The Lattice Molecular Automaton(LMA): A Simulation System for Constructive Molecular Dynamics

Abstract

Molecular self-assembly is frequently encountered in biochemical systems generating higher order structures with well-defined functionalities. However, the driving forces underlying these processes are not well understood. The Lattice Molecular Automaton (LMA) is a deterministic computational tool suitable for simulation of self-organization processes in large scale, molecular systems. This paper introduces the basic computational concepts needed to formulate molecular dynamics and self-assembly in a discrete field, cellular automaton environment: Molecular objects are encoded as data structures on a 2D triangular lattice. Propagating force particles together with kinetic and potential energy terms define simulation objects that specify molecular dynamics and force field properties. As an example, the simulation of polymer dynamics in an aqueous environment is shown. In this paper we focus on the mathematical and algorithmic formulation of a variety of intra- and intermolecular interactions. Thermodynamical characteristics together with a variety of other physico-chemical properties of the LMA are discussed in detail in Ref. 1.