Le sujet de cette thèse est le développement de méthodes itératives permettant la résolution degrands systèmes linéaires creux d'équations présentant plusieurs seconds membres simultanément. Ces méthodes seront en particulier utilisées dans le cadre d'une application géophysique : la migration sismique visant à simuler la propagation d'ondes sous la surface de la terre. Le problème prend la forme d'une équation d'Helmholtz dans le domaine fréquentiel en trois dimensions, discrétisée par des différences finies et donnant lieu à un système linéaire creux, complexe, non-symétrique, non-hermitien. De plus, lorsque de grands nombres d'onde sont considérés, cette matrice possède une taille élevée et est indéfinie. Du fait de ces propriétés, nous nous proposons d'étudier des méthodes de Krylov préconditionnées par des techniques hiérarchiques deux niveaux. Un tel pre-conditionnement s'est montré particulièrement efficace en deux dimensions et le but de cette thèse est de relever le défi de l'adapter au cas tridimensionel. Pour ce faire, des méthodes de Krylov sont utilisées à la fois comme lisseur et comme méthode de résolution du problème grossier. Ces derniers choix induisent l'emploi de méthodes de Krylov dites flexibles. / The topic of this PhD thesis is the development of iterative methods for the solution of large sparse linear systems of equations with possibly multiple right-hand sides given at once. These methods will be used for a specific application in geophysics - seismic migration - related to the simulation of wave propagation in the subsurface of the Earth. Here the three-dimensional Helmholtz equation written in the frequency domain is considered. The finite difference discretization of the Helmholtz equation with the Perfect Matched Layer formulation produces, when high frequencies are considered, a complex linear system which is large, non-symmetric, non-Hermitian, indefinite and sparse. Thus we propose to study preconditioned flexible Krylov subspace methods, especially minimum residual norm methods, to solve this class of problems. As a preconditioner we consider multi-level techniques and especially focus on a two-level method. This twolevel preconditioner has shown efficient for two-dimensional applications and the purpose of this thesis is to extend this to the challenging three-dimensional case. This leads us to propose and analyze a perturbed two-level preconditioner for a flexible Krylov subspace method, where Krylov methods are used both as smoother and as approximate coarse grid solver.

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Much of the vibration in fast moving vehicles is caused bydistributed random excitation, such as turbulent flow and roadroughness. Piping systems transporting fast flowing fluid isanother example, where distributed random excitation will causeunwanted vibration. In order to reduce these vibrations andalso the noise they cause, it is important to have accurate andcomputationally efficient prediction methods available. The aim of this thesis is to present such a method. Thefirst step towards this end was to extend an existing spectralfinite element method (SFEM) to handle excitation of planetravelling pressure waves. Once the elementary response tothese waves is known, the response to arbitrary homogeneousrandom excitation can be found. One example of random excitation is turbulent boundary layer(TBL) excitation. From measurements a new modified Chase modelwas developed that allowed for a satisfactory prediction ofboth the measured wall pressure field and the vibrationresponse of a turbulence excited plate. In order to model morecomplicated structures, a new spectral super element method(SSEM) was formulated. It is based on a waveguide formulation,handles all kinds of boundaries and its elements are easily putinto an assembly with conventional finite elements. Finally, the work to model fluid-structure interaction withanother wave based method is presented. Similar to the previousmethods it seems to be computationally more efficient thanconventional finite elements. / <p>NR 20140805</p>

De nombreuses techniques de lithographie sont proposées aujourd'hui pour structurer des surfaces à l'échelle micrométrique et nanométrique. Parmi elles, la lithographie colloïdale est intéressante en raison notamment du faible coût du procédé. Dans cette thèse, nous avons développé une nouvelle technique appelée « lithographie électro-colloïdale » qui est basée sur l'utilisation de particules colloïdales soumises à des champs électriques continus et alternatifs. Avec des temps de préparation courts et une instrumentation peu coûteuse, des surfaces structurées polymériques et métalliques ont été produites puis testées pour différentes applications (immobilisation de protéines, réseaux de microélectrodes, surfaces superhydrophobes). / Many lithography techniques have been developed to structure surfaces at the micrometer and sub-micrometer ranges. Among them, colloidal lithography is interesting because the process is inexpensive and does not require the use complex instruments. In this thesis, we have developed a new technique called « electro-colloidal lithography » which is based on the use of colloidal particles organized using alternating and direct electric fields. With short preparation times and inexpensive instruments, polymeric and metallic structured surfaces have been prepared and tested for different applications (protein immobilization, microelectrode arrays, superhydrophobic surfaces)

This thesis focuses on inductive base sensor design at MHz range frequency. The background theory, design, experiments and results for a new magnetic particles sensor is presented. A new magnetic sensor based on a planar coil was investigated for DNA pathogen detection. Change in inductance of the planar coil due to the presence of magnetic particles with varying mass was measured. The experimental set-up consisted of different sized planar coil with associated electronics for inductance measurements. The best sensor performance was accomplished using two different inductors while oscillating at frequencies 2.4MHz using 9.5μH inductor and 7.2MHz with 85μH inductor. The sensor has very large signal to noise ratio (580×103), while the average amount of frequency drift was 0.58. This sensor was tested with various types of magnetic particles. In addition, iron-oxide nanoparticles were synthesized through water in oil microemulsion method and with an average size of 25nm. The best sensitivity achieved for detection of 50μg iron-oxide particles was with the bead size of 10nm. 81Hz frequency shift was attained in regard to that amount of particles. This research shows that increasing the resonance frequency to 7.2MHz can cause the larger output signal difference (frequency shift) in the presence of magnetic particles; however, the sensor stability is the most important factor for determining the detection resolution and sensitivity. The sensitivity is better if the sensor can detect smaller amount of magnetic sample. The results of this research demonstrate that while the sample consists of smaller size particles, the sensor can detect the lower amount of sample. This is due to the heating effect of nanoparticles. On the other hand the sample distance from the sensor has a major impact on the sensitivity too; the shorter the distance, the higher the sensitivity. This technique can potentially be extended to detect several different types of bacterial pathogens and can be modified for multiplex quantitative detection. This sensing technique will be incorporated into a handheld, disposable microfluidic chip for point-of-care diagnostics for sexually transmitted diseases.

Abstract Interacting many-body problems are central to most fields of physics. In condensed matter physics, the systems of interest consists of a number of bodies on the order of Avogadro's constant, ~10²³. The precise modeling of such systems is usually impossible. Under certain circumstances however, even these problems can become tractable. One such circumstance is that of a Fermi liquid. At sufficiently low temperatures, in describing the dynamics of a system of interacting fermions, it is possible to forgo description of the fermions themselves, and instead concentrate on the collective excitations of the entire fermion system. These collective excitations are called quasiparticles. In this thesis we study two phenomena related to the motion of objects in a Fermi liquid. First, we study the transmission of transverse oscillations through a thin film of normal Fermi liquid. The dynamics of normal Fermi liquid are described by Landau's Fermi liquid theory. Landau's theory predicts the existence of new modes of sound under conditions where sound ordinarily would not propagate. Using the equations of motion for the Fermi liquid quasiparticles, we calculate the linear response of a Fermi liquid film to the transverse oscillations of a planar substrate under a wide range of conditions. We present the linear response in terms of the film's acoustic impedance and study the effects of quasiparticle collisions and of the Fermi liquid interactions. The second phenomenon we study is the supercritical motion of a wire in a superfluid Fermi liquid. The prevailing assumption is that if the velocity of an object moving in a superfluid Fermi liquid surpasses a characteristic critical velocity, the object experiences a sudden onset of viscous forces. This viscosity is caused by the escape of quasiparticles, produced by pair breaking on the surface of the object, into the surrounding superfluid. We study Andreev reflection of the quasiparticles by the surrounding superfluid flow field, and modifications to the flow caused by pair breaking, as possible mechanisms for low-dissipation motion above the critical velocity. / Original publications The original publications are not included in the electronic version of the dissertation. Kuorelahti, J. A., Tuorila, J. A., &amp; Thuneberg, E. V. (2016). Fermi liquid theory applied to a film on an oscillating substrate. Physical Review B, 94(18). https://doi.org/10.1103/physrevb.94.184103 Kuorelahti, J. A., &amp; Thuneberg, E. V. (2018). Two-parameter boundary condition applied to transverse acoustic impedance of a Fermi liquid. Journal of Physics: Conference Series, 969, 12010. https://doi.org/10.1088/1742-6596/969/1/012010 http://jultika.oulu.fi/Record/nbnfi-fe2018060425173 Kuorelahti, J. A., Laine, S. M., &amp; Thuneberg, E. V. (2018). Models for supercritical motion in a superfluid Fermi liquid. Physical Review B, 98(14). https://doi.org/10.1103/physrevb.98.144512 http://jultika.oulu.fi/Record/nbnfi-fe2018112148794

La microscopie optique est un outil indispensable pour la recherche de la neurobiologie et médecine qui permet l’étude des cellules dans leur environnement natif. Les processus sous-cellulaires restent néanmoins cachés derrière les limites de la résolution optique, ce qui rend la résolution des structures plus petites que ~300nm impossible. Récemment, les techniques de la localisation des molécules individuelles (SML) ont permis le suivi des protéines de l’échelle nanométrique grâce à l’ajustement des molécules uniques à la réponse impulsionnelle du système optique. Ce processus dépend de la quantité de lumière recueilli et rend ces techniques très sensibles aux imperfections de la voie d’imagerie, nommé des aberrations, qui limitent l’application de SML aux cultures cellulaires sur les lamelles de verre. Un système commercial d’optiques adaptatives est implémenté pour compenser les aberrations du microscope, et un flux de travail est défini pour corriger les aberrations dépendant de la profondeur qui rend la 3D SML possible dans les milieux biologiques complexes. Une nouvelle méthode de SML est présentée qui utilise deux objectifs pour détecter le spectre d’émission des molécules individuelles pour des applications du suivi des particules uniques dans 5 dimensions (x,y,z,t,λ) sans compromis ni de la résolution spatiotemporelle ni du champ de vue. Pour faciliter les analyses de manière quantitative des Go de données générés, le développement des outils biochimiques, numériques et optiques est présenté. Ensemble, ces approches ont le but d’amener l’imagerie quantitative des molécules uniques dans les échantillons biologiques complexes / Optical microscopy is an indispensable tool for research in neurobiology and medicine, enabling studies of cells in their native environment. However, subcellular processes remain hidden behind the resolution limits of diffraction-limited optics which makes structures smaller than ~300nm impossible to resolve. Recently, single molecule localization (SML) and tracking has revolutionized the field, giving nanometer-scale insight into protein organization and dynamics by fitting individual fluorescent molecules to the known point spread function of the optical imaging system. This fitting process depends critically on the amount of collected light and renders SML techniques extremely sensitive to imperfections in the imaging path, called aberrations, that have limited SML to cell cultures on glass coverslips. A commercially available adaptive optics system is implemented to compensate for aberrations inherent to the microscope, and a workflow is defined for depth-dependent aberration correction that enables 3D SML in complex biological environments. A new SML technique is presented that employs a dual-objective approach to detect the emission spectrum of single molecules, enabling 5-dimensional single particle imaging and tracking (x,y,z,t,λ) without compromising spatiotemporal resolution or field of view. These acquisitions generate ~GBs of data, containing a wealth of information about the localization and environment of individual proteins. To facilitate quantitative acquisition and data analysis, the development of biochemical, software and hardware tools are presented. Together, these approaches aim to enable quantitative SML in complex biological samples.

Les travaux présentés dans ce manuscrit sont relatifs à la conception et au développement d’antennes basées sur les structures artificielles – métamatériaux. La première antenne conçue et réalisée est une antenne bi-fonction en bande L (~1GHz) (GPS et DME) à diversité de bande/de polarisation, destinée aux applications aéronautiques. Ces travaux rentrent dans le cadre du projet MSIE (pôle de compétitivité ASTHEC) pour lequel notre LEME a été très actif. Les partenaires industriels de ce projet sont EADS/IW, Dassault aviation, INEO-Défense, SATIMO. Les résultats montrent la faisabilité d’une antenne unique pouvant avoir simultanément deux fonctions avec une diversité de polarisation et de bande spectrale. L’utilisation des métamatériaux a permis en particulier le maintien de la polarisation circulaire de l’antenne GPS -L1 à L5. La fonction DME a été consolidée avec le maintien de son gain. La seconde antenne est une antenne cavité Fabry-Pérot mettant en œuvre une structure partiellement réfléchissante double couche. Nous avons démontré le phénomène physique d’inversion de la phase du coefficient de réflexion de la PRS. Nous avons obtenu un gradient positif de phase sur une bande de 5 GHz autour de 80GHz. Grace à ce profil nouveau de la phase obtenu par la structure métamatériau PRS, on dispose d’une avance linéaire de la phase qui compense le retard du à la cavité Fabry-Pérot. Ainsi on maintient les conditions de résonance de la cavité sur une large bande, 5GHz. Nous démontrons, que la mise en œuvre de cette structure aux caractéristiques inédites permet de réaliser une antenne cavité ultra-directive sur une très large bande spectrale de 5GHz. Les performances atteintes sont une directivité de 35 à 40dBi sur 5 GHz, une adaptation parfaite (gain ~ directivité) avec très peu de sources primaires. L’antenne est compacte avec une hauteur totale inférieure au 10mm (connecteur compris) et une surface de 100mmx100mm. / The work presented in this manuscript is related to the design and development of antennas based on artificial structures - metamaterials. The first designed and built antenna is a GPS and DME dual-function in the L (~ 1GHz). It is an antenna designed with polarization and spectral diversities for aeronautical applications. The work is within the MSIE project of ASTHEC cluster for which our laboratory (LEME) was very active. The industrial partners of the project are EADS/IW, Dassault Aviation, INEO-Defense SATIMO. The results show the feasibility of a single antenna having simultaneously two functions with a diversity of polarization and spectral band. The use of metamaterials enabled in particular the preservation of circular polarization of the GPS antenna on the bands ranging from L1 to L2. The DME function was consolidated with the same gain.The second antenna is an antenna Fabry-Perot cavity employing a partially reflective structure (PRS) Double-layer. We have demonstrated by numerical simulation and experimental characterization, the physical phenomenon of inversion phase of the reflection coefficient PRS. We obtain a positive gradient of the phase over a broad band of 5 GHz around 80GHz. Thanks to this new profile obtained by the PRS metamaterial structure, it has a linear advance of the phase which compensates for the delay of the Fabry-Perot cavity. Thus the cavity resonance conditions are maintained over a wide band, 5GHz. We demonstrate that the implementation of this structure with unique features allows a highly directive antenna cavity over a very wide spectral band 5GHz. The performance are a directivity of 35-40 dBi over 5 GHz, a perfect adaptation (gain ~ directivity) with very few primary sources.

Ce travail de thèse porte sur la conception et la réalisation de capteurs optiques ultracompacts et sensibles utilisant le mode d’interrogation en intensité pour la détection d’analytes chimiques et biologiques. Deux approches, l’intégration hybride et l’intégration monolithique, ont été explorées durant cette thèse. Après un descriptif des outils d’analyse et de conception de guides d’onde et de micro résonateurs en anneaux, le manuscrit présente l’intégration hybride d’un laser Fabry-Perot en semiconducteur III-V avec un résonateur en anneau basé sur du matériau SOI. Le laser Fabry-Perot à faible coût fonctionnant en multimode longitudinal a été utilisé comme peigne de référence pour le résonateur en anneau en contact avec un échantillon liquide. L’effet Vernier a été implanté dans le système de détection en utilisant le mode d’interrogation en intensité. La largeur spectrale étroite du laser avec sa densité de puissance élevée ont permis d’obtenir un capteur de plus haute sensitivité en comparaison avec le capteur en double anneaux réalisé précédemment. Une étude numérique d’un capteur composé d’un laser Fabry-Perot et deux résonateurs en anneaux permettant de compenser la fluctuation de température a été ensuite présentée. Concernant l'intégration monolithique, l'interface entre oxyde et non-oxyde après l’oxydation de AlGaAs a été étudiée au Central de Technologies du LPN/CNRS. Un phénomène d’oxydation verticale de GaAs ou AlGaAs avec une faible teneur en aluminium activée par une couche voisine oxydée de AlGaAs avec une forte teneur en aluminium a été identifié expérimentalement. Afin de limiter l’oxydation verticale et de réduire la rugosité des interfaces, des guides d’onde basés respectivement sur une structure intégrant un super-réseau et sur une structure standard ont été fabriqués et caractérisés. L’impact de l'hydrogène sur l'activation du processus d'oxydation de GaAs ou AlGaAs avec une faible teneur en Al a été mis en évidence. Enfin, ce manuscrit décrit la réalisation et la caractérisation d’un laser Fabry-Perot fonctionnant en mode TM. Ce laser constitue une brique important vers l’intégration monolithique d’un capteur extrêmement sensible. / The objective of the thesis is to realize the integrated optical sensors with high sensitivity using intensity interrogation method for chemical and biological analyte detection. For this purpose, two approaches, hybrid integration and monolithic integration, have been explored theoretically and experimentally during this thesis. After a review of the design and analysis tools of optical waveguide and micro-ring resonators, the manuscript reports an experimental demonstration of a highly-sensitive intensity-interrogated optical sensor based on cascaded III-V semiconductor Fabry-Perot laser and silicon-on-insulator ring resonator. The low-cost easy-to-fabricate Fabry-Perot laser serves as a reference comb for the sensing ring in contact with liquid sample. The Vernier effet has been exploited in the detection scheme using intensity interrogation mode. The sharp emission peaks of the FP laser with high spectral power density result in a high sensitivity for the sensor compared to previously investigated all-passive double-ring sensor. The temperature compensation method has also been investigated numerically to improve the performance of the sensor. Concerning the potential monolithic integration of laser and sensing waveguide, the interface between oxide and non-oxide after wet oxidation of buried AlGaAs has been investigated at the Technology Centre of LPN/CNRS. The vertical oxidation of GaAs or AlGaAs with low Al content activated by a neighbouring oxidized Al-rich AlGaAs layer has been discovered experimentally. To limit the vertical oxidation and reduce the roughness of the interface, the waveguides with buried oxide layer on superlattice sample and standard sample have been fabricated and characterised. The key role of hydrogen incorporation in the activation of the oxidation process for GaAs or AlGaAs materials with low Al content has been shown experimentally. Finally, this thesis reports the fabrication and the characterisation results of a Fabry-Perot laser working on TM mode which is an important building block for highly-sensitive monolithically-integrated circuit.

There are many clinical situations where magnetic resonance imaging (MRI) is preferable over other imaging modalities, while the major disadvantage is the relatively long scan time. Due to limited resources, this means that not all patients can be offered an MRI scan, even though it could provide crucial information. It can even be deemed unsafe for a critically ill patient to undergo the examination. In MRI, there is a trade-off between resolution, signal-to-noise ratio (SNR) and the time spent gathering data. When time is of utmost importance, we seek other methods to increase the resolution while preserving SNR and imaging time. In this work, I have studied one of the most promising methods for this task. Namely, constructing super-resolution algorithms to learn the mapping from a low resolution image to a high resolution image using convolutional neural networks. More specifically, I constructed networks capable of transferring high frequency (HF) content, responsible for details in an image, from one kind of image to another. In this context, contrast or weight is used to describe what kind of image we look at. This work only explores the possibility of transferring HF content from T1-weighted images, which can be obtained quite quickly, to T2-weighted images, which would take much longer for similar quality. By doing so, the hope is to contribute to increased efficacy of MRI, and reduce the problems associated with the long scan times. At first, a relatively simple network was implemented to show that transferring HF content between contrasts is possible, as a proof of concept. Next, a much more complex network was proposed, to successfully increase the resolution of MR images better than the commonly used bicubic interpolation method. This is a conclusion drawn from a test where 12 participants were asked to rate the two methods (p=0.0016) Both visual comparisons and quality measures, such as PSNR and SSIM, indicate that the proposed network outperforms a similar network that only utilizes images of one contrast. This suggests that HF content was successfully transferred between images of different contrasts, which improves the reconstruction process. Thus, it could be argued that the proposed multi-contrast model could decrease scan time even further than what its single-contrast counterpart would. Hence, this way of performing multi-contrast super-resolution has the potential to increase the efficacy of MRI.