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

Cellular automata can be designed that allow the simulation of a large vari ety of polymer problems including isolated polymers in dilute solution, pol ymers in high density melts and polymers embedded in media. The two-space a lgorithm is a particularly efficient algorithm for polymer simulation that is easy to implement and generalize on both conventional serial hardward an d Cellular Automaton (CA) Machines. We describe the implementation of this algorithm and two applications: two dimensions (2-D) melts and polymer coll apse. Simulations of high density melts in 2-D show that contrary to expect ations polymers do not segregate at high density, there is significant inte rpenetration 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 reprodu cibly restrict the possible conformations that are explored during protein folding. This suggests that the kinetics of collapse may help lead to the d esired folded conformation of proteins. (C) 2001 Elsevier Science B.V. All rights reserved.