VictorJuiz/thesis huggingface dataset:
The butterfly effect in solvable quantum many-body systems [electronic resource]

The butterfly effect, as an icon for the chaotic dynamics, refers to the exponential sensitivity on the initial conditions. This phenomenon is common in daily life, e.g. it explains the difficulty of long time weather reports. For physicists, the idea of the chaotic dynamics helps to understand the ergodicity of a classical complex system and therefore is essential for the statistical mechanics and thermodynamics. In the microscopic many-body systems governed by quantum mechanics, the chaotic dynamics is also expected to be generic and ultimately helpful for the understanding of the quantum thermalization. What I will show in this dissertation is that the quantum butterfly effect could also provide precise information about the nontrivial properties of the many-body interacting systems, such as thermal transport and topological properties. I will employ two classes of solvable models: the Sachdev-Ye-Kitaev model in high dimensions and the rational conformal field theories in two dimensions to explicitly present the unexpected connection between the butterfly effect and other aspects of the model.

Keywords: Physics.
Advisor: Qi Xiaoliang primary advisor. Thesis advisor
Shenker Stephen Hart
Zhang Shoucheng advisor. Thesis advisor
Campaign Effects On The Stock Market: The Case Of The 2016 Election

The 2016 presidential election displayed at least one candidate who used strong enough campaign rhetoric about potential economic policy change that may have affected market wide stock market indicators. Trump’s candidacy represented a lot of unknowns. As an unknown candidate with unknown economic policies, it can be expected that increases in his polling numbers – widely covered in the media – will depress the value of the stock market and vice- versa. In the context of the 2016 presidential election, I anticipate that Donald Trump’s use of extreme rhetoric about economic policy and his popularity through the polls may have been associated with immediate effects on market wide economic indicators.

Keywords:  Department of Communication
Stock Market Indicators
Election
Campaigns
2016 presidential elections
Stanford University Department of Communication
Donald Trump 1946-
Thesis
Advisor: Reeves Byron
Capturing dynamic correlation with variational explicitly correlated wavefunctions [electronic resource]

In this dissertation, we describe, implement, and test wavefunctions that describe short-range, so called dynamic correlation effects through the use of explicitly correlated geminal pair functions. We present both a single-configuration explicitly correlated analogue of a Hartree-Fock wavefunction, and a multi- configurational variant, a Geminal-augmented Complete Active Space Self Consistent Field method. These methods are designed to efficiently include dynamic correlation effects during variational optimization of the wavefunction, rather than resorting to a post hoc perturbation description. We test both methods on a number of model systems and show that the geminal-augmented wavefunction is capable of describing short-range correlation effects. In addition, we present a fully exact implementation of the algorithms necessary to evaluate the many-electron integrals that arise in explicitly correlated wavefunctions.

Keywords: Chemistry.
Advisor: Martinez Todd J. (Todd Joseph)
Fayer Michael D. advisor. Thesis advisor
Markland Thomas E.
Cascading behavior in social networks [electronic resource]

Cascades occur in social networks when information and behavior spreads from person to person. However, as these cascades grow through complex macro- and micro-level processes, their future behavior is difficult to predict. In this thesis, we study the mechanisms through which cascades propagate in networks. Specifically, we present a framework for predicting a cascade's future trajectory, and develop methods that combine data mining and crowdsourcing techniques to explain how behavior spreads from individual to individual. First, we examine the growth and recurrence of information cascades on Facebook. In contrast to prior work that argued that such cascades are unpredictable, we show how the size, structure, and recurrence of a cascade can be predicted, even over long periods of time. Second, we study how behavior cascades by looking at how antisocial behavior such as trolling may spread from person to person. While past literature has characterized such behavior as confined to a vocal, antisocial minority, we instead demonstrate that ordinary people, under the right circumstances, can become trolls, and that such behavior can percolate and escalate through a community. Altogether, this research explores a future where systems can better mediate information sharing and interpersonal interaction, and thus promote the development of prosocial communities.

Advisor: Leskovec Jurij primary advisor. Thesis advisor
Bernstein Michael S.
Kleinberg Jon
Causes and consequences of news media content [electronic resource]

The nature of the news media's political influence depends crucially on the type and volume of political information that citizens encounter when they read, listen and watch the news. This dissertation examines the causes and consequences of this political coverage. The first paper introduces a new empirical approach to test two long-standing accounts of media bias in the mainstream press. Studying election predictions offered by several specialized media outlets that receive a prominent place in news coverage of congressional elections, I find evidence of an institutional bias in which media ratings are overly favorable towards the electoral prospects of incumbent politicians relative to their challengers. At the same time, this approach offers no evidence of a partisan bias in which these outlets favor candidates from one political party at the expense of the other. The second paper examines the consequences of the political information environment for the public's reliance on party labels to evaluate politicians. Using a doubly-randomized conjoint experiment and an observational study of voting in congressional elections, I show that greater amounts of information reduce the role of partisanship in candidate choice. These findings challenge competing claims that partisan cues inhibit responsiveness to such a degree that voters fail to use other information or that high-information environments increase voter reliance on partisanship. The third paper explores the consequences of a recent change in the local media environment. Newspapers produce political coverage read by a large number of readers, yet they do so with 30% fewer reporters and editors than a decade ago. This rapid decline is thought to pose a threat to the provision of political news. This paper employs two new sources of data to directly measure changes in newspaper staffing and examine their effect on newspapers' attention to local, state and national politics. I show that declines in staffing lead to less political coverage, an effect that is particularly pronounced for local political news. Given that newspapers serve as the primary source of original reporting on local politics, this suggests staffing declines have broad consequences for the local media environment.

Keywords: Political Science.
Advisor: Iyengar Shanto primary advisor. Thesis advisor
Grimmer Justin advisor. Thesis advisor
Hamilton James
Cell fate control by spatiotemporally regulated signaling pathways [electronic resource]

Cells must coordinate their behaviors to occur at the correct time and place. Asymmetric cell division, which underlies cellular differentiation across the kingdoms of life, presents a major coordination challenge. Cell fate signaling proteins must respond to cell cycle progression cues, interpreting these signals in the context of their subcellular location. We studied how the bacterium Caulobacter crescentus, a model organism for the study of asymmetric division, coordinates cell polarity, differentiation, and DNA replication. Caulobacter couples these processes through spatiotemporal control of the phosphorylation state of a master regulator, CtrA. Beginning with an investigation of the ordered assembly of a G1/S signaling complex that downregulates the level of active CtrA~P, we find that disruptions to the expression level or localization of this G1/S complex creates major cell polarity aberrations. We further investigate how CtrA becomes reactivated by a multi-sensor histidine kinase, CckA, in late S-phase. CckA switches between kinase and phosphatase activity towards CtrA in response to multiple spatially controlled upstream signals. CckA detects these signals, which include its own membrane surface density, the second messenger c-di-GMP, and a pseudokinase, DivL, through distinct sensory PAS domains. Our study of CckA's signal transduction illustrates how multi-sensor kinases enable complex bacterial decision making based on an array of spatially and temporally oscillating inputs.

Keywords: Biochemistry.
Advisor: Shapiro Lucy primary advisor. Thesis advisor
Straight Aaron
Long Sharon R. advisor. Thesis advisor
Spudich James A.
Cell-autonomous mechanisms that suspend PVD dendrite outgrowth during dauer diapause

Development in animals is not merely an intrinsically programmed event. Response to environmental conditions plays a large role in an organism’s development. The nematode species C. elegans develop from egg to adulthood through a life cycle known as reproductive development, but in environments of stress, such as starvation, overcrowding, or high temperatures typically found in nature, the worms will enter a dormant larval stage called dauer diapause. Recent work has shown that during the dauer diapause, dendrite outgrowth of the mechanosensory neuron PVD in C. elegans is suspended. Yet, the molecular mechanisms governing the arrest of the development of this neuron remain unknown. To identify the factors involved in pausing PVD dendrite outgrowth during dauer, we tested whether overexpression of four genes that are required for dendrite outgrowth of the PVD neuron during reproductive development (dma-1, mec-3, mbl-1, and rig-1) could bypass the dauer-induced dendrite growth suspension. Additionally, we conducted a forward genetic screen to isolate mutants that fail to suspend PVD development during dauer. The two methods, though, were unsuccessful in identifying the factors governing this phenomenon. Over-expression of the four genes did not cause complete development of PVD’s dendritic arbor, suggesting these genes, individually, do not control the suspension of PVD’s dendritic outgrowth. Also, a mutant of interest with complete development of dendritic outgrowth was not found in the forward genetic screen. However, a mutant with a peculiar phenotype was identified; the PVD neuron of the worm looks like wild-type in reproductive development, but in dauer, the PVD neuron develops abnormally. The mutant is still being studied to understand which gene is affected, but it seems there are multiple genetic events governing the phenotype.

Keywords:  Department of Biology
dma-1
mec-3
mbl-1
rig-1
PVD neuron
dauer diapause
forward genetic screen
Thesis
Advisor: Shen Kang
McConnell Susan
Richardson Claire
Characterization of NF90 as a transcriptional activator with histone acetyl transferase activity

Eukaryotic gene expression is tightly controlled on multiple levels. Proteins that bind both DNA and RNA are involved in multilevel gene expression by regulating both transcriptional and posttranscriptional processes. Nuclear Factor 90 (NF90) is a DNA- and RNA-binding protein encoded by the Interleukin enhancer-binding factor 3 (Ilf3) gene first cloned based on inducible binding to the Nuclear Factor of Activated T cell (NF-AT) target DNA sequence in the IL-2 promoter. NF90 has been widely studied as a double-stranded RNA-binding protein that participates in stabilization of transcript, splicing, and export of mRNA. The role of NF90 in regulating gene expression as a DNA-binding transcription factor has not been systematically studied. In Jurkat T cells, chromatin immunoprecipitation (ChIP) demonstrated inducible binding of NF90 and NF45 at the IL2 and Pdcd1 promoters in vivo upon T cell activation. In K562 cells, ChIP followed by deep sequencing (ChIP-seq) was used to characterize genome-wide binding patterns of NF90. Proteomic analysis elucidated stimulation-dependent post-translational modifications in Jurkat T cells. NF90 showed a sequence-specific DNA binding activity to a highly-conserved purine-rich motif in its genome-wide binding sites. NF90 colocalizes with histone marks H3K9ac at active promoters and H3K27ac at enhancers, closely associates with core histones in the nucleus, and exhibits a novel histone acetyl transferase activity. Taken together, these results characterize NF90 as a transcriptional activator with histone acetyl transferase activity.

Keywords:  Department of Biology
Biology
NF90
ILF3
histone acetyl transferase
transcription factor
chromatin remodeling
epigenetics
Thesis
Advisor: Kao Peter N.
Simon Michael
Characterizing genetic and environmental regulation of RNA editing and gene expression in Drosophila [electronic resource]

Before translation of proteins takes place in cells, RNA transcripts are expressed and modified to form different isoforms which make up the diverse transcriptome. One such transcriptional modification is A-to-I RNA editing, which transforms the sequence information of RNA and can consequently lead to other changes in protein regulation and function. Gene expression and RNA editing levels can be fine-tuned in response to different environments and stresses, but relatively little is known about how these processes are regulated. In this dissertation, I use two different approaches to examine the regulatory mechanisms of RNA editing and gene expression in the fruit fly Drosophila melanogaster. First, I describe a screen for trans-regulators of RNA editing, in which mutants that share phenotypes with flies lacking RNA editing are tested for altered RNA editing levels. Although no novel trans-regulators were identified, the results from this screen demonstrate that cis-regulation of RNA editing is more widespread than originally thought. Then, I explore how gene expression and RNA editing levels differ in flies from two contrasting microclimates, and illustrate the importance of cis-regulation in guiding these transcriptional differences. For two neighboring recoding RNA editing sites that show the largest editing level changes between the fly populations, I experimentally confirm that a genetic mutation in the adjacent intron contributes to their editing level differences. I also demonstrate that temperature and population genetic differences likely affect editing levels through modulating the RNA structure, and regulate editing levels largely independently of each other. Together, this dissertation provides insights into how environmental factors shape gene expression and RNA editing levels, and the regulatory architecture underlying these transcriptional processes.

Advisor: Li Jin (Billy) primary advisor. Thesis advisor
Clandinin Thomas R. (Thomas Robert)
Lipsick Joseph Steven
Montgomery Stephen
Characterizing Infrared Filters for Large Aperture Millimeter Wave Telescopes

Ground based telescopes operating in the millimeter wave regime are attempting to image the sky with increasing sensitivity and depth by employing larger arrays of cryogenically cooled detectors. However, the increase in aperture is accompanied by a corresponding increase in the infrared (IR) loading. This poses a significant challenge for the cryogenic system. BICEP3 met this challenge by developing laser etching as a fabrication technique for producing large aperture metal-mesh infrared filters. Because metal-mesh filters are crucial to the heat load balance of the cryogenic system, we conducted a systematic investigation into the quality, repeatability of production and improvement in the yield of filters.

Keywords:  Department of Physics
Infrared Filtering
BICEP3
Millimeter Waves
Thesis
Advisor: Kuo Chao-Lin
Church Sarah
Characterizing the interaction between cell identity and cell-cycle regulation in the stomatal lineage of Arabidopsis

Asymmetric cell division is an important process that can link stem cell development to the cell cycle. Arabidopsis stomatal guard cell development, a model for plant stem cell lineages, requires asymmetric divisions and has been well characterized in terms of the distinct developmental stages and the transcription factors involved with each transition. To date, the effects or linkages of these developmental transitions on the cell cycle have not been defined in this system. Further, the existence and effects on the cell cycle of the putative plant DREAM complex, whose homologues regulate the cell cycle in animals, has not yet been demonstrated. In this thesis, I implemented two different methods of visualizing cell cycle stages in Arabidopsis leaves: a method that monitors nucleotide incorporation during DNA synthesis (EdU staining) and the CDT1A reporter line that marks the S and G2 stages of the cell cycle for live cell visualization. The latter method was used to begin to characterize how cell cycle timing is affected by differentiation or by members of the DREAM complex. Here, I present evidence that the critical transcription factors for stomatal development appear beginning in G1 and persist, likely with activity, through G2, as well as evidence that the DREAM complex is active from G1 through G2. To facilitate quantitative measurements of cell behaviors, I developed tutorials for MorphoGraphX, a software program that can segment and measure cell size, shape, and growth over time and that will be essential for continued studies of cell cycle and fate.

Keywords:  Department of Biology
Biology
Cell Biology
Molecular Biology
Developmental Biology
Genetics
Plant Biology
Thesis
Advisor: Bergmann Dominique
Walbot Virginia
Chemical sensing with capacitive micromachined ultrasonic transducers [electronic resource]

There is a wide array of potential applications for chemical sensors that are sensitive, but also small and inexpensive. Such sensors could be used for detection of dangerous chemicals, air quality monitoring, or even health monitoring. Gravimetric chemical sensors based on capacitive micromachined ultrasonic transducers (CMUTs) are a good candidate technology for such sensors, given their high sensitivity and low cost due to batch fabrication. In this work, we demonstrate an electronic nose using CMUT chemical sensors. We show that this electronic nose, in conjunction with machine learning algorithms, is able to distinguish between several chemicals, recognize ammonia in a background of water vapor, and distinguish coffee beans of different origin. We discuss the design and fabrication of the chemical sensor chip, the electronic circuits used to operate it, and efforts to reduce the drift of the sensor.

Keywords: Applied Physics.
Advisor: Fejer Martin M. (Martin Michael) primary advisor. Thesis advisor
Khuri-Yakub Butrus T.
Greenleaf William James advisor. Thesis advisor
Children's literature, the common law, and other disputable arts [electronic resource]

This is a dissertation on children's literature as a source of law. Literature produced for and read by children far precedes the 1744 date generally given for the start of Anglo-American children's literature. Not coincidentally a generation after the novel's rise, what this date actually represents is the beginning of the possibility of a distinct form, created to address the socialization threat posed by mass literacy in a market already crowded by delightfully questionable chapbooks and questionably delightful religious tracts. The extent to which children's literature can fairly be considered a genre is in direct proportion to the perceived distance between childhood and adulthood. When this perception emphasized lack (of literacy, of knowledge, etc.), the texts were skill-based socialization tools of varying styles in a host of competing forms—fairy tales, hybrid chapbooks, adaptations of adult novels—which directly addressed parents with promises to "lay up the laws" in children's hearts. As the perception of difference (innocence, naturalness, etc.) gained momentum as a priority in the nineteenth century, a set of tastes and affinities are attributed to childhood which are tied to certain formal and thematic expectations to which adults could now assume that a children's text would adhere. In terms of legal socialization, then, the much lauded transition from didactic to imaginative work in the mid-nineteenth century, characterized by a general relaxation of overt moralizing, was, rather than an end to didacticism, a displacement at the point of application: from general distribution of juridical pronouncements (religious law, custom, criminal law, etc.) to one of judgment embedded in narrative. Children's literature starts to constitute a distinct genre and achieves some measure of critical success through this process of formal sublimation, one which, while perhaps proving a more effective means of producing consent to law—or rather, a more literary means—does so at the expense of an interpretative monopoly on what law is or should be. Not monopoly, then, but compromise: this is what I found by following form and law, an alternative legal history, neither realistic nor utopic, but a bit of both, a place we tell our children not how to live in this world but how this world could be livable.

Advisor: Moretti Franco
Meyler Bernadette advisor. Thesis advisor
Moya Paula M. L. advisor. Thesis advisor
China enchanted [electronic resource] : transformations of knowledge in the enlightenment world

This study shows that European scholars gave up on China as a rational model for civilization and came to see it instead as an esoteric alternative, through genuine engagement with indigenous Chinese traditions of history and natural philosophy. Toward the end of the Enlightenment, the philosophes began to criticize the civilization of China because it seemed stuck in the past; other savants came to praise it for the very same reason. For those who challenged the emerging view of progress, China still had much to offer. Like gunpowder, printing, and the compass, other Western knowledge might have also had ancient Chinese antecedents: Had the sage-king Yu the Great known the secrets of modern astronomy? Was the theory of animal magnetism prefigured by yin-yang cosmology? French Scholars looked to Beijing to investigate. There, the ex-Jesuit missionary Joseph-Marie Amiot fostered a global conversation between a French statesman, a Swiss Freemason, a Chinese barber, and a Manchu prince. Together, they searched for Atlantis, discovered kung fu, and invented tarot card fortune-telling. In the process, they cemented the idea of China as a land enchanted. Where early-modern missionaries and scholars had once seen a model of Confucian reason, modern sinologists and philosophers instead saw an alternative of Daoist magic, establishing a new intellectual relationship between China and the West.

Keywords: History.
Advisor: Findlen Paula primary advisor. Thesis advisor
Baker Keith
Jami Catherine
Riskin Jessica advisor. Thesis advisor
Sommer Matthew Harvey