Multiscale Modeling of Complex Systems Conformational Transitions in Proteins

Abstract : This project concerns development of new simulation methods for modeling protein conformational changes. The purpose is to develop accurate methods for generating a coarse Hamiltonian for use in Monte Carlo simulation. Our method is unique in that we derive the coarse scale energy function based on fine scale (all atom) simulation. We are developing a general scheme which employs both replica exchange (multiple temperatures) with resolution exchange (multiple scales). The method will lead to order-of-magnitude speedup in accurate simulations of loop conformations and protein folding more generally.