Related papers: Metastable tight knots in a worm-like polymer
Advanced Monte Carlo simulations are used to study the effect of nano-slit confinement on metric and topological properties of model DNA chains. We consider both linear and circularised chains with contour lengths in the 1.2--4.8 $\mu$m…
By performing Monte Carlo sampling of $N$-steps self-avoiding polygons embedded on different Bravais lattices we explore the robustness of universality in the entropic, metric and geometrical properties of knotted polymer rings. In…
We introduce an efficient, scalable Monte Carlo algorithm to simulate cross-linked architectures of freely-jointed and discrete worm-like chains. Bond movement is based on the discrete tractrix construction, which effects conformational…
Building on the results of our computer simulation (ArXiv cond-mat/0503573)we develop a theoretical description of the motion of a bead, embedded in a network of semiflexible polymers, and responding to an applied force. The theory reveals…
We analyze several continuum models of polymers: worm-like chains, ribbons and Fourier knots. We show that the torsion of worm-like chains diverges and conclude that such chains can not be described by the Frenet-Serret (FS) equation of…
Twisting a given knot $K$ about an unknotted circle $c$ a full $n \in \mathbb{N}$ times, we obtain a "twist family" of knots $\{ K_n \}$. Work of Kouno-Motegi-Shibuya implies that for a non-trivial twist family the crossing numbers…
We investigate entropy minimization problems for quantum states subject to convex block-separable constraints. Our principal result is a quantitative stability theorem: under a natural confining (fixed-support) hypothesis, if a state has…
The dynamic structure factor of semiflexible polymers in solution is derived from the wormlike chain model. Special attention is paid to the rigid constraint of an inextensible contour and to the hydrodynamic interactions. For the cases of…
We have evaluated a universal ratio between diffusion constants of the ring polymer with a given knot $K$ and a linear polymer with the same molecular weight in solution through the Brownian dynamics under hydrodynamic interaction. The…
We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some monomeric proteins of this kind should have considerable…
The entanglement entropy in clean, as well as in random quantum spin chains has a logarithmic size-dependence at the critical point. Here, we study the entanglement of composite systems that consist of a clean and a random part, both being…
We study the influence of some quenched disorder in the sequence of monomers on the entropic elasticity of long polymeric chains. Starting from the Kratky-Porod model, we show numerically that some randomness in the favoured angles between…
The interplay of nematic order and phase separation in solutions of semiflexible polymers in solvents of variable quality is investigated by density functional theory (DFT) and molecular dynamics (MD) simulations. We studied coarse-grained…
Despite their considerable practical and biological applications, the link between molecular properties, assembly conditions and self-organized structure in confined polymer solutions remains elusive. Here, we explore the lyotropic nematic…
We present a scaling theory and Monte Carlo (MC) simulation results for a flexible polymer chain slowly dragged by one end into a nanotube. We also describe the situation when the completely confined chain is released and gradually leaves…
Polymer chains decorated with a fraction of monomers capable of forming reversible bonds form transient polymer networks that are important in soft and biological systems. If chains are flexible and the attractive monomers are all of the…
We present experimental results on knotting in off-lattice self-avoiding polygons in the bead-chain model. Using Clisby's tree data structure and the scale-free pivot algorithm, for each $k$ between $10$ and $27$ we generated $2^{43-k}$…
We present computer simulations to examine probability distributions of gyration radius for the no-thickness closed polymers of N straight segments of equal length. We are particularly interested in the conditional distributions when the…
For a hyperbolic knot and a natural number n, we consider the Alexander polynomial twisted by the n-th symmetric power of a lift of the holonomy. We establish the asymptotic behavior of these twisted Alexander polynomials evaluated at unit…
We study near-alternating links whose diagrams satisfy conditions generalized from the notion of semi-adequate links. We extend many of the results known for adequate knots relating their colored Jones polynomials to the topology of…