Dissertations / Theses on the topic 'Microfluidics applications'

Drop-based microfluidic technology has been attracting great attention since the prevalence of soft-lithography techniques in poly-dimethylsiloxane (PDMS) microfluidic device fabrication a decade ago. The miniaturized isolated confinement of the droplet provides an ideal environment to study single cell behaviors in vitro that might otherwise be buried in the ensemble measurements. The effective confinement of the target and its secretion, together with the high-throughput processing capability, holds the promise for efficient target search through large-scale library screening. In fact, in the past seven years, considerable efforts have been made in developing this platform towards the applications in biology and great advances in drops have been reported in areas such as directed evolution, DNA sequencing, drug screening, etc. This thesis systematically describes our work that has been done in advancing the biological application of drop-based microfluidics through three major projects that are of significance in both fundamental research and clinical applications. Encapsulating in vitro transcription and translation reactions in the 0.5 pL drops enables us to synthesize a variety of functional RNAs and proteins from the single DNA templates in a drop environment, which not only provides a novel approach for single DNA molecule detection, but also paves the way for the high-throughput screening of the artificial proteins with drop-based microfluidics. Through successful enrichment of the restriction enzyme genes from a library consisting its truncated mutants, we demonstrated the high-throughput sorting capability of microfluidics for target gene screening that is beneficial for gene therapy applications. Finally, a non-invasive hydrogel synthesis method with microfluidic drop-maker and pico-injector is described, as a demonstration of microfluidic platform in the application of controllable synthesis of micro-sized gel particles as the 3D scaffold of, for example, mesenchymal stem cells, for the in vitro study of cell behaviors induced by cell-cell interactions and cell-environment interactions.
Chemical Physics

Microfluidic droplets are a powerful tool for screening large populations of cells, molecules, and biochemical reactions. Droplet systems are able to encapsulate, incubate, screen, and sort millions of samples, providing access to large number statistics that make searching for rare events feasible. Initial development of the microfluidic devices and methods has attracted applications in biology, biochemistry, and material science, but the set of tools remains incomplete. Efforts are required to develop micro-scale droplet analogs for all bulk-scale bench top procedures and instruments. The droplet analogs must be versatile, robust, and process samples rapidly.
Engineering and Applied Sciences

In this project we, for the first time, integrated microfluidics with thermo-plasmonics. While microfluidics is a popular platform allowing experiments with small volumes of fluid, thermo-plasmonics can be used for powerful particle manipulation including capturing, mixing, filtering and projection. Combined, these two techniques give us an opportunity to work with numerous complex fluids containing particles, cells, and micro-beads. Here we designed, developed and tested several devices demonstrating various aspects of this exciting hybrid technology. This required use of soft lithography, metal deposition, 3D printing, oxygen plasma treatment and several other surface modification techniques. Additional challenges were in the fabrication of a multi-layer chip with several types of surfaces binding at several interfaces. The detailed design optimization was conducted, and many characteristics of the microfluidic channel were varied. After that, optimal flow patterns were determined using high-quality syringe pumps. An experiment with the simultaneous flow of two colored solutions through the same microfluidic chip demonstrated controlled laminar flow with minimal mixing. Next, thermo-plasmonic experiments were conducted in optimized micro-fluidic channels. Efficient capturing of microbeads were demonstrated using low power green laser with a wavelength 532 nm. In future, these experiments have many important applications including separation of bacteria from blood on a microfluidic chip. This might help with treatment of sepsis, analysis of blood pathogens and better prescription of antibiotics.

Microfluidics has been emerging as a feasible platform technology with broad applications in chemical synthesis, food safety, environmental monitoring, and especially, biomedical diagnostics. As a promising off-channel platform with many intrinsic properties compatible with digital microfluidics, liquid marbles (LMs) play an important role for a range of biochemical applications, such as three-dimensional cell culture and polymerase chain reactions of nucleic acids. LMs are micro-scale liquid droplets encapsulated by a protective coating of hydrophobic micro- or nanoparticles. Due to the non-wetting property, LMs can move freely as an individual soft system on various solid and liquid surfaces with low friction. LMs, especially floating LMs, evaporate slower than bare droplets on a superhydrophobic surface while stably keeping their near-spherical shapes. In a LM, the porous solid coating isolates the liquid core from the external environment, which avoids cross-contamination, but enables an excellent permeability towards vapours. These features allow LMs to potentially serve as reservoirs, sensors, pumps and reactors at the microscale for versatile chemical and biological applications. To maximise the potentials and fulfil multiple microfluidic functions in sequence as a separate digital microfluidic platform, LMs need to be manipulated continuously via a reliable actuation scheme. However, no convenient, efficient and cost-effective manipulation method for controllable and automated transport of LMs is yet available. This thesis reports a novel and feasible manipulation technique for LMs, investigates the process of LM coalescence, explores different controlled marble motions, and finally generalises the boundary conditions for actuating LMs in practical applications using dynamic analysis and analytical modelling. In the thesis, the effect of dielectrophoresis was first applied to manipulate the movement of sessile and floating LMs. The dielectrophoretic (DEP) force produced in a highly inhomogeneous direct-current (DC) electric field was utilised to pick up and release sessile LMs to induce marble coalescence. The same method was used to drag, trap and position floating LMs. After a brief introduction to the research project, a systematic literature review on LM coalescence was provided. LM coalescence is essential to understand marble robustness, enabling LMs to serve as micromixers and microreactors. This chapter reviews the state-of-the-art studies focusing on the coalescence process of droplets and, more recently, of LMs. An overview was given on how droplet coalescence and LM coalescence can be induced using external fields. Subsequently, recent developments in manipulation schemes of LMs were discussed based on the nature of actuation energies, and LMs’ diverse applications in various chemical and biological assays were also summarised. The easy actuation and broad applications of LMs enable them to implement more functions in micro total analysis systems. A series of theoretical and experimental works were carried out after these two literature reviews to demonstrate the feasibility of dielectrophoresis for controlled manipulation of LMs. The coalescence process was studied for two identical sessile LMs in vertical collisions aided by DEP handling to elaborate the underlying mechanisms and critical conditions of LM coalescence. By experimentally varying marble volumes, impact velocities and offset ratios, it is concluded that LM coalescence may occur through the coating pore opening mechanism. High-speed imaging was used to investigate the dynamic behaviours of colliding LMs such as the radius change of the liquid bridge between two coalescing marbles, and to derive the generalised conditions of LM coalescence. Furthermore, the DEP method was extended to manipulating floating LMs that move on a free liquid surface with less evaporation. A relatively simple setup was used for dragging floating LMs of various sizes (2.5–30 mL) back and forth across the water surface at high speeds up to 30 mm s􀀀1, allowing for stirring and mixing inside LMs. The manipulation technique and the corresponding analytical model for predicting marble motions reported here potentially facilitate high-throughput and efficient handling of floating LMs containing sensitive biochemical samples. As trapping is essential for efficient sample handling, the investigation on trapping LMs is the key for understanding controlled transport of LM-based digital microfluidic platforms. Due to the simple actuation and the long lifespan, floating LMs are selected as the research object for the dynamic analysis. First, the trapping process of a floating LM utilising dielectrophoresis was experimentally and analytically investigated. Static LMs with volumes up to 50 mL could be effectively trapped by the attractive DEP force from a working distance up to 60 mm under applied voltages ranging from 1.6 to 5 kV. Based on the relationship between the static friction coefficient and the Bond number of floating LMs, operation maps showing critical trapping voltages were derived for successful trapping of the LMs. Next, the two-dimensional DEP trapping process of floating LMs was further investigated. The dynamic behaviours of moving LMs on a free water surface in trapping cases via spiral movements and escaping cases were analysed experimentally and theoretically. More importantly, a governing equation describing successful trapping was generalised from the energy balance. In addition, DEP handling technique could manipulate LMs with a complex electrode configuration. The concept of accurately positioning a floating LM using a pair of identical electrodes is presented. High voltages applied to each electrode generated a non-uniform electric field, which attracted the floating LM towards the corresponding electrode by a DEP force. The combined DEP forces from the electrode pair could accurately position the LM by controlling the voltages separately. The effects of electrode arrangements on positioning capability were also studied by measuring the relative position of the LM to the electrodes at different voltage ratios. An analytical model was formulated to describe the DEP forces of the two-electrode system and a governing equation that determines the LM position for various electrode configurations was then obtained. Besides, the effective working range of this setup and future work with three or more electrodes for positioning a floating LM in two dimensions were discussed. Finally, the thesis concludes with main findings of the research and some perspectives on future studies of LMs. The novel DEP manipulation approach reported in this thesis provides a greater versatility for practical applications of LM-based digital microfluidic platforms. The research outcomes contribute to enhancing the uptake of LM-based digital microfluidics in multidisciplinary research and to broadening the user base of this promising technology. It is expected that the DEP handling technique of LMs will enable the concept of “lab-in-a-marble” with multi-functional microfluidic modules.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Eng & Built Env
Science, Environment, Engineering and Technology
Full Text

Woven textile fabrics were designed and constructed from hydrophilic and hydrophobic spun yarns to give planar substrates containing amphiphilic microchannels with defined orientations and locations. Polypropylene fibers were spun to give hydrophobic yarns, and the hydrophilic yarns were spun from a poly(ethylene terephthalate) copolyester. Water wicking rates into the fabrics were measured by video microscopy and longitudinal wicking tests from single drops and from reservoirs. Intra-yarn microchannels in the hydrophilic polyester yarns were shown to selectively transport aqueous fluids, with the flow path governed by the placement of the hydrophilic yarns in the fabric. Simultaneous wicking of an aqueous and hydrocarbon fluid into the hydrophilic and hydrophobic microchannels of an amphiphilic fabric was successfully demonstrated. The high degree of interfacial contact and micron-scale diffusion lengths of such co-flowing immiscible fluid streams inside amphiphilic fabrics suggest potential applications as highly scalable and affordable microcontactors for industrial liquid-liquid extractions. The efficiency of liquid-liquid extractions carried out with the amphiphilic fabrics was evaluated. Solvent extraction efficiencies were shown to reach up to ~98%.

This work proposes a gas-liquid contactor study in microfluidics field, using dense membrane working with a concentration gradient; a microfluidic gas-liquid contactor was developed for CO2 removal and the general idea is to transport CO2 through a polymer dense membrane, followed by its capture by a liquid solvent with chemical absorption. Like recent studies demonstrate, this kind of devices could solve problems related to extracorporeal lung oxygenation (Garofalo, C. Quintavalle, G. Romano, C.M. Croce, 2013) for critical surgical support and critical care medicine, it can work like a real lung because can mimic the architecture of the human vasculature better than the existing technologies. Applications in this fields are related for example to the separation of Xenon from CO2 in anaesthesia. Xe is a very expensive element perfect for anaesthesia, is hemodynamically stable, low soluble in liquid and produces high regional blood flow reducing the risk of hypoxia (Malankowska et al., 2018). The major advantage of using microfluidics devices is that they could be reach a high surface to volume ratio and thanks to miniaturization can be tested reducing the time as well as the production of waste, thus increasing the number of experimental tests can be achieved. In the present thesis in particular one alveolar design channel based of literature results (Malankowska et al., 2018) was realized with soft lithography and tested in different experimental conditions. In particular, for the present geometry the transport of CO2 through the membrane was monitored, calculating the overall mass transfer coefficient and the molar flow of the gas through the membrane in different operating conditions. In additions, the production of other two microfluidics device with different channels configurations was attempted by using a 3-D printing technique that allows the generations of complex structures with high surface to volume ratio.

In this thesis, the mechanical characterization of thin films, bulk materials, compliant MEMS and Microfluidics has been discussed. In chapter1 and chapter 2, the Indentation Size Effect (ISE) has been studied for single crystal aluminum and the substrate effect has also been studied for 200 nm gold film on mica substrate and 50 nm gold film on (100) silicon wafer substrate. The mechanical characterization of super hard SiC films (prepared by CVD) has also been discussed. In chapter 3, the actuation of compliant MEMS devices with a nanoindentation apparatus has been investigated. Friction forces become important at the device level, and the conical tip always makes a crack at the edge of the sliders, thus the slider design needs to be optimized to account for the probe geometry. In chapter 4, the measurement of electrowetting has been outlined. The "airscratch" mode was used to capture the lateral force and normal force during an electrowetting test. With the appearance of surface delamination on the solid surface, the unexpected normal forces can been measured.

The work in the dissertation expands the applications of DIEF and describes the development of incorporating DIEF in a microfluidic chip to create a comprehensive proteomics tool. Proof-of-concept DIEF experiments have been done previously, so the focus of this work is to explore the capabilities of DIEF. Dynamic isoelectric focusing (DIEF) is a separation technique invented by Dr. Luke Tolley. It is similar to capillary isoelectric focusing except it uses four high voltage electrodes to form a pH gradient instead of only two. The additional two electrodes are able to manipulate the pH gradient resulting in selection of the region and of the range of pH within a pre-defined sampling or extraction point. One of the first applications described for DIEF was to isolate a single protein from a complex mixture. The protein isolated was a cellulase enzyme capable of degrading multiple cellulose materials over a wide range of environmental conditions. DIEF did isolate the protein in a pH span of 0.005 which is equivalent to 0.075% of the total pH range. Fractions were collected for sequencing analysis, but the fractions were contaminated with keratin both times. DIEF was also successfully performed in an open air channel. Though other electromigration techniques have been successfully done in open air channels, these techniques were severely time and pH limited. In contrast, DIEF in an open air channel is capable of using the entire 3-10 pH range and can perform isolations until the proteins are completely separated. The device developed was also an improvement on increasing sample capacity. The channel was significantly bigger than the traditional glass capillaries used. Since the channel was open, fraction collection was made simpler by collecting using a pipette. This work also demonstrated that DIEF can be made through the use of silicone molding compounds and polyurethane. The amount of milling needed is reduced, the pieces are produced quickly, and a single mold can produce several pieces. Machining pieces with fragile bits is not needed to be done as much since only one acrylic piece is required produce a mold. The mold can produce several polyurethane pieces. This fabrication method has proven useful for making DIEF holders. The next step was to make DIEF a truly comprehensive proteomic tool by incorporating it into a microfluidic chip. Multiple sample fractions are rapidly generated on chip through the use of multiple bubbles simultaneously injected into the separation channel. This stops the separation and, since each droplet is isolated from others by a bubble on each side, the protein peaks are not able to broaden. This novel use of digital microfluidics is still a work in progress, but the fundamentals have been demonstrated. The fabrication protocol for making molds and PDMS casts was developed using materials and procedures that can be done in a common laboratory environment. DIEF is a separation technique still in its infancy, with a wide variety of available applications. DIEF will continue to be tested in other areas and developed into a comprehensive proteomic tool.

Magnetic particles with active functional groups offer numerous advantages for use in μ-TAS (Micro Total Analytical Systems). The functional site allows chemical binding of the particle with the target species in the fluid sample. Selection of the functional group establishes the target molecule and vice versa under assumptions of highly specific biding. The particles hence act as mobile reaction substrates with high surface to volume ratios owing to their small size. The concept of action at a distance allows their use as agents for separation in microchannels based on relatively simple design. It is possible to manipulate magnetic particles and bound target species using an externally applied magnetic field. Hence, the particles can be effectively separated from the flow of a carrier fluid. Magnetic fields create dipolar interactions causing the particles to form interesting structures and aggregates. Depending upon the applied field, the microstructure evolution of the aggregate is interesting in its own right, e.g. related to improvements in material properties and bottom-up self assembly. The shape of the aggregates can be determined a priori if the interaction between the particles is well characterized. The dominant competing forces that influence magnetic particle dynamics in a flow are magnetic and viscous. There are a number of physical parameters such as viscosity, magnetic susceptibility, fluid velocity, etc. which are varied to study their individual effects. Initially dilute suspensions are studied experimentally and numerically using a particle based dynamics approach. Once established, a force model for particle interaction is investigated for concentrated suspensions. A Lagrangian particle tracking algorithm that returns positions of the particles is used for this work that focuses on studying the dynamics of these particles. A mathematical model is proposed and investigated for functionalization between magnetic and non-magnetic particles. Having characterized the collection of magnetic particles, the effect of relative concentrations is investigated on the collection of the non-magnetic species.
Ph. D.

This thesis is concerned with computational methods for fluid flows on the microscale, also known as microfluidics. This is motivated by current research in biological physics and miniaturization technology, where there is a need to understand complex flows involving microscale structures. Numerical simulations are an important tool for doing this. The first, and smaller, part of the thesis presents a numerical method for simulating multiphase flows involving insoluble surfactants and moving contact lines. The method is based on an interface decomposition resulting in local, Eulerian grid representations. This provides a natural setting for solving the PDE governing the surfactant concentration on the interface. The second, and larger, part of the thesis is concerned with a framework for simulating large systems of rigid particles in three-dimensional, periodic viscous flow using a boundary integral formulation. This framework can solve the underlying flow equations to high accuracy, due to the accurate nature of surface quadrature. It is also fast, due to the natural coupling between boundary integral methods and fast summation methods. The development of the boundary integral framework spans several different fields of numerical analysis. For fast computations of large systems, a fast Ewald summation method known as Spectral Ewald is adapted to work with the Stokes double layer potential. For accurate numerical integration, a method known as Quadrature by Expansion is developed for this same potential, and also accelerated through a scheme based on geometrical symmetries. To better understand the errors accompanying this quadrature method, an error analysis based on contour integration and calculus of residues is carried out, resulting in highly accurate error estimates.
Denna avhandling behandlar beräkningsmetoder för strömning på mikroskalan, även känt som mikrofluidik. Detta val av ämne motiveras av aktuell forskning inom biologisk fysik och miniatyrisering, där det ofta finns ett behov av att förstå komplexa flöden med strukturer på mikroskalan. Datorsimuleringar är ett viktigt verktyg för att öka den förståelsen. Avhandlingens första, och mindre, del beskriver en numerisk metod för att simulera flerfasflöden med olösliga surfaktanter och rörliga kontaktlinjer. Metoden är baserad på en uppdelning av gränsskiktet, som tillåter det att representeras med lokala, Euleriska nät. Detta skapar naturliga förutsättningar för lösning av den PDE som styr surfaktantkoncentrationen på gränsskiktets yta. Avhandlingens andra, och större, del beskriver ett ramverk för att med hjälp av en randintegralformulering simulera stora system av styva partiklar i tredimensionellt, periodiskt Stokesflöde. Detta ramverk kan lösa flödesekvationerna mycket noggrant, tack vare den inneboende höga noggrannheten hos metoder för numerisk integration på släta ytor. Metoden är också snabb, tack vare den naturliga kopplingen mellan randintegralmetoder och snabba summeringsmetoder. Utvecklingen av ramverket för partikelsimuleringar täcker ett brett spektrum av ämnet numerisk analys. För snabba beräkningar på stora system används en snabb Ewaldsummeringsmetod vid namn spektral Ewald. Denna metod har anpassats för att fungera med den randintegralformulering för Stokesflöde som används. För noggrann numerisk integration används en metod kallad expansionskvadratur (eng. Quadrature by Expansion), som också har utvecklats för att passa samma Stokesformulering. Denna metod har även gjorts snabbare genom en nyutvecklad metod baserad på geometriska symmetrier. För att bättre förstå kvadraturmetodens inneboende fel har en analys baserad på konturintegraler och residykalkyl utförts, vilket har resulterat i väldigt noggranna felestimat.

QC 20160427

The use of biosensors and microfluidics devices is often limited by constraints in terms of volumetric throughput due to the small dimensions of devices in microfluidics and of expensive and complicated sample preparation steps necessary to ensure the operation of biosensing platforms. This can be due to high initial sample volume with low concentration analytes or complex media matrices from which analytes are extracted. While working to analyse Cryptosporidium presence in drinking water a novel technique was developed. The huge advantages from using a label-free, buffer-free hydrodynamic mechanism in terms of cost, coupled with the ease of simply scaling a single design to match any target size and the ability manufacture these quickly and easily using cheap and readily available robust materials (i.e. acrylic sheet) may allow a revolution in the scope of microfluidics applications. Using a cascaded array of hydrodynamic focusing devices uniquely designed for parallelised operation from a single pump or pressure source, the array can be tailored to meet the specific requirements of many applications, in particular high volume and low concentration target analyte enrichment from complex media.

Optical manipulation covers a wide range of techniques to guide and trap cells using only the forces exerted by light. Another optical tool is photoporation, the technique of injecting membrane-impermeable molecules using light, which has become an important alternative to other injection techniques. Together they provided sterile tools for manipulation and molecule delivery at the single-cell level. In this thesis, the properties of low Reynolds fluid flows are exploited to guide cells though a femtosecond Bessel beam. This design allows for high-throughput optical injection of cells without the need to individually target cells. A method of 'off-chip' hydrodynamic focusing was evaluated and was found to confine 95.6% of the sample within a region which would receive a femtosecond dose compared to 20% without any hydrodynamic focusing. The system was tested using two cell lines to optically inject the membrane-impermeable dye, propidium iodide. This resulted in an increase of throughput by an order of magnitude compared to the previous microfluidic design (to up to 10 cells per second). Next optical trapping and photoporation were combined to create a multimodal workstation. The system provides 3D beam control using spatial light modulators integrated into a custom user interface. The efficiency of optical injection of adherent cells and trapping capabilities were tested. The development of the system provides the groundwork for exploration of the parameters required for photoporation of non-adherent cells. Finally optical trapping is combined with temporally focused multiphoton illumination for scanless imaging. The axial resolution of the system was measured using different microscope objectives before imaging cells stained with calcein. Both single and a pair of recently trypsinised cells were optically trapped and imaged. The position of the trapped cells was manipulated using a spatial light modulator in order to obtain a z-stack of images without adjusting the objective position.

Cette thèse traite le développement de dispositifs, basés sur la technologie "laboratoire sur puce"(LOC) qui visent à contrôler l'environnement des systèmes biologiques pour des applications macro et microbiologiques. En effet, les caractéristiques de la microfluidique permettent de manipuler l'environnement cellulaire à un niveau supérieur à celui du degré de contrôle atteignable avec les techniques ordinaires. Dans ce travail de thèse sera explorée la possibilité de profiter de ces fonctions afin de développer des outils de diagnostic peu coûteux et pourtant efficaces. En particulier, on rapporte le développement de systèmes microfluidiques permettant une perfusion des médias fluide et rapide, ainsi qu'une plateforme LOC capable de réaliser des PCRq hautement multiplexes. Au sujet des systèmes de perfusion, le but était d'obtenir une substitution du médium entourant les particules afin d'augmenter les capacités de séparation des modules de tri microfluidiques couplés. L'efficacité de notre approche a été validée par les hauts taux de séparation obtenus (>90%) avec l'utilisation de notre système de perfusion microfluidique couplé à une puce d'acoustophorèse. De plus, nous avons conçu et développé un système de thermalisation microfluidique capable d'opérer des changements de température en moins de 1s. Plus spécifiquement, cette plateforme exploite l'échange de chaleur entre un liquide de thermalisation qui circule dans une puce microfluidique et l'échantillon. Ces performances de thermalisation, et le rapport surface/volume élevé typique des appareils microfluidiques, ont permis d'effectuer 50 cycles de PCRq et l'analyse de courbe de fusion en moins de dix minutes
The topic of this manuscript is the development of microdevices, based on "lab on chip" (LOC) technology, aimed to the environmental control and regulation of biological systems for macro and microbiological applications. Indeed, microfluidics possesses some inherent features which allow the manipulation of the environment at the cell and sub-cell level which are superior than the degree of control achievable with standard techniques. In this thesis work the possibility to leverage these features to develop inexpensive yet effective diagnostic tools is explored. In particular, we report the development of microfluidic systems which allow seamless and fast media perfusion and a novel LOC platform capable of performing highly multiplexed real-time PCR assays. Concerning the microfluidic perfusion systems, the aim was to achieve in-flow substitution of the particles' surrounding media in order to enhance the separation capabilities of the coupled microfluidic sorting modules. The effectiveness of our approach was validated by obtaining high separation purities (>90%) using our microfluidic perfusion system coupled with an acoustophoresis chip to discern two population of micro-sized beads. Moreover, we conceived and developed a microfluidic thermalisation system capable of sub-second temperature switches. Specifically, this platform relies on conductive heat exchange between a thermalisation liquid flowing inside a microfluidic chip and the biological sample. These thermalisation performances, and the high surface to volume ratio typical of microfluidic devices, allowed to perform 50 qPCR cycles and subsequent melting curve analysis in less than ten minutes

Optical microlasers have been used in different engineering fields and for sensing various applications. They have been used in biomedical fields in applications such as for detecting protein biomarkers for cancer and for measuring biomechanical properties. The goal of this work is to propose a microfluidic-based fabrication method for fabricating optical polymer based microlasers, which has advantages, over current methods, such us the fabrication time, the contained cost, and the reproducibility of the microlaser's size. The microfluidic setup consisted of microfluidic pumps and a flow focusing droplet generator chip made of polydimethylsiloxane (PDMS). Parameters such as the flow rate (Q) and the pressure (P) of both continuous and dispersed phases are taken into account for determining the microlaser's size and a MATLAB imaging tool is used to reduce the microlaser's diameter estimation. In addition, two applications are discussed: i) electric field measurements via resonator doped with Di-Anepps-4 voltage sensitive dye, and ii) strain measurements in a 3D printed bone-like structure to mimic biomedical implantable sensors.

Les progrès récents des capteurs interférométriques basés sur la réinjection optique dans une diode laser ont démontré la possibilité de mesurer des débits d’écoulements et des profils de vitesses d’écoulement à l'échelle micrométrique. Ce type de capteurs compacts et intégrés est très prometteur pour un domaine - la microfluidique - qui est en expansion, aux frontières de la physique, de la chimie, de la biologie et du biomédical. Cependant, la mesure du débit ou de la vitesse locale en haute résolution reste un problème très complexe et les capteurs proposés jusqu’à présent n’ont pas fourni d’informations sur la nature des particules qui s’écoulent. La présente thèse porte sur la mise en œuvre, la validation et l'évaluation des performances de détection de la technologie OFI dans les domaines d'applications chimiques et biomédicaux. L'élaboration d'une nouvelle génération de capteurs qui fourniront à la fois une haute résolution spatiale pour l’imagerie Doppler 2D est présentée ainsi qu’une approche novatrice permettant de fournir des informations supplémentaires sur la concentration et / ou les dimensions des particules en mouvement. Ensuite, un imageur Doppler par réinjection optique, embarqué dans un système compact pour la débitmétrie a été réalisé à l'aide d'un micro-miroir monté sur des systèmes microélectromécaniques (MEMS), tirant ainsi pleinement parti de la compacité offerte par le système de détection par réinjection optique. Alors que les travaux précédents sur la débitmétrie par réinjection optique ont été limités aux fluides à haute densité de particules dans des régimes de diffusion simples ou multiples, nous présentons également une technique permettant la détection de particules uniques de dimensions micro et nanométriques à travers l'effet Doppler-Fizeau. Grâce au traitement du signal proposé, cette technique de détection peut détecter la présence de micro/nanosphères de polystyrène sphériques uniques ensemencées dans des suspensions aqueuses et mesurer leur vitesse d'écoulement, même lorsque leur diamètre est inférieur à la moitié de la longueur d'onde du laser. Cette méthode présente de nombreux avantages par rapport aux méthodes habituelles qui nécessitent une manipulation du fluide, dans des volumes toujours plus petits avec un contrôle précis du débit et de la concentration. L’ensemble des aspects traités dans cette thèse représente une avancée majeure pour l’utilisation des capteurs par réinjection dans les applications d’ingénierie chimique ou biomédicale implicant des écoulements à micro-échelle
Recent progress of interferometric sensors based on the optical feedback in a laser diode have demonstrated possibility for measurement of flow rates and flow-profiles at the micro-scale. That type of compact and embedded sensors is very promising for a research and industrial field –microfluidics – that is a growing domain of activities, at the frontiers of the physics, the chemical science, the biology and the biomedical. However, the acquisition of flow rate or local velocity at high resolution remains a very challenging issue, and the sensors that have been proposed so far did not have been giving sufficient information on the nature of the particles flowing. The present thesis is driven to the implementation, validation and evaluation of the sensing performances of the optical feedback interferometry technology in both chemical and biomedical fields of applications. The elaboration of a new generation of sensors that will provide both a high spatial resolution for 2D Doppler imaging is presented, as well as a methodology that gives further information on the flowing particles concentration and/or dimensions. Then, a new embedded optical feedback interferometry imager for flowmetry has been realized using a 2-axis beamsteering mirror mounted on Micro-Electro-Mechanical Systems (MEMS) thus taking the full advantage of the compactness offered by the optical feedback interferometry sensing scheme. While previous works on optical feedback interferometry flowmetry have been limited to high particle densities fluids in single or multiple scattering regimes, we present also a sensing technique based on the optical feedback interferometry scheme in a laser diode that enables single particle detection at micro and nanoscales through the Doppler-Fizeau effect. Thanks to the proposed signal processing, this sensing technique can detect the presence of single spherical polystyrene micro/nanospheres seeded in watery suspensions, and measure their flow velocity, even when their diameter is below half the laser wavelength. It discriminates particle by their diameter up to a ratio of 5 between large and small ones while most of the technologies for particle characterization is bulk and requires manipulation of the fluid with small volume handling, precise flow and concentration control. Altogether, the results presented in this thesis realize a major improvement for the use of optical feedback interferometry in the chemical engineering or biomedical applications involving micro-scale flows

Surface acoustic wave (SAW) devices based on the piezoelectric principle have been used extensively in telecommunication applications over the last 20 years, but have recently shown promise in the area of biomedical applications due to their efficient micro-fluidic functions and highly sensitive and label-free detection of pathogens, bacteria, cells, DNA and proteins. There are two types of surface acoustic wave modes: i.e., Rayleigh SAW (R-SAW) and shear horizontal SAW (SH-SAW). R-SAW is widely used for microfluidics and sensing in dry conditions, whereas SH-SAW is mainly used for sensing in liquid conditions. This thesis firstly reviewed the current theoretical and research progress related to these devices and application within the biomedical fields to date, and then the SH-SAW was applied into a novel lab-on-chip combining both bio-sensing and micro-fluidic functions. Simulations of the SH-SAW propagation on 36o Y-cut LiTaO3 were undertaken. Results showed a weak vertical wave component, and at a 90° rotation cut, the crystal was able to support a vertical Rayleigh component showing mixed sensing and streaming possibilities on a single crystal. Experimental investigation of the SH-SAW identified the ability for the shear wave to support mixing, pumping, heating, nebulisation and ejection of sessile droplets on the surface of the crystal with a theoretical explanation for the behaviour presented. A comparison with a standard R-SAW devices made of 128o Y-cut LiNbO3 and sputtered ZnO films was performed. This novel behaviour of digital microfludics, i.e., using sessile droplet with the SH-SAW, demonstrated by this work offers the possibility to manufacture a fully integrated micro-fluidic bio-sensing platform using a single crystal to realise a range of micro-fluidic functions.

This thesis describes the use of proton beam writing (PBW) for the fabrica- tion for microfluidic and microelectromechanical system (MEMS) devices. In particular, the fabrication of three-dimensional (3D) micro or nanostruc- tures with high aspect ratios is of growing interest in these fields. PBW is the only technique that has the capability to satisfy these requirements while providing full control of the geometrical parameters, such as the sur- face roughness and side wall angle. This technique is a direct microfabri- cation method that employs a focused, energetic (MeV) proton beam to structure the input pattern in resist materials. In the present work, a network of buried channels is fabricated as part of a project to develop a functional microfluidic device for neuronal studies and self-powered microfluidics (capillary micropump). Proton beam with energies of 0.75 to 2.5 MeV is used to fabricate the channels in 3D with a minimum feature size of approximately 1 μm and depths of 40 to 60 μm. The roughness of the sidewalls of the written channels is approximately 3 nm root mean square roughness (Rrms). Radio frequency (RF) MEMS switches, which consist of an overhanging structure, are also written using PBW, and new MEMS switch designs are proposed. These designs are constructed so as to provide full control of the main cantilever beam parameters, such as the thickness, spring constant, and actuation. The three main stages of the lithography process, i.e., pre-exposure, expo- sure, and post-exposure, are investigated and optimised for application to poly(methyl methacrylate)(PMMA), pure SU-8 polymer, and SU-8/silver- nanoparticle nanocomposites (SU-8/AgNp). During the exposure process, the proton beam energies, doses, and scanning method are also optimised, in order to attain a good-quality structure (i.e., a robust structure with smooth and straight walls). The mechanical and electrical properties of the nanocomposites, which are irradiated with a range of proton beam doses, are measured. Note that the structures written in this work are numerically validated prior to the writing process using COMSOL Multiphysics �R software. The fluid flow in the written buried channels is investigated using numerical methods.

Microfluidic biosensors and bioreactors based on immobilized biomaterials are described in this dissertation. Photocrosslinkable hydrogel or polymeric microbeads were used as a supporting matrix for immobilizing E.coli or enzymes in a microfluidic device. This dissertation covers a microfluidic bioreactor based on hydrogel-entrapped E.coli, a microfluidic biosensor based on an array of hydrogel-entrapped enzymes, and a microfluidic bioreactor based on microbead-immobilized enzymes. Hydrogel micropatches containing E.coli were fabricated within a microfluidic channel by in-situ photopolymerization. The cells were viable in the hydrogel micropatch and their membranes could be porated by lysating agents. Entrapment of viable cells within hydrogels, followed by lysis, could provide a convenient means for preparing biocatalysts without the need for enzyme extraction and purification. Our results suggested that hydrogel-entrapped cells, immobilized within microfluidic channels, can act as sensors for small molecules and as bioreactors for carrying out reactions. A microfluidic biosensor based on an array of hydrogel-entrapped enzymes could be used to simultaneously detect different concentrations of the same analyte or multiple analyte in real time. The concentration of an enzyme inhibitor could be quantified using the same basic approach. Isolations of the microchannels within different microfluidic channels could eliminate the possibility of cross talk between enzymes. Finally, we characterized microfluidic bioreactors packed with microbead-immobilized enzymes that can carry out sequential, two-step enzyme-catalyzed reactions under flow conditions. The overall efficiency of the reactors depended on the spatial relationship of the two enzymes immobilized on the beads. Digital simulations confirmed the experimental results.

The goal of this research was to develop acoustic sensors and actuators for microfluidic applications. To this end, capacitive micromachined ultrasonic transducers (cMUTs) were developed which generate guided acoustic waves in fluid half-spaces and microchannels. An interdigital transducer structure and a phased excitation scheme were used to selectively excite guided acoustic modes which propagate in a single lateral direction. Analytical models were developed to predict the geometric dispersion of the acoustic modes and to determine the sensitivity of the modes to changes in material and geometric parameters. Coupled field finite element models were also developed to predict the effect of membrane spacing and phasing on mode generation and directionality. After designing the transducers, a surface micromachining process was developed which has a low processing temperature of 250C and has the potential for monolithically integrating cMUTs with CMOS electronics. The fabrication process makes extensive use of PECVD silicon nitride depositions for membrane formation and sealing. The fabricated interdigital cMUTs were placed in microfluidic channels and demonstrated to sense changes in fluid sound speed and flow rate using Scholte waves and other guided acoustic modes. The minimum detectable change in sound speed was 0.25m/s, and the minimum detectable change in flow rate was 1mL/min. The unique nature of the Scholte wave allowed for the measurement of fluid properties of a semi-infinite fluid using two transducers on a single substrate. Changes in water temperature, and thus sound speed, were measured and the minimum detectable change in temperature was found to be 0.1C. For fluid pumping, interdigital cMUTs were integrated into microchannels and excited with phase-shifted, continuous wave signals. Highly directional guided waves were generated which in turn generated acoustic streaming forces in the fluid. The acoustic streaming forces caused the fluid to be pumped in a single, electronically-controlled direction. For a power consumption of 43mW, a flow rate of 410nL/min was generated against a pressure of 3.4Pa; the thermodynamic efficiency was approximately 5x10-8%. Although the efficiency and pressure head are low, these transducers can be useful for precisely manipulating small amounts of fluid around microfluidic networks.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2005.
Includes bibliographical references (leaves 123-125).
Microfluidics, microfabricated suspended heaters and electronic field effect sensors have been successfully integrated on a single device chip. This integration enables spatial cycling of as little as 11nL of reagents over different thermally isolated temperature zones, to be coupled with the field effect sensing capabilities, for label-free detection of biomolecules such as DNA. The microfluidic valves provide control over reagent flow, and flow rates of up to 1.8nLs⁻¹ have been demonstrated with the on-chip pumps. Initial characterization of the suspended heaters was successfully carried out using thermochromic crystals. Functionality of the heaters was shown and a rough calibration was obtained. The subsequent implementation of temperature measurement using fluorescent dyes, enabled real-time spatial temperature mapping. This method demonstrated the capability of monitoring fluid temperatures in microfluidic channels with 5̊C accuracy at 2[mu]m² resolution. Thermal isolation of the suspended heaters was clearly observed from the steep gradients in the spatial temperature profiles captured. Finally, localized boiling of water in the microfluidic channels was achieved, with only 30mW supplied to the heaters. In order to evaluate the sensors, tests were carried out to determine its sensitivity to surface charge. Buffer solutions of different pH were injected, and the sensors have been able to measure pH values ranging from 2.2 - 7.4 and demonstrate sensitivity of up to 38.8mV per pH unit change. Highly charged poly-electrolytes were also investigated as model systems to validate sensor detection of charged biomolecules.
(cont.) The adsorption and layer-by-layer deposition of multiple poly-electrolyte layers to the sensor surface have been successfully detected. This device paves the way for future integration of multiple microfluidic compo- nents, for lab-on-a-chip applications.
by Tzu Liang Loh.
S.M.

This thesis focuses on fundamental aspects of microfluidic systems and applies relevant findings to innovative designs for advanced particle manipulation applications. Computational Fluid Dynamics (CFD) is adopted for fluid modeling, based on the Finite Volume method. The accuracy of the solutions obtained is confirmed by grid sensitivity analysis and by comparisons with experimental work. Curved microchannel features and the induced Dean flow are studied through a parametric space exploration and simulations. The Lagrange-Euler coupling method – Surface Marker Point methodology – is applied to simulate large-size particles (of comparable size to the channel). Through this simulation approach, all the forces on such particles are directly derived through solving the governing equations and the influence of these particles on the flow is considered in a fully coupled manner. A new approach – the Frozen Flow & Flow Correction Coefficient method – is developed, making trans-relaxation-time simulations possible and improving computational efficiency significantly, for 3D simulations of arbitrary shape and size microparticles in complicated microfluidic channels. Detailed comparisons between simulation results and experiments involving particle sedimentation and particle equilibrium position have been conducted for methodology validation. Mechanisms of hydrodynamic particle manipulation are then studied, including hydrodynamic focusing and separation. It is found that the Tubular Pinch effect, Dean flow and the Radial Pressure Gradient effect interact to yield two distinct particle separation mechanisms. For advanced applications, particle focusing, non-magnetic and magnetic separation for neutrally buoyant particles are proposed, based on newly gained insight on the above-mentioned mechanisms. Appropriate channel designs have been proposed both for particle focusing and size-based particle separation, while the vertical-magnetic-Dean separation scheme is highlighted for magnetic separation. Finally, a new integrated system is proposed, that combines the above novel designs into a device-like ensemble. It promises to offer functionality for biomaterial separation and detection, including different types of cells, antigens and biomarkers.

Le phage display est une méthode généralement utilisée pour l'évolution dirigée de protéines, elle permet de produire une immense diversité de variants de protéines exprimés sur la membrane de particules virales. Ces variants de protéines peuvent être sélectionnés soit pour leur affinité de liaison (p. Ex. Les anticorps) soit pour leur activité catalytique (p. Ex. Les enzymes). La sélection d'enzymes pour leur activité catalytique requiert néanmoins l'utilisation de substrats et/ou produits immobilisés, ce qui empêche la sélection de protéines sur plusieurs cycles catalytiques. Le but de ce projet de thèse était de développer une méthode nous permettant d'outrepasser ces limites : la compartimentation dans des systèmes microfluidiques de particules virales exprimant des variants de protéines unique sur leur surface. L'encapsulation de ces particules dans des gouttes nous a permit d'utiliser des substrats/produits solubles et donc la sélection pour de multiples cycles catalytiques a été possible. L'utilisation d'un système d'expression mammifère a permit aux protéines de subir les modifications post-traductionnelles (ponts disulfure, glycosylations) nécessaires. Ce système permet de monitorer l'activité enzymatique, de variants de protéines uniques d'une banque, exprimés sur la membrane de particules virales. En plus, nous avons développé un système nous permettant de trier des virus en utilisant comme critère la présence ou l'absence d'activité enzymatique
Phage display is a widely used method for directed evolution of proteins, allowing the generation of an enormous diversity of protein variants displayed on the viral particles (library diversity <1012). These protein variants can then either be selected for binding affinity (e. G. Antibodies) or for catalytic activity (e. G. Enzymes). However, since selection for catalytic activity requires immobilized substrates and/or products, selection for multiple turnover or maximum rate acceleration remains challenging. To overcome these limitations a new method has been developed: Microfluidic-based compartmentalisation of viral particles displaying single protein variants on their surface. Encapsulation of these particles into picoliter drops allows the use of soluble substrates/products and therefore the selection for multiple turnover. The model system used here is based on retroviral particles displaying tPA (tissue plasminogen activator), a protein used in current emergency therapies of myocardial infarction and stroke, and a non-related control protein (neuraminidase, NA, inactive particles). Single particles displaying tPA and NA variants were encapsulated into aqueous droplets and the enzymatic activity was monitored using a fluorescence assay. Active variants could be sorted from a mixture of active and inactive variants

Magnetic micro-robots are small robots under 1mm in size, made of magnetic materials, with relatively simple structures and functionalities. Such micro-robots can be actuated and controlled remotely by externally applied magnetic fields, and hence have the potential to access small and enclosed spaces. Most of the existing magnetic micro-robots can operate in wet environments. When the robots are actuated by the applied magnetic field to move inside a viscous liquid, they invoke flow motions around them inside the liquid. The induced flows are relatively local as the velocity of these flows decays rapidly with the distance from a moving robot, and the flow patterns are highly correlated with the motions of the micro-robots which are controllable by the applied magnetic field. Therefore, it is possible to generate local flow patterns that cannot be easily done using other microfluidic techniques. In this work we propose to use rotational motion of the magnetic micro-robots for local manipulation of flows. We employ electromagnetic techniques to successfully deliver actuation and motion control onto the micro-robots. Rotational magnetic field is applied to induce rotational motion of micro-robots both when they stay near a surface and are suspended in the liquid. Rotational flows are locally generated in the vicinity of micro-robots inside the viscous liquid. Implementation of three major applications using the flows generated by the rotating micro-robots are demonstrated in this work: 1) Two-dimensional (2D) non-contact manipulation of micro-objects. 2) Three-dimensional (3D) propulsion for the micro-robot to swim in a liquid. 3) Size-based sorting of micro-particles in microfluidic channels under continuous flow. The first two applications occur in otherwise quiescent liquid, while the third requires the presence of non-zero background flow. For the first application, we propose two methods to achieve precise positioning of the microrobots on a surface: 1) Using visual-feedback-control to adjust the rotation for one single microrobot. Micro-robot can be precisely positioned at any location on a surface using this method. 2) Using a specially prepared surface with magnetic micro-docks embedded in it, which act as local magnetic traps for multiple micro-robots to hold their positions and operate in parallel. Physical models are established for both the micro-robot and the micro-objects present in the induced rotational flow. The rotational flows induced by rotating micro-robots are studied with numerical simulations. Experimental demonstrations are first given at sub-millimeter scale to verify the proposed method. Micro-manipulation of polymer beads is performed with both positioncontrol methods. Automated micro-manipulation is also achieved using visual-feedback. Micromanipulation at micron-scale is then performed to demonstrate the scalability and versatility of the proposed method. Non-contact manipulation is achieved for various micro-objects, including biological samples, using a single spherical micro-robot. Inspired by flagellated microorganisms in nature, we explore the hydrodynamics of an elastic rod-like structure - the artificial flagellum, and verify by both simulation and experiments that rotation and deformation of such structure can result in a propulsive force on a micro-robot it is attached to. Optimization of flagellum geometry is achieved for a single flagellum. A swimming micro-robot design with multiple flexible flagella is proposed and fabricated via an inexpensive micro-fabrication process involving photolithography, micro-molding and manual assembly. Experiments are perform to characterize the propulsive force generation and the resulting swimming performance of the fabricated micro-robots. It is demonstrated that the swimming speed can be improved by increasing the number of attached flagella. For the size-based sorting application, we integrate the micro-robots into microfluidic channels by using the substrate embedded with magnetic micro-docks, which are capable of holding the robots under continuous flow inside the channels while the robots spin. Numerical analysis is carried out of the flows inside the microfluidic channel in the presence of rotating micro-robots, and a physical model is established and discussed for size-based lateral migration of spherical micro-objects inside the induced rotational flows. Experimental demonstrations are performed for using the induced rotational flows to divert the trajectories of micro-particles based on their sizes under continuous flow. In addition, we propose the method of using the two photon polymerization (TPP) technique to fabricate magnetic micro-robots with complex shapes. The method could also achieve fabrication of arrays of micro-robots for more sophisticated applications. However, experimental results prove that the TPP is insufficient to achieve magnetic micro-robots that meet our needs for size-based sorting application due to physical limitations of the materials. Despite that, it is potentially powerful and suitable for fabrication of micro-robots with complex structures at small scales.

Many scientists and engineers are turning to lab-on-a-chip systems for cheaper and high throughput analysis of chemical reactions and biomolecular interactions. In this work, we developed several lab-on-a-chip modules based on novel manipulations of individual microbeads inside microchannels. The first manipulation method employs arrays of soft ferromagnetic patterns fabricated inside a microfluidic channel and subjected to an external rotating magnetic field. We demonstrated that the system can be used to assemble individual beads (1-3µm) from a flow of suspended beads into a regular array on the chip, hence improving the integrated electrochemical detection of biomolecules bound to the bead surface. In addition, the microbeads can follow the external magnet rotating at very high speeds and simultaneously orbit around individual soft magnets on the chip. We employed this manipulation mode for efficient sample mixing in continuous microflow. Furthermore, we discovered a simple but effective way of transporting the microbeads on-chip in the rotating field. Selective transport of microbeads with different size was also realized, providing a platform for effective sample separation on a chip. The second manipulation method integrates magnetic and dielectrophoretic manipulations of the same microbeads. The device combines tapered conducting wires and fingered electrodes to generate desirable magnetic and electric fields, respectively. By externally programming the magnetic attraction and dielectrophoretic repulsion forces, out-of-plane oscillation of the microbeads across the channel height was realized. Furthermore, we demonstrated the tweezing of microbeads in liquid with high spatial resolutions by fine-tuning the net force from magnetic attraction and dielectrophoretic repulsion of the beads. The high-resolution control of the out-of-plane motion of the microbeads has led to the invention of massively parallel biomolecular tweezers.

Immune cell migration and chemotaxis plays a key role in immune response. Further research to study the mechanisms of immune cell migration and to develop clinical applications requires advanced experimental tools. Microfluidic devices can precisely apply chemical gradient signals to cells, which is advantageous in quantifying cell migratory response. However, most existing microfluidic systems are impractical to use without specialized facilities and research skills, which hinders their broad use in biological and medical research communities. In this thesis, we integrated several new developments in microfluidic gradient generating devices, compact imaging systems, on-chip cell isolation, cell patterning, and rapid data analysis, to provide an easy-to-use and practical solution for immune cell migration and chemotaxis experiments. Using these systems, we quantitatively studied neutrophil migration for both research and clinical applications. First, we developed a compact USB microscope-based Microfluidic Chemotaxis Analysis System (UMCAS), which integrates microfluidic devices, live cell imaging, environmental control, and data analysis to provide an inexpensive and compact solution for rapid microfluidic cell migration and chemotaxis experiments with real-time result reporting. To eliminate the lengthy cell preparation from large amounts of blood, we developed a simple all-on-chip method for magnetic isolation of untouched neutrophils directly from small volumes of blood, followed by chemotaxis testing on the same microfluidic device. Using these systems, we studied neutrophil migration in gradients of different chemoattractants, such as interleukin-8 (IL-8), N-formyl-methionyl-leucyl-phenylalanine (fMLP), and clinical sputum samples from Chronic Obstructive Pulmonary Disease (COPD) patients. Previous studies have shown that COPD is correlated with neutrophil infiltration into the airways through chemotactic migration. The thesis work is the first application of the microfluidic platform to quantitatively characterizing neutrophil chemotaxis to sputum samples from COPD patients. Our results show increased neutrophil chemotaxis to COPD sputum compared to control sputum from healthy individuals. The level of COPD sputum induced neutrophil chemotaxis was correlated with the patient’s spirometry data. Collectively, the research in this thesis provides novel microfluidic systems for neutrophil migration and chemotaxis analysis in both basic research and clinical applications. The developed microfluidic systems will find broad use in cell migration related applications.
May 2016

Micro-electro-mechanical systems (MEMS) technology has had an increasing impact on industry and our society. A wide range of MEMS devices are used in every aspects of our life, from microaccelerators and microgyroscopes to microscale drug-delivery systems. The increasing complexity of microsystems demands diverse microfabrication methods and actuation strategies to realize. Currently, it is challenging for existing microfabrication methods—particularly 3D microfabrication methods—to integrate multiple materials into the same component. This is a particular challenge for some applications, such as microrobotics and microfluidics, where integration of magnetically-responsive materials would be beneficial, because it enables contact-free actuation. In addition, most existing microfabrication methods can only fabricate flat, layered geometries; the few that can fabricate real 3D microstructures are not cost efficient and cannot realize mass production. This dissertation explores two solutions to these microfabrication problems: first, a method for integrating magnetically responsive regions into microstructures using photolithography, and second, a method for creating three-dimensional freestanding microstructures using a modified micromolding technique. The first method is a facile method of producing inexpensive freestanding photopatternable polymer micromagnets composed NdFeB microparticles dispersed in SU-8 photoresist. The microfabrication process is capable of fabricating polymer micromagnets with 3 µm feature resolution and greater than 10:1 aspect ratio. This method was used to demonstrate the creation of freestanding microrobots with an encapsulated magnetic core. A magnetic control system was developed and the magnetic microrobots were moved along a desired path at an average speed of 1.7 mm/s in a fluid environment under the presence of external magnetic field. A microfabrication process using aligned mask micromolding and soft lithography was also developed for creating freestanding microstructures with true 3D geometry. Characterization of this method and resolution limits were demonstrated. The combination of these two microfabrication methods has great potential for integrating several material types into one microstructure for a variety of applications.

This project aimed at exploring new hybrid materials to be used for acoustophoresis applications. Acoustophoresis can be used to manipulate particles inside a microfluidic channel by creating ultrasound standing waves within the channel [1]. This can be used for cell separation [2] or trapping of particles [3]. The intent of this project was to create materials for use in microfluidic channels that would be cheaper and easier to manufacture than those traditionally used, while still having adequate acoustic properties to allow for use in acoustopheresis. This was done by investigating whether the addition of glass-beads or glass-bubbles could increase the acoustic properties of an off-stoichiometry-thiol-enes (OSTE) based polymer. Hybrid samples with different volume fractions of glass-beads or glass-bubbles added to the OSTE polymer were manufactured and characterised according to their acoustic properties using the pulse-echo buffer-rod method. The acoustic properties measured were the density, attenuation, acoustic impedance and the reflection coefficient between water and the material. The addition of glass-beads was found to increase the acoustic impedance while the inverse was found for the addition of glass-bubbles. Both the addition of glass-beads and glass-bubbles were found to increase the attenuation. The hybrid material that was found to have the most suitable acoustic properties was OSTE/Glass-beads 40%, whose acoustic impedance had been increased ∼60% compared to pure OSTE. Consequently, the OSTE/Glass-beads 40% material was used to manufacture a microfluidic channel. A particle trapping experiment showed that the OSTE/Glass-beads 40% microfluidic channel was able to obtain bead trapping. This means that a standing wave was able to be generated within the channel and that it was strong enough to trap particles in the centre of the channel. However, evaluation of the particle trapping efficiency of the channel showed that it was not as effective as those using traditional materials. Therefore, future work is recommended to optimise a channel design for the OSTE/Glass-beads 40% material to increase the particle trapping efficiency.
I detta projekt undersöktes ett nytt hybridmaterial för användning i applikationer inom akustofores. Akustofores kan användas till att manipulera partiklar inuti mikrofluidkkanaler genom att generera ståendevågor i kanalen med hjälpav ultraljud [1]. Detta kan användas till cellseparation [2] eller till att fånga partiklar [3]. Målet i detta projekt var att skapa material som skulle bli billigare och möjliggöra enklare fabricering av kanalerna som används inom akustofores än de material som traditionellt används, med bibehållande av tillräckliga akustiskaegenskaper. Detta genomfördes genom att undersöka om tillsättning av glaspärlor eller glasbubblor kunde förbättra de akustiska egenskaperna av en off-stoichiometry-thiol-enes (OSTE) baserad polymer. Hybridprover gjorda på OSTE-polymeren med olika volymandelar av glaspärloroch glasbubblor tillverkades och kategoriserades med avseende på deras akustiska egenskaper med hjälp av pulseeko buffertstång metoden. De akustiska egenskaperna som uppmättes var densitet, attenuering, akustisk impedans och reflektions koefficienten mellan vatten och materialet. Resultatet av projektet visade att tillsättning av glaspärlor ökade den akustiska impedansen  i motsatts till glasbubblorna som visade sig minska den. Vidare visade det sig att både tillsättningen av glaspärlor och glasbubblor ökade attenueringen. Det hybridmaterial som visade sig ha de mest lämpliga akustiska egenskaperna var OSTE/glaspärlor med en 40% volymandel av glaspärlor. Den akustiska impedansen hade förhöjts med cirka 60% jämfört med vanlig OSTE. Därför valdes det hybrid-materialet till att tillverka en mikrofluidikkanal. Därefter genomfördes ett partikelfångstexperiment som visade att, OSTE/glaspärlor med en 40% volymandel av glaspärlor, kunde erhålla partikelfångst i kanalen. Detta innebär att en stående våg kunde genereras i kanalen och att den var tillräckligt stark för att kunna fånga partiklarna i mitten av kanalen. Däremot visade utvärdering av kanalens partikelfångsteffektivitet att den inte var lika effektiv som kanaler gjorda av traditionellt använda material. Därför rekommenderas framtida arbete till att designa en optimerad kanaldesign med OSTE/Glas-pärlor 40% materialets egenskaper i åtanke för att förhoppningsvis kunna öka partikelfångst effektivitet.

ZnO nanostructures have been investigated for quite a long time. However, only recently they triggered much interest due to advances in materials synthesis and characterization, as well as emerging demand for new nanostructured materials in novel device implementations. A large part of the work was devoted to exploring new methodology for patterning growth sites and controlling nanowires morphology using the deposition methods that are compatible with integrated circuits (IC) processing. Microcontact printing was used to pattern the seeding layer, and, subsequently, ZnO nanowires through a resistless soft lithography process. When considering hydrothermal growth of ZnO nanowires in the framework of IC compatible techniques, it is favorable to keep the chemistry of the process constant, while tailoring morphological properties of ZnO nanowires through other means. Therefore, control over morphology of ZnO nanowires was realized by setting the physical properties of seeding layers. Atomic Layer Deposition (ALD) was used to deposit seeding layer required for hydrothermal growth and the effect of the physical properties of ALD thin films on resultant ZnO nanowires was studied. Opto-electrochemical properties of ZnO nanowires were studied in various electrolytes and performance of ZnO nanowires as an electrode material for multifunctional applications was investigated. Also, bulk nucleation and growth of novel aster-like nanostructures was investigated. These nanostructures may prove useful for creation of mechanically reinforced biocompatible polymers. Another key objective of the present work was to create strategies for controlled growth of ZnO nanowires on substrates previously unavailable for conventional hydrothermal growth of ZnO nanowires. The newly developed approach greatly facilitates growth of ZnO nanowires in confined microstructures, which greatly enhances the possibilities for the usage of ZnO nanowires in applications where they act as a porous electrode. These novel techniques open wide possibilities for improving performance of devices such as dye sensitized solar cells or supercapacitors.

In recent years, the LOC community has focused most of its research in the biomedical and biotechnology fields, due to the need of portable, low power consumption and low cost theranostics microdevices. Some developing countries do not have suitable medical diagnostics technologies and the supply and storage of the reagents is in many cases limited as well as the access to energy. Furthermore, developed countries are experimenting population aging needing novel low cost efficient disease-screening technologies. The introduction of LOC and microfluidics allow the integration of complex functions that could lead to the developing of more accurate, cheap and reliable theranostic tools. Current focus of application is focused mostly in drug delivery 1, cellular analysis 2, and disease diagnosis 3. Microfluidics is improving the developing of novel point-of-care devices, but there are some challenges that are slowing down the massive production of these LOC. These areas include new methods for sample collection, world-to-chip interfaces, sample pre-treatment, improvement of long-term stability of reagents, working with complex sample specimens, multiple detection of biomarkers and simplify the read-out 4. The main aim of this thesis work was to create novel, cheap and with a high degree of automatization miniaturized biosensing devices with the objective to facilitate Point-of-Care diagnostics in the near future. Our efforts have been focused into developing a LOC system with electrochemical sensing capabilities adjustable to any biomarker, depending only on sample volumes and required analysis times. The devices integrate low-cost label-free biosensors exploiting microfluidics-based self-functionalization, or specialization. The biosensor functionalization takes place in situ and selectively, just before the sensing, and their area keeps dry and inactive until the test starts. The reagents and the sensing parts are kept separated and brought into contact just before the test, avoiding the need of complex fabrication and storage methods to guarantee functionalization integrity. The novel design reduces the cost of the final instrumentation, by simplifying the measurements, while keeping sensitivities and LODs relevant for the application. Furthermore, since the interaction of antibody and protein is time and concentration dependent, our device has the capability to adjust its sensitivity. We have tuned and characterized our system sensitivity using different biomarkers. The development of our novel devices was possible by exploiting synergies in disciplines previously studied in our group. Particularly, in fields such as microfluidics 5-8, surface functionalization 9-14 and electrochemical biosensors 15-19. Summarizing, we are proposing novel microfluidic devices with integrated biosensors. The systems are based on the principle of laminar co-flow in order to perform an on-chip selective surface bio-functionalization of LOC integrated biosensors. This method has the advantage of performing the surface modification protocols “in situ” before the detection. The system can be easily scaled to incorporate several sensors with different biosensing targets in a single chip. We are proposing a novel voltage and impedance differential measurements; that allow us to simplify the read-out. As biomedical application we focus our attention on the detection of prostate cancer biomarkers. Bibliography 1. I. U. Khan, C. A. Serra, N. Anton and T. Vandamme, Journal of Controlled Release, 2013, 172, 1065-1074. 2. H. Andersson and A. Van den Berg, Sensors and Actuators B: Chemical, 2003, 92, 315-325. 3. M. J. Cima, Annual Review of Chemical and Biomolecular Engineering, 2011, 2, 355-378. 4. C. D. Chin, V. Linder and S. K. Sia, Lab on a Chip, 2012, 12, 2118-2134. 5. R. Rodriguez-Trujillo, C. A. Mills, J. Samitier and G. Gomila, Microfluidics and Nanofluidics, 2007, 3, 171-176. 6. R. Rodriguez-Trujillo, O. Castillo-Fernandez, M. Garrido, M. Arundell, A. Valencia and G. Gomila, Biosensors and Bioelectronics, 2008, 24, 290-296. 7. O. Castillo-Fernandez, R. Rodriguez-Trujillo, G. Gomila and J. Samitier, Microfluidics and Nanofluidics, 2014, 16, 91-99. 8. J. Comelles, V. Hortigüela, J. Samitier and E. Martínez, Langmuir, 2012, 28, 13688-13697. 9. E. Prats-Alfonso, F. García-Martín, N. Bayo, L. J. Cruz, M. Pla-Roca, J. Samitier, A. Errachid and F. Albericio, Tetrahedron, 2006, 62, 6876-6881. 10. J. Vidic, M. Pla-Roca, J. Grosclaude, M.-A. Persuy, R. Monnerie, D. Caballero, A. Errachid, Y. Hou, N. Jaffrezic-Renault, R. Salesse, E. Pajot-Augy and J. Samitier, Analytical Chemistry, 2007, 79, 3280-3290. 11. Y. Hou, S. Helali, A. Zhang, N. Jaffrezic-Renault, C. Martelet, J. Minic, T. Gorojankina, M.-A. Persuy, E. Pajot-Augy, R. Salesse, F. Bessueille, J. Samitier, A. Errachid, V. Akimov, L. Reggiani, C. Pennetta and E. Alfinito, Biosensors and Bioelectronics, 2006, 21, 1393-1402. 12. S. Rodríguez Seguí, M. Pla, J. Minic, E. Pajot‐Augy, R. Salesse, Y. Hou, N. Jaffrezic‐Renault, C. A. Mills, J. Samitier and A. Errachid, Analytical Letters, 2006, 39, 1735-1745. 13. A. Lagunas, J. Comelles, E. Martínez and J. Samitier, Langmuir, 2010, 26, 14154-14161. 14. A. Lagunas, J. Comelles, S. Oberhansl, V. Hortigüela, E. Martínez and J. Samitier, Nanomedicine: Nanotechnology, Biology and Medicine, 2013, 9, 694-701. 15. M. Castellarnau, N. Zine, J. Bausells, C. Madrid, A. Juárez, J. Samitier and A. Errachid, Materials Science and Engineering: C, 2008, 28, 680-685. 16. M. Castellarnau, N. Zine, J. Bausells, C. Madrid, A. Juárez, J. Samitier and A. Errachid, Sensors and Actuators B: Chemical, 2007, 120, 615-620. 17. M. Kuphal, C. A. Mills, H. Korri-Youssoufi and J. Samitier, Sensors and Actuators B: Chemical, 2012, 161, 279-284. 18. D. Caballero, E. Martinez, J. Bausells, A. Errachid and J. Samitier, Analytica Chimica Acta, 2012, 720, 43-48. 19. M. Barreiros dos Santos, J. P. Agusil, B. Prieto-Simón, C. Sporer, V. Teixeira and J. Samitier, Biosensors and Bioelectronics, 2013, 45, 174-180.
En años recientes, la comunidad de LOC ha enfocado todos sus esfuerzos en la investigación de nuevas aplicaciones para la biomedicina y biotecnología. Algunos países en vías de desarrollados no tienen tecnologías de diagnóstico adecuadas, además el suministro y almacenamiento de los reactivos es en muchos casos limitado, y en ocasiones cuentan con un acceso limitado al consumo de energía. Por otra parte, los países desarrollados se han encontrado con una población envejecida, y por lo tanto se ha generado la necesidad de contar con nuevas tecnologías para el diagnóstico de enfermedades las cuales sean accesibles y orientadas a una terapia más personalizada. Tanto la microfluídica como los LOC han permitido la integración de funciones de análisis complejas capaces de desarrollar herramientas de diagnostico más precisas, de bajo coste y confiables. Actualmente toda la atención se ha centrado en el diseño de aplicaciones para administración de fármacos 1, análisis celular 2 y diagnostico de enfermedades 3. La introducción de la microfluídica ha servido para mejorar el desarrollo de nuevos dispositivos point-of-care, pero todavía existen algunos problemas que han evitado la producción masiva de estos LOC. Las áreas en las que se pretende conseguir una mejora son la recolección de la muestra, mejora de la interfaz entre el chip y el usuario, tratamiento previo de la muestra, mejorar la estabilidad de los reactivos, trabajo con muestras complejas, detección múltiple de biomarcadores y simplificación del sistema de medida 4. Nuestros esfuerzos se han dedicado en desarrollar un sistema LOC con capacidad de detección electroquímica ajustable a cualquier biomarcador, dependiendo únicamente en la cantidad de muestra y los tiempos de análisis. Nuestros dispositivos microfluídicos cuentan con biosensores integrados de bajo coste con capacidad de auto-funcionalización. La funcionalización de los biosensores se realiza in-situ y selectivamente, antes de la detección, manteniendo el área de detección inerte hasta el inicio de la prueba. Los reactivos y el área de detección se almacenan por separado y entran en contacto hasta el inicio del experimento, lo cual facilita el método de fabricación. Se ha podido desarrollar este trabajo gracias a los estudios previos realizados en nuestro grupo en distintas disciplinas, tales como: microfluídica 5-8, funcionalización de superficies 9-14 y biosensores electroquímicos 15-19. Bibliografía 1. I. U. Khan, C. A. Serra, N. Anton and T. Vandamme, Journal of Controlled Release, 2013, 172, 1065-1074. 2. H. Andersson and A. Van den Berg, Sensors and Actuators B: Chemical, 2003, 92, 315-325. 3. M. J. Cima, Annual Review of Chemical and Biomolecular Engineering, 2011, 2, 355-378. 4. C. D. Chin, V. Linder and S. K. Sia, Lab on a Chip, 2012, 12, 2118-2134. 5. R. Rodriguez-Trujillo, C. A. Mills, J. Samitier and G. Gomila, Microfluidics and Nanofluidics, 2007, 3, 171-176. 6. R. Rodriguez-Trujillo, O. Castillo-Fernandez, M. Garrido, M. Arundell, A. Valencia and G. Gomila, Biosensors and Bioelectronics, 2008, 24, 290-296. 7. O. Castillo-Fernandez, R. Rodriguez-Trujillo, G. Gomila and J. Samitier, Microfluidics and Nanofluidics, 2014, 16, 91-99. 8. J. Comelles, V. Hortigüela, J. Samitier and E. Martínez, Langmuir, 2012, 28, 13688-13697. 9. E. Prats-Alfonso, F. García-Martín, N. Bayo, L. J. Cruz, M. Pla-Roca, J. Samitier, A. Errachid and F. Albericio, Tetrahedron, 2006, 62, 6876-6881. 10. J. Vidic, M. Pla-Roca, J. Grosclaude, M.-A. Persuy, R. Monnerie, D. Caballero, A. Errachid, Y. Hou, N. Jaffrezic-Renault, R. Salesse, E. Pajot-Augy and J. Samitier, Analytical Chemistry, 2007, 79, 3280-3290. 11. Y. Hou, S. Helali, A. Zhang, N. Jaffrezic-Renault, C. Martelet, J. Minic, T. Gorojankina, M.-A. Persuy, E. Pajot-Augy, R. Salesse, F. Bessueille, J. Samitier, A. Errachid, V. Akimov, L. Reggiani, C. Pennetta and E. Alfinito, Biosensors and Bioelectronics, 2006, 21, 1393-1402. 12. S. Rodríguez Seguí, M. Pla, J. Minic, E. Pajot‐Augy, R. Salesse, Y. Hou, N. Jaffrezic‐Renault, C. A. Mills, J. Samitier and A. Errachid, Analytical Letters, 2006, 39, 1735-1745. 13. A. Lagunas, J. Comelles, E. Martínez and J. Samitier, Langmuir, 2010, 26, 14154-14161. 14. A. Lagunas, J. Comelles, S. Oberhansl, V. Hortigüela, E. Martínez and J. Samitier, Nanomedicine: Nanotechnology, Biology and Medicine, 2013, 9, 694-701. 15. M. Castellarnau, N. Zine, J. Bausells, C. Madrid, A. Juárez, J. Samitier and A. Errachid, Materials Science and Engineering: C, 2008, 28, 680-685. 16. M. Castellarnau, N. Zine, J. Bausells, C. Madrid, A. Juárez, J. Samitier and A. Errachid, Sensors and Actuators B: Chemical, 2007, 120, 615-620. 17. M. Kuphal, C. A. Mills, H. Korri-Youssoufi and J. Samitier, Sensors and Actuators B: Chemical, 2012, 161, 279-284. 18. D. Caballero, E. Martinez, J. Bausells, A. Errachid and J. Samitier, Analytica Chimica Acta, 2012, 720, 43-48. 19. M. Barreiros dos Santos, J. P. Agusil, B. Prieto-Simón, C. Sporer, V. Teixeira and J. Samitier, Biosensors and Bioelectronics, 2013, 45, 174-180.

Thesis advisor: Michelle Meyer
The primary bacterial targets for most antibiotics are well known. To survive the stress of an antibiotic a bacterium must decrease the antibiotic to target binding ratio to escape from harmful effects. This can occur through a number of different functions including down-regulation of the target, mutation of the binding site on the target, and decreasing the intake or increasing the efflux of the antibiotic. However, it is becoming more evident that an antibiotic stress response influences more than just the primary target, and that a wave of secondary responses can be triggered throughout the bacterium. As a result resistance mutations may arise in genes that are indirectly affected by the initial interaction between the antibiotic and target. These indirect responses have been found to be associated with metabolism, regulation, cell division, oxidative stress, and other critical pathways. One technique recently developed in our lab, called transposon insertion sequencing (Tn-seq), can be used to further understand the complexity of these indirect responses by profiling growth rates (fitness) of mutants at a genome-wide level. However, Tn-seq is normally performed with large libraries of pooled mutants and thus it remains unclear how this may influence fitness of some independent mutants that may be compensated by others in the population. Additionally, since the original method has only utilized planktonic culture, it is also not clear how higher order bacterial structures, such as biofilms or microcolonies, influence bacterial fitness. To better understand the dynamics of pooled versus individual mutant culture, as well as the effect of community structure in microcolony development on the influence of fitness, we adapted a droplet microfluidics-based technique to encapsulate and culture single mutants. We were able to successfully encapsulate at least 7 different species of bacterial pathogens, including Streptococcus pneumoniae, and culture them planktonically, or as microcolonies, in either monodisperse liquid or agarose droplets. These experiments, however, raised an important challenge: the DNA yield from one encapsulation experiment is insufficient to generate samples for sequencing by means of the traditional Tn-seq method. This led us to develop a novel Tn-seq DNA library preparation method, which is able to generate functional Tn-seq library molecules from picogram amounts of DNA. This method is not ideal yet because fitness data generated through the new method currently does not correlate well with data from traditional Tn-seq library preparation. However, we have identified one major culprit that should be easily solvable. We expect by modifying the binding site of the primer used for linear amplification of transposon ends that the new preparation method will be able recapitulate results from the traditional Illumina preparation method for Tn-seq. This will enable us to prepare robust Tn-seq samples from very small amounts of DNA in order to probe stress responses in single mutants as well as in microcolonies in a high-throughput manner
Thesis (MS) — Boston College, 2016
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology

Thanks to their capability of transmitting light with low loss, optical fibers have found a wide range of applications in illumination, imaging, and telecommunication. However, since the light guided in a regular optical fiber is well confined in the core and effectively isolated from the environment, the fiber does not allow the interactions between the light and matters around it, which are critical for many sensing and actuation applications. Specially shaped optical fibers endow the guided light in optical fibers with the capability of interacting with the environment by modifying part of the fiber into a special shape, while still preserving the regular fiber’s benefit of low-loss light delivering. However, the existing specially shaped fibers have the following limitations: 1) limited light coupling efficiency between the regular optical fiber and the specially shaped optical fiber, 2) lack special shape designs that can facilitate the light-matter interactions, 3) inadequate material selections for different applications, 4) the existing fabrication setups for the specially shaped fibers have poor accessibility, repeatability, and controllability. The overall goal of this dissertation is to further the fundamental understanding of specially shaped fibers and to develop novel specially shaped fibers for different applications. In addition, the final part of this dissertation work proposed a microfluidic platform that can potentially improve the light-matter interactions of the specially shaped fibers in fluidic environments. The contributions of this dissertation work are summarized as follows: 1) An enhanced fiber tapering system for highly repeatable adiabatic tapered fiber fabrications. An enhanced fiber tapering system based on a novel heat source and an innovative monitoring method have been developed. The novel heat source is a low-cost ceramic housed electric furnace (CHEF). The innovative monitoring method is based on the frequency-domain optical transmission signal from the fiber that is being tapered. The enhanced fiber tapering system can allow highly repeatable fabrication of adiabatically tapered fibers. 2) A lossy mode resonance (LMR) sensor enabled by SnO2 coating on a novel specially shaped fiber design has been developed. The developed LMR sensor has a D-shape fiber tip with SnO2 coating. It has the capability of relative humidity and moisture sensing. The fiber-tip form factor can allow the sensor to be used like a probe and be inserted into/removed from a tight space. 3) Specially shaped tapered fibers with novel designs have been developed for integrated photonic and microfluidic applications. Two novel specially tapered fibers, the tapered fiber loop and the tapered fiber helix have been developed. The tapered fiber loop developed in this work has two superiority that differentiated itself from previous works: a) the mechanical stability of the tapered fiber loop in this work is significantly better. b) the tapered fiber loops in this work can achieve a diameter as small as 15 ?m while still have a high intrinsic optical quality factor of 32,500. The tapered fiber helix developed in this work has a 3D structure that allows it to efficiently deliver light to locations out of the plane defined by its two regular fiber arms. Applications of the tapered fiber helices in both integrated photonic device characterizations and microparticle manipulations have been demonstrated. 4) Developed an acrylic-tape hybrid microfluidic platform that can allow function reconfiguration and optical fiber integration. A low-cost, versatile microfluidic platform based on reconfigurable acrylic-tape hybrid microfluidic devices has been developed. To the best of the author’s knowledge, this is the first time that the fabrication method of sealing the acrylic channel with a reconfigurable functional tape has been demonstrated. The tape-sealing method is compatible with specially shaped fiber integrations.

Surfactant coated microbubbles are widely used as contrast agents (UCA) in medical ultrasound imaging, due to their high echogenicity and non-linear response to acoustic excitation. Controlling the stability of microbubbles in vivo represents a considerable challenge. Understanding the characteristics of the bubble surface and how they change with production method, composition and environment is key to addressing this problem. The aim of this thesis is to investigate viscosity, bubble dissolution, and acoustic response as functions of their composition, manufacturing method and environment. Bubbles were made using combinations of phospholipid and an emulsifier in different molar ratios. Adding the emulsifier decreased both the size and the surface viscosity of the bubbles and caused changes in the scattered pressure amplitude of bubbles under ultrasound. To increase microbubble stability, solid inorganic nanoparticles were adsorbed on to the microbubble surface. These particles behaved as Pickering stabilisers, and deterred Ostwald ripening. The nanoparticles also enhanced the nonlinear behaviour of bubbles at low acoustic pressures. Three manufacturing methods (sonication, cross-flow and flow focusing) were investigated in order to verify stability differences. Sonication produced bubbles with surface viscosities hundreds of centipoise greater than those produced by microfluidics. Both pressure amplitude and harmonic content for sonicated bubbles were found to be much larger due to a higher liposomal adhesion rate at the surface. Solution temperature and bubble age were also investigated. When the solutions were heated above the phospholipid gelling temperature, microfluidic bubbles showed an increased surface viscosity, due to increased liposome adhesion caused by the increased temperature. Bubble composition, manufacturing method and environment were found to vary the surface characteristics of the microbubbles. Further investigations into the affects of the filling gas, in vitro studies, and low temperature TEM characterisation should be conducted to produce a microbubble with the full range of desired characteristics.

Les laboratoires sur puce visent à miniaturiser et à intégrer les fonctions couramment utilisées dans les laboratoires d'analyse afin de cibler des applications en santé avec un impact prometteur sur le diagnostic médical au lit du patient. Les membranes poreuses sont d'un grand intérêt pour la préparation et l'analyse d'échantillon sur puce car elles permettent la séparation par taille/charge de molécules, mais également leur pré-concentration. Parmi les matériaux disponibles pour constituer des membranes poreuses, le silicium poreux présente de nombreux avantages tels que le contrôle précis de la taille des pores et de la porosité, une chimie de surface pratique et des propriétés optiques uniques. Les membranes de silicium poreux sont généralement intégrées dans des puces fluidiques en les montant entre deux couches comportant des micro-canaux, formant ainsi des réseaux fluidiques à trois dimensions, peu pratiques et peu adaptés à l'observation directe par microscopie. Dans ces travaux de thèse, nous avons développé deux méthodes de fabrication de membranes de silicium à pores latéraux qui permettent leur intégration monolithique dans des systèmes microfluidiques planaires. Le premier procédé est fondé sur l'utilisation d'électrodes localement structurées afin de guider la formation de pores de manière horizontale, en combinaison avec des substrats type silicium sur isolant (SOI) pour localiser spatialement la formation de silicium poreux dans la profondeur du canal. La deuxième méthode repose sur le fait que la formation de silicium poreux par anodisation est fortement dépendante du type de dopant et de sa concentration. Bien que nous utilisons encore le même type d'électrodes structurées sur les parois latérales de la membrane pour injecter le courant lors de l'anodisation, le dopage par implantation permet de confiner la membrane, de façon analogue mais à la place de l'oxyde enterré du SOI. Des membranes à pores latéraux ont été fabriquées par ces deux méthodes et leur fonctionnalité a été démontrée en réalisant des expériences de filtrage. En plus de la filtration d'échantillon, les membranes ont été utilisées pour étudier la possibilité d'effectuer de la pré-concentration électrocinétique et de la détection interférométrique. La sélectivité ionique des membranes microporeuse permet la pré-concentration moléculaire avec des facteurs de concentration pouvant atteindre jusqu'à 103 en 10 min en appliquant moins de 9 V. Ces résultats sont comparables à ceux rapportés dans la littérature à l'aide par exemple de nanocanaux avec une consommation d'énergie beaucoup plus faible. Enfin, nous avons pu détecter une variation de l'indice de réfraction du silicium poreux par le décalage du spectre d'interférence lors du chargement de différents liquides injectés dans les membranes. Le travail présenté dans cette thèse constitue la première étape dans la démonstration de l'intérêt du silicium poreux pour la préparation d'échantillon et la biodétection dans des laboratoires sur puce planaires
Lab on a chip devices aim at integrating functions routinely used in medical laboratories into miniaturized chips to target health care applications with a promising impact foreseen in point-of-care testing. Porous membranes are of great interest for on-chip sample preparation and analysis since they enable size- and charge-based molecule separation, but also molecule pre-concentration by ion concentration polarization. Out of the various materials available to constitute porous membranes, porous silicon offers many advantages, such as tunable pore properties, large porosity, convenient surface chemistry and unique optical properties. Porous silicon membranes are usually integrated into fluidic chips by sandwiching fabricated membranes between two layers bearing inlet and outlet microchannels, resulting in three-dimensional fluidic networks that lack the simplicity of operation and direct observation accessibility of planar microfluidic devices. To tackle this constraint, we have developed two methods for the fabrication of lateral porous silicon membranes and their monolithic integration into planar microfluidics. The first method is based on the use of locally patterned electrodes to guide pore formation horizontally within the membrane in combination with silicon-on-insulator (SOI) substrates to spatially localize the porous silicon within the channel depth. The second method relies on the fact that the formation of porous silicon by anodization is highly dependent on the dopant type and concentration. While we still use electrodes patterned on the membrane sidewalls to inject current for anodization, the doping via implantation enables to confine the membrane analogously to but instead of the SOI buried oxide box. Membranes with lateral pores were successfully fabricated by these two methods and their functionality was demonstrated by conducting filtering experiments. In addition to sample filtration, we have achieved electrokinetic pre-concentration and interferometric sensing using the fabricated membranes. The ion selectivity of the microporous membrane enables to carry out sample pre-concentration by ion concentration polarization with concentration factors that can reach more than 103 in 10 min by applying less than 9 V across the membrane[TL1]. These results are comparable to what has already been reported in the literature using e.g. nanochannels with much lower power consumption. Finally, we were able to detect a change of the porous silicon refractive index through the shift of interference spectrum upon loading different liquids into the membrane. The work presented in this dissertation constitutes the first step in demonstrating the interest of porous silicon for all-in-one sample preparation and biosensing into planar lab on a chip

THz spectroscopy is an emerging technique for studying the dynamics and interactions of cells and biomolecules, but many practical challenges still remain in experimental studies. We present a prototype of simple and inexpensive cell-trapping microfluidic chip for THz spectroscopic study of live cells. Cells are transported, trapped and concentrated into the THz exposure region by applying an AC bias signal while the chip maintains a steady temperature at 37 degrees C by resistive heating. We conduct some preliminary experiments on E. coli and T-cell solution and compare the transmission spectra of empty channels, channels filled with aqueous media only, and channels filled with aqueous media with un-concentrated and concentrated cells.