Related papers: Following Knots Down Their Energy Gradients
The topological effects on the thermal properties of several knot configurations are investigated using Monte Carlo simulations. In order to check if the topology of the knots is preserved during the thermal fluctuations we propose a method…
In this work the thermodynamic properties of short polymer knots (up to 120 segments) defined on a simple cubic lattice are studied with the help of the Wang-Landau Monte Carlo algorithm. The sampling process is performed using pivot…
Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native…
We have studied numerically Faddeev-Hopf knots, which are defined as those unit-vector fields in $R^3$ that have a nontrivial Hopf charge and minimize Faddeev's Lagrangian. A given initial configuration was allowed to relax into a (local)…
We study a 1-form which can be given by a vector in a conformally invariant way. We then study conformally invariant functionals associated to a ``Y-diagram'' on the space of knots which are made from the 1-form.
Simulations of knotting and unknotting in polymers or other filaments rely on random processes to facilitate topological changes. Here we introduce a method of \textit{topological steering} to determine the optimal pathway by which a…
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.
Knotted proteins embed a physical (i.e., open) knot within their native structures. For decades, significant effort has been devoted to elucidating the functional role of knots in proteins, yet no consensus has been reached. Here, using…
We estimate by Monte Carlo simulations the configurational entropy of $N$-steps polygons in the cubic lattice with fixed knot type. By collecting a rich statistics of configurations with very large values of $N$ we are able to analyse the…
Knotted molecules occur naturally and are designed by scientists to gain special biological and material properties. Understanding and utilizing knotting require efficient methods to recognize and generate knotted structures, which are…
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…
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…
A knot is a circle piecewise-linearly embedded into the 3-sphere. The topology of a knot is intimately related to that of its exterior, which is the complement of an open regular neighborhood of the knot. Knots are typically encoded by…
The presence of slipknots in configurations of proteins and DNA has been shown to affect their functionality, or alter it entirely. Historically, polymers are modeled as polygonal chains in space. As an alternative to space curves, we…
Knots and links are fascinating and intricate topological objects. Their influence spans from DNA and molecular chemistry to vortices in superfluid helium, defects in liquid crystals and cosmic strings in the early universe. Here, we find…
Besides mathematical interest, knots and knot theory have important applications in physics, chemistry, and biology. Stasiak and colleagues devised a constructive method for a knot "energy" using a Metropolis Monte Carlo algorithm to…
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 explore the application of automated reasoning techniques to unknot detection, a classical problem of computational topology. We adopt a two-pronged experimental approach, using a theorem prover to try to establish a positive result…
Energy bounds of knotted and linked vortex states in a charged two-component system are considered. It is shown that a set of local minima of free energy contains new classes of universality. When the mutual linking number of vector order…
We investigate the trajectories of point charges in the background of finite-action vacuum solutions of Maxwell's equations known as knot solutions. More specifically, we work with a basis of electromagnetic knots generated by the so-called…