The Omega deformed B-model for rigid N=2 theories

We give an interpretation of the Omega deformed B-model that leads naturally to the generalized holomorphic anomaly equations. Direct integration of the latter calculates topological amplitudes of four dimensional rigid N=2 theories explicitly in general Omega-backgrounds in terms of modular forms. These amplitudes encode the refined BPS spectrum as well as new gravitational couplings in the effective action of N=2 supersymmetric theories. The rigid N=2 field theories we focus on are the conformal rank one N=2 Seiberg-Witten theories. The failure of holomorphicity is milder in the conformal cases, but fixing the holomorphic ambiguity is only possible upon mass deformation. Our formalism applies irrespectively of whether a Lagrangian formulation exists. In the class of rigid N=2 theories arising from compactifications on local Calabi-Yau manifolds, we consider the theory of local P2. We calculate motivic Donaldson-Thomas invariants for this geometry and make predictions for generalized Gromov-Witten invariants at the orbifold point.Comment: 73 pages, no figures, references added and typos correcte

Counting fermionic zero modes on M5 with fluxes

We study the Dirac equation on an M5 brane wrapped on a divisor in a Calabi--Yau fourfold in the presence of background flux. We reduce the computation of the normal bundle U(1) anomaly to counting the solutions of a finite--dimensional linear system on cohomology. This system depends on the choice of flux. In an example, we find that the presence of flux changes the anomaly and allows instanton corrections to the superpotential which would otherwise be absent.Comment: 14 pages. v2: reference added, typos corrected, few change

Surface Operator, Bubbling Calabi-Yau and AGT Relation

Surface operators in N=2 four-dimensional gauge theories are interesting half-BPS objects. These operators inherit the connection of gauge theory with the Liouville conformal field theory, which was discovered by Alday, Gaiotto and Tachikawa. Moreover it has been proposed that toric branes in the A-model topological strings lead to surface operators via the geometric engineering. We analyze the surface operators by making good use of topological string theory. Starting from this point of view, we propose that the wave-function behavior of the topological open string amplitudes geometrically engineers the surface operator partition functions and the Gaiotto curves of corresponding gauge theories. We then study a peculiar feature that the surface operator corresponds to the insertion of the degenerate fields in the conformal field theory side. We show that this aspect can be realized as the geometric transition in topological string theory, and the insertion of a surface operator leads to the bubbling of the toric Calabi-Yau geometry.Comment: 36 pages, 14 figures. v2: minor changes and typos correcte

Non-compact Topological Branes on Conifold

We consider non-compact branes in topological string theories on a class of Calabi-Yau spaces including the resolved conifold and its mirror. We compute the amplitudes of the insertion of non-compact Lagrangian branes in the A-model on the resolved conifold in the context of the topological vertex as well as the melting crystal picture. They all agree with each other and also agree with the results from Chern-Simons theory, supporting the large N duality. We find that they obey the Schr\"odinger equation confirming the wavefunction behavior of the amplitudes. We also compute the amplitudes of the non-compact B-branes in the DV matrix model which arises as a B-model open string field theory on the mirror manifold of the deformed conifold. We take the large N duality to consider the B-model on the mirror of the resolved conifold and confirm the wave function behavior of this amplitude. We find appropriate descriptions of non-compact branes in each model, which give complete agreements among those amplitudes and clarify the salient features including the role of symmetries toward these agreements.Comment: 32 pages, 9 figures, a reference added, typos fixe

Open string wavefunctions in flux compactifications

We consider compactifications of type I supergravity on manifolds with SU(3) structure, in the presence of RR fluxes and magnetized D9-branes, and analyze the generalized Dirac and Laplace-Beltrami operators associated to the D9-brane worldvolume fields. These compactifications are T-dual to standard type IIB toroidal orientifolds with NSNS and RR 3-form fluxes and D3/D7 branes. By using techniques of representation theory and harmonic analysis, the spectrum of open string wavefunctions can be computed for Lie groups and their quotients, as we illustrate with explicit twisted tori examples. We find a correspondence between irreducible unitary representations of the Kaloper-Myers algebra and families of Kaluza-Klein excitations. We perform the computation of 2- and 3-point couplings for matter fields in the above flux compactifications, and compare our results with those of 4d effective supergravity.Comment: 89 pages, 4 figures. v3: more typos corrected, version published in JHE

Taming open/closed string duality with a Losev trick

A target space string field theory formulation for open and closed B-model is provided by giving a Batalin-Vilkovisky quantization of the holomorphic Chern-Simons theory with off-shell gravity background. The target space expression for the coefficients of the holomorphic anomaly equation for open strings are obtained. Furthermore, open/closed string duality is proved from a judicious integration over the open string fields. In particular, by restriction to the case of independence on continuous open moduli, the shift formulas of [7] are reproduced and shown therefore to encode the data of a closed string dual.Comment: 22 pages, no figures; v.2 Refs. and a comment added

How the structure of the large subunit controls function in an oxygen-tolerant [NiFe]-hydrogenase

Salmonella enterica is an opportunistic pathogen that produces a [NiFe]-hydrogenase under aerobic conditions. In the present study, genetic engineering approaches were used to facilitate isolation of this enzyme, termed Hyd-5. The crystal structure was determined to a resolution of 3.2 Å and the hydro-genase was observed to comprise associated large and small subunits. The structure indicated that His(229) from the large subunit was close to the proximal [4Fe–3S] cluster in the small subunit. In addition, His(229) was observed to lie close to a buried glutamic acid (Glu(73)), which is conserved in oxygen-tolerant hydrogenases. His(229) and Glu(73) of the Hyd-5 large subunit were found to be important in both hydrogen oxidation activity and the oxygen-tolerance mechanism. Substitution of His(229) or Glu(73) with alanine led to a loss in the ability of Hyd-5 to oxidize hydrogen in air. Furthermore, the H229A variant was found to have lost the overpotential requirement for activity that is always observed with oxygen-tolerant [NiFe]-hydrogenases. It is possible that His(229) has a role in stabilizing the super-oxidized form of the proximal cluster in the presence of oxygen, and it is proposed that Glu(73)could play a supporting role in fine-tuning the chemistry of His(229) to enable this function

Heterotic Flux Attractors

We find attractor equations describing moduli stabilization for heterotic compactifications with generic SU(3)-structure. Complex structure and K\"ahler moduli are treated on equal footing by using SU(3)xSU(3)-structure at intermediate steps. All independent vacuum data, including VEVs of the stabilized moduli, is encoded in a pair of generating functions that depend on fluxes alone. We work out an explicit example that illustrates our methods.Comment: 37 pages, references and clarifications adde