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Directed paths have been used extensively in the scientific literature as a model of a linear polymer. Such paths models in particular the conformational entropy of a linear polymer and the effects it has on the free energy. These directed models are simplifi
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The enumeration of lattice paths in wedges poses unique mathematical challenges. These models are not translationally invariant, and the absence of this symmetry complicates both the derivation of a functional recurrence for the generating function, and solving for it. In this paper we consider a model of partially directed walks from the origin in the square lattice confined to both a symmetric wedge defined by $Y = pm pX$, and an asymmetric wedge defined by the lines $Y= pX$ and Y=0, where $p > 0$ is an integer. We prove that the growth constant for all these models is equal to $1+sqrt{2}$, independent of the angle of the wedge. We derive functional recursions for both models, and obtain explicit expressions for the generating functions when $p=1$. From these we find asymptotic formulas for the number of partially directed paths of length $n$ in a wedge when $p=1$. The functional recurrences are solved by a variation of the kernel method, which we call the ``iterated kernel method. This method appears to be similar to the obstinate kernel method used by Bousquet-Melou. This method requires us to consider iterated compositions of the roots of the kernel. These compositions turn out to be surprisingly tractable, and we are able to find simple explicit expressions for them. However, in spite of this, the generating functions turn out to be similar in form to Jacobi $theta$-functions, and have natural boundaries on the unit circle.
In this Letter we present evidences of the occurrence of a tricritical filling transition for an Ising model in a linear wedge. We perform Monte Carlo simulations in a double wedge where antisymmetric fields act at the top and bottom wedges, decorated with specific field acting only along the wegde axes. A finite-size scaling analysis of these simulations shows a novel critical phenomenon, which is distinct from the critical filling. We adapt to tricritical filling the phenomenological theory which successfully was applied to the finite-size analysis of the critical filling in this geometry, observing good agreement between the simulations and the theoretical predictions for tricritical filling.
By extending the Kac-Rice approach to manifolds of finite internal dimension, we show that the mean number $leftlanglemathcal{N}_mathrm{tot}rightrangle$ of all possible equilibria (i.e. force-free configurations, a.k.a. equilibrium points) of an elastic line (directed polymer), confined in a harmonic well and submitted to a quenched random Gaussian potential in dimension $d=1+1$, grows exponentially $leftlanglemathcal{N}_mathrm{tot}rightranglesimexp{(r,L)}$ with its length $L$. The growth rate $r$ is found to be directly related to the generalised Lyapunov exponent (GLE) which is a moment-generating function characterising the large-deviation type fluctuations of the solution to the initial value problem associated with the random Schrodinger operator of the 1D Anderson localization problem. For strong confinement, the rate $r$ is small and given by a non-perturbative (instanton, Lifshitz tail-like) contribution to GLE. For weak confinement, the rate $r$ is found to be proportional to the inverse Larkin length of the pinning theory. As an application, identifying the depinning with a landscape topology trivialization phenomenon, we obtain an upper bound for the depinning threshold $f_c$, in the presence of an applied force, for elastic lines and $d$-dimensional manifolds, expressed through the mean modulus of the spectral determinant of the Laplace operators with a random potential. We also discuss the question of counting of stable equilibria. Finally, we extend the method to calculate the asymptotic number of equilibria at fixed energy (elastic, potential and total), and obtain the (annealed) distribution of the energy density over these equilibria (i.e. force-free configurations). Some connections with the Larkin model are also established.
A method for reconstructing the energy landscape of simple polypeptidic chains is described. We show that we can construct an equivalent representation of the energy landscape by a suitable directed graph. Its topological and dynamical features are shown to yield an effective estimate of the time scales associated with the folding and with the equilibration processes. This conclusion is drawn by comparing molecular dynamics simulations at constant temperature with the dynamics on the graph, defined by a temperature dependent Markov process. The main advantage of the graph representation is that its dynamics can be naturally renormalized by collecting nodes into hubs, while redefining their connectivity. We show that both topological and dynamical properties are preserved by the renormalization procedure. Moreover, we obtain clear indications that the heteropolymers exhibit common topological properties, at variance with the homopolymer, whose peculiar graph structure stems from its spatial homogeneity. In order to obtain a clear distinction between a fast folder and a slow folder in the heteropolymers one has to look at kinetic features of the directed graph. We find that the average time needed to the fast folder for reaching its native configuration is two orders of magnitude smaller than its equilibration time, while for the bad folder these time scales are comparable. Accordingly, we can conclude that the strategy described in this paper can be successfully applied also to more realistic models, by studying their renormalized dynamics on the directed graph, rather than performing lengthy molecular dynamics simulations.
We explore the effect of an attractive interaction between parallel-aligned polymers, which are perpendicularly grafted on a substrate. Such an attractive interaction could be due to, e.g., reversible cross-links. The competition between permanent grafting favoring a homogeneous state of the polymer brush and the attraction, which tends to induce in-plane collapse of the aligned polymers, gives rise to an instability of the homogeneous phase to a bundled state. In this latter state the in-plane translational symmetry is spontaneously broken and the density is modulated with a finite wavelength, which is set by the length scale of transverse fluctuations of the grafted polymers. We analyze the instability for two models of aligned polymers: directed polymers with a line tension and weakly bending chains with a bending stiffness.
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