Unknown Values in the Table of 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. -
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. -
(1,1)-Decompositions of Rational Pretzel Knots
East Asian Math. J. Vol. 32 (2016), No. 1, pp. 077{084 http://dx.doi.org/10.7858/eamj.2016.008 (1,1)-DECOMPOSITIONS OF RATIONAL PRETZEL KNOTS Hyun-Jong Song* Abstract. We explicitly derive diagrams representing (1,1)-decompositions of rational pretzel knots Kβ = M((−2; 1); (3; 1); (j6β + 1j; β)) from four unknotting tunnels for β = 1; −2 and 2. 1. Preliminaries Let V be an unknotted solid torus and let α be a properly embedded arc in V . We say that α is trivial in V if and only if there exists an arc β in @V joining the two end points of α , and a 2-disk D in V such that the boundary @D of D is a union of α and β. Such a disk D is called a cancelling disk of α. Equivalently α is trivial in V if and only if H = V − N(α)◦, the complement of the open tubular neighbourhood N(α) of α in V is a handlebody of genus 2. Note that a cancelling disk of the trivial arc α and a meridian disk of V disjoint from α contribute a meridian disk system of the handlebody H A knot K in S3 is referred to as admitting genus 1, 1-bridge decomposition 3 or (1,1)-decomposition for short if and only if (S ;K) is split into pairs (Vi; αi) (i = 1; 2) of trivial arcs in solid tori determined by a Heegaard torus T = @Vi of S3. Namely we have: 3 (S ;K) = (V1; α1) [T (V2; α2) . -
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. .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .... .. .... .... .... .... .... .... .... .... .... ... -
Of the American Mathematical Society August 2017 Volume 64, Number 7
ISSN 0002-9920 (print) ISSN 1088-9477 (online) of the American Mathematical Society August 2017 Volume 64, Number 7 The Mathematics of Gravitational Waves: A Two-Part Feature page 684 The Travel Ban: Affected Mathematicians Tell Their Stories page 678 The Global Math Project: Uplifting Mathematics for All page 712 2015–2016 Doctoral Degrees Conferred page 727 Gravitational waves are produced by black holes spiraling inward (see page 674). American Mathematical Society LEARNING ® MEDIA MATHSCINET ONLINE RESOURCES MATHEMATICS WASHINGTON, DC CONFERENCES MATHEMATICAL INCLUSION REVIEWS STUDENTS MENTORING PROFESSION GRAD PUBLISHING STUDENTS OUTREACH TOOLS EMPLOYMENT MATH VISUALIZATIONS EXCLUSION TEACHING CAREERS MATH STEM ART REVIEWS MEETINGS FUNDING WORKSHOPS BOOKS EDUCATION MATH ADVOCACY NETWORKING DIVERSITY blogs.ams.org Notices of the American Mathematical Society August 2017 FEATURED 684684 718 26 678 Gravitational Waves The Graduate Student The Travel Ban: Affected Introduction Section Mathematicians Tell Their by Christina Sormani Karen E. Smith Interview Stories How the Green Light was Given for by Laure Flapan Gravitational Wave Research by Alexander Diaz-Lopez, Allyn by C. Denson Hill and Paweł Nurowski WHAT IS...a CR Submanifold? Jackson, and Stephen Kennedy by Phillip S. Harrington and Andrew Gravitational Waves and Their Raich Mathematics by Lydia Bieri, David Garfinkle, and Nicolás Yunes This season of the Perseid meteor shower August 12 and the third sighting in June make our cover feature on the discovery of gravitational waves -
Arxiv:1208.5857V2 [Math.GT] 27 Nov 2012 Hscs Ecncnie Utetspace Quotient a Consider Can We Case This Hoe 1.1
A GOOD PRESENTATION OF (−2, 3, 2s + 1)-TYPE PRETZEL KNOT GROUP AND R-COVERED FOLIATION YASUHARU NAKAE Abstract. Let Ks bea(−2, 3, 2s+1)-type Pretzel knot (s ≧ 3) and EKs (p/q) be a closed manifold obtained by Dehn surgery along Ks with a slope p/q. We prove that if q > 0, p/q ≧ 4s + 7 and p is odd, then EKs (p/q) cannot contain an R-covered foliation. This result is an extended theorem of a part of works of Jinha Jun for (−2, 3, 7)-Pretzel knot. 1. Introduction In this paper, we will discuss non-existence of R-covered foliations on a closed 3-manifold obtained by Dehn surgery along some class of a Pretzel knot. A codimension one, transversely oriented foliation F on a closed 3-manifold M is called a Reebless foliation if F does not contain a Reeb component. By the theorems of Novikov [13], Rosenberg [17], and Palmeira [14], if M is not homeo- morphic to S2 × S1 and contains a Reebless foliation, then M has properties that the fundamental group of M is infinite, the universal cover M is homeomorphic to R3 and all leaves of its lifted foliation F on M are homeomorphic to a plane. In this case we can consider a quotient space T = M/F, and Tfis called a leaf space of F. The leaf space T becomes a simplye connectedf 1-manifold, but it might be a non-Hausdorff space. If the leaf space is homeomorphicf e to R, F is called an R- covered foliation. -
Mutant Knots and Intersection Graphs 1 Introduction
Mutant knots and intersection graphs S. V. CHMUTOV S. K. LANDO We prove that if a finite order knot invariant does not distinguish mutant knots, then the corresponding weight system depends on the intersection graph of a chord diagram rather than on the diagram itself. Conversely, if we have a weight system depending only on the intersection graphs of chord diagrams, then the composition of such a weight system with the Kontsevich invariant determines a knot invariant that does not distinguish mutant knots. Thus, an equivalence between finite order invariants not distinguishing mutants and weight systems depending on intersections graphs only is established. We discuss relationship between our results and certain Lie algebra weight systems. 57M15; 57M25 1 Introduction Below, we use standard notions of the theory of finite order, or Vassiliev, invariants of knots in 3-space; their definitions can be found, for example, in [6] or [14], and we recall them briefly in Section 2. All knots are assumed to be oriented. Two knots are said to be mutant if they differ by a rotation of a tangle with four endpoints about either a vertical axis, or a horizontal axis, or an axis perpendicular to the paper. If necessary, the orientation inside the tangle may be replaced by the opposite one. Here is a famous example of mutant knots, the Conway (11n34) knot C of genus 3, and Kinoshita–Terasaka (11n42) knot KT of genus 2 (see [1]). C = KT = Note that the change of the orientation of a knot can be achieved by a mutation in the complement to a trivial tangle. -
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. -
Fibered Knots and Potential Counterexamples to the Property 2R and Slice-Ribbon Conjectures
Fibered knots and potential counterexamples to the Property 2R and Slice-Ribbon Conjectures with Bob Gompf and Abby Thompson June 2011 Berkeley FreedmanFest Theorem (Gabai 1987) If surgery on a knot K ⊂ S3 gives S1 × S2, then K is the unknot. Question: If surgery on a link L of n components gives 1 2 #n(S × S ), what is L? Homology argument shows that each pair of components in L is algebraically unlinked and the surgery framing on each component of L is the 0-framing. Conjecture (Naive) 1 2 If surgery on a link L of n components gives #n(S × S ), then L is the unlink. Why naive? The result of surgery is unchanged when one component of L is replaced by a band-sum to another. So here's a counterexample: The 4-dimensional view of the band-sum operation: Integral surgery on L ⊂ S3 $ 2-handle addition to @B4. Band-sum operation corresponds to a 2-handle slide U' V' U V Effect on dual handles: U slid over V $ V 0 slid over U0. The fallback: Conjecture (Generalized Property R) 3 1 2 If surgery on an n component link L ⊂ S gives #n(S × S ), then, perhaps after some handle-slides, L becomes the unlink. Conjecture is unknown even for n = 2. Questions: If it's not true, what's the simplest counterexample? What's the simplest knot that could be part of a counterexample? A potential counterexample must be slice in some homotopy 4-ball: 3 S L 3-handles L 2-handles Slice complement is built from link complement by: attaching copies of (D2 − f0g) × D2 to (D2 − f0g) × S1, i. -
The Tree of Knot Tunnels
Geometry & Topology 13 (2009) 769–815 769 The tree of knot tunnels SANGBUM CHO DARRYL MCCULLOUGH We present a new theory which describes the collection of all tunnels of tunnel number 1 knots in S 3 (up to orientation-preserving equivalence in the sense of Hee- gaard splittings) using the disk complex of the genus–2 handlebody and associated structures. It shows that each knot tunnel is obtained from the tunnel of the trivial knot by a uniquely determined sequence of simple cabling constructions. A cabling construction is determined by a single rational parameter, so there is a corresponding numerical parameterization of all tunnels by sequences of such parameters and some additional data. Up to superficial differences in definition, the final parameter of this sequence is the Scharlemann–Thompson invariant of the tunnel, and the other parameters are the Scharlemann–Thompson invariants of the intermediate tunnels produced by the constructions. We calculate the parameter sequences for tunnels of 2–bridge knots. The theory extends easily to links, and to allow equivalence of tunnels by homeomorphisms that may be orientation-reversing. 57M25 Introduction In this work we present a new descriptive theory of the tunnels of tunnel number 1 knots in S 3 , or equivalently, of genus–2 Heegaard splittings of tunnel number 1 knot exteriors. At its heart is a bijective correspondence between the set of equivalence classes of all tunnels of all tunnel number 1 knots and a subset of the vertices of a certain tree T . In fact, T is bipartite, and the tunnel vertex subset is exactly one of its two classes of vertices. -
Non-Orientable Lagrangian Cobordisms Between Legendrian Knots
NON-ORIENTABLE LAGRANGIAN COBORDISMS BETWEEN LEGENDRIAN KNOTS ORSOLA CAPOVILLA-SEARLE AND LISA TRAYNOR 3 Abstract. In the symplectization of standard contact 3-space, R × R , it is known that an orientable Lagrangian cobordism between a Leg- endrian knot and itself, also known as an orientable Lagrangian endo- cobordism for the Legendrian knot, must have genus 0. We show that any Legendrian knot has a non-orientable Lagrangian endocobordism, and that the crosscap genus of such a non-orientable Lagrangian en- docobordism must be a positive multiple of 4. The more restrictive exact, non-orientable Lagrangian endocobordisms do not exist for any exactly fillable Legendrian knot but do exist for any stabilized Legen- drian knot. Moreover, the relation defined by exact, non-orientable La- grangian cobordism on the set of stabilized Legendrian knots is symmet- ric and defines an equivalence relation, a contrast to the non-symmetric relation defined by orientable Lagrangian cobordisms. 1. Introduction Smooth cobordisms are a common object of study in topology. Motivated by ideas in symplectic field theory, [19], Lagrangian cobordisms that are cylindrical over Legendrian submanifolds outside a compact set have been an active area of research interest. Throughout this paper, we will study 3 Lagrangian cobordisms in the symplectization of the standard contact R , 3 t namely the symplectic manifold (R×R ; d(e α)) where α = dz−ydx, that co- incide with the cylinders R×Λ+ (respectively, R×Λ−) when the R-coordinate is sufficiently positive (respectively, negative). Our focus will be on non- orientable Lagrangian cobordisms between Legendrian knots Λ+ and Λ− and non-orientable Lagrangian endocobordisms, which are non-orientable Lagrangian cobordisms with Λ+ = Λ−.