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In this paper we define novel topological invariants of doubly periodic tangles (DP tangles). DP tangles are embeddings of curves in the thickened plane with translational symmetries in two independent directions. We first organize the components of a DP tangle into different interlinked compounds, which are invariants of a DP tangle. The notion of interlinked compound leads to the classification of DP tangles according to their directional type. We then prove that the directional type is an invariant of DP tangles using the concept of axis-motif, which can be viewed as the blueprint of a DP tangle.

In this paper we present recent results on the computation of skein modules of 3-manifolds using braids and appropriate knot algebras. Skein modules generalize knot polynomials in $S^3$ to knot polynomials in arbitrary 3-manifolds and they have become extremely essential algebraic tools in the study of 3-manifolds. In this paper we present the braid approach to the HOMFLYPT and the Kauffman bracket skein modules of the Solid Torus ST and the lens spaces $L(p,1)$ and $S^1\times S^2$., Comment: 34 pages, 31 figures. arXiv admin note: text overlap with arXiv:2005.00737, arXiv:2204.00410, arXiv:1702.06290, arXiv:2307.12275

Doubly periodic tangles, or \textit{DP tangles}, are embeddings of curves in the thickened plane that are periodically repeated in two directions. They are completely defined by their generating cells, the {\it flat motifs}, which can be chosen in infinitely many ways. DP tangles are used in modelling materials and physical systems of entangled filaments. In this paper we establish the mathematical framework of the topological theory of DP tangles. We first introduce a formal definition of DP tangles as topological objects and proceed with an exhaustive analysis in order to characterize the notion of {\it equivalence} between DP tangles and between their flat motifs. We further generalize our results to other diagrammatic categories, such as framed, virtual, singular, pseudo and bonded DP tangles, which could be used in novel applications.

In this paper we present two different ways for computing the Kauffman bracket skein module of $S^1\times S^2$, ${\rm KBSM}\left(S^1\times S^2\right)$, via braids. We first extend the universal Kauffman bracket type invariant $V$ for knots and links in the Solid Torus ST, which is obtained via a unique Markov trace constructed on the generalized Temperley-Lieb algebra of type B, to an invariant for knots and links in $S^1\times S^2$. We do that by imposing on $V$ relations coming from the {\it braid band moves}. These moves reflect isotopy in $S^1\times S^2$ and they are similar to the second Kirby move. We obtain an infinite system of equations, a solution of which, is equivalent to computing ${\rm KBSM}\left(S^1\times S^2\right)$. We show that ${\rm KBSM}\left(S^1\times S^2\right)$ is not torsion free and that its free part is generated by the unknot (or the empty knot). We then present a diagrammatic method for computing ${\rm KBSM}\left(S^1\times S^2\right)$ via braids. Using this diagrammatic method we also obtain a closed formula for the torsion part of ${\rm KBSM}\left(S^1\times S^2\right)$., Comment: 25 pages, 20 figures. arXiv admin note: substantial text overlap with arXiv:2204.00410

In this paper we develop a braid theoretic approach for computing the Kauffman bracket skein module of the lens spaces $L(p,q)$, KBSM($L(p,q)$), for $q\neq 0$. For doing this, we introduce a new concept, that of an {\it unoriented braid}. Unoriented braids are obtained from standard braids by ignoring the natural top-to-bottom orientation of the strands. We first define the {\it generalized Temperley-Lieb algebra of type B}, $TL_{1, n}$, which is related to the knot theory of the solid torus ST, and we obtain the universal Kauffman bracket type invariant, $V$, for knots and links in ST, via a unique Markov trace constructed on $TL_{1, n}$. The universal invariant $V$ is equivalent to the KBSM(ST). For passing now to the KBSM($L(p,q)$), we impose on $V$ relations coming from the band moves (or slide moves), that is, moves that reflect isotopy in $L(p,q)$ but not in ST, and which reflect the surgery description of $L(p,q)$, obtaining thus, an infinite system of equations. By construction, solving this infinite system of equations is equivalent to computing KBSM($L(p,q)$). We first present the solution for the case $q=1$, which corresponds to obtaining a new basis, $\mathcal{B}_{p}$, for KBSM($L(p,1)$) with $(\lfloor p/2 \rfloor +1)$ elements. We note that the basis $\mathcal{B}_{p}$ is different from the one obtained by Hoste \& Przytycki. For dealing with the complexity of the infinite system for the case $q>1$, we first show how the new basis $\mathcal{B}_{p}$ of KBSM($L(p,1)$) can be obtained using a diagrammatic approach based on unoriented braids, and we finally extend our result to the case $q>1$., Comment: 30 pages, 17 figures

In this paper we compute the Kauffman bracket skein module of the complement of $(2, 2p+1)$-torus knots, $KBSM(T_{(2, 2p+1)}^c)$, via braids. We start by considering geometric mixed braids in $S^3$, the closure of which are mixed links in $S^3$ that represent links in the complement of $(2, 2p+1)$-torus knots, $T_{(2, 2p+1)}^c$. Using the technique of parting and combing, we obtain algebraic mixed braids, that is, mixed braids that belong to the mixed braid group $B_{2, n}$ and that are followed by their ``coset'' part, that represents $T_{(2, 2p+1)}^c$. In that way we show that links in $T_{(2, 2p+1)}^c$ may be pushed to the genus 2 handlebody, $H_2$, and we establish a relation between $KBSM(T_{(2, 2p+1)}^c)$ and $KBSM(H_2)$. In particular, we show that in order to compute $KBSM(T_{(2, 2p+1)}^c)$ it suffices to consider a basis of $KBSM(H_2)$ and study the effect of combing on elements in this basis. We consider the standard basis of $KBSM(H_2)$ and we show how to treat its elements in $KBSM(T_{(2, 2p+1)}^c)$, passing through many different spanning sets for $KBSM(T_{(2, 2p+1)}^c)$. These spanning sets form the intermediate steps in order to reach at the set $\mathcal{B}_{T_{(2, 2p+1)}^c}$, which, using an ordering relation and the notion of total winding, we prove that it forms a basis for $KBSM(T_{(2, 2p+1)}^c)$. We finally consider c.c.o. 3-manifolds $M$ obtained from $S^3$ by surgery along the trefoil knot and we discuss steps needed in order to compute the Kauffman bracket skein module of $M$. We first demonstrate the process described before for computing the Kauffman bracket skein module of the complement of the trefoil, $KBSM(Tr^c)$, and we study the effect of braid band moves on elements in the basis of $KBSM(Tr^c)$. These moves reflect isotopy in $M$ and are similar to the second Kirby moves., Comment: 27 pages, 18 figures

In this paper we introduce and study the theory of pseudo links in the genus $g$ handlebody, $H_g$. Pseudo links are links with some missing crossing information that naturally generalize the notion of knot diagrams. The motivation for studying these relatively new knotted objects lies in the fact that pseudo links may be used to model DNA knots, since it is not uncommon for biologists to obtain DNA knots for which it is not possible to tell a positive from a negative crossing. We consider pseudo links in $H_g$ as mixed pseudo links in $S^3$ and we generalize the Kauffman bracket polynomial for the category of pseudo links in $H_g$. We then pass on the category of mixed pseudo braids, that is, pseudo braids whose closures are pseudo links in $H_g$, and we formulate the analogue of the Alexander theorem. It is worth mentioning that the theory of pseudo links is close related to the theory of singular links and that all results in this paper may be used for studying singular links in $H_g$., Comment: 17 pages, 22 figures. Compared to the previous file, some remarks and a figure have been added. To appear in the Bulletin of the Hellenic Mathematical Society. arXiv admin note: substantial text overlap with arXiv:2101.03538

In this paper we study the theory of knotoids and braidoids and the theory of pseudo knotoids and pseudo braidoids on the torus T. In particular, we introduce the notion of {\it mixed knotoids} in $S^2$, that generalize the notion of mixed links in $S^3$, and we present an isotopy theorem for mixed knotoids. We then generalize the Kauffman bracket polynomial, $<;>$, for mixed knotoids and we present a state sum formula for $<;>$. We also introduce the notion of {\it mixed pseudo knotoids}, that is, multi-knotoids on two components with some missing crossing information. More precisely, we present an isotopy theorem for mixed pseudo knotoids and we extend the Kauffman bracket polynomial for pseudo mixed knotoids. Finally, we introduce the theories of {\it mixed braidoids} and {\it mixed pseudo braidoids} as counterpart theories of mixed knotoids and mixed pseudo knotoids respectively. With the use of the $L$-moves, that we also introduce here for mixed braidoid equivalence, we formulate and prove the analogue of the Alexander and the Markov theorems for mixed knotoids. We also formulate and prove the analogue of the Alexander theorem for mixed pseudo knotoids., Comment: 23 pages, 32 figures

In this paper we introduce and study the theories of pseudo links and singular links in the Solid Torus, ST. Pseudo links are links with some missing crossing information that naturally generalize the notion of knot diagrams, and that have potential use in molecular biology, while singular links are links that contain a finite number of self-intersections. We consider pseudo links and singular links in ST and we set up the appropriate topological theory in order to construct invariants for these types of links in ST. In particular, we formulate and prove the analogue of the Alexander theorem for pseudo links and for singular links in ST. We then introduce the mixed pseudo braid monoid and the mixed singular braid monoid, with the use of which, we formulate and prove the analogue of the Markov theorem for pseudo links and for singular links in ST. \smallbreak Moreover, we introduce the pseudo Hecke algebra of type A, $P\mathcal{H}_n$, the cyclotomic and generalized pseudo Hecke algebras of type B, $P\mathcal{H}_{1, n}$, and discuss how the pseudo braid monoid (cor. the mixed pseudo braid monoid) can be represented by $P\mathcal{H}_{n}$ (cor. by $P\mathcal{H}_{1, n}$). This is the first step toward the construction of HOMFLYPT-type invariants for pseudo links in $S^3$ and in ST. We also introduce the cyclotomic and generalized singular Hecke algebras of type B, $S\mathcal{H}_{1, n}$, and we present two sets that we conjecture that they form linear bases for $S\mathcal{H}_{1, n}$. Finally, we generalize the bracket polynomial for pseudo links in ST., Comment: 25 pages, 16 figures

In this paper we study the theory of {\it pseudo knots}, which are knots with some missing crossing information, and we introduce and study the theory of {\it pseudo tied links} and the theory of {\it pseudo knotoids}. In particular, we first present a braiding algorithm for pseudo knots and we then introduce the $L$-moves in that setting, with the use of which we formulate a sharpened version of the analogue of the Markov theorem for pseudo braids. Then we introduce and study the theory of {\it tied pseudo links}, that generalize the notion of tied links, and we exploit the relation between tied pseudo links and tied singular links. We first present an $L$-move braid equivalence for tied singular braids. Then, we introduce the tied pseudo braid monoid and we formulate and prove analogues of the Alexander and Markov theorems for tied pseudo links. Finally, we introduce and study the theory of {\it pseudo knotoids}, that generalize the notion of knotoids. We present an isotopy theorem for pseudo knotoids and we then pass to the level of braidoids. We further introduce and study the {\it pseudo braidoids} by introducing the {\it pseudo} $L${\it -moves} and by presenting the analogues of the Alexander and Markov theorems for pseudo knotoids. We also discuss further research related to {\it tied (multi)-knotoids and tied pseudo (multi)-knotoids}. The theory of pseudo knots may serve as a strong tool in the study of DNA, while tied links have potential use in other aspects of molecular biology., Comment: 27 pages, 32 figures

Tied links in $S^3$ were introduced by Aicardi and Juyumaya as standard links in $S^3$ equipped with some non-embedded arcs, called {\it ties}, joining some components of the link. Tied links in the Solid Torus were then naturally generalized by Flores. In this paper we study this new class of links in other topological settings. More precisely, we study tied links in the lens spaces $L(p,1)$, in handlebodies of genus $g$, and in the complement of the $g$-component unlink. We introduce the tied braid groups $TB_{g, n}$ by combining the algebraic mixed braid groups defined by Lambropoulou and the tied braid monoid, and we state and prove Alexander's and Markov's theorems for tied links in the 3-manifolds mentioned above. Finally, we emphasize on further steps needed in order to study tied links in knot complements and c.c.o. 3-manifolds, which is the subject of a sequel paper., Comment: 20 pages, 25 figures

In this paper we work toward the HOMFLYPT skein module of $L(p, 1)$, $\mathcal{S}(L(p,1))$, via braids. Our starting point is the linear Turaev-basis, $\Lambda^{\prime}$, of the HOMFLYPT skein module of the solid torus ST, $\mathcal{S}({\rm ST})$, which can be decomposed as the tensor product of the "positive" ${\Lambda^{\prime}}^+$ and the "negative" ${\Lambda^{\prime}}^-$ sub-modules, and the Lambropoulou invariant, $X$, for knots and links in ST, that captures $S({\rm ST})$. It is a well-known result by now that $\mathcal{S}(L(p, 1))=\frac{\mathcal{S}(ST)}{}$, where bbm's (braid band moves) denotes the isotopy moves that correspond to the surgery description of $L(p, 1)$. Namely, a HOMFLYPT-type invariant for knots and links in ST can be extended to an invariant for knots and links in $L(p, 1)$ by imposing relations coming from the performance of bbm's and solving the infinite system of equations obtained that way. \smallbreak In this paper we work with a new basis of $\mathcal{S}({\rm ST})$, $\Lambda$, and we relate the infinite system of equations obtained by performing bbm's on elements in $\Lambda^+$ to the infinite system of equations obtained by performing bbm's on elements in $\Lambda^-$ via a map $I$. More precisely we prove that the solutions of one system can be derived from the solutions of the other. Our aim is to reduce the complexity of the infinite system one needs to solve in order to compute $\mathcal{S}(L(p,1))$ using the braid technique. Finally, we present a generating set and a potential basis for $\frac{\Lambda^+}{}$ and thus, we obtain a generating set and a potential basis for $\frac{\Lambda^-}{}$. We also discuss further steps needed in order to compute $\mathcal{S}(L(p,1))$ via braids., Comment: 26 pages, 6 figures. arXiv admin note: text overlap with arXiv:1802.09376, arXiv:1702.06290

In this paper we present two new bases, $B^{\prime}_{H_2}$ and $\mathcal{B}_{H_2}$, for the Kauffman bracket skein module of the handlebody of genus 2 $H_2$, KBSM($H_2$). We start from the well-known Przytycki-basis of KBSM($H_2$), $B_{H_2}$, and using the technique of parting we present elements in $B_{H_2}$ in open braid form. We define an ordering relation on an augmented set $L$ consisting of monomials of all different "loopings" in $H_2$, that contains the sets $B_{H_2}$, $B^{\prime}_{H_2}$ and $\mathcal{B}_{H_2}$ as proper subsets. Using the Kauffman bracket skein relation we relate $B_{H_2}$ to the sets $B^{\prime}_{H_2}$ and $\mathcal{B}_{H_2}$ via a lower triangular infinite matrix with invertible elements in the diagonal. The basis $B^{\prime}_{H_2}$ is an intermediate step in order to reach at elements in $\mathcal{B}_{H_2}$ that have no crossings on the level of braids, and in that sense, $\mathcal{B}_{H_2}$ is a more natural basis of KBSM($H_2$). Moreover, this basis is appropriate in order to compute Kauffman bracket skein modules of c.c.o. 3-manifolds $M$ that are obtained from $H_2$ by surgery, since isotopy moves in $M$ are naturally described by elements in $\mathcal{B}_{H_2}$., Comment: 14 pages, 15 figures

In this paper we give an alternative basis, $\mathcal{B}_{\rm ST}$, for the Kauffman bracket skein module of the solid torus, ${\rm KBSM}\left({\rm ST}\right)$. The basis $\mathcal{B}_{\rm ST}$ is obtained with the use of the Tempereley--Lieb algebra of type B and it is appropriate for computing the Kauffman bracket skein module of the lens spaces $L(p, q)$ via braids., Comment: 14 pages, 5 figures

We prove that, in order to derive the HOMFLYPT skein module of the lens spaces $L(p,1)$ from the HOMFLYPT skein module of the solid torus, $\mathcal{S}({\rm ST})$, it suffices to solve an infinite system of equations obtained by imposing on the Lambropoulou invariant $X$ for knots and links in the solid torus, braid band moves that are performed only on the first moving strand of elements in a set $\Lambda^{aug}$, augmenting the basis $\Lambda$ of $\mathcal{S}({\rm ST})$., Comment: 20 pages, 5 figures. arXiv admin note: substantial text overlap with arXiv:1702.06290, arXiv:1604.06163

In this paper we present recent results toward the computation of the HOMFLYPT skein module of the lens spaces $L(p,1)$, $\mathcal{S}\left(L(p,1) \right)$, via braids. Our starting point is the knot theory of the solid torus ST and the Lambropoulou invariant, $X$, for knots and links in ST, the universal analogue of the HOMFLYPT polynomial in ST. The relation between $\mathcal{S}\left(L(p,1) \right)$ and $\mathcal{S}({\rm ST})$ is established in \cite{DLP} and it is shown that in order to compute $\mathcal{S}\left(L(p,1) \right)$, it suffices to solve an infinite system of equations obtained by performing all possible braid band moves on elements in the basis of $\mathcal{S}({\rm ST})$, $\Lambda$, presented in \cite{DL2}. The solution of this infinite system of equations is very technical and is the subject of a sequel paper \cite{DL3}., Comment: 28 pages, 21 Figures. arXiv admin note: substantial text overlap with arXiv:1604.06163, arXiv:1412.3642

In this paper we work toward the Homflypt skein module of the lens spaces $L(p,1)$, $\mathcal{S}(L(p,1))$, using braids. In particular, we establish the connection between $\mathcal{S}({\rm ST})$, the Homflypt skein module of the solid torus ST, and $\mathcal{S}(L(p,1))$ and arrive at an infinite system, whose solution corresponds to the computation of $\mathcal{S}(L(p,1))$. We start from the Lambropoulou invariant $X$ for knots and links in ST, the universal analogue of the Homflypt polynomial in ST, and a new basis, $\Lambda$, of $\mathcal{S}({\rm ST})$ presented in \cite{DL1}. We show that $\mathcal{S}(L(p,1))$ is obtained from $\mathcal{S}({\rm ST})$ by considering relations coming from the performance of braid band moves (bbm) on elements in the basis $\Lambda$, where the braid band moves are performed on any moving strand of each element in $\Lambda$. We do that by proving that the system of equations obtained from diagrams in ST by performing bbm on any moving strand is equivalent to the system obtained if we only consider elements in the basic set $\Lambda$. The importance of our approach is that it can shed light to the problem of computing skein modules of arbitrary c.c.o. $3$-manifolds, since any $3$-manifold can be obtained by surgery on $S^3$ along unknotted closed curves. The main difficulty of the problem lies in selecting from the infinitum of band moves some basic ones and solving the infinite system of equations., Comment: 24 pages, 16 figures. arXiv admin note: text overlap with arXiv:1412.3642

In this paper we give a new basis, $\Lambda$, for the Homflypt skein module of the solid torus, $\mathcal{S}({\rm ST})$, which was predicted by Jozef Przytycki, using topological interpretation. The basis $\Lambda$ is different from the basis $\Lambda^{\prime}$, discovered independently by Hoste--Kidwell \cite{HK} and Turaev \cite{Tu} with the use of diagrammatic methods. For finding the basis $\Lambda$ we use the generalized Hecke algebra of type B, $\textrm{H}_{1,n}$, defined by the second author in \cite{La2}, which is generated by looping elements and braiding elements and which is isomorphic to the affine Hecke algebra of type A. Namely, we start with the well-known basis of $\mathcal{S}({\rm ST})$, $\Lambda^{\prime}$, and an appropriate linear basis $\Sigma_n$ of the algebra $\textrm{H}_{1,n}$. We then convert elements in $\Lambda^{\prime}$ to linear combinations of elements in the new basic set $\Lambda$. This is done in two steps: First we convert elements in $\Lambda^{\prime}$ to elements in $\Sigma_n$. Then, using conjugation and the stabilization moves, we convert these elements to linear combinations of elements in $\Lambda$ by managing gaps in the indices of the looping elements and by eliminating braiding tails in the words. Further, we define an ordering relation in $\Lambda^{\prime}$ and $\Lambda$ and prove that the sets are totally ordered. Finally, using this ordering, we relate the sets $\Lambda^{\prime}$ and $\Lambda$ via a block diagonal matrix, where each block is an infinite lower triangular matrix with invertible elements in the diagonal and we prove linear independence of the set $\Lambda$. The infinite matrix is then "invertible" and thus, the set $\Lambda$ is a basis for $\mathcal{S}({\rm ST})$. The aim of this paper is to provide the basic algebraic tools for computing skein modules of c.c.o. $3$-manifolds via algebraic means., Comment: 28 pages, 10 figures

In this paper we describe braid equivalence for knots and links in a 3-manifold $M$ obtained by rational surgery along a framed link in $S^3$. We first prove a sharpened version of the Reidemeister theorem for links in $M$. We then give geometric formulations of the braid equivalence via mixed braids in $S^3$ using the $L$-moves and the braid band moves. We finally give algebraic formulations in terms of the mixed braid groups $B_{m,n}$ using cabling and the techniques of parting and combing for mixed braids. We also provide concrete formuli of the braid equivalence in the case where $M$ is a lens space, a Seifert manifold or a homology sphere obtained from the trefoil. The algebraic classification of knots and links in a $3$-manifold via mixed braids is a useful tool for studying skein modules of $3$-manifolds., Comment: 38 pages, 44 figures