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Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic equilibrium we derive a compact formulation exhibiting at the same time the structure of the complex graph and the stoichiometry of the network, and which admits a direct thermodynamical interpretation. This formulation allows us to easily characterize the set of equilibria and their stability properties. Furthermore, we develop a framework for interconnection of chemical reaction networks. Finally we discuss how the established framework leads to a new approach for model reduction.

BackgroundIn this paper we propose a model reduction method for biochemical reaction networks governed by a variety of reversible and irreversible enzyme kinetic rate laws, including reversible Michaelis-Menten and Hill kinetics. The method proceeds by a stepwise reduction in the number of complexes, defined as the left and right-hand sides of the reactions in the network. It is based on the Kron reduction of the weighted Laplacian matrix, which describes the graph structure of the complexes and reactions in the network. It does not rely on prior knowledge of the dynamic behaviour of the network and hence can be automated, as we demonstrate. The reduced network has fewer complexes, reactions, variables and parameters as compared to the original network, and yet the behaviour of a preselected set of significant metabolites in the reduced network resembles that of the original network. Moreover the reduced network largely retains the structure and kinetics of the original model.ResultsWe apply our method to a yeast glycolysis model and a rat liver fatty acid beta-oxidation model. When the number of state variables in the yeast model is reduced from 12 to 7, the difference between metabolite concentrations in the reduced and the full model, averaged over time and species, is only 8%. Likewise, when the number of state variables in the rat-liver beta-oxidation model is reduced from 42 to 29, the difference between the reduced model and the full model is 7.5%.ConclusionsThe method has improved our understanding of the dynamics of the two networks. We found that, contrary to the general disposition, the first few metabolites which were deleted from the network during our stepwise reduction approach, are not those with the shortest convergence times. It shows that our reduction approach performs differently from other approaches that are based on time-scale separation. The method can be used to facilitate fitting of the parameters or to embed a detailed model of interest in a more coarse-grained yet realistic environment.

Abstract-Recently it has been reported that rangemeasurement inconsistency, or equivalently mismatches in prescribed inter-agent distances, may prevent the popular gradient controllers from guiding rigid formations of mobile agents to converge to their desired shape, and even worse from standing still at any location. In this paper, instead of treating mismatches as the source of ill performance, we take them as design parameters and show that by introducing such a pair of parameters per distance constraint, distributed controller achieving simultaneously both formation and motion control can be designed that not only encompasses the popular gradient control, but more importantly allows us to achieve constant collective translation, rotation or their combination while guaranteeing asymptotically no distortion in the formation shape occurs. Such motion control results are then applied to (a) the alignment of formations' orientations and (b) enclosing and tracking a moving target. Besides rigorous mathematical proof, experiments using mobile robots are demonstrated to show the satisfying performances of the proposed formation-motion distributed controller.

An input-to-state stability theory, which subsumes results of circle criterion type, is developed in the context of a class of infinite-dimensional systems. The generic system is of Lur'e type: a feedback interconnection of a well-posed infinite-dimensional linear system and a nonlinearity. The class of nonlinearities is subject to a (generalized) sector condition and contains, as particular subclasses, both static nonlinearities and hysteresis operators of Preisach type.