Related papers: Untying molecular friction knots
Dense particulate suspensions often exhibit a dramatic increase in viscosity in response to external deformation. This shear thickening behavior has been related to a transition from lubricated, unconstrained pairwise motion to a frictional…
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…
We propose a mechanism in which two molecular knots pass through each other and swap positions along a polymer strand. Associated free energy barriers in our simulations only amount to a few $k_{B}T$, which may enable the interchange of…
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…
We investigate the sliding strength of thin filaments in frictional contact with a translating cylinder, perpendicular to the filaments' axes, in knotted (clove hitch) and unknotted (capstan) configurations. Recent work reported superlinear…
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…
In the first part of this work a summary is provided of some recent experiments and theoretical results which are relevant in the research of systems of polymer rings in nontrivial topological conformations. Next, some advances in modeling…
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 use computer simulations to compare the dynamical behaviour of torus and even-twist knots in polymers under tension. The knots diffuse through a mechanism similar to reptation. Their friction coefficients grow linearly with average knot…
We present Monte Carlo computer simulations for melts of semiflexible randomly knotted and randomly concatenated ring polymers on the fcc lattice and in slit confinement. Through systematic variation of the slit width at fixed melt density,…
Friction between ring-polymer brushes at melt densities sliding past each other are studied using extensive course-grained molecular dynamics simulations and scaling arguments, and the results are compared to the friction between…
The most tight conformations of prime knots are found with the use of the SONO algorithm. Their curvature and torsion profiles are calculated. Symmetry of the knots is analysed. Connections with the physics of polymers are discussed.
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or…
We study the geometry of interacting knotted solitons. The interaction is local and advances either as a three-body or as a four-body process, depending on the relative orientation and a degeneracy of the solitons involved. The splitting…
It is common to study polymer physics through the use of idealized single-chain models, and the most popular of these is the freely jointed chain model. In certain thermodynamic ensembles, statistical mechanical treatment of this model is…
Semiflexible polymer models are widely used as a paradigm to understand structural phases in biomolecules including folding of proteins. Since stable knots are not so common in real proteins, the existence of stable knots in semiflexible…
An analysis of extensive simulations of interacting self-avoiding polygons on cubic lattice shows that the frequencies of different knots realized in a random, collapsed polymer ring decrease as a negative power of the ranking order, and…
Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally…
Elucidating the physics of a concentrated suspension of ring polymers, or of an ensemble of ring polymers in a complex environment, is an important outstanding question in polymer physics. Many of the characteristic features of these…
Single-chain elasticity is of fundamental importance in polymer physics, as it underlies many of the unique properties of polymer systems. Recently, there has been interest in characterizing the elastic properties of catenanes, molecular…