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New Constructions in Cellular Automata$
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David Griffeath and Cristopher Moore

Print publication date: 2003

Print ISBN-13: 9780195137170

Published to Oxford Scholarship Online: November 2020

DOI: 10.1093/oso/9780195137170.001.0001

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Constructive Molecular Dynamics Lattice Gases: Three-Dimensional Molecular Self-Assembly

Constructive Molecular Dynamics Lattice Gases: Three-Dimensional Molecular Self-Assembly

Chapter:
(p.182) (p.183) Constructive Molecular Dynamics Lattice Gases: Three-Dimensional Molecular Self-Assembly
Source:
New Constructions in Cellular Automata
Author(s):

Martin Nilsson

Steen Rasmussen

Publisher:
Oxford University Press
DOI:10.1093/9780195137170.003.0011

Realistic molecular dynamics and self-assembly is represented in a lattice simulation where water, water-hydrocarbons, and water-amphiphilic systems are investigated. The details of the phase separation dynamics and the constructive self-assembly dynamics are discussed and compared to the corresponding experimental systems. The method used to represent the different molecular types can easily be expended to include additional molecules and thus allow the assembly of more complex structures. This molecular dynamics (MD) lattice gas fills a modeling gap between traditional MD and lattice gas methods. Both molecular objects and force fields are represented by propagating information particles and all microscopic interactions are reversible. Living systems, perhaps the ultimate constructive dynamical systems, is the motivation for this work and our focus is a study of the dynamics of molecular self-assembly and self-organization. In living systems, matter is organized such that it spontaneously constructs intricate functionalities at all levels from the molecules up to the organism and beyond. At the lower levels of description, chemical reactions, molecular selfassembly and self-organization are the drivers of this complexity. We shall, in this chapter, demonstrate how molecular self-assembly and selforganization processes can be represented in formal systems. The formal systems are to be denned as a special kind of lattice gas and they are in a form where an obvious correspondence exists between the observables in the lattice gases and the experimentally observed properties in the molecular self-assembly systems. This has the clear advantage that by using these formal systems, theory, simulation, and experiment can be conducted in concert and can mutually support each other. However, a disadvantage also exists because analytical results are difficult to obtain for these formal systems due to their inherent complexity dictated by their necessary realism. The key to novelt simpler molecules (from lower levels), dynamical hierarchies are formed [2, 3]. Dynamical hierarchies are characterized by distinct observable functionalities at multiple levels of description. Since these higher-order structures are generated spontaneously due to the physico-chemical properties of their building blocks, complexity can come for free in molecular self-assembly systems. Through such processes, matter apparently can program itself into structures that constitute living systems [11, 27, 30].

Keywords:   London forces, amphiphilic polymers, bicontinuous structures, charge-charge interactions, dispersion forces, excluded volumes of molecules, hydrocarbons, intermolecular interactions, kinetic energies, micellar structures

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