Related papers: The Transition State in a Noisy Environment
Classical transition state theory (TST) is the cornerstone of reaction rate theory. It postulates a partition of phase space into reactant and product regions, which are separated by a dividing surface that reactive trajectories must cross.…
Transition State Theory is a central cornerstone in reaction dynamics. Its key step is the identification of a dividing surface that is crossed only once by all reactive trajectories. This assumption is often badly violated, especially when…
Chemical reactions subjected to time-varying external forces cannot generally be described through a fixed bottleneck near the transition state barrier or dividing surface. A naive dividing surface attached to the instantaneous, but moving,…
The accuracy of rate constants calculated using transition state theory depends crucially on the correct identification of a recrossing--free dividing surface. We show here that it is possible to define such optimal dividing surface in…
When a chemical reaction is driven by an external field, the transition state that the system must pass through as it changes from reactant to product -for example, an energy barrier- becomes time-dependent. We show that for periodic…
We study a simple chemical reaction system and effects of the internal noise. The chemical reaction system causes the same transition phenomenon discussed by Togashi and Kaneko [Phys. Rev. Lett. 86 (2001) 2459; J. Phys. Soc. Jpn. 72 (2003)…
Transition state theory formally provides a simplifying approach for determining chemical reaction rates and pathways. Given an underlying potential energy surface for a reactive system, one can determine the dividing surface in phase space…
In the past the study of reaction-diffusion systems has greatly contributed to our understanding of the behavior of many-body systems far from equilibrium. In this paper we aim at characterizing the properties of diffusion limited reactions…
The fundamental assumption of conventional transition state theory is the existence of a dividing surface having the property that trajectories originating in reactants must cross the surface only once and then proceed to products. Recently…
Dynamics between reactants and products are often mediated by a rate-determining barrier and an associated dividing surface leading to the transition state theory rate. This framework is challenged when the barrier is time-dependent because…
A model is proposed for studying the reaction dynamics in complex quantum systems in which the complete mixing of states is hindered by an internal barrier. Such systems are often treated by the transition-state theory, also known in…
Transition path theory provides a statistical description of the dynamics of a reaction in terms of local spatial quantities. In its original formulation, it is limited to reactions that consist of trajectories flowing from a reactant set A…
Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor…
A description in terms of transition rates among cells is used to analyze self-diffusion of hard spheres in the fluid phase. Cell size is assumed much larger than the mean free path. Transition state theory is used to obtain an equation…
Kramers' theory frames chemical reaction rates in solution as reactants overcoming a barrier in the presence of friction and noise. For weak coupling to the solution, the reaction rate is limited by the rate at which the solution can…
We study fluctuations in diffusion-limited reaction systems driven out of their stationary state. Using a numerically exact method, we investigate fluctuation ratios in various systems which differ by their level of violation of microscopic…
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…
A one-dimensional reaction-diffusion model consisting of two species of particles and vacancies on a ring is introduced. The number of particles in one species is conserved while in the other species it can fluctuate because of creation and…
Transition phenomena between thermal noise state and turbulent state observed in a submarginal turbulent plasma are analyzed with statistical theory. Time-development of turbulent fluctuation is obtained by numerical simulations of Langevin…
Stochastic dynamics of chemical reactions in a mutually repressing two-gene circuit is numerically simulated. The circuit has a rich variety of different states when the kinetic change of DNA status is slow. The stochastic switching…