Driven polymer translocation through nanopores: slow versus fast dynamics

We investigate the dynamics of polymer translocation through nanopores under external driving by 3D Langevin Dynamics simulations, focusing on the scaling of the average translocation time $\tau$ versus the length of the polymer, $\tau\sim N^{\alpha}$. For slow translocation, i.e., under low driving force and/or high friction, we find $\alpha \approx 1+\nu \approx 1.588$ where $\nu$ denotes the Flory exponent. In contrast, $\alpha\approx 1.37$ is observed for fast translocation due to the highly deformed chain conformation on the trans side, reflecting a pronounced non-equilibrium situation. The dependence of the translocation time on the driving force is given by $\tau \sim F^{-1}$ and $\tau \sim F^{-0.80}$ for slow and fast translocation, respectively. These results clarify the controversy on the magnitude of the scaling exponent $\alpha$ for driven translocation.Comment: 6 pages, 7 figures, to appear in EPL (Europhysics Letters

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 has been shown previously to have different interactions with the pore. We study DNA with repeating blocks $A_nC_n$ for various values of $n$, and find that the translocation time depends strongly on the {\em block length} $2n$ as well as on the {\em orientation} of which base entering the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences are contained in the periodicity of the residence time of the individual nucleotides inside the pore.Comment: 4 pages, 4 figures, minor change

Dynamics of DNA translocation through an attractive nanopore

We investigate the dynamics of single-stranded DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions to study how the translocation dynamics depend on the details of the DNA sequences. We consider a coarse-grained model of DNA built from two bases A and C, having different base-pore interactions, e.g., a strong (weak) attractive force between the pore and the base A (C) inside the pore. From a series of studies on hetero-DNAs with repeat units AmCn, we find that the translocation time decreases exponentially as a function of the volume fraction fC of the base C. For longer A sequences with fC⩽0.5, the translocation time strongly depends on the orientation of DNA, namely which base enters the pore first. Our studies clearly demonstrate that for a DNA of certain length N with repeat units AmCn, the pattern exhibited by the waiting times of the individual bases and their periodicity can unambiguously determine the values of m, n, and N, respectively. Therefore, a prospective experimental realization of this phenomenon may lead to fast and efficient sequence detection.Peer reviewe

Polymer translocation through a nanopore under a pulling force

We investigate polymer translocation through a nanopore under a pulling force using Langevin dynamics simulations. We concentrate on the influence of the chain length N and the pulling force F on the translocation time τ. The distribution of τ is symmetric and narrow for strong F. We find that τ∼N2 and translocation velocity v∼N−1 for both moderate and strong F. For infinitely wide pores, three regimes are observed for τ as a function of F. With increasing F, τ is independent of F for weak F, and then τ∼F−2+ν−1 for moderate F, where ν is the Flory exponent, which finally crosses over to τ∼F−1 for strong force. For narrow pores, even for moderate force τ∼F−1. Finally, the waiting time, for monomer s and monomer s+1 to exit the pore, has a maximum for s close to the end of the chain, in contrast to the case where the polymer is driven by an external force within the pore.Peer reviewe

Heteropolymer translocation through nanopores

We investigate the translocation dynamics of heteropolymers driven through a nanopore using a constant temperature Langevin thermostat. Specifically, we consider heteropolymers consisting of two types of monomers labeled A and B, which are distinguished by the magnitude of the driving force that they experience inside the pore. From a series of studies on polymers with sequences AnBn+m we identify both universal as well as sequence specific properties of the translocating chains. We find that the scaling of the average translocation time as a function of the chain length N remains unaffected by the heterogeneity, while the residence time of each bead is a strong function of the sequence for short repeat units. We further discover that for a symmetric heteropolymer AnBn of fixed length, the pattern exhibited by the residence time of the individual monomer has striking similarity with an interference pattern for an optical grating with N/(2n) slits. These results are relevant for designing nanopore based sequencing techniques.Comment: 13 Pages, 6 Figure

Translocation Dynamics with Attractive Nanopore-Polymer Interactions

Using Langevin dynamics simulations, we investigate the influence of polymer-pore interactions on the dynamics of biopolymer translocation through nanopores. We find that an attractive interaction can significantly change the translocation dynamics. This can be understood by examining the three components of the total translocation time $\tau \approx \tau_1+\tau_2+\tau_3$ corresponding to the initial filling of the pore, transfer of polymer from the \textit{cis} side to the \textit{trans} side, and emptying of the pore, respectively. We find that the dynamics for the last process of emptying of the pore changes from non-activated to activated in nature as the strength of the attractive interaction increases, and $\tau_3$ becomes the dominant contribution to the total translocation time for strong attraction. This leads to a new dependence of $\tau$ as a function of driving force and chain length. Our results are in good agreement with recent experimental findings, and provide a possible explanation for the different scaling behavior observed in solid state nanopores {\it vs.} that for the natural $\alpha$-hemolysin channel.Comment: 8 pages, 11 figure

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 translocation probability. At the same time, it also increases translocation time slowly for weak attraction while exponential dependence is observed for 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 non-monotonic behavior as a function of the chain length. Our simulations results are in good agreement with recent experimental data.Comment: 4 pages, 5 figures, Submitted to Phys. Rev. Let

Polymer translocation through a nanopore under an applied external field

We investigate the dynamics of polymer translocation through a nanopore under an externally applied field using the 2D fluctuating bond model with single-segment Monte Carlo moves. We concentrate on the influence of the field strength $E$, length of the chain $N$, and length of the pore $L$ on forced translocation. As our main result, we find a crossover scaling for the translocation time $\tau$ with the chain length from $\tau \sim N^{2\nu}$ for relatively short polymers to $\tau \sim N^{1 + \nu}$ for longer chains, where $\nu$ is the Flory exponent. We demonstrate that this crossover is due to the change in the dependence of the translocation velocity v on the chain length. For relatively short chains $v \sim N^{- \nu}$, which crosses over to $v \sim N^{- 1}$ for long polymers. The reason for this is that with increasing $N$ there is a high density of segments near the exit of the pore, which slows down the translocation process due to slow relaxation of the chain. For the case of a long nanopore for which $R_\parallel$, the radius of gyration $R_{g}$ along the pore, is smaller than the pore length, we find no clear scaling of the translocation time with the chain length. For large $N$, however, the asymptotic scaling $\tau \sim N^{1 + \nu}$ is recovered. In this regime, $\tau$ is almost independent of $L$. We have previously found that for a polymer, which is initially placed in the middle of the pore, there is a minimum in the escape time for $R_\parallel \approx L$. We show here that this minimum persists for a weak fields $E$ such that $EL$ is less than some critical value, but vanishes for large values of $EL$.Comment: 25 Pages, 10 figures. Submitted to J. Chem. Phys. J. Chem. Phys. 124, in press (2006