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We have studied the aging effect on the dynamics of unbinding of a double stranded directed polymer in a random medium. By using the Monte Carlo dynamics of a lattice model in two dimensions, for which disorder is known to be relevant, the…
Randomly branching polymers with {\em annealed} connectivity are model systems for ring polymers and chromosomes. In this context, the branched structure represents transient folding induced by topological constraints. Here we present…
The generating function for spanning forests on a lattice is related to the q-state Potts model in a certain q -> 0 limit, and extends the analogous notion for spanning trees, or dense self-avoiding branched polymers. Recent works have…
We study energy relaxation in a phenomenological model for polymer built from rheological considerations: a one dimensional nonlinear lattice with dissipative couplings. These couplings are well known in polymer's community to be possibly…
We consider flexible branched polymer, with quenched branch structure, and show that its conformational entropy as a function of its gyration radius $R$, at large $R$, obeys, in the scaling sense, $\Delta S \sim R^2/(a^2L)$, with $a$ bond…
We investigate the spectral properties of balanced trees and dendrimers, with a view toward unifying and improving the existing results. Here we find a semi-factorized formula for their characteristic polynomials. Afterwards, we determine…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…
Athermal (i.e. zero-temperature) under-constrained systems are typically floppy, but they can be rigidified by the application of external strain, which is theoretically well understood. Here and in the companion paper, we extend this…
Polymer entanglements lead to complicated topological constraints and interactions between neighbouring chains in a dense solution or melt. Entanglements can be treated in a mean field approach, within the famous reptation model, since they…
A lattice model is presented for the simulation of dynamics in polymeric systems. Each polymer is represented as a chain of monomers, residing on a sequence of nearest-neighbor sites of a face-centered-cubic lattice. The polymers are self-…
The packing of elastic sheets is investigated in a quasi two-dimensional experimental setup: a sheet is pulled through a rigid hole acting as a container, so that its configuration is mostly prescribed by the cross-section of the sheet in…
We present a unified theory for the longitudinal dynamic response of a stiff polymer in solution to various external perturbations (mechanical excitations, hydrodynamic flows, electrical fields, temperature quenches ...) that can be…
Using Monte Carlo simulations, we have studied the relaxation of energy of the three-dimensional Ising spin-glass model in aging process. Our finite-size-scaling analysis on the isothermal energy decay after the quench suggests strongly…
Single molecule force spectroscopy provide details of the underlying energy surfaces of proteins which are essential to the understanding of their unfolding process. Recently, it has been observed experimentally that by pulling proteins in…
I develop a kinetic mechanism to explain chain folding in polymer crystallization which is based on the competition between the formation of stems, which is due to frequent occupations of trans states along the chains in the supercooled…
The folding of naturally occurring, single domain proteins is usually well-described as a simple, single exponential process lacking significant trapped states. Here we further explore the hypothesis that the smooth energy landscape this…
We define a lattice model for the interaction of a polymer with water. We solve the model in a suitable approximation. In the case of a non-polar homopolymer, for reasonable values of the parameters, the polymer is found in a non-compact…
The conformational statistics of ring polymers in melts or dense solutions is strongly affected by their quenched microscopic topological state. The effect is particularly strong for non-concatenated unknotted rings, which are known to…
Based on experiments of the compaction of granular materials under periodic shear of a packing of glass beads, a minimal model for the dynamics of the packing density as a function of time is proposed. First, a random ``energy landscape''…
The kinetic behavior of a three-dimensional off-lattice heteropolymer model is studied in terms of the time dependence of the average mean-square displacement between configurations. It is found that at short time-scales similar behavior is…