Cellular automata for polymer simulation with application to polymer melts and polymer collapse including implications for protein folding

Abstract

Cellular automata can be designed that allow the simulation of a large variety of polymer problems including isolated polymers in dilute solution, polymers in high density melts and polymers embedded in media. The two-space algorithm is a particularly efficient algorithm for polymer simulation that is easy to implement and generalize on both conventional serial hardward and Cellular Automaton (CA) Machines. We describe the implementation of this algorithm and two applications: two dimensions (2-D) melts and polymer collapse. Simulations of high density melts in 2-D show that contrary to expectations polymers do not segregate at high density, there is significant interpenetration as there is in 3-D. Polymer collapse is studied in the regime far from equilibrium. Collapse is found to be dominated by migration of the chain ends. The kinetic process of collapse can systematically and reproducibly restrict the possible conformations that are explored during protein folding. This suggests that the kinetics of collapse may help lead to the desired folded conformation of proteins.