This dissertation investigates the emulsification of aqueous liquid in immiscible organic liquid in various microfluidic environments, and addresses both experimental characterization and theoretical interpretation of the dynamics and design guidelines, as well as an application of microfluidic emulsification in fabrication of disk-like colloidal particle suspensions for studying its sedimentation behavior. In an attempt to understand the dynamics of drop formation in flow-focusing microfluidic channels, especially for an explanation of a transition from unique drop size to bimodal oscillating drop sizes as observed in the experiments, numerical simulation is developed to use the volume-of-fraction method to model the drop formation, and the simulation results help to interpret the transition in the theory of saddle-node transition in drop formation, as well as show the importance of selecting proper orifice length in flow-focusing microfluidic channel design. The electric technique for controlling of microfluidic emulsification is explored by a detailed study on low-frequency alternating-current electro-flow-focusing (EFF) emulsification in microfluidic channels. It is found that the droplet size variation is not a monotonic function of the electric field as in the case of direct-current EFF emulsification, which originates from the relaxation oscillation of the flow rate through the Taylor cone, and a power-law droplet size distribution was obtained at the voltage ramping-up stage. This emulsification process was modeled in analog to the charge accumulation and release in a resistor-capacitor electric circuit with an adjustable resistor, and the simulated data exhibit good agreement with the experiments. As an application of the microfluidic emulsification, a method of fabricating disk-like wax colloidal particle suspensions using electrospray is reported. Based on this technique, the first measurement of the hindrance function for sedimentation and creaming of disk-shaped colloids via the analytical centrifugation is reported. Disks align with the external flow right above the volume fraction of a few percent and this effect is extremely sensitive to the aspect ratio of disks. Due to this alignment effect, disk sedimentation/creaming demonstrate distinct trends in dilute and semi-dilute region.

Combination chemotherapies that introduce multi-agent treatments to target cancer cells are emerging as new paradigms to overcome chemotherapy resistance and side effects involved with conventional monotherapies. In environmental toxicology, characterizing effects of mixtures of toxins rather than simply analyzing the effect of single toxins are of significant interest. In order to determine such combination effects, it is necessary to systematically investigate interactions between different concentration-dependent components of a mixture. Conventional microtiter plate format based assays are efficient and cost-effective, however are not practical as the number of combinations increases drastically. Although robotic pipetting systems can overcome the labor-intensive and time-consuming limitations, they are too costly for general users. Microfluidic live cell screening platforms can allow precise control of cell culture microenvironments by applying accurate doses of biomolecular mixtures with specific mixing ratios generated through integrated on-chip microfluidic gradient generators. This thesis first presents a live cell array platform with integrated microfluidic network-based gradient generator which enables generation and dosing of 64 unique combinations of two cancer drugs at different concentrations to an 8 by 8 cell culture chamber array. We have developed the system into a fully automated microfluidic live cell screening platform with uniform cell seeding capability and pair-wise gradient profile generation. This platform was utilized to investigate the gene expression regulation of colorectal cancer cells in response to combination cancer drug treatment. The resulting cell responses indicate that the two cancer drugs show additive effect when sequential drug treatment scheme is applied, demonstrating the utility of the microfluidic live cell assay platform. However, large reagent consumption and difficulties of repeatedly generating the exact same concentrations and mixture profiles from batch to batch and device to device due to the fact that the generated gradient profiles or mixing ratios of chemicals have to rely on stable flow at optimized flow rate throughout the entire multi-day experiment limit the widespread use of this method. Moreover, producing three or more reagent mixtures require complicated microchannel structures and operating procedures when using traditional microfluidic network-based gradient generators. Therefore, an on-demand geometric metering-based mixture generator which facilitates robust, scalable, and accurate multi-reagent mixing in a high-throughput fashion has been developed and incorporated with a live cell array as a microfluidic screening platform for conducting combination drug or toxin assays. Integrated single cell trapping array allowed single cell resolution analysis of drugs and toxin effects. Reagent mixture generation and precise application of the mixtures to arrays of cell culture chambers repeatedly over time were successfully demonstrated, showing significantly improved repeatability and accuracy than those from conventional microfluidic network-based gradient generators. The influence of this improved repeatability and accuracy in generating concentration specified mixtures on obtaining more reliable and repeatable biological data sets were studied.

The use of mass spectrometry in the biosciences has undergone huge growth in re- cent years due to sustained effort in the development of new ionisation techniques, more powerful mass analysers and better bioinformatic tools. These developments mean that it is now possible to introduce complex crude biological-mixtures into a mass spectrometric platform and to obtain detailed information about the sample. The front-end sample handling techniques used for sample preparation have, for the most part, not changed despite the recent advances in hyphenation of liquid- chromatography and mass spectrometry required to tackle the issue of increased sample complexity. In this thesis the possibility of using Digital Microfluidics (DMF) for front-end sample preparation prior to mass-spectrometric analysis of protein samples has been investigated. DMF is a micro-electromechanical system (MEMS) technology used for manipulation of sub-microlitre droplets. The movement of discrete droplets of liquid is exploited using the Coulombic forces arising due to free charge polarisation. Droplets can be split, joined, dispensed and moved over a sub-surface electrode array. In this thesis a range of DMF devices have been designed, manufactured and coupled with mass spectrometric platforms for protein analysis. A variety of techniques for mass spectrometry- based analysis of biological samples from the fluidic chips have been investigated. A robotic system has been developed to automate sample introduction, manipulation and removal. Finally the application of on-chip sample purification and enzymatic digestion have been demonstrated, providing proof of concept for digital microfluidic sample preparation in mass spectrometry-based proteomics.

Rapid creation of devices with microscale features is a vital step in the commercialization of a wide variety of technologies, such as microfluidics, fuel cells and self-healing materials. The current standard for creating many of these microstructured devices utilizes the inexpensive, flexible material poly-dimethylsiloxane (PDMS) to replicate microstructured molds. This process is inexpensive and fast for small batches of devices, but lacks scalability and the ability to produce large surface-area materials. The novel fabrication process presented in this paper uses a cylindrical mold with microscale surface patterns to cure liquid PDMS prepolymer into continuous microstructured films. Results show that this process can create continuous sheets of micropatterned devices at a rate of 1.9 in2/sec (~1200 mm2/sec), almost an order of magnitude faster than soft lithography, while still retaining submicron patterning accuracy.

Thrombosis is the pathological formation of platelet aggregates that cause stroke and heart attack\textemdash the leading causes of death in developed nations. Determining effective dosages for platelet therapies (e.g. aspirin, Integrilin, and Plavix) to prevent thrombosis is a persistent medical challenge (studies estimate up to 45% of patients exhibit insufficient responses to these drugs) and recent studies have implicated pathological flow conditions of high shear rates and stenosis morphology as primary factors. However, there are currently no diagnostic instruments able to recapitulate a range of such pathological flow conditions for evaluating thrombosis with and without these drugs. In this work, a microfluidic device and associated optical system were designed and fabricated for simultaneous measurement of platelet aggregation at multiple initial wall shear rates within multiple stenotic channels in label-free whole blood and used to characterize thrombosis at varying dosages of two platelet therapies: acetyl-salicylic acid (aspirin) and eptifibatide (Integrilin). Results from our studies show the effects of pathologically high shear rates on enhancing platelet thrombosis and demonstrate the widely varied, shear-dependent efficacy of each therapy. This study lays the foundation for the future development of a medical diagnostic for optimizing the type and dosage of patient platelet therapy and to better understand their mechanisms of action.

No description available.

<p>Promising applications in the design of various biological systems hold critical implications as heralded in the rising field of synthetic biology. But, to achieve these goals, the ability to synthesize in situ DNA constructs of any size or sequence rapidly, accurately and economically is crucial. Today, the process of DNA oligonucleotide synthesis has been automated but the overall development of gene and genome synthesis technology has far lagged behind that of gene and genome sequencing. This has meant that numerous ideas go unfulfilled due to scale, cost and impediments in the quality of DNA due to synthesis errors. </p><p>This thesis presents the development of a multi-tool ensemble platform targeted at gene synthesis. An inkjet oligonucleotide synthesizer is constructed to synthesize DNA microarrays onto silica functionalized cylic olefin copolymer substrates. The arrays are married to microfluidic wells that provide a chamber to for enzymatic amplification and assembly of the DNA from the microarrays into a larger construct. Harvested product is then amplified off-chip and error corrected using a mismatch endonuclease-based reaction. This platform has the potential to be particularly low-cost since it employs standard phosphoramidite reagents and parts that are cheaper than optical and electrochemical systems. Genes sized 160 bp to 993 bp were successfully harvested and, after error correction, achieved up to 94% of intended functionality.</p> / Dissertation

Transport in nanostructures and on-chip detection using nanohole arrays are investigated using a combination of analytical, numerical and experimental techniques. The first half of the thesis describes a fundamental theoretical contribution to the study of nanofluidic species transport. The second half of the thesis describes an applied experimental application of nanostructure-based species detection in a microfluidic framework. A continuum based analytical solution and numerical model are developed to quantify ionic dispersion of charged and neutral species in nanochannels and identify fundamental dispersion mechanisms unique to nanoscale flows. Ionic dispersion for circular cross-section nanochannels is quantified as a function of a valance parameter. the relative electrical double layer thickness. and the form of the velocity profile. Two unique mechanisms governing ionic dispersion in both pressure- and electrokinetically driven flows are identified. The results of the analytical solution are supported and extended by the results of the numerical model. Collectively, these results indicate that dispersion of ionic species in nanoscale channels is markedly charge dependent and substantially deviates from that of neutral solutes in the same flow. A microfluidic device with a set of embedded nanohole array surface plasmon resonance sensors is developed and successfully demonstrated experimentally as a chemical/biological sensor. The device takes advantage of the unique optical properties. the surface-based sensitivity, the transmission mode operation. relatively small footprint, and repeatability characteristic of nanohole arrays. Proof-of-concept measurements are performed on-chip to detect changes in liquid refractive index at the array surface. proportional to change in near wall concentration or indicative of a surface binding event. Employing a cross-stream array of nanohole arrays. the device is applied to detect microfluidic concentration gradients as well as to detect surface binding in the assembly process of a cysteamine monolayer-biotin-streptavidin system.

Optical confinement and manipulation of matter, or optical trapping, is widely adopted at micro-scales as a research tool in disciplines of biology, engineering, and physics. Microfluidic systems arc attractive from the standpoint of low sample volumes, laminar flow, and viscous damping and offer an ideal environment for trapping of miniaturized objects and microorganisms. Various trapping configurations are presented in this thesis using a custom fabricated consumer-grade optofluidic chip and are of significant scientific and practical importance. Microfluidics and fiber optics are integrated in-plane to achieve several flow-dependent particle trapping mechanisms on-chip. Each mechanism results from a combination of fluid drag and optical scattering forces. Parallel and offset fibers, orthogonally oriented to the flow, show cyclic cross-stream particle transit with flow-dependent particle trajectories and loss. Upstream-angled fibers with flow result in circulatory particle trajectories. Asymmetric angled fibers result in continuous particle circulation whereas symmetry with respect to the flow axis enables both stable trapping and circulation modes. Stable trapping of single particles, self-guided multi-particle arrays and stacked particle assemblies are demonstrated with a single upstream-oriented fiber. Size tuning of trapped multiple particle assemblies is also presented. The planar interaction of fluid drag and optical forces results in novel possibilities for cost-effective on-chip diagnostics, mixing, flow rate monitoring, and cell analysis. An opto-hydrodynamic theory is adopted to verify experimentally observed particle array dynamics in a dual-beam fiber-optic trap. When applied to dielectric microsphere particles, the theory confirms the inhomogeneous self-organization and the spontaneous emergence of self-sustained oscillations in particle arrays. In the presence of small-scale symmetry-breaking, self-sustained oscillations are shown to occur spontaneously from an exchange between the optical scattering and the gradient optical forces, in the absence of inertia that is central to the dynamics of ion traps. Experimental results show non-uniform equilibrium particle spacing and spontaneous self-sustained oscillation for large particle numbers. Self-organization and oscillation is of general interest to other systems involving multi-particle optical interactions.

This work revolves around the development of microfluidic technology for use in biomedical diagnostics with a specific focus on analyte concentration. At the reduced scale inherent with microfluidic technologies the sensing of target species can be difficult since the sample volume is reduced to nanolitres leading to low amounts of target species. This necessitates the need to preconcentrate samples prior to the sensing step. The exclusion-enrichment phenomenon associated with concentration polarization has been used within microfluidic platforms for the purpose of analyte concentration though methods have all been inherently 1-D, axial configurations. Within this work a novel radial concentration strategy based on a single microfluidic layer on a uniform nanoporous film is presented. The active nanostructured region is defined by the microfluidics, providing flexibility and opening opportunities beyond the single-channel axial configurations to date. Radial geometries have not been previously shown operating as CP based concentration devices, though the unique geometry offers enhanced flux at the perimeter and the capability to focus samples down to small central regions. This focusing ability allows the concentration to take place on a separate layer and does not compete for space with other analysis fluidics. This radial configuration is numerically modeled and experimentally demonstrated.