Search results for "knots"
showing 10 items of 13 documents
Entropic Interactions between Two Knots on a Semiflexible Polymer.
2017
Two knots on a string can either be separated or intertwined, and may even pass through each other. At the microscopic scale, such transitions may occur spontaneously, driven by thermal fluctuations, and can be associated with a topological free energy barrier. In this manuscript, we study the respective location of a trefoil ( 3 1 ) and a figure-eight ( 4 1 ) knot on a semiflexible polymer, which is parameterized to model dsDNA in physiological conditions. Two cases are considered: first, end monomers are grafted to two confining walls of varying distance. Free energy profiles and transition barriers are then compared to a subset of free chains, which contain exactly one 3 1 and one 4 1 kn…
Are There Knots in Chromosomes?
2017
Recent developments have for the first time allowed the determination of three-dimensional structures of individual chromosomes and genomes in nuclei of single haploid mouse embryonic stem (ES) cells based on Hi⁻C chromosome conformation contact data. Although these first structures have a relatively low resolution, they provide the first experimental data that can be used to study chromosome and intact genome folding. Here we further analyze these structures and provide the first evidence that G1 phase chromosomes are knotted, consistent with the fact that plots of contact probability vs sequence separation show a power law dependence that is intermediate between that of a fractal globule …
On hyperbolic type involutions
2001
We give a bound on the number of hyperbolic knots which are double covered by a fixed (non hyperbolic) manifold in terms of the number of tori and of the invariants of the Seifert fibred pieces of its Jaco-Shalen-Johannson decomposition. We also investigate the problem of finding the non hyperbolic knots with the same double cover of a hyperbolic one and give several examples to illustrate the results.
Branch Points of Algebraic Functions and the Beginnings of Modern Knot Theory
1995
Many of the key ideas which formed modern topology grew out of “normal research” in one of the mainstream fields of 19th-century mathematical thinking, the theory of complex algebraic functions. These ideas were eventually divorced from their original context. The present study discusses an example illustrating this process. During the years 1895-1905, the Austrian mathematician, Wilhelm Wirtinger, tried to generalize Felix Klein's view of algebraic functions to the case of several variables. An investigation of the monodromy behavior of such functions in the neighborhood of singular points led to the first computation of a knot group. Modern knot theory was then formed after a shift in mat…
Non-equivalent hyperbolic knots
2002
We construct, for each integer n 3, pairs of non-equivalent hyperbolic knots with the same 2fold and n-fold cyclic branched covers. We also discuss necessary conditions for such pairs of knots to exist. 2001 Elsevier Science B.V. All rights reserved. MSC: primary 57M25; secondary 57M12, 57M50
Detection and visualization of physical knots in macromolecules
2010
Abstract This manuscript provides a pedagogical introduction on how to determine and visualize simple physical knots occurring in polymers, proteins and DNA. We explain how the Alexander polynomial is computed and implemented in a simulation code, and how the structure can be simplified beforehand to save computer time. The concept of knottedness can also be extended in a statistical framework to chains which are not closed. The latter is exemplified by comparing statistics of knots in open random walks and closed random loops.
The HOMFLY-PT polynomials of sublinks and the Yokonuma–Hecke algebras
2016
We describe completely the link invariants constructed using Markov traces on the Yokonuma-Hecke algebras in terms of the linking matrix and the HOMFLYPT polynomials of sublinks.
When the seasons don't fit: Speedy molt as a routine carry-over cost of reproduction
2013
The failure of animals to fit all life-cycle stages into an annual cycle could reduce the chances of successful breeding. In some cases, non-optimal strategies will be adopted in order to maintain the life-cycle within the scope of one year. We studied trade-offs made by a High Arctic migrant shorebird, the red knot Calidris canutus islandica, between reproduction and wing feather molt carried out in the non-breeding period in the Dutch Wadden Sea. We compared primary molt duration between birds undertaking the full migratory and breeding schedule with birds that forego breeding because they are young or are maintained in captivity. Molt duration was ca. 71 days in breeding adults, which wa…
Protein knot server: detection of knots in protein structures
2007
KNOTS (http://knots.mit.edu) is a web server that detects knots in protein structures. Several protein structures have been reported to contain intricate knots. The physiological role of knots and their effect on folding and evolution is an area of active research. The user submits a PDB id or uploads a 3D protein structure in PDB or mmCIF format. The current implementation of the server uses the Alexander polynomial to detect knots. The results of the analysis that are presented to the user are the location of the knot in the structure, the type of the knot and an interactive visualization of the knot. The results can also be downloaded and viewed offline. The server also maintains a regul…
Topological characterization of virtual braids
2015
The purpose of this thesis is to give a topological characterization of virtual braids. Virtual braids are equivalence classes of planar braid-like diagrams identified up to isotopy, Reidemeister and virtual Reidemeister moves. The set of virtual braids admits a group structure and is called the virtual braid group. In Chapter 1 we present a general introduction to the theory of virtual knots, and we discuss some properties of virtual braids and their relations with classical braids. In Chapter 2 we introduce braid-Gauss dia- grams, and we prove that they are a good combinatorial reinterpretation of virtual braids. In particular this generalizes some results known in virtual knot theory. As…