Polymer translocation through a gradient channel

Abstract

The translocation of polymer through a channel with a gradient interaction between the polymer and the channel is studied. The interaction is expressed by E = E0 + kx, where E0 is the initial potential energy at the entrance, x is the position of the monomer inside the channel, and k is the energy gradient. The mean first passage time τ is calculated by using Fokker-Planck equation for two cases (1) N > L and (2) N < L under the assumption that the diffusion rate D is a constant, here N is the polymer length and L is the length of channel. Results show that there is a minimum of τ at k = k(c) for both cases, and the value kc is dependent on E0 and driving force f. At large f, the scaling relation τ ∼ N is observed for long polymer chains. But the scaling relation is dependent on the energy gradient k for an unforced driving translocation.

Regimes of streaming potential in cylindrical nano-pores in presence of finite sized ions and charge induced thickening: An analytical approach

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Non-monotonous polymer translocation time across corrugated channels: Comparison between Fick-Jacobs approximation and numerical simulations

“…Moreover, due to technological applications such as polymer separation, DNA sequencing and protein sensing, polymer translocation phenomena has been largely investigated in recent years [6][7][8][9][10][11][12][13][14][15][16][17][18][19][20].…”

Translocation time of a polymer chain through an energy gradient nanopore

“…Based on the free-energy landscape, the mean first passage time was obtained by applying the Fokker-Planck equation with reflecting-absorbing boundary conditions. We found that the first passage time was dependent on the energy gradient and the time would reach a minimum at a proper gradient interaction [43]. Besides the pH value, the interaction between DNA and the nanopore could be changed by surface modification [44,45] or by surface-biased voltage [46].…”

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