NDLI: A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions

Content Provider	PubMed Central
Author	Chevalier, Michael W. Hana, El-samad
Copyright Year	2014
Abstract	Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-to-cell variability even in clonal populations. Stochastic biochemical networks have been traditionally modeled as continuous-time discrete-state Markov processes whose probability density functions evolve according to a chemical master equation (CME). In diffusion reaction systems on membranes, the Markov formalism, which assumes constant reaction propensities is not directly appropriate. This is because the instantaneous propensity for a diffusion reaction to occur depends on the creation times of the molecules involved. In this work, we develop a chemical master equation for systems of this type. While this new CME is computationally intractable, we make rational dimensional reductions to form an approximate equation, whose moments are also derived and are shown to yield efficient, accurate results. This new framework forms a more general approach than the Markov CME and expands upon the realm of possible stochastic biochemical systems that can be efficiently modeled.
Related Links	http://dx.doi.org/10.1063/1.4902239
Starting Page	214108
File Format	PDF
ISSN	00219606
e-ISSN	10897690
Journal	The Journal of Chemical Physics
Issue Number	21
Volume Number	141
Language	English
Publisher	American Institute of Physics
Publisher Date	2014-12-07
Access Restriction	Open
Rights Holder	American Institute of Physics
Subject Keyword	Physical and Theoretical Chemistry Physics and Astronomy(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Physics and Astronomy Medicine Physical and Theoretical Chemistry

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