A thin film model for corotational Jeffreys fluids under strong slip

We derive a thin film model for viscoelastic liquids under strong slip which obey the stress tensor dynamics of corotational Jeffreys fluids.Comment: 3 pages, submitted to Eur. Phys. J.

Compositionality, stochasticity and cooperativity in dynamic models of gene regulation

We present an approach for constructing dynamic models for the simulation of gene regulatory networks from simple computational elements. Each element is called a ``gene gate'' and defines an input/output-relationship corresponding to the binding and production of transcription factors. The proposed reaction kinetics of the gene gates can be mapped onto stochastic processes and the standard ode-description. While the ode-approach requires fixing the system's topology before its correct implementation, expressing them in stochastic pi-calculus leads to a fully compositional scheme: network elements become autonomous and only the input/output relationships fix their wiring. The modularity of our approach allows to pass easily from a basic first-level description to refined models which capture more details of the biological system. As an illustrative application we present the stochastic repressilator, an artificial cellular clock, which oscillates readily without any cooperative effects.Comment: 15 pages, 8 figures. Accepted by the HFSP journal (13/09/07

Stability domains of actin genes and genomic evolution

In eukaryotic genes the protein coding sequence is split into several fragments, the exons, separated by non-coding DNA stretches, the introns. Prokaryotes do not have introns in their genome. We report the calculations of stability domains of actin genes for various organisms in the animal, plant and fungi kingdoms. Actin genes have been chosen because they have been highly conserved during evolution. In these genes all introns were removed so as to mimic ancient genes at the time of the early eukaryotic development, i.e. before introns insertion. Common stability boundaries are found in evolutionary distant organisms, which implies that these boundaries date from the early origin of eukaryotes. In general boundaries correspond with introns positions of vertebrates and other animals actins, but not much for plants and fungi. The sharpest boundary is found in a locus where fungi, algae and animals have introns in positions separated by one nucleotide only, which identifies a hot-spot for insertion. These results suggest that some introns may have been incorporated into the genomes through a thermodynamic driven mechanism, in agreement with previous observations on human genes. They also suggest a different mechanism for introns insertion in plants and animals.Comment: 9 Pages, 7 figures. Phys. Rev. E in pres

Exons, introns and DNA thermodynamics

The genes of eukaryotes are characterized by protein coding fragments, the exons, interrupted by introns, i.e. stretches of DNA which do not carry any useful information for the protein synthesis. We have analyzed the melting behavior of randomly selected human cDNA sequences obtained from the genomic DNA by removing all introns. A clear correspondence is observed between exons and melting domains. This finding may provide new insights in the physical mechanisms underlying the evolution of genes.Comment: 4 pages, 8 figures - Final version as published. See also Phys. Rev. Focus 15, story 1

Slip vs viscoelasticity in dewetting thin films

Ultrathin polymer films on non-wettable substrates display dynamic features which have been attributed to either viscoelastic or slip effects. Here we show that in the weak and strong slip regime effects of viscoelastic relaxation are either absent or not distinguishable from slip effects. Strong-slip modifies the fastest unstable mode in a rupturing thin film, which questions the standard approach to reconstruct the effective interface potential from dewetting experiments.Comment: 4 pages, submitted to Eur. Phys. J.

Crackling Noise, Power Spectra and Disorder Induced Critical Scaling

Crackling noise is observed in many disordered non-equilibrium systems in response to slowly changing external conditions. Examples range from Barkhausen noise in magnets to acoustic emission in martensites to earthquakes. Using the non-equilibrium random field Ising model, we derive universal scaling predictions for the dependence of the associated power spectra on the disorder and field sweep rate, near an underlying disorder-induced non-equilibrium critical point. Our theory applies to certain systems in which the crackling noise results from avalanche-like response to a (slowly) increasing external driving force, and is characterized by a broad power law scaling regime of the power spectra. We compute the critical exponents and discuss the relevance of the results to experiments.Comment: 27 Latex Pages, 14 eps figure

Order of the phase transition in models of DNA thermal denaturation

We examine the behavior of a model which describes the melting of double-stranded DNA chains. The model, with displacement-dependent stiffness constants and a Morse on-site potential, is analyzed numerically; depending on the stiffness parameter, it is shown to have either (i) a second-order transition with "nu_perpendicular" = - beta = 1, "nu_parallel" = gamma/2 = 2 (characteristic of short range attractive part of the Morse potential) or (ii) a first-order transition with finite melting entropy, discontinuous fraction of bound pairs, divergent correlation lengths, and critical exponents "nu_perpendicular" = - beta = 1/2, "nu_parallel" = gamma/2 = 1.Comment: 4 pages of Latex, including 4 Postscript figures. To be published in Phys. Rev. Let

Numerical evidence for relevance of disorder in a Poland-Scheraga DNA denaturation model with self-avoidance: Scaling behavior of average quantities

We study numerically the effect of sequence heterogeneity on the thermodynamic properties of a Poland-Scheraga model for DNA denaturation taking into account self-avoidance, i.e. with exponent c_p=2.15 for the loop length probability distribution. In complement to previous on-lattice Monte Carlo like studies, we consider here off-lattice numerical calculations for large sequence lengths, relying on efficient algorithmic methods. We investigate finite size effects with the definition of an appropriate intrinsic length scale x, depending on the parameters of the model. Based on the occurrence of large enough rare regions, for a given sequence length N, this study provides a qualitative picture for the finite size behavior, suggesting that the effect of disorder could be sensed only with sequence lengths diverging exponentially with x. We further look in detail at average quantities for the particular case x=1.3, ensuring through this parameter choice the correspondence between the off-lattice and the on-lattice studies. Taken together, the various results can be cast in a coherent picture with a crossover between a nearly pure system like behavior for small sizes N < 1000, as observed in the on-lattice simulations, and the apparent asymptotic behavior indicative of disorder relevance, with an (average) correlation length exponent \nu_r >= 2/d (=2).Comment: Latex, 33 pages with 15 postscript figure

From nonwetting to prewetting: the asymptotic behavior of 4He drops on alkali substrates

We investigate the spreading of 4He droplets on alkali surfaces at zero temperature, within the frame of Finite Range Density Functional theory. The equilibrium configurations of several 4He_N clusters and their asymptotic trend with increasing particle number N, which can be traced to the wetting behavior of the quantum fluid, are examined for nanoscopic droplets. We discuss the size effects, inferring that the asymptotic properties of large droplets correspond to those of the prewetting film

Effects of confinement and surface enhancement on superconductivity

Within the Ginzburg-Landau approach a theoretical study is performed of the effects of confinement on the transition to superconductivity for type-I and type-II materials with surface enhancement. The superconducting order parameter is characterized by a negative surface extrapolation length $b$. This leads to an increase of the critical field $H_{c3}$ and to a surface critical temperature in zero field, $T_{cs}$, which exceeds the bulk $T_c$. When the sample is {\em mesoscopic} of linear size $L$ the surface induces superconductivity in the interior for $T T_{cs}$. In analogy with adsorbed fluids, superconductivity in thin films of type-I materials is akin to {\em capillary condensation} and competes with the interface delocalization or "wetting" transition. The finite-size scaling properties of capillary condensation in superconductors are scrutinized in the limit that the ratio of magnetic penetration depth to superconducting coherence length, $\kappa \equiv \lambda/\xi$, goes to zero, using analytic calculations. While standard finite-size scaling holds for the transition in non-zero magnetic field $H$, an anomalous critical-point shift is found for H=0. The increase of $T_c$ for H=0 is calculated for mesoscopic films, cylindrical wires, and spherical grains of type-I and type-II materials. Surface curvature is shown to induce a significant increase of $T_c$, characterized by a shift $T_c(R)-T_c(\infty)$ inversely proportional to the radius $R$.Comment: 37 pages, 5 figures, accepted for PR