VictorJuiz/thesis huggingface dataset:
An analysis of stability of the flux reconstruction formulation with applications to shock capturing [electronic resource]

High-order methods in Computational Fluid Dynamics (CFD) have been growing in popularity due to their promise of increased computational efficiency and fidelity to flow physics. Amongst a plethora of methods proposed over the last few decades, Discontinuous Galerkin (DG) type (Finite Element Methods (FEM)) have drawn great attention due to their attractive accuracy and stability properties, facility for performing arbitrarily high order computations and the capability to handle complex unstructured geometries, among other features. The Flux Reconstruction (FR) approach to high-order methods is a flexible, robust and simple to implement framework that has proven to be a promising alternative to the traditional DG schemes on parallel architectures like Graphical Processing Units (GPUs) since it pairs exceptionally well with explicit time-stepping methods. While high order methods have already successfully displayed significant improvements over low order methods on certain fronts, one of the major reasons limiting their industry-wide adoption is their inferior robustness relative to low order methods. These high order schemes are prone to developing instabilities while solving nonlinear problems and the issue compounds with increasing order, thereby requiring a com- promise between accuracy and stability. Instabilities due to discontinuous solutions or shocks that develop in compressible flows and aliasing instabilties are two of the most important ones. This dissertation is divided into two major parts. In the first part, the stability of the FR framework for solving linear advection and advection-diffusion equations on tensor product elements has been investigated and the approach has been proven to be stable for both problems. In the second part, a robust and simple to implement shock capturing method which can be adopted in any unstructured high order Finite Element (FE)-type method has been developed. The proposed method does not sabotage the accuracy of the solution in smooth regions and shows great promise in our numerical simulations.

Keywords: Aeronautics and Astronautics.
Advisor: Jameson Antony
Alonso Juan José
Lele Sanjiva K. (Sanjiva Keshava)
The anatomy of creative computing [electronic resource] : enabling novices to prototype smart devices

Can we enable anyone to create anything? The physical computing tools of a rising Maker Movement are enabling the next generation of artists, designers, clinicians, and children, to create complex electronic prototypes. However, technical novices often struggle with the circuitry and programming required to make a smart device. Affordable sensors, actuators and novice microcomputer toolkits are the building blocks of the field we refer to as Creative Computing - and here we examine the core properties of toolkits specifically designed to enhance creative problem solving. In this dissertation I explore the question: "How can we support technical novices in crossing the gap between idea and electronic prototype?" In doing so, I document the tradeoffs that influence the usability of an electronics toolkit, demonstrate the ability to systematically measure the prototyping experience with design tools, and illustrate a significant increase in a novice designer's ability and confidence with electronics through a one-hour design exercise. We examine each of these areas through a series of prototyping experiments with novices, and show how toolkits combining (1) modular hardware, (2) hackable software, and (3) accessible low-resolution materials such as paper, can encourage novices to: make more prototypes, generate more novel ideas, and increase creative confidence.

Keywords: Mechanical Engineering.
Advisor: Leifer Larry J. primary advisor. Thesis advisor
Srivastava Sakti primary advisor. Thesis advisor
Blikstein Paulo
Shluzas Lauren
Androgynous glamour [electronic resource] : an examination of gender, politics, and male Dan actors in Jingju from the early 1900s through the 1950s

In the early 20th century, Chinese theatre witnessed the establishment of the Jingju (Beijing Opera, or Peking Opera) as the country's "national drama". It acquired a new dimension that attracted considerable number of people: it was not just a remnant and a memory of the past, but signaled the beginning of the reconstruction at the dawn of a new era and the waves of cultural revival in the modern era. In my dissertation, I will argue that Mei Lanfang (1894--1961), Cheng Yanqiu (1904--1958), and Xun Huisheng (1900--1968), the foremost male dan (female role) actors in the early 20th century, involved in the re-creation of the Jingju in specific ways, offered and modeled new paradigms by which to reformulate the aesthetics of Jingju, and thus, contributed to the development of this form of theatre in the modern era. My project is distinct from others that focus upon the discussions of the material conditions of the theatre, or treatment of the modern intellectuals' contributions to the development of the Chinese theatre in the modern era. I attempt to build a framework to schematize these actors' contributions to the field of Jingju. I also discuss their individual strengths, their approaches to Jingju, and the features of their acting. I propose to describe how these actors affected theatrical discourses. For Mei, the struggle occurred between a lyricized dramatic mode versus a more theatrical one. Cheng crafted new positions within the theatrical world that encompassed aesthetic and political ideologies. Xun's choice of the huadan female roles adopted an inherently critical stance, and constituted the decision to re-examine the female characters that could be categorized as "the sensual.".

Keywords: East Asian Languages and Cultures.
Advisor: Wang Ban
Berman Russell A.
Egan Ronald
Llamas Regina advisor. Thesis advisor
Anybuddy: A kid-programmed conversational toy for social cognitive development

Anybuddy is a learning toy that aims to help kids ages 6-9 practice social skills related to theory of mind by allowing them to turn almost anything in their world into a talking, listening character. By programming the toy to carry a conversation with another person, kids are required to make decisions about what Anybuddy should say, when it should listen, and what it should listen for. Anybuddy consists of a set of separate facial features that can be attached to magnetic objects to create various emotional expressions such as happy, sad, mad, or scared. The logic of Anybuddy’s conversations is programmed by kids using a companion app that utilizes a visual, block-based programming language. Anybuddy was designed to work using automatic speech recognition technology. Usability testing was conducted with a prototype of this design, and through in-home observations. Expected benefits of this learning technology were an increased understanding and competency in developmentally-appropriate social skills, particularly perspective-taking.

Keywords: learning
design
technology
toy
education
anybuddy
jessie renee hopkins
smart toy
theory of mind
social skills
perspective-taking
conversational AI
Thesis
Application and characterization of optogenetic systems based on cryptochrome 2/CIB1 [electronic resource]

Various cellular processes are dependent on the regulation of protein activities. In particular, some cellular processes, including migration, division and differentiation, require sophisticated coordination of protein activities in space and time. Therefore, a method capable of perturbing protein activities with precise spatial and temporal control is indispensable for understanding cellular behaviors. However, conventional means, such as genetic or pharmacological perturbation, are either relatively slow to implement, difficult to design, or spatiotemporally uncontrollable. Approaches using inducible chemical genetic enable the control of protein activities by using chemical inducers to trigger engineered proteins. However, these approaches suffer from irreversibility and cannot achieve spatial control. The emerging area of optogenetic actuators provides opportunities to temporally and spatially regulate protein activities. Several pairs of light-induced dimerization proteins have been developed, including the light-oxygen-voltage domain, phytochrome B and cryptochrome 2 (CRY2). CRY2 and its binding partner CIB1 are the optogenetic dimerizers utilized in my research due to their rapidness, reversibility and no need for exogenous cofactor. In my thesis, I develop the optogenetic strategies to optically manipulate two processes: signaling pathway and organelle activity, both of which are determined by protein activities. The light-induced CRY2/CIB1 interaction is complicated by the light-induced CRY2 homo-oligomerization. Therefore, in this thesis, I also study the dual characteristics of CRY2 homo-oligomerization and hetero-dimerization. This thesis consists of three chapters. In the first chapter, I demonstrate the strategies designed to optically activate the RAF/ERK and AKT/FOXO signaling pathways with temporal control, which can help to dissect and resolve the signaling pathways in a quantitative manner. Next, I construct an optogenetic method that exploits light to manipulate organelle distribution and reshaping with reversibility and subcellular spatial precision. This method will be useful to establish a direct linkage between organelle distribution/shaping and cellular functions. Finally, I characterize the CRY2 homo-oligomerization and its interplay with CRY2/CIB1 hetero-dimerization. The results can serve as a guide to the usage of CRY2/CIB1 system.

Keywords: Chemistry.
Advisor: Cui Bianxiao primary advisor. Thesis advisor
Dai Hongjie
Fayer Michael D. advisor. Thesis advisor
Application of a designer histone platform to elucidate new roles for lysine methylation in chromatin regulation [electronic resource]

Lysine methylation is a signaling mechanism conserved from yeast to humans that is critical for many basic cellular processes. Moreover, these processes have been linked to many human diseases like developmental disorders and cancer. While many proteins related to lysine methylation signaling have been identified and characterized, many components of methyl-lysine signaling are poorly understood and require further mechanistic insight. In this work, we further to our understanding of methyl-lysine signaling by addressing technical and biological queries related to methyltransferase activity and identification and characterization of methyl-lysine binding proteins. In Chapter 2, we perform a systematic characterization of lysine methyltransferases on histone H3, a concentrated center for nuclear signaling, and put forth data highlighting the importance of nucleosomes when characterizing histone-modifying enzymes. In Chapter 3, we identify the PZP domain of AF10 to bind unmodified H3K27 and this binding event is regulated by modification of that residue. In cells, the binding interaction between H3 and AF10 regulates DOT1L and the deposition of H3K79 methylation, which manifests in leukemia cells sensitive to H3K79, suggesting a possible target for pharmaceutical intervention. H3K79 methylation is an important modification thought to be important for transcriptional elongation, however the mechanism linking these processes remains elusive. In Chapter 4, we suggest that the FACT complex may provide this link that can read H3K79 methylation signals. FACT is a histone chaperone complex important for relaxation chromatin ahead of RNA polymerase II to facilitate transcription elongation. Modest efficiency in remodeling H3K79me2 histones coupled with compensation of H3K79 depletion with increased FACT complex provide the strongest experimental links between H3K79 methylation and transcription elongation. Together, we contribute to the field of lysine methylation signaling by characterizing the biochemical and biological properties of writer and reader proteins with special consideration to how recombinant chromatin reagents may influence the results.

Keywords: Biology.
Advisor: Gozani Or Pinchas primary advisor. Thesis advisor
Frydman Judith advisor. Thesis advisor
Morrison Ashby J.
Straight Aaron
Architecture of interphase chromosomes [electronic resource]

How DNA folds within nuclei and chromosomes is a great unanswered question in biology. A technology which employs chemical cross-linking of chromatin followed by restriction digestion, proximity ligation, and high-throughput DNA sequencing (Hi-C) has revealed regions of chromatin more likely to interact with themselves than with their neighbors, known as "topologically associating domains" (TADs), separated by regions of little or no such interaction. TADs regulate gene expression by modulating enhancer-promoter communication, but the physical nature of TADs remains unresolved. I have found that TADs and the regions between them correspond to the bands and interbands of the polytene chromosomes of Drosophila melanogaster. Polytene TADs are conserved with diploid TADs, identifying the polytene band-interband pattern as the principle underlying axial chromosome organization. Based on direct measurements from polytene chromosomes, TADs represent a stable state of chromatin condensation up to 30-fold more condensed than a fully extended, "beads-on-a-string" chromatin fiber. Hi-C at sub-kilobase resolution revealed the location of Drosophila chromatin loops, which commonly reside within TADs and are bound by the polycomb group protein, Polycomb. These loops are associated with gene repression and are located at some of the most important developmentally regulated genes. By combining molecular analysis with direct observation from cytology, the architecture of interphase chromosomes is revealed.

Advisor: Kornberg Roger D.
Weis William I. advisor. Thesis advisor
Wysocka Joanna
Argus [electronic resource] : a 16-pixel millimeter-wave spectrometer

This thesis presents the development and deployment of Argus, a 16-pixel millimeter-wave spectrometer for the 100 m Robert C. Byrd Green Bank Telescope (GBT). Argus enables astronomical imaging at state-of-the-art mapping speeds and high angular resolution over the 76-116 GHz band. Its applications include studies of star formation, comets, astrobiology, and astrochemistry. Argus was installed on the GBT and measured rst light in March 2016. It will be available to the general radio astronomy community beginning in the winter 2016 observing semester. This work has demonstrated a novel scalable approach to building a focal plane array. The Argus array is built in 4-pixel subunits, which are tiled together to form the 16-pixel array. In principle, these subunits could be used as the building blocks of an even larger array. Every part is designed to be compact, mass-producible, and as economical as possible. The core technology is based on miniaturized receiver modules, which integrate low-noise ampli ers, a bandpass lter, and a mixer into a single compact unit that would be amenable to automated assembly. The Argus receiver array achieved low noise performance over a very wide bandwidth, which both enables a number of new scienti c opportunities in the near term while demonstrating the viability of the design concept for future receiver designs.

Keywords: Physics.
Advisor: Church Sarah Elizabeth primary advisor. Thesis advisor
Burchat P. (Patricia)
Kuo Chao-Lin (Physics professor) advisor. Thesis advisor
Arsenic and carbon cycling during hydrologically driven soil redox transitions [electronic resource]

Groundwater arsenic contamination affects the health of millions of people worldwide. Although industrial contamination affects localized aquifers, the vast majority of individuals are exposed to arsenic in drinking water that is geogenic in origin. Throughout Asia, geogenic arsenic originates from weathering rocks of the Himalaya and is transported to depositional environments where it is buried during sediment deposition and delta formation. Arsenic comprises only a minor component of these sediments, about 10 ppm, but even such small amounts of arsenic can lead to groundwater concentrations orders of magnitude higher than the World Health Organization drinking water standard of 10 ppb. Once deposited and buried, sediments no longer in contact with the atmosphere are quickly depleted of oxygen, and in the absence of oxygen, microbes utilize alternative electron acceptors such as Mn(IV), Fe(III), As(V), and sulfate to oxidize carbon to gain energy. The result of these reactions is the dissolution of insoluble Fe(III) minerals that are largely responsible for trapping arsenic in the solid phase. The limiting component of these reactions, and thus the key to predicting arsenic concentrations in groundwater, is the supply and fate of microbially reactive organic carbon needed to sustain reducing conditions conducive to arsenic solubilization. In essence, the fate of organic carbon is the determinant of dissolved arsenic concentrations within the groundwater systems (including surface-subsurface exchange) of Asia. In this thesis, I examine how surface and groundwater hydrology control the conditions dictating microbial metabolism of organic carbon and the ensuing impacts on dissolved arsenic concentrations. I use the Yangtze River Basin to illustrate changes in groundwater chemistry arising from surface-groundwater exchange that control arsenic concentrations, and the Mekong Delta of Cambodia to demonstrate how variation in surface hydrology leads to different carbon fates and thus dissolved concentrations of arsenic.

Keywords: Environmental Earth System Science.
Advisor: Fendorf Scott primary advisor. Thesis advisor
Francis Christopher advisor. Thesis advisor
Welander Paula advisor. Thesis advisor
Art-directed muscle simulation for high-end facial animation [electronic resource]

This dissertation presents a system for generating high-end facial animation using muscle simulation. While the rendering of still faces has become quite realistic, facial animation techniques still suffer from a variety of artifacts. The traditional blendshape approach for animating faces often suffers from visual artifacts and requires the time-consuming process of sculpting high-quality facial shapes for a variety of expressions. Alternatively, one could build an anatomically accurate face simulation model and actuate facial muscles to deform the flesh and skin. However, the results are often of lower quality compared to those obtained from other production facial animation techniques. This dissertation addresses these issues by describing an algorithm to automatically build anatomical face simulation models as well as a new framework for the simulation of these models that significantly improves the quality of the results allowing for the immediate mainstream use of anatomical face simulation models in a high-end production quality pipeline.

Advisor: Fedkiw Ronald P.
Bhat Kiran
Hanrahan P. M. (Patrick Matthew) advisor. Thesis advisor
Artist under technocracy [electronic resource] : Gyorgy Kepes and the Cold War avant-garde

This dissertation explores the fraught relationship between art and science during the Cold War through the work of artist, designer, and visual theorist Gyorgy Kepes (1906-2001). Faced with a crisis of confidence in the contemporary relevance of the arts, Kepes cultivated collaborations with the sciences at Chicago's New Bauhaus and especially at the Massachusetts Institute of Technology (MIT), where he taught from 1946 until his retirement in 1974. Kepes evocatively termed his interdisciplinary mission "interthinking" and "interseeing." This study examines the aesthetics and politics of these powerful, and still timely, ideas. It asks: Can the "two cultures"—art and science—actually work together for a common purpose? Or are they fundamentally incompatible, condemned to mutual skepticism of their respective motivations and methodologies? What is the purpose of art in a world dominated by science and technology? Scholars have previously described Kepes's ambitions as a reactionary glorification of the imagery and ideology of science. This study does not ignore the regressive associations of Kepes's work, but it also considers its progressive potential and provides a more nuanced, and conflicted, account of Kepes's contradictory practice. Using new archival evidence, this dissertation puts forth two major arguments. First, it demonstrates how Kepes developed a hitherto unrecognized paradigm for aesthetic practice in a scientific context: the "artist under technocracy." This figure operated within rather than against a scientific institution; seeking refuge, he retreated from the art studio to the research laboratory. Second, it situates Kepes as the major artistic figure within a startling constellation of experts engaged in sophisticated war and weapons research. While many artists renounced this technocratic culture—many also encouraged Kepes to do so—Kepes instead chose to remain part of it. He attempted to shift and shape this technocratic culture from a unique position under it. This study tracks these themes across four chronological chapters and examines Kepes's study of camouflage during World War II; his development of visual design at MIT in the 1950s; his work in the 1960s on an unfinished and unpublished magnum opus he called "The Light Book"; and the Center for Advanced Visual Studies that he founded at MIT in 1967. "Artist under Technocracy" provides a genealogy for interdisciplinary phenomena that are commonplace in both the academy and the art world today, such as the study of visual culture and the use of new media.

Keywords: Art and Art History.
Advisor: Lee Pamela M. primary advisor. Thesis advisor
Nemerov Alexander advisor. Thesis advisor
Troy Nancy J. advisor. Thesis advisor
Turner Fred advisor. Thesis advisor
The artwork of the people [electronic resource] : a history of the Gesamtkunstwerk from Richard Wagner to Kim Jong IL

It is well known that the Democratic People's Republic of Korea is no stranger to mass spectacle. Less widely known, however, is that Kim Jong Il is credited with the authorship of several aesthetic treatises on the principles of North Korean music and drama. Somewhat surprisingly, these principles accord remarkably with many of those of the Wagnerian Gesamtkunstwerk, even though Wagner's works, whether prose or musical, are virtually unknown in the DPRK. The prospect of direct influence is thus minimal. My dissertation explores these unlikely parallels by tracing the evolution and development of the Gesamtkunstwerk idea from Wagner's Germany to Stalin's Soviet Union, Mao's China, and finally Kim Jong Il's DPRK. I argue that Wagner's ideas resonate at least as strongly with the political and artistic aims of these states as they do with those of the West, as evinced by the flowering of the total work of art across Eurasia that took place in the twentieth century.

Keywords: Music.
Advisor: Grey Thomas S.
Schultz Anna C.
Zur Dafna advisor. Thesis advisor