The steady-state degree and mixed volume of a chemical reaction network

DOI10.1016/J.AAM.2021.102254MaRDI QIDQ820932zbMATH OpenOpenAlexFDO

Authors Elizabeth Gross, Cvetelina Hill

Publication date 29 September 2021

Published in Advances in Applied Mathematics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1909.06652

Mathematics Subject Classification ID

Classical flows, reactions, etc. in chemistry (92E20)

Abstract: The steady-state degree of a chemical reaction network is the number of complex steady-states, which is a measure of the algebraic complexity of solving the steady-state system. In general, the steady-state degree may be difficult to compute. Here, we give an upper bound to the steady-state degree of a reaction network by utilizing the underlying polyhedral geometry associated with the corresponding polynomial system. We focus on three case studies of infinite families of networks, each generated by joining smaller networks to create larger ones. For each family, we give a formula for the steady-state degree and the mixed volume of the corresponding polynomial system.

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Cites work

• A survey of methods for deciding whether a reaction network is multistationary
• Algebraic systems biology: a case study for the Wnt pathway
• Algorithm 795
• An algebraic approach to signaling cascades with n layers
• Biochemical reaction networks: An invitation for algebraic geometers
• HOM4PS-2.0: a software package for solving polynomial systems by the polyhedral homotopy continuation method
• Joining and decomposing reaction networks
• Lectures on Polytopes
• Lower bounds for positive roots and regions of multistationarity in chemical reaction networks
• Multistationarity and bistability for fewnomial chemical reaction networks
• Multistationarity in sequential distributed multisite phosphorylation networks
• Multistationarity in the space of total concentrations for systems that admit a monomial parametrization
• Numerically solving polynomial systems with Bertini
• On the number of steady states in a multiple futile cycle
• Oscillations and bistability in a model of ERK regulation
• Parameter regions that give rise to \(2\lfloor \frac{n}{2} \rfloor +1\) positive steady states in the \(n\)-site phosphorylation system
• Regions of multistationarity in cascades of Goldbeter-Koshland loops
• Sign conditions for injectivity of generalized polynomial maps with applications to chemical reaction networks and real algebraic geometry
• Solving polynomial systems via homotopy continuation and monodromy
• The Euclidean distance degree of an algebraic variety
• The maximum likelihood degree
• Triangulations. Structures for algorithms and applications
• Unmixing the mixed volume computation
• \(n\)-site phosphorylation systems with \(2n-1\) steady states

Cited in

(4)

• Newton-Okounkov bodies of chemical reaction systems
• Mixed volumes of networks with binomial steady-states
• Mixed volume of small reaction networks
• scientific article; zbMATH DE number 7576617 (Why is no real title available?)

Describes a project that uses

Uses Software

• libtropicana
• MonodromySolver
• Bertini
• PHCpack
• HOM4PS

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