Related papers: Dynamics of end-pulled polymer translocation throu…
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…
We study the driven translocation of a flexible polymer through an interacting conical pore using Langevin dynamics simulations. We find that, for a fixed value of externally applied force and pore polymer interaction strength, the mean…
Theoretical derivation and numerical confirmation are provided for the scaling of pore-blockade times as $N^{2+\nu}$ for unbiased translocation in two and three dimensions, with $N$ as the polymer length and $\nu$ as the Flory exponent of…
We introduce an anisotropic mean-field approach for the dynamics of semiflexible polymers under intermediate tension, the force range where a chain is partially extended but not in the asymptotic regime of a nearly straight contour. The…
We present a numerical study of forced polymer translocation by using two separate pore models. Both of them have been extensively used in previous forced translocation studies. We show that variations in the pore model affect the forced…
Transport of tracer particles through mesh-like environments such as biological hydrogels and polymer matrices is ubiquitous in nature. These tracers could be passive, such as colloids or active (self-propelled), such as synthetic…
Numerical results on the translocation of long biopolymers through mid-sized and wide pores are presented. The simulations are based on a novel methodology which couples molecular motion to a mesoscopic fluid solvent. Thousands of events of…
DNA capture with high fidelity is an essential part of nanopore translocation. We report several important aspects of the capture process and subsequent translocation of a model DNA polymer through a solid-state nanopore in presence of an…
We study translocation dynamics of a driven compressible semi-flexible chain consisting of alternate blocks of stiff ($S$) and flexible ($F$) segments of size $m$ and $n$ respectively for different chain length $N$ in two dimension (2D).…
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
We consider the escape of a flexible, self-avoiding polymer chain out of a confined geometry. By means of simulations, we demonstrate that the translocation time can be described by a simple scaling law that exhibits a nonlinear dependence…
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…
We study pore blockade times for a translocating polymer of length $N$, driven by a field $E$ across the pore in three dimensions. The polymer performs Rouse dynamics, i.e., we consider polymer dynamics in the absence of hydrodynamical…
The transport of biomolecules across a cell membrane is an important phenomena that plays a pivotal role in the functioning of biological cells. In this paper, we investigate such processes by modeling the translocation of polymers through…
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 propose a simple scaling theory describing the variation of the mean first passage time (MFPT) $\tau(N,M)$ of a regular block copolymer of chain length $N$ and block size $M$ which is dragged through a selective liquid-liquid interface…
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…
Polymer translocation is a promising strategy for the next-generation DNA sequencing technologies. The use of biological and synthetic nano-pores, however, still suffers from serious drawbacks. In particular, the width of the membrane layer…
Here we report on the translocation of folded polymers through nano-pores using molecular dynamic simulations. Two cases are studied; one in which a folded molecule unfolds upon passage and one in which the folding remains intact as the…