Effective simulation techniques for biological systems

Kevin Burrage, Tianhai Tian

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

2 Citations (Scopus)

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. Stochastic simulation methods, chemical reaction systems, multi-scaled approaches, parallel computing, biological applications.

Original languageEnglish
Title of host publicationProceedings of SPIE - The International Society for Optical Engineering
Subtitle of host publicationFluctuations and Noise in Biological, Biophysical, and Biomedical Systems II; Maspalomas; ; 26 May 2004 through 28 May 2004
Pages311-325
Number of pages15
Volume5467
DOIs
Publication statusPublished - 13 Sep 2004
EventFluctuations and Noise in Biological, Biophysical, and Biomedical Systems II - Maspalomas
Duration: 26 May 200428 May 2004

Publication series

NameProceedings of SPIE - The International Society for Optical Engineering
PublisherSPIE
ISSN (Print)0277-786X

Conference

ConferenceFluctuations and Noise in Biological, Biophysical, and Biomedical Systems II
CityMaspalomas
Period26/05/0428/05/04

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