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Register a new userAn efficient characterization of complex-balanced, detailed-balanced, and weakly reversible systems
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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.
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A complex balanced kinetic system is absolutely complex balanced (ACB) if every positive equilibrium is complex balanced. Two results on absolute complex balancing were foundational for modern chemical reaction network theory (CRNT): in 1972, M. Feinberg proved that any deficiency zero complex balanced system is absolutely complex balanced. In the same year, F. Horn and R. Jackson showed that the (full) converse of the result is not true: any complex balanced mass action system, regardless of its deficiency, is absolutely complex balanced. In this paper, we revive the study of ACB systems first by providing a partial converse to Feinbergs Theorem. In the spirit of Horn and Jacksons result, we then describe several methods for constructing new classes of ACB systems with positive deficiency and present classes of power law kinetic systems for each method. Furthermore, we illustrate the usefulness of the ACB property for obtaining new results on absolute concentration robustness (ACR) in a species, a concept introduced for mass action systems by Shinar and Feinberg in 2010, for a class of power law systems. Finally, we motivate the study of ACB in poly-PL systems, i.e. sums of power law systems, and indicate initial results.
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.
This paper studies chemical kinetic systems which decompose into weakly reversible complex factorizable (CF) systems. Among power law kinetic systems, CF systems (denoted as PL-RDK systems) are those where branching reactions of a reactant complex have identical rows in the kinetic order matrix. Mass action and generalized mass action systems (GMAS) are well-known examples. Schmitzs global carbon cycle model is a previously studied non-complex factorizable (NF) power law system (denoted as PL-NDK). We derive novel conditions for the existence of weakly reversible CF-decompositions and present an algorithm for verifying these conditions. We discuss methods for identifying independent decompositions, i.e., those where the stoichiometric subspaces of the subnetworks form a direct sum, as such decompositions relate positive equilibria sets of the subnetworks to that of the whole network. We then use the results to determine the positive equilibria sets of PL-NDK systems which admit an independent weakly reversible decomposition into PL-RDK systems of PLP type, i.e., the positive equilibria are log-parametrized, which is a broad generalization of a Deficiency Zero Theorem of Fortun et al. (2019).
Mass-action kinetics and its generalizations appear in mathematical models of (bio-)chemical reaction networks, population dynamics, and epidemiology. The dynamical systems arising from directed graphs are generally non-linear and difficult to analyze. One approach to studying them is to find conditions on the network which either imply or preclude certain dynamical properties. For example, a vertex-balanced steady state for a generalized mass-action system is a state where the net flux through every vertex of the graph is zero. In particular, such steady states admit a monomial parametrization. The problem of existence and uniqueness of vertex-balanced steady states can be reformulated in two different ways, one of which is related to Birchs theorem in statistics, and the other one to the bijectivity of generalized polynomial maps, similar to maps appearing in geometric modelling. We present a generalization of Birchs theorem, by providing a sufficient condition for the existence and uniqueness of vertex-balanced steady states.
The use of two-site Lindblad dissipator to generate thermal states and study heat transport raised to prominence since [J. Stat. Mech. (2009) P02035] by Prosen and v{Z}nidariv{c}. Here we propose a variant of this method based on detailed balance of internal levels of the two site Hamiltonian and characterize its performance. We study the thermalization profile in the chain, the effective temperatures achieved by different single and two-site observables, and we also investigate the decay of two-time correlations. We find that at a large enough temperature the steady state approaches closely a thermal state, with a relative error below 1% for the inverse temperature estimated from different observables.
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