Force induced stretched state: Effects of temperature

A model of self avoiding walks with suitable constraint has been developed to study the effect of temperature on a single stranded DNA (ssDNA) in the constant force ensemble. Our exact calculations for small chains show that the extension (reaction co-ordinate) may increase or decrease with the temperature depending upon the applied force. The simple model developed here which incorporates semi-microscopic details of base direction provide an explanation of the force induced transitions in ssDNA as observed in experiments.Comment: 5 pages, 8 figures, RevTex

Experimental evidence of accelerated energy transfer in turbulence

We investigate the vorticity dynamics in a turbulent vortex using scattering of acoustic waves. Two ultrasonic beams are adjusted to probe simultaneously two spatial scales in a given volume of the flow, thus allowing a dual channel recording of the dynamics of coherent vorticity structures. Our results show that this allows to measure the average energy transfer time between different spatial length scales, and that such transfer goes faster at smaller scales.Comment: 5 pages, 5 figure

Interplay between the Beale-Kato-Majda theorem and the analyticity-strip method to investigate numerically the incompressible Euler singularity problem

Numerical simulations of the incompressible Euler equations are performed using the Taylor-Green vortex initial conditions and resolutions up to $4096^3$. The results are analyzed in terms of the classical analyticity strip method and Beale, Kato and Majda (BKM) theorem. A well-resolved acceleration of the time-decay of the width of the analyticity strip $\delta(t)$ is observed at the highest resolution for $3.7<t<3.85$ while preliminary 3D visualizations show the collision of vortex sheets. The BKM criterium on the power-law growth of supremum of the vorticity, applied on the same time-interval, is not inconsistent with the occurrence of a singularity around $t \simeq 4$. These new findings lead us to investigate how fast the analyticity strip width needs to decrease to zero in order to sustain a finite-time singularity consistent with the BKM theorem. A new simple bound of the supremum norm of vorticity in terms of the energy spectrum is introduced and used to combine the BKM theorem with the analyticity-strip method. It is shown that a finite-time blowup can exist only if $\delta(t)$ vanishes sufficiently fast at the singularity time. In particular, if a power law is assumed for $\delta(t)$ then its exponent must be greater than some critical value, thus providing a new test that is applied to our $4096^3$ Taylor-Green numerical simulation. Our main conclusion is that the numerical results are not inconsistent with a singularity but that higher-resolution studies are needed to extend the time-interval on which a well-resolved power-law behavior of $\delta(t)$ takes place, and check whether the new regime is genuine and not simply a crossover to a faster exponential decay

A one-dimensional model for theoretical analysis of single molecule experiments

In this paper we compare two polymer stretching experiments. The outcome of both experiments is a force-extension relation. We use a one-dimensional model to show that in general the two quantities are not equal. In certain limits, however, both force-extension relations coincide.Comment: 11 pages, 5 figure

Effects of Eye-phase in DNA unzipping

The onset of an "eye-phase" and its role during the DNA unzipping is studied when a force is applied to the interior of the chain. The directionality of the hydrogen bond introduced here shows oscillations in force-extension curve similar to a "saw-tooth" kind of oscillations seen in the protein unfolding experiments. The effects of intermediates (hairpins) and stacking energies on the melting profile have also been discussed.Comment: RevTeX v4, 9 pages with 7 eps figure

DNA unzipped under a constant force exhibits multiple metastable intermediates

Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the unzipped length as a function of time is characterized by jumps during which the strands separate rapidly, followed by long pauses where the number of separated base pairs remains constant. Here, we report previously uncharacterized observations of this striking behavior carried out on a number of identical single molecules simultaneously. When several single lphage molecules are subject to the same applied force, the pause positions are reproducible in each. This reproducibility shows that the positions and durations of the pauses in unzipping provide a sequence-dependent molecular fingerprint. For small forces, the DNA remains in a partially unzipped state for at least several hours. For larger forces, the separation is still characterized by jumps and pauses, but the double-stranded DNA will completely unzip in less than 30 min

Non-equilibrium Lorentz gas on a curved space

The periodic Lorentz gas with external field and iso-kinetic thermostat is equivalent, by conformal transformation, to a billiard with expanding phase-space and slightly distorted scatterers, for which the trajectories are straight lines. A further time rescaling allows to keep the speed constant in that new geometry. In the hyperbolic regime, the stationary state of this billiard is characterized by a phase-space contraction rate, equal to that of the iso-kinetic Lorentz gas. In contrast to the iso-kinetic Lorentz gas where phase-space contraction occurs in the bulk, the phase-space contraction rate here takes place at the periodic boundaries

Ideal evolution of MHD turbulence when imposing Taylor-Green symmetries

We investigate the ideal and incompressible magnetohydrodynamic (MHD) equations in three space dimensions for the development of potentially singular structures. The methodology consists in implementing the four-fold symmetries of the Taylor-Green vortex generalized to MHD, leading to substantial computer time and memory savings at a given resolution; we also use a re-gridding method that allows for lower-resolution runs at early times, with no loss of spectral accuracy. One magnetic configuration is examined at an equivalent resolution of $6144^3$ points, and three different configurations on grids of $4096^3$ points. At the highest resolution, two different current and vorticity sheet systems are found to collide, producing two successive accelerations in the development of small scales. At the latest time, a convergence of magnetic field lines to the location of maximum current is probably leading locally to a strong bending and directional variability of such lines. A novel analytical method, based on sharp analysis inequalities, is used to assess the validity of the finite-time singularity scenario. This method allows one to rule out spurious singularities by evaluating the rate at which the logarithmic decrement of the analyticity-strip method goes to zero. The result is that the finite-time singularity scenario cannot be ruled out, and the singularity time could be somewhere between $t=2.33$ and $t=2.70.$ More robust conclusions will require higher resolution runs and grid-point interpolation measurements of maximum current and vorticity.Comment: 18 pages, 13 figures, 2 tables; submitted to Physical Review