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

Bernd Mayer () and Steen Rasmussen ()
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Bernd Mayer: Institute for Theoretical Chemistry and Radiation Chemistry, University of Vienna, UZAII Althanstrasse 14, A-1090 Vienna, Austria
Steen Rasmussen: EES-5 MS-D407 and T-CNLS MS-B258, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, USA;

International Journal of Modern Physics C (IJMPC), 1998, vol. 09, issue 01, 157-177

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.TheLattice 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.

Keywords: Molecular Dynamics; Molecular Self-Assembly; Lattice Gas; Discrete Field Automata (search for similar items in EconPapers)
Date: 1998
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DOI: 10.1142/S0129183198000133

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