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

Asymptotic Scaling of the Diffusion Coefficient of Fluctuating "Pulled" Fronts

We present a (heuristic) theoretical derivation for the scaling of the diffusion coefficient $D_f$ for fluctuating ``pulled'' fronts. In agreement with earlier numerical simulations, we find that as $N\to\infty$, $D_f$ approaches zero as $1/\ln^3N$, where $N$ is the average number of particles per correlation volume in the stable phase of the front. This behaviour of $D_f$ stems from the shape fluctuations at the very tip of the front, and is independent of the microscopic model.Comment: Some minor algebra corrected, to appear in Rapid Comm., Phys. Rev.

Monomer dynamics of a wormlike chain

We derive the stochastic equations of motion for a tracer that is tightly attached to a semiflexible polymer and confined or agitated by an externally controlled potential. The generalised Langevin equation, the power spectrum, and the mean-square displacement for the tracer dynamics are explicitly constructed from the microscopic equations of motion for a weakly bending wormlike chain by a systematic coarse-graining procedure. Our accurate analytical expressions should provide a convenient starting point for further theoretical developments and for the analysis of various single-molecule experiments and of protein shape fluctuations.Comment: 6 pages, 4 figure

Fluctuating "Pulled" Fronts: the Origin and the Effects of a Finite Particle Cutoff

Recently it has been shown that when an equation that allows so-called pulled fronts in the mean-field limit is modelled with a stochastic model with a finite number $N$ of particles per correlation volume, the convergence to the speed $v^*$ for $N \to \infty$ is extremely slow -- going only as $\ln^{-2}N$. In this paper, we study the front propagation in a simple stochastic lattice model. A detailed analysis of the microscopic picture of the front dynamics shows that for the description of the far tip of the front, one has to abandon the idea of a uniformly translating front solution. The lattice and finite particle effects lead to a ``stop-and-go'' type dynamics at the far tip of the front, while the average front behind it ``crosses over'' to a uniformly translating solution. In this formulation, the effect of stochasticity on the asymptotic front speed is coded in the probability distribution of the times required for the advancement of the ``foremost bin''. We derive expressions of these probability distributions by matching the solution of the far tip with the uniformly translating solution behind. This matching includes various correlation effects in a mean-field type approximation. Our results for the probability distributions compare well to the results of stochastic numerical simulations. This approach also allows us to deal with much smaller values of $N$ than it is required to have the $\ln^{-2}N$ asymptotics to be valid.Comment: 26 pages, 11 figures, to appear in Phys. rev.

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

Anomalous zipping dynamics and forced polymer translocation

We investigate by Monte Carlo simulations the zipping and unzipping dynamics of two polymers connected by one end and subject to an attractive interaction between complementary monomers. In zipping, the polymers are quenched from a high temperature equilibrium configuration to a low temperature state, so that the two strands zip up by closing up a "Y"-fork. In unzipping, the polymers are brought from a low temperature double stranded configuration to high temperatures, so that the two strands separate. Simulations show that the unzipping time, $\tau_u$, scales as a function of the polymer length as $\tau_u \sim L$, while the zipping is characterized by anomalous dynamics $\tau_z \sim L^\alpha$ with $\alpha = 1.37(2)$. This exponent is in good agreement with simulation results and theoretical predictions for the scaling of the translocation time of a forced polymer passing through a narrow pore. We find that the exponent $\alpha$ is robust against variations of parameters and temperature, whereas the scaling of $\tau_z$ as a function of the driving force shows the existence of two different regimes: the weak forcing ($\tau_z \sim 1/F$) and strong forcing ($\tau_z$ independent of $F$) regimes. The crossover region is possibly characterized by a non-trivial scaling in $F$, matching the prediction of recent theories of polymer translocation. Although the geometrical setup is different, zipping and translocation share thus the same type of anomalous dynamics. Systems where this dynamics could be experimentally investigated are DNA (or RNA) hairpins: our results imply an anomalous dynamics for the hairpins closing times, but not for the opening times.Comment: 15 pages, 9 figure

Logarithmic perturbation theory for radial Klein-Gordon equation with screened Coulomb potentials via ℏ\hbar expansions

The explicit semiclassical treatment of logarithmic perturbation theory for the bound-state problem within the framework of the radial Klein-Gordon equation with attractive real-analytic screened Coulomb potentials, contained time-component of a Lorentz four-vector and a Lorentz-scalar term, is developed. Based upon $\hbar$-expansions and suitable quantization conditions a new procedure for deriving perturbation expansions is offered. Avoiding disadvantages of the standard approach, new handy recursion formulae with the same simple form both for ground and excited states have been obtained. As an example, the perturbation expansions for the energy eigenvalues for the Hulth\'en potential containing the vector part as well as the scalar component are considered.Comment: 14 pages, to be submitted to Journal of Physics

CAUSES OF DISPOSAL OF MURRAH BUFFALO FROM AN ORGANISED HERD

The present study comprised of 602 disposal records of adult Murrah buffaloes , spread over a period of 16 years from 1985 to 2000 at NDRI, Karnal, Haryana. Analysed data showed that the reproductive problems (38.62), low milk production (24.01) and udder problems (22.76) were the three major reasons of culling in adult Murrah buffaloes . The culling of cows due to involuntary reason (reproductive problems, udder problems and locomotive disorders) accounted for nearly 63.68 percent of total culling in Murrah buffaloes in the NDRI herd. The data revealed that maximum mortality occurred due to digestive problems accounting for 30.89 percent followed by cardio-vascular problems (26.02 percent), respiratory problems (21.14 percent), parasitic problems (8.13 percent) and uro-genital problems (5.69 percent). The results showed that there is a scope for further improvement in production and reproductive efficiency through better monitoring of reproduction and udder health status of the buffaloes. The high involuntary culling rate not only makes the dairy enterprises economically less profitable but also reduces the genetic improvement by lowering the selection differential for milk production

The Weakly Pushed Nature of "Pulled" Fronts with a Cutoff

The concept of pulled fronts with a cutoff $\epsilon$ has been introduced to model the effects of discrete nature of the constituent particles on the asymptotic front speed in models with continuum variables (Pulled fronts are the fronts which propagate into an unstable state, and have an asymptotic front speed equal to the linear spreading speed $v^*$ of small linear perturbations around the unstable state). In this paper, we demonstrate that the introduction of a cutoff actually makes such pulled fronts weakly pushed. For the nonlinear diffusion equation with a cutoff, we show that the longest relaxation times $\tau_m$ that govern the convergence to the asymptotic front speed and profile, are given by $\tau_m^{-1} \simeq [(m+1)^2-1] \pi^2 / \ln^2 \epsilon$, for $m=1,2,...$.Comment: 4 pages, 2 figures, submitted to Brief Reports, Phys. Rev.