Generalized binomial tau-leap method for biochemical kinetics incorporating both delay and intrinsic noise

Leier, André, Marquez-Lago, Tatiana T. and Burrage, Kevin (2008) Generalized binomial tau-leap method for biochemical kinetics incorporating both delay and intrinsic noise. Journal of Chemical Physics, 128 20: 205107-1-205107-14. doi:10.1063/1.2919124

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Author Leier, André
Marquez-Lago, Tatiana T.
Burrage, Kevin
Title Generalized binomial tau-leap method for biochemical kinetics incorporating both delay and intrinsic noise
Formatted title
Generalized binomial τ-leap method for biochemical kinetics incorporating both delay and intrinsic noise
Journal name Journal of Chemical Physics   Check publisher's open access policy
ISSN 0021-9606
1520-9032
1089-7690
Publication date 2008-05-01
Sub-type Article (original research)
DOI 10.1063/1.2919124
Open Access Status File (Publisher version)
Volume 128
Issue 20
Start page 205107-1
End page 205107-14
Total pages 14
Place of publication Lancaster, U.S.A.
Publisher American Institute of Physics
Language eng
Subject 0306 Physical Chemistry (incl. Structural)
Formatted abstract
The delay stochastic simulation algorithm (DSSA) by Barrio et al. [Plos Comput. Biol. 2, 117(E) (2006)] was developed to simulate delayed processes in cell biology in the presence of intrinsic noise, that is, when there are small-to-moderate numbers of certain key molecules present in a chemical reaction system. These delayed processes can faithfully represent complex interactions and mechanisms that imply a number of spatiotemporal processes often not explicitly modeled such as transcription and translation, basic in the modeling of cell signaling pathways. However, for systems with widely varying reaction rate constants or large numbers of molecules, the simulation time steps of both the stochastic simulation algorithm (SSA) and the DSSA can become very small causing considerable computational overheads. In order to overcome the limit of small step sizes, various τ-leap strategies have been suggested for improving computational performance of the SSA. In this paper, we present a binomial -DSSA method that extends the τ-leap idea to the delay setting and avoids drawing insufficient numbers of reactions, a common shortcoming of existing binomial τ-leap methods that becomes evident when dealing with complex chemical interactions. The resulting inaccuracies are most evident in the delayed case, even when considering reaction products as potential reactants within the same time step in which they are produced. Moreover, we extend the framework to account for multicellular systems with different degrees of intercellular communication. We apply these ideas to two important genetic regulatory models, namely, the hes1 gene, implicated as a molecular clock, and a Her1/Her 7 model for coupled oscillating cells. ©2008 American Institute of Physics
Keyword Biochemistry
Molecular biophysics
Noise
Reaction rate constants
Q-Index Code C1
Q-Index Status Provisional Code

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
Institute for Molecular Bioscience - Publications
 
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Created: Thu, 03 Sep 2009, 20:00:36 EST by Mr Andrew Martlew on behalf of Institute for Molecular Bioscience