VictorJuiz/thesis huggingface dataset:
Observations of Boundary Layer Dynamics in South San Francisco Bay

Estuarine sediment transport is an important process in determining the fate and transport of contaminants. While physical models exist to describe spherical non-flocculating particles in a fluid, cohesive sediments are poorly modeled from first principles. We conducted field work in South San Francisco Bay during the summer of 2018 to take detailed observations of sediment and water motion near the bed in the shallow eastern shoals. Data collected by a Nortek Vectrino Profiler provides insight into the patterns of flow in the wave-current boundary layer and nearby log layer, as well as the physical forcing behind bed behavior. I compare these profiles with accepted fitting models for flow over a canopy and with measurements taken higher in the water column by an Acoustic Doppler Profiler deployed at the same site. Velocity profiles at 64 Hz for 12 minutes every hour at a 1 mm resolution for 2 mm overlapping the bed are highly detailed in space and time relative to previous field measurements of similar variables, and permit the study of friction velocity and turbulent Reynolds stress in and above the wave-current boundary layer. Velocity profiles in the shallow shoals of South Bay are modeled by the canopy log law. Waves are a major contributor to instantaneous velocity profile deviations from the 12-minute mean profile, and cause corresponding variations in turbulence Reynolds stress and friction velocity. Phase-averaged velocity profiles and turbulence statistics are presented for different tide and wave environments to describe the results of complex wave-current interactions in the boundary layer. This work has implications for interpreting time-averaged velocity profile measurements and presents detailed measurements of parameters relevant to understanding sediment transport in an economically important estuary system.

Keywords:  Department of Civil and Environmental Engineering
estuary
canopy flow
boundary layer
wave Reynolds stress
stanford university
civil &amp; environmental engineering
cee
sediment transport
cohesive sediment
fluid mechanics
san francisco bay
south san francisco bay
Thesis
Advisor: Fringer Oliver
Observing structures and dynamic behavior in biological cells using single-molecule based super-resolution fluorescence microscopy

For the last three decades, the ability to detect single molecules at high spatiotemporal resolutions has revolutionized the way we observe and understand the cells that harbor life. This research uses super-resolution imaging and single-molecule tracking to uncover nanoscale structural details and dynamics for mammalian cells and bacteria. By optically separating out each individual emitter in time using an active-control mechanism, every localization provides spatial information with a resolution much better than the diffraction limit to yield super-resolution microscopy. To address the fact that biological systems are inherently three-dimensional, the microscope detection path is further extended to include a "4f system" configuration, which provides easy access to the conjugate back focal plane. By strategically placing a phase mask here, the emission can be optically transformed in way which breaks the symmetry of the detected intensity profile of a single-molecule emitter above and below the focal plane to give precise axial positions. However, it still remains a challenge to obtain a clear picture of the surface features of small, crowded biological structures in their natural habitat in both a non-invasive and precise manner. This dissertation describes how super-resolution fluorescence microscopy and surface meshing algorithms are used in conjunction to quantify the surface topology of two main biological systems: the primary cilium of mammalian cells and the surface of the bacterium, Caulobacter crescentus.

Keywords: Applied Physics.
Advisor: Moerner W. E. (William Esco)
Greenleaf William James 
Stearns Tim
Oceanic rumblings : midtrophic responses to oceanographic variability observed through acoustic and diet analyses

Open ocean ecosystems are the largest on the planet, containing an enormous diversity of organisms boasting incredible adaptations to life in a mostly dark, seemingly featureless habitat. Despite the heavy reliance on marine resources by countries across the globe, there remains a large gap in our basic understanding of marine ecosystems, particularly with respect to the organisms at the center of open ocean food webs: micronekton. These small, swimming animals are notoriously difficult to quantify, commonly avoiding conventional sampling methods and occurring across large areas that are costly to sample. In this dissertation I collaborated with existing monitoring programs to generate timeseries that capture variability in the composition, abundance, and distribution of micronekton communities with respect to environmental variability. I examined changes in diet composition and prey availability for Humboldt squid, Dosidicus gigas, in the Gulf of California (GOC), Mexico between 1996 and 2017. Humboldt squid in this oceanographically-variable region have exhibited a large range in mature size (15-85 cm mantle length) associated with the El Niño Southern Oscillation (ENSO), but it is unclear how their role in the ecosystem changes with respect to body size or how their prey respond to ENSO. I demonstrated that Humboldt squid diet in the GOC is more different between squid collected in different environmental conditions than between individuals of different sizes. Prey responses to environmental variability were directly assessed with nighttime acoustic observations in the same region. In conjunction with strong El Niño events, I observed significant reductions in forage biomass, which remained depressed for 2-3 years following the event regardless of subsequent environmental conditions. I also described variability in the diet of longnose lancetfish, Alepisaurus ferox, across the central North Pacific Ocean using specimens collected by federal fisheries observers in the Hawaii-based deep-set longline fishery, and demonstrated that continued monitoring of lancetfish diet could be used to quantify environmental responses of their diverse micronektonic prey. My work provides unique insights into large-scale spatiotemporal variability in two open ocean forage communities and contributes to our understanding of the role micronektonic organisms will play in mitigating or exacerbating the effects of ocean warming on marine resources.

Keywords: Biology.
Advisor: Gilly William 
Hazen Elliott Lee
Micheli Fiorenza 
Somero George N. 
Benoit-Bird Kelly
Octans, chart your constellation of support: A web platform for adolescents to identify and expand their social support networks to explore interest-driven learning pathways

We all belong to social networks. A social network is comprised of the set of social actors and relationships among these actors. Social capital refers to the embedded resources in these social networks that an individual actor can access, build and utilize to achieve personal interests. Hence, social capital is a key determinant in our academic and career trajectories. However, social capital is not evenly distributed across individual actors. Historical and institutional processes have resulted in unequal opportunities for different social groups based on characteristics like gender and race. Fortunately, social networks are dynamic, and we can learn to recognize, nurture, and employ social capital to improve these networks.
Octans seeks to empower high school students, particularly marginalized youth, by raising their awareness of the importance of social capital and guiding them to notice, act upon and expand their surrounding resources. As a web platform, Octans features (1) interactive narratives of how relevant role models have used social capital, (2) a visualization tool that helps students identify and reflect on their social networks, and (3) a goal-setting and action-planning journal with prompts and strategies to build social capital. Along with other mentoring resources, Octans aspires to prepare learners to pursue interest-driven learning pathways using their social networks.
Interviews and user testing with target learners have shown that after using Octans, learners are more aware of and grateful for their social networks. Learners are better able to articulate the types of support they encounter in their social networks. Finally, they feel a greater sense of agency to work towards their goals knowing that they have the support from these bonds and the possibility of building new ones.

Keywords: Learning Design and Technology
Graduate School of Education
social networks
social capital
social support
high school students
marginalized youth
mentoring
advising
learning experience design
Thesis
Offset and noise behavior of microfabricated aluminum gallium nitride-gallium nitride two-dimensional electron gas hall-effect sensors

Magnetic sensors are quite common in everyday life, with a variety of uses in mobile devices, electric machines, cars, motors, navigation, and planetary exploration. They are incredibly useful due to their non-perturbing nature. For example, they infer information about position, velocity, and current in power systems. Silicon Hall-effect sensors are popular for many applications due to their low cost and ease of integration with silicon circuits. However, silicon Hall-effect plates cannot operate at extreme temperatures (below -100 degrees C or above 300 degrees C) due to carrier freeze out or intrinsic carrier leakage, respectively. In addition, Hall-effect plates have challenges with thermal drift, offset, and flicker noise. In this PhD thesis, I start with an in-depth focus on the fabrication of high aspect ratio trenches (18.5:1) in 4H-SiC for potential use in direct hot-spot cooling of GaN-on-SiC power devices as well as extreme environment SiC microelectromechanical system (MEMS) applications. I then switch gears and describe an AlGaN/GaN 2DEG Hall-effect plate with ~100 ppm/K constant-current sensitivity drift, 0.5 micro-Tesla offset, and 200 Hz corner frequency. These metrics surpass state-of-the-art silicon Hall-effect sensors with a larger temperature operation range, stability of sensitivity, and lower offset and noise floor. I then describe the fundamental limits of offset in GaN devices and present an examination of the flicker noise of these devices. Through this work, I have achieved a record-low offset in GaN 2DEG Hall devices, presented the first framework for studying noise in GaN Hall sensors, and have demonstrated a world record aspect ratio in bulk 4H-SiC machining. These contributions will enable a future monolithically integrated GaN-on-SiC platform for extreme environment sensors and power electronics. I conclude with proposing future work, including a path forward for implementing these devices in extreme environment systems.

Keywords: Electrical Engineering.
Advisor: Senesky Debbie 
Howe Roger Thomas 
Plummer James D.
On applications of Szemerédi's regularity lemma

Szemeredi's regularity lemma is an important and powerful tool in graph theory. One of its prevalent application is the graph removal lemma, which has numerous applications to extremal problems for graphs and hypergraphs, additive combinatorics, discrete geometry, and theoretical computer science. In this thesis, we initiate and prove a new removal lemma with respect to a stronger metric on graphs, which is a strengthening of the usual graph removal lemma. We also prove a new application of the regularity lemma. The Ramsey number r(H) of a graph H is the minimum integer n such that any two-coloring of the edges of the complete graph Kn contains a monochromatic copy of H. Determining the Ramsey number for all graphs is a famously difficult question. A more general question is to study the minimum total number of monochromatic copies of H over all two-colorings of Kn. When n = r(H), this quantity is referred to as the threshold Ramsey multiplicity of H. Addressing a problem of Harary and Prins forty years ago, we proved the first quantitative sharp bound for cycles and paths. This thesis describes the work for path and even cycles. Although the regularity lemma is powerful, a notable drawback is that applications of the regularity lemma will result in very weak quantitative estimates. One important application of the regularity lemma is the field of property testing, whose goal is to very quickly distinguish between objects that stratify a certain property from those that are epsilon-far from satisfying that property. Some of the most general results in this area give ``constant query complexity" algorithms, which means the amount of information it looks at is independent of the input size. These results are proved using regularity lemmas or graph limits. Unfortunately, typically the proofs come with no explicit bound for the query complexity, or enormous bounds, of tower-type or worse, as a function of 1/epsilon, making them impractical. We show by entirely new methods that for permutations property testing, such general results still hold with query complexity only polynomial in 1/epsilon.

Keywords: Mathematics.
Advisor: Fox Jacob
Chatterjee Sourav 
Vondrak Ján (Mathematician)
On manifold bundles over classifying spaces

This thesis comprises the results of three independent research projects in high-dimensional geometric topology. The first one exhibits, for various manifolds as fibers, smooth bundles over the classifying space of SU(2) not induced from an action. The second project is joint work with M. Krannich. It gives conditions on when a manifold is, up to bordism, the total space of a fiber bundle over a surface with highly-connected and almost-parallelizable fiber M, including a computation of the corresponding characteristic numbers. As a corollary, we determine an explicit basis for the second integral cohomology of BDiff(M) up to torsion in terms of generalized Miller—Morita—Mumford classes. Finally, the third project analyzes models for higher parametrized cobordism categories, with a special focus on the case where the parametrizing space is a circle.

Keywords: Mathematics.
Advisor: Cohen Ralph L.
Galatius Søren
Ionel Eleny
On the arithmetic of weight two Eisenstein series

This thesis contains two separate results on the arithmetic of Eisenstein series. The first is a new proof of theorems of Merel and Lecouturier on the relationship between Mazur's Eisenstein ideal and special values of Dirichlet L-functions. The second is a computation of the Galois representations and mixed Hodge structures associated to certain Eisenstein series on Hilbert modular varieties.

Keywords: Mathematics.
Advisor: Venkatesh Akshay
Conrad Brian
Taylor R. L. (Richard Lawrence)
On the methods of construction and evaluation of reaction coordinates from direct dynamics

With the emerging interest in using non-linear dimensionality reduction (NLDR) methods to study and generate meaningful reaction coordinates for complex dynamical systems, it is important not only to find methods most suited for these types of data but to have methods of evaluating the quality of these different mappings. Methods that perform well for lower energy, simpler ground state reactions are not necessarily suitable for describing the reaction path of more complex ground state reactions or high energy excited state reactions. NLDR is a good candidate for finding reaction coordinates for excited such systems where assumptions used to generate reaction coordinates for ground state reactions do not hold. In this dissertation we explore how different data featurizations and NLDR methods affect the mapping quality of excited state dynamics simulation of ethylene and RPSB analogue. We also introduce techniques to determine the quality of these mappings using several existing, general techniques for comparing the different NLDR mappings and by adapting those general techniques to specifically evaluate the mappings of molecular dynamics simulation data. Having a metric to compare the quality of different NLDR mapping allows us to approach the construction of reaction coordinates in a systematic way.

Keywords: Chemistry.
Advisor: Martinez Todd J. (Todd Joseph)
Markland Thomas E.
Zare Richard N.
On the orderability up to conjugation of certain open contact manifolds

In this thesis, we define and study the orderability up to conjugation problem for groups of compactly supported contactomorphisms of certain open contact manifolds. In particular, we show that the groups of compactly supported contactomorphisms of certain subsets of odd-dimensional spheres are orderable up to conjugation. This class of manifolds has recently showed its importance in the flexible side of contact topology. Along the way, we prove non-squeezing-type results for prequantizations of hyperboloids in the product of an even-dimensional Euclidean space with a circle, which may be of independent interest. The main tool is an equivariant version of contact homology, adapted to subdomains of the product of an even-dimensional Euclidean space with a circle.

Keywords: Mathematics.
Advisor: Eliashberg Y.
Cohen Ralph L.
Ionel Eleny
On the scale dependence of flow structures and transport in chaotic electroconvection

Electroconvection (EC) is a hydrodynamic instability that occurs when dissolved ions are driven from a bulk fluid towards an ion-selective surface under a sufficiently large applied voltage. When the applied voltage exceeds a threshold, chaotic features arise from the coupling between ion-transport, fluid flow, and electrostatic forces near the ion-selective interface. This greatly enhances ion transport, impacting mass transfer and ion residence times and plays a significant role in a wide range of electrochemical applications. Simulating EC in regimes relevant to industrial applications is challenging; its wide range of spatiotemporal scales requires costly computations with extremely high resolutions. This dissertation considers aspects of electroconvection that would inform future modeling of these complex flows in the highly chaotic regime.

Keywords: Mechanical Engineering.
Advisor: Mani Ali (Professor of mechanical engineering) 
Moin Parviz 
Santiago Juan G.
Oncogenic control of aberrant glycosylation in murine and human hematopoietic cancers

Upwards of 50% of cancers exhibit deregulation of MYC, a transcription factor that controls evasion of immune system detection and other aspects of cancer growth. MYC has also been implicated in the modification of the glycolcalyx, or cellular forest of sugars (glycans), and the production of sialic acid, a specific glycan modifier. Alterations to the glycocalyx broadly characterize a variety of cancers. Certain glycans containing sialic acid (sialoglycans) are known to inhibit immune function by binding to Siglecs, a family of inhibitory receptors present on most immune cells. However, the pathways leading to elevated sialoglycan synthesis (hypersialylation) in cancer are not well characterized. In this project, we explore a possible role for oncogenes in promoting sialoglycan production by upregulating transcription of sialyltransferases, which transfer sialic acids to nascent glycans, in murine and human MYC-driven hematopoieitic cancers.
Chemical and genetic MYC inhibition resulted in reduced Siglec ligands and altered glycosylation on murine and human T-ALL cells. Titration of MYC broadly altered transcriptional expression of sialoglycan biosynthetic enzymes; expression of several sialyltransferases, most notably ST6GALNAC4, decreased following MYC suppression. Deletion of ST6GALNAC4 in murine and human hematopoietic cancers reduced the expression of Siglec ligands and increased susceptibility to NK cell killing. While MYC has been implicated in a variety of cancer-promoting activities, our results offer a new connection between MYC and cancer immunoevasion through the glycocalyx in hematological malignancies. While current therapies targeting MYC have been unsuccessful, a better understanding of sialoglycan biosynthesis may provide novel prognostic markers and therapeutic targets.

Keywords:  Department of Biology
Sialoglycan
Myc
Sialic acid
Thesis
Advisor: Bertozzi Carolyn
Gozani Or
Optical Control of the Motion and Spin of Cold Atoms for Quantum Simulations with Long-Range Interactions

Systems of laser-cooled atoms can be precisely controlled and detected with light, making them ideal platforms for understanding and engineering matter from the ground up. Long-range interactions, mediated either by Rydberg excitations or by photons in a high-finesse optical cavity, open up a wide range of possibilities for designing Hamiltonians and performing quantum simulations. A key component of these quantum simulations is the ability to prepare both the internal states and positions of the atoms prior to turning on the long-range interactions. We initialize states by deflecting light onto cold atoms using an acousto-optic deflector (AOD). The precise control over the position of deflected beams enables local control over the atoms’ motional and spin degrees of freedom. By manipulating the internal spin states of rubidium atoms, we prepare a spin texture within an optical cavity. We further demonstrate the creation of large arrays of optical tweezers, consisting of focused Gaussian beams of light, to trap and rearrange cesium atoms in a two-dimensional optical lattice. Arbitrary spin textures and re-configurable atomic arrays will enable future efforts towards enhanced spin-squeezing for metrological applications, the study of frustrated triangular lattices, and gate operations for quantum information applications.

Keywords:  Department of Physics
optical tweezers
cold atoms
quantum simulation
light-matter interaction
Thesis
Advisor: Schleier-Smith Monika
Hogan Jason
Optical scanning using MEMS phased array for 3D display

This thesis describes a direct view 3D display that utilizes a micro-electromechanical systems (MEMS) phased array to steer and focally scan a patterned line to create an image at a desired depth. First, the steering and variable focus operation of the phased array device is analyzed. Then, the optical setup of the 3D display is explained and images with depth are shown. Finally, the thesis demonstrates 3D video frame generation using a clustered depth map approach and ends with a discussion of alternate holographic techniques.

Keywords: Electrical Engineering.
Advisor: Solgaard Olav 
Howe Roger Thomas 
Wetzstein Gordon