Related papers: Evolution of Fragments Formed at the Rupture of a …
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 study the dynamics of a knot in a semiflexible polymer confined to a narrow channel of width comparable to the polymers' persistence length. Using a combination of Brownian dynamics simulations and a coarse-grained stochastic model, we…
Spontaneous formation of knots in long polymers at equilibrium is inevitable but becomes rare in sufficiently short chains. Here, we show that knotting and knot complexity increase by orders of magnitude in diblock polymers with a fraction…
Many experiments have been done to determine the relative strength of different knots, and these show that the break in a knotted rope almost invariably occurs at a point just outside the `entrance' to the knot. The influence of knots on…
We develop a theoretical description of the topological disentanglement occurring when torus knots reach the ends of a semi-flexible polymer under tension. These include decays into simpler knots and total unknotting. The minimal number of…
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…
The breakage of a polymer chain of segments, coupled by anharmonic bonds with applied constant external tensile force is studied by means of Molecular Dynamics simulation. We show that the mean life time of the chain becomes progressively…
The formation of chain-folded structures from the melt is observed in molecular dynamics simulations resembling the lamellae of polymer crystals. Crystallization and subsequent melting temperatures are related linearly to the inverse…
The interplay of topological constraints and Coulomb interactions in static and dynamic properties of charged polymers is investigated by numerical simulations and scaling arguments. In the absence of screening, the long-range interaction…
Motivated by recent advances in single molecule manipulation techniques that enabled several groups to tie knots in individual polymer strands and to monitor their dynamics, we have used computer simulations to study "friction knots"…
We study knotted polymers in equilibrium with an array of obstacles which models confinement in a gel or immersion in a melt. We find a crossover in both the geometrical and the topological behavior of the polymer. When the polymers' radius…
We consider the rupture dynamics of a homopolymer chain pulled at one end at a constant loading rate r. Compared to single bond breaking, the existence of the chain introduces two new aspects into rupture dynamics: the non-Markovian aspect…
We use numerical simulations to study tangentially active flexible ring polymers with different knot topologies. Simple, unknotted active rings display a transition from an extended phase to a collapsed one upon increasing the degree of…
Progressive damage, which eventually leads to failure, is ubiquitous in biological and synthetic polymers. The simplest case to consider is that of elastomeric materials, which can undergo large reversible deformations with negligible rate…
The presence of slipknots in configurations of proteins and DNA has been shown to affect their functionality, or alter it entirely. Historically, polymers are modeled as polygonal chains in space. As an alternative to space curves, we…
We report on a computational study of the statics and dynamics of long flexible linear polymers that spontaneously knot and unknot. Specifically, the equilibrium self-entanglement properties, such as the knotting probability, knot length…
We investigate the sedimentation of knotted polymers by means of stochastic rotation dynamics, a molecular dynamics algorithm that takes hydrodynamics fully into account. We show that the sedimentation coefficient s, related to the terminal…
We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical…
A growing number of proteins have been shown to adopt knotted folds. Yet the biological roles and biophysical properties of these knots remain poorly understood. We have used protein engineering and atomic force microscopy to explore…
Knotted proteins embed a physical (i.e., open) knot within their native structures. For decades, significant effort has been devoted to elucidating the functional role of knots in proteins, yet no consensus has been reached. Here, using…