Intermediates, Catalysts, Persistence, and Boundary Steady States

For dynamical systems arising from chemical reaction networks, persistence is the property that each species concentration remains positively bounded away from zero, as long as species concentrations were all positive in the beginning. We describe two graphical procedures for simplifying reaction networks without breaking known necessary or sufficient conditions for persistence, by iteratively removing so-called intermediates and catalysts from the network. The procedures are easy to apply and, in many cases, lead to highly simplified network structures, such as monomolecular networks. For specific classes of reaction networks, we show that these conditions for persistence are equivalent to one another. Furthermore, they can also be characterized by easily checkable strong connectivity properties of a related graph. In particular, this is the case for (conservative) monomolecular networks, as well as cascades of a large class of post-translational modification systems (of which the MAPK cascade and the $n$-site futile cycle are prominent examples). Since one of the aforementioned sufficient conditions for persistence precludes the existence of boundary steady states, our method also provides a graphical tool to check for that.Comment: The main result was made more general through a slightly different approach. Accepted for publication in the Journal of Mathematical Biolog

A network dynamics approach to chemical reaction networks

A crisp survey is given of chemical reaction networks from the perspective of general nonlinear network dynamics, in particular of consensus dynamics. It is shown how by starting from the complex-balanced assumption the reaction dynamics governed by mass action kinetics can be rewritten into a form which allows for a very simple derivation of a number of key results in chemical reaction network theory, and which directly relates to the thermodynamics of the system. Central in this formulation is the definition of a balanced Laplacian matrix on the graph of chemical complexes together with a resulting fundamental inequality. This directly leads to the characterization of the set of equilibria and their stability. Both the form of the dynamics and the deduced dynamical behavior are very similar to consensus dynamics. The assumption of complex-balancedness is revisited from the point of view of Kirchhoff's Matrix Tree theorem, providing a new perspective. Finally, using the classical idea of extending the graph of chemical complexes by an extra 'zero' complex, a complete steady-state stability analysis of mass action kinetics reaction networks with constant inflows and mass action outflows is given.Comment: 18 page

A Projection Argument for Differential Inclusions, with Applications to Persistence of Mass-Action Kinetics

Motivated by questions in mass-action kinetics, we introduce the notion of vertexical family of differential inclusions. Defined on open hypercubes, these families are characterized by particular good behavior under projection maps. The motivating examples are certain families of reaction networks -- including reversible, weakly reversible, endotactic, and strongly endotactic reaction networks -- that give rise to vertexical families of mass-action differential inclusions. We prove that vertexical families are amenable to structural induction. Consequently, a trajectory of a vertexical family approaches the boundary if and only if either the trajectory approaches a vertex of the hypercube, or a trajectory in a lower-dimensional member of the family approaches the boundary. With this technology, we make progress on the global attractor conjecture, a central open problem concerning mass-action kinetics systems. Additionally, we phrase mass-action kinetics as a functor on reaction networks with variable rates.Comment: v5: published version; v3 and v4: minor additional edits; v2: contains more general version of main theorem on vertexical families, including its accompanying corollaries -- some of them new; final section contains new results relating to prior and future research on persistence of mass-action systems; improved exposition throughou