VictorJuiz/thesis huggingface dataset:
Superconducting Nanobridge SQUID Magnetometer for Spin Sensing

As the cutting edge of science and technology pushes towards smaller length scales, sensing technologies with nanoscale precision become increasingly important. In this thesis I will discuss the optimization and application of a 3D nanobridge SQUID magnetometer for studying solid state spin systems, in particular for sensing impurity spins in diamond. Solid state spins have proposed applications in memory and computation for both classical and quantum computing. Isolated spins typically have longer coherence times, making them attractive qubit candidates, but necessitating the development of very sensitive detectors for readout./nThis 3D nanobridge SQUID combines the exquisite spatial sensitivity of a traditional nanoSQUID with a large non-linearity on par with a tunnel junction SQUID. This allows us to build a highly sensitive magnetometer which can act as both an efficient flux transducer as well as a nearly quantum limited lumped Josephson Parametric Amplifier. We show that the device has a minimum flux noise of 17 ± 0.9 nΦ0/Hz1/2 with only a factor of ∼2.5 increase in flux noise up to 61 mT. A second generation device with a smaller capacitor achieves field tolerance up to 75 mT. The maximal bandwidth values range from 25-40 MHz in the parametric amplification regime to 70 MHz in the linear regime. This combination of large bandwidth, low flux noise, large flux coupling and field tolerance make this sensor a promising candidate for near-single-spin dynamics measurements./nIn the last part of this thesis we begin to demonstrate the utility of a nanobridge SQUID magnetometer for characterizing spin systems in the solid state. We use the magnetometer to measure the decay characteristics of P1 centers in diamond. We find that the spin-lattice relaxation time varies with temperature, with an order of magnitude decrease in the decay time between 25 mK and 370 mK.

Advisor: Siddiqi, Irfan
Studies of the Cosmos Using Spiderweb Absorber Transition Edge Sensor

Transition edge sensor (TES) bolometer technology has been at the core of advancements/nin experimental cosmic microwave background (CMB) science for the/npast few decades. Theoretical and experimental work has built a robust model of/nthe universe. Despite tremendous progress, there are several key pieces of experimental/nevidence missing to complete our understanding of the universe. This dissertation/ncovers the work done by Benjamin Grey Westbrook at the University of California/nBerkeley between 2007 and 2014. It is centered around the use of spider-web absorber/ntransition edge sensor (SWATES) bolometers to study the cosmos by the/nAtcama Pathnder Experiment - Sunyaev Zel'dolvich (APEX-SZ) and the E and/nB Experiment (EBEX). Both of which help complete our model of the universe in/ncomplimentary ways./nAPEX-SZ is a ground-based experiment that made observations of galaxy clusters/nvia the Sunyaev-Zel'dovich Eect from the Chajnantor Plateau in Northern Chile/nfrom 2005 to 2010. It observed galaxy clusters at 150 GHz with 300 SWATES detectors/nwith a resolution of 10. Galaxy clusters are the largest gravitationally bound/nobjects in the present day universe and are excellent for studying the properties of/nthe universe. The primary goal of APEX-SZ was to understand the complex physics/nof galaxy clusters. By understanding their composition, number density, and evolution/nwe can better our understanding of the evolution of the universe into its present/nstate./nEBEX is a balloon-borne experiment that made observations of the CMB and/ncosmic foreground during a science/night from the Long Duration Balloon (LDB)/nfacility outside of McMurdo Station, Antarctica over the 2012-2013 austral summer./nIt made observations of 6000 square degrees of sky using 872, 436, and 256 SWATES/nbolometers at 150, 250, and 410 GHz detectors (respectively) with 80 resolution

Advisor: Lee, Adrian T
Distill for orchestra and electric guitar

Distill is a musical composition for orchestra and electric guitar. The work marshals the power of the electric guitar to create a huge variety of tone color and texture ranging from intense noise to the purest harmony, a power that is also shared by the symphony orchestra. These two sonic forces interact with each other in a slowly evolving soundscape based on an underlying chord progression. Over the course of the piece this chord progression becomes progressively simpler until eventually it is distilled to its barest essence, that of a single note and its overtones.

Advisor: Campion, Edmund
Writing from the Periphery: W. G. Sebald and Outsider Art

This study focuses on a major aspect of literature and culture in the later twentieth century: the intersection of psychiatry, madness and art. As the antipsychiatry movement became an international intervention, W. G. Sebald's fascination with psychopathology rapidly developed. While Sebald collected many materials on Outsider Artists and has several annotated books on psychiatry in his personal library, I examine how Sebald's thought and writings, both academic and literary, were particularly influenced by Ernst Herbeck's poems. Herbeck, a diagnosed schizophrenic, spent decades under the care of Dr. Leo Navratil at the psychiatric institute in Maria Gugging. Sebald became familiar with Herbeck via the book, Schizophrenie und Sprache (1966), in which Navratil analyzed his patients' creative writings in order to illustrate commonalities between pathological artistic productions and canonical German literature, thereby blurring the lines between genius and madness. In 1980, Sebald travelled to Vienna to meet Ernst Herbeck and this experience inspired him to compose two academic essays on Herbeck and the semi-fictionalized account of their encounter in his novel Vertigo (1990)./nIn this study, I reveal how Sebald incorporated Herbeck within his works over a thirty year period in order to provide a social commentary. Sebald looks to Herbeck to examine what had become the standards of normality in Western Germany following the Second World War from a critical perspective. Not only is Sebald's empathetic identification with the outsider Herbeck in itself a political and social act of protest, but I show how Sebald recognized in Herbeck's language an embodiment of his own viewpoints regarding (eco)politics and critical theory. Since his understanding of Herbeck is informed by a number of disciplines, various cultural discourses assist in my clarification: I turn to Sebald's interest in the Frankfurt School thinkers, such as Max Horkheimer and Theodor Adorno; Gilles Deleuze and Félix Guattari's ideas on minor literature; political viewpoints as posed by filmmakers such as Alexander Kluge and Werner Herzog; and also the socio-anthropological writings of Pierre Bertaux, Michel Foucault and Claude Lévi-Strauss. I furthermore provide close readings of Herbeck's poems to argue that Sebald imitates Herbeck's style. Focusing initially on archival material, I locate within Sebald's unpublished poetry and prose several thematic, linguistic and semantic characteristics which are typical of Herbeck's poetry. I then expand this analysis to incorporate how these features also reappear in Sebald's published novels. In uncovering underexplored intertextuality, this study sheds new light both on Sebald's novels, since recognizing Herbeck's voice within his prose calls for a reevaluation of what is "Sebaldian", as well as on the broader, yet underexplored cultural movement from which I focus on Herbeck as the apex. It also locates Sebald's key political ideas and his values concerning poetics and morality as derivatives of a particular historical and psychological discourse.

Advisor: Kudszus, Winfried
Modeling the Impacts of Climate Change on the Douglas-fir Forest within the San Francisco Peninsula Watershed using GIS and LiDAR

Quantifying the impacts of climate change on flora is of interest to many watershed and land managers, but has been challenging to study and distinguish from other disturbances that can reshape the landscape. This dissertation has found new tools to assist watershed managers in modeling the impacts of climate change by utilizing large comprehensive spatial datasets derived from remote sensing technology. To understand the recent expansion of the Douglas-fir (Pseudotsuga menziesii) forest within the San Francisco Peninsula Watershed across spatial-temporal scales with respect to increased precipitation over the past century, GIS models were developed using Light Detection And Ranging (LiDAR). The Douglas-fir was selected to be studied within the San Francisco Peninsula Watershed primarily because of its impact on replacing oak woodland, chaparral and grassland vegetation types. Secondly, Douglas-fir has a minimum mean annual precipitation requirement of around 34 inches, which allows it to be more competitive in formerly drier parts of the watershed. Extensive daily precipitation records spanning the last 100 years were recorded by the Spring Valley Water Company and later by the San Francisco Public Utilities Commission (SFPUC), which has provided a unique opportunity to study the Douglas-fir spread pattern influenced by increased rainfall./nThe SFPUC rain gauges showed an increase in mean annual precipitation of approximately 15 cm over the past century, which is consistent with independent data on climate research for the central California coast. Using LiDAR, over 12,000 individual overstory Douglas-fir trees were identified and their heights measured. Tree cores were taken of Douglas-fir inhabiting different microclimates to determine their age and rate of growth in the study area of the San Francisco Peninsula Watershed, allowing a species distribution model (SDM) of Douglas-fir to be devised. The high density of rain gauge stations encompassing the Douglas-fir forest spanning the last 100 years provided a unique opportunity to model the advancement pattern of the Douglas-fir forest with respect to historical and future climate scenarios. The results show the Douglas-fir advances more quickly with increased annual precipitation across the entire study area.

Advisor: McBride, Joe R
Flooded by Progress: Law, Natural Resources, and Native Rights in the Postwar Pacific Northwest

This dissertation examines the politics of federal Indian law and the changing economic and environmental landscape of the postwar Pacific Northwest. In particular, it contends that the changing legal status of Native lands and resources was instrumental in both the massive industrial expansion, and subsequent environmental transformation, of the postwar Pacific Northwest. It traces the relations between economic and environmental changes and their connections to the dramatic policy shift in Indian affairs from the early 1950s, when the federal government unilaterally terminated tribal status of 109 Native communities, most of them in the Pacific Northwest, to the Native sovereignty movement, which precipitated new national policies of self-determination in the 1970s. Not only does the dissertation illuminate how Native communities in the Pacific Northwest were inequitably burdened by the region's environmental and economic transformations in the second half of the 20th century, it also demonstrates how these transformations fueled the national economy in the postwar years as well as the emergence of Native activism, and how Native communities actively navigated and influenced seminal directions in federal Indian policy. Lastly, it illustrates how Native communities in the Pacific Northwest responded to the economic and environmental struggles of the early sovereignty era. This dissertation remaps the field of Native American history, by foregrounding its critical intersections with 20th-century environmental and economic histories. It relies heavily on materials from the National Archives & Records Administration Regional Office in Seattle, Washington, and agency archives from the Bonneville Power Administration, US Army Corps of Engineers, Bureau of Indian Affairs, and Columbia River Inter-Tribal Fish Commission, all in Portland, Oregon. In addition, the dissertation utilizes a variety of additional evidentiary support, and records from tribes in the Pacific Northwest.

Advisor: Biolsi, Thomas
Multiple Orders in Multiple Venues: The Reform of Married Women's Property Rights, 1839-1920

Beginning in 1839 and continuing through the early twentieth century, the American states passed increasingly liberal laws expanding married women's property rights. These Married Women's Property Laws extended to married women a range of new economic rights, including rights to own property, take out mortgages, sign and enforce contracts, and appear in court under their own name. In almost every state, these significant legal changes took place before women had the right to vote, and they were largely driven by male constitutional convention delegates, legislators, and judges. These male actors, working in a range of political venues, pushed for reforms for reasons rooted in the political orders of liberalism and gender hierarchy. This episode of rights expansion helps us understand both the possible pathways for rights reform when the group in question does not have the vote, and the ways in which an indirect reform process can lead to incomplete liberalization of rights. I analyze the passage of MWPAs from a variety of perspectives, incorporating analyses of political change in multiple venues (state legislatures, state courts, and state constitutional conventions), four case studies from different regions, and quantitative analyses using data on all 48 states. I then examine the longer-term impact of these laws in a discussion of protective labor legislation during the Progressive Era.

Advisor: Schickler, Eric
Reconstitution of Partially Recombinant 26S Proteasome Reveals Functional Asymmetries in its Heterohexameric AAA+ Unfoldase

The 26S proteasome is the major eukaryotic ATP-dependent protease, yet the detailed mechanisms utilized by the proteasomal heterohexameric AAA+ unfoldase to drive substrate degradation remain poorly understood. To perform systematic mutational analyses of individual ATPase subunits, I heterologously expressed the unfoldase, also known as the base subcomplex, from Saccharomyces cerevisiae in Escherichia coli and reconstituted partially recombinant 26S proteasomes in vitro. My studies demonstrate that the six ATPases play distinct roles in degradation, corresponding to their positions in spiral staircases adopted by the AAA+ domains in the absence and presence of substrate. ATP hydrolysis in subunits at the top of the staircases is critical for substrate engagement and translocation. While the unfoldase relies on this vertical asymmetry for substrate processing, interaction of the base with the core peptidase exhibits three-fold symmetry with contributions from every other subunit. Preliminary data on establishing a bulk kinetic assay utilizing substrates of varying lengths to experimentally deconvolute the processes of substrate engagement and translocation is presented. The diverse structural and functional asymmetries explored in this body of work demonstrate how the mechanisms of substrate engagement and processing may differ between the eukaryotic 26S proteasome and other simpler, homomeric AAA+ proteases. My findings provide an initial framework for elucidating the mechanochemical operating principles of the heterohexameric proteasomal motor. Future studies will be required to determine whether emerging mechanistic models of ATP-dependent substrate translocation established for homomeric AAA+ proteases can be generalized to the 26S proteasome.

Advisor: Martin, Andreas
Analysis of Roles of Laccases in Lignin Biosynthesis in Arabidopsis thaliana

Laccases (benzenediol: oxygen oxidoreductase; EC 1.10.3.2) are multi-copper oxidases that have a loose substrate definition, capable of oxidizing a wide range of phenolic compounds, and transferring electrons to molecular oxygen to generate water. Previous genetic studies identified roles for Arabidopsis Lac 4 and 17 in lignin deposition, but did not address the mechanism of their actions. In this study, I further characterized T-DNA insertion lines in the lac4 and lac17 genes. I reproduced the xylem collapsed phenotype and the reduced lignin content from lac 4-2/17 double knock out mutant. I also complemented the double mutant by using a native promoter of Lac4 or Lac17 to drive the expression of Lac4 or Lac17 coding DNA sequence. I showed that the transgene restored the Mäule stain phenotype of lac4-2/17, making them become indistinguishable from wild type plants. Lignin from lac4-2/17 double mutant in Arabidopsis thaliana was further characterized using 2D NMR spectroscopy. My collaborator and I found that the Guaiacyl (G) unit was reduced, and the phenylcoumaran inter-unit linkages almost disappeared in lignin samples of the double mutant compared to that of the wild type. I then tested whether changing the ratio of guaiacyl (G) and sinapyl (S) subunit of lignin up-stream of laccase could rescue the lignin content of the laccase double mutant. The lac4-2/17/fah1-2/C4H-F5H quadruple hybrid was generated by transforming the lac4-2/17/fah1-2 triple mutant with the C4H-F5H construct. The lignin of the quadruple hybrid lines was rich in S and very low in G unit. However, the lignin content was not restored to the wild type level, which indicated that the two laccases, 4 and 17, were not specific to either S or G. Efforts to express and purify Lac4 from heterologous hosts to study the enzyme property were not successful. I further investigated whether other laccases were interchangeable with Lac4 and 17 by attempting to complement the Mäule stain phenotype of 4-2/17 plants with one of the other laccases from A. thaliana, Rhus vernicifera, or Trametes versicolor. I found that Lac10, 11 and 17 fully restored the phenotype of 4-2/17, while Lac 1, 2, 5, 12 restored the phenotype only partially. Lac 3, 15, and Laccases from R. vernicifera, T. versicolor did not complement. The results indicated that not all laccases in A. thaliana were functionally equivalent.

Advisor: Somerville, Chris R
Study of Variability in Advanced Transistor Technologies

As transistor dimensions are scaled down in accordance with Moore's Law to provide for improved performance and cost per function, variability in transistor performance grows in significance and can present a major challenge for achieving high yield in the manufacture of integrated circuits utilizing transistors with sub-30 nm gate lengths. Increased variability in the threshold voltage (VT) of a transistor ultimately limits the minimum operating voltage for six-transistor (6T) static memory (SRAM) cells, hinders aggressive scaling of cell area, and causes performance degradation in analog circuits. Better understanding and accurate assessment of device variation are needed in order to minimize yield loss and design margin./nSeveral variability reduction techniques and variability characterization/modeling methodologies are explored in this work. Device simulations are performed to assess the benefit of super-steep retrograde (SSR) channel doping to reduce variability in transistor performance and thereby extend the scalability of planar bulk-Si CMOS technology with minimal incremental cost. Variability analysis of a 32nm high-permittivity-dielectric/metal gate (HKMG) stack CMOS technology using current-vs.-voltage characteristics of transistors operated in forward (F) and reverse (R) modes measurements is used to explain variabilities in VT and in drain-induced barrier lowering (DIBL) and their correlations, which cannot be captured by a traditional SPICE modeling. Test chips are designed for characterization of systematic and random variability in 16nm and 28nm generation Fully Depleted Silicon-On-Insulator (FDSOI) technologies via device arrays and padded-out SRAM cells./nThe effect of random variability on the performance of a tunnel-field effect transistor (TFET) is also examined. The TFET has emerged as a promising candidate to replace the MOSFET for low-power applications, due to its promise of achieving higher ION/IOFF at low operating voltages. Three-dimensional (3D) device simulations are used to simulate the effects of random dopant fluctuations and line edge roughness on the performance of planar Ge-source and a raised-Ge-source TFET structures.

Advisor: King Liu, Tsu-Jae
Newton Polytopes of Cluster Variables

We study Newton polytopes of cluster variables in type A cluster algebras, whose cluster and coefficient variables are indexed by the diagonals and boundary segments of a polygon. Our main results include an explicit description of the affine hull and facets of the Newton polytope of the Laurent expansion of any cluster variable, with respect to any cluster. In particular, we show that every Laurent monomial in a Laurent expansion of a type A cluster variable corresponds to a vertex of the Newton polytope. We also describe the face lattice of each Newton polytope via an isomorphism with the lattice of elementary subgraphs of the associated snake graph. Other results include a geometric interpretation of the proper Laurent property in type A based on Newton polytopes, and a proof that the Newton polytope of a type A cluster variable has no relative interior lattice points. We also consider extensions of these ideas, results, and methods to other cluster algebras.

Advisor: Williams, Lauren K