O objetivo principal desta tese foi desenvolver dispositivos microfluídicos do tipo língua eletrônica baseada em espectroscopia de impedância para análise de líquidos complexos. Dois tipos de língua eletrônica foram desenvolvidos. O primeiro com unidades sensoriais fabricadas com eletrodos interdigitados de ouro sobre vidro, selados com microcanal de PDMS, e recobertos com filmes automontados de polímeros condutores, materiais orgânicos e semicondutores. Essa língua eletrônica foi usada para diferenciar os sabores básicos, representados por soluções aquosas de NaCl (salgado), sacarose (doce), cafeína (amargo), HCl (azedo) e glutamato monosódico (umami), distinguir diferentes tipos de cafés, e detectar a presença de gliadina em soluções e alimentos. A distinção foi possível processando-se os dados de magnitude da capacitância com técnicas de projeção multidimensional IDMAP (Interactive Document Map) e análise de componentes principais (PCA). O segundo tipo de língua foi produzido com eletrodos interdigitados de carbono impressos sobre papel com canal hidrofílico e barreiras hidrofóbicas também impresso, modificado com hidrogel funcionalizado com ácido fenil-borônico (PBA) ou polilíquido iônico (PIL). Com dados de capacitância tratados com PCA e IDMAP, a língua foi usada para distinguir soluções dos açúcares glicose, frutose e sacarose, em diferentes concentrações, e diferentes marcas de suco de maçã. Nesta última língua, empregou-se a capacidade de intumescimento de hidrogéis contendo PBA na presença de açúcares, principalmente frutose, que também foi explorada na confecção de sensores com eletrodos de papel que puderam detectar concentrações baixas de glicose, próximas às encontrados no suor humano. Com a tecnologia de sensores em papel e microfluídica, podem-se conceber aplicações futuras, de baixo custo, em sensores na forma de emplastro para monitorar o nível de glicose no suor humano de maneira não invasiva e língua eletrônica para verificar a presença de glúten em alimentos. / The main aim of this thesis was to develop microfluidic devices of electronic tongue (e-tongue) type based on impedance spectroscopy to analyze complex liquids. Two types of e-tongue were developed. The first had sensing units fabricated with gold interdigitated electrodes onto glass with a microchannel sealed with PDMS and coated with layer-by-layer films of conducting polymers, organic and semiconductors. This e-tongue was used to distinguish the basic tastes, represented by aqueous solutions of NaCl (salty), sucrose (sweet), caffeine (bitter), HCl (sour) and monosodium glutamate (umami), to distinguish different types of coffees, and detect the presence of gliadin in solutions and food. The distinction was made possible by processing the capacitance data with the multidimensional projection techniques IDMAP (Interactive Document Map) and principal component analysis (PCA). The second type of e-tongue was produced with carbon interdigitated electrodes printed on paper with a hydrophilic channel with hydrophobic barriers, also printed, modified with functionalized hydrogel with phenylboronic acid (PBA) or poly(ionic liquid) (PIL). With capacitance data treated with PCA and IDMAP, the e-tongue was used to distinguish solutions at various concentrations of glucose, fructose and sucrose, in addition to different brands of apple juice. In this latter e-tongue, use was made of the ability of the hydrogel containing PBA to swell in the presence of sugars, mainly fructose, which was exploited in producing sensors with paper electrodes that could detect low concentrations of glucose, close to the values found in human sweat. With the technology of paper-based sensors and microfluidics, one may envisage future low cost applications, including patch sensors to monitor glucose in human sweat in a non-invasive manner and e-tongues to determine the presence of gluten in food.

Ce projet de thèse portait sur le développement d’outils microfluidiques pour la toxicologie et la recherche contre le cancer. En permettant l’analyse simultanée d’un très grand nombre de réactions biologiques ou chimiques réalisés dans des compartiments indépendants (ie. gouttelettes), la microfluidique de gouttes offre une sensibilité de détection et une précision sans précédent pour l’analyse de molécules biologiques, telles que l’ADN ou les Anticorps, en comparaison des expériences réalisées conventionnellement en tubes ou en microplaques (essais en « bulk » ou volume). Ce format permet également de réaliser des expériences à très haut débit et est particulièrement pertinent pour la toxicologie, où des analyses robustes de l’effet des médicaments sont nécessaires. De même, ces procédures sont également très adaptées à l’analyse de cellules uniques pour le séquençage ADN ou ARN et l’épigénomique. Tout cela fait de la microfluidique en goutte un outil puissant pour la toxicologie et la recherche sur le cancer. En premier temps, une méthode du comptage précise des cellules encapsulée dans des microgouttelettes, nommée « hémocytométrie microfluidique », a été développée. Un nouvel algorithme de comptage a été proposé. Des cellules bactériennes (Escherichia Coli) et des cellules de 2 lignées humaines différentes (HL60 and H1975) ont été testées. Le nombre de chaque type de cellules a été déterminé avec une haute corrélation entre la théorie (basée sur la distribution de Poisson) et les résultats expérimentaux. Avec ces résultats robustes, un protocole de microfluidique en goutte a été mis en place pour interroger la viabilité cellulaire et la prolifération des 2 lignées humaines. Ces résultats sont en concordance avec ceux de la littérature. Pour la toxicologie, 3 différents modèles, y compris des microsomes (extrait de cellules d’insectes infectées par un baculovirus exprimant le cytochrome P450 3A4 humain, CYP3A4), HepG2-CYP3A4 (modifiée génétiquement pour exprimer le gène CYP3A4 humain), et HepaRG, une lignée hépatique, ont été évaluées pour l’activité enzymatique du CYP3A4, une enzyme largement utilisée en routine pour le criblage de médicament candidat. Les microsomes ont permis de développer un essai fluorogénique permettant de mesurer l’inhibition du CYP3A4. Cependant, ni l’utilisation des microsomes ni des cellules HepG2 exprimant CYP3A4 n’a donné de résultats satisfaisants en microgouttelettes. L’utilisation des cellules HepaRG, une lignée cellulaire qui conserve la majorité de l’expression des cytochromes P450 et des récepteurs nucléaires nécessaire à leur expression, a montré des résultats encourageant à la fois sur les tests de mesure de l’activité enzymatique et d’analyse de l’induction du CYP3A4. Pour la recherche sur le cancer, 4 essais originaux de PCR digitale en gouttes ont été mis en place pour la détection et la quantification de mutations (NRAS, DNMT3A, SF3B1 and JAK2) importante pour les syndromes myélodysplasiques, un groupe hétérogène de maladies touchant les cellules souches hématopoïétiques caractérisées par une hématopoïèse inefficace et des cytopénies périphériques. Finalement, un essai de PCR sur cellule unique encapsulées au sein de billes agarose a été proposé. / This thesis project consists in developing droplet-based microfluidic tools for toxicology and cancer research. Owing to its large numbers of discretized volumes, sensitivity of detection of droplet-based microfluidics for biological molecules such as DNA and antibody is much higher than bulk assays. This high throughput format is particularly suitable for experiments where a robust dose-response curve is needed, as well as for single cell analysis with applications in genomic or sequencing and epigenetics. All above makes droplet-based microfluidics a powerful tool for toxicology and cancer research. In a first part of the work, an accurate cell counting method, named “microfluidics hemocytometry”, has been developed. A new counting algorithm was proposed to count the cells within each droplet. Escherichia Coli and two different human cell lines (HL60 and H1975) were used to validate our strategy. The number of each type of cells in droplets was determined with a high consistency between theory (Poisson distribution) and experimental results. With these robust results, a droplet-based microfluidic protocol has then been established to inquiry both cell viability and proliferation for the two human cell lines. The results are in good agreement with the one of the literature. For the toxicology, 3 different biological models, including microsomes (extracted from baculovirus-infected insect cell expressing human CYP3A4), HepG2-CYP3A4 (genetically modified to express the human CYP3A4 gene) and HepaRG liver cells lines were evaluated for enzymatic activity of cytochromes P450 (CYP3A4), a routinely used enzyme for drug candidate screening. Microsome-based assays were used to validate a fluorogenic inhibition assay. However neither microsome-based assay nor the assay using CYP3A4 expressing HepG2 gave satisfying results in droplet-based format. However, HepaRG cells, a hepatic function-conserved cell line with most cytochrome and related nuclear receptors, demonstrated high relevance both for enzymatic activity testing and CYP3A4 expression induction study. For cancer research, 4 different picoliter droplet-based PCR assays were developed for the detection and quantification of mutations (NRAS, DNMT3A, SF3B1 and JAK2) present in Myelodysplastic syndromes, a heterogeneous group of clonal bone marrow hematopoietic stem cell disorders characterized by ineffective hematopoiesis and peripheral cytopenias. Furthermore, a single cell multistep PCR assay using encapsulation of target DNA in agarose droplets was proposed.

Este trabalho apresenta a síntese de nanopartículas (NPs) de NaYF4 dopadas com íons terras raras a partir de sistemas microfluídicos projetados e desenvolvidos em parceria entre o Laboratório de Crescimento de Cristais e a Central de Processamento de Materiais a Laser no Centro de Laser e Aplicações IPEN. O objetivo foi o estudo de diferentes circuitos microfluídicos usinados a laser para síntese de NPs de fluoretos em geral. Como material teste foi escolhido o NaYF4:Yb3+:Er3+, visando sua obtenção na fase hexagonal com dimensões definidas. Experiências de síntese deste material por co-precipitação, sem uso de surfactantes, foram realizadas para comparação com as sínteses obtidas via microfluídica. Por co-precipitação foram obtidas partículas esféricas, na fase cubica do NaYF4. Foram projetados e fabricados, via usinagem a laser de pulsos ultracurtos em substrato de vidro ótico BK7, três circuitos microfluídicos. Nas experiências de sínteses realizadas nestes chips foram obtidas NPs de NaYF4:Yb3+:Er3+ tanto na fase cubica quanto na fase hexagonal, em diferentes proporções, dependendo dos fluxos de injeção dos precursores no micro reator, da temperatura e da taxa de residência. As NPs obtidas neste trabalho foram caracterizadas através de DRX e analise pelo método de Rietveld, para a identificação das fases do material, MET para definição de forma e tamanho da nanopartículas e MEV para estudo dos microcanais dos chips usinados a lasers. Os melhores resultados foram observados em chips com microcanais da ordem de 400-600μm, pois minimizam o problema de obstrução. Contudo, o controle da temperatura precisa ser otimizado para evitar trincas nos microcircuitos. As NPs obtidas via microfluídica apresentaram distribuição de tamanho na faixa de 5 a 200nm e fases com estrutura hexagonal e cubica. Foi possível obter NPs de fase única cubica, mas o mesmo não ocorreu para fase hexagonal do NaYF4. O presente estudo permitiu definir vários fatores para a obtenção das NPs de NaYF4 via microfluídica e também referente a fabricação, montagem e uso dos chips, porém para obter NPs desse material com controle da dimensão e fases serão necessários estudos complementares. / This work presents the synthesis of NaYF4 nanoparticles (NPs), doped with rare earth ions, using microfluidic systems designed and fabricated at IPEN through Crystal Growth Lab and Materials Laser Processing Lab partnership. The aim of this work was the study of different microfluidic chips laser machined for use in fluoride NPs synthesis. The compound NaYF4:Yb3+:Er3+ (Yb 10 mole%; Er 0.5 mole %) was chosen to test the fabricated microfluidic chips aiming the production of NPs with hexagonal structure with defined dimensions. Synthesis experiments by co-precipitation method of this material without any surfactant were performed to compare with microfluidics synthesis. By this method spherical particles, were obtained with the cubic NaYF4 crystalline structure. Three different chips were designed and fabricated, using a femtosecond laser to machine BK7 optical glass substrate. The synthesis experiments with these chips resulted in NaYF4:Yb3+:Er3+ NPs with both cubic and hexagonal crystalline structure, in different proportions, depending of precursors flux rates, temperature and resident time. The obtained materials of all experiments were characterized by X-ray diffraction and Rietveld analysis, to define crystalline structures parameters; transmission microscopy to define shape and size of NPs and scanning electron microscopy to characterize the chips micro channels machined by laser. The best results were observed for chips with channels of 400-600μm, in view of the obstruction decrease in the chips. The NPs obtained with microfluidics presented sizes from 5nm up to 200nm and hexagonal and cubic crystallographic structures. Cubic single phase NPs were obtained, but the same did not happened with the NaYF4 hexagonal phase. The present study allowed establishing many different parameters for NaYF4 NPs synthesis through microfluidics and concerning fabrication, assembly and experimental use of microfluidic chips, however, additional experiments will be necessary to obtain the fluoride NPs with controlled size and shape.

Este trabalho apresenta a síntese de nanopartículas (NPs) de NaYF4 dopadas com íons terras raras a partir de sistemas microfluídicos projetados e desenvolvidos em parceria entre o Laboratório de Crescimento de Cristais e a Central de Processamento de Materiais a Laser no Centro de Laser e Aplicações IPEN. O objetivo foi o estudo de diferentes circuitos microfluídicos usinados a laser para síntese de NPs de fluoretos em geral. Como material teste foi escolhido o NaYF4:Yb3+:Er3+, visando sua obtenção na fase hexagonal com dimensões definidas. Experiências de síntese deste material por co-precipitação, sem uso de surfactantes, foram realizadas para comparação com as sínteses obtidas via microfluídica. Por co-precipitação foram obtidas partículas esféricas, na fase cubica do NaYF4. Foram projetados e fabricados, via usinagem a laser de pulsos ultracurtos em substrato de vidro ótico BK7, três circuitos microfluídicos. Nas experiências de sínteses realizadas nestes chips foram obtidas NPs de NaYF4:Yb3+:Er3+ tanto na fase cubica quanto na fase hexagonal, em diferentes proporções, dependendo dos fluxos de injeção dos precursores no micro reator, da temperatura e da taxa de residência. As NPs obtidas neste trabalho foram caracterizadas através de DRX e analise pelo método de Rietveld, para a identificação das fases do material, MET para definição de forma e tamanho da nanopartículas e MEV para estudo dos microcanais dos chips usinados a lasers. Os melhores resultados foram observados em chips com microcanais da ordem de 400-600μm, pois minimizam o problema de obstrução. Contudo, o controle da temperatura precisa ser otimizado para evitar trincas nos microcircuitos. As NPs obtidas via microfluídica apresentaram distribuição de tamanho na faixa de 5 a 200nm e fases com estrutura hexagonal e cubica. Foi possível obter NPs de fase única cubica, mas o mesmo não ocorreu para fase hexagonal do NaYF4. O presente estudo permitiu definir vários fatores para a obtenção das NPs de NaYF4 via microfluídica e também referente a fabricação, montagem e uso dos chips, porém para obter NPs desse material com controle da dimensão e fases serão necessários estudos complementares. / This work presents the synthesis of NaYF4 nanoparticles (NPs), doped with rare earth ions, using microfluidic systems designed and fabricated at IPEN through Crystal Growth Lab and Materials Laser Processing Lab partnership. The aim of this work was the study of different microfluidic chips laser machined for use in fluoride NPs synthesis. The compound NaYF4:Yb3+:Er3+ (Yb 10 mole%; Er 0.5 mole %) was chosen to test the fabricated microfluidic chips aiming the production of NPs with hexagonal structure with defined dimensions. Synthesis experiments by co-precipitation method of this material without any surfactant were performed to compare with microfluidics synthesis. By this method spherical particles, were obtained with the cubic NaYF4 crystalline structure. Three different chips were designed and fabricated, using a femtosecond laser to machine BK7 optical glass substrate. The synthesis experiments with these chips resulted in NaYF4:Yb3+:Er3+ NPs with both cubic and hexagonal crystalline structure, in different proportions, depending of precursors flux rates, temperature and resident time. The obtained materials of all experiments were characterized by X-ray diffraction and Rietveld analysis, to define crystalline structures parameters; transmission microscopy to define shape and size of NPs and scanning electron microscopy to characterize the chips micro channels machined by laser. The best results were observed for chips with channels of 400-600μm, in view of the obstruction decrease in the chips. The NPs obtained with microfluidics presented sizes from 5nm up to 200nm and hexagonal and cubic crystallographic structures. Cubic single phase NPs were obtained, but the same did not happened with the NaYF4 hexagonal phase. The present study allowed establishing many different parameters for NaYF4 NPs synthesis through microfluidics and concerning fabrication, assembly and experimental use of microfluidic chips, however, additional experiments will be necessary to obtain the fluoride NPs with controlled size and shape.

La fusion cellulaire est une méthode de génération de cellules hybrides combinant les propriétés spécifiques des cellules mères. Initialement développée pour la production d’anticorps, elle est maintenant aussi investiguée pour l’immunothérapie du cancer. L’électrofusion consiste à produire ces hybrides en utilisant un champ électrique pulsé. Cette technique présente de meilleurs rendements que les fusions chimiques ou virales, sans introduire de contaminant. L’électrofusion est actuellement investiguée en cuve d’électroporation où le champ électrique n’est pas contrôlable avec précision et le placement cellulaire impossible, produisant de faibles rendements binucléaires. Afin d’augmenter le rendement et la qualité de fusion, la capture et l’appariement des cellules s’avèrent alors nécessaires.Notre objectif a été de développer et de réaliser des biopuces intégrant des microélectrodes et des canaux microfluidiques afin de positionner et d’apparier les cellules avant leur électrofusion. Une première structure de piégeage se basant sur des plots isolants et l’utilisation de la diélectrophorèse a été réalisée. Afin d’effectuer des expérimentations sous flux, une méthode de scellement des canaux, biocompatible et étanche a été développée. Puis, le milieu d’expérimentation a été adapté pour l’électrofusion. En confrontant les résultats des expériences biologiques aux simulations numériques, nous avons pu démontrer que l’application d’impulsions électriques induisait la diminution de la conductivité cytoplasmique. Nous avons ensuite validé la structure par l’électrofusion de cellules. Un rendement de 55% avec une durée de fusion membranaire de 6 s a été obtenu. Dans un second temps, nous avons proposé deux microstructures de piégeage pour l’électrofusion haute densité. La première se base sur un piégeage fluidique, alors que la seconde, utilise ladiélectrophorèse sans adressage électrique à l’aide de plots conducteurs. Jusqu’à 75% des cellules fusionnent dans cette dernière structure. Plus de 97% des hybridomes produits sont binucléaires. Le piégeage étant réversible, les hybridomes peuvent ensuite être collectés pour des études ultérieures. / Cell fusion is a method to generate a hybrid cell combing the specific properties of its progenitor cells. Initially developed for antibody production, it is now also investigated for cancer immunotherapy. Electrofusion consists on the production of hybridoma using electric pulses. Compared to viral or chemical methods, electrofusion shows higher yields and this system is contaminant free. Actually, electrofusion is investigated in electroporation cuvettes, where the electric field is not precisely controllable and cell placement impossible, resulting in low binuclear hibridoma yields. To improve the fusion quality and yield, cell capture and pairing are necessary.Our objective was the development and realization of biochips involving microelectrodes and microfluidic channels to place and pair cells prior to electrofusion. A first trapping structure based on insulators and the use of dielectrophoresis has been achieved. In order to perform fluidic experiments, a biocompatible irreversible packaging was developed. Then, the experimental medium was optimized for electrofusion. Confronting the biological experiments and the numerical simulations, we showed that the application of electric pulses leads to a decrease of the cytoplasmic conductivity. The microstructure was validated by cell electrofusion. A yield of 55%, with a membrane fusion duration of 6 s has been achieved. Secondly, we proposed two trapping microstructures for high density electrofusions. The first one is based on a fluidic trapping while the second one uses dielectrophoresis, free of electric wiring, thanks to conductive pads. Up to 75% of paired cells were successfully electrofused with the conductive pads. More than 97% of the hybridoma were binuclear. The trapping being reversible, the hybridoma can be collected for further analysis.

O desenvolvimento de dispositivos microfluídicos biomiméticos, \"órgãos-em-chip\", tem permitido melhores respostas em ensaios que carecem de uma correlação fisiológica mais próxima da in vivo. Explorando as tecnologias da microfluídica e microfabricação, esses dispositivos recapitulam aspectos específicos de estruturas e funções dos órgãos. Ainda, os avanços obtidos em culturas tridimensionais de células, modelos de matrizes extracelulares e tecnologias direcionadas às células tronco, têm consolidado os órgãos-em-chip como uma ferramenta fundamental para a compreensão de diversas respostas biológicas do corpo humano frente às aplicações biomédicas, farmacêuticas, químicas e ambientais. Com os avanços da nanotecnologia e ciência dos materiais, inúmeros progressos têm sido alcançados na farmácia e na medicina. Devido à redução da escala, propriedades que se diferenciam substancialmente daquelas encontradas na escala macro são obtidas. As nanopartículas de dióxido de titânio (NPs TiO2) têm apresentado múltiplas aplicações na medicina e na indústria. Em vista disso, faz-se necessário a investigação dos efeitos tóxicos dessas nanopartículas, seja na saúde ou no meio ambiente. É bem documentado que as NPs TiO2 podem chegar à corrente sanguínea e alcançar vários órgãos, causando reações inflamatórias e interações celulares que podem ser patogenicamente relevantes. Assim, o presente trabalho propõe o estudo dos efeitos das NPs TiO2 em células endoteliais (HUVEC) cultivadas em um dispositivo microfluídico fabricado em poliéster-toner (PT), uma tecnologia simples que alia rapidez e baixo custo de produção. A viabilidade do uso dos microchips de PT foi avaliada por meio do teste MTT e produção de NO e verificou-se serem adequados para a cultura de células endoteliais. As células no sistema microfluídico foram expostas às NPs TiO2, e os resultados comparados a um sistema estático (placas de cultura de células) submetido às condições semelhantes. Os sobrenadantes de ambos os sistemas foram utilizados para determinação da produção de VEGF-A. Ademais, foram avaliadas a produção de aníon superóxido e a indução de apoptose. Os resultados esclarecem os mecanismos de toxicidade das NPs TiO2 e são correlacionados com as patologias que eventualmente estão associadas a esses efeitos. Por meio deste estudo, demonstrou-se o grande potencial dos microchips de PT para estudos em biologia celular, os quais podem fornecer a base para ensaios pré-clinicos com maior poder preditivo, alternativos ao uso de animais e cobaias na pesquisa científica. / The development of biomimetic microfluidic devices, \"organ-on-chips\", has allowed better responses in assays that need a closer in vivo physiological correlation. Exploring the technologies of microfluidics and microfabrication, these devices recapitulate specific aspects of structures and functions of the organs. In addition, the progress made in 3D cell cultures, extracellular matrix models, and stem cells technologies, have consolidated the organ-on-chips as a key tool for understanding various biological responses of the human body in face of biomedical, pharmaceutical, chemical, and environmental applications. With the advances in nanotechnology and materials science, much progress has been made in pharmacy and medicine. Due to the scale reduction, properties that differ substantially from those found on the macro scale are obtained. Titanium dioxide nanoparticles (TiO2 NPs) have found many applications in medicine and industry. In view of this fact, it is necessary to investigate the toxic effects of nanoparticles, either on health or in the environment. It has been well documented that TiO2 NPs can reach the bloodstream and affect various organs, causing inflammatory reactions and cellular interactions that can be pathogenetically relevant. Thus, this work proposes the study of the effects of TiO2 NPs in endothelial cells (HUVEC) cultured in a microfluidic device made of polyester toner (PT), a simple technology that combines speed and low cost of production. The viability of the use of PT microchips was evaluated by MTT assay and production of NO and we found that it is suitable for culturing of endothelial cells. The HUVEC in the microfluidic system were exposed to TiO2 NPs and the results compared to a static system (cell culture plates) subjected to similar conditions. Supernatants from both systems were used for determining the production of the VEGF-A. Furthermore, we have evaluated superoxide anion production and induction of apoptosis. The results clarify the mechanisms of toxicity of NPs TiO2 and are correlated with the pathologies that eventually are associated with these effects. Through this study, we demonstrated the great potential of PT microchips for studies in cell biology, which may provide the basis for pre-clinical trials with greater predictive power, alternative to the use of animals in scientific research.

One goal of synthetic biology is to design and build genetic circuits in living cells for a range of applications with implications in health, materials, and sensing. Computational design methodologies allow for increased performance and reliability of these circuits. Major challenges that remain include increasing the scalability and robustness of engineered biological systems and streamlining and automating the synthetic biology workflow of “specify-design-build-test.” I summarize the advances in microfluidic technology, particularly microfluidic large scale integration, that can be used to address the challenges facing each step of the synthetic biology workflow for genetic circuits. Microfluidic technologies allow precise control over the flow of biological content within microscale devices, and thus may provide more reliable and scalable construction of synthetic biological systems. However, adoption of microfluidics for synthetic biology has been slow due to the expert knowledge and equipment needed to fabricate and control devices. I present an end-to-end workflow for a computer-aided-design (CAD) tool, Fluigi, for designing microfluidic devices and for integrating biological Boolean genetic circuits with microfluidics. The workflow starts with a ``netlist" input describing the connectivity of microfluidic device to be designed, and proceeds through placement, routing, and design rule checking in a process analogous to electronic computer aided design (CAD). The output is an image of the device for printing as a mask for photolithography or for computer numerical control (CNC) machining. I also introduced a second workflow to allocate biological circuits to microfluidic devices and to generate the valve control scheme to enable biological computation on the device. I used the CAD workflow to generate 15 designs including gradient generators, rotary pumps, and devices for housing biological circuits. I fabricated two designs, a gradient generator with CNC machining and a device for computing a biological XOR function with multilayer soft lithography, and verified their functions with dye. My efforts here show a first end-to-end demonstration of an extensible and foundational microfluidic CAD tool from design concept to fabricated device. This work provides a platform that when completed will automatically synthesize high level functional and performance specifications into fully realized microfluidic hardware, control software, and synthetic biological wetware.

This thesis aims at contributing to the characterization of the dynamics of bubbles in microfluidics through modeling and experiments. Two flow regimes encountered in microfluidics are studied, namely, the bubbly flow regime and the Taylor flow regime (or slug flow).In particular, the first part of this thesis focuses on the dynamics of a bubbly flow inside a horizontal, cylindrical microchannel in the presence of surfactants using numerical simulations. A numerical method allowing to simulate the transport of surfactants along a moving and deforming interface and the Marangoni stresses created by an in-homogeneous distribution of these surfactants on this interface is implemented in the Level set module of the research code. The simulations performed with this code regarding the dynamics of a bubbly flow give insights into the complexity of the coupling of the different phenomena controlling the dynamics of the studied system. Fo example it shows that the confinement imposed by the microchannel walls results in a significantly different distribution of surfactants on the bubble surface, when compared to a bubble rising in a liquid of infinite extent. Indeed, surfactants accumulate on specific locations on the bubble surface, and create local Marangoni stresses, that drastically influence the dynamics of the bubble. In some cases, the presence of surfactants can even cause the bubble to burst, a mechanism that is rationalized through a normal stress balance at the back of the bubble. The numerical method implemented in this thesis is also used for a practical problem, regarding the artisanal production of Mezcal, an alcoholic beverage from Mexico.The second part of the thesis deals with the dynamics of a Taylor flow regime, through experiments and analytical modeling. An experimental technique that allows to measure the thickness of the lubrication film forming between a pancake-like bubble and the microchannel wall is developed. The method requires only a single instantaneous bright-field image of a pancake-like bubble translating inside a microchannel. In addition to measuring the thickness of the lubrication film, the method also allows to measure the depth of a microchannel. Using the proposed method together with the measurment of the bubble velocity allows to infer the surface tension of the interface between the liquid and the gaz. In the last chapter of this thesis, the effect of buoyancy on the dynamics of a Taylor flow is quantified. Though often neglected in microfluidics, it is shown that buoyancy effects can have a significant impact on the thickness of the lubrication film and consequently on the dynamics of the Taylor flow. These effects are quantified using experiments and analytical modeling. This work was performed at Princeton University with Professor Howard A. Stone during an eight month stay. / Doctorat en Sciences de l'ingénieur et technologie / info:eu-repo/semantics/nonPublished

Particle-particle interactions are of paramount importance in every multi-body system as they determine the collective behaviour and coupling strength. Many well-known interactions like electro-static, van der Waals or screened Coulomb, decay exponentially or with negative powers of the particle spacing r. Similarly, hydrodynamic interactions between particles undergoing Brownian motion decay as 1/r in bulk, and are assumed to decay in small channels. Such interactions are ubiquitous in biological and technological systems. Here I confine multiple particles undergoing Brownian motion in narrow, microfluidic channels and study their coupling through hydrodynamic interactions. Our experiments show that the hydrodynamic particle-particle interactions are distance-independent in these channels. We also show that these interactions affect actively propelled particles via electrophoresis or gravity, resulting in non-linear transport phenomena. These findings are of fundamental importance for understanding transport of dense mixtures of particles or molecules through finite length, water-filled channels or pore networks.

Ultrasound, applied in combination with microbubbles, has potential as a means to enhance the uptake of therapeutic agents, which could include drugs and nucleic acids, into biological cells. This process is commonly referred to as 'sonoporation', and the enhanced uptake can be caused through the incident ultrasonic pressure fi eld causing radial oscillations (cavitation) in the microbubbles, amongst other possibilities. However, the mechanisms responsible for any resultant increase in cell membrane permeability are not yet fully understood. This project focussed on achieving a more fundamental understanding of these salient processes by building on a platform of previous work within the group. One strand of the project involved a complete characterisation of the performance of a rotating mirror high speed camera (Cordin 550-62) that was previously used by our group [and others] to investigate microbubble cavitation phenomena and interactions with proximal cell membranes. Speci cally, I present herein an investigation into the image formation process with this type of camera, the essence of which stymied previous data interpretations. I demonstrate that an inherent asynchrony in the exposure of pixels within individual image frames leads to a temporal anomaly. This was achieved using low cost, flashing LED lights and resulted in the extraction of an algorithm to correct for the temporal anomaly. In a slightly diff erent context, the delivery of suitable ultrasonic fields is necessary to achieve a uniform treatment across a therapeutic target. This thesis also reports on a study on the design of ultrasonic lenses to alter the focal region of a focussed ultrasound transducer with the aim of producing focal regions that can enable sonoporation of tumours of varying sizes. We show that the use of lenses can be an inexpensive alternative to more complex systems such as phased array transducers. Design modelling and experimental testing of lens prototypes are presented along with preliminary results with tissue mimicking polyacrylamide gel phantoms. The target environment in which the process of sonoporation will be clinically useful (i.e. in the physiological circulation) can be simpli ed as a microfluidic system. One strategy for bubble mediated therapy involves the use of a pro-drug approach, that is, when two otherwise benign ingredients are loaded onto separate microbubble populations, but can become mixed at the anatomical target site by the action of focussed ultrasound whereupon a potent drug is produced. The required mixing can be achieved by the violent coalescence of nearby cavitating bubbles, their reaction product then being released and di ffused into the interiour of nearby cells through sonoporation. A study related to this field is presented here where laser induced thermocapillary flows are shown to cause mixing of the content of a drop in a microfluidic channel in a bid to understand the mixing process at a level that may assist future microbubble engineering strategy. To summarise then, the work presented in this thesis has consolidated earlier unpublished data sets achieved by the group, providing new and exacting experimental evidence and an accurate algorithm that will facilitate post-processing of that earlier data (Chapters 2-3). Moreover, group aspirations to translate earlier in-vitro work on sonoporation towards next phase medical-phantom exposures have been boosted through the provision of a new direction involving acoustic lensing, the experimental data from which was used to completely validate existing models for our own design scenarios (Chapter 4). Finally, previous unpublished observations on microbubble coalescence undertaken by the group suggested a means to implement pro-drug delivery with direct in-situ mixing. Such suggestions were explored within microfluidic contexts using lasers to control and visualise the mixing processes that might arise in such situations (Chapter 5). All of these new insights have served to consolidate the group's previous and as yet unpublished data, opening the way for dissemination with confidence in the integrity of that data, and have also extended group capability and expertise in the areas of MHz-rate high speed framing cameras, the fabrication of acoustic lenses, and with microfluidic mixing.