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Huntress, Mark. "An Analysis of Artificial Rhodopsin Mimics Using Multiconfigurational Ab Initio Computations". Bowling Green State University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1339875459.
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Kang, Kisuk. "Designing new electrode materials for energy devices by integrating ab initio computations with experiments". Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/36213.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2006.Includes bibliographical references (p. 152-161).
Utilization of Ni2+/Ni4+ double redox couple in electrochemical reactions has been tested as a way to gauge useful properties such as high capacity in electrode materials. The feasibility of a Ni2+/Ni4+ active redox couple is confirmed in a new layered electrode material, Lio.gNi045Ti5502. First principles calculations combined with experiments show that the degree of cation disordering in the material arising from both synthesis conditions and the electrochemical reaction is critical in performance of this material as the electrode. In an attempt to fully utilize Ni2+/Ni4+ double redox couple, Li2NiO2 in the Immm structure was successfully synthesized and its electrochemical behavior upon delithiation was evaluated. The material shows a high specific charge capacity of about 320 mAh/g and discharge capacity of about 240 mAh/g at the first cycle. The stability of Li2NiO2 in the Immm structure is attributed to the more favorable Li arrangement possible as compared to a Li2NiO2 structure with octahedral Ni. The electrochemical data, first principles calculation and EXAFS analysis all indicate that the orthorhombic Immm structure is rather prone to phase transformation to a close-packed layered structure during the electrochemical cycling.
(cont.) The possibility of stabilizing the orthorhombic Immm structure during the electrochemical cycling by partial substitution of Ni is also evaluated. First principles computations of some chemically substituted materials identified Pt substitution as a way of stabilizing the Li2(Ni,M)O2 composition in the Immm structure but found no elements that would likely stabilize the material upon Li removal. The second part of the thesis is focused on designing high rate capable electrode materials. We systematically investigated several of the factors that influence the migration barrier for Li motion in layered oxides with the 03 structure using first principles methods, and found that the two dominant effects are the Li slab spacing which determines the compressive stress on Li when it is in the tetrahedral site, and the electrostatic repulsion Li experiences there from the transition metal ion. The other factors investigated (non-transition metal doping, Li-metal site exchange) can be reduced to the effect they have on the electrostatic and Li-slab factor. We have used these first principles results as key strategies for increasing the rate capability of layered cathode materials and applied them to Li(NiO.5MnO.5)02, a safe, inexpensive material that has been thought to have poor intrinsic rate capability.
(cont.) Structural modification of Li(Nio.sMno.5)2 according to first principles guideline leads this novel material to retain its capacity at high rates in agreement with the theoretical predictions. The rate capability tests show that even at a 6C discharge rate (C= 280mA/g) it can deliver over 180mAh/g. The best electrochemical data published for this material shows that it can deliver about 130mAh/g at a 2C rate, and there is no data available for a rate as high as 6C. The electron microscopy shows that the particle size of this material is about two times bigger than- the conventional Li(Nio.5Mno.5)O2. This implies that with proper engineering optimization in processing (i.e. synthesis temperature, time etc.) this material can show even better rate capability.
by Kisuk Kang.
Ph.D.
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Colin, Aristide. "Design and magnetic behavior of redox-switchable polynuclear complexes". Electronic Thesis or Diss., université Paris-Saclay, 2024. http://www.theses.fr/2024UPASF093.
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Parmi la vaste classe des complexes de coordination moléculaire, certains composés présentent des propriétés magnétiques, pour un environnement de coordination approprié. Par exemple, ces propriétés incluent le comportement de molécule aimant, lorsque qu'il y a une barrière d'énergie à l'inversion de l'aimantation, ou des propriétés de bit quantique lorsque la dégénérescence de l'état fondamental est complètement levée. Combiner ces propriétés magnétiques avec d'autres, comme la luminescence ou la commutabilité magnétique dans des matériaux multifonctionnels est particulièrement intéressant. En effet, des applications telles que la manipulation et le stockage d'information, l'information quantique, les dispositifs spintroniques, les capteurs chimiques ou les micro-thermomètres peuvent être envisagées. Bien que prometteuse, la conception de tels complexes moléculaires magnétiques répondant à des stimuli externes représente un défi à la fois au niveau de la synthèse et au niveau de l'analyse des composés. Les ligands pontants redox-actifs sont connus comme unités de construction pour la conception de complexes polynucléaires avec des interactions d'échange ajustables entre les centres magnétiques. Précédemment, notre groupe a contribué à l'émergence de la famille des composés moléculaires construits autour du ligand non-innocent hexahydroxytriphénylène (HHTP), avec un complexe trinucléaire à base de nickel montre des propriétés prometteuses pour la modulation redox du comportement magnétique. Le ligand HHTP est particulièrement intéressant car il possède sept états redox théoriques, passant, via des événements monoélectroniques successifs, de l'état tris-quinone à l'état tris-catécholate. Dans cette thèse, l'accent est mis sur les complexes de coordination conçus autour du ligand HHTP. Leur synthèse est développée, leurs différents états redox sont isolés et leurs propriétés magnétiques sont étudiées à l'état solide par magnétométrie SQUID. Le comportement magnétique attendu est une modulation on/off de l'interaction d'échange entre les centres magnétiques, en fonction de la présence (ou absence) d'électrons non appariés sur le HHTP. Des complexes trinucléaires de nickel et de cobalt, ainsi qu'un dimère hexanucléaire de nickel avec le ligand HHTP sont rapportés. L'étude des différents états redox isolés met en évidence la modulation des propriétés magnétiques par le commutateur redox. Le comportement observé de commutation du comportement magnétique via le switch redox est rationalisé par des calculs ab initio, révélant la structure électronique du HHTP et les mécanismes de l'interaction de spin en son sein. En outre, il est fait état d'explorations ayant pour but de synthétiser des complexes trinucléaires à base de lanthanides autour du ligand HHTP et des complexes binucléaires autour du ligand chloroanilateAmong the large class of molecular coordination complexes, some compounds exhibit magnetic properties, given a suitable coordination environment of their metallic ions. For instance, these properties can be the single molecule magnet behavior, when there is an energy barrier to the reversal of the magnetization, or qubit properties when the degeneracy of the ground state is fully lifted. Combining these magnetic properties with others like luminescence or magnetic switchability into multifunctional materials is of interest for applications such as, data manipulation and storage, quantum information, spintronic devices, chemisensors or microthermometers. Although very promising, designing such magnetic molecular complexes that respond to external stimuli is both a synthetic and analytical challenge. Redox-active bridge ligands are well-known as building blocks to design polynuclear complexes with tunable exchange interaction between magnetic centers. Previously our group contributed to the emerging family of compounds based on the hexahydroxytripenylene (HHTP) non-innocent ligand with a trinuclear nickel-based complex showing promising magneto-redox coupled properties. The HHTP ligand is particularly interesting as it has seven theoretical redox states going, through successive monoelectronic events, from the tris-quinone to the tris-catecholate state. In this work the focus is on coordination complexes designed around the HHTP ligand. Their synthesis is developed, isolation of their different redox states is carried out and their magnetic properties are investigated in the solid state by SQUID magnetometry. The expected magnetic behavior is an on/off switch of the exchange coupling between the magnetic centers depending on the presence (or absence) of unpaired electrons on the HHTP. Trinuclear complexes of nickel ions and cobalt ions are reported along with an hexanuclear nickel HHTP dimer. The study on the different isolated redox states puts in evidence the modulation of the magnetic properties with the redox switch. The observed magneto-redox switch behavior is rationalized by ab initio calculations unveiling the electronic structure of HHTP and the internal mechanisms of spin interaction. Additionally, explorations to synthesize lanthanide-based trinuclear complexes around the HHTP and binuclear complexes around the chloroanilate ligand are reported
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Wetzel, Thiele Lee. "Ab initio computational studies". Thesis, Georgia Institute of Technology, 1993. http://hdl.handle.net/1853/26023.
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Mintz, Benjamin. "Reducing the Computational Cost of Ab Initio Methods". Thesis, University of North Texas, 2008. https://digital.library.unt.edu/ark:/67531/metadc9061/.
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In recent years, advances in computer technology combined with new ab initio computational methods have allowed for dramatic improvement in the prediction of energetic properties. Unfortunately, even with these advances, the extensive computational cost, in terms of computer time, memory, and disk space of the sophisticated methods required to achieve chemical accuracy - defined as 1 kcal/mol from reliable experimental data effectively - limits the size of molecules [i.e. less than 10-15 non-hydrogen atoms] that can be studied. Several schemes were explored to help reduce the computational cost while still maintaining chemical accuracy. Specifically, a study was performed to assess the accuracy of ccCA to compute atomization energies, ionization potentials, electron affinities, proton affinities, and enthalpies of formation for third-row (Ga-Kr) containing molecules. Next, truncation of the correlation consistent basis sets for the hydrogen atom was examined as a possible means to reduce the computational cost of ab initio methods. It was determined that energetic properties could be extrapolated to the complete basis set (CBS) limit utilizing a series of truncated hydrogen basis sets that was within 1 kcal/mol of the extrapolation of the full correlation consistent basis sets. Basis set truncation for the hydrogen atom was then applied to ccCA in the development of two reduced basis set composite methods, ccCA(aug) and ccCA(TB). The effects that the ccCA(aug) and ccCA(TB) methods had upon enthalpies of formation and the overall percent disk space saved as compared to ccCA was examined for the hydrogen containing molecules of the G2/97 test suite. Additionally, the Weizmann-n (Wn) methods were utilized to compute the several properties for the alkali metal hydroxides as well as the ground and excited states of the alkali monoxides anion and radicals. Finally, a multi-reference variation to the correlation consistent Composite Approach [MR-ccCA] was presented and utilized in the computation of the potential energy surfaces for the N2 and C2 molecules.
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Mintz, Benjamin Wilson Angela K. "Reducing the computational cost of Ab Initio methods". [Denton, Tex.] : University of North Texas, 2008. http://digital.library.unt.edu/permalink/meta-dc-9061.
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Temelso, Berhane. "Computation of Molecular Properties at the Ab Initio Limit". Diss., Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/14638.
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The accuracy of a quantum chemical calculation inherently depends on the ability to account for the completeness of the one- and n-particle spaces. The size of the basis set used can be systematically increased until it reaches the complete one-particle basis set limit (CBS) while the n-particle space approaches its exact full configuration interaction (FCI) limit by following a hierarchy of electron correlation methods developed over the last seventy years. If extremely high accuracy is desired, properly correcting for very small effects such as those resulting the Born-Oppenheimer approximation and the neglect of relativistic effects becomes indispensable. For a series of chemically interesting and challenging systems, we identify the limits of conventional approaches and use state-of-the-art quantum chemical methods along with large basis sets to get the “right answer for the right reasons.” First, we quantify the importance of small effects that are ignored in conventional quantum chemical calculations and manage to achieve spectroscopic accuracy (agreement of 1 cm−1 or less with experimental harmonic vibrational frequencies) for BH, CH+ and NH. We then definitively resolve the global minimum structure for Li₆ , Li₆⁺ , and Li₆- using high accuracy calculations of the binding energies, ionization potentials, electron affinities and vertical excitation spectra for the competing isomers. The same rigorous approach is used to study a series of hydrogen transfer reactions and validate the necessary parameters for the hydrogen abstraction and donation steps in the mechanosynthesis of diamondoids. Finally, in an effort to overcome the steep computational scaling of most high-level methods, a new hybrid methodology which scales as O(N⁵) but performs comparably to O(N⁶) methods is benchmarked for its performance in the equilibrium and dissociation regimes.
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Schmidt, am Busch Marcel. "Ab initio computation of pKa values and redox potentials". [S.l.] : [s.n.], 2006. http://www.diss.fu-berlin.de/2006/122/index.html.
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Monari, Antonio <1976>. "Ab initio computation of electric properties and intermolecular forces". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2007. http://amsdottorato.unibo.it/468/1/tesi.pdf.
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Monari, Antonio <1976>. "Ab initio computation of electric properties and intermolecular forces". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2007. http://amsdottorato.unibo.it/468/.
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Parra, Farré Genís. "Computational identification of genes: ab initio and comparative approaches". Doctoral thesis, Universitat Pompeu Fabra, 2004. http://hdl.handle.net/10803/7082.
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El trabajo que aquí se presenta, estudia el reconocimiento de las señales que delimitan y definen los genes que codifican para proteínas, así como su aplicabilidad en los programas de predicción de genes. La tesis que aquí se presenta, también explora la utilitzación de la genómica comparativa para mejorar la identificación de genes en diferentes especies simultaniamente. También se explica el desarrollo de dos programas de predicción computacional de genes: geneid y sgp2. El programa geneid identifica los genes codificados en una secuencia anónima de DNA basandose en sus propiedades intrínsecas (principalmente las señales de splicing y el uso diferencial de codones). sgp2 permite utilitzar la comparación entre dos genomas, que han de estar a una cierta distancia evolutiva óptima, para mejorar la predicción de genes, bajo la hipotesis que las regiones codificantes están mas conservadas que las regiones que no codifican para proteínas.The motivation of this thesis is to give a little insight in how genes are encoded and recognized by the cell machinery and to use this information to find genes in unannotated genomic sequences. One of the objectives is the development of tools to identify eukaryotic genes through the modeling and recognition of their intrinsic signals and properties. This thesis addresses another problem: how the sequence of related genomes can contribute to the identification of genes. The value of comparative genomics is illustrated by the sequencing of the mouse genome for the purpose of annotating the human genome. Comparative gene predictions programs exploit this data under the assumption that conserved regions between related species correspond to functional regions (coding genes among them). Thus, this thesis also describes a gene prediction program that combines ab initio gene prediction with comparative information between two genomes to improve the accuracy of the predictions.
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Li, Zheng. "Accelerating Catalyst Discovery via Ab Initio Machine Learning". Diss., Virginia Tech, 2019. http://hdl.handle.net/10919/95915.
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In recent decades, machine learning techniques have received an explosion of interest in the domain of high-throughput materials discovery, which is largely attributed to the fastgrowing development of quantum-chemical methods and learning algorithms. Nevertheless, machine learning for catalysis is still at its initial stage due to our insufficient knowledge of the structure-property relationships. In this regard, we demonstrate a holistic machine-learning framework as surrogate models for the expensive density functional theory to facilitate the discovery of high-performance catalysts. The framework, which integrates the descriptor-based kinetic analysis, material fingerprinting and machine learning algorithms, can rapidly explore a broad range of materials space with enormous compositional and configurational degrees of freedom prior to the expensive quantum-chemical calculations and/or experimental testing. Importantly, advanced machine learning approaches (e.g., global sensitivity analysis, principal component analysis, and exploratory analysis) can be utilized to shed light on the underlying physical factors governing the catalytic activity on a diverse type of catalytic materials with different applications. Chapter 1 introduces some basic concepts and knowledge relating to the computational catalyst design. Chapter 2 and Chapter 3 demonstrate the methodology to construct the machine-learning models for bimetallic catalysts. In Chapter 4, the multi-functionality of the machine-learning models is illustrated to understand the metalloporphyrin's underlying structure-property relationships. In Chapter 5, an uncertainty-guided machine learning strategy is introduced to tackle the challenge of data deficiency for perovskite electrode materials design in the electrochemical water splitting cell.Doctor of Philosophy
Machine learning and deep learning techniques have revolutionized a range of industries in recent years and have huge potential to improve every aspect of our daily lives. Essentially, machine-learning provides algorithms the ability to automatically discover the hidden patterns of data without being explicitly programmed. Because of this, machine learning models have gained huge successes in applications such as website recommendation systems, online fraud detection, robotic technologies, image recognition, etc. Nevertheless, implementing machine-learning techniques in the field of catalyst design remains difficult due to 2 primary challenges. The first challenge is our insufficient knowledge about the structure-property relationships for diverse material systems. Typically, developing a physically intuitive material feature method requests in-depth expert knowledge about the underlying physics of the material system and it is always an active field. The second challenge is the lack of training data in academic research. In many cases, collecting a sufficient amount of training data is not always feasible due to the limitation of computational/experimental resources. Subsequently, the machine learning model optimized with small data tends to be over-fitted and could provide biased predictions with huge uncertainties. To address the above-mentioned challenges, this thesis focus on the development of robust feature methods and strategies for a variety of catalyst systems using the density functional theory (DFT) calculations. Through the case studies in the chapters, we show that the bulk electronic structure characteristics are successful features for capturing the adsorption properties of metal alloys and metal oxides. While molecular graphs are robust features for the molecular property, e.g., energy gap, of metal-organics compounds. Besides, we demonstrate that the adaptive machine learning workflow is an effective strategy to tackle the data deficiency issue in search of perovskite catalysts for the oxygen evolution reaction.
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Lawrence, A. Raelene. "A computational investigation of inorganic systems using ab initio methods /". free to MU campus, to others for purchase, 2000. http://wwwlib.umi.com/cr/mo/fullcit?p9998495.
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Herrero, Saboya Gabriela. "Les défauts dans le silicium : revisiter les modèles théoriques pour guider les calculs ab initio". Thesis, Toulouse 3, 2020. http://www.theses.fr/2020TOU30239.
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Dans cette thèse, nous décrivons l'effet des défauts localisés sur les propriétés électroniques du silicium. Après 60 ans de production industrielle de dispositifs à base de silicium, on pourrait s'attendre à ce que tous les caractéristiques de ce matériau soient parfaitement comprises, surtout si l'on considère que la fabrication des transistors actuels à l'échelle du nanomètre nécessite une précision quasi atomique. Cependant, en conséquence directe de cette miniaturisation extrême, la création accidentelle d'un seul défaut peut suffire à modifier les propriétés électroniques souhaitées de l'échantillon, devenant ainsi l'un des phénomènes les plus redoutés de l'industrie. Historiquement, l'identification de ces centres a été possible grâce au développement et à l'amélioration des techniques de caractérisation, capables de cibler des propriétés de défaut spécifiques, par exemple, liées à la position des états induits par le centre dans la bande interdite du semi-conducteur (absorption optique infrarouge, spectroscopie DLTS) ou aux distorsions atomiques déclenchées par la forme de la densité électronique localisée (spectroscopie EPR). Une telle quantité de données expérimentales a motivé le développement de modèles simples basés sur la symétrie, reproduisant qualitativement les caractéristiques fondamentales des défauts. Plus récemment l'augmentation exponentielle de la puissance de calcul a fait des calculs ab initio le modèle théorique parfait pour fournir une représentation quantitatif des défauts ponctuels dans les semi-conducteurs. Les simulations numériques à l'échelle atomique dans le silicium, basées sur la théorie de la fonctionnelle de la densité, ciblent cependant généralement des propriétés spécifiques des défauts, ne donnant pas une image théorique complète du système, et négligeant souvent les modèles précédents et les preuves expérimentales. Dans cette thèse, nous apportons une nouvelle vision sur les défauts emblématiques du silicium par la quantification de modèles identifiés de longue date, en établissant un lien explicite avec les techniques de caractérisation. Notre exploration détaillée de la surface d'énergie potentielle du "E-center" du silicium, guidée par un modèle simple de Jahn-Teller, a confirmé la dynamique des défauts observée à différents régimes de température, nous permettant de relier la présence d'un tel défaut ponctuel à un bruit électronique dans les capteurs d'images. De plus, nous étudions l'hypothèse d'une amélioration de l'absorption des photons dans les cellules solaires en silicium dopé au titane en décrivant les effets à plusieurs corps à l'aide de l'approximation GW. De cette manière, on attribue les excitations électroniques chargées aux transitions entre les états du titane, précédemment décrits par un modèle phénoménologique pour les métaux de transition dans le silicium. Nous proposons également une généralisation des toy-models préexistants pour aborder les centres complexes, pour lesquels une controverse notoire au sein de la communauté ab initio existe toujours, montrant explicitement les limites des approches de champ moyen lorsqu'elles ciblent des densités électroniques hautement localisées. Nous concluons par une brève revue critique de la caractérisation théorique de l'activité électronique des défauts, et en particulier de la section efficace de capture des transitions non radiativesIn this thesis, we describe the effect of localized defects on the electronic properties of silicon. After 60 years of silicon devices production, one might expect all details of this material to be fully understood, especially considering that the manufacture of nowadays nanometer-sized transistors requires quasi-atomic accuracy. However, as a direct result of such extreme miniaturization, the accidental creation of even one single trapping center can be sufficient to alter the desired electronic properties of the sample, becoming one of the most feared phenomena in the industry. Since the early years, the identification of these centers has been possible through the development of characterization techniques, capable of targeting specific defect properties, related to the position of the center-induced states within the semiconductor gap (infrared optical absorption, DLTS spectroscopy) or to the atomic distortions triggered by the form of the localized electronic density (EPR spectroscopy). Such collection of experimental data motivated the development of simple symmetry-based models, qualitatively reproducing the basic features of defects. The later exponential increase in computational power made ab-initio calculations the perfect candidate to give a quantitative theoretical model of point-defects in semiconductors. Atomistic numerical simulations in silicon, based on the Density Functional Theory, do however typically target specific defect-properties, not giving a complete theoretical picture of the system, often overlooking previous models and experimental evidence. In the present thesis, we provide new insight into iconic defects in silicon through the quantification of long-established atomistic models, making an explicit link with the characterization techniques. Our detailed exploration of the DFT energy surface of the silicon E-center, guided by a simple Jahn-Teller model, confirmed the observed defect-dynamics at different temperature regimes, allowing us to link the presence of such point-like defect to a burst noise in image sensors. Moreover, we investigate the hypothesis of enhancing photon-absorption in titanium-doped silicon solar cells by describing many-body effects in the form of the GW approximation, assigning the charged electronic excitations to transitions between Ti-related states, previously depicted by a phenomenological model for transition metals in silicon. We also propose a generalization of the preexisting toy-models to tackle complex centers, for which a notorious controversy within the ab-initio community still exists, showing explicitly the limitations of mean-field approaches when targeting highly localized electronic densities. We conclude with a brief critical review of the theoretical characterization of the defects electronic activity, and in particular the capture cross section of non-radiative transitions
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Lima, Filipe Camargo Dalmatti Alves. "Modelagem ab initio da interação proteína-carboidrato". Universidade de São Paulo, 2010. http://www.teses.usp.br/teses/disponiveis/43/43134/tde-21102010-110913/.
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A Frutalina é uma proteína tetramérica ligante de carboidratos obtida através de sementes Artocarpus incisa. Os interesses biomédicos da Frutalina estão em sua alta afnidade de ligação por carboidratos presentes em algumas células tumorais específicas. Até agora, nenhum estudo teórico computacional foi realizado para investigar as características de ligação da Frutalina. Neste trabalho, através de um estudo multidisciplinar, investigamos as propriedades de ligação e óticas da Frutalina com carboidratos. Utilizamos um modelo-corte teórico, considerando apenas o sítio ativo de ligação com o carboidrato construído com o auxílio de docking molecular e mecânica molecular clássica. As energias de ligação são obtidas através de uma abordagem quântica ab initio all electron, dentro da Teoria do Funcional da Densidade (DFT), no espaço recíproco que combina o método Projector Augmented Waves (PAW) e a dinâmica molecular de Car-Parrinello (CP). Uma metodologia Hartree-Fock (HF) semi-empírica é utilizada para obter as propriedades óticas. A investigação deste problema muito complexo pode ser dividido em seis etapas principais: a) estudamos as propriedades estruturais da proteína para avaliar a sua mobilidade e escolhemos um conjunto de dados de raios-X para descrever o sistema; b) aplicamos a técnica de docking molecular para ligar quatro carboidratos ( alfa-metil-D-galactose, beta-D-galactose, O1-metil-manose e alfa-metil-D-glucopiranose) na proteína; c) otimizamos a geometria do sistema lectina-carboidrato utilizando mecânica molecular clássica; d) criamos o modelo-corte ; e) investigamos as propriedades óticas utilizando HF; f) estudamos as propriedades eletrônicas do sistema proteína-carboidrato e calculamos energias de ligação através do cálculo DFT. O modelo aqui proposto, além de apresentar uma adequada concordância com dados experimentais, abre a possibilidade de investigar propriedades eletrônicas através de uma abordagem quântica estado da arte na área de estrutura eletrônica.Frutalin is a tetrameric carbohydrate-binding protein obtained from breadfruit seeds. Biomedical interest on Frutalin comes from the high afinity exhibited by these molecules toward carbohydrates expressed by specific tumor cells. So far, no theoretical computational studies have been carried out to investigate the binding characteristics of frutalin, which is probably due to the large number of atoms that should be considered for in silicon calculations. We investigate the binding of frutalin and optical properties with specific carbohydrate molecules using a theoretical cutmodel considering only the carbohydrate binding site. This model has been constructed with the aid of molecular docking and classical molecular mechanics. We use the ab initio all electron reciprocal space Projector Augmented Waves (PAW) method and the Car-Parrinello scheme as embodied in the CP-PAW code to obtain the binding energies. To evaluate the optical properties, we employed the Hartree-Fock Semi-empirical ZINDO method from the Materials Studio 4.0 computational package. The investigation of this very complex problem can be divided into 6 main steps. Firstly, we study the structural properties of the protein to evaluate its mobility and we choose a x-ray data to describe reliably the system. In the second step, we performed molecular docking to link up four carbohydrates (alpha-methyl-D-galactoside, beta-D-galactoside, O1-methyl-mannose and methyl-alpha-D-glucopyranoside) in the protein. We optimize the geometry of the system lectin-carbohydrate using molecular mechanics in the third step. In the fourth step, we created the cutmodel based on the final geometries obtained in the previous step. In the fifth and sixth steps we investigate the quantum interaction of the protein with each carbohydrate. Our theoretical results are compared with available measurements in each step. The study of the interaction between the active binding site and carbohydrates allows us to demonstrate that our methodology is well suited to predict the electronic properties of the system.
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Sun, Weiwei. "Ab initio study of transition metal carbides and actinide compounds". Doctoral thesis, KTH, Materialteknologi, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-158005.
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Two classes of materials are investigated using ab intio methods based on density functional theory. The structural properties, electronic structure and thermodynamic properties of binary and ternary transition metal carbides are discussed in details. In addition, two actinide compounds will be presented. A new actinide monoxide, ThO, is predicted to be stable under pressure, and the weakly correlated UN is investigated as regards to its magnetic properties and electronic structure. The atomic and electronic structures of various types of single defects in TiC such as vacancies, interstitial defects, and antisite defects are investigated systematically. Both the C-poor and C-rich off-stoichiometric Ti1-cCc composition (0.49≤c≤0.51) have been studied. For the electronic structure, the difference of density of states (dDOS) is introduced to characterize the changes produced by the defects. Concerning the atomic structures, both interstitial defects and antisites are shown to induce the formation of C dumbbells or Ti dumbbells. To date, the Ti self-diffusion mechanism in TiC has not been fully understood, and particularly the Ti diffusion is much less studied in comparison with the C diffusion. Therefore, the self-diffusion of Ti in sub-stoichiometric TiC is studied, and the formation energies, migration barriers for Ti interstitials, dumbbells and dumbbell-vacancy clusters are reported. Some of the calculated activation energies are close to the experimental values, and the migration of Ti dumbbell terminated by C vacancies gives the lowest activation energy, which is in good agreement with the experimental data. These studies must be continued to obtain a full description (including phonon contributions, prefactors, etc.) of all the feasible diffusion mechanisms in TiC. The focus is then shifted from the light transition metal carbides to the heavy transition metal carbides. Various structures of Ru2C under ambient conditions are explored by using an unbiased swarm structure searching algorithm. The structures with R3m (one formula unit) and R-3m symmetry (two formula units) have been found to be lower in energy than the P-3m1 structure, and also to be dynamically stable at ambient conditions. The R-3m structure is characterized by emergence of the Ru-Ru metallic bonding, which has a crucial role in diminishing the hardness of this material. The study of correlation and relativistic effects in Ta2AlC is also presented. We have shown that going from a scalar relativity to a fully relativistic description does not have a significant effect on the computed electronic and mechanical properties of Ta2AlC. In addition, the calculations show that the structural and mechanical properties of Ta2AlC are strongly dependent on other details of theoretical treatment, such as the value of the Hubbard U parameter. The comparison between our results and experimental data point to that Ta2AlC is a weakly correlated system, which originates from that the 5d band is relatively wide in comparison with that of the 3d band. The existence of a rock salt Thorium monoxide (ThO) under high pressure is theoretically predicted. A chemical reaction between Th and ThO2 can produce a novel compound thorium monoxide under sufficient external pressure. To determine the pressure range where this reaction can be observed, we have identified two extreme boundaries by means of different theoretical approaches. The first one is given by a fully relativity DFT code in local density approximation (LDA). The second one is given by a scalar relativistic DFT code in generalized gradient approximation (GGA). It is found that ThO is energetically favored between 14 and 26 GPa. The f orbitals are filled at the expense of s and d electrons states of Th metal, under the action of pressure. The d-p hybridization leads to the stability of metallic ThO. Dynamical stability is also investigated by computing the phonon dispersions for the considered structures at high pressure. The electronic structure and magnetic properties of a promising nuclear fuel material, uranium mononitride (UN), are studied by means of density functional theory (DFT) and several extensions, such as dynamical mean-field theory (DMFT), disordered local moment (DLM) approach, and the GW method. The role of the relativistic corrections is analyzed for different levels of approximation. The importance of correlation effects is assessed through a detailed comparison between calculated electronic structure and measured photoemission spectrum, which helps to clarify the dual itinerant/localized nature of the 5f states of U in UN. Important effects are also observed for the 2p states of nitrogen, which are positioned at much lower energies that are difficult to be well treated in the conventional electronic structure calculations.QC 20141219
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Heady, Lucy Clare. "Inhibiting CDK2 : a computational study with ab-initio and classical methods". Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.613729.
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Moha, Verena [Verfasser]. "Computational chemistry of supramolecular systems : ab initio and DFT studies / Verena Moha". Aachen : Hochschulbibliothek der Rheinisch-Westfälischen Technischen Hochschule Aachen, 2012. http://d-nb.info/1027607667/34.
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Jain, Deepak. "An ab initio study of defects in solids using parallel computational methods". Thesis, University of Newcastle Upon Tyne, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.360240.
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Richard, Ryan. "Increasing the computational efficiency of ab initio methods with generalized many-body expansions". The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1385570237.
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Srepusharawoot, Pornjuk. "Computational Studies of Hydrogen Storage Materials : Physisorbed and Chemisorbed Systems". Doctoral thesis, Uppsala universitet, Materialteori, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-132875.
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This thesis deals with first-principles calculations based on density functional theory to investigate hydrogen storage related properties in various high-surface area materials and the ground state crystal structures in alkaline earth dicarbide systems. High-surface area materials have been shown to be very promising for hydrogen storage applications owing to them containing numerous hydrogen adsorption sites and good kinetics for adsorption/desorption. However, one disadvantage of these materials is their very weak interaction with adsorbed hydrogen molecules. Hence, for any feasible applications, the hydrogen interaction energy of these materials must be enhanced. In metal organic frameworks, approaches for improving the hydrogen interaction energy are opening the metal oxide cluster and decorating hydrogen attracting metals, e.g. Li, at the adsorption sites of the host. In covalent organic framework-1, the effects of the H2-H2 interaction are also found to play a significant role for enhancing the hydrogen adsorption energy. Moreover, ab initio molecular dynamics simulations reveal that hydrogen molecules can be trapped in the host material due to the blockage from adjacent adsorbed hydrogen molecules. In light metal hydride systems, hydrogen ions play two different roles, namely they can behave as "promoter" and "inhibitor" of Li diffusion in lithium imide and lithium amide, respectively. By studying thermodynamics of Li+ and proton diffusions in the mixture between lithium amide and lithium hydride, it was found that Li+ and proton diffusions inside lithium amide are more favorable than those between lithium amide and lithium hydride. Finally, our results show that the ground state configuration of BeC2 and MgC2 consists of five-membered carbon rings connected through a carbon atom forming an infinitely repeated chain surrounded by Be/Mg ions, whereas the stable crystal structure of the CaC2, SrC2 and BaC2 is the chain type structure, commonly found in the alkaline earth dicarbide systems.Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 712
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Adriaanse, Christopher John. "Computation of adiabatic and vertical ionisation energies of aqueous anions using ab initio molecular dynamics". Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609155.
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Camur, Yakup. "A Computational Study On Nitrotriazine Derivatives". Master's thesis, METU, 2008. http://etd.lib.metu.edu.tr/upload/12609362/index.pdf.
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In this study, all possible mono, di and trinitro-substituted triazine compounds as potential candidates for high energy density materials (HEDMs) have been investigated by using quantum chemical treatment. Computational chemistry is a valuable tool for estimating the potential candidates for high energy density materials. Geometric features and electronic structures of these nitro-substituted triazines have been systematically studied using ab initio and density functional theory (DFT, B3LYP) at the level of 6-31G(d,p), 6-31+G(d,p), 6-311G(d,p), 6-311+G(d,p), cc-pVDZ. Detonation performances were evaluated by the Kamlet-Jacobs equations based on the calculated densities and heats of formation. It is found that 2G derivative with the predicted densities of 1.9 g/cm3, detonation velocities of 9.43 km/s, and detonation pressures of 40.68 GPa may be novel potential candidates of high energy density materials (HEDMs). Moreover, thermal stabilities were investigated by calculating bond dissociation energies (BDE) at B3LYP/6-311G(d,p) level. Detailed molecular orbital (MO) investigation have been performed on these potential HEDMs.
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Asiri, Yazeed. "Ab Initio and Semi-Empirical Calculations of Cyanoligated Rhodium Dimer Complexs". Digital Commons @ East Tennessee State University, 2017. https://dc.etsu.edu/etd/3177.
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Molecular modeling, using both ab initio and semi-empirical methods has been undertaken for a series of dirhodium complexes in order to improve the understanding of the nature of the chemical bonding in this class of homogeneous catalysts. These complexes, with carboxylamidate and carboxylate ligands, are extremely functional metal catalysts used in the synthesis of pharmaceuticals and agrochemicals. The X-ray crystallography shows anomalies in the bond angles that have potential impact on understanding the catalysis. To resolve these issues, minimum energy structures of several examples (e.g. Rh2(NHCOCH3)4, Rh2(NHCOCH3)4NC, Rh2(CO2CH3)4, Rh2(CO2CH3)4NC, Rh2(CHO2)4, and Rh2(CHO2)4NC) were calculated using Hatree-Fock and Density Functional Theory/B3LYP with the LANL2DZ ECP (Rh), and cc-pVDZ (all other atoms) basis sets.
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Laury, Marie L. "Accurate and Reliable Prediction of Energetic and Spectroscopic Properties Via Electronic Structure Methods". Thesis, University of North Texas, 2013. https://digital.library.unt.edu/ark:/67531/metadc500071/.
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Computational chemistry has led to the greater understanding of the molecular world, from the interaction of molecules, to the composition of molecular species and materials. Of the families of computational chemistry approaches available, the main families of electronic structure methods that are capable of accurate and/or reliable predictions of energetic, structural, and spectroscopic properties are ab initio methods and density functional theory (DFT). The focus of this dissertation is to improve the accuracy of predictions and computational efficiency (with respect to memory, disk space, and computer processing time) of some computational chemistry methods, which, in turn, can extend the size of molecule that can be addressed, and, for other methods, DFT, in particular, gain greater insight into which DFT methods are more reliable than others. Much, though not all, of the focus of this dissertation is upon transition metal species – species for which much less method development has been targeted or insight about method performance has been well established. The ab initio approach that has been targeted in this work is the correlation consistent composite approach (ccCA), which has proven to be a robust, ab initio computational method for main group and first row transition metal-containing molecules yielding, on average, accurate thermodynamic properties, i.e., within 1 kcal/mol of experiment for main group species and within 3 kcal/mol of experiment for first row transition metal molecules. In order to make ccCA applicable to systems containing any element from the periodic table, development of the method for second row transition metals and heavier elements, including lower p-block (5p and 6p) elements was pursued. The resulting method, the relativistic pseudopotential variant of ccCA (rp-ccCA), and its application are detailed for second row transition metals and lower p-block elements. Because of the computational cost of ab initio methods, DFT is a popular choice for the study of transition metals. Despite this, the most reliable density functionals for the prediction of energetic properties (e.g. enthalpy of formation, ionization potential, electron affinity, dissociation energy) of transition metal species, have not been clearly identified. The examination of DFT performance for first and second row transition metal thermochemistry (i.e., enthalpies of formation) was conducted and density functionals for the study of these species were identified. And, finally, to address the accuracy of spectroscopic and energetic properties, improvements for a series of density functionals have been established. In both DFT and ab initio methods, the harmonic approximation is typically employed. This neglect of anharmonic effects, such as those related to vibrational properties (e.g. zero-point vibrational energies, thermal contributions to enthalpy and entropy) of molecules, generally results in computational predictions that are not in agreement with experiment. To correct for the neglect of anharmonicity, scale factors can be applied to these vibrational properties, resulting in better alignment with experimental observations. Scale factors for DFT in conjunction with both the correlation and polarization consistent basis sets have been developed in this work.
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South, Christopher James. "Quantum Chemistry Calculations of Energetic and Spectroscopic Properties of p- and f-Block Molecules". Thesis, University of North Texas, 2016. https://digital.library.unt.edu/ark:/67531/metadc862830/.
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Quantum chemical methods have been used to model a variety of p- and f-block chemical species to gain insight about their energetic and spectroscopic properties. As well, the studies have provided understanding about the utility of the quantum mechanical approaches employed for the third-row and lanthanide species. The multireference ab initio correlation consistent Composite Approach (MR-ccCA) was utilized to predict dissociation energies for main group third-row molecular species, achieving energies within 1 kcal mol-1 on average from those of experiment and providing the first demonstration of the utility of MR-ccCA for third-row species. Multireference perturbation theory was utilized to calculate the electronic states and dissociation energies of NdF2+, providing a good model of the Nd-F bond in NdF3 from an electronic standpoint. In further work, the states and energies of NdF+ were determined using an equation of motion coupled cluster approach and the similarities for both NdF2+ and NdF were noted. Finally, time-dependent density functional theory and the static exchange approximation for Hartree-Fock in conjunction with a fully relativistic framework were used to calculate the L3 ionization energies and electronic excitation spectra as a means of characterizing uranyl (UO22+) and the isoelectronic compounds NUO+ and UN2.
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Lai, Jinfeng. "Models of chemical structure and dynamics via nuclear magnetic resonance and ab initio computational chemistry". Diss., [Riverside, Calif.] : University of California, Riverside, 2009. http://proquest.umi.com/pqdweb?index=0&did=1899476641&SrchMode=2&sid=1&Fmt=2&VInst=PROD&VType=PQD&RQT=309&VName=PQD&TS=1269360290&clientId=48051.
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Thesis (Ph. D.)--University of California, Riverside, 2009.Includes abstract. Available via ProQuest Digital Dissertations. Title from first page of PDF file (viewed March 10, 2010). Includes bibliographical references. Also issued in print.
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Brommer, Karl Daniel. "Ab initio study of the Si(111)-(7x7) surface reconstruction : a challenge for massively parallel computation". Thesis, Massachusetts Institute of Technology, 1993. http://hdl.handle.net/1721.1/12658.
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Tarazona, Vasquez Francisco. "Computational study of the complexation of metal ion precursors in dendritic polymers". [College Station, Tex. : Texas A&M University, 2007. http://hdl.handle.net/1969.1/ETD-TAMU-2459.
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Paulla, Kirti Kant K. "Computational Modeling of Nanosensors Based on Graphene Nanoribbons Including Electron-Phonon Effects". Wright State University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=wright1377374382.
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Sale, Matthew John. "Computational and Experimental Studies of Magnetism in Melilites". Thesis, The University of Sydney, 2019. http://hdl.handle.net/2123/20879.
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The melilite class of materials offers many avenues for research into magnetic interactions. The melilite crystal structure has the chemical formula A2BC2D7 and can accommodate many different elements on the A-, B-, C- and D-sites. For compounds with magnetic transition metal atoms on the B-site, the layered nature of the material produces a nearly two dimensional magnetic sub-lattice. Also, due to the non-centrosymmetric space group which is found in several versions of this structure, multiferroic ordering and magnetoelectric coupling can be observed. Our literature review of the melilite class of materials shows that while there is detailed information available for several magnetic melilite compounds, the magnetic properties of most magnetic melilites have not been studied. Ab initio theoretical calculations of the 1-2-5-2 and 2-2-4-2 manganese melilites and other related materials confirmed the stability of the melilite phase and identified a predominant G-type magnetic ordering. However, several melilite materials including Ba2MnSi2O7 were predicted to have a C-type ordering. Theoretical and experimental studies concerning structural and magnetic properties were performed on K2CoP2O7 twisted melilite and Ba2MnSi2O7 melilite materials which confirmed our theoretical modelling. Further studies outside of the melilite family of materials using similar methodologies were also performed on ZrMn2-xCoxGe4O12 and glaserite Ba3MnSi2O8. However, this thesis mainly focuses on the melilite family of materials as these offer a large scope for further research.
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DE, VICO LUCA. "Biological Photoreceptors as Models for the Computer Design of Light Driven Molecular Rotors". Doctoral thesis, Università di Siena, 2005. http://hdl.handle.net/11365/1006844.
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This thesis represents a step towards the detailed comprehension of the photoisomerization processes and their exploitation. State-of-the-art ab initio quantum chemical calculations will be used to achieve various objectives. When a molecule undergoes an excitation to an higher electronic energy level, one of the main features to study is the way followed by the molecule to relax back on the electronic fundamental state. This implies the computation of the molecular structures where radiationless deactivation is most probable: conical intersections and singlet/triplet crossings. Such crossings provide effective channels for the radiationless deactivation to the ground state. During the last fifteen years the quantum chemical methods mentioned above have been successfully applied to the investigation of the mechanism of both the internal conversion and
photochemical transformation of isolated molecules. First objective of this thesis is about retinal chromophores and the relationship between their structure and the ultrafastness and stereospecificity of the photoisomerization in the protein environment. The acquired experience will be used to investigate for possible applications of molecules that can undergo a cis-trans photoisomerization. In fact, the second objective of this thesis is the study of a chromophore, N-methylthioacetammide
(NMTAA), model for a thio-substituted peptide bond. The last part of the thesis, and its third objective, is committed to the development of new tools for the geometry optimization of potential energy surfaces crossings, with high level ab initio computations.
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Sangiovanni, Davide G. "Transition Metal Nitrides : Alloy Design and Surface Transport Properties using Ab-initio and Classical Computational Methods". Doctoral thesis, Linköpings universitet, Tunnfilmsfysik, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-91379.
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Enhanced toughness in brittle ceramic materials, such as transition metal nitrides (TMN), is achieved by optimizing the occupancy of shear-sensitive metallic electronic-states. This is the major result of my theoretical research, aimed to solve an inherent long-standing problem for hard ceramic protective coatings: brittleness. High hardness, in combination with high toughness, is thus one of the most desired mechanical/physical properties in modern coatings. A significant part of this PhD Thesis is dedicated to the density functional theory (DFT) calculations carried out to understand the electronic origins of ductility, and to predict novel TMN alloys with optimal hardness/toughness ratios. Importantly, one of the TMN alloys identified in my theoretical work has subsequently been synthesized in the laboratory and exhibits the predicted properties. The second part of this Thesis concerns molecular dynamics (MD) simulations of Ti, N, and TiNx adspecies diffusion on TiN surfaces, chosen as a model material, to provide unprecedented detail of critical atomic-scale transport processes, which dictate the growth modes of TMN thin films. Even the most advanced experimental techniques cannot provide sufficient information on the kinetics and dynamics of picosecond atomistic processes, which affect thin films nucleation and growth. Information on these phenomena would allow experimentalists to better understand the role of deposition conditions and fine tune thin films growth modes, to tailor coatings properties to the requirements of different applications. The MD simulations discussed in the second part of this PhD Thesis, predict that Ti adatoms and TiN2 admolecules are the most mobile species on TiN(001) terraces. Moreover, these adspecies are rapidly incorporated at island descending steps, and primarily contribute to layer-by-layer growth. In contrast, TiN3 tetramers are found to be essentially stationary on both TiN(001) terraces and islands, and thus constitute the critical nuclei for three-dimensional growth.
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Flores, Livas José. "Computational and experimental studies of sp3-materials at high pressure". Thesis, Lyon 1, 2012. http://www.theses.fr/2012LYO10127.
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Nous présentons des études expérimentales et théoriques de disiliciures alcalino-terreux, le disilane (Si2H6) et du carbone à haute pression. Nous étudions les disiliciures et en particulier le cas d’une phase plane de BaSI2 qui a une structure hexagonale avec des liaisons sp3 entre les atomes de silicium. Cet environnement électronique conduit à un gaufrage de feuilles du silicium. Nous démontrons alors une amélioration de la température de transition supraconductrice de 6 à 8.9 K lorsque les couches de silicium s’aplanissent dans cette structure. Des calculs ab initio basés sur DFT ont guidé la recherche expérimentale et permettent d’expliquer comment les propriétés électroniques et des phonons sont fortement affectés par les fluctuations du flambage des plans de silicium. Nous avons aussi étudié les phases cristallines de disilane à très haute pression et une nouvelle phase métallique est proposé en utilisant les méthodes de prédiction de structure cristalline. Les températures de transition calculées donnant un supraconducteur autour de 20 K à 100 GPa. Ces valeurs sont significativement plus faibles comparées à celles avancées dans la littérature. Finalement, nous présentons des études de structures de carbone à haute pression à travers une recherche de structure systématique. Nous avons trouvé une nouvelle forme allotropique du carbone avec une symétrie Cmmm que nous appelons Z-carbone. Cette phase est prévue pour être plus stable que le graphite pour des pressions supérieures à 10 GPa. Des expériences et simulation de rayon-X et spectre Raman sugèrent l’existence de Z-carbone dans des micro-domaines de graphite sous pressionWe present experimental and theoretical studies of sp3 materials, alkaline-earth-metal (AEM) disilicides, disilane (Si2H6) and carbon at high pressure. First, we study the AEM disilicides and in particular the case of a layered phase of BaSi2 which has an hexagonal structure with sp3 bonding of the silicon atoms. This electronic environment leads to a natural corrugated Si-sheets. Extensive ab initio calculations based on DFT guided the experimental research and permit explain how electronic and phonon properties are strongly affected by changes in the buckling of the silicon plans. We demonstrate experimentally and theoretically an enhancement of superconducting transition temperatures from 6 to 8.9 K when silicon planes flatten out in this structure. Second, we investigated the crystal phases of disilane at the megabar range of pressure. A novel metallic phase of disilane is proposed by using crystal structure prediction methods. The calculated transition temperatures yielding a superconducting Tc of around 20 K at 100 GPa and decreasing to 13 K at 220 GPa. These values are significantly smaller than previously predicted Tc’s and put serious drawbacks in the possibility of high-Tc superconductivity based on silicon-hydrogen systems. Third, we studied the sp3-carbon structures at high pressure through a systematic structure search. We found a new allotrope of carbon with Cmmm symmetry which we refer to as Z-carbon. This phase is predicted to be more stable than graphite for pressures above 10 GPa and is formed by sp3-bonds. Experimental and simulated XRD, Raman spectra suggest the existence of Z-carbon in micro-domains of graphite under pressure
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Parab, Prajakta Rajaram [Verfasser]. "Computational Chemical Kinetics of Biofuel Combustion Using Ab-Initio Methods and Statistical Rate Theories / Prajakta Rajaram Parab". Aachen : Shaker, 2018. http://d-nb.info/1161299246/34.
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Hetzer, Georg. "Multipolnäherungen für lokale Korrelationsverfahren". [S.l.] : Universität Stuttgart , Fakultät Chemie , Institut für Theoretische Chemie, 2000. http://www.bsz-bw.de/cgi-bin/xvms.cgi?SWB8733291.
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Kumar, Ashutosh. "Computation Assisted Study of Silicon Carbide: A Potential Candidate Material for Radiation Detector Devices". The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1376960400.
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Takatani, Tait. "Truth and tractability: compromising between accuracy and computational cost in quantum computational chemistry methods for noncovalent interactions and metal-salen catalysis". Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/34764.
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Computational chemists are concerned about two aspects when choosing between the myriad of theoretical methodologies: the accuracy (the
"truth") and the computational cost (the tractability). Among the least expensive methods are the Hartree-Fock (HF), density functional theory (DFT), and second-order Moller-Plesset perturbation theory (MP2) methods. While each of these methods yield excellent results in many
cases, the inadequate inclusion of certain types of electron correlation (either high-orders or nondynamical) can produce erroneous results.
The compromise for the computation of noncovalent interactions often comes from empirically scaling DFT and/or MP2 methods to fit benchmark
data sets. The DFT method with an empirically fit dispersion term (DFT-D) often yields semi-quantitative results. The spin-component
scaled MP2 (SCS-MP2) method parameterizes the same- and opposite-spin correlation energies and often yields less than 20% error for prototype
noncovalent systems compared to chemically accurate CCSD(T) results. There is no simple fix for cases with a large degree of nondynamical
correlation (such as transition metal-salen complexes). While testing standard and new DFT functionals on the spin-state energy gaps of
transition metal-salen complexes, no DFT method produced reliable results compared to very robust CASPT3 results. Therefore each metal-salen
complex must be evaluated on a case-by-case basis to determine which methods are the most reliable. Utilizing a combination of DFT-D and SCS-MP2 methods, the reaction mechanism for the addition of cyanide to unsaturated imides catalyzed by the Al(Cl)-salen complex was performed. Various experimental observations are rationalized through this mechanism.
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Fernandez, Garcia Guglielmo. "Lanthanide-based SMMs : from molecular properties to surface grafting exploiting multi-level ab initio techniques". Thesis, Rennes 1, 2017. http://www.theses.fr/2017REN1S171/document.
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Cette thèse de doctorat a été réalisée en cotutelle entre les Universités de Rennes 1 en France et de Florence en Italie. L’objectif de ce travail est tout d’abord de rationaliser les propriétés inter- et intramoléculaires de molécules-aimants (Single Molecule Magnet – SMM) à base d’ions lanthanides (“partie moléculaire”) et puis leur évolution une fois absorbé sur surface (''partie sur surface''). Ces deux aspects ont été examinés dans un cadre théorique et computationnel, en utilisant différentes techniques multi-niveaux, de periodic Density Functional Theory (pDFT) en utilisant une approche post-Hartree-Fock, en fonction de la variable expérimentale d’intérêt. Les molécules-aimants sont d'un intérêt particulier pour le design de nouveaux matériaux magnétiques dans la science des surfaces (comme la spintronique), mais elles permettent également une connaissance des propriétés électroniques et magnétiques approfondie est également nécessaireThe Ph.D. project was a joint agreement between two universities: Université de Rennes 1 in France and Università di Firenze in Italy. The project aimed to shed light on the rationalization of the inter- and intramolecular properties of novel lanthanide-based Single Molecule Magnets, SMMs, (“molecular part”) and their evolution once adsorbed on surface (“surface part”). Both aspects are examined within a theoretical and computational framework, with different multi-level techniques ranging from periodic Density Functional Theory (pDFT) to post-Hartree-Focks approaches, depending on the experimental observable of interest. SMMs are, indeed, at the cutting-edge in the design of novel magnetic materials in surface science (as spintronics or memory storage devices), but for their exploitation a deep understanding of their electronic and magnetic properties is needed
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Santos, Leonardo Sabino dos. "Um estudo ab-initio de propriedades estruturais e mecânicas de nanofios de óxido de magnésio". Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/43/43134/tde-03052010-100505/.
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Nanofios são estruturas em forma de fio com diâmetros da ordem de nanômetros. Estas estruturas têm sido bastante estudadas ultimamente, pois prometem aplicações tecnológicas na área de eletrônica e sensores. Neste trabalho, foram estudados nanofios finos de oxido de magnésio (MgO) com diâmetros de até 2 nm, utilizando cálculos ab-initio baseados na Teoria do Funcional da Densidade com uma base de ondas planas. No total foram estudados 12 fios, com diferentes tamanhos e formas. Entre os resultados obtidos, leis de escala são propostas para relacionar as propriedades dos nanofios com o inverso de seus perímetros. Além disso, verificamos que o módulo de elasticidade (ou módulo de Young) dos nanofios é muito maior que o do material sólido. Também construímos um modelo que relaciona a estabilidade dos nanofios com o número de vizinhos de cada átomo.Nanowires are structures in the shape of wires with diameters on the order of nanometers. These structures have been widely studied recently, as they are promising candidates for technological applications in electronic components and sensors. In this work, we have studied very thin magnesium oxide (MgO) nanowires with diameters below 2 nm through Density Functional Theory-based ab-initio calculations with a plane wave basis set. A total of 12 nanowires of different sizes and shapes was studied. Among the obtained results, we have described scaling laws that relate the nanowire properties to the inverse of the wire perimeter. Moreover, we have found that the nanowires elasticity modulus (or Young modulus) is much larger than that of the solid material. We have also built a model that relates the stability of these nanowires to the number of neighbors of each atom.
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Mak, Lora. "Computational approaches to protein structure and function : from 'Ab Initio' electronic structure calculations to 3D molecular structure description and comparison". Thesis, University of East Anglia, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.443086.
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Eleno, Luiz Tadeu Fernandes. "Dados empíricos e ab initio no método CALPHAD: os sistemas Fe-Cr-Mo-C e Nb-Ni-Si". Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/3/3133/tde-05122012-165651/.
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O objetivo do presente projeto é a combinação de abordagens experimentais e teóricas para o desenvolvimento de bancos de dados termodinâmicos, visando o modelamento de aços e ligas de alto desempenho. Entre esses materiais estão as superligas fundidas por centrifugação para aplicações em fornos de reforma e pirólise, bem como aços-ferramenta reforçados por fases intermetálicas. Os métodos teóricos mencionados correspondem à combinação de cálculos de estrutura eletrônica e modelamento termodinâmico em temperaturas finitas, através do protocolo Calphad. Esta metodologia vem sendo aplicada com sucesso por vários grupos de pesquisa brasileiros e internacionais. Utilizando-nos de dados experimentais para o sistema Fe-Cr-Mo-C, obtidos recentemente em nosso laboratório, e cálculos de primeiros princípios para o sistema Ni-Nb-Si, aliados a outros resultados experimentais da literatura, aperfeiçoamos os bancos de dados termodinâmicos existentes para estes dois sistemas, minimizando as inconsistências quanto às evidências experimentais em relação aos campos de estabilidade e equilíbrio entre fases. No sistema Fe-Cr-Mo-C, utilizamo-nos de dados experimentais para uma reotimização da descrição termodinâmica. Adotamos novas descrições para os binários Cr-Fe, C-Cr e C-Fe, com novos modelos para as fases cementita no sistema C-Fe e sigma no sistema Cr-Fe. Com essas alterações, fomos levados a reavaliar todas as descrições dos ternários, reotimizando-os quando necessário (C-Cr-Fe) ou apenas revalidando os modelamentos pré-existentes (C-Cr-Mo). Por fim, reotimizamos o quaternário como um todo, chegando a resultados satisfatórios quando comparados a resultados experimentais. As propriedades termodinâmicas do sistema Nb-Ni-Si são pouquíssimo conhecidas. Por este motivo, não há dados suficientes na literatura para realizar um assessment completo deste sistema. Por isto, decidimos realizar cálculos de primeiros princípios de estrutura eletrônica, para a determinação de energias de formação dos compostos ternários presentes neste sistema. Os sistemas binários Nb-Ni, Nb-Si e Ni-Si, por outro lado, são bem conhecidos, cada um deles contando com diversas descrições termodinâmicas publicadas ao longo dos últimos anos. Por esta razão, adotamos as mais recentes descrições termodinâmicas dos binários como ponto de partida para o modelamento do sistema ternário. O resultado do modelamento, quando comparado aos poucos dados experimentais disponíveis, é bastante satisfatório.The aim of this project is the combination of advanced experimental and theoretical approaches for the development of thermodynamic databases dedicated to modelling steels and high performance alloys. Examples of materials are centrifugally-cast superalloys designed for use in reforming and pyrolisis furnaces, as well as intermetallic-reinforced tool steels. The theoretical methods are the combination of electronic structure calculations and thermodynamic modeling at finite temperatures using the CALPHAD method. This methodology has been used by different scientific groups, both in Brazil and around the world. Using experimental data in the Fe-Cr-Mo-C sytem, recently determined in our laboratory, and first principles calculations in the Nb-Ni-Si system, together with other experimental results from the literature, we improved the existing thermodynamic databases for these two systems, minimizing discrepancies regarding the experimental evidence about phase stability fields and phase equilibria. In the Fe-Cr-Mo-C system, we employed experimental data for a reoptimization of the thermodynamic description. We adopted new descriptions for the binary Cr-Fe, C-Cr, and C-Fe systems, with new models for cementite in the C-Fe system, and sigma in the Cr-Fe system. Because of these alterations, a reevaluation of the ternary descriptions was necessary, reassessing them when required (C-Cr-Fe) or just revalidating existing models (C-Cr-Mo). After that, we re-optimized the quaternary system, arriving at satisfactory results, in comparison with experimental data. The thermodynamic properties of the Ni-Nb-Si system is almost completely unknown. For that reason, there are not enough data in the literature to perform a complete assessment of the system. With that in mind, we decided to perform first-principles electronic structure calculations, in order to determine the formation energies of the ternary compounds. The binary systems, on the other hand, are very well-known, each one of them with several published thermodynamic assessments during the last few years. For this reason, we adopted the most recent thermodynamic descriptions of the binaries as a starting point for the modelling of the ternary system. The result of the modelling is very satisfactory, in comparison with the few experimental information available.
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Gaiotti, Sebastiano <1993>. "Modeling and analysis of the (H2C2)n(HCN)m gas-phase clusters by ab initio and DFT computational methods for astrochemical applications". Master's Degree Thesis, Università Ca' Foscari Venezia, 2021. http://hdl.handle.net/10579/20099.
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Among the different purposes of astrochemistry, there is the study of chemical processes in the Interstellar Medium (ISM), and the corresponding reaction pathways that may lead to the formation of biological molecules. Within this framework, in recent years some gas-phase clusters have been investigated since they may constitute the first steps involved in these reaction networks.
The study presented in this thesis aims to illustrate different types of clusters involving hydrogen cyanide and acetylene, such molecules present a lot of interesting interactions including Van der Waals and dispersion forces. For each cluster, geometry, energy and other parameters have been optimized through many ab initio and Density Function Theory (DFT) methods (also including some of the semiempirical Grimme's density functionals).
Finally, non-covalent interactions were investigated through the Quantum Theory of Atoms in Molecules (QTAIM) to identify the nature of the interactions that lead to the stability of (H2C2)n, (HCN)m and mixed structures (H2C2)n(HCN)m.
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Vendrusculo, Bruno de Oliveira. "Estudo por dinâmica molecular da transição de fase estrutural de nanotubos de carbono por indução de pressão: um método ab initio". Universidade Federal de Santa Maria, 2012. http://repositorio.ufsm.br/handle/1/9232.
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Conselho Nacional de Desenvolvimento Científico e TecnológicoThis work aims to study the computational training of new phases of materials based on carbon nanotubes using as precursor materials. The procedure consists in simulate bundle formed by carbon nanotubes (NTC) (5, 5), (6, 6) and (7, 7) under hydrostatic pressure of 10, 15, 20, 25 and 30 GPa The present study was through the method of ab initio molecular dynamics, as implemented in the SIESTA code. The bundles of nanotubes were studied through a unit cell containing four nanotubes, using the periodic boundary conditions. As a result, for nanotubes (5, 5) of 10 GPa it has occurred a phase transition similar to graphite, which has graphene sheets stacked with the atoms distant from the first neighboring 1.42 Å, indicating the formation of a structure rich in sp2 hybridization. By applying to the nanotubes 30 GPa (5, 5) and (7, 7), there was an amorphous structure similar to cubic diamond with carbon atoms distant from the first neighboring 1.54 Å, indicating a phase with rich sp3 bonds. Finally, for all other combinations, the results were the transition to amorphous structures, varying according to the diameter of the nanotube and the pressure applied, the ratios of sp2 and sp3 carbon, as well as the distances found for the first neighbors were approximately 1.48 Å indicating the formation of transitional phases between sp2 and sp3 hybridizations.
O presente trabalho tem por objetivo o estudo computacional da formação de novas fases de materiais à base de carbono utilizando nanotubos como materiais precursores. O procedimento consiste em simular feixes formados por nanotubos de carbono (NTC) (5, 5), (6, 6) e (7, 7) sob pressão hidrostática de 10, 15, 20, 25 e 30 GPa. A realização desse estudo se deu através do método de Dinâmica Molecular ab initio, conforme implementada no código SIESTA. Os feixes de nanotubos foram estudados através de uma célula unitária contendo quatro nanotubos, valendo-se das condições periódicas de contorno. Como resultado, para os nanotubos (5, 5) à 10 GPa ocorreu a transição para uma fase semelhante ao grafite, a qual possui folhas de grafeno empilhadas, com átomos distantes a 1,42 Å dos primeiros vizinhos, indicando a formação de uma estrutura rica em hibridizações sp2. Para a aplicação de 30 GPa aos nanotubos (5, 5) bem como aos (7, 7), observou-se uma estrutura amorfa, semelhante ao diamante cúbico, com átomos de carbono distantes 1,54 Å dos primeiros vizinhos, indicando uma fase rica em ligações sp3. Finalmente, para as demais combinações, os resultados foram a transição para estruturas amorfas, variando conforme o diâmetro do nanotubo e a pressão aplicada, a relação de carbonos sp2 e sp3, bem como as distâncias encontradas para os primeiros vizinhos, que foram de aproximadamente 1,48 Å, indicando a formação de fases transitórias entre as hibridizações sp2 e sp3.
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Eklund, Robert. "Computational Analysis of Carbohydrates : Dynamical Properties and Interactions". Doctoral thesis, Stockholm : Department of Organic Chemistry, Stockholm University, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-538.
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Zheng, Lixin. "Properties of Liquid Water and Solvated Ions Based on First Principles Calculations". Diss., Temple University Libraries, 2018. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/527565.
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PhysicsPh.D.
Water is of essential importance for life on earth, yet the physics concerning its various anomalous properties has not been fully illuminated. This thesis is dedicated to the understanding of liquid water from aspects of microscopic structures, dynamics, electronic structures, X-ray absorption spectra, and proton transfer mechanism. This thesis use the computational simulation techniques including density functional theory (DFT), ab initio molecular dynamics (AIMD), and theoretical models for X-ray absorption spectra (XAS) to investigate the dynamics and electronic structures of liquid water system. The topics investigated in this thesis include a comprehensive evaluation on the simulation of liquid water using the newly developed SCAN meta-GGA functional, a systematic modeling of the liquid-water XAS using advanced ab initio approaches, and an explanation for a long-puzzling question that why hydronium diffuses faster than hydroxide in liquid water. Overall, significant contributions have been made to the understanding of liquid water and ionic solutions in the microscopic level through the aid of ab initio computational modeling.
Temple University--Theses
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SOSSO, GABRIELE CESARE. "A neural network potential for the phase change material gete: large scale molecular dynamics simulations with close to ab initio accuracy". Doctoral thesis, Università degli Studi di Milano-Bicocca, 2013. http://hdl.handle.net/10281/40098.
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Phase change materials based on chalcogenide alloys are attracting an increasing interest
worldwide due to their ability to undergo reversible and fast transitions between the amorphous
and crystalline phases upon heating. This property is exploited in rewritable
optical media (CD, DVD, Blu-Ray Discs) and electronic nonvolatile memories of new
concept, the Phase Change Memories (PCM). The strong optical and electronic
contrast between the crystal and the amorphous allows discriminating between the two
phases that correspond to the two bits of binary information zero and one. The material
of choice for applications is the ternary compound Ge2Sb2Te5 (GST). However, the
related binary alloy GeTe has also been thoroughly investigated because of its higher
crystallization temperature and better data retention at high temperature with respect
to GST.
PCM devices, born thanks to the work of Ovshinsky in the late 1960s, offer extremely
fast programming, extended cycling endurance, good reliability and inexpensive,
easy integration. A PCM is essentially a resistor of a thin film of the chalcogenide alloy
with a low field resistance that changes by several orders of magnitude across the phase
change. In memory operations, cell read out is performed at low bias. Programming the
memory requires instead a relatively large current to heat up the chalcogenide and induce
the phase change, either the melting of the crystal and subsequent amorphization
(RESET) or the recrystallization of the amorphous (SET).
In the last few years, atomistic simulations based on density functional theory (DFT)
have provided useful insights into the properties of phase change materials. However,
several key issues such as the thermal conductivity at the nanoscale or the origin of
the fast crystallization, just to name a few, are presently beyond the reach of ab initio
simulations due to the high computational cost. In fact, first principles simulations can
deal at most with 10^2 atoms on the timescale of 10^2 ps, while many properties like thermal
conductivity or direct simulations of the crystallization process require at least 10^3 atoms
on the timescale of 10^3 ps.
The development of reliable classical interatomic potentials is a possible route to
overcome the limitations in system size and time scale of ab initio molecular dynamics.
However, traditional approaches based on the fitting of simple functional forms for the
interatomic potentials are very challenging due to the complexity of the chemical bonding in the crystalline and amorphous phases revealed by the ab initio simulations. A possible
solution has been proposed recently by Behler and Parrinello, who developed highdimensional
interatomic potentials with close to ab initio accuracy employing artificial
neural networks (NN).
In this thesis work, we developed a classical interatomic potential for the bulk phases
of GeTe employing this NN technique. The potential was validated by comparing results
on the structural and dynamical properties of liquid, amorphous, and crystalline GeTe
derived from NN-based simulations with the ab initio data obtained here and in previous
works [10]. The NN potential displays an accuracy close to that of the underlying DFT
framework at a much reduced computational load that scales linearly with the size of the
system. It allows us to simulate several thousands of atoms for tens of ns, which is well
beyond present-day capabilities of DFT MD. The development of a reliable interatomic
potential with close to DFT accuracy is thus a breakthrough in the modeling of phase
change materials.
To date, we employed our NNP in order to investigate three issues:
1. the thermal conductivity of the amorphous phase
2. the viscosity and atomic mobility in the supercooled liquid and overheated amorphous
phases
3. the dynamics of homogeneous crystallization of the liquid and amorphous phases
Thermal conductivity is a key property for the PCM operation, as the phase changes
corresponding to the memory writing/erasing processes strongly depend upon heat dissipation
and transport. Moreover, thermal cross-talks among the different bits is a crucial
reliability issue in PCM. Although experimental data on thermal conductivity are available
for few materials in this class it is unclear whether the value measured in the
bulk phase could also describe the behavior of the material in nanoscaled devices (10-20
nm) which might be smaller than the phonon mean free path. This is particularly relevant
for PCM architectures based on nanostructures employing nanowires, colloidal nanoparticles,
thin bridges and nanotubes. In fact, amorphous materials can also display
propagating phonons with mean free path as long as 0.5 μm. This has been demonstrated
for amorphous Si where propagating modes with long mean free path contribute to
half of the total thermal conductivity. It is therefore of great technological relevance to
assess whether similar propagating modes with long mean free path might be present
in amorphous phase change materials as well. Atomistic simulations can provide crucial
insights into the thermal transport properties of phase change materials suitable to aid
a reliable modelling of the device operation. However, the calculation of the thermal conductivity
in an amorphous system requires very long simulations (on the ns scale) of large
models (thousands of atoms) that are presently beyond the reach of fully DFT simulations.
The use of NN potentials allowed us to compute the mean free path of phonons in
a-GeTe and to assess that ballistic transport is inhibited by disorder even at the nanoscale. The key property that makes some chalcogenide alloys suitable for applications in
PCM is the high speed of the transformation which leads to full crystallization on the
time scale of 10-100 ns upon Joule heating. What makes some compounds alloys so special
in this respect and so different from most amorphous semiconductors is, however, still a
matter of debate. The driving force for crystallization of the supercooled liquid is actually
the free energy difference between the crystal and the supercooled liquid. However, the
crystallization is controlled both by the driving force and by the atomic mobility. The
driving force vanishes at melting and increases upon cooling. A large atomic mobility at
high supercooling can thus boost the crystallization speed. These conditions can actually
be met by fragile liquids. In fact, supercooled liquids are classified as fragile or strong
on the basis of the temperature dependence of their viscosity [16]. An ideal strong liquid
shows an Arrhenius behavior of the viscosity η from the melting temperature Tm down
to the glass transition temperature Tg. On the contrary, in a fragile liquid η is very low
down to a crossover temperature T∗, below which a steep rise of the viscosity (and thus
a steep decrease in the mobility) is observed. If T∗ is sufficiently far from the melting
temperature (Tm), high supercooling and large atomic mobility can be met at the same
time. The question is thus whether phase change materials are fragile liquids or not. Due
to the high crystallization speed it is unfortunately not possible to measure η below Tm
experimentally. We have thus addressed this problem by MD simulations and we have
demonstrated that indeed GeTe is a very fragile liquid (fragility index ∼ 100). Moreover
a breakdown of the Stokes-Einstein relation between the viscosity and the diffusion coefficient
is found, which further increase the atomic mobility down to temperatures very
close to Tg. Hysteretic effects in the heating of the amorphous phase above Tg have been
addressed as well.
Finally, we have performed direct simulations of the homogeneous crystallization of
the supercooled liquid and amorphous phases with 4000-atom models and simulation
times of several ns. Although similar simulations have been previously performed by fully
DFT simulations, the limitations in size (about 200 atoms) and time scale (500 ps)
prevented a reliable estimate of the size of the critical nucleus and of the crystallization
speed, which are instead accessible by our large scale simulations.
This thesis is organised as follows: in the introductory chapter 1 I provide essential
information about phase change materials and phase change memories. Chapter 2 is
dedicated to theory and methods, while chapters 3,4,5 and 6 are devoted to the results
on the thermal conductivity of the amorphous phase of GeTe, on the properties of its
supercooled liquid phase and on the homogeneous crystallization from the melt and the
overheated amorphous phase.
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Parab, Prajakta Rajaram Verfasser], Karl Alexander [Akademischer Betreuer] [Heufer y Ravi Xavier Filipe [Akademischer Betreuer] Fernandes. "Computational Chemical Kinetics of Biofuel Combustion Using Ab-Initio Methods and Statistical Rate Theories / Prajakta Rajaram Parab ; Karl Alexander Heufer, Ravi Xavier Filipe Fernandes". Aachen : Universitätsbibliothek der RWTH Aachen, 2018. http://d-nb.info/1162503394/34.
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Parab, Prajakta Rajaram [Verfasser], Karl Alexander [Akademischer Betreuer] Heufer y Ravi Xavier Filipe [Akademischer Betreuer] Fernandes. "Computational Chemical Kinetics of Biofuel Combustion Using Ab-Initio Methods and Statistical Rate Theories / Prajakta Rajaram Parab ; Karl Alexander Heufer, Ravi Xavier Filipe Fernandes". Aachen : Universitätsbibliothek der RWTH Aachen, 2018. http://nbn-resolving.de/urn:nbn:de:101:1-2018071009355498809069.
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Osborn, Tim H. "COMPUTATIONAL DESIGN AND CHARACTERIZATION OF SILICENE NANOSTRUCTURES FOR ELECTRICAL AND THERMAL TRANSPORT APPLICATIONS". Wright State University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=wright1401712678.
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