<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

Microresonators are devices that confine light in small volumes through total internal reflection. Introducing an emissive species into a microresonator allows for resonance enhanced emission at frequencies where the spectrum of the emissive species overlaps with the resonant frequencies of the microresonator. Previous research has led to a good understanding of these phenomena in 1D and 2D microresonators, but many 3D microresonator geometries have not yet been investigated. This work details the successful creation and demonstration of a cubic polymeric optical microresonator.

This thesis theoretically and experimentally studies the characteristics of integrated microresonators (MRs) built by passive (no gain) and non-magnetic materials and characterized by both Hermitian and non-Hermitian Hamiltonians. In particular, I have studied three different microresonators: a typical Microring Resonator (MR), a Taiji Microresonator (TJMR), which consists of a microresonator with an embedded S-shaped waveguide, and a new geometry called the Infinity-Loop Microresonator (ILMR), which is characterized by a microresonator shaped like the infinity symbol coupled at two points to the bus waveguide. To get an accurate picture of the three devices, they were modeled using both the transfer matrix method and the temporal coupled mode theory. Neglecting propagation losses, the MR is described by a Hermitian Hamiltonian, while the TJMR and the ILMR are described by a non-Hermitian one. An important difference between Hermitian and non-Hermitian systems concerns their degeneracies. Hermitian degeneracies are called Diabolic Points (DPs) and are characterized by coincident eigenvalues and mutually orthogonal eigenvectors. In contrast, non-Hermitian degeneracies are called Exceptional Points (EPs). At the EP, both the eigenvalues and the eigenvectors coalesce. The MR is at a DP instead, and the TJMR and the ILMR are at an EP. Since the TJMR and ILMR are at an EP, they have interesting features such as the possibility of being unidirectional reflectors. Here, it is shown experimentally how in the case of the TJMR this degeneracy can also be used to break Lorentz reciprocity in the nonlinear regime (high incident laser powers), discussing the effect of the Fabry-Perot of the bus waveguide facets. The effect of backscattering, mainly due to the waveguide surface-wall roughness, on the microresonators is also studied. This phenomenon induces simultaneous excitation of the clockwise and counterclockwise modes, leading to eigenvalue splitting. This splitting makes the use of typical quality factor estimation methods unfeasible. To overcome this problem and mitigate the negative effects of backscattering, a new experimental technique called interferometric excitation is introduced. This technique involves coherent excitation of the microresonator from both sides of the bus waveguide, allowing selective excitation of a single supermode. By adjusting the relative phase and amplitude between the excitation fields, the splitting in the transmission spectrum can be eliminated, resulting in improved quality factors and eigenvalue measurements. It is shown that this interferometric technique can be exploited under both stationary and dynamic conditions of time evolution. The thesis also investigates the sensing performance of the three microresonators as a function of a backscattering perturbation, which could be caused, for example, by the presence of a molecule or particle near the microresonator waveguide. It is shown that the ILMR has better performance in terms of responsivity and sensitivity than the other two microresonators. In fact, it has both the enhanced sensitivity due to the square root dependence of the splitting on the perturbation (characteristic of EPs) and the ability to completely eliminate the region of insensitivity as the backscattering perturbation approaches zero, which is present in both the other two microresonators. To validate the models used, they were compared with experimental measurements both in the linear regime and, for TJMR, also in the nonlinear regime, with excellent agreement.

Recent instrument development for aerosol measurement has focussed on small-scale, on-line measurements that can be incorporated into miniaturised sensor nodes as part of ambient or personal air quality monitoring networks. As a result, optical particle counters (OPCs) have risen in popularity given their ability to consistently size and count individual particles. OPCs have limitations, however, in their inability to detect ultrafine particles (considered the most influential to human health) or to measure particle mass directly (the standard metric for air quality). The growing field of microelectromechanical systems (MEMS) offers a potential alternative by implementing microresonators as mass sensors. MEMS resonators have high mass sensitivities and have recently seen implementation as particulate matter (PM) monitors. The field of MEMS PM instruments is still limited with a variety of implemented resonator topologies and sampling mechanisms. In general, however, they offer real-time, high sensitivity measurements at low flow rates. The aim of this thesis was to further examine the viability of implementing MEMS resonators for PM measurement with a focus on practical considerations for real-world applications. To this end, a new microresonator-based impactor was developed - the MEMS Impactor Stage (MIS) - capable of accommodating various nozzle and resonator combinations. Square lateral bulk acoustic resonators were the primary topology, but the results within the thesis are widely applicable. A series of laboratory studies covered the resonator lifetime, reusability, detection limits, and response to environmental changes. The resonator displayed a high sensitivity throughout, capable of detecting ultrafine particles, but is vulnerable to misinterpretation. Beyond mass measurement, studies introduced possible extensions to hygroscopicity and compositional applications. Ambient particle measurements with the MIS, simulating a real-world application to air quality monitoring, showed the capabilities as a PM instrument while highlighting concerns to be addressed for future instrument design. A microresonator-based impactor has potential as an alternative to OPCs, but its cross sensitivity to deposition patterns and environmental effects must be accounted for prior to implementation as PM monitor.

<p>Integrated sensing systems are designed to address a variety of problems, including clinical diagnosis, water quality testing, and air quality testing. The growing prevalence of tropical diseases in the developing world, such as malaria, trypanosomiasis (sleeping sickness), and tuberculosis, provides a clear and present impetus for portable, low cost diagnostics both to improve treatment outcomes and to prevent the development of drug resistance in a population. The increasing scarcity of available clean, fresh water, especially noticeable in the developing world, also presents a motivation for low-cost water quality diagnostic tools to prevent exposure of people to contaminated water supplies and to monitor those water supplies to effectively mitigate their contamination. In the developed world, the impact of second-hand cigarette smoke is receiving increased attention, and measuring its effects on public health have become a priority. The `point-of-need' technologies required to address these sensing problems cannot achieve a widespread and effective level of use unless low-cost, small form-factor, portable sensing devices can be realized. Optical sensors based on low cost polymer materials have the potential to address the aforementioned `point-of-need' sensing problems by leveraging low-cost materials and fabrication processes. For portable clinical diagnostics and water quality testing in particular, on-chip sample preparation is a necessity. Electrowetting-on-dielectric (EWD) technology is an enabling technology for chip-scale sample preparation, due to its very low power consumption compared to other microfluidics technologies and the ability to move fluids without bulky external pumps. Potentially, these technologies could be combined into a cell phone sized portable sensing device.</p><p>Towards the goal of developing a portable diagnostic device using EWD microfluidics with an embedded polymer microresonator sensor, this thesis describes a viable fabrication process for the system and explores the design trade-offs of such a system. The main design challenges for this system are optimization of the sensor's limit-of-detection, minimization of the insertion loss of the optical system, and maintaining the ability to actuate droplets onto and off of the sensor embedded in the microfluidic system. The polymer microresonator sensor was designed to optimize the limit-of-detection (LOD) using SU-8 polymer as the bus waveguide and microresonator material and SiO2 as the substrate cladding material. The fabrication process and methodology were explored with test devices using a tunable laser system working around a wavelength of 1550 nm using glucose solutions as a refractive index standard. This sensor design was then utilized to embed the sensor and bus waveguides into an EWD top plate in order to minimize the impact of the sensor integration on microfluidic operations. Finally, the performance of the embedded sensor embedded was evaluated in the same manner and compared to the performance of the sensor without the microfluidic system.</p><p>The primary result of this research was the successful demonstration of a high performance polymer microresonator sensor embedded in the top plate of an electrowetting microfluidic device. The embedded sensor had the highest reported figure-of-merit for any microresonator integrated with electrowetting microfluidics. The embedded microresonator sensor was also the first fully-embedded microresonator in an EWD system. Because the sensor was embedded in the top plate, full functionality of the EWD system was maintained, including the ability to move droplets onto and off of the sensor and to address the sensor with single droplets. Furthermore, the highest figure-of-merit for an SU-8 microresonator sensor yet reported at a probe wavelength of 1550 nm was measured on a test device fabricated with the embedded sensor structure described herein. Optimization of the sensor sensitivity utilized recently developed waveguide sensor design theory, which accurately predicted the measured sensitivity of the sensors. Altogether, the results show that embedding of a microresonator sensor in an EWD microfluidics system is a viable approach to develop a portable diagnostic system with the high efficiency sample preparation capability provided by EWD microfluidics and the versatile sensing capability of the microresonator sensor.</p> / Dissertation

The need for miniaturized frequency-selective components in electronic systems is clear. The questions are whether and how micro-electro-mechanical systems (MEMS) can satisfy the need. This dissertation aims to address these questions from a scientific perspective. Silicon is the focus of this work, as it can benefit from scaling of the semiconductor industry. Silicon also offers many technical advantages. The characteristics of silicon resonators from 32 kHz to 1 GHz are described. The temperature stability and phase noise of a 6-MHz temperature-compensated oscillator and a 100-MHz temperature-controlled oscillator are reported. Silicon resonator design and characterization, with a focus on quality factor, linearity, and the electrical equivalent circuit, are included. Electrical tuning, electromechanical coupling, finite element modeling, and unexpected findings of these resonators are also described. A manufacturability technique employing batch process compensation is demonstrated. Results indicate that silicon is an excellent material for micromechanical resonators. The aim of this research is to explore the fundamental limitations, provide a foundation for future work, and also paint a clearer picture on how micromechanical resonators can complement alternative technologies.

This thesis explored fundamental concepts of linear optics focusing on the modal interaction within waveguide/microresonator systems. In addition, it investigated a nonlinear process of stimulated degenerate four-wave mixing in a channel waveguide exploiting the analogy between photons and cold boson atoms. The backscattering phenomenon due to the surface wall roughness of a microresonator is addressed by adding to the usual conservative (Hermitian) coupling coefficient, a dissipative (non-Hermitian) term. This allows explaining the experimental measurements of a multimodal microresonator, which exhibits an asymmetrical resonance splitting characterized by a difference in the peak depths of the transmission spectra. It is shown theoretically, numerically and experimentally that the stochastic nature of the roughness along with the inter-modal dissipative coupling could give rise to a different exchange of energy between the co-propagating and the counter-propagating mode. The unbalanced exchange of energy between the two modes with opposite angular momenta can generate a different reflection by swapping the injection of the light between the input and the output ports. This effect lies at the heart of the realization of an unidirectional reflection device and it finds an explanation in the physics of the exceptional points. The realization of an optical setup based on a Mach-Zehnder interferometer, which exploits some particular techniques of data acquisition, allows obtaining a full knowledge of the complex electric field of a propagating mode. In this way, the spectrum of a wedge microresonator vertically coupled to a bus waveguide is explained using analysis methods based on parametric phasors and inverse complex representations. In addition, the energy exchange between the co-propagating and counter-propagating modes is studied from a temporal point of view by extrapolating a simple model based on the Green function. In particular, it is discussed the analytical temporal response of a microring resonator excited through a bus waveguide by an optical rectangular pulse. Here, it is shown theoretically and experimentally, how the temporal response leads to the characterization of the coupling regime simply from the knowledge of the electric field intensity. In this thesis, the isomorphism between the Schroedinger’s equation and the Helmholtz wave equation is analyzed in the nonlinear case. Considering a bulk nonlinear medium of the Kerr type, the complex amplitude of the optical field is a slowly varying function of space and time, which satisfies a nonlinear Schroedinger equation. The well-known nonlinear optical phenomenon of stimulated degenerate four wave mixing is reformulated in the language of the Bogoliubov theory. This parallelism between photons and cold atoms allows showing that the phase of the signal assumes a peculiar sound-like dispersion under proper assumptions.

This thesis reports design and implementation of a MEMS based resonant mass sensor for cell detection applications. The main objective of the thesis is the real-time detection of captured cells inside liquid medium and obtaining the detection results by electronic means, without the aid of any external optical instruments. A new resonant mass sensor architecture is presented that has various advantages over its conventional counterparts. The device oscillates in the lateral direction, eliminating squeeze film damping. A thin parylene layer coated on the device prevents liquids from entering the narrow gaps of the device, further improving the quality factor. The resonator is embedded on the floor of a microchannel. A gold film on the proof mass facilitates antibody based cell capture on the device. Theoretical background regarding resonator operation is investigated. Various resonator designs are presented, taking into account design trade-offs, application v considerations, and fabrication limitations. The design procedure is verified with MATLAB Simulink modeling results and finite element simulations. A new process flow has been developed for resonator fabrication, combining SOI, glass, and polymer micromachining. Modifications have been done on the flow for the solution of problems encountered during device fabrication. Each device has a foot print area of 1.5 x 0.5 cm2. The majority of this area is occupied by fluidic connections and reservoirs. Resonance characterization results in air and water have shown that there is significant quality factor enhancement with the parylene coating method. The quality factor decreases to only 170 in water from 610 in air, when the resonator is coated with a thin layer of parylene. Uniformity and linearity tests revealed that the devices have a standard deviation of only 1.9% for different analyte capture sites and an R2 of 0.997 for mass loads as high as 2.7 ng. Detection of Saccharomyces cerevisiae type yeast cells has been done using the resonators. Mass measurement of single yeast cell (13 pg) and yeast clusters (102 pg) have been performed. Antibody and thiol-gold chemistry based Candida Albicans type bacteria capture and detection has also been made in both air and water environments. The mass of several captured bacterial cells in air has been measured as 95pg. Two bacterial cells have been captured on one device inside water and their mass has been measured as 85 pg. It is worthy to note that all mass measurements are consistent with theoretical expectations.

La détection d'espèces (bio)chimiques à de très faibles concentrations représente un enjeu croissant dans les domaines de la santé, de l’environnement et de la défense. Un microrésonateur optique en polymère, sans marqueurs fluorescents, associé à un canal microfluidique, forme un capteur optofluidique, ce qui permet la détection d'analytes par interaction entre un champ évanescent à la surface du microrésonateur et la solution contenant l’espèce à étudier. Cette thèse présente la conception et la réalisation de capteurs optofluidiques à base de microrésonateurs optiques et de circuits microfluidiques en polymères, pour une très faible limite de détection et un temps de réponse rapide. De très bons résultats ont été obtenus en termes de limite de détection de polluants de type ions lourds dans l'eau, en abordant le problème sous différents angles : conception et réalisation de circuits optiques et microfluidiques, optimisation de l’interrogation optique du capteur par l’élaboration d’une méthodologie de mesure rapide et précise et un traitement du signal adéquat, étude des propriétés physico-chimiques des surfaces polymères, mise au point d’une instrumentation adaptée. Le capteur a permis la détection d'ions cadmium, ions hautement toxiques, jusqu'à une décision limite de détection de 50 pmol/L dans l'eau déionisée et 500 pmol/L dans l'eau du robinet grâce à un greffage sur la surface du microrésonateur de 2,2’- ((4-Amino-1,2-Phénylène) Bis (Carboxylatoazanédyil)) Diacétate. Une étude de régénération de la surface fonctionnalisée des microrésonateurs pour la détection d’ions cadmium a été réalisée et ce capteur a pu être régénéré pour plus de soixante mesures consécutives. D’autre part, l'analyse simultanée de deux polarisations orthogonales entre elles TE et TM de la réponse optique du capteur permet d’optimiser la sensibilité de mesure. Une étude de mesure différentielle consistant à comparer simultanément les mesures sur deux microrésonateurs identiques placés dans les même conditions physiques, l’un jouant le rôle de référence et l’autre étant un capteur spécifique, a permis de s’affranchir des différentes perturbations externes (pression, température, attachements non spécifiques). Ces instruments « multi-capteurs » sont également essentiels pour une compréhension détaillée des mécanismes de réactions de surface, une évaluation de l'efficacité d'accrochage de différents protocoles de fonctionnalisation et des mesures en multiplexage. / High sensitivity biochemical sensing is a concern for health, environment and defense. Thanks to the interaction between an analyte and an evanescent field at their surface, label-free polymer microring resonators, in association with a microfluidic channel, form an optofluidic sensor that can be used for biosensing. This thesis shows the realization of versatile optofluidic sensors based on polymer microring resonators combining a high detection limit with a short response time. High limit of detection of heavy ions in tap water was obtained after a careful optimization of the optical and microfluidic designs, signal processing, methodology of detection, surface chemistry and instrumentation. By functionalizing the resonator surface with 2,2’-((4Amino-1,2- Phenylene)Bis(Carboxylatoazanedyil))Diacetate, we obtained a limit of detection of 50 pmol/L in deionized water and 500 pmol/L in tap water. It should be stressed that the functionalized surface of the resonator was regenerated more than 60 times, enabling several sensing experiments with the same resonator. Besides, we were able to optimize the measurement sensitivity by an analysis of the orthogonal polarizations TE and TM from the sensor optical response. The simultaneous use of at least two microresonators in parallel (providing a reference signal and allowing multiplexing) enabled us to improve measurement accuracy and to compensate the signal from various external perturbations such as pressure, temperature and non-specific bindings. These “multi-sensors” are essential for (i) an in-depth understanding of surface reaction mechanism, (ii) an evaluation of the binding efficiency of different functionalization protocols and (iii) a high throughput characterization tool for multiple detections of pollutants.

This dissertation presents the investigation of three thin film materials used in microelectromechanical systems (MEMS): alumina, silicon, and nickel. For this purpose, novel experimental techniques to test thin films under MEMS-relevant loading conditions were developed in order to study environmental effects and the underlying fatigue mechanisms of amorphous alumina ultra-thin coatings, mono-crystalline brittle silicon thin films, and poly-crystalline ductile nickel thin films. Knowledge of these mechanisms is necessary to improve the reliability of MEMS, especially of those devices operating in harsh environments. MEMS resonators were used to investigate both the fatigue and time-dependent behavior of alumina, silicon, and nickel. While micro-resonators were used in prior studies to research the fatigue properties of mono- and polycrystalline silicon, this work is the first in (1) using them to investigate fatigue properties of ultra-thin coatings and metallic films and in (2) using micro-resonators to investigate the time-dependent fatigue behavior of silicon films. For fatigue testing, the micro-resonators were subjected to fully-reversed loading at resonance (≈40 kHz for alumina-coated silicon, ≈8 kHz for nickel). Experiments were conducted in air at 30 °C, 50% relative humidity (RH) or 80 °C, 90% RH and testing was carried out over a broad range of applied stresses. The resonance frequency evolution proved to be a metric for the accumulated damage, which could be further quantified using finite element analysis. In addition, scanning and transmission electron microscopy were used to examine the extent of fatigue damage. For testing under static loads, the resonators were subjected to external loading using a micromanipulator and probe-tip. Experiments with atomic-layer-deposited alumina investigated the cohesive and interfacial fatigue properties of alumina coatings of four different thicknesses, ranging from nominally 4.2 nm to 50.0 nm on silicon micro-resonators. Fatigue loading led to both cohesive and interfacial damage, while static loading did not result in any damage. Both the cohesive and interfacial fatigue crack growth rates are approximately one order of magnitude higher at 80 °C, 90% RH than at 30 °C, 50% RH and seem to increase with increasing strain energy release rate. A combination of compressive loading and the silicon sidewall's surface roughness is believed to cause the observed fatigue behavior. Experiments with 10-micrometer-thick deep reactive ion etched silicon micro-resonators investigated two aspects: whether surface oxidation is the critical parameter in silicon thin film fatigue and time-dependent failure in silicon as a potential underlying cause of resonator failures in the low cycle fatigue (LCF, <17 cycles, corresponding to ≈5 min) regime. To confirm whether surface oxidation is the critical parameter in silicon thin film fatigue, the influence of oxygen diffusion barrier alumina coatings on the fatigue behavior was investigated. The coatings led to an increase in fatigue life by at least two orders of magnitude compared to uncoated devices in the harsh environment, which not only confirms reaction layer fatigue (RLF) as governing fatigue mechanism in silicon thin films, but also constitutes a practical solution to significantly increase fatigue lifetimes. Previous LCF data were inconsistent with the RLF model, given that thick surface oxidation is unrealistic for tests lasting only few minutes. Accordingly, time-dependent failure in silicon was investigated as underlying cause and the observation of resonator failures under static loading indeed suggest that time-dependent crack growth may be responsible for LCF failures. Experiments with metallic micro-resonators investigated the fatigue crack initiation in 20-micrometer-thick electro-deposited nickel under MEMS-relevant conditions, such as extreme stress gradients resulting in non-propagating cracks, fully-reversed loading (over a large range of stress amplitudes), exposure to mild and harsh environments, and accumulation of billions of cycles. Under these circumstances, extrusions form locally at the notch root (within few million cycles at high stress amplitudes). Very thick local oxides (only at the location of the extrusions) of up to 1100 nm were observed in the harsh environment, with thinner oxides (up to 700 nm) in the mild environment. Micro-cracks form in the oxide but do not propagate given the extreme stress gradients. Finite element analysis confirmed that oxidation and micro-cracking lead to changes in the resonance frequency, which are consistent with the experimental results. Accumulation of cyclic plasticity appears to also lead to a decrease in resonance frequency which scales with applied strain.