Microfluidics is the science of processing microliters or less of fluid at a time in a channel with dimensions on the order of microns. The small size of the channels allows fluid properties to be studied in a world dominated by viscosity, surface tension, and diffusion rather than gravity and inertia. Microfluidic droplet generation is a well studied and understood phenomena, which has attracted attention due to its potential applications in biology, medicine, chemistry and a wide range of industries. This dissertation adds to the field of microfluidic droplet studies by studying individual droplet deformation and the process of scaling-up microfluidic devices for industrial use. The study of droplet deformation under extensional and mixed shear and extensional flows was performed within a microfluidic device. Droplets were generated using a flow-focusing device and then sent through a hyperbolic contraction downstream of the droplet generator. The hyperbolic contraction allowed the smallest droplets to be deformed by purely extensional flows and for the larger droplets to experience mixed extensional and shear flows. The shear resulted from the proximity of the droplet to the walls of the microfluidic channel. The continuous phase in all of these devices was oil and the dispersed phase was water, an aqueous surfactant solution, or an aqueous suspension of colloidal particles. Droplet deformation dynamics are affected by the use of surfactants and colloidal particles, which are commonly used to stabilize emulsion droplets again coalescence. Microfluidic droplet generating devices have many potential industrial applications, however, due to the low output of product from a single droplet generating device, their potential has not been realized. Using six parallel flow-focusing droplet generators on a single chip, the process of microfluidic droplet formation can be scaled up, thus resulting in a higher output of droplets. The tuning of droplet size and production frequency can be achieved on chip by varying the outlet tubing lengths, thus allowing for a single device to be used to generate a range of droplet sizes.

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This research aims to investigate how particles assemble together through thermodynamic and kinetic control. Particle assembly with thermodynamic control is achieved in part due to electrostatic attraction between particles. Electrostatic attraction between particles can be achieved by functionalizing polystyrene or SiO2 particles with different charges. Particles with different charges will come together in solution slowly and self-assemble to form ordered crystals with different patterns based on size and charge ratios of two oppositely charged particles. Kinetic control of particle assembly is achieved by pattern aided exponential amplification of nanoscale structures. Some of these nanoscale structures are difficult to build with other conventional synthetic methods. On the other hand, as for kinetically controlled particle replication, the patterns can be synthesized by one of two ways i) crystal products which are produced by thermodynamically controlled particle assembly or ii) single particle deposition. Specifically, kinetically controlled particle assembly focuses on constructing SiO2 particles. Exponential replication of SiO2 particles is achieved by growing a "bridge layer", between templates of SiO2 particles and next generation SiO2 replicas. By dissolving the bridge layer, two times the amount of the SiO2 particles with the shape of the original templates can be formed. In the next generation, all the particles serve as template particles. Thus, after n cycles of replication, 2n amount of products can be formed. If successful, particle assembly can be thermodynamic controlled and particle exponential replication can be kinetical controlled, which will enable new ways to build particles with well-defined shapes from readily available building blocks.

abstract: Environmentally responsive microgels have drawn significant attention due to their intrinsic ability to change volume in response to various external stimuli such as pH, temperature, osmotic pressure, or electric and magnetic fields. The extent of particle swelling is controlled by the nature of the polymer-solvent interaction. This thesis focuses on design and synthesis of environmentally responsive microgels and their composites, and encompasses methods of utilizing microgel systems in applications as vehicles for the adsorption, retention, and targeted delivery of chemical species. Furthermore, self-assembled microgel particles at ionic liquid (IL)-water interfaces demonstrate responsive colloidal lattice morphology. The thesis first reports on the fundamental aspects of synthesis, functionalization, and characteristic properties of multifunctional environmentally responsive microgels derived from poly(N-isopropylacrylamide) (PNIPAm) and other functional co-monomers. In particular, the uptake and release of active chemical species such as rheology modifiers into and from these ionic microgels is demonstrated. Moreover, a facile tunable method for the formation of organic-inorganic composites with Fe3O4 nanoparticles adsorbed and embedded within ionic microgel particles is explored. Additionally, the development of zwitterionic microgels (ZI-MG) is presented. These aqueous ZI-MG dispersions exhibit reversible parabolic swelling as a function of pH and display a minimum hydrodynamic diameter at a tunable isoelectric point (IEP). This study also elucidates the controlled uptake and release of surfactants from these particle systems. The extent of surfactant loading and the ensuing relative swelling/deswelling behaviors within the polymer networks are explained in terms of their binding interactions. The latter part of this thesis highlights the versatility of fluorescently labeled microgel particles as stabilizers for IL-water droplets. When the prepared particles form monolayers and equilibrate at the liquid-liquid interface, the colloidal lattice organization may re-order itself depending on the surface charge of these particles. Finally, it is shown that the spontaneously formed and densely packed layers of microgel particles can be employed for extraction applications, as the interface remains permeable to small active species. / Dissertation/Thesis / Doctoral Dissertation Chemical Engineering 2015

Les virus bactériens (bactériophages), durant leur co-évolution avec les bactéries, ont su trouver de nombreuses voies pour détourner les machineries cellulaires dans le but de se multiplier efficacement. L’infection par le phage dès son entrée dans le cytoplasme est un bouleversement pour la bactérie en termes de ressources monopolisées à ses dépens et probablement de restructuration de l’espace cytoplasmique. Dans ce travail de thèse, l’impact de l’infection de la bactérie Gram-positive Bacillus subtilis par le bactériophage SPP1 a été étudié.La réplication de l’ADN est initiée par des protéines précoces virales. Elle mène au chargement de l’hélicase virale gp40 sur l’origine de réplication de SPP1 dont les brins d’ADN ont été ouverts par la protéine de liaison à l’origine, gp38. Le réplisome bactérien est ensuite recruté de manière massive au sein de l’usine de réplication formant un foyer défini dans le cytoplasme bactérien. L’interaction de gp40 avec les protéines cellulaires DnaX et DnaG assure fort probablement le recrutement du complexe cellulaire au foyer de réplication. La quantité d’ADN viral synthétisée représente presque 500 copies d’ADN viral par bactérie après 30 minutes d’infection, ce qui est équivalent à la taille de 5 génomes de B. subtilis. Des études de FRAP (Fluorescence Recovery After Photobleaching) montrent que l’usine de réplication est très dynamique. Ce comportement est inhibé par la présence de HPUra montrant qu’il dépend de la présence d’un réplisome actif.Les concatémères résultant de la réplication de l’ADN viral sont le substrat pour l’encapsidation du génome de SPP1 dans des procapsides préformées. La maturation de ces procapsides en particules virales infectieuses suit une voie d’assemblage spécifique. Deux protéines rapportrices de différentes étapes de cette voie ont été suivies : la protéine d’échafaudage gp11, présente à l’intérieur de la procapside avant encapsidation de l’ADN, et la protéine auxiliaire gp12, qui se fixe à la surface de la capside pendant l’encapsidation. Les procapsides colocalisent partiellement avec l’usine de réplication du génome viral. Après encapsidation de l’ADN, les capsides vont s’accumuler dans des foyers de stockage qui ont une localisation indépendante du foyer de réplication. Cette organisation est également observée dans des bactéries très allongées où deux régions de stockage sont retrouvées situées de part et d’autre de l’usine de réplication mais éloignées des pôles cellulaires. La microscopie électronique combinée à des immuno-marquages révèlent que cette compartimentation corrèle avec une réorganisation majeure de l’ultrastructure du cytoplasme bactérien.L’assemblage et la dynamique des foyers viraux dans la bactérie ont été suivis pendant toute la durée du cycle viral dans un système de microfluidique. Elle montre que les étapes de réplication de l’ADN viral et la formation de la particule du phage sont des processus compartimentés dans le cytoplasme de la bactérie tant spatialement que temporellement. Bien que la croissance cellulaire soit retardée, les bactéries continuent de s’allonger et de se diviser pendant l’infection par SPP1. Le virus exploite donc de manière efficace les machineries cellulaires et l’architecture de la bactérie pour une multiplication optimale. Ces stratégies sont probablement utilisées par de nombreux phages pour remodeler la cellule bactérienne à leur avantage. / During the co-evolution of viruses and cells, viruses exploited numerous ways to hijack cell machineries for their optimal multiplication and dissemination. Phage infection is a major challenge to bacteria, exploiting extensively cellular biosynthetic ressources and possibly re-organizing the cytoplasm space. The work in this thesis investigated the cellular impact of infection by SPP1, a well-characterized model tailed bacteriophage that infects the Gram-positive bacterium Bacillus subtilis.Viral DNA replication is initiated by early phage proteins whose activity culminates in loading of the SPP1 helicase gp40 at the melted phage origin of replication. The bacterial replisome is then massively recruited to the phage replication factory that is localized at a defined position of the cytoplasm. The interaction of gp40 with its two cellular partners DnaX and DnaG mediates most likely the hijacking of the B. subtilis replication machinery. More than 500 copies of the viral genome are synthesized within 30 minutes after initiation of infection, which is roughly the equivalent to five B. subtilis genomes. FRAP (Fluorescence Recovery After Photobleaching) experiments showed that the viral DNA factory is highly dynamic, a behavior that depends on active DNA replication.The concatemers resulting from DNA replication are the substrate for encapsidation of the SPP1 genome into preformed procapsids. Maturation of procapsids to infectious viral particles follows a defined pathway. The SPP1 scaffolding protein gp11, that occupies the interior of the procapsid before DNA packaging, and gp12, that binds to capsids during DNA packaging, were followed to dissect the steps of this process. Procapsids partially co-localize with DNA replication factories. After packaging the DNA-filled capsids fully segregate to spatially distinct warehouses where viral particles accumulate. Recruitment of SPP1 proteins to these compartments recapitulates the sequential order of their assembly to build the viral particle. The replication factory is most frequently flanked by two warehouses. Such pattern is also observed in very elongated cells where the viral compartments remain localized nearby each others and far from the bacterial poles. Immuno-electron microscopy of cryo-sections from infected cells highlights a complete remodelling of the bacterial cytoplasm dedicated to virus multiplication.The assembly and dynamics of the SPP1 replication factory and virions warehouses were visualized during the complete phage infection cycle in microfluidics experiments. The viral compartments are well individualized in the cytoplasm both in terms of space and time. Although bacterial growth is retarded, cells continue to elongate and to divide during SPP1 infection. Structuration of viral factories appears as a very efficient way for SPP1 to exploit bacterial resources and cytoplasmic space to optimize its multiplication. This strategy might be widely used by phages for remodelling the bacterial cell.