Comment on " A simple model for DNA denaturation"

The replacment of mutual avoidance of polymers by a long-range interaction of the type proposed by Garel etal (Europhys. Lett. 55, 132 (2001), cond-mat/0101058) is inconsistent with the prevalent renormalization group arguments.Comment: 2 pages, Comment on Garel etal. Europhys. Lett 55, 132(2001) cond-mat/0101058. Appeared in Europhys Let

Overlap properties and adsorption transition of two Hamiltonian paths

We consider a model of two (fully) compact polymer chains, coupled through an attractive interaction. These compact chains are represented by Hamiltonian paths (HP), and the coupling favors the existence of common bonds between the chains. Using a ($n=0$ component) spin representation for these paths, we show the existence of a phase transition for strong coupling (i.e. at low temperature) towards a ``frozen'' phase where one chain is completely adsorbed onto the other. By performing a Legendre transform, we obtain the probability distribution of overlaps. The fraction of common bonds between two HP, i.e. their overlap $q$, has both lower ($q_m$) and upper ($q_M$) bounds. This means in particuliar that two HP with overlap greater than $q_M$ coincide. These results may be of interest in (bio)polymers and in optimization problems.Comment: 13 pages, 2 figure

Phase diagram of a semiflexible polymer chain in a θ\theta solvent: application to protein folding

We consider a lattice model of a semiflexible homopolymer chain in a bad solvent. Beside the temperature $T$, this model is described by (i) a curvature energy $\varepsilon_h$, representing the stiffness of the chain (ii) a nearest-neighbour attractive energy $\varepsilon_v$, representing the solvent (iii) the monomer density $\rho={N \over \Omega}$, where $N$ and $\Omega$ denote respectively the number of monomers and the number of lattice sites. This model is a simplified view of the protein folding problem, which encompasses the geometrical competition between secondary structures (the curvature term modelling helix formation) and the global compactness (modeled here by the attractive energy), but contains no side chain information...Comment: 17 pages, plain tex, 2 figures available upon reques

A novel approach for the assessment of morphological evolution based on observed water levels in tide-dominated estuaries

Assessing the impacts of both natural (e.g., tidal forcing from the ocean) and human-induced changes (e.g., dredging for navigation, land reclamation) on estuarine morphology is particularly important for the protection and management of the estuarine environment. In this study, a novel analytical approach is proposed for the assessment of estuarine morphological evolution in terms of tidally averaged depth on the basis of the observed water levels along the estuary. The key lies in deriving a relationship between wave celerity and tidal damping or amplification. For given observed water levels at two gauging stations, it is possible to have a first estimation of both wave celerity (distance divided by tidal travelling time) and tidal damping or amplification rate (tidal range difference divided by distance), which can then be used to predict the morphological changes via an inverse analytical model for tidal hydrodynamics. The proposed method is applied to the Lingdingyang Bay of the Pearl River Estuary, located on the southern coast of China, to analyse the historical development of the tidal hydrodynamics and morphological evolution. The analytical results show surprisingly good correspondence with observed water depth and volume in this system. The merit of the proposed method is that it provides a simple approach for understanding the decadal evolution of the estuarine morphology through the use of observed water levels, which are usually available and can be easily measured.National Key R&D of China (Grant No. 2016YFC0402601), National Natural Science Foundation of China (Grant No. 51979296, 51709287, 41706088, 41476073), Fundamental Research Funds for the Central Universities (No.18lgpy29) and from the Water Resource Science and Technology Innovation Program of Guangdong Province (Grant No. 2016-20, 2016-21). The work of the second author was supported by FCT research contracts IF/00661/2014/CP1234.info:eu-repo/semantics/submittedVersio

Statistics of first-passage times in disordered systems using backward master equations and their exact renormalization rules

We consider the non-equilibrium dynamics of disordered systems as defined by a master equation involving transition rates between configurations (detailed balance is not assumed). To compute the important dynamical time scales in finite-size systems without simulating the actual time evolution which can be extremely slow, we propose to focus on first-passage times that satisfy 'backward master equations'. Upon the iterative elimination of configurations, we obtain the exact renormalization rules that can be followed numerically. To test this approach, we study the statistics of some first-passage times for two disordered models : (i) for the random walk in a two-dimensional self-affine random potential of Hurst exponent $H$, we focus on the first exit time from a square of size $L \times L$ if one starts at the square center. (ii) for the dynamics of the ferromagnetic Sherrington-Kirkpatrick model of $N$ spins, we consider the first passage time $t_f$ to zero-magnetization when starting from a fully magnetized configuration. Besides the expected linear growth of the averaged barrier $\bar{\ln t_{f}} \sim N$, we find that the rescaled distribution of the barrier $(\ln t_{f})$ decays as $e^{- u^{\eta}}$ for large $u$ with a tail exponent of order $\eta \simeq 1.72$. This value can be simply interpreted in terms of rare events if the sample-to-sample fluctuation exponent for the barrier is $\psi_{width}=1/3$.Comment: 8 pages, 4 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

Effects of tidal-forcing variations on tidal properties along a narrow convergent estuary

A 1D analytical framework is implemented in a narrow convergent estuary that is 78 km in length (the Guadiana, Southern Iberia) to evaluate the tidal dynamics along the channel, including the effects of neap-spring amplitude variations at the mouth. The close match between the observations (damping from the mouth to ∼ 30 km, shoaling upstream) and outputs from semi-closed channel solutions indicates that the M2 tide is reflected at the estuary head. The model is used to determine the contribution of reflection to the dynamics of the propagating wave. This contribution is mainly confined to the upper one third of the estuary. The relatively constant mean wave height along the channel (< 10% variations) partly results from reflection effects that also modify significantly the wave celerity and the phase difference between tidal velocity and elevation (contradicting the definition of an “ideal” estuary). Furthermore, from the mouth to ∼ 50 km, the variable friction experienced by the incident wave at neap and spring tides produces wave shoaling and damping, respectively. As a result, the wave celerity is largest at neap tide along this lower reach, although the mean water level is highest in spring. Overall, the presented analytical framework is useful for describing the main tidal properties along estuaries considering various forcings (amplitude, period) at the estuary mouth and the proposed method could be applicable to other estuaries with small tidal amplitude to depth ratio and negligible river discharge.info:eu-repo/semantics/publishedVersio

Adsorption of polymers on a fluctuating surface

We study the adsorption of polymer chains on a fluctuating surface. Physical examples are provided by polymer adsorption at the rough interface between two non-miscible liquids, or on a membrane. In a mean-field approach, we find that the self--avoiding chains undergo an adsorption transition, accompanied by a stiffening of the fluctuating surface. In particular, adsorption of polymers on a membrane induces a surface tension and leads to a strong suppression of roughness.Comment: REVTEX, 9 pages, no figure

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

Lyapunov exponents as a dynamical indicator of a phase transition

We study analytically the behavior of the largest Lyapunov exponent $\lambda_1$ for a one-dimensional chain of coupled nonlinear oscillators, by combining the transfer integral method and a Riemannian geometry approach. We apply the results to a simple model, proposed for the DNA denaturation, which emphasizes a first order-like or second order phase transition depending on the ratio of two length scales: this is an excellent model to characterize $\lambda_1$ as a dynamical indicator close to a phase transition.Comment: 8 Pages, 3 Figure