VictorJuiz/thesis huggingface dataset:
Twisted chimera states and multi-core spiral chimera states on a two-dimension torus

This thesis studies systems of nonlocal phase-coupled oscillators. Various types of solutions have been discovered and analyzed with a combination of analytical and numerical methods. The work is motivated by recent interest in chimera states, in which domains of coherent and incoherent oscillators coexist. A major part focuses on the model/nequation/n\begin{equation}/n\frac{\partial \theta(x,t)}{\partial t}=\omega -\int G(x-y)\sin[\theta(x,t)-\theta(y,t)+\alpha]\,dy, \label{eq:abstract_phase_eq}/n\end{equation}/nand its two-dimensional generalization./nIn one-dimensional systems, the cases where $\omega$ is either a constant or space-dependent are investigated. When $\omega$ is a constant, we propose a class of coupling functions in which chimera states develop from random initial conditions. Several classes of chimera states have been found: (a) stationary multi-cluster states with evenly distributed coherent clusters, (b) stationary multi-cluster states with unevenly distributed clusters, and (c) a single cluster state traveling with a constant speed across the system. Traveling chimera states are also identified. A self-consistent continuum description of these states is provided and their stability properties analyzed through a combination of linear stability analysis and numerical simulation. When $\omega$ is space-dependent, two types of spatial inhomogeneity, localized and spatially periodic, are considered and their effects on the existence and properties of multi-cluster and traveling chimera states are explored. The inhomogeneity is found to break up splay states, to pin the chimera states to specific locations, and to trap traveling chimeras. Many of these states can be studied by constructing an evolution equation for a complex order parameter. Solutions of this equation are in good agreement with the results of numerical simulations./nThe above mentioned solutions have counterparts in two-dimensional systems. However, some of these lose stability in two dimensions and hence cannot be obtained from numerical simulation with random initial conditions. In addition, some solutions which are unique in two dimensions have been found: (a) twisted chimera states with phase that varies uniformly across the coherent domain, and (b) multi-core spiral wave chimera states with evenly distributed phase-randomized cores. Similar stability analysis as for one-dimensional systems is provided.

Advisor: Knobloch, Edgar
Shaping Issues: News Media Framing of Proof of Citizenship Requirements to Register to Vote

Voter eligibility in nearly every jurisdiction in the United States is limited to US citizens age 18 or over. In 1993, federal law established that citizenship and age eligibility are “proven” by an applicant swearing under penalty of perjury that she is citizen age 18 or over. In 2004, Arizona voters approved an initiative requiring documentary proof of citizenship in order to register. Four other states passed similar laws and an additional five states instituted administrative procedures to purge suspected non-citizens from their voter rolls. There is very little evidence of non-citizens voting, and in most of the few cases uncovered, non-citizens without intent to commit fraud. In addition, there is evidence that the laws in Arizona and Kansas prevented more than 50,000 people from registering to vote because their applications lacked proof of citizenship, and that administrative efforts to remove registered non-citizens mistakenly identified US citizens for removal. Nevertheless, the few public opinion polls available show public support for proof of citizenship requirements is high./nThis dissertation uses a content analysis of 181 news stories about non-citizen voting or proof of citizenship requirements to identify media frames used in news coverage of these issues. It finds that media coverage about non-citizen voting and proof of citizenship increased substantially after 2008 even though there was no increase in cases of non-citizen voting; this helped to raise visibility of the “problem.” It identifies seven frames in support of proof of citizenship and seven frames in opposition and finds that news stories analyzed were more likely to use supporting frames than opposing frames. In addition, it finds that most stories analyzed employed a “he said/she said” style of reported consisting of repeating truth-claims from advocates for and against proof of citizenship. This style allowed political elites to present their partisan frames directly to the public, usually without interrogation into the factual basis of those claims. Moreover, reporting style had a significant impact on frames presented, with stories that used a “fact-checking” style far more likely to present frames that proof of citizenship was not necessary and would disenfranchise citizens. Finally, the analysis of two examples from the stories of “valence framing” – different but logically equivalent presentations of the same information – demonstrate how media frames can influence public perception.

Advisor: Luker, Kristin
One and Two Locus Likelihoods Under Complex Demography

The coalescent is a random process that describes the genealogy relating a sample of individuals, and provides a probability model that can be used for likelihood-based inference on genetics data. For example, coalescent models may include recombination, natural selection, population size crashes and growth, and migrations, and thus can be used to learn the strength of these biological and demographic forces. Unfortunately, computing the likelihood of data remains a challenging problem in many of these coalescent models./nIn this dissertation, I develop new equations and algorithms for computing coalescent likelihoods at one or two loci, and apply them to inference problems in a composite likelihood framework. I begin by developing an algorithm for the one-locus case, computing the site frequency spectrum (the distribution of mutant allele counts) under complex demographic histories with population size changes (including exponential growth), population splits, population mergers, and admixture events. This method improves on the runtime and numerical stability of previous approaches, and can successfully infer demographic histories that would otherwise be too computationally challenging to consider. I then consider the two- locus case, and derive a formula for the likelihood at a pair of sites under a variable population size history; this formula scales to tens of individuals. In addition to this exact formula, I also develop a highly efficient importance sampler to compute the same likelihood. I apply these results to the problem of inferring recombination rates under variable population size.

Advisor: Song, Yun S.
Engineered Biosynthesis of Fluorinated Polyketides

Natural products use exquisite structural complexity to tailor a limited repertoire of functional groups for different molecular functions. These molecules have been adopted or adapted by humans to create a large fraction of current therapeutics. However, those adaptations have not always been able to combine the chemical diversity possible for totally synthetic compounds with the many advantages of biosynthesis. Extremely rare in nature but ubiquitous in synthetic pharmaceuticals, fluorine is a unique tool for molecular design, and an excellent candidate for expanding biosynthetic diversity. This dissertation describes our work to enable efficient fluorine incorporation into complex biosynthetic pathways, both in vitro and in the context of a whole organism, and our progress in enabling fluorinated polyketide biosynthesis. We hope to set the stage for a dramatic expansion in polyketide structural diversity via engineered biosynthesis, using a design element that could improve bioactive properties and furnish new therapeutics.

Advisor: Chang, Michelle C Y
The Ricci Flow on Riemannian Groupoids

We study the Ricci flow on Riemannian groupoids. We assume that these groupoids are closed and that the space of orbits is compact and connected. We derive maximum principles for groupoids and give some applications for immortal Ricci flow solutions on closed manifolds. We prove the short time existence and uniqueness of the Ricci flow on groupoids. We also define a F-functional and derive the corresponding results for steady breathers on these groupoids.

Advisor: Lott, John W
Learning Through the Use of Instructional Materials: Secondary Mathematics Teachers’ Enactment of Formative Assessment Lessons

This dissertation is an exploratory study that investigates what and how teachers learn from use of instructional materials. Over the course of one school year, eight secondary mathematics teachers in two urban schools interspersed their usual instruction with “formative assessment lessons” (FALs), based on lessons and lesson guides designed to allow teachers to use student thinking to inform instructional decision-making. The focus of the study was on understanding how the teachers interpreted the goals and uses of these materials for their own and their students’ learning and how the materials supported teachers’ learning about formative assessment./nTeachers were expected to enact five FALs, which they selected from the Mathematics Assessment Project web site (map.mathshell.org) to place in curriculum units in accordance with their instructional goals. The lessons were planned and enacted without formal professional development. However, five collaboration meetings allowed teachers time to plan with colleagues and reflect on their experiences. Teacher surveys, classroom observations, and classroom artifacts were analyzed in order to examine the placement and enactment of the lessons as well as the influence of enacting the lessons on teachers’ classroom practices and use of formative assessment. The teachers’ choices in selecting, placing, planning, and implementing the lessons significantly limited their potential to support teacher learning. However, analyses of student explanations and the teachers’ interactions with small groups of students provide evidence of changes in classroom practices that allowed instruction to be better informed by student thinking./nTwo case studies detail how teachers’ knowledge, goals, and beliefs, their perceptions of the lesson designers’ intentions, and the school environment influenced their use of the FALs and other materials, e.g., a monitoring sheet. Although the materials provided affordances that could support a range of teacher learning, the teachers’ choices played a fundamental role in determining what they learned from teaching the FALs and using the materials. In one case, the teacher developed and refined new classroom routines that reflected his goals for his students about communication and accountability. In the other case, the teacher began to change her teaching practices when using the FALs and monitoring sheet, but later adapted her use of the FALs and altered the monitoring sheet to be more consistent with her routine instruction, limiting her opportunities for exploration and learning. The implications of these findings for research on teacher learning, for revision of the FALs, and for professional development are discussed.

Advisor: Schoenfeld, Alan H
Bio-Inspired Artificial Olfactory System

The escalating statistical variation of device behaviors in the nano-scale era has led to a search for alternative computational paradigms where randomness can be treated as opportunities rather than nuisance. This will allow computational systems to be built with circuits designed at the nominal case and have better access to the advantages of scaled technologies. Such computational paradigms may emerge as we explore the information processing in the biological sensory systems, which achieve unparalleled performance and energy efficiency with mediocre and unreliable components. Implementations of signal processing tasks such as feature extraction, learning, or recognition can especially benefit from bio-inspired computational models. In this thesis, we present a bio-inspired artificial olfactory system, which consists of an analog feature extraction front end that operates efficiently in the low-precision regime and a spike pattern classifier that exploits the randomness in circuits./nThe analog front end implements a novel trainable feature extraction algorithm for metal-oxide gas sensor arrays. The algorithm extracts one composite feature of all analytes and transforms the sensor responses into concentration-invariant spike patterns. This composite feature is extracted by performing the gradient decent algorithm during training. This 6-channel analog frond end consumes 519 nW/channel in the training mode, and 463 nW/channel in the recognition mode./nThe spike pattern classifier consists of a transformation of the input spikes into high-dimensional sparse vectors and a cortical memory model. The transformation is based on a random sampling scheme that can be efficiently performed with circuits exhibiting large parametric variations. Moreover, sparse representations allow fast and robust pattern storage and retrieval with associative memories such as the correlation matrix memory. It’s realized today that hyper-dimensional computing architectures like this may be a perfect match to the emerging nano-scale devices. We show how this classifier can be densely and efficiently implemented in a 3-D CNFET-RRAM technology.

Advisor: Rabaey, Jan
A Computational Assessment of Solar Fuels-Producing Devices from Thermal, Optical and Energy Yield Perspectives

The use of optically concentrating lenses integrated with wireless photoelectrochemical cells provides a mechanism to potentially reduce the energy input required to manufacture solar fuels-producing devices. In this work, a modeling approach is used to assess the annual fuel production from such integrated devices. The model captures optical, heat transfer, photoelectrochemical and climactic phenomena. The variation of design parameters such as cell dimensions, lens type, photovoltaic cell type, optical reflection management coatings and deployment location is investigated for a system that uses an optical concentration ratio of 10. The model then predicts the system’s operating temperature, operating current density and solar fuel production efficiency for every hour of the year in any location for which sufficient weather data is available./nIt is found that the devices that perform most efficiently are sufficiently small to enable effective optical capture and minimize potential losses in the electrolyte. Small ion exchange membrane coverage fractions are sufficient to enable optimal light capture while exhibiting small ohmic drops in the photoelectrochemical cell. Careful management of antireflection coatings and protection layers is required to maximize optical transmission to the current-limiting junction in the device’s photovoltaic cell. Employing simple passive cooling to maintain sufficiently low cell temperatures during extreme, quiescent ambient conditions can be achieved in certain climates but not in others. Additional measures must be undertaken to prevent electrolyte freezing in colder climates. However, despite these challenges, annual weighted average solar to hydrogen efficiency of 11.2% can be realized in high insolation locations, and stably efficient operation is possible with proper cell design. Locations with very poor direct solar irradiation resources can still exhibit annual weighted average solar to hydrogen efficiencies in excess of 9%. Additionally, the model’s predictions of device temperature are found to be in agreement with results produced in COMSOL Multiphysics. These investigations therefore help to elucidate the potential research and development work needed for future development and deployment of this technology.

Advisor: Zohdi, Tarek I
High Level Ensemble Perception

In a brief glance, we experience a rich percept of our visual environment, despite extremely limited visual capacity. What contributes to this seemingly paradoxical phenomenon? We propose that ensemble perception, the ability to extract statistical information from groups of redundant objects, is a substantial contributing factor to rich, complex visual perception. In support of this proposal, we demonstrate that ensemble perception includes high-level visual percepts, such as multi-viewpoint representations —not merely low-level or texture perception./nWe also demonstrate that ensemble perception can bypass attentional and capacity bottlenecks, and successfully function when detailed, single item analysis is unfeasible. Finally, we demonstrate that ensemble representations are functionally beneficial to visual perception, conferring precision unmatched by single-item analysis and effectively operating when other visual processes are impaired. Our investigation of ensemble coding under different visual conditions and within different patient populations provides new evidence that ensemble codes are fundamental components of conscious visual perception

Advisor: Whitney, David
Exploring the Intersections of School Discipline, Discrimination, Connectedness, and Mental Health for African American High School Students

Mixed-methods research was conducted to investigate the experiences of African American students in the school discipline system. The relationships between school discipline experiences and gender, perceptions of racial discrimination, feelings of school connectedness, and mental health were also explored. The investigation utilized survey, interview, and observational data. Findings suggest that the majority of African American participants had negative contact with the school discipline system and nearly half of the participants perceived that they had been discriminated against because of their race in school discipline interactions within the current school year. There were no significant gender differences in relation to students' school discipline experiences or their perceptions of discrimination. Findings further indicated a moderate positive correlation between perceived discrimination in school discipline interactions and depressive symptoms. Students' perceptions of discrimination were also positively correlated with their attitude towards teachers and school, but not overall school connectedness. Students' level of contact with the school discipline system was not predictive of their perceptions of discrimination. However, students who had higher levels of contact with the school discipline system (Saturday school and detention consequences) reported using more engaged coping mechanisms, such as speaking up about their experiences and trying to change things, in response to their negative discipline experiences. Overall, findings highlight the frequency with which students have negative and perceived discriminatory school discipline experiences and draws attention to the important internalizing consequences for African American students coming into contact with the school discipline system. The generalizability of findings is limited by the small sample size and selection biases; however, the study nevertheless calls for additional research regarding the variables investigated.

Advisor: Suad Nasir, Na'ilah
The Triangular Traffic in Women, Plants, and Gold: Along the Interoceanic Road in Brazil, Peru, and Bolivia

Abstract/nThe Triangular Traffic in Women, Plants, and Gold: Along the Interoceanic Road In Brazil, Peru, and Bolivia/nby/nRuth Elizabeth Goldstein/nDoctor of Philosophy in Medical Anthropology/nUniversity of California, Berkeley/nCharles L. Briggs, Chair/n“The Triangular Traffic in Women, Plants, and Gold: On the Interoceanic Road in Brazil, Peru, and Bolivia” focuses on Peru’s Amazonian region of Madre de Dios. Situated near the borders of Brazil and Bolivia, this region has earned the nickname “El Wild Wild West” for the implosion of lawlessness and prostitution reminiscent of the North American gold rush. With the fall of the dollar and international rise in the price of gold, Madre de Dios has seen a massive migration of people—male gold miners and female sex-workers, initially from the Andes. Now men and women from Ecuador, Colombia, and Brazil also make their way to the mines. This dissertation examines the triangular traffic in women destined for the sex-trade, plants employed for reproductive health – often en route to pharmaceutical analysis, and the gold, brought into solid form via mercury that fuels interdependent economies. “Mines are like women,” went a common refrain in the illegal rainforest gold mines, “because both are for exploitation,” placing the investigation of what constitutes “the human” and human-environmental interactions into the realm of human-environmental extraction. From rainforest to laboratory, brothel to bank, “traffic” depicts physical encounters, collisions, and jams, as well as functioning as an analytic to examine entwined questions of (non)human vitality and the dynamic value of people and things traveling across borders and through global commodity-chains.

Advisor: Briggs, Charles L
From Rehabilitation to Punishment: The Institutionalization of Suspension Policies in Post-World War II New York City Schools

The disproportionate suspension and criminalization of black students, referred to in the literature as "disproportionality" "over-representation" and in a nod to the achievement gap, as the "discipline gap," has become the subject of increased concern and analysis in recent years. In this dissertation, I apply concepts from Historical Institutionalism to the formation of exclusionary and criminalizing disciplinary policies in post-war New York City. First, I identify and illuminate how actors, in framing the problem of school disorder, deployed competing logics of discipline. Next I explore how the context, in particular tensions regarding school integration, influenced the framing of school disorder and contributed to the rising salience of logics that individualized school disorder and decontextualized it from the conditions of racism. Finally, I examine how school personnel engaged with and deployed these logics in their participation in the expansion and institutionalization of punitive, exclusionary and criminalizing disciplinary policies. This analysis demonstrates that punitive and criminalizing disciplinary policies were never neutral, but rather emerged out of a context of fraught racial politics that favored policies and actors that individualized, criminalized and racialized school disorder. Ultimately I demonstrate that the policies under-girding contemporary disproportionality in discipline were contested, contingent with pressure for integration and supported by educators and school personnel. This complicates existing explanations for the discipline gap that conceptualize the disproportionate punishment, exclusion and criminalization of black students as “unintended” and “unconscious.” It also highlights the organizational and ideological forces embedded in the institutional environment of schools that may pose challenges to reform efforts.

Advisor: Perlstein, Daniel H
Coburn, Cynthia E