In both, cell secretome analysis and bacteria evolution, controlled handling of particles with a few to sub-micrometers in size and media exchange are inevitable in order to investigate body fluid’s proteins or change the surrounding culture conditions for pivoted evolution. Typically, nanofiltration and ultra-centrifugation are employed which can lead to cell damage, need large sample volumes and have a high sample loss. Using contactless and label-free acoustic cell manipulation, disadvantages of other magnetic, dielectric or hydrodynamic methods can be avoided. Here, a novel design using acoustic forces for small particle trapping and media exchange is thoroughly numerically investigated including first- and second-order acoustic effects. The device comprises parallel aligned medium and air channels separated by a thin wall. Particle trapping occurs at this thin wall. The medium channel dimensions (height and width) and thin wall thickness are optimized with respect to trapping forces. Thinnest walls are preferable and an aspect ratio of 0.8. First preliminary experimental variation with polystyrene particles showed good agreement with the simulations. Thereby the particle trapping efficiency is evaluated under quiescent flow conditions. For particle trapping, a device with a channel height of 290μm and an aspect ratio of 0.7 is superior which supports the numerical results. Finally, medium exchange of E. coli bacteria is demonstrated with best results for a device with a channel height of 450μm and an aspect ratio of 0.8 showing that 13.4% of the initial bacteria were released after medium exchange which can be used for further processing.

Ultrasound directed self-assembly (DSA) utilizes the acoustic radiation force associated with a standing ultrasound wave field to organize particles dispersed in a fluid medium into specific patterns. The ability to tailor the organization and packing density of spherical particles using ultrasound DSA in a viscous fluid medium is crucial in the context of (additive) manufacturing of engineered materials with tailored properties. However, the fundamental physics of the ultrasound DSA process in a viscous fluid medium, and the relationship between the ultrasound DSA process parameters and the specific patterns of particles that result from it, are not well-understood. Researchers have theoretically described the acoustic radiation force and the acoustic interaction force that act on spherical particles in a standing ultrasound wave field in both inviscid and viscous media. In addition, they have solved the forward and inverse ultrasound DSA problem in an inviscid medium, in which they relate the patterns of particles and the ultrasound DSA operating parameters. However, no theoretical model exists that allows simulating the steady-state and transient local particle packing density in a viscous medium during ultrasound DSA. Thus, in this dissertation, we (i) theoretically derive and experimentally validate a model to determine the steady-state locations where spherical particles assemble during ultrasound DSA as a function of medium viscosity and particle volume fraction. (ii) We also theoretically derive and experimentally validate a model to quantify the steady-state and transient local packing density of spherical particles within the pattern features that result from ultrasound DSA. Using these models, we quantify and predict the locations where spherical particles assemble during ultrasound DSA in a viscous medium, considering the effects of medium viscosity and particle volume fraction. We demonstrate that the deviation between locations where particles assemble in viscous and inviscid media first increases and then decreases with increasing particle volume fraction and medium viscosity, which we explain by means of the sound propagation velocity of the mixture. In addition, we quantify and predict the steady-state and transient local packing density of spherical particles within the pattern features, using ultrasound DSA in combination with vat photopolymerization (VP). We show that the steady-state local particle packing density increases with increasing particle volume fraction and increases with decreasing particle size. We also show that the transient local particle packing density increases with increasing particle volume fraction, decreasing particle size, and decreasing fluid medium viscosity. Increasing particle size and decreasing fluid medium viscosity decreases the time to reach steady-state. Finally, we implement single and multiple scattering in the calculation of the acoustic radiation force for spherical particles in a viscous medium and quantify their relative contributions to the calculation of the acoustic radiation force as a function of ultrasound DSA operating parameters and material properties. We demonstrate that the deviation between considering single and multiple scattering may reach up to 100%, depending on the ultrasound DSA process parameters and material properties. Also, increasing the particle volume fraction increases the need to account for multiple scattering. Quantifying and predicting the local packing density of spherical particles during ultrasound DSA in a viscous medium, as a function of ultrasound DSA process parameters is crucial towards using ultrasound DSA in engineering applications, in particular (additive) manufacturing of engineered polymer matrix composite materials with tailored properties whose properties depend on the spatial organization and packing density of particles in the matrix material. / Doctor of Philosophy / Ultrasound directed self-assembly (DSA) is a technique that uses ultrasound waves to arrange small particles submerged in a fluid into specific patterns. When combined with other manufacturing techniques, ultrasound DSA can be used to fabricate composite materials that derive their properties from the spatial organization of particles in a matrix material. However, ultrasound DSA in viscous fluids is not well-understood. Researchers have studied the forces associated with ultrasound waves that move small spherical particles in an inviscid fluid medium (fluids that experience little to no internal resistance to flow), and they have demonstrated intricate control of the patterns of particles that form using ultrasound DSA. However, that knowledge is not currently available for ultrasound DSA in viscous media. In this dissertation, we develop and evaluate theoretical models to understand ultrasound DSA of small spherical particles in a viscous fluid medium. We simulate where particles organize and how densely they pack together. We also determine the difference of the time-dependent motion of particles in a viscous fluid compared to that in an inviscid fluid medium and relate the difference to the number of particles submerged in the fluid and the viscosity of the fluid. Additionally, we examine the effect of particle size and fluid viscosity on the speed by which the particles reach their final location. We also study how ultrasound waves interact with multiple small particles in a viscous fluid, focusing on the forces that move these particles. We explore two models that account for single and multiple ultrasound wave scattering. Scattering is the process by which ultrasound waves deflect in different directions when they encounter a particle. The results show that the difference between single and multiple scattering models can be significant, depending on the ultrasound DSA process parameters and the properties of the fluid and particles. In general, the importance of accounting for multiple scattering increases with the number of particles submerged in the fluid. Understanding particle packing density when using ultrasound DSA in a viscous fluid is essential in many engineering applications, in particular manufacturing of composite materials that derive their properties from the spatial arrangement of particles in a matrix material.

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Le cancer du sein est le cancer le plus fréquent chez la femme. Il demeure la cause de mortalité la plus importante chez les femmes âgées entre 35 et 55 ans. Au Canada, plus de 20 000 nouveaux cas sont diagnostiqués chaque année. Les études scientifiques démontrent que l'espérance de vie est étroitement liée à la précocité du diagnostic. Les moyens de diagnostic actuels comme la mammographie, l'échographie et la biopsie comportent certaines limitations. Par exemple, la mammographie permet de diagnostiquer la présence d’une masse suspecte dans le sein, mais ne peut en déterminer la nature (bénigne ou maligne). Les techniques d’imagerie complémentaires comme l'échographie ou l'imagerie par résonance magnétique (IRM) sont alors utilisées en complément, mais elles sont limitées quant à la sensibilité et la spécificité de leur diagnostic, principalement chez les jeunes femmes (< 50 ans) ou celles ayant un parenchyme dense. Par conséquent, nombreuses sont celles qui doivent subir une biopsie alors que leur lésions sont bénignes. Quelques voies de recherche sont privilégiées depuis peu pour réduire l`incertitude du diagnostic par imagerie ultrasonore. Dans ce contexte, l’élastographie dynamique est prometteuse. Cette technique est inspirée du geste médical de palpation et est basée sur la détermination de la rigidité des tissus, sachant que les lésions en général sont plus rigides que le tissu sain environnant. Le principe de cette technique est de générer des ondes de cisaillement et d'en étudier la propagation de ces ondes afin de remonter aux propriétés mécaniques du milieu via un problème inverse préétabli. Cette thèse vise le développement d'une nouvelle méthode d'élastographie dynamique pour le dépistage précoce des lésions mammaires. L'un des principaux problèmes des techniques d'élastographie dynamiques en utilisant la force de radiation est la forte atténuation des ondes de cisaillement. Après quelques longueurs d'onde de propagation, les amplitudes de déplacement diminuent considérablement et leur suivi devient difficile voir impossible. Ce problème affecte grandement la caractérisation des tissus biologiques. En outre, ces techniques ne donnent que l'information sur l'élasticité tandis que des études récentes montrent que certaines lésions bénignes ont les mêmes élasticités que des lésions malignes ce qui affecte la spécificité de ces techniques et motive la quantification de d'autres paramètres mécaniques (e.g.la viscosité). Le premier objectif de cette thèse consiste à optimiser la pression de radiation acoustique afin de rehausser l'amplitude des déplacements générés. Pour ce faire, un modèle analytique de prédiction de la fréquence de génération de la force de radiation a été développé. Une fois validé in vitro, ce modèle a servi pour la prédiction des fréquences optimales pour la génération de la force de radiation dans d'autres expérimentations in vitro et ex vivo sur des échantillons de tissu mammaire obtenus après mastectomie totale. Dans la continuité de ces travaux, un prototype de sonde ultrasonore conçu pour la génération d'un type spécifique d'ondes de cisaillement appelé ''onde de torsion'' a été développé. Le but est d'utiliser la force de radiation optimisée afin de générer des ondes de cisaillement adaptatives, et de monter leur utilité dans l'amélioration de l'amplitude des déplacements. Contrairement aux techniques élastographiques classiques, ce prototype permet la génération des ondes de cisaillement selon des parcours adaptatifs (e.g. circulaire, elliptique,…etc.) dépendamment de la forme de la lésion. L’optimisation des dépôts énergétiques induit une meilleure réponse mécanique du tissu et améliore le rapport signal sur bruit pour une meilleure quantification des paramètres viscoélastiques. Il est aussi question de consolider davantage les travaux de recherches antérieurs par un appui expérimental, et de prouver que ce type particulier d'onde de torsion peut mettre en résonance des structures. Ce phénomène de résonance des structures permet de rehausser davantage le contraste de déplacement entre les masses suspectes et le milieu environnant pour une meilleure détection. Enfin, dans le cadre de la quantification des paramètres viscoélastiques des tissus, la dernière étape consiste à développer un modèle inverse basé sur la propagation des ondes de cisaillement adaptatives pour l'estimation des paramètres viscoélastiques. L'estimation des paramètres viscoélastiques se fait via la résolution d'un problème inverse intégré dans un modèle numérique éléments finis. La robustesse de ce modèle a été étudiée afin de déterminer ces limites d'utilisation. Les résultats obtenus par ce modèle sont comparés à d'autres résultats (mêmes échantillons) obtenus par des méthodes de référence (e.g. Rheospectris) afin d'estimer la précision de la méthode développée. La quantification des paramètres mécaniques des lésions permet d'améliorer la sensibilité et la spécificité du diagnostic. La caractérisation tissulaire permet aussi une meilleure identification du type de lésion (malin ou bénin) ainsi que son évolution. Cette technique aide grandement les cliniciens dans le choix et la planification d'une prise en charge adaptée. / Breast cancer is the most frequent cancer in women and the leading cause of death for women between 35 and 55 years old. In Canada, more than 20,000 new cases are diagnosed each year. Most of the previous works have shown that life expectancy is closely related to the precocity of diagnosis. Current diagnostic imaging methods such as mammography, sonography, MRI present limitations such as irradiation (mammography), low specificity and low resolution (sonography) and high cost (MRI). For example, about 95% of abnormalities detected by mammography are proven to be benign lesions after complementary examinations (biopsy). Sonography is useful as a complementary examination but the low resolution of its images, its low specificity (54% for women less than 50 years) and its operator dependent interpretation seriously limit the use of this modality alone. MRI is a non-invasive technique with a relatively high sensitivity (86% for women below 50 years), but its limitations are the high cost and the waiting time for medical examination, which dedicate it as a monitoring technique in high-risk patients. It is therefore necessary to examine new noninvasive and cost effective methods. In this context, dynamic elastography is a promising approach. It is an emerging quantitative medical imaging technique inspired from palpation and based on the determination of elastic properties (stiffness) of tissues. This thesis aims the development of a novel dynamic ultrasound elastography method for early detection of breast lesions. One of the main problems of dynamic elastography techniques using remote palpation (acoustic radiation force) is the strong attenuation of shear waves. After few wavelengths of propagation, displacement amplitudes considerably decrease and their tracking becomes difficult even impossible. This problem greatly affects biological tissue characterization. Moreover, these techniques give only the information about elasticity while recent studies show that some benign lesions have the same elasticity as malignant lesions which affect the specificity of these techniques and motivate investigation of other physical parameters (e.g. viscosity). The first objective of this thesis is to optimize the acoustic radiation force using frequency adaptation to enhance the amplitude of displacements. An analytical model has been developed to predict the optimal frequency for the generation of the radiation force. Once validated on phantoms (in vitro), this model was used for the prediction of the optimal frequencies for the generation of the radiation force in tissue mimicking phantoms and ex vivo human breast cancer samples obtained after total mastectomy. Gains in magnitude were between 20% to158% for in vitro measurements on agar-gelatin phantoms, and 170% to 336% for ex vivo measurements on a human breast sample, depending on focus depths and attenuations of tested samples. The signal-to-noise ratio was also improved by more than four folds with adapted sequences. We conclude that frequency adaptation is a complementary technique that is efficient for the optimization of displacement amplitudes. This technique can be used safely to optimize the deposited local acoustic energy, without increasing the risk of damaging tissues and transducer elements. In the second part of this thesis, a prototype of an ultrasound probe for the generation of a specific type of adaptive shear waves called ''adaptive torsional shear waves'' has been developed. The goal was to use the optimized radiation force (developed in the first part) to generate adaptive torsional shear wave, and prove their utility in improving the amplitude of displacement. During their inward propagation, the amplitude of displacement generated by torsional shear waves was enhanced and the signal to noise ratio improved due to the constructive interferences. Torsional shear waves can also resonate heterogeneities which further enhance the displacement contrast between suspicious masses and its surrounding medium. Finally, in the context of assessment of mechanical proprieties of tissue, the last step of this thesis is to develop an inverse problem based on the propagation of adaptive torsional shear waves to estimate the viscoelastic parameters. A finite element method (FEM) model was developed to solve the inverse wave propagation problem and obtain viscoelastic properties of interrogated media. The inverse problem was formulated and solved in the frequency domain and its robustness was evaluated. The proposed model was validated in vitro with two independent rheology methods on several homogeneous and heterogeneous breast tissue mimicking phantoms over a broad range of frequencies (up to 400Hz). The obtained results were in good agreement with reference rheology methods with discrepancies between 8% and 38% for shear modulus and from 9% to 67% for loss modulus. The robustness study showed that the proposed inverse problem solution yielded a good estimation of the storage (19%) and loss moduli (32%) even with very noisy signals.

La thèse s’articule autour du développement des thermothérapies hépatique et cardiaque guidées par Imagerie de Résonance Magnétique (IRM). La première partie est axée sur le développement d’une méthode permettant d’augmenter la taille des lésions induites par ultrasons focalisés de haute intensité (HIFU). Le seuil de d’intensité acoustique fut déterminé par IRM de la force de radiation acoustique et l’effet caractérisé par IRM de température ex vivo et in vivo dans le foie de porc. La deuxième partie présente le développement d’une méthode permettant une focalisation HIFU hépatique intercostale avec utilisation de la déflection électronique du faisceau pour le suivi du mouvement respiratoire ou /et une ablation multipoint. La méthode proposée repose sur une mise à jour des éléments du transducteur HIFU à désactiver en fonction du point de focalisation sélectionné, à partir d’une projection géométrique de l’ombre des côtes sur la surface du transducteur, mesurée sur des images IRM anatomiques. Nous avons montré qu’il est possible de réduire significativement le chauffage des côtes tout en conservant une élévation de température dans le foie suffisante pour induire une lésion thermique. La troisième partie expose la mise en place de l’IRM de température pour le monitoring des ablations par radiofréquences (RF) dans le cœur. Plusieurs aspects sont abordés, notamment la précision de la thermométrie, la possibilité de réaliser des ablations thermiques par cathéter RF sous IRM de température in vivo dans le cœur de brebis, ainsi que l’utilisation du cathéter comme sonde d’imagerie dans l’objectif d’accroitre la précision de la thermométrie cardiaque. / My manuscript studies the development of mini and non invasive thermotherapies guided by magnetic resonance imaging (MRI) in the treatment of hepatic and cardiac diseases. The first part was the development of a method to increase the lesion size, induced by HIFU, and based on bubble enhanced heating (BEH). The acoustic power threshold of the BEH was determined by MR acoustic radiation force imaging (MR-ARFI) and the thermal effect was characterized by MR thermometry on ex vivo and in vivo in pig livers. The second part developed a strategy to perform HIFU through the rib cage using beam steering to track the respiratory movement or to performed multipoint ablation while avoiding heating of ribs. Transducer elements localized in the geometric projection of the shadow of ribs, relatively to the targeted focal point, were switched off.The third part was the development of the MR thermometry on the heart for the monitoring of radiofrequency ablation (RFA). Several aspects were investigated, in particular the thermometry precision, the feasibility to perform catheter radiofrequency ablation under MR thermometry in vivo in a sheep heart, the possibility to use the catheter as an MR antenna to increase spatial resolution of MR thermometry images.