Related papers: Following Knots Down Their Energy Gradients
Knots are entangled structures that cannot be untangled without a cut. Topological stability of knots is one of the many examples of their important properties that can be used in information storage and transfer. Knot dynamics is important…
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…
We investigate the entanglement properties in semiconductor quantum dot systems modeled by extended Hubbard model, focusing on the impact of potential energy variations and electron interactions within a four-site quantum dot spin chain.…
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 describe a method to track particles undergoing large displacements. Starting with a list of particle positions sampled at different time points, we assign particle identities by minimizing the sum across all particles of the trace of…
Studying the physics of quantum correlations has gained new interest after it has become possible to measure entanglement entropies of few body systems in experiments with ultracold atomic gases. Apart from investigating trapped atom…
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…
We develop a model characterizing all possible knots and links arising from recombination starting with a twist knot substrate, extending previous work of Buck and Flapan. We show that all knot or link products fall into three…
A new type of knot energy is presented via real life experiments involving a thin resilient metallic tube. Knotted in different ways, the device mechanically acquires a uniquely determined (up to isometry) normal form at least when the…
The goal of this paper is to discuss the possibility of finding an algorithm that can give all distinct knots up to a desired complexity. Two such algorithms are presented, one based on projections on a plane, the other on closed…
The interplay between the topological and geometrical properties of a polymer ring can be clarified by establishing the entanglement trapped in any portion (arc) of the ring. The task requires to close the open arcs into a ring, and the…
An extensive study of single block copolymer knots containing two kinds of monomers $A$ and $B$ is presented. The knots are in a solution and their monomers are subjected to short range interactions that can be attractive or repulsive. In…
Computational studies of basic models of strongly-correlated electron systems can provide guidance in the search for new materials as well as insight into the physical mechanisms responsible for their properties. Here, we illustrate this by…
We introduce a method of exploring potential energy contours in complex dynamical systems based on potentiostatic kinematics wherein the systems are evolved with minimal changes to their potential energy. We construct a simple iterative…
We propose a thought experiment to detect low-energy Quantum Gravity phenomena using Quantum Optical Information Technologies. Gravitational field perturbations, such as gravitational waves and quantum gravity fluctuations, decohere the…
This paper is a survey of knot theory and invariants of knots and links from the point of view of categories of diagrams. The topics range from foundations of knot theory to virtual knot theory and topological quantum field theory.
Link prediction in complex networks has attracted increasing attention from both physical and computer science communities. The algorithms can be used to extract missing information, identify spurious interactions, evaluate network evolving…
We investigate simplified models of computer data networks and examine how the introduction of additional random links influences the performance of these net works. In general, the impact of additional random links on the performance of…
An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows to understand important characteristics like thermodynamic,…
We probe the character of knotting in open, confined polymers, assigning knot types to open curves by identifying their projections as virtual knots. In this sense, virtual knots are transitional, lying in between classical knot types,…