相关论文: Fundamental Decompositions and Multistationarity o…

In the first part of this paper, we propose new optimization-based methods for the computation of preferred (dense, sparse, reversible, detailed and complex balanced) linearly conjugate reaction network structures with mass action dynamics.…

We provide a category theoretical framework capturing two approaches to graph-based models of chemistry: formal reactions and disconnection rules. We model a translation from the latter to the former as a functor, which is faithful, and…

In this and a companion paper we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first…

In Systems Biology there is a growing interest in the question, whether or not a given mathematical model can admit more than one steady state. As parameter values are often unknown or subject to a very high uncertainty, one is often…

A central challenge in materials science is characterizing chemical processes that are elusive to direct measurement, particularly in functional materials operating under realistic conditions. Here, we demonstrate that mechanical strain…

Chemical reaction network theory provides powerful tools for rigorously understanding chemical reactions and the dynamical systems and differential equations that represent them. A frequent issue with mathematical analyses of these networks…

We define a subclass of Chemical Reaction Networks called Post-Translational Modification systems. Important biological examples of such systems include MAPK cascades and two-component systems which are well-studied experimentally as well…

We describe a large class of chemical reaction networks, those endowed with a subtle structural property called concordance. We show that the class of concordant networks coincides precisely with the class of networks which, when taken with…

Autocatalytic Sets are reaction networks theorised as networks at the basis of life. Their main feature is the ability of spontaneously emerging and self-reproducing. The Reflexively and Food-generated theory provides a formal definition of…

We mathematically prove that chemical reaction networks without hidden layers can solve tasks for which spiking neural networks require hidden layers. Our proof uses the deterministic mass-action kinetics formulation of chemical reaction…

We define catalytic networks as chemical reaction networks with an essentially catalytic reaction pathway: one which is on in the presence of certain catalysts and off in their absence. We show that examples of catalytic networks include…

In the analysis of High-Energy Physics data, it is frequently desired to separate resonant signals from a smooth, non-resonant background. This paper introduces a new technique - functional decomposition (FD) - to accomplish this task. It…

Which reaction networks, when taken with mass-action kinetics, have the capacity for multiple steady states? There is no complete answer to this question, but over the last 40 years various criteria have been developed that can answer this…

A natural condition on the structure of the underlying chemical reaction network, namely weak reversibility, is shown to guarantee the existence of an equilibrium (steady state) in each positive stoichiometric compatibility class for the…

We present conditions which guarantee a parametrization of the set of positive equilibria of a generalized mass-action system. Our main results state that (i) if the underlying generalized chemical reaction network has an effective…

We derive a reduction formula for singularly perturbed ordinary differential equations (in the sense of Tikhonov and Fenichel) with a known parameterization of the critical manifold. No a priori assumptions concerning separation of slow and…

Under suitable assumptions, the dynamic behaviour of a chemical reaction network is governed by an autonomous set of polynomial ordinary differential equations over continuous variables representing the concentrations of the reactant…

For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive…

Chemical reaction networks taken with mass-action kinetics are dynamical systems that arise in chemical engineering and systems biology. In general, determining whether a chemical reaction network admits multiple steady states is difficult,…

The dual phosphorylation network provides an essential component of intracellular signaling, affecting the expression of phenotypes and cell metabolism. For particular choices of kinetic parameters, this system exhibits multistationarity, a…