Related papers: Controlling polymer translocation with crowded med…
The flow of fluids in channels, pipes or ducts, as in any other wall-bounded flow (like water along the hulls of ships or air on airplanes) is hindered by a drag, which increases many-folds when the fluid flow turns from laminar to…
Depletion-induced interactions between colloids in colloid-polymer mixtures depend in range and strength on size, shape, and concentration of depletants. Crowding by colloids in turn affects shapes of polymer coils, such as biopolymers in…
We perform, with the help of cloud computing resources, extensive Langevin simulations which provide compelling evidence in favor of a general markovian framework for unbiased polymer translocation. Our statistical analysis consists of…
Here using LAMMPS molecular dynamics (MD) software, we simulate polymer translocation in 2 dimensions. We do the simulations for weak and moderate forces and for different pore diameters. Our results show that in both non-equilibrium and…
We investigate the translocation of a stiff polymer consisting of M monomers through a nanopore in a membrane, in the presence of binding particles (chaperones) that bind onto the polymer, and partially prevent backsliding of the polymer…
Polymer translocation through a nano-pore in a thin membrane is studied using a coarse-grained bead-spring model and Langevin dynamics simulation with a particular emphasis to explore out of equilibrium characteristics of the translocating…
We study a model of directed polymers in random environment in dimension $1+d$, given by a Brownian motion in a Poissonian potential. We study the effect of the density and the strength of inhomogeneities, respectively the intensity…
Mesh-like structures, such as mucus gel or cytoskeleton networks, are ubiquitous in biological systems. These intricate structures are composed of cross-linked, semi-flexible bio-filaments, crucial to numerous biological processes. In many…
In this chapter we review the rich behavior of polymer chains embedded in a quenched random environment. We first consider the problem of a Gaussian chain free to move in a random potential with short-ranged correlations. We derive the…
We explore the transport features of a single flexible polymer chain that walks on a periodic ratchet potential coupled with spatially varying temperature. At steady state the polymer exhibits a fast unidirectional motion where the…
Recent Monte Carlo simulations of a grafted semiflexible polymer in 1+1 dimensions have revealed a pronounced bimodal structure in the probability distribution of the transverse (bending) fluctuations of the free end, when the total contour…
We computationally investigate the active transport of tangentially-driven polymers with varying degrees of flexibility and activity in two-dimensional square lattices of obstacles. Tight periodic confinement induces notable conformational…
The effect of the microscopic structure of a pore on polymer translocation is studied using Langevin dynamics simulation, and the consequence of introducing patterned stickiness inside the pore is investigated. It is found that the…
The dynamics of flexible polymer molecules are often assumed to be governed by hydrodynamics of the solvent. However there is considerable evidence that internal dissipation of a polymer contributes as well. Here we investigate the dynamics…
We investigate the dynamics of a particle moving randomly along a disordered hetero-polymer subjected to rapid conformational changes which induce superdiffusive motion in chemical coordinates. We study the antagonistic interplay between…
We consider the drift of a polymer chain in a disordered medium, which is caused by a constant force applied to the one end of the polymer, under neglecting the thermal fluctuations. In the lowest order of the perturbation theory we have…
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…
A polymer placed in chaotic flow with large mean shear tumbles, making a-periodic flips. We describe the statistics of angular orientation, as well as of tumbling time (separating two subsequent flips) of polymers in this flow. The…
Polar polymer activity is a fundamental mechanism behind a large number of cellular dynamical processes. The number and location of the active sites on the polymer backbone play a central role in their dynamics and conformational…
We consider the internal dynamics of the polymer molecule which is injected in the chaotic flow with strong mean shear component. The flow geometry corresponds to the recent experiments on the elastic turbulence (Groisman, Steinberg 2000).…