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

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

2008-09-05

arxiv.org/abs/0809.1035v1

Phys. Rev. E, 78 036704 (2008)

Physics

Biological Physics

7 pages, 5 figures. to appear in Phys. Rev. E

Scientific paper

10.1103/PhysRevE.78.036704

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.

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