Browsing by Author "Dandy, David S., committee member"
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Item Open Access A CMOS compatible optical biosensing system based on local evanescent field shift mechanism(Colorado State University. Libraries, 2011) Yan, Rongjin, author; Lear, Kevin L., advisor; Dandy, David S., committee member; Chandrasekar, V., committee member; Notaros, Branislav, committee memberThe need for label-free integrated optical biosensors has dramatically increased in recent years. Integrated optical biosensors have many advantages, including low-cost, and portability. They can be applied to many fields, including clinical diagnostics, food safety, environmental monitoring, and biosecurity applications. One of the most important applications is point-of-care diagnosis, which means the disease could be tested at or near the site of patient care rather than in a laboratory. We are exploring the issues of design, modeling and measurement of a novel chip-scale local evanescent array coupled (LEAC) biosensor, which is an ideal platform for point-of-care diagnosis. Until now, three generations of LEAC samples have been designed, fabricated and tested. The 1st generation of LEAC sensor without a buried detector array was characterized using a commercial near field scanning optical microscope (NSOM). The sample was polished and was end-fire light coupled using single mode fiber. The field shift mechanism in this proof-to-concept configuration without buried detector arrays has been validated with inorganic adlayers [1], photoresist [2] and different concentrations of CRP proteins [3]. Mode beating phenomena was predicted by the beam propagation method (BPM) and was observed in the NSOM measurement. A 2nd generation LEAC sensor with a buried detector array was fabricated using 0.35μm CMOS process at the Avogo Technologies Inc., Fort Collins, Colorado. Characterizations with both single layer patternings, including photoresist as well as BSA [4] and immunoassay complexes [5] were done with cooperative efforts from various research groups. The BPM method was used to study the LEAC sensor, and the simulation results demonstrated the sensitivity of the LEAC sensor is 16%/nm, which was proved to match well with the experimental data [6]. Different antigen/antibodies, including mouse IgG and Hspx (a tuberculosis reactive antigen), have been used to test the immunoassay ability of LEAC sensor [7]. Many useful data have been collected by using the 2nd generation LEAC chip. However, during the characterization of the Avago chips, some design problems were revealed, including incompatibility with microfluidic integration, restricted detection region, strong sidewall scattering and uncoupled light interference from the single mode fiber. To address these problems, the 3rd generation LEAC sensor chip with buried detector arrays was designed to allow real-time monitoring and compatibility with microfluidic channel integration. 3rd generation samples have been fabricated in the CSU cleanroom and the mesa detector structure has been replaced with the thin insulator detector structure to solve the problems encountered during the characterizations. PDMS microfluidic channels and a multichannel measurement system consisting of a probe card, a multiplexing/amplification circuit and a LabVIEW program have been implemented into the LEAC system. In recent years, outbreaks of fast spreading viral diseases, such as bird flu and H1N1, have drawn a lot of concern of the point-of-care virus detection techniques. To test the virus detection ability of LEAC sensor, 40nm and 200nm polystyrene nanoparticles were immobilized onto the waveguide, and the increased scattered light was collected. Sensitivities of 1%/particle and 0.04%/particle were observed for 200nm and 40nm particles respectively.Item Open Access A reduced chemical kinetic mechanism for computational fluid dynamics simulations of high brake mean effective pressure, lean-burn natural gas engines(Colorado State University. Libraries, 2012) Martinez Morett, David, author; Marchese, Anthony J., advisor; Olsen, Daniel B., committee member; Dandy, David S., committee memberRecent developments in numerical techniques and computational processing power now permit time-dependent, multi-dimensional computational fluid dynamics (CFD) calculations with detailed chemical kinetic mechanisms using commercially available software. Such computations have the potential to be highly effective tools for designing lean-burn, high brake mean effective pressure (BMEP) natural gas engines that achieve high fuel efficiency and low emissions. Specifically, these CFD simulations can provide the analytical tools required to design highly optimized natural gas engine components such as pistons, intake ports, pre-combustion chambers, fuel systems and ignition systems. To accurately model the transient, multi-dimensional chemically reacting flows present in these systems, detailed chemical kinetic mechanisms are needed that accurately reproduce measured combustion data at high pressures and lean conditions, but are of reduced size to enable reasonable computational times. Prior to the present study, these CFD models could not be used as accurate design tools for application in high BMEP lean-burn gas engines because existing reduced chemical kinetic mechanisms failed to accurately reproduce experimental flame speed and ignition delay data for natural gas at high pressure (40 atm and higher) and lean (0.6 equivalence ratio and lower) conditions. Existing methane oxidation mechanisms had typically been validated with experimental conditions at atmospheric and intermediate pressures (1 to 20 atm) and relatively rich stoichiometry. Accordingly, these kinetic mechanisms were not adequate for CFD simulation of natural gas combustion for which elevated pressures and very lean conditions are typical. This thesis describes an analysis, based on experimental data, of the laminar flame speed computed from numerous, detailed chemical kinetic mechanisms for methane combustion at pressures and equivalence ratios necessary for accurate high BMEP, lean-burn natural gas engine modeling. A reduced mechanism that was shown previously to best match data at moderately lean and high pressure conditions was updated for the conditions of interest by performing sensitivity analysis using CHEMKIN. The reaction rate constants from the most sensitive reactions were appropriately adjusted to obtain better agreement at high pressure lean conditions. An evaluation of two new reduced chemical kinetic mechanisms for methane combustion was performed using Converge CFD software. The results were compared to engine data and a significant improvement on combustion performance prediction was obtained with the new mechanisms.Item Open Access Development of electrochemical imaging methods using micro-electrode arrays and microfluidic networks(Colorado State University. Libraries, 2016) Wydallis, John B., author; Henry, Charles S., advisor; Van Orden, Alan, committee member; Barisas, B. George, committee member; McNaughton, Brian R., committee member; Dandy, David S., committee memberDistribution of molecules over space and time drive a multitude of macroscopic and microscopic biological processes. There is a need to design novel imaging techniques that can map molecular distributions with spatiotemporal resolution. In this thesis, new electrochemical approaches to provide spatiotemporal imaging are presented. The bulk of this work utilizes high-density platinum micro-electrode arrays fabricated using complementary metal oxide semiconductor (CMOS) fabrication techniques as well as microfluidics and carbon-based electrodes fabricated using soft lithography fabrication techniques. The systems described in this dissertation focus on quantification of biologically relevant neurotransmitters, mainly catecholamines and nitric oxide with concentration ranges from nM to mM. The pitch, or resolution between two "pixels" of electrochemical data, was 250 µm for microfluidic based sampling methods and 12.5 µm for the CMOS based sensors. Descriptions of fabrication methods for the carbon based electrodes and CMOS electrodes are described in this work. Finally, potential future directions of this technology is discussed in the final chapter.Item Open Access Energy storage and conversion materials: Part 1, Synthesis and characterization of ruthenium tris-bipyridine based fullerene charge transfer salts as a new class of tunable thermoelectric materials; Part 2, Synthesis and characterization of polymer thin films for use as a lithium ion battery separator(Colorado State University. Libraries, 2013) Bates, Daniel James, author; Elliott, C. Michael, advisor; Prieto, Amy L., advisor; Finke, Richard G., committee member; Van Orden, Alan, committee member; Crans, Debbie C., committee member; Dandy, David S., committee memberTo view the abstract, please see the full text of the document.Item Open Access Fiber optic enzymatic biosensors and biosensor arrays for measurement of chlorinated ethenes(Colorado State University. Libraries, 2011) Zhong, Zhong, author; Reardon, Kenneth F., advisor; Lear, Kevin, committee member; Dandy, David S., committee member; Henry, Charles S., committee memberChlorinated ethenes such as trichloroethylene (TCE), tetrachloroethylene (PCE), three isomers of dichloroethylene (DCEs) and vinyl chloride (VC) are used as solvents and cleaners in a variety of industrial and commercial areas. Chlorinated ethenes have become one of the most common environmental pollutants in groundwater contamination sites due to their widespread usage, moderate solubility compared with other organic pollutants and recalcitrance to natural attenuation. Fiber optic enzymatic biosensor was developed in this study as a continuous, real time and in situ measurement principle. TOM biosensor, first reported enzymatic biosensor, was initiated with toluene measurement in aqueous solution as proof-of-concept experiments. The subsequent success of TOM and TOM-Green in TCE analysis showed great potential of biosensor measurement for chlorinated ethenes, despite the ubiquitous problem for monooxygenase-based biosensor with NADH consumption overtime and after usage. In addition, epoxide toxicity also increased the difficulty of biosensor application for measurement of chlorinated ethenes, although several TOM-Green transformants could mitigate the toxicity with rapid epxoide degradation. Plasmid transformation with was introduced to manipulate the construction of new TOM and TOM-Green transformants with capability of intracellular NADH regeneration. FDH regeneration system was studied for both TOM and TOM-Green cells, while TOM+FDH showed great activity retention and regeneration ability and TOM-Green+FDH was able to retain activity over prolonged storage but failed on regeneration after repeated usage due to the toxicity of TCE epoxide. Biosensor array was built with pH-based biosensor to measure a group of haloalkanes. The design concept of biosensor array and detection instrumentation was successful. Linear approach in array data analysis was simple and fast but lacked of accuracy, while nonlinear approach increased the complexity of data analysis to a new level with precision in sacrifice of efficiency. Multivariable chemometric approach was also introduced in array data analysis, providing a high-throughput alternative and a means of quantitatively assessing matrix effects. This project demonstrates the potential of fiber optic enzymatic biosensor and biosensor array as measurements for different analyte are described. This is also one of the first comprehensive studies in oxygen-based biosensor and its application and great potential in food, clinical, and environmental monitoring, industrial process control and other related areas.Item Open Access Investigations of the identity of the true catalyst in three systems, including the development of catalyst poisoning methodology(Colorado State University. Libraries, 2012) Bayram, Ercan, author; Finke, Richard G., advisor; Chen, Eugene Y.-X., committee member; Prieto, Amy L., committee member; Bernstein, Elliot R., committee member; Dandy, David S., committee memberFollowing brief reviews of the pertinent "who is the catalyst?" and "M4 (M= transition-metal) cluster catalysis" literature, the research presented herein is focused on the investigations of the true catalyst for three different catalytic systems. The studies include: (i) the investigation of the true catalyst for neat benzene hydrogenation beginning with commercially available [Ir(cod)Cl]2 (cod= 1,5-cyclooctadiene) at 22 °C and 40 psig initial H2 pressure; (ii) the investigation of the true catalyst for benzene hydrogenation beginning with commercially available [RhCp*Cl2]2 (Cp*= pentamethylcyclopentadienyl) at 100 °C and 50 atm (740 psig) initial H2 pressure; and (iii) the investigation of the true catalyst for cyclohexene hydrogenation beginning with the well-characterized, site isolated [Ir(C2H4)2]/zeolite-Y complex at 22 °C and 40 psig initial H2 pressure, studies done collaboratively with Professor Bruce C. Gates and his group at the University of California-Davis. All three investigations aimed at identifying the true catalyst were studied via an arsenal of complimentary techniques including kinetics, in operando and post-catalysis X-ray absorption fine structure (XAFS) spectroscopy, kinetic quantitative poisoning experiments, transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), and high-angle annular dark-field scanning electron microscopy (HAADF-STEM). The data obtained for each system presented herein provide compelling evidence that the proposed species in each chapter are the true catalyst of the given system, specifically (and respectively) for (i), (ii), and (iii) above Ir(0)n nanoparticles and aggregates, Rh4 sub-nanometer clusters, and atomically dispersed, mononuclear Ir1/zeolite Y catalysts. The results emphasize the need to use complimentary, multiple methods in order to correctly identify the true catalyst in such catalytic systems. The final study elucidates kinetic quantitative catalyst poisoning via two model catalysts: Rh(0)n nanoparticles and Rh4 clusters, providing detailed analyses of linear as well as non-linear kinetic quantitative poisoning plots. The resulting quantitative kinetic catalyst poisoning studies of Rh(0)n nanoparticles and Rh4 clusters led to estimates of the equivalents of poison bound, quantitative catalyst poisoning association constants, and the numbers of active sites for each catalyst.Item Open Access Low temperature solution synthesis of ZnSb, MnSb, and Sr-Ru-O compounds(Colorado State University. Libraries, 2011) Noblitt, Jennifer Lenkner, author; Prieto, Amy L., advisor; Dandy, David S., committee member; Elliot, C. Michael, committee member; Fisher, Ellen R., committee member; Van Orden, Alan K., committee memberIncreasing energy demands are fueling research in the area of renewable energy and energy storage. In particular, Li-ion batteries and superconducting wires are attractive choices for energy storage. Improving safety, simplifying manufacturing processes, and advancing technology to increase energy storage capacity is necessary to compete with current marketed energy storage devices. These advancements are accomplished through the study of new materials and new morphologies. Increasing dependence on and rising demand for portable electronic devices has continued to drive research in the area of Li-ion batteries. In order to compete with existing batteries and be applicable to future energy needs such as powering hybrid vehicles, the drawbacks of Li-ion batteries must be addressed including (i) low power density, (ii) safety, and (iii) high manufacturing costs. These drawbacks can be addressed through new materials and morphologies for the anode, cathode, and electrolyte. New intermetallic anode materials such as ZnSb, MnSb, and Mn2Sb are attractive candidates to replace graphite, the current industry standard anode material, because they are safer while maintaining comparable theoretical capacity. Electrodeposition is an inexpensive method that could be used for the synthesis of these electrode materials. Direct electrodeposition allows for excellent electrical contact to the current collector without the use of a binder. To successfully electrodeposit zinc and manganese antimonides, metal precursors with excellent solubility in water were needed. To promote solubility, particularly for the antimony precursor, coordinating ligands were added to the deposition bath solutions. This work shows that the choice of coordinating ligand and metal-ligand speciation can alter both the electrochemistry and the film composition. This work focuses on the search for appropriate coordinating ligands, solution pH, and bath temperatures so that high quality films of ZnSb, MnSb, and Mn2Sb may be electrochemically deposited on a conducting substrate. Increasing use of natural resources for energy generation has driven research in the area of energy storage using superconducting materials. To meet energy storage needs the materials must have the following features: (i) safety, (ii) superconductivity at or above liquid nitrogen temperature (77 K), (iii) low cost manufacturing processes, and (iv) robustness. The search for materials that meet all of these criteria is on-going, specifically in the area of high temperature superconductivity. The precise mechanism of superconductivity is not known. A few theories explain some of the phenomenological aspects, but not all. In order to logically select and synthesize high temperature superconductors for industrial applications, the precise mechanism must first be elucidated. Additionally, a synthetic method that yields pure, high quality crystals is required because transition temperatures have been shown to vary depending on the preparation method due to impurities. Before measuring properties of superconductors, the development of a synthesis method that yields pure, high quality crystals is required. Most superconductors are synthesized using traditional solid state methods. This synthesis route precludes formation of kinetically stable phases. Low temperature synthesis is useful for probing thermodynamic verses kinetic stability of compounds as well as producing high quality single crystals. A novel low temperature hydrothermal synthesis of Sr-Ru-O compounds has been developed. These materials are important because of their interesting properties including superconductivity and ferromagnetism. Sr2RuO4 is particularly interesting as it is superconducting and isostructural to La2CuO4, which is only superconducting when doped. Therefore, Sr2RuO4 is a good choice for study of the mechanism of superconductivity. Additionally, new kinetically stable phases of the Sr-Ru-O family may be formed which may also be superconducting. Sr-Ru-O compounds were previously synthesized via the float zone method. There is one report of using hydrothermal synthesis, but the temperatures used were 480-630 °C. In general, hydrothermal methods are advantageous because of the potential for moderate temperatures and pressures to be used. Additionally, the reaction temperature, precursor choice, and reaction time can all be used to tune the composition and morphology of the product. Hydrothermal methods are inexpensive and a one-step synthesis which is very convenient to scale up for industrial application. This work shows how a hydrothermal method at temperatures between 140 °C and 210 °C was developed for the synthesis of the Sr-Ru-O family of compounds.Item Open Access Molecular diagnostic platforms for point-of-need pathogen detection(Colorado State University. Libraries, 2021) Jain, Sidhartha, author; Henry, Charles S., advisor; Geiss, Brian J., advisor; Dandy, David S., committee member; Magzamen, Sheryl L., committee memberRapid, accurate, reliable nucleic acid testing (NAT) platforms are essential in the diagnosis and management of diseases. The inherent complexity associated with NAT requires that such testing be performed in centralized laboratories by highly trained personnel. Modified molecular technologies that can be used at the point-of-care (POC) are needed to improve the turnaround times of results and lower the global burden of infectious diseases. To help address this urgent need, we have developed a nucleic acid sensor platform utilizing nuclease protection and lateral flow detection for rapid, point-of-need nucleic acid analysis. We have also improved the analytical performance of the assay by pairing it with isothermal padlock rolling circle amplification (RCA). RCA is one of the simplest and most versatile isothermal amplification techniques as it only requires one primer and a strand-displacing polymerase. Utilizing our rolling circle amplification lateral flow platform, we have developed assays for beta-lactamase resistance genes for antimicrobial resistance monitoring and severe acute respiratory virus coronavirus 2 (SARS-CoV-2). We have also explored the use of exponential isothermal amplification to further improve the assay limit of detection. We also propose a microfluidic device to rapidly detect the RCA amplicons. The device allows programmable sequential delivery of reagents to a detection region, reducing the number of user steps. With further development, such microfluidic devices can be used to develop fully integrated sample-to-result molecular diagnostic platforms that integrate sample pretreatment, amplification, and detection in an easy-to-use, point-of-need nucleic acid sensor platform. Chapter 1 presents a brief review of the nucleic acid testing landscape, the challenges associated with the development of point-of-need nucleic acid sensors and recent successes utilizing paper-based devices for fully integrated sample-to-result sensors. Chapters 2 and 3 discuss the development of the nuclease protection lateral flow assay and padlock probe-based rolling circle amplification lateral flow assay. Chapter 4 describes our work on the use of exponential RCA to improve the limit of detection of the SARS-CoV-2 assay. In Chapter 5, we present our work on a paper-plastic microfluidic device for the rapid detection of the RCA amplicon. We believe that such devices can be used for the development of integrated molecular diagnostic sensor platforms that can be used at the point-of-need in resource-limited settings.Item Open Access Pump-free magnetophoresis for improved point-of-care diagnostics(Colorado State University. Libraries, 2022) Call, Zachary D., author; Henry, Charles S., advisor; Reynolds, Melissa M., committee member; Dandy, David S., committee member; Snow, Christopher D., committee memberInfectious diseases are one of the largest health burdens for low-income countries and claim millions of lives every year. The loss of life in low-income countries is largely due to the lack of access to preventative healthcare and appropriate diagnostic testing. Several health agencies have recognized the need for improved diagnostics to reduce the burden of infectious diseases. The following works described in this thesis are focused on improving the capabilities of point-of-care (POC) testing to improve patient healthcare. Microfluidic devices are a popular approach for diagnostics because they offer reduced assay times, reduced sample volume, and are small (<10 cm). Additionally, microfluidic devices can be used with magnetophoresis to improve sensitivity and specificity. However, traditional microfluidic devices have difficulty translating to the POC because of tedious and expensive fabrication. Microfluidic paper-based analytical devices (µPADs) are a popular alternative to traditional microfluidics due to the natural capillary action through cellulose fibers and simple fabrication. µPADs are portable, low-cost, and do not require external instrumentation, making them ideal for POC settings. However, µPADs often suffer from poor analytical performance resulting in failing to translate to POC testing. In Chapters 2, 3 and 4 of this thesis, I described combining µPADs with magnetophoresis to improve the analytical performance without sacrificing the advantages of µPADs. Coupling magnetophoresis with µPADs is a novel approach and was not reported until the publication of chapter two. Chapter 2 of this thesis describes the first reported example of paper-based magnetophoresis. Magnetophoresis has always needed external pumps to drive flow, however we demonstrate the ability to perform magnetophoresis completely pump-free in a µPAD. We demonstrated the ability to detect E.coli at 105 colony forming units (CFU/mL) with a fluorescent label in a pooled human urine sample. Chapter 3, describes improvements to the device described in chapter two. The limit of detection was improved by three orders of magnitude and calculated at 4.67 x 102 CFU/mL in pooled human urine, which is below detection limits for commercial urinary tract infection tests. Colorimetric detection was used instead of fluorescence detection to eliminate any instrumentation needed and create an easy read-by-eye assay. Additionally, the device design was modified to incorporate a burst valve to generate more consistent laminar flow and simplify user-end steps. We envision this technology to be used a platform for future paper-based devices incorporating magnetophoresis for improved POC devices. In Chapter 4 of this thesis, we describe a new platform for microfluidic magnetophoresis that simplifies user-end steps further through a simple magnet sliding operation. Here we introduce a MagnEtophoresis Slider Assay (MeSA) for sequential binding and washing steps without the need for any external instrumentation. A competitive biotin assay and a sandwich immunoassay are demonstrated to display the functionality of this new platform. The limit of detection was calculated at 1.62 x 103 CFU/mL using colorimetric detection. The MeSA is extremely user-friendly, provides sensitive and rapid results (<15 min), and can be applied to a wide range of applications.Item Open Access Reaction network model for the prediction of mammalian metabolism of benzo[a]pyrene(Colorado State University. Libraries, 2004) Liao, Kai-Hsin, author; Yang, Raymond Shih-hsien, 1940-, advisor; Reardon, Kenneth F., advisor; Dandy, David S., committee member; Andersen, Melvin E., committee memberHumans are exposed to mixtures of environmental pollutants on daily bases. Many of these chemicals undergo biotransformation in our body and often produce toxic metabolites. The biotransformation of mixtures involves complex reaction networks that are difficult to study using conventional experimental techniques. As a first step of developing a predictive tool for the biotransformation of chemical mixtures, a chemical engineering approach, Reaction Network (RN) modeling, was utilized to study the mammalian metabolism of benzo[ a ]pyrene (BaP), a priority environmental carcinogen. A RN pathway model which predicts the theoretically possible reaction network for BaP was first developed based on the existing modeling technology for predicting the reaction networks in petroleum refinery processes, mechanistic organic chemistry, as well as the commonly observed biochemical reactions for mammalian metabolism of BaP. The resulting RN pathway model for BaP predicts that 246 reactions can occur, resulting in unique 150 products in the presence of mammalian cytochrome P450 and epoxide hydrolase. Some of these predicted products might not be experimentally detected due to the slow reactions for their formation or the production of reactive species. A RN kinetics model which reflects the experimentally measurable metabolic pathways was then established to determine the reaction rates of BaP metabolism. To obtain proper separation of eleven BaP metabolites with high detection sensitivities, high-performance liquid chromatography methods were developed and validated. The RN kinetics model was calibrated and validated using experimental data of BaP metabolism catalyzed by recombinant human enzymes. The biotransformation of BaP and the production of nine BaP metabolites were accurately described by the RN kinetics model. Finally, the RN kinetics model of BaP was linked to a physiologically based pharmacokinetic (PBPK) model to describe the distribution and disposition of BaP and its metabolites in rats. The major advantages of applying RN modeling to study toxicology are: (1) their capabilities of handling complex metabolic systems; (2) their potential for predicting reaction networks of chemicals with limited knowledge on their metabolic pathways; and (3) their abilities to predict the reactive intermediates that are not readily measurable in experiments.Item Open Access Retardation and reaction in low permeability layers in groundwater plumes(Colorado State University. Libraries, 2013) Wahlberg, Jennifer J., author; Sale, Thomas C., advisor; Shackelford, Charles D., committee member; Dandy, David S., committee memberTo view the abstract, please see the full text of the document.Item Open Access The development of portable electrochemical sensors for environmental and clinical analysis(Colorado State University. Libraries, 2020) Kava, Alyssa A., author; Henry, Charles S., advisor; Shores, Matthew P., committee member; Sambur, Justin B., committee member; Dandy, David S., committee memberThe ability to perform chemical and biochemical analysis at the point-of-need (PON) has become increasingly sought. PON sensing is critical in both environmental and clinical monitoring applications to reduce cost and time of analysis and achieve early detection of potentially harmful pollution and health indicators. Electroanalysis is very well suited to PON sensing applications with miniaturized instrumentation available, fast analysis times, high sensitivity, low detection limits and the ability to be interfaced with both conventional and paper-based microfluidics (μPADs). The primary focus of this thesis is to improve electrochemical sensors for PON applications by: 1) reducing the number of liquid handling steps required by the end user, 2) further development of better performing disposable electrode materials and 3) the proper integration of electrodes with disposable microfluidic paper-based devices. The first half of this thesis, Chapter 2 through Chapter 4, focuses on the development of a new functionality in μPADs coupled with high quality boron doped diamond paste electrodes (BDDPESs). The electrochemical PAD (ePAD) is referred to as the Janus-ePAD after the two- faced Greek god. The Janus-ePAD developed in Chapter 2 takes advantage of the ability to store reagents within porous paper matrices. In the Janus-ePAD, reagents were stored in two separate channels connected by a sample inlet to adjust the sample pH and perform multiplexed electrochemical detection at two analytes' optimal pH conditions. Therefore, the device is able to carry out several liquid handling and operator steps in situ, further simplifying electrochemical PON sensing. In Chapter 3, fundamental electrochemical characteristics of the BDDPEs are then studied in order to improve their electroanalytical utility, providing a guide to the use of this new composite electrode material. Then, in Chapter 4, a second generation Janus-ePAD is developed to overcome several problems typically encountered in ePADs, namely, slow flow rates and analysis times and lowered electrochemical detection sensitivities due to the paper-electrode interface. Both of these problems are addressed by developing a multi-layer Janus-ePAD that consists of a wax-patterned paper layer taped to a transparency film layer, generating microfluidic channel in the gap between the two layers. Passive fluid transport is still achieved within the channel gap via capillary action but at much faster flow rates decreasing analysis time by over 20 times compared to a one-layer Janus- ePAD. The paper-electrode interface is removed by placing screen-printed carbon electrodes (SPCEs) on the transparency film layer, providing increased reproducibility and bulk solution sensitivity. The second main focus of this thesis is the development of better performing electrode materials that retain the simplicity and disposability required for on-site electroanalysis. In Chapter 5, this goal is accomplished by the development of a novel SPCE composition using glassy carbon (GC) microparticles as the active electrode component and a conductive commercial ink as the binder component of this composite electrode material. The GC-SPE is then applied to the detection of the toxic heavy metals Cd and Pb using anodic stripping voltammetry (ASV). The use of GC microparticles as opposed to the widely used graphite powders in the bulk SPCE formulation allows for the GC-SPE to sensitively and quantitatively detect Cd and Pb at environmentally relevant levels without the need for any post-fabrication modification which is typically required for graphite based SPCEs. Following the development of the GC-SPE in Chapter 5, in Chapter 6, a systematic study was carried out to understand the relationship between SPCE composition, or carbon particle type, and electrochemical performance with the goal of improving the electrochemical performance of these single-use, mass producible, inexpensive and disposable electrode materials in their native, or unmodified state. Significantly, it was found that SPCE composition can be optimized and tuned to provide electrochemical sensing performance on par with other types of carbon composites historically believed to outperform SPCEs. The work contained within this thesis achieves the goal of developing better performing PON electrochemical sensing motifs while retaining maximum simplicity of fabrication and operation of ePADs and SPCEs. Through automation of liquid handling steps using a paper-based device, further simplification of sensitive multiplexed electrochemical detection was achieved. The fundamental understanding of the electrochemical performance of SPCEs allowed for further applications without extensive post-fabrication modifications which have historically hindered their translation from academic to real-world settings. The work presented herein can be used to guide further development of electrochemical PON sensors for a variety of environmental and clinical applications.Item Open Access The role of plasma-surface interactions in process chemistry: mechanistic studies of a-CNx deposition and SF6/O2 etching of silicon(Colorado State University. Libraries, 2010) Stillahn, Joshua Michael, author; Fisher, Ellen R., advisor; Bernstein, E. R. (Elliot R.), committee member; Dandy, David S., committee member; Levinger, Nancy E., committee member; Prieto, Amy L. (Amy Lucia), committee memberThe molecular level chemistry of a-CNx deposition in plasma discharges was studied with emphasis on the use of CH3CN and BrCN as single source precursors for these films. Characterization of the global deposition behavior in these systems indicates that the resulting films are relatively smooth and contain significant levels of N-content, with N/C > 0.3. Notably, films obtained from BrCN plasmas are observed to delaminate upon their exposure to atmosphere, and preliminary investigation of this behavior is presented. Detailed chemical investigation of the deposition process focuses primarily on the contributions of CN radicals, which were characterized from their origin in the gas phase to their reaction at the a-CNx film surface. Laser-induced fluorescence studies suggest that CN is formed through electron impact dissociation of the precursor species and that this breakdown process produces CN with high internal energies, having rotational and vibrational temperatures on the order of 1000 K and 5000 K, respectively. Measurement of CN surface reactivity coefficients in CH3CN plasmas show that CN reacts with a probability of ~94%, irrespective of the deposition conditions; this information, combined with gas phase and film characterization data, leads to the conclusion that CN internal energies exert a strong influence on their surface reactivity and that these surface reactions favor their incorporation into the a-CNx film. Moreover, this correlation is shown to hold for several other plasma radicals studied in our lab, suggesting the potential for developing a general model for predicting surface interactions of activated gas phase species. This dissertation also presents results from studies of SF6/O2 etching of Si. Addition of O2 to the feed gas leads to the generation of SO2, among other species, and gas phase characterization data suggest that SO2 may act as a sink for atomic S, preventing the reformation of SOxFy (y > 0) and thus promoting generation of atomic F. The surface scatter coefficient of SO2 was also measured in an effort to understand its role in the formation of gas phase species. These measurements suggest that SO2 does not undergo surface reaction during etching and therefore does not contribute to the generation of gaseous SOxFy species.