Hypergraphic Oriented Matroid Relational Dependency Flow Models of Chemical Reaction Networks

TL;DR

This paper introduces hypergraphic oriented matroids to analyze variable interdependencies in chemical reaction networks, providing a novel mathematical framework for understanding complex biochemical systems.

Contribution

It develops a new hypergraphic oriented matroid model for chemical reaction networks, linking matroid theory with non-linear dynamical systems in biochemistry.

Findings

Generated dual matroids for hyperspanning trees and hypercycles.

Applied the model to MAP Kinase cascade pathway.

Demonstrated solution sets for non-linear reaction systems.

Abstract

In this paper we derive and present an application of hypergraphic oriented matroids for the purpose of enumerating the variable interdependencies that define the chemical complexes associated with the kinetics of non-linear dynamical system representations of chemical kinetic reaction flow networks. The derivation of a hypergraphic oriented matroid is obtained by defining a closure operator on families of n-subsets of signed multi-sets from which a "Z-module" is obtained. It has been observed that every instantiation of the closure operator on the signed multiset families define a matroid structure. It is then demonstrated that these structures generate a pair of dual matroids corresponding respectively to hyperspanning trees and hypercycles obtained from the corresponding directed hypergraphs. These structures are next systematically evaluated to obtain solution sets that satisfy systems of non-linear chemical kinetic reaction flow networks in the MAP Kinase cascade cell-signaling pathway.