Characterization of Minimal Degenerate Zero-One Reaction Networks

Abstract

A fundamental problem in the algebraic study of biochemical reaction networks is to characterize degeneracy. Two-dimensional zero-one networks, where each reactant appears with stoichiometric coefficient zero or one, constitute the smallest biologically relevant class capable of exhibiting degeneracy. In this paper, we provide a complete classification: a two-dimensional zero-one network without trivial species is degenerate if and only if it is a consistent subnetwork of a species refinement of one of two prototypical networks, namely the complete paired-exchange network or the catalytic-pair conversion network. Equivalently, in matrix-theoretic terms, degeneracy is determined entirely by the row patterns of the stoichiometric and reactant matrices, and can be verified by purely structural inspection without computation. Remarkably, every such degenerate network has a steady-state system consisting entirely of binomials, so its steady-state variety is toric. These results also bear on absolute concentration robustness: since any network exhibiting this property necessarily contains a degenerate subnetwork, the minimal degenerate networks characterized here serve as fundamental building blocks for constructing such networks.