相关论文: Fixed Points for Stochastic Open Chemical Systems

Living systems are maintained out-of-equilibrium by external driving forces. At stationarity, they exhibit emergent selection phenomena that break equilibrium symmetries and originate from the expansion of the accessible chemical space due…

Recent research in both the experimental and mathematical communities has focused on biochemical interaction systems that satisfy an "absolute concentration robustness" (ACR) property. The ACR property was first discovered experimentally…

We formulate a local picture of strongly correlated systems as a Feynman sum over atomic configurations. The hopping amplitudes between these atomic configurations are identified as the renormalization group charges, which describe the…

Some ideas from quantum theory are just beginning to percolate back to classical probability theory. For example, there is a widely used and successful theory of "chemical reaction networks", which describes the interactions of molecules in…

A new tool for modeling electrochemical kinetics is presented. An extension of the Stochastic Simulation Algorithm framework to electrochemical systems is proposed. The physical justifications and constraints for the derivation of a…

How stochastic, microscopic events generate deterministic, macroscopic properties is a fundamental question in physics. We address this question by developing a quantum master equation model for concentrated radical solutions, where random…

We analyzed the stochastic behavior of systems controlled by autocatalytic reaction A+X -> X+X. Assuming the distribution of reacting particles in the system volume to be uniform, we introduced the notion of the point model of reaction…

All biological processes are controlled by complex systems of enzymatic chemical reactions. Although the majority of enzymatic networks have very elaborate structures, there are many experimental observations indicating that some turnover…

We introduce a class of Boltzmann equations on the real line, which constitute extensions of the classical Kac caricature. The collisional gain operators are defined by smoothing transformations with quite general properties. By…

Boltzmann provided a scenario to explain why individual macroscopic systems composed of a large number $N$ of microscopic constituents are inevitably (i.e., with overwhelming probability) observed to approach a unique macroscopic state of…

Studying systems where many individual bodies in motion interact with one another is a complex and interesting area. Simple mechanisms that may be determined for biological, chemical, or physical reasons can lead to astonishingly complex…

This article shows how to specify and construct a discrete, stochastic, continuous-time model specifically for ecological systems. The model is more broad than typical chemical kinetics models in two ways. First, using time-dependent hazard…

The catalytic reaction system (CRS) formalism by Hordijk and Steel is a versatile method to model autocatalytic biochemical reaction networks. It is particularly suited, and has been widely used, to study self-sustainment and…

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…

All known up to now models of chemical oscillations are based exclusively on kinetic considerations. The chemical gross-process equation is split usually by elementary steps, each step is supplied by an arrow and a differential equation,…

Chemical reaction networks (CRNs) provide a convenient language for modelling a broad variety of biological systems. These models are commonly studied with respect to the time series they generate in deterministic or stochastic simulations.…

How smart can a micron-sized bag of chemicals be? How can an artificial or real cell make inferences about its environment? From which kinds of probability distributions can chemical reaction networks sample? We begin tackling these…

Stochastic and dynamical processes lie at the heart of all physical, chemical, and biological systems. However, kinetic and thermodynamic properties which characterize these processes have largely been treated separately as they can be…

While the analytical solution for the marginal distribution of a stochastic chemical reaction network has been extensively studied, its joint distribution, i.e. the solution of a high-dimensional chemical master equation, has received much…

Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to…