Share Email Print
cover

Proceedings Paper

Effective simulation techniques for biological systems
Author(s): Kevin Burrage; Tianhai Tian
Format Member Price Non-Member Price
PDF $14.40 $18.00
cover GOOD NEWS! Your organization subscribes to the SPIE Digital Library. You may be able to download this paper for free. Check Access

Paper 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.

Paper Details

Date Published: 25 May 2004
PDF: 15 pages
Proc. SPIE 5467, Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems II, (25 May 2004); doi: 10.1117/12.548672
Show Author Affiliations
Kevin Burrage, Univ. of Queensland (Australia)
Tianhai Tian, Univ. of Queensland (Australia)


Published in SPIE Proceedings Vol. 5467:
Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems II
Derek Abbott; Sergey M. Bezrukov; Andras Der; Angel Sanchez, Editor(s)

© SPIE. Terms of Use
Back to Top