POLYMER SIMULATION USING CELLULAR AUTOMATA: 2-D MELTS, GEL-ELECTROPHORESIS AND POLYMER COLLAPSE

Simulations using simple cellular automata algorithms can be used to study various abstract polymer problems. We describe the two-space algorithm where interactions of a monomer are only with monomers in the other space. It is a particularly efficient algorithm for polymer simulation that is easy to implement and generalize. Three applications: 2-D melts, gel-electrophoresis and polymer collapse, are described. Simulations of high density melts in 2-D show that contrary to expectations polymers do not completely segregate at high density -- there is significant interpenetration. Preliminary simulations of gel-electrophoresis show its behavior in the diffusive regime and demonstrate the use of Cellular Automaton Machines (CAMs). Polymer collapse is studied in the regime of large departures from good solvent conditions. In this regime kinetics plays a significant role. Collapse is found to be dominated (nucleated) 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.