期刊
COMMUNICATIONS IN COMPUTATIONAL PHYSICS
卷 9, 期 1, 页码 89-112出版社
GLOBAL SCIENCE PRESS
DOI: 10.4208/cicp.280110.070510a
关键词
Constant-number Monte Carlo; stochastic simulation algorithm; gene expression; heterogeneous population dynamics
资金
- National Science and Engineering Research Council of Canada (NSERC)
- Canadian Institutes of Health Research (CIHR)
- Academy of Finland [129657, 124615]
- Tampere Graduate School in Information Science and Engineering (TISE)
- Academy of Finland (AKA) [124615, 124615] Funding Source: Academy of Finland (AKA)
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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