Knot Module Lecture Notes (As of June 2005) Day 1 - Crossing and Linking Number
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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. -
Complete Invariant Graphs of Alternating Knots
Complete invariant graphs of alternating knots Christian Soulié First submission: April 2004 (revision 1) Abstract : Chord diagrams and related enlacement graphs of alternating knots are enhanced to obtain complete invariant graphs including chirality detection. Moreover, the equivalence by common enlacement graph is specified and the neighborhood graph is defined for general purpose and for special application to the knots. I - Introduction : Chord diagrams are enhanced to integrate the state sum of all flype moves and then produce an invariant graph for alternating knots. By adding local writhe attribute to these graphs, chiral types of knots are distinguished. The resulting chord-weighted graph is a complete invariant of alternating knots. Condensed chord diagrams and condensed enlacement graphs are introduced and a new type of graph of general purpose is defined : the neighborhood graph. The enlacement graph is enriched by local writhe and chord orientation. Hence this enhanced graph distinguishes mutant alternating knots. As invariant by flype it is also invariant for all alternating knots. The equivalence class of knots with the same enlacement graph is fully specified and extended mutation with flype of tangles is defined. On this way, two enhanced graphs are proposed as complete invariants of alternating knots. I - Introduction II - Definitions and condensed graphs II-1 Knots II-2 Sign of crossing points II-3 Chord diagrams II-4 Enlacement graphs II-5 Condensed graphs III - Realizability and construction III - 1 Realizability -
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. -
Tait's Flyping Conjecture for 4-Regular Graphs
CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector Journal of Combinatorial Theory, Series B 95 (2005) 318–332 www.elsevier.com/locate/jctb Tait’s flyping conjecture for 4-regular graphs Jörg Sawollek Fachbereich Mathematik, Universität Dortmund, 44221 Dortmund, Germany Received 8 July 1998 Available online 19 July 2005 Abstract Tait’s flyping conjecture, stating that two reduced, alternating, prime link diagrams can be connected by a finite sequence of flypes, is extended to reduced, alternating, prime diagrams of 4-regular graphs in S3. The proof of this version of the flyping conjecture is based on the fact that the equivalence classes with respect to ambient isotopy and rigid vertex isotopy of graph embeddings are identical on the class of diagrams considered. © 2005 Elsevier Inc. All rights reserved. Keywords: Knotted graph; Alternating diagram; Flyping conjecture 0. Introduction Very early in the history of knot theory attention has been paid to alternating diagrams of knots and links. At the end of the 19th century Tait [21] stated several famous conjectures on alternating link diagrams that could not be verified for about a century. The conjectures concerning minimal crossing numbers of reduced, alternating link diagrams [15, Theorems A, B] have been proved independently by Thistlethwaite [22], Murasugi [15], and Kauffman [6]. Tait’s flyping conjecture, claiming that two reduced, alternating, prime diagrams of a given link can be connected by a finite sequence of so-called flypes (see [4, p. 311] for Tait’s original terminology), has been shown by Menasco and Thistlethwaite [14], and for a special case, namely, for well-connected diagrams, also by Schrijver [20]. -
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. -
Introduction to Vassiliev Knot Invariants First Draft. Comments
Introduction to Vassiliev Knot Invariants First draft. Comments welcome. July 20, 2010 S. Chmutov S. Duzhin J. Mostovoy The Ohio State University, Mansfield Campus, 1680 Univer- sity Drive, Mansfield, OH 44906, USA E-mail address: [email protected] Steklov Institute of Mathematics, St. Petersburg Division, Fontanka 27, St. Petersburg, 191011, Russia E-mail address: [email protected] Departamento de Matematicas,´ CINVESTAV, Apartado Postal 14-740, C.P. 07000 Mexico,´ D.F. Mexico E-mail address: [email protected] Contents Preface 8 Part 1. Fundamentals Chapter 1. Knots and their relatives 15 1.1. Definitions and examples 15 § 1.2. Isotopy 16 § 1.3. Plane knot diagrams 19 § 1.4. Inverses and mirror images 21 § 1.5. Knot tables 23 § 1.6. Algebra of knots 25 § 1.7. Tangles, string links and braids 25 § 1.8. Variations 30 § Exercises 34 Chapter 2. Knot invariants 39 2.1. Definition and first examples 39 § 2.2. Linking number 40 § 2.3. Conway polynomial 43 § 2.4. Jones polynomial 45 § 2.5. Algebra of knot invariants 47 § 2.6. Quantum invariants 47 § 2.7. Two-variable link polynomials 55 § Exercises 62 3 4 Contents Chapter 3. Finite type invariants 69 3.1. Definition of Vassiliev invariants 69 § 3.2. Algebra of Vassiliev invariants 72 § 3.3. Vassiliev invariants of degrees 0, 1 and 2 76 § 3.4. Chord diagrams 78 § 3.5. Invariants of framed knots 80 § 3.6. Classical knot polynomials as Vassiliev invariants 82 § 3.7. Actuality tables 88 § 3.8. Vassiliev invariants of tangles 91 § Exercises 93 Chapter 4. -
CALIFORNIA STATE UNIVERSITY, NORTHRIDGE P-Coloring Of
CALIFORNIA STATE UNIVERSITY, NORTHRIDGE P-Coloring of Pretzel Knots A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Mathematics By Robert Ostrander December 2013 The thesis of Robert Ostrander is approved: |||||||||||||||||| |||||||| Dr. Alberto Candel Date |||||||||||||||||| |||||||| Dr. Terry Fuller Date |||||||||||||||||| |||||||| Dr. Magnhild Lien, Chair Date California State University, Northridge ii Dedications I dedicate this thesis to my family and friends for all the help and support they have given me. iii Acknowledgments iv Table of Contents Signature Page ii Dedications iii Acknowledgements iv Abstract vi Introduction 1 1 Definitions and Background 2 1.1 Knots . .2 1.1.1 Composition of knots . .4 1.1.2 Links . .5 1.1.3 Torus Knots . .6 1.1.4 Reidemeister Moves . .7 2 Properties of Knots 9 2.0.5 Knot Invariants . .9 3 p-Coloring of Pretzel Knots 19 3.0.6 Pretzel Knots . 19 3.0.7 (p1, p2, p3) Pretzel Knots . 23 3.0.8 Applications of Theorem 6 . 30 3.0.9 (p1, p2, p3, p4) Pretzel Knots . 31 Appendix 49 v Abstract P coloring of Pretzel Knots by Robert Ostrander Master of Science in Mathematics In this thesis we give a brief introduction to knot theory. We define knot invariants and give examples of different types of knot invariants which can be used to distinguish knots. We look at colorability of knots and generalize this to p-colorability. We focus on 3-strand pretzel knots and apply techniques of linear algebra to prove theorems about p-colorability of these knots. -
Arxiv:Math/9807161V1
FOUR OBSERVATIONS ON n-TRIVIALITY AND BRUNNIAN LINKS Theodore B. Stanford Mathematics Department United States Naval Academy 572 Holloway Road Annapolis, MD 21402 [email protected] Abstract. Brunnian links have been known for a long time in knot theory, whereas the idea of n-triviality is a recent innovation. We illustrate the relationship between the two concepts with four short theorems. In 1892, Brunn introduced some nontrivial links with the property that deleting any single component produces a trivial link. Such links are now called Brunnian links. (See Rolfsen [7]). Ohyama [5] introduced the idea of a link which can be independantly undone in n different ways. Here “undo” means to change some set of crossings to make the link trivial. “Independant” means that once you change the crossings in any one of the n sets, the link remains trivial no matter what you do to the other n − 1 sets of crossings. Philosophically, the ideas are similar because, after all, once you delete one component of a Brunnian link the result is trivial no matter what you do to the other components. We shall prove four theorems that make the relationship between Brunnian links and n-triviality more precise. We shall show (Theorem 1) that an n-component Brunnian link is (n − 1)-trivial; (Theorem 2) that an n-component Brunnian link with a homotopically trivial component is n-trivial; (Theorem 3) that an (n − k)-component link constructed from an n-component Brunnian link by twisting along k components is (n − 1)-trivial; and (Theorem 4) that a knot is (n − 1)-trivial if and only if it is “locally n-Brunnian equivalent” to the unknot. -
A Computation of Knot Floer Homology of Special (1,1)-Knots
A COMPUTATION OF KNOT FLOER HOMOLOGY OF SPECIAL (1,1)-KNOTS Jiangnan Yu Department of Mathematics Central European University Advisor: Andras´ Stipsicz Proposal prepared by Jiangnan Yu in part fulfillment of the degree requirements for the Master of Science in Mathematics. CEU eTD Collection 1 Acknowledgements I would like to thank Professor Andras´ Stipsicz for his guidance on writing this thesis, and also for his teaching and helping during the master program. From him I have learned a lot knowledge in topol- ogy. I would also like to thank Central European University and the De- partment of Mathematics for accepting me to study in Budapest. Finally I want to thank my teachers and friends, from whom I have learned so much in math. CEU eTD Collection 2 Abstract We will introduce Heegaard decompositions and Heegaard diagrams for three-manifolds and for three-manifolds containing a knot. We define (1,1)-knots and explain the method to obtain the Heegaard diagram for some special (1,1)-knots, and prove that torus knots and 2- bridge knots are (1,1)-knots. We also define the knot Floer chain complex by using the theory of holomorphic disks and their moduli space, and give more explanation on the chain complex of genus-1 Heegaard diagram. Finally, we compute the knot Floer homology groups of the trefoil knot and the (-3,4)-torus knot. 1 Introduction Knot Floer homology is a knot invariant defined by P. Ozsvath´ and Z. Szabo´ in [6], using methods of Heegaard diagrams and moduli theory of holomorphic discs, combined with homology theory. -
Alternating Knots
ALTERNATING KNOTS WILLIAM W. MENASCO Abstract. This is a short expository article on alternating knots and is to appear in the Concise Encyclopedia of Knot Theory. Introduction Figure 1. P.G. Tait's first knot table where he lists all knot types up to 7 crossings. (From reference [6], courtesy of J. Hoste, M. Thistlethwaite and J. Weeks.) 3 ∼ A knot K ⊂ S is alternating if it has a regular planar diagram DK ⊂ P(= S2) ⊂ S3 such that, when traveling around K , the crossings alternate, over-under- over-under, all the way along K in DK . Figure1 show the first 15 knot types in P. G. Tait's earliest table and each diagram exhibits this alternating pattern. This simple arXiv:1901.00582v1 [math.GT] 3 Jan 2019 definition is very unsatisfying. A knot is alternating if we can draw it as an alternating diagram? There is no mention of any geometric structure. Dissatisfied with this characterization of an alternating knot, Ralph Fox (1913-1973) asked: "What is an alternating knot?" black white white black Figure 2. Going from a black to white region near a crossing. 1 2 WILLIAM W. MENASCO Let's make an initial attempt to address this dissatisfaction by giving a different characterization of an alternating diagram that is immediate from the over-under- over-under characterization. As with all regular planar diagrams of knots in S3, the regions of an alternating diagram can be colored in a checkerboard fashion. Thus, at each crossing (see figure2) we will have \two" white regions and \two" black regions coming together with similarly colored regions being kitty-corner to each other.