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Associated with each oriented link is the two variable Homflypt polynomial. The Morton-Franks-Williams (MFW) inequality gives rise to an expression for the Homflypt polynomial with MFW coefficient polynomials. These MFW coefficient polynomials are labelled in a braid-dependent manner and may be zero, but display a number of interesting relations. One consequence is an expression for the first three Laurent coefficient polynomials in z as a function of the other coefficient polynomials and three link invariants: the minimum v-degree and v-span of the Homflypt polynomial, and the Conway polynomial. These expressions are used to derive additional properties of the Homflypt polynomial for general n-braid links. One specific result is that the Jones and Homflypt polynomials distinguish the same three-braid links., Comment: 20 pages; this version was rewritten for readability, expands the prior results, and removes a result for 3-braids whose proof was flawed (prop. 2.8 on monotonic properties). This version is the unrevised version accepted for publication, so the theorem, equation, etc. numbering differs from the published version due to those further revisions

Two Dehn surgeries on a knot are called {\it purely cosmetic}, if they yield manifolds that are homeomorphic as oriented manifolds. Suppose there exist purely cosmetic surgeries on a knot in $S^3$, we show that the two surgery slopes must be the opposite of each other. One ingredient of our proof is a Dehn surgery formula for correction terms in Heegaard Floer homology., Comment: v2: 19 pages, incorporates referee's comments

In "Width complexes for knots and 3-manifolds," Jennifer Schultens defines the width complex for a knot in order to understand the different positions a knot can occupy in the 3-sphere and the isotopies between these positions. She poses several questions about these width complexes; in particular, she asks whether the width complex for a knot can have local minima that are not global minima. In this paper, we find an embedding of the unknot that is a local minimum but not a global minimum in its width complex. We use this embedding to exhibit for any knot K infinitely many distinct local minima that are not global minima of the width complex for K., Comment: 9 pages, 4 figures

Thin position for knots in the 3-sphere was introduced by Gabai and has been used in a variety of contexts. We conjecture an analogue to a theorem of Schubert and Schultens concerning the bridge number of satellite knots. For a satellite knot K, we use the companion torus T to provide a lower bound for w(K), proving the conjecture for K with a 2-bridge companion. As a corollary, we find thin position for any satellite knot with a braid pattern and 2-bridge companion., Comment: 10 pages, 3 figures

We introduce colored Jones polynomials of nanowords and their categorification. We also prove the existence of a Khovanov-type bicomplex which has three grades., Comment: For Section 2, the author noticed that we did not have a bicomplex that yields a new link invariant yet in this manuscript. Thus, it should be withdrawn

For a knot K the cube number is a knot invariant defined to be the smallest n for which there is a cube diagram of size n for K. We will show that the cube number detects chirality in all cases computed thus far, and distinguishes certain legendrian knots.

For an oriented knot $K$, we construct a functor from the category of pointed quandles to the category of quandles in three different ways. We also extend the quandle cocycle invariants of knots by using these quandle-valued invariant of knots, and study their properties., Comment: 17 pages, 7 figures, typos and inconsintent notations are corrected

We establish an existence and uniqueness theorem for prime decompositions of theta-curves in $3$-manifolds., Comment: 9 pages, 3 figures

Homologically fibered knots are knots whose exteriors satisfy the same homological conditions as fibered knots. In our previous paper, we observed that for such a knot, higher-order Alexander invariants defined by Cochran, Harvey and Friedl are generally factorized into the part of the Magnus matrix and that of a certain Reidemeister torsion, both of which are known as invariants of homology cylinders over a surface. In this paper, we study more details of the invariants and give some concrete calculations by restricting to the case of the invariants associated with metabelian quotients of their knot groups. We provide examples of explicit calculations of the invariants for all the 12 crossings non-fibered homologically fibered knots., Comment: 25 pages, 18 figures, to appear in Journal of Knot Theory and Its Ramifications

We give formulas expressing Milnor invariants of an n-component link L in the 3-sphere in terms of the HOMFLYPT polynomial as follows. If the Milnor invariant \bar{\mu}_J(L) vanishes for any sequence J with length at most k, then any Milnor \bar{\mu}-invariant \bar{\mu}_I(L) with length between 3 and 2k+1 can be represented as a combination of HOMFLYPT polynomial of knots obtained from the link by certain band sum operations. In particular, the `first non vanishing' Milnor invariants can be always represented as such a linear combination., Comment: Entirely revised version (20 pages). The main result was generalized and extended to Milnor invariants of links, using new arguments. Several corollaries are given, in particular one containing the main result of the previous version. Example and References added

Garoufalidis conjectured a relation between the boundary slopes of a knot and its colored Jones polynomials. According to the conjecture, certain boundary slopes are detected by the sequence of degrees of the colored Jones polynomials. We verify this conjecture for adequate knots, a class that vastly generalizes that of alternating knots., Comment: 7 pages, 3 figures. To appear in Proceedings of the AMS

In the present paper, we construct a simple invariant which provides a sliceness obstruction for {\em free knots}. This obstruction provides a new point of view to the problem of studying cobordisms of curves immersed in 2-surfaces, a problem previously studied by Carter, Turaev, Orr, and others. The obstruction to sliceness is constructed by using the notion of {\em parity} recently introduced by the author into the study of virtual knots and their modifications. This invariant turns out to be an obstruction for cobordisms of higher genera with some additional constraints., Comment: A result on cobordisms of higher genus with some constraints is added; A list of problems is added

We find a formula for the L2 signature of a (p,q) torus knot, which is the integral of the omega-signatures over the unit circle. We then apply this to a theorem of Cochran-Orr-Teichner to prove that the n-twisted doubles of the unknot, for n not 0 or 2, are not slice. This is a new proof of the result first proved by Casson and Gordon., Comment: 11 pages, Version 2 contains a note explaining that the main theorem of the paper has already been proved in earlier work by Kirby and Melvin

We show for an alternating knot the minimal boundary slope of an essential spanning surface is given by the signature plus twice the minimum degree of the Jones polynomial and the maximal boundary slope of an essential spanning surface is given by the signature plus twice the maximum degree of the Jones polynomial. For alternating Montesinos knots, these are the minimal and maximal boundary slopes., Comment: 8 pages, 4 figures

We introduce some chain maps between Khovanov complexes. Each of the chain maps commutes with a chain homotopy map and a retraction maps which obtain a Reidemeister invariance of Khovanov homology., Comment: 7 pages

Link-homotopy and self Delta-equivalence are equivalence relations on links. It was shown by J. Milnor (resp. the last author) that Milnor invariants determine whether or not a link is link-homotopic (resp. self Delta-equivalent) to a trivial link. We study link-homotopy and self Delta-equivalence on a certain component of a link with fixing the rest components, in other words, homotopy and Delta-equivalence of knots in the complement of a certain link. We show that Milnor invariants determine whether a knot in the complement of a trivial link is null-homotopic, and give a sufficient condition for such a knot to be Delta-equivalent to the trivial knot. We also give a sufficient condition for knots in the complements of the trivial knot to be equivalent up to Delta-equivalence and concordance., Comment: 17 pages, 16 figures

It is shown that if the exterior of a link L in the three sphere admits a genus 2 Heegaard splitting, then L has Generalized Property R., Comment: 5 pages, 1 figure; main theorem strengthened to cover all handle number one links; simplified proof for 2-component links; minor style changes

It has been conjectured that for knots $K$ and $K'$ in $S^3$, $w(K#K')= w(K)+w(K')-2$. Scharlemann and Thompson have proposed potential counterexamples to this conjecture. For every $n$, they proposed a family of knots ${K^n_i}$ for which they conjectured that $w(B^n#K^n_i)=w(K^n_i)$ where $B^n$ is a bridge number $n$ knot. We show that for $n>2$ none of the knots in ${K^n_i}$ produces such counterexamples., Comment: 12 pages, 11 figures

It is well known that any two diagrams representing the same oriented link are related by a finite sequence of Reidemeister moves O1, O2 and O3. Depending on orientations of fragments involved in the moves, one may distinguish 4 different versions of each of the O1 and O2 moves, and 8 versions of the O3 move. We introduce a minimal generating set of four oriented Reidemeister moves, which includes two O1 moves, one O2 move, and one O3 move. We then study which other sets of up to 5 oriented moves generate all moves, and show that only few of them do. Some commonly considered sets are shown not to be generating. An unexpected non-equivalence of different O3 moves is discussed., Comment: 14 pages, many figures; v2: significantly improved results; v3: minor changes, publication information

We construct a bicomplex for the categorification of the colored Jones polynomial. This work is motivated by the problem suggested by Anna Beliakova and Stephan Wehrli who discussed the categorification of the colored Jones polynomial in their paper., Comment: 4 pages, 2 figures, Figure 2 and the references were revised; Added a reference and explanation. Corrected a typo, Revised some presentation; version 4, removed some needles parts from section 2: version 5, revised proof and some presentation, version 6, revised proof and some presentation, added important remark, version 7, Revised Section 2

It has been conjectured that the algebraic crossing number of a link is uniquely determined in minimal braid representation. This conjecture is true for many classes of knots and links. The Morton-Franks-Williams inequality gives a lower bound for braid index. And sharpness of the inequality on a knot type implies the truth of the conjecture for the knot type. We prove that there are infinitely many examples of knots and links for which the inequality is not sharp but the conjecture is still true. We also show that if the conjecture is true for K and L, then it is also true for the (p,q)-cable of K and for the connect sum of K and L., Comment: This is the version published by Algebraic & Geometric Topology on 8 December 2006

Two categorifications are given for the arrow polynomial, an extension of the Kauffman bracket polynomial for virtual knots. The arrow polynomial extends the bracket polynomial to infinitely many variables, each variable corresponding to an integer {\it arrow number} calculated from each loop in an oriented state summation for the bracket. The categorifications are based on new gradings associated with these arrow numbers, and give homology theories associated with oriented virtual knots and links via extra structure on the Khovanov chain complex. Applications are given to the estimation of virtual crossing number and surface genus of virtual knots and links. Key Words: Jones polynomial, bracket polynomial, extended bracket polynomial, arrow polynomial, Miyazawa polynomial, Khovanov complex, Khovanov homology, Reidemeister moves, virtual knot theory, differential, partial differential, grading, dotted grading, vector grading., Comment: 34 pages; small stylistic changes

We show that any two diagrams of the same knot or link are connected by a sequence of Reidemeister moves which are sorted by type., Comment: This is the version published by Algebraic & Geometric Topology on 18 May 2006

The Reidemeister torsion construction can be applied to the chain complex used to compute the Khovanov homology of a knot or a link. This defines a volume form on Khovanov homology. The volume form transforms correctly under Reidemeister moves to give an invariant volume on the Khovanov homology. In this paper, its construction and invariance under these moves is demonstrated. Also, some examples of the invariant are presented for particular choices for the bases of homology groups to obtain a numerical invariant of knots and links. In these examples, the algebraic torsion seen in the Khovanov chain complex when homology is computed over $\mathbb{Z}$ is recovered., Comment: 29 pages, 15 figures, 2 tables

Using computer calculations and working with representatives of pretzel tangles we established general adequacy criteria for different classes of knots and links. Based on adequate graphs obtained from all Kauffman states of an alternating link we defined a new numerical invariant: adequacy number, and computed adequacy polynomial which is the invariant of alternating link families. Adequacy polynomial distinguishes (up to mutation) all families of alternating knots and links whose generating link has at most $n=12$ crossings.

We explore Jaeger's state model for the HOMFLYPT polynomial. We reformulate this model in the language of Gauss diagrams and use it to obtain Gauss diagram formulas for a two-parameter family of Vassiliev invariants coming from the HOMFLYPT polynomial. These formulas are new already for invariants of degree 3., Comment: 12 pages, many figures. v2: multiple changes; part on virtual links removed

We describe the Polyak-Viro arrow diagram formulas for the coefficients of the Conway polynomial. As a consequence, we obtain the Conway polynomial as a state sum over some subsets of the crossings of the knot diagram. It turns out to be a simplification of a special case of Jaeger's state model for the HOMFLY polynomial., Comment: 9 pages, many figures

The unknotting number of a knot is bounded from below by its slice genus. It is a well-known fact that the genera and unknotting numbers of torus knots coincide. In this note we characterize quasipositive knots for which the genus bound is sharp: the slice genus of a quasipositive knot equals its unknotting number, if and only if the given knot appears in an unknotting sequence of a torus knot., Comment: 7 pages, 5 figures

We propose to generalize the volume conjecture to knotted trivalent graphs and we prove the conjecture for all augmented knotted trivalent graphs. As a corollary we find that for any link L there is a link containing L for which the volume conjecture holds., Comment: 28 pages, 14 figures Corrected typos, added corollary about arithmeticity

Motivated by the study of ribbon knots we explore symmetric unions, a beautiful construction introduced by Kinoshita and Terasaka in 1957. For symmetric diagrams we develop a two-variable refinement $W_D(s,t)$ of the Jones polynomial that is invariant under symmetric Reidemeister moves. Here the two variables $s$ and $t$ are associated to the two types of crossings, respectively on and off the symmetry axis. From sample calculations we deduce that a ribbon knot can have essentially distinct symmetric union presentations even if the partial knots are the same. If $D$ is a symmetric union diagram representing a ribbon knot $K$, then the polynomial $W_D(s,t)$ nicely reflects the geometric properties of $K$. In particular it elucidates the connection between the Jones polynomials of $K$ and its partial knots $K_\pm$: we obtain $W_D(t,t) = V_K(t)$ and $W_D(-1,t) = V_{K_-}(t) \cdot V_{K_+}(t)$, which has the form of a symmetric product $f(t) \cdot f(t^{-1})$ reminiscent of the Alexander polynomial of ribbon knots., Comment: 28 pages; v2: some improvements and corrections suggested by the referee

For every n-component ribbon link L we prove that the Jones polynomial V(L) is divisible by the polynomial V(O^n) of the trivial link. This integrality property allows us to define a generalized determinant det V(L) := [V(L)/V(O^n)]_(t=-1), for which we derive congruences reminiscent of the Arf invariant: every ribbon link L = (K_1,...,K_n) satisfies det V(L) = det(K_1) >... det(K_n) modulo 32, whence in particular det V(L) = 1 modulo 8. These results motivate to study the power series expansion V(L) = \sum_{k=0}^\infty d_k(L) h^k at t=-1, instead of t=1 as usual. We obtain a family of link invariants d_k(L), starting with the link determinant d_0(L) = det(L) obtained from a Seifert surface S spanning L. The invariants d_k(L) are not of finite type with respect to crossing changes of L, but they turn out to be of finite type with respect to band crossing changes of S. This discovery is the starting point of a theory of surface invariants of finite type, which promises to reconcile quantum invariants with the theory of Seifert surfaces, or more generally ribbon surfaces., Comment: 38 pages, reformatted in G&T style; minor changes suggested by the referee

It is shown that any closed three-manifold M obtained by integral surgery on a knot in the three-sphere can always be constructed from integral surgeries on a 3-component link L with each component being an unknot in the three-sphere. It is also interesting to notice that infinitely many different integral surgeries on the same link L could give the same three-manifold M., Comment: 10 pages, 8 figures

Pairs of genus 2 mutant knots can have different Homfly polynomials, for example some 3-string satellites of Conway mutant pairs. We give examples which have different Kauffman 3-variable polynomials, answering a question raised by Dunfield et al in their study of genus 2 mutants. While pairs of genus 2 mutant knots have the same Jones polynomial, given from the Homfly polynomial by setting v=s^2, we give examples whose Homfly polynomials differ when v=s^3. We also give examples which differ in a Vassiliev invariant of degree 7, in contrast to satellites of Conway mutant knots., Comment: 16 pages, 20 figures

We determine the smooth concordance order of the 3-stranded pretzel knots P(p,q,r) with p,q,r odd. We show that each one of finite order is, in fact, ribbon, thereby proving the slice-ribbon conjecture for this family of knots. As corollaries we give new proofs of results first obtained by Fintushel-Stern and Casson-Gordon., Comment: 21 pages, 5 figures. Significantly expanded version, mistake in previous proof corrected

This paper gives an explicit formula for the SL_2(C)-non-abelian Reidemeister torsion as defined in [Dub06] in the case of twist knots. For hyperbolic twist knots, we also prove that the non-abelian Reidemeister torsion at the holonomy representation can be expressed as a rational function evaluated at the cusp shape of the knot., Comment: 36 pages and 4 figures. Title and Abstract are modified. typos and inconsistent notations corrected. minor changes. to appear in Journal of Knot Theory and Its Ramifications

We consider the operation of Whitehead double on a component of a link and study the behavior of Milnor invariants under this operation. We show that this operation turns a link whose Milnor invariants of length < k are all zero into a link with vanishing Milnor invariants of length < 2k, and we provide formulas for the first non-vanishing ones. As a consequence, we obtain statements relating the notions of link-homotopy and self Delta-equivalence via the Whitehead double operation. By using our result, we show that a Brunnian link L is link-homotopic to the unlink if and only if a link L with a single component Whitehed doubled is self Delta-equivalent to the unlink., Comment: 9 pages, 5 figures. Some minor modifications in this final version

We show that nontrivial classical pretzel knots L(p,q,r) are hyperbolic with eight exceptions which are torus knots. We find Conway polynomials of n-pretzel links using a new computation tree. As applications, we compute the genera of n-pretzel links using these polynomials and find the basket number of pretzel links by showing that the genus and the canonical genus of a pretzel link are the same.

We prove the volume conjecture for an infinite family of links called Whitehead chains that generalizes both the Whitehead link and the Borromean rings., Comment: 11 pages, 1 figure. See also http://www.science.uva.nl/~riveen/papers.html New in version two is a computation for the constant term in the asymptotic expansion. The proof of lemma 5 has been omitted because it is almost the same as that of lemma 4

A classical result states that the determinant of an alternating link is equal to the number of spanning trees in a checkerboard graph of an alternating connected projection of the link. We generalize this result to show that the determinant is the alternating sum of the number of quasi-trees of genus j of the dessin of a non-alternating link. Furthermore, we obtain formulas for other link invariants by counting quantities on dessins. In particular we will show that the $j$-th coefficient of the Jones polynomial is given by sub-dessins of genus less or equal to $j$., Comment: 18 pages, 8 figures; extended version

Bing doubling is an operation which produces a 2-component boundary link B(K) from a knot K. If K is slice, then B(K) is easily seen to be boundary slice. In this paper, we investigate whether the converse holds. Our main result is that if B(K) is boundary slice, then K is algebraically slice. We also show that the Rasmussen invariant can tell that certain Bing doubles are not smoothly slice., Comment: This is the version published by Algebraic & Geometric Topology on 13 December 2006

A C_n-move is a local move on links defined by Habiro and Goussarov, which can be regarded as a `higher order crossing change'. We use Milnor invariants with repeating indices to provide several classification results for links up to C_n-moves, under certain restrictions. Namely, we give a classification up to C_4-moves of 2-component links, 3-component Brunnian links and n-component C_3-trivial links, and we classify n-component link-homotopically trivial Brunnian links up to C_{n+1}-moves., Comment: 16 pages

We define the basket number, the flat plumbing number and the flat plumbing basket number of a link. Then we provide some upperbounds for these plumbing numbers by using Seifert's algorithm. We study the relation between these plumbing numbers and the genera of links., Comment: This paper has been withdrawn by the author due to a crucial error in Theorem 2.2 and 2.4

The purpose of the paper is twofold. First, we give a short proof using the Kontsevich integral for the fact that the restriction of an invariant of degree 2n to (n+1)-component Brunnian links can be expressed as a quadratic form on the Milnor mu-bar link-homotopy invariants of length n+1. Second, we describe the structure of the Brunnian part of the degree 2n-graded quotient of the Goussarov--Vassiliev filtration for (n+1)-component links., Comment: This is the version published by Algebraic & Geometric Topology on 25 September 2006

In this paper, by using the regulator map of Beilinson-Deligne, we show that the quantization condition posed by Gukov is true for the SL_2(\mathbb{C}) character variety of the hyperbolic knot in S^3. Furthermore, we prove that the corresponding \mathbb{C}^{*}-valued 1-form is a secondary characteristic class (Chern-Simons) arising from the vanishing first Chern class of the flat line bundle over the smooth part of the character variety, where the flat line bundle is the pullback of the universal Heisenberg line bundle over \mathbb{C}^{*}\times \mathbb{C}^{*}. The second part of the paper is to define an algebro-geometric invariant of 3-manifolds resulting from the Dehn surgery along a hyperbolic knot complement in $S^3$. We establish a Casson type invariant for these 3-manifolds. In the last section, we explicitly calculate the character variety of the figure-eight knot and discuss some applications., Comment: 19 pages, this is the revised and corrected version

We determine the algebraic structure underlying the geometric complex associated to a link in Bar-Natan's geometric formalism of Khovanov's link homology theory (n=2). We find an isomorphism of complexes which reduces the complex to one in a simpler category. This reduction enables us to specify exactly the amount of information held within the geometric complex and thus state precisely its universality properties for link homology theories. We also determine its strength as a link invariant relative to the different topological quantum field theories (TQFTs) used to create link homology. We identify the most general (universal) TQFT that can be used to create link homology and find that it is "smaller" than the TQFT previously reported by Khovanov as the universal link homology theory. We give a new method of extracting all other link homology theories (including Khovanov's universal TQFT) directly from the universal geometric complex, along with new homology theories that hold a controlled amount of information. We achieve these goals by making a classification of surfaces (with boundaries) modulo the 4TU/S/T relations, a process involving the introduction of genus generating operators. These operators enable us to explore the relation between the geometric complex and its algebraic structure., Comment: This is the version published by Algebraic & Geometric Topology on 1 November 2006

We describe a way of representing finite biquandles with n elements as 2n x 2n block matrices. Any finite biquandle defines an invariant of virtual knots through counting homomorphisms. The counting invariants of non-quandle biquandles can reveal information not present in the knot quandle, such as the non-triviality of the virtual trefoil and various Kishino knots. We also exhibit a virtual knot which is distinguished from its obverse and its reverse by a finite biquandle counting invariant. We classify biquandles of order 2, 3 and 4 and provide a URL for our Maple programs for computing with finite biquandles., Comment: 20 pages. Version 4: changes made as suggested by the referee. To appear in Homology, Homotopy and Applications

Non-classical virtual knots may have non-isomorphic upper and lower quandles. We exploit this property to define the quandle difference invariant, which can detect non-classicality by comparing the numbers of homomorphisms into a finite quandle from a virtual knot's upper and lower quandles. The invariants for small-order finite quandles detect non-classicality in several interesting virtual knots. We compute the difference invariant with the six smallest connected quandles for all non-evenly intersticed Gauss codes with 3 and 4 crossings. For non-evenly intersticed Gauss codes with 4 crossings, the difference invariant detects non-classicality in 86% of codes which have non-trivial upper or lower counting invariant values., Comment: 10 pages. Version 3: Changes made as suggested by referee. To appear in Topology Proceedings

In this article we take up the calculation of the minimum number of colors needed to produce a non-trivial coloring of a knot. This is a knot invariant and we use the torus knots of type (2, n) as our case study. We calculate the minima in some cases. In other cases we estimate upper bounds for these minima leaning on the features of modular arithmetic. We introduce a sequence of transformations on colored diagrams called Teneva Transformations. Each of these Transformations reduces the number of colors in the diagrams by one (up to a point). This allows us to further decrease the upper bounds on these minima. We conjecture on the value of these minima. We apply these Transformations to rational knots., Comment: Final version accepted for publication in Adv. in Appl. Math

A theorem of Kirby states that two framed links in the 3-sphere produce orientation-preserving homeomorphic results of surgery if they are related by a sequence of stabilization and handle-slide moves. The purpose of the present paper is twofold: First, we give a sufficient condition for a sequence of handle-slides on framed links to be able to be replaced with a sequences of algebraically canceling pairs of handle-slides. Then, using the first result, we obtain a refinement of Kirby's calculus for integral homology spheres which involves only +/-1-framed links with zero linking numbers., Comment: This is the version published by Geometry & Topology on 18 September 2006

The theory of link-homotopy, introduced by Milnor, is an important part of the knot theory, with Milnor's mu-bar-invariants being the basic set of link-homotopy invariants. Skein relations for knot and link invariants played a crucial role in the recent developments of knot theory. However, while skein relations for Alexander and Jones invariants are known for quite a while, a similar treatment of Milnor's mu-bar-invariants was missing. We fill this gap by deducing simple skein relations for link-homotopy mu-invariants of string links., Comment: Published by Algebraic and Geometric Topology at http://www.maths.warwick.ac.uk/agt/AGTVol5/agt-5-58.abs.html