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Stochastic simulation of chemical reactions in spatially complex media

Nicolau, Dan & Burrage, Kevin (2008) Stochastic simulation of chemical reactions in spatially complex media. Computers and Mathematics with Applications, 55(5), pp. 1007-1018.

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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.

Impact and interest:

4 citations in Scopus
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5 citations in Web of Science®

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ID Code: 44632
Item Type: Journal Article
Keywords: Stochastic simulation, Chemical reactions, Anomalous diffusion, Obstacles, Lateral segregation, Monte Carlo
DOI: 10.1016/j.camwa.2006.12.085
ISSN: 0898-1221
Subjects: Australian and New Zealand Standard Research Classification > MATHEMATICAL SCIENCES (010000) > APPLIED MATHEMATICS (010200)
Australian and New Zealand Standard Research Classification > MATHEMATICAL SCIENCES (010000) > NUMERICAL AND COMPUTATIONAL MATHEMATICS (010300)
Australian and New Zealand Standard Research Classification > INFORMATION AND COMPUTING SCIENCES (080000) > COMPUTATION THEORY AND MATHEMATICS (080200)
Divisions: Past > QUT Faculties & Divisions > Faculty of Science and Technology
Past > Schools > Mathematical Sciences
Deposited On: 24 Aug 2011 22:13
Last Modified: 29 Feb 2012 14:35

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