Graphical reduction of reaction networks by linear elimination of species
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Publication:504070
DOI10.1007/S00285-016-1028-YzbMATH Open1357.92034arXiv1509.03153OpenAlexW2963773794WikidataQ46543011 ScholiaQ46543011MaRDI QIDQ504070FDOQ504070
Authors: Meritxell Sáez, Carsten Wiuf, Elisenda Feliu 
Publication date: 25 January 2017
Published in: Journal of Mathematical Biology (Search for Journal in Brave)
Abstract: The quasi-steady state approximation and time-scale separation are commonly applied methods to simplify models of biochemical reaction networks based on ordinary differential equations (ODEs). The concentrations of the "fast" species are assumed effectively to be at steady state with respect to the "slow" species. Under this assumption the steady state equations can be used to eliminate the "fast" variables and a new ODE system with only the slow species can be obtained. We interpret a reduced system obtained by time-scale separation as the ODE system arising from a unique reaction network, by identification of a set of reactions and the corresponding rate functions. The procedure is graphically based and can easily be worked out by hand for small networks. For larger networks, we provide a pseudo-algorithm. We study properties of the reduced network, its kinetics and conservation laws, and show that the kinetics of the reduced network fulfil realistic assumptions, provided the original network does. We illustrate our results using biological examples such as substrate mechanisms, post-translational modification systems and networks with intermediates (transient) steps.
Full work available at URL: https://arxiv.org/abs/1509.03153
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Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45) Chemical kinetics in thermodynamics and heat transfer (80A30)
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