Due to the widespread use of molecular similarity assessments in drug design, numerous methods for the calculation of similarity scores of organic molecules have been developed. When applied to other types of molecules, such as inorganic and organometallic compounds, these methods face significant challenges. To overcome these challenges, we here introduce Hypershape Recognition (HSR), a versatile framework for moment-based similarity assessment of three-dimensional (3D) chemical representations annotated with atomic features. In a default, general-purpose, implementation of the framework, features containing information about the atomic number, the isotope (the number of neutrons), and the formal charge of each atom are combined with its Cartesian coordinates to form the N-dimensional objects, termed hypershapes, that are compared. The hypershapes may account for any atomic features, including, as the first moment-based similarity method, any user-provided numerical values. Thus, the HSR framework can be tailored for specific applications, such as that of distinguishing between isotopologues and transition-metal complexes with different oxidation states, not handled by other moment-based molecular similarity methods. Moreover, by placing each hypershape in a reference system consisting of its own principal components (PCs, derived from principal component analysis, PCA, of the centered N-dimensional coordinates and features of the hypershape) and using reference points located on PCs instead of on atoms to generate distance distributions and their moments, HSR similarity scores are continuous across geometry fluctuations. The PC-based reference system also enables HSR to distinguish between enantiomers. HSR is available as open source at https://github.com/denoptim-project/HSR.

Computational methods for automated molecular design, many of which have been built around genetic algorithms inspired by natural selection and evolution, have been used for decades in drug discovery. The last decade has seen a rapid development of such methods and strategies also in design of other functional molecules, such as transition-metal catalysts. To help introduce new researchers to this emerging field, the fundamentals of genetic algorithms and how they are implemented for molecular design are presented along with practical and tutorial-like information. The emphasis is on methods, implementations, and advice of particular relevance for design of transition-metal compounds and catalysts.

A new release of the Monte Carlo event generator Herwig++ (version 2.7) is now available. This version comes with a number of improvements including: an interface to the Universal FeynRules Output (UFO) format allowing the simulation of a wide range of new-physics models; developments of the Matchbox framework for next-to-leading order (NLO) simulations; better treatment of QCD radiation in heavy particle decays in new-physics models; a new tune of underlying event and colour connection parameters that allows a good simultaneous description of both Tevatron and LHC underlying event data and the effective cross-section parameter for double-parton scattering.

First released in 2010, the Rivet library forms an important repository for analysis code, facilitating comparisons between measurements of the final state in particle collisions and theoretical calculations of those final states. We give an overview of Rivet's current design and implementation, its uptake for analysis preservation and physics results, and summarise recent developments including propagation of MC systematic-uncertainty weights, heavy-ion and ep physics, and systems for detector emulation. In addition, we provide a short user guide that supplements and updates the Rivet user manual.

A new release of the Monte Carlo event generator Herwig (version 7.2) is now available. This version introduces a number of improvements over the major version 7.0, notably: multi-jet merging with the dipole shower at LO and NLO QCD; spin correlations in both the dipole and angular-ordered parton showers; an improved choice of evolution variable in the angular-ordered parton shower; improvements to mass effects and top decays in the dipole shower, improvements to the simulation of multiple-parton interactions, including diffractive processes; a new model for baryonic colour reconnection; improvements to strangeness production; as well as a new tune of the hadronisation parameters and support for generic Lorentz structures in BSM models. This article illustrates new features of versions 7.1 and 7.2.

We present the activities of the `New Physics' working group for the `Physics at TeV Colliders' workshop (Les Houches, France, 5–23 June, 2017). Our report includes new physics studies connected with the Higgs boson and its properties, direct search strategies, reinterpretation of the LHC results in the building of viable models and new computational tool developments.

A new release of the Monte Carlo event generator Herwig (version 7.1) is now available. This version introduces a number of improvements, notably: multi-jet merging with the dipole shower at LO and NLO QCD; a new model for soft interactions and diffraction; improvements to mass effects and top decays in the dipole shower, as well as a new tune of the hadronisation parameters.

Johannes Bellm1,2, Stefan Gieseke1, David Grellscheid2, Simon Plätzer2,3, Michael Rauch1, Christian Reuschle ∗ 1,4, Peter Richardson2,5, Peter Schichtel2, Michael H. Seymour3, Andrzej Siódmok5,6, Alexandra Wilcock2, Nadine Fischer1, Marco A. Harrendorf7, Graeme Nail3, Andreas Papaefstathiou5, Daniel Rauch1 1Institute for Theoretical Physics, Karlsruhe Institute of Technology 2IPPP, Department of Physics, Durham University 3Particle Physics Group, School of Physics and Astronomy, University of Manchester 4HEP Theory Group, Department of Physics, Florida State University 5CERN, PH-TH, Geneva 6The Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences 7Institut of Experimental Nuclear Physics, Karlsruhe Institute of Technology

A 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.

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.

With the advent and recent extension of the BLHA standard to interface Monte Carlo event generators and one-loop matrix element providers, the Herwig++ event generator has expanded its range of applicability to a multitude of underlying hard processes at NLO QCD.The new NLO development is centered around the Matchbox framework, which turns fixed NLO QCD calculations into parton shower matched calculations -to be matched to the two parton shower variants of Herwig++.Matchbox provides thereby for the automated setup of the underlying fixed NLO QCD calculations and the interface to the one-loop matrix element providers, as well as for an efficient and automated multi-channel phase space sampling, and forms the basis for the NLO capabilities of the new release of Herwig++.Along with several other new features and developments, the new release marks the end of distinguishing Herwig++ and (Fortran) HERWIG, and constitutes the first major release of version 7 of the Herwig event generator.

This Report summarizes the proceedings of the 2015 Les Houches workshop on Physics at TeV Colliders. Session 1 dealt with (I) new developments relevant for high precision Standard Model calculations, (II) the new PDF4LHC parton distributions, (III) issues in the theoretical description of the production of Standard Model Higgs bosons and how to relate experimental measurements, (IV) a host of phenomenological studies essential for comparing LHC data from Run I with theoretical predictions and projections for future measurements in Run II, and (V) new developments in Monte Carlo event generators.

Herwig++ is the successor of the event generator HERWIG. In its present version 2.2.1 it provides a program for full LHC event generatio n which is superior to the previous program in many respects. We briefly su mmarize its features and describe present work and some future plans.

This is the manual and user guide for the Rivet system for the validation and tuning of Monte Carlo event generators for high energy physics. 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.

A large number of computational scientific research projects make use of open source software packages. However, the development process of such tools frequently differs from conventional software development; partly because of the nature of research, where the problems being addressed are not always fully understood; partly because the majority of the development is often carried out by scientists with limited experience and exposure to best practices of software engineering. Often the software development suffers from the pressure to publish scientific results and that credit for software development is limited in comparison. Fundamental components of software engineering like modular and reusable design, validation, documentation, and software integration as well as effective maintenance and user support tend to be disregarded due to lack of resources and qualified specialists. Thus innovative developments are often hindered by steep learning curves required to master development for legacy software packages full of ad hoc solutions. The growing complexity of research, however, requires suitable and maintainable computational tools, resulting in a widening gap between the potential users (often growing in number) and contributors to the development of such a package. In this paper we share our experiences aiming to improve the situation by training particularly young scientists, through disseminating our own experiences at contributing to open source software packages and practicing key components of software engineering adapted for scientists and scientific software development. Specifically we summarize the outcome of the Workshop in Advanced Techniques for Scientific Programming and Collaborative Development of Open Source Software Packages run at the Abdus Salam International Centre for Theoretical Physics in March 2013, and discuss our conclusions for future efforts.

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.

In this note we compare the latest 1.04 fb−1 LHC searches for squarks and gluinos from jets and missing transverse momentum (MET) with constraints arising from the LEP Higgs bound. For General Gauge Mediation models with moderate values of tan(β) we find that the zero-lepton MET searches of supersymmetry at the LHC are only starting to be competitive with the Higgs bounds from LEP. From this perspective and for such models, the SUSY searches at the LHC are still very much in the beginning.

A new release of the Monte Carlo event generator Herwig++ (version 2.6) is now available. This version comes with a number of improvements including: a new structure for the implementation of next-to-leading order matrix elements; an improved treatment of wideangle gluon radiation; new hard-coded next-to-leading order matrix elements for deep inelastic scattering and weak vector boson fusion; additional models of physics beyond the Standard Model, including the production of colour sextet particles; a statistical colour reconnection model; automated energy scaling of underlying-event tunes.

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.