329 research outputs found
Automation methodologies and large-scale validation for , towards high-throughput calculations
The search for new materials, based on computational screening, relies on
methods that accurately predict, in an automatic manner, total energy,
atomic-scale geometries, and other fundamental characteristics of materials.
Many technologically important material properties directly stem from the
electronic structure of a material, but the usual workhorse for total energies,
namely density-functional theory, is plagued by fundamental shortcomings and
errors from approximate exchange-correlation functionals in its prediction of
the electronic structure. At variance, the method is currently the
state-of-the-art {\em ab initio} approach for accurate electronic structure. It
is mostly used to perturbatively correct density-functional theory results, but
is however computationally demanding and also requires expert knowledge to give
accurate results. Accordingly, it is not presently used in high-throughput
screening: fully automatized algorithms for setting up the calculations and
determining convergence are lacking. In this work we develop such a method and,
as a first application, use it to validate the accuracy of using the
PBE starting point, and the Godby-Needs plasmon pole model
(@PBE), on a set of about 80 solids. The results of the
automatic convergence study utilized provides valuable insights. Indeed, we
find correlations between computational parameters that can be used to further
improve the automatization of calculations. Moreover, we find that
@PBE shows a correlation between the PBE and the
@PBE gaps that is much stronger than that between and
experimental gaps. However, the @PBE gaps still describe
the experimental gaps more accurately than a linear model based on the PBE
gaps.Comment: 12 pages, 11 figure
Room temperature Peierls distortion in small radius nanotubes
By means of {\it ab initio} simulations, we investigate the phonon band
structure and electron-phonon coupling in small 4-\AA diameter nanotubes. We
show that both the C(5,0) and C(3,3) tubes undergo above room temperature a
Peierls transition mediated by an acoustical long-wavelength and an optical
phonons respectively. In the armchair geometry, we verify that the
electron-phonon coupling parameter originates mainly from phonons at
and is strongly enhanced when the diameter decreases. These results
question the origin of superconductivity in small diameter nanotubes.Comment: submitted 21oct2004 accepted 6jan2005 (Phys.Rev.Lett.
Band Offsets at the Si/SiO Interface from Many-Body Perturbation Theory
We use many-body perturbation theory, the state-of-the-art method for band
gap calculations, to compute the band offsets at the Si/SiO interface. We
examine the adequacy of the usual approximations in this context. We show that
(i) the separate treatment of band-structure and potential lineup
contributions, the latter being evaluated within density-functional theory, is
justified, (ii) most plasmon-pole models lead to inaccuracies in the absolute
quasiparticle corrections, (iii) vertex corrections can be neglected, (iv)
eigenenergy self-consistency is adequate. Our theoretical offsets agree with
the experimental ones within 0.3 eV
Origin of magnetism and quasiparticles properties in Cr-doped TiO
Combining LSDA+ and an analysis of superexchange interactions beyond DFT,
we describe the magnetic ground states in rutile and anatase Cr-doped TiO.
In parallel, we correct our LSDA+ ground state through GW corrections
(@LSDA+) that reproduce the position of impurity states and the band
gaps in satisfying agreement with experiments. Because of the different
topological coordinations of Cr-Cr bonds in the ground states of rutile and
anatase, superexchange interactions induce either ferromagnetic or
antiferromagnetic couplings of Cr ions. In Cr-doped anatase, this interaction
leads to a new mechanism which stabilizes a ferromagnetic ground state, in
keeping with experimental evidence, without the need to invoke F-center
exchange.Comment: 5<pages, 4 figure
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
Analysis of 22 mutations within milk protein genes in Italian Friesian cattle
The bovine milk protein caseins, αS1-CN, β-CN, αS2-CN, and κ-CN are codified by four well characterized genes, named CSN1S1, CSN2, CSN1S2, and CSN3 respectively and clustered in a region of 250-kb of chromosome 6. A recent revision of milk protein nomenclature considering only protein polymorphisms indicates 8 αS1-CN, 4 αS2-CN, 12 β-CN, and 11 κ-CN variants within the genus Bos. Other mutations were found in the non-coding regions of the cluster, such as the promoter regions or the 3'UTR. Many of these polymorphisms, together with others in various genes, such as the one coding for β-lactoglobulin (LGB), show important associations with different milk quality traits. Analyzing all these polymorphisms could help clarify the role of both the casein haplotype and the other polymorphisms in milk composition and cheese-making properties, and could explain which polymorphisms are really or mostly involved. The mPCR-LDR-UA approach recently developed to test simultaneously 22 SNPs in DNA regions responsible for milk protein expression was used to type 250 Italian Friesian cattle. In perfect agreement with literature, the most frequent alleles were CSN1S1*B, CSN2*A2, CSN3*A, variant 2 of CSN1S1 promoter, and variant A of Bov-A2 element. A quite balanced frequency was observed for the LGB*A and LGB*B. No CSN2*C, CSN3*C, and CSN3*H alleles were found. The CSN1S1*C, CSN2*A3, CSN2*I alleles were detected only at the heterozygous condition and at a frequency lower than 2%. The method allowed also finding some unusual intragenic haplotype, such as the Bov-A2 element-CSN3 haplotypes A-B and B-E. As to LGB one of the four SNPs tested was always homozygous for the same mutation, as already noticed. This finding confirms that this synonymous SNP is probably a sequencing mistake or a rare mutation not decisive for the LGB typing in the Italian Friesian. Reducing cost and time for typing simultaneously many SNPs, the method will be applied to a greater number of individuals and to other breeds, aiming to find out a number of animals for each haplotype sufficient for accurate statistical analysis to give a better understanding of the significance of milk protein polymorphism
The bandstructure of gold from many-body perturbation theory
The bandstructure of gold is calculated using many-body perturbation theory
(MBPT). Different approximations within the GW approach are considered.
Standard single shot G0W0 corrections shift the unoccupied bands up by ~0.2 eV
and the first sp-like occupied band down by ~0.4 eV, while leaving unchanged
the 5d occupied bands. Beyond G0W0, quasiparticle self-consistency on the
wavefunctions lowers the occupied 5d bands by 0.35 eV. Globally, many-body
effects achieve an opening of the interband gap (5d-6sp gap) of 0.35 to 0.75 eV
approaching the experimental results. Finally, the quasiparticle bandstructure
is compared to the one obtained by the widely used HSE (Heyd, Scuseria, and
Ernzerhof) hybrid functional
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