Rare-earth impurities in gallium nitride: The role of the Hubbard potential

We performed a first principles investigation on the electronic properties of 4f-rare earth substitutional impurities in zincblende gallium nitride (GaN:REGa, with RE=Eu, Gd, Tb, Dy, Ho, Er and Tm). The calculations were performed within the all electron methodology and the density functional theory. We investigated how the introduction of the on-site Hubbard U potential (GGA + U) corrects the electronic properties of those impurities. We showed that a self-consistent procedure to compute the Hubbard potential provides a reliable description on the position of the 4f-related energy levels with respect of the GaN valence band top. The results were compared to available data coming from a recent phenomenological model. (C) 2012 Elsevier B.V. All rights reserved.

First principles calculations for vacancies and antisites in PbSe and PbTe: bulk and nanowire.

The energetic stability and the electronic properties of vacancies (VX) and antisites (XY) in PbSe and PbTe are investigated. PbSe and PbTe are narrow band gap semiconductors and have the potential to be used in infrared detectors, laser, and diodes. They are also of special interest for thermoelectric devices (TE). The calculations are based in the Density Functional Theory (DFT) and the General Gradient Approximation (GGA) for the exchange-correlation term, as implemented in the VASP code. The core and valence electrons are described by the Projected Augmented Wave (PAW) and the Plane Wave (PW) methods, respectively. The defects are studied in the bulk and nanowire (NW) system. Our results show that intrinsec defects (vacancies and antisites) in PbTe have lower formation energies in the NW as compared to the bulk and present a trend in migrate to the surface of the NW. For the PbSe we obtain similar results when compare the formation energy for the bulk and NW. However, the Pb vacancy and the antisites are more stable in the core of the NW. The intrinsec defects are shallow defects for the bulk system. For both PbSe and PbTe VPb is a shallow acceptor defect and VSe and VT e are shallow donor defects for the PbSe and PbTe, respectively. Similar electronic properties are observed for the antisites. For the Pb in the anion site we obtain an n-type semiconductor for both PbSe and PbTe, SeP b is a p-type for the PbSe, and T eP b is a n-type for PbTe. Due the quantum con¯nement effects present in the NW (the band gap open), these defects have different electronic properties for the NW as compared to the bulk. Now these defects give rise to electronic levels in the band gap of the PbTe NW and the VT e present a metallic character. For the PbSe NW a p-type and a n-type semiconductor is obtained for the VP b and P bSe, respectively. On the other hand, deep electronic levels are present in the band gap for the VSe and SePb. These results show that due an enhanced in the electronic density of states (DOS) near the Fermi energy, the defective PbSe and PbTe are candidates for efficient TE devices.

Computational studies on the structure and stabilities of magnetic inter-metallic compounds

The purpose of this thesis is to further the understanding of the structural, electronic and magnetic properties of ternary inter-metallic compounds using density functional theory (DFT). Four main problems are addressed. First, a detailed analysis on the ternary Heusler compounds is made. It has long been known that many Heusler compounds ($X_2YZ$; $X$ and $Y$ transition elements, $Z$ main group element) exhibit interesting half-metallic and ferromagnetic properties. In order to understand these, the dependence of magnetic and electronic properties on the structural parameters, the type of exchange-correlation functional and electron-electron correlation was examined. It was found that almost all Co$_2YZ$ Heusler compounds exhibit half-metallic ferromagnetism. It is also observed that $X$ and $Y$ atoms mainly contribute to the total magnetic moment. The magnitude of the total magnetic moment is determined only indirectly by the nature of $Z$ atoms, and shows a trend consistent with Slater-Pauling behaviour in several classes of these compounds. In contrast to experiments, calculations give a non-integer value of the magnetic moment in certain Co$_2$-based Heusler compounds. To explain deviations of the calculated magnetic moment, the LDA+$U$ scheme was applied and it was found that the inclusion of electron-electron correlation beyond the LSDA and GGA is necessary to obtain theoretical description of some Heusler compounds that are half-metallic ferromagnets. The electronic structure and magnetic properties of substitutional series of the quaternary Heusler compound Co$_2$Mn$_{1-x}$Fe$_x$Si were investigated under LDA+$U$. The calculated band structure suggest that the most stable compound in a half-metallic state will occur at an intermediate Fe concentration. These calculated findings are qualitatively confirmed by experimental studies. Second, the effect of antisite disordering in the Co$_2$TiSn system was investigated theoretically as well as experimentally. Preservation of half-metallicity for Co$_2$TiSn was observed with moderate antisite disordering and experimental findings suggest that the Co and Ti antisites disorder amounts to approximately 10~% in the compound. Third, a systematic examination was carried out for band gaps and the nature (covalent or ionic) of bonding in semiconducting 8- and 18-electron or half-metallic ferromagnet half-Heusler compounds. It was found that the most appropriate description of these compounds from the viewpoint of electronic structures is one of a $YZ$ zinc blende lattice stuffed by the $X$ ion. Simple valence rules are obeyed for bonding in the 8- and 18-electron compounds. Fourth, hexagonal analogues of half-Heusler compounds have been searched. Three series of compounds were investigated: GdPdSb, GdAutextit{X} (textit{X} = Mn, Cd and In) and EuNiP. GdPdSb is suggested as a possible half-metallic weak ferromagnet at low temperature. GdAutextit{X} (textit{X} = Mn, Cd and In) and EuNiP were investigated because they exhibit interesting bonding, structural and magnetic properties. The results qualitatively confirm experimental studies on magnetic and structural behaviour in GdPdSb, GdAutextit{X} (textit{X} = Mn, Cd and In) and EuNiP compounds. ~

Development of parallelizable flood inundation models for large scale analysis

Flood disasters are a major cause of fatalities and economic losses, and several studies indicate that global flood risk is currently increasing. In order to reduce and mitigate the impact of river flood disasters, the current trend is to integrate existing structural defences with non structural measures. This calls for a wider application of advanced hydraulic models for flood hazard and risk mapping, engineering design, and flood forecasting systems. Within this framework, two different hydraulic models for large scale analysis of flood events have been developed. The two models, named CA2D and IFD-GGA, adopt an integrated approach based on the diffusive shallow water equations and a simplified finite volume scheme. The models are also designed for massive code parallelization, which has a key importance in reducing run times in large scale and high-detail applications. The two models were first applied to several numerical cases, to test the reliability and accuracy of different model versions. Then, the most effective versions were applied to different real flood events and flood scenarios. The IFD-GGA model showed serious problems that prevented further applications. On the contrary, the CA2D model proved to be fast and robust, and able to reproduce 1D and 2D flow processes in terms of water depth and velocity. In most applications the accuracy of model results was good and adequate to large scale analysis. Where complex flow processes occurred local errors were observed, due to the model approximations. However, they did not compromise the correct representation of overall flow processes. In conclusion, the CA model can be a valuable tool for the simulation of a wide range of flood event types, including lowland and flash flood events.

"Hot spot" in the PROP1 gene responsible for combined pituitary hormone deficiency.

As pituitary function depends on the integrity of the hypothalamic-pituitary axis, any defect in the development and organogenesis of this gland may account for a form of combined pituitary hormone deficiency (CPHD). Although pit-1 was 1 of the first factors identified as a cause of CPHD in mice, many other homeodomain and transcription factors have been characterized as being involved in different developmental stages of pituitary gland development, such as prophet of pit-1 (prop-1), P-Lim, ETS-1, and Brn 4. The aims of the present study were first to screen families and patients suffering from different forms of CPHD for PROP1 gene alterations, and second to define possible hot spots and the frequency of the different gene alterations found. Of 73 subjects (36 families) analyzed, we found 35 patients, belonging to 18 unrelated families, with CPHD caused by a PROP1 gene defect. The PROP1 gene alterations included 3 missense mutations, 2 frameshift mutations, and 1 splice site mutation. The 2 reported frameshift mutations could be caused by any 2-bp GA or AG deletion at either the 148-GGA-GGG-153 or 295-CGA-GAG-AGT-303 position. As any combination of a GA or AG deletion yields the same sequencing data, the frameshift mutations were called 149delGA and 296delGA, respectively. All but 1 mutation were located in the PROP1 gene encoding the homeodomain. Importantly, 3 tandem repeats of the dinucleotides GA at location 296-302 in the PROP1 gene represent a hot spot for CPHD. In conclusion, the PROP1 gene seems to be a major candidate gene for CPHD; however, further studies are needed to evaluate other genetic defects involved in pituitary development.

Human TNF receptor p75/80 gene structure and promoter characterization

Tumor necrosis factor receptor p75/80 ((TNF-R p75/80) is a 75 kDa type 1 transmembrane protein expressed predominately on cells of hematopoietic lineage. TNF-R p75/80 belongs to the TNF receptor superfamily characterized by cysteine-rich extracellular regions composed of three to six disulfide-linked domains. In the present report, we have characterized, for the first time, the complete gene structure for human TNF-R p75/80 which spans approximately 43 kbp. The gene consists of 10 exons (ranging from 34 bp to 2.5 kbp) and 9 introns (343 bp to 19 kbp). Consensus elements for transcription factors involved in T cell development and activation were noted in the 5$\sp\prime$ flanking region including TCF-1, Ikaros, AP-1, CK-2, IL-6RE, ISRE, GAS, NF-$\kappa$B and SP1, as well as an unusually high GC content and CpG frequency that appears characteristic of some TNF-R family members. The unusual (GATA)$\sb{\rm n}$ and (GAA)(GGA) repeats found within intron 1 may prove useful for further genome analysis within the 1p36 chromosomal locus. The human TNF-R p75/80 gene structure will permit further assessment of its involvement in normal hematopoietic cell development and function, autoimmune disease, and non-random translocations in hematopoietic malignancies. The region 1.8 kb 5$\sp\prime$ of the ATG was able to drive luciferase expression when transfected into cell lines expressing TNF-R p75/80. Further characterization of the 5$\sp\prime$-regulatory region will aid in determining factors and signal transduction pathways involved in regulating TNF-R p75/80 expression. ^

Theoretical study of band alignment in nano-porous ZnO interacting with substituted Phthalocyanines

The aim of this work is the theoretical study of the band alignment between the two components of a hybrid organic-inorganic solar-cell. The working organic molecules are metal tetra-sulphonated phthalocyanines (M-Pc) and the inorganic material is nano-porous ZnO growth in the 001 direction. The theoretical calculations are being made using the density functional theory (DFT) using a GGA functional with the SIESTA code, which projects electron wave functions and density onto a real space grid and uses as basis set a linear combination of numerical, finite-range localized atomic orbitals. We also used the DFT+U method included in the code that allows a semi-empirical inclusion of electronic correlations in the description of electronic spectra for systems such as zinc oxide.

Computación evolutiva de bosques de expansión mínimos con restricción de grado y de rol

Encontrar el árbol de expansión mínimo con restricción de grado de un grafo (DCMST por sus siglas en inglés) es un problema NP-complejo ampliamente estudiado. Una de sus aplicaciones más importantes es el dise~no de redes. Aquí nosotros tratamos una nueva variante del problema DCMST, que consiste en encontrar el árbol de expansión mínimo no solo con restricciones de grado, sino también con restricciones de rol (DRCMST), es decir, a~nadimos restricciones para restringir el rol que los nodos tienen en el árbol. Estos roles pueden ser nodo raíz, nodo intermedio o nodo hoja. Por otra parte, no limitamos el número de nodos raíz a uno, por lo que, en general, construiremos bosques de DRCMSTs. El modelado en los problemas de dise~no de redes puede beneficiarse de la posibilidad de generar más de un árbol y determinar el rol de los nodos en la red. Proponemos una nueva representación basada en permutaciones para codificar los bosques de DRCMSTs. En esta nueva representación, una permutación codifica simultáneamente todos los árboles que se construirán. Nosotros simulamos una amplia variedad de problemas DRCMST que optimizamos utilizando ocho algoritmos de computación evolutiva diferentes que codifican los individuos de la población utilizando la representación propuesta. Los algoritmos que utilizamos son: algoritmo de estimación de distribuciones (EDA), algoritmo genético generacional (gGA), algoritmo genético de estado estacionario (ssGA), estrategia evolutiva basada en la matriz de covarianzas (CMAES), evolución diferencial (DE), estrategia evolutiva elitista (ElitistES), estrategia evolutiva no elitista (NonElitistES) y optimización por enjambre de partículas (PSO). Los mejores resultados fueron para el algoritmo de estimación de distribuciones utilizado y ambos tipos de algoritmos genéticos, aunque los algoritmos genéticos fueron significativamente más rápidos.---ABSTRACT---Finding the degree-constrained minimum spanning tree (DCMST) of a graph is a widely studied NP-hard problem. One of its most important applications is network design. Here we deal with a new variant of the DCMST problem, which consists of finding not only the degree- but also the role-constrained minimum spanning tree (DRCMST), i.e., we add constraints to restrict the role of the nodes in the tree to root, intermediate or leaf node. Furthermore, we do not limit the number of root nodes to one, thereby, generally, building a forest of DRCMSTs. The modeling of network design problems can benefit from the possibility of generating more than one tree and determining the role of the nodes in the network. We propose a novel permutation-based representation to encode the forest of DRCMSTs. In this new representation, one permutation simultaneously encodes all the trees to be built. We simulate a wide variety of DRCMST problems which we optimize using eight diferent evolutionary computation algorithms encoding individuals of the population using the proposed representation. The algorithms we use are: estimation of distribution algorithm (EDA), generational genetic algorithm (gGA), steady-state genetic algorithm (ssGA), covariance matrix adaptation evolution strategy (CMAES), diferential evolution (DE), elitist evolution strategy (ElististES), non-elitist evolution strategy (NonElististES) and particle swarm optimization (PSO). The best results are for the estimation of distribution algorithm and both types of genetic algorithms, although the genetic algorithms are significantly faster. iv

A single G-to-C change causes human centromere TGGAA repeats to fold back into hairpins.

Recently, we established that satellite III (TGGAA)n tandem repeats, which occur at the centromeres of human chromosomes, pair with themselves to form an unusual "self-complementary" antiparallel duplex containing (GGA)2 motifs in which two unpaired guanines from opposite strands intercalate between sheared G.A base pairs. In separate studies, we have also established that the GCA triplet does not form bimolecular (GCA)2 motifs but instead promotes the formation of hairpins containing a GCA-turn motif in which the loop contains a single cytidine closed by a sheared G.A pair. Since TGCAA is the most frequent variant of TGGAA found in satellite III repeats, we reasoned that the potential of this variant to form GCA-turn miniloop fold-back structures might be an important factor in modulating the local structure in natural (TGGAA)n repeats. We report here the NMR-derived solution structure of the heptadecadeoxynucleotide (G)TGGAATGCAATGGAA(C) in which a central TGCAA pentamer is flanked by two TGGAA pentamers. This 17-mer forms a rather unusual and very stable hairpin structure containing eight base pairs in the stem, only four of which are Watson-Crick pairs, and a loop consisting of a single cytidine residue. The stem contains a (GGA)2 motif with intercalative 14G/4G stacking between two sheared G.A base pairs; the loop end of the stem consists of a sheared 8G.10A closing pair with the cytosine base of the 9C loop stacked on 8G. The remarkable stability of this unusual hairpin structure (Tm = 63 degrees C) suggests that it probably plays an important role in modulating the folding of satellite III (TGGAA)n repeats at the centromere.