相关论文: Reaction Kinetics in a Tight Spot

Compartmentalization of biochemical processes underlies all biological systems, from the organelle to the tissue scale. Theoretical models to study the interplay between noisy reaction dynamics and compartmentalization are sparse, and…

We consider local bifurcations of equilibria in dynamical systems arising from chemical reaction networks with mass action kinetics. In particular, given any mass action network admitting a local bifurcation of equilibria, assuming only a…

Numerical simulations of a simple reaction--diffusion model reveal a surprising variety of irregular spatio--temporal patterns. These patterns arise in response to finite--amplitude perturbations. Some of them resemble the steady irregular…

A zone of reactions is determined and then exploited as a tool in studying the space-time structure of an interacting system formed in a collision of relativistic nuclei. The time dependence of the reaction rates integrated over spatial…

It has recently been shown that structural conditions on the reaction network, rather than a 'fine-tuning' of system parameters, often suffice to impart 'absolute concentration robustness' on a wide class of biologically relevant,…

The efficiency of an encounter-controlled two-channel reaction between two independently-mobile reactants on a lattice is characterized by the mean number $\rt$ of steps to reaction. The two reactants are distinguished by their mass with…

Reaction networks are systems in which the populations of a finite number of species evolve through predefined interactions. Such networks are found as modeling tools in many biological disciplines such as biochemistry, ecology,…

We analyzed the stochastic behavior of systems controlled by autocatalytic reaction A+X -> X+X, X+X -> A+X, X -> B provided that the distribution of reacting particles in the system volume is uniform, i.e. the point model of reaction…

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…

Stochastic reaction networks with mass-action kinetics provide a useful framework for understanding processes -- biochemical and otherwise -- in homogeneous environments. However, cellular reactions are often compartmentalized, either at…

Nuclear reaction rates determine the abundances of isotopes in stellar burning processes. A multitude of reactions determine the reaction flow pattern which is described in terms of reaction network simulations. The reaction rates are…

In the study of reaction networks and the polynomial dynamical systems that they generate, special classes of networks with important properties have been identified. These include reversible, weakly reversible}, and, more recently,…

We consider a class of nonequilibrium systems of interacting agents with pairwise interactions and quenched disorder in the dynamics featuring, in the thermodynamic limit, phase transitions. We provide conditions on the microscopic…

Diffusion mediated reaction models are particularly ubiquitous in the description of physical, chemical or biological processes. The random walk schema is a useful tool for formulating these models. Recently, evanescent random walk models…

Reaction systems are discrete dynamical systems that model biochemical processes in living cells using finite sets of reactants, inhibitors, and products. We investigate the computational complexity of a comprehensive set of problems…

We investigate the dynamics of chemical reaction networks (CRNs) with the goal of deriving an upper bound on their reaction rates. This task is challenging due to the nonlinear nature and discrete structure inherent in CRNs. To address…

To what extent do the characteristic features of a chemical reaction network reflect its purpose and function? In general, one argues that correlations between specific features and specific functions are key to understanding a complex…

Reaction coordinates are widely used throughout chemical physics to model and understand complex chemical transformations. We introduce a definition of the natural reaction coordinate, suitable for condensed phase and biomolecular systems,…

A numerically effective procedure for determining weakly reversible chemical reaction networks that are linearly conjugate to a known reaction network is proposed in this paper. The method is based on translating the structural and…

We study the dynamics of a system made up of particles of two different species undergoing irreversible quadratic autocatalytic reactions: $A + B \to 2A$. We especially focus on the reaction velocity and on the average time at which the…