S.D. Barrett

STM observations of Cu(100)−c(2×2)N surfaces: evidence for attractive interactions and an incommensurate c(2 × 2) structure

Abstract STM studies of N on Cu (100), adsorbed via activated ion bombardment, reveal behaviour consistent with attractive interactions and an incommensurate c(2×2)N structure. For extremely low N doses, images of the resultant surface show roughly square shaped islands with island edges running along the 〈001〉 directions. The islands have an internal c(2 × 2) periodicity and while tending to group together do not coalesce. For higher N doses, island coalescence occurs simultaneously with the appearance of trench-like defect structures running in the 〈011〉) directions and small one-atomic layer high islands. Lack of island coalescence at low coverages and the appearance of trench-like defects at higher coverages are interpreted as strain-relief mechanisms for an incommensurate c(2×2)N structure. To derive the N adsorption site, S has also been coadsorbed along with the c(2×2)N islands to form coexisting p(2×2)S domains. The spatial relationships between features in both domains show that the protrusions observed in the c(2 × 2)N areas are located above four-fold hollow sites. Finally, in order to compare our work with previous studies, we have obtained detailed LEED I–V data from the various Cu(100)−c(2×2)N surfaces studied with STM.

Image Analysis in Earth Sciences

Part I Looking at Images.- 1 Images and Microstructures.- 2 Acquiring Images.- 3 Digital Image Processing.- 4 Pre-processing.- Part II Segmentation: Finding and Defining the Object.- 5 Segmentation by Point Operations.- 6 Post-processing.- 7 Segmentation by Neighborhood Operations.- 8 Image Analysis.- 9 Test Images.- Part III Measuring Size and Volume.- 10 Volume Determinations.- 11 2-D Grain Size Distributions.- 12 3-D Grain Size.- 13 Fractal Grain Size Distributions.- Part IV Quantifying Shape and Orientation.- 14 Particle Fabrics.- 15 Surface Fabrics.- 16 Strain Fabrics.- 17 Shape Descriptors.- Part V Spatial Relationships.- 18 Spatial Distributions.- 19 Spatial Frequencies.- 20 Autocorrelation Function.- Part VI Orientation Imaging.- 21 Crystal Orientation and Interference Color.- 22 Computer-Integrated Polarization Microscopy.- 23 Orientation and Misorientation Imaging.- Index.

Household Air Pollution Causes Dose-dependent Inflammation and Altered Phagocytosis in Human Macrophages

Three billion people are exposed to household air pollution from biomass fuel use. Exposure is associated with higher incidence of pneumonia, and possibly tuberculosis. Understanding mechanisms underlying these defects would improve preventive strategies. We used human alveolar macrophages obtained from healthy Malawian adults exposed naturally to household air pollution and compared them with human monocyte-derived macrophages exposed in vitro to respirable-sized particulates. Cellular inflammatory response was assessed by IL-6 and IL-8 production in response to particulate challenge; phagosomal function was tested by uptake and oxidation of fluorescence-labeled beads; ingestion and killing of Streptococcus pneumoniae and Mycobacterium tuberculosis were measured by microscopy and quantitative culture. Particulate ingestion was quantified by digital image analysis. We were able to reproduce the carbon loading of naturally exposed alveolar macrophages by in vitro exposure of monocyte-derived macrophages. Fine carbon black induced IL-8 release from monocyte-derived and alveolar macrophages (P < 0.05) with similar magnitude responses (log10 increases of 0.93 [SEM = 0.2] versus 0.74 [SEM = 0.19], respectively). Phagocytosis of pneumococci and mycobacteria was impaired with higher particulate loading. High particulate loading corresponded with a lower oxidative burst capacity (P = 0.0015). There was no overall effect on killing of M. tuberculosis. Alveolar macrophage function is altered by particulate loading. Our macrophage model is comparable morphologically to the in vivo uptake of particulates. Wood smoke-exposed cells demonstrate reduced phagocytosis, but unaffected mycobacterial killing, suggesting defects related to chronic wood smoke inhalation limited to specific innate immune functions.

The structure of the mixed OH+H2O overlayer on Pt{111}

The structure of the mixed p(3 x 3)-(3OH + 3H2O) phase on Pt[111] has been investigated by low-energy electron diffraction-IV structure analysis. The OH + H2O overlayer consists of hexagonal rings of coplanar oxygen atoms interlinked by hydrogen bonds. Lateral shifts of the O atoms away from atop sites result in different O-O separations and hexagons with only large separations (2.81 and 3.02 angstroms) linked by hexagons with alternating separations of 2.49 and 2.813.02 angstroms. This unusual pattern is consistent with a hydrogen-bonded network in which water is adsorbed in cyclic rings separated by OH in a p(3 x 3) structure. The top-most two layers of the Pt atoms relax inwards with respect to the clean surface and both show vertical buckling of up to 0.06 angstroms. In addition, significant shifts away from the lateral bulk positions have been found for the second layer of Pt atoms.

The Structure of Rare-Earth Metal Surfaces

Introduction to the Rare Earths The Basics of Surface Structure Surface Structure Techniques Crystal Growth and Surface Preparation Rare-Earth Surface Science Quantitative Low-Energy Electron Diffraction Quantitative LEED Results Summary - Past, Present and Future.

Visualization of Bacterial Microcompartment Facet Assembly Using High-Speed Atomic Force Microscopy

Bacterial microcompartments (BMCs) are proteinaceous organelles widespread among bacterial phyla. They compartmentalize enzymes within a selectively permeable shell and play important roles in CO2 fixation, pathogenesis, and microbial ecology. Here, we combine X-ray crystallography and high-speed atomic force microscopy to characterize, at molecular resolution, the structure and dynamics of BMC shell facet assembly. Our results show that preformed hexamers assemble into uniformly oriented shell layers, a single hexamer thick. We also observe the dynamic process of shell facet assembly. Shell hexamers can dissociate from and incorporate into assembled sheets, indicating a flexible intermolecular interaction. Furthermore, we demonstrate that the self-assembly and dynamics of shell proteins are governed by specific contacts at the interfaces of shell proteins. Our study provides novel insights into the formation, interactions, and dynamics of BMC shell facets, which are essential for the design and engineering of self-assembled biological nanoreactors and scaffolds based on BMC architectures.

Angle-resolved photoemission and LEED from rare-earth metals

Abstract Angle-resolved photoemission and LEED studies of single-crystal surfaces of the rare-earth metals are still relatively few in number. The reasons for this are outlined and comparisons are made between the procedures used to obtain clean and well-ordered surfaces suitable for study. Valence-band photoemission spectra are compared with surface electronic structure and photocurrent calculations in order to identify surface and bulk features. Core-level spectroscopy indicates that the 5p levels of the lanthanides show intensity variations with emission angle that are not explicable in terms of a simple core-level shift. Although the 4p levels of Y have some band character, detailed comparison of the 4p photoemission lineshape with those produced by photocurrent calculations enables the surface core-level shift to be determined. Quantitative LEED studies of close-packed (0001) surfaces show essentially a bulk-terminated structure for Sc, a structural reconstruction of the divalent surface of Sm and a magnetic reconstruction of ferromagnetic Gd. The more open (11 2 0) and (10 1 0) surfaces of all the rare-earth metals studied undergo extensive reconstructions into a close-packed structure almost identical to that of a (0001) surface. Angle-resolved photoemission and LEED have yet to distinguish between these structures, indicating a reconstruction depth of at least five atomic layers.

A software tool to straighten curved chromosome images

A software tool for straightening curved chromosomes has been developed and integrated into the freely available image analysis application Image SXM (available via the Internet at http://reg.ssci.liv.ac.uk). This new tool straightens curvilinear objects in one simple step after minimal input from the user. The ends of a curvilinear chromosome are identified by the user using the mouse and a window is opened displaying the object as it would appear if it was straightened out. This image processing produces linear images of chromosomes with no loss of resolution or spatial calibration, making subsequent analysis significantly more straightforward.

The growth of epitaxial Yb silicide: a study with STM

Abstract The formation of epitaxial Yb silicide phases on Si(111) substrates has been investigated by scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS). The STM images demonstrate that the morphology of the silicide thin film phases depends critically on the conditions of preparation. For evaporation of Yb at room temperature followed by annealing up to 600°C a closed silicide film with flat terraces and many domain boundaries is observed, in which epitaxial order can only be inferred from the hexagonally shaped terrace boundaries. Heating of this phase to 650–700°C introduces the break-up of the silicide film and the formation of large flat silicide islands with outdiffused Si agglomerates on their top surfaces and a (2 × 1) YbSi superstructure in between them. Evaporation of Yb onto heated Si(111) substrates yields crystallographically well defined silicide islands of completely different shape: “three-dimensional” hexagonal or trigonal structures surrounded by a (2 × 1) YbSi layer. The pyramidal island shapes suggest that the islands have grown in a layer-by-layer fashion, and the epitaxial order in this phase is directly reflected in STM images displaying atomic resolution. The overall silicide growth mechanism, however, appears to follow the Stranski-Krastanov type irrespective of the detailed growth conditions.

Angle-resolved UV photoemission from Y(0001)

We observe a number of well defined peaks in the photoemission spectra from Y(0001) over the photon energy range 25 eV<hv<60 eV. We believe that one of the features with a binding energy of 1.7 eV is due to emission from states near the upper band edge at the Γ point and that a second nearEForiginates from a surface state. We find a large peak at a binding energy of 9.6 eV which is sensitive to the quality of the surface.