VictorJuiz/thesis huggingface dataset:
Biophysical Mass Spectrometry Techniques for Probing the Higher-Order Structure of Proteins and Complexes

Electrospray ionization mass spectrometry (ESI-MS) is a powerful analytical platform for answering a wide variety of questions about the identity, quantity, structure, function, dynamics and energetics of biological molecules. Key advantages of ESI-MS include unrivaled specificity, attomole sensitivity, and the capacity for simultaneous analysis of complex mixtures with analyte masses that differ by less than 1 ppm. The low flow rates and sub-micron sized droplets formed with "nano" ESI allows biomolecular ions to be readily formed from purely aqueous or buffered aqueous solutions, and these ions have been shown to retain a "memory" of their solution-phase structures so that higher-order structural information can be obtained directly from a gas-phase measurement. All of the work described in this dissertation was undertaken in an effort to develop new nanoESI-based techniques that augment the existing array of biophysical mass spectrometry techniques for probing the structure/function relationships of biological molecules in their native environments. In part one, a hypothesis for the origin of nanoESI "supercharging" is developed and exhaustively tested utilizing a variety of solution- and gas-phase techniques with a range of different proteins and protein complexes. The results of all of these studies support the hypothesis that the origin of aqueous solution supercharging is the rapid chemical and/or thermal denaturation of a protein or protein complex analyte in an evaporating ESI droplet due to enrichment of the reagent caused by its high boiling point relative to that of water. Aqueous solution supercharging has recently been used in a variety of new applications and an understanding of its underlying mechanism is therefore essential. In part two, two new biophysical mass spectrometry applications are described. The first is a tandem-MS application of aqueous solution supercharging for obtaining hydrogen/deuterium exchange (HDX) rate constants in real-time with nearly single amino acid spatial resolution, and the second describes an MS method to obtain the quaternary structure of protein complexes that require high concentrations of essential salts. Finally, two ideas for new HDX-MS methods that capitalize on the mechanism of aqueous solution supercharging are outlined.

Advisor: Williams, Evan R.
Design Considerations for CMOS-Integrated Hall-effect Magnetic Bead Detectors for Biosensor Applications

This dissertation presents a design methodology for on-chip magnetic bead label detectors based on Hall-effect sensors to be used for biosensor applications. Signal errors caused by the label binding process and other factors that place constraints on the minimum detector area are quantified and adjusted to meet assay accuracy standards. The methodology is demonstrated by designing an 8,192 element Hall sensor array implemented in a commercial 0.18 um CMOS process with single mask post-processing. The array can quantify a one percent surface coverage of 2.8 um beads in thirty seconds with a coefficient of variation of 7.4%. This combination of accuracy and speed makes this technology a suitable detection platform for biological assays based on magnetic bead labels.

Advisor: Boser, Bernhard E
Randomized Algorithms for Scalable Machine Learning

Many existing procedures in machine learning and statistics are computationally intractable in the setting of large-scale data. As a result, the advent of rapidly increasing dataset sizes, which should be a boon yielding improved statistical performance, instead severely blunts the usefulness of a variety of existing inferential methods. In this work, we use randomness to ameliorate this lack of scalability by reducing complex, computationally difficult inferential problems to larger sets of significantly smaller and more tractable subproblems. This approach allows us to devise algorithms which are both more efficient and more amenable to use of parallel and distributed computation. We propose novel randomized algorithms for two broad classes of problems that arise in machine learning and statistics: estimator quality assessment and semidefinite programming. For the former, we present the Bag of Little Bootstraps (BLB), a procedure which incorporates features of both the bootstrap and subsampling to obtain substantial computational gains while retaining the bootstrap's accuracy and automation; we also present a novel diagnostic procedure which leverages increasing dataset sizes combined with increasingly powerful computational resources to render existing estimator quality assessment methodology more automatically usable. For semidefinite programming, we present Random Conic Pursuit, a procedure that solves semidefinite programs via repeated optimization over randomly selected two-dimensional subcones of the positive semidefinite cone. As we demonstrate via both theoretical and empirical analyses, these algorithms are scalable, readily benefit from the use of parallel and distributed computing resources, are generically applicable and easily implemented, and have favorable theoretical properties.

Advisor: Jordan, Michael I
Statistical Methods for Enhanced Metrology in Semiconductor/Photovoltaic Manufacturing

As semiconductor technology is aggressively scaling to finer feature sizes, manufacturing complexity increases dramatically. This drives the need for extensive control on processing equipment and on the efficiency of the associated metrology. Similarly, in the field of photovoltaic (PV) manufacturing, processing technology is driven by cost reduction while increasing output power per cell. In either case, the variability impact on the final performance is critical./nIn this thesis, we focus on the application of statistical methods for enhanced metrology in both semiconductor and PV manufacturing. The work falls into three main topics: Wafer-to-Wafer (W2W) Virtual Metrology (VM) via predictive modeling, Site-to-Site (S2S) metrology modeling for Fault Detection and Classification (FDC), and predictive variability modeling for solar PV./nThe first topic is on creating predictive VM models for W2W control in plasma etching, one of the bottlenecked processes for technology node scaling. The idea is to utilize equipment sensor data to predict the wafer processing results, so that actual wafer measurements can be reduced or eliminated. VM comprises four main steps: data extraction, outlier removal, variable selection, and model creation. They aim to deal with the special characteristics of equipment sensor data which are high dimensional, collinear and non stationary. VM models are trained and tested with approximately one production year worth of wafer data collected from a single plasma etching tool. The best model result is obtained by a hybrid model that utilizes step-wsie parameter selection and Neural Network (NN) based prediction, which achieved a testing R2 of 0.75./nThe second topic aims to develop FDC schemes for wafer-level S2S metrology. We first focus on utilizing spatial and multivariate statistics for detecting outlier wafers. Spatial and multivariate methods are preferred given the temporal and spatial varying nature of wafer level metrology data. We then focus on selecting the optimal measurement sites for process monitoring. Various site selection schemes are evaluated within the FDC application, showing than more than 70% metrology savings with no discernable reduction in performance is possible./nThe third topic addresses modeling the variability of solar cells. The impact of environmental and manufacturing variability is simulated and discussed. A predictive model for manufacturing variability-induced mismatch power loss is proposed and evaluated with various PV array configurations. Finally, spatial statistics are used to model the non-uniformities of solar cell properties. A SPICE-based distributive solar cell simulator is constructed to estimate electrical performance for various defect distribution patterns. Finally, a statistical model is created in order to correlate the spatial characteristics of defect patterns with the corresponding electrical performance.

Advisor: Spanos, Costas J
Bicrystal-Array Fabrication

The continued optimization of technologically advanced ceramics, such as bone implants, computer components, and thermal barrier coatings, is necessary to continue the improvement of their lifetimes, effectiveness, and energy efficiencies. Properties of polycrystalline ceramics can be controlled by varying processing conditions. In order to fully understand the morphological development of grains in polycrystalline material during processing, one must understand the structure and movement of their grain boundaries, both individually and as a group. For many materials, the average group behavior has been measured, but little is known about the qualities of individual boundaries, which comprise a wide range of geometries and misorientations. A more complete understanding of the structure and motion of a collection of interfaces can only be obtained by creating and studying a range of individual interfaces with known misorientations. Many methods currently exist for creating one - or a few - isolated grain boundaries, also called "bicrystals," in a sample. However, this then represents only a tiny fraction of the grain boundaries present in advanced polycrystals and until now, there has been no method for creating a wide and representative collection of bicrystals within a single ceramic sample. This research project involves the development of an experimental method that results in hundreds of ceramic island-grain bicrystals on a single sample in order to facilitate combinatorial studies of a wide range of interfaces. These samples could then be used to observe correlations such as interface structure vs. misorientation, kinetic behavior vs. misorientation, and relative surface energy by measurement of dihedral angle relative to misorientation. Additionally, changes in samples that have been chemically doped or annealed under different conditions could be compared. A clear understanding of these relationships is expected to shed light on bulk polycrystalline behavior and therefore provide more complete understanding of the energetic and kinetic properties and characteristics of interfaces in ceramics and therefore more opportunities to control and improve bulk polycrystalline ceramics.

Advisor: Glaeser, Andreas
On Wealth and Wrongdoing: How Social Class Influences Unethical Behavior

Social class is an individual-level characteristic that reflects a person's objective material resources (e.g., income, education, and occupational prestige) and corresponding subjective perceptions of rank vis-à-vis others in the social hierarchy (Kraus, Piff, & Keltner, 2011). Drawing on theories of cultural psychology and social cognition, emerging psychological research suggests that social class influences people's social and cognitive tendencies, significantly shaping how they perceive, interpret, and react to their environments (Kraus, Piff, Mendoza-Denton, Rheinschmidt, & Keltner, in press; Piff, Kraus, Côté, Cheng, & Keltner, 2010). Specifically, the confluence of increased resources and rank, greater personal control, decreased vulnerability to environmental threat, and increased independence from others gives rise to self-focused social cognitive tendencies among upper-class individuals. By contrast, the confluence of decreased resources and rank, less personal control, increased vulnerability to threat, and increased dependence on others gives rise to other-focused social cognitive tendencies among lower-class individuals. Following from this theoretical framework, I tested the hypothesis that upper-class individuals, relative to lower-class individuals, engage in increased unethical behavior, and do so, in part, because of their more favorable attitudes toward greed./nSeven studies using experimental and naturalistic methods yielded evidence that supported this hypothesis. In my first two studies, upper-class individuals proved more likely than lower-class individuals to break the law while driving by cutting off other vehicles at a four-way intersection (Study 1) or failing to yield for a pedestrian at a crosswalk (Study 2). Follow-up laboratory studies further tested the association between social class and unethical tendencies. In Study 3, upper-class individuals were more likely than lower-class individuals to exhibit unethical decision-making tendencies. In Study 4, inducing in participants an upper-class mindset caused them to take more valued goods from others compared to participants who experienced a lower-class mindset. In Study 5, upper-class individuals were more likely than lower-class individuals to endorse lying in a hypothetical negotiation. In Study 6, upper-class individuals were more likely than lower-class individuals to cheat in a game to increase their chances of winning a prize. Finally, in Study 7, upper-class individuals endorsed more unethical behavior at work than lower-class individuals. Across studies, I provide mediator and moderator data in support of the hypothesis that upper-class individuals' unethical tendencies are driven, in part, by their more favorable attitudes toward greed.

Advisor: Keltner, Dacher
Improved Positive Electrode Materials for Li-ion Batteries

The introduction of the first commercially produced Li-ion battery by Sony in 1990 sparked a period of unprecedented growth in the consumer electronics industry. Now, with increasing efforts to move away from fossil-fuel-derived energy sources, a substantial amount of current research is focused on the development of an electrified transportation fleet. Unfortunately, existent battery technologies are unable to provide the necessary performance for electric vehicles (EV's) and plug-in hybrid electric vehicles (PHEV's) vehicles at a competitive cost. The cost and performance metrics of current Li-ion batteries are mainly determined by the positive electrode materials. The work here is concerned with understanding the structural and electrochemical consequences of cost-lowering mechanisms in two separate classes of Li-ion cathode materials; the LiMO2 (M = Ni, Mn, Co) layered oxides and the LiMPO4 olivine materials; with the goal of improving performance./nAl-substitution for Co in LiNizMnzCo1-2zO2 ("NMC") materials not only decreases the costly Co-content, but also improves the safety aspects and, notably, enhances the cycling stability of the layered oxide electrodes. The structural and electrochemical effects of Al- substitution are investigated here in a model NMC compound, LiNi0.45Mn0.45Co0.1-yAlyO2. In addition to electrochemical measurements, various synchrotron-based characterization methods are utilized, including high-resolution X-ray diffraction (XRD), in situ X-ray diffraction, and X-ray absorption spectroscopy (XAS). Al-substitution causes a slight distortion of the as-synthesized hexagonal layered oxide lattice, lowering the inherent octahedral strain within the transition metal layer. The presence of Al also is observed to limit the structural variation of the NMC materials upon Li-deintercalation, as well as extended cycling of the electrodes./nVarious olivine materials, LiMPO4 (M=Fe,Co) are produced using a custom-built spray pyrolysis system. Spray pyrolysis is a simple, inexpensive, and scalable method used to produce highly uniform and phase-pure particle materials. The materials are synthesized here as porous, carbon-coated spherical particles with micron-sized diameters and nanoscale primary particles. The LiMPO4 (M=Fe,Co) olivine electrodes display exceptional electrochemical properties, in terms of high discharge capacities, rate capability, and cycling stability. The excellent performance is due to the particle morphologies that include a hierarchical pore structure and conductive carbon network throughout the particles. This allows liquid electrolyte penetration into the particle interiors, thus limiting the necessary solid-state diffusion distances, as well as efficient charge transfer and collection.

Advisor: De Jonghe, Lutgard C.
Cox Rings and Partial Amplitude

In algebraic geometry, we often study algebraic varieties by looking at their codimension one subvarieties, or divisors. In this thesis we explore the relationship between the global geometry of a variety $X$ over $\mathbb{C}$ and the algebraic, geometric, and cohomological properties of divisors on $X$. Chapter 1 provides background for the results proved later in this thesis. There we give an introduction to divisors and their role in modern birational geometry, culminating in a brief overview of the minimal model program./nIn chapter 2 we explore criteria for Totaro's notion of $q$-amplitude. A line bundle $L$ on $X$ is $q$-ample if for every coherent sheaf $\mathcal{F}$ on $X$, there exists an integer $m_0$ such that $m\geq m_0$ implies $H^i(X,\mathcal{F}\otimes \mathcal{O}(mL))=0$ for $i>q$. We show that a line bundle $L$ on a complex projective scheme $X$ is $q$-ample if and only if the restriction of $L$ to its augmented base locus is $q$-ample. In particular, when $X$ is a variety and $L$ is big but fails to be $q$-ample, then there exists a codimension $1$ subscheme $D$ of $X$ such that the restriction of $L$ to $D$ is not $q$-ample./nIn chapter 3 we study the singularities of Cox rings. Let $(X,\Delta)$ be a log Fano pair, with Cox ring $R$. It is a theorem of Birkar, Cascini, Hacon and McKernan that $R$ is finitely generated as a $\C$ algebra. We show that Spec $R$ has log terminal singularities.

Advisor: Eisenbud, David
Californians and their Earthquakes: Post-Earthquake Public Information Infrastructures

This dissertation analyzes Californians' information infrastructure after three Bay Area earthquakes: 1868 Hayward Fault Earthquake, 1906 San Francisco Earthquake and Fire, and 1989 Loma Prieta Earthquake. I use qualitative and historical research approaches, focusing on documents produced by state and local governments, newspapers and letters by Californians. In my analysis, I employ the construct of "information infrastructure" from the field of Science and Technology Studies to describe the complex constellation of practices, technology and institutions that underpins the public sphere. Four themes help develop the idea of public information infrastructure: continuity, reach, informational authority and multiple infrastructures. First, major disruptions such as earthquakes challenge the continuity of public information infrastructure while making infrastructure visible. For example, after the 1906 earthquake and fire, refugees had to reassemble their social geography. Friends, loved ones, employers and employees all wanted to locate each other and notify others of their well-being. While the physical information infrastructure was destroyed, the ways that people worked and organized was not. Thus, with some work-arounds, information infrastructure within San Francisco was reassembled to working order. Second, I look at one of the qualities of information infrastructure that is considered fundamental - that of the reach of infrastructure across space. In 1868, the circulation of documents to far away audiences shaped the earthquake narrative locally. Third, I examine claims to informational authority. My dissertation begins in 1868, at a time when there were not shared scientific earthquake descriptors such as magnitude, when it took weeks for a newspaper to travel from San Francisco to New York, and when there was no professionalized class of "responders" or specialized government response. The Chamber of Commerce claimed the authority to explain the earthquake. The bureaucratization of disaster response and the rise of scientific explanations for earthquakes shaped infrastructure and information practices, such that by the 1989 earthquake government officials claimed the authority to explain what had happened. The intertwining of science, the state, and infrastructure helped constitute and legitimize a new set of informational authorities, and provide a lens with which to design post-disaster information systems and policy today. Last, I argue that there is not just one information infrastructure, but multiple infrastructures supporting multiple publics. Alternate infrastructures supported Chinese people in 1906 and Spanish-speakers in 1989 when attempting to get aid or find loved ones. My research ties together how technology, media organizations, government institutions, and scientific explanations of earthquakes contribute to a sensemaking epistemology for Californians.

Advisor: Saxenian, AnnaLee
Duguid, Paul
Late antique and medieval Islamic legal histories: contextual changes and comparative (re)considerations

This dissertation demonstrates the contingent and contextual nuances of Islamic legal history by balancing precise legal case studies with broad-spectrum jurisprudential surveys. This work places Islamic legal history within diverse late antique (seventh to tenth centuries CE) and medieval (tenth to fifteenth centuries CE) contexts through specific comparisons with rabbinic legal traditions. By delineating intricate legal changes involving several generations of jurists, my research demonstrates the flexibility, expansiveness, and contingency of Islamic legal traditions within a meta-narrative about the transformations of law in the "Near East." I offer a historical understanding of the ambiguous and mutable nature of law and illustrate the complexity of legal pluralism and the struggle for legal-politcal authority that underlies the formation of orthodoxy. This research challenges common reifications of "Islamic law" as an inevitable outcome or a static, monolithic whole.

Advisor: Lapidus, Ira
Atmosphere as Culture: Ambient Media and Postindustrial Japan

Ambient media are oriented towards tinting the space around them with a particular mood or emotional tone, which their users can then attune to. The dissertation begins by tracing how this use of media as a mood regulator emerges in postindustrial Japan, drawing from the longer histories of background music, environmental art, and therapy culture. What follows theorizes this aesthetics of atmosphere as found in music, animation, literature, and video art./nThe analysis explores the relationship between ambient media and landscape, dreams, the cosmos, domesticity and gender, the rhythms of urban life, cosubjectivity, and information overload. In each case, discussion focuses on how the aesthetics of atmosphere reimagines subjectivity vis-à-vis the surrounding environment, shifting the postindustrial self away from a social identity based in interpersonal relations and towards a more abstract sensing body developed with and through the moods afforded by mediated space./nThe central concern here is how the aesthetics of ambient media serve to erase other people from the sensible horizons of postindustrial life, while at the same time expanding the environmental affordances of the human body in new directions. The dissertation theorizes the dynamics of ambient subjectivity to reveal how the aesthetics of atmosphere are both radical and regressive, offering an aesthetic solution to the coexistence of diverse objects in space, yet at the same time denying the possibility of any direct encounter with difference.

Advisor: Tansman, Alan