Path Sampling Based Coupling of Fast and Slow Dynamical Modes in Biomolecular Reactions: Implications for Enzyme Catalysis and Implications for Mixed Quantum Mechanics Molecular Mechanics Simulations
Ravi Radhakrishnan, Department of Bioengineering, University of Pennsylvania, 120 Hayden Hall, 3320 Smithwalk, Philadelphia, PA 19104 |
Modeling Large-Scale Protein Conformational Changes with the Elastic Network Model: an Approach Based on the Empirical Valence Bond Theory
Jhih-Wei Chu, Center for Biophysical Modeling and Simulation and the Department of Chemistry, University of Utah, Room 2020, 315 S 1400 E, Salt Lake City, UT 84112 and Gregory A. Voth, Center for Biophysical Modeling and Simulation and the Department of Chemistry, University of Utah, Room 2020, 315 S 1400 E, Salt Lake City, UT 84112 |
Combining Multilevel Methods with Modern Sampling Schemes
Andreas Heyden, Department of Chemistry, University of Minnesota, 228 Smith Hall, 207 Pleasant Street S.E., Minneapolis, MN 55455 and Donald G. Truhlar, Chemistry, University of Minnesota, 247 Smith Hall, 207 Pleasant St SE, Minneapolis, MN 55455 |
Improved Density of States Monte-Carlo Method Based on Recycling of Rejected States
Manan Chopra and Juan J. De Pablo, Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706-1691 |
Monte Carlo Simulation Using Reversible Mapping between Local Energy Minima
Doros N. Theodorou, Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Zografou Campus, Athens, 157 80, Greece and Alfred Uhlherr, High Performance Scientific Computing, CSIRO, GPO Box 1289, Melbourne, VIC 3001, Australia |
A Generalized Hamiltonian-Based Algorithm for Rigorous Nonequilibrium Molecular Dynamics Simulation in the Nvt Ensemble
Joseph G. Rajkumar, Chemical Engineering, The University of Tennessee, 419 Dougherty Hall, Knoxville, TN 37996-2200, David J. Keffer, The University of Tennessee, 617 Dougherty Hall Dougherty Hall, Knoxville, TN 37996-2200, Brian J. Edwards, The University of Tennessee, Department of Chemical Engineering, Knoxville, TN 37917 and Chunggi Baig, Chemical Engineering, The University of Tennessee, Knoxville, TN 37996-2200 |
Sequential Updating Algorithms for Grand Canonical Monte Carlo Simulations
Ruichao Ren, Chemical Engineering, University of California, Los Angeles, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095 and Gerassimos Orkoulas, University of California, Los Angeles, Departmet of Chemical and Biomolecular Engineering, 5531 Boelter Hall, Los Angeles, CA 90095-1590 |
Ensemble Optimization Based on a Rigorous Overlap Function
M. Scott Shell, Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, Box 2240, San Francisco, CA 94143 |
Obtaining Reaction Coordinates by Likelihood Maximization
Baron Peters, Chemical Engineering, Massachusetts Institute of Technology, 77 Mass. Ave. E19-528, Cambridge, MA 02139 and Bernhardt L. Trout, Massachusetts Institute of Technology, 77 Mass. Ave. E19-502B, Cambridge, MA 02139 |
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