Conformation Change, Tension Propagation and Drift-Diffusion Properties of Polyelectrolyte in Nanopore Translocation

Abstract

Using Langevin dynamics simulations, conformational, mechanical and dynamical properties of charged polymers threading through a nanopore are investigated. The shape descriptors display different variation behaviors for the cis-and trans-side sub-chains, which reflects a strong cis-trans dynamical asymmetry, especially when the driving field is strong. The calculation of bond stretching shows how the bond tension propagates on the chain backbone, and the chain section straightened by the tension force is determined by the ratio of the direct to the contour distances of the monomer to the pore. With the study of the waiting time function, the threading process is divided into the tension-propagation stage and the tail-retraction stage. At the end, the drift velocity, diffusive property and probability density distribution are explored. Owing to the non-equilibrium nature, translocation is not a simple drift-diffusion process, but exhibits several intermediate behaviors, such as ballistic motion, normal diffusion and super diffusion, before ending with the last, negative-diffusion behavior.

Translocation of Charged Polymers through a Nanopore in Monovalent and Divalent Salt Solutions: A Scaling Study Exploring over the Entire Driving Force Regimes

“…The role of chain stiffness on driven translocation was analyzed; the scaling regimes have been classified into the rigid-chain (α=2), the Gaussian-chain (α=1.5) and the excluded-volume chain (α=1+ν) regimes and verified by simulations [69,70]. To understand tension propagation on a chain, two-dimensional intensity maps of the tensile force have been studied in the translocation simulations [47,71,72,73]; the calculations involved, at the same time, the study of the variations of the local monomer velocity, the bond length, the monomer-to-pore distance, etc.…”

“…In the simulations, the majority of the works investigated translocation using neutral chains as the studying models. Only a few papers used charged chains with explicit ions to explore the dynamics of translocation [48,72,74,75,76,77]. As we know, the biomacromolecules concerned in the applications of translocation, such as DNA, RNA and proteins, are mostly ionizable molecules in aqueous solutions and belong to a general category of linear polymer, called “polyelectrolyte”.…”

“…Decreasing the size of counterions was found to slow down the DNA translocation [82]. Recently, we performed a detailed translocation study, using polyelectrolytes in the simulations [48,72]. The scaling behavior of translocation time, the conformational change of the chain, the condensation of ions, the distribution of monomers on the cis and trans sides, the tension propagation, the waiting time function and the drift-diffusion properties have been analyzed.…”

Polyelectrolyte Translocation through a Corrugated Nanopore

“…For this purpose, a normalized time t n is defined as t n = t/τ, where τ is the translocation time recorded for a particular run. [24,[35][36][37] The time interval of 0 ≤ t n ≤ 1 is divided into 20 sub-intervals, each having a duration of 0.05. Various chain properties were averaged over all 200 successful runs in each sub-interval.…”

Star Polymer Translocation into a Spheroidal Cavity

“…The normalized time t n is defined as t n = t/τ s , where τ s is the translocation time recorded for a particular run. [16,27,42,43] Moreover, R gi denotes the component of the radius of gyration along a particular direction i. the linear chain, R gx attains a maximum at t n = 0.125 and 0.486 for R = 4.2 and 9.0 respectively. For R = 9.0, the chain is maximally extended along the x-direction when the branch point enters the pore.…”