<p>The aim of the Master’s Thesis work is to study and develop algorithms for autonomous travel of a UGV (Unmanned Ground Vehicle). A vehicle for the mounting of sensors has been constructed in order to perform the work. Since the UGV is to be used outdoor in urban areas, GPS can be used. To improve precision and robustness, inertial navigation is used in addition to GPS, since GPS reception is likely to be diminished in such areas. The sensors used for navigation are consequently GPS, magnetometers, accelerometers, gyroscopes, tachometers and ultra sonic sensors measuring distance to be used in detection of obstacles. The system has been implemented in Matlab. Two alternative methods of navigation with sensor fusion have been developed; one is a decentralized method with Kalman filtering using an error model and the other is a centralized particle filter using an all-embracing model of the vehicle. The two methods have been evaluated and compared. Test results show that the two methods perform equivalently.</p><p>The autonomous travel is undertaken between predetermined waypoints. In order to steer the vehicle a PID-controller based on the error between heading and its reference value is used. The computation of the reference value is based on position and heading in comparison to the desired path. The system has been tested using different routes and the results show an evident improvement of the precision in navigation compared to using only GPS-data. This holds for both navigation methods. Simulation of collision avoidance using virtual force fields shows satisfying results as well as terrain navigation with coordinate map referencing.</p> / <p>Examensarbetet är en studie i utveckling av algoritmer för autonom förflyttning av en UGV (eng Unmanned Ground Vehicle). För ändamålet har en farkost konstruerats där budgetsensorer för navigering används. Farkosten är tänkt att färdas utomhus i tätbebyggt område och GPS används. För förbättring av noggrannhet och robusthet vid dålig GPS-mottagning används även sensorer för tröghetsnavigering vilket här innebär magnetometrar, accelerometrar, gyron och tachometrar. För hinderdetektering finns avståndsmätande ultraljudssonar. Systemet som tagits fram har implementerats i realtid i Matlab. Två olika navigeringsmetoder med sensorfusion har utprovats; en decentraliserad variant med kalmanfilter som är uppbyggd kring felmodeller och en centraliserad variant med ett partikelfilter som använder en helhetsmodell för farkosten. De båda navigeringsmetoderna har utvärderats och jämförts. Resultat visar att de båda metoderna presterar likvärdigt.</p><p>Den autonoma förflyttningen utförs mellan förutbestämda brytpunkter. För att styra farkosten har en PID-regulator baserad på felet mellan kurs och börvärde använts. Börvärdet på kurs baseras på nuvarande position och riktning relativt den önskade färdvägen. Olika körsituationer har testats och resultaten visar en markant förbättring av navigeringsprecisionen jämfört med endast GPS-mätningar för både kalman- och partikelfilter. Simuleringar på vektorfältsstyrning med virtuella kraftfält för att undvika hinder har utförts med goda resultat liksom simuleringar av kartreferenspositionering.</p>

The aim of the Master’s Thesis work is to study and develop algorithms for autonomous travel of a UGV (Unmanned Ground Vehicle). A vehicle for the mounting of sensors has been constructed in order to perform the work. Since the UGV is to be used outdoor in urban areas, GPS can be used. To improve precision and robustness, inertial navigation is used in addition to GPS, since GPS reception is likely to be diminished in such areas. The sensors used for navigation are consequently GPS, magnetometers, accelerometers, gyroscopes, tachometers and ultra sonic sensors measuring distance to be used in detection of obstacles. The system has been implemented in Matlab. Two alternative methods of navigation with sensor fusion have been developed; one is a decentralized method with Kalman filtering using an error model and the other is a centralized particle filter using an all-embracing model of the vehicle. The two methods have been evaluated and compared. Test results show that the two methods perform equivalently. The autonomous travel is undertaken between predetermined waypoints. In order to steer the vehicle a PID-controller based on the error between heading and its reference value is used. The computation of the reference value is based on position and heading in comparison to the desired path. The system has been tested using different routes and the results show an evident improvement of the precision in navigation compared to using only GPS-data. This holds for both navigation methods. Simulation of collision avoidance using virtual force fields shows satisfying results as well as terrain navigation with coordinate map referencing. / Examensarbetet är en studie i utveckling av algoritmer för autonom förflyttning av en UGV (eng Unmanned Ground Vehicle). För ändamålet har en farkost konstruerats där budgetsensorer för navigering används. Farkosten är tänkt att färdas utomhus i tätbebyggt område och GPS används. För förbättring av noggrannhet och robusthet vid dålig GPS-mottagning används även sensorer för tröghetsnavigering vilket här innebär magnetometrar, accelerometrar, gyron och tachometrar. För hinderdetektering finns avståndsmätande ultraljudssonar. Systemet som tagits fram har implementerats i realtid i Matlab. Två olika navigeringsmetoder med sensorfusion har utprovats; en decentraliserad variant med kalmanfilter som är uppbyggd kring felmodeller och en centraliserad variant med ett partikelfilter som använder en helhetsmodell för farkosten. De båda navigeringsmetoderna har utvärderats och jämförts. Resultat visar att de båda metoderna presterar likvärdigt. Den autonoma förflyttningen utförs mellan förutbestämda brytpunkter. För att styra farkosten har en PID-regulator baserad på felet mellan kurs och börvärde använts. Börvärdet på kurs baseras på nuvarande position och riktning relativt den önskade färdvägen. Olika körsituationer har testats och resultaten visar en markant förbättring av navigeringsprecisionen jämfört med endast GPS-mätningar för både kalman- och partikelfilter. Simuleringar på vektorfältsstyrning med virtuella kraftfält för att undvika hinder har utförts med goda resultat liksom simuleringar av kartreferenspositionering.

Cette thèse porte sur deux projets visant au développement de nouvelles approches pour simuler les dynamiques moléculaire et électronique avec application à des biomolécules étendues. Dans la première partie nous cherchons à améliorer significativement la précision des simulations des propriétés rédox des protéines. Dans ce contexte, l'objectif est de recourir à de champ de force reposant sur une description multipolaire des interactions électrostatiques (AMOEBA) pour estimer les potentiels redox d'hémoprotéines. Nous avons dérivé des paramètres pour AMOEBA afin de décrire précisément les interactions électrostatiques avec l'hème. Une amélioration très encourageante est obtenue par rapport aux champs de forces standard. Le second projet vise à développer de nouvelles méthodes pour étudier la dynamique des électrons dans des biomolécules à l'échelle attoseconde en incluant les effets d'environnement. Nous avons conçu un couplage original entre la théorie de la fonctionnelle de la densité dépendant du temps (RT-TDDFT) et un modèle de mécanique moléculaire polarisable (MMpol). Une implémentation efficace et robuste de cette méthode a été réalisée dans le logiciel deMon2k. L'utilisation de techniques d'ajustements de densités électroniques auxiliaires permet de réduire drastiquement le coût de calcul des propagations RT-TDDFT/MMpol. La méthode est appliquée à l'analyse de la dissipation d'énergie dans l'environnement d'un peptide excité par un impulsion laser. / This thesis involves two projects devoted to the development of advanced approaches for simulating molecular and electron dynamics in extended biomolecules. The first project aims at significantly improving the accuracy of redox potentials of proteins by numerical simulations. A sophisticated force field relying on a multipolar description of electrostartic interactions (AMOEBA) is used to perform molecular dynamics simulations onheme proteins. We derived parameters for AMOEBA to accurately describe electrostatic interactions with hemein both ferrous and ferric states. Very encouraging improvements are obtained compared to the standard force fields. The second project aims at developing original approaches for simulating ultrafast electron dynamics in biomolecules in contact to polarizable environments. We devised acombination of Real-time Time-Dependent Density Functional Theory (RT-TDDFT) and polarizable Molecular Mechanics (MMpol). An efficient and robust implementation of this method has been realized in deMon2k software. Density fitting techniques allow to reduce the computational cost of RT-TDDFT/MMpol propagations. The methodology is applied to understand the mechanisms of energy dissipation of a peptide excited by a laser pulse.

La spectroscopie de dissociation par absorption de photons infrarouges (IRPD) permet d’obtenir les signatures vibrationnelles d’espèces chargées en phase gazeuse, telles que de petits peptides ou des ions hydratés dans des agrégats d’eau. L’attribution des modes de vibration pour établir une relation entre le spectre expérimental et une structure moléculaire est une tâche délicate et nécessite le recours à la modélisation moléculaire.Ce manuscrit présente un ensemble d’outils théoriques pour le calcul et l’attribution de spectres vibrationnels, basée principalement sur la dynamique moléculaire classique et le champ de forces polarisable AMOEBA, ainsi que son application à des ions gazeux de tailles diverses. Les ions hydratés dans des agrégats d’eau M(H2O)n (n allant de 6 à 100) sont caractérisés par une dynamique importante, et leur spectre expérimental ne peut pas être décrit par une seule structure. La signature des peptides évolue avec la température et les effets d’anharmonicité dynamique. Ils peuvent également être le siège de mécanismes de transfert de proton, présentant une signature vibrationnelle très caractéristique.La surface d’énergie potentielle de ces systèmes est explorée par la dynamique moléculaire classique en trajectoires individuelles ou avec échange de répliques, afin d’engendrer des structures énergétiquement stables. Pour les plus petits systèmes, les méthodes quantiques DFT et post-HF sont utilisées pour confirmer les structures de plus basse énergie, calculer leurs spectres IR statiques et proposer des attributions des modes de vibration. Pour les plus systèmes de plus grandes tailles, c’est-à-dire les ions dans des gouttes d’eau de plusieurs dizaines de molécules, la simulation des spectres IR à température finie est basée sur la transformée de Fourier de la fonction d’autocorrélation du moment dipolaire (DACF), calculée pour une trajectoire de dynamique moléculaire classique. Cette méthode n’offrant pas d’accès direct aux modes normaux de vibration, nous avons implémenté une méthode d’attribution dynamique, basée sur la Driven Molecular Dynamics (DMD) et couplée au DACF. La combinaison AMOEBA/DACF/DMD a été utilisée pour reproduire et attribuer le spectre du dipeptide Ace-Phe-Ala-NH2, et ceux d’ions hydratés dans des agrégats d’eau.Enfin, la signature vibrationnelle d’un transfert de proton ne peut être décrite, ni par des méthodes statiques quantiques, ni par la dynamique classique. Sa modélisation a nécessité le développement d’un modèle Empirical Valence Bond (EVB) à deux états, couplé au champ de forces polarisable AMOEBA. Le modèle EVB a été implémenté dans la suite logicielle Tinker. Il permet de reproduire le comportement dynamique du transfert de proton au sein de petits peptides et de diacides déprotonés, ainsi que la signature spectroscopique observée expérimentalement.Une partie importante des applications de ces développements concerne des ions simples hydratés dans des nano-gouttelettes, et en particulier l’ion sulfate de grande importance environnementale. Nous avons pu reproduire de façon satisfaisante, pour la première fois, les spectres d’agrégats contenant jusqu’à 100 molécules d’eau. Le principal contributeur à cette spectroscopie expérimentale est l’équipe d’E. Williams à l’université de Californie à Berkeley. Nous avons établi avec eux une collaboration pour compléter ce travail en modélisant les spectres IR d’ions sulfates hydratés [SO4(H2O)n=9-36]2-, dont ils ont obtenu les signatures expérimentales. / Spectroscopy dissociation by absorption of infrared photons (IRPD) provides vibrational signatures of charged species in the gas phase, such as small peptides or hydrated ions in water clusters. The vibrational normal modes assignment to establish a relationship between the experimental spectrum and molecular structure is a delicate task and requires the use of molecular modeling.This manuscript presents a set of theoretical tools for calculation and assignment of vibrational spectra, based mainly on classical molecular dynamics and polarizable AMOEBA force field, and its application to gaseous ions of various sizes. Hydrated ions in water clusters M(H2O)n (n in 6-100 range) are characterized by a dynamic behavior, and their experimental spectrum can not be described by a single structure. The signature of peptides changes with temperature and dynamic anharmonicity effects. They can also be the site of proton transfer mechanisms, with a very characteristic vibrational signature.The potential energy surface of these systems is explored by classical molecular dynamics in individual trajectories or replica exchange to generate energetically stable structures. For smaller systems, quantum methods, as DFT and post-HF, are used to confirm the lowest energy structures, calculate their static IR and propose normal modes assignments. For larger systems, i.e ions in water drops of several tens of molecules, the simulation of IR spectra at finite temperature is based on the Fourier transform of the autocorrelation function of the dipole moment (DACF), calculated during a classical molecular dynamics trajectory. As this method does not allow direct access to the vibrational normal modes, we implemented a method of dynamic assigments, based on the Driven Molecular Dynamics (DMD) and coupled to the DACF. The combination AMOEBA /DACF / DMD was used to reproduce and assign the spectrum of the dipeptide Ace-Phe-Ala-NH2, and those of hydrated ions in water clusters.Finally, the vibrational signature of a proton transfer can not be described by quantum static methods or by classical dynamics. Its modeling required the development of a two states Empirical Valence Bond Model (EVB), coupled with AMOEBA polarizable force field. The two states EVB model was implemented in the software TINKER. It can reproduce the dynamic behavior of proton transfer in small peptides and deprotonated acids, as well as the spectroscopic signatures observed experimentally.An important part of the applications of these developments relates simple hydrated ions in nano-droplets, and in particular the sulfate ion of great environmental importance. We were able to reproduce satisfactorily, for the first time, the spectra of clusters containing up to 100 water molecules. The main contributor to this experimental spectroscopy is the team of E. Williams from the University of California of Berkeley. We have established cooperation with them to complete this work by modeling the IR spectra of hydrated sulfates ions [SO4(H2O) n=9-36]2-, for which they obtained experimental signatures.

No description available.

Nesta tese de doutorado apresentamos os resultados de quatro tópicos referentes a estudos de propriedades elétricas que são interpretados com o auxílio da Teoria Quântica de Átomos em Moléculas (QTAIM). No primeiro deles, foram calculados momentos de dipolo e suas derivadas através de um novo formalismo de divisão de átomos em moléculas, baseado em campos de forças de Ehrenfest (CFE), sendo que estes dados são comparados com aqueles advindos da QTAIM. Desta forma, um modelo alternativo de partição em carga - fluxo de carga - fluxo de dipolo (CFCFD) é discutido para derivadas do momento dipolar. Os resultados gerais obtidos pelo formalismo CFE foram satisfatórios em termos quantitativos, embora QTAIM ainda fornece uma descrição mais apropriada destes fenômenos das polarizações atômicas e de suas variações durante vibrações. Na sequência, investigamos os Atratores Não Nucleares (NNAs), que são identificados através de uma análise QTAIM da densidade eletrônica. O nosso intuito foi descobrir novas moléculas que apresentam essa peculiaridade, bem como encontrar padrões entre os casos encontrados que permitam contribuir para o entendimento dos fatores que levam ao seu aparecimento. Para isso trabalhamos com moléculas diatômicas homonucleares de elementos representativos com números atômicos que variavam de Z=1 até Z=38 e moléculas heteronucleares formadas pela combinação dos mesmos. Os nossos dados mostram que NNAs podem ser encontrados em alguns pontos dentro da faixa de distâncias internucleares investigada para quase todos os sistemas diatômicos homonucleares, exceto para as moléculas de Hidrogênio, Hélio e Estrôncio. Por sua vez, encontramos trinta casos de NNAs em sistemas heteronucleares, muitos dos quais ainda inéditos na literatura. Descobrimos também que a polarizabilidade atômica aparentemente tem um papel importante na explicação dos casos encontrados. Tratamos também de moléculas contendo interações fracas como as de Van der Waals (moléculas tri-atômicas contendo um gás nobre ligado a um composto diatômico iônico) de modo a investigar os valores de dipolos atômicos QTAIM de uma maneira mais direta, ou seja, via comparação com um modelo simples para estes compostos. Por fim, estudamos moléculas em estados excitados, sendo que nossa análise focou em dois casos peculiares (CO e de CF2N2) que apresentam momento de dipolo nulo no estado fundamental, enquanto valores significativos desta propriedade são observados em seus primeiros estados excitados. Desta forma, QTAIM foi fundamental para compreender como o processo de excitação pode levar à mudanças tão significativas em tais propriedades elétricas. / In this PhD thesis we present the results of four different topics that refer to a study of electric properties interpreted with The Quantum Theory of Atoms and Molecules (QTAIM). First, dipole moments and their derivatives were calculated from a new formalism based on Ehrenfest Force Fields (EFF) and a comparison with data from QTAIM is carried out. Therefore, the Charge-Charge Flux-Dipole Flux (CCFDF) model was discussed for the dipole moment derivatives. The results from EFF were satisfactory in quantitative terms although QTAIM still seems to be better for the description of atomic polarization and its variations during vibrations. In the sequence, we investigated the Non-Nuclear Attractors (NNAs) that could be identified with the QTAIM formalism. Our intention was to discover new molecules that present this peculiarity, as well as to find trends among these cases that allow contributing for the understanding of the factors that lead to their appearance. For this purpose, we selected homonuclear diatomic molecules of elements presenting atomic numbers ranging from Z=1 to Z=38 and heteronuclear diatomic molecules containing these same elements. Our data shows that NNAs could be found in almost every homonuclear molecule expect by the systems formed by Hydrogen, Helium, and Strontium. On other hand, we have found 30 cases of NNAs in heteronuclear molecules, many of them seen for the first time. We also have noticed that the atomic polarizabilities play a main role in the understanding of these cases. We also treated molecules containing weak Van der Waals interactions (triatomic complexes presenting a noble gas bonded to a diatomic ionic molecule) in order to investigate the atomic dipole values obtained with QTAIM in a direct way, that is, by means of a comparison using a simple model for this kind of bonding. Finally, we studied molecules in excited states. Our focus was in two peculiar cases (CO and CF2N2), which present null dipole moments in their ground states but exhibit significant dipole moment values in their first excited states. Therefore, QTAIM was fundamental to understand how the excitation process can lead to important changes in electric properties.

Nesta tese de doutorado apresentamos os resultados de quatro tópicos referentes a estudos de propriedades elétricas que são interpretados com o auxílio da Teoria Quântica de Átomos em Moléculas (QTAIM). No primeiro deles, foram calculados momentos de dipolo e suas derivadas através de um novo formalismo de divisão de átomos em moléculas, baseado em campos de forças de Ehrenfest (CFE), sendo que estes dados são comparados com aqueles advindos da QTAIM. Desta forma, um modelo alternativo de partição em carga - fluxo de carga - fluxo de dipolo (CFCFD) é discutido para derivadas do momento dipolar. Os resultados gerais obtidos pelo formalismo CFE foram satisfatórios em termos quantitativos, embora QTAIM ainda fornece uma descrição mais apropriada destes fenômenos das polarizações atômicas e de suas variações durante vibrações. Na sequência, investigamos os Atratores Não Nucleares (NNAs), que são identificados através de uma análise QTAIM da densidade eletrônica. O nosso intuito foi descobrir novas moléculas que apresentam essa peculiaridade, bem como encontrar padrões entre os casos encontrados que permitam contribuir para o entendimento dos fatores que levam ao seu aparecimento. Para isso trabalhamos com moléculas diatômicas homonucleares de elementos representativos com números atômicos que variavam de Z=1 até Z=38 e moléculas heteronucleares formadas pela combinação dos mesmos. Os nossos dados mostram que NNAs podem ser encontrados em alguns pontos dentro da faixa de distâncias internucleares investigada para quase todos os sistemas diatômicos homonucleares, exceto para as moléculas de Hidrogênio, Hélio e Estrôncio. Por sua vez, encontramos trinta casos de NNAs em sistemas heteronucleares, muitos dos quais ainda inéditos na literatura. Descobrimos também que a polarizabilidade atômica aparentemente tem um papel importante na explicação dos casos encontrados. Tratamos também de moléculas contendo interações fracas como as de Van der Waals (moléculas tri-atômicas contendo um gás nobre ligado a um composto diatômico iônico) de modo a investigar os valores de dipolos atômicos QTAIM de uma maneira mais direta, ou seja, via comparação com um modelo simples para estes compostos. Por fim, estudamos moléculas em estados excitados, sendo que nossa análise focou em dois casos peculiares (CO e de CF2N2) que apresentam momento de dipolo nulo no estado fundamental, enquanto valores significativos desta propriedade são observados em seus primeiros estados excitados. Desta forma, QTAIM foi fundamental para compreender como o processo de excitação pode levar à mudanças tão significativas em tais propriedades elétricas. / In this PhD thesis we present the results of four different topics that refer to a study of electric properties interpreted with The Quantum Theory of Atoms and Molecules (QTAIM). First, dipole moments and their derivatives were calculated from a new formalism based on Ehrenfest Force Fields (EFF) and a comparison with data from QTAIM is carried out. Therefore, the Charge-Charge Flux-Dipole Flux (CCFDF) model was discussed for the dipole moment derivatives. The results from EFF were satisfactory in quantitative terms although QTAIM still seems to be better for the description of atomic polarization and its variations during vibrations. In the sequence, we investigated the Non-Nuclear Attractors (NNAs) that could be identified with the QTAIM formalism. Our intention was to discover new molecules that present this peculiarity, as well as to find trends among these cases that allow contributing for the understanding of the factors that lead to their appearance. For this purpose, we selected homonuclear diatomic molecules of elements presenting atomic numbers ranging from Z=1 to Z=38 and heteronuclear diatomic molecules containing these same elements. Our data shows that NNAs could be found in almost every homonuclear molecule expect by the systems formed by Hydrogen, Helium, and Strontium. On other hand, we have found 30 cases of NNAs in heteronuclear molecules, many of them seen for the first time. We also have noticed that the atomic polarizabilities play a main role in the understanding of these cases. We also treated molecules containing weak Van der Waals interactions (triatomic complexes presenting a noble gas bonded to a diatomic ionic molecule) in order to investigate the atomic dipole values obtained with QTAIM in a direct way, that is, by means of a comparison using a simple model for this kind of bonding. Finally, we studied molecules in excited states. Our focus was in two peculiar cases (CO and CF2N2), which present null dipole moments in their ground states but exhibit significant dipole moment values in their first excited states. Therefore, QTAIM was fundamental to understand how the excitation process can lead to important changes in electric properties.

Cette thèse présente le développement et les applications d'un formalisme hybride quantique-classique pour décrire la structure électronique d'un système actif avec un environnement cryogénique (agrégat ou matrice d'atomes de gaz rare). La description quantique de la structure électronique du système actif est faite dans le cadre d'une approximation de type Liaisons Fortes de la Théorie de la Fonctionnelle de la Densité, avec charges atomiques autocohérentes (SCC-DFTB). L'environnement de gaz rare est décrit par des potentiels classiques atome-atome (FF). L'interaction entre le sytème actif et les atomes de l'environnement cryogénique est représentée par des opérateurs matriciels locaux anisotropes électron-atome, ainsi que par des contributions de polarisation et de dispersion. La détermination des opérateurs et des paramètres d'interaction est extraite de calculs ab initio post Hartree-Fock (CCSD-T) sur les paires atome actif/atome d'argon. Les applications concernent les interactions entre hydrocarbures, agrégats d'eau isolés ou complexes hydrocarbures/eau avec des agrégats et ou des matrices d'argon. Le modèle est validé sur de petits systèmes (molécule C6H6 , molécule H2O) en interaction avec des atomes et agrégats d'argon. Nous avons ainsi déterminé les données structurales et énergétiques pour les agrégats (C6H6)Arn (n < 55) qui ont été comparées à des données ab initio (DFT, CCSD-T) pour les plus petits agrégats, ou à des calculs de champ de force publiés dans la littérature pour les agrégats de plus grande taille. Le modèle permet également un traitement unifié de différentes situations électroniques permettant ainsi la détermination de l'évolution des potentiels d'ionisation du système actif en fonction de la taille n de l'agrégat solvatant. Le modèle DFTB/FF a ensuite été appliqué à des molécules et nano-agrégats d'eau (H2O)n (n=2-6) insérés dans des matrices d'argon, représentées par des sous-ensembles finis du réseau cristallin cubique faces centrées. Des données structurales et énergétiques ont été obtenues. Des études de dynamique moléculaire ont permis la détermination de spectres infrarouges (IR) à température finie. La comparaison des spectres IR théoriques caractérisant une molécule d'eau en matrice avec les données expérimentales nous a permis de valider l'approche DFTB/FF. Le cas de l'hexamère (H2O)6, plus petit agrégat présentant une structure tri-dimensionnelle et caractérisé par plusieurs isomères stables, a été étudié de façon exhaustive : l'effet de la matrice sur les structures de certains de ces isomères a été mis en évidence, ainsi que des effets différentiels sur leur stabilités respectives. Une influence sur les positions des bandes IR des agrégats a également été montrée. Les résultats obtenus permettent une interprétation satisfaisante des données expérimentales existantes pour les plus petits agrégats. L'assignation des spectres expérimentaux de l'hexamère demeure incertaine. Enfin, des résultats préliminaires sur les structures, l'énergétique et les spectres IR à température finie ont été obtenus pour des complexes d'Hydrocarbures Aromatiques Polycycliques avec l'eau (HAP-H2O) en matrices d'argon. L'ensemble des données obtenues pour ces complexes est discuté en relation avec les résultats expérimentaux en environnement cryogénique obtenus dans l'équipe de Joëlle Mascetti de l'Institut des Sciences Moléculaires de l'Université Bordeaux I, dans le cadre d'une collaboration ANR (ANR PARCS no 13-BS08-0005). Ce travail a bénéficié d'une allocation de thèse co-financée par l'Institut de Physique du CNRS et le Conseil Régional de la région Midi-Pyrénées. / This thesis presents the development and applications of an hybrid quantum-classical formalism in order to describe the electronic structure of an active system in a cryogenic environment (cluster or rare gas matrix). The quantum description of the electronical structure of the active system is based on a a tight-binding approximation of the density functional theory, with self-consistency regarding the charges (SCC-DFTB). The rare gaz environment is described via classical atom-atom potential (FF). The interaction between the active system and the atoms of the cryogenic environment is represented by local anisotropic matricial electron-atom operators, as well as by polarisation and dispersion contributions. Operators and interaction parameters are extracted from post Hartree-Fock \textit{ab initio} calculations (CCSD-T) of active atom/argon atom pairs. The applications involve hydrocarbons, isolated water clusters or hydrocarbon/water complexes in interaction with argon clusters or matrices. The model has been validated on small systems (C6H6 molecule, H2O molecule) in interaction with argon atoms and clusters. We have been able to determine structural and energetic data for (C6H6)Arn (n < 55) clusters which are benchmarked against ab initio results (DFT,CCSD-T) for the smaller sizes, or with respect to FF calculations, available in the literature, for larger sized clusters. The model enables to treat various electronic situations, allows in particular to determine the evolution of the ionization potentials of the active system as a function of the inert cluster size. The SCC-DFTB/FF model has then been applied to water molecules and water nano-clusters (H2O)n (n=2-6) embedded in argon matrices, represented by finite size cristal pieces of the face centered cubic lattice. Structural and energetical data have been obtained. Molecular dynamics studies have enabled the determination of finite temperature infrared (IR) spectra. Comparison between the theoretical and experimental spectra of the water monomer embedded in the matrix validates the SCC-DFTB/FF approach. The case of the water hexamer (H2O)6, the smallest cluster presenting a three-dimensional structure and caracterized by several low-energy isomers, has been investigated exhaustively : the effect of the matrix on the structures of some isomers has been shown as well as differential effects on their respective stabilities. An influence on IR lines positions has also been highlighted. Our theoretical study allows for a satisfactory interpretation of the experimental data for the smallest clusters (n<4). The assignment of the experimental spectra of the hexamer remains in discussion. Finally, preliminary results on structures, energetics and finite temperature IR spectra have been obtained for Polycyclic Aromatic Hydrocarbons (PAH) /water complexes. The results for the complexes are discussed in relation with experimental data obtained in the team of Joëlle Mascetti at the Institute of Molecular Sciences (University of Bordeaux I), in the context of an ANR collaborative project (ANR PARCS no 13-BS08-0005). The thesis has been co-financed by the CNRS Institute of Physics and Conseil Regional of Region Midi-Pyrénées.

This thesis is concerned with theoretical concepts of phenomenological and statistical thermodynamics and their computational realization. The main goal of this thesis is to provide efficient workflows for an accurate description of thermodynamic properties of molecules and solid state materials. The Cp-MD workflow developed within this thesis is applied to characterize binary battery materials, such as lithium silicides.This workflow enables a numerically efficient description of macroscopic thermodynamic properties. For battery materials and metal-organic frameworks, it is shown that some macroscopic properties are dominantly controlled by microscopic properties. These microscopic properties are well described by respective small clusters or molecules.Given their reduced size, these systems can be calculated using more accurate and numerically more demanding methods. Standard density functional theory (DFT) and the so called Fermi-Löwdin orbital self-interaction correction (FLO-SIC) method are used for further investigations. It will be shown that SIC is able to overcome some of the problems of DFT. Given further workflows, it is demonstrated how a combination of different computational methods can speed up thermodynamic calculations and is able to deepen the understanding of the driving forces of macroscopic thermodynamic properties.:1 Introduction 2 Open-source and open-science I Theoretical basics 3 Computational methods 4 Computation of thermodynamic properties II Thermodynamics of solid state systems 5 Methodical developments 6 Lithium silicides 7 Metal-organic frameworks III Thermodynamics of nuclei and electrons 8 Electrons and bonding information 9 Thermodynamic properties IV Summary 10 Conclusion 11 Outlook V Appendix / Diese Arbeit befasst sich mit theoretischen Konzepten der phänomenologischen und statistischen Thermodynamik und deren numerischer Umsetzung. Das Hauptziel dieser Arbeit ist es, Arbeitsabläufe für die akurate Beschreibung von thermodynamischen Eigenschaften von Molekülen und Festkörpern zur Verfügung zu stellen. Der während dieser Arbeit entwickelte Cp -MD Arbeitsablauf wird angewandt um binäre Batteriemateralien, wie Lithiumsilizide, zu charakterisieren. Dieser Arbeitsablauf ermöglicht eine numerisch effiziente Beschreibung von makroskopischen thermodynamischen Eigenschaften. Für Batteriemateralien und metallorganische Gerüstverbindungen wird gezeigt, dass einige makroskopische Eigenschaften hauptsächlich von mikroskopischen Eigenschaften kontrolliert sind. Diese mikroskopischen Eigenschaften können mittels zugehöriger Cluster oder Moleküle beschrieben werden. Aufgrund ihrer reduzierten Größe können diese Systeme mit genaueren und numerisch aufwendigeren Methoden berechnet werden. Standard Dichtefunktionaltheorie (DFT) und die Fermi-Löwdin-Orbital Selbstwechselwirkungskorrektur (FLO-SWK) werden für weitere Untersuchungen verwendet. Es wird gezeigt, dass die SWK einige Probleme der DFT überwinden kann. Anhand weiterer Arbeitsabläufe wird gezeigt, wie eine Kombination von verschiedenen numerischen Methoden thermodynamische Berechnungen beschleunigen kann und in der Lage ist das Verständnis der Triebkräfte von makroskopischen thermodynamischen Eigenschaften zu vertiefen.:1 Introduction 2 Open-source and open-science I Theoretical basics 3 Computational methods 4 Computation of thermodynamic properties II Thermodynamics of solid state systems 5 Methodical developments 6 Lithium silicides 7 Metal-organic frameworks III Thermodynamics of nuclei and electrons 8 Electrons and bonding information 9 Thermodynamic properties IV Summary 10 Conclusion 11 Outlook V Appendix

Gasphasenabscheidungen werden zur Produktion dünner Schichten in der Mikro- und Nanoelektronik benutzt, um eine präzise Kontrolle der Schichtdicke im Sub-Nanometer-Bereich zu erreichen. Elektronische Eigenschaften der Schichten werden dabei von strukturellen Eigenschaften determiniert, deren Bestimmung mit hohem experimentellem Aufwand verbunden ist. Die vorliegende Arbeit erweitert ein hochparalleles Modell zur atomistischen Simulation des Wachstums und der Struktur von Dünnschichten, welches Molekulardynamik (MD) und Kinetic Monte Carlo-Methoden (KMC) kombiniert, um die Beschreibung beliebiger Gasphasenabscheidungen. KMC-Methoden erlauben dabei die effiziente Betrachtung der Größenordnung ganzer Nano-Bauelemente, während MD für atomistische Genauigkeit sorgt. Erste Ergebnisse zeigen, dass das Parsivald genannte Modell Abscheidungen in Simulationsräumen mit einer Breite von 0.1 µm x 0.1 µm effizient berechnet, aber auch bis zu 1 µm x 1 µm große Räume mit 1 Milliarden Atomen beschreiben kann. Somit lassen sich innerhalb weniger Tage Schichtabscheidungen mit einer Dicke von 100 Å simulieren. Die kristallinen und amorphen Schichten zeigen glatte Oberflächen, wobei auch mehrlagige Systeme auf die jeweilige Lagenrauheit untersucht werden. Die Struktur der Schicht wird hauptsächlich durch die verwendeten molekulardynamischen Kraftfelder bestimmt, wie Untersuchungen der physikalischen Gasphasenabscheidung von Gold, Kupfer, Silizium und einem Kupfer-Nickel-Multilagensystem zeigen. Stark strukturierte Substrate führen hingegen zu Artefakten in Form von Nanoporen und Hohlräumen aufgrund der verwendeten KMC-Methode. Zur Simulation von chemischen Gasphasenabscheidungen werden die Precursor-Reaktionen von Silan mit Sauerstoff sowie die Hydroxylierung von alpha-Al2O3 mit Wasser mit reaktiven Kraftfeldern (ReaxFF) berechnet, allerdings ist weitere Arbeit notwendig, um komplette Abscheidungen auf diese Weise zu simulieren. Mit Parsivald wird somit die Erweiterung einer Software präsentiert, die Gasphasenabscheidungen auf großen Substraten effizient simulieren kann, dabei aber auf passende molekulardynamische Kraftfelder angewiesen ist.