Related papers: Transition State Theory for dissipative systems wi…
We examine the phase space structures that govern reaction dynamics in the absence of critical points on the potential energy surface. We show that in the vicinity of hyperbolic invariant tori it is possible to define phase space dividing…
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…
Many chemical reactions can be formulated in terms of particle diffusion in a complex energy landscape. Transition path theory (TPT) is a theoretical framework for describing the direct (reaction) pathways from reactant to product states…
A practical method for finding free energy barriers for transitions in high-dimensional classical and quantum systems is presented and used to calculate the dissociative sticking probability of H2 on a metal surface within transition state…
Transition state theory is a standard framework for predicting the rate of a chemical reaction. Although the transition state theory has been successfully applied to numerous chemical reaction analyses, many experimental and theoretical…
The time evolution of many physical, chemical, and biological systems can be modelled by stochastic transitions between the minima of the potential energy surface describing the system of interest. We show that in cases where there are two…
Many processes in chemistry, physics, and biology involve rare events in which the system escapes from a metastable state by surmounting an activation barrier. Examples range from chemical reactions, protein folding, and nucleation events…
In chemical or physical reaction dynamics, it is essential to distinguish precisely between reactants and products for all time. This task is especially demanding in time-dependent or driven systems because therein the dividing surface (DS)…
A one-dimensional model on a line of the length L is investigated, which involves particle diffusion as well as single particle annihilation. There are also creation and annihilation at the boundaries. The static and dynamical behaviors of…
Simulating chemical reactions is a central challenge in computational chemistry, characterized by an uneven difficulty profile: while equilibrium reactant and product geometries are often classically tractable, intermediate transition…
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…
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…
Mass-conserving reaction-diffusion systems with bistable nonlinearity are useful models for studying cell polarity formation, which is a key process in cell division and differentiation. We rigorously show the existence and stability of…
Many classic questions of structural theory concern discrete changes, such as the formation or dissolution of groups, role turnover, or faction realignment. Here, we consider a basic framework combining prior work on change paths and recent…
The main goal of this paper is to understand the formation of hexagonal patterns from the dynamical transition theory point of view. We consider the transitions from a steady state of an abstract nonlinear dissipative system. To shed light…
Rare events such as conformational changes in biomolecules, phase transitions, and chemical reactions are central to the behavior of many physical systems, yet they are extremely difficult to study computationally because unbiased…
In many biological situations, a species arriving from a remote source diffuses in a domain confined between two parallel surfaces until it finds a binding partner. Since such a geometric shape falls in between two- and three-dimensional…
In Part I [J. Chem. Phys. 138, 084108 (2013)] we derived a quantum transition-state theory by taking the t->0+ (short-time) limit of a new form of quantum flux-side time-correlation function containing a ring-polymer dividing surface. This…
Determining the kinetic bottlenecks that make transitions between metastable states difficult is key to understanding important physical problems like crystallization, chemical reactions, or protein folding. In all these phenomena, the…
The time evolution of the thermally activated decay rates is considered. This evolution is of particular importance for the recent nanoscale experiments discussed in the literature, where the potential barrier is relatively low (or the…