Simulation and Dynamics of Entropy Driven, Molecular Self-Assembly Processes

Molecular self-assembly is frequently found to generate higher order, functional structures in biochemical systems. One such example is the self-assembly of lipids in aqueous solution forming membranes, micelles and vesicles, another is the dynamic formation and rearrangement of the cytoskeleton. These processes are often driven by local, short range forces and, therefore, the dynamics is solely based on local interactions. In this paper, we introduce a cellular automata based simulation, the Lattice Molecular Automaton, in which data structures, representing different molecular entities like water, hydrophilic and hydrophobic monomers, share locally propagated force information on a hexagonal, 2D lattice. The purpose of this level of description is the simulation of entropic and enthalpic flows in a microcanonical, molecular ensemble to gain insight about entropy-driven processes in molecular many-particle systems. Three applications are shown, i.e., modeling structural features of a polar solvent, cluster-formation of hydrop-hobic monomers in a polar environment, and the self-assembly of polymers. Processes leading to phase-separation on a molecular level are discussed. A thorough discussion of the computational details, advantages, and limitations of the Lattice Molecular Automaton approach can be found in reference [1].