Related papers: Falling chains as variable mass systems: theoretic…
The steady state reached by a system of particles sliding down a fluctuating surface has interesting properties. Particle clusters form and break rapidly, leading to a broad distribution of sizes and large fluctuations. The density-density…
Force chains form heterogeneous physical structures that can constrain the mechanical stability and acoustic transmission of granular media. However, despite their relevance for predicting bulk properties of materials, there is no agreement…
We investigate a flexible polymer chain made up of chiral active Brownian particles in two dimensions using computer simulations. In the presence of chiral active Brownian forces, the radius of gyration of the chain reduces significantly.…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
We study the effect of the spatial distribution of active force dipoles on the folding pathways and mechanical stability of rigid-elastic networks using Langevin dynamics simulations. While it has been shown in Majumdar et al., J. Chem.…
Can active forces be exploited to drive the consistent collapse of an active polymer into a folded structure? In this paper we introduce and perform numerical simulations of a simple model of active colloidal folders, and show that a…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Collapse and reverse to collapse explosion transition in self-gravitating systems are studied by molecular dynamics simulations. A microcanonical ensemble of point particles confined to a spherical box is considered; the particles interact…
The transport of polymers with folded configurations across membrane pores is investigated theoretically by analyzing simple discrete stochastic models. The translocation dynamics is viewed as a sequence of two events: motion of the folded…
The motion of flexible fibers through structured fluidic environments is ubiquitous in nature and industrial applications. Most often, their dynamics results from the complex interplay between internal elastic stresses, contact forces and…
We discuss the method of folding for discrete planar systems and use it to establish the existence or non-existence of cycles or chaos in planar systems of rational difference equations with variable coefficients. These include some systems…
We study the creep rupture of fiber composites in the framework of fiber bundle models. Two novel fiber bundle models are introduced based on different microscopic mechanisms responsible for the macroscopic creep behavior. Analytical and…
The unjamming transition of granular systems is investigated in a seismic fault model via three dimensional Molecular Dynamics simulations. A two--time force--force correlation function, and a susceptibility related to the system response…
We investigate the folding and forced-unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe biologically relevant phenomena that include adhesive interactions between proteins…
Fiber bundles with statistically distributed thresholds for breakdown of individual fibers are interesting models of the static and dynamics of failures in materials under stress. They can be analyzed to an extent that is not possible for…
The mechanical resistance of a polyethylene strand subject to tension and the way its properties are affected by the presence of a knot is studied using first-principles molecular dynamics calculations. The distribution of strain energy for…
We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of…
We analyze the freezing and collapse transition of a simple model for flexible polymer chains on simple cubic and face-centered cubic lattices by means of sophisticated chain-growth methods. In contrast to bond-fluctuation polymer models in…
Granular systems confined in vertically vibrated shallow horizontal boxes (quasi two-dimensional geometry) present a liquid to solid phase transition when the frequency of the periodic forcing is increased. An effective model, where grains…
It has been claimed that quasistatic granular materials, as well as nanoscale materials, exhibit departures from elasticity even at small loadings. It is demonstrated, using 2D and 3D models with interparticle harmonic interactions, that…