This thesis is devoted to first-principles simulations of bio- and nano-materials,focusing on various soft x-ray spectra, ground-state energies and structures of isolated largemolecules, bulk materials, and small molecules in ambient solutions. K-edge near-edge x-ray absorption fine structure (NEXAFS) spectra, x-ray emission spectra, andresonant inelastic x-ray scattering spectra of DNA duplexes have been studied by means oftheoretical calculations at the density functional theory level. By comparing a sequence of DNAduplexes with increasing length, we have found that the stacking effect of base pairs has verysmall influence on all kinds of spectra, and suggested that the spectra of a general DNA can bewell reproduced by linear combinations of composed base pairs weighted by their ratio. The NEXAFS spectra study has been extended to other realistic systems. We have used cluster modelswith increasing sizes to represent the infinite crystals of nucleobases and nucleosides, infinitegraphene sheet, as well as a short peptide in water solution. And the equivalent core holeapproximation has been extensively adopted, which provides an efficient access to these largesystems. We have investigated the influence of external perturbations on the nitrogen NEXAFSspectra of guanine, cytosine, and guanosine crystals, and clarified early discrepancies betweenexperimental and calculated spectra. The effects of size, stacking, edge, and defects to theabsorption spectra of graphene have been systematically analyzed, and the debate on theinterpretation of the new feature has been resolved. We have illustrated the influence of watersolvent to a blocked alanine molecule by using the snapshots generated from molecular dynamics. Multi-scale computational study on four short peptides in a self-assembled cage is presented. It isshown that the conformation of a peptide within the cage does not corresponds to its lowest-energyconformation in vacuum, due to the Zn-O bond formed between the peptide and the cage, and theconfinement effect of the cage. Special emphasis has been paid on a linear-scaling method, the generalized energy basedfragmentation energy (GEBF) approach. We have derived the GEBF energy equation at the Hartree-Focklevel with the Born approximation of the electrostatic potential. Numerical calculations for amodel system have explained the accuracy of the GEBF equation and provides a starting point forfurther refinements. We have also presented an automatic and efficient implementation of the GEBFapproach which is applicable for general large molecules. / QC 20110404

Le but de ce mémoire est d’expliciter en détail et de voir la portée d'un passage bien précis du traité des Topiques, ouvrage où Aristote tente d'élaborer une méthode qui permettra de raisonner de manière dialectique. Dans le deuxième chapitre du premier livre (I, 2), il énonce de manière succincte trois utilités que le traité en question peut procurer à celui qui possède et maîtrise adéquatement cette méthode. En premier lieu, la dialectique servirait de gymnastique intellectuelle pour former l'esprit et lui donner plus de souplesse dans ses raisonnements. Dans un second temps, elle serait utile dans les rencontres de tous les jours avec autrui parce qu’elle permettrait de discuter et d'argumenter sur un sujet donné avec le premier venu. Enfin, il semble également que la dialectique soit utile pour les «connaissances de caractère philosophique», en ce sens qu'elle permettrait de développer les apories et ultimement, d'établir les principes ou les notions premières de chaque science. Dans ce travail, je me propose donc d’examiner chacune de ces prétendues utilités afin de voir comment, et dans quelle mesure, nous pouvons réellement affirmer que la dialectique s’avère profitable pour chacun des services énumérés en Topiques I, 2. / The purpose of this dissertation is to explain in detail the importance of a very precise passage of the Topics, treatise where Aristotle tries to find a method which will allow to reason in a dialectical way. In the second chapter of the first book (I, 2), he expresses in a brief way three utilities that the treatise in question can provide to those who own and control this method properly. First of all, the dialectic would serve as a mental gymnastic to train the mind and give it more flexibility in its reasoning. Secondly, it would be useful in the everyday encounters with others, because it would allow to discuss and argue on any given subject with the first person we could meet. Finally, it also seems that the dialectic would be useful for the "philosophical knowledge ", in the sense that it would go through the puzzles and ultimately, would establish the first principles of each science. In this work, I thus suggest examining each of its claimed utilities to see how, and in which measures, we can really assert that the dialectic turns out profitable for each of the services enumerated in Topics I, 2.

The (001) surface of silicon has been the topic of our study in this thesis. The clean surface, an-adatom or submonolayer adsorption on the surface, the monolayer adsorption and its stability conditions as well as growth simulation on the surface were investigated using the state of the art techniques. We have used ab initio density functional calculations based on norm-conserving pseudopotentials to investigate the Mg adsorption on the Si(001) surface for 1/4, 1/2 and 1 monolayer (ML) coverages. For both 1/4 and 1/2 ML coverages it has been found that the most favorable site for the Mg adsorption is the cave site between two dimer rows consistent with recent experiments. For the 1 ML coverage (2 Mg atoms per 2X1 unit cell) we have found that the most preferable configuration is when both Mg atoms on 2X1 reconstruction occupy the two shallow sites. We have found that the minimum energy configurations for 1/4 ML coverage is a 2X2 reconstruction while for the 1/2 and 1 ML coverages they are 2X1. Same method was also used to investigate the surface stress and energetics of the clean-, Sb-adsorbed-, and Sb-interdiffused-Si(001) surface. It is found that interdiffusion of Sb into deeper layers of Si(001) leads to a more isotropic surface stress but corresponds to a higher total energy configuration. As a result of competition between stress relief and energy gain, the surface with all the Sb atoms adsorbed on top of Si(001) surface layer is predicted to have a less ordered geometry and roughness in z-direction. We have repeated the similar calculations on the Ge(001) surface for comparison. Finally using empirical molecular dynamics method, we have investigated the crystalline growth of silicon on Si(001) as a function of substrate temperature and incident particle energy. Our results show that the increase of substrate temperature enhances the crystallinity in the film grown on the Si(001) surface, on the other hand, the crystalline growth can be enhanced at low temperature by using higher incidence energy.

Ferritic superalloys strengthened by coherent ordered NiAl B2-type precipitates are promising candidates for ultra-supercritical steam-turbine applications, due to their superior resistance to creep, coarsening, oxidation, and steam corrosion as compared to Cr ferritic steels at high temperatures. Combined computational and experimental tools have been employed to investigate the interrelationships among the composition, microstructure, and mechanical behavior, and provide insight into deformation micromechanisms at elevated temperatures. Self and impurity diffusivities in a body-centered-cubic (bcc) iron are calculated using first-principles methods. Calculated self and impurity diffusivities compare favorably with experimental measurements in both ferromagnetic and paramagnetic states of bcc Fe. The calculated impurity diffusivities of W and Mo are larger than the self diffusivity of Fe, mainly owing to the lower activation energies. The microstructural attributes of NiAl-type B2 precipitates are investigated in several designed ferritic superalloys. Ultra-small-angle X-ray scattering in conjunction with transmission electron microscopy is employed to quantify the average size, size distribution, inter-particle spacing, and volume fraction of the primary precipitates. It is observed that as the Al amount increases from 4 to 10 mass%, there is a decrease in the average inter-particle spacing and average particle diameter. An alloy with 6.5 weight percent Al exhibits the optimal creep resistance and an associated maximum Orowan stress at 973 K. The dislocations-particle interaction mode during the secondary creep regime is identified as a combination of Orowan looping and dislocation climb. In-situ neutron diffraction experiments during tensile and creep deformations reveal the intergranular and interphase load-sharing mechanisms during plastic deformation at elevated temperatures. The change of deformation mechanisms from dislocation slip below 773 K to power-law creep above 873 K is well captured by the evolution of the different lattice strains. High-temperature deformation above 873 K is possibly assisted by the relaxation processes, e.g., grain-boundary sliding and/or diffusional flow along grain boundaries and matrixparticle interfaces. The evolution of lattice strains during high-temperature deformation is further verified by crystal-plasticity finite-element simulations. The significant findings in the present work provide the crucial baseline information for further alloy optimization and improvement in high-temperature creep resistance of ferritic superalloys.

In the first part of this work, the influence of hydrogen on the structural and magnetic properties of Fe/V(001) superlattices was studied. The local structure of the vanadium-hydride layers was determined by extended x-ray absorption fine structure (EXAFS) measurements. The magnetic ordering in a weakly coupled Fe/V(001) superlattice was investigated using the magneto-optical Kerr effect (MOKE). The interlayer exchange coupling is weakened upon alloying with hydrogen and a phase with short-range magnetic order was observed. The second part is concerned with first-principles calculations of magnetic materials, with a focus on magnetic recording applications. The uniaxial magnetic anisotropy energy (MAE) of Fe, Co, and Ni was calculated for tetragonal and trigonal structures. Based on an analysis of the electronic states of tetragonal Fe and Co at the center of the Brillouin zone, tetragonal Fe-Co alloys were proposed as a material that combines a large uniaxial MAE with a large saturation magnetization. This was confirmed by experimental studies on (Fe,Co)/Pt superlattices. The large uniaxial MAE of L10 FePt is caused by the large spin-orbit interaction on the Pt sites in connection with a strong hybridization between Fe and Pt. Furthermore, it was shown that the uniaxial MAE can be increased by alloying the Fe sublattice with Mn. The combination of the high-moment rare-earth (RE) metals with the high-TC 3d transition metals in RE/Cr/Fe multilayers (RE = Gd, Tb, Dy) gives rise to a strong ferromagnetic effective exchange interaction between the Fe layers and the RE layer. The MAE of hcp Gd was found to have two principal contributions, namely the dipole interaction of the large localized 4f spins and the band electron magnetic anisotropy due to the spin-orbit interaction. The peculiar temperature dependence of the easy axis of magnetization was reproduced on a qualitative level.

Molecular electronics is envisioned as a possible next step in device miniaturization. It is usually taken to mean the design and manufacturing of electronic devices and applications where organic molecules work as the fundamental functioning unit. It involves the measurement and manipulation of electronic response and transport in molecules attached to conducting leads. Organic molecules have the advantages over conventional solid state electronics of inherent small sizes, endless chemical diversity and ambient temperature low cost manufacturing. In this thesis we investigate the switching and conducting properties of photoswitching dithienylethene derivatives. Such molecules change their conformation in solution when acted upon by light. Photochromic molecules are attractive candidates for use in molecular electronics because of the switching between different states with different conducting properties. The possibility of optically controlling the conductance of the molecule attached to conducting leads may lead to new device implementations. The switching reaction is investigated with potential energy calculations for different values of the reaction coordinate between the closed and the open isomer. The electronic and atomic structure calculations are performed with Density Functional Theory (DFT). The potential energy barrier separating the open and closed isomer is investigated, as well as the nature of the excited states involved in the switching. The conducting properties of the molecule inserted between gold, silver and nickel leads is calculated within the Non Equilibrium Green Function theory (NEGF). The molecule is found to be a good conductor in both conformations, with the low-bias current for the closed one being about 20 times larger than that of the open in the case of gold contacts, and over 30 times larger in the case of silver contacts. For the Ni leads the current for the closed isomer is almost 40 times larger than that of the open. Importantly, the current-voltage characteristics away from the linear response is largely determined by molecular orbital re-hybridization in an electric field, in close analogy to what happens for Mn12 molecules. However in the case of dithienylethene attached to Au and Ag such a mechanism is effective also in conditions of strong electronic coupling to the electrodes. In reality these molecules are in constant motion, and the dynamical properties has to be considered. In this thesis such a line of work is initiated. In order to facilitate efficient and stable dynamical simulations of molecular systems the extended Lagrangian formulation of Born-Oppenheimer molecular dynamics have been implemented in two different codes. The extended Lagrangian framework enables the geometric integration of both the nuclear and electronic degrees of freedom. This provides highly efficient simulations that are stable and energy conserving even under incomplete and approximate self-consistent field (SCF) convergence. In the density functional theory code FreeON, different symplectic integrators up to the 6th order have been adapted and optimized. It is shown how the accuracy can be significantly improved compared to a conventional Verlet integration at the same level of computational cost, in particular for the case of very high accuracy requirements. Geometric integration schemes, including a weak dissipation to remove numerical noise, are developed and implemented in the self-consistent tight-binding code LATTE. We find that the inclusion of dissipation in the symplectic integration methods gives an efficient damping of numerical noise or perturbations that otherwise may accumulate from finite arithmetics in a perfect reversible dynamics. The modification of the integration breakes symplecticity and introduces a global energy drift. The systematic driftin energy and the broken symplecticity can be kept arbitrarily small without significant perturbations of the molecular trajectories. / QC 20101202

Recent carbon allotropes such as carbon nanotubes (CNTs), fullerenes (C60s) and graphene have attracted great interests in both science and engineering due to their unique properties such as excellent electrical and mechanical properties as well as its vast surface area, and have led to many commercial applications. Especially, CNTs have been considered to be one of the promising candidates in the Li ion battery system because of its outstanding properties. However, the experimental results in the pristine CNT system have shown just slight improvement than original graphitic carbon material, which has been attributed to the weak adsorption of Li on CNTs. In this study, we investigated two types of CNT-C60 hybrid system consisting of CNTs and C60s to improve Li adsorption capabilities and predict its performance through quantum mechanical (QM) computations. First, we investigated adsorption energy of lithium (Li) on dilute CNT-C60 hybrid and CNT-C60 nanobud system as well as various electronic properties such as band structure, density of states (DOS), molecular orbital and charge distribution. Then, we expanded our interest to the more realistic condensed structure of CNT-C60 hybrid and nanobud system to examine actual electrochemical characteristics. The study of the condensed structure has been expanded to the very unique CNT-C60 nano-network system and examined mechanical strength as well as electronic properties. Finally, Li adsorption on other carbon allotropes system such as graphene-C60 hybrid and graphene-C60 bud system was investigated in order to provide fundamental understanding of electronic interaction between carbon allotrope and effect of Li adsorption.

Orientador: Prof. Dr. Caetano Rodrigues Miranda / Tese (doutorado) - Universidade Federal do ABC, Programa de Pós-Graduação em Nanociências e Materiais Avançados, 2015. / A presente Tese baseia-se nas aplicacoes das propriedades de Ressonancia Magnetica Nuclear (RMN) de Liquidos e de Estado Solido para entender alguns processos que ocorrem na dinamica de sistemas de interesse para a Industria do Petroleo via simulacoes computacionais moleculares. Portanto, na primeira parte, utilizou-se metodos de primeiros principios para caracterizar o processo de degradacao da pasta cimenticia e, a adsorcao de hidrocarbonetos em superficies minerais. Dessa forma, foi possivel avaliar sistemas de diferentes dimensoes desde de estruturas 3D ate 0D a partir de simulacoes baseadas na Teoria do Funcional da Densidade, com e sem van der Waals (vdW) para calcular os parametros espectrais de RMN. Por meio de simulacoes de RMN de Estado Solido, investigou-se o processo de degradacao da pasta cimenticia, conhecido como ataque tardio da etringita que ocorre por meio de reacoes do gesso hidratado (CaSO4.2H2O) com o aluminato tricalcico (Ca3Al2O6) formando o composto chamado etringita (Ca6Al2(OH)12.(SO4)3.26H2O). Os resultados para as tres estruturas bulk ou 3D, a partir dos nucleos de 43Ca, 33S, 27Al e 17O, mostraram, em particular, que os nucleos de calcio garantem indicacoes suficientes da estrutura que esta sendo avaliada, principalmente para o caso da etringita. Isso mostra que a coordenacao altera os espectros, uma vez que afeta o ambiente quimico local. Os sistemas de 2D representados pelas superficies de calcita (CaCO3 ) e silica (SiO2 ¿¿-quartzo (0001) hidrofobica e hidrofilica) foram igualmente abordados via simulacoes computacionais de RMN do Estado Solido. A calcita e a silica sao os principais constituintes das rochas sedimentares nos reservatorios de petroleo e uma caracterizacao detalhada da interacao dessas superficies minerais com hidrocarbonetos representativos do oleo e bastante oportuna. Para a primeira superficie, os espectros dos sitios de calcio garantiram informacoes a respeito local e o tipo de adsorbato. Similarmente para a segunda, as assinaturas dos nucleos de 17O permitiram observar a presenca dos adsorbatos na superficie bem como o tipo de superficie analisada. A segunda parte do estudo abrange as estruturas 0D, em que utilizou-se nanoparticulas (NPs) de SiO2 funcionalizadas com etileno glicol (EG) e acido sulfonico (AS) em solucao para obtencao dos tempos de relaxacao de RMN transversal (T2). A partir de simulacoes de Dinamica Molecular Classica pode-se observar que os sinais de T2 das moleculas de agua para o sistema bulk aproximam-se dos valores obtidos experimentalmente, validando o metodo. Com a adicao das NPs, os sinais de T2 sao devido a forte adsorcao da superficie hidrofilica das NPs de SiO2 com as moleculas de agua. Assim, podemos sugerir que a tecnica de RMN simulada pode ser uma ferramenta poderosa na analise de reservatorios, uma vez que perturbacoes no sistema podemser, efetivamente, detectadas. Alem de exercer papel importante na Recuperacao Avancada de Petroleo. / In this Thesis we explore computational applications of Nuclear Magnetic Resonance (NMR) properties to understand some dynamic processes that occur in the oil reservoir systems. Therefore, we used first principles methods to characterize the delayed ettringite attack (DEA) and the adsorption of hydrocarbon molecules in the mineral surfaces. In this way, it was possible to evaluate different system dimensions since 3D to 0D nanostructures by computational simulations based on Density Functional Theory, with or without van der Waals (vdW) dispersion corrections, to achieve the Solid State Nuclear Magnetic Resonance (SSNMR) parameters. Through SSNMR simulations, cement phases: gypsum dihydrate (CaSO4.2H2O), tricalcium aluminate (Ca3Al2O6) and ettringite (Ca6Al2(OH)12.(SO4)3.26H2O), which are directly involved on DEA process were investigated. The results for the three bulk or 3D nanostructures from 43Ca, 33S, 27Al and 17O nuclei, shown in particular that calcium nuclei ensure sufficient guidance of the structure which is being evaluated, especially in the case of ettringite. This study shows that the coordination change the spectra, since it affects local chemical environment. The 2D systems represented by calcite (CaCO3 ) and silica (SiO2 ¿¿-quartzo (0001) hidrofobica e hidrofilica) surfaces were analyzed via ab initio SSNMR. Since calcite and silica is a major constituent of sedimentary rocks in oil reservoir, a more detailed characterization of the interaction between hydrocarbon molecules and mineral surfaces is highly desirable. Our results show a chemical shift differentiation for atoms located on different sites (bulk and surface) for calcite and silicate systems. Interestingly, the presence of hydrocarbon molecules also modifies the chemical shift of adsorbed the Ca and O sites for both surfaces, respectively. The second part concerns the 0D nanostructures, which is represented by SiO2 nanoparticles functionalized with ethylene glycol (EG) and sulfonic acid (SA). These NPs were immersed on water solution to obtain the relaxation time distribution, especially T2, by Molecular Dynamics simulations. It was found that the correlation function of water when the SiO2 is present takes longer because the water molecules can not rotate easily because the hydrophilic silica surface has a strong adsorption property. Therefore, T2 relaxation time is decreased compared to the bulk water and this is probably related to the fact that there is a hydrophilic silica surface in the system. Thus, we suggest that the simulated NMR technique can be a powerful tool in the analysis containers, since disturbances in the system can be effectively detected. In addition to play an important role in Enhanced Oil Recovery (EOR).

Matériaux multiferroïques ont suscité beaucoup d'intérêt au cours des dernières années. Notre étude est consacrée à un système prototype: manganite d'yttrium. En particulier, nous nous concentrons sur les propriétés ferroélectriques sous forme massive monocristalline et sous forme de couches minces. Manganite d'yttrium appartient à la classe des composés ABO3. La plupart des études théoriques de la ferroélectricité à ce jour se sont concentrées sur perovskite cubique ABO3. Manganite d'yttrium est hexagonale et est un ferroélectrique impropre. Nous nous sommes intéressés à étudier théoriquement et expérimentalement comment ces deux fonctions se comportent sous forme de film mince. / Multiferroic materials have attracted much interest during the recent years. Our study is devoted to a prototypic system: yttrium manganite. In particular, we focus on the ferroelectric properties in bulk and in thin film form. Yttrium manganite belongs to the class of ABO3 compounds. Most theoretical studies of ferroelectricity to date were concentrated on cubic perovskite ABO3. Yttrium manganite is hexagonal and is an improper ferroelectric. We were interested to study theoretically and experimentally how these two features behave in thin film form.

Made available in DSpace on 2016-08-18T18:19:26Z (GMT). No. of bitstreams: 1 Nilton Ferreira Frazao.pdf: 1298809 bytes, checksum: 5aca0b703a735a7fb605b7bdee658bdd (MD5) Previous issue date: 2009-03-30 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Recently, the existence of nanoribbon of Boron Nitride with finite size was discovered experimentally, in porous nanoesferas of BN (100-400 nm of diameter), synthesized for the reaction of B2O3 with carbon spheres contend nanoporos filled for Nitrogen to a temperature of 17500C. However a theoretical inquiry of the properties of this nanometerial did not exist. Then, in this present work, we carry through simulation of molecular mechanics using field of universal force (forcefild) to optimize the structure of some of these nanoribbon of Boron Nitride, with objective to find a conformation more steady, that is, of lesser energy for these nanostructures. Later, we investigate the electronic properties of these nanoribbon of Boron Nitride (NRBN) in the finite form (not-periodic) of two types: nanoribbon of Boron Nitride of the type to armchair (a-NRBN) and nanoribbon of Boron Nitride of the type zigzag (z-NRBN). The study of these properties they had been carried through of calculations of first principles based in the Density Functional Theory, with the local density approximation (LDA). Through our calculations, we observe that all the nanoribbon are metallic when we made the analysis of the density of states (DOS). Result not waited, but surprising, therefore of literature we know that material nanostructuralized of Boron Nitride they are always semiconductors. However, our calculations had shown that as much a-NRBN as z-NRBN had presented a conducting electronic character. The simulations had been carried through for many cases of nanoribbon of width (L) and length (C), forming a pair of indices (L, C), with the objective to facilitate the identification of these nanostructures. However we will present the results of but twelve of these, being: (1,3), (1,6), (1,9), (2,3), (2,6) e (2,9) in such a way of the types a-NRBN and z-NRBN. / Recentemente, foi descoberto experimentalmente a existência de Nanofitas de Nitreto de Boro (BN) de tamanho finito, em nanoesferas porosas de BN (100-400 nm de diâmetro), sintetizada pela reação de B2O3 com esferas de carbono contendo nanoporos preenchidos por Nitrogênio a uma temperatura de 17500C. No entanto não existia uma investigação teórica das propriedades desses nanocompósitos. Então, neste presente trabalho, realizamos simulações de mecânica molecular usando campo de força universal (forcefild) para otimizar a estrutura de algumas destas nanofitas de Nitreto de Boro, com objetivo de encontrar uma conformação mais estável, ou seja, de menor energia para essas nanoestruturas. Depois, investigamos as propriedades eletrônicas dessas nanofitas de Nitreto de Boro (NRBN) na forma finita (não-periódica) de dois tipos: nanofitas de Nitreto de Boro do tipo armchair (a-NRBN) e nanofitas de Nitreto de Boro do tipo zigzag (z-NRBN). O estudo destas propriedades foram realizados através de cálculos de primeiros princípios baseados na Teoria do Funcional da Densidade, com a aproximação da densidade local (LDA). Através de nossos cálculos, observamos que todas as nanofitas são metálicas quando fizemos a análise da densidade de estados eletrônicos (DOS). Resultado não esperado, mas surpreendente, pois da literatura sabemos que materiais nanoestruturados de Nitreto de Boro são sempre semicondutores. No entanto, nossos cálculos mostraram que tanto as a- NRBN como as z-NRBN apresentaram um caráter eletrônico condutor. As simulações foram realizadas para muitos casos de nanofitas de largura (L) e comprimento (C), formando um par de índices (L, C), com o objetivo de facilitar a identificação dessas nanoestruturas. No entanto apresentaremos os resultados de apenas doze dessas, sendo: (1,3), (1,6), (1,9), (2,3), (2,6) e (2,9) tanto dos tipos a-NRBN e z-NRBN.