arXiv subjects

Enzo Orlandini

Publications and source records attributed to Enzo Orlandini.

85 records · Page 5Linked to original sources

arXiv2002

A simple model of DNA denaturation and mutually avoiding walks statistics

Recently Garel, Monthus and Orland (Europhys. Lett. v 55, 132 (2001)) considered a model of DNA denaturation in which excluded volume effects within each strand are neglected, while mutual avoidance is included. Using an approximate scheme they found a first order denaturation. We show that a first order transition for this model follows from exact results for the statistics of two mutually avoiding random walks, whose reunion exponent is c > 2, both in two and three dimensions. Analytical estimates of c due to the interactions with other denaturated loops, as well as numerical calculations, indicate that the transition is even sharper than in models where excluded volume effects are fully incorporated. The probability distribution of distances between homologous base pairs decays as a power law at the transition.

cond-mat.stat-mech↗

arXiv2002

Roles of stiffness and excluded volume in DNA denaturation

The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated loops of length l, $P \sim l^{-c}$. If excluded volume effects are fully taken into account, c= 2.10(4) is consistent with a first order transition. The stiffness of the double stranded chain has the effect of sharpening the transition, if it is continuous, but not of changing its order and the value of the exponent c, which is also robust with respect to inclusion of specific base-pair sequence heterogeneities.

cond-mat.stat-mech↗

arXiv2001

Mechanical denaturation of DNA: existence of a low temperature denaturation

Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs of self avoiding walks (SAW) which are pulled apart by a force applied at the two extremities. The whole phase diagram is spanned by extensive Monte Carlo (MC) simulations and the existence of a low temperature denaturation is confirmed. The basic features of the phase diagram and the re-entrant phase boundary are also obtained with a simple heuristic argument based on an energy-entropy estimate.

cond-mat.stat-mech↗

arXiv2001

Peculiar scaling of self-avoiding walk contacts

The nearest neighbor contacts between the two halves of an N-site lattice self-avoiding walk offer an unusual example of scaling random geometry: for N going to infinity they are strictly finite in number but their radius of gyration Rc is power law distributed, ~ Rc^{-τ}, where τ>1 is a novel exponent characterizing universal behavior. A continuum of diverging lengths scales is associated to the Rc distribution. A possibly super-universal τ=2 is also expected for the contacts of a self-avoiding or random walk with a confining wall.

cond-mat.stat-mech↗

arXiv2001

Phase Ordering in Nematic Liquid Crystals

We study the kinetics of the nematic-isotropic transition in a two-dimensional liquid crystal by using a lattice Boltzmann scheme that couples the tensor order parameter and the flow consistently. Unlike in previous studies, we find the time dependences of the correlation function, energy density, and the number of topological defects obey dynamic scaling laws with growth exponents that, within the numerical uncertainties, agree with the value 1/2 expected from simple dimensional analysis. We find that these values are not altered by the hydrodynamic flow. In addition, by examining shallow quenches, we find that the presence of orientational disorder can inhibit amplitude ordering.

cond-mat.soft↗

arXiv2000

Simulations of liquid crystals in Poiseuille flow

Lattice Boltzmann simulations are used to explore the behavior of liquid crystals subject to Poiseuille flow. In the nematic regime at low shear rates we find two possible steady state configurations of the director field. The selected state depends on both the shear rate and the history of the sample. For both director configurations there is clear evidence of shear-thinning, a decrease in the viscosity with increasing shear rate. Moreover, at very high shear rates or when the order parameter is large, the system transforms to a log-rolling state with boundary layers that may exhibit oscillatory behavior.

cond-mat.soft↗

arXiv2000

Lattice Boltzmann Simulations of Liquid Crystal Hydrodynamics

We describe a lattice Boltzmann algorithm to simulate liquid crystal hydrodynamics. The equations of motion are written in terms of a tensor order parameter. This allows both the isotropic and the nematic phases to be considered. Backflow effects and the hydrodynamics of topological defects are naturally included in the simulations, as are viscoelastic properties such as shear-thinning and shear-banding.

cond-mat.soft↗

arXiv2000

Zipping and collapse of diblock copolymers

Using exact enumeration methods and Monte Carlo simulations we study the phase diagram relative to the conformational transitions of a two dimensional diblock copolymer. The polymer is made of two homogeneous strands of monomers of different species which are joined to each other at one end. We find that depending on the values of the energy parameters in the model, there is either a first order collapse from a swollen to a compact phase of spiral type, or a continuous transition to an intermediate zipped phase followed by a first order collapse at lower temperatures. Critical exponents of the zipping transition are computed and their exact values are conjectured on the basis of a mapping onto percolation geometry, thanks to recent results on path-crossing probabilities.

cond-mat.stat-mech↗

arXiv1999

Sequence randomness and polymer collapse transitions

Contrary to expectations based on Harris' criterion, chain disorder with frustration can modify the universality class of scaling at the theta transition of heteropolymers. This is shown for a model with random two-body potentials in 2D on the basis of exact enumeration and accurate Monte Carlo results. When frustration grows beyond a certain finite threshold, the temperature below which disorder becomes relevant coincides with the theta one and scaling exponents definitely start deviating from those valid for homopolymers.

cond-mat.soft↗

arXiv1999

Monte Carlo Results for Projected Self-Avoiding Polygons: A Two-dimensional Model for Knotted Polymers

We introduce a two-dimensional lattice model for the description of knotted polymer rings. A polymer configuration is modeled by a closed polygon drawn on the square diagonal lattice, with possible crossings describing pairs of strands of polymer passing on top of each other. Each polygon configuration can be viewed as the two- dimensional projection of a particular knot. We study numerically the statistics of large polygons with a fixed knot type, using a generalization of the BFACF algorithm for self-avoiding walks. This new algorithm incorporates both the displacement of crossings and the three types of Reidemeister transformations preserving the knot topology. Its ergodicity within a fixed knot type is not proven here rigorously but strong arguments in favor of this ergodicity are given together with a tentative sketch of proof. Assuming this ergodicity, we obtain numerically the following results for the statistics of knotted polygons: In the limit of a low crossing fugacity, we find a localization along the polygon of all the primary factors forming the knot. Increasing the crossing fugacity gives rise to a transition from a self-avoiding walk to a branched polymer behavior.

cond-mat.stat-mech↗

arXiv1997

Reaction-Diffusion Processes from Equivalent Integrable Quantum Chains

One-dimensional reaction-diffusion systems are mapped through a similarity transformation onto integrable (and a priori non-stochastic) quantum chains. Time-dependent properties of these chemical models can then be found exactly. The reaction-diffusion processes related to free fermion systems with site-independent interactions are classified. The time-dependence of the mean particle density is calculated. Furthermore new integrable stochastic processes related to the Heisenberg XXZ chain are identified and the relaxation times for the particle density and density correlation for these systems are found.

cond-mat.stat-mech↗

arXiv1995

A Lattice Boltzmann Model of Binary Fluid Mixture

We introduce a lattice Boltzmann for simulating an immiscible binary fluid mixture. Our collision rules are derived from a macroscopic thermodynamic description of the fluid in a way motivated by the Cahn-Hilliard approach to non-equilibrium dynamics. This ensures that a thermodynamically consistent state is reached in equilibrium. The non-equilibrium dynamics is investigated numerically and found to agree with simple analytic predictions in both the one-phase and the two-phase region of the phase diagram.

comp-gas↗

arXiv1995

EQUIVALENCES BETWEEN STOCHASTIC SYSTEMS

Time-dependent correlation functions of (unstable) particles undergoing biased or unbiased diffusion, coagulation and annihilation are calculated. This is achieved by similarity transformations between different stochastic models and between stochastic and soluble {\em non-stochastic} models. The results agree with experiments on one-dimensional annihilation-coagulation processes.

cond-mat↗