Proteins are commonly found molecules in biological systems: our fingernails, hair, skin, blood, muscle, and eyes are all made of protein. Many diseases simply arise because a protein is not folded properly. Therefore, knowledge of protein structure is considered a prerequisite to understanding protein function and, by extension, a cornerstone for drug design and for the development of therapeutic agents. Protein crystallography is a tool that allows structural biologists to discern protein structures to the highest degree of detail possible in three dimensions. The recording of x-ray diffraction data from the protein crystal is a central part of protein crystallography. As such, an important challenge in protein crystallography research is to design x-ray detectors to accurately determine the structures of proteins. This research presents the design and evaluation of a solid-state large area at panel detector for protein crystallography based on an amorphous selenium (a-Se) x-ray sensitive photoconductor operating in avalanche mode integrated with an amorphous silicon (a-Si:H) charge storage and readout pixel. The advantages of the proposed detector over the existing imaging plate (IP) and charge coupled device (CCD) detectors are large area, high dynamic range coupled to single x-ray detection capability, fast readout, high spatial resolution, and inexpensive manufacturing process. The requirement of high dynamic range is crucial for protein crystallography since both weak and strong diffraction spots need to be imaged. The main disadvantage of a-Si:H thin film transistor (TFT) array is its high electronic noise which prohibits quantum noise limited operation for the weak diffraction spots. To overcome the problem, the x-ray to charge conversion gain of a-Se is increased by using its internal avalanche multiplication gain. Since the detector can be made approximately the same size as the diffraction pattern, it eliminates the need for image demagnification. The readout time of the detector is usually within the ms range, so it is appropriate for crystallographic application. The optimal detector parameters (such as, detector size, pixel size, thickness of a-Se layer), and operating parameters (such as, electric field across the a-Se layer) are determined based on the requirements for protein crystallography. A complete model of detective quantum efficiency (DQE) of the detector is developed to predict and optimize the performance of the detector. The performance of the detector is evaluated in terms of readout time (< 1 s), dynamic range (~10^5), and sensitivity (~ 1 x-ray photon), thus validating the detector's efficacy for protein crystallography. The design of an in-house a-Si:H TFT pixel array for integration with an avalanche a-Se layer is detailed. Results obtained using single pixel are promising and highlight the feasibility of a-Si:H pixels coupled with avalanche a-Se layer for protein crystallography application.

A series of experiments was carried out to compare the structural and electronic properties of intrinsic nanocrystalline silicon (nc-Si:H) thin films deposited via continuous wave (cw) and pulsed (p)-PECVD at 150°C substrate temperature. Working at this temperature allows for the easy transfer of film recipes from glass to plastic substrates in the future. During the p-PECVD process the pulsing frequency was varied from 0.2 to 50 kHz at 50% duty cycle. Approximately 15% drop in the deposition rate was observed for the samples fabricated in p-PECVD compared to cw-PECVD. The optimum crystallinity and photo (σph) and dark conductivity (σD) were observed at 5 kHz pulsing frequency, with ~10% rise in crystallinity and about twofold rise in the σph and σD compared to cw-PECVD. However, for both the cw and p-PECVD nc-Si:H films, the observed σph and σD were one to two orders and three orders of magnitude higher respectively than those reported in literature. The average activation energy (EA) of 0.16 ∓ 0.01 eV for nc-Si:H films deposited using p-PECVD confirmed the presence of impurities, which led to the observation of the unusually high conductivity values. It was considered that the films were contaminated by the impurity atoms after they were exposed to air. Following the thin film characterization procedure, the optimized nc-Si:H film recipes, from cw and p-PECVD, were used to fabricate the absorber layer of thin film solar cells. The cells were then characterized for J-V and External Quantum Efficiency (EQE) parameters. The cell active layer fabricated from p-PECVD demonstrated higher power conversion efficiency (η) and a maximum EQE of 1.7 ∓ 0.06 % and 54.3% respectively, compared to 1.00 ∓ 0.04 % and 48.6% respectively for cw-PECVD. However, the observed η and EQE of both the cells were lower than a reported nc-Si:H cell fabricated via p-PECVD with similar absorber layer thickness. This was due to the poor Short-circuit Current Density (Jsc), Open-circuit Voltage (Voc), and Fill Factor (FF) of the cw and p-PECVD cells respectively, compared to the reported cell. The low Jsc resulted from the poor photocarrier collection at longer and shorter wavelengths and high series resistance (Rseries). On the other hand, the low Voc stemmed from the low shunt resistance (Rsh). It was inferred that the decrease in the Rsh occurred due to the inadequate electrical isolation of the individual cells and the contact between the n – layer and the front TCO contact at the edge of the p-i-n deposition area. Additionally, the net effect of the high Rseries and the low Rsh led to a decrease in the FF of the cells.

Magnetic nanoscale devices have shown great promise in both research and industry. Magnetic nanostructures have potential for non-volatile data storage applications, reconfigurable logic devices, biomedical devices and many more. The S-state magnetic element is one of the promising structures for non-volatile data storage applications and reconfigurable logic devices. It is a single-layer logic element that can be integrated in magnetoresistive structures. We present a detailed micromagnetic analysis of the geometrical parameter space in which the logic operation is carried out. The influence of imperfections, such as sidewall roughness and roundness of the edge is investigated. Magnetic nanowires are highly attractive materials that has potential for applications in ultrahigh magnetic recording, logic operation devices, and micromagnetic and spintronic sensors. To utilize applications, manipulation and assembly of nanowires into ordered structures is needed. Magnetic self-alignment is a facile technique for assembling nanowires into hierarchical structures. In my thesis, I focus on synthesizing and assembling nickel nanowires. The magnetic behaviour of a single nickel nanowire with 200~nm diameter is investigated in micromagnetic simulations. Nickel nanowires with Au caps at the ends were synthesized by electrochemical deposition into nanopores in alumina templates. One-dimensional alignment, which forms chains and two-dimensional alignment, which forms T-junctions as well as cross-junctions are demonstrated. Attempts to achieve three-dimensional alignment were not successful yet. I will discuss strategies to improve the alignment process.

This thesis describes the development and application of solid phase microextraction (SPME) as a sample preparation technique for in vivo determination of pharmaceutical residues in fish tissue and wastewater. The occurrence, distribution and fate of pharmaceuticals in the environment are a subject of concern across the globe due to the impact they may have on human life and aquatic organisms. To address this challenge from an analytical perspective, a simplified and reliable analytical methodology is required to investigate and determine the concentration (bioconcentration factors) of trace pharmaceutical residue in fish tissue and environmental water samples (exposure). An improved SPME method, coupled with liquid chromatography with tandem mass spectrometry has been developed and applied to both controlled laboratory and field-caged fish exposed to wastewater effluent for quantitative determination of pharmaceutical residue in fish specific tissue. A new SPME configuration based on C18 thin film (blade) was developed and optimized to improve SPME sensitivity for in vivo determinations of trace pharmaceuticals in live fish. The C18 thin film extraction phase successfully quantified bioconcentrated fluoxetine, venlafaxine, sertraline, paroxetine, and carbamazapine in the dorsal-epaxial muscle of living fish at concentrations ranging from 1.7 to 259 ng/g. The reproducibility of the method in spiked fish muscle was 9-18% RSD with limits of detection and quantification ranging from 0.08 - 0.21 ng/g and 0.09 - 0.64 ng/g (respectively) for the analytes examined. Fish were sampled by in vivo SPME for 30 min to detect pharmaceutical uptake and bioconcentration, with experimental extracts analyzed using liquid chromatography coupled with tandem mass spectrometry. In addition, a simplified analytical methodology based on SPME was developed and optimized for determination and bioconcentration factor of different classes of pharmaceuticals residues in fish bile. The reproducibility of the method in spiked fish Rainbow Trout bile was 3-7% RSD with limits of detection (LOD) ranging from 0.3 – 1.4 ng/mL for the analytes examined. The field application of SPME sampling was further demonstrated in Fathead Minnow (Pimephales promelas), a small-bodied fish caged upstream and downstream of a local wastewater treatment plant where fluoxetine, atorvastatin, and sertraline were detected in fish bile at the downstream location. Also, a simple automated analytical method using high throughput robotic system was developed for the simultaneous extraction of pharmaceutical compounds detected in surface waters. The proposed method successfully determined concentrations of carbamazepine, fluoxetine, sertraline, and paroxetine in treated effluent at concentrations ranging from 240 - 3820 ng/L with a method detection limit of 2-13 ng/L, and a relative standard deviation of less than 16%. Application of the method was demonstrated using wastewater from pilot-scale municipal treatment plants and environmental water samples from wastewater-dominated reaches of the Grand River (Waterloo, ON). Finally, 4 and 8-d laboratory exposures were carried out with Rainbow Trout exposed to wastewater effluent collected from pilot scale at Burlington, ON. Additionally, wild fish, White Sucker (Catostomus commersonii) were collected and sampled from Waterloo and Kitchener downstreams containing local municipal effluent. Bioconcentration factors of the selected compounds were determined in both fish muscle and bile samples. The results show that anti-depressant drugs such fluoxetine, sertraline and paroxetine were uptake in the fish muscle and fish bile for both laboratory and field exposure. In summary, exposure of fish to micro-pollutants such as pharmaceuticals may be monitored through the analysis of bile, particularly at low concentration exposure of pharmaceuticals, where the sensitivity of analytical method may be challenged. SPME is a promising simple analytical tool which can potentially be used for monitoring of pharmaceuticals in fish tissue and wastewater.

<p>The integration of planar on-chip light sources is a bottleneck in the implementation of portable planar chip-scale photonic integrated sensing systems, integrated optical interconnects, and optical signal processing systems on platforms such as Silicon (Si) and Si-CMOS integrated circuits. A III/V on-chip laser source integrated onto Si needs to use standard semiconductor fabrication techniques, operate at low power, and enable efficient coupling to other devices on the Si platform.</p><p>In this thesis, thin film strain compensated InGaAs/GaAs single quantum well (SQW) separate confinement heterostructure (SCH) edge emitting lasers (EELs) have been implemented with patterning on both sides of the thin film laser under either growth or host substrate support, with the devices metal/metal bonded to Si and SiO₂/Si substrates. Gain and index guided lasers in various configurations fabricated using standard semiconductor manufacturing processes were simulated, fabricated, and experimentally characterized. Low threshold current densities in the range of 250 A/cm<super>2</super> were achieved. These are the lowest threshold current densities achieved for thin film single quantum well (SQW) lasers integrated on Si reported to date, and also the lowest reported, for thin film lasers operating in the 980 nm wavelength window.</p><p>These thin film EELs were also integrated with photolithographically patterned polymer (SU-8) waveguides on the same SiO₂/Si substrate. Coupling of the laser and waveguide was compared for the cases where an air gap existed between the thin film laser and the waveguide, and in which one facet of the thin film laser was embedded in the waveguide. The laser to waveguide coupling was improved by embedding the laser facet into the waveguide, and eliminating the air gap between the laser and the waveguide. Although the Fresnel reflectivity of the embedded facet was reduced by embedding the facet in the polymer waveguide, leading to a 27.2% increase in threshold current density for 800 &mum long lasers, the slope efficiency of the L-I curves was higher due to preferential power output from the front (now lower reflectivity) facet. In spite of this reduced mirror reflectivity, threshold current densities of 260 A/cm<super>2</super> were achieved for 1000 &mum long lasers. This passively aligned structure eliminates the need for precise placement and tight tolerances typically found in end-fire coupling configurations on separate substrates.</p> / Dissertation

The goal of this thesis is to experimentally characterize the flyability of current generation read/write heads over media patterned to densities above the superparamagnetic limit. The superparamagnetic limit is the physical limit to magnetic storage density. In magnetic storage, superparamagnetism is the uncontrollable switching of stored bits during the lifespan of a hard disk. Theoretical analysis has predicted that densities of ~50 Gbit/in2 are not possible using traditional continuous media. One strategy to achieve high storage density, above the superparamagnetic limit, is patterned media. With patterned media the physical separation of magnetic domains increases their stability. One of the major challenges of development of patterned media is achieving acceptable flyability of the read/write head. In that vein, a test stand is built to measure head liftoff speed, head to disk intermittent contact and head fly height. Tangential friction, an indicator of head liftoff is measured by a Wheatstone bridge strain circuit attached to a cantilever beam. Intermittent contact is quantified by the amount of noise emanating from the interface, which is measured by a high frequency acoustic emission sensor. Head fly height is measured indirectly with a capacitance circuit built around the head to disk interface. Experimental samples of current generation read/write heads and media are obtained from industry. Current generation media is patterned using focused ion beam milling to a density of 10 Gbit/in2. Other, extremely dense samples, above 700 Gbit/in2, are created via thin film self assembly on silicon substrate. Conclusions on slider head flyability over patterned media are based on comparison with flyability over non-patterned media. It is demonstrated that loss of hydrodynamic lubrication is small for small pattern regions with high conserved surface area ratio. Conserved surface area ratio is defined as total surface area minus etched surface area all divided by the total surface area of the storage media. For wafer scale patterned media with low conserved surface area ratio, head liftoff cannot be achieved at designed normal load. However, a 50% reduction of load allows slider head liftoff.

No description available.

The objective of this work is to understand how the thin film characteristics of p-type organic and polymer semiconductors affect their electronic properties in microelectronic applications. To achieve this goal, three main objectives were drawn out: (1) to create single-crystal organic field-effect transistors and measure the intrinsic charge carrier mobility, (2) to develop a platform for measuring and depositing polymer thin films for organic field-effect transistors, and (3) to deposit polythiophene thin films for inorganic-organic hybrid solar cells and determine how thin film properties effect device performance. Pentacene single-crystal field-effect transistors (OFETs) were successfully manufactured on crystals grown via horizontal vapor-phase reactors designed for simultaneous ultrapurification and crystal growth. These OFETs led to calculated pentacene field-effect mobility of 2.2 cm2/Vs. During the sublimation of pentacene at atmospheric pressure, a pentacene disporportionation reaction was observed whereby pentacene reacted with itself to form a peripentacene, a 2:1 cocrystal of pentacene:6,13-dihydropentacene and 6,13-dihydropentacene. This has led to the proposal of a possible mechanism for the observed disproportionation reaction similar to other polyaromatic hydrocarbons, which may be a precursor for explaining the formation of graphite. Several silicon-based and PET-based field-effect transistor platforms were developed for the measurement of mobility of materials in the thin film state. These platforms were critically examined against one another and the single-crystal devices in order to determine the optimal device design for highest possible mobility data, both theoretically based on silicon technology and commercially based on individual devices on flexible substrates. Novel FET device designs were constructed with a single gate per device on silicon and PET as well as the commonly used common-gate device. It was found that the deplanarization effects and poor gate insulator quality of the individual gate devices led to lower overall performance when compared to the common gate approach; however, good transistor behavior was observed with field modulation. Additionally, these thin films were implemented into inorganic-organic hybrid and purely organic solid-state photovoltaic cells. A correlation was drawn between the thin film properties of the device materials and the overall performance of the device. It was determined that each subsequent layer deposited on the device led to a planarization effect, and that the more pristine the individual layer, the better device performance. The hybrid cells performed at VOC = 0.8V and JSC = 55A/cm2.

In this study, we want to realize the influence of temperature and mechanical rubbing on the surface free energy and wettability of liquid crystal(LC) of polyimide(PI) thin films. In different surface conditions, we use the LC that was dropped on to the surface of the sample and become stable to explore the wettability of the surface. We also observe the phenomenon and influence of the LC on the PI with increasing surface temperature. We utilize hot stage and contact angle measuring system to obtain the surface free energy to realize the surface of the PI and measure the contact angle of LC in different temperature to realize the wettability of the PI. We found that the increase of the surface temperature leads to the decrease in the surface free energy of the PI and the contact angle of the FLC on the PI. The increase of the surface temperature causes the stabilization in the surface polar energy and the LC contact angle of the unrubbed PI. But the increase of the surface temperature causes the increase in the surface polar energy and the decrease of the LC contact angle of the rubbed PI. In the anti-parallel-direction to the rubbing direction the rubbed PI exhibits better wettability.

A non-crosslinking approach that covalently bonds nitroxide polymer brushes onto the ITO substrates via surface-initiated atom transfer radical polymerization (ATRP) was develpoed. Since the indium tin oxide (ITO)-silane covalent bonding providesvery strong chemical bonds to adsorb the nitroxide polymer brushes on ITO, it prevents polymers from dissolving into electrolyte solvent and thus improves its electrochemical properties. Moreover, micro-contact printing technology was used to pattern nitroxide polymer brushes on an ITO surface for the potential application in microbatteries. The morphology of electrodes was observed by atomic force microscopy.The electrochemical properties of the cathode were also studies.