Related papers: Spanning trees for the geometry and dynamics of co…

While Flory theories provide an extremely useful framework for understanding the behavior of interacting, randomly branching polymers, the approach is inherently limited. Here we use a combination of scaling arguments and computer…

Many-body systems relaxing to equilibrium can exhibit complex dynamics even if their steady state is trivial. At low temperatures or high densities their evolution is often dominated by steric hindrances affecting particle motion [1,2,3].…

Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…

Kinetic equations are analyzed for thermal degradation of polymers. The governing relations are based on the fragmentation-annihilation concept. Explicit solutions to these equations are derived in two particular cases of interest. For…

Based on large-scale Monte Carlo simulations on lattice the energy probability distribution functions are investigated for a large set of primary sequences in distinct models of copolymers at low temperatures below transitions to compacted…

Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…

We consider membranes adhered through specific receptor-ligand bonds. Thermal undulations of the membrane induce effective interactions between adhesion sites. We derive an upper bound to the free energy that is independent of interaction…

In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…

We study the statistics of branching polymers with excluded-volume interactions, by modeling them as single self-avoiding trees on a generic regular periodic lattice with coordination number $q$. Each lattice site can be occupied at most by…

Using molecular dynamics simulations we examine the dynamics of a family of model polymers with varying chain length and torsional potential barriers. We focus on features of the dynamics of polymers that are seen experimentally but absent…

In this article, we try to give a rather complete picture of the behavior of the free energy for a model of directed polymer in a random environment, in which the polymer is a simple symmetric random walk on the lattice $\Z^d$, and the…

In this work, we study the dynamics of complex systems with time-dependent transition rates, focusing on $p$-adic analysis in modeling such systems. Starting from the master equation that governs the stochastic dynamics of a system with a…

We present an in-depth multi-scale analysis of the conformations and dynamics of polar active polymers, comparing very dilute and very dense conditions. We unveil characteristic length and time scales, common to both dilute and dense…

How useful it is to think about the potential energy landscape of a complex many-body system depends in large measure on how direct the connection is to the system's dynamics. In this paper we show that, within what we call the potential…

Compact polymers are self-avoiding random walks which visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform…

Using extensive molecular dynamics simulations, we investigate the slowing down of dynamics in a 3D system of ring polymers by varying the ambient pressure and the stiffness of the rings. Our study demonstrates that the stiffness of the…

We study the thermally assisted relaxation of a directed elastic line in a two dimensional quenched random potential by solving numerically the Edwards-Wilkinson equation and the Monte Carlo dynamics of a solid-on-solid lattice model. We…

We study the effect of physical aging on the mechanical properties of a model polymer glass using molecular dynamics simulations. The creep compliance is determined simultaneously with the structural relaxation under a constant uniaxial…

The aging dynamics and the fluctuation-dissipation relation between the spontaneous diffusion induced by a random noise and the drift motion induced by a small stirring force are numerically investigated in a 3D schematic model of…

Active polymers are ubiquitous in nature, and often kicked by persistent noises that break detailed balance. In order to capture the out-of-equilibrium dynamics of such active polymers, we propose a simple yet reliable analytical framework…