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The aim of this paper is two-fold. First, we give a fully geometric description of the HOMFLYPT homology of Khovanov-Rozansky. Our method is to construct this invariant in terms of the cohomology of various sheaves on certain algebraic…
We extend the construction of upsilon-type invariants to null-homologous knots in rational homology three-spheres. By considering $m$-fold cyclic branched covers with $m$ a prime power, this extension provides new knot concordance…
There exists a simplified Bar-Natan Khovanov complex for open 2-braids. The Khovanov cohomology of a knot diagram made by gluing tangles of this type is therefore often amenable to calculation. We lift this idea to the level of the…
We propose a framework for unifying the sl(N) Khovanov-Rozansky homology (for all N) with the knot Floer homology. We argue that this unification should be accomplished by a triply graded homology theory which categorifies the HOMFLY…
We prove that any link admitting a diagram with a single negative crossing is strongly quasipositive. This answers a question of Stoimenow's in the (strong) positive. As a second main result, we give simple and complete characterizations of…
We further study the symplectic Khovanov homology of Seidel and Smith and its generalization to even tangles. This homology theory is a conjectural geometric model for Khovanov homology. In this paper we uncover structures on symplectic…
This paper formulates a generalization of our work on quantum knots to explain how to make quantum versions of algebraic, combinatorial and topological structures. We include a description of previous work on the construction of Hilbert…
We construct explicitly the Khovanov homology theory for virtual links with arbitrary coefficients by using the twisted coefficients method. This method also works for constructing Khovanov homology for ``non-oriented virtual knots'' in the…
We revisit Rozansky's construction of Khovanov homology for links in $S^2\times S^1$, extending it to define Khovanov homology $Kh(L)$ for links $L$ in $M^r=#^r(S^2\times S^1)$ for any $r$. The graded Euler characteristic of $Kh(L)$ can be…
This is an expository paper discussing various versions of Khovanov homology theories, interrelations between them, their properties, and their applications to other areas of knot theory and low-dimensional topology.
We characterize the para-associative ternary quasigroups (flocks) applicable to knot theory, and show which of these structures are isomorphic. We enumerate them up to order 64. We note that the operation used in knot-theoretic flocks has…
We equip a knot $K$ with a set of colored bonds, that is, colored intervals properly embedded into $\mathbb{R}^3 \setminus K$. Such a construction can be viewed as a structure that topologically models a closed protein chain including any…
This paper is a computation of the homotopy type of K, the space of long knots in R^3, the same space of knots studied by Vassiliev via singularity theory. Each component of K corresponds to an isotopy class of long knot, and we `enumerate'…
We introduce the notion of partial presimplicial set and construct its geometric realization. We show that any semiadequate diagram yields a partial presimplicial set leading to a geometric realization of the almost-extreme Khovanov…
We show the $n$ colored Jones polynomials of a highly twisted link approach the Kauffman bracket of an $n$ colored skein element. This is in the sense that the corresponding categorifications of the colored Jones polynomials approach the…
We construct an algebra of non-trivial homological operations on Khovanov homology with coefficients in $\mathbb Z_2$ generated by two Bockstein operations. We use the unified Khovanov homology theory developed by the first author to lift…
Wilson-loop averages in Chern-Simons theory (HOMFLY polynomials) can be evaluated in different ways -- the most difficult, but most interesting of them is the hypercube calculus, the only one applicable to virtual knots and used also for…
We introduce a refinement of Bar-Natan homology for involutive links, extending the work of Lobb-Watson and Sano. We construct a new suite of numerical invariants and derive bounds for the genus of equivariant cobordisms between strongly…
We consider a family of chaotic Bose-Hubbard Hamiltonians (BHH) parameterized by the coupling strength $k$ between neighboring sites. As $k$ increases the eigenstates undergo changes, reflected in the structure of the Local Density of…
We conjecture the existence of four independent gradings in the colored HOMFLY homology. We describe these gradings explicitly for the rectangular colored homology of torus knots and make qualitative predictions of various interesting…