VictorJuiz/thesis huggingface dataset:
Chinese Letters and Intellectual Life in Medieval Japan: The Poetry and Political Philosophy of Chūgan Engetsu

This dissertation explores the writings of the fourteenth-century poet and intellectual Chūgan Engetsu 中巌円月, a leading figure in the literary movement known to history as Gozan (“Five Mountains”) literature. In terms of modern disciplinary divisions, Gozan literature straddles the interstices of several distinct areas of study, including classical Chinese poetry and poetics, Chinese philosophy and intellectual history, Buddhology, and the broader tradition of “Sinitic” poetry and prose (kanshibun) in Japan./nAmong the central contentions of this dissertation are the following: (1) that Chūgan was the most original Confucian thinker in pre-Tokugawa Japanese history, the significance of his contributions matched only by those of early-modern figures such as Ogyū Sorai, and (2) that kanshi and kanbun were creative media, not merely displays of erudition or scholastic mimicry. Chūgan’s expository writing demonstrates that the enormous multiplicity of terms and concepts animating the Chinese philosophical tradition were very much alive to premodern Japanese intellectuals, and that they were subject to thoughtful reinterpretation and application to specifically Japanese sociohistorical phenomena. No less intrepid in the realm of poetry, Chūgan candidly addressed themes such as illness, war, and poverty, and experimented with unusual Sinitic forms such as hexasyllabic quatrains and the vernacular “song lyric” or ci 詞, which though popular in China was very seldom seen in Japan./nThe thematic and stylistic breadth of Chūgan’s oeuvre reveals the catholicity of Gozan literary culture and suggests directions for further research into Japanese intellectual history and Sinitic poetry during the medieval era.

Advisor: Horton, H. Mack
Cavity and Microwave Experiments on Electron Plasma

A new technique for rapidly generating a sequence of target plasmas in a Penning-Malmberg trap is presented and applied in the first demonstration of cavity-resonant cooling in a plasma. This ``reservoir'' technique further enables the in situ magnetic field to be measured to high precision by microwave ECR spectroscopy. A precision antihydrogen gravity experiment being constructed at CERN will rely on this method, as there is no other method with comparable absolute, spatial, and temporal resolution which can be implemented in the Penning-Malmberg trap. These cavity and microwave measurements require accessing new regimes with the plasma parallel energy analyzer, to which end the sensitivity of the latter technique has been increased twenty-fold.

Advisor: Fajans, Joel
The Lover’s Voice: The Poetics of Direct Discourse in Medieval French Romance

This dissertation proposes that the frequent inclusion of characters’ speech in medieval romance is more than a formal marker of genre; rather, certain romance texts use dialogue between male and female protagonists to portray varied experiences of affect and desire, and to explore questions of subjectivity and gender difference. While scholars often assume that asymmetrical models of gender difference are deeply entrenched in twelfth-century courtly literature, I argue that an ephemeral subgenre of early romance not only problematizes such models, but also reaches toward an ethos of collaboration between men and women. In the Old French adaptation of Ovid’s “Pyramus and Thisbe,” the adaptor grants his protagonists lengthy paired monologues that illuminate their interiority and agency, suggesting a humanistic affirmation of subjectivity. At first glance, the Old French text might seem to depart from its Latin model mostly in form; however, the adaptor’s interest in his character’s speech marks a more profound commitment to a poetics of dialogue. Chrétien de Troyes’s romance Érec et Énide might be read as a repudiation of such a poetics, given its unusual problematization of dialogue between its titular couple: Énide’s speech is not represented until after her marriage to Érec, and when she does speak, her words disrupt rather than repair the couple’s peaceful marriage. I argue that, despite Énide’s troubled speaking status, this romance shows how a female subject might navigate courtly society by focalizing Énide’s subjectivity; furthermore, although conversation within the couple rarely leads to greater accord, mutual touch offers an alternate form of communication. Direct discourse is less fraught but no less charged in the Tristan legend; this chapter analyzes three Tristanian texts in order to examine the role of evocation in the narrative and in the way communication between Tristan and Yseut is portrayed. I advocate for a reconsideration of the “fragmented” Tristan tradition, and propose reading it as episodic instead, a shift that reveals the ways in which different authors evoke a larger narrative. This relationship of the part to the whole is echoed by the way communication between Tristan and Yseut is treated as both exceptionally seamless and oddly overwrought: these lovers understand each other so effortlessly that their speech must be glossed for the reader, in order to explain the evocative nature of their dialogue. These three chapters reveal romance’s exquisite sensitivity to its characters’ speech, and outline a model of the medieval love relationship that champions a cooperation and dynamism that can only be represented in dialogue.

Advisor: Hult, David F
Guynn, Noah D
Mechanical regulation of cell shape by actomyosin stress fibers

Cell migration is a key process underlying embryogenesis, wound healing, and cancer progression. The actomyosin stress fiber (SF) network enables mechanosensing of the extracellular matrix (ECM) environment by generating forces to probe substrate stiffness, topography, and adhesive properties, which in turn, collectively influence SF organization. Migrating cells actively rearrange three SF subtypes—dorsal SFs, transverse arcs, and ventral SFs (including apical SFs and basal SFs)—to maintain a polarized shape needed for directional movement. There have been several efforts to dissect contributions of specific SF subtypes in generating and maintaining tension, which have produced important new insights into the field’s understanding of SF subtype function. However, they remain indirect measures of SF mechanical properties. Furthermore, many of these studies were conducted on cells cultured on flat, rigid substrates which do not recapitulate many of the salient features of the complex microenvironments found in vivo./nIn this dissertation, we seek to understand how cells regulate tension in their SF network during polarization and migration, and how substrate geometry influences SF organization. Using laser nanosurgery, we systematically sever single SFs belonging to each subtype in order to measure their retraction kinetics. We find that SF subtypes are arranged in a mechanically integrated network and that SF subtypes have distinct mechanical properties that are dependent on intrinsic structure, external connections to other SFs, and formation history. Next, we examine the role of cofilin in remodeling the SF network during polarization, the first step in directed cell migration. We find that cofilin remodels SF tension by facilitating the fusion of thin, weakly contractile SFs into thicker, more contractile structures that break tensional symmetry and enable front-back polarization. Finally, we explore the influence of substrate curvature on SF network organization and mechanics. Apical and basal SFs are oriented perpendicular to one another, and bear different amounts of prestress, suggesting that they each have distinct roles in shaping the cell./nIn summary, this dissertation systematically examines the mechanical contributions of SF subtypes to determining cell shape and establishing tensional asymmetry in the cell. We also examine the influence of substrate topography and adhesive patterns on cell shape and SF tension, which are important in understanding how cells interact with ECMs that vary in topography and adhesion. These findings enhance our understanding of how cells mechanically organize their SF network to build a contractile, integrated network for migration.

Advisor: Kumar, Sanjay
Design and Fabrication of VCSELs for 3D Sensing

Vertical-cavity surface-emitting lasers (VCSELs) are critical components in many optical systems. They already drive the transmission of data in massive datacenters and supercomputers, and they are becoming the state of the art in 3D sensing systems that allow computers to perceive the world more like humans. These systems have important applications in medicine, autonomous vehicles, facial recognition, and gesture detection. VCSELs have shown the promise of improving resolution while decreasing module cost due to their extremely scalable fabrication process./nThe first 3D sensing mechanisms that VCSELs promise to improve are swept-source optical coherence tomography and frequency-modulated continuous-wave LIDAR. These techniques use a wavelength tunable source to probe the distance to reflectors in the beam path. The resolution of these systems is limited by the fractional tuning range of the source. This work presents a method to increase the fractional tuning range of tunable VCSELs by coupling the energy in the cavity out of the gain medium and into the tuning gap. The design is demonstrated experimentally to increase the tuning range by a factor of two over a comparable tunable/nVCSEL./nThe second family of 3D sensing mechanisms demand high-power, high-efficiency VCSEL arrays to illuminate an entire scene to identify gestures and faces. The final chapter of this dissertation describes a novel fabrication method leveraging the oxidation of AlGaAs to form a high-contrast grating (HCG) reflector in a VCSEL array. The process is scaled from a proof of concept, to the first high-efficiency HCG VCSEL, and finally to an array of HCG VCSELs. The introduction of an HCG to the device reduces the fabrication cost and introduces polarization control to the array, creating a platform for new possibilities in 3D sensing.

Advisor: Chang-Hasnain, Constance J
Data-Driven Appointment Scheduling

Advances in electronic medical records and healthcare databases enable researchers to easily acquire and analyze large amounts of data, and to build data-driven models to improve the system performance. Surgical departments, in particular, utilize a variety of expensive resources, so efficient appointment scheduling and sequencing decisions that minimize patient-surgeon waiting time and the surgeon-operating room idle time substantially reduce costs. We aim to improve the way that schedules are generated by incorporating both dynamically updated data sets, and the opinions of surgeons./nOur research focuses on appointment scheduling of stochastic tasks on a single server where the task durations are challenging to estimate. The task types are known prior to the appointment date but the task duration data is initially limited so that the estimates need to be continuously updated. Appointment scheduling involves both sequencing the tasks and setting the start time of those tasks. Our goal is to develop a data driven appointment scheduling algorithm for sequencing and scheduling tasks. Our research is motivated by a project we have completed with University of California, San Francisco (UCSF) on surgical scheduling where the tasks are the surgical procedures and the server is the operating room./nIn Chapter 1 we introduce the appointment scheduling problem with a motivating example of surgical appointment scheduling. We run some simulations to show patient-surgeon waiting time (tardiness) and the surgeon-operating room idle time (earliness) can be reduced by changing the sequence of the procedures and the start times of the procedures. We go over the appointment scheduling literature with various objective functions. We analyze the objective of minimizing expected earliness and tardiness and bound the performance of the commonly used sequencing heuristic based on the standard deviation of procedure duration./nIn Chapter 2 we focus on data-driven appointment scheduling. Without making any distributional assumptions we use the empirical distributions of the procedures while computing the objective function which is the expectation of weighted earliness and tardiness. We study the continuity and the convexity of the objective function and the conditions under which there is an integral optimal solution. We briefly go over the methods to optimize the objective function and also constrain the search space containing the minimizer. We develop sequencing heuristics tailored for this problem. Lastly we talk about data selection algorithms if there are categorical features such as name of the surgeon or surgeon estimates about how long the next procedure might take.

Advisor: Kaminsky, Philip M
Molecular Mechanisms in Signaling by Target of Rapamycin Complex 2 in Saccharomyces cerevisiae

Protein kinases are enzymes that transfer the γ-phosphate of ATP to acceptor residues, most often serine, threonine or tyrosine, in proteins. Phosphorylation by protein kinases are integral to the signaling processes that control virtually all aspects of cellular physiology and phosphorylation is the most abundant post-translational modification in signal transduction networks. Covalent attachment of a phosphate group to a protein can cause a conformational change, introduce a new epitope that enhances or prevents interaction with another protein, increase or decrease the rate of turnover, and/or affect subcellular localization. In these ways, phosphorylation-dependent events can influence cell metabolism, morphology, and differentiation./nTarget of rapamycin (TOR) complex 2 (TORC2) is an evolutionarily conserved multi-subunit protein kinase and indispensable regulator of plasma membrane homeostasis. Genetic studies in yeast have demonstrated that the sole essential downstream target and effector of TORC2 is the protein kinase Ypk1 (and its paralog Ypk2), whose mammalian ortholog is SGK1. In humans, mutations in the TORC2 signaling network have been implicated in inflammatory disorders, metabolic diseases, and multiple cancers./nIn this doctoral dissertation, I describe the studies I undertook to explore novel aspects of TORC2-Ypk1 signaling. Because a Rab5-specific guanine nucleotide exchange factor (GEF), Muk1, was identified in a prior global screen for candidate Ypk1 targets, I investigated the role of Rab5-type GTPases in the TORC2 signaling network. I confirmed first that Muk1 is a substrate of Ypk1 and demonstrated that Ypk1-mediated phosphorylation stimulates Muk1 function in vivo. Second, and strikingly, I found that yeast lacking its two Rab5 GEFs (Muk1 and Vps9), or its three Rab5 paralogs (Vps21/Ypt51, Ypt52 and Ypt53), or overexpressing Msb3 (a Rab5-directed GTPase-activating protein), all exhibited pronounced reduction in TORC2-mediated phosphorylation and activation of Ypk1. Finally, I showed that Vps21 co-immunoprecipitates with TORC2, and furthermore, that purified GTP-bound Vps21 is able to stimulate in vitro the activity of TORC2 immuno-enriched from Rab5-deficient cells. My findings suggest that TORC2-dependent and Ypk1-mediated activation of Muk1 provides a control circuit for positive (self-reinforcing) up-regulation to sustain TORC2-Ypk1 signaling

Advisor: Thorner, Jeremy W
Quantitative Microscopy using Coded Illumination

Quantitative optical microscopy continues to be a powerful tool for biomedical research and the sciences at-large. Building upon centuries of optical theory, computational microscopy leverages large-scale numerical computation to dramatically extend and improve the capabilities of existing optical microscopes through high-speed capture, super-resolution, or opening new application spaces such as quantitative phase imaging. This dissertation describes the theory and reduction to practice of several novel computational microscopy techniques which make use of jointly-designed coded illumination hardware and physics-based reconstruction algorithms. We first introduce label-free quantitative phase imaging using differential phase contrast, and demonstrate a novel single-shot variant using color-multiplexing. Second, we explore coded illumination for high-throughput imaging, and demonstrate a temporal-coding technique which enables significantly higher SNR for high-speed slide scanning and neuropathology applications. For fluorescent imaging, this method can provide up to a 10x improvement in reconstruction SNR compared to conventional high-speed imaging techniques. Next, we explore the design and fabrication of LED illumination devices, including a quasi-dome LED illuminator which enables high-angle illumination for a variety of applications. To address practical calibration concerns for computational microscopy systems, we demonstrate two examples of algorithmic self-calibration. These include aberration recovery using differential phase contrast as well as source calibration for the quasi-dome LED array, using both image-based calibration and an online method based on Fourier ptychography. These works demonstrate the benefits and practical challenges related to computational optical microscopy with coded illumination.

Advisor: Waller, Laura L.
Transport and topology in strongly correlated two-dimensional systems, using techniques from one dimension

Many of the most interesting problems in theoretical condensed matter physics involve the study of two- and three-dimensional materials, but this is in general very difficult. On the other hand, one-dimensional quantum systems are much better understood, with exact solutions possible using techniques like bosonization, and with extremely efficient numerical approaches based on matrix product states. Thus one promising route to studying higher-dimensional systems is the application of techniques developed for one-dimensional systems. In this dissertation I discuss two research projects in which I use this approach./nIn the first study, motivated by intriguing experiments that have shown two-dimensional polymer films to be promising materials for thermoelectric devices, I consider a two-dimensional material consisting of an array of one-dimensional systems. Each is treated as a strongly-interacting Luttinger liquid, and I assume weak (incoherent) coupling between them, an approximation which I refer to as the ``quasi-atomic limit.'' I find integral expressions for the (interchain) transport coefficients, including the electrical and thermal conductivities and the thermopower, and I extract their power law dependencies on temperature. Luttinger liquid physics is manifested in a violation of the Wiedemann-Franz law; the Lorenz number is larger than the Fermi liquid value by a factor between $\gamma^2$ and $\gamma^4$, where $\gamma\geq 1$ is a measure of the electron-electron interaction strength in the system./nIn the second project, motivated by experimental studies that have found signatures of a quantum spin liquid phase in organic crystals whose structure is well described by the two-dimensional triangular lattice, I study the Hubbard model on this lattice at half filling using the infinite-system density matrix renormalization group (iDMRG) method. On infinite cylinders with finite circumference, I identify an intermediate phase between observed metallic behavior at low interaction strength and Mott insulating spin-ordered behavior at strong interactions. Chiral ordering from spontaneous breaking of time-reversal symmetry, a fractionally quantized spin Hall response, and characteristic level statistics in the entanglement spectrum in the intermediate phase provide strong evidence for the existence of a chiral spin liquid in the full two-dimensional limit of the model.

Advisor: Moore, Joel E
Optical Investigations of Intermolecular Electron Dynamics in Low Dimensional Materials

The interaction of electrons with an electromagnetic field is one of the most important phenomena in physics. The electromagnetic interaction is central to the absorption and emission of light by matter and permits interpretation of physical phenomena in our natural world. This dissertation uses light-matter interactions to probe the behavior of electrons in atomically thin materials and to develop new scientific tools for the study of intermolecular dynamics./nIn Part I, we present and demonstrate a set of principles that permit the rational design of two dimensional covalent organic frameworks with optical and electronic properties not present in their constituent counterparts. We develop a novel low bandgap framework that is characterized under broadband optical spectroscopy, X-ray scattering, transmission electron microscopy, atomic force microscopy, and transport. In inorganic/organic van der Waals heterostructures, we report ultrafast electron dynamics not previously observed in two dimensional covalent organic frameworks with consequences that are relevant to a broad range of materials./nIn Part II, we manipulate light-matter interactions in atomically thin materials to develop an optical sensor capable of imaging electric fields generated by intermolecular dynamics. We combine the unique gate-variable optical transitions in graphene with critically-coupled waveguide amplification to convert electrical activity into optical signals while retaining high spatio-temporal resolution. We apply this technique to living systems and noninvasively image signals from and among electrically active cells.

Advisor: Wang, Feng
Biosynthesis and translational control of terminal-alkyne amino acids

Living systems are remarkably efficient in their ability to build complex molecular function, using a relatively small set of chemical functional groups to drive the wide range of life processes. In contrast, synthetic compounds access a much broader scope of structural and reaction diversity to tune desired chemical properties. However, unusual functional groups can be found in Nature. Many pathways for secondary metabolism produce compounds that could be useful for chemical applications if their biosynthesis could be repurposed. Here, we report the discovery and characterization of a unique pathway to produce a terminal alkyne-containing amino acid, β- ethynylserine, by the microbe Streptomyces cattleya through an unexpected reaction sequence that includes radical halogenation and oxidative C-C bond cleavage, followed by a desaturation that proceeds through a putative allene intermediate. We also report progress in porting the bes pathway into heterologous host, particularly E. coli. Furthermore, we present preliminary work on the discovery of a protein who’s function is to prevent translation of β-ethynylserine by acting as a tRNA proofreading enzyme. This pathway, and the auxiliary proteins related to control of translation of non-standard amino acids, offers the potential to genetically encode the de novo production of halo-, alkene-, and alkyne-labeled proteins and peptides from glucose to provide bioorthogonal functionality for downstream applications.

Advisor: Chang, Michelle CY