Type-dependent irreversible stochastic spin models for genetic regulatory networks at the level of promotion-inhibition circuitry
Authored by J Ricardo G Mendonca, Oliveira Mario J de
Date Published: 2015
DOI: 10.1016/j.physa.2015.08.001
Sponsors:
Brazilian National Council for Scientific and Technological Development (CNPq)
Platforms:
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Model Documentation:
Other Narrative
Mathematical description
Model Code URLs:
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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. (C) 2015 Elsevier B.V.
All rights reserved.
Tags
Evolution
Transitions
Modularity
systems
Biological networks
Expression
Ashkin-teller model
Design principles
Cell
biology
Oscillators