相关论文: When do two networks have the same steady-state id…
Complex systems can be advantageously modeled by formal reaction systems (RS), a.k.a. chemical reaction networks in chemistry. Reaction-based models can indeed be interpreted in a hierarchy of semantics, depending on the question at hand,…
Random graph models have been instrumental in characterizing complex networks, but chemical reaction networks (CRNs) are better represented as hypergraphs. Traditional models of random CRNs often reduce CRNs to bipartite graphs,…
A reaction system exhibits "absolute concentration robustness" (ACR) in some species if the positive steady-state value of that species does not depend on initial conditions. Mathematically, this means that the positive part of the variety…
In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction…
In chemical reaction network theory, ordinary differential equations are used to model the temporal change of chemical species concentration. As the functional form of these ordinary differential equations systems is derived from an…
Network translation has recently been used to establish steady state properties of mass action systems by corresponding the given system to a generalized one which is either dynamically or steady state equivalent. In this work we further…
In this paper we discuss the question of how to decide when a general chemical reaction system is incapable of admitting multiple equilibria, regardless of parameter values such as reaction rate constants, and regardless of the type of…
In this paper we examine some natural ideal conditions and show how graphs can be defined that give a visualization of these conditions. We examine the interplay between the multiplicative ideal theory and the graph theoretic structure of…
Siphons in a chemical reaction system are subsets of the species that have the potential of being absent in a steady state. We present a characterization of minimal siphons in terms of primary decomposition of binomial ideals, we explore…
Universal intermittent dynamics in a random catalytic reaction network, induced by smallness in the molecule number is reported. Stochastic simulations for a random catalytic reaction network subject to a flow of chemicals show that the…
The quasi-steady state approximation and time-scale separation are commonly applied methods to simplify models of biochemical reaction networks based on ordinary differential equations (ODEs). The concentrations of the "fast" species are…
Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most cases, feasible flux configurations can be derived from…
An analytical approach to network dynamics is used to show that when agents copy their state randomly the network arrives to a stationary status in which the distribution of states is independent of the agents degree. The effects of network…
Open dynamical systems are mathematical models of machines that take input, change their internal state, and produce output. For example, one may model anything from neurons to robots in this way. Several open dynamical systems can be…
Dynamic networks consist of interconnected dynamical systems. The subsystems can be viewed as transformations of input signals into output signals, where signals flow from one system into another through interconnections. The signal flows…
We consider a natural class of reaction networks which consist of reactions where either two species can inactivate each other (i.e., sequestration), or some species can be transformed into another (i.e., transmutation), in a way that gives…
A fundamental premise of statistical physics is that the particles in a physical system are interchangeable, and hence the state of each specific component is representative of the system as a whole. This assumption breaks down for complex…
Identifiability conditions for single or multiple modules in a dynamic network specify under which conditions the considered modules can be uniquely recovered from the second-order statistical properties of the measured signals. Conditions…
We present a new conjecture about a necessary condition that a (bio)chemical network has to satisfy for it to exhibit multistationarity. According to a Theorem of Feliu and Wiuf [27, 12], the conjecture is known for strictly monotonic…
This work addresses multistationarity of fully open reaction networks equipped with mass action kinetics. We improve upon the existing results relating existence of positive feedback loops in a reaction network and multistationarity; and we…