By Liz Yokubison, writer, author and mother of Alex, ENG‘21 I’m not sure...
MSE PhD Prospectus Defense of Qing Lu
- 1:00 pm on Thursday, December 13, 2012
- 3:00 pm on Thursday, December 13, 2012
- 110 Cummington Street, Rm 245
Extensions and Applications of Generalized Replica Exchange Method in Complex Molecular Systems ABSTRACT: The proposed research aims to apply the generalized Replica Exchange Method (gREM), a recently developed novel computational algorithm, to address the outstanding computational challenges in effectively simulating strong phase transitions in condensed phase systems. The gREM is built upon Replica Exchange Method, which is an extended ensemble algorithm implemented in Molecular Dynamics (MD) or Monte Carlo (MC) simulations. The key ingredients of gREM are parameterized effective sampling weights, smoothly joining ordered and disordered phases with a succession of unimodal energy distributions by transforming unstable or metastable energy states of canonical ensembles into stable ones. The inverse mapping between the sampling weights and the effective temperature provides a systematic way to design the effective sampling weights and determine a dynamic range of relevant parameters. Preliminary results of the applications of gREM in different systems are presented, including the liquid-solid change of an adapted Dzugutov model and the vapor-liquid phase transition in Lennard-Jones fluids. The gREM simulations are performed at various pressures below and near the critical pressure to see the behavior change of the vaporliquid phase transition at different pressures. This proposal reports the observations of features of first-order phase transition at low pressures, including the backbending in the statistical temperature and the kink in the Gibbs function, and continuous second-order phase transition near the critical pressure. The extension of gREM to Molecular Dynamics is proposed to simulate complex fluids and bimolecules, since MD is a more natural choice than MD due to the difficulty in designing an effective algorithm for generating collective trial moves. Another extension of gREM is proposed as hyrid-gREM to cope the challenges in simulations of systems with a greater complexity of conformational states and the corresponding rugged energy landscape. Application of hybrid-gREM approach is proposed for the simulation of phase separation in lipid bilayers using coarse-grained model with implicit solvent. COMMTTEE: Advisor: Professor John Straub, MSE/Chemistry; Professor David Coker, MSE/Chemistry; Professor Tom Keyes, MSE/Chemistry; Appointed Reader Soumendra N. Basu, MSE/ME