Related papers: Dynamics of polymer ejection from capsid
We investigate several scaling properties of a translocating homopolymer through a thin pore driven by an external field present inside the pore only using Langevin Dynamics (LD) simulation in three dimension (3D). Specifically motivated by…
The function of many membrane-enclosed intracellular structures relies on release of diffusing particles that exit through narrow pores or channels in the membrane. The rate of release varies with pore size, density, and length of the…
We investigate polymer translocation through a nanopore under a pulling force using Langevin dynamics simulations. We concentrate on the influence of the chain length $N$ and the pulling force $F$ on the translocation time $\tau$. The…
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…
During polymer translocation driven by e.g. voltage drop across a nanopore, the segments in the cis-side is incessantly pulled into the pore, which are then pushed out of it into the trans-side. This pulling and pushing polymer segments are…
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…
We study translocation of semiflexible polymers driven by force $f_d$ inside a nanometer-scale pore using our three-dimensional Langevin dynamics model. We show that the translocation time $\tau$ increases with increasing bending rigidity…
The translocation dynamics of a polymer chain through a nanopore in the absence of an external driving force is analyzed by means of scaling arguments, fractional calculus, and computer simulations. The problem at hand is mapped on a one…
We present a numerical study of the effect of knotting on the ejection of flexible and semiflexible polymers from a spherical, virus-like capsid. The polymer ejection rate is primarily controlled by the knot, which moves to the hole in the…
We solve the Chapman-Kolmogorov equation and study the exact splitting probabilities of the general stochastic process which describes polymer translocation through membrane pores within the broad class of Markov chains. Transition…
Using two dimensional Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a fluidic channel with diameter $R$ through a nanopore under a driving force $F$. Due to the crowding effect induced by the…
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…
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…
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…
How fast a post-translational nascent protein escapes from the ribosomal exit tunnel is relevant to its folding and protection against aggregation. Here, by using Langevin molecular dynamics, we show that non-local native interactions help…
We employ 3D Langevin Dynamics simulations to study the dynamics of polymer chains translocating through a nanopore in presence of asymmetric solvent conditions. Initially a large fraction ($>$ 50%) of the chain is placed at the…
The escape dynamics of sticky particles from textured surfaces is poorly understood despite importance to various scientific and technological domains. In this work, we address this challenge by investigating the escape time of adsorbates…
Monte Carlo (MC) simulations are used to study the dynamics of polymer translocation through a nanopore in the limit where the translocation rate is sufficiently slow that the polymer maintains a state of conformational quasi-equilibrium.…
This study deals with polymer looping, an important process in many chemical and biological systems. We investigate basic questions on the looping dynamics of a polymer under tension using the freely-jointed chain (FJC) model. Previous…
We investigate the translocation of stiff polymers in the presence of binding particles through a nanopore by two-dimensional Langevin dynamics simulations. We find that the mean translocation time shows a minimum as a function of the…