Theoretical and experimental modal analysis, i.e., the computation of vibration modes from a mathematical model and from experimental data, respectively, is quite sophisticated and advanced in linear structural dynamics. However, nonlinearity is a frequent occurrence in real-world engineering structures, and the existing linear methodologies fail dramatically in the presence of nonlinear dynamical phenomena. Therefore, the present thesis focuses on the development of a practical nonlinear analog of modal analysis for properly accounting for nonlinearity in mechanical systems. The concept of nonlinear normal mode (NNM) provides solid mathematical and theoretical foundations for a rigorous, yet understandable by the practicing engineer, analysis of nonlinear dynamical behaviors. In this context, a useful framework for nonlinear modal analysis of vibrating structures, which includes the computation of NNMs from finite element models and their identification from experimental data, is proposed in this dissertation. In view of the still limited use of NNMs in structural dynamics, special attention is devoted to progress toward a practical tool that has the potential to deal with large-scale, real-world structures. Targeting an effective and exact computation of NNMs, even in strongly nonlinear regimes of motion, one original contribution of this work is to resort to numerical methods. An algorithm combining a shooting procedure and the so-called pseudo-arclength continuation method is developed. On the other hand, a nonlinear extension of phase resonance testing (also known as force appropriation) is introduced for the experimental identification of NNMs, which is another innovative aspect of the doctoral thesis. In particular, the phase lag quadrature criterion, which is used for linear experimental modal analysis, is generalized in the presence of nonlinear dynamical behavior. Academic examples are first considered to illustrate, in a simple manner, that the proposed methods form an effective and adequate framework for nonlinear modal analysis. Furthermore, more realistic structures, including a full-scale aircraft, are studied to demonstrate the potential applicability of the approach to large-scale, real-life applications.

Molecular dynamics simulations were performed on the influenza A non-structural protein 1 (NS1) RNA binding domain (RBD), a homodimer. Fourteen simulations were performed at 298K, nine ionized with 0.1M KCl and five with no ions. Several analysis techniques were employed to study RBD residue flexibility. The focus of the study was the RNA binding cavity formed by side chains of helix 2 (chain A) and helix 2’ (chain B) and cavity intermonomeric salt bridges. Opening of the salt bridges D29–R46’ and D29’–R46 was observed in several of the trajectories. The RNA binding cavity has large flexibility, where the dimension and shape change during the dynamics. One pair of residues surrounding the cavity and necessary for RNA binding, residues R38 and R38’, have motions during the simulations which cover the top of the cavity. There is correlation between the salt bridge breaking, flexibility of R38 and R38’, and the cavity size and shape changes. Possible RBD small molecule drug targets are these two salt bridges and the pair R38 and R38’. Disrupting the events that occur around these areas could possibly inactivate RNA binding function of the domain. These results could have implications in searching for potential molecules that effectively treat influenza A.

Cette thèse traite de la réduction d’ordre de modèle du phénomène communément rencontré dans la modélisation de microsystèmes, à savoir, dans la littérature anglaise, le « squeeze-film damping ». Dans un premier chapitre sont présentées les différentes méthodes de réduction d’ordre de modèle. Dans le cas des systèmes linéaires, elles ont un cadre théorique bien établi. Ces méthodes peuvent être adaptées pour les systèmes non-linéaires. La validité des modèles réduits résultants sera alors réduite à un certain espace des phases, leur établissement faisant intervenir certaines trajectoires particulières servant d’apprentissage. On présente finalement la méthode des modes normaux non-linéaires dont les modèles résultants ne dépendent pas d’une trajectoire d’apprentissage. Au chapitre 2, on s’intéresse plus particulièrement au phénomène de « squeeze-film damping » régi par l’équation de Reynolds. Après avoir détaillé son établissement à partir de certaines hypothèses, on décrit les différentes méthodes de résolution de l’équation linéaire puis non-linéaire de la littérature. On compare ensuite les résultats d’un modèle de l’équation de Reynolds à des simulations éléments finis de l’équation de Navier-Stokes afin de valider les hypothèses faites pour la dérivation de l’équation de Reynolds. On propose ensuite une résolution originale par changement de variable. On étudie aussi plusieurs autres résolutions possibles ainsi que plusieurs bases de projection parmi celles décrites dans le premier chapitre. Le chapitre 3 est consacré à la modélisation du problème couplé que constitue le micro-interrupteur MEMS qui est un candidat au remplacement des interrupteurs à base de transistors dans les communications RF. Sa modélisation fait intervenir trois domaines, la mécanique, l’électrostatique, et la fluidique à travers l’équation de Reynolds. Après voir décrit les différents modèles de la littérature, on propose un modèle réduit couplé dont le modèle fluidique est basé sur le modèle établi au chapitre 2. Ce modèle est validé par rapport à des modèles différences finies et à des résultats expérimentaux de la littérature.Enfin le quatrième chapitre traite de la réduction du coût d’évaluation du modèle réduit couplé de micro-interrupteur du chapitre 3. La première méthode proposée consiste à trouver une fonction d’approximation de la projection de la force fluidique sur le premier mode mécanique, fonction des coordonnées modales mécaniques position et vitesse. Cette méthode ne se révèle valable que dans le cas incompressible. Dans le cas compressible, la résolution de l’équation de Reynolds restant obligatoire, on utilise la méthode de Rewienski et al. qui consiste à linéariser par morceaux les fonctions régissant la dynamique. Une autre méthode de linéarisation par morceaux, tirant parti d’une particularité du modèle du chapitre 2 et permettant de s’affranchir d’une trajectoire d’apprentissage, est également proposée. / This thesis deals with reduced-order modelling of squeeze-film damping, a fluidic phenomenon that is commonly encountered in MEMS. In the first chapter, reduced-order modelling methods are presented. For linear systems, well-established theories exist. They can be adapted to nonlinear systems. However, the resulting reduced-order models are valid in a certain region of the state-space only, depending on the training trajectory. The method of nonlinear normal modes, which does not depend on a training trajectory is also introduced. Chapter two is focused on the squeeze-film damping phenomenon governed by the Reynolds equation. We first establish the equation from appropriate hypotheses, and then present the different resolutions of its linear and nonlinear form found in literature. The results from a model based on the Reynolds equation are then compared to results from a finite element Navier-Stokes model, in order to validate the various hypotheses made. An original method of resolution based on a change of variable is then proposed. Several other method of resolution are studied as well as different projection bases amongst those presented in chapter one.Chapter three is dedicated to the modelling a micro-switch, a candidate to the replacement of switches based on transistors in RF communications. Its modelling implies the coupling of three domains: mechanics, electrostatics, and fluidics with Reynolds equation. Following a description of the models from literature, a coupled model is proposed, the fluidic model being the one presented in chapter two. This model is validated compared to finite difference models as well as experimental data from the literature.Finally, the fourth chapter aims at reducing the evaluation cost of the coupled micro-switch model established in chapter three. The first method consists in finding an approximation function of the projection of the fluidic force on the first linear mechanical mode as a function of the mechanical modal coordinates, position and speed. This method is applicable in the incompressible case only. In the compressible case, the Reynolds equation has to be solved. The method of Rewienski and al., which consists in piecewise-linearizing the functions governing the dynamics, is used. Another method based on a piecewise-linear approach, taking advantage of the particular structure of the model presented in chapter two, thus not depending on a training trajectory, is proposed.

Buracos negros têm as suas oscilações próprias, que são chamadas modos quase-normais. As oscilações próprias de buracos negros astrofísicos podem ser observadas no futuro mais próximo com a ajuda de detectores de ondas gravitacionais. Os modos quase-normais são também muito importantes no contexto de teste da estabilidade de objetos negros, da correspondência anti-deSitter/ Teoria Campos Conformes (AdS/CFT) e nas teorias em dimensões mais altas, como os cenários de mundo-brana e teoria das cordas. Esta tese revê um numero de trabalhos, que fornecem um estudo completo do espectro quase normal de grande classe de buracos negros em quatro e mais altas dimensões para campos de vários spins e perturbações gravitacionais. Foi estudada numericamente a dependência dos modos quase-normais sobre um numero de fatores, como a presença da constante cosmológica, o parâmetro de Gauss-Bonnet ou o a éter no espaco-tempo, a dependência do espectro sobre os parâmetros do buraco negro e os campos em consideração. Pela analise do espectro quase-normal, foi estudada a estabilidade de buracos negros Reissner-Nordstrom-de Sitter em dimensões mais altas, buracos negros de Kaluza-Klein com horizontes esmagados, buracos negros de Gauss-Bonnet e cordas negras. Uma atenção especial foi prestada à evolução de campos massivos no contexto de vários buracos negros. Foram considerados os seus toques quase-normais e as caudas de tempo tardio. Alem disso, foram apresentadas duas novas técnicas numéricas: uma generalização da melhora de Nollert para do método de Frobenius para problemas em dimensões mais altas e um método qualitativamente novo, que permite calcular freqüências quase-normais de buracos negros, cujas métricas não são conhecidas analiticamente. Também foi considerada uma possibilidade da construção do análogo acústico do buraco negro de Schwarzschild. / Black holes have their proper oscillations, which are called the quasi-normal modes. The proper oscillations of astrophysical black holes can be observed in the nearest future with the help of gravitational wave detectors. Quasi-normal modes are also very important in the context of testing of the stability of black objects, the anti-de Sitter/ Conformal Field Theory (AdS/CFT) correspondence and in higher dimensional theories, such as the brane-world scenarios and string theory. This dissertation reviews a number of works, which provide a thorough study of the quasi-normal spectrum of a wide class of black holes in four and higher dimensions for fields of various spin and gravitational perturbations. We have studied numerically the dependance of the quasi-normal modes on a number of factors, such as the presence of the cosmological constant, the Gauss-Bonnet parameter or the aether in the space-time, the dependance of the spectrum on parameters of the black hole and fields under consideration. By the analysis of the quasi-normal spectrum, we have studied the stability of higher dimensional Reissner-Nordstr¨om-de Sitter black holes, Kaluza-Klein black holes with squashed horizons, Gauss-Bonnet black holes and black strings. Special attention is paid to the evolution of massive fields in the background of various black holes. We have considered their quasi-normal ringing and the late-time tails. In addition, we present two new numerical techniques: a generalisation of the Nollert improvement of the Frobenius method for higher dimensional problems and a qualitatively new method, which allows to calculate quasi-normal frequencies for black holes, which metrics are not known analytically. Also we considered a possibility of construction of the acoustic analogue of the Schwarzschild black hole.

Estudamos a evolução temporal de perturbações escalares na vizinhança de uma estrela com densidade uniforme que colapsa em um buraco negro. O trabalho começa com um estudo básico de gravitação e modos quasi-normais. O objetivo principal é resolver a equação de Klein-Gordon sem massa para a perturbação escalar, cuja solução depende de métodos numéricos. Com este objetivo, tratamos os aspectos teóricos de buracos negros e estrelas a partir da solução prevista pela Relatividade Geral para um buraco negro, estrelas com densidade uniforme e estrelas em colapso. Estudamos também uma maneira de reduzirmos a Equação de Klein-Gordon para uma forma conveniente de ser integrada, assim como os métodos numéricos necessários para resolver essa equação. Encontramos soluções para os modos variando a massa M, o raio inicial R e o rótulo do momento angular l. Essas soluções são irregulares em muitas situações, mas em geral elas são crescentes, de acordo com o comportamente observado de explosões de Supernovas. / This work is a study on the time evolution of scalar perturbations around a star collapsing to a black hole. It starts with a basic study of gravitation and quasi-normal modes. The aim is to derive the solution of the massless Klein-Gordon equation, that depends on numerical methods. Aiming at this goal, we studied theoretical aspects of stars, black holes and gravitational collapse. The methods include coordinate substitutions to modify the Klein-Gordon equation to a simple form. We also studied numerical methods for partial differential equations. Solutions of the quasi-normal modes were found with different values of M, R and l. The solutions are irregular in several situations, but some of them display increasing modes, that could be explained by the explosive behavior of Supernovas.

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / Estuda-se, neste trabalho, aglomerados bidimensionais de partÃculas dipolares magnÃticas, com carga elÃtrica superficial, confinadas em um potencial parabÃlico circular. As partÃculas possuem mesmo mÃdulo de momento de dipolo magnÃtico, assim como mesmos mÃdulo e sinal de carga superficial. O objetivo do presente estudo à a caracterizaÃÃo das configuraÃÃes do estado fundamental e do espectro dos modos normais do aglomerado. O sistema à estudado numericamente atravÃs de simulaÃÃes Monte Carlo, utilizando o algoritmo de Metropolis. Utilizou-se ainda o chamado MÃtodo de Newton Modificado para auxiliar a obtenÃÃo das configuraÃÃes de mÃnima energia. O estudo à dividido em duas partes: i) Na primeira, a dependÃncia das configuraÃÃes de equilÃbrio e modos normais à analisada em funÃÃo da carga superficial, na presenÃa e ausÃncia de campo magnÃtico externo, considerando-se o momento de dipolo magnÃtico constante. ii) Na segunda, a carga superficial e o momento de dipolo magnÃtico sÃo fixados e as configuraÃÃes de equilÃbrio e os modos normais sÃo estudados em funÃÃo da intensidade do campo magnÃtico externo. Nesta parte, calcula-se ainda a magnetizaÃÃo do sistema em funÃÃo do campo externo. O espectro de frequÃncias dos modos normais de vibraÃÃo foram obtidos atravÃs da tÃcnica de aproximaÃÃo harmÃnica. Devido à nÃo-simetria espacial da interaÃÃo magnÃtica dipolar, os modos normais devem apresentar um componente extra de rotaÃÃo. Observa-se que para um intervalo caracterÃstico da carga superficial das partÃculas, o espectro de frequÃncias sofre uma grande variaÃÃo de intensidade. Observa-se que no caso dependente da carga, o sistema apresenta caracterÃsticas que independem do campo magnÃtico aplicado. Observa-se, no caso dependente do campo aplicado, uma menor variedade de configuraÃÃes de equilÃbrio deste tipo de sistema em relaÃÃo ao dependente da carga. / It is studied at this thesis a two-dimensional cluster of magnetic particles, with surface charge, confined by a circular parabolic potential. The particles have the same magnitude of magnetic dipole moment and the same amount and sign of surface charge. The goal of the present study is the characterization of the ground state configurations and the normal mode spectra of the cluster. The numerical study of the system is based on the Monte Carlo simulation technique, using the Metropolis Algorithm. It was also used the called Newton Method technique to reach the ground state configurations . The present study is divided in two parts: i) In the first one, the dependence of the equilibrium configurations and the normal modes is analyzed considering the presence or not of a external magnetic field. The magnetic dipole moment is taken as constant. ii) In the second one, the surface charge and the magnetic dipole moment are taken as constant, and the ground state configurations and the normal modes are studied as function the the external magnetic field intensity. At this part, it is also calculated the magnetization of the system as function of the external magnetic field. It was observed a great number of different ground state configurations, like concentric rings, and chains. The vibrational normal mode frequencies spectra was obtained by using the harmonic approximation. Due to the non-spatial symmetry of the magnetic dipole interaction, the normal modes must show an extra rotational component. It can be noted that due to surface charge of the particles the frequencies spectra can present elevated variation on the intensity. It can also be noted that some properties of the first case system also occurs on the second case system, and these properties are independent of the applied magnetic field, and in the second case system it can be noted that there are less different ground state configurations as compared with the first one.

La Sarcolipine (SLN) est un hélice transmembranaire de 31 résidus dont la function est de reguler l’ATPase-Ca2+ SERCA1a. Ce régulateur peut subir une modification post-traductionnelle chez certaines espèces. Par exemple, chez le lapin, il est palmitoyle ou oleoylé sur le résidu Cys9. Pour comprendre au niveau moléculaire l’effet de cette modification post-traductionnelle sur la SLN, nous avons réalisé des simulations de dynamique moléculaire de la SLN de lapin insérée dans une bicouche de 1-palmitoyl-2-oléoyl-sn-glycéro-3-phosphocholine (POPC), non acylée et palmitoylée. L’analyse de ces simulations démontre que la palmitoylation n’affecte pas la structure secondaire, l’orientation (tilt et azimut), ainsi que l’enfouissemnt de la SLN dans la membrane. De plus, l’analyse de simulations tout atome de la SLN humaine insérée dans une bicouche de POPC montre que la SLN humaine a la même structure secondaire et orientation que la SLN de lapin mais est plus enfouie dans la membraneque celle de lapin, du fait de sa sequence en acides amines N-terminale plus hydrophobe.L’ATPase-Ca2+ SERCA1a, une ATPase de type P, est localisée dans la membrane du reticulum sarcoplasmique des cellules du muscle squelettique. Elle est impliquée dans les processus de contraction/relaxation musculaire en transportant rapidement le Ca2+ cytosolique dans le lumen du reticulum sarcoplasmique grâce à l’énergie fournie par l’hydrolyse de l’ATP. D’importants changements conformationnels de SERCA1a ont lieu durant son cycle catalytique comme le montrent les nombreuses structures cristallines de SERCA1a. En particulier, à l’état E1, la cavité contenant les sites de fixation du Ca2+ est ouverte vers le cytoplasme, tandis qu’à l’état E2, cette cavité est ouverte vers le lumen. La transition de l’état E1 à E2 nécessite la phosphorylation du résidu Asp351. Des structures 3D du complexe SERCA1a-SLN ont été déterminées par diffraction aux rayons X avec SERCA1a dans un état E1-Mg2+. Pour comprendre le mécanisme détaillé de la regulation de SERCA1a par la SLN, des simulations de dynamique moléculaire et des analyses des modes normaux (NMA) ont été réalisées en utilisant la structure 3D du complexe SERCA1a-SLN inséré dans une bicouche de POPC. Les résultats principaux de ces analyses sont les suivants : 1) la SLN régule les transitions E1.Mg2+ → E1.2Ca2+ et E1.Mg2+ → E2 ; 2) l’interaction de la SLN influe sur la structure et la dynamique de SERCA1a et modifie la position de l’hélice transmembranaire TM1 de sorte à ce que la cavité contenant les sites de fixation du Ca2+soit plus ouverte et que les sites soient plus accessibles ; 3) l’interaction de la SLN avec TM6 affecte deux regions de SERCA1a indispensables à sa fonction : en modifiant la structure et la dynamique de TM6, la SLN perturbe la position et la fluctuation des résidus des sites de fixation du Ca2+, leur conférant une conformation inapte à fixer le Ca2+. De même, l’interaction avec TM6 induit la courbure de TM5, ce qui affecte de façon indirecte le site de phosphorylation (éloigné de plus de 35 Å de la SLN) et conduit à l’inhibition de la phosphorylation du résidu Asp351.Nos résultats de cette étude in silico fournissent de nouveaux éléments concernant le mécanisme par lequel la SLN régule SERCA1a et qui pourrait être complétés par des travaux expérimentaux. / Sarcolipin (SLN), a transmembrane helix of 31 residues, binds to and regulates the Ca2+-ATPase SERCA1a. This regulator is post-translationnally modified in some species. For example, in rabbit, it is palmitoylated or oleoylated on its Cys9 residue. To understand at a molecular level, the effect of this post-translationnal modification on SLN, all-atom molecular dynamics simulations of unacylated and palmitoylated rabbit SLN embedded in a POPC bilayer were performed. Analysis of the simulations demonstrates that palmitoylation does not affect the secondary structure, the orientation (tilt and azimuth) as well as the burying of SLN within the membrane. In addition, the analyses of all-atom simulations of human SLN embedded in a POPC bilayer show that human SLN has the same secondary structure and orientation as rabbit SLN but is more buried within the membrane than rabbit SLN as a result of its more hydrophobic N-terminal amino acids sequence.The Ca2+ pump SERCA1a, a P-type ATPase, is localized in the sarcoplasmic reticulum membrane of striated muscle cells. It is involved in the contraction/relaxation process by fast pumping the cytoplasmic Ca2+ from the cytosol to the lumen of the sarcoplasmic reticulum using the energy of ATP hydrolysis. Large conformational changes of SERCA1a occur during its catalytic cycle as evidenced by the various crystal structures of SERCA1a. In particular, in the E1 state, the cavity that contains the Ca2+ binding sites is open toward the cytoplasm while in the E2 state, this cavity is open toward the lumen. The transition from the E1 to the E2 state involves the phosphorylation of Asp351 residue. 3D structures of SERCA1a-SLN complex have been determined by X-Ray diffraction, with SERCA1a in a E1-Mg2+ state. To understand the detailed mechanisms of SERCA1a regulation by SLN, molecular dynamics (MD) simulations and normal mode analysis (NMA) were performed using the 3D structures of SERCA1a-SLN complex embedded in a POPC bilayer. Main results from these analyses are the followings: 1) SLN regulates the E1-Mg2+ → E1-2Ca2+ and E1-Mg2+ → E2 state transitions; 2) interaction of SLN with SERCA1a impact the structure and dynamic of SERCA1a and modifies the position of the transmembrane helix TM1 such that the cavity that contains the Ca2+ binding sites is more widely opened and the Ca2+ binding sites more accessible; 3) SLN interaction with affects two regions essential to its function. By changing the structure and dynamic of TM6, SLN alters the position and fluctuations of residues involved in the Ca2+ binding sites, such that those sites are unable to bind Ca2+. This interaction with TM6 also induces TM5 bending and thus, indirectly modifies the phosphorylation site conformation, leading to the inhibition of Asp351 phosphorylation.Our results from these in silico studies provide new insights into the mechanism by which SLN regulates SERCA1a activity and could be completed by experimental work.

There is a need for reliable methods to determine approximate solutions of nonlinear continuous systems. Recently, it has been proved that finite-degree-of-freedom Galerkin-type discretization procedures applied to some distributed-parameter systems may fail to predict the correct dynamics. By contrast, direct procedures yield reliable approximate solutions. Starting from these results and extending some of these concepts and procedures, we compare the outcomes of these two approaches (the Galerkin discretization and the direct application of a reduction method to the original governing equations) with experimental results. The nonlinear planar vibrations of a buckled beam around its first buckling mode shape are investigated. Frequency-response curves characterizing single-mode responses of the beam under a primary resonance are generated using both approaches and contrasted with experimentally obtained frequency-response curves. It is shown that discretization leads to erroneous quantitative as well as qualitative results in certain ranges of the buckling level, whereas the direct approach predicts the correct dynamics of the system. / Master of Science

Nous considérons un système mécanique en vibration non linéaire, pour lequel nous fournissons une solution approchée par l'utilisation des développements multiples échelles; nous proposons d'abord une étude avec double échelles puis avec triple échelles où nous comparons les deux approches. Une preuve rigoureuse de ces développements a été faite. L'étude de la stabilité de la solution est nécessaire pour montrer la convergence au voisinage de la résonance. Un lien entre l'amplitude de la réponse vibratoire et la fréquence du système en vibration libre a été mis en évidence. / We consider small solutions of a vibrating mechanical system with smooth non-linearities for which we provide an approximate solution by using multiple scale analysis; we first use a double scale analysis; in order to improve the approximation, then we perform a triple scale analysis; a rigorous proof of convergence of the triple scale method is included; for the forced response, a stability result is needed in order to prove convergence in a neighborhood of a primary resonance. The amplitude of the response with respect to the frequency forcing is described and it is related to the frequency of a free periodic vibration.

Les mers Indonésiennes sont le siège de très fort courants de marée qui interagissent avec la topographie pour créer des ondes internes à la fréquence de la marée que l'on appelle marée interne. Certaines d'entres elles, vont se propager et se dissiper dans l'océan intérieur. Le mélange associé provoque la remontée d'eau plus froide et plus riche en nutriments en surface qui influence le climat tropical et toute la chaine des écosystèmes marins. Surveiller les ressources marines est l'objectif du projet INDESO, dont cette thèse fait partie. Prendre en compte le mélange induit par la marée interne n'est pas facile. En effet, le résoudre entièrement n'est pas possible car les échelles concernées par les différents processus des ondes internes varient de plusieurs milliers de kilomètres (propagation) à quelques centimètres/millimètres (dissipation). De plus en plus de scientifiques introduisent le forçage de la marée dans leur modèle mais sans savoir où va l'énergie et comment les ondes sont dissipées. Dans cette thèse nous cherchons à proposer des outils et des débuts de réponses pour participer à cette meilleure compréhension de la dissipation des ondes internes dans le modèle numérique d'océan NEMO. Nous proposons certaines quantifications que nous comparons aux anciennes paramétrisations. J'ai, tout d'abord, contribué à une étude d'INDESO sur la validation de NEMO grâce à de nombreux jeu de données. Ensuite, j'ai cherché à quantifier et à qualifier le mélange induit par l'introduction de la marée explicite dans le modèle, ainsi que son impact sur les masses d'eau. (c'est redit plus loin)Il produit un refroidissement de surface de 0.3°C avec des maxima atteignant 0.8°C au niveau des sites de génération des ondes internes. Le modèle reproduit 75% de l'énergie attendue de génération des ondes internes, en bon accord avec des études précédentes. L'essentiel de la dissipation a lieu horizontalement (19GW) est proche de celle induite par la paramétrisation couramment utilisée (16GW), alors que, dans la réalité, on s'attend principalement à une dissipation réalisée grâce à des processus verticaux. Le modèle, au dessus des zones de génération, est de façon surprenante en très bon accord avec les mesures in situ de dissipation obtenues lors de la campagne INDOMIX. Par contre, dans les régions distantes des sources de génération, le modèle surestime le mélange par rapport aux observations d'INDOMIX. Dans la dernière partie de cette thèse j'ai commencé à apporter des éléments de réponse à la quantification des puits d'énergie dans NEMO. J'ai pour cela travaillé avec le cas test COMODO, qui est une section d'un fluide stratifié constituée d'une plaine abyssale, d'un talus et d'un plateau, forcée par la marée et sans friction de fond. Le modèle T-UGOm, un modèle hydrodynamique de marée, est comparé au modèle NEMO. Dans ce cadre, nous avons développé une méthode originale pour séparer la marée barotrope de la marée barocline. Elle repose sur la projection en modes normaux. Cette méthode donne, à première vue, des résultats similaires à ceux obtenus grâce à la méthode plus classique de soustraction par la moyenne verticale. Cependant, lorsque l'on regarde plus en détail les diagnostiques d'énergie on trouve que la méthode de projection en modes normaux offre une plus grande précision et un plus grand réalisme pour séparer la marée barotrope de la marée barocline. Plus on monte dans des modes élevés plus les longueurs ondes se raccourcissent dans NEMO par rapport à T-UGOm. Par ailleurs, NEMO dissipe la marée barotrope dans la plaine abyssale, alors qu'il n'y a explicitement pas de friction. Ce ne peut pas être la diffusion verticael ou horizontale qui est à l'œuvre ici, car il n'y a pas de raison physique pour une diffusion sur un fond plat. Le meilleur candidat pour expliquer cette diffusion serait le couplage 2D/3D du time splitting de NEMO. Un travail est en cours pour appliquer cette méthode sur l'ensemble de l'archipel Indonésien. / In the Indonesian seas, large tidal currents interact with the rough topography and create strong internal waves at the tidal frequency, called internal tides. Part of them will eventually propagate and dissipate far away from generation sites. Their associated mixing upwells cold and nutrient-rich water that prove to be critical for climate system and for marine resources. This thesis uses the physical ocean general circulation model, NEMO, as part of the INDESO project that aims at monitoring the Indonesian marine living resources. Models not taking into account tidal missing are unable to correctly reproduce the vertical structure of watermasses in Indonesian seas. However, taking into account this mixing is no simple task as the phenomena involved in tidal mixing cover a wide spectrum of spatial scales. Internal tides indeed propagate over thousands of kilometres while dissipation and mixing occurs at centimetric to millimetric scales. A model capable of resolving all these processes at the same time does not exist. Until now scientists either parameterised the tidal mixing or used models which only partly resolve internal tides. More and more scientists introduce explicit tidal forcing in their models but without knowing where the energy is going and how the internal tides are dissipated. This thesis intends to quantify energy dissipation in NEMO forced with explicit tidal forcing and compares it to the dissipation induced by the currently used parameterization. This thesis also provides new results about the quantification of the tidal energy budget in NEMO. I first contributed to an INDESO study that aimed at validating the model against several observation data sets. In a second and third study, I investigated the mixing produced in the model by explicit tidal forcing and its impact on water mass. Explicit tides forcing proves to produce a mixing comparable to the one produced by the parameterization. It also produces a significant cooling of 0.3 °C with maxima reaching 0.8°C in the areas of internal tide generation. The cooling is stronger on austral winter. The spring tides and neap tides modulate this impact by 0.1°C to 0.3°C. The model generates 75% of the expected internal tides energy, in good agreement with other previous studies. In the ocean interior, most of it is dissipated by horizontal momentum dissipation (19 GW), while in reality one would expect dissipation through vertical possesses. This value is close to the dissipation induced by the parameterization (16 GW). The mixing is strong over generation sites, and only 20% remains for far field dissipation mainly in the Banda and Sulawesi Seas. The model and the recent INDOMIX cruise [Koch-Larrouy et al. (2015)], which provided direct estimates of the mixing, are surprisingly in good agreement mainly above straits. However, in regions far away from the energy generation sites where INDOMIX found NO evidence of intensified mixing, the model produces too strong mixing. The bias comes from the lack of specific set up of internal tides in the model. More work is thus needed to improve the modeled dissipation, which is a theme of active research for the scientific community. I dedicated the last part of my thesis to the quantification of tidal energy sinks in NEMO. I first worked on a simple academic case: the COMODO internal tides test case, which analyses the behaviour of a vertically stratified fluid forced by a barotropic flow interacting over an idealized abyssal plain/slope/shelf topography without bottom friction. The results of the finite element T-UGOm hydrodynamic model are compared with those of NEMO. The central issue in calculating tidal energy budget is the separation of barotropic and baroclinic precesses.