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Using a long-standing conjecture from combinatorial group theory, we explore, from multiple angles, the challenges of finding rare instances carrying disproportionately high rewards. Based on lessons learned in the mathematical context defined by the Andrews-Curtis conjecture, we propose algorithmic improvements that can be relevant in other domains with ultra-sparse reward problems. Although our case study can be formulated as a game, its shortest winning sequences are potentially $10^6$ or $10^9$ times longer than those encountered in chess. In the process of our study, we demonstrate that one of the potential counterexamples due to Akbulut and Kirby, whose status escaped direct mathematical methods for 39 years, is stably AC-trivial., Comment: 39 pages, 18 figures, 1 table

We explore statistical properties of BPS q-series for 3d N=2 strongly coupled supersymmetric theories that correspond to a particular family of 3-manifolds Y. We discover that gaps between exponents in the q-series are statistically more significant at the beginning of the q-series compared to gaps that appear in higher powers of q. Our observations are obtained by calculating saliencies of q-series features used as input data for principal component analysis, which is a standard example of an explainable machine learning technique that allows for a direct calculation and a better analysis of feature saliencies., Comment: 11 pages, 4 figures, 3 tables

We consider a finite-dimensional oscillatory integral which provides a "finite-dimensional model" for analytically continued $SU(2)$ Chern-Simons theory on closed 3-manifolds that are described by plumbing trees. This model allows an efficient description of Stokes phenomenon for perturbative expansions in Chern-Simons theory around classical solutions - $SL(2,\mathbb{C})$ flat connections. Moreover, the Stokes coefficients can be categorified, i.e. promoted to graded vector spaces, in terms of this finite-dimensional model. At least naively, the categorification gives BPS spectrum of 5d maximally supersymmetric Yang-Mills theory on the 3-manifold times a line with appropriate boundary conditions. We also comment on necessity of taking into account "flat connections at infinity" to capture Stokes phenomenon for certain 3-manifolds., Comment: 79 pages, 27 figures

Using resurgent analysis we offer a novel mathematical perspective on a curious bijection (duality) that has many potential applications ranging from the theory of vertex algebras to the physics of SCFTs in various dimensions, to q-series invariants in low-dimensional topology that arise, e.g. in Vafa-Witten theory and in non-perturbative completion of complex Chern-Simons theory. In particular, we introduce explicit numerical algorithms that efficiently implement this bijection. This bijection is founded on preservation of relations, a fundamental property of resurgent functions. Using resurgent analysis we find new structures and patterns in complex Chern-Simons theory on closed hyperbolic 3-manifolds obtained by surgeries on hyperbolic twist knots. The Borel plane exhibits several intriguing hints of a new form of integrability. An important role in this analysis is played by the twisted Alexander polynomials and the adjoint Reidemeister torsion, which help us determine the Stokes data. The method of singularity elimination enables extraction of geometric data even for very distant Borel singularities, leading to detailed non-perturbative information from perturbative data. We also introduce a new double-scaling limit to probe 0-surgeries from the limiting $r\to\infty$ behavior of 1/r surgeries, and apply it to the family of hyperbolic twist knots., Comment: 115 pages; 32 figures

Based on the observed behavior of the superconformal index in three-dimensional $\mathcal{N}=2$ theories, we propose a quantity that can be considered as an analogue of the "effective central charge." We discuss the general properties of this quantity and ways of computing it in a variety of different theories, including simple Lagrangian theories as well as more interesting strongly coupled examples that come from 3d-3d correspondence., Comment: 18 pages, 3 figures

We apply Bayesian optimization and reinforcement learning to a problem in topology: the question of when a knot bounds a ribbon disk. This question is relevant in an approach to disproving the four-dimensional smooth Poincar\'e conjecture; using our programs, we rule out many potential counterexamples to the conjecture. We also show that the programs are successful in detecting many ribbon knots in the range of up to 70 crossings., Comment: 23 pages, 10 figures

We study $q$-series invariants of 3-manifolds $\hat{Z}_b$ defined by Gukov--Pei--Putrov--Vafa using techniques from the theory of normal surface singularities such as splice diagrams. This provides a link between algebraic geometry with quantum topology. We show that the (suitably normalized) sum of all $\hat{Z}_b$ depends only on the splice diagram, and in particular, it agrees for manifolds with the same universal Abelian cover. Using these ideas we find simple formulas for $\hat{Z}_b$ invariants of Seifert manifolds that resemble equivariant Poincar\'e series of corresponding quasihomogeneous singularity. Applications include a better understanding of the vanishing of the $q$-series $\hat{Z}_b$., Comment: 39 pages, comments welcome

We initiate explicit computations of Vafa-Witten invariants of 3-manifolds, analogous to Floer groups in the context of Donaldson theory. In particular, we explicitly compute the Vafa-Witten invariants of 3-manifolds in a family of concrete examples relevant to various surgery operations (the Gluck twist, knot surgeries, log-transforms). We also describe the structural properties that are expected to hold for general 3-manifolds, including the modular group action, relation to Floer homology, infinite-dimensionality for an arbitrary 3-manifold, and the absence of instantons., Comment: 27 pages, 5 figures

By studying the properties of $q$-series $\widehat Z$-invariants, we develop a dictionary between 3-manifolds and vertex algebras. In particular, we generalize previously known entries in this dictionary to Lie groups of higher rank, to 3-manifolds with toral boundaries, and to BPS partition functions with line operators. This provides a new physical realization of logarithmic vertex algebras in the framework of the 3d-3d correspondence and opens new avenues for their future study. For example, we illustrate how invoking a knot-quiver correspondence for $\widehat{Z}$-invariants leads to many infinite families of new fermionic formulae for VOA characters., Comment: 85 pages, 3 figures, 6 tables

We generalize the $F_K$ invariant, i.e. $\widehat{Z}$ for the complement of a knot $K$ in the 3-sphere, the knots-quivers correspondence, and $A$-polynomials of knots, and find several interconnections between them. We associate an $F_K$ invariant to any branch of the $A$-polynomial of $K$ and we work out explicit expressions for several simple knots. We show that these $F_K$ invariants can be written in the form of a quiver generating series, in analogy with the knots-quivers correspondence. We discuss various methods to obtain such quiver representations, among others using $R$-matrices. We generalize the quantum $a$-deformed $A$-polynomial to an ideal that contains the recursion relation in the group rank, i.e. in the parameter $a$, and describe its classical limit in terms of the Coulomb branch of a 3d-5d theory. We also provide $t$-deformed versions. Furthermore, we study how the quiver formulation for closed 3-manifolds obtained by surgery leads to the superpotential of 3d $\mathcal{N}=2$ theory $T[M_3]$ and to the data of the associated modular tensor category $\text{MTC} [M_3]$., Comment: 99 pages, 13 figures

We propose and in some cases prove a precise relation between 3-manifold invariants associated with quantum groups at roots of unity and at generic $q$. Both types of invariants are labeled by extra data which plays an important role in the proposed relation. Bridging the two sides - which until recently were developed independently, using very different methods - opens many new avenues. In one direction, it allows to study (and perhaps even to formulate) $q$-series invariants labeled by spin$^c$ structures in terms of non-semisimple invariants. In the opposite direction, it offers new insights and perspectives on various elements of non-semisimple TQFT's, bringing the latter into one unifying framework with other invariants of knots and 3-manifolds that recently found realization in quantum field theory and in string theory.

We introduce natural language processing into the study of knot theory, as made natural by the braid word representation of knots. We study the UNKNOT problem of determining whether or not a given knot is the unknot. After describing an algorithm to randomly generate $N$-crossing braids and their knot closures and discussing the induced prior on the distribution of knots, we apply binary classification to the UNKNOT decision problem. We find that the Reformer and shared-QK Transformer network architectures outperform fully-connected networks, though all perform well. Perhaps surprisingly, we find that accuracy increases with the length of the braid word, and that the networks learn a direct correlation between the confidence of their predictions and the degree of the Jones polynomial. Finally, we utilize reinforcement learning (RL) to find sequences of Markov moves and braid relations that simplify knots and can identify unknots by explicitly giving the sequence of unknotting actions. Trust region policy optimization (TRPO) performs consistently well for a wide range of crossing numbers and thoroughly outperformed other RL algorithms and random walkers. Studying these actions, we find that braid relations are more useful in simplifying to the unknot than one of the Markov moves., Comment: 51 pages, 16 figures, 6 algorithms, 2 tables

Many BPS partition functions depend on a choice of additional structure: fluxes, Spin or Spin$^c$ structures, etc. In a context where the BPS generating series depends on a choice of Spin$^c$ structure we show how different limits with respect to the expansion variable $q$ and different ways of summing over Spin$^c$ structures produce different invariants of homology cobordisms out of the BPS $q$-series., Comment: 30 pages, 4 figures

Reducing a 6d fivebrane theory on a 3-manifold $Y$ gives a $q$-series 3-manifold invariant $\widehat{Z}(Y)$. We analyse the large-$N$ behaviour of $F_K=\widehat{Z}(M_K)$, where $M_K$ is the complement of a knot $K$ in the 3-sphere, and explore the relationship between an $a$-deformed ($a=q^N$) version of $F_{K}$ and HOMFLY-PT polynomials. On the one hand, in combination with counts of holomorphic annuli on knot complements, this gives an enumerative interpretation of $F_K$ in terms of counts of open holomorphic curves. On the other, it leads to closed form expressions for $a$-deformed $F_K$ for $(2,2p+1)$-torus knots. They suggest a further $t$-deformation based on superpolynomials, which can be used to obtain a $t$-deformation of ADO polynomials, expected to be related to categorification. Moreover, studying how $F_K$ transforms under natural geometric operations on $K$ indicates relations to quantum modularity in a new setting., Comment: 42 pages, 4 figures

By studying Rozansky-Witten theory with non-compact target spaces we find new connections with knot invariants whose physical interpretation was not known. This opens up several new avenues, which include a new formulation of $q$-series invariants of 3-manifolds in terms of affine Grassmannians and a generalization of Akutsu-Deguchi-Ohtsuki knot invariants., Comment: 33 pages, 1 figure, 7 tables

One of the main challenges in 3d-3d correspondence is that no existent approach offers a complete description of 3d $N=2$ SCFT $T[M_3]$ --- or, rather, a "collection of SCFTs" as we refer to it in the paper --- for all types of 3-manifolds that include, for example, a 3-torus, Brieskorn spheres, and hyperbolic surgeries on knots. The goal of this paper is to overcome this challenge by a more systematic study of 3d-3d correspondence that, first of all, does not rely heavily on any geometric structure on $M_3$ and, secondly, is not limited to a particular supersymmetric partition function of $T[M_3]$. In particular, we propose to describe such "collection of SCFTs" in terms of 3d $N=2$ gauge theories with "non-linear matter'' fields valued in complex group manifolds. As a result, we are able to recover familiar 3-manifold invariants, such as Turaev torsion and WRT invariants, from twisted indices and half-indices of $T[M_3]$, and propose new tools to compute more recent $q$-series invariants $\hat Z (M_3)$ in the case of manifolds with $b_1 > 0$. Although we use genus-1 mapping tori as our "case study," many results and techniques readily apply to more general 3-manifolds, as we illustrate throughout the paper., Comment: 53 pages, 8 figures

The physical 3d $\mathcal{N}=2$ theory T[Y] was previously used to predict the existence of some 3-manifold invariants $\hat{Z}_{a}(q)$ that take the form of power series with integer coefficients, converging in the unit disk. Their radial limits at the roots of unity should recover the Witten-Reshetikhin-Turaev invariants. In this paper we discuss how, for complements of knots in $S^3$, the analogue of the invariants $\hat{Z}_{a}(q)$ should be a two-variable series $F_K(x,q)$ obtained by parametric resurgence from the asymptotic expansion of the colored Jones polynomial. The terms in this series should satisfy a recurrence given by the quantum A-polynomial. Furthermore, there is a formula that relates $F_K(x,q)$ to the invariants $\hat{Z}_{a}(q)$ for Dehn surgeries on the knot. We provide explicit calculations of $F_K(x,q)$ in the case of knots given by negative definite plumbings with an unframed vertex, such as torus knots. We also find numerically the first terms in the series for the figure-eight knot, up to any desired order, and use this to understand $\hat{Z}_a(q)$ for some hyperbolic 3-manifolds., Comment: 79 pages; final version, to appear in Quantum Topology

We build a connection between topology of smooth 4-manifolds and the theory of topological modular forms by considering topologically twisted compactification of 6d (1,0) theories on 4-manifolds with flavor symmetry backgrounds. The effective 2d theory has (0,1) supersymmetry and, possibly, a residual flavor symmetry. The equivariant topological Witten genus of this 2d theory then produces a new invariant of the 4-manifold equipped with a principle bundle, valued in the ring of equivariant weakly holomorphic (topological) modular forms. We describe basic properties of this map and present a few simple examples. As a byproduct, we obtain some new results on 't Hooft anomalies of 6d (1,0) theories and a better understanding of the relation between 2d (0,1) theories and TMF spectra., Comment: 74 pages

We find and propose an explanation for a large variety of modularity-related symmetries in problems of 3-manifold topology and physics of 3d $\mathcal{N}=2$ theories where such structures a priori are not manifest. These modular structures include: mock modular forms, $SL(2,\mathbb{Z})$ Weil representations, quantum modular forms, non-semisimple modular tensor categories, and chiral algebras of logarithmic CFTs., Comment: 119 pages, 10 figures and 20 tables

We propose a way to define and compute invariants of general smooth 4-manifolds based on topological twists of non-Lagrangian 4d N=2 and N=3 theories in which the problem is reduced to a fairly standard computation in topological A-model, albeit with rather unusual targets, such as compact and non-compact Gepner models, asymmetric orbifolds, N=(2,2) linear dilaton theories, "self-mirror" geometries, varieties with complex multiplication, etc., Comment: 49 pages, 8 figures, 8 tables, v2: a reference added

We propose a way of computing 4-manifold invariants, old and new, as chiral correlation functions in half-twisted 2d $\mathcal{N}=(0,2)$ theories that arise from compactification of fivebranes. Such formulation gives a new interpretation of some known statements about Seiberg-Witten invariants, such as the basic class condition, and gives a prediction for structural properties of the multi-monopole invariants and their non-abelian generalizations., Comment: 67 pages, 11 figures

We provide a physical definition of new homological invariants $\mathcal{H}_a (M_3)$ of 3-manifolds (possibly, with knots) labeled by abelian flat connections. The physical system in question involves a 6d fivebrane theory on $M_3$ times a 2-disk, $D^2$, whose Hilbert space of BPS states plays the role of a basic building block in categorification of various partition functions of 3d $\mathcal{N}=2$ theory $T[M_3]$: $D^2\times S^1$ half-index, $S^2\times S^1$ superconformal index, and $S^2\times S^1$ topologically twisted index. The first partition function is labeled by a choice of boundary condition and provides a refinement of Chern-Simons (WRT) invariant. A linear combination of them in the unrefined limit gives the analytically continued WRT invariant of $M_3$. The last two can be factorized into the product of half-indices. We show how this works explicitly for many examples, including Lens spaces, circle fibrations over Riemann surfaces, and plumbed 3-manifolds., Comment: v2: 80 pages, 7 figures, typos corrected, exposition improved with three newly added subsections (2.3, 2.4, 2.10)

We study resurgence properties of partition function of SU(2) Chern-Simons theory (WRT invariant) on closed three-manifolds. We check explicitly that in various examples Borel transforms of asymptotic expansions posses expected analytic properties. In examples that we study we observe that contribution of irreducible flat connections to the path integral can be recovered from asymptotic expansions around abelian flat connections. We also discuss connection to Floer instanton moduli spaces, disk instantons in 2d sigma models, and length spectra of "complex geodesics" on the A-polynomial curve., Comment: 56 pages, 19 figures. v2: references added

Motivated by physical constructions of homological knot invariants, we study their analogs for closed 3-manifolds. We show that fivebrane compactifications provide a universal description of various old and new homological invariants of 3-manifolds. In terms of 3d/3d correspondence, such invariants are given by the Q-cohomology of the Hilbert space of partially topologically twisted 3d N=2 theory T[M_3] on a Riemann surface with defects. We demonstrate this by concrete and explicit calculations in the case of monopole/Heegaard Floer homology and a 3-manifold analog of Khovanov-Rozansky link homology. The latter gives a categorification of Chern-Simons partition function. Some of the new key elements include the explicit form of the S-transform and a novel connection between categorification and a previously mysterious role of Eichler integrals in Chern-Simons theory., Comment: 85 pages, 14 figures

This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincare polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties., Comment: 160 pages, 69 figures, 4 tables; Don't be intimidated by the length - each section can be read more or less independently.; v2 and v3, minor corrections, a Mathematica file is attached as an ancillary file

We show how networks of Wilson lines realize quantum groups U_q(sl(m)), for arbitrary m, in 3d SU(N) Chern-Simons theory. Lifting this construction to foams of surface operators in 4d theory we find that rich structure of junctions is encoded in combinatorics of planar diagrams. For a particular choice of surface operators we reproduce known mathematical constructions of categorical representations and categorified quantum groups., Comment: 62 pages, 33 figures, minor changes, references added

The goal of this article is twofold. First, we find a natural home for the double affine Hecke algebras (DAHA) in the physics of BPS states. Second, we introduce new invariants of torus knots and links called "hyperpolynomials" that address the "problem of negative coefficients" often encountered in DAHA-based approaches to homological invariants of torus knots and links. Furthermore, from the physics of BPS states and the spectra of singularities associated with Landau-Ginzburg potentials, we also describe a rich structure of differentials that act on homological knot invariants for exceptional groups and uniquely determine the latter for torus knots., Comment: 44 pages, 4 figures

We study complex Chern-Simons theory on a Seifert manifold $M_3$ by embedding it into string theory. We show that complex Chern-Simons theory on $M_3$ is equivalent to a topologically twisted supersymmetric theory and its partition function can be naturally regularized by turning on a mass parameter. We find that the dimensional reduction of this theory to 2d gives the low energy dynamics of vortices in four-dimensional gauge theory, the fact apparently overlooked in the vortex literature. We also generalize the relations between 1) the Verlinde algebra, 2) quantum cohomology of the Grassmannian, 3) Chern-Simons theory on $\Sigma\times S^1$ and 4) index of a spin$^c$ Dirac operator on the moduli space of flat connections to a new set of relations between 1) the "equivariant Verlinde algebra" for a complex group, 2) the equivariant quantum K-theory of the vortex moduli space, 3) complex Chern-Simons theory on $\Sigma \times S^1$ and 4) the equivariant index of a spin$^c$ Dirac operator on the moduli space of Higgs bundles., Comment: 56 pages, 7 figures; v2: misprints corrected, clarifications added, missing factors and terms restored in section 6.2

In fivebrane compactifications on 3-manifolds, we point out the importance of all flat connections in the proper definition of the effective 3d N=2 theory. The Lagrangians of some theories with the desired properties can be constructed with the help of homological knot invariants that categorify colored Jones polynomials. Higgsing the full 3d theories constructed this way recovers theories found previously by Dimofte-Gaiotto-Gukov. We also consider the cutting and gluing of 3-manifolds along smooth boundaries and the role played by all flat connections in this operation., Comment: 43 pages + 1 appendix, 6 figures Version 2: new appendix on flat connections in the 3d-3d correspondence

We describe rules for building 2d theories labeled by 4-manifolds. Using the proposed dictionary between building blocks of 4-manifolds and 2d N=(0,2) theories, we obtain a number of results, which include new 3d N=2 theories T[M_3] associated with rational homology spheres and new results for Vafa-Witten partition functions on 4-manifolds. In particular, we point out that the gluing measure for the latter is precisely the superconformal index of 2d (0,2) vector multiplet and relate the basic building blocks with coset branching functions. We also offer a new look at the fusion of defect lines / walls, and a physical interpretation of the 4d and 3d Kirby calculus as dualities of 2d N=(0,2) theories and 3d N=2 theories, respectively, Comment: 81 pages, 18 figures. v2: misprints corrected, clarifications and references added. v3: additions and corrections about lens space theory, 4-manifold gluing, smooth structures

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 structures and symmetries in the colored homology of general knots. We also give a simple representation-theoretic model for the HOMFLY homology of the unknot colored by any representation. While some of these structures have a natural interpretation in the physical realization of knot homologies based on counting supersymmetric configurations (BPS states, instantons, and vortices), others are completely new. They suggest new geometric and physical realizations of colored HOMFLY homology as the Hochschild homology of the category of branes in a Landau-Ginzburg B-model or, equivalently, in the mirror A-model. Supergroups and supermanifolds are surprisingly ubiquitous in all aspects of this work., Comment: 78 pages

Besides offering a friendly introduction to knot homologies and quantum curves, the goal of these lectures is to review some of the concrete predictions that follow from the physical interpretation of knot homologies. In particular, this interpretation allows one to pose questions that would not have been asked otherwise, such as, "Is there a direct relation between Khovanov homology and the A-polynomial of a knot?" We will explain that the answer to this question is "yes," and introduce a certain deformation of the planar algebraic curve defined by the zero locus of the A-polynomial. This novel deformation leads to a categorified version of the Generalized Volume Conjecture that completely describes the "color behavior" of the colored sl(2) knot homology, and eventually to a similar version for the colored HOMFLY homology. Furthermore, this deformation is strong enough to distinguish mutants, and its most interesting properties include relations to knot contact homology and knot Floer homology., Comment: 48 pages, 9 figures. Comments are welcome

We study singularities of algebraic curves associated with 3d N=2 theories that have at least one global flavor symmetry. Of particular interest is a class of theories T_K labeled by knots, whose partition functions package Poincare polynomials of the S^r-colored HOMFLY homologies. We derive the defining equation, called the super-A-polynomial, for algebraic curves associated with many new examples of 3d N=2 theories T_K and study its singularity structure. In particular, we catalog general types of singularities that presumably exist for all knots and propose their physical interpretation. A computation of super-A-polynomials is based on a derivation of corresponding superpolynomials, which is interesting in its own right and relies solely on a structure of differentials in S^r-colored HOMFLY homologies., Comment: 40 pages, 14 figures

We introduce and compute a 2-parameter family deformation of the A-polynomial that encodes the color dependence of the superpolynomial and that, in suitable limits, reduces to various deformations of the A-polynomial studied in the literature. These special limits include the t-deformation which leads to the "refined A-polynomial" introduced in the previous work of the authors and the Q-deformation which leads, by the conjecture of Aganagic and Vafa, to the augmentation polynomial of knot contact homology. We also introduce and compute the quantum version of the super-A-polynomial, an operator that encodes recursion relations for S^r-colored HOMFLY homology. Much like its predecessor, the super-A-polynomial admits a simple physical interpretation as the defining equation for the space of SUSY vacua (= critical points of the twisted superpotential) in a circle compactification of the effective 3d N=2 theory associated to a knot or, more generally, to a 3-manifold M. Equivalently, the algebraic curve defined by the zero locus of the super-A-polynomial can be thought of as the space of open string moduli in a brane system associated with M. As an inherent outcome of this work, we provide new interesting formulas for colored superpolynomials for the trefoil and the figure-eight knot., Comment: 47 pages, 8 figures; typos and references fixed

The generalized volume conjecture relates asymptotic behavior of the colored Jones polynomials to objects naturally defined on an algebraic curve, the zero locus of the A-polynomial $A(x,y)$. Another "family version" of the volume conjecture depends on a quantization parameter, usually denoted $q$ or $\hbar$; this quantum volume conjecture (also known as the AJ-conjecture) can be stated in a form of a q-difference equation that annihilates the colored Jones polynomials and $SL(2,\C)$ Chern-Simons partition functions. We propose refinements / categorifications of both conjectures that include an extra deformation parameter $t$ and describe similar properties of homological knot invariants and refined BPS invariants. Much like their unrefined / decategorified predecessors, that correspond to $t=-1$, the new volume conjectures involve objects naturally defined on an algebraic curve $A^{ref} (x,y; t)$ obtained by a particular deformation of the A-polynomial, and its quantization $\hat A^{ref} (\hat x, \hat y; q, t)$. We compute both classical and quantum t-deformed curves in a number of examples coming from colored knot homologies and refined BPS invariants., Comment: with an appendix by Hidetoshi Awata; 92 pages, 24 figures

We identify a large class R of three-dimensional N=2 superconformal field theories. This class includes the effective theories T_M of M5-branes wrapped on 3-manifolds M, discussed in previous work by the authors, and more generally comprises theories that admit a UV description as abelian Chern-Simons-matter theories with (possibly non-perturbative) superpotential. Mathematically, class R might be viewed as an extreme quantum generalization of the Bloch group; in particular, the equivalence relation among theories in class R is a quantum-field-theoretic "2-3 move." We proceed to study the supersymmetric index of theories in class R, uncovering its physical and mathematical properties, including relations to algebras of line operators and to 4d indices. For 3-manifold theories T_M, the index is a new topological invariant, which turns out to be equivalent to non-holomorphic SL(2,C) Chern-Simons theory on M with a previously unexplored "integration cycle.", Comment: 67+11 pages, 14 figures

It is known that knot homologies admit a physical description as spaces of open BPS states. We study operators and algebras acting on these spaces. This leads to a very rich story, which involves wall crossing phenomena, algebras of closed BPS states acting on spaces of open BPS states, and deformations of Landau-Ginzburg models. One important application to knot homologies is the existence of "colored differentials" that relate homological invariants of knots colored by different representations. Based on this structure, we formulate a list of properties of the colored HOMFLY homology that categorifies the colored HOMFLY polynomial. By calculating the colored HOMFLY homology for symmetric and anti-symmetric representations, we find a remarkable "mirror symmetry" between these triply-graded theories., Comment: 42 pages, 5 figures, additional references and explanations concerning colored differentials and grading choices, enhanced analysis of examples

We propose a dictionary between geometry of triangulated 3-manifolds and physics of three-dimensional N=2 gauge theories. Under this duality, standard operations on triangulated 3-manifolds and various invariants thereof (classical as well as quantum) find a natural interpretation in field theory. For example, independence of the SL(2) Chern-Simons partition function on the choice of triangulation translates to a statement that S^3_b partition functions of two mirror 3d N=2 gauge theories are equal. Three-dimensional N=2 field theories associated to 3-manifolds can be thought of as theories that describe boundary conditions and duality walls in four-dimensional N=2 SCFTs, thus making the whole construction functorial with respect to cobordisms and gluing., Comment: 59 pages, 24 figures

We study S-dualities in analytically continued SL(2) Chern-Simons theory on a 3-manifold M. By realizing Chern-Simons theory via a compactification of a 6d five-brane theory on M, various objects and symmetries in Chern-Simons theory become related to objects and operations in dual 2d, 3d, and 4d theories. For example, the space of flat SL(2,C) connections on M is identified with the space of supersymmetric vacua in a dual 3d gauge theory. The hidden symmetry "hbar -> - (4 pi^2)/hbar" of SL(2) Chern-Simons theory can be identified as the S-duality transformation of N=4 super-Yang-Mills theory (obtained by compactifying the five-brane theory on a torus); whereas the mapping class group action in Chern-Simons theory on a three-manifold M with boundary C is realized as S-duality in 4d N=2 super-Yang-Mills theory associated with the Riemann surface C. We illustrate these symmetries by considering simple examples of 3-manifolds that include knot complements and punctured torus bundles, on the one hand, and mapping cylinders associated with mapping class group transformations, on the other. A generalization of mapping class group actions further allows us to study the transformations between several distinguished coordinate systems on the phase space of Chern-Simons theory, the SL(2) Hitchin moduli space., Comment: 64 pages, 18 figures

The volume conjecture states that for a hyperbolic knot K in the three-sphere S^3 the asymptotic growth of the colored Jones polynomial of K is governed by the hyperbolic volume of the knot complement S^3\K. The conjecture relates two topological invariants, one combinatorial and one geometric, in a very nonobvious, nontrivial manner. The goal of the present lectures is to review the original statement of the volume conjecture and its recent extensions and generalizations, and to show how, in the most general context, the conjecture can be understood in terms of topological quantum field theory. In particular, we consider: a) generalization of the volume conjecture to families of incomplete hyperbolic metrics; b) generalization that involves not only the leading (volume) term, but the entire asymptotic expansion in 1/N; c) generalization to quantum group invariants for groups of higher rank; and d) generalization to arbitrary links in arbitrary three-manifolds., Comment: 32 pages, 6 figures; acknowledgements updated

We develop several methods that allow us to compute all-loop partition functions in perturbative Chern-Simons theory with complex gauge group G_C, sometimes in multiple ways. In the background of a non-abelian irreducible flat connection, perturbative G_C invariants turn out to be interesting topological invariants, which are very different from finite type (Vassiliev) invariants obtained in a theory with compact gauge group G. We explore various aspects of these invariants and present an example where we compute them explicitly to high loop order. We also introduce a notion of "arithmetic TQFT" and conjecture (with supporting numerical evidence) that SL(2,C) Chern-Simons theory is an example of such a theory., Comment: 60 pages, 9 figures

Topological gauge theories in four dimensions which admit surface operators provide a natural framework for realizing homological knot invariants. Every such theory leads to an action of the braid group on branes on the corresponding moduli space. This action plays a key role in the construction of homological knot invariants. We illustrate the general construction with examples based on surface operators in N=2 and N=4 twisted gauge theories which lead to a categorification of the Alexander polynomial, the equivariant knot signature, and certain analogs of the Casson invariant. This paper is based on a lecture delivered at the International Congress on Mathematical Physics 2006, Rio de Janeiro, and at the RTN Workshop 2006, Napoli., Comment: 37 pages. Based on a talk given at the ICMP 2006 and at the RTN Workshop 2006

We establish a direct map between refined topological vertex and sl(N) homological invariants of the of Hopf link, which include Khovanov-Rozansky homology as a special case. This relation provides an exact answer for homological invariants of the of Hopf link, whose components are colored by arbitrary representations of sl(N). At present, the mathematical formulation of such homological invariants is available only for the fundamental representation (the Khovanov-Rozansky theory) and the relation with the refined topological vertex should be useful for categorifying quantum group invariants associated with other representations (R_1, R_2). Our result is a first direct verification of a series of conjectures which identifies link homologies with the Hilbert space of BPS states in the presence of branes, where the physical interpretation of gradings is in terms of charges of the branes ending on Lagrangian branes., Comment: 38 pages, 5 figures

We clarify and refine the relation between the asymptotic behavior of the colored Jones polynomial and Chern-Simons gauge theory with complex gauge group SL(2,C). The precise comparison requires a careful understanding of some delicate issues, such as normalization of the colored Jones polynomial and the choice of polarization in Chern-Simons theory. Addressing these issues allows us to go beyond the volume conjecture and to verify some predictions for the behavior of the subleading terms in the asymptotic expansion of the colored Jones polynomial., Comment: 15 pages, 7 figures

The topological string interpretation of homological knot invariants has led to several insights into the structure of the theory in the case of sl(N). We study possible extensions of the matrix factorization approach to knot homology for other Lie groups and representations. In particular, we introduce a new triply graded theory categorifying the Kauffman polynomial, test it, and predict the Kauffman homology for several simple knots., Comment: 45 pages, harvmac

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 polynomial. Moreover, this theory should have an additional formal structure of a family of differentials. Roughly speaking, the triply graded theory by itself captures the large N behavior of the sl(N) homology, and differentials capture non-stable behavior for small N, including knot Floer homology. The differentials themselves should come from another variant of sl(N) homology, namely the deformations of it studied by Gornik, building on work of Lee. While we do not give a mathematical definition of the triply graded theory, the rich formal structure we propose is powerful enough to make many non-trivial predictions about the existing knot homologies that can then be checked directly. We include many examples where we can exhibit a likely candidate for the triply graded theory, and these demonstrate the internal consistency of our axioms. We conclude with a detailed study of torus knots, developing a picture which gives new predictions even for the original sl(2) Khovanov homology., Comment: 46 pages, 30 figures. V2: Minor improvements. To appear in Exp. Math

We conjecture a relation between the sl(N) knot homology, recently introduced by Khovanov and Rozansky, and the spectrum of BPS states captured by open topological strings. This conjecture leads to new regularities among the sl(N) knot homology groups and suggests that they can be interpreted directly in topological string theory. We use this approach in various examples to predict the sl(N) knot homology groups for all values of N. We verify that our predictions pass some non-trivial checks., Comment: 25 pages, 2 figures, harvmac; minor corrections, references added

We study three-dimensional Chern-Simons theory with complex gauge group SL(2,C), which has many interesting connections with three-dimensional quantum gravity and geometry of hyperbolic 3-manifolds. We show that, in the presence of a single knotted Wilson loop in an infinite-dimensional representation of the gauge group, the classical and quantum properties of such theory are described by an algebraic curve called the A-polynomial of a knot. Using this approach, we find some new and rather surprising relations between the A-polynomial, the colored Jones polynomial, and other invariants of hyperbolic 3-manifolds. These relations generalize the volume conjecture and the Melvin-Morton-Rozansky conjecture, and suggest an intriguing connection between the SL(2,C) partition function and the colored Jones polynomial., Comment: 67 pages, 13 figures, harvmac