%0 Journal Article %1 ullah_investigatingtwo-moment_2009 %A Ullah, Mukhtar %A Wolkenhauer, Olaf %D 2009 %J Journal of Theoretical Biology %K Cell Mean, Noise, Rostock SBI Two-moment approximation cycle, {(Co)variance,} %N 3 %P 340--352 %R 10.1016/j.jtbi.2009.05.022 %T Investigating the two-moment characterisation of subcellular biochemical networks %U http://www.sciencedirect.com/science/article/B6WMD-4WFG60P-3/2/a715714ac19a22ae365692d291be364f %V 260 %X While ordinary differential equations (ODEs) form the conceptual framework for modelling many cellular processes, specific situations demand stochastic models to capture the influence of noise. The most common formulation of stochastic models for biochemical networks is the chemical master equation (CME). While stochastic simulations are a practical way to realise the CME, analytical approximations offer more insight into the influence of noise. Towards that end, the two-moment approximation (2MA) is a promising addition to the established analytical approaches including the chemical Langevin equation (CLE) and the related linear noise approximation (LNA). The 2MA approach directly tracks the mean and (co)variance which are coupled in general. This coupling is not obvious in CME and CLE and ignored by LNA and conventional ODE models. We extend previous derivations of 2MA by allowing (a) non-elementary reactions and (b) relative concentrations. Often, several elementary reactions are approximated by a single step. Furthermore, practical situations often require the use of relative concentrations. We investigate the applicability of the 2MA approach to the well-established fission yeast cell cycle model. Our analytical model reproduces the clustering of cycle times observed in experiments. This is explained through multiple resettings of M-phase promoting factor (MPF), caused by the coupling between mean and (co)variance, near the G2/M transition.

@article{ullah_investigatingtwo-moment_2009, abstract = {While ordinary differential equations {(ODEs)} form the conceptual framework for modelling many cellular processes, specific situations demand stochastic models to capture the influence of noise. The most common formulation of stochastic models for biochemical networks is the chemical master equation {(CME).} While stochastic simulations are a practical way to realise the {CME,} analytical approximations offer more insight into the influence of noise. Towards that end, the two-moment approximation {(2MA)} is a promising addition to the established analytical approaches including the chemical Langevin equation {(CLE)} and the related linear noise approximation {(LNA).} The {2MA} approach directly tracks the mean and (co)variance which are coupled in general. This coupling is not obvious in {CME} and {CLE} and ignored by {LNA} and conventional {ODE} models. We extend previous derivations of {2MA} by allowing (a) non-elementary reactions and (b) relative concentrations. Often, several elementary reactions are approximated by a single step. Furthermore, practical situations often require the use of relative concentrations. We investigate the applicability of the {2MA} approach to the well-established fission yeast cell cycle model. Our analytical model reproduces the clustering of cycle times observed in experiments. This is explained through multiple resettings of M-phase promoting factor {(MPF),} caused by the coupling between mean and (co)variance, near the {G2/M} transition.}, added-at = {2010-09-17T16:55:15.000+0200}, author = {Ullah, Mukhtar and Wolkenhauer, Olaf}, biburl = {https://www.bibsonomy.org/bibtex/222668b45b986f9055e9f558e1a001105/ra1602}, doi = {10.1016/j.jtbi.2009.05.022}, interhash = {25bd2e3587ab0d9a4d66c56fb9149e85}, intrahash = {22668b45b986f9055e9f558e1a001105}, issn = {0022-5193}, journal = {Journal of Theoretical Biology}, keywords = {Cell Mean, Noise, Rostock SBI Two-moment approximation cycle, {(Co)variance,}}, month = oct, number = 3, pages = {340--352}, timestamp = {2010-09-17T16:55:29.000+0200}, title = {Investigating the two-moment characterisation of subcellular biochemical networks}, url = {http://www.sciencedirect.com/science/article/B6WMD-4WFG60P-3/2/a715714ac19a22ae365692d291be364f}, volume = 260, year = 2009 }