Matching Items (139)
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
Over 2 billion people are using online social network services, such as Facebook, Twitter, Google+, LinkedIn, and Pinterest. Users update their status, post their photos, share their information, and chat with others in these social network sites every day; however, not everyone shares the same amount of information. This thesis explores methods of linking publicly available data sources as a means of extrapolating missing information of Facebook. An application named "Visual Friends Income Map" has been created on Facebook to collect social network data and explore geodemographic properties to link publicly available data, such as the US census data. Multiple predictors are implemented to link data sets and extrapolate missing information from Facebook with accurate predictions. The location based predictor matches Facebook users' locations with census data at the city level for income and demographic predictions. Age and relationship based predictors are created to improve the accuracy of the proposed location based predictor utilizing social network link information. In the case where a user does not share any location information on their Facebook profile, a kernel density estimation location predictor is created. This predictor utilizes publicly available telephone record information of all people with the same surname of this user in the US to create a likelihood distribution of the user's location. This is combined with the user's IP level information in order to narrow the probability estimation down to a local regional constraint.
ContributorsMao, Jingxian (Author) / Maciejewski, Ross (Thesis advisor) / Farin, Gerald (Committee member) / Wang, Yalin (Committee member) / Arizona State University (Publisher)
Created2012
Description
Laboratory automation systems have seen a lot of technological advances in recent times. As a result, the software that is written for them are becoming increasingly sophisticated. Existing software architectures and standards are targeted to a wider domain of software development and need to be customized in order to use them for developing software for laboratory automation systems. This thesis proposes an architecture that is based on existing software architectural paradigms and is specifically tailored to developing software for a laboratory automation system. The architecture is based on fairly autonomous software components that can be distributed across multiple computers. The components in the architecture make use of asynchronous communication methodologies that are facilitated by passing messages between one another. The architecture can be used to develop software that is distributed, responsive and thread-safe. The thesis also proposes a framework that has been developed to implement the ideas proposed by the architecture. The framework is used to develop software that is scalable, distributed, responsive and thread-safe. The framework currently has components to control very commonly used laboratory automation devices such as mechanical stages, cameras, and also to do common laboratory automation functionalities such as imaging.
ContributorsKuppuswamy, Venkataramanan (Author) / Meldrum, Deirdre (Thesis advisor) / Collofello, James (Thesis advisor) / Sarjoughian, Hessam S. (Committee member) / Johnson, Roger (Committee member) / Arizona State University (Publisher)
Created2012
Description
This document presents a new implementation of the Smoothed Particles Hydrodynamics algorithm using DirectX 11 and DirectCompute. The main goal of this document is to present to the reader an alternative solution to the largely studied and researched problem of fluid simulation. Most other solutions have been implemented using the NVIDIA CUDA framework; however, the proposed solution in this document uses the Microsoft general-purpose computing on graphics processing units API. The implementation allows for the simulation of a large number of particles in a real-time scenario. The solution presented here uses the Smoothed Particles Hydrodynamics algorithm to calculate the forces within the fluid; this algorithm provides a Lagrangian approach for discretizes the Navier-Stockes equations into a set of particles. Our solution uses the DirectCompute compute shaders to evaluate each particle using the multithreading and multi-core capabilities of the GPU increasing the overall performance. The solution then describes a method for extracting the fluid surface using the Marching Cubes method and the programmable interfaces exposed by the DirectX pipeline. Particularly, this document presents a method for using the Geometry Shader Stage to generate the triangle mesh as defined by the Marching Cubes method. The implementation results show the ability to simulate over 64K particles at a rate of 900 and 400 frames per second, not including the surface reconstruction steps and including the Marching Cubes steps respectively.
ContributorsFigueroa, Gustavo (Author) / Farin, Gerald (Thesis advisor) / Maciejewski, Ross (Committee member) / Wang, Yalin (Committee member) / Arizona State University (Publisher)
Created2012
Description
Biological soil crusts (BSCs) are critical components of arid and semiarid environments and provide the primary sources of bioavailable macronutrients and increase micronutrient availability to their surrounding ecosystems. BSCs are composed of a variety of microorganisms that perform a wide range of physiological processes requiring a multitude of bioessential micronutrients, such as iron, copper, and molybdenum. This work investigated the effects of BSC activity on soil solution concentrations of bioessential elements and examined the microbial production of organic chelators, called siderophores. I found that aluminum, vanadium, copper, zinc, and molybdenum were solubilized in the action of crusts, while nickel, zinc, arsenic, and zirconium were immobilized by crust activity. Potassium and manganese displayed behavior consistent with biological removal and mobilization, whereas phosphorus and iron solubility were dominated by abiotic processes. The addition of bioavailable nitrogen altered the effects of BSCs on soil element mobilization. In addition, I found that the biogeochemical activites of BSCs were limited by molybdenum, a fact that likely contributes to co-limitation by nitrogen. I confirmed the presence of siderophore producing microbes in BSCs. Siderophores are low-molecular weight organic compounds that are released by bacteria to increase element solubility and facilitate element uptake; siderophore production is likely the mechanism by which BSCs affect the patterns I observed in soil solution element concentrations. Siderophore producers were distributed across a range of bacterial groups and ecological niches within crusts, suggesting that siderophore production influences the availability of a variety of elements for use in many physiological processes. Four putative siderophore compounds were identified using electrospray ionization mass spectrometry; further attempts to characterize the compounds confirmed two true siderophores. Taken together, the results of my work provide information about micronutrient cycling within crusts that can be applied to BSC conservation and management. Fertilization with certain elements, particularly molybdenum, may prove to be a useful technique to promote BSC growth and development which would help prevent arid land degradation. Furthermore, understanding the effects of BSCs on soil element mobility could be used to develop useful biomarkers for the study of the existence and distribution of crust-like communities on ancient Earth, and perhaps other places, like Mars.
ContributorsNoonan, Kathryn Alexander (Author) / Hartnett, Hilairy (Thesis advisor) / Anbar, Ariel (Committee member) / Garcia-Pichel, Ferran (Committee member) / Shock, Everett (Committee member) / Sharp, Thomas (Committee member) / Arizona State University (Publisher)
Created2012
Description
Ponderosa pine forests are a dominant land cover type in semiarid montane areas. Water supplies in major rivers of the southwestern United States depend on ponderosa pine forests since these ecosystems: (1) receive a significant amount of rainfall and snowfall, (2) intercept precipitation and transpire water, and (3) indirectly influence runoff by impacting the infiltration rate. However, the hydrologic patterns in these ecosystems with strong seasonality are poorly understood. In this study, we used a distributed hydrologic model evaluated against field observations to improve our understandings on spatial controls of hydrologic patterns, appropriate model resolution to simulate ponderosa pine ecosystems and hydrologic responses in the context of contrasting winter to summer transitions. Our modeling effort is focused on the hydrologic responses during the North American Monsoon (NAM), winter and spring periods. In Chapter 2, we utilized a distributed model explore the spatial controls on simulated soil moisture and temporal evolution of these spatial controls as a function of seasonal wetness. Our findings indicate that vegetation and topographic curvature are spatial controls. Vegetation controlled patterns during dry summer period switch to fine-scale terrain curvature controlled patterns during persistently wet NAM period. Thus, a climatic threshold involving rainfall and weather conditions during the NAM is identified when high rainfall amount (such as 146 mm rain in August, 1997) activates lateral flux of soil moisture and frequent cloudy cover (such as 42% cloud cover during daytime of August, 1997) lowers evapotranspiration. In Chapter 3, we investigate the impacts of model coarsening on simulated soil moisture patterns during the NAM. Results indicate that model aggregation quickly eradicates curvature features and its spatial control on hydrologic patterns. A threshold resolution of ~10% of the original terrain is identified through analyses of homogeneity indices, correlation coefficients and spatial errors beyond which the fidelity of simulated soil moisture is no longer reliable. Based on spatial error analyses, we detected that the concave areas (~28% of hillslope) are very sensitive to model coarsening and root mean square error (RMSE) is higher than residual soil moisture content (~0.07 m3/m3 soil moisture) for concave areas. Thus, concave areas need to be sampled for capturing appropriate hillslope response for this hillslope. In Chapter 4, we investigate the impacts of contrasting winter to summer transitions on hillslope hydrologic responses. We use a distributed hydrologic model to generate a consistent set of high-resolution hydrologic estimates. Our model is evaluated against the snow depth, soil moisture and runoff observations over two water years yielding reliable spatial distributions during the winter to summer transitions. We find that a wet winter followed by a dry summer promotes evapotranspiration losses (spatial averaged ~193 mm spring ET and ~ 600 mm summer ET) that dry the soil and disconnect lateral fluxes in the forested hillslope, leading to soil moisture patterns resembling vegetation patches. Conversely, a dry winter prior to a wet summer results in soil moisture increases due to high rainfall and low ET during the spring (spatially averaged 78 mm ET and 232 mm rainfall) and summer period (spatially averaged 147 mm ET and 247 mm rainfall) which promote lateral connectivity and soil moisture patterns with the signature of terrain curvature. An opposing temporal switch between infiltration and saturation excess runoff is also identified. These contrasting responses indicate that the inverse relation has significant consequences on hillslope water availability and its spatial distribution with implications on other ecohydrological processes including vegetation phenology, groundwater recharge and geomorphic development. Results from this work have implications on the design of hillslope experiments, the resolution of hillslope scale models, and the prediction of hydrologic conditions in ponderosa pine ecosystems. In addition, our findings can be used to select future hillslope sites for detailed ecohydrological investigations. Further, the proposed methodology can be useful for predicting responses to climate and land cover changes that are anticipated for the southwestern United States.
ContributorsMahmood, Taufique Hasan (Author) / Vivoni, Enrique R. (Thesis advisor) / Whipple, Kelin X. (Committee member) / Shock, Everett (Committee member) / Heimsath, Arjun M. (Committee member) / Ruddell, Benjamin (Committee member) / Arizona State University (Publisher)
Created2012
Description
Alzheimer's Disease (AD) is the most common form of dementia observed in elderly patients and has significant social-economic impact. There are many initiatives which aim to capture leading causes of AD. Several genetic, imaging, and biochemical markers are being explored to monitor progression of AD and explore treatment and detection options. The primary focus of this thesis is to identify key biomarkers to understand the pathogenesis and prognosis of Alzheimer's Disease. Feature selection is the process of finding a subset of relevant features to develop efficient and robust learning models. It is an active research topic in diverse areas such as computer vision, bioinformatics, information retrieval, chemical informatics, and computational finance. In this work, state of the art feature selection algorithms, such as Student's t-test, Relief-F, Information Gain, Gini Index, Chi-Square, Fisher Kernel Score, Kruskal-Wallis, Minimum Redundancy Maximum Relevance, and Sparse Logistic regression with Stability Selection have been extensively exploited to identify informative features for AD using data from Alzheimer's Disease Neuroimaging Initiative (ADNI). An integrative approach which uses blood plasma protein, Magnetic Resonance Imaging, and psychometric assessment scores biomarkers has been explored. This work also analyzes the techniques to handle unbalanced data and evaluate the efficacy of sampling techniques. Performance of feature selection algorithm is evaluated using the relevance of derived features and the predictive power of the algorithm using Random Forest and Support Vector Machine classifiers. Performance metrics such as Accuracy, Sensitivity and Specificity, and area under the Receiver Operating Characteristic curve (AUC) have been used for evaluation. The feature selection algorithms best suited to analyze AD proteomics data have been proposed. The key biomarkers distinguishing healthy and AD patients, Mild Cognitive Impairment (MCI) converters and non-converters, and healthy and MCI patients have been identified.
ContributorsDubey, Rashmi (Author) / Ye, Jieping (Thesis advisor) / Wang, Yalin (Committee member) / Wu, Tong (Committee member) / Arizona State University (Publisher)
Created2012
Description
Early spacecraft missions to Mars, including the Marnier and Viking orbiters and landers revealed a morphologically and compositionally diverse landscape that reshaped widely held views of Mars. More recent spacecraft including Mars Global Surveyor, Mars Odyssey, Mars Express, Mars Reconnaissance Orbiter, and the Mars Exploration Rovers have further refined, enhanced, and diversified our understanding of Mars. In this dissertation, I take a multiple-path approach to planetary and Mars science including data analysis and instrument development. First, I present several tools necessary to effectively use new, complex datasets by highlighting unique and innovative data processing techniques that allow for the regional to global scale comparison of multiple datasets. Second, I present three studies that characterize several processes on early Mars, where I identify a regional, compositionally distinct, in situ, stratigraphically significant layer in Ganges and Eos Chasmata that formed early in martian history. This layer represents a unique period in martian history where primitive mantle materials were emplaced over large sections of the martian surface. While I originally characterized this layer as an effusive lava flow, based on the newly identified regional or global extent of this layer, I find the only likely scenario for its emplacement is the ejecta deposit of the Borealis Basin forming impact event. I also re-examine high thermal inertia, flat-floored craters identified in Viking data and conclude they are typically more mafic than the surrounding plains and were likely infilled by primitive volcanic materials during, or shortly after the Late Heavy Bombardment. Furthermore, the only plausible source for these magmas is directly related to the impact process, where mantle decompression melting occurs as result of the removal of overlying material by the impactor. Finally, I developed a new laboratory microscopic emission and reflectance spectrometer designed to help improve the interpretation of current remote sensing or in situ data from planetary bodies. I present the design, implementation, calibration, system performance, and preliminary results of this instrument. This instrument is a strong candidate for the next generation in situ rover instruments designed to definitively assess sample mineralogy and petrology while preserving geologic context.
ContributorsEdwards, Christopher (Author) / Christensen, Philip R. (Thesis advisor) / Bell, James (Committee member) / Sharp, Thomas (Committee member) / Clarke, Amanda B (Committee member) / Shock, Everett (Committee member) / Arizona State University (Publisher)
Created2012
Description
Single cell analysis has become increasingly important in understanding disease onset, progression, treatment and prognosis, especially when applied to cancer where cellular responses are highly heterogeneous. Through the advent of single cell computerized tomography (Cell-CT), researchers and clinicians now have the ability to obtain high resolution three-dimensional (3D) reconstructions of single cells. Yet to date, no live-cell compatible version of the technology exists. In this thesis, a microfluidic chip with the ability to rotate live single cells in hydrodynamic microvortices about an axis parallel to the optical focal plane has been demonstrated. The chip utilizes a novel 3D microchamber design arranged beneath a main channel creating flow detachment into the chamber, producing recirculating flow conditions. Single cells are flowed through the main channel, held in the center of the microvortex by an optical trap, and rotated by the forces induced by the recirculating fluid flow. Computational fluid dynamics (CFD) was employed to optimize the geometry of the microchamber. Two methods for the fabrication of the 3D microchamber were devised: anisotropic etching of silicon and backside diffuser photolithography (BDPL). First, the optimization of the silicon etching conditions was demonstrated through design of experiment (DOE). In addition, a non-conventional method of soft-lithography was demonstrated which incorporates the use of two positive molds, one of the main channel and the other of the microchambers, compressed together during replication to produce a single ultra-thin (<200 µm) negative used for device assembly. Second, methods for using thick negative photoresists such as SU-8 with BDPL have been developed which include a new simple and effective method for promoting the adhesion of SU-8 to glass. An assembly method that bonds two individual ultra-thin (<100 µm) replications of the channel and the microfeatures has also been demonstrated. Finally, a pressure driven pumping system with nanoliter per minute flow rate regulation, sub-second response times, and < 3% flow variability has been designed and characterized. The fabrication and assembly of this device is inexpensive and utilizes simple variants of conventional microfluidic fabrication techniques, making it easily accessible to the single cell analysis community.
ContributorsMyers, Jakrey R (Author) / Meldrum, Deirdre (Thesis advisor) / Johnson, Roger (Committee member) / Frakes, David (Committee member) / Arizona State University (Publisher)
Created2012
Description
Molybdenum and uranium isotope variations are potentially powerful tools for reconstructing the paleoredox history of seawater. Reliable application and interpretation of these proxies requires not only detailed knowledge about the fractionation factors that control the distribution of molybdenum and uranium isotopes in the marine system, but also a thorough understanding of the diagenetic processes that may affect molybdenum and uranium isotopes entering the rock record. Using samples from the Black Sea water column, the first water column profile of 238U/235U variations from a modern euxinic basin has been measured. This profile allows the direct determination of the 238U/235U fractionation factor in a euxinic marine setting. More importantly however, these data demonstrate the extent of Rayleigh fractionation of U isotopes that can occur in euxinic restricted basins. Because of this effect, the offset of 238U/235U between global average seawater and coeval black shales deposited in restricted basins is expected to depend on the degree of local uranium drawdown from the water column, potentially complicating the interpretation 238U/235U paleorecords. As an alternative to the black shales typically used for paleoredox reconstructions, molybdenum and uranium isotope variations in bulk carbonate sediments from the Bahamas are examined. The focus of this work was to determine what processes, if any, fractionate molybdenum and uranium isotopes during incorporation into bulk carbonate sediments and their subsequent diagenesis. The results demonstrate that authigenic accumulation of molybdenum and uranium from anoxic and sulfidic pore waters is a dominant process controlling the concentration and isotopic composition of these sediments during early diagenesis. Examination of ODP drill core samples from the Bahamas reveals similar behavior for sediments during the first ~780ka of burial, but provides important examples where isolated cores and samples occasionally demonstrate additional fractionation, the cause of which remains poorly understood.
ContributorsRomaniello, Stephen J. (Author) / Anbar, Ariel (Thesis advisor) / Hartnett, Hilairy (Committee member) / Herrmann, Achim (Committee member) / Shock, Everett (Committee member) / Wadhwa, Meenakshi (Committee member) / Arizona State University (Publisher)
Created2012