Parallel exact enumeration of self-avoiding walk on cubic lattices and its applications to protein folding studies
Date of Award
Master of Science in Computer Science - (M.S.)
Computer and Information Science
Lonnie R. Welch
James A. McHugh
Exact enumeration of self-avoiding walk on many lattices have been studied extensively recently. Even a short chain polymer (about 30 monomers) represented as a chain of cubic lattice sites requires a considerable amount of computer time to exhaustively search for all unique conformations. However, self-avoiding walk process can be modified such that it exhibits a high degree of independence among subprocesses. Parallel implementation of such subprocesses can reduce a great amount of enumeration time. Parallel enumeration makes longer chain enumeration possible.
Enumerating only unique conformations requires that all rotation and mirror conformations be removed. An algorithm to avoid generating such symmetrical conformations is presented. A set of parallel algorithms to solve exact enumeration of cubic lattice graphs subjected to various constraints (volume and/or contact constraints) is presented. The speed up and communication cost are analyzed. One of the most important application of lattice enumeration, enumerative kinetics of protein folding, is also discussed.
Vorapanya, Anek, "Parallel exact enumeration of self-avoiding walk on cubic lattices and its applications to protein folding studies" (1994). Theses. 1681.