Structural and ultrametric properties of twenty(L-alanine)

We study local energy minima of twenty(L-alanine). The minima are generated using high-temperature Molecular Dynamics and Chain-Growth Monte Carlo simulations, with subsequent minimization. We find that the lower-energy configurations are $\alpha$-helices for a wide range of dielectric constant values $(\epsilon = 1,10,80),$ and that there is no noticeable difference between the distribution of energy minima in $\phi \psi$ space for different values of $\epsilon .$ Ultrametricity tests show that lower-energy $(\alpha$ -helical) $\epsilon =1$ configurations form a set which is ultrametric to a certain degree, providing evidence for the presence of fine structure among those minima. We put forward a heuristic argument for this fine structure. We also find evidence for ultrametricity of a different kind among $\epsilon =10$ and $\epsilon =80$ energy minima. We analyze the distribution of lengths of $\alpha$-helical portions among the minimized configurations and find a persistence phenomenon for the $\epsilon =1$ ones, in qualitative agreement with previous studies of critical lengths. Email contact: [email protected]: Saclay-T93/025 Email: [email protected]

Estimation and comparison of signed symmetric covariation coefficient and generalized association parameter for alpha-stable dependence modeling

Accepté à Communications in Statistics - Theory and methodsInternational audienceIn this paper we study the estimators of two measures of dependence: the signed symmetric covariation coefficient proposed by Garel and Kodia and the generalized association parameter put forward by Paulauskas. In the sub-Gaussian case, the signed symmetric covariation coefficient and the generalized association parameter coincide. The estimator of the signed symmetric covariation coefficient proposed here is based on fractional lower-order moments. The estimator of the generalized association parameter is based on estimation of a stable spectral measure. We investigate the relative performance of these estimators by comparing results from simulations

Directed polymer in a random medium of dimension 1+1 and 1+3: weights statistics in the low-temperature phase

We consider the low-temperature $T<T_c$ disorder-dominated phase of the directed polymer in a random potentiel in dimension 1+1 (where $T_c=\infty$) and 1+3 (where $T_c<\infty$). To characterize the localization properties of the polymer of length $L$, we analyse the statistics of the weights $w_L(\vec r)$ of the last monomer as follows. We numerically compute the probability distributions $P_1(w)$ of the maximal weight $w_L^{max}= max_{\vec r} [w_L(\vec r)]$, the probability distribution $\Pi(Y_2)$ of the parameter $Y_2(L)= \sum_{\vec r} w_L^2(\vec r)$ as well as the average values of the higher order moments $Y_k(L)= \sum_{\vec r} w_L^k(\vec r)$. We find that there exists a temperature $T_{gap}<T_c$ such that (i) for $T<T_{gap}$, the distributions $P_1(w)$ and $\Pi(Y_2)$ present the characteristic Derrida-Flyvbjerg singularities at $w=1/n$ and $Y_2=1/n$ for $n=1,2..$. In particular, there exists a temperature-dependent exponent $\mu(T)$ that governs the main singularities $P_1(w) \sim (1-w)^{\mu(T)-1}$ and $\Pi(Y_2) \sim (1-Y_2)^{\mu(T)-1}$ as well as the power-law decay of the moments $\bar{Y_k(i)} \sim 1/k^{\mu(T)}$. The exponent $\mu(T)$ grows from the value $\mu(T=0)=0$ up to $\mu(T_{gap}) \sim 2$. (ii) for $T_{gap}<T<T_c$, the distribution $P_1(w)$ vanishes at some value $w_0(T)<1$, and accordingly the moments $\bar{Y_k(i)}$ decay exponentially as $(w_0(T))^k$ in $k$. The histograms of spatial correlations also display Derrida-Flyvbjerg singularities for $T<T_{gap}$. Both below and above $T_{gap}$, the study of typical and averaged correlations is in full agreement with the droplet scaling theory.Comment: 13 pages, 29 figure

Numerical study of the disordered Poland-Scheraga model of DNA denaturation

We numerically study the binary disordered Poland-Scheraga model of DNA denaturation, in the regime where the pure model displays a first order transition (loop exponent $c=2.15>2$). We use a Fixman-Freire scheme for the entropy of loops and consider chain length up to $N=4 \cdot 10^5$, with averages over $10^4$ samples. We present in parallel the results of various observables for two boundary conditions, namely bound-bound (bb) and bound-unbound (bu), because they present very different finite-size behaviors, both in the pure case and in the disordered case. Our main conclusion is that the transition remains first order in the disordered case: in the (bu) case, the disorder averaged energy and contact densities present crossings for different values of $N$ without rescaling. In addition, we obtain that these disorder averaged observables do not satisfy finite size scaling, as a consequence of strong sample to sample fluctuations of the pseudo-critical temperature. For a given sample, we propose a procedure to identify its pseudo-critical temperature, and show that this sample then obeys first order transition finite size scaling behavior. Finally, we obtain that the disorder averaged critical loop distribution is still governed by $P(l) \sim 1/l^c$ in the regime $l \ll N$, as in the pure case.Comment: 12 pages, 13 figures. Revised versio

Statistics of low energy excitations for the directed polymer in a 1+d1+d random medium (d=1,2,3d=1,2,3)

We consider a directed polymer of length $L$ in a random medium of space dimension $d=1,2,3$. The statistics of low energy excitations as a function of their size $l$ is numerically evaluated. These excitations can be divided into bulk and boundary excitations, with respective densities $\rho^{bulk}_L(E=0,l)$ and $\rho^{boundary}_L(E=0,l)$. We find that both densities follow the scaling behavior $\rho^{bulk,boundary}_L(E=0,l) = L^{-1-\theta_d} R^{bulk,boundary}(x=l/L)$, where $\theta_d$ is the exponent governing the energy fluctuations at zero temperature (with the well-known exact value $\theta_1=1/3$ in one dimension). In the limit $x=l/L \to 0$, both scaling functions $R^{bulk}(x)$ and $R^{boundary}(x)$ behave as $R^{bulk,boundary}(x) \sim x^{-1-\theta_d}$, leading to the droplet power law $\rho^{bulk,boundary}_L(E=0,l)\sim l^{-1-\theta_d}$ in the regime $1 \ll l \ll L$. Beyond their common singularity near $x \to 0$, the two scaling functions $R^{bulk,boundary}(x)$ are very different : whereas $R^{bulk}(x)$ decays monotonically for $0<x<1$, the function $R^{boundary}(x)$ first decays for $0<x<x_{min}$, then grows for $x_{min}<x<1$, and finally presents a power law singularity $R^{boundary}(x)\sim (1-x)^{-\sigma_d}$ near $x \to 1$. The density of excitations of length $l=L$ accordingly decays as $\rho^{boundary}_L(E=0,l=L)\sim L^{- \lambda_d}$ where $\lambda_d=1+\theta_d-\sigma_d$. We obtain $\lambda_1 \simeq 0.67$, $\lambda_2 \simeq 0.53$ and $\lambda_3 \simeq 0.39$, suggesting the possible relation $\lambda_d= 2 \theta_d$.Comment: 15 pages, 25 figure

On the multifractal statistics of the local order parameter at random critical points : application to wetting transitions with disorder

Disordered systems present multifractal properties at criticality. In particular, as discovered by Ludwig (A.W.W. Ludwig, Nucl. Phys. B 330, 639 (1990)) on the case of diluted two-dimensional Potts model, the moments $\bar{\rho^q(r)}$ of the local order parameter $\rho(r)$ scale with a set $x(q)$ of non-trivial exponents $x(q) \neq q x(1)$. In this paper, we revisit these ideas to incorporate more recent findings: (i) whenever a multifractal measure $w(r)$ normalized over space $\sum_r w(r)=1$ occurs in a random system, it is crucial to distinguish between the typical values and the disorder averaged values of the generalized moments $Y_q =\sum_r w^q(r)$, since they may scale with different generalized dimensions $D(q)$ and $\tilde D(q)$ (ii) as discovered by Wiseman and Domany (S. Wiseman and E. Domany, Phys Rev E {\bf 52}, 3469 (1995)), the presence of an infinite correlation length induces a lack of self-averaging at critical points for thermodynamic observables, in particular for the order parameter. After this general discussion valid for any random critical point, we apply these ideas to random polymer models that can be studied numerically for large sizes and good statistics over the samples. We study the bidimensional wetting or the Poland-Scheraga DNA model with loop exponent $c=1.5$ (marginal disorder) and $c=1.75$ (relevant disorder). Finally, we argue that the presence of finite Griffiths ordered clusters at criticality determines the asymptotic value $x(q \to \infty) =d$ and the minimal value $\alpha_{min}=D(q \to \infty)=d-x(1)$ of the typical multifractal spectrum $f(\alpha)$.Comment: 17 pages, 20 figure

Random wetting transition on the Cayley tree : a disordered first-order transition with two correlation length exponents

We consider the random wetting transition on the Cayley tree, i.e. the problem of a directed polymer on the Cayley tree in the presence of random energies along the left-most bonds. In the pure case, there exists a first-order transition between a localized phase and a delocalized phase, with a correlation length exponent $\nu_{pure}=1$. In the disordered case, we find that the transition remains first-order, but that there exists two diverging length scales in the critical region : the typical correlation length diverges with the exponent $\nu_{typ}=1$, whereas the averaged correlation length diverges with the bigger exponent $\nu_{av}=2$ and governs the finite-size scaling properties. We describe the relations with previously studied models that are governed by the same "Infinite Disorder Fixed Point". For the present model, where the order parameter is the contact density $\theta_L=l_a/L$ (defined as the ratio of the number $l_a$ of contacts over the total length $L$), the notion of "infinite disorder fixed point" means that the thermal fluctuations of $\theta_L$ within a given sample, become negligeable at large scale with respect to sample-to-sample fluctuations. We characterize the statistics over the samples of the free-energy and of the contact density. In particular, exactly at criticality, we obtain that the contact density is not self-averaging but remains distributed over the samples in the thermodynamic limit, with the distribution ${\cal P}_{T_c}(\theta) = 1/(\pi \sqrt{\theta (1-\theta)})$.Comment: 15 pages, 1 figur

Anderson localization transition with long-ranged hoppings : analysis of the strong multifractality regime in terms of weighted Levy sums

For Anderson tight-binding models in dimension $d$ with random on-site energies $\epsilon_{\vec r}$ and critical long-ranged hoppings decaying typically as $V^{typ}(r) \sim V/r^d$, we show that the strong multifractality regime corresponding to small $V$ can be studied via the standard perturbation theory for eigenvectors in quantum mechanics. The Inverse Participation Ratios $Y_q(L)$, which are the order parameters of Anderson transitions, can be written in terms of weighted L\'evy sums of broadly distributed variables (as a consequence of the presence of on-site random energies in the denominators of the perturbation theory). We compute at leading order the typical and disorder-averaged multifractal spectra $\tau_{typ}(q)$ and $\tau_{av}(q)$ as a function of $q$. For $q<1/2$, we obtain the non-vanishing limiting spectrum $\tau_{typ}(q)=\tau_{av}(q)=d(2q-1)$ as $V \to 0^+$. For $q>1/2$, this method yields the same disorder-averaged spectrum $\tau_{av}(q)$ of order $O(V)$ as obtained previously via the Levitov renormalization method by Mirlin and Evers [Phys. Rev. B 62, 7920 (2000)]. In addition, it allows to compute explicitly the typical spectrum, also of order $O(V)$, but with a different $q$-dependence $\tau_{typ}(q) \ne \tau_{av}(q)$ for all $q>q_c=1/2$. As a consequence, we find that the corresponding singularity spectra $f_{typ}(\alpha)$ and $f_{av}(\alpha)$ differ even in the positive region $f>0$, and vanish at different values $\alpha_+^{typ} > \alpha_+^{av}$, in contrast to the standard picture. We also obtain that the saddle value $\alpha_{typ}(q)$ of the Legendre transform reaches the termination point $\alpha_+^{typ}$ where $f_{typ}(\alpha_+^{typ})=0$ only in the limit $q \to +\infty$.Comment: 13 pages, 2 figures, v2=final versio

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

THERMODYNAMICS OF A BROWNIAN BRIDGE POLYMER MODEL IN A RANDOM ENVIRONMENT

We consider a directed random walk making either 0 or $+1$ moves and a Brownian bridge, independent of the walk, conditioned to arrive at point $b$ on time $T$. The Hamiltonian is defined as the sum of the square of increments of the bridge between the moments of jump of the random walk and interpreted as an energy function over the bridge connfiguration; the random walk acts as the random environment. This model provides a continuum version of a model with some relevance to protein conformation. The thermodynamic limit of the specific free energy is shown to exist and to be self-averaging, i.e. it is equal to a trivial --- explicitly computed --- random variable. An estimate of the asymptotic behaviour of the ground state energy is also obtained.Comment: 20 pages, uuencoded postscrip