Pore-blockade Times for Field-Driven Polymer Translocation

We study pore blockade times for a translocating polymer of length $N$, driven by a field $E$ across the pore in three dimensions. The polymer performs Rouse dynamics, i.e., we consider polymer dynamics in the absence of hydrodynamical interactions. We find that the typical time the pore remains blocked during a translocation event scales as $\sim N^{(1+2\nu)/(1+\nu)}/E$, where $\nu\simeq0.588$ is the Flory exponent for the polymer. In line with our previous work, we show that this scaling behaviour stems from the polymer dynamics at the immediate vicinity of the pore -- in particular, the memory effects in the polymer chain tension imbalance across the pore. This result, along with the numerical results by several other groups, violates the lower bound $\sim N^{1+\nu}/E$ suggested earlier in the literature. We discuss why this lower bound is incorrect and show, based on conservation of energy, that the correct lower bound for the pore-blockade time for field-driven translocation is given by $\eta N^{2\nu}/E$, where $\eta$ is the viscosity of the medium surrounding the polymer.Comment: 14 pages, 6 figures, slightly shorter than the previous version; to appear in J. Phys.: Cond. Ma

Probabilistic Phase Space Trajectory Description for Anomalous Polymer Dynamics

It has been recently shown that the phase space trajectories for the anomalous dynamics of a tagged monomer of a polymer --- for single polymeric systems such as phantom Rouse, self-avoiding Rouse, Zimm, reptation, and translocation through a narrow pore in a membrane; as well as for many-polymeric system such as polymer melts in the entangled regime --- is robustly described by the Generalized Langevin Equation (GLE). Here I show that the probability distribution of phase space trajectories for all these classical anomalous dynamics for single polymers is that of a fractional Brownian motion (fBm), while the dynamics for polymer melts between the entangled regime and the eventual diffusive regime exhibits small, but systematic deviations from that of a fBm.Comment: 8 pages, two figures, 3 eps figure files, minor changes, supplementary material included moved to the appendix, references expanded, to appear in J. Phys.: Condens. Matte

Amplitude and Frequency Spectrum of Thermal Fluctuations of A Translocating RNA Molecule

Using a combination of theory and computer simulations, we study the translocation of an RNA molecule, pulled through a solid-state nanopore by an optical tweezer, as a method to determine its secondary structure. The resolution with which the elements of the secondary structure can be determined is limited by thermal fluctuations. We present a detailed study of these thermal fluctuations, including the frequency spectrum, and show that these rule out single-nucleotide resolution under the experimental conditions which we simulated. Two possible ways to improve this resolution are strong stretching of the RNA with a back-pulling voltage across the membrane, and stiffening of the translocated part of the RNA by biochemical means.Comment: Significantly expanded compared to previous version, 13 pages, 4 figures, to appear in J. Phys.: Condens. Matte

Polymers grafted to porous membranes

We study a single flexible chain molecule grafted to a membrane which has pores of size slightly larger than the monomer size. On both sides of the membrane there is the same solvent. When this solvent is good, i.e. when the polymer is described by a self avoiding walk, it can fairly easily penetrate the membrane, so that the average number of membrane crossings tends, for chain length $N\to\infty$, to a positive constant. The average numbers of monomers on either side of the membrane diverges in this limit, although their ratio becomes infinite. For a poor solvent, in contrast, the entire polymer is located, for large $N$, on one side of the membrane. For good and for theta solvents (ideal polymers) we find scaling laws, whose exponents can in the latter case be easily understood from the behaviour of random walks.Comment: 4 pages, 6 figure

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

Polymer translocation out of planar confinements

Polymer translocation in three dimensions out of planar confinements is studied in this paper. Three membranes are located at z = -h, z = 0 and z = h(1). These membranes are impenetrable, except for the middle one at z = 0, which has a narrow pore. A polymer with length N is initially sandwiched between the membranes placed at z = -h and z = 0 and translocates through this pore. We consider strong confinement (small h), where the polymer is essentially reduced to a two-dimensional polymer, with a radius of gyration scaling as R-g((2D)) similar to N-nu 2D; here, nu(2D) = 0.75 is the Flory exponent in two dimensions. The polymer performs Rouse dynamics. On the basis of theoretical analysis and high-precision simulation data, we show that in the unbiased case h = h(1), the dwell time tau(d) scales as N2+nu 2D, in perfect agreement with our previously published theoretical framework. For h(1) = infinity, the situation is equivalent to field-driven translocation in two dimensions. We show that in this case tau(d) scales as N-2 nu 2D, in agreement with several existing numerical results in the literature. This result violates the earlier reported lower bound N1+nu for tau(d) for field-driven translocation. We argue, on the basis of energy conservation, that the actual lower bound for tau(d) is N-2 nu and not N1+nu. Polymer translocation in such theoretically motivated geometries thus resolves some of the most fundamental issues that have been the subject of much heated debate in recent times

Anomalous dynamics of unbiased polymer translocation through a narrow pore

We consider a polymer of length N translocating through a narrow pore in the absence of external fields. The characterization of its purportedly anomalous dynamics has so far remained incomplete. We show that the polymer dynamics is anomalous up to the Rouse time tau(R) similar to N1+2 nu ., with a mean square displacement through the pore consistent with t((1+nu)/( 1+ 2 nu)), with nu approximate to 0.588 the Flory exponent. This is shown to be directly related to a decay over time of the excess monomer density near the pore as t(-(1+nu)/(1+2 nu)) exp(-t/tau(R)). Beyond the Rouse time, translocation becomes diffusive. In consequence of this, the dwell time tau(d), the time a translocating polymer typically spends within the pore, scales as N2+nu, in contrast to previous claims

Unwinding dynamics of double-stranded polymers

We consider the unwinding of two lattice polymer strands of length N that are initially wound around each other in a double-helical conformation and evolve through Rouse dynamics. The problem relates to quickly bringing a double-stranded polymer well above its melting temperature, i.e., the binding interactions between the strands are neglected, and the strands separate from each other as it is entropically favorable for them to do so. The strands unwind by rotating around each other until they separate. We find that the process proceeds from the ends inward; intermediate conformations can be characterized by a tightly wound inner part, from which loose strands are sticking out, with length l 3c t^0.39. The total time needed for the two strands to unwind scales as a power of N as \u3c4_u 3c N^2.57\ub10.03. We present a theoretical argument, which suggests that during this unwinding process, these loose strands are far out of equilibrium