Hydrodynamic correlations in the translocation of biopolymer through a nanopore: theory and multiscale simulations

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 $\alpha$ $\approx 1.2$. The actual value of the exponent from the simulations is $\alpha =1.28\pm 0.01$, 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.

arXiv comment7 pages, 5 figures. to appear in Phys. Rev. E

References in corpus (12)

• Fast DNA translocation through a solid-state nanopore
• Polymer Translocation througha Pore in a Membrane
• Driven Polymer Translocation Through a Narrow Pore
• Anomalous Dynamics of Forced Translocation
• Influence of polymer-pore interactions on translocation
• Langevin Dynamics Simulations of Polymer Translocation through Nanopores
• Driven polymer translocation through a nanopore: a manifestation of anomalous diffusion
• Multiscale coupling of molecular dynamics and hydrodynamics: application to DNA translocation through a nanopore
• Quantized current blockade and hydrodynamic correlations in biopolymer translocation through nanopores: evidence from multiscale simulations
• Elasticity from the Force Network Ensemble in Granular Media
• Translocation of polymers with folded configurations across nanopores
• Exploring DNA translocation through a nanopore via a multiscale Lattice-Boltzmann Molecular-Dynamics methodology

Cited by in corpus (22)

• Driven polymer translocation through nanopores: slow versus fast dynamics
• Autonomous Motility of Active Filaments due to Spontaneous Flow-Symmetry Breaking
• Dynamics of forced biopolymer translocation
• Scaling theory of driven polymer translocation
• Process Time Distribution of Driven Polymer Transport
• Mesoscale Structures at Complex Fluid-Fluid Interfaces: a Novel Lattice Boltzmann / Molecular Dynamics Coupling
• Through the Eye of the Needle: Recent Advances in Understanding Biopolymer Translocation
• Mesoscopic simulations at the physics-chemistry-biology interface
• Dynamics of DNA translocation through an attractive nanopore
• The chain sucker: translocation dynamics of a polymer chain into a long narrow channel driven by longitudinal flow
• Simulations of Two-Dimensional Unbiased Polymer Translocation Using the Bond Fluctuation Model
• Multiscale method based on coupled lattice-Boltzmann and Langevin-dynamics for direct simulation of nanoscale particle/polymer suspensions in complex flows
• Non-Equilibrium Dynamics of Single polymer Adsorption to Solid Surfaces
• Pore-polymer interaction reveals non-universality in forced polymer translocation
• Dynamics of driven translocation of semiflexible polymers
• Quantification of tension to explain bias dependence of driven polymer translocation dynamics
• Current fluctuations in nanopores: the effects of electrostatic and hydrodynamic interactions
• Quantized biopolymer translocation through nanopores: departure from simple scaling
• Response of Single Polymers to Localized Step Strains
• Force-dependent diffusion coefficient of molecular Brownian ratchets
• Coupling Lattice Boltzmann with Atomistic Dynamics for the multiscale simulation of nano-biological flows
• Numerical simulation of conformational variability in biopolymer translocation through wide nanopores