Physics – Chemical Physics
Scientific paper
2008-06-25
J. Chem. Phys. 129, 044108 (2008)
Physics
Chemical Physics
8 pages, 3 figures
Scientific paper
10.1063/1.2957462
We study an approximation scheme based on a second quantization method for a chemical master equation. Small systems, such as cells, could not be studied by the traditional rate equation approach because fluctuation effects are very large in such small systems. Although a Fokker-Planck equation obtained by the system size expansion includes the fluctuation effects, it needs large computational costs for complicated chemical reaction systems. In addition, discrete characteristics of the original master equation are neglected in the system size expansion scheme. It has been shown that the usage of the second quantization description and a variational method achieves tremendous reduction in the dimensionality of the master equation approximately, without loss of the discrete characteristics. We here propose a new scheme for the choice of variational functions, which is applicable to multivariate cases. It is revealed that the new scheme gives better numerical results than old ones and the computational cost increases only slightly.
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