On the Helix-Coil transition in grafted chains

The helix-coil transition is modified by grafting to a surface. This modification is studied for short peptides capable of forming $\alpha$-helices. Three factors are involved: (i) the grafting can induced change of the boundary free energy of the helical domain (ii) the van der Waals attraction between the helices and (iii) the crowding induced stretching of the coils. As a result the helix-coil transition acquires ``all or nothing'' characteristics. In addition the transition temperature is elevated and the transition itself sharpens as the grafting density increases.Comment: 6 pages, 1 figures, europhys.sty and euromacro.sty Submitted to Europhys. Let

Reply to A. Louis Comment

Reply to A. Louis Comment: Fluid-solid phase-separation in hard-sphere mixtures is unrelated to bond-percolationComment: Reply to a comment of PRL 82 p960 To be published in PR

Rigorous Bounds to Retarded Learning

We show that the lower bound to the critical fraction of data needed to infer (learn) the orientation of the anisotropy axis of a probability distribution, determined by Herschkowitz and Opper [Phys.Rev.Lett. 86, 2174 (2001)], is not always valid. If there is some structure in the data along the anisotropy axis, their analysis is incorrect, and learning is possible with much less data points.Comment: 1 page, 1 figure. Comment accepted for publication in Physical Review Letter

Finite size scaling of the bayesian perceptron

We study numerically the properties of the bayesian perceptron through a gradient descent on the optimal cost function. The theoretical distribution of stabilities is deduced. It predicts that the optimal generalizer lies close to the boundary of the space of (error-free) solutions. The numerical simulations are in good agreement with the theoretical distribution. The extrapolation of the generalization error to infinite input space size agrees with the theoretical results. Finite size corrections are negative and exhibit two different scaling regimes, depending on the training set size. The variance of the generalization error vanishes for $N \rightarrow \infty$ confirming the property of self-averaging.Comment: RevTeX, 7 pages, 7 figures, submitted to Phys. Rev.

Kovacs effect and fluctuation-dissipation relations in 1D kinetically constrained models

Strong and fragile glass relaxation behaviours are obtained simply changing the constraints of the kinetically constrained Ising chain from symmetric to purely asymmetric. We study the out-of-equilibrium dynamics of those two models focusing on the Kovacs effect and the fluctuation--dissipation relations. The Kovacs or memory effect, commonly observed in structural glasses, is present for both constraints but enhanced with the asymmetric ones. Most surprisingly, the related fluctuation-dissipation (FD) relations satisfy the FD theorem in both cases. This result strongly differs from the simple quenching procedure where the asymmetric model presents strong deviations from the FD theorem.Comment: 13 pages and 7 figures. To be published in J. Phys.

Phase transitions in optimal unsupervised learning

We determine the optimal performance of learning the orientation of the symmetry axis of a set of P = alpha N points that are uniformly distributed in all the directions but one on the N-dimensional sphere. The components along the symmetry breaking direction, of unitary vector B, are sampled from a mixture of two gaussians of variable separation and width. The typical optimal performance is measured through the overlap Ropt=B.J* where J* is the optimal guess of the symmetry breaking direction. Within this general scenario, the learning curves Ropt(alpha) may present first order transitions if the clusters are narrow enough. Close to these transitions, high performance states can be obtained through the minimization of the corresponding optimal potential, although these solutions are metastable, and therefore not learnable, within the usual bayesian scenario.Comment: 9 pages, 8 figures, submitted to PRE, This new version of the paper contains one new section, Bayesian versus optimal solutions, where we explain in detail the results supporting our claim that bayesian learning may not be optimal. Figures 4 of the first submission was difficult to understand. We replaced it by two new figures (Figs. 4 and 5 in this new version) containing more detail

Optical conductivity of URu2_2Si2_2 in the Kondo Liquid and Hidden-Order Phases

We measured the polarized optical conductivity of URu$_2$Si$_2$ from room temperature down to 5 K, covering the Kondo state, the coherent Kondo liquid regime, and the hidden-order phase. The normal state is characterized by an anisotropic behavior between the ab plane and c axis responses. The ab plane optical conductivity is strongly influenced by the formation of the coherent Kondo liquid: a sharp Drude peak develops and a hybridization gap at 12 meV leads to a spectral weight transfer to mid-infrared energies. The c axis conductivity has a different behavior: the Drude peak already exists at 300 K and no particular anomaly or gap signature appears in the coherent Kondo liquid regime. When entering the hidden-order state, both polarizations see a dramatic decrease in the Drude spectral weight and scattering rate, compatible with a loss of about 50 % of the carriers at the Fermi level. At the same time a density-wave like gap appears along both polarizations at about 6.5 meV at 5 K. This gap closes respecting a mean field thermal evolution in the ab plane. Along the c axis it remains roughly constant and it "fills up" rather than closing.Comment: 10 pages, 7 figure

The Effects of Stacking on the Configurations and Elasticity of Single Stranded Nucleic Acids

Stacking interactions in single stranded nucleic acids give rise to configurations of an annealed rod-coil multiblock copolymer. Theoretical analysis identifies the resulting signatures for long homopolynucleotides: A non monotonous dependence of size on temperature, corresponding effects on cyclization and a plateau in the extension force law. Explicit numerical results for poly(dA) and poly(rU) are presented.Comment: 4 pages and 2 figures. Accepted in Phys. Rev. E Rapid Com

Topological Quantum Glassiness

Quantum tunneling often allows pathways to relaxation past energy barriers which are otherwise hard to overcome classically at low temperatures. However, this is not always the case. In this paper we provide simple exactly solvable examples where the barriers each system encounters on its approach to lower and lower energy states become increasingly large and eventually scale with the system size. If the environment couples locally to the physical degrees of freedom in the system, tunnelling under large barriers requires processes whose order in perturbation theory is proportional to the width of the barrier. This results in quantum relaxation rates that are exponentially suppressed in system size: For these quantum systems, no physical bath can provide a mechanism for relaxation that is not dynamically arrested at low temperatures. The examples discussed here are drawn from three dimensional generalizations of Kitaev's toric code, originally devised in the context of topological quantum computing. They are devoid of any local order parameters or symmetry breaking and are thus examples of topological quantum glasses. We construct systems that have slow dynamics similar to either strong or fragile glasses. The example with fragile-like relaxation is interesting in that the topological defects are neither open strings or regular open membranes, but fractal objects with dimension $d^* = ln 3/ ln 2$.Comment: (18 pages, 4 figures, v2: typos and updated figure); Philosophical Magazine (2011

Pocket Monte Carlo algorithm for classical doped dimer models

We study the correlations of classical hardcore dimer models doped with monomers by Monte Carlo simulation. We introduce an efficient cluster algorithm, which is applicable in any dimension, for different lattices and arbitrary doping. We use this algorithm for the dimer model on the square lattice, where a finite density of monomers destroys the critical confinement of the two-monomer problem. The monomers form a two-component plasma located in its high-temperature phase, with the Coulomb interaction screened at finite densities. On the triangular lattice, a single pair of monomers is not confined. The monomer correlations are extremely short-ranged and hardly change with doping.Comment: 6 pages, REVTeX