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

Author

Listed:
  • 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;
    The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico, 87501, USA)

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.

Suggested Citation

  • Bernd Mayer & Steen Rasmussen, 1998. "The Lattice Molecular Automaton(LMA): A Simulation System for Constructive Molecular Dynamics," International Journal of Modern Physics C (IJMPC), World Scientific Publishing Co. Pte. Ltd., vol. 9(01), pages 157-177.
    • Handle: RePEc:wsi:ijmpcx:v:09:y:1998:i:01:n:s0129183198000133
    DOI: 10.1142/S0129183198000133
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    Cited by:

    1. Bernd Mayer & Steen Rasmussen, 1998. "Self-Reproduction of Dynamical Hierarchies in Chemical Systems," Working Papers 98-05-038, Santa Fe Institute.

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