arXiv subjects

Jean-Charles Walter

Publications and source records attributed to Jean-Charles Walter.

25 records · Page 2Linked to original sources

arXiv2012

Fractional Brownian motion and the critical dynamics of zipping polymers

We consider two complementary polymer strands of length $L$ attached by a common end monomer. The two strands bind through complementary monomers and at low temperatures form a double stranded conformation (zipping), while at high temperature they dissociate (unzipping). This is a simple model of DNA (or RNA) hairpin formation. Here we investigate the dynamics of the strands at the equilibrium critical temperature $T=T_c$ using Monte Carlo Rouse dynamics. We find that the dynamics is anomalous, with a characteristic time scaling as $τ\sim L^{2.26(2)}$, exceeding the Rouse time $\sim L^{2.18}$. We investigate the probability distribution function, the velocity autocorrelation function, the survival probability and boundary behaviour of the underlying stochastic process. These quantities scale as expected from a fractional Brownian motion with a Hurst exponent $H=0.44(1)$. We discuss similarities and differences with unbiased polymer translocation.

cond-mat.stat-mech↗

arXiv2011

Relaxation at finite temperature in Fully-Frustrated Ising Models

We consider by means of Monte Carlo simulations the relaxation in the paramagnetic phase of the anti-ferromagnetic Ising model on a triangular lattice and of a fully-frustrated Ising model on a square lattice. In contradistinction to previous studies of the second model, we show that spin-spin correlation functions do not decay with a stretched-exponential law at low temperature but that both models display an exponential decay with logarithmic corrections that are interpreted as the signature of topological defects.

cond-mat.stat-mech↗

arXiv2011

Equilibrium winding angle of a polymer around a bar

The winding angle probability distribution of a planar self-avoiding walk has been known exactly since a long time: it has a gaussian shape with a variance growing as $<θ^2>\sim \ln L$. For the three-dimensional case of a walk winding around a bar, the same scaling is suggested, based on a first-order epsilon-expansion. We tested this three-dimensional case by means of Monte Carlo simulations up to length $L\approx25\,000$ and using exact enumeration data for sizes $L\le20$. We find that the variance of the winding angle scales as $<θ^2>\sim (\ln L)^{2α}$, with $α=0.75(1)$. The ratio $γ= <θ^4>/<θ^2>^2=3.74(5)$ is incompatible with the gaussian value $γ=3$, but consistent with the observation that the tail of the probability distribution function $p(θ)$ is found to decrease slower than a gaussian function. These findings are at odds with the existing first-order $ε$-expansion results.

cond-mat.stat-mech↗

arXiv2011

Nonequilibrium effects in DNA microarrays: a multiplatform study

It has recently been shown that in some DNA microarrays the time needed to reach thermal equilibrium may largely exceed the typical experimental time, which is about 15h in standard protocols (Hooyberghs et al. Phys. Rev. E 81, 012901 (2010)). In this paper we discuss how this breakdown of thermodynamic equilibrium could be detected in microarray experiments without resorting to real time hybridization data, which are difficult to implement in standard experimental conditions. The method is based on the analysis of the distribution of fluorescence intensities I from different spots for probes carrying base mismatches. In thermal equilibrium and at sufficiently low concentrations, log I is expected to be linearly related to the hybridization free energy $ΔG$ with a slope equal to $1/RT_{exp}$, where $T_{exp}$ is the experimental temperature and R is the gas constant. The breakdown of equilibrium results in the deviation from this law. A model for hybridization kinetics explaining the observed experimental behavior is discussed, the so-called 3-state model. It predicts that deviations from equilibrium yield a proportionality of $\log I$ to $ΔG/RT_{eff}$. Here, $T_{eff}$ is an effective temperature, higher than the experimental one. This behavior is indeed observed in some experiments on Agilent arrays. We analyze experimental data from two other microarray platforms and discuss, on the basis of the results, the attainment of equilibrium in these cases. Interestingly, the same 3-state model predicts a (dynamical) saturation of the signal at values below the expected one at equilibrium.

q-bio.BM↗

arXiv2009

Numerical investigation of the aging of the Fully-Frustrated XY model

We study the out-of-equilibrium dynamics of the fully-frustrated XY model. At equilibrium, this model undergoes two phase transitions at two very close temperatures: a Kosterlitz-Thouless topological transition and a second-order phase transition between a paramagnetic phase and a low-temperature phase where the chiralities of the lattice plaquettes are anti-ferromagnetically ordered. We compute by Monte Carlo simulations two-time spin-spin and chirality-chirality autocorrelation and response functions. From the dynamics of the spin waves in the low temperature phase, we extract the temperature-dependent exponent $η$. We provide evidences for logarithmic corrections above the Kosterlitz-Thouless temperature and interpret them as a manifestation of free topological defects. Our estimates of the autocorrelation exponent and the fluctuation-dissipation ratio differ from the XY values, while $η(T_{\rm KT})$ lies at the boundary of the error bar. Indications for logarithmic corrections at the second-order critical temperature are presented. However, the coupling between angles and chiralities is still strong and explains why autocorrelation exponent and fluctuation-dissipation ratio are far from the Ising values and seems stable.

cond-mat.stat-mech↗

arXiv2008

Extended Scaling in High Dimensions

We apply and test the recently proposed "extended scaling" scheme in an analysis of the magnetic susceptibility of Ising systems above the upper critical dimension. The data are obtained by Monte Carlo simulations using both the conventional Wolff cluster algorithm and the Prokof'ev-Svistunov worm algorithm. As already observed for other models, extended scaling is shown to extend the high-temperature critical scaling regime over a range of temperatures much wider than that achieved conventionally. It allows for an accurate determination of leading and sub-leading scaling indices, critical temperatures and amplitudes of the confluent corrections.

cond-mat.stat-mech↗

arXiv2008

Logarithmic corrections in the aging of the fully-frustrated Ising model

We study the dynamics of the critical two-dimensional fully-frustrated Ising model by means of Monte Carlo simulations. The dynamical exponent is estimated at equilibrium and is shown to be compatible with the value $z_c=2$. In a second step, the system is prepared in the paramagnetic phase and then quenched at its critical temperature $T_c=0$. Numerical evidences for the existence of logarithmic corrections in the aging regime are presented. These corrections may be related to the topological defects observed in other fully-frustrated models. The autocorrelation exponent is estimated to be $λ=d$ as for the Ising chain quenched at $T_c=0$.

cond-mat.stat-mech↗