Families of toric chemical reaction networks
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Publication:2201046
DOI10.1007/S10910-020-01162-XzbMATH Open1448.92071arXiv1906.03931OpenAlexW3080139355MaRDI QIDQ2201046FDOQ2201046
Authors: Michael F. Adamer, Martin Helmer 
Publication date: 24 September 2020
Published in: Journal of Mathematical Chemistry (Search for Journal in Brave)
Abstract: We study families of chemical reaction networks whose positive steady states are toric, and therefore can be parameterized by monomials. Families are constructed algorithmically from a core network; we show that if a family member is multistationary, then so are all subsequent networks in the family. Further, we address the questions of model selection and experimental design for families by investigating the algebraic dependencies of the chemical concentrations using matroids. Given a family with toric steady states and a constant number of conservation relations, we construct a matroid that encodes important information regarding the steady state behaviour of the entire family. Among other things, this gives necessary conditions for the distinguishability of families of reaction networks with respect to a data set of measured chemical concentrations. We illustrate our results using multi-site phosphorylation networks.
Full work available at URL: https://arxiv.org/abs/1906.03931
Recommendations
Biochemistry, molecular biology (92C40) Systems biology, networks (92C42) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)
Cites Work
- Ideals, varieties, and algorithms. An introduction to computational algebraic geometry and commutative algebra
- Introduction to Toric Varieties. (AM-131)
- Title not available (Why is that?)
- Algebraic systems biology: a case study for the Wnt pathway
- Complex-linear invariants of biochemical networks
- Chemical reaction systems with toric steady states
- Toric varieties
- The red book of varieties and schemes. Includes the Michigan lectures (1974) on ``Curves and their Jacobians.
- Binomial ideals
- Recursively constructible families of graphs
- The rational parameterisation theorem for multisite post-translational modification systems
- Toric dynamical systems
- Sign conditions for injectivity of generalized polynomial maps with applications to chemical reaction networks and real algebraic geometry
- A global convergence result for processive multisite phosphorylation systems
- From max-plus algebra to nonexpansive mappings: A nonlinear theory for discrete event systems.
- Multistationarity in structured reaction networks
- Multistationarity in sequential distributed multisite phosphorylation networks
- \(n\)-site phosphorylation systems with \(2n-1\) steady states
- Atoms of multistationarity in chemical reaction networks
- Detecting binomiality
- Multistationarity in the space of total concentrations for systems that admit a monomial parametrization
- Joining and decomposing reaction networks
- A Survey of Methods for Deciding Whether a Reaction Network is Multistationary
- The multistationarity structure of networks with intermediates and a binomial core network
- Algebraic Tools for the Analysis of State Space Models
- The Inheritance of Nondegenerate Multistationarity in Chemical Reaction Networks
Cited In (8)
- Polar degrees and closest points in codimension two
- Gröbner bases of reaction networks with intermediate species
- Chemical reaction systems with toric steady states
- Families of polynomials in the study of biochemical reaction networks
- Parametric toricity of steady state varieties of reaction networks
- The Disguised Toric Locus and Affine Equivalence of Reaction Networks
- Torsion in biochemical reaction networks
- The structure of the toric locus of a reaction network
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