Author:

Keywords:

Science & Technology, Life Sciences & Biomedicine, Biology, Mathematical & Computational Biology, Life Sciences & Biomedicine - Other Topics, Reaction network, Stoichiometric matrix, Hypergraph, Conserved moiety, Moiety matrix splitting, Mathematical modelling, PRINCIPLE, TOOL, Cell Physiological Phenomena, Mathematics, 01 Mathematical Sciences, 06 Biological Sciences, 08 Information and Computing Sciences, Evolutionary Biology, 31 Biological sciences, 49 Mathematical sciences

Abstract:

Characterising biochemical reaction network structure in mathematical terms enables the inference of functional biochemical consequences from network structure with existing mathematical techniques and spurs the development of new mathematics that exploits the peculiarities of biochemical network structure. The structure of a biochemical network may be specified by reaction stoichiometry, that is, the relative quantities of each molecule produced and consumed in each reaction of the network. A biochemical network may also be specified at a higher level of resolution in terms of the internal structure of each molecule and how molecular structures are transformed by each reaction in a network. The stoichiometry for a set of reactions can be compiled into a stoichiometric matrix N∈Zm×n, where each row corresponds to a molecule and each column corresponds to a reaction. We demonstrate that a stoichiometric matrix may be split into the sum of m-rank(N) moiety transition matrices, each of which corresponds to a subnetwork accessible to a structurally identifiable conserved moiety. The existence of this moiety matrix splitting is a property that distinguishes a stoichiometric matrix from an arbitrary rectangular matrix.