相关论文: Reaction kinetics in open reactors and serial tran…

We introduce thermodynamic networks, a general framework for autonomous, physics-based computation using non-equilibrium steady states. These networks are modeled as a collection of finite-size reservoirs that exchange conserved…

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…

Similarly to gear systems in vehicles, most chemical reaction networks (CRNs) involved in energy transduction have at their disposal multiple transduction pathways, each characterized by distinct efficiencies. We conceptualize these…

The classical theory of linear response applies to statistical mechanics close to equilibrium. Away from equilibrium, one may describe the microscopic time evolution by a general differentiable dynamical system, identify nonequilibrium…

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…

A stochastic theory is developed to predict the spectral signature of proton-transfer processes and applied to infrared spectra computed from ab initio molecular-dynamics simulations of a single H$_5$O$_2{}^{+}$ cation. By constraining the…

Continuous time recurrent neural networks (CTRNN) are systems of coupled ordinary differential equations that are simple enough to be insightful for describing learning and computation, from both biological and machine learning viewpoints.…

Reaction-diffusion equations are widely used as the governing evolution equations for modeling many physical, chemical, and biological processes. Here we derive reaction-diffusion equations to model transport with reactions on a…

Stochastic network-dynamics are typically assumed to be memory-less. Involving prolonged dwells interrupted by instantaneous transitions between nodes such Markov networks stand as a coarse-graining paradigm for chemical reactions, gene…

In this chapter, we illustrate recently obtained thermodynamic bounds for a number of enzymatic networks by focusing on simple examples of unicyclic or multi-cyclic networks. We also derive complementary relations which constrain the…

Stochastic models of reaction networks are becoming increasingly important in Systems Biology. In these models, the dynamics is generally represented by a continuous-time Markov chain whose states denote the copy-numbers of the constituent…

We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…

This paper is motivated by examples from stochastic reaction network theory. The $Q$-matrix of a stochastic reaction network can be derived from the reaction graph, an edge-labelled directed graph encoding the jump vectors of an associated…

Stochastic Structural Stability Theory (SSST) provides an autonomous, deterministic, nonlinear dynamical system for evolving the statistical mean state of a turbulent system. In this work SSST is applied to the problem of understanding the…

The paper gives an account of a detailed investigation of the thermodynamic branch as a path of the chemical system deviation from its isolated thermodynamic equilibrium under an external impact. For a combination of direct and reverse…

In this paper I show that, for a class of reaction networks, the discrete stochastic nature of the reacting species and reactions results in qualitative and quantitative differences between the mean of exact stochastic simulations and the…

Analysis of large continuous-time stochastic systems is a computationally intensive task. In this work we focus on population models arising from chemical reaction networks (CRNs), which play a fundamental role in analysis and design of…

With the help of time-dependent scattering theory on the observable algebra of infinitely extended quasifree fermionic chains, we introduce a general class of so-called right mover/left mover states which are inspired by the nonequilibrium…

Nuclear reaction rates are one of the most important ingredients in describing how stars evolve. The study of the nuclear reactions involved in different astrophysical sites is thus mandatory to address most questions in nuclear…

We study diffusion-controlled processes in nonequilibrium steady states, where standard rate theory assumptions break down. Using transition path theory, we generalize the relations between reactive probability fluxes and measures of the…