Related papers: Siphons in chemical reaction networks
This paper presents new results about the optimization based generation of chemical reaction networks (CRNs) of higher deficiency. Firstly, it is shown that the graph structure of the realization containing the maximal number of reactions…
Computer algebra methods for analyzing reaction networks often rely on the assumption of mass-action kinetics, which transform the governing ODEs into polynomial systems amenable to techniques such as Gr\"obner basis computation and related…
The spatially distributed reaction networks are indispensable for the understanding of many important phenomena concerning the development of organisms, coordinated cell behavior, and pattern formation. The purpose of this brief discussion…
Chemical and biological networks can describe a wide variety of processes, from gene regulatory networks to biochemical oscillations. Modeled by chemical master equations, these processes are inherently stochastic, as fluctuations dominate…
The research concerns the dynamics of complex autonomous Kauffman networks. The article defines and shows using simulation experiments half-chaotic networks, which exhibit features much more similar to typically modeled systems like a…
The trend to equilibrium for reaction-diffusion systems modelling chemical reaction networks is investigated, in the case when reaction processes happen on subsets of the domain. We prove the convergence to equilibrium by directly showing…
This paper analyses of a stochastic model of a chemical reaction network with three types of chemical species ${\cal R}$, ${\cal M}$ and ${\cal U}$ that interact to transform a flow of external resources, the chemical species ${\cal Q}$, to…
Coupled chemical interactions in a well-mixed solution are commonly formalized as chemical reaction networks (CRNs). However, despite the widespread use of CRNs in the natural sciences, the range of computational behaviors exhibited by CRNs…
Kinetic proofreading mechanisms explain the extraordinary accuracy observed in central biological events in terms of the enhanced specificity of substrate selection networks under a nonequilibrium environment. The nonequilibrium steady…
Reaction networks taken with mass-action kinetics arise in many settings, from epidemiology to population biology to systems of chemical reactions. Bistable reaction networks are posited to underlie biochemical switches, which motivates the…
The emergence of an autocatalytic network from an available set of elements is a fundamental step in early evolutionary processes, such as the origin of metabolism. Given a set of elements, the reactions between them (chemical or…
A key problem in the study and design of complex systems is the apparent disconnection between the microscopic and the macroscopic. It is not straightforward to identify the local interactions that give rise to an observed global…
We develop tools from computational algebraic geometry for the study of steady state features of autonomous polynomial dynamical systems via elimination of variables. In particular, we obtain nontrivial bounds for the steady state…
Chimera states occur in networks of coupled oscillators, and are characterized by having some fraction of the oscillators perfectly synchronized, while the remainder are desynchronized. Most chimera states have been observed in networks of…
The software for chemical interaction networks (SCINE) project aims at pushing the frontier of quantum chemical calculations on molecular structures to a new level. While calculations on individual structures as well as on simple relations…
The problem of "what is 'system'?" is in the very foundations of modern quantum mechanics. Here, we point out the interest in this topic in the information-theoretic context. E.g., we point out the possibility to manipulate a pair 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…
One of the hypothesized functions of biomolecular condensates is to act as chemical reactors, where chemical reactions can be modulated, i.e. accelerated or slowed down, while substrate molecules enter and products exit from the condensate.…
We develop a thermodynamic framework for closed and open chemical networks applicable to non-elementary reactions that do not need to obey mass action kinetics. It only requires the knowledge of the kinetics and of the standard chemical…
Statistical mechanics provides an effective framework to investigate information processing in biochemical reactions. Within such framework far-reaching analogies are established among (anti-) cooperative collective behaviors in chemical…