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Register a new userNew Approach to the Stability of Chemical Reaction Networks: Piecewise Linear in Rates Lyapunov Functions
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Piecewise-Linear in Rates (PWLR) Lyapunov functions are introduced for a class of Chemical Reaction Networks (CRNs). In addition to their simple structure, these functions are robust with respect to arbitrary monotone reaction rates, of which mass-action is a special case. The existence of such functions ensures the convergence of trajectories towards equilibria, and guarantee their asymptotic stability with respect to the corresponding stoichiometric compatibility class. We give the definition of these Lyapunov functions, prove their basic properties, and provide algorithms for constructing them. Examples are provided, relationship with consensus dynamics are discussed, and future directions are elaborated.
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We present a framework to transform the problem of finding a Lyapunov function of a Chemical Reaction Network (CRN) in concentration coordinates with arbitrary monotone kinetics into finding a common Lyapunov function for a linear parameter varying system in reaction coordinates. Alternative formulations of the proposed Lyapunov function is presented also. This is applied to reinterpret previous results by the authors on Piecewise Linear in Rates Lyapunov functions, and to establish a link with contraction analysis. Persistence and uniqueness of equilibria are discussed also.
We consider the relationship between stationary distributions for stochastic models of reaction systems and Lyapunov functions for their deterministic counterparts. Specifically, we derive the well known Lyapunov function of reaction network theory as a scaling limit of the non-equilibrium potential of the stationary distribution of stochastically modeled complex balanced systems. We extend this result to general birth-death models and demonstrate via example that similar scaling limits can yield Lyapunov functions even for models that are not complex or detailed balanced, and may even have multiple equilibria.
Recent work of M.D. Johnston et al. has produced sufficient conditions on the structure of a chemical reaction network which guarantee that the corresponding discrete state space system exhibits an extinction event. The conditions consist of a series of systems of equalities and inequalities on the edges of a modified reaction network called a domination-expanded reaction network. In this paper, we present a computational implementation of these conditions written in Python and apply the program on examples drawn from the biochemical literature, including a model of polyamine metabolism in mammals and a model of the pentose phosphate pathway in Trypanosoma brucei. We also run the program on 458 models from the European Bioinformatics Institutes BioModels Database and report our results.
In 1961, Renyi discovered a rich family of non-classical Lyapunov functions for kinetics of the Markov chains, or, what is the same, for the linear kinetic equations. This family was parameterised by convex functions on the positive semi-axis. After works of Csiszar and Morimoto, these functions became widely known as $f$-divergences or the Csiszar--Morimoto divergences. These Lyapunov functions are universal in the following sense: they depend only on the state of equilibrium, not on the kinetic parameters themselves. Despite many years of research, no such wide family of universal Lyapunov functions has been found for nonlinear reaction networks. For general non-linear networks with detailed or complex balance, the classical thermodynamics potentials remain the only universal Lyapunov functions. We constructed a rich family of new universal Lyapunov functions for {em any non-linear reaction network} with detailed or complex balance. These functions are parameterised by compact subsets of the projective space. They are universal in the same sense: they depend only on the state of equilibrium and on the network structure, but not on the kinetic parameters themselves. The main elements and operations in the construction of the new Lyapunov functions are partial equilibria of reactions and convex envelopes of families of functions.
Homochirality, i.e. the dominance across all living matter of one enantiomer over the other among chiral molecules, is thought to be a key step in the emergence of life. Building on ideas put forward by Frank and many others, we proposed recently one such mechanism in G. Laurent et al., PNAS (2021) based on the properties of large out of equilibrium chemical networks. We showed that in such networks, a phase transition towards an homochiral state is likely to occur as the number of chiral species in the system becomes large or as the amount of free energy injected into the system increases. This paper aims at clarifying some important points in that scenario, not covered by our previous work. We first analyze the various conventions used to measure chirality, introduce the notion of chiral symmetry of a network, and study its implications regarding the relative chiral signs adopted by different groups of molecules. We then propose a generalization of Franks model for large chemical networks, which we characterize completely using methods of random matrices. This analysis can be extended to sparse networks, which shows that the emergence of homochirality is a robust transition.
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