Related papers: Following Knots Down Their Energy Gradients
We examine computer experiments that can be performed to understand the dynamics of knots under self-repulsion. In the course of specific computer exploration we use the knot theory of rational knots and rational tangles to produce classes…
Knot and link energies can be computed from sets of closed curves in three dimensional space, and each type of knot or link has a minimum energy associated with it. Here, we consider embeddings of links that locally or globally minimize the…
Knots are fascinating topological structures that have been observed in various contexts, ranging from micro-worlds to macro-systems, and are conjectured to play a fundamental role in their respective fields. In order to characterize their…
The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling…
This an article about some elementary geometric and combinatorial natures of various knot energies. A related "new" knot invariant -- the X-crossing number -- is introduced.
We discuss a semi-implicit numerical scheme that allows for minimizing the bending energy of curves within certain isotopy classes. To this end we consider a weighted sum of the bending energy and the tangent-point functional. Based on…
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…
New results on the groundstate energy of tight, magnetic knots are presented. Magnetic knots are defined as tubular embeddings of the magnetic field in an ideal, perfectly conducting, incompressible fluid. An orthogonal, curvilinear…
Knotted proteins, when forced through the pores, can get stuck if the knots in their backbone tighten under force. Alternatively, the knot can slide off the chain, making translocation possible. We construct a simple energy landscape model…
In this paper we study a model of random knots obtained by fixing a space curve in $n$-dimensional Euclidean space with $n>3$, and orthogonally projecting the space curve on to random $3$ dimensional subspaces. By varying the space curve we…
We make use of the 3D nature of knots and links to find savings in computational complexity when computing knot invariants such as the linking number and, in general, most finite type invariants. These savings are achieved in comparison…
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…
This project explores the mathematical study of knots and links in topology, focusing on differentiating between the two-component Unlink and the Hopf Link using a computational tool named LINKAGE. LINKAGE employs the linking number,…
In this paper, knot physics on entangled vortex-membranes are studied including classification, knot dynamics and effective theory. The physics objects in this paper are entangled vortex-membranes that are called composite knot-crystals.…
We investigate low energy structures of a lattice with dislocations in the context of nonlinear elasticity. We show that these low energy configurations exhibit in the limit a Cosserat-like behavior. Moreover, we give bounds from above and…
We study numerically the minimum energy path and energy barriers for dislocation nucleation in a two-dimensional atomistic model of strained epitaxial layers on a substrate with lattice misfit. Stress relaxation processes from coherent to…
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…
We present a methodology to simulate the mechanics of knots in elastic rods using geometrically nonlinear, full three-dimensional (3D) finite element analysis. We focus on the mechanical behavior of knots in tight configurations, for which…
We present the structures of putative global potential energy minima for clusters bound by the Stockmayer (Lennard-Jones plus point dipole) potential. A rich variety of structures is revealed as the cluster size and dipole strength are…
While the problem of knot classification is far from solved, it is possible to create computer programs that can be used to tabulate knots up to a desired degree of complexity. Here we discuss the main ideas on which such programs can be…