Structure of SPH (Self-Incompatibility Protein Homologue) Proteins: a Widespread Family of Small, Highly Stable, Secreted Proteins

SPH proteins are a large family of small, disulphide-bonded, secreted proteins, initially found in the self-incompatibility response in the field poppy , but now known to be widely distributed in plants, many containing multiple members of this protein family. Using the Origami strain of , we expressed one member of this family, SPH15 from , as a folded thioredoxin-fusion protein and purified it from the cytosol. The fusion protein was cleaved and characterised by analytical ultracentrifugation, circular dichroism, and NMR spectroscopy. This showed that SPH15 is monomeric and temperature stable, with a beta-sandwich structure. The four strands in each sheet have the same topology as the unrelated proteins; human transthyretin, bacterial TSSJ, and pneumolysin, with no discernable sequence similarity. The NMR-derived structure was compared with a model, made using a new deep learning algorithm based on co-evolution/correlated mutations, DeepCDPred, validating the method. The DeepCDPred method and homology modelling to SPH15 were then both used to derive models of the 3D structure of the three known PrsS proteins from , which have only 15-18% sequence homology to SPH15. The DeepCDPred method gave models with lower Discreet Optimised Protein Energy (DOPE) scores than the homology models. Three loops at one end of the poppy structures are postulated to interact with their respective pollen receptors to instigate programmed cell death in pollen tubes. [Abstract copyright: ©2019 The Author(s).

Ab initio Quantum and ab initio Molecular Dynamics of the Dissociative Adsorption of Hydrogen on Pd(100)

The dissociative adsorption of hydrogen on Pd(100) has been studied by ab initio quantum dynamics and ab initio molecular dynamics calculations. Treating all hydrogen degrees of freedom as dynamical coordinates implies a high dimensionality and requires statistical averages over thousands of trajectories. An efficient and accurate treatment of such extensive statistics is achieved in two steps: In a first step we evaluate the ab initio potential energy surface (PES) and determine an analytical representation. Then, in an independent second step dynamical calculations are performed on the analytical representation of the PES. Thus the dissociation dynamics is investigated without any crucial assumption except for the Born-Oppenheimer approximation which is anyhow employed when density-functional theory calculations are performed. The ab initio molecular dynamics is compared to detailed quantum dynamical calculations on exactly the same ab initio PES. The occurence of quantum oscillations in the sticking probability as a function of kinetic energy is addressed. They turn out to be very sensitive to the symmetry of the initial conditions. At low kinetic energies sticking is dominated by the steering effect which is illustrated using classical trajectories. The steering effects depends on the kinetic energy, but not on the mass of the molecules. Zero-point effects lead to strong differences between quantum and classical calculations of the sticking probability. The dependence of the sticking probability on the angle of incidence is analysed; it is found to be in good agreement with experimental data. The results show that the determination of the potential energy surface combined with high-dimensional dynamical calculations, in which all relevant degrees of freedon are taken into account, leads to a detailed understanding of the dissociation dynamics of hydrogen at a transition metal surface.Comment: 15 pages, 9 figures, subm. to Phys. Rev.

Decoherence and CPT Violation in a Stringy Model of Space-Time Foam

I discuss a model inspired from the string/brane framework, in which our Universe is represented as a three brane, propagating in a bulk space time punctured by D0-brane (D-particle) defects. As the D3-brane world moves in the bulk, the D-particles cross it, and from an effective observer on D3 the situation looks like a ``space-time foam'' with the defects ``flashing'' on and off (``D-particle foam''). The open strings, with their ends attached on the brane, which represent matter in this scenario, can interact with the D-particles on the D3-brane universe in a topologically non-trivial manner, involving splitting and capture of the strings by the D0-brane defects. Such processes are described by logarithmic conformal field theories on the world-sheet. Physically, they result in effective decoherence of the string matter on the D3 brane, and as a result, of CPT Violation, but of a type that implies an ill-defined nature of the effective CPT operator. Due to electric charge conservation, only electrically neutral (string) matter can exhibit such interactions with the D-particle foam. This may have unique, experimentally detectable, consequences for electrically-neutral entangled quantum matter states on the brane world, in particular the modification of the pertinent EPR Correlation of neutral mesons in a meson factory.Comment: 41 pages Latex, five eps figures incorporated. Uses special macro

Nuclear Alpha-Particle Condensates

The $\alpha$-particle condensate in nuclei is a novel state described by a product state of $\alpha$'s, all with their c.o.m. in the lowest 0S orbit. We demonstrate that a typical $\alpha$-particle condensate is the Hoyle state ($E_{x}=7.65$ MeV, $0^+_2$ state in $^{12}$C), which plays a crucial role for the synthesis of $^{12}$C in the universe. The influence of antisymmentrization in the Hoyle state on the bosonic character of the $\alpha$ particle is discussed in detail. It is shown to be weak. The bosonic aspects in the Hoyle state, therefore, are predominant. It is conjectured that $\alpha$-particle condensate states also exist in heavier $n\alpha$ nuclei, like $^{16}$O, $^{20}$Ne, etc. For instance the $0^+_6$ state of $^{16}$O at $E_{x}=15.1$ MeV is identified from a theoretical analysis as being a strong candidate of a $4\alpha$ condensate. The calculated small width (34 keV) of $0^+_6$, consistent with data, lends credit to the existence of heavier Hoyle-analogue states. In non-self-conjugated nuclei such as $^{11}$B and $^{13}$C, we discuss candidates for the product states of clusters, composed of $\alpha$'s, triton's, and neutrons etc. The relationship of $\alpha$-particle condensation in finite nuclei to quartetting in symmetric nuclear matter is investigated with the help of an in-medium modified four-nucleon equation. A nonlinear order parameter equation for quartet condensation is derived and solved for $\alpha$ particle condensation in infinite nuclear matter. The strong qualitative difference with the pairing case is pointed out.Comment: 71 pages, 41 figures, review article, to be published in "Cluster in Nuclei (Lecture Notes in Physics) - Vol.2 -", ed. by C. Beck, (Springer-Verlag, Berlin, 2011

Linking Grass Pollen Biodiversity and Human Health: an Environmental Genomic Approach

In Europe and the UK, grass pollen is the single most important outdoor aeroallergen; 27% of the population are sensitised to grass pollen. Grass pollen allergy has been linked to increased risk of allergic asthma exacerbations, which can lead to hospitalisation and fatalities. Sensitivity towards grass pollen varies between species, of which there are over 150 in the UK. However, due to few unique morphological features, grass pollen from different species cannot be discriminated using traditional observational methods. Currently, there is no way of detecting, modelling or forecasting the aerial-dispersion of pollen from the biodiversity of UK grasses. Consequently, grasses are coalesced into a single group in the UK forecast. PollerGEN is an interdisciplinary NERC project with the aim of revolutionising the way that pollen dispersion is measured and forecast, with concomitant synergies for understanding the ecology of aerial dispersed pollen. In collaboration with the UK Met Office, a key goal is to build a more accurate forecast of individual grass pollen species. Using environmental genomics, we will identify which species of grass pollen are present during the summer months across 16 specific collection sites in the UK, and measure the abundance of the different allergenic species of grass. The information will be used to model the spatial and temporal deposition of different species of grass pollen and identify linkages to human health. The project therefore aims to provide a paradigm shift in our understanding of the ecology of windborne pollen in time and space and inform the public about the timing and environmental factors that put them at risk of exposure to pollen they are allergic to; a key strategy in the prevention of allergy and asthma attacks

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results

Jet size dependence of single jet suppression in lead-lead collisions at sqrt(s(NN)) = 2.76 TeV with the ATLAS detector at the LHC

Measurements of inclusive jet suppression in heavy ion collisions at the LHC provide direct sensitivity to the physics of jet quenching. In a sample of lead-lead collisions at sqrt(s) = 2.76 TeV corresponding to an integrated luminosity of approximately 7 inverse microbarns, ATLAS has measured jets with a calorimeter over the pseudorapidity interval |eta| < 2.1 and over the transverse momentum range 38 < pT < 210 GeV. Jets were reconstructed using the anti-kt algorithm with values for the distance parameter that determines the nominal jet radius of R = 0.2, 0.3, 0.4 and 0.5. The centrality dependence of the jet yield is characterized by the jet "central-to-peripheral ratio," Rcp. Jet production is found to be suppressed by approximately a factor of two in the 10% most central collisions relative to peripheral collisions. Rcp varies smoothly with centrality as characterized by the number of participating nucleons. The observed suppression is only weakly dependent on jet radius and transverse momentum. These results provide the first direct measurement of inclusive jet suppression in heavy ion collisions and complement previous measurements of dijet transverse energy imbalance at the LHC.Comment: 15 pages plus author list (30 pages total), 8 figures, 2 tables, submitted to Physics Letters B. All figures including auxiliary figures are available at http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HION-2011-02

Measurement of the polarisation of W bosons produced with large transverse momentum in pp collisions at sqrt(s) = 7 TeV with the ATLAS experiment

This paper describes an analysis of the angular distribution of W->enu and W->munu decays, using data from pp collisions at sqrt(s) = 7 TeV recorded with the ATLAS detector at the LHC in 2010, corresponding to an integrated luminosity of about 35 pb^-1. Using the decay lepton transverse momentum and the missing transverse energy, the W decay angular distribution projected onto the transverse plane is obtained and analysed in terms of helicity fractions f0, fL and fR over two ranges of W transverse momentum (ptw): 35 < ptw < 50 GeV and ptw > 50 GeV. Good agreement is found with theoretical predictions. For ptw > 50 GeV, the values of f0 and fL-fR, averaged over charge and lepton flavour, are measured to be : f0 = 0.127 +/- 0.030 +/- 0.108 and fL-fR = 0.252 +/- 0.017 +/- 0.030, where the first uncertainties are statistical, and the second include all systematic effects.Comment: 19 pages plus author list (34 pages total), 9 figures, 11 tables, revised author list, matches European Journal of Physics C versio

Observation of a new chi_b state in radiative transitions to Upsilon(1S) and Upsilon(2S) at ATLAS

The chi_b(nP) quarkonium states are produced in proton-proton collisions at the Large Hadron Collider (LHC) at sqrt(s) = 7 TeV and recorded by the ATLAS detector. Using a data sample corresponding to an integrated luminosity of 4.4 fb^-1, these states are reconstructed through their radiative decays to Upsilon(1S,2S) with Upsilon->mu+mu-. In addition to the mass peaks corresponding to the decay modes chi_b(1P,2P)->Upsilon(1S)gamma, a new structure centered at a mass of 10.530+/-0.005 (stat.)+/-0.009 (syst.) GeV is also observed, in both the Upsilon(1S)gamma and Upsilon(2S)gamma decay modes. This is interpreted as the chi_b(3P) system.Comment: 5 pages plus author list (18 pages total), 2 figures, 1 table, corrected author list, matches final version in Physical Review Letter

Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS

We present the results of a search for new, heavy particles that decay at a significant distance from their production point into a final state containing charged hadrons in association with a high-momentum muon. The search is conducted in a pp-collision data sample with a center-of-mass energy of 7 TeV and an integrated luminosity of 33 pb^-1 collected in 2010 by the ATLAS detector operating at the Large Hadron Collider. Production of such particles is expected in various scenarios of physics beyond the standard model. We observe no signal and place limits on the production cross-section of supersymmetric particles in an R-parity-violating scenario as a function of the neutralino lifetime. Limits are presented for different squark and neutralino masses, enabling extension of the limits to a variety of other models.Comment: 8 pages plus author list (20 pages total), 8 figures, 1 table, final version to appear in Physics Letters