Theses and Dissertations at Montana State University (MSU)
Permanent URI for this collectionhttps://scholarworks.montana.edu/handle/1/733
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Item Development and characterization of a novel isothermal DNA amplification reaction(Montana State University - Bozeman, College of Engineering, 2021) Ozay, Burcu; Chairperson, Graduate Committee: Scott McCalla; This is a manuscript style paper that includes co-authored chapters.Isothermal nucleic acid amplification chemistries are gaining popularity as nucleic acid detection tools that can replace the current gold standard methods, PCR and its derivatives, with their simplicity, speed and applicability to point-of-care applications. In this work, we have developed and characterized a novel isothermal amplification chemistry, ultrasensitive DNA amplification reaction (UDAR). UDAR differs from similar chemistries with its unique, biphasic response with a high-gain output that can be captured with a cell-phone camera. The switch-like, nonlinear characteristics provide a definitive on/off signal for potential use in applications such as molecular diagnostics and DNA circuits. Tunability of the reaction was explored and the relationship between thermodynamic properties of the reaction templates and the reaction output was established. Limitations on fluorescent staining of reaction components by two popular commercial nucleic acid stains, SYBR Green II and SYBR Gold, were determined for a more accurate evaluation of the reaction output and reaction product analysis. A mathematical model of the reaction output was built and outputs from three different UDAR templates were successfully simulated. This model revealed important information on reaction pathways and helped identify the impact of individual reaction events. A comprehensive literature review of enhancement strategies for isothermal amplification reactions was conducted to serve as a guide to improve and modify these reactions according to different needs and applications. Lastly, UDAR was applied to microRNA detection, which are putative biomarkers for diseases such as cancer, malaria, and traumatic brain injury. Five different miRNAs were successfully detected by UDAR, down to 10 fM concentration. UDAR-based miRNA quantification is possible, with linear calibration curves provided between 10fM and 1 nM. This work has significant contributions to the growing field of isothermal nucleic acid amplification based-molecular detection systems by introducing a unique isothermal amplification chemistry, establishing design and manipulation techniques, and guiding improvement efforts of these technologies.Item Exploring exchange and transport dynamics in complex systems through nuclear magnetic resonance(Montana State University - Bozeman, College of Letters & Science, 2021) Nelson, Madison Lee; Chairperson, Graduate Committee: Joseph D. Seymour and Sarah L. Codd (co-chair); This is a manuscript style paper that includes co-authored chapters.Nuclear magnetic resonance (NMR) is uniquely qualified for non-invasive studies of systems providing insights into macro-, meso-, and microscale structures. NMR relaxation and diffusion methods are applied to characterize transport and magnetization exchange dynamics in various complex systems. These techniques are highly sensitive to molecular mobility restrictions which correlate to the ability to monitor thermodynamic phase transitions and changes in molecular environment. NMR diffusion and relaxation measurements are applied to characterize the effect of xylose on transport within zeolite beads. The ability for NMR to explore the transport phenomenon on multiple length and time scales is exploited to characterize how the introduction of xylose effects the transport structure of the bead. Eigenvector simulations of magnetization evolution within a coupled pore system during multidimensional NMR measurements, T1-T2 relaxation correlation experiments, allowed for insights into complex diffusion and exchange occurring within multiple systems. Additionally, multidimensional relaxation NMR measurements, in the form of varying echo-time spin-spin relaxation dispersion T2(tau) and spin-spin relaxation exchange T2-T2 experiments, are demonstrated to successfully characterize thermodynamic structural rearrangements of two natural straight-chained hydrocarbons and a natural wax. Temperature dependent magnetization exchange was found in both the longitudinal and transverse magnetization. The results indicate the ability of NMR relaxometry to detect magnetization exchange without mass or molecular exchange, also known as spin diffusion, including in the transverse magnetization. Spatial domain extent can be inferred from the exchange timescale and an estimate of the spin diffusion coefficient. NMR relaxometry methods were extended to glycerol behenate, a common pharmaceutical component. Glycerol behenate was decomposed into its three base components to explore how polymorphic structure and exchange depend on temperature within each pure lipid through T2(tau) and T2-T2 NMR relaxation experiments. These methods allowed for in-situ monitoring of thermodynamic dependent exchange across domains in addition to decoupling of transverse and longitudinal exchange. The results allow for calculation of exchange length scales across the micro- and mesoscales within the lipids. Ultimately, multidimensional NMR relaxometry is successfully demonstrated to be an effective technique for characterizing and monitoring structural changes in lipids across various phase transition temperatures and time and length scales.Item A thermodynamic and optical assessment of soluble carbon particulate effects on lipid film structure and organization(Montana State University - Bozeman, College of Letters & Science, 2022) Shaikh, Nida; Chairperson, Graduate Committee: Robert Walker; This is a manuscript style paper that includes co-authored chapters.Research described in this thesis investigates the effects of carbonaceous particulate matter on model biological membrane structure, organization, and function. Although the harmful impacts of black carbon are well-documented, researchers lack the chemically-specific, mechanistic information necessary for understanding how black carbon aerosols affect lung surfactant spreading and compression. Surface specific optical spectroscopy methods together with complementary thermodynamic methods are used to measure how carbon nanoparticles, a model for black carbon aerosols that are a component of particulate matter (PM 2.5 ), change average lipid conformation, orientation, thickness, and compressibility in monolayers, and how these changes affect overall membrane organization. Addressing these questions requires a suite of independent, but complementary, experimental techniques including Langmuir trough and surface tension measurements, surface specific nonlinear optical spectroscopy measurements including both second harmonic generation and sum frequency generation, and spectroscopic ellipsometry measurements. Work presented in this thesis discusses cooperative adsorption as a possible mechanism to explain the interactions between DPPC monolayers and PHFs at biologically-relevant aqueous - air interfaces. The experiments forthcoming represent a detailed investigation of 1) the mechanism(s) responsible for accumulation of carbon particulates at the aqueous/monolayer/air interface present in the lungs, and 2) how specific thermodynamic behavior and optical properties (i.e. structure, composition, membrane integrity, orientation, thickness, and organization) at the aqueous/monolayer/air interface change with the inclusion of non-biological, nano-sized materials. Motivating this work is a need to develop a predictive understanding of black carbon - lung surfactant interactions and how non-biological, nano-sized materials impact membrane structure and function.Item Diode-laser-based high spectral resolution LIDAR(Montana State University - Bozeman, College of Engineering, 2021) Colberg, Luke Stewart; Chairperson, Graduate Committee: Kevin S. RepaskyThis thesis describes the design, construction, and testing of a high spectral resolution lidar (HSRL) as a part of a combined HSRL and differential absorption lidar (DIAL) system. The combined HSRL and DIAL instrument is constructed using the MicroPulse DIAL (MPD) architecture and uses distributed Bragg reflector lasers. The MPD architecture is unique because it is eye-safe and cost-effective; therefore, it is ideal for creating a network of ground-based lidars. This instrument is designed for thermodynamic profiling of the lower troposphere. A network of these instruments would be helpful for wide-scale atmospheric monitoring for weather forecasting and climate science. The purpose of the HSRL is to retrieve the optical properties of aerosols in the lower troposphere. The HSRL uses the DIAL offline laser, which has a wavelength of 770.1085 nm, and a potassium vapor cell as the spectral filter. The data retrieved from the HSRL provides the aerosol backscatter coefficient and the backscatter ratio up to an altitude of 7 km during nighttime operation and 5 km during daytime operation. The time resolution for these measurements is 5 minutes, and the range resolution is 150 m. These aerosol optical properties are valuable for aerosol studies and climate modeling; aerosols introduce the most significant degree of uncertainty in modeling the heat flux of the atmosphere. Additionally, these aerosol optical properties can be used to find the planetary boundary layer height (PBLH). The planetary boundary layer controls the exchange of heat, water vapor, aerosols, and momentum between the surface and the atmosphere. It has been demonstrated that the PBLH strongly affects turbulent mixing, convective transport, and cloud entrainment, which makes the PBLH an important parameter for weather forecasting and climate modeling. Despite its significance in atmospheric science, there is no standard method for defining the PBLH. A retrieval method for finding the daytime PBLH using HSRL data is proposed, and data comparisons to radiosonde PBLH retrievals are provided. The algorithm shows a good agreement with the radiosonde retrievals for conditions with a well-behaved boundary layer.Item Results of a micro pulse differential absorption LIDAR for temperature profiling and analysis code(Montana State University - Bozeman, College of Engineering, 2021) Cruikshank, Owen Daniel; Chairperson, Graduate Committee: Kevin S. RepaskyThermodynamic profiling of the lower troposphere is necessary for the study of weather and climate. The micropulse DIAL (differential absorption lidar), or MPD, presented here is designed to fill the need. The MPD is eye-safe and can run autonomously for continuous measurements compared to technologies with similar measurement capabilities like Raman lidar. Using a temperature-sensitive absorption line of O 2, the MPD system can measure the absorption of O 2 in the lower troposphere as a function of range and convert that measurement to temperature as a function of range. This process relies on a perturbative correction to the absorption retrieval to account for the fact that the O 2 absorption spectral linewidth is similar to the molecular Rayleigh scattering linewidth. An ancillary measurement of the ratio of aerosol backscatter to molecular backscatter is required for the correction. The integrated high spectral resolution lidar (HSRL) uses a heated potassium vapor notch filter to make the aerosol-to-molecular ratio measurement. An analysis program in MATLAB was written to take in raw lidar data and produce a temperature product of range and time. Results presented from a campaign at the Atmospheric Radiation Measurements program Southern Great Plains site in Oklahoma in spring 2019 show temperature comparisons with radiosonde measurements with a mean difference between radiosonde and MPD measurements of -1.1K and a standard deviation of 2.7 K. Further results from an instrument on the Montana State University campus in Bozeman and at the National Center for Atmospheric Research in Boulder, Colorado have shown that the MPD instrument can produce measurements autonomously for periods of weeks to months.Item Combining spectral and polarimetric methods to classify cloud thermodynamic phase(Montana State University - Bozeman, College of Engineering, 2019) Tauc, Martin Jan; Chairperson, Graduate Committee: Joseph A. Shaw; David W. Riesland, Laura M. Eshelman, Wataru Nakagawa and Joseph A. Shaw were co-authors of the article, 'Radiance ratios for CTP discrimination' submitted to the journal 'Journal of applied remote sensing' which is contained within this thesis.; Wataru Nakagawa and Joseph A. Shaw were co-authors of the article, 'The SWIR three-channel polarimeter for cloud thermodynamic phase detection' in the journal 'Optical engineering' which is contained within this thesis.Cloud thermodynamic phase--whether a cloud is composed of spherical water droplets or polyhedral ice crystals--is an important parameter for optical communication with space-based instruments, remote sensing of the atmosphere, and, perhaps most importantly, understanding weather and climate. Although some methods exist to detect the phase of clouds, there is still a need for passive remote sensing of cloud thermodynamic phase due to its low-cost, scalability, and ease of use. Two methods for cloud thermodynamic phase classification employ spectral radiance ratios in the short-wave infrared, and the S 1 Stokes parameter, a polarimetric quantity. In this dissertation, the combination of the two methods is realized in an instrument called the short-wave infrared three-channel polarimeter. The coalescence of radiance ratios in the short-wave infrared and polarization channels oriented parallel and perpendicular to the scattering plane provides better classification of cloud phase than either method independently. Despite the improvement, the low-cost system suffered from hardware and software limitations, which caused an increase in noise and polarimetric artifacts. These errors are analyzed and a subset of low-noise data shows even better classification ability. All together, the results attained from the deployment of the polarimeter in early 2019 showed promise that the combination of the two methods is an improvement over past techniques.Item The role of adsorbed phase volume on the thermodynamics of supercritical methane adsorption on microporous carbon(Montana State University - Bozeman, College of Engineering, 2019) Remington, Emily Lynn; Chairperson, Graduate Committee: Sarah L. Codd; Nicholas P. Stadie (co-chair)Experimental determination of the isosteric heat of adsorption at the fluidsolid interface is an important undertaking in the chemical sciences since this fundamental thermodynamic quantity is closely related to the binding energy of the adsorbate on the adsorbent surface. The usual methods employed to calculate the isosteric heat from measured gas adsorption equilibria, however, are unsuited to the treatment of adsorption under a high-pressure adsorptive fluid (where the difference in molar volume between the two phases becomes small and depends significantly on that of the adsorbed phase). Herein we employ a methodological approach to the thermodynamic analysis of adsorption up to high pressures in the supercritical regime, with a specific focus on methane adsorption on microporous carbonaceous materials at T/T c between 1.25-2.75 and P/P c up to 2. The aim is to achieve a meritorious description of the thermodynamics of the adsorbed phase with as few independent parameters as possible. We compare several simple approaches to estimating the molar volume of the adsorbed phase, and demonstrate that among the several well-known sources of error involved in the isosteric approach, that attributed to molar volume estimations is not itself prohibitive to achieving meritorious results. We contrast the isosteric approach with that of the so-called 'isoexcess' methodology, and thereby shed new insights into the key role of the finite adsorbed phase volume in assessments of adsorption thermodynamics.Item The development and validation of a snow/icepack pavement temperature thermodynamic model(Montana State University - Bozeman, College of Engineering, 2002) Bristow, Jeffrey RyanItem Tricritical point in KHâ‚‚Oâ‚„(Montana State University - Bozeman, College of Letters & Science, 1977) Bacon, Charles RobertItem Pressure induced tricritical point in the ferroelectric phase transition of potassium dihydrogen phosphate(Montana State University - Bozeman, College of Letters & Science, 1976) Western, Arthur B.