Tom Keyes, Boston University, "Statistical temperature molecular dynamics (STMD) and generalized replica exchange (GREM) algorithms for enhanced sampling of biomolecules and first order phase transitions"

Feb 19 2013, 11:00 am
Distinguished Lecture Series Guest Speaker: 

Tom Keyes

Professor
Department of Chemistry
Boston University

Date & Time: 
Tuesday, February 19, 2013, 11:00AM
Location: 
Klaus 1116E
Host: 
Jeffrey Skolnick
Abstract: 
Systems with multiple free energy minima pose challenges to conventional methods of computer simulation due to broken ergodicity, which may be overcome or mitigated with generalized ensembles. STMD [1] is a MD algorithm sampling a flat-energy distribution, and GREM [2] is a replica exchange algorithm in which the replicas are explicitly designed to sample states with coexisting phases. The application and performance of STMD, the replica exchange version, RESTMD [3], and the GREM will be detailed for biomolecules and for phase equilibrium. 1. Jae Gil Kim, J. E. Straub and T. Keyes, Statistical Temperature Monte Carlo and Molecular Dynamics Algorithms, Phys. Rev. Lett. 97, 050601 (2006); Jae Gil Kim and T. Keyes, The Influence of Energetic Frustration on the Global Shapes of Energy Landscapes in beta-Barrel Forming Model Proteins: Inherent Structure Analysis and Statistical Temperature Molecular Dynamics Simulation, J. Phys. Chem. B 112, 954 (2008). 2. Jaegil Kim, Thomas Keyes and John E. Straub, Generalized Replica Exchange Method, J. Chem. Phys. 132, 224107 (2010). 3. Jaegil Kim, John E. Straub and Tom Keyes, Replica Exchange Statistical Temperature Molecular Dynamics Algorithm, J. Phys. Chem. B 116, 8646 (2012).
Additional Info: 

Tom Keyes studies biomolecules and water using fundamental statistical mechanics and computer simulation, simultaneously developing algorithms for fast and efficient sampling of large systems.

Faculty Profile

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