Numerical and theoretical study on the mechanism of biopolymer translocation process through a nano-pore

Abstract

We conducted a numerical study on the translocation of a biopolymer from the cis side to the trans side of a membrane through a synthetic nano-pore driven by an external electric field in the presence of hydrodynamic interactions (HIs). The motion of the polymer is simulated by 3D Langevin dynamics technique using a worm-like chain model of N identical beads, while HI between the polymer and fluid are incorporated by the lattice Boltzmann equation. The translocation process is induced by electrophoretic force, which sequentially straightens out the folds of the initial random configuration of the polymer chain on the cis side. Our simulation results on translocation time and velocity are in good quantitative agreement with the corresponding experimental ones when the surface charge on the nano-pore and the HI effect are considered explicitly. We found that the translocation velocity of each bead inside the nano-pore mainly depends upon the length of the straightened portion of the polymer in forced motion near the pore. We confirmed this by a theoretical formula. After performing simulations with different pore lengths, we observed that translocation velocity mainly depends upon the applied potential difference rather than upon the electric field inside the nano-pore.

Influence of polymer-pore interaction on the translocation of a polymer through a nanopore

“…The latter is consistent with their experimental result α = 1.27. Langevin dynamics simulation gave α = 1.24 and 1.32 for a 3D SAW chain with and without hydrodynamic interaction [32], whereas Kantor and Kardar predicted α = 1 + ν for Rouse dynamics. Their simulation showed that the exponent increased with the polymer length and might eventually reach 1 + ν [33].…”

Effect of Nanopore Length on the Translocation Process of a Biopolymer: Numerical Study

“…They could match the value α = 1.24 as well as the results of the translocation time and velocity with the corresponding experimental values [4]. They also found that the reason for the variation of translocation velocity relative to the polymer length is due to the variation of the fluid drag force acting on the polymer on the cis side [20]. …”

“…We use LBE to include the effect of HI between the polymer and the fluid. This work is the extension of our earlier work [19,20]. The main aim of this study is to know the effect of nanopore length on the polymer’s translocation speed inside the pore and to find the reason for the decrease of the translocation velocity within the elongated nanopore.…”

“…They observed that biopolymers undertake multi-folded configurations when they are passing through wide nanopores [16,17]. Alapati et al [19,20] conducted numerical studies on the translocation process by considering the HI explicitly using LBE. They could match the value α = 1.24 as well as the results of the translocation time and velocity with the corresponding experimental values [4].…”

Simulation by using the lattice Boltzmann method of microscopic particle motion induced by artificial cilia

“…. ., b), which is chosen such that, after the time step Δt, the particle arrives at the n th neighboring grid point [16]. The subscript n denotes the link number of a lattice.…”