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Dynamic cellular automata: an alternative to cellular simulation

Par Conseil national de recherches du Canada

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FormatTexte, Article
Sujetcellular simulation; cellular automata; E. coli; genetic circuit
Résumé
A wide variety of approaches, ranging from Petri nets to systems of partial differential equations, have been used to model very specific aspects of cellular or biochemical functions. Here we describe how an agent-based or dynamic cellular automata (DCA) approach can be used as a very simple, yet very general method to model many different kinds of cellular or biochemical processes. Specifically, using simple pair wise interaction rules coupled with random object moves to simulate Brownian motion, we show how the DCA approach can be used to easily and accurately model diffusion, viscous drag, enzyme rate processes, metabolism (the Kreb's cycle), and complex genetic circuits (the repressilator). We also demonstrate how DCA approaches are able to accurately capture the stochasticity of many biological processes. The success and simplicity of this technique suggests that many other physical properties and significantly more complicated aspects of cellular behavior could be modeled using DCA methods. An easy-to-use, graphically-based computer program, called SimCell, was developed to perform the DCA simulations described here. It is available at http://wishart.biology.ualberta.ca/SimCell/.
Date de publication
Maison d’éditionIOP
Dans
  • In Silico Biology 5, nº 2 : 139–161.
Publications évaluées par des pairsOui
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IdentificateurNRC-NINT-148
Numéro NPARC8926197
Exporter la noticeExporter en format RIS
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Identificateur de l’enregistrement8a0e66ad-ff4f-4a21-ab3d-b5d3ca95d141
Enregistrement créé2009-04-23
Enregistrement modifié2020-04-07
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