Related papers: Kink motion in the Kramers problem for a chain mol…
We study a system of non-interacting active particles, propelled by colored noises, characterized by an activity time $\tau$, and confined by a double-well potential. A straightforward application of this system is the problem of barrier…
I develop a kinetic mechanism to explain chain folding in polymer crystallization which is based on the competition between the formation of stems, which is due to frequent occupations of trans states along the chains in the supercooled…
Freestanding thin polymer films with high molecular weights exhibit an anomalous decrease in the glass-transition temperature with film thickness. Specifically, in such materials, the measured glass-transition temperature evolves in an…
Kramer's approach to the rate of the thermally activated escape from a metastable state is extended to field theory. Diffusion rate in the 1+1-dimensional Sine-Gordon model as a function of temperature and friction coefficient is evaluated…
The reptation concept in polymer dynamics is studied for model chains with added stiffness. The main idea of a chain diffusing inside a tube can be transferred from fully flexible chains. However, the picture, which renormalizes the chain…
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…
We extend the Rouse model of polymer dynamics to situations of non-stationary chain growth. For a dragged polymer chain of length $N(t) = t^\alpha$, we find two transitions in conformational dynamics. At $\alpha= 1/2$, the propagation of…
We revisit the Fokker-Planck based theory of driven polymer translocation through a narrow nanopore. A bead-spring model of a uniformly charged polyelectrolyte chain translocating through a semi-implicit model of a nanopore embedded in a…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
The dynamics of active particles is of interest at many levels and is the focus of theoretical and experimental research. There have been many attempts to describe the dynamics of particles affected by random active forces in terms of an…
We analyze the behavior of a Brownian particle moving in a double-well potential. The escape probability of this particle over the potential barrier from a metastable state toward another state is known as the Kramers problem. In this work…
Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…
The classical Kramers problem of the kinetic theory is analytically solved. The Kramers problem about isothermal sliding for quantum Fermi gases is considered. Quantum gases with the velocity-dependent collision frequency are considered.…
The usual Kramers theory of reaction rates in a condensed medium predict the rate to have an $\eta^{-1}$ dependence, $\eta$ being the viscosity of the medium. However, experiments on ligand binding to proteins performed long ago, showed the…
We present a modified version of our "sliding model", where chain arcs, between two contacts at the surface, may move if all the barriers along the arc are weaker than a certain threshold.An important advance of the revised model is that…
We investigate the mechanism of chain exchange in diblock copolymer micelles using two distinct yet complementary simulation techniques. First, enhanced sampling method is combined with coarse-grained molecular dynamics to compute a…
We consider the motion of a particle in a force field subjected to adiabatic, fluctuations of external origin. We do not put the restriction on the type of stochastic process that the noise is Gaussian. Based on a method developed earlier…
We investigate the deconfinement transition driven by excitations in long-range spin models. At low temperatures, these models exhibit a confined phase where domain-wall (or kinks) are localized. As temperature increases, kinks interact and…
Theories that are used to extract energy-landscape information from single-molecule pulling experiments in biophysics are all invariably based on Kramers' theory of thermally-activated escape rate from a potential well. As is well known,…
We investigate conformations and dynamics of a polymer considering its monomers to be active Brownian particles. This active polymer shows very intriguing physical behavior which is absent in an active Rouse chain. The chain initially…