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 $q=2k_F$ phonons respectively. In the armchair geometry, we verify that the electron-phonon coupling parameter $\lambda$ originates mainly from phonons at $q=2k_F$ 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.

Origin of magnetism and quasiparticles properties in Cr-doped TiO2_2

Combining LSDA+$U$ and an analysis of superexchange interactions beyond DFT, we describe the magnetic ground states in rutile and anatase Cr-doped TiO$_2$. In parallel, we correct our LSDA+$U$ ground state through GW corrections ($GW$@LSDA+$U$) 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

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

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

Accuracy of generalized gradient approximation functionals for density functional perturbation theory calculations

We assess the validity of various exchange-correlation functionals for computing the structural, vibrational, dielectric, and thermodynamical properties of materials in the framework of density-functional perturbation theory (DFPT). We consider five generalized-gradient approximation (GGA) functionals (PBE, PBEsol, WC, AM05, and HTBS) as well as the local density approximation (LDA) functional. We investigate a wide variety of materials including a semiconductor (silicon), a metal (copper), and various insulators (SiO$_2$ $\alpha$-quartz and stishovite, ZrSiO$_4$ zircon, and MgO periclase). For the structural properties, we find that PBEsol and WC are the closest to the experiments and AM05 performs only slightly worse. All three functionals actually improve over LDA and PBE in contrast with HTBS, which is shown to fail dramatically for $\alpha$-quartz. For the vibrational and thermodynamical properties, LDA performs surprisingly very good. In the majority of the test cases, it outperforms PBE significantly and also the WC, PBEsol and AM05 functionals though by a smaller margin (and to the detriment of structural parameters). On the other hand, HTBS performs also poorly for vibrational quantities. For the dielectric properties, none of the functionals can be put forward. They all (i) fail to reproduce the electronic dielectric constant due to the well-known band gap problem and (ii) tend to overestimate the oscillator strengths (and hence the static dielectric constant)

Characterization of the casein gene complex in West Africa goats and description of a new αs1-casein polymorphism

The analysis of casein polymorphisms was carried out in West Africa goat populations: Red Sokoto (n = 57), West African Dwarf Nigeria (n = 27), West African Dwarf Cameroon (n = 39), and Borno (n = 37). The 4 casein genes alphas1 (CSN1S1), beta (CSN2), alphas2 (CSN1S2), and kappa (CSN3) were typed at the DNA level. No null alleles were found in any of the genes analyzed. A PCR single-strand conformation polymorphism method was implemented for the identification of CSN1S1*F allele simultaneously with A/01, B/E, N and the new allele. The allele differed from CSN1S1*B by a synonymous transversion TCG->TCT in the codon corresponding to Ser66 of the mature protein. The new allele, named CSN1S1*B', occurred at a high frequency in all the populations, ranging from 0.295 (West African Dwarf Cameroon) to 0.405 (Borno). A greater frequency was found for alleles associated with high alphas1-casein quantity, as has already been observed in the goat populations from the Mediterranean area. The intermediate E allele occurred only in the Red Sokoto and at a low frequency. The faint F allele occurred in 3 populations at frequencies lower than 0.03. Linkage disequilibrium occurred in all the populations, with highly significant differences in Borno, Red Sokoto, and West Africa Dwarf Nigeria, and significant differences in West Africa Dwarf Cameroon. Only 10 haplotypes showed frequencies >= 0.05 in at least 1 of the 4 populations considered, and the overall frequency was >0.1 only for 4 haplotypes: BAAB, B'ACA, ACAB, and BACA (in the order CSN1S1-CSN2-CSN1S2-CSN3). Haplotype BAAB, postulated as an ancestral haplotype in previous studies, was the most common haplotype in all breeds except Borno, where B'ACA was predominant. The results obtained are of considerable significance given that very little information exists on the subject for African goats. The high frequency of strong alleles in the calcium-sensitive caseins as well as the high linkage disequilibrium found among the casein genes in the African breeds analyzed may suggest that specific casein haplotypes have already been selected due to their advantages for nutrition. Haplotypes providing greater protein and casein content would increase the energy content of milk, thus resulting in more favorable growth and survival of young goats and humans consuming the milk

Epitaxially strained [001]-(PbTiO3_3)1_1(PbZrO3_3)1_1 superlattice and PbTiO3_3 from first principles

The effect of layer-by-layer heterostructuring and epitaxial strain on lattice instabilities and related ferroelectric properties is investigated from first principles for the [001]-(PbTiO$_3$)$_1$(PbZrO$_3$)$_1$ superlattice and pure PbTiO$_3$ on a cubic substrate. The results for the superlattice show an enhancement of the stability of the monoclinic r-phase with respect to pure PbTiO$_3$. Analysis of the lattice instabilities of the relaxed centrosymmetric reference structure computed within density functional perturbation theory suggests that this results from the presence of two unstable zone-center modes, one confined in the PbTiO$_3$ layer and one in the PbZrO$_3$ layer, which produce in-plane and normal components of the polarization, respectively. The zero-temperature dielectric response is computed and shown to be enhanced not only near the phase boundaries, but throughout the r-phase. Analysis of the analogous calculation for pure PbTiO$_3$ is consistent with this interpretation, and suggests useful approaches to engineering the dielectric properties of artificially structured perovskite oxides.Comment: 8 pages, 5 figure

Short communication: Carora cattle shows high variability at αsl-casein

The objective of this study was to analyze the genetic variability of milk proteins of the Carora, a shorthorned Bos taurus cattle breed in Venezuela and in other Southern American countries that is primarily used for milk production. A total of 184 individual milk samples were collected from Carora cattle in 5 herds in Venezuela. The milk protein genes alphas1-casein (CN) (CSN1S1), alphas2-CN (CSN2), beta-CN (CSN3), and beta-lactoglobulin (LGB) were typed at the protein level by isoelectrofocusing. It was necessary to further analyze CSN1S1 at the DNA level by a PCR-based method to distinguish CSN1S1*G from B. Increased variation was found in particular at the CSN1S1 gene, where 4 variants were identified. The predominant variant was CSN1S1*B (frequency = 0.8). The second most common CSN1S1 variant was CSN1S1*G (0.101), followed by CSN1S1*C (0.082). Moreover, a new isoelectrofocusing pattern was identified, which may result from a novel CSN1S1 variant, named CSN1S1*I, migrating at an intermediate position between CSN1S1*B and CSN1S1*C. Six cows carried the variant at the heterozygous condition. For the other loci, predominance of CSN2*A2 (0.764), CSN3*B (0.609), and LGB*B (0.592) was observed. Haplotype frequencies (AF) at the CSN1S1-CSN2-CSN3 complex were also estimated by taking association into account. Only 7 haplotypes showed AF values >0.05, accounting for a cumulative frequency of 0.944. The predominant haplotype was B-A2-B (frequency = 0.418), followed by B-A2-A (0.213). The occurrence of the G variant is at a rather high frequency, which is of interest for selection within the Carora breed because of the negative association of this variant with the synthesis of the specific protein. From a cheese-making point of view, this variant is associated with improved milk-clotting parameters but is negatively associated with cheese ripening. Thus, milk protein typing should be routinely carried out in the breed, with particular emphasis on using a DNA test to detect the CSN1S*G variant. The CSN1S*G allele is likely to have descended from the Brown Swiss, which contributed to the Carora breed and also carries this allele

The Garfagnina goat: A zootechnical overview of a local dairy population

Domestic livestock with a limited distribution are increasingly recognized in the action plans of the European Union as a reason for protecting rural land. The preservation and enhancement of the native germplasm and traits selected through the ages in different areas of farming is the first step in increasing typical products at a time when high quality products are increasingly in demand. This is the first time that a zootechnical overview has been performed on the Italian native goat population named "Garfagnina", which is registered on the Tuscan regional repertory of genetic resources at risk of extinction. The aim of the study was to give added value to this population by focusing on particular traits that could be used for promoting typical products. Data on the size of the local goats, zoometric measures, breeding system, milk quality, and genetic polymorphisms were collected to get insight into the current state of the population of this type of goat. The native goat population is reared in Tuscany in central Italy, mostly for its milk. The local goat farms considered in our study are located in the hills and mountains of the northwestern Tuscan Apennine area. For every farm we measured at least 10% of the reproductive females (273), randomly chosen, and all reproductive males (47) for a total of 320 subjects. Regarding the management of the animals and the feeding system, semi-extensive farming is practiced in all the flocks. From a morphological point of view the animals are relatively homogeneous, especially in terms of zoometric data, whereas they show a wider variability regarding coat. Milk gross and fatty acid composition were similar to that reported in the literature for bulk goat milk. Moreover, the average of somatic cell count and standard plate count found in Garfagnina goat milk indicated good hygienic farm management and correct milking practices, although milking is mainly manual. The average number of globules per milliliter found in Garfagnina goat milk was almost double compared with the literature, whereas the average diameter was lower. Milk coagulation properties were scarce, thus indicating poor cheesemaking aptitude of Garfagnina milk. Selecting haplotypes carrying alleles associated with a higher expression of the specific casein could help improve milk cheesemaking aptitude. Moreover, the rather high frequency of the faint CSN1S1*F allele and the occurrence of CSN2*0 might suggest that Garfagnina goat milk could be used, after an appropriate selection, for direct consumption of milk at low casein content for intolerant human subjects