Simulation of electron energy loss spectra with the turboEELS and thermo-pw codes

For some materials like noble metals, electron energy loss spectra have a complex structure that makes them difficult to analyze without the help of ab initio calculations. Various theoretical approaches can be used for this purpose, among which the time-dependent density functional perturbation theory (TDDFPT) which has been widely used to study plasmons in a number of bulk and surface systems. In the present paper we present a comparison of the results and performance of two different numerical implementations of TDDFPT: the Sternheimer and Liouville-Lanczos methods. The former approach is implemented in the thermo-pw module and the latter one in the turboEELS code of the QUANTUM ESPRESSO package for electronic structure calculations. In the present paper a comparison is made for bulk bismuth, a semimetal, taking into account spin-orbit coupling, as well as for bulk gold, a noble metal. We show that for these two examples, both codes gives identical results and the turboEELS code has a better performance than the thermo-pw code, and point out in which cases the usage of thermo-pw alone or of both codes can be advantageous

Atomic structure and vibrational properties of icosahedral B4_4C boron carbide

The atomic structure of icosahedral B$_4$C boron carbide is determined by comparing existing infra-red absorption and Raman diffusion measurements with the predictions of accurate {\it ab initio} lattice-dynamical calculations performed for different structural models. This allows us to unambiguously determine the location of the carbon atom within the boron icosahedron, a task presently beyond X-ray and neutron diffraction ability. By examining the inter- and intra-icosahedral contributions to the stiffness we show that, contrary to recent conjectures, intra-icosahedral bonds are harder.Comment: 9 pages including 3 figures, accepted in Physical Review Letter

Pressure-induced metallization in solid boron

Different phases of solid boron under high pressure are studied by first principles calculations. The $\alpha$-B$_{12}$ structure is found to be stable up to 270 GPa. Its semiconductor band gap (1.72 eV) decreases continuously to zero around 160 GPa, where the material transforms to a weak metal. The metallicity, as measured by the density of states at the Fermi level, enhances as the pressure is further increased. The pressure-induced metallization can be attributed to the enhanced boron-boron interactions that cause bands overlap. These results are consist with the recently observed metallization and the associated superconductivity of bulk boron under high pressure (M.I.Eremets et al, Science{\bf 293}, 272(2001)).Comment: 14 pages, 5 figure

Phonons and related properties of extended systems from density-functional perturbation theory

This article reviews the current status of lattice-dynamical calculations in crystals, using density-functional perturbation theory, with emphasis on the plane-wave pseudo-potential method. Several specialized topics are treated, including the implementation for metals, the calculation of the response to macroscopic electric fields and their relevance to long wave-length vibrations in polar materials, the response to strain deformations, and higher-order responses. The success of this methodology is demonstrated with a number of applications existing in the literature.Comment: 52 pages, 14 figures, submitted to Review of Modern Physic

Understanding and retention of the informed consent process among parents in rural northern Ghana

<p>Abstract</p> <p>Background</p> <p>The individual informed consent model remains critical to the ethical conduct and regulation of research involving human beings. Parental informed consent process in a rural setting of northern Ghana was studied to describe comprehension and retention among parents as part of the evaluation of the existing informed consent process.</p> <p>Methods</p> <p>The study involved 270 female parents who gave consent for their children to participate in a prospective cohort study that evaluated immune correlates of protection against childhood malaria in northern Ghana. A semi-structured interview with questions based on the informed consent themes was administered. Parents were interviewed on their comprehension and retention of the process and also on ways to improve upon the existing process.</p> <p>Results</p> <p>The average parental age was 33.3 years (range 18–62), married women constituted a majority (91.9%), Christians (71.9%), farmers (62.2%) and those with no formal education (53.7%). Only 3% had ever taken part in a research and 54% had at least one relation ever participate in a research. About 90% of parents knew their children were involved in a research study that was not related to medical care, and 66% said the study procedures were thoroughly explained to them. Approximately, 70% recalled the study involved direct benefits compared with 20% for direct risks. The majority (95%) understood study participation was completely voluntary but only 21% recalled they could withdraw from the study without giving reasons. Younger parents had more consistent comprehension than older ones. Maternal reasons for allowing their children to take part in the research were free medical care (36.5%), better medical care (18.8%), general benefits (29.4%), contribution to research in the area (8.8%) and benefit to the community (1.8%). Parental suggestions for improving the consent process included devoting more time for explanations (46.9%), use of the local languages (15.9%) and obtaining consent at home (10.3%).</p> <p>Conclusion</p> <p>Significant but varied comprehension of the informed consent process exists among parents who participate in research activities in northern Ghana and it appears the existing practices are fairly effective in informing research participants in the study area.</p

Gastric and intestinal barrier impairment in tropical enteropathy and HIV: limited impact of micronutrient supplementation during a randomised controlled trial

<p>Abstract</p> <p>Background</p> <p>Although micronutrient supplementation can reduce morbidity and mortality due to diarrhoea, nutritional influences on intestinal host defence are poorly understood. We tested the hypothesis that micronutrient supplementation can enhance barrier function of the gut.</p> <p>Methods</p> <p>We carried out two sub-studies nested within a randomised, double-blind placebo-controlled trial of daily micronutrient supplementation in an urban community in Lusaka, Zambia. In the first sub-study, gastric pH was measured in 203 participants. In the second sub-study, mucosal permeability, lipopolysaccharide (LPS) and anti-LPS antibodies, and serum soluble tumour necrosis factor receptor p55 (sTNFR55) concentrations were measured in 87 participants. Up to three stool samples were also analysed microbiologically for detection of asymptomatic intestinal infection. Gastric histology was subsequently analysed in a third subset (n = 37) to assist in interpretation of the pH data. Informed consent was obtained from all participants after a three-stage information and consent process.</p> <p>Results</p> <p>Hypochlorhydria (fasting gastric pH > 4.0) was present in 75 (37%) of participants. In multivariate analysis, HIV infection (OR 4.1; 95%CI 2.2-7.8; <it>P </it>< 0.001) was associated with hypochlorhydria, but taking anti-retroviral treatment (OR 0.16; 0.04-0.67; <it>P </it>= 0.01) and allocation to micronutrient supplementation (OR 0.53; 0.28-0.99; <it>P </it>< 0.05) were protective. Hypochlorhydria was associated with increased risk of salmonellosis. Mild (grade 1) gastric atrophy was found in 5 participants, irrespective of <it>Helicobacter pylori </it>or HIV status. Intestinal permeability, LPS concentrations in serum, anti-LPS IgG, and sTNFR55 concentrations did not differ significantly between micronutrient and placebo groups. Anti-LPS IgM was reduced in the micronutrient recipients (<it>P <</it>0.05).</p> <p>Conclusions</p> <p>We found evidence of a specific effect of HIV on gastric pH which was readily reversed by anti-retroviral therapy and not mediated by gastric atrophy. Micronutrients had a modest impact on gastric pH and one marker of bacterial translocation.</p> <p>Trial Registration</p> <p>Current Controlled Trials ISRCTN31173864</p

Study of multi-carbide B4C-SiC/(Al, Si) reaction infiltrated composites by SEM with EBSD

In the definition of conceptual developments and design of new materials with singular or unique properties, characterisation takes a key role in clarifying the relationships of composition, properties and processing that define the new material. B4C has a rare combination of properties that makes it suitable for a wide range of applications in engineering: high refractoriness, thermal stability, high hardness and abrasion resistance coupled to low density. However, the low self-diffusion coefficient of B4C limits full densification by sintering. A way to overturn this constraint is by using an alloy, for example Al-Si, forming composites with B4C. Multi-carbide B4C-SiC/(Al, Si) composites were produced by the reactive melt infiltration technique at 1200 - 1350 degrees C with up to 1 hour of isothermal temperature holds. Pressed preforms made from C-containing B4C were spontaneously infiltrated with Al-Si alloys of composition varying from 25 to 50 wt% Si. The present study involves the characterisation of the microstructure and crystalline phases in the alloys and in the composites by X-ray diffraction and SEM/EDS with EBSD. Electron backscatter diffraction is used in detail to look for segregation and spatial distribution of Si and Al containing phases during solidification of the metallic infiltrate inside the channels of the ceramic matrix when the composite cools down to the eutectic temperature (577 degrees C). It complements elemental maps of the SEM/EDS. The production of a flat surface by polishing is intrinsically difficult and the problems inherent to the preparation of EBSD qualified finishing in polished samples of such type of composites are further discussed

Advanced capabilities for materials modelling with Quantum ESPRESSO

Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches. Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement theirs ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software