Response of Single Polymers to Localized Step Strains

In this paper, the response of single three-dimensional phantom and self-avoiding polymers to localized step strains are studied for two cases in the absence of hydrodynamic interactions: (i) polymers tethered at one end with the strain created at the point of tether, and (ii) free polymers with the strain created in the middle of the polymer. The polymers are assumed to be in their equilibrium state before the step strain is created. It is shown that the strain relaxes as a power-law in time $t$ as $t^{-\eta}$. While the strain relaxes as $1/t$ for the phantom polymer in both cases; the self-avoiding polymer relaxes its strain differently in case (i) than in case (ii): as $t^{-(1+\nu)/(1+2\nu)}$ and as $t^{-2/(1+2\nu)}$ respectively. Here $\nu$ is the Flory exponent for the polymer, with value $\approx0.588$ in three dimensions. Using the mode expansion method, exact derivations are provided for the $1/t$ strain relaxation behavior for the phantom polymer. However, since the mode expansion method for self-avoiding polymers is nonlinear, similar theoretical derivations for the self-avoiding polymer proves difficult to provide. Only simulation data are therefore presented in support of the $t^{-(1+\nu)/(1+2\nu)}$ and the $t^{-2/(1+2\nu)}$ behavior. The relevance of these exponents for the anomalous dynamics of polymers are also discussed.Comment: 10 pages, 1 figure; minor errors corrected, introduction slightly modified and references expanded; to appear in Phys. Rev.

Extreme Associated Functions: Optimally Linking Local Extremes to Large-scale Atmospheric Circulation Structures

We present a new statistical method to optimally link local weather extremes to large-scale atmospheric circulation structures. The method is illustrated using July-August daily mean temperature at 2m height (T2m) time-series over the Netherlands and 500 hPa geopotential height (Z500) time-series over the Euroatlantic region of the ECMWF reanalysis dataset (ERA40). The method identifies patterns in the Z500 time-series that optimally describe, in a precise mathematical sense, the relationship with local warm extremes in the Netherlands. Two patterns are identified; the most important one corresponds to a blocking high pressure system leading to subsidence and calm, dry and sunny conditions over the Netherlands. The second one corresponds to a rare, easterly flow regime bringing warm, dry air into the region. The patterns are robust; they are also identified in shorter subsamples of the total dataset. The method is generally applicable and might prove useful in evaluating the performance of climate models in simulating local weather extremes.Comment: 10 pages, 7 figures, 14 eps figure files; to appear in J. Atmos. Chem. Phy

Rouse Modes of Self-avoiding Flexible Polymers

Using a lattice-based Monte Carlo code for simulating self-avoiding flexible polymers in three dimensions in the absence of explicit hydrodynamics, we study their Rouse modes. For self-avoiding polymers, the Rouse modes are not expected to be statistically independent; nevertheless, we demonstrate that numerically these modes maintain a high degree of statistical independence. Based on high-precision simulation data we put forward an approximate analytical expression for the mode amplitude correlation functions for long polymers. From this, we derive analytically and confirm numerically several scaling properties for self-avoiding flexible polymers, such as (i) the real-space end-to-end distance, (ii) the end-to-end vector correlation function, (iii) the correlation function of the small spatial vector connecting two nearby monomers at the middle of a polymer, and (iv) the anomalous dynamics of the middle monomer. Importantly, expanding on our recent work on the theory of polymer translocation, we also demonstrate that the anomalous dynamics of the middle monomer can be obtained from the forces it experiences, by the use of the fluctuation-dissipation theorem.Comment: 16 pages (double spaced), 5 figures, small changes and corrections, to appear in J. Chem. Phy

Fluctuating Fronts as Correlated Extreme Value Problems: An Example of Gaussian Statistics

In this paper, we view fluctuating fronts made of particles on a one-dimensional lattice as an extreme value problem. The idea is to denote the configuration for a single front realization at time $t$ by the set of co-ordinates $\{k_i(t)\}\equiv[k_1(t),k_2(t),...,k_{N(t)}(t)]$ of the constituent particles, where $N(t)$ is the total number of particles in that realization at time $t$. When $\{k_i(t)\}$ are arranged in the ascending order of magnitudes, the instantaneous front position can be denoted by the location of the rightmost particle, i.e., by the extremal value $k_f(t)=\text{max}[k_1(t),k_2(t),...,k_{N(t)}(t)]$. Due to interparticle interactions, $\{k_i(t)\}$ at two different times for a single front realization are naturally not independent of each other, and thus the probability distribution $P_{k_f}(t)$ [based on an ensemble of such front realizations] describes extreme value statistics for a set of correlated random variables. In view of the fact that exact results for correlated extreme value statistics are rather rare, here we show that for a fermionic front model in a reaction-diffusion system, $P_{k_f}(t)$ is Gaussian. In a bosonic front model however, we observe small deviations from the Gaussian.Comment: 6 pages, 3 figures, miniscule changes on the previous version, to appear in Phys. Rev.

Validity of the Brunet-Derrida formula for the speed of pulled fronts with a cutoff

We establish rigorous upper and lower bounds for the speed of pulled fronts with a cutoff. We show that the Brunet-Derrida formula corresponds to the leading order expansion in the cut-off parameter of both the upper and lower bounds. For sufficiently large cut-off parameter the Brunet-Derrida formula lies outside the allowed band determined from the bounds. If nonlinearities are neglected the upper and lower bounds coincide and are the exact linear speed for all values of the cut-off parameter.Comment: 8 pages, 3 figure

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

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

Front Propagation and Diffusion in the A <--> A + A Hard-core Reaction on a Chain

We study front propagation and diffusion in the reaction-diffusion system A $\leftrightharpoons$ A + A on a lattice. On each lattice site at most one A particle is allowed at any time. In this paper, we analyze the problem in the full range of parameter space, keeping the discrete nature of the lattice and the particles intact. Our analysis of the stochastic dynamics of the foremost occupied lattice site yields simple expressions for the front speed and the front diffusion coefficient which are in excellent agreement with simulation results.Comment: 5 pages, 5 figures, to appear in 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