Applications > lammps

Publications

Users of this package associated the following 32 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.

  • 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
  • David Wright (University College, London), S. Kashif Sadiq, Gianni De Fabritiis, Peter V. Coveney, (July2012) "Thumbs Down for HIV: Domain Level Rearrangements Do Occur in the NNRTI-Bound HIV-1 Reverse Transcriptase", Journal of the American Chemical Society 134 / 31, 12885-12888. http://dx.doi.org/10.1021/ja301565k
  • 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
  • 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
  • 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
  • Benjamin A. Hall, David Wright (University College, London), Shantenu Jha, Peter V. Coveney, (August2012) "Quantized Water Access to the HIV-1 Protease Active Site as a Proposed Mechanism for Cooperative Mutations in Drug Affinity", Biochemistry 51 / 33, 6487-6489. http://dx.doi.org/10.1021/bi300432u
  • 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
  • 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
  • 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
  • Ryan Lang (University of Akron), David Simmons (University of Akron), (2013) "Interfacial Dynamic Length Scales in the Glass Transition of a Model Freestanding Polymer Film and Their Connection to Cooperative Motion", Macromolecules 46 / 24, 9818-9825. http://dx.doi.org/10.1021/ma401525q
  • 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
  • S. Wan, David Wright (University College, London), P. V. Coveney, (August2012) "Mechanism of Drug Efficacy within the Epidermal Growth Factor Receptor Revealed by Microsecond Molecular Dynamics Simulation", Molecular Cancer Therapeutics undefined / undefined, . http://dx.doi.org/10.1158/1535-7163.MCT-12-0644-T
  • Qijun Hong (California Institute of Technology), Axel van de Walle, (September2012) "Direct first-principles chemical potential calculations of liquids", The Journal of Chemical Physics 137 / 9, 094114. http://dx.doi.org/10.1063/1.4749287
  • 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
  • Davoud Ebrahimi, Andrew J. Whittle, Roland J.-M. Pellenq, (2014) "Mesoscale properties of clay aggregates from potential of mean force representation of interactions between nanoplatelets", The Journal of Chemical Physics 140 / 15, 154309. http://dx.doi.org/10.1063/1.4870932
  • 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
  • M. B. Prigozhin, Yanxin Liu, A. J. Wirth, S. Kapoor, R. Winter, K. Schulten, M. Gruebele, (May2013) "Misplaced helix slows down ultrafast pressure-jump protein folding", Proceedings of the National Academy of Sciences 110 / 20, 8087-8092. http://dx.doi.org/10.1073/pnas.1219163110
  • Peter L. Freddolino, Christopher B. Harrison, Yanxin Liu, Klaus Schulten, (October2010) "Challenges in protein-folding simulations", Nature Physics 6 / 10, 751-758. http://dx.doi.org/10.1038/nphys1713
  • Boon Chong Goh (University of Illinois at Urbana-Champaign), Michael J Rynkiewicz, Tanya R Cafarella, Mitchell R White, Kevan L Hartshorn, Kimberly Allen, Erika C Crouch, Oliviana Calin, Peter H Seeberger, Klaus Schulten, Barbara A Seaton, (November2013) "Molecular Mechanisms of Inhibition of Influenza by Surfactant Protein D Revealed by Large-Scale Molecular Dynamics Simulation", Biochemistry 52 / 47, 8527-8538. http://dx.doi.org/10.1021/bi4010683
  • Mark Mackura (University of Akron), David Simmons (University of Akron), (2014) "Enhancing heterogenous crystallization resistance in a bead-spring polymer model by modifying bond length", Journal of Polymer Science Part B: Polymer Physics 52 / 2, 134-140. http://dx.doi.org/10.1002/polb.23398
  • 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
  • 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
  • David Wright (University College, London), Benjamin A. Hall, Paul Kellam, Peter V. Coveney, (June2012) "Global Conformational Dynamics of HIV-1 Reverse Transcriptase Bound to Non-Nucleoside Inhibitors", Biology 1 / 2, 222-244. http://dx.doi.org/10.3390/biology1020222
  • 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
  • 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
  • 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
  • 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
  • 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