相关论文: Determining the Equivalence of Small Zero-one Reac…

Mass-action kinetics is frequently used in systems biology to model the behaviour of interacting chemical species. Many important dynamical properties are known to hold for such systems if they are weakly reversible and have a low…

Resilience is an ability of a system with which the system can adjust its activity to maintain its functionality when it is perturbed. To study resilience of dynamics on networks, Gao et al. proposed a theoretical framework to reduce…

A chemical reaction network (CRN) is composed of reactions that can be seen as interactions among entities called species, which exist within the system. Endowed with kinetics, CRN has a corresponding set of ordinary differential equations…

This paper develops the concept of decomposition for chemical reaction networks, based on which a network decomposition technique is proposed to capture the stability of large-scale networks characterized by a high number of species, high…

The goal of this paper is to gather and develop some necessary and sufficient criteria for injectivity and multistationarity in vector fields associated with a chemical reaction network under a variety of more or less general assumptions on…

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 consider the problem of binomiality of the steady state ideals of biochemical reaction networks. We are interested in finding polynomial conditions on the parameters such that the steady state ideal of a chemical reaction network is…

Multistationary chemical reaction networks are of interest to scientists and mathematicians alike. While some criteria for multistationarity exist, obtaining explicit reaction rates and steady states that exhibit multistationarity for a…

The nuclear reaction network is usually studied via precise calculation of differential equation sets, and much research interest has been focused on the characteristics of nuclides, such as half-life and size limit. In this paper, however,…

Many biological systems can be modeled as a chemical reaction network with unknown parameters. Data available to identify these parameters are often in the form of a stationary distribution, such as that obtained from measurements of a cell…

Boolean networks have been used successfully in modeling biological networks and provide a good framework for theoretical analysis. However, the analysis of large networks is not trivial. In order to simplify the analysis of such networks,…

Stochastic reaction networks (SRNs) provide models of many real-world networks. Examples include networks in epidemiology, pharmacology, genetics, ecology, chemistry, and social sciences. Here, we model stochastic reaction networks by…

The aim of this work is to make available to the community a large collection of mass-action reaction networks of a given size for further research. The set is limited to what can be computed on a modern multi-core desktop in reasonable…

The steady-state degree of a chemical reaction network is the number of complex steady-states for generic rate constants and initial conditions. One way to bound the steady-state degree is through the mixed volume of the steady-state system…

We present a systematic procedure for testing whether reaction networks exhibit non-expansivity or monotonicity. This procedure identifies explicit norms under which a network is non-expansive or cones for which the system is monotone-or…

Deciding whether and where a system of parametrized ordinary differential equations displays bistability, that is, has at least two asymptotically stable steady states for some choice of parameters, is a hard problem. For systems modeling…

We establish a new relationship between monotonicity and contractivity and use this connection to describe a new general class of weakly contractive reaction networks. The new class is characterized by the stoichiometry matrix of the…

Motivation: A Chemical Reaction Network (CRN) is a set of chemical reactions, which can be very complex and difficult to analyze. Indeed, dynamical properties of CRNs can be described by a set of non-linear differential equations that…

Bistability and multistationarity are properties of reaction networks linked to switch-like responses and connected to cell memory and cell decision making. Determining whether and when a network exhibits bistability is a hard and open…

We investigate six operations on chemical reaction networks, all of which have been proven to preserve important dynamical properties, namely, the capacity for nondegenerate multistationarity (multiple steady states) and periodic orbits.…