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For Chern-Simons-matter theories in three dimensions, gauge invariance may require the Chern-Simons level k to be half-integral, in which case parity is violated. As noted by Pasquetti for abelian theories with N=2 supersymmetry, the partition function on the ellipsoid also admits a suitable holomorphic factorization precisely when the value of k is properly quantized. Using known formulas for the partition function, we investigate analytic aspects of this factorization for non-abelian gauge groups and general matter representations. We verify that factorization occurs in accord with the parity anomaly for the classical matrix groups and for the exceptional group G_2. In an appendix, we discuss the analytic continuation of torus knot observables in the SU(2) Chern-Simons-matter theory., Comment: 220 pages, tikz figures; v2: references added

The Thurston-Bennequin invariant provides one notion of self-linking for any homologically-trivial Legendrian curve in a contact three-manifold. Here we discuss related analytic notions of self-linking for Legendrian knots in Euclidean space. Our definition is based upon a reformulation of the elementary Gauss linking integral and is motivated by ideas from supersymmetric gauge theory. We recover the Thurston-Bennequin invariant as a special case., Comment: 42 pages, many figures; v2: minor revisions, published version

In three dimensions, a free, periodic scalar field is related by duality to an abelian gauge field. Here I explore aspects of this duality when both theories are quantized on a Riemann surface of genus g. At higher genus, duality involves an identification of winding with momentum on the Jacobian variety of the Riemann surface. I also consider duality for monopole and loop operators on the surface and exhibit the operator algebra, a refinement of the Wilson-'t Hooft algebra., Comment: 53 pages, 1 figure, v2: references added

In three dimensions, an abelian gauge field is related by duality to a free, periodic scalar field. Though usually considered on Euclidean space, this duality can be extended to a general three-manifold M, in which case topological features of M become important. Here I comment upon several of these features as related to the partition function on M. In a companion article, arXiv:1405.2483, I discuss similarly the algebra of operators on a surface of genus g., Comment: 62 pages, 1 figure, v2: references added

As noted long ago by Atiyah and Bott, the classical Yang-Mills action on a Riemann surface admits a beautiful symplectic interpretation as the norm-square of a moment map associated to the Hamiltonian action by gauge transformations on the affine space of connections. Here I explain how certain Wilson loop observables in Chern-Simons gauge theory on a Seifert three-manifold can be given an analogous symplectic description. Among other results, this symplectic description implies that the stationary-phase approximation to the Wilson loop path integral is exact for torus knots, an empirical observation made previously by Lawrence and Rozansky. This article reviews selected material from the larger work "Localization for Wilson Loops in Chern-Simons Theory," arXiv:0911.2687., Comment: 17 pages, to appear in the proceedings of the conference "Chern-Simons Gauge Theory: 20 Years After"

We reconsider Chern-Simons gauge theory on a Seifert manifold M, which is the total space of a nontrivial circle bundle over a Riemann surface, possibly with orbifold points. As shown in previous work with Witten, the path integral technique of non-abelian localization can be used to express the partition function of Chern-Simons theory in terms of the equivariant cohomology of the moduli space of flat connections on M. Here we extend this result to apply to the expectation values of Wilson loop operators which wrap the circle fibers of M. Under localization, such a Wilson loop operator reduces naturally to the Chern character of an associated universal bundle over the moduli space. Along the way, we demonstrate that the stationary-phase approximation to the Wilson loop path integral is exact for torus knots, an observation made empirically by Lawrence and Rozansky prior to this work., Comment: 227 pages, 1 figure, harvmac, v2: references added

We consider realizations of GUT models in F-theory. Adopting a bottom up approach, the assumption that the dynamics of the GUT model can in principle decouple from Planck scale physics leads to a surprisingly predictive framework. An internal U(1) hypercharge flux Higgses the GUT group directly to the MSSM or to a flipped GUT model, a mechanism unavailable in heterotic models. This new ingredient automatically addresses a number of puzzles present in traditional GUT models. The internal U(1) hyperflux allows us to solve the doublet-triplet splitting problem, and explains the qualitative features of the distorted GUT mass relations for lighter generations due to the Aharanov-Bohm effect. These models typically come with nearly exact global symmetries which prevent bare mu terms and also forbid dangerous baryon number violating operators. Strong curvature around our brane leads to a repulsion mechanism for Landau wave functions for neutral fields. This leads to large hierarchies of the form exp(-c/B^(2*g)) where c and g are order one parameters and B ~ M_(GUT)/(M_(pl)*alpha_(GUT)). This effect can simultaneously generate a viably small mu term as well as an acceptable Dirac neutrino mass on the order of 0.5 * 10^(-2 +/- 0.5) eV. In another scenario, we find a modified seesaw mechanism which predicts that the light neutrinos have masses in the expected range while the Majorana mass term for the heavy neutrinos is ~ 3 * 10^(12 +/- 1.5) GeV. Communicating supersymmetry breaking to the MSSM can be elegantly realized through gauge mediation. In one scenario, the same repulsion mechanism also leads to messenger masses which are naturally much lighter than the GUT scale., Comment: v3: 203 pages, 8 figures, typos corrected, references added

Motivated by potential phenomenological applications, we develop the necessary tools for building GUT models in F-theory. This approach is quite flexible because the local geometrical properties of singularities in F-theory compactifications encode the physical content of the theory. In particular, we show how geometry determines the gauge group, matter content and Yukawa couplings of a given model. It turns out that these features are beautifully captured by a four-dimensional topologically twisted N=4 theory which has been coupled to a surface defect theory on which chiral matter can propagate. From the vantagepoint of the four-dimensional topological theory, these defects are surface operators. Specific intersection points of these defects lead to Yukawa couplings. We also find that the unfolding of the singularity in the F-theory geometry precisely matches to properties of the topological theory with a defect., Comment: v2: 121 pages, 5 figures, reference and clarification added

It is argued, using an M-theory lift, that the IIA partition function on a euclidean AdS_2 x S^2 x CY_3 attractor geometry computes the modified elliptic genus Z_BH of the associated black hole in a large charge expansion. The partition function is then evaluated using the Green-Schwarz formalism. After localizing the worldsheet path integral with the addition of an exact term, contributions arise only from the center of AdS_2 and the north and south poles of S^2. These are the toplogical and anti-topological string partition functions Z_top and {\bar Z_top} respectively. We thereby directly reproduce the perturbative relation Z_BH = |Z_top|^2., Comment: 19 pages, no figures

We describe a new class of instanton effects in string compactifications that preserve only N=1 supersymmetry in four dimensions. As is well-known, worldsheet or brane instantons in such a background can sometimes contribute to an effective superpotential for the moduli of the compactification. We generalize this phenomenon by showing that such instantons can also contribute to new multi-fermion and higher-derivative F-terms in the low-energy effective action. We consider in most detail the example of heterotic compactification on a Calabi-Yau threefold X with gauge bundle V, in which case we study worldsheet instanton effects that deform the complex structure of the moduli space associated to X and V. We also give new, slightly more economical derivations of some previous results about worldsheet instantons in Type IIA Calabi-Yau compactifications., Comment: 49 pages, harvmac, v2: references added

We reconsider Chern-Simons gauge theory on a Seifert manifold M (the total space of a nontrivial circle bundle over a Riemann surface). When M is a Seifert manifold, Lawrence and Rozansky have shown from the exact solution of Chern-Simons theory that the partition function has a remarkably simple structure and can be rewritten entirely as a sum of local contributions from the flat connections on M. We explain how this empirical fact follows from the technique of non-abelian localization as applied to the Chern-Simons path integral. In the process, we show that the partition function of Chern-Simons theory on M admits a topological interpretation in terms of the equivariant cohomology of the moduli space of flat connections on M., Comment: 131 pages, harvmac, v2: references added

In supersymmetric QCD with SU(N_c) gauge group and N_f flavors, it is known that instantons generate a superpotential if N_f=N_c-1 and deform the moduli space of vacua if N_f=N_c. But the role of instantons has been unclear for N_f>N_c. In this paper, we demonstrate that for N_f>N_c, on the moduli space of vacua, instantons generate a more subtle chiral operator containing (for example) non-derivative interactions of 2(N_f-N_c)+4 fermions. Upon giving masses to some flavors, one can integrate out some fermions and recover the standard results for N_f=N_c and N_f=N_c-1. For N_f=N_c, our analysis gives, in a sense, a more systematic way to demonstrate that instantons deform the complex structure of the moduli space of vacua., Comment: 40 pp

We reconsider the question of which Calabi-Yau compactifications of the heterotic string are stable under world-sheet instanton corrections to the effective space-time superpotential. For instance, compactifications described by (0,2) linear sigma models are believed to be stable, suggesting a remarkable cancellation among the instanton effects in these theories. Here, we show that this cancellation follows directly from a residue theorem, whose proof relies only upon the right-moving world-sheet supersymmetries and suitable compactness properties of the (0,2) linear sigma model. Our residue theorem also extends to a new class of "half-linear" sigma models. Using these half-linear models, we show that heterotic compactifications on the quintic hypersurface in CP^4 for which the gauge bundle pulls back from a bundle on CP^4 are stable. Finally, we apply similar ideas to compute the superpotential contributions from families of membrane instantons in M-theory compactifications on manifolds of G_2 holonomy., Comment: 47 pages

We elucidate the relationship between supersymmetric D3-branes and chiral baryonic operators in the AdS/CFT correspondence. For supersymmetric backgrounds of the form AdS_5 x H, we characterize via holomorphy a large family of supersymmetric D3-brane probes wrapped on H. We then quantize this classical family of probe solutions to obtain a BPS spectrum which describes D3-brane configurations on H. For the particular examples H = T^{1,1} and H = S^5, we match the BPS spectrum to the spectrum of chiral baryonic operators in the dual gauge theory., Comment: 28 pages, harvmac

We consider the breaking of N=1 supersymmetry by non-zero G-flux when M-theory is compactified on a smooth manifold X of G_2 holonomy. Gukov has proposed a superpotential W to describe this breaking in the low-energy effective theory. We check this proposal by comparing the bosonic potential implied by W with the corresponding potential deduced from the eleven-dimensional supergravity action. One interesting aspect of this check is that, though W depends explicitly only on G-flux supported on X, W also describes the breaking of supersymmetry by G-flux transverse to X., Comment: 15 pages, harvmac, v2: reference added

We investigate field theories on the worldvolume of a D3-brane transverse to partial resolutions of a $\Z_3\times\Z_3$ Calabi-Yau threefold quotient singularity. We deduce the field content and lagrangian of such theories and present a systematic method for mapping the moment map levels characterizing the partial resolutions of the singularity to the Fayet-Iliopoulos parameters of the D-brane worldvolume theory. As opposed to the simpler cases studied before, we find a complex web of partial resolutions and associated field-theoretic Fayet-Iliopoulos deformations. The analysis is performed by toric methods, leading to a structure which can be efficiently described in the language of convex geometry. For the worldvolume theory, the analysis of the moduli space has an elegant description in terms of quivers. As a by-product, we present a systematic way of extracting the birational geometry of the classical moduli spaces, thus generalizing previous work on resolution of singularities by D-branes., Comment: 52 pages, 9 figures