Structural model of the CopA copper ATPase of Enterococcus hirae based on chemical cross-linking

The CopA copper ATPase of Enterococcus hirae belongs to the family of heavy metal pumping CPx-type ATPases and shares 43% sequence similarity with the human Menkes and Wilson copper ATPases. Due to a lack of suitable protein crystals, only partial three-dimensional structures have so far been obtained for this family of ion pumps. We present a structural model of CopA derived by combining topological information obtained by intramolecular cross-linking with molecular modeling. Purified CopA was cross-linked with different bivalent reagents, followed by tryptic digestion and identification of cross-linked peptides by mass spectrometry. The structural proximity of tryptic fragments provided information about the structural arrangement of the hydrophilic protein domains, which was integrated into a three-dimensional model of CopA. Comparative modeling of CopA was guided by the sequence similarity to the calcium ATPase of the sarcoplasmic reticulum, Serca1, for which detailed structures are available. In addition, known partial structures of CPx-ATPase homologous to CopA were used as modeling templates. A docking approach was used to predict the orientation of the heavy metal binding domain of CopA relative to the core structure, which was verified by distance constraints derived from cross-links. The overall structural model of CopA resembles the Serca1 structure, but reveals distinctive features of CPx-type ATPases. A prominent feature is the positioning of the heavy metal binding domain. It features an orientation of the Cu binding ligands which is appropriate for the interaction with Cu-loaded metallochaperones in solution. Moreover, a novel model of the architecture of the intramembranous Cu binding sites could be derived.

Jet energy measurement with the ATLAS detector in proton-proton collisions at sqrt(s) = 7 TeV

The jet energy scale (JES) and its systematic uncertainty are determined for jets measured with the ATLAS detector at the LHC in proton-proton collision data at a centre-of-mass energy of sqrt(s) = 7 TeV corresponding to an integrated luminosity of 38 inverse pb. Jets are reconstructed with the anti-kt algorithm with distance parameters R=0.4 or R=0.6. Jet energy and angle corrections are determined from Monte Carlo simulations to calibrate jets with transverse momenta pt > 20 GeV and pseudorapidities eta<4.5. The JES systematic uncertainty is estimated using the single isolated hadron response measured in situ and in test-beams. The JES uncertainty is less than 2.5% in the central calorimeter region (eta<0.8) for jets with 60 < pt < 800 GeV, and is maximally 14% for pt < 30 GeV in the most forward region 3.2proton-proton collisions in the same bunch crossing is less than 1.5% per additional collision for jets with pt > 50 GeV after a dedicated correction for this effect. The JES is validated for jet transverse momenta up to 1 TeV to the level of a few percent using several in situ techniques by comparing a well-known reference such as the recoiling photon pt, the sum of the transverse momenta of tracks associated to the jet, or a system of low-pt jets recoiling against a high-pt jet. More sophisticated jet calibration schemes are presented based on calorimeter cell energy density weighting or hadronic properties of jets, providing an improved jet energy resolution and a reduced flavour dependence of the jet response. The JES systematic uncertainty determined from a combination of in situ techniques are consistent with the one derived from single hadron response measurements over a wide kinematic range. The nominal corrections and uncertainties are derived for isolated jets in an inclusive sample of high-pt jets.

Jet energy measurement with the ATLAS detector in proton-proton collisions at sqrt(s) = 7 TeV

The jet energy scale (JES) and its systematic uncertainty are determined for jets measured with the ATLAS detector at the LHC in proton-proton collision data at a centre-of-mass energy of sqrt(s) = 7 TeV corresponding to an integrated luminosity of 38 inverse pb. Jets are reconstructed with the anti-kt algorithm with distance parameters R=0.4 or R=0.6. Jet energy and angle corrections are determined from Monte Carlo simulations to calibrate jets with transverse momenta pt > 20 GeV and pseudorapidities eta<4.5. The JES systematic uncertainty is estimated using the single isolated hadron response measured in situ and in test-beams. The JES uncertainty is less than 2.5% in the central calorimeter region (eta<0.8) for jets with 60 < pt < 800 GeV, and is maximally 14% for pt < 30 GeV in the most forward region 3.2proton-proton collisions in the same bunch crossing is less than 1.5% per additional collision for jets with pt > 50 GeV after a dedicated correction for this effect. The JES is validated for jet transverse momenta up to 1 TeV to the level of a few percent using several in situ techniques by comparing a well-known reference such as the recoiling photon pt, the sum of the transverse momenta of tracks associated to the jet, or a system of low-pt jets recoiling against a high-pt jet. More sophisticated jet calibration schemes are presented based on calorimeter cell energy density weighting or hadronic properties of jets, providing an improved jet energy resolution and a reduced flavour dependence of the jet response. The JES systematic uncertainty determined from a combination of in situ techniques are consistent with the one derived from single hadron response measurements over a wide kinematic range. The nominal corrections and uncertainties are derived for isolated jets in an inclusive sample of high-pt jets.

Search for squarks and gluinos with the ATLAS detector in final states with jets and missing transverse momentum using 4.7 fb⁻¹ of sqrts=7 TeV proton-pro collision data

A search for squarks and gluinos in final states containing jets, missing transverse momentum and no high-p(T) electrons or muons is presented. The data represent the complete sample recorded in 2011 by the ATLAS experiment in 7 TeV proton-proton collisions at the Large Hadron Collider, with a total integrated luminosity of 4.7 fb(-1). No excess above the Standard Model background expectation is observed. Gluino masses below 860 GeV and squark masses below 1320 GeV are excluded at the 95% confidence level in simplified models containing only squarks of the first two generations, a gluino octet and a massless neutralino, for squark or gluino masses below 2 TeV, respectively. Squarks and gluinos with equal masses below 1410 GeV are excluded. In minimal supergravity/constrained minimal supersymmetric Standard Model models with tan beta = 10, A(0) = 0 and mu > 0, squarks and gluinos of equal mass are excluded for masses below 1360 GeV. Constraints are also placed on the parameter space of supersymmetric models with compressed spectra. These limits considerably extend the region of supersymmetric parameter space excluded by previous measurements with the ATLAS detector.

Search for long-lived, heavy particles in final states with a muon and multi-track displaced vertex in proton-proton collisions at sqrts=7 TeV with the ATLAS detector

Many extensions of the Standard Model posit the existence of heavy particles with long lifetimes. In this Letter, results are presented of a search for events containing one or more such particles, which decay at a significant distance from their production point, using a final state containing charged hadrons and an associated muon. This analysis uses a data sample of proton-proton collisions at root s = 7 TeV corresponding to an integrated luminosity of 4.4 fb(-1) collected in 2011 by the ATLAS detector operating at the Large Hadron Collider. Results are interpreted in the context of R-parity violating supersymmetric scenarios. No events in the signal region are observed and limits are set on the production cross section for pair production of supersymmetric particles, multiplied by the square of the branching fraction for a neutralino to decay to charged hadrons and a muon, based on the scenario where both of the produced supersymmetric particles give rise to neutralinos that decay in this way. However, since the search strategy is based on triggering on and reconstructing the decay products of individual long-lived particles, irrespective of the rest of the event, these limits can easily be reinterpreted in scenarios with different numbers of long-lived particles per event. The limits are presented as a function of neutralino lifetime, and for a range of squark and neutralino masses.

Measurement of the underlying event in jet events from 7 TeV proton-proton collisions with the ATLAS detector

Distributions sensitive to the underlying event in QCD jet events have been measured with the ATLAS detector at the LHC, based on 37 pb−1 of proton–proton collision data collected at a centre-of-mass energy of 7 TeV. Chargedparticle mean pT and densities of all-particle ET and chargedparticle multiplicity and pT have been measured in regions azimuthally transverse to the hardest jet in each event. These are presented both as one-dimensional distributions and with their mean values as functions of the leading-jet transverse momentum from 20 to 800 GeV. The correlation of chargedparticle mean pT with charged-particle multiplicity is also studied, and the ET densities include the forward rapidity region; these features provide extra data constraints for Monte Carlo modelling of colour reconnection and beamremnant effects respectively. For the first time, underlying event observables have been computed separately for inclusive jet and exclusive dijet event selections, allowing more detailed study of the interplay of multiple partonic scattering and QCD radiation contributions to the underlying event. Comparisonsto the predictions of different Monte Carlo models show a need for further model tuning, but the standard approach is found to generally reproduce the features of the underlying event in both types of event selection.

Characterization of the dose distribution in the halo region of a clinical proton pencil beam using emulsion film detectors

Proton therapy is a high precision technique in cancer radiation therapy which allows irradiating the tumor with minimal damage to the surrounding healthy tissues. Pencil beam scanning is the most advanced dose distribution technique and it is based on a variable energy beam of a few millimeters FWHM which is moved to cover the target volume. Due to spurious effects of the accelerator, of dose distribution system and to the unavoidable scattering inside the patient's body, the pencil beam is surrounded by a halo that produces a peripheral dose. To assess this issue, nuclear emulsion films interleaved with tissue equivalent material were used for the first time to characterize the beam in the halo region and to experimentally evaluate the corresponding dose. The high-precision tracking performance of the emulsion films allowed studying the angular distribution of the protons in the halo. Measurements with this technique were performed on the clinical beam of the Gantry1 at the Paul Scherrer Institute. Proton tracks were identified in the emulsion films and the track density was studied at several depths. The corresponding dose was assessed by Monte Carlo simulations and the dose profile was obtained as a function of the distance from the center of the beam spot.

Study of the radioactivity induced in air by a 15-MeV proton beam.

Radioactivity induced by a 15-MeV proton beam extracted into air was studied at the beam transport line of the 18-MeV cyclotron at the Bern University Hospital (Inselspital). The produced radioactivity was calculated and measured by means of proportional counters located at the main exhaust of the laboratory. These devices were designed for precise assessment of air contamination for radiation protection purposes. The main produced isotopes were 11C, 13N and 14O. Both measurements and calculations correspond to two different irradiation conditions. In the former, protons were allowed to travel for their full range in air. In the latter, they were stopped at the distance of 1.5 m by a beam dump. Radioactivity was measured continuously in the exhausted air starting from 2 min after the end of irradiation. For this reason, the short-lived 14O isotope gave a negligible contribution to the measured activity. Good agreement was found between the measurements and the calculations within the estimated uncertainties. Currents in the range of 120–370 nA were extracted in air for 10–30 s producing activities of 9–22 MBq of 11C and 13N. The total activities for 11C and 13N per beam current and irradiation time for the former and the latter irradiation conditions were measured to be (3.60 ± 0.48) × 10−3 MBq (nA s)−1 and (2.89 ± 0.37) × 10−3 MBq (nA s)−1, respectively.