Magazine 3 / 1, 20-28. http://dx.doi.org/10.1109/MNANO.2008.931112
  • Yuan Zhang (Columbia University in the City of New York), (2012) "Identifying Highly Conserved and Unique Structural Elements in Myosin VI", CELLULAR AND MOLECULAR BIOENGINEERING , .
  • Kai Zhang, Li Wang, Yanxin Liu, Kwok-Yan Chan, Xiaoyun Pang, Klaus Schulten, Zhiyang Dong, Fei Sun, (June2013) "Flexible interwoven termini determine the thermal stability of thermosomes", Protein & Cell 4 / 6, 432-444. http://dx.doi.org/10.1007/s13238-013-3026-9
  • Shawn P Coleman (University of Arkansas), Mehrdad M. M Sichani, Douglas E Spearot (University of Arkansas), (2014) "A Computational Algorithm to Produce Virtual X-ray and Electron Diffraction Patterns from Atomistic Simulations", JOM 66 / 3, 408-416. http://dx.doi.org/10.1007/s11837-013-0829-3
  • Georgios A Tritsaris (Harvard University), Brad D Malone (Harvard University), Efthimios Kaxiras (Harvard University), (June2014) "Structural stability and electronic properties of low-index surfaces of SnS", Journal of Applied Physics 115, 173702. http://dx.doi.org/10.1063/1.4874775
  • Alexei Bazavov (University of Arizona), C. Bouchard (U. of Illinois), Carleton DeTar (University of Utah), A. X. El-Khadra (U. of Illinois), E. Freeland (Washington U.), E. Gamiz (Fermi National Accelerator Laboratory), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), A. Kronfeld (Fermi National Accelerator Laboratory), John Laiho (U. of Glasgow), Ludmila Levkova (University of Utah), Paul Mackenzie (Fermi National Accelerator Laboratory), M. Oktay (University of Utah), James Simone (Fermi National Accelerator Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Brookhaven National Laboratory), (2010) "Semileptonic decays of K and D mesons in 2+1 flavor QCD", Lattice 2010 Villasimius, Sardinia Italy , . http://arxiv.org/pdf/1011.2423.pdf
  • Rogan Carr (University of Illinois at Urbana-Champaign), Jeffrey Comer (University of Illinois at Urbana-Champaign), Mark D. Ginsberg, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2011) "Modeling Pressure-Driven Transport of Proteins Through a Nanochannel", IEEE Transactions on Nanotechnology 10 / 1, 75-82. http://dx.doi.org/10.1109/TNANO.2010.2062530
  • Utkur Mirsaidov, Jeffrey Comer (University of Illinois at Urbana-Champaign), Valentin Dimitrov, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Gregory Timp, (2010) "Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix", Nanotechnology 21 / 39, 395501. http://dx.doi.org/10.1088/0957-4484/21/39/395501
  • Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Robert Brunner, Eduardo Cruz-Chu, Jeffrey Comer (University of Illinois at Urbana-Champaign), Klaus Schulten, (2009) "Modeling transport through synthetic nanopores", IEEE Nanotechnology Magazine 3 / 1, 20-28. http://dx.doi.org/10.1109/MNANO.2008.931112
  • Yan Zhang, Fan Zhang, Jason Bakos, (2011) "Frequent Itemset Mining on Large-Scale Shared Memory Machines", 2011 IEEE International Conference on Cluster Computing Austin, TX , 585-589. http://dx.doi.org/10.1109/CLUSTER.2011.69
  • Christopher Maffeo (University of Illinois at Urbana-Champaign), Robert Schöpflin, Hergen Brutzer, René Stehr, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Gero Wedemann, Ralf Seidel, (2010) "DNA–DNA Interactions in Tight Supercoils Are Described by a Small Effective Charge Density", Physical Review Letters 105 / 15, 158101. http://dx.doi.org/10.1103/PhysRevLett.105.158101
  • Bala Murali Venkatesan, James Polans, Jeffrey Comer (University of Illinois at Urbana-Champaign), Supriya Sridhar, David Wendell, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Rashid Bashir, (2011) "Lipid bilayer coated Al2O3 nanopore sensors: towards a hybrid biological solid-state nanopore", Biomedical Microdevices 13 / 4, 671-682. http://dx.doi.org/10.1007/s10544-011-9537-3
  • J. Bailey (Seoul National University), Alexei Bazavov (Brookhaven National Laboratory), A. X. El-Khadra (U. of Illinois), Steven Gottlieb (Indiana University), R. Jain (U. of Illinois), A. Kronfeld (Fermi National Accelerator Laboratory), Ruth Van de Water (Fermi National Accelerator Laboratory), Ran Zhou (Indiana University), (2011) "D semileptonic form factors and |V_{cs}(d)| from 2+1 flavor lattice QCD", Lattice 2011 Squaw Valley, CA , . http://arxiv.org/pdf/1111.5471.pdf
  • Swati Bhattacharya (University of Illinois at Urbana-Champaign), Julien Muzard (Ecole Supérieure de Physique et Chimie Industrielles, ParisTech, Centre National de la Recherche Scientifique, France), Linda Payet (Ecole Supérieure de Physique et Chimie Industrielles, ParisTech, Centre National de la Recherche Scientifique, France), Jerome Mathe (Ecole Supérieure de Physique et Chimie Industrielles, ParisTech, Centre National de la Recherche Scientifique, France), Ulrich Bockelmann (Ecole Supérieure de Physique et Chimie Industrielles, ParisTech, Centre National de la Recherche Scientifique, France), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Virgile Viasnoff (Ecole Supérieure de Physique et Chimie Industrielles, ParisTech, Centre National de la Recherche Scientifique, France), (February2011) "Rectification of the Current in α-Hemolysin Pore Depends on the Cation Type: The Alkali Series Probed by Molecular Dynamics Simulations and Experiments", Journal of Physical Chemistry C 115, 4255. http://pubs.acs.org/doi/abs/10.1021/jp111441p
  • Meni Wanunu (Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States), Swati Bhattacharya (University of Illinois at Urbana-Champaign), Yun Xie (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States), Yitzhak Tor (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Marija Drndik (Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania), (November2011) "Nanopore Analysis of Individual RNA/Antibiotic Complexes", ACS Nano 5, 9345. http://pubs.acs.org/doi/abs/10.1021/nn203764j#cor1
  • Noa Marom (University of Texas at Austin), Jonathan Moussa (University of Texas at Austin), Xinguo Ren, Alexandre Tkatchenko, James Chelikowsky (University of Texas at Austin), (December2011) "Electronic structure of dye-sensitized TiO_{2} clusters from many-body perturbation theory", Physical Review B 84 / 24, 245115. http://dx.doi.org/10.1103/PhysRevB.84.245115
  • Noa Marom (University of Texas at Austin), Xinguo Ren, Jonathan Moussa (University of Texas at Austin), James Chelikowsky (University of Texas at Austin), Leeor Kronik, (2011) "Electronic structure of copper phthalocyanine from G_{0}W_{0} calculations", Physical Review B 84 / 19, 195143. http://dx.doi.org/10.1103/PhysRevB.84.195143
  • Jason Naylor (University of North Dakota), Matthew Gilmore (University of North Dakota), (September2012) "Environmental factors influential to the duration and intensity of tornadoes in simulated supercells.", Geophysical Research Letters 39/L17802, 5. http://www.agu.org/pubs/crossref/2012/2012GL053041.shtml
  • Alexei Bazavov (University of Arizona), Claude Bernard (Washington University in St. Louis), Carleton DeTar (University of Utah), X. Du (Washington U.), Walter Freeman (University of Arizona), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), John Laiho (U. of Glasgow), Ludmila Levkova (University of Utah), M. Oktay (University of Utah), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Brookhaven National Laboratory), (2010) "Staggered chiral perturbation theory in the two-flavor case and SU(2) analysis of the MILC data", Lattice 2010 Villasimius, Sardinia Italy , . http://arxiv.org/pdf/1011.1792.pdf
  • Swati Bhattacharya (University of Illinois at Urbana-Champaign), Ian M. Derrington (Department of Physics, University of Washington Seattle, 3910 15th Avenue, Seattle, Washington, 98195, United States ), Mikhail Pavlenok (Department of Microbiology, University of Alabama at Birmingham, 609 Bevill Biomedical Research Building, 845 19th Street South, Birmingham, Alabama 35294, United States), Michael Niederweis (Department of Microbiology, University of Alabama at Birmingham, 609 Bevill Biomedical Research Building, 845 19th Street South, Birmingham, Alabama 35294, United States), Jens H. Gundlach (Department of Physics, University of Washington Seattle, 3910 15th Avenue, Seattle, Washington, 98195, United States ), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2012) "Molecular Dynamics Study of MspA Arginine Mutants Predicts Slow DNA Translocations and Ion Current Blockades Indicative of DNA Sequence", ACS Nano 6 / 8, 6960-6968. http://dx.doi.org/10.1021/nn3019943
  • Christopher Maffeo (University of Illinois at Urbana-Champaign), Binquan Luan (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2012) "End-to-end attraction of duplex DNA", Nucleic Acids Research 40 / 9, 3812-3821. http://dx.doi.org/10.1093/nar/gkr1220
  • David Wells (University of Illinois at Urbana-Champaign), Volha Abramkina, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2007) "Exploring transmembrane transport through α-hemolysin with grid-steered molecular dynamics", The Journal of Chemical Physics 127 / 12, 125101. http://dx.doi.org/10.1063/1.2770738
  • Alexei Bazavov (University of Arizona), Claude Bernard (Washington University in St. Louis), Carleton DeTar (University of Utah), X. Du (Washington U.), Walter Freeman (University of Arizona), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), John Laiho (Washington University in St. Louis), Ludmila Levkova (University of Utah), M. Oktay (University of Utah), James Osborn (Argonne National Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Brookhaven National Laboratory), (2009) "MILC results for light pseudoscalars", Lattice 2009 Beijing, China , . http://arxiv.org/pdf/0910.2966.pdf
  • S. Samudrala (Iowa State University), Olga Wodo (Iowa State University), S.K. Suram (Iowa State University), S. Broderick (Iowa State University), K. Rajan (Iowa State University), B. Ganapathysubramanian (Iowa State University), (2013) "A graph-theoretic approach for characterization of precipitates from atom probe tomography data", Computational Materials Science 77 / undefined, 335-342. http://dx.doi.org/10.1016/j.commatsci.2013.04.038
  • David Wells (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2010) "Mechanical Properties of a Complete Microtubule Revealed through Molecular Dynamics Simulation", Biophysical Journal 99 / 2, 629-637. http://dx.doi.org/10.1016/j.bpj.2010.04.038
  • Olga Wodo (Iowa State University), Baskar Ganapathysubramanian (Iowa State University), (2012) "Modeling morphology evolution during solvent-based fabrication of organic solar cells", Computational Materials Science 55 / undefined, 113-126. http://dx.doi.org/10.1016/j.commatsci.2011.12.012
  • Olga Wodo (Iowa State University), Baskar Ganapathysubramanian (Iowa State University), (2011) "Computationally efficient solution to the Cahn–Hilliard equation: Adaptive implicit time schemes, mesh sensitivity analysis and the 3D isoperimetric problem", Journal of Computational Physics 230 / 15, 6037-6060. http://dx.doi.org/10.1016/j.jcp.2011.04.012
  • Jesmin Jahan Tithi (SUNY at Stony Brook), (May2013) "Avoiding Locks and Atomic Instructions in Shared-Memory Parallel BFS Using Optimistic Parallelization", IPDPSW, MTAAP'2013 BOSTON, MA , .
  • Luca Larini (Rutgers, the State University of New Jersey), Joan-Emma Shea (University of California-Santa Barbara), (2013) "Double Resolution Model for Studying TMAO/Water Effective Interactions", The Journal of Physical Chemistry B 117 / 42, 13268-13277. http://dx.doi.org/10.1021/jp403635g
  • Yoo-shin Kim, Feng Li, Ren Kong, Yang Bai, King Li, Yubo Fan (University of Houston-Downtown), Brian E. O’Neill, Zheng Li, (August2013) "Multivalency of non-peptide integrin αVβ3 antagonist slows tumor growth", Molecular Pharmaceutics undefined / undefined, 130820125717008. http://dx.doi.org/10.1021/mp400096z
  • Peikai Chen, Y. S. Hung, Tsz-Kwong Man, Ching C. Lau, Yubo Fan (University of Houston-Downtown), (2012) "A gene signature based method for identifying subtypes and subtype-specific drivers in cancer with an application to medulloblastoma", 2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS) Stan Fulton Building, UNLV, Las Vegas, Nevada , 1-6. http://dx.doi.org/10.1109/ICCABS.2012.6182629
  • Peikai Chen, Yubo Fan (University of Houston-Downtown), Tsz-kwong Man, YS Hung, Ching C Lau, (November2013) "A gene signature based method for identifying subtypes and subtype-specific drivers in cancer with an application to medulloblastoma", BMC Bioinformatics 14 / Suppl 18, S1. http://dx.doi.org/10.1186/1471-2105-14-S18-S1
  • HyeongJun Kim, Jen Hsin, Yanxin Liu, Paul R. Selvin, Klaus Schulten, (November2010) "Formation of Salt Bridges Mediates Internal Dimerization of Myosin VI Medial Tail Domain", Structure 18 / 11, 1443-1449. http://dx.doi.org/10.1016/j.str.2010.09.011
  • Cemil S. Geyik, Fangzhou Wei (University of Texas at Austin), Jackson Massey (University of Texas at Austin), Ali Yilmaz (University of Texas at Austin), (July2012) "FDTD vs. AIM for bioelectromagnetic analysis", Proceedings of the 2012 IEEE International Symposium on Antennas and Propagation Chicago, IL , 1-2. http://dx.doi.org/10.1109/APS.2012.6348964
  • Zheqiang Shi (San Diego State University), Steven M. Day, (March2013) "Rupture dynamics and ground motion from 3-D rough-fault simulations", Journal of Geophysical Research: Solid Earth 118 / 3, 1122-1141. http://dx.doi.org/10.1002/jgrb.50094
  • Fangzhou Wei (University of Texas at Austin), Jackson W. Massey, Cemil S. Geyik, Ali Yilmaz (University of Texas at Austin), (July2012) "Error measures for comparing bioelectromagnetic simulators", Proceedings of the 2012 IEEE International Symposium on Antennas and Propagation Chicago, IL , 1-2. http://dx.doi.org/10.1109/APS.2012.6348016
  • Luca Larini (University of California-Santa Barbara), Lanyuan Lu (University of Utah), Gregory Voth (University of Chicago), (April2010) "The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials", The Journal of Chemical Physics 132 / 16, 164107. http://dx.doi.org/10.1063/1.3394863
  • David Wells (University of Illinois at Urbana-Champaign), Maxim Belkin (University of Illinois at Urbana-Champaign), Jeffrey Comer (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (July2012) "Assessing Graphene Nanopores for Sequencing DNA", Nano Letters 12 / 8, 4117-4123. http://dx.doi.org/10.1021/nl301655d
  • Luca Larini (University of California-Santa Barbara), Joan-Emma Shea (University of California-Santa Barbara), (July2012) "Coarse-Grained Modeling of Simple Molecules at Different Resolutions in the Absence of Good Sampling", The Journal of Physical Chemistry B 116 / 29, 8337-8349. http://dx.doi.org/10.1021/jp2097263
  • Akshaya Shankar (Lehigh University), Anand Jagota (Lehigh University), Jeetain Mittal (Lehigh University), (2012) "DNA Base Dimers Are Stabilized by Hydrogen-Bonding Interactions Including Non-Watson–Crick Pairing Near Graphite Surfaces", The Journal of Physical Chemistry B 116 / 40, 12088-12094. http://dx.doi.org/10.1021/jp304260t
  • Brett Olsen (Washington University in St. Louis), Paul H. Schlesinger (Washington University in St. Louis), Daniel S. Ory (Washington University in St. Louis), Nathan A. Baker (Pacific Northwest National Labs), (2011) "25-Hydroxycholesterol Increases the Availability of Cholesterol in Phospholipid Membranes", Biophysical Journal , .
  • Jacobo Bielak (Carnegie Mellon University), Haydar Karaoglu (Carnegie Mellon University), Ricardo Taborda (University of Memphis), (2011) "Memory-efficient displacement-based internal friction for wave propagation simulation", GEOPHYSICS 76 / 6, T131-T145. http://dx.doi.org/10.1190/geo2011-0019.1
  • Yigit Isbiliroglu (Carnegie Mellon University), Ricardo Taborda (University of Memphis), Jacobo Bielak (Carnegie Mellon University), (2013) "Coupled Soil-Structure Interaction Effects of Building Clusters During Earthquakes", Earthquake Spectra undefined / undefined, 131030142624007. http://dx.doi.org/10.1193/102412EQS315M
  • C. Stavis, T. L. Clare, J. E. Butler, A. D. Radadia, Rogan Carr (University of Illinois at Urbana-Champaign), H. Zeng, W. P. King, J. A. Carlisle, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), R. Bashir, R. J. Hamers, (2010) "Surface Chemistry Special Feature: Surface functionalization of thin-film diamond for highly stable and selective biological interfaces", Proceedings of the National Academy of Sciences 108 / 3, 983-988. http://dx.doi.org/10.1073/pnas.1006660107
  • Jason Naylor (NorthWest Research Associates), Matthew Gilmore (University of North Dakota), (March2014) "Vorticity evolution leading to tornadogenesis and tornadogenesis failure in simulated supercells.", Journal of the Atmospheric Sciences 71/3, 1201-1217. http://journals.ametsoc.org/doi/pdf/10.1175/JAS-D-13-0219.1
  • Jason Naylor (University of North Dakota), Matthew Gilmore (University of North Dakota), (October2012) "Convective initiation in an idealized cloud model using an updraft nudging technique", Monthly Weather Review 140, . http://journals.ametsoc.org/doi/pdf/10.1175/MWR-D-12-00163.1
  • E. Gamiz (U. de Granada), Carleton DeTar (University of Utah), A. X. El-Khadra (U. of Illinois), A. Kronfeld (Fermi National Accelerator Laboratory), Paul Mackenzie (Fermi National Accelerator Laboratory), James Simone (Fermi National Accelerator Laboratory), (2011) "K --> pi l nu form factors with staggered quarks", Lattice 2011 Squaw Valley, CA , . http://arxiv.org/pdf/1111.2021.pdf
  • Claude Bernard (Washington University in St. Louis), C. Bouchard (U. of Illinois), A. X. El-Khadra (U. of Illinois), E. Free (Benedictine U.), E. Gamiz (Gr), A. Kronfeld (Fermi National Accelerator Laboratory), John Laiho (U. of Glasgow), Ruth Van de Water (Fermi National Accelerator Laboratory), (2011) "B Mixing in the Standard Model and Beyond: Lattice QCD", 19th Particles and Nuclei International Conference (PANIC11) Cambridge, MA , . http://arxiv.org/pdf/1111.2968.pdf
  • Claude Bernard (Washington University in St. Louis), Carleton DeTar (University of Utah), M. Di Pierro (DePaul U.), A. El-Khadra (U. of Illinois), R. Evans (U. of Illinois), E. Freeland (Benedictine U.), E. Gamiz (U. de Granada), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), A. Kronfeld (Fermi National Accelerator Laboratory), John Laiho (Washington University in St. Louis), Ludmila Levkova (University of Utah), Paul Mackenzie (Fermi National Accelerator Laboratory), M. Okamoto (Fermi National Accelerator Laboratory), M. Oktay (U. of Utah), James Simone (Fermi National Accelerator Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Brookhaven National Laboratory), (August2009) "Visualization of semileptonic form factors from lattice QCD", Physical Review D 80 / 3, . http://dx.doi.org/10.1103/PhysRevD.80.034026
  • Alexei Bazavov (Brookhaven National Laboratory), T. Bhattacharya (Los Alamos National Laboratory), M. Cheng (Lawrence Livermore National Laboratory), N. Christ (Columbia U.), Carleton DeTar (University of Utah), S. Ejiri (Brookhaven National Laboratory), Steven Gottlieb (Indiana University), Rajan Gupta (Los Alamos National Laboratory), Urs Heller (American Physical Society), K. Huebner (Brookhaven National Laboratory), C. Jung (Brookhaven National Laboratory), F. Karsch (Brookhaven National Laboratory), E. Laermann (U. Bielefeld), Ludmila Levkova (University of Utah), C. Miao (Brookhaven National Laboratory), R. Mawhinney (Columbia U.), P. Petreczky (Brookhaven National Laboratory), C. Schmidt (U. Bielefeld), R. Soltz (Lawrence Livermore National Laboratory), W. Soeldner (U. Darmstadt), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Pavlos M. Vranas (Lawrence Livermore National Laboratory), (July2009) "Equation of state and QCD transition at finite temperature", Physical Review D 80 / 1, . http://dx.doi.org/10.1103/PhysRevD.80.014504
  • Carleton DeTar (University of Utah), Ludmila Levkova (University of Utah), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), (June2010) "QCD thermodynamics with nonzero chemical potential at N_{t}=6 and effects from heavy quarks", Physical Review D 81 / 11, . http://dx.doi.org/10.1103/PhysRevD.81.114504
  • Claude Bernard (Washington University in St. Louis), Carleton DeTar (University of Utah), M. Di Pierro (DePaul U.), A. X. El-Khadra (U. of Illinois), R. T. Evans (U. of Illinois), E. D. Freeland (Benedictine U.), E. Gámiz (U. de Granada), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), A. S. Kronfeld (Fermi National Accelerator Laboratory), John Laiho (Washington University in St. Louis), Ludmila Levkova (University of Utah), Paul Mackenzie (Fermi National Accelerator Laboratory), James Simone (Fermi National Accelerator Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Brookhaven National Laboratory), (February2011) "Tuning Fermilab heavy quarks in 2+1 flavor lattice QCD with application to hyperfine splittings", Physical Review D 83 / 3, . http://dx.doi.org/10.1103/PhysRevD.83.034503
  • Alexei Bazavov (Brookhaven National Laboratory), Claude Bernard (Washington University in St. Louis), Carleton DeTar (University of Utah), Walter Freeman (George Washington University), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), John Laiho (U. of Glasgow), Ludmila Levkova (University of Utah), M. Oktay (U. of Utah), J. Osborn (Lawrence Berkeley National Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Brookhaven National Laboratory), (October2010) "Scaling studies of QCD with the dynamical highly improved staggered quark action", Physical Review D 82 / 7, . http://dx.doi.org/10.1103/PhysRevD.82.074501
  • Alexei Bazavov (U. of Arizona), Douglas Toussaint (University of Arizona), Claude Bernard (Washington University in St. Louis), John Laiho (Washington University in St. Louis), B. Billeter (U. of Utah), Carleton DeTar (University of Utah), L. Levkova (U. of Utah), M. B. Oktay (U. of Utah), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), James Osborn (Argonne National Laboratory), Robert Sugar (University of California-Santa Barbara), Ruth Van de Water (Brookhaven National Laboratory), (June2010) "Topological susceptibility with the asqtad action", Physical Review D 81 / 11, . http://dx.doi.org/10.1103/PhysRevD.81.114501
  • Alexei Bazavov (Brookhaven National Laboratory), Douglas Toussaint (University of Arizona), Claude Bernard (Washington University in St. Louis), John Laiho (Washington University in St. Louis), Carleton DeTar (University of Utah), Ludmila Levkova (University of Utah), M. B. Oktay (U. of Utah), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), Paul Mackenzie (Fermi National Accelerator Laboratory), Robert Sugar (University of California-Santa Barbara), Ruth Van de Water (Brookhaven National Laboratory), (May2010) "Nonperturbative QCD simulations with 2+1 flavors of improved staggered quarks", Reviews of Modern Physics 82 / 2, 1349-1417. http://dx.doi.org/10.1103/RevModPhys.82.1349
  • Yuri A. Nedialkov, Kristopher Opron (Michigan State University), Fadi Assaf, Irina Artsimovitch, Maria L. Kireeva, Mikhail Kashlev, Robert Cukier (Michigan State University), Evgeny Nudler, Zachary Burton (Michigan State University), (November2012) "The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation", Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms undefined / undefined, . http://dx.doi.org/10.1016/j.bbagrm.2012.11.005
  • Alexei Bazavov (University of Arizona), Claude Bernard (Washington University in St. Louis), Carleton DeTar (University of Utah), E. Freeland (Washington U.), E. Gamiz (U. of Illinois), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), A. X. El-Khadra (U. of Illinois), A. Kronfeld (Fermi National Accelerator Laboratory), John Laiho (Washington University in St. Louis), Ludmila Levkova (University of Utah), Paul Mackenzie (Fermi National Accelerator Laboratory), M. Oktay (University of Utah), M. Di Pierro (DePaul U.), James Simone (Fermi National Accelerator Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Brookhaven National Laboratory), (2009) "The D_s and D^+ Leptonic Decay Constants from Lattice QCD", Lattice 2009 Beijing, China , . http://arxiv.org/pdf/0912.5221.pdf
  • Alexei Bazavov (Brookhaven National Laboratory), Claude Bernard (Washington University in St. Louis), Carleton DeTar (University of Utah), Walter Freeman (University of Arizona), Steven Gottlieb (Indiana University), Urs Heller (American Physical Society), James Hetrick (University of the Pacific), J. Kim (University of Arizona), John Laiho (U. of Glasgow), Ludmila Levkova (University of Utah), M. Lightman (Washington U.), M. Oktay (University of Utah), James Osborn (Argonne National Laboratory), Robert Sugar (University of California-Santa Barbara), Douglas Toussaint (University of Arizona), Ruth Van de Water (Fermi National Accelerator Laboratory), (2011) "Properties of light pseudoscalars from lattice QCD with HISQ ensembles", Lattice 2011 Squaw Valley, CA , . http://arxiv.org/pdf/1111.4314.pdf
  • Kim Olsen (San Diego State University), Steven Day (San Diego State University), Luis Dalguer (ETH Zurich), John Mayhew (San Diego State University), Yifeng Cui (University of California-San Diego), Jun Zhou (University of California-San Diego), Victor Cruz-Atienza (Universidad Nacional Autonoma de Mexico), Daniel Roten (ETH Zurich), Philip Maechling (University of Southern California), Thomas Jordan (University of Southern California), David Okaya (University of Southern California), Amit Chourasia (University of California-San Diego), (February2009) "ShakeOut-D: Ground motion estimates using an ensemble of large earthquakes on the southern San Andreas fault with spontaneous rupture propagation", Geophysical Research Letters 36 / 4, . http://dx.doi.org/10.1029/2008GL036832
  • Jackson Massey (University of Texas at Austin), Fangzhou Wei (University of Texas at Austin), Ali Yilmaz (University of Texas at Austin), (July2013) "Mixed basis functions for fast analysis of antennas near voxel-based human models", 2013 USNC-URSI Radio Science Meeting (Joint with AP-S Symposium) Orlando, FL , . http://dx.doi.org/10.1109/USNC-URSI.2013.6715406
  • Fangzhou Wei (University of Texas at Austin), Ali Yilmaz (University of Texas at Austin), (July2013) "A scalable nested preconditioner for improving the AIM-accelerated analysis of antennas near the human body", 2013 USNC-URSI Radio Science Meeting (Joint with AP-S Symposium) Orlando, FL , 214-214. http://dx.doi.org/10.1109/USNC-URSI.2013.6715520
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