Effective simulation techniques for biological systems

Kevin Burrage; Tianhai Tian

doi:10.1117/12.548672

25 May 2004 Effective simulation techniques for biological systems

Kevin Burrage, Tianhai Tian

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Proceedings Volume 5467, Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems II; (2004) https://doi.org/10.1117/12.548672
Event: Second International Symposium on Fluctuations and Noise, 2004, Maspalomas, Gran Canaria Island, Spain

Abstract

In this paper we give an overview of some very recent work on the stochastic simulation of 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 discuss how novel computing implementations can enhance the performance of these simulations.

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Kevin Burrage and Tianhai Tian "Effective simulation techniques for biological systems", Proc. SPIE 5467, Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems II, (25 May 2004); https://doi.org/10.1117/12.548672

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