VictorJuiz/thesis huggingface dataset:
Absorbing Boundary Conditions for Scalar and Elastic Waves in the Time-Domain

Absorbing boundary conditions are a requisite element of many computational wave prop-/nagation problems. With our main motivation being the anchor loss simulations of Micro-/nelectromechanical Systems (MEMS) in three dimensions, efficient time-domain absorbing/nboundary conditions which do work well for elastodynamics are in demand. In this work/nwe investigate three classes of absorbing boundary conditions which we believe are promis-/ning, viz., perfectly matched layers (PMLs), perfectly matched discrete layers (PMDLs), and/nhigh-order absorbing boundary conditions (HOABCs). We first devise a PML formulation on/nspherical domains which is particularly suited for the simulation of a large class of MEMS-/nresonator systems. What distinguishes our original PML formulation from most existing/nPML formulations is that it works with standard numerical solvers such as discontinuous/nGalerkin methods on unstructured meshes and that it allows for a natural application of/nNeumann boundary conditions on traction-free surfaces. It is also of significant impor-/ntance in large three-dimensional problems that our formulation has fewer number of degrees/nof freedom than any existing PML formulations. We demonstrate the applicability of our/nspherical PML formulation to large problems via a simulation of a three-dimensional double-/ndisk resonator in the time-domain using a discontinuous Galerkin method and an explicit/nfourth-order Runge-Kutta method. PMDL methods and HOABC methods are alternatives/nto PML methods, which in the context of the scalar wave equation surpass PML methods in/ntheir overall behavior. Unfortunately, their mathematical properties are not as well under-/nstood in the context of elastodynamics and, at least in a certain setting, they are known to/nresult in unstable systems. Due to its involved nature, we focus in this work on the analysis/nof PMDLs/HOABCs for the scalar wave equation and prove several useful identities which/nwill also be useful in the analysis of PMDLs/HOABCs for elastodynamics.

Advisor: Govindjee, Sanjay
The Effect of Ferric Chloride on Charge Injection into Polyethylene

DC charge injection from aqueous electrolytes into low density polyethylene was investigated. Among the electrolytes surveyed, it was found that much higher current densities were recorded when solutions containing both ferric ions and chloride ions were electrochemically oxidized at the polyethylene interface. It was found that exposure to ferric chloride solutions both with and without applied voltage rendered the polyethylene susceptible to charge injection from other solutions that did not contain ferric and chloride ions. Characterization with electrochemical impedance spectroscopy of polyethylene after the application of voltage in the presence of ferric chloride electrolytes did not reveal significant changes, but oxidation products on the exposed surface of polyethylene were detected by both fluorescence spectroscopy and X-ray photoelectron spectroscopy. The effect of oxidation of the surface of polyethylene on charge injection is investigated./nA mechanism of the action of the ferric chloride solutions is proposed by which complexes of ferric ions and chloride ions catalyze the oxidation of a component in the electrolyte. The electron produced by this oxidation reaction is injected into a surface state in the polyethylene. The identity of the complex in ferric chloride solutions responsible for this catalytic behavior is believed to be FeCl4-. The presence of atmospheric oxygen in the electrolyte is thought to be necessary for the production of the oxidation groups on the surface of polyethylene that lead to enhanced charge injection with other electrolytes.

Advisor: Devine, Thomas M
Dispersion and Tidal Dynamics of Channel-Shoal Estuaries

Estuaries, and the varied ecosystems they support, are affected by human action in many ways. One of the fundamental environmental questions pertaining to estuaries is how material is mixed into ambient waters and transported within and beyond the estuary. Characterizing transport and mixing is essential for tackling local environmental questions, such as gauging the water-quality impacts of a wastewater outfall, or how dredging may alter estuarine circulation. In many estuaries the dominant physical dispersion mechanism is shear dispersion. A fundamental and idealized approach to the scalar transport problem is undertaken, in which canonical shear dispersion regimes are augmented with a new, intermediate regime. This mode of shear dispersion, in which the longitudinal variance of the plume increase with the square of time, is likely to occur in channel-shoal basins where bathymetric transitions can create sheared velocity profiles. A key tool in the engineer's arsenal for pursuing studies of scalar transport is the numerical model, but care must be taken to separate physical mixing effects from numerical artifacts. Unstructured models are particularly well-suited to estuarine problems as the grid can be adapted to complex local topography, but the numerical errors of these models can be difficult to characterize with standard methods. An in-depth error analysis reveals a strong dependence of numerical diffusion on the orientation of the grid relative to the flow. Flexible grid generation methods allow for optimizing the grid in light of this dependence, and can decrease across-flow numerical diffusion by a factor of two./nThe most far-reaching impact of our actions, though, must certainly be global climate change. A period of rising sea level is being ushered in by climate change, and the final research-oriented chapter seeks to further our understanding of how rising sea levels will affect basin-scale tidal dynamics. Numerical and analytic approaches show that as basins get deeper tidal amplification becomes more effective and tidal range increases. The crux of the analysis, though, is the inclusion of inundation within these scenarios. Inundated areas dissipate incident tidal energy, countering the added amplification due to basins becoming deeper. The net effect, in the case of San Francisco Bay, is that tidal amplification under sea level rise actually decreases, such that a particular rise in mean higher high water in the/ncoastal ocean is predicted to raise mean higher high water within the bay by a lesser amount.

Advisor: Stacey, Mark T
The Borders of Friendship: Transnational Travel and Tourism in the East Bloc, 1972-1989

The "borders of friendship" was an open border travel project between Czechoslovakia, East Germany, and Poland starting in 1972. The project allowed ordinary citizens to cross borders with a police-issued personal identification card, and citizens of member countries were initially allowed to exchange unlimited amounts of foreign currency. In this episode of liberalized travel - still largely unknown in the West - the number of border-crossings between member states grew from the tens of thousands to the tens of millions within a very brief period./nThis dissertation analyses the political, economic, social and cultural effects of this open border policy. It first clarifies what motivated authorities in Poland, East Germany, and Czechoslovakia to promote unorganized foreign tourism in the 1970s and 1980s. Then, it explores how authorities encouraged citizens to become tourists. Governments wanted the "borders of friendship" to be successful, but they were unsure how to define success. Each government had different understandings about what the project was supposed to entail. Whatever the case, officials worked to ensure that their population reaped the greatest rewards from the open border./nFor ordinary citizens, the "borders of friendship" were popular, but were fraught with problems. They liked being able to go abroad, but felt uneasy about foreigners entering their own lands, often plagued by shortages. Additionally, border guards and custom officials harassed people going abroad. Furthermore, people had not forgotten unpleasant chapters of World War II, including forced population movements and genocide. Finally, even if people gained a greater sense of "freedom" through open borders, few forgot the looming presence of the totalitarian state./nYet the open border project (like the travel it was meant to encourage) was not organized by the state. Contrary to commonplace views of the East bloc, officials did not act in unison, but rather struggled unsuccessfully to control undesirable travel and to gain reliable information to disseminate to socialist neighbors. Additionally complicating matters was the fact that everyone had different understandings as to what the open border project was meant to entail. Nevertheless, even if locals were chagrinned by shortages in their supermarkets, the open border project provided everyday individuals with a new social environment. By 1989, travel had become engrained in the habitus not only of citizens in the West, but of East Central Europe, as well./nIn sum, I paint a picture of late state socialism which, on the one hand, alters our commonplace perceptions of life behind the "Iron Curtain," but on the other, which also confirms views of governments hyper-sensitive to change.

Advisor: Connelly, John
Ultrastructural Characterization of Cellular Interactions Within Resting, Developing and Tumorigenic Breast Epithelium

Epithelial to mesenchymal transition (EMT) and collective cell migration events are of interest for understanding cancer progression and metastasis. The use of in vitro cell lines to model these processes are widely used and help to shed light upon the mechanisms that lead to tumorigenesis. Here we use two such models: the human mammary epithelial cell line HMT-3522 and ex vivo mouse mammary primary culture epithelial organoids. The HMT-3522 cell line provides an encapsulated system to study cancer progression, however detailed ultrastructural analyses of this cell line are lacking. To study collective cell migration we used the murine ex vivo epithelial "organoid" system, which upon growth factor stimulation undergoes branching morphogenesis. Growth of these systems in 3D cell culture is an important component in understanding the highly dynamic and complex processes of EMT and collective cell migration. High resolution imaging via transmission electron microscopy and three dimensional scanning electron microscopy provide a way to discern ultrastructural features of both collective cell migration and EMT./nElectron microscopy imaging of the HMT-3522 S1 cell line, grown in 3D to form acini, demonstrated an abundance of membrane protrusions at all interior lateral and apical surfaces. Furthermore, these acinar structures were determined to have a semi-polarized state as defined by the appearance of a basement membrane, but lack all hallmarks of apical polarization. Three dimensional imaging of the membrane protrusions revealed they have a variety of lengths and an interdigitated nature. Determining this semi-polarized state to be more representative of a transitive tissue state, we sought to image the transient terminal end bud (TEB) of organoids undergoing branching morphogenesis. Ultrastructural analysis of in vivo murine mammary gland and ex vivo un-stimulated organoids revealed nearly identical tissue organization, with typical apico-basal polarity and almost no intercellular membrane protrusions. However, data of the stimulated organoids and specifically the TEB revealed a semi-polarized state of the cells very similar to the HMT-3522 S1 acini, with prolific membrane protrusions. Hypothesizing these membrane protrusions were aiding in normal collective cell migration, we investigated whether disruption of actin polymerization via drug treatments within the TEB would recapitulate the ultrastructure of the tumorigenic cell line HMT-3522 T4-2. RhoA kinase inhibition lead to a remarkably similar tissue and cellular morphology between the two cell types.

Advisor: Gray, Joe
Liu, Fenyong
Romantic Etymology and Language Ecology

This dissertation brings to light an etymological poetics in European and American Romanticism, through natural figures of temporal process that changed language's shape. I argue that the supposed "primitivism" of theories that root language in nature can often be better understood as efforts to model a simultaneous solidity and liquidity in language's forms, using metaphors borrowed from natural history. These theories react against arbitrary or conventional Lockean "signs" and the rational agents who invent them, while at the same time avoiding the stability of traditional "naturalisms," such as Cratylic or Adamic myths of naming. By demonstrating the ethical insufficiency of words alienated from their disorderly contexts, the practice of "Romantic etymology" reconstructs not derivations of individual words, but linguistic philosophy itself.

Advisor: Francois, Anne-Lise
Cell Wall- and Glycolipid-related Functions of Arabidopsis Glycosyltransferase Family Eight Proteins

Glycosyltransferases catalyze the transfer of sugars from activated phosphate sugar substrates to various acceptor molecules ranging from primary metabolites to glycolipids to plant cell walls. The model plant Arabidopsis encodes about 500 glycosyltransferase proteins. Forty-one of these are members of Glycosyltransferase Family 8. These enzymes are thought to function in synthesis of diverse compounds including the disaccharide galactinol, and the cell wall polymer pectin, and the energy storage polysaccharide starch. This thesis will describe evidence that allowed us to assign additional functions of members of this family: five of these enzymes synthesize the cell wall polymer glucuronoxylan, while one synthesizes glycosyl inositol phosphoryl-ceramide sphingolipids./nThe eight Plant Glycogenin-like Starch Initiation Proteins (PGSIPs) were named based on their homology to glycogenin, a protein in fungi and animals that initiates glycogen synthesis by glucosylating itself. The PGSIP proteins were proposed to initiate starch synthesis in a similar manner. However, two of these proteins, PGSIP1 and PGSIP3, are highly coexpressed with glucuronoxylan biosynthetic proteins. Mutations in PGSIP1 cause a decrease in cell wall glucuronoxylan content and microsomal xylan:glucuronosyltransferase activity, leading to the re-annotation of five of the PGSIP proteins as Glucuronic Acid Substitution of Xylan (GUX). Heterologously expressed and purified GUX1, GUX2, and GUX4 show xylan glucuronosyltransferase activity in vitro. These proteins transferred glucuronic acid to a xylooligomer acceptor with different patterns, showing that these related proteins have subtle differences in specificity./nAnother protein, PGSIP6, is related to both the GUX proteins and the galactinol synthase (GolS) proteins, which transfer galactose onto the acceptor inositol. The phylogenetic placement of PGSIP6 between the GUX and GolS proteins led us to suspect that this enzyme catalyzes the transfer of glucuronic acid to the inositol moiety of glycosyl inositol phosphorylceramides, a class of glycosphingolipids that are abundant in plant plasma membranes. Expression of PGSIP6 in yeast led to production of glucuronic acid linked to inositol phosphorylceramide. Overexpressing PGSIP6 in Nicotiana benthamiana plants led to an increase in inositol phosphorylceramide glucuronosyltransferase activity, while silencing expression of PGSIP6 led to a decrease in activity. PGSIP6 has now been renamed Inositol Phosphorylceramide Glucuronosyltransferase 1 (IPGT1).

Advisor: Scheller, Henrik V
Pauly, Markus
Merging Horizons: Authority, Hermeneutics, and the Zuo Tradition from Western Han to Western Jin (2nd c. BCE -3rd c. CE)

This dissertation examines the central forms of exegetical authority in early to early medieval China, focusing on the reception history of the Zuo Tradition from Western Han to Western Jin (2nd c. BCE-3rd c. CE). Most modern scholarly works treat the Zuo Tradition as a historical narrative of great literary value about China's Spring and Autumn period (722-468 BCE). My research, however, studies the value and status of this text as an exegetical tradition from the perspective of classicists spanning five centuries. These early scholars on the Zuo Tradition measured its worth according to how well it preserved and explicated the visions of Confucius as lodged in the wording of Annals the Classic. Conceptions about the Zuo Tradition evolved through a series of debates and arguments in expository letters, memorials, and essays, as well as commentaries on the Annals and Zuo Tradition./nDuring the Western Han (206 BCE-9 CE), the Shiji advanced the conception of the Zuo Tradition as a corrective to the divergent interpretations of the Annals. In late Western Han, Liu Xin (46 BCE-23 CE) vied to establish the Zuo Tradition on equal footing with officially sponsored exegetical traditions. But during early Eastern Han (25-220 CE), the Fan Sheng (fl. 28 CE) versus Chen Yuan (fl. 28 CE) debate showed that doubts remained about the authority of the text as an interpretation of Confucius' messages. Implicitly responding to such doubts, Ban Gu's (32-92) writings elaborated on previous accounts about the authorship, transmission, and official precedence of the Zuo Tradition. During the mid-Eastern Han, Jia Kui (30-101) represented the Zuo Tradition as a source of legitimization for the imperial house, while other scholars added to the myths about the Zuo Tradition. The Western Jin (265-317) scholar Du Yu (222-284) worked to further shore up the text's authority by both redefining conceptions about the Annals and privileging the Zuo Tradition as an exclusive system of interpretation of the Classic./nIn the period under study, successive generations of Zuo Tradition scholars made steps to secure its status in a range of ways, all of them aiming to strengthen the text's relationship to the Classic. These incremental steps enabled the Zuo Tradition to attain definitive authority in the early Tang (7th c. CE), allowing us to observe a process fraught with conflicting ideas about the text. Thus the study of this historical process helps to merge the intellectual horizons of modern scholars with those of classicists.

Advisor: Ashmore, Robert
The Role of Spontaneous Activity in the Development of Retinal Direction Selectivity

ABSTRACT/nThe Role of Spontaneous Activity in the Development of Retinal Direction Selectivity/nBy/nAaron Michael Hamby/nDoctor of Philosophy in Molecular & Cell Biology/nUniversity of California, Berkeley/nProfessor Marla B. Feller, Chair/nOne of the most fascinating and distinctive features of the nervous system is that a vast number of neuronal cell-types arise from a limited number of precursors to assume a multitude of unique morphological and functional units throughout the brain. Furthermore, this mass of unique cell-types wire together with exquisite precision to form the neural circuits that do much of the work of the mature nervous system. How these highly specific and well-ordered assemblies of neurons achieve their ultimate structure and functional state is therefore one of the most important and challenging questions in modern neurobiology./nThe direction selective circuit of the mammalian retina serves as a canonical example of how heterologous cell-types can be arranged in the nervous system to perform complex operations on sensory or synaptic input and transform noisy or mixed signals into specific channels that carry information about the outside world or internal states. How the specific synaptic connections underlying direction selectivity are specified, or how elements of the circuit acquire their unique identities is unclear. Both evoked and spontaneously generated neural activity have been well-documented to shape the assembly of neural circuits in diverse parts of the nervous system. Here, using a combination of multi-electrode array recordings, patch-clamp electrophysiology and anatomical and immunohistochemical techniques we test for a role of spontaneous activity in the development of retinal direction selectivity in mouse./nBy developing transgenic mouse lines to identify direction selective ganglion cells for targeted investigation we identify a critical period of inhibitory synapse development crucial to the direction selective responses of these cells that occurs over the second post-natal week, a period dominated by glutamatergic retinal waves. Through the use of pharmacological and genetic manipulations to alter or block these retinal activity patterns we show that manipulations sufficient to disrupt the activity-dependent process of eye-specific segregation have no effect on the emergence of robust direction selective responses, indistinguishable from age-matched wild type controls. These results indicate that spontaneous activity does not play a critical role in the development of the direction selective circuit in retina.

Advisor: Feller, Marla B
Three Essays on Network Analysis and Patent Citation Networks

Patent statistics provide insight into a range of economic phenomena in the economics of innovation. Since the earliest research using patent data, it was recognized that patents are highly heterogeneous with a minority of patents having much greater impact and value than others. Citation counts are a key measurement of patents, observable directly from patent bibliographic data, which carries information about patent characteristics. But patent citations form a complex network that carries more information about patents than the number of a patent's immediate neighbors./nThis dissertation explores network measures that exploit this structure to extract more information about patents. The first chapter of this dissertation is addressed to network centrality and the measurement of patent value. The centrality of a patent is negatively related, after controls for citation counts, to public company market value. This establishes that centrality measurements carry information about patent attributes beyond citation counts, and suggests a clear market saturation phenomenon that may drive the result./nThe next chapter considers whether patent centrality measurements can detect probable holdup in the economic space of patents. Patent pools associated with technical standards, such as the MPEG-2 video compression method, can relate to inventions subject to many competing rights. Centrality measurements are lower for patents that are in the patent pool, suggesting a line of research into the measurement of patent complementarity and substitute relationships./nThe remaining chapter concerns technology identification from patent citations. Classifying patents by technology is a common necessity in patent empirics, and existing approaches using administrative classification suffer certain inevitable limitations due to the nature of the classification system. Community detection algorithms can use citations to break patents into natural groups. An empirical analysis shows that the communities thus produced contain more information than administrative classifications and can detect underlying technological changes before the classification system does.

Advisor: Hall, Bronwyn H.