Related papers: Equilibrium shapes of flat knots
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…
We introduce a two-dimensional lattice model for the description of knotted polymer rings. A polymer configuration is modeled by a closed polygon drawn on the square diagonal lattice, with possible crossings describing pairs of strands of…
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…
Using a combination of the replica-exchange Monte Carlo algorithm and the multicanonical method, we investigate the influence of bending stiffness on the conformational phases of a bead-stick homopolymer model and present the pseudo-phase…
We use Brownian dynamics simulations and advanced topological profiling methods to characterize the out-of-equilibrium evolution of self-entanglement in linear polymers confined into nano-channels and under periodic compression. We…
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 mechanical properties of polymer knots under stretching in a bad or good solvent are investigated by applying a given force $F$ to a point of the knot while keeping another point fixed. The Monte Carlo sampling of the polymer…
The relaxation of a single knotted ring polymer is studied by Brownian dynamics simulations. The relaxation rate lambda_q for the wave number q is estimated by the least square fit of the equilibrium time-displaced correlation function to a…
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…
Large scale molecular dynamics simulations on graphic processing units (GPUs) are employed to study the scaling behavior of ring polymers with various topological constraints in melts. Typical sizes of rings containing $3_1$, $5_1$ knots…
Scaling arguments are used to analyze the size of topologically constrained closed ring polymer with excluded volume. It is found that there exists a finite range of polymer thickness (excluded volume) in which self-avoidance is unimportant…
We investigate the effect of knot type on the properties of a ring polymer confined to a slit. For relatively wide slits, the more complex the knot, the more the force exerted by the polymer on the walls is decreased compared to an…
A coarse-grained computational model is used to investigate how the bending rigidity of a polymer under tension affects the formation of a trefoil knot. Thermodynamic integration techniques are applied to demonstrate that the free-energy…
The shape of semiflexible polymer rings is studied over their whole range of flexibility. Investigating the joint distribution of asphericity and nature of asphericity as well as their respective averages we find two distinct shape regimes…
The entropic pressure in the vicinity of a cubic lattice knot is examined as a model of the entropic pressure near a knotted ring polymer in a good solvent. A model for the scaling of the pressure is developed and this is tested numerically…
The role of the topology and its relation with the geometry of biopolymers under different physical conditions is a nontrivial and interesting problem. Aiming at understanding this issue for a related simpler system, we use Monte Carlo…
We construct an algorithm that lists all closed essential surfaces in the complement of a knot that lies on the fiber of a trefoil or figure eight knot. Such knots are Berge knots and hence admit lens space surgeries. Furthermore they may…
We define homotopy-theoretic invariants of knots in prime 3-manifolds. Fix a knot J in a prime 3-manifold M. Call a knot K in M concordant to J if it cobounds a properly embedded annulus with J in MxI, and call K J-characteristic if there…
It is known that any tame hyperbolic 3-manifold with infinite volume and a single end is the geometric limit of a sequence of finite volume hyperbolic knot complements. Purcell and Souto showed that if the original manifold embeds in the…
The interplay of topological constraints and persistence length of ring polymers in their own melt is investigated by means of dynamical Monte Carlo simulations of a three dimensional lattice model. We ask if the results are consistent with…