Exact model reduction with delays: closed-form distributions and extensions to fully bi-directional monomolecular reactions

Abstract

In order to systematically understand the qualitative and quantitative behaviour of chemical reaction networks, scientists must derive and analyse associated mathematical models. However, biochemical systems are often very large, with reactions occurring at multiple time scales, as evidenced by signalling pathways and gene expression kinetics. Owing to the associated computational costs, it is then many times impractical, if not impossible, to solve or simulate these systems with an appropriate level of detail. By consequence, there is a growing interest in developing techniques for the simplification or reduction of complex biochemical systems. Here, we extend our recently presented methodology on exact reduction of linear chains of reactions with delay distributions in two ways. First, we report that it is now possible to deal with fully bi-directional monomolecular systems, including degradations, synthesis and generalized bypass reactions. Second, we provide all derivations of associated delays in analytical, closed form. Both advances have a major impact on further reducing computational costs, while still retaining full accuracy. Thus, we expect our new methodology to respond to current simulation needs in pharmaceutical, chemical and biological research.