Diffraction intensities from a crystallographic experiment include contributions from the entire unit cell of the crystal: the macromolecule, the solvent around it and eventually other compounds. These contributions cannot typically be well described by an atomic model alone, i.e. using point scatterers. Indeed, entities such as disordered (bulk) solvent, semi-ordered solvent (e.g. lipid belts in membrane proteins, ligands, ion channels) and disordered polymer loops require other types of modeling than a collection of individual atoms. This results in the model structure factors containing multiple contributions. Most macromolecular applications assume two-component structure factors: one component arising from the atomic model and the second one describing the bulk solvent. A more accurate and detailed modeling of the disordered regions of the crystal will naturally require more than two components in the structure factors, which presents algorithmic and computational challenges. Here an efficient solution of this problem is proposed. All algorithms described in this work have been implemented in the computational crystallography toolbox (CCTBX) and are also available within Phenix software. These algorithms are rather general and do not use any assumptions about molecule type or size nor about those of its components.

A fundamental prerequisite for implementing new procedures of atomic model refinement against neutron diffraction data is the efficient handling of hydrogen atoms. The riding hydrogen model, which constrains hydrogen atom parameters to those of the non-hydrogen atoms, is a plausible parameterization for refinements. This work describes the implementation of the riding hydrogen model in the Computational Crystallography Toolbox and in Phenix. Riding hydrogen atoms can be found in several different configurations that are characterized by specific geometries. For each configuration, the hydrogen atom parameterization and the expressions for the gradients of refinement target function with respect to non-hydrogen parameters are described.

Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.

© Published by the American Physical Society. Measurements of normalized differential cross sections for top-quark pair production are presented as a function of the top-quark transverse momentum, and of the mass, transverse momentum, and rapidity of the tt¯ system, in proton-proton collisions at a center-of-mass energy of s=7TeV. The data set corresponds to an integrated luminosity of 4.6fb-1, recorded in 2011 with the ATLAS detector at the CERN Large Hadron Collider. Events are selected in the lepton+jets channel, requiring exactly one lepton and at least four jets with at least one of the jets tagged as originating from a b-quark. The measured spectra are corrected for detector efficiency and resolution effects and are compared to several Monte Carlo simulations and theory calculations. The results are in fair agreement with the predictions in a wide kinematic range. Nevertheless, data distributions are softer than predicted for higher values of the mass of the tt¯ system and of the top-quark transverse momentum. The measurements can also discriminate among different sets of parton distribution functions.

This Letter presents a search for the Standard Model Higgs boson in the decay channel H→ZZ (*) →ℓ + ℓ - ℓ '+ ℓ '- , where ℓ, ℓ ' =e or μ, using proton-proton collisions at √s=7 TeV recorded with the ATLAS detector and corresponding to an integrated luminosity of 4.8 fb -1 . The four-lepton invariant mass distribution is compared with Standard Model background expectations to derive upper limits on the cross section of a Standard Model Higgs boson with a mass between 110 GeV and 600 GeV. The mass ranges 134-156 GeV, 182-233 GeV, 256-265 GeV and 268-415 GeV are excluded at the 95% confidence level. The largest upward deviations from the background-only hypothesis are observed for Higgs boson masses of 125 GeV, 244 GeV and 500 GeV with local significances of 2.1, 2.2 and 2.1 standard deviations, respectively. Once the look-elsewhere effect is considered, none of these excesses are significant. © 2012 CERN.

A search is presented for a narrow resonance decaying to a pair of Z bosons using data corresponding to 1.02fb -1 of integrated luminosity collected by the ATLAS experiment from pp collisions at √s=7TeV. Events containing either four charged leptons (ℓℓℓℓ) or two charged leptons and two jets (ℓℓjj) are analyzed and found to be consistent with the Standard Model background expectation. Lower limits on a resonance mass are set using the Randall-Sundrum (RS1) graviton model as a benchmark. Using both ℓℓℓℓ and ℓℓjj events, an RS1 graviton with k/m-pl=0.1 and mass between 325 and 845 GeV is excluded at 95% confidence level. In addition, the ℓℓℓℓ events are used to set a model-independent fiducial cross section limit of σ fid (pp→X→ZZ)<0.92pb at 95% confidence level for any new sources of ZZ production with m ZZ greater than 300 GeV. © 2012 CERN.

A blind analysis searching for the decay Bs0→μ+μ- has been performed using proton-proton collisions at a centre-of-mass energy of 7 TeV recorded with the ATLAS detector at the LHC. With an integrated luminosity of 2.4 fb-1 no excess of events over the background expectation is found and an upper limit is set on the branching fraction BR(Bs0→μ+μ-)<2.2(1.9)×10-8 at 95% (90%) confidence level. © 2012 CERN.

© CERN for the benefit of the ATLAS collaboration. Ameasurement is presented of the φ×BR(φ → K⁺K⁻) production cross section at √s = 7 TeV using pp collision data corresponding to an integrated luminosity of 383 μb^-1, collected with theATLAS experiment at the LHC. Selection of φ(1020) mesons is based on the identification of charged kaons by their energy loss in the pixel detector. The differential cross section ismeasured as a function of the transverse momentum, pT,φ , and rapidity, yφ, of the φ(1020) meson in the fiducial region 500< pT,φ <1200MeV, |yφ| < 0.8, kaon pT,K > 230 MeV and kaon momentum pK < 800 MeV. The integrated φ(1020)-meson production cross section in this fiducial range is measured to be σφ×BR(φ → K⁺K⁻) = 570 ± 8 (stat) ± 66 (syst) ± 20 (lumi) μb.

A search for the Standard Model Higgs boson in the H→WW (⋆) →ℓνℓν (ℓ=e, μ) decay mode is presented. The search is performed using proton-proton collision data corresponding to an integrated luminosity of 4.7 fb -1 at a centre-of-mass energy of 7 TeV collected during 2011 with the ATLAS detector at the Large Hadron Collider. No significant excess of events over the expected background is observed. An upper bound is placed on the Higgs boson production cross section as a function of its mass. A Standard Model Higgs boson with mass in the range between 133 GeV and 261 GeV is excluded at 95% confidence level, while the expected exclusion range is from 127 GeV to 233 GeV. © 2012 CERN.

A search is presented for production of a heavy up-type quark (t ' ) together with its antiparticle, assuming a significant branching ratio for subsequent decay into a W boson and a b quark. The search is based on 4.7 fb -1 of pp collisions at s=7TeV recorded in 2011 with the ATLAS detector at the CERN Large Hadron Collider. Data are analyzed in the lepton+jets final state, characterized by a high-transverse-momentum isolated electron or muon, large missing transverse momentum and at least three jets. The analysis strategy relies on the substantial boost of the W bosons in the t't¯' signal when mt'?400GeV. No significant excess of events above the Standard Model expectation is observed and the result of the search is interpreted in the context of fourth-generation and vector-like quark models. Under the assumption of a branching ratio BR(t ' ?Wb)=1, a fourth-generation t ' quark with mass lower than 656GeV is excluded at 95% confidence level. In addition, in light of the recent discovery of a new boson of mass ~126GeV at the LHC, upper limits are derived in the two-dimensional plane of BR(t ' ?Wb) versus BR(t ' ?Ht), where H is the Standard Model Higgs boson, for vector-like quarks of various masses. © 2012 CERN.