Model building with intersecting D6-branes on smooth Calabi-Yau manifolds

We study intersecting D6-branes in Calabi-Yau manifolds that are smooth hypersurfaces in weighted projective spaces. We develop the techniques for calculating intersection numbers between special Lagrangian sub-manifolds defined as fixed loci of anti-holomorphic involutions. We present global Pati-Salam and MSSM-like models that are supersymmetric up to a decoupled hidden sector.Comment: 29p

Gauge Threshold Corrections for Local Orientifolds

We study gauge threshold corrections for systems of fractional branes at local orientifold singularities and compare with the general Kaplunovsky-Louis expression for locally supersymmetric N=1 gauge theories. We focus on branes at orientifolds of the C^3/Z_4, C^3/Z_6 and C^3/Z_6' singularities. We provide a CFT construction of these theories and compute the threshold corrections. Gauge coupling running undergoes two phases: one phase running from the bulk winding scale to the string scale, and a second phase running from the string scale to the infrared. The first phase is associated to the contribution of N=2 sectors to the IR beta functions and the second phase to the contribution of both N=1 and N=2 sectors. In contrast, naive application of the Kaplunovsky-Louis formula gives single running from the bulk winding mode scale. The discrepancy is resolved through 1-loop non-universality of the holomorphic gauge couplings at the singularity, induced by a 1-loop redefinition of the twisted blow-up moduli which couple differently to different gauge nodes. We also study the physics of anomalous and non-anomalous U(1)s and give a CFT description of how masses for non-anomalous U(1)s depend on the global properties of cycles.Comment: 44 page

Genome-wide association analysis and accuracy of genome-enabled breeding value predictions for resistance to infectious hematopoietic necrosis virus in a commercial rainbow trout breeding population

International audienceAbstractBackgroundInfectious hematopoietic necrosis (IHN) is a disease of salmonid fish that is caused by the IHN virus (IHNV). Under intensive aquaculture conditions, IHNV can cause significant mortality and economic losses. Currently, there is no proven and cost-effective method for IHNV control. Clear Springs Foods, Inc. has been applying selective breeding to improve genetic resistance to IHNV in their rainbow trout breeding program. The goals of this study were to elucidate the genetic architecture of IHNV resistance in this commercial population by performing genome-wide association studies (GWAS) with multiple regression single-step methods and to assess if genomic selection can improve the accuracy of genetic merit predictions over conventional pedigree-based best linear unbiased prediction (PBLUP) using cross-validation analysis.ResultsTen moderate-effect quantitative trait loci (QTL) associated with resistance to IHNV that jointly explained up to 42% of the additive genetic variance were detected in our GWAS. Only three of the 10 QTL were detected by both single-step Bayesian multiple regression (ssBMR) and weighted single-step GBLUP (wssGBLUP) methods. The accuracy of breeding value predictions with wssGBLUP (0.33–0.39) was substantially better than with PBLUP (0.13–0.24).ConclusionsOur comprehensive genome-wide scan for QTL revealed that genetic resistance to IHNV is controlled by the oligogenic inheritance of up to 10 moderate-effect QTL and many small-effect loci in this commercial rainbow trout breeding population. Taken together, our results suggest that whole genome-enabled selection models will be more effective than the conventional pedigree-based method for breeding value estimation or the marker-assisted selection approach for improving the genetic resistance of rainbow trout to IHNV in this population

Froggatt-Nielsen models from E8 in F-theory GUTs

This paper studies F-theory SU(5) GUT models where the three generations of the standard model come from three different curves. All the matter is taken to come from curves intersecting at a point of enhanced E8 gauge symmetry. Giving a vev to some of the GUT singlets naturally implements a Froggatt-Nielsen approach to flavour structure. A scan is performed over all possible models and the results are filtered using phenomenological constraints. We find a unique model that fits observations of quark and lepton masses and mixing well. This model suffers from two drawbacks: R-parity must be imposed by hand and there is a doublet-triplet splitting problem.Comment: 42 pages; v2:journal version; v3:corrected typo in neutrino masse

Moduli Redefinitions and Moduli Stabilisation

Field redefinitions occur in string compactifications at the one loop level. We review arguments for why such redefinitions occur and study their effect on moduli stabilisation and supersymmetry breaking in the LARGE volume scenario. For small moduli, although the effect of such redefinitions can be larger than that of the $\alpha'$ corrections in both the K\"ahler and scalar potentials, they do not alter the structure of the scalar potential. For the less well motivated case of large moduli, the redefinitions can dominate all other terms in the scalar potential. We also study the effect of redefinitions on the structure of supersymmetry breaking and soft terms.Comment: 21 pages, 3 figures; v2. references adde

D-Terms from Generalized NS-NS Fluxes in Type II

Orientifolds of type II string theory admit a certain set of generalized NS-NS fluxes, including not only the three-form field strength H, but also metric and non-geometric fluxes, which are related to H by T-duality. We describe in general how these fluxes appear as parameters of an effective N=1 supergravity theory in four dimensions, and in particular how certain generalized NS-NS fluxes can act as charges for R-R axions, leading to D-term contributions to the effective scalar potential. We illustrate these phenomena in type IIB with the example of a certain orientifold of T^6/Z_4.Comment: 31+1 pages, uses utarticle.cls; v2: references adde

Analysis of BAC-end sequences in rainbow trout: Content characterization and assessment of synteny between trout and other fish genomes

<p>Abstract</p> <p>Background</p> <p>Rainbow trout (<it>Oncorhynchus mykiss</it>) are cultivated worldwide for aquaculture production and are widely used as a model species to gain knowledge of many aspects of fish biology. The common ancestor of the salmonids experienced a whole genome duplication event, making extant salmonids such as the rainbow trout an excellent model for studying the evolution of tetraploidization and re-diploidization in vertebrates. However, the lack of a reference genome sequence hampers research progress for both academic and applied purposes. In order to enrich the genomic tools already available in this species and provide further insight on the complexity of its genome, we sequenced a large number of rainbow trout BAC-end sequences (BES) and characterized their contents.</p> <p>Results</p> <p>A total of 176,485 high quality BES, were generated, representing approximately 4% of the trout genome. BES analyses identified 6,848 simple sequence repeats (SSRs), of which 3,854 had high quality flanking sequences for PCR primers design. The first rainbow trout repeat elements database (INRA RT rep1.0) containing 735 putative repeat elements was developed, and identified almost 59.5% of the BES database in base-pairs as repetitive sequence. Approximately 55% of the BES reads (97,846) had more than 100 base pairs of contiguous non-repetitive sequences. The fractions of the 97,846 non-repetitive trout BES reads that had significant BLASTN hits against the zebrafish, medaka and stickleback genome databases were 15%, 16.2% and 17.9%, respectively, while the fractions of the non-repetitive BES reads that had significant BLASTX hits against the zebrafish, medaka, and stickleback protein databases were 10.7%, 9.5% and 9.5%, respectively. Comparative genomics using paired BAC-ends revealed several regions of conserved synteny across all the fish species analyzed in this study.</p> <p>Conclusions</p> <p>The characterization of BES provided insights on the rainbow trout genome. The discovery of specific repeat elements will facilitate analyses of sequence content (e.g. for SNPs discovery and for transcriptome characterization) and future genome sequence assemblies. The numerous microsatellites will facilitate integration of the linkage and physical maps and serve as valuable resource for fine mapping QTL and positional cloning of genes affecting aquaculture production traits. Furthermore, comparative genomics through BES can be used for identifying positional candidate genes from QTL mapping studies, aid in future assembly of a reference genome sequence and elucidating sequence content and complexity in the rainbow trout genome.</p

AdS Vacua, Attractor Mechanism and Generalized Geometries

We consider flux vacua attractor equations in type IIA string theory compactified on generalized geometries with orientifold projections. The four-dimensional N=1 superpotential in this compactification can be written as the sum of the Ramond-Ramond superpotential and a term described by (non)geometric flux charges. We exhibit a simple model in which supersymmetric AdS and Minkowski solutions are classified by means of discriminants of the two superpotentials. We further study various configurations without Ramond-Ramond flux charges. In this case we find supersymmetric AdS vacua both in the case of compactifications on generalized geometries with SU(3) x SU(3) structures and on manifolds with an SU(3)-structure without nongeometric flux charges. In the latter case, we have to introduce correction terms into the prepotential in order to realize consistent vacua.Comment: 35 pages, accepted version in JHE

On hypercharge flux and exotics in F-theory GUTs

We study SU(5) Grand Unified Theories within a local framework in F-theory with multiple extra U(1) symmetries arising from a small monodromy group. The use of hypercharge flux for doublet-triplet splitting implies massless exotics in the spectrum that are protected from obtaining a mass by the U(1) symmetries. We find that lifting the exotics by giving vacuum expectation values to some GUT singlets spontaneously breaks all the U(1) symmetries which implies that proton decay operators are induced. If we impose an additional R-parity symmetry by hand we find all the exotics can be lifted while proton decay operators are still forbidden. These models can retain the gauge coupling unification accuracy of the MSSM at 1-loop. For models where the generations are distributed across multiple curves we also present a motivation for the quark-lepton mass splittings at the GUT scale based on a Froggatt-Nielsen approach to flavour.Comment: 38 pages; v2: emphasised possibility of avoiding exotics in models without a global E8 structure, added ref, journal versio

Non-geometric flux vacua, S-duality and algebraic geometry

The four dimensional gauged supergravities descending from non-geometric string compactifications involve a wide class of flux objects which are needed to make the theory invariant under duality transformations at the effective level. Additionally, complex algebraic conditions involving these fluxes arise from Bianchi identities and tadpole cancellations in the effective theory. In this work we study a simple T and S-duality invariant gauged supergravity, that of a type IIB string compactified on a $T^6/(Z_2 x Z_2)$ orientifold with O3/O7-planes. We build upon the results of recent works and develop a systematic method for solving all the flux constraints based on the algebra structure underlying the fluxes. Starting with the T-duality invariant supergravity, we find that the fluxes needed to restore S-duality can be simply implemented as linear deformations of the gauge subalgebra by an element of its second cohomology class. Algebraic geometry techniques are extensively used to solve these constraints and supersymmetric vacua, centering our attention on Minkowski solutions, become systematically computable and are also provided to clarify the methods.Comment: 47 pages, 10 tables, typos corrected, Accepted for Publication in Journal of High Energy Physic