Collapse transitions of a periodic hydrophilic hydrophobic chain

We study a single self avoiding hydrophilic hydrophobic polymer chain, through Monte Carlo lattice simulations. The affinity of monomer $i$ for water is characterized by a (scalar) charge $\lambda_{i}$, and the monomer-water interaction is short-ranged. Assuming incompressibility yields an effective short ranged interaction between monomer pairs $(i,j)$, proportional to $(\lambda_i+\lambda_j)$. In this article, we take $\lambda_i=+1$ (resp. ($\lambda_i=- 1$)) for hydrophilic (resp. hydrophobic) monomers and consider a chain with (i) an equal number of hydro-philic and -phobic monomers (ii) a periodic distribution of the $\lambda_{i}$ along the chain, with periodicity $2p$. The simulations are done for various chain lengths $N$, in $d=2$ (square lattice) and $d=3$ (cubic lattice). There is a critical value $p_c(d,N)$ of the periodicity, which distinguishes between different low temperature structures. For $p >p_c$, the ground state corresponds to a macroscopic phase separation between a dense hydrophobic core and hydrophilic loops. For $p <p_c$ (but not too small), one gets a microscopic (finite scale) phase separation, and the ground state corresponds to a chain or network of hydrophobic droplets, coated by hydrophilic monomers. We restrict our study to two extreme cases, $p \sim O(N)$ and $p\sim O(1)$ to illustrate the physics of the various phase transitions. A tentative variational approach is also presented.Comment: 21 pages, 17 eps figures, accepted for publication in Eur. Phys. J.

Phase diagram of magnetic polymers

We consider polymers made of magnetic monomers (Ising or Heisenberg-like) in a good solvent. These polymers are modeled as self-avoiding walks on a cubic lattice, and the ferromagnetic interaction between the spins carried by the monomers is short-ranged in space. At low temperature, these polymers undergo a magnetic induced first order collapse transition, that we study at the mean field level. Contrasting with an ordinary $\Theta$ point, there is a strong jump in the polymer density, as well as in its magnetization. In the presence of a magnetic field, the collapse temperature increases, while the discontinuities decrease. Beyond a multicritical point, the transition becomes second order and $\Theta$-like. Monte Carlo simulations for the Ising case are in qualitative agreement with these results.Comment: 29 pages, 15 eps figures (one color figure). Submitted for publication to Eur.Phys.J.

Tidally-averaged currents and bedload transport over the Kwinte Bank, southern North Sea

The short-term dynamics of a dredged tidal sandbank (the Kwinte Bank, southern North Sea) are examined, on the basis of field measurements and 1D sediment transport modelling. The field measurements include current data from shipborne Acoustic Doppler Current Profiler (ADCP) and from moorings (ADCP and electromagnetic S4), collected across the bank during a nominal (spring) tidal cycle, and during 7 tidal cycles, respectively. The dynamics of the bank are described in terms of tidally-averaged (residual) currents and (net) bedload transport. The results indicate a predominance of ebb flow during the period of study. Convergence of (net) bedload transport is predicted, from both flanks towards the crest of the bank. The exact location of the sand transport convergence zone varies, in the short-term, according to the prevailing tidal currents. The observation of clockwise veering of the peak ebb and flood currents over the bank indicates that this sediment transport pattern relates, at least partially, to tidal rectification of the flow. In relation to dredging, the present study suggests that the presence of a (dredged) depression at the crest of the bank influences locally the short-term hydrodynamics. The currents are channelised, and the across-bank peak (near-bed) flow is enhanced towards the crest. Net erosion of the depression is predicted, over the tidal cycle considered. More data are needed to evaluate the morphological evolution of the trough over the long-term

Delocalization transition of the selective interface model: distribution of pseudo-critical temperatures

According to recent progress in the finite size scaling theory of critical disordered systems, the nature of the phase transition is reflected in the distribution of pseudo-critical temperatures $T_c(i,L)$ over the ensemble of samples $(i)$ of size $L$. In this paper, we apply this analysis to the delocalization transition of an heteropolymeric chain at a selective fluid-fluid interface. The width $\Delta T_c(L)$ and the shift $[T_c(\infty)-T_c^{av}(L)]$ are found to decay with the same exponent $L^{-1/\nu_{R}}$, where $1/\nu_{R} \sim 0.26$. The distribution of pseudo-critical temperatures $T_c(i,L)$ is clearly asymmetric, and is well fitted by a generalized Gumbel distribution of parameter $m \sim 3$. We also consider the free energy distribution, which can also be fitted by a generalized Gumbel distribution with a temperature dependent parameter, of order $m \sim 0.7$ in the critical region. Finally, the disorder averaged number of contacts with the interface scales at $T_c$ like $L^{\rho}$ with $\rho \sim 0.26 \sim 1/\nu_R$.Comment: 9 pages,6 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

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

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

Probing the tails of the ground state energy distribution for the directed polymer in a random medium of dimension d=1,2,3d=1,2,3 via a Monte-Carlo procedure in the disorder

In order to probe with high precision the tails of the ground-state energy distribution of disordered spin systems, K\"orner, Katzgraber and Hartmann \cite{Ko_Ka_Ha} have recently proposed an importance-sampling Monte-Carlo Markov chain in the disorder. In this paper, we combine their Monte-Carlo procedure in the disorder with exact transfer matrix calculations in each sample to measure the negative tail of ground state energy distribution $P_d(E_0)$ for the directed polymer in a random medium of dimension $d=1,2,3$. In $d=1$, we check the validity of the algorithm by a direct comparison with the exact result, namely the Tracy-Widom distribution. In dimensions $d=2$ and $d=3$, we measure the negative tail up to ten standard deviations, which correspond to probabilities of order $P_d(E_0) \sim 10^{-22}$. Our results are in agreement with Zhang's argument, stating that the negative tail exponent $\eta(d)$ of the asymptotic behavior $\ln P_d (E_0) \sim - | E_0 |^{\eta(d)}$ as $E_0 \to -\infty$ is directly related to the fluctuation exponent $\theta(d)$ (which governs the fluctuations $\Delta E_0(L) \sim L^{\theta(d)}$ of the ground state energy $E_0$ for polymers of length $L$) via the simple formula $\eta(d)=1/(1-\theta(d))$. Along the paper, we comment on the similarities and differences with spin-glasses.Comment: 13 pages, 16 figure

On Heteropolymer Shape Dynamics

We investigate the time evolution of the heteropolymer model introduced by Iori, Marinari and Parisi to describe some of the features of protein folding mechanisms. We study how the (folded) shape of the chain evolves in time. We find that for short times the mean square distance (squared) between chain configurations evolves according to a power law, $D \sim t ^\nu$. We discuss the influence of the quenched disorder (represented by the randomness of the coupling constants in the Lennard-Jones potential) on value of the critical exponent. We find that $\nu$ decreases from $\frac{2}{3}$ to $\frac{1}{2}$ when the strength of the quenched disorder increases.Comment: 12 pages, very simple LaTeX file, 6 figures not included, sorry. SCCS 33