相关论文: Characteristic time of crossing a long free energy…
The classical theory of chemical reactions can be understood in terms of diffusive barrier crossing, where the rate of a reaction is determined by the inverse of the mean first passage time (FPT) to cross a free energy barrier. Whenever a…
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…
Biochemical processes typically involve huge numbers of individual reversible steps, each with its own dynamical rate constants. For example, kinetic proofreading processes rely upon numerous sequential reactions in order to guarantee the…
A phenomenological model for a measurement of barrier traversal times for particles is proposed. Two idealized detectors for passage and arrival provide entrance and exit times for the barrier traversal. The averaged traversal time is…
An approximate method for studying activation over a fluctuating barrier of potential is proposed. It involves considering separately the slow and fast components of barrier fluctuations, and it applies for any value of their correlation…
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…
Biomolecular folding, at least in simple systems, can be described as a two state transition in a free energy landscape with two deep wells separated by a high barrier. Transition paths are the short part of the trajectories that cross the…
The analytic solution for the kinetic description of binary reactions can be seen as the continuum version of a basic discrete iterate mapping. This fact allows a clear definition of the reaction characteristic time which takes the backward…
Thermally activated escape over a potential barrier in the presence of periodic driving is considered. By means of novel time-dependent path-integral methods we derive asymptotically exact weak-noise expressions for both the instantaneous…
Many biological, chemical, and physical systems are underpinned by stochastic transitions between equilibrium states in a potential energy. Here, we consider such transitions in a minimal model with two possible competing pathways, both…
An activated process consists of energy activation and barrier crossing; the former is a prerequisite for the latter. Barrier crossing has been studied extensively, but energy activation has been overlooked due to a lack of means to gauge…
The non-crossing rule for the energy levels of a parameter-dependent Hamiltonian is revisited and a flaw in a commonly accepted proof is revealed. Some aspects of avoided crossings are illustrated by means of simple models. One of them…
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,…
We calculate crossing probabilities and one-sided last exit time densities for a class of moving barriers on an interval $[0,T]$ via Schwartz distributions. We derive crossing probabilities and first hitting time densities for another class…
We investigate the hopping dynamics of a colloidal particle across a potential barrier and within a viscoelastic, i.e., non-Markovian bath, and report two clearly separated time scales in the corresponding waiting time distributions. While…
The time needed for a particle to exit a confining domain through a small window, called the narrow escape time (NET), is a limiting factor of various processes, such as some biochemical reactions in cells. Obtaining an estimate of the mean…
The thermal activation process by which a system passes from one local energy minimum to another is a recurring motif in physics, chemistry, and biology. For instance, biopolymer chains are typically modeled in terms of energy landscapes,…
We introduce a formalism for the calculation of the time of arrival t at a detector of particles traveling through interacting environments. We develop a general formulation that employs quantum canonical transformations from the free to…
We propose algorithms for determining both lower and upper bounds for the energy barriers encountered by a flux line in moving through a two-dimensional random potential. Analytical arguments, supported by numerical simulations, suggest…
We consider the generalization of the Kramers escape over a barrier problem to the case of a long chain molecule. The problem involves the motion of a chain molecule of $N$ segments across a region where the free energy per segment is…