Related papers: Dynamics of forced biopolymer translocation
Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between…
We consider the statics and dynamics of a flexible polymer confined between parallel plates both in the presence and absence of hydrodynamic interactions. The hydrodynamic interactions are described at the level of the fluctuating,…
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 use the Bond Fluctuation Model (BFM) to study the pore-blockade times of a translocating polymer of length $N$ in two dimensions, in the absence of external forces on the polymer (i.e., unbiased translocation) and hydrodynamic…
Motivated by identifying the origin of the bias dependence of tension propagation we investigate methods for measuring tension propagation quantitatively in computer simulations of driven polymer translocation. Here the motion of flexible…
We show the presence of both a minimum and clear oscillations in the frequency dependence of the translocation time of a polymer described as a unidimensional Rouse chain driven by a spatially localized oscillating linear potential. The…
One of the most fundamental quantities associated with polymer translocation through a nanopore is the translocation time $\tau$ and its dependence on the chain length $N$. Our simulation results based on both the bond fluctuation Monte…
We study the dynamics of an ideal polymer chain in a crowded, viscoelastic medium and in the presence of active forces. The motion of the centre of mass and of individual monomers is calculated. On time scales that are comparable to the…
Poroelastic materials, consisting of a permeable solid matrix infiltrated with fluid, are ubiquitous in natural and engineering contexts. In poroelastic polymer solids, the elastic matrix swells to equilibrium when immersed in a solvent…
We investigate the effect of hydrodynamic interactions on the non-equilibrium drift dynamics of an ideal flexible polymer pulled by a constant force applied at one end of the polymer using the perturbation theory and the renormalization…
Translocation of a polymer out of curved surface or membrane is studied via mean first passage time approach. Membrane curvature gives rise to a constraint on polymer conformation, which effectively drives the polymer to the outside of…
We report a numerical study of the diffusiophoresis of short polymers using non-equilibrium molecular dynamics simulations. More precisely, we consider polymer chains in a fluid containing a solute which has a concentration gradient, and…
While the characteristics of the driven translocation for asymptotically long polymers are well understood, this is not the case for finite-sized polymers, which are relevant for real-world experiments and simulation studies. Most notably,…
Using Langevin dynamics simulations in three dimensions (3D), we investigate the dynamics of polymer translocation into the regions between two parallel plane walls with separation $R$ under a driving force $F$, respectively. Compared with…
In this paper, we investigate the microscopic dynamics of a polymer of length $N$ translocating through a narrow pore. Characterization of its purportedly anomalous dynamics has so far remained incomplete. We show that the polymer dynamics…
In this work we study the noise induced effects on the dynamics of short polymers crossing a potential barrier, in the presence of a metastable state. An improved version of the Rouse model for a flexible polymer has been adopted to mimic…
We investigate the voltage-driven translocation of an inhomogeneously charged polymer through a nanopore by utilizing discrete and continuous stochastic models. As a simplified illustration of the effect of charge distribution on…
We analyze the nonequilibrium dynamics of single inextensible semiflexible biopolymers as stretching forces are applied at the ends. Based on different (contradicting) heuristic arguments, various scaling laws have been proposed for the…
We study the translocation of polymers across varying-section channels. Using systematic approximations, we derive a simplified model that reduces the problem of polymer translocation through varying-section channels to that of a point-like…
We propose a method for the theoretical investigation of polymer translocation through composite pore structures possessing arbitrarily specified geometries. Translocation through each constituent part of the composite is treated as being…