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- Genre: Masters Thesis
- Status: Published
Description
Microbially induced calcium carbonate precipitation (MICP) is attracting increasing attention as a sustainable means of soil improvement. While there are several possible MICP mechanisms, microbial denitrification has the potential to become one of the preferred methods for MICP because complete denitrification does not produce toxic byproducts, readily occurs under anoxic conditions, and potentially has a greater carbonate yield per mole of organic electron donor than other MICP processes. Denitrification may be preferable to ureolytic hydrolysis, the MICP process explored most extensively to date, as the byproduct of denitrification is benign nitrogen gas, while the chemical pathways involved in hydrolytic ureolysis processes produce undesirable and potentially toxic byproducts such as ammonium (NH4+). This thesis focuses on bacterial denitrification and presents preliminary results of bench-scale laboratory experiments on denitrification as a candidate calcium carbonate precipitation mechanism. The bench-scale bioreactor and column tests, conducted using the facultative anaerobic bacterium Pseudomonas denitrificans, show that calcite can be precipitated from calcium-rich pore water using denitrification. Experiments also explore the potential for reducing environmental impacts and lowering costs associated with denitrification by reducing the total dissolved solids in the reactors and columns, optimizing the chemical matrix, and addressing the loss of free calcium in the form of calcium phosphate precipitate from the pore fluid. The potential for using MICP to sequester radionuclides and metal contaminants that are migrating in groundwater is also investigated. In the sequestration process, divalent cations and radionuclides are incorporated into the calcite structure via substitution, forming low-strontium calcium carbonate minerals that resist dissolution at a level similar to that of calcite. Work by others using the bacterium Sporosarcina pasteurii has suggested that in-situ sequestration of radionuclides and metal contaminants can be achieved through MICP via hydrolytic ureolysis. MICP through bacterial denitrification seems particularly promising as a means for sequestering radionuclides and metal contaminants in anoxic environments due to the anaerobic nature of the process and the ubiquity of denitrifying bacteria in the subsurface.
ContributorsHamdan, Nasser (Author) / Kavazanjian, Edward (Thesis advisor) / Rittmann, Bruce E. (Thesis advisor) / Shock, Everett (Committee member) / Arizona State University (Publisher)
Created2013
Description
Cancer claims hundreds of thousands of lives every year in US alone. Finding ways for early detection of cancer onset is crucial for better management and treatment of cancer. Thus, biomarkers especially protein biomarkers, being the functional units which reflect dynamic physiological changes, need to be discovered. Though important, there are only a few approved protein cancer biomarkers till date. To accelerate this process, fast, comprehensive and affordable assays are required which can be applied to large population studies. For this, these assays should be able to comprehensively characterize and explore the molecular diversity of nominally "single" proteins across populations. This information is usually unavailable with commonly used immunoassays such as ELISA (enzyme linked immunosorbent assay) which either ignore protein microheterogeneity, or are confounded by it. To this end, mass spectrometric immuno assays (MSIA) for three different human plasma proteins have been developed. These proteins viz. IGF-1, hemopexin and tetranectin have been found in reported literature to show correlations with many diseases along with several carcinomas. Developed assays were used to extract entire proteins from plasma samples and subsequently analyzed on mass spectrometric platforms. Matrix assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) mass spectrometric techniques where used due to their availability and suitability for the analysis. This resulted in visibility of different structural forms of these proteins showing their structural micro-heterogeneity which is invisible to commonly used immunoassays. These assays are fast, comprehensive and can be applied in large sample studies to analyze proteins for biomarker discovery.
ContributorsRai, Samita (Author) / Nelson, Randall (Thesis advisor) / Hayes, Mark (Thesis advisor) / Borges, Chad (Committee member) / Ros, Alexandra (Committee member) / Arizona State University (Publisher)
Created2012
Description
Microfluidic platforms have been exploited extensively as a tool for the separation of particles by electric field manipulation. Microfluidic devices can facilitate the manipulation of particles by dielectrophoresis. Separation of particles by size and type has been demonstrated by insulator-based dielectrophoresis in a microfluidic device. Thus, manipulating particles by size has been widely studied throughout the years. It has been shown that size-heterogeneity in organelles has been linked to multiple diseases from abnormal organelle size. Here, a mixture of two sizes of polystyrene beads (0.28 and 0.87 μm) was separated by a ratchet migration mechanism under a continuous flow (20 nL/min). Furthermore, to achieve high-throughput separation, different ratchet devices were designed to achieve high-volume separation. Recently, enormous efforts have been made to manipulate small size DNA and proteins. Here, a microfluidic device comprising of multiple valves acting as insulating constrictions when a potential is applied is presented. The tunability of the electric field gradient is evaluated by a COMSOL model, indicating that high electric field gradients can be reached by deflecting the valve at a certain distance. Experimentally, the tunability of the dynamic constriction was demonstrated by conducting a pressure study to estimate the gap distance between the valve and the substrate at different applied pressures. Finally, as a proof of principle, 0.87 μm polystyrene beads were manipulated by dielectrophoresis. These microfluidic platforms will aid in the understanding of size-heterogeneity of organelles for biomolecular assessment and achieve separation of nanometer-size DNA and proteins by dielectrophoresis.
ContributorsOrtiz, Ricardo (Author) / Ros, Alexandra (Thesis advisor) / Hayes, Mark (Committee member) / Borges, Chad (Committee member) / Arizona State University (Publisher)
Created2021
Description
Traditional Reinforcement Learning (RL) assumes to learn policies with respect to reward available from the environment but sometimes learning in a complex domain requires wisdom which comes from a wide range of experience. In behavior based robotics, it is observed that a complex behavior can be described by a combination of simpler behaviors. It is tempting to apply similar idea such that simpler behaviors can be combined in a meaningful way to tailor the complex combination. Such an approach would enable faster learning and modular design of behaviors. Complex behaviors can be combined with other behaviors to create even more advanced behaviors resulting in a rich set of possibilities. Similar to RL, combined behavior can keep evolving by interacting with the environment. The requirement of this method is to specify a reasonable set of simple behaviors. In this research, I present an algorithm that aims at combining behavior such that the resulting behavior has characteristics of each individual behavior. This approach has been inspired by behavior based robotics, such as the subsumption architecture and motor schema-based design. The combination algorithm outputs n weights to combine behaviors linearly. The weights are state dependent and change dynamically at every step in an episode. This idea is tested on discrete and continuous environments like OpenAI’s “Lunar Lander” and “Biped Walker”. Results are compared with related domains like Multi-objective RL, Hierarchical RL, Transfer learning, and basic RL. It is observed that the combination of behaviors is a novel way of learning which helps the agent achieve required characteristics. A combination is learned for a given state and so the agent is able to learn faster in an efficient manner compared to other similar approaches. Agent beautifully demonstrates characteristics of multiple behaviors which helps the agent to learn and adapt to the environment. Future directions are also suggested as possible extensions to this research.
ContributorsVora, Kevin Jatin (Author) / Zhang, Yu (Thesis advisor) / Yang, Yezhou (Committee member) / Praharaj, Sarbeswar (Committee member) / Arizona State University (Publisher)
Created2021
Description
Dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC) are crucial nutrients for autotrophic and heterotrophic microbial life, respectively, in hydrothermal systems. Biogeochemical processes that control amounts of DIC and DOC in Yellowstone hot springs can be investigated by measuring carbon abundances and respective isotopic values. A decade and a half of field work in 10 regions within Yellowstone National Park and subsequent geochemical lab analyses reveal that sulfate-dominant acidic regions have high DOC (Up to 57 ppm C) and lower DIC (up to 50 ppm C) compared to neutral-chloride regions with low DOC (< 2 ppm C) and higher DIC (up to 100 ppm C). Abundances and isotopic data suggest that sedimentary rock erosion by acidic hydrothermal fluids, fresh snow-derived meteoric water, and exogenous carbon input allowed by local topography may affect DOC levels. Evaluating the isotopic compositions of DIC and DOC in hydrothermal fluids gives insight on the geology and microbial life in the subsurface between different regions. DIC δ13C values range from -4‰ to +5‰ at pH 5-9 and from -10‰ to +3‰ at pH 2-5 with several springs lower than -10‰. DOC δ13C values parkwide range from -10‰ to -30‰. Within this range, neutral-chloride regions in the Lower Geyser Basin have lighter isotopes than sulfate-dominant acidic regions. In hot springs with elevated levels of DOC, the range only varies between -20‰ and -26‰ which may be caused by local exogenous organic matter runoff. Combining other geochemical measurements, such as differences in chloride and sulfate concentrations, demonstrates that some regions contain mixtures of multiple fluids moving through the complex hydrological system in the subsurface. The mixing of these fluids may account for increased levels of DOC in meteoric sulfate-dominant acidic regions. Ultimately, the foundational values of dissolved carbon and their isotopic composition is provided in a parkwide study, so results can be combined with future studies that apply different sequencing analyses to understand specific biogeochemical cycling and microbial communities that occur in individual hot springs.
ContributorsBarnes, Tanner (Author) / Shock, Everett (Thesis advisor) / Meyer-Dombard, D'Arcy (Committee member) / Hartnett, Hilairy (Committee member) / Arizona State University (Publisher)
Created2023
Description
Trace evidence is an essential component of forensic investigations. Anthropogenicmaterials such as fibers and glass have been well studied for use in forensic trace evidence, but the potential use of retroreflective beads found in soils for forensic investigations is largely unexplored. Retroreflective glass beads are tiny spheres mixed into pavement markings to create reflective surfaces to reduce lane departure accidents. Retroreflective glass beads are a potentially new source of trace evidence for forensic investigations.
Analysis of the spatial distribution and chemical compositions of retroreflective glass beads recovered from 17 soil samples were analyzed and compared to see if there are striking variations that can distinguish samples by source. Soil samples taken near marked roads showed significantly higher concentrations of glass beads, averaging from 0.18 bead/g of soil sample to 587 beads/g of soil, while soil samples taken near unmarked roads had average range of concentration of 0 bead/g of soil to 0.21 bead/g of soil. Retroreflective glass beads come from pavement markings, thus soil samples near marked roads are expected to have higher concentrations of glass beads. Analysis of spatial distribution of glass beads showed that as sample collection moved further from the road, concentration of glass beads decreased.
ICP-MS results of elemental concentrations for each sample showed discriminative differences between samples, for most of the elements. An analysis of variance for elemental concentrations was conducted, and results showed statistically significant differences, beyond random chance alone for half of the elements analyzed. For forensic comparisons, a significant difference in even just one element is enough to conclude that the samples came from different sources. The elemental concentrations of glass beads collected from the same location, but of varying differences, was also analyzed. ANOVA results show significant differences for only one or two elements. A pair-wise t-test was conducted to determine which elements are most discriminative among all the samples. Rubidium was found to be the most discriminative, showing significant difference for 67% of the pairs. Beryllium, potassium, and manganese were also highly discriminative, showing significant difference for at least 50% of all the pairs.
ContributorsGomez, Janelle Kate Pacifico (Author) / Montero, Shirly (Thesis advisor) / Herckes, Pierre (Thesis advisor) / Borges, Chad (Committee member) / Gordon, Gwyneth (Committee member) / Arizona State University (Publisher)
Created2023
Description
Public transportation is considered a solution to congestion and a tool for reducing greenhouse gas emissions. It is becoming popular even in cities with the harshest climate conditions as these cities grow rapidly and are trying to provide sustainable alternatives for their vehicle-oriented communities. A lot must be taken into consideration whendesigning transit systems to reduce riders' vulnerability to heat in cities with high temperatures averaging 40°C during the summer and humidity levels reaching 90 percent. Using transit systems in Dubai, United Arab Emirates, and Phoenix Metropolitan, United States, as case studies, this paper focuses on both qualitative and quantitative research methods to observe the built environment around public transit stations and measure the temperatures and humidity levels to compare with the experienced temperatures and the built environment observations. The results show that the design of transit stations and the public realm significantly impacts a rider's experience. The findings show that passive cooling, shading, and vegetation as the best practices in the two case studies. Both transit systems have certain elements that work efficiently and other elements that need improvement to provide a better rider experience. Identifying these best practices helps develop recommendations for the future of designing transit systems in desert cities worldwide.
ContributorsAlbastaki, Mohamed (Author) / King, David (Thesis advisor) / Salon, Deborah (Committee member) / Kelley, Jason (Committee member) / Arizona State University (Publisher)
Created2022
Description
Transit agencies are struggling to regain ridership lost during the pandemic. Research shows that riding transit was among the most feared activities during the pandemic due to people’s high perceived risk of infection. Transit agencies have responded by implementing a variety of pandemic-related safety measures in stations and vehicles, but there is little literature assessing how these safety measures affect passengers’ perception of safety. This study implements surveys, interviews, and observations in Berlin, Germany to assess how passengers’ demographic characteristics and experiences with safety measures are related to their perception of safety using transit. Females and older age groups were more likely to perceive transit as riskier than males and younger age groups. The results provide little evidence to suggest that safety measures have a significant impact on passengers’ perception of safety, however. If this result is supported by future research, it suggests that transit agency investments in pandemic safety measures may not help them to regain ridership.
ContributorsKatt, Noah (Author) / Salon, Deborah (Thesis advisor) / Meerow, Sara (Committee member) / King, David (Committee member) / Arizona State University (Publisher)
Created2022
Description
For cold chain tracking systems, precision and versatility across varying time intervals and temperature ranges remain integral to effective application in clinical, commercial, and academic settings. Therefore, while electronic and chemistry/physics based cold chain tracking mechanisms currently exist, both have limitations that affect their application across various biospecimens and commercial products, providing the initiative to develop a time temperature visual indicator system that resolves challenges with current cold chain tracking approaches. As a result, a permanganate/oxalic acid time temperature visual indicator system for cold chain tracking has been proposed. At thawing temperatures, the designed permanganate/oxalic acid reaction system undergoes a pink to colorless transition as permanganate, Mn(VII), is reduced to auto-catalytic Mn(II), while oxalate is oxidized to CO2. Therefore, when properly stored and vitrified or frozen, the proposed visual indicator remains pink, whereas exposure to thawing conditions will result in an eventual, time temperature dependent, designed color transition that characterizes compromised biospecimen integrity. To design visual indicator systems for targeted times at specific temperatures, absorbance spectroscopy was utilized to monitor permanganate kinetic curves by absorbance at 525 nm. As a result, throughout the outlined research, the following aims were demonstrated: (i) Design and functionality of 1x (0.5 mM KMnO4) visual indicator systems across various time intervals at temperatures ranging from 25°C to -20°C, (ii) Design and functionality of high concentration, 5x, visual indicator systems across varying targeted time intervals at temperatures ranging from 25°C to 0°C, (iii) Pre-activation stability and long-term stability of the proposed visual indicator systems.
ContributorsLjungberg, Emil (Author) / Borges, Chad (Thesis advisor) / Levitus, Marcia (Committee member) / Williams, Peter (Committee member) / Arizona State University (Publisher)
Created2024
Description
Insulator-based dielectrophoresis (iDEP) has attracted considerable attention due to its ability to precisely capture and manipulate nanoparticles and biomolecules. A distinctive approach for effective manipulation of nanometer-sized proteins employing iDEP technique by generating higher electric field (E) and gradient (??2) in the iDEP microfluidic devices is delineated. Strategies to generate higher ??2 in the iDEP devices were outlined using numerical simulations. Intriguingly, the numerical simulation results demonstrated that by decreasing the post-to-post gap in the iDEP microfluidic devices, the ??2 was increased by ⁓12 fold. Furthermore, the inclusion of channel constrictions, such as rectangular constriction or curved constriction into the straight channel iDEP microfluidic device led to a significant increase in ??2. In addition, the inclusion of rectangular constrictions in the straight channel iDEP microfluidic device resulted in a greater increase in ??2 compared to the incorporation of curved constrictions in the same device. Moreover, the straight channel device with horizontal post-to-post gap of 20 μm and vertical post-to-post gap of 10 μm generated the lowest ??2 and the ??2 was uniform across the device. The rectangular constriction device with horizontal and vertical post-to-post gap of 5 μm generated the highest ??2 and the ??2 was non-uniform across the device. Subsequently, suitable candidate devices were fabricated using soft lithography as well as high resolution 3D printing and the DEP behavior of ferritin examined under various experimental conditions. Positive streaming DEP could be observed for ferritin at low frequency in the device generating the lowest ??2, whereas at higher frequency of 10 kHz no DEP trapping characteristics were apparent in the same device. Importantly, in the device geometry resulting in the highest ??2 at 10 kHz, labeled ferritin exhibited pDEPtrapping characteristics. This is an indication that the DEP force superseded diffusion and became the dominant force.
ContributorsMAHMUD, SAMIRA (Author) / Ros, Alexandra (Thesis advisor) / Borges, Chad (Committee member) / Mills, Jeremy (Committee member) / Arizona State University (Publisher)
Created2024