Accession Number : ADA339000

Title :   Effective Energy Methods for Global Optimization for Biopolymer Structure Prediction.

Descriptive Note : Final Technical rept. 1 Jan 94-31 Dec 97

Corporate Author : CORNELL UNIV ITHACA NY

Personal Author(s) : Shalloway, David

PDF Url : ADA339000

Report Date : 20 FEB 1998

Pagination or Media Count : 35

Abstract : We developed the fundamental theory and algorithms of the new "Packet Annealing Method" for analyzing biopolymers 3-dimensional structures and tested it on small systems. We showed that the method provides a natural and powerful computational approximation to the stochastic description of biopolymer motions and encompasses other competing "potential smoothing" methods as special cases. Its main strength is that it uncovers and exploits the intrinsic "hidden structures" of biopolymer energy landscapes to efficiently perform global minimization using a hierarchical search procedure which concentrates parallel computing effort on a sequence of * selected regions of decreasing size. Each search region corresponds to a metastable macrostate of the system, a region of conformation space that is isolated from the remainder of the space by effective energy barriers. The effective energy includes both energetic contributions from the energy potential function and entropic contributions resulting from thermal fluctuations of the biopolymer. It determines the thermodynamic macrostate free-energies which (rather than the energies) determine biopolymer structures. In addition, new methods for computing macromolecular conformational transitions and for molecular dynamics simulation were developed.:

Descriptors :   *GLOBAL, *OPTIMIZATION, *MOLECULAR PROPERTIES, THERMAL PROPERTIES, ALGORITHMS, FUNCTIONS, SIMULATION, COMPUTATIONS, STOCHASTIC PROCESSES, PREDICTIONS, DYNAMICS, POLYMERS, ENERGY, STRUCTURES, MOTION, PARALLEL PROCESSING, REGIONS, VARIATIONS, ORGANIC MATERIALS, SEARCHING, STRENGTH(GENERAL), BARRIERS, HIERARCHIES.

Subject Categories : Operations Research
      Atomic and Molecular Physics and Spectroscopy

Distribution Statement : APPROVED FOR PUBLIC RELEASE