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In this thesis, acoustical and other physical properties of soft submicron suspensions were investigated in order to provide invaluable clues for their adaptation in theragnostic applications. Two types of dispersions were studied: fluorocarbon droplets stabilised with a polymeric (PLGA, PLGA-PEG) shell or a semifluorinated surfactant (called FTAC) shell. Since preparation of polymeric particles had been already developed, we first studied factors affecting mean diameter, size distribution, and coarsening of emulsions made of FTAC stabilising droplets of various fluorocarbons. Mechanical parameters used for emulsion synthesis and surfactants length were optimised to get the smallest droplets (~200 nm in diameter) that stay mainly submicrometric for several weeks. In addition, a full characterisation of surfactant properties was conducted. Next, for ultrasonic theragnostic purpose, it was necessary to improve our understanding in the mechanisms underlying interactions between ultrasonic waves and particles of a suspension. To do so, ultrasound propagation studies through dilute suspensions were carried out in a large frequency range (3-90 MHz) with subsequent modelling. The model could fit with a good accuracy our experimental data on polymeric particles and reveals information about unknown parameters of the shell: the geometrical parameters (shell thickness) and the viscoelastic parameters of the shell (speed of sound, shear moduli at infinite and zero frequencies, and the relaxation frequency). Therefore, such a model provides the required feedback for tuning the physicochemical parameters of nanoparticles in order to optimize their design.

Dans cette thèse, des propriétés acoustiques et physiques de suspensions nanométriques ont été étudiées afin de fournir des éléments importants permettant leurs modifications en vue d'application théragnostique. Deux types de suspensions ont été considérées: des gouttelettes fluorocarbonées stabilisées par une capsule soit polymérique (PLGA, PLGA-PEG), soit composé d'un tensioactif semifluoré (FTAC). La préparation des particules polymériques ont déjà été développés. Nous avons donc commencé par l'étude des facteurs influant sur le diamètre moyen, la distribution en taille, et le comportement temporel de gouttelettes stabilisées par du FTAC. Les paramètres mécaniques durant l'émulsification ainsi que la longueur des FTAC ont été optimisé pour obtenir les gouttelettes les plus petites possibles (~200 nm de diamètre) et qui restent principalement nanométriques pendant plusieurs semaines. De plus, une caractérisation des tensioactifs a été menée. Pour les applications envisagées, il fallait améliorer notre connaissance des mécanismes d'interactions entre ultrasons et particules en suspension. La propagation ultrasonore à travers des suspensions diluées a étudiée sur une large gamme de fréquences (3-90 MHz) et fut associée au développement d'un modèle analytique. Le modèle a ajusté correctement nos résultats sur les particules polymériques et des paramètres difficilement mesurables de la coque ont été déduit : épaisseur, vitesse du son, coefficient de cisaillement et fréquence de relaxation. Un tel modèle permet donc de fournir des éléments indispensables permettant de savoir quels paramètres physico-chimiques il faut modifier afin de les optimiser. / In this thesis, acoustical and other physical properties of soft submicron suspensions were investigated in order to provide invaluable clues for their adaptation in theragnostic applications. Two types of dispersions were studied: fluorocarbon droplets stabilised with a polymeric (PLGA, PLGA-PEG) shell or a semifluorinated surfactant (called FTAC) shell. Since preparation of polymeric particles had been already developed, we first studied factors affecting mean diameter, size distribution, and coarsening of emulsions made of FTAC stabilising droplets of various fluorocarbons. Mechanical parameters used for emulsion synthesis and surfactants length were optimised to get the smallest droplets (~200 nm in diameter) that stay mainly submicrometric for several weeks. In addition, a full characterisation of surfactant properties was conducted. Next, for ultrasonic theragnostic purpose, it was necessary to improve our understanding in the mechanisms underlying interactions between ultrasonic waves and particles of a suspension. To do so, ultrasound propagation studies through dilute suspensions were carried out in a large frequency range (3-90 MHz) with subsequent modelling. The model could fit with a good accuracy our experimental data on polymeric particles and reveals information about unknown parameters of the shell: the geometrical parameters (shell thickness) and the viscoelastic parameters of the shell (speed of sound, shear moduli at infinite and zero frequencies, and the relaxation frequency). Therefore, such a model provides the required feedback for tuning the physicochemical parameters of nanoparticles in order to optimize their design.

It is estimated that mind-boggling 14.1 million new cases of cancer occurred worldwide in 2012 alone. This number is alarming. Although healthy lifestyle may reduce a risk of developing cancer, there is always some probability that cancer would develop even in an absolutely fit individual. There are two main conditions for successful treatment of cancer. Firstly, early diagnostic is absolutely crucial. Secondly, there is a need for suitable surgical methods for affected tissue removal. Ultrasound has a great potential to be used for both purposes as a non-invasive method. Photoacoustic spectroscopy is imaging method for tumor detection of great properties making the use of ultrasound while High-Intensity Focused Ultrasound (HIFU) is non-invasive surgical method. These methods would be impossible without precise ultrasound propagation simulations. The k-Wave is an open source MATLAB toolbox implementing such simulations. So, why are not these methods already deployed in treatment? Unfortunately, the simulation of ultrasound propagation is a very time consuming task, which makes it ineffective for medical purposes. However, there are a few options how to accelerate these simulations. The use of GPU is a very promising way to accelerate simulation.   The main topic of this thesis is the acceleration of the simulation of soundwaves propagation in bones and hard tissue. The implementation developed as a part of this thesis was benchmarked on various supercomputers including Anselm in Ostrava and Piz Daint in Lugano. The implemented solution provides remarkable acceleration compared to the original MATLAB prototype. It was able to accelerate the simulation around 160 times in the best case. It means that the simulation, which would otherwise last for 6.5 days, can be now computed in one hour. This acceleration was achieved using an NVIDIA Tesla P100 to run the simulation with the domain size of 416x416x416 grid points. The thesis includes performance benchmarks on different GPUs to provide complex image acceleration capabilities of developed implementation and provides discussion about memory usage and numerical accuracy. Thanks to the implemented solution harnessing the power of modern GPUs, doctors and researchers all around the world have a powerful tool in hands.

Extensions to k-Wave toolbox used for ultrasound modelling are described. Aim of extensions is to reduce time and space complexity by presenting alternative representations of tissues and transducers in simulation. This project clarifies basic principles and features of k-Wave, describes design of new representations and finally describes implementation of the suggested extensions.

Simulácia šírenia ultrazvuku prostredníctvom mäkkých biologických tkanív má širokú škálu praktických aplikácií. Patria sem dizajn prevodníkov pre diagnostický a terapeutický ultrazvuk, vývoj nových metód spracovania signálov a zobrazovacích techník, štúdium anomálií ultrazvukových lúčov v heterogénnych médiách, ultrazvuková klasifikácia tkanív, učenie rádiológov používať ultrazvukové zariadenia a interpretáciu ultrazvukových obrazov, modelové vrstvenie medicínskeho obrazu a plánovanie liečby pre ultrazvuk s vysokou intenzitou. Ultrazvuková simulácia však predstavuje výpočtovo zložitý problém, pretože simulačné domény sú veľmi veľké v porovnaní s akustickými vlnovými dĺžkami, ktoré sú predmetom záujmu. Ale ak je problém osovo symetrický, problém môže byť riešený v 2D.To umožňuje spúšťanie simulácií na mriežke s väčším počtom bodov, s menším využitím výpoč- tových zdrojov za kratšiu dobu. Táto práca modeluje a implementuje zrýchlenie vlnovej nelineárnej ultrazvukovej simulácie v axisymetrickom súradnicovom systéme realizovanom v Matlabe pomocou Mex súborov pre diskrétne sínové a kosínové transformácie. Axisymetrická simulácia bola implementovaná v C++ ako open source rozšírenie K-WAVE toolboxu. Kód je optimalizovaný na beh na jednom uzle superpočítaču Salomon (IT4Innovations, Ostrava, Česká republika) s dvoma dvanásť-jadrovými procesormi Intel Xeon E5-2680v3. Na maximalizáciu výpočtovej efektívnosti boli vykonané viaceré optimalizácie kódu. Po prvé, fourierové tramsformácie boli vypočítané pomocou real-to-complex FFT z knižnice FFTW. V porovnaní s complex-to-complex FFT to znížilo čas výpočtu a pamäť spojenú s výpočtom FFT o takmer 50%. Taktiež diskrétne sínové a kosínové transformácie sa počítali pomocou knižnice FFTW, ktoré v Matlab verzii museli byť vyvolané z dynamicky načítaných MEX súborov. Po druhé, aby sa znížilo zaťaženie priepustnosti pamäte, boli všetky operácie počítané jednoduchej presnosti pohyblivej rádovej čiarky. Po tretie, elementárne operá- cie boli paralelizované pomocou OpenMP a potom vektorizované pomocou rozšírení SIMD (SSE). Celkový výpočet C++ verzie je až do 34-násobne rýchlejší a využíva menej ako tretinu pamäte ako Matlab verzia simulácie. Simulácia ktorá by trvala takmer dva dni tak môže byť vypočítaná za jeden a pol hodinu. Toto všetko umožňuje počítať simuláciu na výpočetnej mriežke s veľkosťou 16384 × 8192 bodov v primeranom čase.