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The aim of this paper is to provide a new characterization of isomorphism classes of generalized Alexander quandles in terms of the underlying groups and their automorphisms. This extends the previous result [4, Theorem 1.4]. Additionally, we compute the number of generalized Alexander quandles up to quandle isomorphism arising from groups up to order 127 and their group automorphisms., Comment: 12 pages

The affine index polynomial and the $n$-writhe are invariants of virtual knots which are introduced by Kauffman and by Satoh and Taniguchi independently. They are defined by using indices assigned to each classical crossing, which we call affine indices in this paper. We discuss a relationship between the invariants and generalize them to invariants of virtual links. The invariants for virtual links can be also computed by using cut systems. We also introduce invariants of twisted links by using affine indices.

Twisted knot theory introduced by M. Bourgoin is a generalization of knot theory. It leads us to the notion of twisted virtual braids. In this paper we show theorems for twisted links corresponding to the Alexander theorem and the Markov theorem in knot theory. We also provide a group presentation and a reduced group presentation of the twisted virtual braid group.

Twisted links are a generalization of classical links and correspond to stably equivalence classes of links in thickened surfaces. In this paper we introduce twisted intersection colorings of a diagram and construct two invariants of a twisted link using such colorings. As an application, we show that there exist infinitely many pairs of twisted links such that for each pair the two twisted links are not equivalent but their double coverings are equivalent. We also introduce a method of constructing a pair of twisted links whose double coverings are equivalent.

A doodle is a collection of immersed circles without triple intersections in the $2$-sphere. It was shown by the second author and P.~Tayler that doodles induce commutator identities (identities amongst commutators) in a free group. In this paper we observe this idea more closely by concentrating on doodles with proper noose systems and elementary commutator identities. In particular we show that there is a bijection between cobordism classes of colored doodles and weak equivalence classes of elementary commutator identities.

We present an algorithm that takes as input any element $B$ of the loop braid group and constructs a polynomial $f:\mathbb{R}^5\to\mathbb{R}^2$ such that the intersection of the vanishing set of $f$ and the unit 4-sphere contains the closure of $B$. The polynomials can be used to create real analytic time-dependent vector fields with zero divergence and closed flow lines that move as prescribed by $B$. We also show how a family of surface braids in $\mathbb{C}\times S^1\times S^1$ without branch points can be constructed as the vanishing set of a holomorphic polynomial $f:\mathbb{C}^3\to\mathbb{C}$ on $\mathbb{C}\times S^1\times S^1\subset\mathbb{C}^3$. Both constructions allow us to give upper bounds on the degree of the polynomials., Comment: 32 pages, 4 figures

A quandle is an algebra with two binary operations satisfying three conditions which are related to Reidemeister moves in knot theory. In this paper we introduce the notion of the (canonical) tensor product of a quandle. The tensor product of the knot quandle or the knot symmetric quandle of a surface-link in $4$-space can be used to classify or construct invariants of $1$-handles attaching to the surface-link.

Biquandles and multiple conjugation biquandles are algebras which are related to links and handlebody-links in $3$-space. Cocycles of them can be used to construct state-sum type invariants of links and handlebody-links. In this paper we discuss cocycles of a certain class of biquandles and multiple conjugation biquandles, which we call $G$-Alexander biquandles and $G$-Alexander multiple conjugation biquandles, with a relationship with group cocycles. We give a method to obtain a (biquandle or multiple conjugation biquandle) cocycle of them from a group cocycle., Comment: 31 pages

A virtual doodle is an equivalence class of virtual diagrams under an equivalence relation generated by flat version of classical Reidemesiter moves and virtual Reidemsiter moves such that Reidemeister moves of type 3 are forbidden. In this paper we discuss colorings of virtual diagrams using an algebra, called a doodle switch, and define an invariant of virtual doodles. Besides usual colorings of diagrams, we also introduce doubled colorings.

We discuss Gauss codes of virtual diagrams and virtual doodles. The notion of a left canonical Gauss code is introduced and it is shown that oriented virtual doodles are uniquely presented by left canonical Gauss codes.

A virtual link is a generalization of a classical link that is defined as an equivalence class of certain diagrams, called virtual link diagrams. It is further generalized to a twisted link. Twisted links are in one-to-one correspondence with stable equivalence classes of links in oriented thickenings of (possibly non-orientable) closed surfaces. By definition, equivalent virtual links are also equivalent as twisted links. In this paper, we discuss when two virtual links are equivalent as twisted links, and give a necessary and sufficient condition for this to be the case.

In this paper we compute a presentation for the group of ring motions of the split union of a Hopf link with Euclidean components and a Euclidean circle. A key part of this work is the study of a short exact sequence of groups of ring motions of general ring links in $\mathbb{R}^3$. This sequence allowed us to build the main result from the previously known case of the ring group with one component, which a particular case of the ring groups studied by Brendle and Hatcher. This work is a first step towards the computation of a presentation for groups of motions of H-trivial links with an arbitrary number of components., Comment: v2: corrected acknowledgements (grant number), and minor typos

In this paper, we discuss the (co)homology theory of biquandles, derived biquandle cocycle invariants for oriented surface-links using broken surface diagrams and how to compute the biquandle cocycle invariants from marked graph diagrams. We also develop the shadow (co)homology theory of biquandles and construct the shadow biquandle cocycle invariants for oriented surface-links., Comment: 34 pages, 28 figures. arXiv admin note: text overlap with arXiv:1502.01450

In this paper, we introduce the (co)homology group of a multiple conjugation biquandle. It is the (co)homology group of the prismatic chain complex, which is related to the homology of foams introduced by J. S. Carter, modulo a certain subchain complex. We construct invariants for $S^1$-oriented handlebody-links using $2$-cocycles. When a multiple conjugation biquandle $X\times\mathbb{Z}_{\operatorname{type}X_Y}$ is obtained from a biquandle $X$ using $n$-parallel operations, we provide a $2$-cocycle (or $3$-cocycle) of the multiple conjugation biquandle $X\times\mathbb{Z}_{\operatorname{type}X_Y}$ from a $2$-cocycle (or $3$-cocycle) of the biquandle $X$ equipped with an $X$-set $Y$., Comment: arXiv admin note: text overlap with arXiv:1702.01363; text overlap with arXiv:1704.07792 by other authors

It is well known that surface-links in 4-space can be presented by diagrams on the plane of 4-valent spatial graphs with makers on the vertices, called marked graph diagrams. In this paper we extend the method of presenting surface-links by marked graph diagrams to presenting immersed surface-links. We also give some moves on marked graph diagrams that preserve the ambient isotopy classes of their presenting immersed surface-links.

We introduce a multiple conjugation biquandle, and show that it is the universal algebra to define a semi-arc coloring invariant for handlebody-links. A multiple conjugation biquandle is a generalization of a multiple conjugation quandle. We extend the notion of $n$-parallel biquandle operations for any integer $n$, and show that any biquandle gives a multiple conjugation biquandle with them.

Doodles were introduced in [R. Fenn and P. Taylor, Introducing doodles, Topology of low-dimensional manifolds, pp. 37--43, Lecture Notes in Math., 722, Springer, Berlin, 1979] but were restricted to embedded circles in the 2-sphere. Khovanov, [M. Khovanov, Doodle groups, Trans. Amer. Math. Soc. 349 (1997), 2297--2315], extended the idea to immersed circles in the 2-sphere. In this paper we further extend the range of doodles to any closed orientable surface. Uniqueness of minimal representatives is proved, and various example of doodles are given with their minimal representatives. We also introduce the notion of virtual doodles, and show that there is a natural one-to-one correspondence between doodles on surfaces and virtual doodles on the plane.

We introduce the notion of a ribbon-clasp surface-link, which is a generalization of a ribbon surface-link. We generalize the notion of a normal form on embedded surface-links to the case of immersed surface-links and prove that any (immersed) surface-link can be described in a normal form. It is known that an embedded surface-link is a ribbon surface-link if and only if it can be described in a symmetric normal form. We prove that an (immersed) surface-link is a ribbon-clasp surface-link if and only if it can be described in a symmetric normal form. We also introduce the notion of a ribbon-clasp normal form, which is a simpler version of a symmetric normal form.

It is known that every surface-link can be presented by a marked graph diagram, and such a diagram presentation is unique up to moves called Yoshikawa moves. G. Kuperberg introduced a regular isotopy invariant, called the quantum A_2 invariant, for tangled trivalent graph diagrams. In this paper, a polynomial for a marked graph diagram is defined by use of the quantum A_2 invariant and it is studied how the polynomial changes under Yoshikawa moves. The notion of a ribbon marked graph is introduced to show that this polynomial is useful for an invariant of a ribbon 2-knot., Comment: 31 pages, 22 figures

Twisted links are a generalization of virtual links. As virtual links correspond to abstract links on orientable surfaces, twisted links correspond to abstract links on (possibly non-orientable) surfaces. In this paper, we introduce the notion of the double covering of a twisted link. It is defined by considering the orientation double covering of an abstract link or alternatively by constructing a diagram called a double covering diagram. We also discuss links in thickened surfaces, their diagrams and their stable equivalence classes. Bourgoin's twisted knot group is understood as the virtual knot group of the double covering.

We define a new invariant $w$ for hyperelliptic Lefschetz fibrations over closed oriented surfaces, which counts the number of Dirac braids included intrinsically in the monodromy, by using chart description introduced by the second author. As an application, we prove that two hyperelliptic Lefschetz fibrations of genus $g$ over a given base space are stably isomorphic if and only if they have the same numbers of singular fibers of each type and they have the same value of $w$ if $g$ is odd. We also give examples of pair of hyperelliptic Lefschetz fibrations with the same numbers of singular fibers of each type which are not stably isomorphic., Comment: 30 pages, 32 figures; (v2) the title changed, Section 1 rewritten, remarks added. arXiv admin note: text overlap with arXiv:1403.7946

By using the cohomology theory of quandles, quandle cocycle invariants and shadow quandle cocycle invariants are defined for oriented links and surface-links via broken surface diagrams. By using symmetric quandles, symmetric quandle cocycle invariants are also defined for unoriented links and surface-links via broken surface diagrams. A marked graph diagram is a link diagram possibly with $4$-valent vertices equipped with markers. S. J. Lomonaco, Jr. and K. Yoshikawa introduced a method of describing surface-links by using marked graph diagrams. In this paper, we give interpretations of these quandle cocycle invariants in terms of marked graph diagrams, and introduce a method of computing them from marked graph diagrams., Comment: 40 pages, 29 figures

A. S. Lipson constructed two state models yielding the same classical link invariant obtained from the Kauffman polynomial $F(a,z)$. In this paper, we apply Lipson's state models to marked graph diagrams of surface-links, and observe when they induce surface-link invariants., Comment: 21 pages, 16 figures

Quandle cocycle invariants form a powerful and well developed tool in knot theory. This paper treats their variations - namely, positive and twisted quandle cocycle invariants, and shadow invariants. We interpret the former as particular cases of the latter. As an application, several constructions from the shadow world are extended to the positive and twisted cases. Another application is a sharpening of twisted quandle cocycle invariants for multi-component links., Comment: 13 pages. In version 2, a new co-author was added, and Section 4 was considerably extended

We employ a certain labeled finite graph, called a chart, in a closed oriented surface for describing the monodromy of a(n achiral) Lefschetz fibration over the surface. Applying charts and their moves with respect to Wajnryb's presentation of mapping class groups, we first generalize a signature formula for Lefschetz fibrations over the 2-sphere obtained by Endo and Nagami to that for Lefschetz fibrations over arbitrary closed oriented surface. We then show two theorems on stabilization of Lefschetz fibrations under fiber summing with copies of a typical Lefschetz fibration as generalizations of a theorem of Auroux., Comment: 30 pages, 29 figures; (v2) a co-author added; (v3) proofs simplified, remarks and references added, typos corrected; (v4) symbols simplified, examples added, typos corrected

J. Boyle classified 1-handles attached to surface-knots, that are closed and connected surfaces embedded in the Euclidean 4-space, in the case that the surfaces are oriented and 1-handles are orientable with respect to the orientations of the surfaces. In that case, the equivalence classes of 1-handles correspond to the equivalence classes of cords attached to the surface-knot, and correspond to the double cosets of the peripheral subgroup of the knot group. In this paper, we classify cords and cords with local orientations attached to (possibly non-orientable) surface-knots. And we classify 1-handles attached to surface-knots in the case that the surface-knots are oriented and 1-handles are non-orientable, and in the case that the surface-knots are non-orientable., Comment: It will appear in Boletin de la Sociedad Matematica Mexicana

A symmetric quandle is a quandle with a good involution. For a knot in \$R^3\$, a knotted surface in \$R^4\$ or an \$n\$-manifold knot in \$R^{n+2}\$, the knot symmetric quandle is defined. We introduce the notion of a symmetric quandle presentation, and show how to get a presentation of a knot symmetric quandle from a diagram., Comment: 13 pages. It will appear in Banach Center Publications

In this paper, we study quandles of cyclic type, which form a particular subclass of finite quandles. The main result of this paper describes the set of isomorphism classes of quandles of cyclic type in terms of certain cyclic permutations. By using our description, we give a direct classification of quandles of cyclic type with cardinality up to $12$., Comment: 14 pages

The notion of a braid is generalized into two and three dimensions. Two-dimensional braids are described by braid monodromies or graphics called charts. In this paper we introduce the notion of curtains, and show that three-dimensional braids are described by braid monodromies or curtains., Comment: Eight color figures

Chart descriptions are a graphic method to describe monodromy representations of various topological objects. Here we introduce a chart description for hyperelliptic Lefschetz fibrations, and show that any hyperelliptic Lefschetz fibration can be stabilized by fiber-sum with certain basic Lefschetz fibrations., Comment: 19 pages, 22 figures. arXiv admin note: substantial text overlap with arXiv:1106.0569

Techniques for constructing codimension 2 embeddings and immersions of the 2 and 3-fold branched covers of the 3 and 4-dimensional spheres are presented. These covers are in braided form, and it is in this sense that they are folded. More precisely the composition of the embedding (or immersion) and the canonical projection induces the branched covering map. In the case of the 3-sphere, the branch locus is a knotted or linked curve in space, the 2-fold branched cover always embeds, and the 3-fold branch cover might be immersed. In the case of the 4-sphere, the branch locus is a knotted or linked orientable surface (surface knot or link), and the 2-fold branched cover is always embedded. We give an explicit embedding of the 3-fold branched cover of the 4-sphere when the branch set is the spun trefoil., Comment: 28 pages. Lots of color figures

We study simple branched coverings of degree d of the 2- and 3- dimensional sphere branched over oriented links. We demonstrate how to use braid charts to develop embeddings of these into $S^k \times D^2$ for $k=2,3 when $d=2,3$. This is an initial part of our study and represents the manuscript submitted to the RIMS workshop at Intelligence of Low Dimensional Topology., Comment: 18 pages, 19 figures

We introduce two kinds of structures, called v-structures and t-structures, on biquandles. These structures are used for colorings of diagrams of virtual links and twisted links such that the numbers of colorings are invariants. Given a biquandle or a quandle, we give a method of constructing a biquandle with these structures. Using the numbers of colorings, we show that Bourgoin's twofoil and non-orientable virtual $m$-foils do not represent virtual links.

Chart descriptions are a graphic method to describe monodromy representations of various topological objects. Here we introduce a chart description for genus-two Lefschetz fibrations, and show that any genus-two Lefschetz fibration can be stabilized by fiber-sum with certain basic Lefschetz fibrations., Comment: 17 pages, 18 figures

In this article, we generalize the classification of genus one Lefschetz fibrations to genus one simplified broken Lefschetz fibrations, which have fibers of genera one and zero. We classify genus one Lefschetz fibrations over the 2-disk with certain non-trivial global monodromies using chart descriptions, and identify the 4-manifolds admitting genus one simplified broken Lefschetz fibrations., Comment: 22 pages, 14 figures. Included a previously overlooked case in the proof of Theorem 13