Orientador: Alex Antonelli / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Física Gleb Wataghin / Made available in DSpace on 2018-08-29T05:01:21Z (GMT). No. of bitstreams: 1 CajahuaringaMacollunco_OscarSamuel_D.pdf: 15985103 bytes, checksum: f54d17d6335170c62196c9e329f257d9 (MD5) Previous issue date: 2015 / Resumo: Apesar de serem substâncias muito diferentes, silício e gálio, na fase líquida, compartilham muitas anomalias nas suas propriedades termodinâmicas. Evidências teóricas e experimentais sugerem que esses líquidos podem sofrer a chamada transição de fase líquido-líquido (LLPT). Especula-se que este tipo de transição é acompanhada por uma transição dinâmica entre um líquido frágil e um líquido forte, com base nas hipóteses de que o surgimento de um "dip" na função auto-intermediária de espalhamento logo após o regime balístico e o aparecimento do excesso de modos vibracionais em baixas frequências após a LLPT estariam relacionados com o comportamento de líquidos fortes. Foi realizado um estudo da dinâmica desses sistemas através das funções de correlação nas vizinhanças da LLPT usando simulações clássicas. Observamos apenas no caso do silício o aparecimento do "dip" na função auto-intermediária de espalhamento. A densidade de estados vibracionais reduzida de ambos os líquidos apresenta picos em baixas frequências, sugerindo que ambos os líquidos seriam fortes. Desta forma, nos dois casos estudados, as duas hipóteses não são conclusivas. Visando um melhor entendimento, determinamos a viscosidade de cisalhamento de ambos os líquidos em um amplo intervalo de temperatura. A apresentação desses resultados no chamado gráfico de Angell, indica que, em ambos os casos, a LLPT é acompanhada de uma transição de um líquido frágil para um líquido menos frágil, o que não dá suporte às especulações de uma transição frágil-forte. Além de investigar a LLPT em gálio "bulk", foi também estudado o gálio líquido confinado em nanofendas, ou seja, um sistema quase-bidimensional. Foi observada a transição de fase de primeira ordem entre um líquido isotrópico e um líquido ordenado. Por meio de uma série de análises estruturais, tanto de ordem translacional quanto orientacional, conseguimos identificar o líquido ordenado como a fase hexática, que é prevista ocorrer em sistemas bidimensionais segundo a teoria de Kosterlitz-Thouless-Halperin-Nelson-Young (KTHNY). Como a LLPT em gálio bulk foi identificada em simulações de dinâmica clássica, realizamos um estudo visando obter evidência da LLPT em simulações de primeiros princípios, que são em princípio mais realísticas. Utilizando o chamado método-Z, que permite estimar a temperatura de fusão, determinamos que o regime super-resfriado do gálio líquido descrito por cálculos de primeiros princípios ocorre em temperaturas abaixo de 400 K. Partindo de um líquido em equilíbrio em 500 K, realizamos simulações a pressão constante igual a zero em que o líquido foi resfriado para 260 K em um intervalo de 145 ps. Não foi observada uma mudança abrupta no volume durante o resfriamento. A fim de melhorar a amostragem em nossas simulações de primeiros princípios, realizamos um estudo de dinâmica molecular a volume constante com troca de réplicas. Foram usadas um total de 10 réplicas entre 400 K e 260 K, em simulações com a duração de 100 ps. Neste caso, a pressão decresceu monotonicamente com a temperatura, o que é característico de líquidos simples que não sofrem LLPT. Cabe ressaltar que nas simulações clássicas que identificaram a LLPT em gálio, a taxa de resfriamento foi muito mais lenta, da ordem de nano-segundos, que seria inexequível para simulações de primeiros princípios / Abstract: Despite of being very different substances, silicon and gallium, in their liquid phase, share several anomalous thermodynamic properties. Theoretical and experimental evidence suggest that these liquids can undergo the so-called liquid-liquid phase transition (LLPT). There has been speculated that this transition is accompanied by a dynamic transition form a fragile liquid to a strong liquid, based on the hypothesis that the development of a dip in the self-intermediate scattering function, just after the ballistic regime, and the appearance of excess low frequency vibrational modes just after the LLPT would be related to the behavior of strong liquids. It was performed a study of the dynamics of these systems through the correlation functions in the vicinity of the LLPT using classical simulations. We observed the development of a dip in the self-intermediate scattering function only in the case o silicon. The reduced density of vibrational states of both liquids exhibits peaks in low frequencies, suggesting both liquids to be strong. Therefore, for the two cases we studied, the two hypotheses are not conclusive. In order to achieve a better understanding, we determined the shear viscosity of both liquids for a wide range of temperatures. By plotting the data in the so-called Angell plot one can see that, in both cases, the LLPT is accompanied by a transition of a fragile liquid to a less fragile liquid, which does not give support to the speculations of a fragile-to-strong transition. Aside from investigating the LLPT in bulk gallium, it was also studied liquid gallium confined in nanoslits. i.e., a quasi two-dimensional system. It was observed a first-order transition between an isotropic liquid and an ordered liquid. Through a series of structural analyses, both translational and orientational, we were able to identify the ordered liquid as the hexatic phase, which is predict to occur in two-dimensional systems according to the Kosterlitz-Thouless-Halperin-Nelson-Young (KTHNY) theory. Since the LLPT in gallium has been found in classical molecular dynamics simulations, we performed a study aimed to obtain evidence of the LLPT in first-principles simulations, which are, in principle, more realistic. Using the so-called Z-method, which allows one to estimate the melting temperature, we determined the supercooled regime of liquid gallium, described by first-principles, to occur below 400 K. Starting from an equilibrated liquid at 500 K, we performed simulations at zero pressure in which the liquid was cooled down to 260 K in an interval of 145 ps. No abrupt change in the volume was observed as the liquid was cooled. In order to improve sampling in our first-principles simulations, we performed a study using constant volume molecular dynamics with replica exchange. Ten replicas were used between 400 K and 260 K, in simulations 100 ps long. In this case, pressure decreased monotonically with temperature, which is the behavior of simple liquids, which do not exhibit the LLPT. It should be emphasized that in the classical simulations that identified the LLPT in gallium, the cooling rates were much slower, of the order of nanoseconds, which would be unfeasible for first-principles simulations / Doutorado / Física / Doutor em Ciências / 1000949 / CAPES

As proteínas são moléculas que desempenham funções essenciais para a vida. Para entender a função de uma proteína é preciso conhecer sua estrutura tridimensional. No entanto, encontrar a estrutura da proteína pode ser um processo caro e demorado, exigindo profissionais altamente qualificados. Neste sentido, métodos computacionais têm sido investigados buscando predizer a estrutura de uma proteína a partir de uma sequência de aminoácidos. Em geral, tais métodos computacionais utilizam conhecimentos de estruturas de proteínas já determinadas por métodos experimentais, para tentar predizer proteínas com estrutura desconhecida. Embora métodos computacionais como, por exemplo, o Rosetta, I-Tasser e Quark tenham apresentado sucesso em suas predições, são apenas capazes de produzir estruturas significativamente semelhantes às já determinadas experimentalmente. Com isso, por utilizarem conhecimento a priori de outras estruturas pode haver certa tendência em suas predições. Buscando elaborar um algoritmo eficiente para Predição de Estruturas de Proteínas livre de tendência foi desenvolvido um Algoritmo de Estimação de Distribuição (EDA) específico para esse problema, com modelagens full-atom e algoritmos ab initio. O fato do algoritmo proposto ser ab initio é mais interessante para aplicação envolvendo proteínas com baixa similaridade, com relação às estruturas já conhecidas. Três tipos de modelos probabilísticos foram desenvolvidos: univariado, bivariado e hierárquico. O univariado trata o aspecto de multi-modalidade de uma variável, o bivariado trata os ângulos diedrais (Φ Ψ) de um mesmo aminoácido como variáveis correlacionadas. O hierárquico divide o problema em subproblemas e tenta tratá-los separadamente. Os resultados desta pesquisa mostraram que é possível obter melhores resultados quando considerado a relação bivariada (Φ Ψ). O hierárquico também mostrou melhorias nos resultados obtidos, principalmente para proteínas com mais de 50 resíduos. Além disso, foi realiza uma comparação com algumas heurísticas da literatura, como: Busca Aleatória, Monte Carlo, Algoritmo Genético e Evolução Diferencial. Os resultados mostraram que mesmo uma metaheurística pouco eficiente, como a Busca Aleatória, pode encontrar a solução correta, porém utilizando muito conhecimento a priori (predição que pode ser tendenciosa). Por outro lado, o algoritmo proposto neste trabalho foi capaz de obter a estrutura da proteína esperada sem utilizar conhecimento a priori, caracterizando uma predição puramente ab initio (livre de tendência). / Proteins are molecules that perform critical roles in the living organism and they are essential for their lifes. To understand the function of a protein, its 3D structure should be known. However, to find the protein structure is an expensive and a time-consuming task, requiring highly skilled professionals. Aiming to overcome such a limitation, computational methods for Protein Structure Prediction (PSP) have been investigated, in order to predict the protein structure from its amino acid sequence. Most of computational methods require knowledge from already determined structures from experimental methods in order to predict an unknown protein. Although computational methods such as Rosetta, I-Tasser and Quark have showed success in their predictions, they are only capable to predict quite similar structures to already known proteins obtained experimentally. The use of such a prior knowledge in the predictions of Rosetta, I-Tasser and Quark may lead to biased predictions. In order to develop a computational algorithm for PSP free of bias, we developed an Estimation of Distribution Algorithm applied to PSP with full-atom and ab initio model. A computational algorithm with ab initio model is mainly interesting when dealing with proteins with low similarity with the known proteins. In this work, we developed an Estimation of Distribution Algorithm with three probabilistic models: univariate, bivariate and hierarchical. The univariate deals with multi-modality of the distribution of the data of a single variable. The bivariate treats the dihedral angles (Proteins are molecules that perform critical roles in the living organism and they are essential for their lifes. To understand the function of a protein, its 3D structure should be known. However, to find the protein structure is an expensive and a time-consuming task, requiring highly skilled professionals. Aiming to overcome such a limitation, computational methods for Protein Structure Prediction (PSP) have been investigated, in order to predict the protein structure from its amino acid sequence. Most of computational methods require knowledge from already determined structures from experimental methods in order to predict an unknown protein. Although computational methods such as Rosetta, I-Tasser and Quark have showed success in their predictions, they are only capable to predict quite similar structures to already known proteins obtained experimentally. The use of such a prior knowledge in the predictions of Rosetta, I-Tasser and Quark may lead to biased predictions. In order to develop a computational algorithm for PSP free of bias, we developed an Estimation of Distribution Algorithm applied to PSP with full-atom and ab initio model. A computational algorithm with ab initio model is mainly interesting when dealing with proteins with low similarity with the known proteins. In this work, we developed an Estimation of Distribution Algorithm with three probabilistic models: univariate, bivariate and hierarchical. The univariate deals with multi-modality of the distribution of the data of a single variable. The bivariate treats the dihedral angles (Φ Ψ) within an amino acid as correlated variables. The hierarchical approach splits the original problem into subproblems and attempts to treat these problems in a separated manner. The experiments show that, indeed, it is possible to achieve better results when modeling the correlation (Φ Ψ). The hierarchical model also showed that is possible to improve the quality of results, mainly for proteins above 50 residues. Besides, we compared our proposed techniques among other metaheuristics from literatures such as: Random Walk, Monte Carlo, Genetic Algorithm and Differential Evolution. The results show that even a less efficient metaheuristic such as Random Walk managed to find the correct structure, however using many prior knowledge (prediction that may be biased). On the other hand, our proposed EDA for PSP was able to find the correct structure with no prior knowledge at all, so we can call this prediction as pure ab initio (biased-free).

This diploma thesis is focused on a theoretical study of the phase stability of solid solutions in selected aluminium and silver alloys. The ab initio calculations were performed using projected augmented waves method and the thermal dependencies of thermodynamic quantities were acquired using phonon calculations. The main focus of this work is the of aluminium-germanium alloy, while the other examined alloys (Al-Pb, Ag-Ge and Ag-Pb) serve the purpose of comparison of the solid solubility prediction and its reliability in systems with different composition. The temperatures, at which the solid solutions become stable, were evaluated using the energy difference between possible states and this evaluation was carried out for different contributions to the total energy. Also the electronic and phonon densities of states were calculated for all pure elements and solid solutions. The temperatures of solubility were compared to the experimental ones provided by the CALPHAD method and the individual contributions to the total energy were determined and depicted. The results obtained in this work tend to underestimate temperatures of solubility of individual solid solutions by hundreds of Kelvin.

This Master‘s thesis is focused on theoretical study of twinning in magnetic shape memory alloys based on Ni2MnGa using ab initio calculations of electronic structure within the projector augmented wave method. In particular, the effect of increasing concentration of manganese at the expense of gallium was studied on total energy and stress profiles along different deformation paths in the (10-1)[101] shear system of non-modulated martensite. Further, this work deals with the effect of the concentration of manganese on the energy of planar fault caused by presence of partial dislocation due to motion of twin boundary. The results show that the shear modulus in studied shear system increases with the increasing concentration of manganese as well as energy barrier and deformation characteristics along shear deformation paths increases, which makes the shear more difficult in Mn-rich alloys. Increasing concentration of manganese also leads to rising the planar fault energy. All these effects can be responsible for lower mobility of twin boundaries in alloys with higher concentration of manganese.

This Master’s thesis is focused on theoretical study of the high entropy alloy CoCrNi using ab initio calculations. The focus was on the effect of short range order on the relative stability of FCC and HCP structures and the value of stacking fault energy.The results show increase of stability in both types of structures wtih decreasing number of Cr-Cr nearest neighbours. The effect of the number of Cr-Cr nearest neighbours on the stacking fault energy previously shown in literature was not observed. However the strong dependency was found on the change of short range order caused by the shift of (1 1 1) planes after the transformation from the FCC to HCP structure. The effect of interstitial atoms C a N was also studied. Both these interstitials stabilise FCC structure and thus cause the increase of stacking fault energy. Both interstitials prefer octahedral positions with higher amount of Cr in their nearest neighbour shell.

Pomocí molekulového modelování je možné předpovídat chování nových látek a napomáhá při jinak obtížné interpretaci experimentálních dat. Cílem práce byla predikce vybraných vlastností polymeračních katalyzátorů na bázi karbenů, predikce jejich struktur a spektrálních charakteristik a studie mechanismu polymerace za otevření kruhu laktidu. K ověření chování karbenů a jejich prekurzorů ve formě chloridů byly studovány vybrané charakteristiky molekuly. Byl proveden výpočet vybraných molekulových orbitalů a elektrostatických map. Následně pomocí počítačových programů byly získány teoretické vazebné délky a úhly vybraných imidazolových a imidazolinových sloučenin, karbenů a jejich možných produktů hydrolýzy. Data strukturně podobných, již charakterizovaných sloučenin, byla získána z CCDC (Cambridge Crystallographic Data Centre) a následně byla konfrontována s vypočítanými daty. Byla změřena infračervená a Ramanova spektra imidazolové soli a infračervené spektrum příslušného karbenu. Tato spektra byla konfrontována s napredikovanými. Pro lepší interpretaci spekter byla spočítána spektra možných produktů hydrolýzy. Následně byl studován mechanismus polymerace za otevření kruhu laktidu. Na základě spočítaných energií stacionárních bodů byl navržen nový mechanismus polymerace.

This work deals with study of stability of solid crystals under isotropic loading. Ab initio methods were used for this purpose. Crystals of four fcc metals (Al, Cu, Ir, Au) and diamond were subjected to simulated isotropic tensile deformation and maximum value of isotropic stress was evaluated for them. Consequently, phonon spectra were calculated for several strain values in order to assess crystal stability. Phonon instabilities in dispersion curves of diamond, Al, Ir and Au appeared at strains lower than those corresponding to their decohesion. This appearance of instability determinates the value of ideal strength. However, significant reduction (by about 20%) was found only in the cases of Au and Ir.

Le travail porte sur les propriétés vibrationnelles de semi-conducteurs innovants, notamment les composés Cu2ZnSnSe4, Cu2ZnSnS4 de type kesterite, qui, dans le domaine du photovoltaïque, soutiennent la comparaison avec les matériaux leaders de type chalcopyrite, Cu(In,Ga)Se2. Un intérêt pratique immédiat pressenti est que les spectres de vibration devraient permettre de distinguer entre différentes phases structurales possibles à une composition donnée. Les modes de vibration sont abordés en utilisant une approche théorique premiers principes. Le manuscrit est divisé en cinq chapitres, dont le contenu est le suivant : (1) Une brève introduction sur le principe et les enjeux du photovoltaïque, les cellules solaires à base de composés semi-conducteur multinaires; le chapitre se termine par une description du diagramme de phase du système Cu-Zn-Sn-Se. (2) L’exposé de la théorie de la fonctionnelle de la densité (DFT) et la mise en œuvre de simulations numériques via le logiciel SIESTA. (3) Les propriétés vibrationnelles de Cu2ZnSnSe4 dans ses deux phases kesterite et stannite, étudiées par une méthode premiers principes, en faisant une comparaison détaillée et une analyse minutieuse mode par mode. (4) Les propriétés vibrationnelles de la phase secondaire Cu2SnSe3, une concurrente habituelle de la phase Cu2ZnSnSe4 lors de la croissance des échantillons. (5) Le calcul des phonons dans la structure Cu2ZnSnS4 contenant des défauts intrinsèques (lacunes; antisites), avec comme objectif l'évaluation des contributions vibrationnelles à l'entropie, et l'élaboration du diagramme de phases composition – température dans ce système multinaire. La conclusion générale récapitule les résultats, qui sont publiés dans 5 articles / The works addresses vibrational properties of novel semiconductors, specifically the Cu2ZnSnSe4 and Cu2ZnSnS4 compounds of the kesterite structure, which, in the domain of photovoltaics, become competitive with leading materials of chalcopyrite type, notably Cu(In,Ga)Se2. The anticipated immediate practical interest of such study is that the vibration spectra are likely to make possible a distinction between different structural phases, possible for a given composition. The vibration modes are accessed by using a first-principle theory approach. The manuscript is divided into five chapters, with the following contents: (1) A brief introduction into the work principle and the problematics of photovoltaics, specifically of the solar cells based on multinary semiconductors; the chapter closes by the description of the phase diagram of the Cu-Zn-Sn-Se system. (2) An overview of the density functional theory (DFT) and of the technics of numerical simulations using the SIESTA code. (3) The vibrational properties of Cu2ZnSnSe4 in its two phases, kesterite and stannite, as studied by first-principles method, with a detailed comparison being done along with a thorough mode-by-mode analysis. (4) Vibrational properties of a secondary phase Cu2SnSe3, which often competes with the Cu2ZnSnSe4 phase in the process of sample growth. (5) Calculation of phonons in the Cu2ZnSnS4 structure containing intrinsic defects (vacances; anti sites), with the objective of estimating vibrational contributions to entropy and the correction of the composition - temperature phase diagram in this multi nary system. The general conclusion summarises the results which are published in 5 articles

The thesis aims at the study of conformation of a dimethyl tartrate molecule using the methods of vibrational optical activity (VOA), namely vibrational circular dichroism (VCD) and Raman optical activity (ROA). Based on the theoretical background of both VOA methods and current state of research of the studied molecule there was a sample of dimethyl tartrate dissolved in different solvents and its properties were measured using VCD and ROA spectrometers. In addition to the experiment, ab initio calculations were carried out in order to compare calculated and experimental spectra. Based on the comparison, the possible conformations present in water solution of the studied molecule are described in detail.

Nanoelectronics and spintronics are concerned with writing, transporting, and reading information stored in electronic charge and spin degrees of freedom at the nanoscale. Past few years have shown that two spintronics effects discovered in the 19th century, namely anisotropic magnetoresistance and anomalous Hall effect, can be used also for sensing antiferromagnetism which opened the field of antiferromagnetic spintronics. The more than a century of controversial studies of these effects have shown their relativistic spin-orbit coupling and spin-polarisation symmetry breaking origin. However, a complete understanding of these effects and a fully predictive theory capable of identifying novel suitable antiferromagnetic materials are still lacking. Here, by extending modern symmetry and topology concepts in condensed matter physics, we have further developed the theory of anisotropic magnetoresistance and spontaneous Hall effect. Our approach is based on magnetic symmetry and topology analysis of antiferromagnetic energy bands, Bloch spectral functions, and Berry curvatures calculated from the state-of-the- art first-principle theory. This guided us to the prediction of two novel, previously unanticipated effects: relativistic metal-insulator transition from antiferromagnetic Dirac fermions, and crystal Hall...