512 research outputs found
The PseudoDojo: Training and grading a 85 element optimized norm-conserving pseudopotential table
First-principles calculations in crystalline structures are often performed
with a planewave basis set. To make the number of basis functions tractable two
approximations are usually introduced: core electrons are frozen and the
diverging Coulomb potential near the nucleus is replaced by a smoother
expression. The norm-conserving pseudopotential was the first successful method
to apply these approximations in a fully ab initio way. Later on, more
efficient and more exact approaches were developed based on the ultrasoft and
the projector augmented wave formalisms. These formalisms are however more
complex and developing new features in these frameworks is usually more
difficult than in the norm-conserving framework. Most of the existing tables of
norm- conserving pseudopotentials, generated long ago, do not include the
latest developments, are not systematically tested or are not designed
primarily for high accuracy. In this paper, we present our PseudoDojo framework
for developing and testing full tables of pseudopotentials, and demonstrate it
with a new table generated with the ONCVPSP approach. The PseudoDojo is an open
source project, building on the AbiPy package, for developing and
systematically testing pseudopotentials. At present it contains 7 different
batteries of tests executed with ABINIT, which are performed as a function of
the energy cutoff. The results of these tests are then used to provide hints
for the energy cutoff for actual production calculations. Our final set
contains 141 pseudopotentials split into a standard and a stringent accuracy
table. In total around 70.000 calculations were performed to test the
pseudopotentials. The process of developing the final table led to new insights
into the effects of both the core-valence partitioning and the non-linear core
corrections on the stability, convergence, and transferability of
norm-conserving pseudopotentials. ...Comment: abstract truncated, 17 pages, 25 figures, 8 table
A model for the formation energies of alanates and boranates
We develop a simple model for the formation energies (FEs) of alkali and
lkaline earth alanates and boranates, based upon ionic bonding between metal
cations and (AlH4)- or (BH4)- anions. The FEs agree well with values obtained
from first principles calculations and with experimental FEs. The model shows
that details of the crystal structure are relatively unimportant. The small
size of the (BH4)- anion causes a strong bonding in the crystal, which makes
boranates more stable than alanates. Smaller alkali or alkaline earth cations
do not give an increased FE. They involve a larger ionization potential that
compensates for the increased crystal bonding.Comment: 3 pages, 2 figure
DFT Study of Planar Boron Sheets: A New Template for Hydrogen Storage
We study the hydrogen storage properties of planar boron sheets and compare
them to those of graphene. The binding of molecular hydrogen to the boron sheet
(0.05 eV) is stronger than that to graphene. We find that dispersion of alkali
metal (AM = Li, Na, and K) atoms onto the boron sheet markedly increases
hydrogen binding energies and storage capacities. The unique structure of the
boron sheet presents a template for creating a stable lattice of strongly
bonded metal atoms with a large nearest neighbor distance. In contrast, AM
atoms dispersed on graphene tend to cluster to form a bulk metal. In particular
the boron-Li system is found to be a good candidate for hydrogen storage
purposes. In the fully loaded case this compound can contain up to 10.7 wt. %
molecular hydrogen with an average binding energy of 0.15 eV/H2.Comment: 19 pages, 7 figures, and 3 table
Electronic structure and optical properties of lightweight metal hydrides
We study the electronic structures and dielectric functions of the simple
hydrides LiH, NaH, MgH2 and AlH3, and the complex hydrides Li3AlH6, Na3AlH6,
LiAlH4, NaAlH4 and Mg(AlH4)2, using first principles density functional theory
and GW calculations. All these compounds are large gap insulators with GW
single particle band gaps varying from 3.5 eV in AlH3 to 6.5 eV in the MAlH4
compounds. The valence bands are dominated by the hydrogen atoms, whereas the
conduction bands have mixed contributions from the hydrogens and the metal
cations. The electronic structure of the aluminium compounds is determined
mainly by aluminium hydride complexes and their mutual interactions. Despite
considerable differences between the band structures and the band gaps of the
various compounds, their optical responses are qualitatively similar. In most
of the spectra the optical absorption rises sharply above 6 eV and has a strong
peak around 8 eV. The quantitative differences in the optical spectra are
interpreted in terms of the structure and the electronic structure of the
compounds.Comment: 13 pages, 10 figure
The high-pressure phase of boron, {\gamma}-B28: disputes and conclusions of 5 years after discovery
{\gamma}-B28 is a recently established high-pressure phase of boron. Its
structure consists of icosahedral B12 clusters and B2 dumbbells in a NaCl-type
arrangement (B2){\delta}+(B12){\delta}- and displays a significant charge
transfer {\delta}~0.5- 0.6. The discovery of this phase proved essential for
the understanding and construction of the phase diagram of boron. {\gamma}-B28
was first experimentally obtained as a pure boron allotrope in early 2004 and
its structure was discovered in 2006. This paper reviews recent results and in
particular deals with the contentious issues related to the equation of state,
hardness, putative isostructural phase transformation at ~40 GPa, and debates
on the nature of chemical bonding in this phase. Our analysis confirms that (a)
calculations based on density functional theory give an accurate description of
its equation of state, (b) the reported isostructural phase transformation in
{\gamma}-B28 is an artifact rather than a fact, (c) the best estimate of
hardness of this phase is 50 GPa, (d) chemical bonding in this phase has a
significant degree of ionicity. Apart from presenting an overview of previous
results within a consistent view grounded in experiment, thermodynamics and
quantum mechanics, we present new results on Bader charges in {\gamma}-B28
using different levels of quantum-mechanical theory (GGA, exact exchange, and
HSE06 hybrid functional), and show that the earlier conclusion about
significant degree of partial ionicity in this phase is very robust
Ionic high-pressure form of elemental boron
Boron is an element of fascinating chemical complexity. Controversies have
shrouded this element since its discovery was announced in 1808: the new
'element' turned out to be a compound containing less than 60-70 percent of
boron, and it was not until 1909 that 99-percent pure boron was obtained. And
although we now know of at least 16 polymorphs, the stable phase of boron is
not yet experimentally established even at ambient conditions. Boron's
complexities arise from frustration: situated between metals and insulators in
the periodic table, boron has only three valence electrons, which would favour
metallicity, but they are sufficiently localized that insulating states emerge.
However, this subtle balance between metallic and insulating states is easily
shifted by pressure, temperature and impurities. Here we report the results of
high-pressure experiments and ab initio evolutionary crystal structure
predictions that explore the structural stability of boron under pressure and,
strikingly, reveal a partially ionic high-pressure boron phase. This new phase
is stable between 19 and 89 GPa, can be quenched to ambient conditions, and has
a hitherto unknown structure (space group Pnnm, 28 atoms in the unit cell)
consisting of icosahedral B12 clusters and B2 pairs in a NaCl-type arrangement.
We find that the ionicity of the phase affects its electronic bandgap, infrared
adsorption and dielectric constants, and that it arises from the different
electronic properties of the B2 pairs and B12 clusters and the resultant charge
transfer between them.Comment: Published in Nature 453, 863-867 (2009
Predictors for grade 6 reading in children at familial risk of dyslexia
The present study investigates whether grade 6 reading outcomes, reading fluency, and reading comprehension can be predicted by grade 3 reading fluency, familial risk of dyslexia (FR), and grade 3 reading related skills: rapid automatized naming (RAN), phonological awareness (PA), and vocabulary. In a sample of 150 children, of whom 83 had a parent with dyslexia, correlation and regression analyses were performed. FR, measured on a continuous scale, was by itself related to all outcomes. However, FR did not explain any variance on top of grade 3 reading fluency. Grade 3 reading fluency strongly predicted grade 6 reading fluency and was also related to reading comprehension. RAN improved the prediction of grade 6 reading fluency, though the additional explained variance was small. Vocabulary and PA fully explained the variance that grade 3 reading fluency explained in grade 6 reading comprehension. Vocabulary explained a substantial amount of variance in grade 6 reading comprehension making it an interesting clinical target. As we used continuous measures of reading fluency and FR, our findings are not biased by distinct diagnostic criteria
Fully Automated Fluorescent in situ Hybridization (FISH) Staining and Digital Analysis of HER2 in Breast Cancer:A Validation Study
HER2 assessment is routinely used to select patients with invasive breast cancer that might benefit from HER2-targeted therapy. The aim of this study was to validate a fully automated in situ hybridization (ISH) procedure that combines the automated Leica HER2 fluorescent ISH system for Bond with supervised automated analysis with the Visia imaging D-Sight digital imaging platform. HER2 assessment was performed on 328 formalin-fixed/paraffin-embedded invasive breast cancer tumors on tissue microarrays (TMA) and 100 (50 selected IHC 2+ and 50 random IHC scores) full-sized slides of resections/biopsies obtained for diagnostic purposes previously. For digital analysis slides were pre-screened at 20x and 100x magnification for all fluorescent signals and supervised-automated scoring was performed on at least two pictures (in total at least 20 nuclei were counted) with the D-Sight HER2 FISH analysis module by two observers independently. Results were compared to data obtained previously with the manual Abbott FISH test. The overall agreement with Abbott FISH data among TMA samples and 50 selected IHC 2+ cases was 98.8% (κ = 0.94) and 93.8% (κ = 0.88), respectively. The results of 50 additionally tested unselected IHC cases were concordant with previously obtained IHC and/or FISH data. The combination of the Leica FISH system with the D-Sight digital imaging platform is a feasible method for HER2 assessment in routine clinical practice for patients with invasive breast cancer
Quasiparticle interfacial level alignment of highly hybridized frontier levels: HO on TiO(110)
Knowledge of the frontier levels' alignment prior to photo-irradiation is
necessary to achieve a complete quantitative description of HO
photocatalysis on TiO(110). Although HO on rutile TiO(110) has been
thoroughly studied both experimentally and theoretically, a quantitative value
for the energy of the highest HO occupied levels is still lacking. For
experiment, this is due to the HO levels being obscured by hybridization
with TiO(110) levels in the difference spectra obtained via ultraviolet
photoemission spectroscopy (UPS). For theory, this is due to inherent
difficulties in properly describing many-body effects at the
HO-TiO(110) interface. Using the projected density of states (DOS) from
state-of-the-art quasiparticle (QP) , we disentangle the adsorbate and
surface contributions to the complex UPS spectra of HO on TiO(110). We
perform this separation as a function of HO coverage and dissociation on
stoichiometric and reduced surfaces. Due to hybridization with the TiO(110)
surface, the HO 3a and 1b levels are broadened into several peaks
between 5 and 1 eV below the TiO(110) valence band maximum (VBM). These
peaks have both intermolecular and interfacial bonding and antibonding
character. We find the highest occupied levels of HO adsorbed intact and
dissociated on stoichiometric TiO(110) are 1.1 and 0.9 eV below the VBM. We
also find a similar energy of 1.1 eV for the highest occupied levels of HO
when adsorbed dissociatively on a bridging O vacancy of the reduced surface. In
both cases, these energies are significantly higher (by 0.6 to 2.6 eV) than
those estimated from UPS difference spectra, which are inconclusive in this
energy region. Finally, we apply self-consistent QP (scQP1) to obtain
the ionization potential of the HO-TiO(110) interface.Comment: 12 pages, 12 figures, 1 tabl
Interactions of Shiga-like toxin with human peripheral blood monocytes
The cytotoxic effect of Shiga-like toxin (Stx; produced by certain Escherichia coli strains) plays a central role in typical hemolytic uremic syndrome (HUS). It damages the renal endothelium by inhibiting the cellular protein synthesis. Also, the monocyte has a specific receptor for Stx but is not sensitive for the cytotoxic effect. In this work, monocytes were studied as a potential transporter for Stx to the renal endothelium. Coincubation of isolated human monocytes loaded with Stx and target cells (vero cells and human umbilical vascular endothelial cells) were performed. Transfer was determined by measuring the protein synthesis of target cells and by flow cytometry. Furthermore, the effect of a temperature shift on loaded monocytes was investigated. Stx-loaded monocytes reduced the protein synthesis of target cells. After adding an antibody against Stx, incomplete recovery occurred. Also, adding only the supernatant of coincubation was followed by protein synthesis inhibition. Stx detached from its receptor on the monocyte after a change in temperature, and no release was detected without this temperature shift. Although the monocyte plays an important role in the pathogenesis of HUS, it has no role in the transfer of Stx
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