VictorJuiz/thesis huggingface dataset:
The Deaths of Massive Stars: Core-Collapse Supernovae and Pre-Explosion Mass Loss

This thesis addresses some of the gaps in our current understanding of the deaths of massive stars using observations of supernovae (SNe) obtained at frequencies from the radio up to the ultraviolet. I use new data collected by myself and the other researchers in the Berkeley SN research group using telescopes at the Lick and Keck Observatories; new data collected by my collaborators using many different telescopes, from the Very Large Array to the Hubble Space Telescope; and every category of relevant archived data available. Most of this work is organized by event: SNe 1998S and 2011dh provide representative case studies of their types (the interacting Type IIn SNe and the stripped-envelope Type IIb SNe, respectively), and I use SNe 2015G and 2015U to explore the properties of the rare and confounding subclass of Type Ibn SNe (which are both stripped-envelope and interacting). In addition to these focused analyses of single SNe, I use a curated sample of events to refine our measures of the relative rates of core-collapse SNe in an effort to better understand the populations of massive stars from which these events arise.

Advisor: Filippenko, Alexei
Total positivity for Grassmannians and amplituhedra

Total positivity is the mathematical study of spaces and their positive parts, which can have interesting combinatorial properties as well as applications in areas such as analysis, representation theory, and theoretical physics. In this dissertation, I study total positivity in the Grassmannian Gr(k,n), which is the space of k-dimensional subspaces of R^n. The totally nonnegative Grassmannian is the subset of Gr(k,n) where all Plücker coordinates are nonnegative. In Chapter 2, I generalize a result of Gantmakher and Krein, who showed that an element V of Gr(k,n) is totally nonnegative if and only if every vector in V, when viewed as a sequence of n numbers and ignoring any zeros, changes sign at most k-1 times. I characterize when the vectors in V change sign at most k-1+m times for any m, in terms of the Plücker coordinates of V. I then apply this result to solve the problem of determining when Grassmann polytopes, generalizations of polytopes into the Grassmannian studied by Lam, are well defined. In Chapter 3, which is joint work with Lauren Williams, we study the (tree) amplituhedron A(n,k,m), the image in Gr(k,k+m) of the totally nonnegative part of Gr(k,n) under a (map induced by a) linear map which is totally positive. It was introduced by Arkani-Hamed and Trnka in 2013 in order to give a geometric basis for computing scattering amplitudes in N=4 supersymmetric Yang-Mills theory. We take an orthogonal point of view and define a related "B-amplituhedron" B(n,k,m), which we show is isomorphic to A(n,k,m), and use the results of Chapter 2 to describe the amplituhedron in terms of sign variation. Then we use this reformulation to give a cell decomposition of the amplituhedron in the case m=1, using the images of a collection of distinguished cells of the totally nonnegative Grassmannian. We also identify A(n,k,1) with the complex of bounded faces of a cyclic hyperplane arrangement, and deduce that A(n,k,1) is homeomorphic to a ball. In Chapter 4, I study the action of the cyclic group of order n on the totally nonnegative part of Gr(k,n). I show that the cyclic action has a unique fixed point, given by taking n equally spaced points on the trigonometric moment curve (if k is odd) or the symmetric moment curve (if k is even). More generally, I show that the cyclic action on the entire complex Grassmannian has exactly n choose k fixed points, corresponding to k-subsets of nth roots of (-1)^(k-1). I explain how these fixed points also appear in the study of the quantum cohomology ring of the Grassmannian.

Advisor: Williams, Lauren K.
Characterization of a Novel Population of Olfactory Neurons

Zebrafish have become a useful model for understanding olfactory circuitry and social behaviors. Combined with the benefits of optical transparency and fast developmental speed, the large clutch sizes of zebrafish larvae make this animal a desirable choice for large scale drug screens that may be affecting the olfactory system (McCarroll et al., 2016). Zebrafish olfactory anatomy consists of one olfactory epithelium (OE) that exposes at least five classes of olfactory sensory neurons (OSNs) to chemical ligands in the water (Ahuja et al., 2014; Wakisaka et al., 2017; Yoshihara, 2008). OSNs then project axons to the olfactory bulb, which then send projections to higher order brain regions (Yoshihara, 2014). In each step of the olfactory signaling process, ligand information is coded in the receptors, OSNs, and brain areas that each ligand, or suite of ligands, activates. However, to make comparisons with the mammalian olfactory systems, we need to understand how the circuitry of the zebrafish olfactory system differs from mammals. In mice, for instance, two different olfactory systems exist in the nose: the main olfactory epithelium (MOE) and the vomeronasal olfactory system (VNO). These two sensory systems contain OSNs that diverge in morphology and projection targets. Some are important in learned behaviors while others play a role in innate behaviors. In zebrafish, there is only one epithelium that contains a variety of cell types and projection targets. How does this system differentiate between learned and innate behaviors? Understanding why these differences have evolved this way might help us make better comparative studies between different animal groups. New behavioral assays and gene trap techniques have emerged as a powerful way to probe the structure and function of zebrafish olfactory behaviors (Koide et al., 2009; Yabuki et al., 2016). This dissertation examines the circuitry of the zebrafish olfactory system and innate behaviors using gene trapping, single cell RNA sequencing, immunohistochemistry, in situ hybridization, and novel behavioral assays. The following was determined: (1) A new class of unipolar olfactory sensory neuron (OSN) exists in zebrafish larvae that projects directly to the telencephalon and fish amygdala from the anterior olfactory epithelium (OE); (2) Two types of bipolar OSNs project to the mG2 and mG3 glomeruli of the olfactory bulb and express the ora4 and ora6 receptors respectively; (3) Larval zebrafish display thigmotaxis when exposed to fish skin extract; (4) This behavior is absent in fish with olfactory nerve lesions; and (5) Ablation of telencephalon projecting OSNs suggest that these neurons may play a role in thigmotaxis. These results provide a new look at how olfactory circuitry is organized in the larval zebrafish and how these circuits may play a role in innate fear behavior.

Advisor: Ngai, John
Tools for Trustworthy Autonomy: Robust Predictions, Intuitive Control, and Optimized Interaction

In the near future, robotics will impact nearly every aspect of life. Yet for technology to smoothly integrate into society, we need interactive systems to be well modeled and predictable; have robust decision making and control; and be trustworthy to improve cooperation and interaction. To achieve these goals, we propose taking a human-centered approach to ease the transition into human-dominated fields. In this work, our modeling methods and control schemes are validated through user studies in a realistic motion simulator and demonstrate improved interaction, predictability, and trustworthiness. Autonomous vehicles are a great motivating example, due to the wealth of interesting problems that arise with human-in-the-loop control and multi-agent interaction and cooperation. While autonomous vehicles will likely be publicly available soon, it can be assumed that the transition will not be instantaneous, suggesting that: (1) levels of autonomy will be introduced incrementally, and (2) autonomous vehicles will have to be capable of driving in a mixed environment, with both humans and autonomy. In both cases, the human drivers must be modeled in an accurate and precise manner that easily integrates into control frameworks./nWe present a data-driven approach to hybrid system tools, that approximates the forward reachable set of a coupled human-robot system. This empirical reachable set is an alternative look at a classic control theoretic safety metric and allows us to predict driver behavior over long time horizons in a robust, yet informative, manner. This method is compared to an extension of traditional reachability, in which the optimal disturbances are uncovered using empirical metrics with probabilistic guarantees. Applications of this work include the design of minimally invasive intervention schemes for semi-autonomous vehicles and of planning nuanced interactions between humans and autonomy in interactive maneuvers. We also consider concerns that arise with shared control. Given a fixed semi-autonomous framework, we model the communication between the human and automation using information theory metrics. By controlling information flow, we observe an information/performance trade-off that follows a strongly concave relationship. This is formulated as an optimization paradigm, giving a model-based approach to interface design for optimizing interaction.

Advisor: Bajcsy, Ruzena
An Imaging-Based Human Embryonic Stem Cell Assay for Teratogenic Activity

In this work a human pluripotent stem cell (hPSC) assay was proposed as a novel imaging-based screen for identifying substances (teratogens) likely to cause birth defects in humans. The assay was engineered to leverage lessons from the validated mouse Embryonic Stem Cell Test (EST). An automated fluid handler was repurposed to support printing stem cells and biological materials to an innovative two-part microculture platform, the pillar/well chip system. Key milestones were met, demonstrating the applicability of the microculture platform to hPSC cultures over the duration of the proposed assay. Three proof-of-principle experimental data sets were acquired using statistical experimental design to eliminate confounding systematic variation and uncontrolled variables. Changes in cell population and expression of four protein biomarkers were observed with automated fluorescence microscopy and quantified by image analysis. Toxic molecules were found to show similar inhibition of viability to literature values. Further work is needed to optimize quantification and reduce variability in these signals to assess the effects of candidate teratogens on cell differentiation.

Advisor: Clark, Douglas
Schaffer, David
Deciphering structural heterogeneity in metal-organic frameworks towards an understanding of structure-property relationships

The work presented herein describes the relevance and study of structural heterogeneity in the porous crystalline metal-organic framework (MOF) materials. These frameworks, which consist of metal clusters bridged by organic linking units, frequently contain defects or other components that are not described simply by the unit cell of the framework. Intriguingly, even if the features make up a small part of the overall structure, these can dominate a given material’s properties. This is evidenced in Chapters 2 and 3, which focus on characterizing the structural heterogeneity on a molecular level, specifically of the ‘missing linker’ defects in UiO-66 and the origin of superacidity in sulfated MOF-808 respectively. The former displays Lewis acidic sites and different protonation states while the latter has superacidic Brønsted acid sites following exchange of sulfuric acid into the pristine MOF-808 framework. These sites are dependent on the post-synthetic treatment of the material, and are a direct result of the heterogeneous chemical features that are not necessarily ordered in a long-range manner. Chapter 4 extends the characterization of sulfated MOF-808 by investigating other oxides that may be incorporated into the framework, focusing on their structural characterization./nThe concept of structural heterogeneity is not limited to defects and other features that are not ordered over long-range. MOFs can be developed into smart solid-state materials by incorporating multiple types of functional groups with the capacity for different reactivity and chemistry within the same material. This is the focus of Chapter 5, which discusses the synthesis and characterization of MOFs containing phosphonate groups with multiple binding modes and protonation states, carboxylate-based MOFs with disulfide units, and the incorporation of peptide units into the MOF linker to stabilize alkali metal-based clusters./nFinally, the full potential of these materials with complex structural landscapes can only be realized through careful structural characterization and analysis. Chapter 6 highlights the case study of fifteen mixed-linker zeolitic imidazolate frameworks (ZIFs) and how their single crystal structures are characterized from low resolution data. While the information at low resolution is clearly less than what can be uncovered at high resolution, there is still much structural information to be gained. The procedures to obtain the data and model the structures, the limitations and methods used, are described.

Advisor: Yaghi, Omar M
Ru

This piece borrows its title from an installation work by Kosovar artist Petrit Halilaj that depicts a landscape of migratory birds and their ephemeral nests. In Halilaj’s work, the title RU represents Runik, the artist’s birthplace and the site of numerous Neolithic artifacts and musical instruments, serving as material representations of a distant cultural memory. His work describes ideas of presence and absence that are important to me and my music. The presence of a sonic body, as it manifests in various permutational musical spaces and situations, briefly inscribes its activity and resonance within the environment, before fading away. This composition is an extension of my research on sonic embodiment that preserves and renews these sociocultural memories.

Advisor: Ueno, Ken
Ultrafast Dynamics of Adenine Derivatives Studied by Time-Resolved Photoelectron Spectroscopy in Water Microjets

Femtosecond time-resolved photoelectron spectroscopy (TRPES) in liquid microjets is a powerful tool for elucidating the ultrafast photoinduced dynamics of species in the condensed phase. A pump pulse first excites the molecule of interest and is then followed by a probe pulse, which detaches the nascent electron distribution to vacuum at varying time-delays. The transient lifetimes, solvation timescales, and binding energies of the molecule can then be elucidated by tracking the time-evolving photoelectron distribution with a magnetic bottle time-of-flight spectrometer./nOf particular interest to many fields of chemistry and biology is the process by which DNA and its nucleic acid (NA) constituents shed excess energy imparted by UV radiation. Beyond their intrinsic interest, study of UV-photoexcited NA constituents can also provide fundamental insights into the non-adiabatic processes of organic molecules generally. DNA components are known to undergo rapid de-excitation through a slew of conical intersections that involve ring-puckering modes of the nitrogenous base. Importantly, the local environment and small structural changes in the NA constituent are known to drastically affect these dynamics. For this reason, a bottom up approach to DNA photophysics is necessary./nThis dissertation explores the photodeactivation of the NA constituents adenosine and adenosine monophosphate in aqueous solution. In a series of pseudo-degenerate experiments, 4.69-4.97eV and 6.20eV photons were used as both the pump and probe pulses. The lowest ππ* excited state was populated by photons ranging in energy from 4.69-4.97eV, and this state was found to decay via internal conversion to vibrationally hot ground state on a sub-ps timescale. Another non-adiabatic channel was seen at an excitation energy of 6.20eV, and was tentatively assigned to the decay of a higher-lying ππ* excited state./nThese experiments mark the first reported use of a 6.20eV pulse to study the photoinduced dynamics in NA constituents with TRPES in liquid microjets. As a probe pulse, the 6.20eV pulse provides a fuller picture of the excited state relaxation dynamics. When used as a pump, this pulse is posited to interrogate different excited states than previously studied by others. Regardless, in both cases, information about the ground electronic state is energetically inaccessible./nThe lack of information regarding the ground state dynamics of NA constituents, and, in fact, many solvated species, remains an outstanding issue for TRPES in liquid microjets. The second half of this dissertation focuses on remedying this through the implementation of a new XUV source. High harmonic generation in a semi-infinite gas cell will be used to produce a femtosecond probe pulse ranging in energy from 20-100eV. With a more energetic probe, new regimes of fundamental physical chemistry in the condensed phase will be accessible.

Advisor: Neumark, Daniel M
Investigating noncoding RNA biogenesis and function during mitosis

Mitosis is one of the most dramatic and complex processes in the life of a cell. Although first observed over 100 years ago, there are still many gaps in our understanding of this crucial process. Years of research into the mechanisms of cell division have uncovered many of the protein players required for the faithful execution of this essential process. However, very little is known about the roles of RNAs during mitosis. In my thesis work, I established several biological functions and regulatory modes employed by RNAs and the RNA biogenesis machinery that are essential for cell division. Using a variety of techniques, I showed that RNA biogenesis during mitosis is an essential step in the assembly of the mitotic spindle and mitotic chromatin. I also provided evidence that RNAs are required for microtubule generation, microtubule organization, and chromatin assembly. In addition, I developed automated image analysis tools to systematically assess mitotic spindle morphology for Xenopus egg extract spindle assembly reactions, a very challenging image analysis application. My work suggests that RNAs should be included as a broad class of regulatory molecules that are essential for the execution of eukaryotic cell division.

Advisor: Heald, Rebecca
Resonances in Middle High German: New Methodologies in Prosody

For years, scholars of medieval German have grappled with how to analyze formal characteristics of the lyric and epic poetry while taking into consideration performance, musicality, mouvance, linguistic variation, and aggressive editing practices. The scholarship has justifiably resorted to restricted explorations of specific texts or poets, or heavily criticized region-specific descriptions with several caveats. The many challenges this multifaceted poetry presents has also obscured one of its most central features—–the medieval voice. With the little evidence we have often being ambiguous or contradictory, how are we to understand the role of the medieval voice in the German corpus as a whole? This project seeks to shed light on this forgotten aspect by taking advantage of computational methods to demonstrate/nrelative formal and thematic relationships based on sound and voice. In doing so, it presents several new prosodic analytical methods./nThe first chapter of this project underlines the importance of sound and voice to medieval performance and composition. It additionally justifies the syllable as the foundation of the novel formal methods presented in the following chapters. Chapter two presents a new/nsyllabification algorithm that combines two linguistic principles: the Sonority Sequencing Principle and the Legality Principle. This algorithm is then customized and computationally implemented to perform accurately on medieval German across dialects and editing practices. Chapter three employs this syllabification algorithm to characterize different phonological soundscapes in reference to theme and voice using a modest corpus of only medieval German lyric poetry. While chapter three intends to quantify the vocal affect of a soundscape, chapter four aims to account for the sequencing of these soundscapes within the larger text and corpus. Chapter three therefore lays the foundation for a structural model of medieval German form. Finally, chapter five reduces the corpus once again to a very small subset of medieval German Vierheber (epic poetry with four stresses per line). It presents a supervised machine learning model to predict scansion for these texts according to the theory proposed by Andreas Heusler, and draws conclusions from how different poets took advantage of the freedom this structure allowed./nIn each chapter, I present the aggregate statistics to confirm and supplement our knowledge of the medieval German corpus as a whole. Yet more importantly, I return to individual texts in order to demonstrate how these newly discovered formal soundscapes manifest and function within a smaller narrative. This combination of “distant reading” and “close reading” supports my overarching argument that medieval German form and content were demonstrably and quantifiably highly intertwined. In many cases markedly different formal, phonologically-influenced structures were implemented to trigger connections to related texts and formats. This project thus creates a new understanding of intertextual relations in medieval German literature.

Advisor: Largier, Niklaus