Abstract
We investigate the process of biopolymer translocation through a narrow pore using a multiscale approach which explicitly accounts for the hydrodynamic interactions of the molecule with the surrounding solvent. The simulations confirm that the coupling of the correlated molecular motion to hydrodynamics results in significant acceleration of the translocation process. Based on these results, we construct a phenomenological model which incorporates the statistical and dynamical features of the translocation process and predicts a power-law dependence of the translocation time on the polymer length with an exponent alpha approximately 1.2. The actual value of the exponent from the simulations is alpha=1.28+/-0.01, which is in excellent agreement with experimental measurements of DNA translocation through a nanopore, and is not sensitive to the choice of parameters in the simulation. The mechanism behind the emergence of such a robust exponent is related to the interplay between the longitudinal and transversal dynamics of both translocated and untranslocated segments. The connection to the macroscopic picture involves separating the contributions from the blob shrinking and shifting processes, which are both essential to the translocation dynamics.
Highlights
Translocation of biopolymers, such as DNA and RNA, plays a vital role in many important biological processes, such as viral infection by phages, inter-bacterial DNA transduction or gene therapy [1]
Compared to other numerical methods, the present lattice Boltzmann-Molecular Dynamics (LB-MD) scheme has certain computational advantages, namely, it permits to take into account self-consistent hydrodynamic correlations at computational cost scaling linearly with the polymer length
N0 i=1 γ(ui vi), where again vi is the bead velocity, ui is the fluid velocity at the Summarizing, we have investigated the process of polymer translocation through a narrow pore using a multiscale approach which explicitly accounts for the hydromonomer location and γ is the friction coefficient
Summary
Translocation of biopolymers, such as DNA and RNA, plays a vital role in many important biological processes, such as viral infection by phages, inter-bacterial DNA transduction or gene therapy [1]. Some universal features of the translocation process can be analyzed by means of suitably simplified statistical models [7, 8, 9, 10], and non-hydrodynamic coarse-grained or microscopic models [11, 12, 13, 14], a quantitative description of this complex phenomenon calls for realistic, stateof-the-art computational modeling Work along these lines has been recently reported by several groups, beginning with the first multiscale simulations by the present authors [15, 16], followed by Langevin dynamics simulations [17] and more recently by coupled molecular-fluid dynamics [18, 20].
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