Stochastic simulation of chemical reactions in spatially complex media
Description
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:
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ID Code: | 44632 | ||
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Item Type: | Contribution to Journal (Journal Article) | ||
Refereed: | Yes | ||
ORCID iD: |
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Measurements or Duration: | 12 pages | ||
Keywords: | Anomalous diffusion, Chemical reactions, Lateral segregation, Monte Carlo, Obstacles, Stochastic simulation | ||
DOI: | 10.1016/j.camwa.2006.12.085 | ||
ISSN: | 0898-1221 | ||
Pure ID: | 33644462 | ||
Divisions: | Past > QUT Faculties & Divisions > Faculty of Science and Technology | ||
Copyright Owner: | Consult author(s) regarding copyright matters | ||
Copyright Statement: | This work is covered by copyright. Unless the document is being made available under a Creative Commons Licence, you must assume that re-use is limited to personal use and that permission from the copyright owner must be obtained for all other uses. If the document is available under a Creative Commons License (or other specified license) then refer to the Licence for details of permitted re-use. It is a condition of access that users recognise and abide by the legal requirements associated with these rights. If you believe that this work infringes copyright please provide details by email to qut.copyright@qut.edu.au | ||
Deposited On: | 24 Aug 2011 22:13 | ||
Last Modified: | 03 Mar 2024 14:48 |
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