A moment closure method for stochastic reaction networks

被引:79
|
作者
Lee, Chang Hyeong [1 ]
Kim, Kyeong-Hun [2 ]
Kim, Pilwon [3 ]
机构
[1] Worcester Polytech Inst, Dept Math Sci, Worcester, MA 01609 USA
[2] Korea Univ, Dept Math, Seoul 136701, South Korea
[3] Ohio State Univ, Dept Math, Columbus, OH 43210 USA
来源
JOURNAL OF CHEMICAL PHYSICS | 2009年 / 130卷 / 13期
关键词
algebra; differential equations; master equation; reaction kinetics theory; reaction rate constants; series (mathematics); statistical analysis; SIMULATION; SYSTEMS;
D O I
10.1063/1.3103264
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
In this paper we present a moment closure method for stochastically modeled chemical or biochemical reaction networks. We derive a system of differential equations which describes the dynamics of means and all central moments from a chemical master equation. Truncating the system for the central moments at a certain moment term and using Taylor approximation, we obtain explicit representations of means and covariances and even higher central moments in recursive forms. This enables us to deal with the moments in successive differential equations and use conventional numerical methods for their approximations. Furthermore, we estimate the errors in the means and central moments generated by the approximation method. We also find the moments at equilibrium by solving truncated algebraic equations. We show in examples that numerical solutions based on the moment closure method are accurate and efficient by comparing the results to those of stochastic simulation algorithms.
引用
收藏
页数:15
相关论文
共 50 条
  • [1] A Moment Closure Method for Stochastic Chemical Reaction Networks with General Kinetics
    Lee, Chang Hyeong
    [J]. MATCH-COMMUNICATIONS IN MATHEMATICAL AND IN COMPUTER CHEMISTRY, 2013, 70 (03) : 785 - 800
  • [2] A moment-convergence method for stochastic analysis of biochemical reaction networks
    Zhang, Jiajun
    Nie, Qing
    Zhou, Tianshou
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2016, 144 (19):
  • [3] Stochastic analysis of gene regulatory networks using moment closure
    Singh, Abhyudai
    Hespanha, Joao Pedro
    [J]. 2007 AMERICAN CONTROL CONFERENCE, VOLS 1-13, 2007, : 2800 - 2805
  • [4] Maximum-entropy moment-closure for stochastic systems on networks
    Rogers, Tim
    [J]. JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT, 2011,
  • [5] Adaptive moment closure for parameter inference of biochemical reaction networks
    Schilling, Christian
    Bogomolov, Sergiy
    Henzinger, Thomas A.
    Podelski, Andreas
    Ruess, Jakob
    [J]. BIOSYSTEMS, 2016, 149 : 15 - 25
  • [6] Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks
    Bogomolov, Sergiy
    Henzinger, Thomas A.
    Podelski, Andreas
    Ruess, Jakob
    Schilling, Christian
    [J]. COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY, CMSB 2015, 2015, 9308 : 77 - 89
  • [7] A modified Gaussian moment closure method for nonlinear stochastic differential equations
    Makarem, H.
    Pishkenari, H. Nejat
    Vossoughi, G. R.
    [J]. NONLINEAR DYNAMICS, 2017, 89 (04) : 2609 - 2620
  • [8] A modified Gaussian moment closure method for nonlinear stochastic differential equations
    H. Makarem
    H. Nejat Pishkenari
    G. R. Vossoughi
    [J]. Nonlinear Dynamics, 2017, 89 : 2609 - 2620
  • [9] Moment closure and the stochastic logistic model
    Nåsell, I
    [J]. THEORETICAL POPULATION BIOLOGY, 2003, 63 (02) : 159 - 168
  • [10] Moment closure for biochemical networks
    Hespanha, Joao
    [J]. 2008 3RD INTERNATIONAL SYMPOSIUM ON COMMUNICATIONS, CONTROL AND SIGNAL PROCESSING, VOLS 1-3, 2008, : 142 - 147