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J Chem Phys. 2012 Apr 21;136(15):154105. doi: 10.1063/1.3702848.

A study of the accuracy of moment-closure approximations for stochastic chemical kinetics.

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1
School of Biological Sciences, University of Edinburgh, United Kingdom.

Abstract

Moment-closure approximations have in recent years become a popular means to estimate the mean concentrations and the variances and covariances of the concentration fluctuations of species involved in stochastic chemical reactions, such as those inside cells. The typical assumption behind these methods is that all cumulants of the probability distribution function solution of the chemical master equation which are higher than a certain order are negligibly small and hence can be set to zero. These approximations are ad hoc and hence the reliability of the predictions of these class of methods is presently unclear. In this article, we study the accuracy of the two moment approximation (2MA) (third and higher order cumulants are zero) and of the three moment approximation (3MA) (fourth and higher order cumulants are zero) for chemical systems which are monostable and composed of unimolecular and bimolecular reactions. We use the system-size expansion, a systematic method of solving the chemical master equation for monostable reaction systems, to calculate in the limit of large reaction volumes, the first- and second-order corrections to the mean concentration prediction of the rate equations and the first-order correction to the variance and covariance predictions of the linear-noise approximation. We also compute these corrections using the 2MA and the 3MA. Comparison of the latter results with those of the system-size expansion shows that: (i) the 2MA accurately captures the first-order correction to the rate equations but its first-order correction to the linear-noise approximation exhibits the wrong dependence on the rate constants. (ii) the 3MA accurately captures the first- and second-order corrections to the rate equation predictions and the first-order correction to the linear-noise approximation. Hence while both the 2MA and the 3MA are more accurate than the rate equations, only the 3MA is more accurate than the linear-noise approximation across all of parameter space. The analytical results are numerically validated for dimerization and enzyme-catalyzed reactions.

PMID:
22519313
DOI:
10.1063/1.3702848
[Indexed for MEDLINE]
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