Newton-Okounkov bodies of chemical reaction systems

DOI10.1016/J.AAM.2024.102672MaRDI QIDQ6153619zbMATH OpenWikidataFDO

Authors Nida Kazi Obatake

Publication date 14 February 2024

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

Full work available at URL https://arxiv.org/abs/2203.03840

Mathematics Subject Classification ID

Solving polynomial systems; resultants (13P15) Toric varieties, Newton polyhedra, Okounkov bodies (14M25) Computational aspects in algebraic geometry (14Qxx) Biochemistry, molecular biology (92C40)

Abstract: Despite their noted potential in polynomial-system solving, there are few concrete examples of Newton-Okounkov bodies arising from applications. Accordingly, in this paper, we introduce a new application of Newton-Okounkov body theory to the study of chemical reaction networks, and compute several examples. An important invariant of a chemical reaction network is its maximum number of positive steady states, which is realized as the maximum number of positive real roots of a parametrized polynomial system. Here, we introduce a new upper bound on this number, namely the `Newton-Okounkov body bound' of a chemical reaction network. Through explicit examples, we show that the Newton-Okounkov body bound of a network gives a good upper bound on its maximum number of positive steady states. We also compare this Newton-Okounkov body bound to a related upper bound, namely the mixed volume of a chemical reaction network, and find that it often achieves better bounds.

Recommendations

• Mixed volume of small reaction networks
• scientific article; zbMATH DE number 7774177
• The steady-state degree and mixed volume of a chemical reaction network
• Multiple Equilibria in Complex Chemical Reaction Networks: I. The Injectivity Property
• Biochemical reaction networks: An invitation for algebraic geometers

Cites work

• A Product-Decomposition Bound for Bezout Numbers
• A survey of methods for deciding whether a reaction network is multistationary
• Algebraic systems biology: a case study for the Wnt pathway
• Algorithms in invariant theory
• Biochemical reaction networks: An invitation for algebraic geometers
• Certification for polynomial systems via square subsystems
• Convex bodies associated to linear series
• Foundations of chemical reaction network theory
• scientific article; zbMATH DE number 3550860 (Why is no real title available?)
• scientific article; zbMATH DE number 3795757 (Why is no real title available?)
• scientific article; zbMATH DE number 4196114 (Why is no real title available?)
• Ideals, varieties, and algorithms. An introduction to computational algebraic geometry and commutative algebra
• Khovanskii bases, higher rank valuations, and tropical geometry
• Mixed volume and an extension of intersection theory of divisors
• Mixed volume of small reaction networks
• Multistationarity in structured reaction networks
• Newton-Okounkov bodies, semigroups of integral points, graded algebras and intersection theory
• Numerical homotopies from Khovanskii bases
• Okounkov bodies and toric degenerations
• Oscillations and bistability in a model of ERK regulation
• Sign conditions for injectivity of generalized polynomial maps with applications to chemical reaction networks and real algebraic geometry
• The number of roots of a system of equations
• The steady-state degree and mixed volume of a chemical reaction network
• Weakly reversible mass-action systems with infinitely many positive steady states

Cited in

(3)

• \texttt{SubalgebraBases} in Macaulay2
• The algebraic degree of coupled oscillators
• Generic consistency and nondegeneracy of vertically parametrized systems

This page was built for publication: Newton-Okounkov bodies of chemical reaction systems

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q6153619)