Casian Pantea

Fatma Mohamed, Casian Pantea, Adrian Tudorascu

We show that solutions of the chemical reaction-diffusion system associated to $A+B\rightleftharpoons C$ in one spatial dimension can be approximated in $L^2$ on any finite time interval by solutions of a space discretized ODE system which models the corresponding chemical reaction system replicated in the discretization subdomains where the concentrations are assumed spatially constant. Same-species reactions through the virtual boundaries of adjacent subdomains lead to diffusion in the vanishing limit. We show convergence of our numerical scheme by way of a consistency estimate, with features generalizable to reaction networks other than the one considered here, and to multiple space dimensions. In particular, the connection with the class of complex-balanced systems is briefly discussed here, and will be considered in future work.

Matthew D. Johnston, Casian Pantea, Pete Donnell

We introduce a mixed-integer linear programming (MILP) framework capable of determining whether a chemical reaction network possesses the property of being endotactic or strongly endotactic. The network property of being strongly endotactic is known to lead to persistence and permanence of chemical species under genetic kinetic assumptions, while the same result is conjectured but as yet unproved for general endotactic networks. The algorithms we present are the first capable of verifying endotacticity of chemical reaction networks for systems with greater than two constituent species. We implement the algorithms in the open-source online package CoNtRol and apply them to several well-studied biochemical examples, including the general $n$-site phosphorylation / dephosphorylation networks and a circadian clock mechanism.