Lecture 3 Some Simple Knot Invariants in This
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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. -
The Khovanov Homology of Rational Tangles
The Khovanov Homology of Rational Tangles Benjamin Thompson A thesis submitted for the degree of Bachelor of Philosophy with Honours in Pure Mathematics of The Australian National University October, 2016 Dedicated to my family. Even though they’ll never read it. “To feel fulfilled, you must first have a goal that needs fulfilling.” Hidetaka Miyazaki, Edge (280) “Sleep is good. And books are better.” (Tyrion) George R. R. Martin, A Clash of Kings “Let’s love ourselves then we can’t fail to make a better situation.” Lauryn Hill, Everything is Everything iv Declaration Except where otherwise stated, this thesis is my own work prepared under the supervision of Scott Morrison. Benjamin Thompson October, 2016 v vi Acknowledgements What a ride. Above all, I would like to thank my supervisor, Scott Morrison. This thesis would not have been written without your unflagging support, sublime feedback and sage advice. My thesis would have likely consisted only of uninspired exposition had you not provided a plethora of interesting potential topics at the start, and its overall polish would have likely diminished had you not kept me on track right to the end. You went above and beyond what I expected from a supervisor, and as a result I’ve had the busiest, but also best, year of my life so far. I must also extend a huge thanks to Tony Licata for working with me throughout the year too; hopefully we can figure out what’s really going on with the bigradings! So many people to thank, so little time. I thank Joan Licata for agreeing to run a Knot Theory course all those years ago. -
Oriented Pair (S 3,S1); Two Knots Are Regarded As
S-EQUIVALENCE OF KNOTS C. KEARTON Abstract. S-equivalence of classical knots is investigated, as well as its rela- tionship with mutation and the unknotting number. Furthermore, we identify the kernel of Bredon’s double suspension map, and give a geometric relation between slice and algebraically slice knots. Finally, we show that every knot is S-equivalent to a prime knot. 1. Introduction An oriented knot k is a smooth (or PL) oriented pair S3,S1; two knots are regarded as the same if there is an orientation preserving diffeomorphism sending one onto the other. An unoriented knot k is defined in the same way, but without regard to the orientation of S1. Every oriented knot is spanned by an oriented surface, a Seifert surface, and this gives rise to a matrix of linking numbers called a Seifert matrix. Any two Seifert matrices of the same knot are S-equivalent: the definition of S-equivalence is given in, for example, [14, 21, 11]. It is the equivalence relation generated by ambient surgery on a Seifert surface of the knot. In [19], two oriented knots are defined to be S-equivalent if their Seifert matrices are S- equivalent, and the following result is proved. Theorem 1. Two oriented knots are S-equivalent if and only if they are related by a sequence of doubled-delta moves shown in Figure 1. .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .. .... .... .... .... .... .... .... .... .... ... -
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. -
On the Number of Unknot Diagrams Carolina Medina, Jorge Luis Ramírez Alfonsín, Gelasio Salazar
On the number of unknot diagrams Carolina Medina, Jorge Luis Ramírez Alfonsín, Gelasio Salazar To cite this version: Carolina Medina, Jorge Luis Ramírez Alfonsín, Gelasio Salazar. On the number of unknot diagrams. SIAM Journal on Discrete Mathematics, Society for Industrial and Applied Mathematics, 2019, 33 (1), pp.306-326. 10.1137/17M115462X. hal-02049077 HAL Id: hal-02049077 https://hal.archives-ouvertes.fr/hal-02049077 Submitted on 26 Feb 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. On the number of unknot diagrams Carolina Medina1, Jorge L. Ramírez-Alfonsín2,3, and Gelasio Salazar1,3 1Instituto de Física, UASLP. San Luis Potosí, Mexico, 78000. 2Institut Montpelliérain Alexander Grothendieck, Université de Montpellier. Place Eugèene Bataillon, 34095 Montpellier, France. 3Unité Mixte Internationale CNRS-CONACYT-UNAM “Laboratoire Solomon Lefschetz”. Cuernavaca, Mexico. October 17, 2017 Abstract Let D be a knot diagram, and let D denote the set of diagrams that can be obtained from D by crossing exchanges. If D has n crossings, then D consists of 2n diagrams. A folklore argument shows that at least one of these 2n diagrams is unknot, from which it follows that every diagram has finite unknotting number. -
On Computation of HOMFLY-PT Polynomials of 2–Bridge Diagrams
. On computation of HOMFLY-PT polynomials of 2{bridge diagrams . .. Masahiko Murakami . Joint work with Fumio Takeshita and Seiichi Tani Nihon University . December 20th, 2010 1 Masahiko Murakami (Nihon University) On computation of HOMFLY-PT polynomials December 20th, 2010 1 / 28 Contents Motivation and Results Preliminaries Computation Conclusion 1 Masahiko Murakami (Nihon University) On computation of HOMFLY-PT polynomials December 20th, 2010 2 / 28 Contents Motivation and Results Preliminaries Computation Conclusion 1 Masahiko Murakami (Nihon University) On computation of HOMFLY-PT polynomials December 20th, 2010 3 / 28 There exist polynomial time algorithms for computing Jones polynomials and HOMFLY-PT polynomials under reasonable restrictions. Computational Complexities of Knot Polynomials Alexander polynomial [Alexander](1928) Generally, polynomial time Jones polynomial [Jones](1985) Generally, #P{hard [Jaeger, Vertigan and Welsh](1993) HOMFLY-PT polynomial [Freyd, Yetter, Hoste, Lickorish, Millett, Ocneanu](1985) [Przytycki, Traczyk](1987) Generally, #P{hard [Jaeger, Vertigan and Welsh](1993) 1 Masahiko Murakami (Nihon University) On computation of HOMFLY-PT polynomials December 20th, 2010 4 / 28 Computational Complexities of Knot Polynomials Alexander polynomial [Alexander](1928) Generally, polynomial time Jones polynomial [Jones](1985) Generally, #P{hard [Jaeger, Vertigan and Welsh](1993) HOMFLY-PT polynomial [Freyd, Yetter, Hoste, Lickorish, Millett, Ocneanu](1985) [Przytycki, Traczyk](1987) Generally, #P{hard [Jaeger, Vertigan -
Mathematics and Computation
Mathematics and Computation Mathematics and Computation Ideas Revolutionizing Technology and Science Avi Wigderson Princeton University Press Princeton and Oxford Copyright c 2019 by Avi Wigderson Requests for permission to reproduce material from this work should be sent to [email protected] Published by Princeton University Press, 41 William Street, Princeton, New Jersey 08540 In the United Kingdom: Princeton University Press, 6 Oxford Street, Woodstock, Oxfordshire OX20 1TR press.princeton.edu All Rights Reserved Library of Congress Control Number: 2018965993 ISBN: 978-0-691-18913-0 British Library Cataloging-in-Publication Data is available Editorial: Vickie Kearn, Lauren Bucca, and Susannah Shoemaker Production Editorial: Nathan Carr Jacket/Cover Credit: THIS INFORMATION NEEDS TO BE ADDED WHEN IT IS AVAILABLE. WE DO NOT HAVE THIS INFORMATION NOW. Production: Jacquie Poirier Publicity: Alyssa Sanford and Kathryn Stevens Copyeditor: Cyd Westmoreland This book has been composed in LATEX The publisher would like to acknowledge the author of this volume for providing the camera-ready copy from which this book was printed. Printed on acid-free paper 1 Printed in the United States of America 10 9 8 7 6 5 4 3 2 1 Dedicated to the memory of my father, Pinchas Wigderson (1921{1988), who loved people, loved puzzles, and inspired me. Ashgabat, Turkmenistan, 1943 Contents Acknowledgments 1 1 Introduction 3 1.1 On the interactions of math and computation..........................3 1.2 Computational complexity theory.................................6 1.3 The nature, purpose, and style of this book............................7 1.4 Who is this book for?........................................7 1.5 Organization of the book......................................8 1.6 Notation and conventions..................................... -
Knots, Links, Spatial Graphs, and Algebraic Invariants
689 Knots, Links, Spatial Graphs, and Algebraic Invariants AMS Special Session on Algebraic and Combinatorial Structures in Knot Theory AMS Special Session on Spatial Graphs October 24–25, 2015 California State University, Fullerton, CA Erica Flapan Allison Henrich Aaron Kaestner Sam Nelson Editors American Mathematical Society 689 Knots, Links, Spatial Graphs, and Algebraic Invariants AMS Special Session on Algebraic and Combinatorial Structures in Knot Theory AMS Special Session on Spatial Graphs October 24–25, 2015 California State University, Fullerton, CA Erica Flapan Allison Henrich Aaron Kaestner Sam Nelson Editors American Mathematical Society Providence, Rhode Island EDITORIAL COMMITTEE Dennis DeTurck, Managing Editor Michael Loss Kailash Misra Catherine Yan 2010 Mathematics Subject Classification. Primary 05C10, 57M15, 57M25, 57M27. Library of Congress Cataloging-in-Publication Data Names: Flapan, Erica, 1956- editor. Title: Knots, links, spatial graphs, and algebraic invariants : AMS special session on algebraic and combinatorial structures in knot theory, October 24-25, 2015, California State University, Fullerton, CA : AMS special session on spatial graphs, October 24-25, 2015, California State University, Fullerton, CA / Erica Flapan [and three others], editors. Description: Providence, Rhode Island : American Mathematical Society, [2017] | Series: Con- temporary mathematics ; volume 689 | Includes bibliographical references. Identifiers: LCCN 2016042011 | ISBN 9781470428471 (alk. paper) Subjects: LCSH: Knot theory–Congresses. | Link theory–Congresses. | Graph theory–Congresses. | Invariants–Congresses. | AMS: Combinatorics – Graph theory – Planar graphs; geometric and topological aspects of graph theory. msc | Manifolds and cell complexes – Low-dimensional topology – Relations with graph theory. msc | Manifolds and cell complexes – Low-dimensional topology – Knots and links in S3.msc| Manifolds and cell complexes – Low-dimensional topology – Invariants of knots and 3-manifolds. -
Planar and Spherical Stick Indices of Knots
PLANAR AND SPHERICAL STICK INDICES OF KNOTS COLIN ADAMS, DAN COLLINS, KATHERINE HAWKINS, CHARMAINE SIA, ROB SILVERSMITH, AND BENA TSHISHIKU Abstract. The stick index of a knot is the least number of line segments required to build the knot in space. We define two analogous 2-dimensional invariants, the planar stick index, which is the least number of line segments in the plane to build a projection, and the spherical stick index, which is the least number of great circle arcs to build a projection on the sphere. We find bounds on these quantities in terms of other knot invariants, and give planar stick and spherical stick constructions for torus knots and for compositions of trefoils. In particular, unlike most knot invariants,we show that the spherical stick index distinguishes between the granny and square knots, and that composing a nontrivial knot with a second nontrivial knot need not increase its spherical stick index. 1. Introduction The stick index s[K] of a knot type [K] is the smallest number of straight line segments required to create a polygonal conformation of [K] in space. The stick index is generally difficult to compute. However, stick indices of small crossing knots are known, and stick indices for certain infinite categories of knots have been determined: Theorem 1.1 ([Jin97]). If Tp;q is a (p; q)-torus knot with p < q < 2p, s[Tp;q] = 2q. Theorem 1.2 ([ABGW97]). If nT is a composition of n trefoils, s[nT ] = 2n + 4. Despite the interest in stick index, two-dimensional analogues have not been studied in depth. -
MUTATIONS of LINKS in GENUS 2 HANDLEBODIES 1. Introduction
PROCEEDINGS OF THE AMERICAN MATHEMATICAL SOCIETY Volume 127, Number 1, January 1999, Pages 309{314 S 0002-9939(99)04871-6 MUTATIONS OF LINKS IN GENUS 2 HANDLEBODIES D. COOPER AND W. B. R. LICKORISH (Communicated by Ronald A. Fintushel) Abstract. A short proof is given to show that a link in the 3-sphere and any link related to it by genus 2 mutation have the same Alexander polynomial. This verifies a deduction from the solution to the Melvin-Morton conjecture. The proof here extends to show that the link signatures are likewise the same and that these results extend to links in a homology 3-sphere. 1. Introduction Suppose L is an oriented link in a genus 2 handlebody H that is contained, in some arbitrary (complicated) way, in S3.Letρbe the involution of H depicted abstractly in Figure 1 as a π-rotation about the axis shown. The pair of links L and ρL is said to be related by a genus 2 mutation. The first purpose of this note is to prove, by means of long established techniques of classical knot theory, that L and ρL always have the same Alexander polynomial. As described briefly below, this actual result for knots can also be deduced from the recent solution to a conjecture, of P. M. Melvin and H. R. Morton, that posed a problem in the realm of Vassiliev invariants. It is impressive that this simple result, readily expressible in the language of the classical knot theory that predates the Jones polynomial, should have emerged from the technicalities of Vassiliev invariants. -
On Framings of Knots in 3-Manifolds
ON FRAMINGS OF KNOTS IN 3-MANIFOLDS RHEA PALAK BAKSHI, DIONNE IBARRA, GABRIEL MONTOYA-VEGA, JÓZEF H. PRZYTYCKI, AND DEBORAH WEEKS Abstract. We show that the only way of changing the framing of a knot or a link by ambient isotopy in an oriented 3-manifold is when the manifold has a properly embedded non-separating S2. This change of framing is given by the Dirac trick, also known as the light bulb trick. The main tool we use is based on McCullough’s work on the mapping class groups of 3-manifolds. We also relate our results to the theory of skein modules. Contents 1. Introduction1 1.1. History of the problem2 2. Preliminaries3 3. Main Results4 3.1. Proofs of the Main Theorems5 3.2. Spin structures and framings7 4. Ramications and Connections to Skein Modules8 4.1. From the Kauman bracket skein module to spin twisted homology9 4.2. The q-homology skein module9 5. Future Directions 10 6. Acknowledgements 11 References 11 1. Introduction We show that the only way to change the framing of a knot in an oriented 3-manifold by ambient isotopy is when the manifold has a properly embedded non-separating S2. More precisely the only change of framing is by the light bulb trick as illustrated in the Figure1. Here the change arXiv:2001.07782v1 [math.GT] 21 Jan 2020 of framing is very local (takes part in S2 × »0; 1¼ embedded in the manifold) and is related to the fact that the fundamental group of SO¹3º is Z2. Furthermore, we use the fact that 3-manifolds possess spin structures given by the parallelization of their tangent bundles.