Natural parameter conditions for singular perturbations of chemical and biochemical reaction networks

TL;DR

This paper develops a method to derive small parameters for reaction network reductions, based on eigenvalue ratios, enabling better understanding and approximation of complex biochemical systems.

Contribution

It introduces a novel eigenvalue-based approach to identify parameters for singular perturbation reductions in chemical and biochemical networks, especially for systems of arbitrary dimension.

Findings

Derived new parameters for three-dimensional enzyme systems

Validated parameters through numerical simulations

Provided insights into reduction accuracy and limitations

Abstract

We consider reaction networks that admit a singular perturbation reduction in a certain parameter range. The focus of this paper is on deriving "small parameters" (briefly for small perturbation parameters), to gauge the accuracy of the reduction, in a manner that is consistent, amenable to computation and permits an interpretation in chemical or biochemical terms. Our work is based on local timescale estimates via ratios of the real parts of eigenvalues of the Jacobian near critical manifolds. This approach modifies the one introduced by Segel and Slemrod and is familiar from computational singular perturbation theory. While parameters derived by this method cannot provide universal quantitative estimates for the accuracy of a reduction, they represent a critical first step toward this end. Working directly with eigenvalues is generally unfeasible, and at best cumbersome. Therefore we focus on the coefficients of the characteristic polynomial to derive parameters, and relate them to timescales. Thus, we obtain distinguished parameters for systems of arbitrary dimension, with particular emphasis on reduction to dimension one. As a first application, we discuss the Michaelis--Menten reaction mechanism system in various settings, with new and perhaps surprising results. We proceed to investigate more complex enzyme catalyzed reaction mechanisms (uncompetitive, competitive inhibition and cooperativity) of dimension three, with reductions to dimension one and two. The distinguished parameters we derive for these three-dimensional systems are new. In fact, no rigorous derivation of small parameters seems to exist in the literature so far. Numerical simulations are included to illustrate the efficacy of the parameters obtained, but also to show that certain limitations must be observed.