The Use of Reaction Network Theory for Finding Network Motifs in Oscillatory Mechanisms and Kinetic Parameter Estimation
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Stoichiometric network analysis (SNA) is a method of studying stability of steady states of reaction systems obeying mass action kinetics. Reaction rates are expressed as a linear combination of elementary subnetworks with nonnegative coefficients (convex parameters) as opposed to standard formulation using rate coefficients and input parameters (kinetic parameters). We present examples of core reaction subnetworks that provide for oscillatory instability. Frequently there is an autocatalytic cycle in the core subnetwork, but in biochemical reactions such cycle is often replaced by a pathway called competitive autocatalysis. Rate coefficients in complex networks are often only partly known. We present a method of estimating the unknown rate coefficients, in which known/measured kinetic parameters and steady state concentrations are used to determine convex parameters, which in turn allows for determination of unknown rate coefficients by solving a set of constraint equations.
KeywordsStoichiometric networks Oscillating (bio) chemical reactions Dynamical instabilities Parameter estimation
This work has been supported by the grant 18-24397S from the Czech Science Foundation.
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