David Grellscheid

UFO – The Universal FeynRules Output

We present a new model format for automatized matrix-element generators, the so- called Universal FeynRules Output (UFO). The format is universal in the sense that it features compatibility with more than one single generator and is designed to be flexible, modular and agnostic of any assumption such as the number of particles or the color and Lorentz structures appearing in the interaction vertices. Unlike other model formats where text files need to be parsed, the information on the model is encoded into a Python module that can easily be linked to other computer codes. We then describe an interface for the Mathematica package FeynRules that allows for an automatic output of models in the UFO format.

Rivet user manual

This is the manual and user guide for the Rivet system for the validation and tuning of Monte Carlo event generators. As well as the core Rivet library, this manual describes the usage of the rivet program and the AGILe generator interface library. The depth and level of description is chosen for users of the system, starting with the basics of using validation code written by others, and then covering sufficient details to write new Rivet analyses and calculational components. Program summary Program title: Rivet Catalogue identifier: AEPS_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEPS_v1_0.html Program obtainable from: CPC Program Library, Queens University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 571126 No. of bytes in distributed program, including test data, etc.: 4717522 Distribution format: tar.gz Programming language: C++, Python. Computer: PC running Linux, Mac. Operating system: Linux, Mac OS. RAM: 20 MB Classification: 11.9, 11.2. External routines: HepMC (https://savannah.cern.ch/projects/hepmc/), GSL (http://www.gnu.org/software/gsl/manual/gsl-ref.html), FastJet (http://fastjet.fr/), Python (http://www.python.org/), Swig (http://www.swig.org/), Boost (http://www.boostsoftware.com/), YAML (http://www.yaml.org/spec/1.2/spec.html) Nature of problem: Experimental measurements from high-energy particle colliders should be defined and stored in a general framework such that it is simple to compare theory predictions to them. Rivet is such a framework, and contains at the same time a large collection of existing measurements. Solution method: Rivet is based on HepMC events, a standardised output format provided by many theory simulation tools. Events are processed by Rivet to generate histograms for the requested list of analyses, incorporating all experimental phase space cuts and histogram definitions. Restrictions: Cannot calculate statistical errors for correlated events as they appear in NLO calculations. Unusual features: It is possible for the user to implement and use their own custom analysis as a module without having to modify the main Rivet code/installation. Running time: Depends on the number and complexity of analyses being applied, but typically a few hundred events per second

General-purpose event generators for LHC physics

We review the physics basis, main features and use of general-purpose Monte Carlo event generators for the simulation of proton-proton collisions at the Large Hadron Collider. Topics included are: the generation of hardscattering matrix elements for processes of interest, at both leading and nextto-leading QCD perturbative order; their matching to approximate treatments of higher orders based on the showering approximation; the parton and dipole shower formulations; parton distribution functions for event generators; non-perturbative aspects such as soft QCD collisions, the underlying event and diractive processes; the string and cluster models for hadron formation; the treatment of hadron and tau decays; the inclusion of QED radiation and beyond-Standard-Model processes. We describe the principal features of the Ariadne, Herwig++, Pythia 8 and Sherpa generators, together with the Rivet and Professor validation and tuning tools, and discuss the physics philosophy behind the proper use of these generators and tools. This review is aimed at phenomenologists wishing to understand better how parton-level predictions are translated into hadron-level events as well as experimentalists wanting a deeper insight into the tools available for signal and background simulation at the LHC.

Herwig 7.0/Herwig++ 3.0 release note

A major new release of the Monte Carlo event generator Herwig++ (version 3.0) is now available. This release marks the end of distinguishing Herwig++ and HERWIG development and therefore constitutes the first major release of version 7 of the Herwig event generator family. The new version features a number of significant improvements to the event simulation, including: built-in NLO hard process calculation for virtually all Standard Model processes, with matching to both angular-ordered and dipole shower modules via both subtractive (MC@NLO-type) and multiplicative (Powheg-type) algorithms; QED radiation and spin correlations in the angular-ordered shower; a consistent treatment of perturbative uncertainties within the hard process and parton showering. Several of the new features will be covered in detail in accompanying publications, and an update of the manual will follow in due course.

Identification of evolutionarily conserved exons as regulated targets for the splicing activator Tra2β in development

Alternative splicing amplifies the information content of the genome, creating multiple mRNA isoforms from single genes. The evolutionarily conserved splicing activator Tra2β (Sfrs10) is essential for mouse embryogenesis and implicated in spermatogenesis. Here we find that Tra2β is up-regulated as the mitotic stem cell containing population of male germ cells differentiate into meiotic and post-meiotic cells. Using CLIP coupled to deep sequencing, we found that Tra2β binds a high frequency of exons and identified specific G/A rich motifs as frequent targets. Significantly, for the first time we have analysed the splicing effect of Sfrs10 depletion in vivo by generating a conditional neuronal-specific Sfrs10 knock-out mouse (Sfrs10fl/fl; Nestin-Cretg/+). This mouse has defects in brain development and allowed correlation of genuine physiologically Tra2β regulated exons. These belonged to a novel class which were longer than average size and importantly needed multiple cooperative Tra2β binding sites for efficient splicing activation, thus explaining the observed splicing defects in the knockout mice. Regulated exons included a cassette exon which produces a meiotic isoform of the Nasp histone chaperone that helps monitor DNA double-strand breaks. We also found a previously uncharacterised poison exon identifying a new pathway of feedback control between vertebrate Tra2 proteins. Both Nasp-T and the Tra2a poison exon are evolutionarily conserved, suggesting they might control fundamental developmental processes. Tra2β protein isoforms lacking the RRM were able to activate specific target exons indicating an additional functional role as a splicing co-activator. Significantly the N-terminal RS1 domain conserved between flies and humans was essential for the splicing activator function of Tra2β. Versions of Tra2β lacking this N-terminal RS1 domain potently repressed the same target exons activated by full-length Tra2β protein.

The splicing landscape is globally reprogrammed during male meiosis

Meiosis requires conserved transcriptional changes, but it is not known whether there is a corresponding set of RNA splicing switches. Here, we used RNAseq of mouse testis to identify changes associated with the progression from mitotic spermatogonia to meiotic spermatocytes. We identified ∼150 splicing switches, most of which affect conserved protein-coding exons. The expression of many key splicing regulators changed in the course of meiosis, including downregulation of polypyrimidine tract binding protein (PTBP1) and heterogeneous nuclear RNP A1, and upregulation of nPTB, Tra2β, muscleblind, CELF proteins, Sam68 and T-STAR. The sequences near the regulated exons were significantly enriched in target sites for PTB, Tra2β and STAR proteins. Reporter minigene experiments investigating representative exons in transfected cells showed that PTB binding sites were critical for splicing of a cassette exon in the Ralgps2 mRNA and a shift in alternative 5′ splice site usage in the Bptf mRNA. We speculate that nPTB might functionally replace PTBP1 during meiosis for some target exons, with changes in the expression of other splicing factors helping to establish meiotic splicing patterns. Our data suggest that there are substantial changes in the determinants and patterns of alternative splicing in the mitotic-to-meiotic transition of the germ cell cycle.

New constraints on gauge mediation and beyond from LHC SUSY searches at 7 TeV

The first results from the LHC on jets plus missing energy provide powerful new data to test SUSY models. Initial theoretical interpretations of these data have concentrated on gravity mediation, usually the CMSSM and its variations. In this paper we confront a large class of gauge mediation models with these new data. More precisely we consider models of pure general gauge mediation (pure GGM) and confront them with the recent experimental results of the ATLAS collaboration. We use Herwig++ and RIVET, incorporating the full set of experimental cuts, to calculate the signal rates and compare them to the data. Although based on only 35pb−1 of integrated luminosity, we show that these new data probe and exclude a portion of previously allowed parameter space of GGM. In addition we investigate the viability of standard SUSY benchmark points, including the Snowmass, CMS and ATLAS sets which encompass other mediation scenarios such as gravity, anomaly and gaugino mediation.

Selecting Supersymmetric String Scenarios From Sparticle Spectra

We approach the following question: if supersymmetry is discovered, how can we select among different supersymmetric extensions of the Standard Model? In particular, we perform an analysis of the sparticle spectrum in low-energy string effective theories, asking which observables best distinguish various scenarios. We examine scenarios differing by the fundamental string scale and concentrate on GUT and intermediate scale models. We scan over four parameters (two goldstino angles, tan β and the gravitino mass) in each scenario, finding ratios of sparticle masses that provide the maximum discrimination between them. The necessary accuracy for discrimination is determined in each case. We find that the required accuracy on various sparticle mass ratios is at the few percent level, a precision that may be achieved in future linear colliders. We also map out phenomenologically viable regions of parameter space.

Molecular design of a splicing switch responsive to the RNA binding protein Tra2β

Tra2β regulates a number of splicing switches including activation of the human testis-specific exon HIPK3-T in the Homeodomain Interacting Protein Kinase 3 gene. By testing HIPK3-T exons of different intrinsic strengths, we found Tra2β most efficiently activated splicing inclusion of intrinsically weak exons, although these were spliced at a lower overall level. Both the RRM and N-terminal RS-rich region of Tra2β were required for splicing activation. Bioinformatic searches for splicing enhancers and repressors mapped four physically distinct exonic splicing enhancers (ESEs) within HIPK3-T, each containing the known Tra2β AGAA-rich binding site. Surprisingly disruption of each single ESE prevented Tra2β-mediated activation, although single mutated exons could still bind Tra2β protein by gel shifts and functional splicing analyses. Titration experiments indicate an additive model of HIPK3-T splicing activation, requiring availability of an array of four distinct ESEs to enable splicing activation. To enable this efficient Tra2β-mediated splicing switch to operate, a closely adjacent downstream and potentially competitive stronger 5′-splice site is actively repressed. Our data indicate that a novel arrangement of multiple mono-specific AGAA-rich ESEs coupled to a weak 5′-splice site functions as a responsive gauge. This gauge monitors changes in the specific nuclear concentration of the RNA binding protein Tra2β, and co-ordinately regulates HIPK3-T exon splicing inclusion.

Constraining new physics with collider measurements of Standard Model signatures

A bstractA new method providing general consistency constraints for Beyond-the-Standard-Model (BSM) theories, using measurements at particle colliders, is presented. The method, ‘Constraints On New Theories Using Rivet’, Contur, exploits the fact that particle-level differential measurements made in fiducial regions of phase-space have a high degree of model-independence. These measurements can therefore be compared to BSM physics implemented in Monte Carlo generators in a very generic way, allowing a wider array of final states to be considered than is typically the case. The Contur approach should be seen as complementary to the discovery potential of direct searches, being designed to eliminate inconsistent BSM proposals in a context where many (but perhaps not all) measurements are consistent with the Standard Model. We demonstrate, using a competitive simplified dark matter model, the power of this approach. The Contur method is highly scaleable to other models and future measurements.