Type-dependent irreversible stochastic spin models for genetic regulatory networks at the level of promotion–inhibition circuitry

J. Ricardo G. Mendonça and Mário J. de Oliveira

Physica A: Statistical Mechanics and its Applications, 2015, vol. 440, issue C, 33-41

Abstract: We describe an approach to model genetic regulatory networks at the level of promotion–inhibition circuitry through a class of stochastic spin models that includes spatial and temporal density fluctuations in a natural way. The formalism can be viewed as an agent-based model formalism with agent behaviour ruled by a classical spin-like pseudo-Hamiltonian playing the role of a local, individual objective function. A particular but otherwise generally applicable choice for the microscopic transition rates of the models also makes them of independent interest. To illustrate the formalism, we investigate (by Monte Carlo simulations) some stationary state properties of the repressilator, a synthetic three-gene network of transcriptional regulators that possesses oscillatory behaviour.

Keywords: Genetic regulatory network; Stochastic spin model; Nonequilibrium statistical mechanics; Repressilator; Biochemical oscillations (search for similar items in EconPapers)
Date: 2015
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Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:440:y:2015:i:c:p:33-41

DOI: 10.1016/j.physa.2015.08.001

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