Wavefunctions and the Point of E8 in F-theory

In F-theory GUTs interactions between fields are typically localised at points of enhanced symmetry in the internal dimensions implying that the coefficient of the associated operator can be studied using a local wavefunctions overlap calculation. Some F-theory SU(5) GUT theories may exhibit a maximum symmetry enhancement at a point to E8, and in this case all the operators of the theory can be associated to the same point. We take initial steps towards the study of operators in such theories. We calculate wavefunctions and their overlaps around a general point of enhancement and establish constraints on the local form of the fluxes. We then apply the general results to a simple model at a point of E8 enhancement and calculate some example operators such as Yukawa couplings and dimension-five couplings that can lead to proton decay.Comment: 46 page

Novel Branches of (0,2) Theories

We show that recently proposed linear sigma models with torsion can be obtained from unconventional branches of conventional gauge theories. This observation puts models with log interactions on firm footing. If non-anomalous multiplets are integrated out, the resulting low-energy theory involves log interactions of neutral fields. For these cases, we find a sigma model geometry which is both non-toric and includes brane sources. These are heterotic sigma models with branes. Surprisingly, there are massive models with compact complex non-Kahler target spaces, which include brane/anti-brane sources. The simplest conformal models describe wrapped heterotic NS5-branes. We present examples of both types.Comment: 36 pages, LaTeX, 2 figures; typo in Appendix fixed; references added and additional minor change

On Global Flipped SU(5) GUTs in F-theory

We construct an SU(4) spectral divisor and its factorization of types (3,1) and (2,2) based on the construction proposed in [1]. We calculate the chiral spectra of flipped SU(5) GUTs by using the spectral divisor construction. The results agree with those from the analysis of semi-local spectral covers. Our computations provide an example for the validity of the spectral divisor construction and suggest that the standard heterotic formulae are applicable to the case of F-theory on an elliptically fibered Calabi-Yau fourfold with no heterotic dual.Comment: 45 pages, 12 tables, 1 figure; typos corrected, footnotes added, and a reference adde

Flipped SU(5) GUTs from E_8 Singularities in F-theory

In this paper we construct supersymmetric flipped SU(5) GUTs from E_8 singularities in F-theory. We start from an SO(10) singularity unfolded from an E_8 singularity by using an SU(4) spectral cover. To obtain realistic models, we consider (3,1) and (2,2) factorizations of the SU(4) cover. After turning on the massless U(1)_X gauge flux, we obtain the SU(5) X U(1)_X gauge group. Based on the well-studied geometric backgrounds in the literature, we demonstrate several models and discuss their phenomenology.Comment: 46 pages, 23 tables, 1 figure, typos corrected, references added, and new examples presente

Emerging Non-Anomalous Baryonic Symmetries in the AdS_5/CFT_4 Correspondence

We study the breaking of baryonic symmetries in the AdS_5/CFT_4 correspondence for D3 branes at Calabi-Yau three-fold singularities. This leads, for particular VEVs, to the emergence of non-anomalous baryonic symmetries during the renormalization group flow. We claim that these VEVs correspond to critical values of the B-field moduli in the dual supergravity backgrounds. We study in detail the C^3/Z_3 orbifold, the cone over F_0 and the C^3/Z_5 orbifold. For the first two examples, we study the dual supergravity backgrounds that correspond to the breaking of the emerging baryonic symmetries and identify the expected Goldstone bosons and global strings in the infra-red. In doing so we confirm the claim that the emerging symmetries are indeed non-anomalous baryonic symmetries.Comment: 65 pages, 15 figures;v2: minor changes, published versio

Evidence for F(uzz) Theory

We show that in the decoupling limit of an F-theory compactification, the internal directions of the seven-branes must wrap a non-commutative four-cycle S. We introduce a general method for obtaining fuzzy geometric spaces via toric geometry, and develop tools for engineering four-dimensional GUT models from this non-commutative setup. We obtain the chiral matter content and Yukawa couplings, and show that the theory has a finite Kaluza-Klein spectrum. The value of 1/alpha_(GUT) is predicted to be equal to the number of fuzzy points on the internal four-cycle S. This relation puts a non-trivial restriction on the space of gauge theories that can arise as a limit of F-theory. By viewing the seven-brane as tiled by D3-branes sitting at the N fuzzy points of the geometry, we argue that this theory admits a holographic dual description in the large N limit. We also entertain the possibility of constructing string models with large fuzzy extra dimensions, but with a high scale for quantum gravity.Comment: v2: 66 pages, 3 figures, references and clarifications adde

Rational F-Theory GUTs without exotics

We construct F-theory GUT models without exotic matter, leading to the MSSM matter spectrum with potential singlet extensions. The interplay of engineering explicit geometric setups, absence of four-dimensional anomalies, and realistic phenomenology of the couplings places severe constraints on the allowed local models in a given geometry. In constructions based on the spectral cover we find no model satisfying all these requirements. We then provide a survey of models with additional U(1) symmetries arising from rational sections of the elliptic fibration in toric constructions and obtain phenomenologically appealing models based on SU(5) tops. Furthermore we perform a bottom-up exploration beyond the toric section constructions discussed in the literature so far and identify benchmark models passing all our criteria, which can serve as a guideline for future geometric engineering.Comment: 27 Pages, 1 Figur

Abelian Gauge Fluxes and Local Models in F-Theory

We analyze the Abelian gauge fluxes in local F-theory models with G_S=SU(6) and SO(10). For the case of G_S=SO(10), there is a no-go theorem which states that for an exotic-free spectrum, there are no solutions for U(1)^2 gauge fluxes. We explicitly construct the U(1)^2 gauge fluxes with an exotic-free bulk spectrum for the case of G_S=SU(6). We also analyze the conditions for the curves supporting the given field content and discuss non-minimal spectra of the MSSM with doublet-triplet splitting.Comment: 43 pages, 15 tables; typos corrected, reference adde

Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment

Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. To compare the performance of different aligners and help detect systematic errors in alignments, a number of benchmarking strategies have been pursued. Here we present an overview of the main strategies--based on simulation, consistency, protein structure, and phylogeny--and discuss their different advantages and associated risks. We outline a set of desirable characteristics for effective benchmarking, and evaluate each strategy in light of them. We conclude that there is currently no universally applicable means of benchmarking MSA, and that developers and users of alignment tools should base their choice of benchmark depending on the context of application--with a keen awareness of the assumptions underlying each benchmarking strategy.Comment: Revie