Optimization methods and their use in low-energy electron-diffraction calculations

The speed of automatic optimization procedures used in surface structure determination by low-energy electron diffraction can be greatly enhanced by the use of linear approximations in the calculation of scattering amplitudes. It is shown how linear approximations can be used in the calculation of derivatives of intensities which are required in the least-squares optimization method. The derivatives with respect to structural and nonstructural parameters are calculated applying a combination of analytic and numerical methods in connection with approximations of the sum over lattice points in the angular momentum representation. Special cases for different structural and nonstructural parameters and simplifications for special geometries are discussed. The computational effort becomes nearly independent of the number of free parameters and enables the analysis of complex surface structures

Manifestation of quantum chaos on scattering techniques: application to low-energy and photo-electron diffraction intensities

Intensities of LEED and PED are analyzed from a statistical point of view. The probability distribution is compared with a Porter-Thomas law, characteristic of a chaotic quantum system. The agreement obtained is understood in terms of analogies between simple models and Berry's conjecture for a typical wavefunction of a chaotic system. The consequences of this behaviour on surface structural analysis are qualitatively discussed by looking at the behaviour of standard correlation factors.Comment: 5 pages, 4 postscript figures, Latex, APS, http://www.icmm.csic.es/Pandres/pedro.ht

Efficient determiniation of multilayer relaxation in the Pt(210) stepped and densely kinked surface

The multilayer relaxation of the Pt(210) stepped and kinked surface is analyzed by low-energy-electron diffraction. This is the first application of the new real-space multiple-scattering theory of LEED, designed specifically for such open surfaces where conventional theories fail. Combined with an automated tensor LEED method, it efficiently detects nonalternating atomic relaxations which are oriented primarily perpendicular to the surface. These relaxations are in qualitative agreement with new embedded-atom-method results

The Static and Dynamic Lattice Changes Induced by Hydrogen Adsorption on NiAl(110)

Static and dynamic changes induced by adsorption of atomic hydrogen on the NiAl(110) lattice at 130 K have been examined as a function of adsorbate coverage. Adsorbed hydrogen exists in three distinct phases. At low coverages the hydrogen is itinerant because of quantum tunneling between sites and exhibits no observable vibrational modes. Between 0.4 ML and 0.6 ML, substrate mediated interactions produce an ordered superstructure with c(2x2) symmetry, and at higher coverages, hydrogen exists as a disordered lattice gas. This picture of how hydrogen interacts with NiAl(110) is developed from our data and compared to current theoretical predictions.Comment: 36 pages, including 12 figures, 2 tables and 58 reference

LEED Holography applied to a complex superstructure: a direct view of the adatom cluster on SiC(111)-(3x3)

For the example of the SiC(111)-(3x3) reconstruction we show that a holographic interpretation of discrete Low Energy Electron Diffraction (LEED) spot intensities arising from ordered, large unit cell superstructures can give direct access to the local geometry of a cluster around an elevated atom, provided there is only one such prominent atom per surface unit cell. By comparing the holographic images obtained from experimental and calculated data we illuminate validity, current limits and possible shortcomings of the method. In particular, we show that periodic vacancies such as cornerholes may inhibit the correct detection of the atomic positions. By contrast, the extra diffraction intensity due to slight substrate reconstructions, as for example buckling, seems to have negligible influence on the images. Due to the spatial information depth of the method the stacking of the cluster can be imaged down to the fourth layer. Finally, it is demonstrated how this structural knowledge of the adcluster geometry can be used to guide the dynamical intensity analysis subsequent to the holographic reconstruction and necessary to retrieve the full unit cell structure.Comment: 11 pages RevTex, 6 figures, Phys. Rev. B in pres

Molecular identification of papillomavirus in ducks

Papillomaviruses infect many vertebrates, including birds. Persistent infections by some strains can cause malignant proliferation of cells (i.e. cancer), though more typically infections cause benign tumours, or may be completely subclinical. Sometimes extensive, persistent tumours are recorded– notably in chaffinches and humans. In 2016, a novel papillomavirus genotype was characterized from a duck faecal microbiome, in Bhopal, India; the sixth papillomavirus genotype from birds. Prompted by this finding, we screened 160 cloacal swabs and 968 faecal samples collected from 299 ducks sampled at Ottenby Bird Observatory, Sweden in 2015, using a newly designed real-time PCR. Twenty one samples (1.9%) from six individuals (2%) were positive. Eighteen sequences were identical to the published genotype, duck papillomavirus 1. One additional novel genotype was recovered from three samples. Both genotypes were recovered from a wild strain domestic mallard that was infected for more than 60 days with each genotype. All positive individuals were adult (P = 0.004). Significantly more positive samples were detected from swabs than faecal samples (P < 0.0001). Sample type data suggests transmission may be via direct contact, and only infrequently, via the oral-faecal route. Infection in only adult birds supports the hypothesis that this virus is sexually transmitted, though more work is required to verify this.Thanks to duck trappers at Ottenby Bird Observatory for support and sample collection, and to Abbtesaim Jawad for DNA extraction. This work was supported by the Crafoord Foundation Sweden (grants number 20160971 and 20170671). This is contribution no. 306 from Ottenby Bird Observatory