Search results for "KNOTS"
showing 10 items of 13 documents
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.
Three-dimensional skyrmions in spin-2 Bose–Einstein condensates
2017
We introduce topologically stable three-dimensional skyrmions in the cyclic and biaxial nematic phases of a spin-2 Bose-Einstein condensate. These skyrmions exhibit exceptionally high mapping degrees resulting from the versatile symmetries of the corresponding order parameters. We show how these structures can be created in existing experimental setups and study their temporal evolution and lifetime by numerically solving the three-dimensional Gross-Pitaevskii equations for realistic parameter values. Although the biaxial nematic and cyclic phases are observed to be unstable against transition towards the ferromagnetic phase, their lifetimes are long enough for the skyrmions to be imprinted…
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…
A cubic defining algebra for the Links-Gould polynomial
2012
We define a finite-dimensional cubic quotient of the group algebra of the braid group, endowed with a (essentially unique) Markov trace which affords the Links-Grould invariant of knots and links. We investigate several of its properties, and state several conjectures about its structure.
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…
Comparing equilibration schemes of high-molecular-weight polymer melts with topological indicators.
2021
Abstract Recent theoretical studies have demonstrated that the behaviour of molecular knots is a sensitive indicator of polymer structure. Here, we use knots to verify the ability of two state-of-the-art algorithms—configuration assembly and hierarchical backmapping—to equilibrate high-molecular-weight (MW) polymer melts. Specifically, we consider melts with MWs equivalent to several tens of entanglement lengths and various chain flexibilities, generated with both strategies. We compare their unknotting probability, unknotting length, knot spectra, and knot length distributions. The excellent agreement between the two independent methods with respect to knotting properties provides an addit…
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.
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…
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 …
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.