We consider the translocation dynamics of a polymer chain forced through a nanopore by an external force on its head monomer on the trans side. For a proper theoretical treatment we generalize the iso-flux tension propagation (IFTP) theory to include friction arising from the trans side subchain. The theory reveals a complicated scenario of multiple scaling regimes depending on the configurations of the cis and the trans side subchains. In the limit of high driving forces f such that the trans subchain is strongly stretched, the theory is in excellent agreement with molecular dynamics simulations and allows an exact analytic solution for the scaling of the translocation time τ as a function of the chain length N0 and f . In this regime the asymptotic scaling exponents for τ ∼ N α 0 f β are α = 2, and β = −1. The theory reveals significant correction-to-scaling terms arising from the cis side subchain and pore friction, which lead to a very slow approach to α = 2 from below as a function of increasing N0.
We probe the influence of polymer-pore interactions on the translocation dynamics using Langevin dynamics simulations. We investigate the effect of the strength and location of the polymer-pore interaction using nanopores that are partially charged either at the entry or the exit or on both sides of the pore. We study the change in the translocation time as a function of the strength of the polymer-pore interaction for a given chain length and under the effect of an externally applied field. Under a moderate driving force and a chain length longer than the length of the pore, the translocation time shows a nonmonotonic increase with an increase in the attractive interaction. Also, an interaction on the cis side of the pore can increase the translocation probability. In the presence of an external field and a strong attractive force, the translocation time for shorter chains is independent of the polymer-pore interaction at the entry side of the pore, whereas an interaction on the trans side dominates the translocation process. Our simulation results are rationalized by a qualitative analysis of the free energy landscape for polymer translocation.
We study the translocation
of a polymer with oppositely charged
segments at both ends of the chain passing through a pore under the
effect of an external electric field in the presence of a pH gradient
using Langevin dynamics simulations. As observed in experiments, the
electrostatic interactions between the pore and the polymer are tuned
by altering the pH gradient. Our simulation studies show that with
the change in charge distribution on the polymer and the pore that
can mimic different pH conditions, the external driving force and
the polymer–pore electrostatic interactions play a significant
role in the translocation process. The external electric forces are
dominant during the entry stage, and the entry time decreases with
increase in the charge asymmetry of the pore-trapped polymer. During
the exit stage, the electrostatic interactions as well as the external
electric field act in concert in determining the exit time through
the pore. Our simulation results can capture many features observed
in experiments. Our results are explained qualitatively by calculating
the free-energy change of the polymer chain during the translocation
process.
We investigate the translocation dynamics of a folded linear polymer which is pulled through a nanopore by an external force. To this end, we generalize the iso-flux tension propagation theory for end-pulled polymer translocation to include the case of two segments of the folded polymer traversing simultaneously trough the pore. Our theory is extensively benchmarked with corresponding molecular dynamics (MD) simulations. The translocation process for a folded polymer can be divided into two main stages. In the first stage, both branches are traversing the pore and their dynamics is coupled. If the branches are not of equal length, there is a second stage where translocation of the shorter branch has been completed. Using the assumption of equal monomer flux of both branches confirmed by MD simulations, we analytically derive the equations of motion for both branches and characterize the translocation dynamics in detail from the average waiting time and its scaling form.
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