This article is concerned with the asymptotic accuracy of the Computational Singular Perturbation (CSP) method developed by Lam and Goussis to reduce the dimensionality of a system of chemical kinetics equations. The method exploits the presence of disparate time scales to model the dynamics by an evolution equation on a lower-dimensional slow manifold. In this article it is shown that the successive applications of the CSP algorithm generate, order by order, the asymptotic expansion of a slow manifold. The results are illustrated on the Michaelis-Menten-Henri equations of enzyme kinetics.
Food scientists at the U.S. Army's Natick Solider Center have developed a model for the lifecyle of the bacteria Staphylococcus aureus in intermediate moisture bread. In this article, we study this model using dynamical systems and Lie symmetry methods. We calculate center manifolds and Lie symmetries for different cases of parameter values and compare our results to those of the food scientists.
Chemical kinetic models in terms of ordinary differential equations correspond to finite dimensional dissipative dynamical systems involving a multiple time scale structure. Most dimension reduction approaches aimed at a slow mode-description of the full system compute approximations of low-dimensional attracting slow invariant manifolds and parameterize these manifolds in terms of a subset of chosen chemical species, the reaction progress variables. The invariance property suggests a slow invariant manifold to be constructed as (a bundle of) solution trajectories of suitable ordinary differen…
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. Schmitz's 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…
In this paper we discuss the question of how to decide when a general chemical reaction system is incapable of admitting multiple equilibria, regardless of parameter values such as reaction rate constants, and regardless of the type of chemical kinetics, such as mass-action kinetics, Michaelis-Menten kinetics, etc. Our results relate previously described linear algebraic and graph-theoretic conditions for injectivity of chemical reaction systems. After developing a translation between the two formalisms, we show that a graph-theoretic test developed earlier in the context of systems with mass …
In this paper, we review the construction of low-dimensional manifolds of reduced description for equations of chemical kinetics from the standpoint of the method of invariant manifold (MIM). MIM is based on a formulation of the condition of invariance as an equation, and its solution by Newton iterations. A review of existing alternative methods is extended by a thermodynamically consistent version of the method of intrinsic low-dimensional manifolds. A grid-based version of MIM is developed, and model extensions of low-dimensional dynamics are described. Generalizations to open systems are s…
This paper deals with the theory of structure, stability, robustness, and stabilization for an appealing class of nonlinear systems which arises in the analysis of chemical networks. The results given here extend, but are also heavily based upon, certain previous work by Feinberg, Horn, and Jackson, of which a self-contained and streamlined exposition is included. The theoretical conclusions are illustrated through an application to the kinetic proofreading model proposed by McKeithan for T-cell receptor signal transduction. (Update includes, among other topics, remarks on extensions to certai…
We consider chemical reaction networks taken with mass action kinetics. The steady states of such a system are solutions to a system of polynomial equations. Even for small systems the task of finding the solutions is daunting. We develop an algebraic framework and procedure for linear elimination of variables. The procedure reduces the variables in the system to a set of "core" variables by eliminating variables corresponding to a set of non-interacting species. The steady states are parameterized algebraically by the core variables, and a graphical condition is given for when a steady state …
In this paper, we analyze the stability, convergence, and bifurcation properties of the Boissonade-De Kepper (BD) model which played a key role in the development of nonlinear chemical dynamics. We first outline conditions for local stability, which may help guide design considerations. Then, we show that the BD model undergoes a Hopf bifurcation when the stability condition gets violated. Using Poincaré normal forms and center manifold theory, we derive explicit analytic expressions for determining the type of the Hopf bifurcation and the stability of the limit cycles. This provides insights …
A frequently desirable characteristic of chemical kinetics systems is that of persistence, the property that if all the species are initially present then none of them may tend toward extinction. It is known that solutions of deterministically modelled mass-action systems may only approach portions of the boundary of the positive orthant which correspond to semi-locking sets (alternatively called siphons). Consequently, most recent work on persistence of these systems has been focused on these sets. In this paper, we focus on a result which states that, for a conservative mass-action system, p…
In dissipative ordinary differential equation systems different time scales cause anisotropic phase volume contraction along solution trajectories. Model reduction methods exploit this for simplifying chemical kinetics via a time scale separation into fast and slow modes. The aim is to approximate the system dynamics with a dimension-reduced model after eliminating the fast modes by enslaving them to the slow ones via computation of a slow attracting manifold. We present a novel method for computing approximations of such manifolds using trajectory-based optimization. We discuss Riemannian geo…
Chemical reaction networks with generalized mass-action kinetics lead to power-law dynamical systems. As a simple example, we consider the Lotka reactions with two chemical species and arbitrary power-law kinetics. We study existence, uniqueness, and stability of the positive equilibrium, in particular, we characterize its global asymptotic stability in terms of the kinetic orders.
Absolute concentration robustness (ACR) is a condition wherein a species in a chemical kinetic system possesses the same value for any positive steady state the network may admit regardless of initial conditions. Thus far, results on ACR center on chemical kinetic systems with deficiency one. In this contribution, we use the idea of dynamic equivalence of chemical reaction networks to derive novel results that guarantee ACR for some classes of power law kinetic systems with deficiency zero. Furthermore, using network decomposition, we identify ACR in higher deficiency networks (i.e. deficiency…
Reversibility, weak reversibility and deficiency, detailed and complex balancing are generally not "encoded" in the kinetic differential equations but they are realization properties that may imply local or even global asymptotic stability of the underlying reaction kinetic system when further conditions are also fulfilled. In this paper, efficient numerical procedures are given for finding complex balanced or detailed balanced realizations of mass action type chemical reaction networks or kinetic dynamical systems in the framework of linear programming. The procedures are illustrated on numer…
We consider stochastically modeled chemical reaction systems with mass-action kinetics and prove that a product-form stationary distribution exists for each closed, irreducible subset of the state space if an analogous deterministically modeled system with mass-action kinetics admits a complex balanced equilibrium. Feinberg's deficiency zero theorem then implies that such a distribution exists so long as the corresponding chemical network is weakly reversible and has a deficiency of zero. The main parameter of the stationary distribution for the stochastically modeled system is a complex balan…
Mass action systems capture chemical reaction networks in homogeneous and dilute solutions. We suggest a notion of generalized mass action systems that admits arbitrary nonnegative power-law rate functions and serves as a more realistic model for reaction networks in intracellular environments. In addition to the chemical complexes and the related stoichiometric subspace, we introduce corresponding kinetic complexes, which represent the nonnegative exponents in the rate functions and determine the kinetic-order subspace. We show that several results of Chemical Reaction Network Theory carry ov…
Chemical kinetics and reaction engineering consists of the phenomenological framework for the disentanglement of reaction mechanisms, optimization of reaction performance and the rational design of chemical processes. Here, we utilize feed-forward artificial neural networks as basis functions to solve ordinary differential equations (ODEs) constrained by differential algebraic equations (DAEs) that describe microkinetic models (MKMs). We present an algebraic framework for the mathematical description and classification of reaction networks, types of elementary reaction, and chemical species. U…
