Uniqueness of weakly reversible and deficiency zero realizations of dynamical systems

DOI10.1016/J.MBS.2021.108720MaRDI QIDQ2066477zbMATH OpenOpenAlexFDO

Authors Jiaxin Jin, Polly Y. Yu, Gheorghe Craciun

Publication date 14 January 2022

Published in Mathematical Biosciences (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/2010.04316

zbMATH Keywords

chemical reaction networkcomplex balancingdeficiency zero theoremdynamical equivalenceinvariant polyhedronlinkage classmass-action kineticsstoichiometric subspaceweakly reversible system

Mathematics Subject Classification ID

Equivalence and asymptotic equivalence of ordinary differential equations (34C41) Qualitative investigation and simulation of ordinary differential equation models (34C60) Stability of solutions to ordinary differential equations (34D20) Dynamical systems in biology (37N25) Biochemistry, molecular biology (92C40) Systems biology, networks (92C42) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45) Classical flows, reactions, etc. in chemistry (92E20) Lyapunov and other classical stabilities (Lagrange, Poisson, (L^p, l^p), etc.) in control theory (93D05)

Abstract: A reaction network together with a choice of rate constants uniquely gives rise to a system of differential equations, according to the law of mass-action kinetics. On the other hand, different networks can generate the same dynamical system under mass-action kinetics. Therefore, the problem of identifying "the" underlying network of a dynamical system is not well-posed, in general. Here we show that the problem of identifying an underlying weakly reversible deficiency zero network is well-posed, in the sense that the solution is unique whenever it exists. This can be very useful in applications because from the perspective of both dynamics and network structure, a weakly reversibly deficiency zero ($extit{WR}_{e}xtit0$) realization is the simplest possible one. Moreover, while mass-action systems can exhibit practically any dynamical behavior, including multistability, oscillations, and chaos, $W{R}_0$ systems are remarkably stable for any choice of rate constants: they have a unique positive steady state within each invariant polyhedron, and cannot give rise to oscillations or chaotic dynamics. We also prove that both of our hypotheses (i.e., weak reversibility and deficiency zero) are necessary for uniqueness.

Review text

The authors address the relationship between chemical reaction networks obeying mass-action kinetics and the topological dynamics of corresponding systems of differential equations. A reaction network together with rate constants gives rise to a specific differential equation. The question is in how far a differential equation determines a relevant reaction network. In general, the differential equation does not select a particular network. The main result tells us that this is nevertheless the case for the simplest and most important class of networks, consisting of those that are weakly reversible and deficiency zero (Theorem 3.12). If different networks show the same dynamics then at most one belongs to this special class. The paper presents a thorough introduction to the pertinent theory together with a description of its development, equipped with numerous references to the literature.

Recommendations

• Source-Only Realizations, Weakly Reversible Deficiency One Networks, and Dynamical Equivalence
• Parametric uniqueness of deficiency zero reaction networks
• The existence and uniqueness of steady states for a class of chemical reaction networks
• Computing weakly reversible linearly conjugate chemical reaction networks with minimal defi\-ciency
• Identifiability of chemical reaction networks

Cites work

• A geometric approach to the global attractor conjecture
• A proof of the global attractor conjecture in the single linkage class case
• An efficient characterization of complex-balanced, detailed-balanced, and weakly reversible systems
• Chemical mechanism structure and the coincidence of the stoichiometric and kinetie subspaces
• Computing weakly reversible linearly conjugate chemical reaction networks with minimal defi\-ciency
• Computing zero deficiency realizations of kinetic systems
• Existence of Positive Steady States for Weakly Reversible Mass-Action Systems
• Foundations of chemical reaction network theory
• From max-plus algebra to nonexpansive mappings: A nonlinear theory for discrete event systems.
• Identifiability of chemical reaction networks
• On the persistence and global stability of mass-action systems
• Parametric uniqueness of deficiency zero reaction networks
• Permanence of Weakly Reversible Mass-Action Systems with a Single Linkage Class
• Persistence and permanence of mass-action and power-law dynamical systems
• Polynomial dynamical systems, reaction networks, and toric differential inclusions
• Polynomial time algorithms to determine weakly reversible realizations of chemical reaction networks
• Realizations of kinetic differential equations
• Structure and stability of certain chemical networks and applications to the kinetic proofreading model of T-cell receptor signal transduction
• Toric dynamical systems
• Weakly reversible mass-action systems with infinitely many positive steady states

Cited in

(17)

• Realizations of kinetic differential equations
• Parametric uniqueness of deficiency zero reaction networks
• scientific article; zbMATH DE number 754895 (Why is no real title available?)
• Takens-type reconstruction theorems of one-sided dynamical systems
• An Algorithm for Finding Weakly Reversible Deficiency Zero Realizations of Polynomial Dynamical Systems
• Source-Only Realizations, Weakly Reversible Deficiency One Networks, and Dynamical Equivalence
• Weakly reversible single linkage class realizations of polynomial dynamical systems: an algorithmic perspective
• Weakly reversible deficiency one realizations of polynomial dynamical systems: an algorithmic perspective
• Boundedness of trajectories for weakly reversible, single linkage class reaction systems
• Generalized Lotka-Volterra systems and complex balanced polyexponential systems
• Realizations through weakly reversible networks and the globally attracting locus
• Some results about the structural properties of the Wnt pathway, its steady states and its non-associative commutative algebra
• Weakly reversible deficiency zero realizations of reaction networks
• Deficiency of chemical reaction networks: the effect of operations that preserve multistationarity and periodic orbits
• First-order endotactic reaction networks
• Comment on ``Identifiability of chemical reaction networks by G. Craciun and C. Pantea
• Computing zero deficiency realizations of kinetic systems

Describes a project that uses

Uses Software

• CRNreals

This page was built for publication: Uniqueness of weakly reversible and deficiency zero realizations of dynamical systems

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2066477)