On Unknotting Numbers and Knot Trivadjacency
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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 -
Jones Polynomial for Graphs of Twist Knots
Available at Applications and Applied http://pvamu.edu/aam Mathematics: Appl. Appl. Math. An International Journal ISSN: 1932-9466 (AAM) Vol. 14, Issue 2 (December 2019), pp. 1269 – 1278 Jones Polynomial for Graphs of Twist Knots 1Abdulgani ¸Sahinand 2Bünyamin ¸Sahin 1Faculty of Science and Letters 2Faculty of Science Department Department of Mathematics of Mathematics Agrı˘ Ibrahim˙ Çeçen University Selçuk University Postcode 04100 Postcode 42130 Agrı,˘ Turkey Konya, Turkey [email protected] [email protected] Received: January 1, 2019; Accepted: March 16, 2019 Abstract We frequently encounter knots in the flow of our daily life. Either we knot a tie or we tie a knot on our shoes. We can even see a fisherman knotting the rope of his boat. Of course, the knot as a mathematical model is not that simple. These are the reflections of knots embedded in three- dimensional space in our daily lives. In fact, the studies on knots are meant to create a complete classification of them. This has been achieved for a large number of knots today. But we cannot say that it has been terminated yet. There are various effective instruments while carrying out all these studies. One of these effective tools is graphs. Graphs are have made a great contribution to the development of algebraic topology. Along with this support, knot theory has taken an important place in low dimensional manifold topology. In 1984, Jones introduced a new polynomial for knots. The discovery of that polynomial opened a new era in knot theory. In a short time, this polynomial was defined by algebraic arguments and its combinatorial definition was made. -
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]. -
Knot Theory: an Introduction
Knot theory: an introduction Zhen Huan Center for Mathematical Sciences Huazhong University of Science and Technology USTC, December 25, 2019 Knots in daily life Shoelace Zhen Huan (HUST) Knot theory: an introduction USTC, December 25, 2019 2 / 40 Knots in daily life Braids Zhen Huan (HUST) Knot theory: an introduction USTC, December 25, 2019 3 / 40 Knots in daily life Knot bread Zhen Huan (HUST) Knot theory: an introduction USTC, December 25, 2019 4 / 40 Knots in daily life German bread: the pretzel Zhen Huan (HUST) Knot theory: an introduction USTC, December 25, 2019 5 / 40 Knots in daily life Rope Mat Zhen Huan (HUST) Knot theory: an introduction USTC, December 25, 2019 6 / 40 Knots in daily life Chinese Knots Zhen Huan (HUST) Knot theory: an introduction USTC, December 25, 2019 7 / 40 Knots in daily life Knot bracelet Zhen Huan (HUST) Knot theory: an introduction USTC, December 25, 2019 8 / 40 Knots in daily life Knitting Zhen Huan (HUST) Knot theory: an introduction USTC, December 25, 2019 9 / 40 Knots in daily life More Knitting Zhen Huan (HUST) Knot theory: an introduction USTC, December 25, 2019 10 / 40 Knots in daily life DNA Zhen Huan (HUST) Knot theory: an introduction USTC, December 25, 2019 11 / 40 Knots in daily life Wire Mess Zhen Huan (HUST) Knot theory: an introduction USTC, December 25, 2019 12 / 40 History of Knots Chinese talking knots (knotted strings) Inca Quipu Zhen Huan (HUST) Knot theory: an introduction USTC, December 25, 2019 13 / 40 History of Knots Endless Knot in Buddhism Zhen Huan (HUST) Knot theory: an introduction -
Categorified Invariants and the Braid Group
PROCEEDINGS OF THE AMERICAN MATHEMATICAL SOCIETY Volume 143, Number 7, July 2015, Pages 2801–2814 S 0002-9939(2015)12482-3 Article electronically published on February 26, 2015 CATEGORIFIED INVARIANTS AND THE BRAID GROUP JOHN A. BALDWIN AND J. ELISENDA GRIGSBY (Communicated by Daniel Ruberman) Abstract. We investigate two “categorified” braid conjugacy class invariants, one coming from Khovanov homology and the other from Heegaard Floer ho- mology. We prove that each yields a solution to the word problem but not the conjugacy problem in the braid group. In particular, our proof in the Khovanov case is completely combinatorial. 1. Introduction Recall that the n-strand braid group Bn admits the presentation σiσj = σj σi if |i − j|≥2, Bn = σ1,...,σn−1 , σiσj σi = σjσiσj if |i − j| =1 where σi corresponds to a positive half twist between the ith and (i + 1)st strands. Given a word w in the generators σ1,...,σn−1 and their inverses, we will denote by σ(w) the corresponding braid in Bn. Also, we will write σ ∼ σ if σ and σ are conjugate elements of Bn. As with any group described in terms of generators and relations, it is natural to look for combinatorial solutions to the word and conjugacy problems for the braid group: (1) Word problem: Given words w, w as above, is σ(w)=σ(w)? (2) Conjugacy problem: Given words w, w as above, is σ(w) ∼ σ(w)? The fastest known algorithms for solving Problems (1) and (2) exploit the Gar- side structure(s) of the braid group (cf. -
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. -
Alexander Polynomial, Finite Type Invariants and Volume of Hyperbolic
ISSN 1472-2739 (on-line) 1472-2747 (printed) 1111 Algebraic & Geometric Topology Volume 4 (2004) 1111–1123 ATG Published: 25 November 2004 Alexander polynomial, finite type invariants and volume of hyperbolic knots Efstratia Kalfagianni Abstract We show that given n > 0, there exists a hyperbolic knot K with trivial Alexander polynomial, trivial finite type invariants of order ≤ n, and such that the volume of the complement of K is larger than n. This contrasts with the known statement that the volume of the comple- ment of a hyperbolic alternating knot is bounded above by a linear function of the coefficients of the Alexander polynomial of the knot. As a corollary to our main result we obtain that, for every m> 0, there exists a sequence of hyperbolic knots with trivial finite type invariants of order ≤ m but ar- bitrarily large volume. We discuss how our results fit within the framework of relations between the finite type invariants and the volume of hyperbolic knots, predicted by Kashaev’s hyperbolic volume conjecture. AMS Classification 57M25; 57M27, 57N16 Keywords Alexander polynomial, finite type invariants, hyperbolic knot, hyperbolic Dehn filling, volume. 1 Introduction k i Let c(K) denote the crossing number and let ∆K(t) := Pi=0 cit denote the Alexander polynomial of a knot K . If K is hyperbolic, let vol(S3 \ K) denote the volume of its complement. The determinant of K is the quantity det(K) := |∆K(−1)|. Thus, in general, we have k det(K) ≤ ||∆K (t)|| := X |ci|. (1) i=0 It is well know that the degree of the Alexander polynomial of an alternating knot equals twice the genus of the knot.