Langevin Dynamics Simulations of Polymer Translocation through Nanopores

We investigate the dynamics of polymer translocation through a nanopore using two-dimensional Langevin dynamics simulations. In the absence of an external driving force, we consider a polymer which is initially placed in the middle of the pore and study the escape time τe required for the polymer to completely exit the pore on either side. The distribution of the escape times is wide and has a long tail. We find that τe scales with the chain length N as τe∼N1+2ν, where ν is the Flory exponent. For driven translocation, we concentrate on the influence of the friction coefficient ξ, the driving force E, and the length of the chain N on the translocation time τ, which is defined as the time duration between the first monomer entering the pore and the last monomer leaving the pore. For strong driving forces, the distribution of translocation times is symmetric and narrow without a long tail and τ∼E−1. The influence of ξ depends on the ratio between the driving and frictional forces. For intermediate ξ, we find a crossover scaling for τ with N from τ∼N2ν for relatively short chains to τ∼N1+ν for longer chains. However, for higher ξ, only τ∼N1+ν is observed even for short chains, and there is no crossover behavior. This result can be explained by the fact that increasing ξ increases the Rouse relaxation time of the chain, in which case even relatively short chains have no time to relax during translocation. Our results are in good agreement with previous simulations based on the fluctuating bond lattice model of polymers at intermediate friction values, but reveal additional features of dependency on friction.Peer reviewe

Multivariate multi-way analysis of multi-source data

Motivation: Analysis of variance (ANOVA)-type methods are the default tool for the analysis of data with multiple covariates. These tools have been generalized to the multivariate analysis of high-throughput biological datasets, where the main challenge is the problem of small sample size and high dimensionality. However, the existing multi-way analysis methods are not designed for the currently increasingly important experiments where data is obtained from multiple sources. Common examples of such settings include integrated analysis of metabolic and gene expression profiles, or metabolic profiles from several tissues in our case, in a controlled multi-way experimental setup where disease status, medical treatment, gender and time-series are usual covariates

Dynamics and Kinetic Roughening of Interfaces in Two-Dimensional Forced Wetting

We consider the dynamics and kinetic roughening of wetting fronts in the case of forced wetting driven by a constant mass flux into a 2D disordered medium. We employ a coarse-grained phase field model with local conservation of density, which has been developed earlier for spontaneous imbibition driven by a capillary forces. The forced flow creates interfaces that propagate at a constant average velocity. We first derive a linearized equation of motion for the interface fluctuations using projection methods. From this we extract a time-independent crossover length $\xi_\times$, which separates two regimes of dissipative behavior and governs the kinetic roughening of the interfaces by giving an upper cutoff for the extent of the fluctuations. By numerically integrating the phase field model, we find that the interfaces are superrough with a roughness exponent of $\chi = 1.35 \pm 0.05$, a growth exponent of $\beta = 0.50 \pm 0.02$, and $\xi_\times \sim v^{-1/2}$ as a function of the velocity. These results are in good agreement with recent experiments on Hele-Shaw cells. We also make a direct numerical comparison between the solutions of the full phase field model and the corresponding linearized interface equation. Good agreement is found in spatial correlations, while the temporal correlations in the two models are somewhat different.Comment: 9 pages, 4 figures, submitted to Eur.Phys.J.

Driven polymer translocation through a nanopore: a manifestation of anomalous diffusion

We study the translocation dynamics of a polymer chain threaded through a nanopore by an external force. By means of diverse methods (scaling arguments, fractional calculus and Monte Carlo simulation) we show that the relevant dynamic variable, the translocated number of segments $s(t)$, displays an {\em anomalous} diffusive behavior even in the {\em presence} of an external force. The anomalous dynamics of the translocation process is governed by the same universal exponent $\alpha = 2/(2\nu +2 - \gamma_1)$, where $\nu$ is the Flory exponent and $\gamma_1$ - the surface exponent, which was established recently for the case of non-driven polymer chain threading through a nanopore. A closed analytic expression for the probability distribution function $W(s, t)$, which follows from the relevant {\em fractional} Fokker - Planck equation, is derived in terms of the polymer chain length $N$ and the applied drag force $f$. It is found that the average translocation time scales as $\tau \propto f^{-1}N^{\frac{2}{\alpha} -1}$. Also the corresponding time dependent statistical moments, $\propto t^{\alpha}$ and $\propto t^{2\alpha}$ reveal unambiguously the anomalous nature of the translocation dynamics and permit direct measurement of $\alpha$ in experiments. These findings are tested and found to be in perfect agreement with extensive Monte Carlo (MC) simulations.Comment: 6 pages, 4 figures, accepted to Europhys. Lett; some references were supplemented; typos were correcte

Chaperone-assisted translocation of a polymer through a nanopore

Using Langevin dynamics simulations, we investigate the dynamics of chaperone-assisted translocation of a flexible polymer through a nanopore. We find that increasing the binding energy $\epsilon$ between the chaperone and the chain and the chaperone concentration $N_c$ can greatly improve the translocation probability. Particularly, with increasing the chaperone concentration a maximum translocation probability is observed for weak binding. For a fixed chaperone concentration, the histogram of translocation time $\tau$ has a transition from long-tailed distribution to Gaussian distribution with increasing $\epsilon$. $\tau$ rapidly decreases and then almost saturates with increasing binding energy for short chain, however, it has a minimum for longer chains at lower chaperone concentration. We also show that $\tau$ has a minimum as a function of the chaperone concentration. For different $\epsilon$, a nonuniversal dependence of $\tau$ on the chain length $N$ is also observed. These results can be interpreted by characteristic entropic effects for flexible polymers induced by either crowding effect from high chaperone concentration or the intersegmental binding for the high binding energy.Comment: 10 pages, to appear in J. Am. Chem. So

The Potential and Challenges of Nanopore Sequencing

A nanopore-based device provides single-molecule detection and analytical capabilities that are achieved by electrophoretically driving molecules in solution through a nano-scale pore. The nanopore provides a highly confined space within which single nucleic acid polymers can be analyzed at high throughput by one of a variety of means, and the perfect processivity that can be enforced in a narrow pore ensures that the native order of the nucleobases in a polynucleotide is reflected in the sequence of signals that is detected. Kilobase length polymers (single-stranded genomic DNA or RNA) or small molecules (e.g., nucleosides) can be identified and characterized without amplification or labeling, a unique analytical capability that makes inexpensive, rapid DNA sequencing a possibility. Further research and development to overcome current challenges to nanopore identification of each successive nucleotide in a DNA strand offers the prospect of ‘third generation’ instruments that will sequence a diploid mammalian genome for ~$1,000 in ~24 h.Molecular and Cellular BiologyPhysic