Gröbner bases of reaction networks with intermediate species
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Publication:2423401
Abstract: In this work we consider the computation of Groebner bases of the steady state ideal of reaction networks equipped with mass-action kinetics. Specifically, we focus on the role of intermediate species and the relation between the extended network (with intermediate species) and the core network (without intermediate species). We show that a Groebner basis of the steady state ideal of the core network always lifts to a Groebner basis of the steady state ideal of the extended network by means of linear algebra, with a suitable choice of monomial order. As illustrated with examples, this contributes to a substantial reduction of the computation time, due mainly to the reduction in the number of variables and polynomials. We further show that if the steady state ideal of the core network is binomial, then so is the case for the extended network, as long as an extra condition is fulfilled. For standard networks, this extra condition can be visually explored from the network structure alone.
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Cited in
(5)- The multistationarity structure of networks with intermediates and a binomial core network
- Multistationarity in the space of total concentrations for systems that admit a monomial parametrization
- Joining and decomposing reaction networks
- Algebraic study of receptor-ligand systems: a dose-response analysis
- When algebra twinks system biology: a conjecture on the structure of Gröbner bases in complex chemical reaction networks
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