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- All Subjects: Civil Engineering
- All Subjects: Biochemistry
- Creators: Zapata, Claudia
- Creators: Yan, Hao
Description
In geotechnical engineering, measuring the unsaturated hydraulic conductivity of fine grained soils can be time consuming and tedious. The various applications that require knowledge of the unsaturated hydraulic conductivity function are great, and in geotechnical engineering, they range from modeling seepage through landfill covers to determining infiltration of water under a building slab. The unsaturated hydraulic conductivity function can be measured using various direct and indirect techniques. The instantaneous profile method has been found to be the most promising unsteady state method for measuring the unsaturated hydraulic conductivity function for fine grained soils over a wide range of suction values. The instantaneous profile method can be modified by using different techniques to measure suction and water content and also through the way water is introduced or removed from the soil profile. In this study, the instantaneous profile method was modified by creating duplicate soil samples compacted into cylindrical tubes at two different water contents. The techniques used in the duplicate method to measure the water content and matric suction included volumetric moisture probes, manual water content measurements, and filter paper tests. The experimental testing conducted in this study provided insight into determining the unsaturated hydraulic conductivity using the instantaneous profile method for a sandy clay soil and recommendations are provided for further evaluation. Overall, this study has demonstrated that the presence of cracks has no significant impact on the hydraulic behavior of soil in high suction ranges. The results of this study do not examine the behavior of cracked soil unsaturated hydraulic conductivity at low suction and at moisture contents near saturation.
ContributorsJacquemin, Sean Christopher (Author) / Zapata, Claudia (Thesis advisor) / Houston, Sandra (Committee member) / Kavazanjian, Edward (Committee member) / Arizona State University (Publisher)
Created2011
Description
The infrastructure is built in Unsaturated Soils. However, the geotechnical practitioners insist in designing the structures based on Saturated Soil Mechanics. The design of structures based on unsaturated soil mechanics is desirable because it reduces cost and it is by far a more sustainable approach. The research community has identified the Soil-Water Characteristic Curve as the most important soil property when dealing with unsaturated conditions. This soil property is unpopular among practitioners because the laboratory testing takes an appreciable amount of time. Several authors have attempted predicting the Soil-Water Characteristic Curve; however, most of the published predictions are based on a very limited soil database. The National Resources Conservation Service has a vast database of engineering soil properties with more than 36,000 soils, which includes water content measurements at different levels of suctions. This database was used in this study to validate two existing models that based the Soil-Water Characteristic Curve prediction on statistical analysis. It was found that although the predictions are acceptable for some ranges of suctions; they did not performed that well for others. It was found that the first model validated was accurate for fine-grained soils, while the second model was best for granular soils. For these reasons, two models to estimate the Soil-Water Characteristic Curve are proposed. The first model estimates the fitting parameters of the Fredlund and Xing (1994) function separately and then, the predicted parameters are fitted to the Fredlund and Xing function for an overall estimate of the degree of saturation. Results show an overall improvement on the predicted values when compared to existing models. The second model is based on the relationship between the Soil-Water Characteristic Curve and the Pore-Size Distribution of the soils. The process allows for the prediction of the entire Soil-Water Characteristic Curve function and proved to be a better approximation than that used in the first attempt. Both models constitute important tools in the implementation of unsaturated soil mechanics into engineering practice due to the link of the prediction with simple and well known engineering soil properties.
ContributorsTorres Hernández, Gustavo (Author) / Zapata, Claudia (Thesis advisor) / Houston, Sandra (Committee member) / Witczak, Matthew (Committee member) / Arizona State University (Publisher)
Created2011
Description
Telomerase is a specialized enzyme that adds telomeric DNA repeats to the chromosome ends to counterbalance the progressive telomere shortening over cell divisions. It has two essential core components, a catalytic telomerase reverse transcriptase protein (TERT), and a telomerase RNA (TR). TERT synthesizes telomeric DNA by reverse transcribing a short template sequence in TR. Unlike TERT, TR is extremely divergent in size, sequence and structure and has only been identified in three evolutionarily distant groups. The lack of knowledge on TR from important model organisms has been a roadblock for vigorous studies on telomerase regulation. To address this issue, a novel in vitro system combining deep-sequencing and bioinformatics search was developed to discover TR from new phylogenetic groups. The system has been validated by the successful identification of TR from echinoderm purple sea urchin Strongylocentrotus purpuratus. The sea urchin TR (spTR) is the first invertebrate TR that has been identified and can serve as a model for understanding how the vertebrate TR evolved with vertebrate-specific traits. By using phylogenetic comparative analysis, the secondary structure of spTR was determined. The spTR secondary structure reveals unique sea urchin specific structure elements as well as homologous structural features shared by TR from other organisms. This study enhanced the understanding of telomerase mechanism and the evolution of telomerase RNP. The system that was used to identity telomerase RNA can be employed for the discovery of other TR as well as the discovery of novel RNA from other RNP complex.
ContributorsLi, Yang (Author) / Chen, Julian Jl (Thesis advisor) / Yan, Hao (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2011
Description
It is estimated that wind induced soil transports more than 500 x 106 metric tons of fugitive dust annually. Soil erosion has negative effects on human health, the productivity of farms, and the quality of surface waters. A variety of different polymer stabilizers are available on the market for fugitive dust control. Most of these polymer stabilizers are expensive synthetic polymer products. Their adverse effects and expense usually limits their use. Biopolymers provide a potential alternative to synthetic polymers. They can provide dust abatement by encapsulating soil particles and creating a binding network throughout the treated area. This research into the effectiveness of biopolymers for fugitive dust control involved three phases. Phase I included proof of concept tests. Phase II included carrying out the tests in a wind tunnel. Phase III consisted of conducting the experiments in the field. Proof of concept tests showed that biopolymers have the potential to reduce soil erosion and fugitive dust transport. Wind tunnel tests on two candidate biopolymers, xanthan and chitosan, showed that there is a proportional relationship between biopolymer application rates and threshold wind velocities. The wind tunnel tests also showed that xanthan gum is more successful in the field than chitosan. The field tests showed that xanthan gum was effective at controlling soil erosion. However, the chitosan field data was inconsistent with the xanthan data and field data on bare soil.
ContributorsAlsanad, Abdullah (Author) / Kavazanjian, Edward (Thesis advisor) / Edwards, David (Committee member) / Zapata, Claudia (Committee member) / Arizona State University (Publisher)
Created2011
Description
A method for evaluating the integrity of geosynthetic elements of a waste containment system subject to seismic loading is developed using a large strain finite difference numerical computer program. The method accounts for the effect of interaction between the geosynthetic elements and the overlying waste on seismic response and allows for explicit calculation of forces and strains in the geosynthetic elements. Based upon comparison of numerical results to experimental data, an elastic-perfectly plastic interface model is demonstrated to adequately reproduce the cyclic behavior of typical geomembrane-geotextile and geomembrane-geomembrane interfaces provided the appropriate interface properties are used. New constitutive models are developed for the in-plane cyclic shear behavior of textured geomembrane/geosynthetic clay liner (GMX/GCL) interfaces and GCLs. The GMX/GCL model is an empirical model and the GCL model is a kinematic hardening, isotropic softening multi yield surface plasticity model. Both new models allows for degradation in the cyclic shear resistance from a peak to a large displacement shear strength. The ability of the finite difference model to predict forces and strains in a geosynthetic element modeled as a beam element with zero moment of inertia sandwiched between two interface elements is demonstrated using hypothetical models of a heap leach pad and two typical landfill configurations. The numerical model is then used to conduct back analyses of the performance of two lined municipal solid waste (MSW) landfills subjected to strong ground motions in the Northridge earthquake. The modulus reduction "backbone curve" employed with the Masing criterion and 2% Rayleigh damping to model the cyclic behavior of MSW was established by back-analysis of the response of the Operating Industries Inc. landfill to five different earthquakes, three small magnitude nearby events and two larger magnitude distant events. The numerical back analysis was able to predict the tears observed in the Chiquita Canyon Landfill liner system after the earthquake if strain concentrations due to seams and scratches in the geomembrane are taken into account. The apparent good performance of the Lopez Canyon landfill geomembrane and the observed tension in the overlying geotextile after the Northridge event was also successfully predicted using the numerical model.
ContributorsArab, Mohamed G (Author) / Kavazanjian, Edward (Thesis advisor) / Zapata, Claudia (Committee member) / Houston, Sandra (Committee member) / Arizona State University (Publisher)
Created2011
Description
The structural design of pavements in both highways and airfields becomes complex when one considers environmental effects and ground water table variation. Environmental effects have been incorporated on the new Mechanistic-Empirical Pavement Design Guide (MEPDG) but little has been done to incorporate environmental effects on airfield design. This work presents a developed code produced from this research study called ZAPRAM, which is a mechanistically based pavement model based upon Limiting Strain Criteria in airfield HMA pavement design procedures. ZAPRAM is capable of pavement and airfield design analyses considering environmental effects. The program has been coded in Visual Basic and implemented in an event-driven, user-friendly educational computer program, which runs in Excel environment. Several studies were conducted in order to insure the validity of the analysis as well as the efficiency of the software. The first study yielded the minimum threshold number of computational points the user should use at a specific depth within the pavement system. The second study was completed to verify the correction factor for the Odemark's transformed thickness equation. Default correction factors were included in the code base on a large comparative study between Odemark's and MLET. A third study was conducted to provide a comparison of flexible airfield pavement design thicknesses derived from three widely accepted design procedures used in practice today: the Asphalt Institute, Shell Oil, and the revised Corps of Engineering rutting failure criteria to calculate the thickness requirements necessary for a range of design input variables. The results of the comparative study showed that there is a significant difference between the pavement thicknesses obtained from the three design procedures, with the greatest deviation found between the Shell Oil approach and the other two criteria. Finally, a comprehensive sensitivity study of environmental site factors and the groundwater table depth upon flexible airfield pavement design and performance was completed. The study used the newly revised USACE failure criteria for subgrade shear deformation. The methodology utilized the same analytical methodology to achieve real time environmental effects upon unbound layer modulus, as that used in the new AASHTO MEPDG. The results of this effort showed, for the first time, the quantitative impact of the significant effects of the climatic conditions at the design site, coupled with the importance of the depth of the groundwater table, on the predicted design thicknesses. Significant cost savings appear to be quite reasonable by utilizing principles of unsaturated soil mechanics into the new airfield pavement design procedure found in program ZAPRAM.
ContributorsSalim, Ramadan A (Author) / Zapata, Claudia (Thesis advisor) / Witczak, Matthew (Thesis advisor) / Kaloush, Kamil (Committee member) / Arizona State University (Publisher)
Created2011
Description
A major goal of synthetic biology is to recapitulate emergent properties of life. Despite a significant body of work, a longstanding question that remains to be answered is how such a complex system arose? In this dissertation, synthetic nucleic acid molecules with alternative sugar-phosphate backbones were investigated as potential ancestors of DNA and RNA. Threose nucleic acid (TNA) is capable of forming stable helical structures with complementary strands of itself and RNA. This provides a plausible mechanism for genetic information transfer between TNA and RNA. Therefore TNA has been proposed as a potential RNA progenitor. Using molecular evolution, functional sequences were isolated from a pool of random TNA molecules. This implicates a possible chemical framework capable of crosstalk between TNA and RNA. Further, this shows that heredity and evolution are not limited to the natural genetic system based on ribofuranosyl nucleic acids. Another alternative genetic system, glycerol nucleic acid (GNA) undergoes intrasystem pairing with superior thermalstability compared to that of DNA. Inspired by this property, I demonstrated a minimal nanostructure composed of both left- and right-handed mirro image GNA. This work suggested that GNA could be useful as promising orthogonal material in structural DNA nanotechnology.
ContributorsZhang, Su (Author) / Chaut, John C (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2011
Description
This dissertation describes development of a procedure for obtaining high quality, optical grade sand coupons from frozen sand specimens of Ottawa 20/30 sand for image processing and analysis to quantify soil structure along with a methodology for quantifying the microstructure from the images. A technique for thawing and stabilizing frozen core samples was developed using optical grade Buehler® Epo-Tek® epoxy resin, a modified triaxial cell, a vacuum/reservoir chamber, a desiccator, and a moisture gauge. The uniform epoxy resin impregnation required proper drying of the soil specimen, application of appropriate confining pressure and vacuum levels, and epoxy mixing, de-airing and curing. The resulting stabilized sand specimen was sectioned into 10 mm thick coupons that were planed, ground, and polished with progressively finer diamond abrasive grit levels using the modified Allied HTP Inc. polishing method so that the soil structure could be accurately quantified using images obtained with the use of an optical microscopy technique. Illumination via Bright Field Microscopy was used to capture the images for subsequent image processing and sand microstructure analysis. The quality of resulting images and the validity of the subsequent image morphology analysis hinged largely on employment of a polishing and grinding technique that resulted in a flat, scratch free, reflective coupon surface characterized by minimal microstructure relief and good contrast between the sand particles and the surrounding epoxy resin. Subsequent image processing involved conversion of the color images first to gray scale images and then to binary images with the use of contrast and image adjustments, removal of noise and image artifacts, image filtering, and image segmentation. Mathematical morphology algorithms were used on the resulting binary images to further enhance image quality. The binary images were then used to calculate soil structure parameters that included particle roundness and sphericity, particle orientation variability represented by rose diagrams, statistics on the local void ratio variability as a function of the sample size, and the local void ratio distribution histograms using Oda's method and Voronoi tessellation method, including the skewness, kurtosis, and entropy of a gamma cumulative probability distribution fit to the local void ratio distribution.
ContributorsCzupak, Zbigniew David (Author) / Kavazanjian, Edward (Thesis advisor) / Zapata, Claudia (Committee member) / Houston, Sandra (Committee member) / Arizona State University (Publisher)
Created2011
Description
As a prelude to a study on the post-liquefaction properties and structure of soil, an investigation of ground freezing as an undisturbed sampling technique was conducted to investigate the ability of this sampling technique to preserve soil structure and properties. Freezing the ground is widely regarded as an appropriate technique to recover undisturbed samples of saturated cohesionless soil for laboratory testing, despite the fact that water increases in volume when frozen. The explanation generally given for the preservation of soil structure using the freezing technique was that, as long as the freezing front advanced uni-directionally, the expanding pore water is expelled ahead of the freezing front as the front advances. However, a literature review on the transition of water to ice shows that the volume of ice expands approximately nine percent after freezing, bringing into question the hypothesized mechanism and the ability of a frozen and then thawed specimen to retain the properties and structure of the soil in situ. Bench-top models were created by pluviation of sand. The soil in the model was then saturated and subsequently frozen. Freezing was accomplished using a pan filled with alcohol and dry ice placed on the surface of the sand layer to induce a unidirectional freezing front in the sample container. Coring was used to recover frozen samples from model containers. Recovered cores were then placed in a triaxial cell, thawed, and subjected to consolidated undrained loading. The stress-strain-strength behavior of the thawed cores was compared to the behavior of specimens created in a split mold by pluviation and then saturated and sheared without freezing and thawing. The laboratory testing provide insight to the impact of freezing and thawing on the properties of cohesionless soil.
ContributorsKatapa, Kanyembo (Author) / Kavazanjian, Edward (Thesis advisor) / Houston, Sandra (Committee member) / Zapata, Claudia (Committee member) / Arizona State University (Publisher)
Created2011
Description
The F1Fo ATP synthase is required for energy conversion in almost all living organisms. The F1 complex is a molecular motor that uses ATP hydrolysis to drive rotation of the γ–subunit. It has not been previously possible to resolve the speed and position of the γ–subunit of the F1–ATPase as it rotates during a power stroke. The single molecule experiments presented here measured light scattered from 45X91 nm gold nanorods attached to the γ–subunit that provide an unprecedented 5 μs resolution of rotational position as a function of time. The product of velocity and drag, which were both measured directly, resulted in an average torque of 63±8 pN nm for the Escherichia coli F1-ATPase that was determined to be independent of the load. The rotational velocity had an initial (I) acceleration phase 15° from the end of the catalytic dwell, a slow (S) acceleration phase during ATP binding/ADP release (15°–60°), and a fast (F) acceleration phase (60°–90°) containing an interim deceleration (ID) phase (75°–82°). High ADP concentrations decreased the velocity of the S phase proportional to 'ADP-release' dwells, and the F phase proportional to the free energy derived from the [ADP][Pi]/[ATP] chemical equilibrium. The decreased affinity for ITP increased ITP-binding dwells by 10%, but decreased velocity by 40% during the S phase. This is the first direct evidence that nucleotide binding contributes to F1–ATPase torque. Mutations that affect specific phases of rotation were identified, some in regions of F1 previously considered not to contribute to rotation. Mutations βD372V and γK9I increased the F phase velocity, and γK9I increased the depth of the ID phase. The conversion between S and F phases was specifically affected by γQ269L. While βT273D, βD305E, and αR283Q decreased the velocity of all phases, decreases in velocity due to βD302T, γR268L and γT82A were confined to the I and S phases. The correlations between the structural locations of these mutations and the phases of rotation they affect provide new insight into the molecular basis for F1–ATPase γ-subunit rotation.
ContributorsMartin, James (Author) / Frasch, Wayne D (Thesis advisor) / Chandler, Douglas (Committee member) / Gaxiola, Roberto (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2012