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Volume 9, Issue 1
An Algorithm for the Stochastic Simulation of Gene Expression and Heterogeneous Population Dynamics

Daniel A. Charlebois, Jukka Intosalmi, Dawn Fraser & Mads Kærn

Commun. Comput. Phys., 9 (2011), pp. 89-112.

Published online: 2011-09

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  • Abstract

We present an algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics. The algorithm combines an exact method to simulate molecular-level fluctuations in single cells and a constant-number Monte Carlo method to simulate time-dependent statistical characteristics of growing cell populations. To benchmark performance, we compare simulation results with steady-state and time-dependent analytical solutions for several scenarios, including steady-state and time-dependent gene expression, and the effects on population heterogeneity of cell growth, division, and DNA replication. This comparison demonstrates that the algorithm provides an efficient and accurate approach to simulate how complex biological features influence gene expression. We also use the algorithm to model gene expression dynamics within "bet-hedging" cell populations during their adaption to environmental stress. These simulations indicate that the algorithm provides a framework suitable for simulating and analyzing realistic models of heterogeneous population dynamics combining molecular-level stochastic reaction kinetics, relevant physiological details and phenotypic variability.

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@Article{CiCP-9-89, author = {Daniel A. Charlebois, Jukka Intosalmi, Dawn Fraser and Mads Kærn}, title = {An Algorithm for the Stochastic Simulation of Gene Expression and Heterogeneous Population Dynamics}, journal = {Communications in Computational Physics}, year = {2011}, volume = {9}, number = {1}, pages = {89--112}, abstract = {

We present an algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics. The algorithm combines an exact method to simulate molecular-level fluctuations in single cells and a constant-number Monte Carlo method to simulate time-dependent statistical characteristics of growing cell populations. To benchmark performance, we compare simulation results with steady-state and time-dependent analytical solutions for several scenarios, including steady-state and time-dependent gene expression, and the effects on population heterogeneity of cell growth, division, and DNA replication. This comparison demonstrates that the algorithm provides an efficient and accurate approach to simulate how complex biological features influence gene expression. We also use the algorithm to model gene expression dynamics within "bet-hedging" cell populations during their adaption to environmental stress. These simulations indicate that the algorithm provides a framework suitable for simulating and analyzing realistic models of heterogeneous population dynamics combining molecular-level stochastic reaction kinetics, relevant physiological details and phenotypic variability.

}, issn = {1991-7120}, doi = {https://doi.org/10.4208/cicp.280110.070510a}, url = {http://global-sci.org/intro/article_detail/cicp/7492.html} }
TY - JOUR T1 - An Algorithm for the Stochastic Simulation of Gene Expression and Heterogeneous Population Dynamics AU - Daniel A. Charlebois, Jukka Intosalmi, Dawn Fraser & Mads Kærn JO - Communications in Computational Physics VL - 1 SP - 89 EP - 112 PY - 2011 DA - 2011/09 SN - 9 DO - http://doi.org/10.4208/cicp.280110.070510a UR - https://global-sci.org/intro/article_detail/cicp/7492.html KW - AB -

We present an algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics. The algorithm combines an exact method to simulate molecular-level fluctuations in single cells and a constant-number Monte Carlo method to simulate time-dependent statistical characteristics of growing cell populations. To benchmark performance, we compare simulation results with steady-state and time-dependent analytical solutions for several scenarios, including steady-state and time-dependent gene expression, and the effects on population heterogeneity of cell growth, division, and DNA replication. This comparison demonstrates that the algorithm provides an efficient and accurate approach to simulate how complex biological features influence gene expression. We also use the algorithm to model gene expression dynamics within "bet-hedging" cell populations during their adaption to environmental stress. These simulations indicate that the algorithm provides a framework suitable for simulating and analyzing realistic models of heterogeneous population dynamics combining molecular-level stochastic reaction kinetics, relevant physiological details and phenotypic variability.

Daniel A. Charlebois, Jukka Intosalmi, Dawn Fraser and Mads Kærn. (2011). An Algorithm for the Stochastic Simulation of Gene Expression and Heterogeneous Population Dynamics. Communications in Computational Physics. 9 (1). 89-112. doi:10.4208/cicp.280110.070510a
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