A multi-scaled approach for simulating chemical reaction systems

Burrage, Kevin, Tian, Tianhai, & Burrage, Pamela (2004) A multi-scaled approach for simulating chemical reaction systems. Progress in Biophysics & Molecular Biology, 85(2-3), pp. 217-234.

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In this paper we give an overview of some very recent work, as well as presenting a new approach, on the stochastic simulation of multi-scaled systems involving chemical reactions. In many biological systems (such as genetic regulation and cellular dynamics) there is a mix between small numbers of key regulatory proteins, and medium and large numbers of molecules. In addition, it is important to be able to follow the trajectories of individual molecules by taking proper account of the randomness inherent in such a system. We describe different types of simulation techniques (including the stochastic simulation algorithm, Poisson Runge-Kutta methods and the balanced Euler method) for treating simulations in the three different reaction regimes: slow, medium and fast. We then review some recent techniques on the treatment of coupled slow and fast reactions for stochastic chemical kinetics and present a new approach which couples the three regimes mentioned above. We then apply this approach to a biologically inspired problem involving the expression and activity of LacZ and LacY proteins in E coli, and conclude with a discussion on the significance of this work. (C) 2004 Elsevier Ltd. All rights reserved.

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ID Code: 57765
Item Type: Journal Article
Refereed: Yes
Keywords: stochastic simulation method, Poisson Runge-Kutta method, chemical reaction system, multi-scaled approaches, biological applications
DOI: 10.1016/j.pbiomolbio.2004.01.004
ISSN: 0079-6107
Subjects: Australian and New Zealand Standard Research Classification > MATHEMATICAL SCIENCES (010000) > STATISTICS (010400) > Stochastic Analysis and Modelling (010406)
Divisions: Past > QUT Faculties & Divisions > Faculty of Science and Technology
Current > Schools > School of Mathematical Sciences
Current > QUT Faculties and Divisions > Science & Engineering Faculty
Deposited On: 04 Mar 2013 23:29
Last Modified: 22 Mar 2013 04:02

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