Related papers: Kink motion in the Kramers problem for a chain mol…
A free particle is constrained to move on a knot obtained by winding around a putative torus. The classical equations of motion for this system are solved in a closed form. The exact energy eigenspectrum, in the thin torus limit, is…
We investigate the problem of polymer translocation through a nanopore in the absence of an external driving force. To this end, we use the two-dimensional (2D) fluctuating bond model with single-segment Monte Carlo moves. To overcome the…
We analyze the motion of individual beads of a polymer chain using a discrete version of De Gennes' reptation model that describes the motion of a polymer through an ordered lattice of obstacles. The motion within the tube can be evaluated…
We make a brief review of the Kramers escape rate theory for the probabilistic motion of a particle in a potential well U(x), and under the influence of classical fluctuation forces. The Kramers theory is extended in order to take into…
We investigate the interplay between post-translational folding and escape of two small single-domain proteins at the ribosomal exit tunnel by using Langevin dynamics with coarse-grained models. It is shown that at temperatures lower or…
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…
We present a dynamical picture of kink-anti-kink scattering in a pair of special, Frankensteinian potentials made of piece-wise quadratic and linear pieces. Specifically, we focus on models that support kinks without skin and core regions.…
The statistical mechanics of a long knotted collapsed polymer is determined by a free-energy with a knot-dependent subleading term, which is linked to the length of the shortest polymer that can hold such knot. The only other parameter…
Kibble-Zurek mechanism is widely known to appear in the transverse-field quantum Ising chain in the thermodynamic limit at zero temperature, having notorious characteristics, like the divergence of its relaxation time. In this work, I…
Dynamics of molecular motor dimers, consisting of rigidly bound particles that move along two parallel lattices and interact with underlying molecular tracks, is investigated theoretically by analyzing discrete-state stochastic…
In this paper we develop a link between the atomic-level modeling of the glide of 1/2<111> screw dislocations at 0 K and the thermally activated motion of these dislocations via nucleation of pairs of kinks. For this purpose, we introduce…
Kramers' rate theory forms a cornerstone for thermally activated barrier crossing. However, its reliance on equilibrium quantities excludes analysis of nonequilibrium dynamics at early times. Most works have thus focused on obtaining rates…
The stiff problem is concerned with a thermal conduction model with a singular barrier of zero volume. In this paper, we shall build the phase transitions for the stiff problems in one-dimensional space. It turns out that every phase…
Nonlinear cubic Euler-Lagrange equations of motion in the traveling variable are usually derived from Ginzburg-Landau free energy functionals frequently encountered in several fields of physics. Many authors considered in the past damped…
Half-space boundary Kramers' problem about isothermal sliding of moderate dense gas with accomodation boundary conditions along a flat firm surface is solving. The new method of the solution of boundary problems of the kinetic theory is…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
The time-dependent barrier passage of an anomalous damping system is studied via the generalized Langevin equation (GLE) with non-Ohmic memory damping friction tensor and corresponding thermal colored noise tensor describing a particle…
We consider the passage of long polymers of length N through a hole in a membrane. If the process is slow, it is in principle possible to focus on the dynamics of the number of monomers s on one side of the membrane, assuming that the two…
We investigate the motion of two overlapping polymers with self-avoidance confined in a narrow 2d box. A statistical model is constructed using blob free-energy arguments. We find spontaneous segregation under the condition: $L > R_{//}$,…
We study the dynamics of a polymer that is pulled by a constant force through a viscoelastic medium. This is a model for a polymer being pulled through a cell by an external force, or for an active biopolymer moving due to a self generated…