Related papers: Knots in Macromolecules in Constraint Space
We investigate knot-theoretic properties of geometrically defined curvature energies such as integral Menger curvature. Elementary radii-functions, such as the circumradius of three points, generate a family of knot energies guaranteeing…
We argue that the mean crossing number of a random polymer configuration is simply a measure of opacity, without being closely related to entanglement as claimed by several authors. We present an easy way of estimating its asymptotic…
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…
Knots have been considered to be useful models for simulating molecular chains such as DNA and proteins. One quantity that we are interested on molecular knots is the minimum number of monomers necessary to realize a knot. In this paper we…
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…
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…
Semiflexible macromolecules in dilute solution under very good solvent conditions are modeled by self-avoiding walks on the simple cubic lattice ($d=3$ dimensions) and square lattice ($d=2$ dimensions), varying chain stiffness by an energy…
This report presents a unified treatment of the density of states for the knots and folds of polymer chains. The physical realization of such systems ranges from DNA molecules to the microscopic configurations of space-time.
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…
The viscous flow of polymer chains in dense melts is dominated by topological constraints whenever the single chain contour length, N, becomes larger than the characteristic scale Ne, defining comprehensively the macroscopic rheological…
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…
We study the interplay between entropy and topological constraints for a polymer chain in which sliding rings (slip-links) enforce pair contacts between monomers. These slip-links divide a closed ring polymer into a number of sub-loops…
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 $2^{43-k}$…
The space writhe of a knot is a property of its three-dimensional embedding that contains information about its underlying topology, but the correspondence between space writhe and other topological invariants is not fully understood. We…
We study the behavior of threads and polymers in a turbulent flow. These objects have finite spatial extension, so the flow along them differs slightly. The corresponding drag forces produce a finite average stretching and the thread is…
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…
Monte Carlo simulations are used to study the conformational behavior of a semiflexible polymer confined to cylindrical and conical channels. The channels are sufficiently narrow that the conditions for the Odijk regime are marginally…
This paper contains linear systems of equations which can distinguish knots without knot invariants. Let $M_n$ be the topological moduli space of all n-component string links and such that a fixed projection into the plane is an immersion.…
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…
We show that for a large class of hyperbolic knots and links, we can determine bounds on the volume of the link complement from combinatorial information given by a link diagram. Specifically, there is a universal constant C such that if a…