Nanofluids, a new class of fluids engineered by suspending nanometer-sized particles in a host liquid, are offered as a new strategy in order to improve heat and mass transfer efficiency. My research was motivated by previous exciting studies on enhanced mass diffusion and the possibility of tailoring mass transport by direct manipulation of molecular diffusion. Therefore, a microfluidic approach capable of directly probing tracer diffusion between nanoparticle-laden fluid streams was developed. Under conditions matching previously reported studies, strong complexation interactions between the dye and nanoparticles at the interface between fluid streams was observed. When the tracer dye and surfactant were carefully chosen to minimize the collective effects of the interactions, no significant change in tracer dye diffusivity was observed in the presence of nanoparticles. Next, adapting tracer dyes for studies involving colloidal nanomaterials was explored. Addition of these charged tracers poses a myriad of challenges because of their propensity to disrupt the delicate balance among physicochemical interactions governing suspension stability. Here it was shown how important it is to select the compatible combinations of dye, nanoparticle, and stabilizing surfactant to overcome these limitations in low volume fraction (< 1 vol%) aqueous suspensions of Al2O3 nanoparticles. A microfluidic system was applied as a stability probe that unexpectedly revealed how rapid aggregation could be readily triggered in the presence of local chemical gradients. Suspension stability was also assessed in conjunction with coordinated measurements of zeta potential, steady shear viscosity and bulk thermal conductivity. These studies also guided our efforts to prepare new refrigerant formulations containing dispersed nanomaterials, including graphene nanosheets, carbon nanotubes and metal oxide and nitride. The influence of key parameters such as particle type, size and volume fraction on the suspension's thermal conductivity was investigated using a standard protocol. Our findings showed that thermal conductivity values of carbon nanotube and graphene nanosheet suspensions were higher than TiO2 nanoparticles, despite some nanoparticles with large particle sizes provided noticeable thermal conductivity enhancements. Significantly, the graphene containing suspensions uniquely matched the thermal conductivity enhancements attained in nanotube suspensions without accompanying viscosity, thus making them an attractive new coolant for demanding applications such as electronics and reactor cooling.

Since the introduction of electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI), there has been an unprecedented growth of biomolecule analysis using mass spectrometry (MS). One of the most popular applications for mass spectrometry is the field of proteomics, which has emerged as the next scientific challenge in the post-genome era. One critical step in proteomic analysis is sample preparation, a major bottleneck that is attributed to many time consuming and labor-intensive steps involved. Microfluidics can play an important role in proteome sample preparation due to its ability to handle small volumes of sample and reagent, and its capability to integrate multiple processes on a single chip with the potential for high-throughput analysis. However, to utilize microfluidic systems for proteome analysis, an efficient interface between microfluidic chip and mass spectrometry is required. This thesis presents several methods for coupling of microfluidic chips with ESI-MS and MALDIMS. III Three microfluidic-ESI interfaces were developed. The first interface involves fabricating a polymer based microchannel at the rectangular corners of the glass substrates using a single photolithography step. The second interface was build upon the previous interface in which a digital microfluidic platform was integrated with the microchannel in a “top-down” format. The integrated microfluidic system was used for inline quantification of amino acids in dried blood spots that have been processed by digital microfluidics. The third interface was formed by sandwiching a pulled glass capillary emitter between two digital microfluidic substrates. This method is a simpler and more direct coupling of digital microfluidics with ESI-MS as compared to the method used for second interface. Finally, a strategy using a removable plastic “skin” was developed to interface digital microfluidics with MALDI-MS for offline sample analysis. We demonstrated the utility of this format by implementing on-chip protein digestion on immobilized enzyme depots.

An all-optical micromanipulation technique is presented in the framework of precise cell selection within a cell culture and multiplexed transport capabilities for microfluidic single cell analysis applications. The technique was developed by combining an optical tweezer setup with a novel integrated waveguide cell propulsion method referred to as end-face waveguide propulsion (EFWP). The EFWP technique delivers optical forces to a particle generating thrust. The thesis is divided into two sections: simulation and experimental validation. In the first section a new simulation technique based on ray optics theory (ROT) and the beam propagation method (BPM) is used to predict particle velocity and trajectory along a microfluidic propagation channel. In this work, the ROT-BPM technique is used to analyse and optimize the waveguide geometry to maximize particle velocity. Analysis of the impact of common microchip manufacturing limitations on velocity is performed to determine acceptable fabrication process tolerances. The second section presents experimental results of polymer microspheres and acute myeloid leukemia (AML) cells as biological targets. The experimental results are compared with simulations performed in the first section. Correction factors are added to the simulations to reflect the experimental device parameters. Thermal e_ects due to photon absorption within the fluidic channels are also investigated and corrected for. The final analysis indicates that the ROT-BPM technique developed in this work can be used to adequately predict particle velocity and trajectory path. EFWP currently delivers the fastest particle velocities compared to other optical micromanipulation techniques currently available in microfluidic applications. While the technique is focused on addressing chemical cytometry precise particle selectivity and high throughput needs, EFWP can also be used in many other single cell applications.

Osteocytes make up the largest cell population in bone and are believed to be the main mechanosensory bone cells. During mechanical disuse and overuse, osteocyte viability is compromised and is found to be co-localized with increased osteoclastic bone resorption. Osteoclasts are recruited to remodel sites of apoptosis or bone microdamage; however, it is unclear whether the apoptotic or neighbouring healthy osteocytes are responsible for targeted bone remodeling. I hypothesized that apoptotic osteocytes are: (a) directly responsible for initiating bone remodeling by recruiting osteoclast precursors and directing osteoclast differentiation, and (b) indirectly responsible by signaling to nearby healthy osteocytes that, in turn, regulate osteoclastogenesis. In this in vitro study, apoptotic osteocytes were found to increase osteoclast precursor migration and osteoclast formation. Inhibition of the osteoclastogenic protein, receptor activator of nuclear factor kappa B ligand (RANKL), in conditioned medium abolished the osteoclastogenic effect of apoptotic osteocytes. Healthy osteocytes surrounded by apoptotic regions were modeled by applying apoptotic osteocyte conditioned medium to healthy osteocytes. These cells also promoted osteoclastogenesis, and had increased expression of macrophage colony stimulating factor (M-CSF) and vascular endothelial growth factor (VEGF). Inhibition of these factors abrogated the pro-osteoclastic effect of healthy osteocytes conditioned by apoptotic osteocytes. These findings support the hypothesis that apoptotic osteocytes directly and indirectly, by signaling to nearby healthy osteocytes, initiate osteoclastogenesis. One limitation of our and other conventional in vitro models is the lack of real-time cell communication and physiologically-relevant mechanical environment. Using a microfluidics approach, a miniature fluid shear delivery system was created for in vitro osteocyte cultures. The purpose of this microsystem was to increase control of the cell microenvironment for subsequent integration into scalable screening platforms or co-culture systems for studying osteocyte mechanobiology under physiological loading conditions. Fluid shear stress was periodically applied without external pumping using a deflecting elastomer membrane, where up to 2 Pa of oscillating shear stress was possible by manipulating membrane dimensions. Osteocyte culture, viability and calcium response were demonstrated in the microdevice. Further studies should attempt to characterize calcium signaling in osteocytes which, using a conventional macro-scale system, was found to dependent on cell-cell communication.

This thesis presents two hybrid luminescence-based biochemical photosensory microsystems: a CMOS/microfluidic chemiluminescence contact imager, and a CMOS/thin-film fluorescence contact imager. A compact, low-power analog-to-digital converter (ADC) architecture for use in such sensory microsystems is also proposed. Both microsystems are prototyped in a standard 0.35um CMOS technology. The CMOS/microfluidic microsystem integrates a 64x128-pixel CMOS imager and a soft polymer microfluidic network. Circuit techniques are employed to reduce the dark current and circuit noise for low-level light sensitivity. Experimental validation is performed by detecting luminol chemiluminescence and electrochemiluminescence. The CMOS/thin-film microsystem integrates an existing 128x128-pixel CMOS imager and a prefabricated, high-performance optical filter. Experimental validation is performed by detecting human DNA labeled with Cyanine-3 fluorescent dye. The proposed ADC architecture employs a novel digital-to-analog converter with a flexible trade-off between the integration area and the conversion speed. The area savings and good linearity of the DAC are verified by simulations.

This thesis presented a microfluidic preparation of bubbles-templated micro-size materials. In particular, this thesis focused on the microfluidic formation and dissolution of CO2 bubbles. First, this thesis described pH-regulated behaviours of CO2 bubbles in the microfluidic channel. This method opened a new way to generate small (<10 µm in diameter) with a narrow size distribution (CV<5%). Second, the microfluidic dissolution of CO2 bubbles possessed the important feature: the local change of pH on the bubble surface. This allowed us to encapsulate the bubbles with various colloidal particles. The bubbles coated with particles showed a high stability against coalescences and Ostwald ripening. The dimensions and shapes of bubbles with a shell of colloidal particle were manipulated by the hydrodynamic and chemical means, respectively. Third, we proposed a microfluidic method for the generation of small and stable bubbles coated with a lysozyme-alginate shell. The local pH decrease at the periphery of CO2 bubbles led to the electrostatic attraction between lysozyme on the bubble surface and alginate in the continuous phase. This produced the bubbles with a shell of biopolymers, which gave a long-term stability (up to a month, at least) against the dissolution and coalescence. Fourth, we presented a single-step method to functionalize bubbles with a variety of nanoparticles. The bubbles showed the corresponding properties of nanoparticles on their surface. Further, we explored the potential applications of these bubbles as contrast agents in ultrasound and magnetic resonance imaging.

Since the introduction of electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI), there has been an unprecedented growth of biomolecule analysis using mass spectrometry (MS). One of the most popular applications for mass spectrometry is the field of proteomics, which has emerged as the next scientific challenge in the post-genome era. One critical step in proteomic analysis is sample preparation, a major bottleneck that is attributed to many time consuming and labor-intensive steps involved. Microfluidics can play an important role in proteome sample preparation due to its ability to handle small volumes of sample and reagent, and its capability to integrate multiple processes on a single chip with the potential for high-throughput analysis. However, to utilize microfluidic systems for proteome analysis, an efficient interface between microfluidic chip and mass spectrometry is required. This thesis presents several methods for coupling of microfluidic chips with ESI-MS and MALDIMS. III Three microfluidic-ESI interfaces were developed. The first interface involves fabricating a polymer based microchannel at the rectangular corners of the glass substrates using a single photolithography step. The second interface was build upon the previous interface in which a digital microfluidic platform was integrated with the microchannel in a “top-down” format. The integrated microfluidic system was used for inline quantification of amino acids in dried blood spots that have been processed by digital microfluidics. The third interface was formed by sandwiching a pulled glass capillary emitter between two digital microfluidic substrates. This method is a simpler and more direct coupling of digital microfluidics with ESI-MS as compared to the method used for second interface. Finally, a strategy using a removable plastic “skin” was developed to interface digital microfluidics with MALDI-MS for offline sample analysis. We demonstrated the utility of this format by implementing on-chip protein digestion on immobilized enzyme depots.

L'expression génétique est un processus cellulaire fondamental réglé de manière ne. Les promoteurs inducibles perme ent de perturber l'expression génétique en changeant l'expression d'une protéine par rapport à son niveau physiologique de référence. Ce e propriété en fait un outil incontournable pour décrypter le fonctionnement des processus biologiques via la comparaison du comportement de la cellule sous divers niveaux d'induction. Toutefois, une limite actuelle à l'utilisation des promoteurs inducibles provient de la difficulté à appliquer des perturbations précises et dynamiques. Les deux obstacles principaux étant: (i) la variabilité intercellulaire ainsi qu'à la nature aléatoire de l'expression génétique qui limite la précision de la perturbation appliquée. (ii) la difficulté à prèdire quantitativement le comporteement des systèmes biologiques sur les longues periodes requises pour des objectifs d'expression variables dans le temps. Or des perturbations précises et changeant dans le temps perme ent d'obtenir de riches informations sur la dynamique d'un système biologique. Est présenté ici une plate-forme de contrôle temps réel en boucle fermée qui permet le contrôle quantitatif sur une longue durée de l'expression génétique chez la levure. Ce e plateforme utilise la microscopie par uorescence pour suivre l'expression génétique, un système micro uidique pour interagir avec l'environnement cellulaire ainsi qu'un logiciel perme ant l'analyse d'image en temps réel et le calcul de la stratégie de contrôle à appliquer. Ce système permet le contrôle de l'expression d'un gène chez la levure, tant au niveau d'un population cellulaire qu'au niveau de la cellule seule et ceci pour un objectif d'expression constant ou dépendant du temps. Le système de réponse au chocs hyper-osmotiques de la levure S. cerevisiae (HOG pathway) a été utilisé pourin uencer l'expression génétique. Toutefois, la possibilité d'utiliser un autre système d'induction sans profondes modi cations de la plate-forme est démontrée. De surcroît au développement de ce e plate-forme est également ici démontré la possibilité de contrôler le système HOG. A n de comprendre la dynamique cellulaire et de pouvoir la quanti er, il est nécessaire de pouvoir appliquer des perturbations précises. La plate-forme de contrôle de l'expression génétique présentée ici permet de perturber avec précision le niveau d'expression d'une protéine et représente donc une contribution majeure dans ce e direction.

Nanoparticles (NPs) are often synthesized in organic solvents due to advantages of superior size and shape control obtainable in a non-polar environment. However, many applications featuring NPs require them to be in aqueous media. To transfer NPs from oil to water, surfactants with amphiphilic (hydrophobic and hydrophilic) groups have been widely used. A popular phase-transfer approach involves formation of oil-in-water emulsions upon which the oil storing the NPs is boiled off. In the process, surfactants form bilayers with hydrophobic groups on the NPs rendering them water-dispersible. This transfer route however is limited in that NPs aggregate to form clusters which results in poor colloidal stability and for the specific case of quantum dots (QDs), adversely impacts optical properties. It has ever since remained a challenge to devise approaches that transfer NPs from oil to water as single particles without compromising NP stability and properties. We have discovered that by simple addition of salt to water during the step of emulsion formation, NP transfer efficiency can be greatly enhanced in "salty-micelles" of surfactants. The strength of this approach lies in its simplicity and generic nature in that the transfer scheme is valid for different NP, surfactant and salt types. Using a model system with cadmium selenide (CdSe) QDs as NPs, Aerosol-OT (AOT) as the surfactant and NaCl as the salt in water, we found >90% of CdSe QDs transferred in salty-micelles of AOT which was significantly higher than the 45-55% QDs that transferred in deionized-water (DI-water) micelles of AOT. In the salty-micelle environment, QDs were found to exist predominantly as single NPs with narrow size distribution, as established by light scattering, analytical ultracentrifugation and electron microscopy. The effects of salt were in lowering aqueous solubility of AOT through "salting-out" action and in screening repulsions between like-charged head groups of AOT molecules. Electrophoresis, thermogravimetric analysis and photoluminescence measurements using a solvatochromic dye established higher surfactant coverage with greater lateral compaction for QDs in salty-micelles over the DI-micelle counterpart. Single NP characteristics along with a hydrophobic environment in laterally compact salty-micelles resulted in better retention of optical properties of QDs. Observations of a secondary effect by salt in inducing spontaneous emulsification of a hydrocarbon (octane)/AOT/brine system were systematically investigated by tracking time-variant octane droplet size and charge. Salinity levels that determine the spontaneous curvature and phase behavior of AOT were seen to influence the initial nucleation of octane droplets and their subsequent growth. The smallest octane drops (sub 50 nm) were nucleated at the optimum cross-over salinity and emergence of the liquid crystalline phase of AOT resulted in slowest growth rates. These factors contributed towards higher transfer efficiency of NPs in salty-micelles. Two applications from formulating aqueous NP suspensions by the new phase-transfer approach are described. In the first, QD and carbon-dot (C-Dot) "nanoreporters" were formulated for oil-field reservoir characterization using Neodol 91-7 (nonionic) and Avanel S150 CGN (hybrid nonionic and anionic) as surfactants. These NPs were stable to aggregation under reservoir-representative conditions (salinities: 1M NaCl, 1M KCl and 0.55M synthetic seawater; temperatures: 70-100 °C) and demonstrated flow and transport through crushed-calcite and quartz-sand columns with high breakthrough and recovery (> 90%). In the second application, tandem assembly of a cationic polymer, multivalent salt, and NPs was investigated in a microfluidic channel where charge ratio of the polymer/salt and shear from flow and device geometry determined their assembly into higher ordered structures such as gels and capsules.

The field of neuroscience has recently seen optogenetics emerge as a highly utilized and powerful method of non-invasive neural activation and inhibition. This thesis seeks to enhance the optogenetic toolbox through the design, construction, and evaluation of a number of hardware and software modules for research in Caenorhabditis elegans neuroscience. In the first aim, we combine optogenetics, microfluidics, and automated image processing, to create a system capable of high-throughput analysis of synaptic function. In the second aim, we develop a multi-modal illumination system for the manipulation of optogenetic reagents. The system is capable of multi-spectral illumination in definable patterns, with the ability to dynamically alter the intensity, color, and shape of the illumination. The illumination system is controlled by a set of software programs introduced in aim three, and is demonstrated through a set of experiments in aim four where we selectively activate and inhibit specific neural nodes expressing optogenetic reagents in freely moving C. elegans. With the ability to target specific nodes in a freely moving animal, we can correlate specific neural states to behaviors allowing for the dissection of neural circuits. Taken together, the developed technologies for optogenetic researchers will allow for experimentation with previously unattainable speed, precision and flexibility.