An Index-Type Invariant of Knot Diagrams and Bounds for Unknotting Framed Knots
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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. -
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. -
RASMUSSEN INVARIANTS of SOME 4-STRAND PRETZEL KNOTS Se
Honam Mathematical J. 37 (2015), No. 2, pp. 235{244 http://dx.doi.org/10.5831/HMJ.2015.37.2.235 RASMUSSEN INVARIANTS OF SOME 4-STRAND PRETZEL KNOTS Se-Goo Kim and Mi Jeong Yeon Abstract. It is known that there is an infinite family of general pretzel knots, each of which has Rasmussen s-invariant equal to the negative value of its signature invariant. For an instance, homo- logically σ-thin knots have this property. In contrast, we find an infinite family of 4-strand pretzel knots whose Rasmussen invariants are not equal to the negative values of signature invariants. 1. Introduction Khovanov [7] introduced a graded homology theory for oriented knots and links, categorifying Jones polynomials. Lee [10] defined a variant of Khovanov homology and showed the existence of a spectral sequence of rational Khovanov homology converging to her rational homology. Lee also proved that her rational homology of a knot is of dimension two. Rasmussen [13] used Lee homology to define a knot invariant s that is invariant under knot concordance and additive with respect to connected sum. He showed that s(K) = σ(K) if K is an alternating knot, where σ(K) denotes the signature of−K. Suzuki [14] computed Rasmussen invariants of most of 3-strand pret- zel knots. Manion [11] computed rational Khovanov homologies of all non quasi-alternating 3-strand pretzel knots and links and found the Rasmussen invariants of all 3-strand pretzel knots and links. For general pretzel knots and links, Jabuka [5] found formulas for their signatures. Since Khovanov homologically σ-thin knots have s equal to σ, Jabuka's result gives formulas for s invariant of any quasi- alternating− pretzel knot. -
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. -
Results on Nonorientable Surfaces for Knots and 2-Knots
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Dissertations, Theses, and Student Research Papers in Mathematics Mathematics, Department of 8-2021 Results on Nonorientable Surfaces for Knots and 2-knots Vincent Longo University of Nebraska-Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/mathstudent Part of the Geometry and Topology Commons Longo, Vincent, "Results on Nonorientable Surfaces for Knots and 2-knots" (2021). Dissertations, Theses, and Student Research Papers in Mathematics. 111. https://digitalcommons.unl.edu/mathstudent/111 This Article is brought to you for free and open access by the Mathematics, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Dissertations, Theses, and Student Research Papers in Mathematics by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. RESULTS ON NONORIENTABLE SURFACES FOR KNOTS AND 2-KNOTS by Vincent Longo A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Doctor of Philosophy Major: Mathematics Under the Supervision of Professors Alex Zupan and Mark Brittenham Lincoln, Nebraska May, 2021 RESULTS ON NONORIENTABLE SURFACES FOR KNOTS AND 2-KNOTS Vincent Longo, Ph.D. University of Nebraska, 2021 Advisor: Alex Zupan and Mark Brittenham A classical knot is a smooth embedding of the circle S1 into the 3-sphere S3. We can also consider embeddings of arbitrary surfaces (possibly nonorientable) into a 4-manifold, called knotted surfaces. In this thesis, we give an introduction to some of the basics of the studies of classical knots and knotted surfaces, then present some results about nonorientable surfaces bounded by classical knots and embeddings of nonorientable knotted surfaces. -
Knot Theory and the Alexander Polynomial
Knot Theory and the Alexander Polynomial Reagin Taylor McNeill Submitted to the Department of Mathematics of Smith College in partial fulfillment of the requirements for the degree of Bachelor of Arts with Honors Elizabeth Denne, Faculty Advisor April 15, 2008 i Acknowledgments First and foremost I would like to thank Elizabeth Denne for her guidance through this project. Her endless help and high expectations brought this project to where it stands. I would Like to thank David Cohen for his support thoughout this project and through- out my mathematical career. His humor, skepticism and advice is surely worth the $.25 fee. I would also like to thank my professors, peers, housemates, and friends, particularly Kelsey Hattam and Katy Gerecht, for supporting me throughout the year, and especially for tolerating my temporary insanity during the final weeks of writing. Contents 1 Introduction 1 2 Defining Knots and Links 3 2.1 KnotDiagramsandKnotEquivalence . ... 3 2.2 Links, Orientation, and Connected Sum . ..... 8 3 Seifert Surfaces and Knot Genus 12 3.1 SeifertSurfaces ................................. 12 3.2 Surgery ...................................... 14 3.3 Knot Genus and Factorization . 16 3.4 Linkingnumber.................................. 17 3.5 Homology ..................................... 19 3.6 TheSeifertMatrix ................................ 21 3.7 TheAlexanderPolynomial. 27 4 Resolving Trees 31 4.1 Resolving Trees and the Conway Polynomial . ..... 31 4.2 TheAlexanderPolynomial. 34 5 Algebraic and Topological Tools 36 5.1 FreeGroupsandQuotients . 36 5.2 TheFundamentalGroup. .. .. .. .. .. .. .. .. 40 ii iii 6 Knot Groups 49 6.1 TwoPresentations ................................ 49 6.2 The Fundamental Group of the Knot Complement . 54 7 The Fox Calculus and Alexander Ideals 59 7.1 TheFreeCalculus ............................... -
How Can We Say 2 Knots Are Not the Same?
How can we say 2 knots are not the same? SHRUTHI SRIDHAR What’s a knot? A knot is a smooth embedding of the circle S1 in IR3. A link is a smooth embedding of the disjoint union of more than one circle Intuitively, it’s a string knotted up with ends joined up. We represent it on a plane using curves and ‘crossings’. The unknot A ‘figure-8’ knot A ‘wild’ knot (not a knot for us) Hopf Link Two knots or links are the same if they have an ambient isotopy between them. Representing a knot Knots are represented on the plane with strands and crossings where 2 strands cross. We call this picture a knot diagram. Knots can have more than one representation. Reidemeister moves Operations on knot diagrams that don’t change the knot or link Reidemeister moves Theorem: (Reidemeister 1926) Two knot diagrams are of the same knot if and only if one can be obtained from the other through a series of Reidemeister moves. Crossing Number The minimum number of crossings required to represent a knot or link is called its crossing number. Knots arranged by crossing number: Knot Invariants A knot/link invariant is a property of a knot/link that is independent of representation. Trivial Examples: • Crossing number • Knot Representations / ~ where 2 representations are equivalent via Reidemester moves Tricolorability We say a knot is tricolorable if the strands in any projection can be colored with 3 colors such that every crossing has 1 or 3 colors and or the coloring uses more than one color. -
ON the VASSILIEV KNOT INVARIANTS Contents 1
ON THE VASSILIEV KNOT INVARIANTS DROR BAR-NATAN Appeared in Topology 34 (1995) 423–472. Abstract. The theory of knot invariants of finite type (Vassiliev invariants) is described. These invariants turn out to be at least as powerful as the Jones polynomial and its numer- ous generalizations coming from various quantum groups, and it is conjectured that these invariants are precisely as powerful as those polynomials. As invariants of finite type are much easier to define and manipulate than the quantum group invariants, it is likely that in attempting to classify knots, invariants of finite type will play a more fundamental role than the various knot polynomials. Contents 1. Introduction 2 1.1. A sketchy introduction to the introduction 2 1.2. Acknowledgement 3 1.3. Weight systems and invariants of finite type 3 1.4. There are many invariants of finite type 5 1.5. The algebra A of diagrams 6 1.6. The primitive elements of A 8 1.7. How big are A, W and P? 9 1.8. Odds and ends 10 1.9. Summary of spaces and maps 10 2. The basic constructions 10 2.1. The classical knot polynomials 10 2.2. Constructing a weight system from a Vassiliev knot invariant 11 2.3. Framed links 12 2.4. Constructing invariant tensors from Lie algebraic information 13 3. The algebra A of diagrams 15 3.1. Proof of theorem 6 15 3.2. Proof of theorem 7 16 4. Kontsevich’s Knizhnik-Zamolodchikov construction 21 4.1. Connections, curvature, and holonomy 21 4.2. -
On L-Space Knots Obtained from Unknotting Arcs in Alternating Diagrams
New York Journal of Mathematics New York J. Math. 25 (2019) 518{540. On L-space knots obtained from unknotting arcs in alternating diagrams Andrew Donald, Duncan McCoy and Faramarz Vafaee Abstract. Let D be a diagram of an alternating knot with unknotting number one. The branched double cover of S3 branched over D is an L-space obtained by half integral surgery on a knot KD. We denote the set of all such knots KD by D. We characterize when KD 2 D is a torus knot, a satellite knot or a hyperbolic knot. In a different direction, we show that for a given n > 0, there are only finitely many L-space knots in D with genus less than n. Contents 1. Introduction 518 2. Almost alternating diagrams of the unknot 521 2.1. The corresponding operations in D 522 3. The geometry of knots in D 525 3.1. Torus knots in D 525 3.2. Constructing satellite knots in D 526 3.3. Substantial Conway spheres 534 References 538 1. Introduction A knot K ⊂ S3 is an L-space knot if it admits a positive Dehn surgery to an L-space.1 Examples include torus knots, and more broadly, Berge knots in S3 [Ber18]. In recent years, work by many researchers provided insight on the fiberedness [Ni07, Ghi08], positivity [Hed10], and various notions of simplicity of L-space knots [OS05b, Hed11, Krc18]. For more examples of L-space knots, see [Hom11, Hom16, HomLV14, Mot16, MotT14, Vaf15]. Received May 8, 2018. 2010 Mathematics Subject Classification. 57M25, 57M27. -
The Conway Knot Is Not Slice
THE CONWAY KNOT IS NOT SLICE LISA PICCIRILLO Abstract. A knot is said to be slice if it bounds a smooth properly embedded disk in B4. We demonstrate that the Conway knot, 11n34 in the Rolfsen tables, is not slice. This com- pletes the classification of slice knots under 13 crossings, and gives the first example of a non-slice knot which is both topologically slice and a positive mutant of a slice knot. 1. Introduction The classical study of knots in S3 is 3-dimensional; a knot is defined to be trivial if it bounds an embedded disk in S3. Concordance, first defined by Fox in [Fox62], is a 4-dimensional extension; a knot in S3 is trivial in concordance if it bounds an embedded disk in B4. In four dimensions one has to take care about what sort of disks are permitted. A knot is slice if it bounds a smoothly embedded disk in B4, and topologically slice if it bounds a locally flat disk in B4. There are many slice knots which are not the unknot, and many topologically slice knots which are not slice. It is natural to ask how characteristics of 3-dimensional knotting interact with concordance and questions of this sort are prevalent in the literature. Modifying a knot by positive mutation is particularly difficult to detect in concordance; we define positive mutation now. A Conway sphere for an oriented knot K is an embedded S2 in S3 that meets the knot 3 transversely in four points. The Conway sphere splits S into two 3-balls, B1 and B2, and ∗ K into two tangles KB1 and KB2 .