<p>Data acquisition and diagnostics for chemical and biological analytes are critical to medicine, security, and the environment. Miniaturized and portable sensing systems are especially important for medical and environmental diagnostics and monitoring applications. Chip scale integrated planar photonic sensing systems that can combine optical, electrical and fluidic functions are especially attractive to address sensing applications, because of their high sensitivity, compactness, high surface specificity after surface customization, and easy patterning for reagents. The purpose of this dissertation research is to make progress toward a chip scale integrated sensing system that realizes a high functionality optical system integration with a digital microfluidics platform for medical diagnostics and environmental monitoring. </p><p>This thesis describes the details of the design, fabrication, experimental measurement, and theoretical modeling of chip scale optical sensing systems integrated with electrowetting-on-dielectric digital microfluidic systems. Heterogeneous integration, a technology that integrates multiple optical thin film semiconductor devices onto arbitrary host substrates, has been utilized for this thesis. Three different integrated sensing systems were explored and realized. First, an integrated optical sensor based upon the heterogeneous integration of an InGaAs thin film photodetector with a digital microfluidic system was demonstrated. This integrated sensing system detected the chemiluminescent signals generated by a pyrogallol droplet solution mixed with H2O2 delivered by the digital microfluidic system. </p><p>Second, polymer microresonator sensors were explored. Polymer microresonators are useful components for chip scale integrated sensing because they can be integrated in a planar format using standard semiconductor manufacturing technologies. Therefore, as a second step, chip scale optical microdisk/ring sensors integrated with digital microfluidic systems were fabricated and measured. . The response of the microdisk and microring sensing systems to the change index of refraction, due to the glucose solutions in different concentrations presented by the digital microfluidic to the resonator surface, were measured to be 95 nm/RIU and 87nm/RIU, respectively. This is a first step toward chip-scale, low power, fully portable integrated sensing systems. </p><p>Third, a chip scale sensing system, which is composed of a planar integrated optical microdisk resonator and a thin film InGaAs photodetector, integrated with a digital microfluidic system, was fabricated and experimentally characterized. The measured sensitivity of this sensing system was 69 nm/RIU. Estimates of the resonant spectrum for the fabricated systems show good agreement with the theoretical calculations. These three systems yielded results that have led to a better understanding of the design and operation of chip scale optical sensing systems integrated with microfluidics.</p> / Dissertation

As digital microfluidics has continued to mature since its advent in the early 1980's, an increase in new and novel applications of this technology have been developed. However, even as this technology has become more common place, a consensus on the physics and force models of the motion of the contact line between the fluid, substrate, and ambient has not been reached. This uncertainty along with the dependence of the droplet geometry on the force to cause its motion has directed much of the research at specific geometries and droplet actuation methods. The goal of this thesis is to help characterize the components of the friction force which opposes droplet motion as a one dimensional system model based upon simple system parameters independent from the actuation method. To this end, the force opposing the motion of a droplet under a thin rectangular glass cover slip was measured for varying cover slip dimensions (widths, length), gap height between the cover slip and substrate, and bulk droplet velocity. The stiffness of the droplet before droplet motion began, the force at which the motion initiated, and the steady-state force opposing the droplet motion were measured. The data was then correlated to hypothesized equations and compared to simple models accounting for the forces due to the contact angle hysteresis, contact line friction, and viscous losses. It was found that the stiffness, breakaway force, and steady-state force of the droplet could be correlated to with an error standard deviation of 8 %, 14%, and 10 % respectively. Much of the error was due to an unexpected height dependence for the breakaway and steady-state forces and testing error associated with the velocity. The models for the stiffness and breakaway force over predicted the results by 36% and 16% respectively. During testing, viii stability issues with the cover slip were observed and simple dye testing was conducted to visualize the droplet flow field.

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<p>This thesis demonstrates a new way to achieve sparse biological sample detection, which uses magnetic bead manipulation on a digital microfluidic device. Sparse sample detection was made possible through two steps: sparse sample capture and fluorescent signal detection. For the first step, the immunological reaction between antibody and antigen enables the binding between target cells and antibody-­‐‑ coated magnetic beads, hence achieving sample capture. For the second step, fluorescent detection is achieved via fluorescent signal measurement and magnetic bead manipulation. In those two steps, a total of three functions need to work together, namely magnetic beads manipulation, fluorescent signal measurement and immunological binding. The first function is magnetic bead manipulation, and it uses the structure of current-­‐‑carrying wires embedded in the actuation electrode of an electrowetting-­‐‑on-­‐‑dielectric (EWD) device. The current wire structure serves as a microelectromagnet, which is capable of segregating and separating magnetic beads. The device can achieve high segregation efficiency when the wire spacing is 50µμm, and it is also capable of separating two kinds of magnetic beads within a 65µμm distance. The device ensures that the magnetic bead manipulation and the EWD function can be operated simultaneously without introducing additional steps in the fabrication process. Half circle shaped current wires were designed in later devices to concentrate magnetic beads in order to increase the SNR of sample detection. The second function is immunological binding. Immunological reaction kits were selected in order to ensure the compatibility of target cells, magnetic bead function and EWD function. The magnetic bead choice ensures the binding efficiency and survivability of target cells. The magnetic bead selection and binding mechanism used in this work can be applied to a wide variety of samples with a simple switch of the type of antibody. The last function is fluorescent measurement. Fluorescent measurement of sparse samples is made possible of using fluorescent stains and a method to increase SNR. The improved SNR is achieved by target cell concentration and reduced sensing area. Theoretical limitations of the entire sparse sample detection system is as low as 1 Colony Forming Unit/mL (CFU/mL).</p> / Dissertation

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.

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.

<p>Digital microfluidics is an emerging technology that provides fluid-handling capability on a chip. Biochips based on digital microfluidics have therefore enabled the automation of laboratory procedures in biochemistry. By reducing the rate of sample and reagent consumption, digital microfluidic biochips allow continuous sampling and analysis for real-time biochemical analysis, with application to clinical diagnostics, immunoassays, and DNA sequencing. Recent advances in technology and applications serve as a powerful driver for research on computer-aided design (CAD) tools for biochips.</p><p>This thesis research is focused on a design automation framework that addresses chip synthesis, droplet routing, control-pin mapping, testing and diagnosis, and error recovery. In contrast to prior work on automated design techniques for digital microfluidics, the emphasis here is on practical CAD optimization methods that can target different design problems in a unified manner. Constraints arising from the underlying technology and the application domain are directly incorporated in the optimization framework.</p><p>The avoidance of cross-contamination during droplet routing is a key design challenge for biochips. As a first step in this thesis research, a droplet-routing method based on disjoint droplet routes has been developed to avoid cross-contamination during the design of droplet flow paths. A wash-operation synchronization method has been developed to synchronize wash-droplet routing steps with sample/reagent droplet-routing steps by controlling the order of arrival of droplets at cross-contamination sites.</p><p>In pin-constrained digital microfluidic biochips, concurrently-implemented fluidic operations may involve pin-actuation conflicts if they are not carefully synchronized. A two-phase optimization method has been proposed to identify and synchronize these fluidic operations. The goal is to implement these fluidic operations without pin-actuation conflict, and minimize the duration of implementing the outcome sequence after synchronization.</p><p>Due to the interdependence between droplet routing and pin-count reduction, this thesis presents two optimization methods to concurrently solve the droplet-routing and the pin-mapping design problems. First, an integer linear programming (ILP)-based optimization method has been developed to minimize the number of control pins. Next an efficient heuristic approach has been developed to tackle the co-optimization problem.</p><p>Dependability is an important system attribute for microfluidic biochips. Robust testing methods are therefore needed to ensure correct results. This thesis presents a built-in self-test (BIST) method for digital microfluidic biochips. This method utilizes digital microfluidic logic gates to implement the BIST architecture. A cost-effective fault diagnosis method has also been proposed to locate a single defective cell, multiple</p><p>rows/columns with defective cells, as well as an unknown number of rows/columns-under-test with defective cells. A BIST method for on-line testing of digital microfluidic biochips has been proposed. An automatic test pattern generation (ATPG) method has been proposed for non-regular digital microfluidic chips. A pin-count-aware online testing method has been developed for pin-constrained designs to support the execution of both fault testing and the target bioassay protocol.</p><p>To better monitor and manage the execution of bioassays, control flow has been incorporated in the design and optimization framework. A synthesis method has been developed to incorporate control paths and an error-recovery mechanism during chip design. This method addresses the problem of recovering from fluidic errors that occur</p><p>during on-chip bioassay execution.</p><p>In summary, this thesis research has led to a set of unified design tools for digital microfluidics. This work is expected to reduce human effort during biochip design and biochip usage, and enable low-cost manufacture and more widespread adoption for laboratory procedures.</p> / Dissertation

<p>Electrowetting-on-dielectric (EWD) digital microfluidics is a droplet-based fluid handling technology capable of radically accelerating the pace of genome engineering research. EWD-based laboratory-on-chip (LoC) platforms demonstrate excellent performance in automating labor-intensive laboratory protocols at ever smaller scales. Until now, there has not been an effective means of gene transfer demonstrated in EWD microfluidic platforms. This thesis describes the theoretical and experimental approaches developed in the demonstration of an EWD-enabled electrotransfer device. Standard microfabrication methods were employed in the integration of electroporation (EP) and EWD device architectures. These devices enabled the droplet-based bulk transformation of E. coli with plasmid and oligo DNA. Peak on-chip transformation efficiencies for the EP/EWD device rivaled that of comparable benchtop protocols. Additionally, ultrasound induced in-droplet microstreaming was developed as a means of improving on-chip electroporation. The advent of electroporation in an EWD platform offers synthetic biologists a reconfigurable, programmable, and scalable fluid handling platform capable of automating next-generation genome engineering methods. This capability will drive the discovery and production of exotic biomaterials by providing the instrumentation necessary for rapidly generating ultra-rich genomic diversity at arbitrary volumetric scales.</p> / Dissertation

Digital microfluidics (DMF) has emerged in the past decade as a novel microfluidic paradigm. As a liquid handling technology, DMF facilitates the electrostatic manipulation of discrete nano- and micro- litre droplets across open electrode arrays providing the advantages of single sample addressability, automation, and parallelization. This thesis presents DMF advances toward improved functionality and compatibility for automated miniaturized cell culture in two and three dimensions. Through the development and integration of surface patterning techniques we demonstrate a virtual microwell method for high precision on-device reagent dispensing in one and two plate DMF geometries. These methods are shown to be compatible with two-dimensional culture of immortalized cell lines on ITO, primary cells on coated surfaces, and for co-culture assays. We further extrapolate this method for the formation of microgels on-demand where form micro scale hydrogel structures through passive dispensing in a wide array of geometries. With this system we interrogate three-dimensional cell culture models, specifically for the recapitulation of kidney epthelialization and the analysis of functional cardiac microgels.