Modeling protein complexes using restraints from Crosslinking Mass Spectrometry

Modeling macromolecular assemblies with restraints from crosslinking mass spectrometry (XL-MS) tends to focus solely on distance violation. Recently, we identified three different modeling features inherent in crosslink data: (1) expected distance between crosslinked residues; (2) violation of the crosslinker's maximum bound; and (3) solvent accessibility of crosslinked residues. Here, we implement these features in a scoring function. cMNXL, and demonstrate that it outperforms the commonlyused crosslink distance violation. We compare the different methods of calculating the distance between crosslinked residues, which shows no significant change in performance when using Euclidean distance compared with the solvent-accessible surface distance. Finally, we create a combined score that incorporates information from 3D electron microscopy maps as well as crosslinking. This achieves, on average, better results than either information type alone and demonstrates the potential of integrative modeling with XL-MS and low-resolution cryoelectron microscopy

CP Phases in Correlated Production and Decay of Neutralinos in the Minimal Supersymmetric Standard Model

We investigate the associated production of neutralinos $e^+e^-\to\tilde{\chi}^0_1\tilde{\chi}^0_2$ accompanied by the neutralino leptonic decay $\tilde{\chi}^0_2\to\tilde{\chi}^0_1 \ell^+\ell^-$, taking into account initial beam polarization and production-decay spin correlations in the minimal supersymmetric standard model with general CP phases but without generational mixing in the slepton sector. The stringent constraints from the electron EDM on the CP phases are also included in the discussion. Initial beam polarizations lead to three CP--even distributions and one CP--odd distribution, which can be studied independently of the details of the neutralino decays. We find that the production cross section and the branching fractions of the leptonic neutralino decays are very sensitive to the CP phases. In addition, the production--decay spin correlations lead to several CP--even observables such as lepton invariant mass distribution, and lepton angular distribution, and one interesting T--odd (CP--odd) triple product of the initial electron momentum and two final lepton momenta, the size of which might be large enough to be measured at the high--luminosity future electron--positron collider or can play a complementary role in constraining the CP phases with the EDM constraints.Comment: Revtex, 37 pages, 12 eps figure

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Indirect Dark Matter Detection from Dwarf Satellites: Joint Expectations from Astrophysics and Supersymmetry

We present a general methodology for determining the gamma-ray flux from annihilation of dark matter particles in Milky Way satellite galaxies, focusing on two promising satellites as examples: Segue 1 and Draco. We use the SuperBayeS code to explore the best-fitting regions of the Constrained Minimal Supersymmetric Standard Model (CMSSM) parameter space, and an independent MCMC analysis of the dark matter halo properties of the satellites using published radial velocities. We present a formalism for determining the boost from halo substructure in these galaxies and show that its value depends strongly on the extrapolation of the concentration-mass (c(M)) relation for CDM subhalos down to the minimum possible mass. We show that the preferred region for this minimum halo mass within the CMSSM with neutralino dark matter is ~10^-9-10^-6 solar masses. For the boost model where the observed power-law c(M) relation is extrapolated down to the minimum halo mass we find average boosts of about 20, while the Bullock et al (2001) c(M) model results in boosts of order unity. We estimate that for the power-law c(M) boost model and photon energies greater than a GeV, the Fermi space-telescope has about 20% chance of detecting a dark matter annihilation signal from Draco with signal-to-noise greater than 3 after about 5 years of observation

The Green, Green Grass of Home: an archaeo-ecological approach to pastoralist settlement in central Kenya

© 2016 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. This paper considers the ecological residues of pastoralist occupation at the site of Maili Sita in Laikipia, central Kenya, drawing links with the archaeological record so as to contribute a fresh approach to the ephemeral settlement sites of mobile herding communities, a methodological aspect of African archaeology that remains problematic. Variations in the geochemical and micromorphological composition of soils along transects across the site are compared with vegetation distributions and satellite imagery to propose an occupation pattern not dissimilar to contemporary Cushitic-speaking groups further north. We argue that Maili Sita exemplifies the broad migratory and cultural exchange networks in place during the mid- to late second millennium AD, with pastoralist occupants who were both physically and culturally mobile.British Academy (2002-5 Funding) European Union - Marie Curie Initiatives (EXT grant 2007-11

Measurement of the View the tt production cross-section using eμ events with b-tagged jets in pp collisions at √s = 13 TeV with the ATLAS detector

This paper describes a measurement of the inclusive top quark pair production cross-section (σtt¯) with a data sample of 3.2 fb−1 of proton–proton collisions at a centre-of-mass energy of √s = 13 TeV, collected in 2015 by the ATLAS detector at the LHC. This measurement uses events with an opposite-charge electron–muon pair in the final state. Jets containing b-quarks are tagged using an algorithm based on track impact parameters and reconstructed secondary vertices. The numbers of events with exactly one and exactly two b-tagged jets are counted and used to determine simultaneously σtt¯ and the efficiency to reconstruct and b-tag a jet from a top quark decay, thereby minimising the associated systematic uncertainties. The cross-section is measured to be: σtt¯ = 818 ± 8 (stat) ± 27 (syst) ± 19 (lumi) ± 12 (beam) pb, where the four uncertainties arise from data statistics, experimental and theoretical systematic effects, the integrated luminosity and the LHC beam energy, giving a total relative uncertainty of 4.4%. The result is consistent with theoretical QCD calculations at next-to-next-to-leading order. A fiducial measurement corresponding to the experimental acceptance of the leptons is also presented

Search for strong gravity in multijet final states produced in pp collisions at √s=13 TeV using the ATLAS detector at the LHC

A search is conducted for new physics in multijet final states using 3.6 inverse femtobarns of data from proton-proton collisions at √s = 13TeV taken at the CERN Large Hadron Collider with the ATLAS detector. Events are selected containing at least three jets with scalar sum of jet transverse momenta (HT) greater than 1TeV. No excess is seen at large HT and limits are presented on new physics: models which produce final states containing at least three jets and having cross sections larger than 1.6 fb with HT > 5.8 TeV are excluded. Limits are also given in terms of new physics models of strong gravity that hypothesize additional space-time dimensions

Search for TeV-scale gravity signatures in high-mass final states with leptons and jets with the ATLAS detector at sqrt [ s ] = 13TeV

A search for physics beyond the Standard Model, in final states with at least one high transverse momentum charged lepton (electron or muon) and two additional high transverse momentum leptons or jets, is performed using 3.2 fb−1 of proton–proton collision data recorded by the ATLAS detector at the Large Hadron Collider in 2015 at √s = 13 TeV. The upper end of the distribution of the scalar sum of the transverse momenta of leptons and jets is sensitive to the production of high-mass objects. No excess of events beyond Standard Model predictions is observed. Exclusion limits are set for models of microscopic black holes with two to six extra dimensions

Search for dark matter produced in association with a hadronically decaying vector boson in pp collisions at sqrt (s) = 13 TeV with the ATLAS detector

A search is presented for dark matter produced in association with a hadronically decaying W or Z boson using 3.2 fb−1 of pp collisions at View the MathML sources=13 TeV recorded by the ATLAS detector at the Large Hadron Collider. Events with a hadronic jet compatible with a W or Z boson and with large missing transverse momentum are analysed. The data are consistent with the Standard Model predictions and are interpreted in terms of both an effective field theory and a simplified model containing dark matter