Bridge scour at piers is a major problem for design and for maintaining old infrastructure. The current methods require their own upkeep and there may be better ways to mitigate scour. I looked to the mangrove forests of coastal environments for inspiration and have developed a 2D model to test the efficacy of placing a mangrove-root inspired system to mitigate scour. My model tests the hydrodynamics of the root systems, but there are additional benefits that can be used as bioinspiration in the future (altering the surrounding chemistry and mechanical properties of the soil).Adding a mangrove inspired minipile system to bridge piers changes scour parameters within my 2D COMSOL models. For the volume of material added, the minipiles compare favorably to larger sacrificial piles as they reduce A_wcz and 〖τ'〗_max by similar (or even better) amounts. These two parameters are indicators of scour in the field. Within the minipile experiments, it is more beneficial to place them upstream of the main bridge pier as their own ‘mangrove forest.’ The value of A_wcz and 〖τ'〗_max for complex 2D models of scour is unclear and physical experiments need to be performed. The model geometry is based on the dimensions of the experimental flume to be used in future studies and the model results have not yet been verified through experiments and field trials. Scale effects may be present which cannot be accounted for in the 2D models. Therefore future work should be conducted to test ‘mangrove forest’ minipile systems in 3D space, in flume experiments, and in field trials.

Urease, an amidohydrolase, is an essential ingredient in the emerging engineering technique of biocementation. When free urease enzyme is used this carbonate precipitation process is often referred to as enzyme induced carbonate precipitation (EICP). To date, most engineering applications of EICP have used commercially available powdered urease. However, the high cost of commercially available urease is a major barrier to adoption of engineering applications of EICP in practice. The objective of this dissertation was to develop a simple and inexpensive enzyme production technique using agricultural resources. The specific objectives of this dissertation were (i) to develop a simple extraction process to obtain urease from common agricultural resources and identify a preferred agricultural resource for further study, (ii) to reduce the cost of enzyme production by eliminating the use of a buffer, centrifugation, and dehusking of the beans during the extraction process, (iii) investigate the stability of the extracted enzyme both in solution and after reduction to a powder by lyophilization (freeze-drying), and (iv) to study the kinetics of the extracted enzyme. The results presented in this dissertation confirmed that inexpensive crude extracts of urease from agricultural products, including jack beans, soybeans, and watermelon seeds, are effective at catalyzing urea hydrolysis for carbonate precipitation. Based upon unit yield, jack beans were identified as the preferred agricultural resource for urease extraction. Results also showed that the jack bean extract retained its activity even after replacing the buffer with tap water and eliminating acetone fractionation, centrifugation, and dehusking. It was also found that the lyophilized crude extract maintained its activity during storage for at least one year and more effectively than either the crude extract solution or rehydrated commercial urease. The kinetics of the extracted enzyme was studied to gain greater insight into the optimum concentration of urea in engineering applications of EICP. Results showed higher values for the half-saturation coefficient of the crude extract compared to the commercial enzymes. The results presented in this dissertation demonstrate the potential for a significant reduction in the cost of applying EICP in engineering practice by mass production of urease enzyme via a simple extraction process.

Earthquake-induced soil liquefaction poses a significant global threat, especially to vulnerable populations. There are no existing cost-effective techniques for mitigation of liquefaction under or around existing infrastructure. Microbially Induced Desaturation and Precipitation (MIDP) via denitrification is a potentially sustainable, non-disruptive bio-based ground improvement technique under existing structures. MIDP has been shown to reduce liquefaction triggering potential under lab conditions in two ways: 1) biogenic gas desaturation in the short-term (treatment within hours to days) and 2) calcium carbonate precipitation and soil strengthening in the long-term (treatment within weeks to months). However, these experiments have not considered MIDP behavior under field stresses and pressures, nor have they considered challenges from process inhibition or microbial competition that may be encountered when upscaled to field applications. This study presents results from centrifuge experiments and simplified modeling to explore scaling effects on biogenic gas formation, distribution, and retention when simulating field pressures and stresses. Experimental results from the centrifuge demonstrated MIDP’s potential to mitigate the potential liquefaction triggering through desaturation. This study also includes the development of a biogeochemical model to explore the impact of water constituents, process inhibition, and alternative biochemical metabolisms on MIDP and the subsequent impact of MIDP on the surrounding environment. The model was used to explore MIDP behavior when varying the source-water used as the substrate recipe solute (i.e., groundwater and seawater) and when varying the electron donor (i.e., acetate, glucose, and molasses) in different substrate recipes. The predicted products and by-products were compared for cases when desaturation was the targeted improvement mechanism and for the case when precipitation was the primary targeted ground improvement mechanism. From these modeling exercises, MIDP can be applied in all tested natural environments and adjusting the substrate recipe may be able to mitigate unwanted long-term environmental impacts. A preliminary techno-economic analysis using information gained from the modeling exercises was performed, which demonstrated MIDP’s potential as a cost-effective technique compared to currently used ground improvement techniques, which can be costly, impractical, and unsustainable. The findings from this study are critical to develop treatment MIDP plans for potential field trials to maximize treatment effectiveness, promote sustainability and cost-effectiveness, and limit unwanted by-products.

Microbially induced desaturation (MID) via denitrification is an emerging ground improvement technique to mitigate liquefaction by stimulating the metabolic processes of native bacteria to produce biogas, biominerals and biomass. The production of biogenic gas gradually lowers the degree of saturation of treated soils, thereby dampening the pore pressure response to cyclic loading. However, the production of these metabolic products also alters the hydraulic and mechanical properties of the soil. A series of four tank tests simulating two-dimensional plane strain conditions were performed to evaluate the effectiveness of MID and the resulting changes to the hydraulic properties of the soils. Previous studies have demonstrated the mechanical response for treated homogenous granular soils at the bench scale via vertical injection methods. However, limited knowledge is available on the impact of partial desaturation on the hydraulic properties of the soil, particularly in stratified formations. Treating larger granular soil specimens via lateral injection methods is important for the up-scaling and future commercialization of the process as it may affect injection strategies, and the distribution of substrates and metabolic products. Tank tests were performed on a layered natural soil sediment collected from Richmond, British Columbia, Canada, as well as layered and unlayered laboratory grade Ottawa sands of different grain size distributions. The results demonstrated the effectiveness of treatment upon macro-scale soil properties, and showed how gas formation, migration and entrapment, and resulting degree of desaturation and hydraulic conductivity are affected by micro and macro-stratifications in granular soils.

Expansive soils pose considerable geotechnical and structural challenges all over the world. Many cities, towns, transport systems, and structures are built on expansive soils. This study evaluates stabilization of expansive soils using silicate solution extracted from rice husk taking advantage of an agricultural material waste. Rice husk ash production was optimized considering several factors including rinsing solution, rinsing temperature, burning time, and burning temperature. Results indicated that washing the rice husk with HCl (1M) produced an ash with surface area of 320 m2/g and 97% of silicon oxide. Two local soils were treated with sodium silicate solution, silica gel at pH 1.5, and silica gel at pH 4 to evaluate its mechanical properties at curing times of 1 day, 7 days, and 14 days. Results indicated that sodium silicate solution reduced the one-dimensional swell by 48% for Soil A, however, swell for soil B remained about the same. Silica gel at pH 1.5 reduced the one-dimensional swell by 67% for soil A and by 35% for soil B. Silica gel at pH 4 did also reduce the free swell by 40% for soil A and by 35% for soil B. Results also indicated that the swell pressures for all treated soils increased significantly compared to untreated soils. Soils treated with sodium silicate solution showed irregular compaction curves. Silica gel-treated soils showed a reduction in the maximum dry unit weight for both soils but optimum water content decreased for soil A and increased for soil B. Atterberg limits were also reduced for sodium silicate and silica gels-treated soils. Swelling index for bentonite showed a reduction by 53% for all treated bentonites. Soil-water characteristics curves (SWCC) for sodium silicate-treated soils remined almost the same as untreated soils. However, silica gels-treated soils retain more water. Surface area (SSA) decreased for sodium silicate-treated soil but increased for all silica gels-treated soils. It was concluded that curing times did not show additional improvement in most of the experiments, but the results remained about the same as 1-day treatment. The study demonstrated that silicate solution is promising and sustainable technique for stabilization of expansive soils.

Water is a vital resource, and its protection is a priority world-wide. One widespread threat to water quality is contamination by chlorinated solvents. These dry-cleaning and degreasing agents entered the watershed through spills and improper disposal and now are detected in 4% of U.S. aquifers and 4.5-18% of U.S. drinking water sources. The health effects of these contaminants can be severe, as they are associated with damage to the nervous, liver, kidney, and reproductive systems, developmental issues, and possibly cancer. Chlorinated solvents must be removed or transformed to improve water quality and protect human and environmental health. One remedy, bioaugmentation, the subsurface addition of microbial cultures able to transform contaminants, has been implemented successfully at hundreds of sites since the 1990s. Bioaugmentation uses the bacteria Dehalococcoides to transform chlorinated solvents with hydrogen, H2, as the electron donor. At advection limited sites, bioaugmentation can be combined with electrokinetics (EK-Bio) to enhance transport. However, challenges for successful bioremediation remain. In this work I addressed several knowledge gaps surrounding bioaugmentation and EK-Bio. I measured the H2 consuming capacity of soils, detailed the microbial metabolisms driving this demand, and evaluated how these finding relate to reductive dechlorination. I determined which reactions dominated at a contaminated site with mixed geochemistry treated with EK-Bio and compared it to traditional bioaugmentation. Lastly, I assessed the effect of EK-Bio on the microbial community at a field-scale site. Results showed the H2 consuming capacity of soils was greater than that predicted by initial measurements of inorganic electron acceptors and primarily driven by carbon-based microbial metabolisms. Other work demonstrated that, given the benefits of some carbon-based metabolisms to microbial reductive dechlorination, high levels of H2 consumption in soils are not necessarily indicative of hostile conditions for Dehalococcoides. Bench-scale experiments of EK-Bio under mixed geochemical conditions showed EK-Bio out-performed traditional bioaugmentation by facilitating biotic and abiotic transformations. Finally, results of microbial community analysis at a field-scale implementation of EK-Bio showed that while there were significant changes in alpha and beta diversity, the impact of EK-Bio on native microbial communities was minimal.

This document presents the assessment of the swelling behavior of expansive clay stabilized with bio-based silica gel and subjected to wetting and drying cycles. The expansive clay used in this research was obtained from Anthem, Arizona. Rice husk is a rich silica by-product of rice production with commercial uses and applications in the industry. Rice husk ash from two different sources -California (named ASU) and India- were subjected to chemical characterization. Fourier Transform Infra-red Spectroscopy was used to verify the functional groups of the gel formed. Results showed differences between the ashes from different sources and confirmed the presence of silica structure bonds. X-Ray Diffraction (XRF) results showed that the ASU ash contained more amorphous silica than the Indian ash.One dimensional swell and consolidation tests were performed to investigate the volume change behavior of the untreated and silica gel treated remoulded samples. The free swell of the clay decreased from 12.3% (untreated sample) to 7.2% (ASU sample) and 11.4% (Indian sample). The effect of the wet and dry cycles on the swelling and consolidation characteristics of the untreated clay demonstrated that the treatment is irreversible after three cycles. Swelling of clay treated with ASU ash was reduced after the first cycle, while that of the clay treated with Indian ash was reduced after three cycles. This was due to the gelation time difference between treatments. Scanning Electron Microscopy images showed that the structure of the untreated clay was discontinuous, flaky and without aggregations whereas particles in the treated samples were aggregated and new bonds were created, decreasing the surface area. The X-Ray Diffraction (XRF) results showed that the main mineral responsible for expansive behavior of the clay studied was illite. The d-spacing of the illite decreased from 4.47Å for the untreated clay to 3.33Å for the treated clay. This study demonstrates a promising technique for clay swelling reduction and a more sustainable solution than that available to current practicing engineering.

The Atlantic razor clam burrows underground with effectiveness and efficiency by coordinating shape changings of its shell and foot. Inspired by the burrowing strategy of razor clams, this research is dedicated to developing a self-burrowing technology for active underground explorations by investigating the burrowing mechanism of razor clams from the perspective of soil mechanics. In this study, the razor clam was observed to burrow out of sands simply by extending and contracting its foot periodically. This upward burrowing gait is much simpler than its downward burrowing gait, which also involves opening/closing of the shell and dilation of the foot. The upward burrowing gait inspired the design of a self-burrowing-out soft robot, which drives itself out of sands naturally by extension and contraction through pneumatic inflation and deflation. A simplified analytical model was then proposed and explained the upward burrowing behavior of the robot and razor clams as the asymmetric nature of soil resistances applied on both ends due to the intrinsic stress gradient of sand deposits. To burrow downward, additional symmetry-breaking features are needed for the robot to increase the resistance in the upward burrowing direction and to decrease the resistance in the downward burrowing direction. A potential approach is by incorporating friction anisotropy, which was then experimentally demonstrated to affect the upward burrowing of the soft robot. The downward burrowing gait of razor clams provides another inspiration. By exploring the analogies between the downward burrowing gait and in-situ soil characterization methods, a clam-inspired shape-changing penetrator was designed and penetrated dry granular materials both numerically and experimentally. Results demonstrated that the shell opening not only contributes to forming a penetration anchor by compressing the surrounding particles, but also reduces the foot penetration resistance temporally by creating a stress arch above the foot; the shell closing facilitates the downward burrowing by reducing the friction resistance to the subsequent shell retraction. Findings from this research shed lights on the future design of a clam-inspired self-burrowing robot.

This thesis is part of a larger research project, conducted by Elizabeth Stallings Young, which aims to improve understanding about the factors controlling the process of MIDP and the interaction between the biochemical reactions and the hydrological properties of soils treated with MIDP. Microbially Induced Desaturation and Precipitation (MIDP) is a bio-geotechnical process by which biogenic gas production and calcite mineral bio-cementation are induced in the pore space between the soil particles, which can mitigate earthquake induced liquefaction (Kavazanjian et al. 2015). In this process substrates are injected which stimulate indigenous nitrate reducing bacteria to produce nitrogen and carbon dioxide gas, while precipitating calcium carbonate minerals. The biogenic gas production has been shown to dampen pore pressure build up under dynamic loading conditions and significantly increase liquefaction resistance (Okamura and Soga 2006), while the precipitation of calcium carbonate minerals cements adjacent granular particles together. The objective of this thesis was to analyze the recorded pore pressure development as a result of biogenic gas formation and migration, over the entire two-dimensional flow field, by generating dynamic pressure contour plots, using MATLAB and ImageJ software. The experiment was run in a mesoscale tank that was approximately 114 cm tall, 114 cm wide and 5.25 cm thick. Substrate was flushed through the soil body and the denitrifying reaction occurred, producing gas and correspondingly, pressure. The pressure across the tank was recorded with pore pressure sensors and was loaded into a datalogger. This time sensitive data file was loaded into a MATLAB script, MIDPCountourGen.m, to create pressure contours for the tank. The results from this thesis include the creation of MIDPContourGen.m and a corresponding How-To Guide and pore pressure contours for the F60 tank. This thesis concluded that the MIDP reaction takes a relatively short amount of time and that the residual pressure in the tank after the water flush on day 17 offers a proof of effect of the MIDP reaction.

This study evaluates the use of plant-extracted silica solution as a bio-based grout material for improvement of granular soils. Although silicate grout is a very well-established and popular technique in the ground improvement market, efforts have been initiated to replace chemically-synthesized silicate grout with plant-extracted silica grout. This initiative will increase the level of sustainability and consequently improve the existing market acceptability. The silica-rich plant source used for extraction was rice husk, which is an abundantly produced agricultural waste. The extraction method includes acid-leaching, temperature-controlled rice husk ash production and the preparation of an aqueous sodium silicate solution from the ash through an alkaline leachate method. Silica ash was in amorphous form containing 95% of silica content which is suitable for soil treatment. Gelation time was controlled in the absence and presence of sand under different pH values. Bio-based silica grouting showed an improvement of the shear strength of the soil as well as the hydraulic conductivity reduction.