Cette thèse est une étude par diffusion neutronique des pyrochlores Tb2Ti2O7 et Pr2Zr2O7. Ces composés, pour lesquels les ions magnétiques sont des ions Non-Kramers (NK), sont présentés comme de potentielles glaces de spin quantiques. Dans Pr2Zr2O7, l'étude des réponses élastique et inélastique et des structures induites sous champ nous amènent à conclure que l'état fondamental serait une recombinaison du doublet fondamental de champ cristallin (CEF) du fait de l'existence de termes multipolaires dans l'Hamiltonien. Ces termes seraient dus à un couplage magnéto-cristallin. Dans l'approximation de champ moyen, un modèle local de distorsion structurale semble en effet reproduire nos résultats. Dans Tb2Ti2O7, malgré de notables différences avec Pr2Zr2O7, nos mesures indiquent qu'un mécanisme semblable de mélange des fonctions d'onde du doublet fondamental de CEF a lieu. Ce mélange impliquerait des termes multipolaires également dus au couplage magnéto-cristallin et nous avons pu observer une signature directe de ce couplage. Les mécanismes en jeu dans ces systèmes ne seraient pas ceux proposés pour les glaces de spin quantiques mais dus à la sensibilité des ions NK à leur environnement. L'étude de composés non-st¿chiométriques montre la réactivité du magnétisme aux perturbations. / This work is the neutron scattering study of the pyrochlores Tb2Ti2O7 and Pr2Zr2O7. These compounds where magnetic ions are Non-Kramers ions are expected to be quantum spin ices. In Pr2Zr2O7, the study of the elastic and inelastic response together with the study of the magnetic structures in applied magnetic field lead to the conclusion that the magnetic ground state is a mixing of the wave functions of the crystal-field ground state doublet because of quadrupolar terms in the Hamiltonian. These terms would originate from a coupling to the lattice. Using the mean-field approximation, a model based on a local structural distortion reproduces quite well our measurements. Despite strong differences with Pr2Zr2O7, our measurements provide evidence for a similar mechanism in Tb2Ti2O7. Again, this would be caused by multipolar terms in the Hamiltonian reflecting a strong coupling of the magnetic moments to the lattice. Then, these pyrochlores would not be quantum spin ices. Instead, the extreme sensibility to the environment characteristic of the Non-Kramers ions would lead to these fluctuations. Our measurements of samples slightly off-stoichiometry emphases the strong reactivity of the magnetic behavior of these compounds.

Today, the investigation of fuel economy improvements in internal combustion engines (ICEs) has become the most significant research interest among the automobile manufacturers and researchers. The scarcity of natural resources, progressively increasing oil prices, carbon dioxide taxation and stringent emission regulations all make fuel economy research relevant and compelling. The enhancement of engine performance solely using incylinder techniques is proving increasingly difficult and as a consequence the concept of exhaust energy recovery has emerged as an area of considerable interest. Three main energy recovery systems have been identified that are at various stages of investigation. Vapour power bottoming cycles and turbo-compounding devices have already been applied in commercially available marine engines and automobiles. Although the fuel economy benefits are substantial, system design implications have limited their adaptation due to the additional components and the complexity of the resulting system. In this context, thermo-electric (TE) generation systems, though still in their infancy for vehicle applications have been identified as attractive, promising and solid state candidates of low complexity. The performance of these devices is limited to the relative infancy of materials investigations and module architectures. There is great potential to be explored. The initial modelling work reported in this study shows that with current materials and construction technology, thermo-electric devices could be produced to displace the alternator of the light duty vehicles, providing the fuel economy benefits of 3.9%-4.7% for passenger cars and 7.4% for passenger buses. More efficient thermo-electric materials could increase the fuel economy significantly resulting in a substantially improved business case. The dynamic behaviour of the thermo-electric generator (TEG) applied in both, main exhaust gas stream and exhaust gas recirculation (EGR) path of light duty and heavy duty engines were studied through a series of experimental and modelling programs. The analyses of the thermo-electric generation systems have highlighted the need for advanced heat exchanger design as well as the improved materials to enhance the performance of these systems. These research requirements led to the need for a systems evaluation technique typified by hardware-in-the-loop (HIL) testing method to evaluate heat exchange and materials options. HIL methods have been used during this study to estimate both the output power and the exhaust back pressure created by the device. The work has established the feasibility of a new approach to heat exchange devices for thermo-electric systems. Based on design projections and the predicted performance of new materials, the potential to match the performance of established heat recovery methods has been demonstrated.

This dissertation has investigated the adsorption, thermal behavior, and radiation (both photon and electron) processing of prebiotically-relevant ices and surfaces. A custom ultra-high vacuum (UHV) chamber has been built that is coupled with a Fourier Transform-Infrared (FT IR) spectrometer and a Temperature Programmed Desorption (TPD) system that utilizes Quadrupole Mass Spectrometry (QMS) to study selected organic:surface systems. Formamide (HCONH₂) has been studied in two related but distinct studies relevant to primitive Earth and interstellar chemistry. First, in collaboration with a theory group, formamide’s interaction with kaolinite (Al6Si6O36H30), a clay mineral relevant to early Earth chemistry, has been studied experimentally and theoretically. Experimental infrared results are compared with calculated infrared frequencies obtained by our collaborators. TPD analysis is compared with the calculated values of adsorption energy, and the optimal kaolinite termination site for adsorption is reported. Second, the first thermal and radiation damage study of pure formamide and HCONH₂:H₂O mixed ices on an interstellar icy grain analog (SiO₂) is reported. A discussion of the pure formamide ice phases identified with FT-IR upon warm-up, as well as the TPD binding energies of HCONH₂ on SiO₂, is presented. The observed Lyman-alpha photochemical products and proposed formation mechanisms from pure formamide ice is reported and discussed. In addition, results of Lyman alpha processing of mixed HCONH₂:H₂O ices are provided. Low-energy electron irradiation of pure HCONH₂ and HCONH₂:H₂O mixed ices has also been reported for the first time. A third investigation has studied acetylene (C₂D₂) and acetonitrile (CH₃CN) interactions and radiation stability in mixed low-temperature ices to simulate possible prebiotic reactions that may occur on Saturn’s moon, Titan. This investigation contributes to understanding the possible consumption, trapping, and degradation of these species on the surface of Titan.

Les grains de poussière se trouvant dans les nuages moléculaires denses jouent un grand rôle dans la formation de molécules organiques complexes. Ces grains sont recouverts d'un manteau glacé contenant des molécules primitives. Au cours de l'évolution des nuages moléculaires vers des systèmes planétaires, les grains sont soumis à des processus énergétiques transformant la matière organique présente dans les glaces. Les grains finissent par être intégrés dans les petits corps du système solaire tels que les comètes et les astéroïdes. Cette thèse cherche à simuler en laboratoire l'évolution chimique de ces glaces. Des analogues de ces glaces sont formés sur un substrat à basse température, et sont irradiés avec des photons UV et/ou réchauffés afin de simuler les processus astrophysiques. On forme ainsi un résidu organique que l'on caractérise grâce à la spectroscopie infrarouge à transformée de Fourier (IRTF) et la spectrométrie de masse à très haute résolution (VHRMS) par Orbitrap.Nous avons d'abord effectué des études mécanistiques centrées autour de la formation d'aminoalcools et d'hydroxynitriles lors du réchauffement de glaces contenant de l'acétaldéhyde (CH$_3$CHO) ou de l'acétone ((CH$_3$)$_2$CO) avec NH$_3$, HCN et H$_2$O. Nous avons ensuite étudié la composition globale de résidus issus de l'irradiation et du réchauffement de glaces contenant H$_2$O, CH$_3$OH, et NH$_3$. Nous présentons une nouvelle approche pour interpréter les données Orbitrap de ces résidus. Les similarités trouvées avec des analyses de matière organique météoritique issues de la littérature laissent à penser qu'une partie de son évolution pourrait être semblable à celle de nos résidus. / Dust grains located in dense molecular clouds play a major role in the formation of complex organic molecules. These grains are covered by icy mantles containing primitive molecules. Dense molecular clouds can collapse and lead to the formation of planetary systems such as our own. During this evolution, the grains are exposed to energetic processes which transform the organic matter inside the ices. The grains are ultimately incorporated into small solar system bodies such as comets and asteroids, which can then contribute to the exogenous delivery of organic matter on Earth. In this context, this thesis focuses on simulating the chemical evolution of ices. To that end, ice analogues are formed by condensing a relevant gas mixture on a cold substrate. These interstellar ice analogues are irradiated with UV photons and/or heated in order to simulate astrophysical processes. An organic residue is formed which we characterized with Fourier transform infrared spectroscopy (FTIR) and very high resolution mass spectrometry (VHRMS) by Orbitrap.First, we performed mechanistic studies focused on the formation of aminoalcohols and hydroxynitriles from the warming of ices containing acetaldehyde (CH$_3$CHO) or acetone ((CH$_3$)$_2$CO) with NH$_3$, HCN and H$_2$O. Secondly, we studied the global composition of residues made from irradiation and warming of ices containing H$_2$O, CH$_3$OH, and NH$_3$. We present a new approach to interpret Orbitrap data of the residues. Similarities observed with meteoritic organic matter analyses found in the literature could mean that some of the evolution that led to meteoritic organic matter is shared with the evolution of our residues.

Les expériences de laboratoire ont montré que la photo-irradiation ultraviolette d'analogues de glaces astrophysiques suivie de leur réchauffement à température ambiante mène à la formation de résidus organiques réfractaires. Ces résidus, solubles dans l'eau, consistent en un riche mélange de composés organiques incluant entre autres des acides aminés, molécules potentiellement importantes pour la chimie prébiotique. Ces résidus sont considérés comme des analogues de la matière organique réfractaire que l'on pense être synthétisée sur les grains de poussière dans les nuages moléculaires et/ou dans les disques protoplanétaires, produit de l'évolution des glaces, et qui pourra être accrétée plus tard en comètes ou en astéroïdes et finalement délivrée sur la Terre primitive. Ainsi, l'étude de ces analogues, produits dans des conditions astrophysiques pertinentes, représente un outil efficace pour explorer les processus à l'origine de la formation des molécules organiques complexes dans le Système Solaire et en particulier la possible introduction d'excès énantiomériques dans les molécules chirales.Ce travail de thèse est consacré à l'étude de ces résidus organiques, leur caractérisation et les applications astrophysiques de ces résultats. Nous avons utilisé différentes techniques d'analyse comme la chromatographie en phase gazeuse couplée à la spectrométrie de masse (GC MS, classique et multidimensionnelle), la spectrométrie de masse par résonnance cyclotronique ionique à transformée de Fourier (FT ICR MS) ou encore la spectroscopie infrarouge. Nous avons mesuré les excès énantiomériques induits dans cinq acides aminés par irradiation de nos analogues avec de la lumière UV polarisée circulairement (UV CPL) et insérons nos résultats dans le cadre d'un scénario astrophysique cohérent pour expliquer l'origine des excès énantiomériques observés dans les acides aminés météoritiques. Nous avons étudié le contenu en acides aminés de la météorite de "Paris" et montré des similarités avec la distribution en acides aminés de nos résidus organiques. Nous avons également produit des analogues plus réalistes de grains interstellaires en incluant une surface silicatée, afin de tester l’effet potentiel de cette surface sur la formation et la nature des résidus organiques. Enfin, nous effectuons une discussion générale à propos de la pertinence de ces résultats dans le contexte astrophysique et soulignons le possible lien entre astrochimie et chimie prébiotique. / Laboratory experiments have shown that ultraviolet photo-irradiation of astrophysical ice analogs and their following warm-up until room temperature lead to the formation of refractory organic residues. These residues consist of rich mixtures of organic compounds, including amino acids, which have a potential importance for prebiotic chemistry. They are considered as analogs of the organic refractory materials that are thought to be synthesized on dust grains in molecular clouds and/or in protoplanetary disks, as a product of ices evolution, and that could be later accreted into comets and asteroids and eventually be delivered to the early Earth. Hence, the study of these analogs, produced under astrophysically relevant conditions, represents a valid tool to investigate the processes at work for the origin of complex organic molecules in the Solar System and in particular the possible introduction of enantiomeric excesses in chiral molecules. This PhD work is devoted to the study of these laboratory organic residues, their characterization and the astrophysical applications of the results. We used different analytical techniques such as gas chromatography mass spectrometry (GC MS, classical and multidimensional), Fourier transform ion cyclotron resonance mass spectrometry (FT ICR MS), and infrared spectroscopy. We measured the enantiomeric excesses induced in five chiral amino acids by UV circularly polarized light (UV CPL) irradiation of our analogs and insert our result in a coherent astrophysical scenario for the origin of the enantiomeric excesses observed in meteoritic amino acids. We studied the amino acid content of the Paris meteorite and evidence some similarities with the distribution of the amino acids in our organic residues. We also produced more realistic analogs of interstellar grains, including a silicate surface, to test the potential effect of such a surface on the formation and nature of organic residues. Finally, we discuss the significance of these results in the astrophysical context and the possible relationship between astrochemistry and prebiotic chemistry.

<div> In recent decades as environmental concerns and the cost and availability of fossil fuels have become more pressing issues, the need to extract more work from each drop of fuel has increased accordingly. Electrification has been identified as a way to address these issues in vehicles powered by internal combustion engines, as it allows existing engines to be operated more efficiently, reducing overall fuel consumption. Two applications of electrification are discussed in the work presented: a series-electric hybrid powertrain from an on-road class 8 truck, and an electrically supercharged diesel engine for use in the series hybrid power system of a wheel loader.</div><div> </div><div> The first application is an experimental powertrain developed by a small start-up company for use in highway trucks. The work presented in this thesis shows test results from routes along (1) Interstate 75 between Florence, KY, and Lexington, KY, and (2) Interstates 74 and 70 east of Indianapolis, during which tests the startup collected power flow data from the vehicle's motor, generator, and battery, and three-dimensional position data from a GPS system. Based on these data, it was determined that the engine-driven generator provided an average of 15% more propulsive energy than required due to electrical losses in the drivetrain. Some of these losses occured in the power electronics, which are shown to be 82% - 92% efficient depending on power flow direction, but the battery showed significant signs of wear, accounting for the remainder of these electrical losses. Overall, most of the system's fuel savings came from its regenerative braking capability, which recaptured between 3% and 12% of the total drive energy output. Routes with significant grade changes maximize this energy recapture percentage, but it is shown minimizing drag and rolling resistance with a more modern truck and trailer could further increase this energy capture to between 8% and 18%.</div><div> </div><div> In the second application, an electrified air handling system is added to a 4.5L engine, allowing it to replace the 6.8L engine in John Deere's 644K hybrid wheel loader. Most of the fuel savings arise from downsizing the engine, so in this case an electrically driven supercharger (eBooster) allows the engine to meet the peak torque requirements of the larger, original engine. In this thesis, a control-oriented nonlinear state space model of the modified 4.5L engine is presented and linearized for use in designing a robust, multi-input multi-output (MIMO) controller which commands the engine's fueling rate, eBooster, eBooster bypass valve, exhaust gas recirculation (EGR) valve, and exhaust throttle. This integrated control strategy will ultimately allow superior tracking of engine speed, EGR fraction, and air-fuel ratio (AFR) targets, but these performance gains over independent single-input single-output control loops for each component demand linear models that accurately represent the engine's gas exchange dynamics. To address this, a physics-based model is presented and linearized to simulate pressures, temperatures, and shaft speeds based on sub-models for exhaust temperature, cylinder charge flow, valve flow, compressor flow, turbine flow, compressor power, and turbine power. The nonlinear model matches the truth reference engine model over the 1200 rpm - 2000 rpm and 100 Nm - 500 Nm speed and torque envelope of interest within 10% in steady state and 20% in transient conditions. Two linear models represent the full engine's dynamics over this speed and torque range, and these models match the truth reference model within 20% in the middle of the operating envelope. However, specifically at (1) low load for any speed and (2) high load at high speed, the linear models diverge from the nonlinear and truth reference models due to nonlinear engine dynamics lost in linearization. Nevertheless, these discrepancies at the edges of the engine's operating envelope are acceptable for control design, and if greater accuracy is needed, additional linear models can be generated to capture the engine's dynamics in this region.</div>

The urgent need to reduce green house gas emissions from the transport sector, particularly from heavy-duty trucks, has underscored the importance of developing more efficient internal combustion engines. Using computational fluid dynamics (CFD), this work investigated the impact of valve seat geometry on in-cylinder swirl, addressing a gap in research. Additionally, the suitability of steady-state simulations for providing valid qualitative data on port flow was assessed. To answer both research questions, two approaches were followed: steady-state port flow RANS simulations, and transient RANS simulations in a running engine setup. The results from the steady-state simulations highlighted the limitations of this approach to qualitatively predict swirl, as this quantity is highly dependent on the mesh. Despite these limitations, the steady-state simulations were still able to capture the trade-off between swirl and discharge coefficient, outlined in the literature. Transient simulations revealed that in-cylinder swirl is affected by the geometry of the valve seats. It was found that valve seats that direct the flow towards the liner, while avoiding strong flow separation tend to promote higher swirl, whereas valve seats that induce strong flow separation lead to lower swirl ratios. Despite the trade-off between swirl and volumetric efficiency, the volumetric efficiency losses were found to be practically negligible. The study emphasizes the need for a more comprehensive set of simulations, including more valve lifts and pressure ratios. Given the unsuitability of the steady-state simulations to predict swirl trends, future investigations should focus on replacing this approach by transient simulations with steady-state geometry and boundary conditions, properly addressing flow time-dependency at relatively low computational cost, and facilitating validation with experimental data.

[Truncated abstract] This thesis examines the bonding interactions and chemical processes associated with irradiated water (H2O) and ammonia (NH3) molecules. The experiments conducted in the present study are designed to replicate the surface chemistry of outer Solar System bodies, particularly the icy surfaces of Saturn's inner moons. Infrared (IR) spectroscopy is used to identify the H2ONH3 complex isolated in an argon (Ar) matrix. An electric discharge is then applied to the H2O and NH3 species to produce the hydroxyl-ammonia (OHNH3) complex and the water-amidogen (H2ONH2) complex. Finally, the ammonia-oxygen (NH3O2) complex is formed in an Ar matrix, complementing previous studies performed by the Quickenden research group, which investigated the conversion of OH radicals into molecular O2 on icy planetary surfaces. ... An electric discharge is applied to the NH3 in Ar mixture, producing the NH2 radical subunit of the complex. Two absorption bands are assigned to the H2O subunit vibrational frequencies of the complex; at 1616.1 cm-1 for the ¿2 HOH bending fundamental and at 3532.1 cm-1 for the ¿1 OH bonded stretching fundamental. Two absorption bands are also assigned to the NH2 radical subunit vibrational frequencies of the complex; at 1498.5 cm-1 for the ¿2 HNH bending fundamental and at 3260.8 cm-1 for the ¿3 NH asymmetric stretching fundamental. These assignments are verified by the isotope substitution method, involving the formation of the deuterated D2OND2 complex analogue in an Ar matrix and the measurement of the isotope induced shifts in peak position in the IR region. The isotopic shifts displayed by the IR absorption bands are in good agreement with the theoretically calculated shifts in vibration frequency when going from the H2ONH2 complex fundamentals to the D2OND2 complex fundamentals. The theoretical calculations also derived an interaction energy of 5.2 kcal mol-1 for the HOHNH2 structure of the H2ONH2 complex. This HOHNH2 structure is also confirmed as the preferred structure of the H2ONH2 complex in the IR experiments, by the observation of a large shift in position of the absorption band associated with the H2O subunit ¿1 OH stretching fundamental, away from the position of the H2O monomer ¿1 OH stretching fundamental. This indicates that the H2O subunit donates a hydrogen for the complex bond in the HOHNH2 complex. The NH3O2 complex is identified in solid Ar matrices at 10.5 K by IR analysis. The NH3O2 complex is formed by the co-deposition of gaseous NH3 in Ar mixtures with O2 in Ar gas mixtures. An absorption band is assigned to the ¿1 OO stretching fundamental for the O2 subunit of the NH3O2 complex at 1552.0 cm-1. This assignment is verified by the isotope substitution method, involving the formation of the deuterated ND3O2 complex analogue in an Ar matrix and the measurement of the isotope induced shift in peak position in the IR region. The isotopic shift displayed by the IR absorption band is in good agreement with the theoretically calculated shift in vibration frequency when going from the NH3O2 complex fundamental to the ND3O2 complex fundamental. The theoretical calculations also derived an interaction energy of 0.28 kcal mol-1 for the NH3O2 complex.

Les éléments génétiques mobiles contribuent grandement à la diversité et à l’évolution des génomes bactériens par le biais du transfert horizontal. Parmi eux, les éléments intégratifs conjugatifs (ICE) codent leur propre excision, leur transfert par conjugaison et leur intégration. En revanche, les éléments intégratifs et mobilisables (IME) ne sont autonomes que pour leur excision et intégration et ne codent seulement que certaines des protéines/fonctions (oriT) dont ils ont besoin pour leur transfert conjugatif. Par conséquent, les IME ont besoin d’un élément conjugatif « helper » pour se transférer. Malgré leur impact sur le flux des gènes et l’évolution des génomes, la prévalence des ICE reste peu étudiée et seulement très peu d’IME avaient été identifiés au début de cette étude. De plus, bien que plusieurs méthodes de détection des ilots génomiques existent, aucune d’elles n’est dédiée aux ICE ou aux IME. Ce qui ne facilite pas l’analyse exhaustive de ces éléments. Le genre Streptococcus appartient au phylum des firmicutes. La quasi-totalité des streptocoques sont des bactéries commensales ou pathogènes de l’homme et d’autres animaux. Aussi, 2 espèces de streptocoques sont utilisées en tant que ferments lactiques lors la production de laits fermentés et divers fromages. Globalement, le genre streptocoques représente un groupe d’intérêt pour l’homme, l’étude du flux de gènes au sein de ces organismes et l’impact qu’il peut avoir sur leur mode vie est primordiale. Au cours de cette thèse, nous avons recherché les ICE et les IME dans 124 souches de streptocoques appartenant à 27 espèces en utilisant une base de données de référence comportant des protéines dites « signatures » d’IME et d’ICE (de leurs modules de conjugaison/mobilisation et d’integration/excision). Cette analyse exhaustive a permis l’identification et la délimitation de 131 ICE ou ICE légèrement dégénérés et 144 IME. Tous ces éléments ont été délimités, ce qui nous a permis de déterminer leur spécificité d’intégration dans les génomes. Au total, 17 spécificités d’intégration ont été identifiées pour les ICE dont 8 encore jamais décrites (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG and ybaB/EbfC) et 18 spécificités pour les IME dont seulement 5 étaient connues chez les firmicutes. Les modules d’intégration des ICE codent soit une intégrase à tyrosine pouvant avoir une faible spécificité (1 famille d’intégrase) ou une forte spécificité (13 spécificités différentes), soit des intégrases à sérine seule ou en triplet (4 spécificités différentes), soit une transposase à DDE. Les IME codent soit des intégrases à tyrosine (10 spécificités différentes) soit des intégrases à serine seule (8 spécificités différentes). Les ICE ont été groupés en 7 familles distinctes selon les protéines codées par leur module de conjugaison. Les IME présentaient une très forte diversité au sein de leur module de mobilisation, empêchant ainsi leur regroupement en famille selon les gènes portés par ce module. Les analyses phylogénétiques des protéines signature codées par tous les ICE et les IME ont montré des échanges de modules d’intégration entre les ICE et les IME et de nombreux échanges entre les modules de mobilisation des IME. L’ensemble de ces résultats révèle la forte prévalence et l’extrême diversité des ICE et des IME au sein des génomes de streptocoques. Une meilleure connaissance et compréhension de ces éléments nous a incité à construire un outil informatique semi-automatisé de détection des ICE et des IME de Streptocoques ainsi que leurs sites d’insertion / Mobile genetic elements largely contribute to the evolution and diversity of bacterial genomes through horizontal gene transfer. Among them, the integrative and conjugative elements (ICEs) encode their own excision, conjugative transfer and integration. On the other hand, integrative mobilizable elements (IMEs) are autonomous for excision and integration but encode only some of the proteins needed for their conjugative transfer. IMEs therefore need a “helper” conjugative element to transfer. Despite their impact on gene flow and genome dynamics, the prevalence of ICEs remains largely underscored and very few IMEs were identified at the beginning of this study. Furthermore, although several in silico methods exist to detect genomic islands, none are dedicated to ICEs or IMEs, thus complicating exhaustive examination of these mobile elements. The Streptococcus genus belongs to the firmicutes’ phylum. Almost all streptococci are commensal bacteria or pathogenes to men and animals. Two species of Streptococcus are also used in the dairy industry as lactic ferments in order to produce fermented milk and different types of cheese. Studying the gene flux of the Steptococci genus and the impact it can have on the lifestyle of these organisms is essential, as it has a lot of interest for human health and activities. In this work, we searched for ICEs and IMEs in 124 strains of streptococci belonging to 27 species using a reference database of ICE and IME signature proteins (from their conjugation, mobilization and integration/excision modules). This exhaustive analysis led to the identification and delimitation of 131 ICEs or slightly decayed ICEs and 144 IMEs. All these elements were delimited, which allowed us to identify their integration specificities in the genomes. In total, 17 ICE integration specificities were identified. Among them, 8 had never been described before (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG and ybaB/EbfC). 18 specificities were also identified for IMEs, among which only 5 were known for the firmicutes. ICEs encode high or low-specificity tyrosine integrases (13 different specificities), single serine intégrases (1 specificity), triplet of serine integrases (3 different specificities), or DDE transposases while IMEs encode either tyrosine integrases (10 different specificities) or single serine integrases (8 different specificities). ICE were grouped in 7 distinct families according to the proteins encoded by their conjugation module whereas the mobilization modules of IMEs were highly diverse, preventing them from grouping into families according to their mobilization modules. The phylogenetic analysis of the signature proteins encoded by all ICEs and IMEs showed integration module exchanges between ICEs and IMEs and several mobilization module exchanges between IMEs. The overall results reveal a strong prevalence and extreme diversity of these elements among Streptococci genomes. Better understanding and knowledge of ICEs and IMEs prompted us to build a semi-automated command-line tool to identify streptococcal ICEs and IMEs as well as to determine their insertion site

Dans cette thèse, nous étudions la stabilité et les propriétés des glaces d’eau de haute pression (entre 5 et 300 GPa) et de haute température (entre 300 et 2000 K) comportant ou non des inclusions de NaCl dans leur structure cristalline. Pour attendre ces conditions propres aux intérieurs des exoplanètes océans, nous utilisons une approche théorique basée sur des dynamiques moléculaires ab initio. Nous montrons que l’analyse de la dynamique des liaisons entre hydrogènes et oxygènes permet de distinguer toutes les phases de la glace présentant une structure cubique volume-centrée. En particulier, nous présentons la première description ab initio de la phase plastique, et nous mettons en évidence la présence de multiples transitions dans la phase superionique. Ensuite, nous montrons que jusqu’à 5.9 % en masse de NaCl peuvent être inclus dans la structure de la glace à 1600 K. L’inclusion des ions Na+ et Cl- stimule le désordre orientationel des molécules d’eau par rapport à la glace d’eau pure. À partir de 2.5 % en masse de NaCl, la conduction superionique s’étend à l’ensemble de la gamme de pression étudiée, et la symétrisation des liaisons hydrogènes se produit à plus haute pression. Enfin, nous décrivons les structures de cœur des dislocations vis ayant des vecteurs de Burgers <110> et <111> dans la glace X à 80 GPa, ce qui constitue une étape préliminaire importante à la construction de lois rhéologiques pour les glaces cubiques de haute pression. / In this thesis we study the stability and the properties of pure and NaCl-bearing dense water ices at high pressure (between 5 and 300 GPa) and high temperature (between 300 and 2000 K). To reach these conditions that correspond to the interiors of ocean exoplanets, we employ a theoretical approach based on ab initio molecular dynamics simulations. We show that a detailed analysis of the hydrogen bond dynamics allows to distinguish all the different ice phases presenting a body-centered cubic sub-lattice of oxygen atoms. In particular, we present the first ab initio description of the plastic phase of water ice. We also reveal the multiple transitions that occur in the superionic domain. Next, we show that ice VII' can incorporate up to 5.9 wt% NaCl in its structure at 1600 K. The inclusion of Na+ and Cl- ions enhances the orientation disorder of the water molecules in comparison to the pure ice. From 2.5 wt% NaCl, superionic conduction expands over the entire pressure range studied, and the hydrogen symmetrisation is shifted towards higher pressures. Last, we describe the <110> and <111> screw dislocation core structures of ice X at 80 GPa. This constitutes a first step towards the construction rheological laws for high-pressure cubic ices.