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We introduce and implement a Monte Carlo scheme to study the equilibrium statistics of polymers in the globular phase. It is based on a model of "interacting elastic lattice polymers" and allows a sufficiently good sampling of long and…
In this paper we develop a Bethe approximation, based on the cluster variation method, which is apt to study lattice models of branched polymers. We show that the method is extremely accurate in cases where exact results are known as, for…
In this chapter we review concepts and theories of polymer dynamics. We think of it as an introduction to the topic for scientists specializing in other subfields of statistical mechanics and condensed matter theory, so, for the readers…
We study asymptotic properties of diffusion and other transport processes (including self-avoiding walks and electrical conduction) on large randomly branched polymers using renormalized dynamical field theory. We focus on the swollen phase…
We consider mechanically generated molecular braids composed of two molecules where long range interactions between them can be considered to be very weak. We describe a model that takes account of the thermal fluctuations of the braid,…
Monte Carlo simulations are used to study the translocation of a polymer into a cavity. Modeling the polymer as a hard-sphere chain with a length up to N=601 monomers, we use a multiple-histogram method to measure the variation of the…
Stretched polymers with attractive interaction are studied in two and three dimensions. They are described by biased self-avoiding random walks with nearest neighbour attraction. The bias corresponds to opposite forces applied to the first…
Uniform spanning trees are a statistical model obtained by taking the set of all spanning trees on a given graph (such as a portion of a cubic lattice in d dimensions), with equal probability for each distinct tree. Some properties of such…
Current theories of heteropolymers are inherently macrpscopic, but are applied to folding proteins which are only mesoscopic. In these theories, one computes the averaged free energy over sequences, always assuming that it is self-averaging…
An important problem in statistical physics concerns the fascinating connections between partition functions of lattice models studied in equilibrium statistical mechanics on the one hand and graph theoretical enumeration problems on the…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
The polymer relaxation dynamic of a sample, stretched up to the stress hardening regime, is measured, at room temperature, as a function of the strain $\lambda$ for a wide range of the strain rate $\dot\gamma$, by an original dielectric…
We derive a microscopic theory of glassy dynamics based on the transport of voids by micro-string motions, each of which involves particles arranged in a line hopping simultaneously displacing one another. Disorder is modeled by a random…
Directed polymers in random environment have usually been constructed with a simple random walk on the integer lattice. It has been observed before that several standard results for this model continue to hold for a more general reference…
We show that the geometry of minimum spanning trees (MST) on random graphs is universal. Due to this geometric universality, we are able to characterise the energy of MST using a scaling distribution ($P(\epsilon)$) found using uniform…
The statistics of randomly branching double-folded ring polymers are relevant to the secondary structure of RNA, the large-scale branching of plectonemic DNA (and thus bacterial chromosomes), the conformations of single-ring polymers…
Describing the complex landscape of infinite-dimensional free energy is generally a challenging problem. This difficulty arises from the existence of numerous minimizers and, consequently, a vast number of saddle points. These factors make…
The dynamical characterization of proteins is crucial to understand protein function. From a microscopic point of view, protein dynamics is governed by the local atomic interactions that, in turn, trigger the functional conformational…
Monte Carlo simulations of coarse-grained polymers provide a useful tool to deepen the understanding of conformational and statistical properties of polymers both in physical as well as in biological systems. In this study we sample compact…
The statistical mechanics of a long knotted collapsed polymer is determined by a free-energy with a knot-dependent subleading term, which is linked to the length of the shortest polymer that can hold such knot. The only other parameter…