Reduction of Chemical Reaction Networks with Approximate Conservation Laws

TL;DR

This paper introduces a novel reduction method for fast-slow chemical reaction networks with approximate conservation laws, using tropical geometry to identify slow variables and hierarchical multiple timescale reductions.

Contribution

It develops a new approach combining tropical geometry and singular perturbation theory to reduce complex networks with approximate conservation laws and multiple timescales.

Findings

Successfully applied to TGF-b signaling pathway model

Provides symbolic algorithms for network reshaping and rescaling

Enables reduction of hierarchical multiple timescale systems

Abstract

Model reduction of fast-slow chemical reaction networks based on the quasi-steady state approximation fails when the fast subsystem has first integrals. We call these first integrals approximate conservation laws. In order to define fast subsystems and identify approximate conservation laws, we use ideas from tropical geometry. We prove that any approximate conservation law evolves slower than all the species involved in it and therefore represents a supplementary slow variable in an extended system. By elimination of some variables of the extended system, we obtain networks without approximate conservation laws, which can be reduced by standard singular perturbation methods. The field of applications of approximate conservation laws covers the quasi-equilibrium approximation, well known in biochemistry. We discuss reductions of slow-fast as well as multiple timescale systems. Networks with multiple timescales have hierarchical relaxation. At a given timescale, our multiple timescale reduction method defines three subsystems composed of (i) slaved fast variables satisfying algebraic equations, (ii) slow driving variables satisfying reduced ordinary differential equations, and (iii) quenched much slower variables that are constant. The algebraic equations satisfied by fast variables define chains of nested normally hyberbolic invariant manifolds. In such chains, faster manifolds are of higher dimension and contain the slower manifolds. Our reduction methods are introduced algorithmically for networks with monomial reaction rates and linear, monomial or polynomial approximate conservation laws. We propose symbolic algorithms to reshape and rescale the networks such that geometric singular perturbation theory can be applied to them, test the applicability of the theory, and finally reduce the networks. As a proof of concept, we apply this method to a model of the TGF-b signaling pathway.