Construction of transferable spherically-averaged electron potentials

A new scheme for constructing approximate effective electron potentials within density-functional theory is proposed. The scheme consists of calculating the effective potential for a series of reference systems, and then using these potentials to construct the potential of a general system. To make contact to the reference system the neutral-sphere radius of each atom is used. The scheme can simplify calculations with partial wave methods in the atomic-sphere or muffin-tin approximation, since potential parameters can be precalculated and then for a general system obtained through simple interpolation formulas. We have applied the scheme to construct electron potentials of phonons, surfaces, and different crystal structures of silicon and aluminum atoms, and found excellent agreement with the self-consistent effective potential. By using an approximate total electron density obtained from a superposition of atom-based densities, the energy zero of the corresponding effective potential can be found and the energy shifts in the mean potential between inequivalent atoms can therefore be directly estimated. This approach is shown to work well for surfaces and phonons of silicon.Comment: 8 pages (3 uuencoded Postscript figures appended), LaTeX, CAMP-090594-

An Effective-Medium Tight-Binding Model for Silicon

A new method for calculating the total energy of Si systems is presented. The method is based on the effective-medium theory concept of a reference system. Instead of calculating the energy of an atom in the system of interest a reference system is introduced where the local surroundings are similar. The energy of the reference system can be calculated selfconsistently once and for all while the energy difference to the reference system can be obtained approximately. We propose to calculate it using the tight-binding LMTO scheme with the Atomic-Sphere Approximation(ASA) for the potential, and by using the ASA with charge-conserving spheres we are able to treat open system without introducing empty spheres. All steps in the calculational method is {\em ab initio} in the sense that all quantities entering are calculated from first principles without any fitting to experiment. A complete and detailed description of the method is given together with test calculations of the energies of phonons, elastic constants, different structures, surfaces and surface reconstructions. We compare the results to calculations using an empirical tight-binding scheme.Comment: 26 pages (11 uuencoded Postscript figures appended), LaTeX, CAMP-090594-

NDM-1 imported from India – first reported case in South Africa

Carbapenem-resistant Enterobacteriaceae have been increasingly reported throughout the world. The first South African report of a New Delhi metallo-beta-lactamase was from Gauteng in August 2011. Despite maintaining a high degree of vigilance, the first such case was seen in KwaZulu-Natal almost a year later. Other cases have been unable to confirm a definite link to any other affected areas; this is the first case in South Africa showing this direct epidemiological link

The influence of surface stress on the equilibrium shape of strained quantum dots

The equilibrium shapes of InAs quantum dots (i.e., dislocation-free, strained islands with sizes >= 10,000 atoms) grown on a GaAs (001) substrate are studied using a hybrid approach which combines density functional theory (DFT) calculations of microscopic parameters, surface energies, and surface stresses with elasticity theory for the long-range strain fields and strain relaxations. In particular we report DFT calculations of the surface stresses and analyze the influence of the strain on the surface energies of the various facets of the quantum dot. The surface stresses have been neglected in previous studies. Furthermore, the influence of edge energies on the island shapes is briefly discussed. From the knowledge of the equilibrium shape of these islands, we address the question whether experimentally observed quantum dots correspond to thermal equilibrium structures or if they are a result of the growth kinetics.Comment: 7 pages, 8 figures, submitted to Phys. Rev. B (February 2, 1998). Other related publications can be found at http://www.rz-berlin.mpg.de/th/paper.htm

First-principles calculations of the self-trapped exciton in crystalline NaCl

The atomic and electronic structure of the lowest triplet state of the off-center (C2v symmetry) self-trapped exciton (STE) in crystalline NaCl is calculated using the local-spin-density (LSDA) approximation. In addition, the Franck-Condon broadening of the luminescence peak and the a1g -> b3u absorption peak are calculated and compared to experiment. LSDA accurately predicts transition energies if the initial and final states are both localized or delocalized, but 1 eV discrepancies with experiment occur if one state is localized and the other is delocalized.Comment: 4 pages with 4 embeddded figure

Sentinel seroprevalence of SARS-CoV-2 in Gauteng Province, South Africa, August - October 2020

Background. Estimates of prevalence of anti-SARS-CoV-2 antibody positivity (seroprevalence) for tracking the COVID-19 epidemic are lacking for most African countries.Objectives. To determine the prevalence of antibodies against SARS-CoV-2 in a sentinel cohort of patient samples received for routine testing at tertiary laboratories in Johannesburg, South Africa.Methods. This sentinel study was conducted using remnant serum samples received at three National Health Laboratory Service laboratories in the City of Johannesburg (CoJ) district. Collection was from 1 August to 31 October 2020. We extracted accompanying laboratory results for glycated haemoglobin (HbA1c), creatinine, HIV, viral load and CD4 T-cell count. An anti-SARS-CoV-2 targeting the nucleocapsid (N) protein of the coronavirus with higher affinity for IgM and IgG antibodies was used. We reported crude as well as population-weighted and test-adjusted seroprevalence. Multivariate logistic regression analysis was used to determine whether age, sex, HIV and diabetic status were associated with increased risk for seropositivity.Results. A total of 6 477 samples were analysed, the majority (n=5 290) from the CoJ region. After excluding samples with no age or sex stated, the model population-weighted and test-adjusted seroprevalence for the CoJ (n=4 393) was 27.0% (95% confidence interval (CI) 25.4 - 28.6). Seroprevalence was highest in those aged 45 - 49 years (29.8%; 95% CI 25.5 - 35.0) and in those from the most densely populated areas of the CoJ. Risk for seropositivity was highest in those aged 18 - 49 years (adjusted odds ratio (aOR) 1.52; 95% CI 1.13 - 2.13; p=0.0005) and in samples from diabetics (aOR 1.36; 95% CI 1.13 - 1.63; p=0.001).Conclusions. Our study conducted between the first and second waves of the pandemic shows high levels of current infection among patients attending public health facilities in Gauteng Province

Competition between Magnetic and Structural Transition in CrN

CrN is observed to undergo a paramagnetic to antiferromagnetic transition accompanied by a shear distortion from cubic NaCl-type to orthorhombic structure. Our first-principle plane wave and ultrasoft pseudopotential calculations confirm that the distorted antiferromagnetic phase with spin configuration arranged in double ferromagnetic sheets along [110] is the most stable. Antiferromagnetic ordering leads to a large depletion of states around Fermi level, but it does not open a gap. Simultaneous occurence of structural distortion and antiferromagnetic order is analyzed.Comment: 10 pages, 10 figure

A Geometric Formulation of Quantum Stress Fields

We present a derivation of the stress field for an interacting quantum system within the framework of local density functional theory. The formulation is geometric in nature and exploits the relationship between the strain tensor field and Riemannian metric tensor field. Within this formulation, we demonstrate that the stress field is unique up to a single ambiguous parameter. The ambiguity is due to the non-unique dependence of the kinetic energy on the metric tensor. To illustrate this formalism, we compute the pressure field for two phases of solid molecular hydrogen. Furthermore, we demonstrate that qualitative results obtained by interpreting the hydrogen pressure field are not influenced by the presence of the kinetic ambiguity.Comment: 22 pages, 2 figures. Submitted to Physical Review B. This paper supersedes cond-mat/000627