Application of the strang splitting to the chemical master equation for simulating biochemical kinetics

MacNamara, Shev, Burrage, Kevin and Sidje, Roger B. (2008) Application of the strang splitting to the chemical master equation for simulating biochemical kinetics. International Journal of Computational Science, 2 3: 402-421.


Author MacNamara, Shev
Burrage, Kevin
Sidje, Roger B.
Title Application of the strang splitting to the chemical master equation for simulating biochemical kinetics
Journal name International Journal of Computational Science   Check publisher's open access policy
ISSN 1992-6669
1992-6677
Publication date 2008
Sub-type Article (original research)
Volume 2
Issue 3
Start page 402
End page 421
Total pages 20
Publisher Global Information Publisher
Language eng
Subject 10 Technology
1006 Computer Hardware
1099 Other Technology
Abstract Recently the Finite State Projection (FSP) algorithm was suggested for the numerical solution of the chemical master equation (CME). The CME is a discrete partial differential equation that describes the probability density function associated with stochastic biochemical kinetic processes. We show that the FSP approximation is an example of operator splitting, giving insight into why the method performs so well for biochemical applications. Furthermore we describe the application of the Strang splitting, in combination with the FSP approximation, to chemical reactions with disparate rates and show how this relates to recent applications of the quasi-steady-state approximation (QSSA) to the CME. The application of the Strang splitting to the direct solution of the CME is demonstrated to be extremely effective on four examples commonly used as test problems in the literature: Michaelis-Menten enzyme kinetics, the Goldbeter-Koshland switch, dual phosphorylation, and a decaying-dimerizing model. Finally, the framework gives a multiscale approach for combining the Strang splitting and QSSA approximations, leading to greater overall computational efficiency.
Keyword Chemical master equation
Strang splitting
Stochastic chemical kinetics
Systems biology
Q-Index Code CX
Q-Index Status Provisional Code

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
School of Chemistry and Molecular Biosciences
 
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Created: Fri, 29 Jan 2010, 08:33:05 EST by Macushla Boyle on behalf of Faculty of Science