An optimized TOPS+ comparison method for enhanced TOPS models

This article has been made available through the Brunel Open Access Publishing Fund.Background Although methods based on highly abstract descriptions of protein structures, such as VAST and TOPS, can perform very fast protein structure comparison, the results can lack a high degree of biological significance. Previously we have discussed the basic mechanisms of our novel method for structure comparison based on our TOPS+ model (Topological descriptions of Protein Structures Enhanced with Ligand Information). In this paper we show how these results can be significantly improved using parameter optimization, and we call the resulting optimised TOPS+ method as advanced TOPS+ comparison method i.e. advTOPS+. Results We have developed a TOPS+ string model as an improvement to the TOPS [1-3] graph model by considering loops as secondary structure elements (SSEs) in addition to helices and strands, representing ligands as first class objects, and describing interactions between SSEs, and SSEs and ligands, by incoming and outgoing arcs, annotating SSEs with the interaction direction and type. Benchmarking results of an all-against-all pairwise comparison using a large dataset of 2,620 non-redundant structures from the PDB40 dataset [4] demonstrate the biological significance, in terms of SCOP classification at the superfamily level, of our TOPS+ comparison method. Conclusions Our advanced TOPS+ comparison shows better performance on the PDB40 dataset [4] compared to our basic TOPS+ method, giving 90 percent accuracy for SCOP alpha+beta; a 6 percent increase in accuracy compared to the TOPS and basic TOPS+ methods. It also outperforms the TOPS, basic TOPS+ and SSAP comparison methods on the Chew-Kedem dataset [5], achieving 98 percent accuracy. Software Availability: The TOPS+ comparison server is available at http://balabio.dcs.gla.ac.uk/mallika/WebTOPS/.This article is available through the Brunel Open Access Publishing Fun

Measurement of the cross-section and charge asymmetry of WW bosons produced in proton-proton collisions at s=8\sqrt{s}=8 TeV with the ATLAS detector

This paper presents measurements of the $W^+ \rightarrow \mu^+\nu$ and $W^- \rightarrow \mu^-\nu$ cross-sections and the associated charge asymmetry as a function of the absolute pseudorapidity of the decay muon. The data were collected in proton--proton collisions at a centre-of-mass energy of 8 TeV with the ATLAS experiment at the LHC and correspond to a total integrated luminosity of 20.2~\mbox{fb^{-1}}. The precision of the cross-section measurements varies between 0.8% to 1.5% as a function of the pseudorapidity, excluding the 1.9% uncertainty on the integrated luminosity. The charge asymmetry is measured with an uncertainty between 0.002 and 0.003. The results are compared with predictions based on next-to-next-to-leading-order calculations with various parton distribution functions and have the sensitivity to discriminate between them.Comment: 38 pages in total, author list starting page 22, 5 figures, 4 tables, submitted to EPJC. All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/STDM-2017-13

Search for chargino-neutralino production with mass splittings near the electroweak scale in three-lepton final states in √s=13 TeV pp collisions with the ATLAS detector

A search for supersymmetry through the pair production of electroweakinos with mass splittings near the electroweak scale and decaying via on-shell W and Z bosons is presented for a three-lepton final state. The analyzed proton-proton collision data taken at a center-of-mass energy of √s=13  TeV were collected between 2015 and 2018 by the ATLAS experiment at the Large Hadron Collider, corresponding to an integrated luminosity of 139  fb−1. A search, emulating the recursive jigsaw reconstruction technique with easily reproducible laboratory-frame variables, is performed. The two excesses observed in the 2015–2016 data recursive jigsaw analysis in the low-mass three-lepton phase space are reproduced. Results with the full data set are in agreement with the Standard Model expectations. They are interpreted to set exclusion limits at the 95% confidence level on simplified models of chargino-neutralino pair production for masses up to 345 GeV

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente

Correlated long-range mixed-harmonic fluctuations measured in pp, p+Pb and low-multiplicity Pb+Pb collisions with the ATLAS detector

For abstract see published article

Measurement of the Higgs boson mass in the H→ZZ ∗ →4ℓ and H→γγ channels with √s =13 TeV pp collisions using the ATLAS detector

The mass of the Higgs boson is measured in the H→ZZ ∗ →4ℓ and in the H→γγ decay channels with 36.1 fb −1 of proton-proton collision data from the Large Hadron Collider at a centre-of-mass energy of 13 TeV recorded by the ATLAS detector in 2015 and 2016. The measured value in the H→ZZ ∗ →4ℓ channel is m ZZ ∗ H =124.79±0.37 GeV, while the measured value in the H→γγ channel is m γγ H =124.93±0.40 GeV. Combining these results with the ATLAS measurement based on 7 TeV and 8 TeV proton-proton collision data yields a Higgs boson mass of m H =124.97±0.24 GeV

Searches for exclusive Higgs and Z boson decays into J/ψγ,ψ(2S)γ,and Υ(nS)γ at √s=13 TeV with the ATLAS detector

Searches for the exclusive decays of the Higgs and Z bosons into a J/ψ,ψ(2S), or Υ(nS)(n=1,2,3) meson and a photon are performed with a pp collision data sample corresponding to an integrated luminosity of 36.1 fb −1 collected at √s =13 TeV with the ATLAS detector at the CERN Large Hadron Collider. No significant excess of events is observed above the expected backgrounds, and 95% confidence-level upper limits on the branching fractions of the Higgs boson decays to J/ψγ, ψ(2S)γ,and Υ(nS)γ of 3.5×10 −4, 2.0×10−3,and(4.9,5.9,5.7)×10 −4,respectively, are obtained assuming Standard Model production. The corresponding 95% confidence-level upper limits for the branching fractions of the Z boson decays are 2.3×10 −6, 4.5×10 −6 and (2.8,1.7,4.8)×10 −6, respectively

Search for Higgs boson decays into a pair of light bosons in the bbμμ final state in pp collision at √s=13 TeV with the ATLAS detector

A search for decays of the Higgs boson into a pair of new spin-zero particles, H→aa, where the a-bosons decay into a b-quark pair and a muon pair, is presented. The search uses 36.1fb−1of proton–proton collision data at √s=13 TeV recorded by the ATLAS experiment at the LHC in 2015 and 2016. No significant deviation from the Standard Model prediction is observed. Upper limits at 95% confidence level are placed on the branching ratio (σH/σSM) ×B(H→aa →bbμμ), ranging from 1.2 ×10−4to 8.4 ×10−4in the a-boson mass range of 20–60GeV. Model-independent limits are set on the visible production cross-section times the branching ratio to the bbμμ final state for new physics, σvis(X) ×B(X→bbμμ), ranging from 0.1fb to 0.73fb for mμμ between 18 and 62GeV

Search for large missing transverse momentum in association with one top-quark in proton-proton collisions at √s = 13 TeV with the ATLAS detector

This paper describes a search for events with one top-quark and large missing transverse momentum in the final state. Data collected during 2015 and 2016 by the ATLAS experiment from 13 TeV proton–proton collisions at the LHC corresponding to an integrated luminosity of 36.1 fb−1 are used. Two channels are considered, depending on the leptonic or the hadronic decays of the W boson from the top quark. The obtained results are interpreted in the context of simplified models for dark-matter production and for the single production of a vector-like T quark. In the absence of significant deviations from the Standard Model background expectation, 95% confidence-level upper limits on the corresponding production cross-sections are obtained and these limits are translated into constraints on the parameter space of the models considered