Development of a Kohn-Sham like potential in the Self-Consistent Atomic Deformation Model

This is a brief description of how to derive the local ``atomic'' potentials from the Self-Consistent Atomic Deformation (SCAD) model density function. Particular attention is paid to the spherically averaged case.Comment: 5 Pages, LaTeX, no figure

First-principles Calculation of the Formation Energy in MgO-CaO Solid Solutions

The electronic structure and total energy were calculated for ordered and disordered MgO-CaO solid solutions within the multiple scattering theory in real space and the local density approximation. Based on the dependence of the total energy on the unit cell volume the equilibrium lattice parameter and formation energy were determined for different solution compositions. The formation energy of the solid solutions is found to be positive that is in agreement with the experimental phase diagram, which shows a miscibility gap.Comment: 11 pages, 3 figure

Aetiology of canine infectious respiratory disease complex and prevalence of its pathogens in Europe

The canine infectious respiratory disease complex (CIRDC) is an endemic worldwide syndrome involving multiple viral and bacterial pathogens. Traditionally, Bordetella bronchiseptica (Bb), canine adenovirus type 2 (CAV-2), canine distemper virus (CDV), canine herpesvirus (CHV) and canine parainfluenza virus (CPiV) were considered the major causative agents. Lately, new pathogens have been implicated in the development of CIRDC, namely canine influenza virus (CIV), canine respiratory coronavirus (CRCoV), canine pneumovirus (CnPnV), Mycoplasma cynos and Streptococcus equi subspecies zooepidemicus. To better understand the role of the different pathogens in the development of CIRDC and their epidemiological relevance in Europe, prevalence data were collected from peer-reviewed publications and summarized. Evidence of exposure to Bb is frequently found in healthy and diseased dogs and client-owned dogs are as likely to be infected as kennelled dogs. Co-infections with viral pathogens are common. The findings confirm that Bb is an important cause of CIRDC in Europe. CAV-2 and CDV recovery rates from healthy and diseased dogs are low and the most likely explanation for this is control through vaccination. Seroconversion to CHV can be demonstrated following CIRDC outbreaks and CHV has been detected in the lower respiratory tract of diseased dogs. There is some evidence that CHV is not a primary cause of CIRDC, but opportunistically re-activates at the time of infection and exacerbates the disease. The currently available data suggest that CIV is, at present, neither a prevalent nor a significant pathogen in Europe. CPiV remains an important pathogen in CIRDC and facilitates co-infection with other viral and bacterial pathogens. CnPnV and CRCoV are important new elements in the aetiology of CIRDC and spread particularly well in multi-dog establishments. M. cynos is common in Europe and is more likely to occur in younger and kennelled dogs. This organism is frequently found together with other CIRDC pathogens and is significantly associated with more severe respiratory signs. S. zooepidemicus infection is not common and appears to be a particular problem in kennels. Protective immunity against respiratory diseases is rarely complete, and generally only a reduction in clinical signs and excretion of pathogen can be achieved through vaccination. However, even vaccines that only reduce and do not prevent infection carry epidemiological advantages. They reduce spread, increase herd immunity and decrease usage of antimicrobials. Recommending vaccination of dogs against pathogens of CIRDC will directly provide epidemiological advantages to the population and the individual dog

Towards a Linear-Scaling DFT Technique: The Density Matrix Approach

A recently proposed linear-scaling scheme for density-functional pseudopotential calculations is described in detail. The method is based on a formulation of density functional theory in which the ground state energy is determined by minimization with respect to the density matrix, subject to the condition that the eigenvalues of the latter lie in the range [0,1]. Linear-scaling behavior is achieved by requiring that the density matrix should vanish when the separation of its arguments exceeds a chosen cutoff. The limitation on the eigenvalue range is imposed by the method of Li, Nunes and Vanderbilt. The scheme is implemented by calculating all terms in the energy on a uniform real-space grid, and minimization is performed using the conjugate-gradient method. Tests on a 512-atom Si system show that the total energy converges rapidly as the range of the density matrix is increased. A discussion of the relation between the present method and other linear-scaling methods is given, and some problems that still require solution are indicated.Comment: REVTeX file, 27 pages with 4 uuencoded postscript figure

A first principles study of sub-monolayer Ge on Si(001)

Experimental observations of heteroepitaxial growth of Ge on Si(001) show a (2xn) reconstruction for sub-monolayer coverages, with dimer rows crossed by missing-dimer trenches. We present first-principles density-functional calculations designed to elucidate the energetics and relaxed geometries associated with this reconstruction. We also address the problem of how the formation energies of reconstructions having different stoichiometries should be compared. The calculations reveal a strong dependence of the formation energy of the missing-dimer trenches on spacing n, and demonstrate that this dependence stems almost entirely from elastic relaxation. The results provide a natural explanation for the experimentally observed spacings in the region of n \~ 8.Comment: 13 pages, 4 figures, submitted to Surface Scienc

The particle-in-cell model for ab initio thermodynamics: implications for the elastic anisotropy of the Earth's inner core

We assess the quantitative accuracy of the particle-in-cell (PIC) approximation used in recent ab initio predictions of the thermodynamic properties of hexagonal-close-packed iron at the conditions of the Earth's inner core. The assessment is made by comparing PIC predictions for a range of thermodynamic properties with the results of more exact calculations that avoid the PIC approximation. It is shown that PIC gives very accurate results for some properties, but that it gives an incorrect treatment of anharmonic lattice vibrations. In addition, our assessment does not support recent PIC-based predictions that the hexagonal c/a ratio increases strongly with increasing temperature, and we point out that this casts doubt on a proposed re-interpretation of the elastic anisotropy of the inner core.Comment: 25 pages, 9 figures, submitted to Physics of the Earth and Planetary Interior

Atomic layering at the liquid silicon surface: a first- principles simulation

We simulate the liquid silicon surface with first-principles molecular dynamics in a slab geometry. We find that the atom-density profile presents a pronounced layering, similar to those observed in low-temperature liquid metals like Ga and Hg. The depth-dependent pair correlation function shows that the effect originates from directional bonding of Si atoms at the surface, and propagates into the bulk. The layering has no major effects in the electronic and dynamical properties of the system, that are very similar to those of bulk liquid Si. To our knowledge, this is the first study of a liquid surface by first-principles molecular dynamics.Comment: 4 pages, 4 figures, submitted to PR

Trace element composition of silicate inclusions in sub-lithospheric diamonds from the Juina-5 kimberlite:Evidence for diamond growth from slab melts

The trace element compositions of inclusions in sub-lithospheric diamonds from the Juina-5 kimberlite, Brazil, are presented. Literature data for mineral/melt partition coefficients were collated, refitted and employed to interpret inclusion compositions. As part of this process an updated empirical model for predicting the partitioning behaviour of trivalent cations for garnet–melt equilibrium calibrated using data from 73 garnet-melt pairs is presented. High levels of trace element enrichment in inclusions interpreted as former calcium silicate perovskite and majoritic garnet preclude their origin as fragments of an ambient deep mantle assemblage. Inclusions believed to represent former bridgmanite minerals also display a modest degree of enrichment relative to mantle phases. The trace element compositions of ‘NAL’ and ‘CF phase’ minerals are also reported. Negative Eu, Ce, and Y/Ho anomalies alongside depletions of Sr, Hf and Zr in many inclusions are suggestive of formation from a low-degree carbonatitic melt of subducted oceanic crust. Observed enrichments in garnet and ‘calcium perovskite’ inclusions limit depths of melting to less than ~ 600 km, prior to calcium perovskite saturation in subducting assemblages. Less enriched inclusions in sub-lithospheric diamonds from other global localities may represent deeper diamond formation. Modelled source rock compositions that are capable of producing melts in equilibrium with Juina-5 ‘calcium perovskite’ and majorite inclusions are consistent with subducted MORB. Global majorite inclusion compositions suggest a common process is responsible for the formation of many superdeep diamonds, irrespective of geographic locality. Global transition zone inclusion compositions are reproduced by fractional crystallisation from a single parent melt, suggesting that they record the crystallisation sequence and melt evolution during this interaction of slab melts with ambient mantle. All observations are consistent with the previous hypothesis that many superdeep diamonds are created as slab-derived carbonatites interact with peridotitic mantle in the transition zone

The axial ratio of hcp iron at the conditions of the Earth's inner core

We present ab initio calculations of the high-temperature axial c/a ratio of hexagonal-close-packed (hcp) iron at Earth's core pressures, in order to help interpret the observed seismic anisotropy of the inner core. The calculations are based on density functional theory, which is known to predict the properties of high-pressure iron with good accuracy. The temperature dependence of c/a is determined by minimising the Helmholtz free energy at fixed volume and temperature, with thermal contributions due to lattice vibrations calculated using harmonic theory. Anharmonic corrections to the harmonic predictions are estimated from calculations of the thermal average stress obtained from ab initio molecular dynamics simulations of hcp iron at the conditions of the inner core. We find a very gradual increase of axial ratio with temperature. This increase is much smaller than found in earlier calculations, but is in reasonable agreement with recent high-pressure, high-temperature diffraction measurements. This result casts doubt on an earlier interpretation of the seismic anisotropy of the inner core