Many-body perturbation theory calculations using the yambo code

International audienceyambo is an open source project aimed at studying excited state properties of condensed matter systems from first principles using many-body methods. As input, yambo requires ground state electronic structure data as computed by density functional theory codes such as quantum-espresso and abinit. yambo's capabilities include the calculation of linear response quantities (both independent-particle and including electron-hole interactions), quasi-particle corrections based on the GW formalism, optical absorption, and other spectroscopic quantities. Here we describe recent developments ranging from the inclusion of important but oft-neglected physical effects such as electron-phonon interactions to the implementation of a real-time propagation scheme for simulating linear and non-linear optical properties. Improvements to numerical algorithms and the user interface are outlined. Particular emphasis is given to the new and efficient parallel structure that makes it possible to exploit modern high performance computing architectures. Finally, we demonstrate the possibility to automate workflows by interfacing with the yambopy and AiiDA software tools

Inhibition of the Nicotinic Acetylcholine Receptors by Cobra Venom α-Neurotoxins: Is There a Perspective in Lung Cancer Treatment?

Nicotine exerts its oncogenic effects through the binding to nicotinic acetylcholine receptors (nAChRs) and the activation of downstream pathways that block apoptosis and promote neo-angiogenesis. The nAChRs of the α7 subtype are present on a wide variety of cancer cells and their inhibition by cobra venom neurotoxins has been proposed in several articles and reviews as a potential innovative lung cancer therapy. However, since part of the published results was recently retracted, we believe that the antitumoral activity of cobra venom neurotoxins needs to be independently re-evaluated

Large-angle production of charged pions by 3 GeV/c - 12 GeV/c protons on carbon, copper and tin targets

A measurement of the double-differential $\pi^{\pm}$ production cross-section in proton--carbon, proton--copper and proton--tin collisions in the range of pion momentum 100 \MeVc \leq p < 800 \MeVc and angle 0.35 \rad \le \theta <2.15 \rad is presented. The data were taken with the HARP detector in the T9 beam line of the CERN PS. The pions were produced by proton beams in a momentum range from 3 \GeVc to 12 \GeVc hitting a target with a thickness of 5% of a nuclear interaction length. The tracking and identification of the produced particles was done using a small-radius cylindrical time projection chamber (TPC) placed in a solenoidal magnet. An elaborate system of detectors in the beam line ensured the identification of the incident particles. Results are shown for the double-differential cross-sections at four incident proton beam momenta (3 \GeVc, 5 \GeVc, 8 \GeVc and 12 \GeVc)

Multiple Integrated Non-clinical Studies Predict the Safety of Lentivirus-Mediated Gene Therapy for \u3b2-Thalassemia

Gene therapy clinical trials require rigorous non-clinical studies in the most relevant models to assess the benefit-to-risk ratio. To support the clinical development of gene therapy for \u3b2-thalassemia, we performed in vitro and in vivo studies for prediction of safety. First we developed newly GLOBE-derived vectors that were tested for their transcriptional activity and potential interference with the expression of surrounding genes. Because these vectors did not show significant advantages, GLOBE lentiviral vector (LV) was elected for further safety characterization. To support the use of hematopoietic stem cells (HSCs) transduced by GLOBE LV for the treatment of \u3b2-thalassemia, we conducted toxicology, tumorigenicity, and biodistribution studies in compliance with the OECD Principles of Good Laboratory Practice. We demonstrated a lack of toxicity and tumorigenic potential associated with GLOBE LV-transduced cells. Vector integration site (IS) studies demonstrated that both murine and human transduced HSCs retain self-renewal capacity and generate new blood cell progeny in the absence of clonal dominance. Moreover, IS analysis showed an absence of enrichment in cancer-related genes, and the genes targeted by GLOBE LV in human HSCs are well known sites of integration, as seen in other lentiviral gene therapy trials, and have not been associated with clonal expansion. Taken together, these integrated studies provide safety data supporting the clinical application of GLOBE-mediated gene therapy for \u3b2-thalassemia

Quest for barley canopy architecture genes in the hortillus population and whealbi germplasm collection

Barley grains are predominantly used for animal feed and malting, and breeding traditionally focused on increase of grain yield by partitioning biomass from straw to grains. The increasing demand for renewable energy sources makes straw, and specially barley straw characterized by the largest content of carbohydrates among the cereals, a valuable product for its potential conversion into biofuels and other products. The BarPLUS project aims at finding genes, alleles and candidate lines related to barley canopy architecture and photosynthesis, to maximize barley biomass and yield (https://barplus.wordpress.com/). In this framework, our research group focuses on identifying genes and alleles controlling tillering, leaf size and leaf angle traits in barley by exploiting both induced and natural allelic variation. Using a forward genetics approach, we screened the HorTILLUS population (Szurman-Zubrzycka et al., 2018) under both field and controlled conditions, identifying 5 mutants with increased tillering and/or erect leaves. After crossing with four reference cultivars, pools of F2 wild-type and mutant plants were selected to map and identify the underlying genes by exome sequencing (Mascher et al., 2014). In parallel, TILLING of the HorTILLUS population identified four lines carrying mutations in the LBO (Lateral branching oxidoreductase) gene involved in tiller number. In order to explore also natural genetic variation, we are taking advantage of the \u2018WHEALBI\u2019 germplasm collection, which includes 403 exome sequenced diverse accessions (BustosKorts et al., 2019): a field trial on a subset of 240 lines (Fiorenzuola d\u2019Arda, Italy) allowed us to conduct a preliminary genome wide association study based on high-throughput phenotyping for leaf angle (PocketPlant3D smartphone app) and quantitative image-analysis for leaf size. Results will be compared with those from a greenhouse experiment on the same 240 accessions to analyze a wide range of morphological traits and identify associated markers and genomic regions

Measurement of the production of charged pions by protons on a tantalum target

A measurement of the double-differential cross-section for the production of charged pions in proton--tantalum collisions emitted at large angles from the incoming beam direction is presented. The data were taken in 2002 with the HARP detector in the T9 beam line of the CERN PS. The pions were produced by proton beams in a momentum range from 3 \GeVc to 12 \GeVc hitting a tantalum target with a thickness of 5% of a nuclear interaction length. The angular and momentum range covered by the experiment (100 \MeVc \le p < 800 \MeVc and 0.35 \rad \le \theta <2.15 \rad) is of particular importance for the design of a neutrino factory. The produced particles were detected using a small-radius cylindrical time projection chamber (TPC) placed in a solenoidal magnet. Track recognition, momentum determination and particle identification were all performed based on the measurements made with the TPC. An elaborate system of detectors in the beam line ensured the identification of the incident particles. Results are shown for the double-differential cross-sections ${{\mathrm{d}^2 \sigma}} / {{\mathrm{d}p\mathrm{d}\theta}}$ at four incident proton beam momenta (3 \GeVc, 5 \GeVc, 8 \GeVc and 12 \GeVc). In addition, the pion yields within the acceptance of typical neutrino factory designs are shown as a function of beam momentum. The measurement of these yields within a single experiment eliminates most systematic errors in the comparison between rates at different beam momenta and between positive and negative pion production.Comment: 49 pages, 31 figures. Version accepted for publication on Eur. Phys. J.

Measurement of the production cross-section of positive pions in the collision of 8.9 GeV/c protons on beryllium

The double-differential production cross-section of positive pions, $d^2\sigma^{\pi^{+}}/dpd\Omega$, measured in the HARP experiment is presented. The incident particles are 8.9 GeV/c protons directed onto a beryllium target with a nominal thickness of 5% of a nuclear interaction length. The measured cross-section has a direct impact on the prediction of neutrino fluxes for the MiniBooNE and SciBooNE experiments at Fermilab. After cuts, 13 million protons on target produced about 96,000 reconstructed secondary tracks which were used in this analysis. Cross-section results are presented in the kinematic range 0.75 GeV/c < $p_{\pi}$ < 6.5 GeV/c and 30 mrad < $\theta_{\pi}$ < 210 mrad in the laboratory frame.Comment: 39 pages, 21 figures. Version accepted for publication by Eur. Phys. J.

Single hadron response measurement and calorimeter jet energy scale uncertainty with the ATLAS detector at the LHC

The uncertainty on the calorimeter energy response to jets of particles is derived for the ATLAS experiment at the Large Hadron Collider (LHC). First, the calorimeter response to single isolated charged hadrons is measured and compared to the Monte Carlo simulation using proton-proton collisions at centre-of-mass energies of sqrt(s) = 900 GeV and 7 TeV collected during 2009 and 2010. Then, using the decay of K_s and Lambda particles, the calorimeter response to specific types of particles (positively and negatively charged pions, protons, and anti-protons) is measured and compared to the Monte Carlo predictions. Finally, the jet energy scale uncertainty is determined by propagating the response uncertainty for single charged and neutral particles to jets. The response uncertainty is 2-5% for central isolated hadrons and 1-3% for the final calorimeter jet energy scale.Comment: 24 pages plus author list (36 pages total), 23 figures, 1 table, submitted to European Physical Journal

Measurement of the flavour composition of dijet events in pp collisions at root s=7 TeV with the ATLAS detector

This paper describes a measurement of the flavour composition of dijet events produced in pp collisions at &#8730;s=7 TeV using the ATLAS detector. The measurement uses the full 2010 data sample, corresponding to an integrated luminosity of 39 pb−1. Six possible combinations of light, charm and bottom jets are identified in the dijet events, where the jet flavour is defined by the presence of bottom, charm or solely light flavour hadrons in the jet. Kinematic variables, based on the properties of displaced decay vertices and optimised for jet flavour identification, are used in a multidimensional template fit to measure the fractions of these dijet flavour states as functions of the leading jet transverse momentum in the range 40 GeV to 500 GeV and jet rapidity |y|&#60;2.1. The fit results agree with the predictions of leading- and next-to-leading-order calculations, with the exception of the dijet fraction composed of bottom and light flavour jets, which is underestimated by all models at large transverse jet momenta. The ability to identify jets containing two b-hadrons, originating from e.g. gluon splitting, is demonstrated. The difference between bottom jet production rates in leading and subleading jets is consistent with the next-to-leading-order predictions

Music-aided affective interaction between human and service robot

This study proposes a music-aided framework for affective interaction of service robots with humans. The framework consists of three systems, respectively, for perception, memory, and expression on the basis of the human brain mechanism. We propose a novel approach to identify human emotions in the perception system. The conventional approaches use speech and facial expressions as representative bimodal indicators for emotion recognition. But, our approach uses the mood of music as a supplementary indicator to more correctly determine emotions along with speech and facial expressions. For multimodal emotion recognition, we propose an effective decision criterion using records of bimodal recognition results relevant to the musical mood. The memory and expression systems also utilize musical data to provide natural and affective reactions to human emotions. For evaluation of our approach, we simulated the proposed human-robot interaction with a service robot, iRobiQ. Our perception system exhibited superior performance over the conventional approach, and most human participants noted favorable reactions toward the music-aided affective interaction.open0