title: Graphical reduction of reaction networks by linear elimination of species.
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.
authors.affiliation: Department of Mathematical Sciences. University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark.
authors.forename: Meritxell
authors.identifier: 0000-0002-2991-3183
authors.initials: M
authors.lastname: Sáez
authors.affiliation: Department of Mathematical Sciences. University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark.
authors.forename: Carsten
authors.identifier: 0000-0002-1302-4445
authors.initials: C
authors.lastname: Wiuf
authors.affiliation: Department of Mathematical Sciences. University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark. efeliu@math.ku.dk.
authors.forename: Elisenda
authors.identifier: 0000-0001-7205-6511
authors.initials: E
authors.lastname: Feliu
mesh_terms: D000465:Algorithms; D001669:Biochemical Phenomena / Q000502:physiology*; D007700:Kinetics; D008954:Models, Biological; D011499:Protein Processing, Post-Translational / Q000502:physiology
keywords: Dynamical system; Noninteracting; Positivity; Quasi-steady-state; Reduced network; Species graph