Browsing by Author "Wilson, Jesse, committee member"
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Item Open Access A biosensor system with an integrated CMOS microelectrode array for high spatio-temporal electrochemical imaging(Colorado State University. Libraries, 2019) Tedjo, William, author; Chen, Thomas, advisor; Tobet, Stuart, committee member; Collins, George, committee member; Wilson, Jesse, committee memberThe ability to view biological events in real time has contributed significantly to research in life sciences. While optical microscopy is important to observe anatomical and morphological changes, it is equally important to capture real-time two-dimensional (2D) chemical activities that drive the bio-sample behaviors. The existing chemical sensing methods (i.e. optical photoluminescence, magnetic resonance, and scanning electrochemical), are well-established and optimized for existing ex vivo or in vitro analyses. However, such methods also present various limitations in resolution, real-time performance, and costs. Electrochemical method has been advantageous to life sciences by supporting studies and discoveries in neurotransmitter signaling and metabolic activities in biological samples. In the meantime, the integration of Microelectrode Array (MEA) and Complementary-Metal-Oxide-Semiconductor (CMOS) technology to the electrochemical method provides biosensing capabilities with high spatial and temporal resolutions. This work discusses three related subtopics in this specific order: improvements to an electrochemical imaging system with 8,192 sensing points for neurotransmitter sensing; comprehensive design processes of an electrochemical imaging system with 16,064 sensing points based on the previous system; and the application of the system for imaging oxygen concentration gradients in metabolizing bovine oocytes. The first attempt of high spatial electrochemical imaging was based on an integrated CMOS microchip with 8,192 configurable Pt surface electrodes, on-chip potentiostat, on-chip control logic, and a microfluidic device designed to support ex vivo tissue experimentation. Using norepinephrine as a target analyte for proof of concept, the system is capable of differentiating concentrations of norepinephrine as low as 8µM and up to 1,024 µM with a linear response and a spatial resolution of 25.5×30.4μm. Electrochemical imaging was performed using murine adrenal tissue as a biological model and successfully showed caffeine-stimulated release of catecholamines from live slices of adrenal tissue with desired spatial and temporal resolutions. This system demonstrates the capability of an electrochemical imaging system capable of capturing changes in chemical gradients in live tissue slices. An enhanced system was designed and implemented in a CMOS microchip based on the previous generation. The enhanced CMOS microchip has an expanded sensing area of 3.6×3.6mm containing 16,064 Pt electrodes and the associated 16,064 integrated read channels. The novel three-electrode electrochemical sensor system designed at 27.5×27.5µm pitch enables spatially dense cellular level chemical gradient imaging. The noise level of the on-chip read channels allow amperometric linear detection of neurotransmitter (norepinephrine) concentrations from 4µM to 512µM with 4.7pA/µM sensitivity (R=0.98). Electrochemical response to dissolved oxygen concentration or oxygen partial pressure (pO2) was also characterized with deoxygenated deionized water containing 10µM to 165 µM pO2 with 8.21pA/µM sensitivity (R=0.89). The enhanced biosensor system also demonstrates selectivity to different target analytes using cyclic voltammetry to simultaneously detect NE and uric acid. In addition, a custom-designed indium tin oxide and Au glass electrode is integrated into the microfluidic support system to enable pH measurement, ensuring viability of bio-samples in ex vivo experiments. Electrochemical images confirm the spatiotemporal performance at four frames per second while maintaining the sensitivity to target analytes. The overall system is controlled and continuously monitored by a custom-designed user interface, which is optimized for real-time high spatiotemporal resolution chemical bioimaging. It is well known that physiological events related to oxygen concentration gradients provide valuable information to determine the state of metabolizing biological cells. Utilizing the CMOS microchip with 16,064 Pt MEA and an improved three-electrode system configuration, the system is capable of imaging low oxygen concentration with limit of detection of 18.3µM, 0.58mg/L, or 13.8mmHg. A modified microfluidic support system allows convenient bio-sample handling and delivery to the MEA surface for sensing. In vitro oxygen imaging experiments were performed using bovine cumulus-oocytes-complexes cells with custom software algorithms to analyze its flux density and oxygen consumption rate. The imaging results are processed and presented as 2D heatmaps, representing the dissolved oxygen concentration in the immediate proximity of the cell. The 2D images and analysis of oxygen consumption provide a unique insight into the spatial and temporal dynamics of cell metabolism.Item Open Access A distributed network of autonomous environmental monitoring systems(Colorado State University. Libraries, 2018) Kinhal, Kiran Krishnamurthy, author; Azimi-Sadjadi, Mahmood R., advisor; Wilson, Jesse, committee member; Ghosh, Sudipto, committee memberAcoustic wireless sensor networks have found applications in various areas including monitoring, assisted living, home automation, security and situational awareness. The process of acoustic detection and classification usually demands significant human involvement in the form of visual and audio examination of the collected data. The accuracy of the detection and classification outcome through this process is often limited by inevitable human errors. In order to overcome this limitation and to automate this process, we present a new fully decentralized decision-making platform referred to as Environmental Monitoring Station (EMS) for sensor-level detection and classification of acoustic airborne sources in national parks. The EMS automatically reports this information to a park station through two wireless communication systems. More specifically, in this thesis, we focus on the implementation of the communication systems on the EMS, and also on the design of 1/3rd octave filter bank that is used for onboard spectral sub-band feature generation. A 1/3rd octave filter bank was implemented on the ARTIX-7 FPGA as a custom hardware unit and was interfaced with the detection and classification algorithm on the MicroBlaze softcore processor. The detection results are stored in an SD card and the source counts are tracked in the MicroBlaze firmware. The EMS board is equipped with two expansion slots for incorporating the XBee as well as GSM communication systems. The XBee modules help to build a self-forming mesh network of EMS nodes and makes it easy to add or remove nodes into the network. The GSM module is used as a gateway to send data to the web server. The EMS system is capable of performing detection, classification, and reporting of the source events in near real-time. A field test was recently conducted in the Lake Mead National Recreation Area by deploying a previously trained system as a slave node and a gateway as a master node to demonstrate and evaluate the detection and classification and the networking abilities of the developed system. It was found that the trained EMS system was able to adequately detect and classify the sources of interest and communicate the results through a gateway to the park station successfully. At the time of writing this document, only two fully functional EMS boards were built. Thus, it was not possible to physically build a mesh network of several EMS systems. Thus, future research should focus on accomplishing this task. During the field test, it was not possible to achieve a high transmission range for XBee, due to RF interference present in the deployment area. An effort needs to be made to achieve a higher transmission range for XBees by using a high gain antenna and keeping the antenna in line-of-sight as much as possible. Due to inadequate training data, the EMS system frequently misclassified the sources and mis-detected interference as sources. Thus, it is necessary to train the detection and classification algorithm by using a larger and more representative data set with considerable variability to make it more robust and less prone to variability in deployment location.Item Embargo A microphysiological system for studying barrier health of live tissues in real time(Colorado State University. Libraries, 2024) Way, Ryan, author; Chen, Thomas W., advisor; Wilson, Jesse, committee member; Chicco, Adam, committee memberEpithelial cells create barriers that protect many different components in the body from their external environment. The gut in particular carries bacteria and other infectious agents. A healthy gut epithelial barrier prevents unwanted substances from accessing the underlying lamina propria while maintaining the ability to digest and absorb nutrients. Increased gut barrier permeability, better known as leaky gut, has been linked to several chronic inflammatory diseases. Yet understanding the cause of leaky gut and developing effective interventions are still elusive due to the lack of tools to maintain tissue's physiological environment while elucidating cellular functions under various stimuli ex vivo. This thesis presents a microphysiological system capable of recording real-time barrier permeability of mouse gut tissues in a realistic physiological environment over extended durations. Key components of the microphysiological system include a microfluidic chamber designed to hold the live tissue explant and create a sufficient microphysiological environment to maintain tissue viability; proper media composition that preserves a microbiome and creates necessary oxygen gradients across the barrier; integrated sensor electrodes and supporting electronics for acquiring and calculating transepithelial electrical resistance (TEER); and a scalable system architecture to allow multiple chambers running in parallel for increased throughput. The experimental results demonstrate that the system can maintain tissue viability for up to 72 hours. The results also show that the custom-built and integrated TEER sensors are sufficiently sensitive to distinguish differing levels of barrier permeability when treated with collagenase and low pH media compared to control. Permeability variations in tissue explants from different positions in the intestinal tract were also investigated using TEER revealing their disparities in permeability. Finally, the results also quantitatively determine the effect of the muscle layer on total epithelial resistance.Item Open Access Automating the derivation of memory allocations for acceleration of polyhedral programs(Colorado State University. Libraries, 2024) Ferry, Corentin, author; Rajopadhye, Sanjay, advisor; Derrien, Steven, advisor; Wilson, Jesse, committee member; Pasricha, Sudeep, committee member; McClurg, Jedidiah, committee member; Sadayappan, Ponnuswamy, committee member; de Dinechin, Florent, committee member; Collange, Caroline, committee memberAs processors compute power keeps increasing, so do their demands in memory accesses: some computations will require a higher bandwidth and exhibit regular memory access patterns, others will require a lower access latency and exhibit random access patterns. To cope with all demands, memory technologies are becoming diverse. It is then necessary to adapt both programs and hardware accelerators to the memory technology they use. Notably, memory access patterns and memory layouts have to be optimized. Manual optimization can be extremely tedious and does not scale to a large number of processors and memories, where automation becomes necessary. In this Ph.D dissertation, we suggest several automated methods to derive data layouts from programs, notably for FPGA accelerators. We focus on getting the best throughput from high-latency, high-bandwidth memories and, for all kinds of memories, the lowest redundancy while preserving contiguity. To this effect, we introduce mathematical analyses to partition the data flow of a program with uniform and affine dependence patterns, propose memory layouts and automation techniques to get optimized FPGA accelerators.Item Open Access Crexens™: an expandable general-purpose electrochemical analyzer(Colorado State University. Libraries, 2019) Yang, Lang, author; Chen, Tom, advisor; Collins, George J., committee member; Wilson, Jesse, committee member; Tobet, Stuart, committee memberElectrochemical analysis has gained a great deal of attention of late due to its low-cost, easy-to-perform, and easy-to-miniaturize, especially in personal health care where accuracy and mobility are key factors to bring diagnostics to patients. According to data from Centers for Medicare & Medicaid Services (CMS) in the US, the share of health expenditure in the US has been kept growing in the past 3 decades and reached 17.9% of its overall Gross Domestic Product till 2016, which is equivalent to $10,348 for every person in the US per year. On the other hand, health care resources are often limited not only in rural area but also appeared in well-developed countries. The urgent need and the lack of health resource brings to front the research interest of Point-of-Care (PoC) diagnosis devices. Electrochemical methods have been largely adopted by chemist and biologist for their research purposes. However, several issues exist within current commercial benchtop instruments for electrochemical measurement. First of all, the current commercial instruments are usually bulky and do not have handheld feature for point-of-care applications and the cost are easily near $5,000 each or above. Secondly, most of the instruments do not have good integration level that can perform different types of electrochemical measurements for different applications. The last but not the least, the existing generic benchtops instruments for electrochemical measurements have complex operational procedures that require users to have a sufficient biochemistry and electrochemistry background to operate them correctly. The proposed Crexens™ analyzer platform is aimed to present an affordable electrochemical analyzerwhile achieving comparable performance to the existing commercial instruments, thus, making general electrochemical measurement applications accessible to general public. In this dissertation, the overall Crexens™ electrochemical analyzer architecture and its evolution are presented. The foundation of the Crexens™ architecture was derived from two separate but related research in electrochemical sensing. One of them is a microelectrode sensor array using CMOS for neurotransmitter sensing; the other one is a DNA affinity-based capacitive sensor for infectious disease, such as ZIKA. The CMOS microelectrode sensor array achieved a 320uM sensitivity for norepinephrine, whereas the capacitive sensor achieved a dynamic range of detection from 1 /uL to 105 /uL target molecules (20 to 2 million targets), which makes it be within the detection range in a typical clinical application environment. This dissertation also covers the design details of the CMOS microelectrode array sensor and the capacitive sensor design as a prelude to the development of the Crexens™ analyzer architecture. Finally, an expandable integrated electrochemical analyzer architecture (Crexens™) has been designed for mobile point-of-care (POC) applications. Electrochemical methods have been explored in detecting various bio-molecules such as glucose, lactate, protein, DNA, neurotransmitter, steroid hormone, which resulted in good sensitivity and selectivity. The proposed system is capable of running electrochemical experiments including cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), electrochemical capacitive spectroscopy (ECS), amperometry, potentiometry, and other derived electrochemical based tests. This system consist of a front-end interface to sensor electrodes, a back-end user interface on smart phone and PC, a base unit as master module, a low-noise add-on module, a high-speed add-on module, and a multi-channel add-on module. The architecture allows LEGO™-like capability to stack add-on modules on to the base-unit for performance enhancements in noise, speed or parallelism. The analyzer is capable of performing up to 1900 V/s CV with 10 mV step, up to 12 kHz EIS scan range and a limit of detection at 637 pA for amperometric applications with the base module. With high performance module, the EIS scan range can be extended upto 5 MHz. The limit of detection can be further improved to be at 333 fA using the low-noise module. The form factor of the electrochemical analyzer is designed for its mobile/point-of-care applications, integrating its entire functionality on to a 70 cm² area of surface space. A glutamine enzymatic sensor was used to valid the capability of the proposed electrochemical analyzer and turned out to give good linearity and reached a limit of detection at 50 uM.Item Open Access Design and implementation of the SBX1: a smart environment chamber for biological research and discovery(Colorado State University. Libraries, 2021) Ball, Daniel S., author; Chen, Thomas, advisor; Wilson, Jesse, committee member; Chicco, Adam, committee memberModern biomedical laboratories make significant use of environmentally controlled chambers for incubation and examination of live cell samples. They require precise control over temperature, humidity, and gas concentration to mimic natural conditions for cell survival and growth. Many incubators and live cell imaging systems exist as commercial products; however, they are prohibitively expensive, costing tens or hundreds of thousands of dollars depending on capabilities of the system. This thesis presents the electrical, optical, mechanical, and software design of the SBX1Smart Environment Chamber. This device aims to fulfill the needs of most users at a lower cost than current commercial offerings, providing an opportunity for less funded labs to pursue biomedical research and development. The chamber provides temperature, humidity, and gas concentration controls, an internal microscope with an automated stage, and an integrated ARM microcomputer to with a graphical user interface for control and monitoring of the system. A patent has been filed for the SBX1; application no. US 2020/0324289 A1.Item Open Access Integrating discrete stochastic models with single-cell and single-molecule experiments(Colorado State University. Libraries, 2019) Fox, Zachary R., author; Munsky, Brian, advisor; Stargell, Laurie, committee member; Wilson, Jesse, committee member; Prasad, Ashok, committee memberModern biological experiments can capture the behaviors of single biomolecules within single cells. Much like Robert Brown looking at pollen grains in water, experimentalists have noticed that individual cells that are genetically identical behave seemingly randomly in the way they carry out their most basic functions. The field of stochastic single-cell biology has been focused developing mathematical and computational tools to understand how cells try to buffer or even make use of such fluctuations, and the technologies to measure such fluctuations has vastly improved in recent years. This dissertation is focused on developing new methods to analyze modern single-cell and single-molecule biological data with discrete stochastic models of the underlying processes, such as stochastic gene expression and single-mRNA translation. The methods developed here emphasize a strong link between model and experiment to help understand, design, and eventually control biological systems at the single-cell level.Item Embargo Investigating the role of chemical additives in the structure and dynamics of electrolyte mixtures via 2D infrared spectroscopy and microscopy(Colorado State University. Libraries, 2022) Tibbetts, Clara Anne, author; Krummel, Amber T., advisor; Wilson, Jesse, committee member; Levinger, Nancy, committee member; Rappe, Anthony, committee memberThe research in this dissertation is focused on the impact that additives have on the chemical structure and dynamics of electrolyte solutions that can be used in electrochemical devices such as batteries or solar devices. Two-dimensional infrared spectroscopy (2D IR) has been used in conjunction with linear Fourier Transform infrared spectroscopy (FTIR), rheology, molecular dynamics, and density functional theory to study organic carbonate and ionic liquid mixtures. In addition, 2D IR microscopy is successfully implemented to study ionic liquid mixtures in different environments including a microdroplet and a copper electrochemical cell. 2D IR and molecular dynamics simulations of organic carbonate mixtures with varied amounts of a common additive, fluoroethylene carbonate (FEC), show that even in small quantities FEC can induce changes in the solvent structure. Experimental results demonstrated that at low concentrations FEC slows spectral diffusion. Cylindrical distribution functions calculated from molecular dynamics simulations in conjunction with experimental results suggest the slowing is due to significant changes in the behavior of one of the solution components, ethylene carbonate. Furthermore, a combination of experimental anisotropy and viscosity, and computational rotational correlation functions shows that local solvent rigidity increases with high amounts of FEC. Moreover, these results show that additional FEC increases macroscopic viscosity which is correlated to global solvent orientational relaxation. In functional batteries FEC is shown to dramatically impact how the solid electrolyte interphase forms, a layer that impacts battery metrics such as lifetime and safety.1–3 Therefore, it is possible that the observed changes in the solvent structure upon addition of FEC has implications in how the solid electrolyte interphase forms. The combination of linear and 2D IR spectroscopy with viscosity measurements is used to study the impact of small amounts of water (between ~1.32 and 21.6% mole fraction water) on the structure and dynamics of room-temperature ionic liquid mixtures. Specifically, the effects of water on a mixture of 1-butyl-3-methylimidazolium tetrafluoroborate (BmimBF4) and 1-butyl-3-methylimidazolium dicyanamide (BmimDCA) room-temperature ionic liquid (RTIL) was investigated by tracking changes in the vibrational features of the dicyanamide anion (DCA). Shifts in the infrared peak frequencies of DCA indicated the formation of water-associated and non-water-associated DCA populations. Time-dependent 2D IR shows differences in the dynamic behavior of the water-associated and non-water-associated populations of DCA at low (below 2.5% χWater), mid (between 2.5% χWater and 9.6% χWater), and high (between 11.6% χWater and 21.6% χWater) water concentrations. The vibrational relaxation occurs more quickly with increasing water content for water-associated populations of DCA, indicating water introduces additional pathways for relaxation, possibly via new bath modes. On the other hand, spectral diffusion of water-associated populations slows significantly with more water, suggesting water induces the formation of distinct and non- or very slowly interchangeable local environments. It is possible that in a functional electrochemical device with a water and RTIL electrolyte the introduction of these diverse local solvent environments might impact device performance. If water could be introduced in a system in a way that increased ion-mobility but does not cause undesirable interfacial interactions near an electrode this could improve device efficiency. Therefore, determining if and how this local heterogeneity presents itself in an operational electrochemical cell is an important next step. Ultrafast 2D IR microscopy is discussed as an emerging imaging platform that is a promising tool for investigating heterogeneous samples across multiple time scales and length scales, including electrochemical devices. However, there are numerous practical considerations in the implementation of 2D IR microscopy. Some of these considerations include mid-IR laser sources, repetition rates, mid-IR pulse shaping, noise reduction, microscope design, and detection limitations. In this work we show the implementation of improvements in spectral resolution and noise reduction and the consequent successful imaging of a BmimDCA:BmimBF4 electrolyte in two different scenarios—a droplet and a copper electrochemical cell. Imaging the BmimDCA:BmimBF4 microdroplet shows how 2D IR imaging can be used to probe dynamics on a spatial scale. Results indicate the solvent dynamics in the microdroplet are spatially homogenous. Imaging experiments of the RTIL electrolyte in a copper cell, demonstrates a practical application of ultrafast 2D IR microscopy to study functional electrochemical devices. 2D IR spectra collected between the copper counter electrode and working electrode showed dramatic changes in peak positions and shapes suggesting the formation of DCA copper complexes. These results suggest 2D IR microscopy will allow chemical exchange dynamics of different species involved in the electrochemical reactions to be monitored as they evolve from the counter electrode to the working electrode. This work establishes 2D IR microscopy as a tool well equipped to connect molecular level condensed phase reaction dynamics to micro- and mesoscale spatial dependence in an electrochemical cell.Item Open Access Ionospheric scintillation effects on GPS measurements and algorithms to improve positioning solution accuracy(Colorado State University. Libraries, 2017) Myer, Gregory Thomas, author; Morton, Y. T. Jade, advisor; Wilson, Jesse, committee member; Shonkwiler, Clayton, committee memberThe ionosphere is an important cause of disturbances on GNSS signals, especially in high latitudes and equatorial areas. Previous studies indicate that while ionospheric scintillation may cause abrupt, random fluctuations in carrier phase measurements, its impact on pseudorange is less serious. Since modern GNSS receivers, especially those for high precision applications, use carrier phase-smoothed pseudoranges to improve accuracy of position solutions, there exists the need to have a better understanding of the scintillation effects on carrier phase measurements and developing means to mitigate scintillation induced errors in navigation solutions. In this thesis, scintillation impacts are demonstrated on carrier phase and pseudorange measurements using real scintillation data collected at high latitudes and equatorial areas, and the effect on positioning is investigated and mitigated. To obtain a more insightful and quantitative understanding of the impact, the data was used to generate position solutions using standard navigation processing algorithms. The results clearly indicate that sudden carrier phase discontinuities during strong scintillation lead to the degradation of carrier-smoothed pseudorange accuracy and consequently, results in large position errors. During strong scintillation with no carrier phase discontinuities, comparatively smaller position errors are found due to phase fluctuations that cause small changes in the range measurements. Based on this analysis, we give examples of several approaches to mitigate these problems, and use these approaches to present adaptive positioning techniques to mitigate scintillation induced position errors. One algorithm simply replaces the carrier-smoothed pseudorange with the unsmoothed pseudorange for satellites that are affected by outages on the carrier phase measurements, or if strong scintillation is detected. Another adaptive algorithm uses the GDOP to determine if a scintillating satellite can be completely removed from the navigation processing to improve positioning accuracy. Results show that the algorithms that substitute the unsmoothed pseudorange increase errors by 24.5% as compared to a conventional technique that repairs cycle slips, which indicates that it is still best to use the carrier-smoothed pseudoranges as long as there are no discontinuities. Results from the adaptive technique based on the analysis of the GDOP show a reduction of maximum errors on average by 13% on all of the data sets when comparing to a conventional algorithm. It was also found that a new carrier-smoothing technique can reduce maximum errors by 7.9% on average. Alternative approaches for future improvements are also discussed.Item Open Access Long range fiber noise cancellation(Colorado State University. Libraries, 2024) Helburn, Noah, author; Sanner, Christian, advisor; Brewer, Sam, committee member; Wilson, Jesse, committee memberOptical atomic clocks are beyond timekeeping applications an increasingly important tool for testing fundamental physics and pushing the quantum science frontier. Being able to compare remote optical clocks by sharing coherent laser light between them opens exciting scientific perspectives. Optical fibers are almost ideal guides for sending light over long distances, but they induce phase noise on the light travelling through them. We demonstrate an actively phase-stabilized optical fiber link over a distance of 80km. A fractional frequency instability of 7 × 10−15 at 1 s and 6.3 × 10−18 after 1800 s was achieved.Item Embargo Multiphoton spatial frequency modulated imaging(Colorado State University. Libraries, 2023) Wernsing, Keith, author; Bartels, Randy, advisor; Squier, Jeff, committee member; Wilson, Jesse, committee member; Borch, Thomas, committee memberFar-field optical microscopy has seen significant development in the last 20 years in its ability to resolve specimen information beyond the diffraction limit. However, nearly all of these super-resolution techniques are predicated on the use of fluorescence as the contrast mechanism in the sample. While the variety of fluorophores available for labeling a sample are a widely-utilized tool, in many instances non-fluorescent contrast mechanisms also provide valuable information. Multiphoton microscopy is one route to probing non-fluorescent contrast mechanisms. It has the benefit of sampling multiple contrast mechanisms at once, including second- and third-harmonic generation and Raman vibrational characteristics, as well as autofluorescence and labeled fluorescence. However, development of super-resolving techniques for coherent scattering processes like harmonic generation or coherent Raman excitation has lagged behind that of incoherent scattering processes like fluorescence. In this work I present the first technique to simultaneously enhance resolution in both real-state (e.g., fluorescence) and virtual-state (e.g. harmonic generation) molecular excitation mechanisms, known as multiphoton spatial-frequency modulated imaging (MP-SPIFI). Standard SPIFI works by projecting spatial cosine patterns onto the sample and gathering object spatial frequency information. Multiphoton SPIFI generates harmonics of these cosine patterns and therein gathers information beyond the frequency passband of the microscope. We demonstrate our initial results with two-photon fluorescence and SHG. An extensive model is built describing the super-resolved image formation process. We then present a method for extending the native, 1D resolution enhancement into two dimensions for an isotropic enhancement. Finally, we present development of two femtosecond, amplified pulsed laser sources tailored to boost SNR in multiphoton processes, through parabolic pulse amplification, and chirped pulse fiber broadening, in order to deliver the high average power & high peak power required by MP-SPIFI for driving nonlinear processes across a line-focus geometry.Item Open Access Non-ionizing tomographic imaging modalities for bedside lung monitoring(Colorado State University. Libraries, 2023) Vieira Pigatto, Andre, author; Mueller, Jennifer L., advisor; Wilson, Jesse, committee member; Rezende, Marlis, committee member; Wang, Zhijie, committee memberThe need for an accurate and non-ionizing imaging modality for pulmonary assessment of patients undergoing mechanical ventilation due to respiratory failure has increased due to COVID. The ability to quickly detect the development of pathologies at an early stage is highly desirable and could help reduce the incidence of complications. It is also clear that mechanical ventilation can cause ventilator-induced lung injuries, which can be avoided by adequately optimizing the positive end-expiratory pressure to induce alveolar recruitment while preventing hyperinflation. Here, I will explore two non-ionizing pulmonary imaging systems that could be used as monitoring systems in the intensive care unit: Ultrasound Computed Tomography (USCT) and Electrical Impedance Tomography (EIT). The most comprehensive part of this research is the development of a Low-Frequency USCT system, which was motivated by recent studies demonstrating that acoustic waves transmitted at frequencies between 10 kHz and 750 kHz penetrate the lungs and may be useful for thoracic imaging. A novel transducer based on Tonpilz was designed, characterized, and calibrated through vibrational, electrical, and acoustic measurements, and a flexible belt that holds up to 32 transducers was constructed. A Verasonics Vantage 64 Low-frequency Research Ultrasound system was programmed to collect data by transmitting and receiving signals at frequencies of 125 and 156 kHz. The data collection and processing algorithms were developed in MATLAB, and the system was tested on phantom and vertebrate animal experiments; image reconstructions were conducted using a Time-Of-Flight algorithm. As a secondary study, SMA-1, COVID, and regular patients were imaged and analyzed using EIT technology; these results are shown through journal and conference articles presented in the Appendix A and C of this document.Item Open Access Off-resonant RF heating of strongly magnetized electrons in ultracold neutral plasma(Colorado State University. Libraries, 2021) Guthrie, John M., author; Roberts, Jacob, advisor; Fairbank, William, Jr., committee member; Gelfand, Martin, committee member; Wilson, Jesse, committee memberMagnetic fields are common in many plasma systems. Ultracold neutral plasmas (UCPs) are capable of not only accessing strong Coulomb coupling physics but also strong and extreme electron magnetization regimes, as well. These magnetization regimes, as defined by Baalrud and Daligault [S. Baalrud and J. Daligault, Phys. Rev. E, 96, 043202 (2017)], are predicted to modify screening or binary collision properties as the electron cyclotron radius approaches or subceeds the relevant plasma length scales. UCPs provide an advantageous testing ground for measuring magnetized electron-ion interactions, such as collisional heating induced by applied off-resonant RF fields. The experiments described in this thesis are focused on observations of RF heating in a UCP made from a photoionized cloud of ultracold 85Rb at three electron magnetization strengths that span the weakly-strongly magnetized boundary to the strongly-extremely magnetized boundary. Relative comparisons between heating rates at different magnetic fields were measured with ~20% precision, and an absolute determination of the heating rate near the weak-strong magnetization boundary is determined with ~40% precision. The results from these experiments were compared to theoretical predictions we developed that account for the finite-RF amplitude conditions used in the UCP measurements. This finite-amplitude heating rate theory is shown to be an extension of low-amplitude magnetized AC conductivity treatments as well as unmagnetized nonlinear collisional radiation absorption treatments. Mixed agreement was discovered between our observations and the theory for the three magnetic fields investigated: 10.6, 65, and 134 G. The measured absolute RF heating rate at 10.6 G and the relative rate between 134 and 10.6 G are in agreement with predictions within uncertainty; the relative rate between 65 and 10.6 G was observed to be a factor of ~3 lower than the predictions, with an absolute difference---in terms of the measurement uncertainty---on the order of 10σ. The implications of this disagreement are discussed, and future measurements that can be conducted with this technique are presented.Item Open Access Optical detection methods for microfluidic devices(Colorado State University. Libraries, 2020) Koepke, Marina M., author; Lear, Kevin L., advisor; Wilson, Jesse, committee member; Gustafson, Daniel, committee memberOptical technology is a common tool integrated onto microfluidic devices to aid in data collection and counting for biological and chemical research. In this study, a simple optical technique was investigated as a detection method for microfluidic impedance cytometry (MIC) devices. The MIC devices were designed to characterize size and structure of parasite eggs through electrical impedance measurements. This data could directly benefit the medical and veterinary communities by providing information to aid in addressing helminth infections in humans and animals. The current MIC device and instrumentation does not provide a robust way to validate which impedance changes correlate to parasite eggs passing through the electrodes. To address this, an optical detection method was designed, implemented and tested on two different types of microfluidic devices: a glass device and printed circuit board (PCB) device. The optical hardware was accompanied by a trigger circuit that was used to process and manipulate the detected light signal. The circuit was designed with a sensitivity that would detect small changes in light from strongyle-type eggs flowing through the microfluidic channel. The trigger circuit was composed of multiple stages of signal amplification and oscillation suppression techniques so the changes in light could clearly be detected by the electronics. This method proved to be successful in detecting voltage changes ranging from 1.7 mV to 6.8 mV which resulted from strongyle egg sized particles (63-75 μm in diameter) flowing through the microfluidic channel. Adaptations for the optics, bench set-up and microfluidic device design were investigated to transfer this method to different laboratory settings. This study outlines the process of utilizing basic lab tools and components to create an easy to implement optical detection method for a variety of chip designs and laboratory set-ups.Item Open Access Polyhedral optimizations of RNA-RNA interaction computations(Colorado State University. Libraries, 2017) Varadarajan, Swetha, author; Rajopadhye, Sanjay, advisor; Bohm, Wim, committee member; Wilson, Jesse, committee memberStudying RNA-RNA interaction has led to major successes in the treatment of some cancers, including colon, breast and pancreatic cancer by suppressing the gene expression involved in the development of these diseases. The problem with such programs is that they are computationally and memory intensive: O(N4) space and O(N6) time complexity. Moreover, the entire application is complicated, and involves many mutually recursive data variables. We address the problem of speeding up a surrogate kernel (named OSPSQ) that captures the main dependence pattern found in two widely used RNA-RNA interaction applications IRIS and piRNA. The structure of the OSPSQ kernel perfectly fits the constraints of the polyhedral model, a well-developed technology for optimizing codes that belong to many specialized domains. However, the current state-of-the-art automatic polyhedral tools do not significantly improve the performance of the baseline implementation of OSPSQ. With simple techniques like loop permutation and skewing, we achieve an average of 17x sequential and 31x parallel speedup on a standard modern multi-core platform (Intel Broadwell, E5-1650v4). This performance represents 75% and 88% of attainable single-core and multi-core L1 bandwidth. For further performance improvement, we describe how to tile all six dimensions and also formulate the associated memory trade-off. In the future, we plan to implement these tiling strategies, explore the performance of the code for various tile sizes and optimize the whole piRNA application.Item Open Access Single pixel computational imaging(Colorado State University. Libraries, 2023) Stockton, Patrick Allen, author; Bartels, Randy A., advisor; Pezeshki, Ali, committee member; Muller, Jennifer, committee member; Wilson, Jesse, committee memberMicroscopy has a long rich history of peering into life's smallest mysteries. Ever since the first microscope, the ability to see objects that would otherwise be impossible to see with the naked eye have allowed new discoveries and modern technology has benefited tremendously. There have been many improvements on microscopes over the centuries with each improvement unlocking more knowledge as we go. Some of these advancements are the modern objective lens correcting for numerous optical aberrations, phase contrast imaging allowing nearly transparent samples to have high contrast, the confocal pinhole allowing an easy method to get optical sectioning, and super resolution microscopy surpassing the diffraction limit by several orders of magnitude. One of the most amazing things about all these discoveries is that they all rely on the same fundamental concepts. This work focuses on expanding the capabilities of single pixel imaging. Single pixel imaging is a class of imaging that encodes spatial information on a temporal signal using a single element detector; having knowledge of the encoding allows the time signal to be reconstructed to generate a spatial image. A canonical example of single pixel imaging is laser scanning microscopy (LSM). More complicated encoding systems have been developed but the basic idea for reconstruction remains the same. There are several advantages conferred to single pixel imaging such as image formation is resistant to scattering, very fast temporal response, flexibility in detector selection at a given wavelength, and exotic imaging information. My research primarily utilizes two techniques, SPatIal Frequency modulated Imaging (SPIFI) and Coherent Holographic Image Reconstruction by Phase Transfer (CHIRPT), both are explained in detail. My research aims to expand the capability's of SPIFI by providing a method for homogenizing the anisotropic resolution observed in the higher orders, additionally, I present a method of solving the inverse problem that allows the measurement matrix to more accurately represent to true image formation process there by increasing the performance of the reconstruction. I present research for CHIRPT which takes advantage of the encoded coherent phase information of two interfering beams to measure the quantitative phase of an object. I also present a new technique utilizing CHIRPT's holographic phase information to extend optical diffraction tomography to incoherent emitters which has long been an illusive task.Item Open Access Study of real-time spatial and temporal behavior of bacterial biofilms using 2D impedance spectroscopy(Colorado State University. Libraries, 2019) Begly, Caleb R., author; Chen, Thomas W., advisor; Wilson, Jesse, committee member; Chicco, Adam, committee memberThe study of biofilms and their effect on disease treatment, prevention, and cures has been increasing in importance in recent years. Bacterial biofilms are colony formations developed by bacteria that allow them to anchor onto a surface and survive hostile environments. The formation of harmful bacteria biofilms on some surfaces can be troublesome, particularly in the case of medical implants. The continuing rise of antibiotic-resistant bacteria over the past decade had escalated the need to study and understand biofilms. This thesis presents the design of a multi-channel impedance spectroscopy instrument to allow 2D spatial and temporal evaluation of biofilm growth. The custom-designed circuits allow measurement updates once per second on the entire set of impedance sensors. The distance between the neighboring sensors is 220 micrometers, allowing realtime observation of biofilm growth. The initial results show that the proposed 2D impedance spectroscopy tool provides the needed accuracy to predict the existence of bacteria biofilm at a given sensor location. The initial results were validated using optical images with fluorescent staining.Item Open Access The development of a thin film sputter deposition system using a novel hidden anode ion source and motion control(Colorado State University. Libraries, 2020) VanGemert, Jack J., author; Williams, John D., advisor; Farnell, Casey, committee member; Menoni, Carmen, committee member; Wilson, Jesse, committee memberThin films consist of metallic or dielectric materials that are commonly deposited onto surfaces where properties, intrinsic to the thin film, are desired. Ranging from a single atomic layer to several microns in thickness, thin films are found to be useful for a broad range of applications. Most thin film applications desire uniform, durable, and adherent coatings with specific optical, electrical, or tribological properties. Therefore it is important that deposition systems can produce thin films with properties suited for the application at hand. The development of a thin film sputter deposition system is presented. The system has been shown to produce large area art pieces at a low cost compared to current deposition systems. The deposition system uses a novel hidden anode ion source (HAIS) to sputter target material, assist film growth, and to clean substrates prior to deposition. To the author's knowledge, an ion source of this design has not been implemented in a deposition system prior to the one discussed. The characterization of a novel ion source is presented in detail along with the other system components. Deposition rates and thin film profiles are used to validate experimental results and predict thin film properties for various operating conditions. Coatings produced by the system are studied and used to determine film characteristics of interest to the application of outdoor art. Structural thin film properties of interest for long outdoor lifetime art work include film adhesion, density, and residual stress. Visual thin film properties important for the artwork are related to optical properties such as reflection, transmission, and absorption. The plasma-based deposition system is shown to be a tool of high potential for creating engaging, long lifetime art pieces.