VictorJuiz/thesis huggingface dataset:
Stipa pulchra in serpentine grasslands host a diverse community of foliar fungal pathogens with little potential impact on the outcomes of plant invasions

The invasion of California grasslands is striking and extensive: since the 19th century, invasive annual grasses from the Mediterranean have come to dominate 9.2 million hectares of grassland previously dominated by native perennial grasses. As in many species invasions, the mechanisms driving the spread of invasive species in these grasslands remain poorly understood. Disease, which may prevent and/or facilitate invasions through its influence on the outcomes of interspecies competition, represents a relatively unexplored but potentially powerful driver in this invasive event. California grassland plant communities found in serpentine soils with high heavy metal content and low essential plant nutrient availability are exceptional in that they remain largely uninvaded and continue to include diverse native grasses and forbs. In these remnant communities, I assessed the potential for foliar disease to play a role in maintaining and/or reducing native plant persistence in California grasslands. To do this, I: 1) measured foliar disease burden in serpentine and nonserpentine populations of the native bunchgrass Stipa pulchra, 2) compared the fungal foliar pathogen communities hosted by the surveyed plants, and 3) analyzed the chemical makeup of serpentine and nonserpentine plant tissue in order to understand potential impacts of soil chemistry on plant health and pathogen community composition. I found that serpentine and nonserpentine Stipa experience low disease pressure from distinct communities of foliar pathogens, and that serpentine plants, like the soil they grow in, have elevated Ni and Mg content and decreased C, N, Ca, and P content compared to nonserpentine plants. The results imply that pathogens are unlikely to affect the persistence of this native plant, but that plants may structure their pathogen communities via either plant community composition or via tissue chemistry. Plant invasions and/or soil type are shown to have potentially far-reaching effects on pathogen diversity and community composition, with implications for efforts to conserve native plant communities and to beneficially shift public perceptions of parasites.

Keywords:  Department of Biology
Biology
Ecology and Evolution
Ecology
Disease Ecology
California grasslands
Stipa pulchra
Stanford University Department of Biology
Thesis
Advisor: Mordecai Erin
Mooney Harold
Stochastic models for flow and transport in heterogeneous porous media

Modeling flow and transport in porous media is an important part of the decision-making process in managing crucial resources such as underground aquifers and hydrocarbon reservoirs, subsurface disposal of contaminants, and the design of battery systems. The multiscale nature of porous media, the heterogeneity of their properties and the uncertainty of our knowledge of these properties pose significant modeling challenges that have been the focus of extensive research. In this work, four important contributions are made to the modeling of flow and transport in porous systems. First, a non-local formulation is rigorously derived to find the average flow solution in multiscale porous media. Second, the stochastic representation of the flow problem is used for quantifying the flow uncertainty in cases with heterogeneous conductivity fields. An algorithm is proposed for using the Feynman-Kac formulation for one-dimensional elliptic problems with piecewise constant conductivity and various schemes were explored to improve the efficiency of particle tracking algorithms for both stochastic and deterministic flow problems. The third contribution of this work is the introduction of the stencil method, a discrete temporal Markov model for modeling transport in networks representing porous material. The stencil method simplifies the temporal models used to simulate mean transport in porous media. Finally, a fast discrete temporal Markov velocity process is introduced to simulate ensemble transport in highly heterogeneous continuum scale conductivity fields. This is the first stochastic model to simulate dispersion in high-variance conductivity fields for both Gaussian and exponential correlation structures.

Keywords: Energy Resources Engineering.
Advisor: Tchelepi Hamdi 
Jenny Patrick
Tartakovsky Daniel
Strain engineering germanium-tin in group IV photonics

The scaling of technology nodes to smaller length scales has enabled unprecedented growth for silicon integrated circuits (IC). The reduction of critical feature dimensions has allowed larger densities of integrated components and improved performance on the device level. At the same time, however, scaling has presented increasing challenges for the performance of global electrical interconnects, which comprise the longest wire lengths on a chip. One solution to overcoming the limitations of electrical interconnect technology is the integration of optical interconnects. While optical communications has already been employed on much larger length scales, the application of optical interconnects for chip-to-chip and on-chip communications has yet to be realized. In the IC industry, the silicon (Si) complementary metal-oxide-semiconductor (CMOS) platform has unified and enabled large-scale integration, but Si performs poorly as an active optical material due to its indirect band gap. As a result, an integrated Si laser has remained elusive in Si photonics, although the ability to leverage this platform for photonic integration has the potential to achieve low cost and high-throughput manufacturing, while maintaining compatibility with CMOS electronics. Developing a tunable direct band gap group IV semiconductor can instead be achieved using the binary germanium-tin system. The incorporation of Sn into the Ge crystal reduces the energy difference between the direct and indirect conduction band minima. A major challenge of the germanium-tin system is lattice mismatch with respect to Si or Ge-buffered Si substrates. Significant compressive strain arises from the coherent epitaxial growth of germanium-tin on these substrates, which inhibits the onset of the fundamental direct gap. This dissertation explores methods of strain engineering pseudomorphic germanium-tin epitaxy to relieve lattice mismatch strain that inhibits the onset of the fundamental direct band gap.

Keywords: Materials Science and Engineering.
Advisor: Harris J. S. (James Stewart)
McIntyre P. (Paul)
Kamins Theodore I.
Strategies to Address Forced Labor in Industries with Globally-Integrated Supply Chains: Lessons Learned from Case Studies in Palm Oil, Prawn Farming, and Cattle Ranching

Nahla Gedeon Achi’s capstone project focused on evaluating the successes and shortcomings of efforts to address forced labor in three industries with globally-integrated supply chains: palm oil, cattle ranching in Brazil, and prawn farming in Thailand. More specifically, Nahla looked to provide a comprehensive overview and analysis of a subset of existing strategies to address human trafficking within these varied industries. As a former research assistant for the Stanford Center for Ocean Solutions (COS), Nahla also tied her capstone project to existing initiatives put forth by COS and the Center for Human Rights and International Justice addressing slavery in tuna supply chains. Nahla hopes that her capstone project not only brings to light grave human rights issues within these industries, but also demonstrates how concerted efforts from governments, corporations, consumers, and communities everywhere will we be able to fully eliminate forced labor from all supply chains.

Keywords: Global supply chains
Forced labor > Law and legislation
Text
Thesis
Stretchable serpentine microwave devices for next-generation wearable systems

Over recent years, the use of patterned serpentine geometries in stretchable wearable electronics has attracted significant attention, especially for health monitoring in fitness and biomedical applications. While stretchable serpentine systems have been demonstrated for direct-current (DC) and low-frequency applications, there is a need to further study the influence of the serpentine geometry on high-frequency characteristics, to avoid potential parasitic effects or impedance issues. Furthermore, the impact of the serpentine stretching mechanics on wireless performance remains relatively unexplored. This work describes a general strategy for producing stretchable microwave components in which rigid, planar metallic structures are deconstructed into stretchable mesh geometries based on subwavelength-scale unit cells. The impact of this conversion strategy on microwave performance is examined for serpentine meshed transmission lines and antennas. Observations of surface current propagation and antenna radiation efficiency indicate an inherent trade-off between mechanical stretchability and microwave performance. Using the insight gained from investigating the performance impacts on transmission lines and antennas, the serpentine conversion strategy is then applied to produce a stretchable electromagnetic device for biomedical wireless power transfer in the electromagnetic midfield. A stretchable microwave phased surface is designed and fabricated to transmit a focused electromagnetic field into the human body to wirelessly power a miniature biomedical implant. Its performance with stretching is characterized in an experimental setup, and results indicate that with proper design, the serpentine phased surface can achieve comparable performance to its solid counterpart. To ensure optimal design decisions for future stretchable microwave systems, a general methodology is developed to model the microwave performance of various serpentine geometries. Serpentine designs are implemented in a microstrip transmission line system, and the effective transmission line parameters are extracted by fitting results to an equivalent transmission line model. This methodology is utilized to benchmark the serpentine microwave performance relative to alternative materials approaches. It is also useful for assessing the performance impacts of changes to the serpentine design. From these demonstrations, it is clear that the proposed methodology is highly useful for evaluating and improving the performance of future wearable systems.

Keywords: Electrical Engineering.
Advisor: Fan Jonathan Albert 
Lee Thomas H.
Arbabian Amin
Stringy nonlocality and black hole physics

We analyze nonlocal effects in string theory near black hole horizons. Due to extended string effects, early infalling matter can be detected by late observers long after they fall into the black hole. The nonlocal effects are derived via an analysis of the six-point string scattering matrix in flat space, as well as by probing the scattering with a background dilaton. We also derive simple new string solutions in three dimensions.

Keywords: Physics.
Advisor: Silverstein Eva
Kachru Shamit
Shenker Stephen Hart
Susskind Leonard
Structural and functional characterizations of mitochondrial calcium uniporter

In this thesis, I mainly worked on the structural and functional characterization of a mitochondrial calcium channel named MCU. Mitochondrial calcium plays critical roles in a wide range of fundamental cellular processes, including controlling the rate of ATP production, regulating the initiation of cell death and shaping cytosolic calcium signaling. Since fifty years ago when it was first demonstrated that fully energized mitochondria can rapidly load up calcium ions (Ca2+), the machinery behind this process has been extensively explored. This uptake is mediated by a highly selective calcium channel called the mitochondrial calcium uniporter (MCU), which resides on the inner mitochondrial membrane. The molecular identity of the uniporter was only uncovered relatively recently. MCU bears no discernable sequence similarity to other known channels and represents a new class in ion channels with its unique selectivity and conductance properties. In this thesis, I used both X-ray crystallography and single-particle cryo-electron microscopy to determine the structures of MCU from two species containing all domains, and I established rapid and efficient functional characterization platforms in cells and in liposomes. Unexpectedly, the stoichiometry, overall architecture, and local structural details of the new structures differed markedly from the NMR cMCU structure. The physiological relevance of those structures was corroborated by the observation of a consistent architecture across species and chemical environments, and by the systematical functional assays. Structural and functional characterizations provided insights into Ca2+ coordination, selectivity, and permeation, establishing a framework for understanding the mechanism of MCU function.

Keywords: Molecular and Cellular Physiology.
Advisor: Feng Liang
Kobilka Brian K. 
Lewis Richard (Richard Sheridan)
Maduke Merritt C.
Structural phase stability and van der Waals computation for two-dimensional materials

Two-dimensional (2D) materials are a family of materials that are atomically thin, with ultra-high surface-to-volume ratio. Multiple 2D materials can be held together by van der Waals interaction to build layered heterostructures. Since the first experimental isolation of a 2D material graphene in 2004, 2D materials have attracted much attention as promising candidate materials for future nanoscale devices. In the first part of the dissertation, I focus on a unique property of a small subset of 2D transition metal dichalcogenide (TMD) monolayers: the potential to exist in multiple competing crystal structures. Phase change materials have wide spread applications from electronics, optics to energy technology. Here, I study the structural phase stability control of a TMD monolayer, MoTe2 monolayer, with surface adsorption of atoms and molecules. Our density functional theory (DFT) calculations reveal the potential for surface adsorption to induce a structural phase change between the competing semiconducting and metallic crystal structures of the monolayer. Further, I find that the MoxW1-xTe2 monolayer alloy composition can be tuned to achieve some degree of molecular selectivity in phase changes, providing a basis for nanoscale molecular sensing applications. I next focus on van der Waals computation for 2D materials. As an alternative to expensive standard electronic-structure approaches, I explore the potential for an electromagnetic approach to describe van der Waals interactions to provide faster computation for layered materials, including some non-pairwise effects which may be important for layered materials. Surprisingly, we find that this electromagnetic approach, based on a modified Lifshitz model, combined with DFT calculations of optical properties can provide total van der Waals interaction energies within 8-20% of the advanced electronic structure calculations for a variety of layered heterostrctures. This method potentially provides a powerful tool for studying van der Waals interactions in layered heterostructure devices. Finally, I applied our defined Lifshitz model to study surface wettability of 2D materials and their layered forms. The literature contains a wide variation of reported water contact angles for graphene, postulated to be associated with contaminations. However, a theoretical understanding of this variation has yet to be quantitatively fully explored. Here, I utilized the Lifshitz model to find that certain forms of contamination can indeed induce the large variation in reported water contact angles for layered materials. I also make predictions on layer dependence and substrate dependence of wettability.

Keywords: Materials Science and Engineering.
Advisor: Reed Evan J. 
Cai Wei
Lindenberg Aaron Michael
The structure and maintenance of centromeric chromatin

When a human cell divides, it pulls its chromosomes into regions that will become new cells. The pull is applied to a single region on each chromosome called the centromere. Centromeres are defined by high concentrations of nucleosomes containing the protein CENP-A instead of the canonical histone H3. CENP-A nucleosomes directly recruit proteins that bridge between the nucleosomes and the forces that pull chromosomes apart. These proteins also affect CENP-A chromatin itself. This thesis examines the role of two proteins that directly interact with CENP-A nucleosomes, CENP-C and CENP-N, in centromere maintenance and structure. It was found that CENP-A nucleosomes have little to no dissociation from centromeric regions. We hypothesized that this lack of dissociation is caused by increased nucleosome stability due to binding to CENP-C and CENP-N. To test this, we generated cell lines where we could induce the degradation of the endogenous proteins. Using these cells, we employed several orthogonal methods to show that CENP-C and CENP-N do not affect CENP-A nucleosome stability at the centromere. Next, we explored the role of these proteins on centromeric chromatin structure. Not much is known about CENP-A chromatin structure due to technical limitations. To overcome this, we instead looked for activities that alter CENP-A chromatin structure. We developed a novel activity-based assay that detects CENP-A nucleosome clustering. Using this assay, we discovered that CENP-C can cluster CENP-A nucleosomes from different strands of DNA. We showed that this activity is specific and depends on CENP-C's ability to bind CENP-A nucleosomes. We identified the minimal domain necessary for the clustering which will serve as the basis for further studies. Lastly, we examined the role of these proteins in disease. We looked at CENP-N mutations associated with familial idiopathic pulmonary fibrosis. We found that one mutation, E46Q, lowered the levels of CENP-T at the centromere. Since CENP-T functions in kinetochore formation, we hypothesize that this leads to impaired kinetochore function and more chromosome segregation errors. Consistent with this, we found that this mutation sensitized the cells to PDMP, a drug that selectively kills aneuploid cells.

Keywords: Biochemistry.
Advisor: Straight Aaron
Ferrell James Ellsworth 
Herschlag Daniel
Studies in structure and electrochemistry of halide perovskite semiconductors and covalently-functionalized carbon with applications in optoelectronic devices, energy storage, and CO₂ capture

Described here are the results of my efforts to understand and control the structural, electrochemical, and transport properties of materials under development for the field of energy generation and storage. I first give the results of transport and defect chemistry studies in halide perovskite semiconductors. These crystalline solids have risen to the forefront of applied materials science research owing to the high performance demonstrated in optoelectronic devices incorporating them as active layers and their easy synthesis at low temperatures. Despite their favorable electronic properties, defect chemistry can be shown to play a pivotal role in halide perovskite properties, and thus its understanding is crucial to the technology that uses these semiconductors. I have measured electronic and ionic conductivities in multiple perovskite compounds, and have found them to change significantly, even in nominally inert environments. The behavior of ionic and electronic transport has led to the development of defect chemistry models that successfully predict how material properties change with component activity, and point to methods to control doping, defects, and conduction in halide perovskites. I next report a method to modify the physical and electronic structure of two-dimensional halide perovskites, which are of interest for solid-state lighting and other optoelectronic applications. These materials have electronic band-gaps in the visible or near UV region of the spectrum, and typically have high exciton binding energies due to 2D electronic confinement. Zwitterionic alkylammonium molecules reliably modify the structure of 2D perovskites by incorporating additional metallic or nonmetallic ions between the 2D perovskite layers. I show that these ions modify the electronic properties; they lower exciton binding energy and introduce light emission from new photoluminescent defect states. I also give an account of the development of quinone-functionalized carbons, materials whose favorable electrochemical properties lead to potential applications as high-power lithium-ion battery electrodes and as a CO2 capture materials in electrochemical CO2 separation process. Due to the particular nature of halide perovskites and other materials included in this work, nonstandard electrochemical and synthetic methods have often been required. I end by describing the tools and techniques developed with the hope that they will help fellow researchers carry out rigorous measurements simply and effectively.

Keywords: Chemistry.
Advisor: Karunadasa Hemamala
Chidsey Christopher E. D. (Christopher Elisha Dunn)
Suzuki Yuri (Applied physicist)
A study of the dynamic response of plasma filled microwave cavity resonators

This dissertation details research done to study microwave cavity resonators and their dynamic actuation using laboratory pulsed plasma discharges. The work is encompassed in a broader research effort to study the utility of gaseous plasmonics in controlling the propagation of electromagnetic waves. In support of this effort, I present numerical and experimental findings that together describe with consistency the transient behavior of laboratory pulsed plasma discharges through their interaction with electromagnetic resonant modes. The research contained in this thesis combines the fields of microwave engineering, plasma physics, and photonic crystals in novel ways that enables actively tunable electromagnetic devices at high frequencies. Two devices are presented, the first consisting of a metallic two-post 14 GHz resonator located inside a WR62 waveguide section, and the second consisting of a hexagonal lattice photonic crystal with a defect state at 27 GHz. The microwave transmission through both devices is measured during a 150 ns pulsed plasma discharge and pulsed microwaves are seen of various widths and delays, depending on the transmission frequency. In this way, the resonant cavities are shown to have pulse shaping properties, with the photonic crystal cavity able to generate pulses with widths and delays ranging from tens of microseconds down to hundreds nanoseconds. A fluid plasma simulation was developed to model with high fidelity the transient dynamics of laboratory plasma discharges. The simulated plasma properties are used in conjunction with microwave theory to predict and provide insight into the experimentally measured microwave transmission signals. The results of the modeling efforts are compared with the experimental findings and show good qualitative and quantitative agreement, such as predicting the magnitude and time of the maximum frequency shift within the cavity within ten percent error. Lastly, the nonlinear coupling between high power microwaves and the plasma-cavity system are studied. It is shown that both resonator devices are capable of microwave plasma breakdown, suggesting that they could be used as nonlinear power limiting devices or plasma sources. Additionally, the coupling between high power microwaves and pulsed plasma discharges is also studied. Here, the previously elusive microwave pulses generated due to plasma ionization were finally captured due to the nonlinear behavior of high power microwaves interacting with the plasma ignition process, and pulse widths and delays were measured as low as several hundred nanoseconds.

Keywords: Aeronautics and Astronautics.
Advisor: Cappelli Mark A. (Mark Antony) 
Close Sigrid
D'Amico Simone