On L-Space Knots Obtained from Unknotting Arcs in Alternating Diagrams
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Conservation of Complex Knotting and Slipknotting Patterns in Proteins
Conservation of complex knotting and PNAS PLUS slipknotting patterns in proteins Joanna I. Sułkowskaa,1,2, Eric J. Rawdonb,1, Kenneth C. Millettc, Jose N. Onuchicd,2, and Andrzej Stasiake aCenter for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92037; bDepartment of Mathematics, University of St. Thomas, Saint Paul, MN 55105; cDepartment of Mathematics, University of California, Santa Barbara, CA 93106; dCenter for Theoretical Biological Physics , Rice University, Houston, TX 77005; and eCenter for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland Edited by* Michael S. Waterman, University of Southern California, Los Angeles, CA, and approved May 4, 2012 (received for review April 17, 2012) While analyzing all available protein structures for the presence of ers fixed configurations, in this case proteins in their native folded knots and slipknots, we detected a strict conservation of complex structures. Then they may be treated as frozen and thus unable to knotting patterns within and between several protein families undergo any deformation. despite their large sequence divergence. Because protein folding Several papers have described various interesting closure pathways leading to knotted native protein structures are slower procedures to capture the knot type of the native structure of and less efficient than those leading to unknotted proteins with a protein or a subchain of a closed chain (1, 3, 29–33). In general, similar size and sequence, the strict conservation of the knotting the strategy is to ensure that the closure procedure does not affect patterns indicates an important physiological role of knots and slip- the inherent entanglement in the analyzed protein chain or sub- knots in these proteins. -
Deep Learning the Hyperbolic Volume of a Knot Arxiv:1902.05547V3 [Hep-Th] 16 Sep 2019
Deep Learning the Hyperbolic Volume of a Knot Vishnu Jejjalaa;b , Arjun Karb , Onkar Parrikarb aMandelstam Institute for Theoretical Physics, School of Physics, NITheP, and CoE-MaSS, University of the Witwatersrand, Johannesburg, WITS 2050, South Africa bDavid Rittenhouse Laboratory, University of Pennsylvania, 209 S 33rd Street, Philadelphia, PA 19104, USA E-mail: [email protected], [email protected], [email protected] Abstract: An important conjecture in knot theory relates the large-N, double scaling limit of the colored Jones polynomial JK;N (q) of a knot K to the hyperbolic volume of the knot complement, Vol(K). A less studied question is whether Vol(K) can be recovered directly from the original Jones polynomial (N = 2). In this report we use a deep neural network to approximate Vol(K) from the Jones polynomial. Our network is robust and correctly predicts the volume with 97:6% accuracy when training on 10% of the data. This points to the existence of a more direct connection between the hyperbolic volume and the Jones polynomial. arXiv:1902.05547v3 [hep-th] 16 Sep 2019 Contents 1 Introduction1 2 Setup and Result3 3 Discussion7 A Overview of knot invariants9 B Neural networks 10 B.1 Details of the network 12 C Other experiments 14 1 Introduction Identifying patterns in data enables us to formulate questions that can lead to exact results. Since many of these patterns are subtle, machine learning has emerged as a useful tool in discovering these relationships. In this work, we apply this idea to invariants in knot theory. -
THE JONES SLOPES of a KNOT Contents 1. Introduction 1 1.1. The
THE JONES SLOPES OF A KNOT STAVROS GAROUFALIDIS Abstract. The paper introduces the Slope Conjecture which relates the degree of the Jones polynomial of a knot and its parallels with the slopes of incompressible surfaces in the knot complement. More precisely, we introduce two knot invariants, the Jones slopes (a finite set of rational numbers) and the Jones period (a natural number) of a knot in 3-space. We formulate a number of conjectures for these invariants and verify them by explicit computations for the class of alternating knots, the knots with at most 9 crossings, the torus knots and the (−2, 3,n) pretzel knots. Contents 1. Introduction 1 1.1. The degree of the Jones polynomial and incompressible surfaces 1 1.2. The degree of the colored Jones function is a quadratic quasi-polynomial 3 1.3. q-holonomic functions and quadratic quasi-polynomials 3 1.4. The Jones slopes and the Jones period of a knot 4 1.5. The symmetrized Jones slopes and the signature of a knot 5 1.6. Plan of the proof 7 2. Future directions 7 3. The Jones slopes and the Jones period of an alternating knot 8 4. Computing the Jones slopes and the Jones period of a knot 10 4.1. Some lemmas on quasi-polynomials 10 4.2. Computing the colored Jones function of a knot 11 4.3. Guessing the colored Jones function of a knot 11 4.4. A summary of non-alternating knots 12 4.5. The 8-crossing non-alternating knots 13 4.6. -
A Knot-Vice's Guide to Untangling Knot Theory, Undergraduate
A Knot-vice’s Guide to Untangling Knot Theory Rebecca Hardenbrook Department of Mathematics University of Utah Rebecca Hardenbrook A Knot-vice’s Guide to Untangling Knot Theory 1 / 26 What is Not a Knot? Rebecca Hardenbrook A Knot-vice’s Guide to Untangling Knot Theory 2 / 26 What is a Knot? 2 A knot is an embedding of the circle in the Euclidean plane (R ). 3 Also defined as a closed, non-self-intersecting curve in R . 2 Represented by knot projections in R . Rebecca Hardenbrook A Knot-vice’s Guide to Untangling Knot Theory 3 / 26 Why Knots? Late nineteenth century chemists and physicists believed that a substance known as aether existed throughout all of space. Could knots represent the elements? Rebecca Hardenbrook A Knot-vice’s Guide to Untangling Knot Theory 4 / 26 Why Knots? Rebecca Hardenbrook A Knot-vice’s Guide to Untangling Knot Theory 5 / 26 Why Knots? Unfortunately, no. Nevertheless, mathematicians continued to study knots! Rebecca Hardenbrook A Knot-vice’s Guide to Untangling Knot Theory 6 / 26 Current Applications Natural knotting in DNA molecules (1980s). Credit: K. Kimura et al. (1999) Rebecca Hardenbrook A Knot-vice’s Guide to Untangling Knot Theory 7 / 26 Current Applications Chemical synthesis of knotted molecules – Dietrich-Buchecker and Sauvage (1988). Credit: J. Guo et al. (2010) Rebecca Hardenbrook A Knot-vice’s Guide to Untangling Knot Theory 8 / 26 Current Applications Use of lattice models, e.g. the Ising model (1925), and planar projection of knots to find a knot invariant via statistical mechanics. Credit: D. Chicherin, V.P. -
CROSSING CHANGES and MINIMAL DIAGRAMS the Unknotting
CROSSING CHANGES AND MINIMAL DIAGRAMS ISABEL K. DARCY The unknotting number of a knot is the minimal number of crossing changes needed to convert the knot into the unknot where the minimum is taken over all possible diagrams of the knot. For example, the minimal diagram of the knot 108 requires 3 crossing changes in order to change it to the unknot. Thus, by looking only at the minimal diagram of 108, it is clear that u(108) ≤ 3 (figure 1). Nakanishi [5] and Bleiler [2] proved that u(108) = 2. They found a non-minimal diagram of the knot 108 in which two crossing changes suffice to obtain the unknot (figure 2). Lower bounds on unknotting number can be found by looking at how knot invariants are affected by crossing changes. Nakanishi [5] and Bleiler [2] used signature to prove that u(108)=2. Figure 1. Minimal dia- Figure 2. A non-minimal dia- gram of knot 108 gram of knot 108 Bernhard [1] noticed that one can determine that u(108) = 2 by using a sequence of crossing changes within minimal diagrams and ambient isotopies as shown in figure. A crossing change within the minimal diagram of 108 results in the knot 62. We then use an ambient isotopy to change this non-minimal diagram of 62 to a minimal diagram. The unknot can then be obtained by changing one crossing within the minimal diagram of 62. Bernhard hypothesized that the unknotting number of a knot could be determined by only looking at minimal diagrams by using ambient isotopies between crossing changes. -
An Introduction to Knot Theory and the Knot Group
AN INTRODUCTION TO KNOT THEORY AND THE KNOT GROUP LARSEN LINOV Abstract. This paper for the University of Chicago Math REU is an expos- itory introduction to knot theory. In the first section, definitions are given for knots and for fundamental concepts and examples in knot theory, and motivation is given for the second section. The second section applies the fun- damental group from algebraic topology to knots as a means to approach the basic problem of knot theory, and several important examples are given as well as a general method of computation for knot diagrams. This paper assumes knowledge in basic algebraic and general topology as well as group theory. Contents 1. Knots and Links 1 1.1. Examples of Knots 2 1.2. Links 3 1.3. Knot Invariants 4 2. Knot Groups and the Wirtinger Presentation 5 2.1. Preliminary Examples 5 2.2. The Wirtinger Presentation 6 2.3. Knot Groups for Torus Knots 9 Acknowledgements 10 References 10 1. Knots and Links We open with a definition: Definition 1.1. A knot is an embedding of the circle S1 in R3. The intuitive meaning behind a knot can be directly discerned from its name, as can the motivation for the concept. A mathematical knot is just like a knot of string in the real world, except that it has no thickness, is fixed in space, and most importantly forms a closed loop, without any loose ends. For mathematical con- venience, R3 in the definition is often replaced with its one-point compactification S3. Of course, knots in the real world are not fixed in space, and there is no interesting difference between, say, two knots that differ only by a translation. -
Berge–Gabai Knots and L–Space Satellite Operations
BERGE-GABAI KNOTS AND L-SPACE SATELLITE OPERATIONS JENNIFER HOM, TYE LIDMAN, AND FARAMARZ VAFAEE Abstract. Let P (K) be a satellite knot where the pattern, P , is a Berge-Gabai knot (i.e., a knot in the solid torus with a non-trivial solid torus Dehn surgery), and the companion, K, is a non- trivial knot in S3. We prove that P (K) is an L-space knot if and only if K is an L-space knot and P is sufficiently positively twisted relative to the genus of K. This generalizes the result for cables due to Hedden [Hed09] and the first author [Hom11]. 1. Introduction In [OS04d], Oszv´ath and Szab´ointroduced Heegaard Floer theory, which produces a set of invariants of three- and four-dimensional manifolds. One example of such invariants is HF (Y ), which associates a graded abelian group to a closed 3-manifold Y . When Y is a rational homologyd three-sphere, rk HF (Y ) ≥ |H1(Y ; Z)| [OS04c]. If equality is achieved, then Y is called an L-space. Examples included lens spaces, and more generally, all connected sums of manifolds with elliptic geometry [OS05]. L-spaces are of interest for various reasons. For instance, such manifolds do not admit co-orientable taut foliations [OS04a, Theorem 1.4]. A knot K ⊂ S3 is called an L-space knot if it admits a positive L-space surgery. Any knot with a positive lens space surgery is then an L-space knot. In [Ber], Berge gave a conjecturally complete list of knots that admit lens space surgeries, which includes all torus knots [Mos71]. -
Hyperbolic Structures from Link Diagrams
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 5-2012 Hyperbolic Structures from Link Diagrams Anastasiia Tsvietkova [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Geometry and Topology Commons Recommended Citation Tsvietkova, Anastasiia, "Hyperbolic Structures from Link Diagrams. " PhD diss., University of Tennessee, 2012. https://trace.tennessee.edu/utk_graddiss/1361 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Anastasiia Tsvietkova entitled "Hyperbolic Structures from Link Diagrams." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Mathematics. Morwen B. Thistlethwaite, Major Professor We have read this dissertation and recommend its acceptance: Conrad P. Plaut, James Conant, Michael Berry Accepted for the Council: Carolyn R. Hodges Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Hyperbolic Structures from Link Diagrams A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Anastasiia Tsvietkova May 2012 Copyright ©2012 by Anastasiia Tsvietkova. All rights reserved. ii Acknowledgements I am deeply thankful to Morwen Thistlethwaite, whose thoughtful guidance and generous advice made this research possible. -
Knots and Links in Lens Spaces
Alma Mater Studiorum Università di Bologna Dottorato di Ricerca in MATEMATICA Ciclo XXVI Settore Concorsuale di afferenza: 01/A2 Settore Scientifico disciplinare: MAT/03 Knots and links in lens spaces Tesi di Dottorato presentata da: Enrico Manfredi Coordinatore Dottorato: Relatore: Prof.ssa Prof. Giovanna Citti Michele Mulazzani Esame Finale anno 2014 Contents Introduction 1 1 Representation of lens spaces 9 1.1 Basic definitions . 10 1.2 A lens model for lens spaces . 11 1.3 Quotient of S3 model . 12 1.4 Genus one Heegaard splitting model . 14 1.5 Dehn surgery model . 15 1.6 Results about lens spaces . 17 2 Links in lens spaces 19 2.1 General definitions . 19 2.2 Mixed link diagrams . 22 2.3 Band diagrams . 23 2.4 Grid diagrams . 25 3 Disk diagram and Reidemeister-type moves 29 3.1 Disk diagram . 30 3.2 Generalized Reidemeister moves . 32 3.3 Standard form of the disk diagram . 36 3.4 Connection with band diagram . 38 3.5 Connection with grid diagram . 42 4 Group of links in lens spaces via Wirtinger presentation 47 4.1 Group of the link . 48 i ii CONTENTS 4.2 First homology group . 52 4.3 Relevant examples . 54 5 Twisted Alexander polynomials for links in lens spaces 57 5.1 The computation of the twisted Alexander polynomials . 57 5.2 Properties of the twisted Alexander polynomials . 59 5.3 Connection with Reidemeister torsion . 61 6 Lifting links from lens spaces to the 3-sphere 65 6.1 Diagram for the lift via disk diagrams . 66 6.2 Diagram for the lift via band and grid diagrams . -
Knots with Unknotting Number 1 and Essential Conway Spheres 1
Algebraic & Geometric Topology 6 (2006) 2051–2116 2051 arXiv version: fonts, pagination and layout may vary from AGT published version Knots with unknotting number 1 and essential Conway spheres CMCAGORDON JOHN LUECKE For a knot K in S3 , let T(K) be the characteristic toric sub-orbifold of the orbifold (S3; K) as defined by Bonahon–Siebenmann. If K has unknotting number one, we show that an unknotting arc for K can always be found which is disjoint from T(K), unless either K is an EM–knot (of Eudave-Munoz)˜ or (S3; K) contains an EM– tangle after cutting along T(K). As a consequence, we describe exactly which large algebraic knots (ie, algebraic in the sense of Conway and containing an essential Conway sphere) have unknotting number one and give a practical procedure for deciding this (as well as determining an unknotting crossing). Among the knots up to 11 crossings in Conway’s table which are obviously large algebraic by virtue of their description in the Conway notation, we determine which have unknotting number one. Combined with the work of Ozsvath–Szab´ o,´ this determines the knots with 10 or fewer crossings that have unknotting number one. We show that an alternating, large algebraic knot with unknotting number one can always be unknotted in an alternating diagram. As part of the above work, we determine the hyperbolic knots in a solid torus which admit a non-integral, toroidal Dehn surgery. Finally, we show that having unknotting number one is invariant under mutation. 57N10; 57M25 1 Introduction Montesinos showed [24] that if a knot K has unknotting number 1 then its double branched cover M can be obtained by a half-integral Dehn surgery on some knot K∗ in S3 . -
Monopole Floer Homology, Link Surgery, and Odd Khovanov Homology
Monopole Floer Homology, Link Surgery, and Odd Khovanov Homology Jonathan Michael Bloom Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2011 c 2011 Jonathan Michael Bloom All Rights Reserved ABSTRACT Monopole Floer Homology, Link Surgery, and Odd Khovanov Homology Jonathan Michael Bloom We construct a link surgery spectral sequence for all versions of monopole Floer homology with mod 2 coefficients, generalizing the exact triangle. The spectral sequence begins with the monopole Floer homology of a hypercube of surgeries on a 3-manifold Y , and converges to the monopole Floer homology of Y itself. This allows one to realize the latter group as the homology of a complex over a combinatorial set of generators. Our construction relates the topology of link surgeries to the combinatorics of graph associahedra, leading to new inductive realizations of the latter. As an application, given a link L in the 3-sphere, we prove that the monopole Floer homology of the branched double-cover arises via a filtered perturbation of the differential on the reduced Khovanov complex of a diagram of L. The associated spectral sequence carries a filtration grading, as well as a mod 2 grading which interpolates between the delta grading on Khovanov homology and the mod 2 grading on Floer homology. Furthermore, the bigraded isomorphism class of the higher pages depends only on the Conway-mutation equivalence class of L. We constrain the existence of an integer bigrading by considering versions of the spectral sequence with non-trivial Uy action, and determine all monopole Floer groups of branched double-covers of links with thin Khovanov homology. -
Arxiv:1809.04186V2 [Math.GT] 3 Jan 2021
SATELLITES OF INFINITE RANK IN THE SMOOTH CONCORDANCE GROUP MATTHEW HEDDEN AND JUANITA PINZÓN-CAICEDO Abstract. We conjecture that satellite operations are either constant or have infinite rank in the concordance group. We reduce this to the difficult case of winding number zero satellites, and use SO(3) gauge theory to provide a general criterion sufficient for the image of a satellite operation to generate an infinite rank subgroup of the smooth concordance group C. Our criterion applies widely; notably to many unknotted patterns for which the corresponding operators on the topological concordance group are zero. We raise some questions and conjectures regarding satellite operators and their interaction with concordance. 1. Introduction Oriented knots are said to be concordant if they cobound a properly embedded cylinder in [0; 1] × S3. One can vary the regularity of the embeddings, and typically one considers either smooth or locally flat continuous embeddings. Either choice defines an equivalence relation under which the set of knots becomes an abelian group using the connected sum operation. These concordance groups of knots are intensely studied, with strong motivation provided by the profound distinction between the groups one defines in the topologically locally flat and smooth categories, respectively. Indeed, many questions pertaining to 4– manifolds with small topology (like the 4–sphere) can be recast or addressed in terms of concordance. Despite the efforts of many mathematicians, the concordance groups are still rather poorly understood. In both categories, for instance, the basic question of whether the groups possess elements of any finite order other than two remains open.