Research Initiation Award: The Rapid Evaluation and Global Minimization of Potential Energy Functions in Molecular and Protein Conformations

点击翻译按钮获取中文摘要

Xue 9409285 The objective of this project is to produce more effective sequential and parallel algorithms and software for the rapid evaluation and global minimization of nonconvex potential energy functions that arise in molecular and protein conformation problems. The proposed research will combine the fast multipole algorithms and automatic differentiation to produce O (n) operation algorithms for both the function evaluation and the gradient vector evaluation for a system of n particles. Since all existing algorithms require at least O (n2) operations to evaluate the gradient vector, this research will improve almost all existing algorithms for molecular and protein conformations where repeated evaluation of the function and gradient is required. This success relies on two programming paradigms: a discrete-continuous programming paradigm that uses physical knowledge on the problem to guide continuous minimization searchers, and a parallel two-level simulated annealing programming paradigm which provides load balancing dynamically and moves from one local minimizer to another in an effort to locate a global minimizer.