Aniket Bhattacharya

Influence of polymer-pore interactions on translocation.

We investigate the influence of polymer-pore interactions on the translocation dynamics using Langevin dynamics simulations. An attractive interaction can greatly improve the translocation probability. At the same time, it also increases the translocation time slowly for a weak attraction while an exponential dependence is observed for a strong attraction. For fixed driving force and chain length the histogram of translocation time has a transition from Gaussian distribution to long-tailed distribution with increasing attraction. Under a weak driving force and a strong attractive force, both the translocation time and the residence time in the pore show a nonmonotonic behavior as a function of the chain length. Our simulations results are in good agreement with recent experimental data.

Sequence dependence of DNA translocation through a nanopore

We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built from two types of bases A and C, which have been shown previously to have different interactions with the pore. We study DNA with repeating blocks A(n)C(n) for various values of n and find that the translocation time depends strongly on the block length 2n as well as on the orientation of which base enters the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through a nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences is contained in the periodicity of the residence time of the individual nucleotides inside the pore.

Dynamical scaling exponents for polymer translocation through a nanopore

Kaifu Luo,1 Tapio Ala-Nissila, 1, 2 See-Chen Ying, 2 Pawel Pomorski, 3 and Mikko Karttunen3 Laboratory of Physics, Helsinki University of Technology, P.O. Box 1100, FIN-02015 TKK, Espoo, Finland Department of Physics, Box 1843, Brown University, Providence, Rhode Island 02912-1843, USA Department of Applied Mathematics, The University of Western Ontario, London, Ontario, Canada (Dated: August 21, 2007)We determine the scaling exponents of polymer translocation (PT) through a nanopore by extensive computer simulations of various microscopic models for chain lengths extending up to N=800 in some cases. We focus on the scaling of the average PT time tau approximately Nalpha and the mean-square change of the PT coordinate, approximately tbeta. We find alpha=1+2nu and beta=2/alpha for unbiased PT in two dimensions (2D) and three dimensions (3D). The relation alphabeta=2 holds for driven PT in 2D, with a crossover from alpha approximately 2nu for short chains to alpha approximately 1+nu for long chains. This crossover is, however, absent in 3D where alpha=1.42+/-0.01 and alphabeta approximately 2.2 for N approximately 40-800.

Scaling exponents of forced polymer translocation through a nanopore

We investigate several properties of a translocating homopolymer through a thin pore driven by an external field present inside the pore only using Langevin Dynamics (LD) simulations in three dimensions (3D). Motivated by several recent theoretical and numerical studies that are apparently at odds with each other, we estimate the exponents describing the scaling with chain length (Nof the average translocation time

Unifying model of driven polymer translocation

\ensuremath \langle\tau\rangle

Heteropolymer translocation through nanopores

, the average velocity of the center of mass

Out-of-equilibrium characteristics of a forced translocating chain through a nanopore

\ensuremath \langle v_{{\rm CM}}\rangle

Influence of non-universal effects on dynamical scaling in driven polymer translocation

, and the effective radius of gyration

Translocation dynamics with attractive nanopore-polymer interactions

\ensuremath \langle {R}_g\rangle

Influence of pore friction on the universal aspects of driven polymer translocation

during the translocation process defined as