相关论文: Modeling of chemical reaction systems with detaile…
We investigate the multi-chain version of the Chemical Master Equation, when there are transitions between different states inside the long chains, as well as transitions between (a few) different chains. In the discrete version, such a…
The detailed balance property is a fundamental property that must be satisfied in all the macroscopic systems with a well defined temperature at each point. On the other hand, many biochemical networks work in non-equilibrium conditions and…
Although coarse-grained models have been widely used to explain exotic phenomena in complex fluids, such as droplet formation in living cells, these conventional approaches often fail to capture the intricate microscopic degrees of freedom…
A general phenomenological reaction-diffusion model for flow-induced phase transitions in complex fluids is presented. The model consists of an equation of motion for a nonconserved composition variable, coupled to a Newtonian stress…
Temperature gradients represent energy sources that can be harvested to generate steady reaction or transport fluxes. Technological developments could lead to the transfer of free energy from heat sources and sinks to chemical systems for…
Wetting and dewetting dynamics of simple and complex liquids is described by kinetic equations in gradient dynamics form that incorporates the various coupled dissipative processes in a fully thermodynamically consistent manner. After…
Making sense of complex inhomogeneous systems composed of many interacting species is a grand challenge that pervades basically all natural sciences. Phase separation and pattern formation in reaction-diffusion systems have been largely…
The use of mathematical methods for the analysis of chemical reaction systems has a very long history, and involves many types of models: deterministic versus stochastic, continuous versus discrete, and homogeneous versus spatially…
This paper is devoted to the development of a theoretical and computational framework to efficiently sample the statistically significant thermally activated reaction pathways, in multi-dimensional systems obeying Langevin dynamics. We show…
The practical description of disordered chemical reactions, where reactions involve multiple species at multiple sites, is presently challenge using correlated electronic structure methods. Here we describe the gradient theory of…
Chemical reaction networks in living cells maintain precise control over thousands of metabolites despite operating far from equilibrium under constant perturbations. While mass action kinetics accurately describe the underlying dynamics,…
A combination of reaction-diffusion models with moving-boundary problems yields a system in which the diffusion (spreading and penetration) and reaction (transformation) evolve the system's state and geometry over time. These systems can be…
We study the asymptotic behaviour of a gradient system in a regime in which the driving energy becomes singular. For this system gradient-system convergence concepts are ineffective. We characterize the limiting behaviour in a different…
Reversibility, weak reversibility and deficiency, detailed and complex balancing are generally not "encoded" in the kinetic differential equations but they are realization properties that may imply local or even global asymptotic stability…
We consider linear reaction systems with slow and fast reactions, which can be interpreted as master equations or Kolmogorov forward equations for Markov processes on a finite state space. We investigate their limit behavior if the fast…
Dynamical system models of complex biochemical reaction networks are usually high-dimensional, nonlinear, and contain many unknown parameters. In some cases the reaction network structure dictates that positive equilibria must be unique for…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
In this paper we study the rate of convergence to the complex balanced equilibrium for some chemical reaction-diffusion systems with boundary equilibria. We first analyze a three-species system with boundary equilibria in some…
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…
We further clarify the relation between detailed-balanced and complex-balanced equilibria of reversible chemical reaction networks. Our results hold for arbitrary kinetics and also for boundary equilibria. Detailed balance, complex balance,…