Computing zero deficiency realizations of kinetic systems

In the literature, there exist strong results on the qualitative dynamical properties of chemical reaction networks (also called kinetic systems) governed by the mass action law and having zero deficiency. However, it is known that different network structures with different deficiencies may correspond to the same kinetic differential equations. In this paper, an optimization-based approach is presented for the computation of deficiency zero reaction network structures that are linearly conjugate to a given kinetic dynamics. Through establishing an equivalent condition for zero deficiency, the problem is traced back to the solution of an appropriately constructed mixed integer linear programming problem. Furthermore, it is shown that weakly reversible deficiency zero realizations can be determined in polynomial time using standard linear programming. Two examples are given for the illustration of the proposed methods. © 2015 Elsevier B.V. All rights reserved

Chemical Reaction Systems, Computer Algebra and Systems Biology

International audienceIn this invited paper, we survey some of the results obtained in the computer algebra team of Lille, in the domain of systems biology. So far, we have mostly focused on models (systems of equations) arising from generalized chemical reaction systems. Eight years ago, our team was involved in a joint project, with physicists and biologists, on the modeling problem of the circadian clock of the green algae Ostreococcus tauri. This cooperation led us to different algorithms dedicated to the reduction problem of the deterministic models of chemical reaction systems. More recently, we have been working more tightly with another team of our lab, the BioComputing group, interested by the stochastic dynamics of chemical reaction systems. This cooperation led us to efficient algorithms for building the ODE systems which define the statistical moments associated to these dynamics. Most of these algorithms were implemented in the MAPLE computer algebra software. We have chosen to present them through the corresponding MAPLE packages

Toward Geometric Time Minimal Control without Legendre Condition and with Multiple Singular Extremals for Chemical Networks. An Extended Version

This article deals with the problem of maximizing the production of a species for a chemical network by controlling the temperature. Under the socalled mass kinetics assumption the system can be modeled as a single-input control system using the Feinberg-Horn-Jackson graph associated to the reactions network. Thanks to Pontryagin's Maximum Principle, the candidates as minimizers can be found among extremal curves, solutions of a (non smooth) Hamiltonian dynamics and the problem can be stated as a time minimal control problem with a terminal target of codimension one. Using geometric control and singularity theory the time minimal syntheses (closed loop optimal control) can be classified near the terminal manifold under generic conditions. In this article, we focus to the case where the generalized Legendre-Clebsch condition is not satisfied, which paves the road to complicated syntheses with several singular arcs. In particular, it is related to the situation for a weakly reversible network like the McKeithan scheme