<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

Prediction of bubble formation during filling of microchambers is often critical for determining the efficacy of microfluidic devices in various applications. In this study experimental validation is performed to verify the predictions from a previously developed numerical model using lumped analyses for simulating bubble formation during the filling of microchambers. The lumped model is used to predict bubble formation in a micro-chamber as a function of the chamber geometry, fluid properties (i.e. viscosity and surface tension), surface condition (contact angle, surface roughness) and operational parameters (e.g., flow rate) as user defined inputs. Several microchambers with different geometries and surface properties were microfabricated. Experiments were performed to fill the microchambers with different liquids (e.g., water and alcohol) at various flow rates to study the conditions for bubble formation inside the microchambers. The experimental data are compared with numerical predictions to identify the limitations of the numerical model. Also, the comparison of the experimental data with the numerical results provides additional insight into the physics of the micro/nano-scale flow phenomena. The results indicate that contact angle plays a significant role on properties of fluids confined within small geometries, such as in microfluidic devices.

This dissertation focuses on the study of inverse temperature transition processes of the poly(N-isopropylacrylamide) (PNIPAM) and the elastin-like polypeptides (ELPs). A novel temperature jump microfluidic system is introduced and this system shows the ability to measure the kinetics of the PNIPAM and the ELPs collapse without a heat transfer problem. The conformational change of the ELPs during the phase transition process is utilized as a nanoscale protein filter to modulate ligandreceptor binding events on supported lipid bilayers (SLBs). This research study is divided into three main parts. The first part is the development of the temperature jump microfluidics. The kinetics of PNIPAM collapse is used as a model system to show the capability of this new device to measure millisecond time scale phase transition processes. The effects of salts on the kinetics of PNIPAM collapse are also shown in this part. To our knowledge, this is the first study which shows the effects of salts on PNIPAM collapse kinetics. The second part of this research is the application of the novel temperature jump microfluidics. The hydrophobic collapse of ELPs composed of identical sequence but different chain length is investigated. By controlling the molecular weight of the ELPs, the thermodynamic contributions from intermolecular hydrophobic interactions, and intramolecular hydrophobic interactions could be calculated individually for this unique system. The third part is the application of the phase transition property of ELPs. The ELPs are conjugated on the surface of the SLBs as a nanoscale protein filter. The conformation of the ELPs can be modulated by ionic strength of the buffer solution or ambient temperature. The ELPs conjugated SLBs platform showed the ability to block IgG binding to biotin conjugated on the SLBs when the ELPs were in the extended coil state and open the access for protein to bind to biotin in compact globule conformation.

This study proposes a novel microfluidic system based on a computer controlled digital image processing (DIP) technique and optical tweezers for automatic cell/microparticle recognition, counting and sorting in a continuous flow environment. In the proposed system, the cells/microparticles are focused electrokinetically into a narrow sample stream and are then driven through the region of interest (ROI), where they are recognized and traced in real time using a proprietary DIP system. Synchronized control signals generated by the DIP system are then used to actuate a focused IR laser beam to displace the target cells from the main sample stream into a neighboring sheath flow, which carries them to a downstream collection channel where they are automatically counted. The proposed approach makes possible the continuous sorting and counting of cell samples without the need for any moving parts or embedded transducers. The experimental results show that the proposed system is capable of sorting 5 £gm or 10 £gm PS bead from a mixture of 5 £gm and 10 £gm samples in the flow speed 300 £gm/sec. The proposed system provides a simple, low-cost, high-performance solution for cell manipulation in microfluidic devices.

Although advances in microfluidic technology have enabled increasingly sophisticated biosensing and bioassay operations to be performed at the microscale, many of these applications employ such small amounts of charged biomolecules (DNA, proteins, peptides) that they must first be pre-concentrated to a detectable level. Efficient strategies for precisely handling minute quantities of biomolecules in microchannel geometries are critically needed, however it has proven challenging to achieve simultaneous concentration, focusing, and metering capabilities with currentgeneration sample injection technology. Using microfluidic chips incorporating arrays of individually addressable microfabricated electrodes, we demonstrate that DNA can be sequentially concentrated, focused into a narrow zone, metered, and injected into an analysis channel. The technique used in this research transports charged biomolecules between active electrodes upon application of a small potential difference (1 V), and is capable of achieving orders of magnitude concentration increases within a small device footprint. The collected samples are highly focused, with sample zone size and shape defined solely by electrode geometry. In addition to achieving the objectives of the research project, this setup was found to provide added functionality as a label-free biomolecule detection technique due to the formation of light scattering phases of charged biomolecules on top of the capture electrode.

Molecular weight and concentration are two most important characteristics of polymers synthesized through chemical or microbial processes. However, current methods for characterizing polymer molecular weight such as Multi-Angle Laser Light Scattering (MALLS) or Gel Permeation Chromatography (GPC) require precise information on concentration as well as extensive sample preparation. Additionally, these current methods are also generally expensive, low throughput, and require large sample titers. These limitations prevent dynamic time-point studies of changes in molecular weight, which would be very useful for monitoring synthesis progress in microbes or in chemical synthesis. In this thesis, we designed, fabricated, and tested a rapid, low cost, high throughput, modular microfluidic system for determining polymer molecular weight in samples of unknown concentrations. To assess the accuracy of this system, we first constructed theoretical predictions for its accuracy, and then compared these to the experimental results from our microfluidic system. The system evaluated molecular weight by correlating the behavior of polymers in various solvent conditions to their molecular weights. The system consists of two modules for measuring fluid viscosity, and for controlling solvent conditions. Results of this study will show that this system is able to evaluate the differences in polymer viscosity for varying molecular weights and solvent conditions. For the solvent control module, we show that salt concentrations in small titers of polymer solutions can be rapidly added or subtracted and evaluated compared with current methods. Next, we will show the efficacy of the viscosity module at rapidly and accurately assessing fluid viscosity over a wide range of molecular weights. Finally, we will show the effects of solvent changes on molecular weight viscosity, and thus the efficacy of the system in determining molecular weight from fluid viscosity. This system will be applied to the evaluation of both the biologically produced polymer Hyaluronic Acid (HA) as well as the synthetically produced polymer Poly-ethylene Oxide (PEO).

Binding of the antigen receptor on T cells initiates a rapid series of signaling events leading to an immune response. To fully understand T cell mediated immunity, underlying regulatory properties of the receptor network must be understood. Monitoring dynamic protein signaling events allows for network analysis. Unfortunately, dynamic data acquisition is often extremely time-consuming and expensive with conventional methods; the number of proteins monitored at the same time on the same sample is limited. Furthermore, with conventional, multi-well plate assays it is difficult to achieve adequate resolution at sub-minute timescales. Microfluidics is a capable alternative, providing uniformity in sample handling to reduce error between experiments and precision in timing, an important factor in monitoring phosphorylation events that occur within minutes of stimulation. We used a two-module microfluidic platform for simultaneous multi-time point stimulation and lysis of T cells to investigate early signaling events with a resolution down to 20 seconds using only small amounts of cells and reagents. The device did not elicit adverse cellular stress in Jurkat cells. The activation of 6 important proteins in the signaling cascade upon stimulation with a soluble form of α-CD3 in the device was quantified and compared under a variety of conditions. First, in comparison to manual pipetting, the microdevice exhibits significantly less error between experiments. Secondly, a comparison between Jurkat cells and primary T cells shows similar dynamic trends across the 6 proteins. Finally, we have used the device to compare properties of long-term vs, short-term cultured primary T cells. As expected, older cells present a much weakened response to antigenic cues, as measured with TCR response markers. This modular microdevice provides a flexible format for investigating cell signaling properties through the use of soluble cue stimuli.

<p>Imagine if you could combine the power and capabilities ofan entire laboratory in the palm of your hand. Advances inmicrofluidic chip technology promise to integrate andminiaturize multiple lab processes into a single palm-sizeddevice. The advantages of these lab-on-a-chip devices,sometimes also referred to as micro total analysis systems(µTAS), compared with conventional bench-scale systems arenumerous and wide ranging and include: less reagentconsumption, low manufacturing costs, increased performance,faster analysis, high sample throughput, integration andautomation possibilities, and disposability. However,microfluidic devices also present challenges such as theinterfacing to the macro world and detection limits.</p><p>In this thesis the focus has been to develop novel discretemicrofluidic components for biotechnology and organic chemicalapplications with the goal to integrate them to formlab-on-chips. A flow-through filter-chamber device has beendesigned, manufactured and evaluated for chemical analysis onbeads. Passive liquid handling has been integrated on the chipin the form of hydrophobic valves at the inlet channels. Anarray format has also been developed to allow parallel analysisof multiple samples. The filter-chamber functions well forsingle nucleotide analysis using pyrosequencing. Initialevaluations on catalyst screening in the filter-chamber devicehas been performed.</p><p>The suitability of valve-less micropumps for biochemicalapplications is presented. Fluids encountered in variousbiochemical methods, including living cells, that areproblematic for other micropumps have been pumped with goodperformance. This thesis also introduces expandablemicrospheres as a novel component in microfluidics includingapplications such as one-shot valves, micropositioning andsurface enlargement.</p><p>A novel technique for bead immobilization in microfluidicdevices based on surface chemistry is presented in this thesis.Beads for both biochemical assays and organic chemistry havebeen self-sorted and self-assembled in line patterns as narrowas 5 µm on both structured and unstructured substrates.This method will greatly facilitate the generation of screeningplatforms, for example.</p><p>To develop a microfluidic device for catalysis-on-chip,ligands for asymmetric catalysis have successfully beenimmobilized in silicon channels by consecutive microcontactprinting, which is a novel technique presented in thisthesis.</p><p><b>Keywords:</b>microfluidics, beads, microspheres, silicon,filter-chamber, flow-through, bead trapping, DRIE, passivevalves, fluorocarbon, microfluidic array, adhesive bonding,valve-less micropump, microcontact printing, PDMS,self-assembly, self-sorting, DNA, SNP, pyrosequencing,allele-specific extension, expandable microspheres, catalysis,chiral ligand, monolayer, miniaturization, lab-on-a-chip,µTAS.</p>

Thesis (Ph.D.)--Brown University, 2008. / Vita. Advisor : Anubhav Tripathi. Includes bibliographical references.

Thesis (M.S.)--Oregon State University, 2010. / Printout. Includes bibliographical references (leaves 77-78). Also available on the World Wide Web.