Related papers: Encounter dynamics of a small target by a polymer …
The dynamics of polymer translocation through a pore has been the subject of recent theoretical and experimental works. We have considered theoretical estimates and performed computer simulations to understand the mechanism of DNA uptake…
We present a scaling theory and Monte Carlo (MC) simulation results for a flexible polymer chain slowly dragged by one end into a nanotube. We also describe the situation when the completely confined chain is released and gradually leaves…
In this paper, we develop an encounter-based model of partial surface adsorption for fractional diffusion in a bounded domain. We take the probability of adsorption to depend on the amount of particle-surface contact time, as specified by a…
The transport of polymers with folded configurations across membrane pores is investigated theoretically by analyzing simple discrete stochastic models. The translocation dynamics is viewed as a sequence of two events: motion of the folded…
When does a diffusing particle reach its target for the first time? This first-passage time (FPT) problem is central to the kinetics of molecular reactions in chemistry and molecular biology. Here we explain the behavior of smooth FPT…
Loop formation in long molecules occurs many places in nature, from solutions of carbon nanotubes to polymers inside a cell. In this article, we review theoretical studies of the static and dynamic properties of polymer loops. For example,…
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…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
The self-avoid random walk algorithm has been extensively used in the study of polymers. In this work we study the basic properties of the trajectories generated with this algorithm when two interactions are added to it: contact and folding…
In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a…
We investigate a diffusive motion of a system of interacting Brownian particles in quasi-one-dimensional micropores. In particular, we consider a semi-infinite 1D geometry with a partially absorbing boundary and the hard-core inter-particle…
A self-interacting polymer with one end attached to a sticky surface has been studied by means of a flat-histogram stochastic growth algorithm known as FlatPERM. We examined the four-dimensional parameter space of the number of monomers up…
Several important biological processes are initiated by the binding of a protein to a specific site on the DNA. The strategy adopted by a protein, called transcription factor (TF), for searching its specific binding site on the DNA has been…
Polymer translocation through a nanopore in a membrane investigated theoretically. Recent experiments on voltage-driven DNA and RNA translocations through a nanopore indicate that the size and geometry of the pore are important factors in…
Long DNA molecules can be mapped by cutting them with restriction enzymes inside a narrow channel. Once cut, the individual fragments thus produced move away from each other due to diffusion and entropic effects. We investigate how long it…
Using molecular dynamics simulations we study the static and dynamic properties of spherical nanoparticles (NPs) embedded in a disordered and polydisperse polymer network. Purely repulsive (RNP) as well as weakly attractive (ANP) polymer-NP…
The diffusion of small molecular penetrants through polymeric materials represents an important fundamental problem, relevant to the design of materials for applications such as coatings and membranes. Polymer networks hold promise in these…
In noisy environments such as the cell, many processes involve target sites that are often hidden or inactive, and thus not always available for reaction with diffusing entities. To understand reaction kinetics in these situations, we study…
In this paper, we investigate random walks in a family of small-world trees having an exponential degree distribution. First, we address a trapping problem, that is, a particular case of random walks with an immobile trap located at the…
We develop a high order asymptotic expansion for the mean first passage time (MFPT) of the capture of Brownian particles by a small elliptical trap in a bounded two dimensional region. This new result describes the effect that trap…