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Open Access Publications from the University of California

Scholarly Works (9 results)

  • Thesis
  • Peer Reviewed
UC Riverside Electronic Theses and Dissertations (2019)

The goal of this work is to understand spin and heat transfer in metal multilayer systems on nanoscale length scales and ultra-fast time scales due to ultra-fast laser pulse heating. Femto-second laser pulses are absorbed at the surface of the metal system. The absorbed energy is deposited in the metal’s electrons. Energy is then redistributed to vibrational and spin degrees of freedom through electron-electron, electron-phonon, and phonon-phonon interactions. Energy is also dispersed spatially through hot electron transport. The heat transfer in these metal systems can be divided into two temporal regimes with the first spanning from 0 to 1ps and the second from 1ps to 12.5ns

I present Time Domain Thermo-Reflectance (TDTR) and Time-Resolved Magneto Optic Kerr Effect (TR-MOKE) results that further our understanding of how heat is transported in these metal multilayer systems. By conducting various TDTR and TR-MOKE experiments, we are able to experimentally obtain fit parameters in order to prepare model predictions of the heat transfer in the metal systems. I also present my work on spin accumulation in Au due to the Spin dependent Seebeck Effect in Au-iron garnet bilayer systems. By varying the iron garnet used in the bilayer system, we are able to see how different magnetic insulators of the same family behave when demagnetized by ultra-fast laser pulses.

    Cover page: Heat Transport and Spin Accumulation in Nanoscale Metal Multilayers
    • Thesis
    • Peer Reviewed
    UC Berkeley Electronic Theses and Dissertations (2017)

    Diseases caused by the family Potyviridae require the interaction of viral genome-linked protein (VPg) and host eukaryotic translation initiation factor 4E (eIF4E) isoforms. Disruption of these host genes responsible for Potyviridae susceptibility confers disease resistance. CRISPR/Cas9 has emerged as a robust and specific gene editing technology. As a proof of concept for CRISPR-mediated susceptibility gene targeting, Arabidopsis thaliana was chosen as a model plant system for editing resistance to Turnip mosaic potyvirus (TuMV). CRISPR/Cas9 was employed to generate eif(iso)4e mutants in A. thaliana. eif(iso)4e mutants exhibited resistance to TuMV systemic spread and symptom development. Precise gene editing of A. thaliana eIF(iso)4E was also achieved in somatic cells via the CRISPR/Cpf1 tool.

    Cassava brown streak disease (CBSD) is a major constraint on cassava yields in East and Central Africa and threatens production in West Africa. CBSD is caused by two species of positive sense RNA viruses belonging to the family Potyviridae, genus Ipomovirus: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Cassava encodes five eIF4E isoforms: eIF4E, eIF(iso)4E-1, eIF(iso)4E-2, novel cap-binding protein-1 (nCBP-1), and nCBP-2. Yeast two-hybrid analysis detected interactions between both CBSV and UCBSV VPg proteins and cassava nCBP-1 and nCBP-2. CRISPR/Cas9-mediated genome editing was employed to generate eif4e, ncbp-1, ncbp-2, and ncbp-1/ncbp-2 mutants in cassava cultivar 60444. Challenge with CBSV showed that ncbp-1/ncbp-2 mutants displayed delayed and attenuated CBSD aerial symptoms, as well as reduced severity and incidence of storage root necrosis. Suppressed disease symptoms were correlated with reduced virus titer in storage roots relative to wild-type controls. However, full resistance to CBSD was not achieved, suggesting that remaining functional eIF4E isoforms may be compensating for the targeted mutagenesis of nCBP-1 and nCBP-2.

    Furthermore, viruses of the family Geminiviridae threaten to global food security through severe crop loss. Tomato yellow leaf curl virus species (TYLCV; genus Begomovirus) cause widespread destruction of the tomato crop. The high levels of genetic variability and persistent insect vector distribution pose significant challenges for conventional and genetic control strategies. In addition to precise genome editing, CRISPR/Cas9 may be employed as a form of molecular immunity against plant DNA viruses. In this study, sgRNA were designed to target a broad range of the TYLCV species, mutagenize a stable region of the TYLCV genome, and disrupt expression of the virus replication machinery. Functionality of multiple TYLCV-targeting CRISPR/Cas9 expression systems was demonstrated in Nicotiana benthamiana. The utility of this TYLCV control strategy was then extended to tomato. CRISPR/Cas9 transgenic tomato lines exhibited reduced TYLCV symptom severity and viral DNA presence. CRISPR-mediated viral interference and viral susceptibility gene mutagenesis reflect the vast potential of the CRISPR technology as a solution to global food challenges.

      Cover page: CRISPR-Mediated Susceptibility Gene Editing and Viral Interference for Plant Disease Resistance
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2023)
      Colloidal silica grouting is a ground improvement technique capable of stabilizing weak problematic soils and achieving large reductions in soil hydraulic conductivities for applications including earthquake-induced liquefaction mitigation and groundwater flow control. In the conventional approach, chemical accelerants are added to colloidal silica suspensions that are introduced into soils targeted for improvement and the formation of a semi-solid silica gel occurs over time at a rate controlled by suspension chemistry and in situ geochemical conditions. Although the process has been extensively investigated, controlling the rate of gel formation in the presence of varying subsurface conditions and the limited ability of conventional methods to effectively monitor the gel formation process has posed practical challenges. In this study, a biomediated soil improvement process is proposed which utilizes enriched fermentative microorganisms to control the gelation of colloidal silica grouts through solution pH reductions and ionic strength increases. Four series of batch experiments were performed to investigate the ability of glucose fermenting microorganisms to be enriched in natural sands to induce geochemical changes capable of mediating silica gel formation and assess the effect of treatment solution composition on pH reduction behaviors. Complementary batch and soil column experiments were subsequently performed to upscale the process and explore the effectiveness of chemical, hydraulic, and geophysical methods to monitor microbial activity, gel formation, and engineering improvements. Results demonstrate that fermentative microorganisms can be successfully enriched and mediate gel formation in suspensions that would otherwise remain highly stable, thereby forgoing the need for chemical accelerants, increasing the reliability and control of colloidal silica grouting, enabling new monitoring approaches, and affording engineering enhancements comparable to conventional colloidal silica grouts.
        Cover page: Biomediated control of colloidal silica grouting using microbial fermentation.Creative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2022)
        Microbially induced calcite precipitation (MICP) is an environmentally conscious ground-improvement method that can enhance the engineering properties of granular soils through the precipitation of calcium carbonate (CaCO3) on soil particle surfaces and contacts. Although numerous studies have shown the ability of biocementation to improve the liquefaction resistance of loose sands, the effects of light cementation levels on undrained cyclic behaviors have remained relatively unexplored. A series of undrained monotonic and cyclic direct simple shear tests were performed to examine the effect of light biocementation (ΔVs<100 m/s and CaCO3 contents <0.9%) on the liquefaction triggering and post-triggering behavior of loose Ottawa F-65 sand subjected to varying loading magnitudes [cyclic stress ratio (CSR)=0.1 to 0.3]. Results suggest that the presence of light biocementation can significantly improve the liquefaction triggering resistance of loose sands, with log-linear increases in the number of cycles required to trigger liquefaction, which consistently correlated with cementation-induced Vs increases. Despite these remarkable pretriggering improvements, almost no improvements were observed in post-triggering strain accumulation and postcyclic reconsolidation behaviors, with Vs measurements indicating that small-strain improvements were largely erased following shearing events.
          Cover page: Effect of Light Biocementation on the Liquefaction Triggering and Post-Triggering Behavior of Loose Sands
          • Article
          • Peer Reviewed
          UC Riverside Previously Published Works (2021)
            Cover page: Ultrafast measurements of the interfacial spin Seebeck effect in Au and rare-earth iron-garnet bilayers
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2022)
            Textured platens are often used to improve the transfer of shear stresses from the platens to the soil specimen during direct simple shear (DSS) tests. However, constant-volume DSS tests when textured platens are used can be affected by inadequate engagement of the soil at the platen-soil interface, leading to large reductions in the vertical stress at the start of shearing. The application of a preconditioning sequence involving small-strain drained cycles prior to constant-volume shearing can improve engagement at the platen-soil interface, but when excessively implemented, it can also have adverse effects on the measured soil behavior (e.g., strength, stiffness). A series of constant-volume cyclic DSS tests preceded by different preconditioning sequences was performed to evaluate the effect of preconditioning on the engagement of sand specimens at the platen-soil interface and the stress-strain response of these specimens. Results showed that textured platens that are properly engaged with sand specimens can reduce slippage at the platen-soil interface. This engagement can be achieved by applying a limited number of small-strain drained cycles at a low vertical stress while still obtaining representative soil behavior during the subsequent equivalent undrained constantvolume cyclic loading. Although the preconditioning protocol presented herein is specific to the testing equipment and materials considered, similar procedures may be adopted to develop preconditioning protocols for other soils, platens, and testing devices.
              Cover page: Development and Evaluation of Preconditioning Protocols for Sand Specimens in Constant-Volume Cyclic Direct Simple Shear Tests
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2019)
              Microbially Induced Calcite Precipitation (MICP) is a bio-mediated cementation process that can improve the engineering properties of granular soils through the precipitation of calcite. The process is made possible by soil microorganisms containing urease enzymes, which hydrolyze urea and enable carbonate ions to become available for precipitation. While most researchers have injected non-native ureolytic bacteria to complete bio-cementation, enrichment of native ureolytic microorganisms may enable reductions in process treatment costs and environmental impacts. In this study, a large-scale bio-cementation experiment involving two 1.7-meter diameter tanks and a complementary soil column experiment were performed to investigate biogeochemical differences between bio-cementation mediated by either native or augmented (Sporosarcina pasteurii) ureolytic microorganisms. Although post-treatment distributions of calcite and engineering properties were similar between approaches, the results of this study suggest that significant differences in ureolysis rates and related precipitation rates between native and augmented microbial communities may influence the temporal progression and spatial distribution of bio-cementation, solution biogeochemical changes, and precipitate microstructure. The role of urea hydrolysis in enabling calcite precipitation through sustained super-saturation following treatment injections is explored.
                Cover page: Biogeochemical Changes During Bio-cementation Mediated by Stimulated and Augmented Ureolytic MicroorganismsCreative Commons 'BY' version 4.0 license
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2019)
                A set of saturated Ottawa sand models was treated with microbially induced calcite precipitation (MICP) and subjected to repeated shaking events using the 1-m radius centrifuge at the UC Davis Center for Geotechnical Modeling. Centrifuge models were constructed to initial relative densities (DR0) of approximately 38% and treated to light, moderate, and heavy levels of cementation (calcium carbonate contents by mass of approximately 0.8%, 1.4%, and 2.2%, respectively) as indicated by shear wave velocities (light≈200 m/s, moderate≈325 m/s, and heavy≈600 m/s). The cemented centrifuge models were compared to a pair of uncemented saturated Ottawa sand models with initial DR0≈38 and 53% and subjected to similar levels of shaking. Cone penetration resistances and shear wave velocities were monitored throughout shaking to investigate (1) the effect of cementation on cone penetration resistance, shear wave velocity, and cyclic resistance to liquefaction triggering; and (2) the effect of shaking on cementation degradation. Accelerometers, pore pressure transducers, and a linear potentiometer were used to monitor the effect of cementation on liquefaction triggering and consequences. Cone penetration resistances and shear wave velocities were sensitive to light, moderate, and heavy levels of cementation (increases in penetration resistance from 2 to 5 MPa, from 2 to 10 MPa, and from 2 to 18 MPa and increases in shear wave velocity from 140 to 200 m/s, from 140 to 325 m/s, and from 140 to 660 m/s, respectively), and were able to capture the effects of cementation degradation.
                  Cover page: Centrifuge Model Testing of Liquefaction Mitigation via Microbially Induced Calcite Precipitation
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2019)
                  Microbially Induced Calcite Precipitation (MICP), or bio-cementation, is a promising bio-mediated technology that can improve the engineering properties of soils through the precipitation of calcium carbonate. Despite significant advances in the technology, concerns regarding the fate of produced NH4+ by-products have remained largely unaddressed. In this study, five 3.7-meter long soil columns each containing one of three different soils were improved using ureolytic bio-cementation, and post-treatment NH4+ by-product removal was investigated during the application of 525 L of a high pH and high ionic strength rinse solution. During rinsing, reductions in aqueous NH4+ were observed in all columns from initial concentrations between ≈100 mM to 500 mM to final values between ≈0.3 mM and 20 mM with higher NH4+ concentrations observed at distances furthest from the injection well. In addition, soil Vs measurements completed during rinse injections suggested that no significant changes in cementation integrity occurred during NH4+ removal. After rinsing and a 12 hour stop flow period, all column solutions achieved cumulative NH4+ removals exceeding 97.9%. Soil samples collected following rinsing, however, contained significant sorbed NH4+ masses that appeared to have a near linear relationship with surrounding aqueous NH4+ concentrations. While these results suggest that NH4+ can be successfully removed from bio-cemented soils, acceptable limits for NH4+ aqueous concentrations and sorbed NH4+ masses will likely be governed by site-specific requirements and may require further investigation and refinement of the developed techniques.
                    Cover page: Investigating Ammonium By-product Removal for Ureolytic Bio-cementation Using Meter-scale ExperimentsCreative Commons 'BY' version 4.0 license
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