Type-dependent irreversible stochastic spin models for biochemical reaction networks

Details Type-dependent irreversible stochastic spin models for biochemical reaction networks Type-dependent irreversible stochastic spin models for biochemical reaction networks

2010-11-23

arxiv.org/abs/1011.4976v2

Physics

Condensed Matter

Statistical Mechanics

Typeset in REVTeX 4.1, 6 pages, 4 figures, references given in full format (titles, DOI etc.). Some extra material and new ref

Scientific paper

We describe an approach to model biochemical reaction networks at the level of promotion-inhibition circuitry through a class of stochastic spin models that depart from the usual chemical kinetics setup and includes spatial and temporal density fluctuations in a most natural way. 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 some stationary state properties of the repressilator, a synthetic three-gene network of transcriptional regulators that possesses a rich dynamical behaviour.

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