Effective simulation techniques for biological systems

Burrage, K. and Tian, T. (2004) Effective simulation techniques for biological systems. Proceedings of the SPIE: The International Society for Optical Engineering, 5467, pp. 311-325. (doi: 10.1117/12.548672)

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.

• Item Type: Articles
• Additional Information: Copyright 2004 Society of Photo-Optical Instrumentation Engineers (SPIE). One print or electronic copy may be made for personal use only. Systematic reproduction and distribution, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper are prohibited.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Tian, Dr Tianhai
• Authors: Burrage, K., and Tian, T.
• Subjects: Q Science > QH Natural history > QH301 Biology; Q Science > QC Physics
• College/School: College of Science and Engineering > School of Mathematics and Statistics > Mathematics
• Journal Name: Proceedings of the SPIE: The International Society for Optical Engineering
• Publisher: SPIE - The International Society for Optical Engineering
• ISSN: 0277-786X
• Published Online: 01 July 2004
• Copyright Holders: Copyright © 2004 SPIE
• First Published: First published in Proceedings of the SPIE - The International Society for Optical Engineering 5467:311-325
• Publisher Policy: Reproduced in accordance with the copyright policy of the publisher.