Stochastic simulation of chemical reactions in spatially complex media

Nicolau Jr., Dan V. and Burrage, Kevin (2008) Stochastic simulation of chemical reactions in spatially complex media. Computers & Mathematics With Applications, 55 5: 1007-1018. doi:10.1016/j.camwa.2006.12.085

Author Nicolau Jr., Dan V.
Burrage, Kevin
Title Stochastic simulation of chemical reactions in spatially complex media
Journal name Computers & Mathematics With Applications   Check publisher's open access policy
ISSN 0898-1221
Publication date 2008-03
Sub-type Article (original research)
DOI 10.1016/j.camwa.2006.12.085
Volume 55
Issue 5
Start page 1007
End page 1018
Total pages 12
Place of publication New York, U.S.
Publisher Pergamon Press
Language eng
Subject 0102 Applied Mathematics
Abstract Discrete stochastic simulations, via techniques such as the Stochastic Simulation Algorithm (SSA) are a powerful tool for understanding the dynamics of chemical kinetics when there are low numbers of certain molecular species. However, an important constraint is the assumption of well-mixedness and homogeneity. In this paper, we show how to use Monte Carlo simulations to estimate an anomalous diffusion parameter that encapsulates the crowdedness of the spatial environment. We then use this parameter to replace the rate constants of bimolecular reactions by a time-dependent power law to produce an SSA valid in cases where anomalous diffusion occurs or the system is not well-mixed (ASSA). Simulations then show that ASSA can successfully predict the temporal dynamics of chemical kinetics in a spatially constrained environment.
Keyword Stochastic simulation
Chemical reactions
Anomalous diffusion
Lateral segregation
Monte Carlo
Q-Index Code C1
Q-Index Status Provisional Code

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
Institute for Molecular Bioscience - Publications
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Citation counts: TR Web of Science Citation Count  Cited 6 times in Thomson Reuters Web of Science Article | Citations
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Created: Thu, 03 Sep 2009, 10:23:33 EST by Mr Andrew Martlew on behalf of Institute for Molecular Bioscience