Dissertations / Theses on the topic 'Ab-initio simulations'
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Hasnip, Philip James. "Ab initio simulations of transition metal surfaces." Thesis, University of Cambridge, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.272735.
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Adams, Donat Jozsef. "Ab initio simulations of Earth forming minerals /." kostenfrei, 2007. http://e-collection.ethbib.ethz.ch/view/eth:30017.
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Astala, Roope Kalle. "Ab initio simulations of defects in strontium titanate." Thesis, University of Cambridge, 2003. https://www.repository.cam.ac.uk/handle/1810/251864.
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Prasongkit, Jariyanee. "Molecular Electronics : Insight from Ab-Initio Transport Simulations." Doctoral thesis, Uppsala universitet, Materialteori, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-160474.
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This thesis presents the theoretical studies of electronic transport in molecular electronic devices. Such devices have been proposed and investigated as a promising new approach that complements conventional silicon-based electronics. To design and fabricate future nanoelectronic devices, it is essential to understand the conduction mechanism at a molecular or atomic level. Our approach is based on the non-equilibrium Green's function method (NEGF) combined with density functional theory (DFT). We apply the method to study the electronic transport properties of two-probe systems consisting of molecules or atomic wires sandwiched between leads. A few molecular electronic devices are characterized; namely, conducting molecular wires, molecular switches and molecular recognition sensors. The considered applications are interconnection of different nanoelectronic units with cumulene molecular wires; adding switching functionality to the molecular connectors by applying stress to the CNT-cumulene-CNT junction or by introducing phthalocyanine unit; sensing of individual nucleotides, e.g., for DNA sequencing applications. The obtained results provide useful insights into the electron transport properties of molecules. Several interesting and significant features are analyzed and explained in particular such as, level pinning, negative differential resistance, interfering of conducting channels etc.
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Craig, M. "Ab initio simulations of minerals using localised basis sets." Thesis, University of Cambridge, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.598117.
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I have applied the recently developed ab initio simulation code, SIESTA, to a variety of studies of mineral systems. The code is designed to be capable of linear scaling, and promises the ability to simulate systems much larger than other ab initio methods. The SIESTA code is used in several studies of cation ordering to calculate small energy differences between structures in which cations are rearranged. The results are compared to those given by other ab initio methods, and by empirical potentials. SIESTA is found to be a useful tool, capable of improving on the accuracy of empirical potential methods, but able to tackle larger systems than traditional ab initio techniques. A study of the high-pressure phase transition in cristobalite is also used as a comparison between SIESTA and other methods. This study shows SIESTA to be capable of giving results comparable to the best ab initio methods, and the quality of results that can be expected at varying levels of convergence are demonstrated. A study of the adsorption of an adenine monolayer on a graphite surface demonstrates the ability of the code to perform calculations on a large unit cell practically, and illustrates some of the issues related to the Basis Set Superposition Error (BSSE) that is a disadvantage of the SIESTA method. A wide general study of adsorption of organic molecules on clay mineral surfaces shows some trends in binding energies of different molecules and cations, and considers the effect of absorbed water on the binding of a molecule. The practical utility of ab initio calculations for this type of study is demonstrated, raising the possibility of future work to fully understand the complex and environmentally important interactions between organic pollutant molecules and clay in soils.
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Kochman, Michal. "Ab initio simulations of reactions occurring in molecular crystals." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/8906.
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Although the solid state may not usually be thought of as an environment suitable for chemical reactions under mild conditions, a growing number of organic compounds are known to undergo interesting and, in many cases, practically useful chemistry in the molecular crystal phase. Of particular interest are photochemical reactions occurring in molecular crystals, which possess a number of characteristic features that make them attractive to study using the methods of theoretical chemistry. Firstly, molecular packing and steric effects strongly influence the mechanistic course of reactions in the crystal phase, which in some cases enables clean and controllable chemistry, including synthetic reactions as well as reversibly switchable isomerisations accompanied by a change of the macroscopic properties of the crystal, such as shape and colour. Secondly, in part due to their fast (subpicosecond) timescales and relatively low conversion rates (of the order of a few per cent), many of these reactions present challenges to experimental techniques, which computer simulation methods are uniquely positioned to overcome. Finally, these systems lend themselves well to simulation using a hybrid combination of two ab initio electronic structure methods, one of which is used to describe the electronic excitation of a reactive molecule while the other is applied to the surrounding bulk lattice. This thesis describes the computational modelling of two such reactions: the syn-anti photoisomerisation of 7-(2-pyridyl)indole and the reversible cis-enol⇄trans-keto photoisomerisation of N-salicylidene-2-chloroaniline. The solid-state mechanisms and rates of both reactions are computed using the TD-DFT/DFT hybrid method, in the latter case validating a previously postulated reaction mechanism. Furthermore, the thermal (ground-state) tautomerisation reaction in the photochromic and non-photochromic polymorphs of N-salicylidene-2-chloroaniline is investigated through calculations at the DFT level of theory. The results of these calculations indicate that both polymorphs are thermochromic, but tautomeric equilibrium in the non-photochromic polymorph is more sensitive to temperature than in the photochromic polymorph. Additionally, a critical assessment is presented of the accuracy of the various emphab initio methods employed throughout this work.
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Bhandari, Ghadendra B. "Synthesis and AB-Initio Simulations of Colloidal PBS Nanosheets." Bowling Green State University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1403519605.
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Musella, Riccardo. "Ab initio simulations of MgO and MgSiO3 for planetary modelling." Sorbonne Paris Cité, 2016. http://www.theses.fr/2016USPCC052.
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Les intérieurs des exoplanètes représentent un domaine au carrefour de la planétologie, de la physique des hautes pressions et de l'astronomie. Les observations semblent indiquer que les planètes rocheuses sont les plus nombreuses. Cependant, avec les technologies actuelles, les planètes de type-Terre sont encore difficilement détectables et seuls de nouveaux programmes scientifiques pourront atteindre la précision nécessaire permettant obtenir un échantillon non biaisé de planète de type Terre. À present, les exoplanètes les plus similaires à la Terre sont presque toutes des planètes rocheuses massives, appelées super-Terres. Dans ce travail, nous avons étudié les composés MgO, MgSiO3 et Fe qui constituent les intérieurs des super-Terres et probablement les coeurs des planètes géantes. Recréer en laboratoire les conditions thermodynamiques que l'on rencontre à l'intérieur de ces corps représente un vrai défi. Dans certains cas, le seul outil disponible est fourni par les simulation numériques. Nous avons utilisé la dynamique moléculaire ab initio sur les composés MgO (jusqu'à —10 TPa) et MgSiO3 (jusqu'à —2 TPa) afin d'obtenir leurs équations d'état, courbe de fusion, métallisation etc. . . Pour Fe nous avons utilisé la dynamique moléculaire sans orbitales afin d'étendre la courbe de fusion jusqu'à —100 TPa. Les résultats que nous avons obtenus pourront donc être utilisés dans le futur pour construire des modèles de planètes plus précis. Les courbes de fusion calculées dans ce travail auront également un fort impact sur les modèles planétairesThe interiors of exosolar planets represent a new fertile field at the interface of planetary science, high pressure physics and astronomy. The observations seem to indicate that rocky planets are the most numerous. Nevertheless, with the current technology, Earth-like planets are still hardly detectable and only new scientific programs could bring enough accuracy to obtain an unbiased sample of Earth-like objects. At present time, the characterized exoplanets more similar to the Earth are massive rocky planets, dubbed super-Earths. In this thesis, we have studied MgO, MgSiO3 and Fe compounds which are the main constituents of the deep interiors of massive rocky planets and possibly of cores of giant planets. The thermodynamic conditions inside these objects are very challenging to reproduce in laboratory; numerical simulations are sometimes the only available tool to explore the phase diagram of the minerais at such extreme conditions. We used ab initio molecular dynamics to provide data on MgO (up to pressure -10 TPa) and MgSiO3 (up to pressure -2 TPa) such as the equation of state, the melting line, the metallization etc. . . For Fe we used the orbital free molecular dynamics in order to extend the iron melting line up to -100 TPa. Our ab initio EOS tables obtained for MgO and MgSiO3 could be used to improve the models of massive exoplanets including aspects such as the influences of phase transitions, of time-evolution and a complete description of the thermal state. Also, the melting lines calculated for MgO, MgSiO3 and Fe may have a strong impact on these models. What language could be considered as their own? For them, when did French cease to be a foreign language ? More generally, what remains of an author who has chosen to express himself in another language?
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Osborn, Tim H. "Ab Initio Simulations of Hydrogen and Lithium Adsorption on Silicene." Wright State University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=wright1283177822.
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Wang, JinJin. "Growth mechanisms of single-walled carbon nanotubes by ab-initio simulations." Thesis, University of Cambridge, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.607748.
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Pedroza, Luana Sucupira. "Desenvolvimento de novas aproximações para simulações ab initio." Universidade de São Paulo, 2010. http://www.teses.usp.br/teses/disponiveis/43/43134/tde-28032011-155857/.
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Simulações computacionais são ferramentas essenciais para a compreensão num nível microscópico de diversos fenômenos que ocorrem na natureza. Em particular, simulações ab initio, isto é, de primeiros princípios, podem predizer novas propriedades e auxiliar na interpretação de resultados experimentais, sem a necessidade de potenciais empíricos os quais são ajustados para uma específica configuração do sistema. No entanto, mesmo para simulações ab initio são necessárias aproximações tanto para o cálculo de estrutura eletrônica quanto para a descrição dos movimentos nucleares. Nesta tese, novas aproximações para o funcional de energia de troca e correlação da Teoria do Funcional da Densidade (DFT) são propostas e testadas no cálculo de estrutura eletrônica de átomos, moléculas e sólidos. Para a descrição dos movimentos nucleares a técnica de Monte Carlo é utilizada, porém as energias totais são obtidas com a DFT. Propomos também uma nova metodologia que permite descrever movimentos intramoleculares de sistemas cujas frequências de vibração não podem ser tratadas classicamente. Como aplicações estudamos aglomerados de água e água líquida, mostrando a relevância dessa nova metodologia na descrição de propriedades estruturais, vibracionais e de momento de dipolo desses sistemas.Computer simulations are essential tools for a microscopic understanding of many processes that occur in nature. In particular, ab initio simulations, i.e., first principles simulations, can predict new properties and support experimental results, without the need to use empirical potentials which are fitted for a specific configuration of the system. However, even in ab initio simulations it is necessary to do approximations for the electronic structure calculations and for the description of the nuclear movements. In this thesis, new approximations for the exchange-correlation energy functional of Density Functional Theory (DFT) are proposed and tested for atoms, molecules and solids. The description of the nuclear movements was done using the Monte Carlo technique, however the total energy calculations were obtained by DFT. We also propose a new methodology which allows the description of intramolecular movements whose vibrational frequencies can not be treated classically. As an illustration, we have studied water clusters and liquid water, showing the relevance of this new methodology on the description of structural, vibrational and of the dipole moment of these systems.
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Cassone, Giuseppe. "Ab initio molecular dynamics simulations of H-bonded systems under an electric field." Thesis, Paris 6, 2016. http://www.theses.fr/2016PA066061/document.
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Malgré le mécanisme de base du transport protonique (PT) dans l'eau ait été proposé en 1806, à ce jour il n'existe pas de théorie complète qui décrive la protolyse. Ce phénomène est à la base du fonctionnement des batteries à hydrogène et de nombreux processus biologiques. Grâce à la technique de dynamique moléculaire Car-Parrinello (CPMD) et à l'aide de l'application d'un champ electrique (EF), une partie de cette thèse a été consacrée à l'étude du PT dans deux phase de la glace: la phase Ih et sa contrepartie ferroélectrique, la glace XI. Certains mécanismes ont été révélés: le rôle joué par les oxygènes lorsque se produit le PT et la contribution du (dés)ordre afin d'assister ce processus [1,2]. Le phénomène du PT est aussi à la base de nombreaux convertisseurs d'énergie constitués par le méthanol tels que le Direct Methanol Fuel Cells et les membranes Nafion. Afin de révéler la nature intime du PT dans le méthanol liquide, une série de simulations CPMD ont été menées sous l'effet d'un EF extérieur. De cette façon il a été possible de comparer le rôle joué par les liasons hydrogène afin d'assister le PT [3]. De plus, quand les intensités du champ sont plus élevées que celles qui donnent lieu au PT, certaines réactions chimiques ont été observées dans le même échantillon "numérique" du méthanol. En exploitant des paramètres typique de la "Théorie de la fonctionnelle de la densité conceptuelle", il a été possible de clarifier les conditions qui donnent lieu à ces réactions chimiques. Enfin, afin de quantifier la contribution du EF à la formation de méthane et de formaldéhyde dans le système, des simulations de métadynamique en conjonction à ceux ab initio ont été menéesAlthough the basic mechanism of the proton transfer (PT) phenomenon in water has been envisaged in 1806, nowadays does not exist a detailed theoretical framework that envelop the protolysis process. This phenomenon is at the base of the operation of hydrogen batteries, as well as of many biological processes. Via the Car-Parrinello Molecular Dynamics (CPMD) technique and by means of the application of an electric field (EF), part of this thesis has been devoted to the detailed study of PT in two ice phases: ice Ih and its ferroelectric counterpart, ice XI. Several previously unknown mechanisms have been shown. As an example, the role played by the oxygens when a PT occurs and the contribution due to (dis)order in assisting this process [1,2]. The PT phenomenon is also at the base of the functioning of some methanol-based energy converters such as Nafion membranes. To the aim of disclosing the intimate nature of PT in liquid methanol, a series of CPMD simulations have been carried out by applying an external EF; the role played by the H-bond network have been also compared with the similar PT mechanism in water [3]. At field strengths higher than those leading to PT, several chemical reactions have been observed in this sample. By exploiting the conceptual Density Functional Theory framework, it has been possible to clarify the circumstances under which a given chemical reaction occurs. Moreover, in order to disclose the role played by the EF in assisting chemical reactions, the mechanism leading to the formation of formaldehyde and methane in the sample has been studied with metadynamics approaches in conjuction with the ab initio ones
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Fang, Wei. "Nuclear quantum effects from ab initio simulations : hydrogen-bonds and tunnelling rates." Thesis, University College London (University of London), 2017. http://discovery.ucl.ac.uk/10039743/.
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The quantum nature of nuclei plays an important role in materials and molecules containing light mass elements, for example in enzymes and water, which are crucial to life and technology. Yet in materials modelling, nuclear quantum effects (NQEs) are often ignored. Using the path integral theory, NQEs in hydrogen bonds and reaction rates for various systems described with density functional theory (DFT) have been examined. A review of the theoretical background, including DFT, path integral molecular dynamics, and the instanton rate theory, is given in Chapter 2. In Chapter 3, the NQEs on the binding energy of DNA base pairs are investigated, revealing that NQEs strengthen the binding of base pairs at room temperature. A counter-intuitive temperature dependence where NQEs are less significant at low temperature was also discovered and explained through a picture of competing quantum effects. In Chapters 4 and 5, hydrogen diffusion on metal surfaces is studied. Calculations show that ``broad-top" diffusion barriers exist on many metal surfaces, and that these have a distinct tunnelling behaviour compared to conventional ``parabolic-top" barriers. The theoretical and experimental implications of this unique behaviour are discussed. In Chapter 5, an improved multidimensional instanton rate theory is tested and applied to hydrogen diffusion on Pd(110), a complex potential energy surface that includes an interesting diffusion pathway over a second order saddle point. Finally, tunnelling assisted water diffusion on Pd(111) is studied using the instanton rate theory combined with DFT. It is found that tunnelling, including the tunnelling of oxygen atoms, plays a role in changing the water dimer diffusion mechanism on this surface at below 40 K. Water monomer and dimer diffusion on a variety of transition metal (111) surfaces have also been studied in this work.
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Li, Lan. "Ab-initio simulations of graphite defects and growth mechanisms of carbon nanotubes." Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.614271.
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Hassan, Ahmed Jama. "Ab Initio Simulations of Graphene-based Nanosensor for Detecting NO2 and Li." Wright State University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=wright1316317509.
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More, Joshua N. "Algorithms and computer code for ab initio path integral molecular dynamics simulations." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:b8ca7471-21e3-4240-95b1-8775e5d6c08f.
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This thesis presents i-PI, a new path integral molecular dynamics code designed to capture nuclear quantum effects in ab initio electronic structure calculations of condensed phase systems. This software has an implementation of estimators used to calculate a wide range of static and dynamical properties and of state-of-the-art techniques used to increase the computational efficiency of path integral simulations. i-PI has been designed in a highly modular fashion, to ensure that it is as simple as possible to develop and implement new algorithms to keep up with the research frontier, and so that users can take maximum advantage of the numerous electronic structure programs which are freely available without needing to rewrite large amounts of code. Among the functionality of the i-PI code is a novel integrator for constant pressure dynamics, which is used to investigate the properties of liquid water at 750 K and 10 GPa, and efficient estimators for the calculation of single particle momentum distri- butions, which are used to study the properties of solid and liquid ammonia. These show respectively that i-PI can be used to make predictions about systems which are both difficult to study experimentally and highly non-classical in nature, and that it can illustrate the relative advantages and disadvantages of different theoretical methods and their ability to reproduce experimental data.
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Pourovskii, Leonid. "Ab Initio Simulations of Transition Metal Alloys: Towards the Multiscale Modeling." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributr], 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3459.
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Totolici, Iacob Emanuel. "Ab initio simulations and neutron scattering studies of structure and dynamics in PdH." Thesis, University of Salford, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.395659.
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Lasoroski, Aurélie. "Etude de complexes de gadolinium d'intérêt pour l'IRM : simulations ab initio et propriétés magnétiques." Phd thesis, Université Pierre et Marie Curie - Paris VI, 2013. http://tel.archives-ouvertes.fr/tel-00876988.
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Lors d'examens IRM des agents de contraste sont utilisés afin d'affiner les diagnostics. Ces agents sont constitués d'un ion paramagnétique, la plupart du temps le gadolinium, chélaté par un ligand linéaire ou macrocyclique afin d'éviter tout relargage et donc toute toxicité. Dans cette thèse, nous étudions les propriétés magnétiques de complexes de gadolinium. Ces propriétés magnétiques influencent la relaxation d'une molécule d'eau coordinée à l'ion central, relaxation à l'origine des contrastes visibles sur les images IRM. Nous nous sommes intéressés à l'agent de contraste commercial ProHance ainsi qu'à des systèmes dérivés. Après avoir réalisé des simulations de dynamique moléculaire ab initio des espèces à étudier, et les avoir analysées, nous avons sur ces systèmes des calculs de structure électronique explicitant les interactions hyperfines en jeu au sein du système, ainsi que le Zero-Field Splitting. Il a ainsi été possible de définir un tenseur hyperfin moyen pour chacun des systèmes étudiés. De plus, une décomposition du terme en fonction de variables collectives géométriques a permis d'expliciter l'origine des fluctuations rapides du tenseur hyperfin dans le cas du ProHance. Enfin, le ZFS a été décomposé en un terme dit transitoire et un terme dit statique. Ceci permettra par la suite de modéliser la relaxation électronique des systèmes étudiés et la relaxation du proton de la molécule d'eau coordinée.
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Altschäffel, Jan [Verfasser]. "Ab initio molecular dynamics simulations of molecular scattering from metal(111) surfaces / Jan Altschäffel." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2021. http://nbn-resolving.de/urn:nbn:de:gbv:7-21.11130/00-1735-0000-0008-58F1-5-3.
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Lasoroski, Aurélie. "Etude de complexes de gadolinium d’intérêt pour l’IRM : simulations ab-initio et propriétés magnétiques." Paris 6, 2013. http://www.theses.fr/2013PA066216.
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Lors d’examens IRM des agents de contraste sont utilisés afin d’affiner les diagnostics. Ces agents sont constitués d’un ion paramagnétique, la plupart du temps le gadolinium, chélaté par un ligand linéaire ou macrocyclique afin d’éviter tout relargage et donc toute toxicité. Dans cette thèse, nous étudions les propriétés magnétiques de complexes de gadolinium. Ces propriétés magnétiques influencent la relaxation d’une molécule d’eau coordinée à l’ion central, relaxation à l’origine des contrastes visibles sur les images IRM. Nous nous sommes intéressés à l’agent de contraste commercial ProHance ainsi qu’à des systèmes dérivés. Après avoir réalisé des simulations de dynamique moléculaire ab initio des espèces à étudier, et les avoir analysées, nous avons sur ces systèmes des calculs de structure électronique explicitant les interactions hyperfines en jeu au sein du système, ainsi que le Zero-Field Splitting. Il a ainsi été possible de définir un tenseur hyperfin moyen pour chacun des systèmes étudiés. De plus, une décomposition du terme en fonction de variables collectives géométriques a permis d’expliciter l’origine des fluctuations rapides du tenseur hyperfin dans le cas du ProHance. Enfin, le ZFS a été décomposé en un terme dit transitoire et un terme dit statique. Ceci permettra par la suite de modéliser la relaxation électronique des systèmes étudiés et la relaxation du proton de la molécule d’eau coordinéeCurrently MRI exams use contrast agents to enhance contrast imaging and so diagnostics. A contrast agent is most of the time a gadolinium complex in which a chelate ligand is used to avoid Gd release, thus preventing toxic ion to spread in patient’s body. In this thesis we studied magnetic properties of gadolinium complexes that affect the relaxation of a water molecule coordinated to Gd, which is the source of contrast imaging. We focused on the commercial contrast agent ProHance, and some derivatives. The first step was to compute ab initio molecular dynamics of the different systems and analyse them. Then we calculated using quantum chemistry hyperfine interaction and Zero-Field Splitting. The analysis of hyperfine tensors was achieved for each system, and average terms were estimated. The origin of tensors’ fast fluctuations in ProHance system was identified thanks to geometrical collectives variables decomposition. ZFS was decomposed into two contributions: static and transient. We can now set up from ab initio all the necessary ingredients for modeling the electronic relaxation time and then the water coordinated molecule proton relaxation for each of the studied systems
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Domain, Christophe. "Simulations atomiques ab initio des effets de l'hydrogène et de l'iode dans le zirconium." Lille 1, 2002. https://pepite-depot.univ-lille.fr/RESTREINT/Th_Num/2002/50376-2002-31.pdf.
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Morawietz, Tobias [Verfasser], Jörg [Akademischer Betreuer] Behler, and Dominik [Akademischer Betreuer] Marx. "Efficient simulations of water with ab initio accuracy / Tobias Morawietz. Gutachter: Jörg Behler ; Dominik Marx." Bochum : Ruhr-Universität Bochum, 2016. http://d-nb.info/1089006381/34.
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Iglesias, Fernández Javier. "Elucidating catalytic mechanisms of glycoside hydrolases and transferases by means of ab initio molecular dynamics simulations." Doctoral thesis, Universitat de Barcelona, 2014. http://hdl.handle.net/10803/283551.
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Carbohydrates play a central role in transport and storage of energy and as molecular building blocks. Additionally, glycoconjugates, specifically glycoproteins and glycolipids, are important components of cell surfaces and the extracellular environment that mediate cellular and molecular interactions. Defects in glycosylation are associated with human diseases while the ability of glycans to modulate immune responses leads to them playing a critical role in susceptibility and resistance to pathogens. This huge amount of glycan structures requires the existence of a diverse group of degrading and remodelling enzymes: glycoside hydrolases (GHs) and glycoside transferases (GTs).
GHs and GTs are highly specific enzymes responsible of the hydrolysis (GHs) and formation (GTs) of glycosidic bonds in carbohydrates. They are responsible for the modification of polysaccharides and glycoconjugates involved in numerous biological processes such as pathogenesis mechanisms, cell-cell recognition and polysaccharide degradation for biofuel processing. Knowledge of their enzymatic mechanism at a molecular level is crucial to understand how carbohydrates are assembled/degraded in organisms, as well as in developing new drugs. The detailed characterization of the transition state of the chemical reaction in which they participate, for instance, is key for the development of TS-analog inhibitors, which are known to be very efficient.
In recent years, our group has investigated the implications of the conformational changes on the substrate during catalysis in several GHs and has related these changes with the conformations that can be sampled by a single sugar unit (e.g. glucose). This was analyzed by adapting sugar puckering coordinates as collective variables in ab initio metadynamics simulations. These studies are having a significant impact not only in the theoretical community but also in biochemistry and biophysics, because of the possibility to predict substrate catalytic itineraries for GHs. In this thesis, we extend these analyses to other sugar molecules to verify the proposed catalytic itineraries and also to GH inhibitors and sugar oxocarbenium ions to gain insights into transition state mimicry.
Unlike GHs, known to operate by means of a double displacement mechanism, the reaction mechanism of retaining GTs is controversial. Both a two-step mechanism (by analogy to retaining glycoside hydrolases) and a one-step mechanism have been proposed and studied by means of quantum mechanics / molecular mechanics (QM/MM) simulations. Here, we applied this methodology to elucidate the catalytic mechanism of an engineered glycoside hydrolase and a glycoside transferase, giving support for a front-face single displacement mechanism.Los azúcares presentan una gran variabilidad estructural que es aprovechada por los diferentes organismos para realizar una multitud de procesos biológicos, que incluyen el almacenamiento de energía, el reconocimiento y la señalización celular. Las glicosil hidrolasas y glicosil transferasas son las enzimas responsables de la hidrólisis y síntesis, respectivamente, de estos biopolímeros y por lo tanto están presentes en una gran variedad de procesos celulares. Las técnicas de modelado molecular permiten analizar estos procesos biológicos, como por ejemplo la reacción de formación de un enlace entre azúcares, a un nivel atomístico. De esta forma, se pueden describir los cambios conformacionales que se producen en el sustrato al unirse a la enzima, identificar el estado de transición de la reacción química y determinar otros aspectos fundamentales de la catálisis enzimática.
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Lord, Adam. "An investigation of metastable electronic states in ab-initio simulations of mixed actinide ceramic oxide fuels." Thesis, Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/45840.
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First-principles calculations such as density functional theory (DFT) employ numerical approaches to solve the Schrodinger equation of a system. Standard functionals employed to determine the cohesive system energy, specifically the local density and generalized gradient approximations (LDA and GGA), underestimate the correlation of 5f electrons to their ions in AO₂ systems (A=U/Pu/Np). The standard correction, the "Hubbard +U," causes the multidimensional energy surface to develop a large number of local minima which do not correspond to the ground state (global minimum). Because all useful energy values derived from DFT calculations depend on small differences between relatively large cohesive energies, comparing systems wherein one or more of the samples are not in the ground state has the potential to introduce large errors. This work presents an analysis of the fundamental issues of metastable states in both pure and binary AO₂ systems, investigates novel methods of handling them, and describes why current literature approaches which appear to work well for the pure compounds are not well-suited for systems containing multiple actinide species.
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Hemmen, Sascha Michael [Verfasser]. "Ab initio simulations of the P-cluster in nitrogenase and multi-scale methods / Sascha Michael Hemmen." [Clausthal-Zellerfeld] : [Univ.-Bibliothek], 2008. http://d-nb.info/988542870/34.
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Thomson, David Ian. "Ab-initio computer simulations in the study of metallic behaviour : gallium impurities in aluminium grain boundaries." Thesis, University of Cambridge, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627347.
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Nassour, Ayoub. "Etude vibrationnelle des alliages semi-conducteurs II-VI et III-V : simulations empirique et ab initio." Thesis, Metz, 2008. http://www.theses.fr/2008METZ040S/document.
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Nos travaux sont consacrés à la promotion du modèle de percolation phénoménologique en employant des méthodes indépendantes et libres de tout paramètre. Nous avons utilisé à cet effet des codes ab initio existants (PWscf et SIESTA) et développé une méthode semi-empirique pour étudier les propriétés vibrationnelles des alliages AxB1 xC. Les paramètres techniques du code PWscf ont été testés sur les composés binaires ZnSe, ZnTe et BeSe pour lesquels nous avons confronté nos résultats aux données expérimentales et théoriques disponibles. La validation du modèle de percolation a et e effectué sur l alliage Zn(Se,Te) appartenant à la catégorie des semi-conducteurs 1-liaison ! 2-modes. Nous avons confirmé le caractère général du comportement bimodal prévu par le modèle de percolation en montrant son existence pour chacune des liaisons Zn Se et Zn Te. Les propriétés vibrationnelles et structurales de Zn(Se,Te) ont et e calculées à différentes concentrations avec des cellules optimisées à 64 atomes. Les résultats obtenus sont en bon accord avec l expérience. Nous présentons en détail notre méthode semi-empirique de calcul de spectre de phonons, applicable en principe à tous les alliages sans restriction sur la taille des super-cellules. La mise au point a été réalisé sur les alliages (Zn,Be)Se et (In,Ga)As avec des cellules à64 atomes relaxées d une façon ab initio. L application de notre méthode à(In,Ga)As à 50% simulé par une super-cellule à 8.103 atomes relaxée avec un potentiel harmonique met en évidence que l étude des phonons demande des super-cellules qui reflètent fidèlement le désordre d un alliageOur work is devoted to promoting the percolation model using phenomenological methods which are independent and free from any need of external parameters. We used for this purpose existing ab initio codes (PWscf and SIESTA) and developed a semiempirical method to study the vibrational properties of AxB1 xC alloys. The technical parameters of the PWscf code were tested on ZnSe, BeSe ZnTe binary compounds, for which we have confronted our results with theoretical and experimental data available. The percolation model validation was done on the alloy Zn(Se, Te) belonging to the category of 1-bond ! 2-modes semi-conductors. We have confirmed the general bimodal behavior provided by the percolation model showing its existence for each bond Zn Se and Zn Te. The vibrational and structural properties of Zn(Se, Te) were calculated for different concentration using optimized cells of 64 atoms. The results are in good agreement with experiments. We present in detail our semi empirical method of calculating the spectrum of phonons, in principle applicable to all alloys without restriction on the size of super-cells. The development was carried out on (Zn, Be)Se and (In, Ga)As alloys with cells of up to 64 atoms relaxed from first principles. The application of our method to (In, Ga)As at 50% simulated by a super-cell of 8.103 atoms with a harmonic relaxation potential underlines the fact that the study of phonons in alloys requires the use of supercells which adequately describe the alloy disorder
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Walbrühl, Martin. "Diffusion in the liquid Co binder of cemented carbides: Ab initio molecular dynamics and DICTRA simulations." Thesis, KTH, Materialvetenskap, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-140880.
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A fundamental quantum mechanical modelling approach is used for calculating liquid diffusion parameters in cemented carbides. Up to now, no detailed description of diffusion for alloying elements in a liquid Co matrix is available. Neither are experimental measurements found in the literature for the self- or impurity diffusion in the liquid Co system. State of the art application is the description of gradient formation in cemented carbide systems using DICTRA. In this work it is assumed that diffusion during sintering of cemented carbides takes place mainly in the liquid Co binder phase. With this assumption one can calculate the diffusion coefficient for different alloying elements like W, Ti, N and C in a liquid Co matrix phase. The mean square displacement (MSD) of the diffusing atoms is used to obtain the diffusion coefficients which could be simulated by Ab initio Molecular Dynamics (AIMD). By fitting the computed temperature dependence with the Arrhenius relation one can determine the frequency factor and the activation energy which allows to give a quantitative description of the diffusion. Three methods will be used for validating the data from this work. Available estimated literature values based on calculations (scaling laws, a modified Sutherland equation and classical molecular dynamics) will be used to compare the results in a first instance. The general agreement for diffusion in liquid metals will be done by comparison with experimental data for the liquid Fe system. In a last step, the diffusion values obtained by this work will be used to create a kinetic database for DICTRA. The gradient simulations will be compared with experimentally measured gradients. The AIMD simulations are performed for binary diffusion systems to investigate the diffusion between the liquid Co matrix and one type of alloying element. In a second approach the diffusion for a multicomponent systems with Co, W, Ti and C has been performed. The results from the present AIMD simulations could be shown to be in good agreement with the literature. Only two DICTRA simulations could be performed within the timeframe of this work. Both are predicting a ~3 times bigger gradient zone whereas the initial choice of the labyrinth factor λ = f could be identified as a possible source of disagreement. A labyrinth factor of λ = f2 with the calculated mobility values from the AIMD calculations should give improved results. Although the results from those simulations are not available to this date. The two approaches of the diffusion simulations in the binary and multicomponent system are giving matching results. The non-metallic elements C and N are diffusing two times faster than the fastest metallic element Co. The diffusivity of Ti is slightly lower than Co and W could be identified as the element with the slowest diffusion within the liquid Co matrix. Further investigations of the liquid structure could indicate the tendency to form bonds between C and W and between C and Ti. This gives slowed down diffusion of C in the multicomponent system compared to the diffusion in the binary Co-C system.
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Houska, Jiri. "New quaternary amorphous materials Si-B-C-N: reactive magnetron sputtering and an ab-initio study." Science, School of Physics, 2007. http://hdl.handle.net/2123/1542.
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Doctor of PhilosophyFirst part of the thesis is focused on experimental preparation of new hard quaternary amorphous materials Si-B-C-N with high thermal stability. Materials were prepared in the form of thin films using reactive magnetron sputtering. The technique used proved to be suitable for reproducible synthesis of these materials. The Si-B-C-N films were generally found to be amorphous with low compressive stress and good adhesion to silicon or glass substrates. The process and film characteristics were controlled by varying the sputter target composition, the Ar fraction in the N2–Ar gas mixture, the negative rf-induced substrate bias, and the substrate temperature. Main conclusions describe the relationships between process parameters, discharge and deposition characteristics and film properties (elemental composition, chemical bonding structure, material hardness, compressive stress or electrical conductivity of materials prepared). Second part of the thesis is focused on ab-initio simulations of structures of experimentally prepared Si-B-C-N materials. In the performed liquid-quench simulations, the Kohn-Sham equations for the valence electrons are expanded in a basis of plane wave functions, while core electrons were represented using Goedecker-type pseudopotentials. We simplified the ion bombardment process by assuming that the primary impact creates a localized molten region of high temperature and sufficiently short cooling time, commonly referred to as a thermal spike. Main conclusions deal with N2 formation in studied materials, effect of implanted Ar on structure and properties of prepared materials, ability of Si to relieve that part of compressive stress which is caused by implanted Ar, and ability of B to improve thermal stability of Si-B-C-N materials. The calculated results are compared with experiment.
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Houska, Jiri. "New quaternary amorphous materials Si-B-C-N: reactive magnetron sputtering and an ab-initio study." Thesis, The University of Sydney, 2006. http://hdl.handle.net/2123/1542.
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First part of the thesis is focused on experimental preparation of new hard quaternary amorphous materials Si-B-C-N with high thermal stability. Materials were prepared in the form of thin films using reactive magnetron sputtering. The technique used proved to be suitable for reproducible synthesis of these materials. The Si-B-C-N films were generally found to be amorphous with low compressive stress and good adhesion to silicon or glass substrates. The process and film characteristics were controlled by varying the sputter target composition, the Ar fraction in the N2–Ar gas mixture, the negative rf-induced substrate bias, and the substrate temperature. Main conclusions describe the relationships between process parameters, discharge and deposition characteristics and film properties (elemental composition, chemical bonding structure, material hardness, compressive stress or electrical conductivity of materials prepared). Second part of the thesis is focused on ab-initio simulations of structures of experimentally prepared Si-B-C-N materials. In the performed liquid-quench simulations, the Kohn-Sham equations for the valence electrons are expanded in a basis of plane wave functions, while core electrons were represented using Goedecker-type pseudopotentials. We simplified the ion bombardment process by assuming that the primary impact creates a localized molten region of high temperature and sufficiently short cooling time, commonly referred to as a thermal spike. Main conclusions deal with N2 formation in studied materials, effect of implanted Ar on structure and properties of prepared materials, ability of Si to relieve that part of compressive stress which is caused by implanted Ar, and ability of B to improve thermal stability of Si-B-C-N materials. The calculated results are compared with experiment.
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Josefsson, Ida. "Ab initio simulations of core level spectra : Towards an atomistic understanding of the dye-sensitized solar cell." Licentiate thesis, Stockholms universitet, Fysikum, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-93098.
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The main focus of this thesis is ab initio modeling of core level spectra with a high-level quantum chemical description both of the chemical interactions and of local atomic multiplet effects. In particular, the combination of calculations and synchrotron-based core-level spectroscopy aims at understanding the local structure of the electronic valence in transition metal complexes, and the details of the solvation mechanisms of electrolyte solutions, systems relevant for the dye-sensitized solar cell. Configurational sampling in solution is included through molecular dynamics simulations. Transition metal complexes are studied with x-ray absorption (XA) and resonant inelastic scattering (RIXS) spectroscopy, characterizing excited states with atomic site specificity. The theoretical multiconfigurational method, applying an active-space partitioning of the molecular orbitals (RASSCF), is used to assign the transitions observed in spectra of hydrated Ni2+ explicitly, including charge transfer and multiplet effects. Furthermore, the solvent-induced binding energy properties of the I- and I3- anions in aqueous, ethanol, and acetonitrile solutions are analyzed using photoelectron spectroscopy (XPS). The study shows that specific ion–solvent interactions are important for the core-level binding energy shifts in solution. The special case with I3- dissolved in water, where hydrogen bonding causes breaking of the molecular symmetry, is treated and proves that the geometry changes influence the photoelectron spectrum of aqueous I3- directly.
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Rancati, Andrea. "Ab initio simulations of topological phase transitions in Dirac semimetal Cd3As2 doped with Zn and Mn impurities." Thesis, Linnéuniversitetet, Institutionen för fysik och elektroteknik (IFE), 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-80767.
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In this work we exploit the unique characteristics of a Dirac semimetal material to be symmetry-protected, to investigate dierent topological phase transitions provided by chemical dopings, focusing in particular on the electronic, magnetic and topological properties of the doped systems, studied by the mean of rst-principles methods based on density functional theory (DFT) approach. In particular these doped systems, besides being of interest for investigating the role of topology in solid state physics, could have a great potential for practical application since the dierent topological phases that come along with the chemical dopings allow one to exploit the unique properties of topological materials. The starting point for our study will be the material called cadmium-arsenide (Cd3As2), an example of a topological Dirac semimetal, which is chemically stable at ambient conditions. Chapter I presents a general introduction to topology, especially in condensed matter physics, and to the main physical properties of the topological materials we mentioned. Then, in chapter II, we briey present the methods and the computational tools that we used for our study. In chapter III a more detailed introduction to our work is given, along with a schemetic view of the path we followed, together with the results that we obtained for pristine Cd3As2, which we use as bench mark for our computational methods. Finally, in chapter IV and V, the results for the doped systems are presented and discussed, respectevely for the non-magnetic (IV) and magnetic (V) dopings. Our study has enabled us to discern how doping can give rise to see dierent topological phase transitions. Specically our work shows that dierent realizations of non-magnetic doping gives rise to dierent topological phases: the topological Weyl semimetal phase, which is of great interest since it can support a robust quantum spin Hall eect, and a very special mixed Dirac + Weyl phase, where surprisingly both a Dirac and a Weyl phase can coexist in the same system. Furthermore, magnetically doped systems show the emergence of a magnetic Weyl phase, which can support a quantum anomalous Hall eect. Our work can be the starting point for future studies, both theoretical and experimental, in which the unique physical properties we found in the doped Cd3As2 systems can be further investigated, in order to exploit them for practical applications.
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Torche, Abderrezak. "Simulations ab-initio des spectres Raman résonants dans le graphène, les multicouches de graphène et le graphite." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066522/document.
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Les multicouches de graphène en empilement rhomboédrique sont considérés comme une phase prometteuse du carbone. Cela est due à la particularité de cette phase de pouvoir exhiber des états à forte corrélation électronique comme le magnétisme ou la supraconductivité à haute température critique. Ce qui est due, a son tour, à l’occurrence d’un état de surface avec une dispersion d’énergie électroniques quasi-nulle à proximité du niveau de Fermi. Malgré que le graphite Bernal soit la forme la plus stable du graphite, des échantillons a trois et quatre couches de graphène en empilement rhomboédrique ont pu être synthétisés. Plus récemment, des flocons d’épaisseur dépassant les 17 couches ont été isolés et provisoirement attribués à des séquences d’empilement rhomboédrique. Cette attribution à été faite via des expériences de spectroscopie Raman sous champ magnétique, bien que l’empreinte Raman des multicouche de graphène en empilement rhomboédrique est actuellement inconnue. Même le cas simple du spectre Raman résonnant à deux phonons (le pic 2D) du graphite Bernal n’est pas totalement compris. Dans ce travail de thèse, nous fournissons une description ab-initio complète du pic Raman 2D dans les systèmes de graphène à trois et quatre couches pour tous les empilements possibles, ainsi que pour le graphite Bernal, rhomboédrique et une alternance de graphite Bernal et rhomboédriqueMulti-layer graphene with rhombohedral ABC stacking is considered as a promising carbon phase possibly displaying correlated states like magnetism or high-T c superconductivity due to the occurrence of an ultraflat electronic surface band at the Fermi level. Despite Bernal graphite being the most stable form of graphite, three and four layers graphene samples with rhombohedral stacking can be synthesized. Recently, flakes of thickness up to 17 layers were tentatively attributed ABC sequences although the Raman fingerprint of rhombohedral multilayer graphene is currently unknown and the 2D two-phonon resonant Raman spectrum of Bernal graphite not completely theoretically understood. Here we provide a complete first principles description of the 2D Raman peak in three and four layer graphene for all possible stackings, as well as for bulk Bernal, rhombohedral and an alternation of Bernal and rhombohedral graphite, that can be seen as a periodic sequence of ABA and ABC trilayers. Calculations for several laser energies are performed and we give practical prescriptions are proposed to identify long range sequences of ABC multi-layer graphene flakes
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Blomqvist, Johanna. "Ab initio and DFT derived potential energy functions in simulations of selected polyesters based on atomistic models." Helsinki : University of Helsinki, 2001. http://ethesis.helsinki.fi/julkaisut/mat/fysii/vk/blomqvist/.
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Bhatti, Asif Iqbal. "Calculs ab-initio et simulations atomistiques des propriétés thermodynamiques et cinétiques de complexes de métaux de transition utilisés comme batteries." Thesis, Université Grenoble Alpes (ComUE), 2018. http://www.theses.fr/2018GREAI092/document.
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Ce travail théorique vise à étudier, via les méthodes Premiers Principes, les propriétés des complexes de métaux de transitions, left[Mleft(dmbpyright)_{3}right]^{n+}nCi^{-} pour un usage en batterie. Pour cette étude ab-initio, les composés mono et bi-nucléaires ont été retenus. La pertinance de notre modélisation a été validée sur les composés mononucléaires. Nous nous sommes interessé au complexes de Fe, Ru et Cu pour lesquels une validation expérimentale était possible. Notre étude a principalement consisté à faire varier les degrés de liberté que nous possédons pour optimiser le voltage et la cinétique de chargement des batteries. Pour cela, nous avons fait varier le TM = Fe, Ru, et Cu, la nature des contre-ions Ci^{-}=PF_{6}^{-}, TFSI^{-} et ClO_{4}^{-} en interaction avec le polymère lors du processus de charge, ainsi que la longeur de la chaîne alkyl qui sépare les deux monomers dans le cas des composés binucléaires. Le composé à base de Fe avec une chaîne -left(CH_{2}right)_{n=6}- a été retenu comme le meilleur candidat pour une application batterie. Le composé à base Ru montre un comportement proche de celui du Fe, quant-au complexe de Cu, il présente des changements de géométrie locale sous chargement trop importants, le rendant peu apte à conduire à une cinétique efficace. Cette étude nous a permis de déterminer que l'approximation PBE était le meilleur choix possible pour modéliser nos complexes dans les conditions de fonctionnement en batterie (dans le champ créé par les contre-ions) et que l'approximation PBE0, généralement utilisée dans la littérature, ne pouvait rendre compte de la physico-chimie de nos composés dans de telles conditions.De surcroît, nous avons dévelopé pour le complexe de Fe, un potentiel atomistique de type “Champ de forces” de manière à pouvoir aborder les aspects dynamiques impliquant de plus grandes tailles de boîte de simulation. Ici, nous modélisons une structure 3D, totalement réticulée à partir de nos monomères à base de Fe. Nous nous sommes servi de la base de donnés DFT que nous avions généré (énergies, géométries, état de spin et fréquences vibrationnelles calculées) pour ajuster les paramètres entrant dans l'écriture du modèle. La construction de la géométrie initiale du polymère 3D a nécessité l'écriture d'un code de calcul visant à produire un arrangement complétement réticulé et à assigner les charges effectives issues des calculs DFT. Ce modèle nous a permis de déterminer les coefficients de diffusion des contre-ions pour les états totalement chargé et non-chargé. Un calcul plus ambitieux vise à déterminer les chemins de diffusion des contre-ions lors d'un processus de chargement en considérant un seul centre de degré d'oxydation 3+ au centre du polymère 3D, pour lequel les centres actifs possèdent un degré d'oxidation 2+. Les contre-ions assurent la neutralité globale.Keyword: Polymer, Electrochemistry, Li-ion Battery, DFT, Force Field development, 3D structure, Atomistic modelingAbstract Standard redox potentials for mono and bi-nuclear transition metal (TM) complexes left[Mleft(dmbpyright)_{3}right]^{n+}nCi^{-}, have been investigated using First Principles Calculation. Three metal centers are investigated: Fe, Ru, and Cu. Our modeling is validated on mono-nuclear compounds. This approach consists in determining the best small polymer (bi-nuclear) made out of these monomers for a battery application. For that, we varied the three available degrees of freedom i.e., the nature of the central TM atom (Fe, Ru, and Cu), counter-ions Ci=PF_{6}^{-}, TFSI^{-} and ClO_{4}^{-} in interaction with the polymer, and the alkyl chain -left(CH_{2}right)_{n}- of length n that connects both mono-nuclear in the bi-nuclear compound. The Iron compound with -left(CH_{2}right)_{n=6}- is found to be the best candidate. The left[Culeft(dmbpyright)_{2}right]^{n+}nCi^{-} complex shows too much structure deformation upon loading, making it less reliable for cathode material. Moreover, we studied two XC functional, PBE and PBE0 and found, for three complexes PBE approximation retains the ligand field picture whereas PBE0 functional induces an exaggerated and unexpected band dispersion by dissolving the ligand field picture expected for the octahedral environment of the TM in the studied complexes. These findings validate that hybrid functional for which it was designed to localize and cancel self-interaction error does not work for all system. More particularly, the PBE0 approximation fails to model the three complexes (Fe, Ru, and Cu) in functional conditions (in the field made by the counter-ions).Abstract Further, we have developed an atomistic potential relying on the Force Field scheme for the Iron complex in order to study the dynamical properties of this compound at larger simulation scale (3D reticulated polymerization made of our Fe complex monomers). We made an intensive use of our DFT data (energies, geometries, spin-state configurations and calculated vibrational properties) to develop the required parameters entering the model. Moreover, computational techniques (written python language) were developed specifically to create a 3D structure of transition metal complexes satisfying the condition to be fully reticulated. Bounding conditions had to be designed and a procedure aiming at fixing reliable and physical effective charges on each atom of the simulation cell (compatible with DFT results) were developed. Our first simulations have been attached to calculate the diffusion coefficients of the counter-ions in both the fully loaded and unloaded states. A more ambitious and realistic calculation aims at investigating the paths of the counter-ions when one single center starts to be loaded in an unloaded environment.Abstract Keyword: Polymer, Electrochemistry, Li-ion Battery, DFT, Force Field development, 3D structure, Atomistic modeling
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Schoof, Tim [Verfasser]. "Configuration Path Integral Monte Carlo : ab initio simulations of fermions in the warm dense matter regime / Tim Schoof." Kiel : Universitätsbibliothek Kiel, 2017. http://d-nb.info/1133492177/34.
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Rasim, Karsten. "Conductivité protonique et structures locales par simulations ab initio d'oxydes utilisés comme électrolyte dans les piles à combustible." Phd thesis, Université de Nantes, 2011. http://tel.archives-ouvertes.fr/tel-00983483.
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Cette thèse porte sur une étude de matériaux oxydes fortement désordonnés de type Brownmillerite et présentant diverses substitutions. Les aspects les plus étudiés sont la conductivité protonique des phases hydratées ainsi que les propriétés structurales des composés anhydres. L'étude repose majoritairement sur des calculs de type DFT (réalisés de manière statique à 0 K et à température élevée en utilisant la dynamique moléculaire ab initio). Elle est complétée de mesures XANES (spectroscopie d'absorption des rayons X) qui ont permi de confirmer certains résultats issus des calculs DFT. Ces approches combinées ont fourni des informations cruciales sur la préférence de coordination chimique de plusieurs substituants, sur la mobilité des protons dans divers composés en fonction de leur contenu cationique ainsi que sur les propriétés vibrationnelles. Le matériau Ba2 In2(1 − x)Ti2xO5+x (BITx) a été le centre d'intérêt de cette thèse, au vu des performances prometteuses dans des piles à combustible de type PC-SOFC. Dans une optique de comparaison et de rationalisation, des composés de formulation voisine Sr2In2(1 − x)Ti 2xO5+x (SITx), Ba2In2(1 − x)Zr2xO5+x (BIZx) et Ba2In2(1 − x)Y2xO5 (BIYx) ont également été étudiés pour préciser le rôle des différents substituants sur le comportement de la conductivité protonique (e.g. les effets de piégeage, la force des liaisons hydrogène, la distinction entre plusieurs arrangements protoniques etc...). Tous ces aspects ont été obtenus grâce à la dynamique moléculaire qui intègre naturellement les effets de température et d'entropie.
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Rimsza, Jessica M. "Reactions and Interfacial Behaviors of the Water–Amorphous Silica System from Classical and Ab Initio Molecular Dynamics Simulations." Thesis, University of North Texas, 2016. https://digital.library.unt.edu/ark:/67531/metadc849660/.
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Due to the wide application of silica based systems ranging from microelectronics to nuclear waste disposal, detailed knowledge of water-silica interactions plays an important role in understanding fundamental processes, such as glass corrosion and the long term reliability of devices. In this dissertation, atomistic computer simulation methods have been used to explore and identify the mechanisms of water-silica reactions and the detailed processes that control the properties of the water-silica interfaces due to their ability to provide atomic level details of the structure and reaction pathways. The main challenges of the amorphous nature of the silica based systems and nano-porosity of the structures were overcome by a combination of simulation methodologies based on classical molecular dynamics (MD) simulations with Reactive Force Field (ReaxFF) and density functional theory (DFT) based ab initio MD simulations.
Through the development of nanoporous amorphous silica structure models, the interactions between water and the complex unhydroxylated internal surfaces identified the unusual stability of strained siloxane bonds in high energy ring structure defects, as well as the hydroxylation reaction kinetics, which suggests the difficulty in using DFT methods to simulate Si-O bond breakage with reasonable efficiency. Another important problem addressed is the development of silica gel structures and their interfaces, which is considered to control the long term residual dissolution rate in borosilicate glasses. Through application of the ReaxFF classical MD potential, silica gel structures which mimic the development of interfacial layers during silica dissolution were created A structural model, consisting of dense silica, silica gel, and bulk water, and the related interfaces was generated, to represent the dissolution gel structure. High temperature evolution of the silica-gel-water (SGW) structure was performed through classical MD simulation of the system, and growth of the gel into the water region occurred, as well as the formation of intermediate range structural features of dense silica. Additionally, hydroxylated silica monomers (SiO4H4) and longer polymerized silica chains were formed in the water region, indicating that glass dissolution is occurring, even at short time frames. The creation of the SGW model provides a framework for a method of identifying how interfacial structures which develop at glass-water interfaces can be incorporated into atomistic models for additional analysis of the dissolution of silicates in water.
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Ouali, Hela. "Simulations numériques ab initio de l'adsorption de l'ozone O3 par des couches d'oxydes de cuivre CuxO pour une application capteurs de gaz." Thesis, Aix-Marseille, 2015. http://www.theses.fr/2015AIXM4380/document.
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Les équipes micro-capteurs (IM2NP) et capteurs de gaz (LMMA) développent des capteurs à base de couches minces de CuxO et étudient leurs réponses électriques sous O3. Les travaux de cette thèse ont pour but de mieux comprendre l’interaction solide-gaz à l’échelle atomique en simulant l’adsorption de l’O3 sur les surfaces (111) du CuO et du Cu2O. Pour cela nous avons utilisé la DF T (Density Functional Theory) dans le cadre de deux approximations de la fonctionnelle : la LDA (Local Density Approximation) et la GGA (Generalized Gradient Approximation).Pour le CuO, la correction de Hubbard (DF T + U) a été également prise en compte pour reproduire correctement les comportements semiconducteuret antiferromagnétique du matériau. Tous les calculs ont été menés avec le code SIESTA et montrent que pour les deux matériaux, l'ozone s’adsorbe sur la surface sans défauts, sans se dissocier, induisant un dopage p du matériau. Ceci est en accord avec la diminution de la résistance électrique mesurée expérimentalement sous ozone. Ensuite, l’ozone se dissocie en formant une molécule de O2 et un atome d’oxygène qui restent adsorbés. Cette étape ne semble pas modifier le dopage. Par contre lorsque le capteur n’est plus en présence d'O3, la molécule d’O2 désorbe et le dopage est annihilé. Dans ce mécanisme les énergies mises en jeu sont du même ordre de grandeur pour CuO ou pour Cu2O (allant de −3 eV à −1 eV). Dans l’objectif de développer un capteur de gaz, le CuO, plus facile à obtenir par les techniques de dépôt courantes en microélectronique, semble donc être plus pertinent que le Cu2O, qui a une réponse similaire (voire moindre) mais dont il est difficile d’obtenir une phase pureMicro-sensors (IM2NP) and gas sensors (LMMA) team develop sensors based on CuO and Cu2O thin layers and study their electrical responses to O3. The aim of this thesis is a better understanding of the solid-gas interactions at the atomic scale by simulating the adsorption of O3 molecule on the (111) surfaces of CuO and Cu2O. Simulations were performed using the DF T (Density Functional Theory) within two functional approximations : the LDA (Local Density Appriximation) and GGA (Generalized Gradient Approximation). In the case of CuO, the Hubbard correction (DF T + U) was taken into account to properly reproduce the semiconductor and antiferromagnetic behaviors of the material. All calculations were performed with the SIESTA code and show that for the CuO as for Cu2O, O3 is adsorbed on the defect-free surface, without dissociating inducing a p-doping of the material. This observation is consistent with the decrease in electrical resistance measured experimentally under ozone. In a second stage ozone dissociates into a molecule of O2 and an oxygen atom which remains adsorbed. This step does not appear to change the doping. However, when the sensor is no longer in the presence of ozone, O2 molecule is desorbed and doping disappears. In this mechanism, the energies involved during the adsorption or the dissociation of ozone are of the same order of magnitude for CuO or Cu2O (ranging from −1 eV to −3 eV). Aiming to develop a gas sensor, and since the CuO material is easier to obtain by standard deposition techniques (RF sputtering), it seems to be more appropriate than the Cu2O, which has a similar response (even lower) but is more difficult to synthesize in a pure phase
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Hambach, Ralf. "Théorie et Simulations numériques ab-initio des propriétés électroniques de nanostructures: vers la spectroscopie de perte d'énergie résolue spatialement." Phd thesis, Ecole Polytechnique X, 2010. http://pastel.archives-ouvertes.fr/pastel-00587080.
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Cette thèse présente les résultats d'études théoriques et numériques des excitations collectives de systèmes de carbone de dimensionnalité différente. D'abord, une méthode combinant la théorie du milieu effectif et des calculs ab-initio a été développée pour décrire les excitations collectives de nanostructures (comme les nanotubes de carbone) à partir de la polarisabilité de leurs blocs élémentaires (graphène). Contrairement à la théorie diélectrique standard, les équations de Maxwell sont résolues pour la fonction diélectrique microscopique dépendant du temps et du moment ε(q,q',ω) du matériau massif. Cette dernière a été calculée à partir des premiers principes dans l'approximation de la phase aléatoire (RPA). Cette méthode a ensuite été appliquée pour calculer les spectres de perte d'énergie d'électrons (EELS) pour le graphène et les nanotubes de carbone monoparoi (SWCNT). L'accord avec les calculs complètement ab-initio sur ces systèmes et avec les expériences correspondantes est très bon. La dispersion du plasmon π dans le graphène et les SWCNT a été analysée et expliquée. La dépendance avec la direction du moment des spectres de perte d'énergie d'électrons des SWCNT est comprise en termes d'excitations des modes normaux. Finalement, l'utilisation des calculs ab-initio en vue de prédire le EELS résolu spatialement a été étudiée. Le facteur de forme mixte dynamique a été analysé et une discontinuité de son comportement pour certaines réflections de Bragg a été prédite. Cet effet a été expliqué par les effets de champ cristallin et a été confirmé par des expériences de IXS sur le graphite et le silicium. L'approche blocs élémentaires a été appliquée au EELS résolu spatialement.
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Hiebel, Fanny. "Etude de l'interface graphène - SiC(000-1) (face carbone) par microscopie à effet tunnel et simulations numériques ab initio." Phd thesis, Université de Grenoble, 2011. http://tel.archives-ouvertes.fr/tel-00680068.
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Le graphène est un cristal bidimensionnel composé d'atomes de carbone arrangés sur un réseau en nids d'abeille. Ce matériau présente des propriétés électroniques intéressantes tant au niveau fondamental qu'en vue d'applications avec notamment une structure de bande exotique en " cône de Dirac " et de grandes mobilités de porteurs. Sa fabrication par graphitisation du SiC est particulièrement adaptée aux applications électroniques. Nous avons étudié ce système par microscopie à effet tunnel (STM) et simulations numériques ab initio avec comme objectif la caractérisation au niveau atomique de l'interface graphène - SiC(000-1) (face carbone) et l'étude de l'impact du substrat sur la structure électronique du graphène. Après un chapitre introductif à la thématique du graphène, suivi d'un chapitre présentant les deux techniques utilisées au cours de ce travail, nous présentons nos échantillons faiblement graphitisés obtenus sous ultra-vide. Nous avons identifié deux types d'interfaces, les reconstructions natives de la surface du SiC(000-1) appelées (2x2)C et (3x3), sur lesquelles reposent les ilots monoplan de graphène, avec un fort désordre rotationnel donnant lieu à des figures de moiré sur les images STM. Nous montrons par imagerie STM et spectroscopie tunnel que l'interaction graphène/(3x3) est très faible. Nous étudions ensuite le cas d'interaction plus forte graphène/(2x2) successivement du point de vue des états du graphène et des états de la reconstruction, dans l'espace direct et réciproque, de façon expérimentale et théorique. Enfin, nous considérons l'effet de défauts observés par STM à l'interface des ilots sur (2x2), modélisés par des adatomes d'hydrogène, sur le dopage et la structure de bande électronique du graphène.
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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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Cheenicode, Kabeer Fairoja [Verfasser]. "Ab initio Molecular Dynamics Simulations of the Structural Response of Solids to Ultrashort Laser and XUV Pulses / Fairoja Cheenicode Kabeer." Kassel : Universitätsbibliothek Kassel, 2015. http://d-nb.info/1069693669/34.
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Dragoni, Alberto. "Corrélations multi-corps dans les simulations ab initio du transport électronique quantique : une application aux dispositifs OxRAM de nouvelle génération." Thesis, Université Grenoble Alpes (ComUE), 2019. http://www.theses.fr/2019GREAY039.
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Les mémoires résistives non volatiles basées sur les oxydes (OxRAM) acquièrent récemment un grand intérêt pour leurs performances, ce qui en fait des candidats prometteurs comme mémoire de stockage pour remplacer la technologie flash, et comme mémoires intégrées pour les applications réseau de neurones. Néanmoins, les dispositifs OxRAM émergents présentent encore certains inconvénients, comme la non-uniformité des paramètres de commutation et les défaillances de commutation. Surmonter ces inconvénients exige une compréhension plus profonde des principes de fonctionnement de l’OxRAM, jusqu’à présent pas complètement compris. Ceci peut être réalisé au moyen de simulations textit{ab initio}. Ce travail présente donc une étude approfondie de HfO₂, qui fait partie des matériaux les plus prometteurs pour la construction de dispositifs OxRAM, au moyen de calculs précis des états de quasi-particules (QP). Une étude des propriétés du transport électronique dans les dispositifs OxRAM est également de première importance. Toutefois, cela nécessite un cadre théorique solide et fiable afin de calculer la conductance des jonctions métal/isolant. L’approche standard, basée sur la théorie fonctionnelle de la densité, le formalisme de la fonction de Green et la formule de Landauer, a quelques limites et soucis de fiabilité. Ce travail propose une approche plus fiable basée sur les calculs QP, qui fournissent une structure électronique plus précise pour calculer la conductance, et teste en grande partie cette nouvelle méthode sur différentes jonctions imitant les dispositifs OxRAMResistive non-volatile memories based on oxides (OxRAM) are recently acquiring a wide interest for their performances, which make them promising candidates as storage memories to replace flash technology, and as embedded memories for neural network applications. Nevertheless, emerging OxRAM devices still present some drawbacks, like non-uniformity of switching parameters and switching failures. Overcoming these drawbacks requires a deeper comprehension of the OxRAM working principles, so far not completely understood. This can be achieved by means of textit{ab initio} simulations. Hence this work presents a careful characterization of HfO₂, which is within the most promising materials to build OxRAM devices, by means of accurate quasi-particle (QP) calculations. A study of the electronic transport properties in OxRAM devices is also of primary importance. However, this requires a robust and reliable theoretical framework to compute the conductance of bulk metal/insulator junctions. The standard approach, based on density functional theory, Green function formalism, and Landauer formula, has some limitations and reliability issues. This work proposes a more reliable approach based on QP calculations, which provide a more accurate electronic structure to compute the conductance, and largely tests this new method on different junctions mimicking OxRAM devices
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Pham, Thanh Tung. "Multiscale modelling and simulation of slip boundary conditions at fluid-solid interfaces." Phd thesis, Université Paris-Est, 2013. http://tel.archives-ouvertes.fr/tel-00980155.
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In most applications concerning a fluid flowing over a solid surface, the no-slip velocity condition was widely used because it is simple and produces the results in agreement with experiments. However, this dynamical boundary condition is not appropriate when the flow under consideration is at a micro or nano length scale.In order to model this effect at the macroscopic scale, the Navier boundary conditions have been introduced, with the slip length as a parameter. When the fluid is a gas, this length is related to the tangential momentum accommodation coefficient (TMAC) and the mean free path, according to the Maxwell model. The aim of this work is to systematically address this model using a multi-scale approach and to extend it by incorporating both the morphology and the anisotropy of a surface. The thesis consists of five chapters. In Chapter 1, the basics of the kinetic theory of gases, the Boltzmann equation and related solutions (Navier-Stokes-Fourier, Burnett, Grad, Direct Simulation Monte Carlo ...) are briefly presented. The models of gas-wall interaction and slip models introduced in the fluid mechanics are also recalled. The chapter ends with a description of the computational method used for the molecular dynamics simulations performed in this work. Chapter 2 is dedicated to the development of a simple technique to simulate the pressure driven flows. The principle is to rely on the atomistic formulas of the stress tensor (Irving Kirkwood, Method of Plane, Virial Stress) and to modify the periodic conditions by maintaining the difference between the kinetic energy of the ingoing and outgoing particles of the simulation domain. Several types of channels are studied with this technique. The results (temperature, velocity ...) are discussed and compared. Chapter 3 deals with the study of the gas-wall interaction potential by the ab-initio method. The code CRYSTAL 09 is used to obtain the potential between an atom of argon (Ar) and a surface of platinum (Pt) <111> as a function of distance. Then the gas-wall potential is decomposed into binary potential and approached by an analytic function. This function is then implemented in a MD code to simulate the gas-wall collisions and determine the TMAC coefficient. In Chapter 4, the effect of morphology is studied. The multi-body Quantum Sutton Chen (QSC) potential is used for Pt <100> solid and the binary potential proposed in the previous chapter for the Ar-Pt couple is employed. The QSC potential is needed to reproduce the surface effects that affect the final results. Different surfaces are treated : smooth, nanostructured surface and, random surface obtained by Chemical vapor deposition (CVD). The TMAC is determined using a generalized approach, i.e. depending on the angle of incident flux of gas atoms on the surface. The surface anisotropy and the scattering kernel are also examined. In Chapter 5, we propose a model of anisotropic slip for fluids based on accommodation tensor. The model is obtained by the analytical approximate calculations developed in the framework of the kinetic theory. We thus generalize Maxwell's equation by showing that the slip length tensor is directly related to the accommodation tensor. The model is in good agreement with the MD results. Thanks to our MD simulations, we develop a suitable technique for reproducing the anisotropy of the accommodation tensor. The thesis ends with a conclusion section in which we suggest some perspectives for a continuation of this work
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Naseem-Khan, Sehr. "Development of a polarizable ab initio force field : From separability of intermolecular interactions to condensed phase properties." Thesis, Sorbonne université, 2018. http://www.theses.fr/2018SORUS564.
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Grâce aux récents progrès de l’informatique, il devient alors possible d’utiliser des champs de forces polarisables sophistiqués tel que SIBFA. En effet, le potentiel intermoléculaire SIBFA et ses gradients sont désormais implémentés dans le code Tinker-HP. La calibration initiale de SIBFA est basée sur la méthode RVS, une méthode de décomposition de l’énergie seulement accessible au niveau Hartree-Fock. Ainsi, les objectifs de ce travail sont double : i) choisir une nouvelle méthode référence de décomposition de l’énergie afin d’obtenir les paramètres de SIBFA au niveau corrélé ; ii) réaliser des simulations de dynamiques moléculaires. La première partie de cette thèse est dédiée à l’étude ab initio de la séparabilité de l’interaction intermoléculaire prédit par les méthodes de décomposition de l’énergie dites variationnelles et perturbationnelles. Nous avons fait des améliorations de l’énergie d’induction au sein de la méthode SAPT(DFT) et nous avons proposé une nouvelle définition du transfert de charge. La seconde partie de cette thèse est dédiée au développement du potentiel polarisable de l’eau de SIBFA, et à notre stratégie pour calculer les propriétés en phase condensée. L’étude ab initio de la séparabilité de l’énergie totale intermoléculaire SAPT(DFT) a mené à une séparabilité totale des contributions du potentiel SIBFA au niveau post Hatree-Fock. Cette thèse marque un réel progrès pour le potentiel SIBFA qui finalise son approche bottom-up : à partir de calculs ab initio en phase gaz vers des simulations de dynamiques moléculaires et des prédictions précises des propriétés en phase condenséeThanks to the recent progresses of computer sciences de-multiplying the available computational resources, the possibility of using sophisticated polarizable force fields such as SIBFA becomes a reality. Indeed, the SIBFA intermolecular potential and its gradients are now implemented in the Tinker-HP package. The original calibration of SIBFA was based on the RVS method, an energy decomposition analysis only available at the Hartree–Fock level of theory. Therefore, the goals of this work are double : i) choosing a new energy decomposition analysis reference scheme in order to upgrade the SIBFA parameters at the correlated level of theory ; ii) performing molecular dynamics. The first part of this thesis is dedicated to the study of the separability of the ab initio intermolecular interaction energy predicted by both variational and perturbational Energy Decomposition Analysis methods. We have made improvements for the induction energy term within the SAPT(DFT) method, and we have proposed a new charge transfer definition. The second part of this thesis is dedicated to the development of the SIBFA polarizable water model and to our definition of a strategy to compute condensed phase properties. The ab initio study of the separability of the total SAPT(DFT) intermolecular interaction energy has led the SIBFA potential to achieve both full separability of its components and high accuracy at the post Hartree-Fock level. This thesis marks a turning-point for the SIBFA potential, finalizing its global bottom-up strategy going from gas phase ab initio computations towards molecular dynamics simulations and accurate condensed phase properties predictions
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Walz, Michael Steffen [Verfasser], and F. [Akademischer Betreuer] Evers. "Ab initio simulations of local current densities in mesoscopic films: Current vortices in functionalized graphene nanoribbons / Michael Steffen Walz. Betreuer: F. Evers." Karlsruhe : KIT-Bibliothek, 2015. http://d-nb.info/1079594876/34.
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Peters, Laurens Dirk Marga [Verfasser], and Christian [Akademischer Betreuer] Ochsenfeld. "Development and application of efficient ab initio molecular dynamics simulations of ground and excited states / Laurens Dirk Marga Peters ; Betreuer: Christian Ochsenfeld." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2020. http://d-nb.info/1209472821/34.
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Traoré, Boubacar. "Etude des cellules mémoires résistives RRAM à base de HfO2 par caractérisation électrique et simulations atomistiques." Thesis, Université Grenoble Alpes (ComUE), 2015. http://www.theses.fr/2015GREAT037/document.
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La mémoire NAND Flash représente une part importante dans le marché des circuits intégrés et a bénéficié de la traditionnelle miniaturisation de l’industrie des sémiconducteurs lui permettant un niveau d’intégration élevé. Toutefois, cette miniaturisation semble poser des sérieux problèmes au-delà du noeud 22 nm. Dans un souci de dépasser cette limite, des solutions mémoires alternatives sont proposées parmi lesquelles la mémoire résistive (RRAM) se pose comme un sérieux candidat pour le remplacement de NAND Flash. Ainsi, dans cette thèse nous essayons de répondre à des nombreuses questions ouvertes sur les dispositifs RRAM à base d’oxyde d’hafnium (HfO2) en particulier en adressant le manque de compréhension physique détaillée sur leur fonctionnement et leur fiabilité. L’impact de la réduction de taille des RRAM, le rôle des électrodes et le processus de formation et de diffusion des défauts sont étudiés. L’impact de l’alliage/dopage de HfO2 avec d’autres matériaux pour l’optimisation des RRAM est aussi abordé. Enfin, notre étude tente de donner quelques réponses sur la formation du filament conducteur, sa stabilité et sa possible compositionAmong non-volatile memory technologies, NAND Flash represents a significant portion in the IC market and has benefitted from the traditional scaling of semiconductor industry allowing its high density integration. However, this scaling seems to be problematic beyond the 22 nm node. In an effort to go beyond this scaling limitation, alternative memory solutions are proposed among which Resistive RAM (RRAM) stands out as a serious candidate for NAND Flash replacement. Hence, in this PhD thesis we try to respond to many open questions about RRAM devices based on hafnium oxide (HfO2), in particular, by addressing the lack of detailed physical comprehension about their operation and reliability. The impact of scaling, the role of electrodes, the process of defects formation and diffusion are investigated. The impact of alloying/doping HfO2 with other materials for improved RRAM performance is also studied. Finally, our study attempts to provide some answers on the conductive filament formation, its stability and possible composition