Related papers: Polymer escape from a confining potential
We study the dynamics of flexible, semiflexible, and self-avoiding polymer chains moving under a Kramers metastable potential. Due to thermal noise, the polymers, initially placed in the metastable well, can cross the potential barrier, but…
The rate of escape of an ideal bead-spring polymer in a symmetric double-well potential is calculated using transition state theory (TST) and the results compared with direct dynamical simulations. The minimum energy path of the transitions…
We investigate the escape rate of an overdamped, self-propelled spherical Brownian particle on a surface from a metastable potential well. Within a modeling in terms of a 1D constant speed of the particle's active dynamics we consider the…
The escape rate of a Brownian particle over a potential barrier is accurately described by the Kramers theory. A quantitative theory explicitly taking the activity of Brownian particles into account has been lacking due to the inherently…
We study the dynamics of one-dimensional active particles confined in a double-well potential, focusing on the escape properties of the system, such as the mean escape time from a well. We first consider a single-particle both in near and…
The probability per unit time for a thermally activated Brownian particle to escape over a potential well is in general well-described by Kramers theory. Kramers showed that the escape time decreases exponentially with increasing barrier…
The recrossing correction to the transition state theory estimate of a thermal rate can be difficult to calculate when the energy barrier is flat. This problem arises, for example, in polymer escape if the polymer is long enough to stretch…
A linear polymer grafted to a hard wall and underneath an AFM tip can be modelled in a lattice as a grafted lattice polymer (or self-avoiding walk) compressed underneath a piston approaching the wall. As the piston approaches the wall the…
Polymer ejection from a capsid through a nanoscale pore is an important biological process with relevance to modern biotechnology. Here, we study generic capsid ejection using Langevin dynamics. We show that even when the ejection takes…
This paper focuses on the escape problem of a harmonically-forced classical particle from a purely-quartic truncated potential well. The latter corresponds to various engineering systems that involve purely cubic restoring force and absence…
We determine the rate of escape from a potential well, and the diffusion coefficient in a periodic potential, of a random walker that moves under the influence of the potential in between successive collisions with the heat bath. In the…
This study deals with polymer looping, an important process in many chemical and biological systems. We investigate basic questions on the looping dynamics of a polymer under tension using the freely-jointed chain (FJC) model. Previous…
We examine the effect of subdividing the potential barrier along the reaction coordinate on Kramers' escape rate for a model potential. Using the known supersymmetric potential approach, we show the existence of an optimal number of…
We examine the ejection of an initially strongly confined flexible polymer from a spherical capsid through a nanoscale pore. We use molecular dynamics for unprecedentedly high initial monomer densities. We show that the time for an…
Brownian escape is key to a wealth of physico-chemical processes, including polymer folding, and information storage. The frequency of thermally activated energy barrier crossings is assumed to generally decrease exponentially with…
Classical escape in 2D Hamiltonian systems with the mixed state has been studied numerically and analytically. The wide class of potentials with the mixed state is presented by polinomial potentials. In potentials, where the mixed state…
The reactive process of barrier escaping from the metastable potential well is studied together with the extension of Kramers' rate formula to the fractional case. Characteristic quantities are computed for an thimbleful of insight into the…
Polymers in confined spaces are compressed and have reduced conformational entropy, and will partially or fully escape from confinement if conditions are suitable. This is in particular the case for a polymer grafted in a pore. The escape…
Most of the theoretical models describing the translocation of a polymer chain through a nanopore use the hypothesis that the polymer is always relaxed during the complete process. In other words, models generally assume that the…
An end-grafted flexible polymer chain in 3d space between two pistons undergoes an abrupt transition from a confined coil to a flower-like conformation when the number of monomers in the chain, N, reaches a critical value. In 2d geometry,…