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In this paper, we provide a graphic formulation of non-isothermal reaction systems and show that a non-isothermal detailed balanced network system converges (locally) asymptotically to the unique equilibrium within the invariant manifold determined by the initial condition. To model thermal effects, the proposed modeling approach extends the classical chemical reaction network by adding two parameters to each direct (reaction) edge, depicting, respectively, the instantaneous internal energy change after the firing of the reaction and the variation of the reaction rate with respect to the temperature. For systems possessing thermodynamic equilibria, our modeling approach provides a compact formulation of the dynamics where reaction topology and thermodynamic information are presented simultaneously. Finally, using this formulation and the Legendre transformation, we show that non-isothermal detailed balanced network systems admit some fundamental properties: dissipativeness, the detailed balancing of each equilibrium, the existence and uniqueness of the equilibrium, and the asymptotic stability of each equilibrium. In general, the analysis and results of this work provide insights into the research of non-isothermal chemical reaction systems.
Very often, models in biology, chemistry, physics, and engineering are systems of polynomial or power-law ordinary differential equations, arising from a reaction network. Such dynamical systems can be generated by many different reaction networks. On the other hand, networks with special properties (such as reversibility or weak reversibility) are known or conjectured to give rise to dynamical systems that have special properties: existence of positive steady states, persistence, permanence, and (for well-chosen parameters) complex balancing or detailed balancing. These last two are related to thermodynamic equilibrium, and therefore the positive steady states are unique and stable. We describe a computationally efficient characterization of polynomial or power-law dynamical systems that can be obtained as complex-balanced, detailed-balanced, weakly reversible, and reversible mass-action systems.
A chemical reaction network (CRN) is composed of reactions that can be seen as interactions among entities called species, which exist within the system. Endowed with kinetics, CRN has a corresponding set of ordinary differential equations (ODEs). In Chemical Reaction Network Theory, we are interested with connections between the structure of the CRN and qualitative properties of the corresponding ODEs. One of the results in Decomposition Theory of CRNs is that the intersection of the sets of positive steady states of the subsystems is equal to the set of positive steady states of the whole system, if the decomposition is independent. Hence, computational approach using independent decompositions can be used as an efficient tool in studying large systems. In this work, we provide a necessary and sufficient condition for the existence of a nontrivial independent decomposition of a CRN, which leads to a novel step-by-step method to obtain such decomposition, if it exists. We also illustrate these results using real-life examples. In particular, we show that a CRN of a popular model of anaerobic yeast fermentation pathway has a nontrivial independent decomposition, while a particular biological system, which is a metabolic network with one positive feedforward and a negative feedback has none. Finally, we analyze properties of steady states of reaction networks of specific influenza virus models.
Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems of polynomial ordinary differential equations. The steady states of these mass action systems have been analysed via a variety of techniques, including elementary flux mode analysis, algebraic techniques (e.g. Groebner bases), and deficiency theory. In this paper, we present a novel method for characterizing the steady states of mass action systems. Our method explicitly links a networks capacity to permit a particular class of steady states, called toric steady states, to topological properties of a related network called a translated chemical reaction network. These networks share their reaction stoichiometries with their source network but are permitted to have different complex stoichiometries and different network topologies. We apply the results to examples drawn from the biochemical literature.
We study two specific measures of quality of chemical reaction networks, Precision and Sensitivity. The two measures arise in the study of sensory adaptation, in which the reaction network is viewed as an input-output system. Given a step change in input, Sensitivity is a measure of the magnitude of the response, while Precision is a measure of the degree to which the system returns to its original output for large time. High values of both are necessary for high-quality adaptation. We focus on reaction networks without dissipation, which we interpret as detailed-balance, mass-action networks. We give various upper and lower bounds on the optimal values of Sensitivity and Precision, characterized in terms of the stoichiometry, by using a combination of ideas from matroid theory and differential-equation theory. Among other results, we show that this class of non-dissipative systems contains networks with arbitrarily high values of both Sensitivity and Precision. This good performance does come at a cost, however, since certain ratios of concentrations need to be large, the network has to be extensive, or the network should show strongly different time scales.
This paper presents novel decomposition classes of chemical reaction networks (CRNs) derived from S-system kinetics. Based on the network decomposition theory initiated by Feinberg in 1987, we introduce the concept of incidence independent decompositions and develop the theory of $mathscr{C}$- and $mathscr{C}^*$- decompositions which partition the set of complexes and the set of nonzero complexes respectively, including their structure theorems in terms of linkage classes. Analogous to Feinbergs independent decomposition, we demonstrate the important relationship between sets of complex balance equilibria for an incidence independent decomposition of weakly reversible subnetworks for any kinetics. We show that the $mathscr{C}^*$-decompositions are also incidence independent. We also introduce in this paper a new realization for an S-system that is analyzed using a newly defined class of species coverable CRNs. This led to the extension of the deficiency formula and characterization of fundamental decompositions of species decomposable reaction networks.