VictorJuiz/thesis huggingface dataset:
Optimization and adjoint-based CFD for the conceptual design of low sonic boom aircraft [electronic resource]

For future civil supersonic aircraft to have the operational flexibility offered by current subsonic aircraft, some means of reducing their sonic boom to acceptable levels is required. An effective technique by which the sonic boom ground signal may be altered, and potentially minimized, is through careful shaping of external features of the aircraft. By considering the detailed aircraft shape using nonlinear flow solvers, accurate assessments of sonic boom can be made during multi-disciplinary conceptual design optimization. Such capability would enable the development of aircraft satisfying not only a requirement on low boom, but also on the range of constraints and mission goals necessary to produce a viable aircraft design. This work presents a multi-level framework for the conceptual design of low sonic boom aircraft. The development of a robust, automated tool using output-driven mesh adaptation enables accurate prediction of sonic boom. Results are validated with available experimental data for a variety of signal forms. An approach combining linear supersonic potential theory with atmospheric propagation and loudness prediction methods is used to generate low-boom near-field signals subject to lift and equivalent area constraints. This signal generator is then used to build a response surface fit that enables a conceptual-level design optimization to develop aircraft configurations with low boom. The imposition of a diverse range of multi-disciplinary design constraints ensures a viable aircraft. Once a satisfactory baseline is obtained, the design is transferred to the CFD domain, where an adjoint-driven inverse design approach is used to determine the detailed aircraft shape. This optimization seeks to match the near-field pressure target associated with the conceptual baseline design, subject to geometric constraints that ensure conceptual-level performance predictions are preserved. An aircraft design example is presented, demonstrating the application of this approach on a supersonic business jet.

Keywords: Aeronautics and Astronautics
Advisor: Kroo Ilan primary advisor. Thesis advisor
Aftosmis Michael J. advisor. Thesis advisor
Alonso Juan José
Farhat Charbel advisor. Thesis advisor
Optimization of a plasmonic-enhanced photodetector design [electronic resource]

This thesis covers the design and investigation of a plasmonic-grating enhanced photodetector structure that consists of a series of concentric gratings around a bull's eye that is split to form a metal-semiconductor-metal photodetector. Finite-difference-time-domain (FDTD) studies were carried out in order to study and simulate the different parameters of the photodetector design. A fabrication process was suggested that makes use of two lithographic mask layers in order to fabricate the basic metal-semiconductor-metal photodetector structure in InGaN where the bull's eye grating is to be patterned on. Initial fabrication work was done on making the concentric gratings and bull's eye structures using focused-ion-beam milling on a metal layer as a test. In addition, these plasmonic-grating enhanced photodetector structures were shown to be wavelength selective, and such a characteristic can be used to design multi-spectrum detectors for bio-sensing. A design for a multi-spectrum biosensor using microfluidic channels and multiple plasmonic-grating enhanced photodetectors is also described in the thesis.

Keywords: Electrical Engineering
Advisor: Harris J. S. (James Stewart)
Optogenetic tool development and application to dissecting dopaminergic circuitry in social behavior [electronic resource]

Social interaction is an essential and highly integrative behavioral task that is impaired in major psychiatric disorders such as autism, schizophrenia, social anxiety disorder, and depression. Current treatments for many of these disorders are based on pharmacological approaches that have been used for decades even though their mechanisms of action are poorly understood and carry many side effects. In particular, treatment of the asocial symptoms of these disorders has remained elusive due to a generally poor understanding of the neural circuitry underlying normal social behavior. In order to move toward a deeper circuit-level understanding of these complex neural processes, our lab has pioneered the use of two light-activated microbial opsins, Channelrhodopsin-2 (ChR2) and Halorhodopsin (NpHR), to achieve precise bidirectional optogenetic control of specific cell types in behaving animals. However, it has become clear that the complexity of the circuitry involved in psychiatric behaviors will require new classes of optogenetic tools to modulate cells in a more refined manner based on characteristics such as projection profile, receptor expression, and endogenous firing patterns. The purpose of this study was thus two-fold: 1) to develop novel optogenetic tools for more physiologically relevant stimulation of different cell types on different timescales, and 2) to apply these tools to define in socializing animals the real-time causal role not only of a specific brain region and cell type, but also of distinct subpopulations defined by projections to different downstream brain regions and distinct downstream cell types. The engineered opsins we develop here will be generalizable to dissect other neural circuits in health and disease, enabling new domains of optogenetic investigation that have thus far been inaccessible, and enhancing the precision of optical neural control in a broad variety of settings.

Keywords: Neurosciences.
Advisor: Deisseroth Karl primary advisor. Thesis advisor
Knutson Brian advisor. Thesis advisor
Malenka Robert C. advisor. Thesis advisor
Shatz Carla J. advisor. Thesis advisor
Order out of chaos [electronic resource] : Fernando Pessoa and Eugeni d'Ors and the crisis of modernism

This is the first study comparing the works of the contemporary intellectuals Fernando Pessoa and Eugeni d'Ors. It examines their use of heteronyms, heterodoxy, and history in approaching the crises that arose in the beginning of the twentieth-century. Each applied an aesthetic understanding to reality. A full understanding of reality required the multiplication of the self in an attempt to achieve an objective--decentralized--perspective. For Pessoa, this meant the creation of a host of heteronyms that led in a progression to a centralizing figure. For d'Ors an internal divine attribute of the human psyche approached objectivity through dialogue. In fact, dialogue is found as a connective theme in Pessoa as well. This aesthetic perspective becomes a gateway into a deeper understanding of reality. This understanding in turn shapes the present and future through the aesthetic works of each of these authors. In this way, Pessoa and d'Ors conceived of a present in which the future could be shaped through an aesthetic understanding of the world. The striking similarities of their approaches speak to the hidden interconnectedness of Iberian cultures.

Keywords: Iberian and Latin American Cultures.
Advisor: Barletta Vincent primary advisor. Thesis advisor
Resina Joan Ramon primary advisor. Thesis advisor
Gumbrecht Hans Ulrich advisor. Thesis advisor
Hoyos Ayala Héctor advisor. Thesis advisor
Organic electronics [electronic resource] : devices, circuits and applications

Organic materials have brought exciting opportunities for flexible, light weight, low cost, and disposable electronics. However, there are still several technical challenges for the wide spread of this technology. In this dissertation, I discuss about the challenges and the improvements of organic electronics. In the first part, I explore device engineering for organic thin film transistors (OTFTs). New device architecture and fabrication methods to improve the OTFT characteristics are proposed. Short channel and self-aligned OTFTs are implemented on a non-planer substrate. The self-aligned structure enables accurate alignment between the electrodes with a pre-defined prism-structure dimension, thus reducing parasitic overlap capacitance. In the second part, circuit engineering based on OTFTs is studied. An OTFT circuit design methodology is proposed to enable accurate analysis and verification in the design stage. Various topologies of digital circuits such as complimentary and unipolar OTFT circuits based on this design methodology are demonstrated. The third part focuses on application engineering, specifically on the implementation of disposable and flexible organic electronic sensors. Wireless temperature sensor based on conductive filled polymer is demonstrated. The stability and reproducibility is improved and the sensitive temperature can be tuned by employing a binary polymer system.

Keywords: Electrical Engineering
Advisor: Bao Zhenan primary advisor. Thesis advisor
Nishi Yoshio
Poon Ada Shuk Yan
Organic geochemical reconstructions of the late quaternary climate history of the Sierra Nevada [electronic resource]

Organic geochemical proxy measurements in sediments from Swamp Lake, Yosemite NP, in the central Sierra Nevada of California provide evidence of climatic change on millennial and centennial timescales over the last ~20,000 years. Proxy measurements in bulk sediments (TOC, TN, C/N, [delta]13Corg, [delta]15N, biogenic silica, magnetic susceptibility) record the response of the lake environment, in terms of primary productivity, OM sources, microbial OM regeneration and secondary production, and detrital input, to climate-driven changes in temperature, seasonal ice cover, lake mixing regimes, runoff and lake level. Parallel changes in the relative abundances of n-alkane biomarkers provide more specific information about lake level during the Holocene epoch. The inferred environmental changes at Swamp lake correlate with other Sierra Nevada paleo-records, and with reconstructed sea surface temperatures along the California margin. Parallel changes in the Swamp Lake and SST records over the past ~20,000 years provide new evidence that continental climate in the Sierra Nevada and the California Current system have responded, on multiple timescales, to common drivers in North Pacific ocean-atmospheric circulation. Measurements of compound-specific hydrogen isotope ratios in sedimentary leaf wax n-alkanes ([delta]Dwax) provide insight into the nature of the link between North Pacific and Sierra Nevada climate over time. The [delta]Dwax composition of Swamp Lake sediments is primarily controlled by changes in the [delta]D of precipitation, which is in turn influenced by the moisture sources and trajectories of winter storms. The Swamp Lake [delta]Dwax record reveals a long-term change in precipitation seasonality and/or storm trajectory over the Holocene, driven by seasonal insolation, as well as centennial- to millennial-scale fluctuations reflecting changes in the relative importance of northerly and southerly storm types. These apparent "regime shifts" in North Pacific atmospheric circulation resemble modern, short timescale responses to ENSO and the PDO, but their underlying causes remain unknown.

Keywords: Geological and Environmental Sciences.
Advisor: Chamberlain C. Page primary advisor. Thesis advisor
Paytan Adina
Diffenbaugh Noah S. advisor. Thesis advisor
Maher Katharine advisor. Thesis advisor
Ravelo Ana Christina advisor. Thesis advisor
Overcoming the last mile of humanitarian and health delivery supply chains [electronic resource] : models and insights

The "last mile" of a supply chain is the final step of that supply chain before the product reaches the end consumer. In humanitarian and health delivery supply chains, the last mile represents the final leg of the journey for health care or other assistance to reach beneficiaries, and is a critical bottleneck contributing to the acutely inadequate health care access in resource-limited regions. Operations research methodology can be used to evaluate, lessen, and ultimately overcome this bottleneck. In this dissertation, we present four models developed for this context. First, we develop an inventory model to analyze the interaction between a stockpile and a downstream relief operation for large humanitarian organizations such as the United Nations High Commissioner for Refugees. Second, we present an optimization model that explicitly includes treatment adherence when integrating a clinic's capacity decisions with population health outcomes. Our final two models investigate the effectiveness, then the efficiency and equity, of fleet management programs for health worker vehicles (e.g., nonprofit Riders for Health) in places like rural sub-Saharan Africa. Health access challenges are fundamentally supply chain problems, and these models are a first step in using operations research tools to improve health delivery in resource-limited regions. Humanitarian organizations must use their financial resources wisely to carry out their mandates, and models such as these can help organizations make the best use of their limited response resources.

Keywords: Management Science and Engineering
Advisor: Brandeau Margaret L. primary advisor. Thesis advisor
Johnson M. Eric
Lee Hau Leung advisor. Thesis advisor
Oxytocin enhances signal-to-noise in hippocampal feed-forward transmission by selective action on targeted interneuron subtypes [electronic resource]

Neural circuits throughout the brain are under the continuous influence of neuromodulators which shape network activity in accordance with behavioral context. Oxytocin is a key neuromodulator that has been linked to social memory and maternal behavior in animals, as well as to autism spectrum disorders, trust, emotion recognition and parenting in humans. Here we show that activation of oxytocin receptors sharpens the responses of the hippocampal circuit, increasing the signal of spike transmission through the network while simultaneously suppressing the noise of background spontaneous activity. Both of these actions are mediated through a depolarization of the fast-spiking interneurons. The resulting increase in inhibitory tone serves to silence spontaneous activity in the CA1 pyramidal cells, while a use-dependent depression of the inhibitory synapses permits enhanced feed-forward spike transmission. Furthermore, we show that oxytocin potently modulates spontaneous hippocampal Sharp-Wave Ripple oscillations in a slice preparation. These results elucidate the action of oxytocin in the hippocampus, while simultaneously shedding light on a novel mechanism by which modulation of fast-spiking interneurons can modify hippocampal circuit activity.

Keywords: Molecular and Cellular Physiology.
Advisor: Tsien R. W. (Richard W.) primary advisor. Thesis advisor
Deisseroth Karl advisor. Thesis advisor
Huguenard John advisor. Thesis advisor
Madison Daniel V.
The page redux [electronic resource] : American literature in the information age

The Page Redux: American Literature in the Information Age argues that American literature of the past three decades has played a central role in reconceptualizing the relationship between literature and technology. The texts analyzed in this dissertation self-consciously approach the book as a technological object and reveal the printed page to be a crucial site for interrogating the capabilities and limitations of several media technologies including cameras, computers, and writing itself. In treating the page as a meaning-bearing graphic interface, this strand of American literature, which includes hybrid texts, graphic novels and experimental fiction, defiantly protests against the alleged obsolescence of print and offers innovative ways for books to remain a viable, valuable communication system in the endless competition between old and new media. The first chapter frames the project's historical arc with an overview of key developments in information inscription and digital culture, showing how these developments have challenged print's dominance as an information storage technology. Building on this analysis in the context of early information age, or pre-digital, literature, the second chapter approaches Theresa Hak Kyung Cha's hybrid text, Dictée (1982), not as the experimental novel that it is often labeled, but as a work of media theory that critiques communication systems and the politics of historiography. The third chapter examines interactions between media technologies and literature in the form of graphic novels. Analyzing Art Spiegelman's Maus (1986; 1991) and Alison Bechdel's Fun Home (2006), this chapter illustrates how word and image combinations work to destabilize various technologies' ability to accurately record information, and in the process generate an ironic authenticity that stems from the traditionally anti-realist comics form. The last two chapters attend to American literature of the new millennium. The first of these situates Mark Z. Danielewski's experimental novel House of Leaves (2000) at the intersection of space, technology and narrative and contends that the text stages a confrontation between analog and digital technologies that exposes the mediatedness of all narrative, regardless of the technology used to record it, and ultimately attests to the value of interpretation in a hypermediated world. To conclude the project, the final chapter considers Jonathan Safran Foer's die-cut book, Tree of Codes (2010), in relation to recent developments in media technologies and digital culture. Grating against intangibility and digital culture's drive to convert atoms into bits, Foer's hypermaterial novel further demonstrates that in the last few decades the physical space of the page has become an increasingly animated site for reconsidering how media technologies affect literary studies and how older media forms, such as the book, reemerge as flexible communication systems capable of co-evolving with the digital rather than being consumed by it.

Advisor: Heise Ursula K.
Elam Michele
Jones Gavin Roger
The palm oil revolution in Asia [electronic resource]

Palm oil has doubled its share of world vegetable oil consumption in the past twenty-five years to become the world's leading source of vegetable oil. Even though the environmental crises associated with oil palm are directly related to its cultivation (tropical forest loss, carbon emissions from drained peat swamps, biodiversity loss), studying supply interventions is insufficient. From a conservation perspective, the demand side of vegetable oils markets matters equally, if not more, since demand patterns affect the incentives facing producers. The dissertation begins by examining demand systems in Indonesia, today the world's largest palm oil producing country and the country with the highest palm oil consumption per capita. In Indonesia, higher palm oil consumption is the result not just of population and income growth but also of government policies that promoted an extraordinary substitution away from an alternative cooking oil. Comparing Indonesia to the other top two palm oil consuming countries in the world, India and China, reveals that Indonesia's experience is not representative of Asia. Different political and economic factors, from livestock production to trade policy, have produced different vegetable oil consumption patterns in each of these three markets. Finally, the dissertation examines the effect that biodiesel has had on vegetable oil demand and describes how a petroleum-price shock might play out in vegetable oils markets. Overall, the dissertation predicts a doubling of palm oil demand over the next twenty-five years and emphasizes how, given the highly substitutable nature of vegetable oils markets, small changes in relative prices can have exaggerated effects on palm oil demand. The elastic, or price sensitive, demand structure that producers face suggests that policies to increase yields are likely to cause more land conversion for oil palm.

Keywords: Environment and Resources.
Advisor: Falcon Walter P.
Naylor Rosamond primary advisor. Thesis advisor
Mooney Harold
Parameter extraction from single cell dynamics using numerical optimization techniques [electronic resource]

Cell signaling networks are complex dynamical systems with mechanisms for adaptation and failure-tolerance such that typical stimulus experiments are often robust to the perturbation of individual components. While such robustness is often advantageous, it also means that the information content of an experiment with respect to internal states and activities is often poor. We treat this problem formally by examining the statistical uncertainty of parameter estimates of corresponding signaling models as a function of experimental protocols that are based on live-cell imaging of fluorescent reporters. The first part of this work uses such model predictions of parameter sensitivity to design numerically optimized live-cell imaging protocols with the goal to maximally constrain the space of possible parameter values. The second part instead uses an experimental approach to define invariant parameters by correlated population estimates in order to reveal changes of regulated parameters in systematic siRNA perturbation experiments. Our results show that the effects of siRNA perturbations on reporter dynamics can be used to infer functional changes of the probed system. We exploit this feature to define not only the key molecules responsible for activity but also direct and indirect regulators.

Keywords: Chemical and Systems Biology.
Advisor: Meyer Tobias primary advisor. Thesis advisor
Covert Markus advisor. Thesis advisor
Dolmetsch Ricardo E. advisor. Thesis advisor
Ferrell James Ellsworth advisor. Thesis advisor
Parkinson's disease phenotypes and treatments with induced pluripotent stem cells [electronic resource]

Studies of Parkinson's disease (PD) have been greatly hindered by lack of access to affected human dopaminergic (DA) neurons. Here, we report generation of induced pluripotent stem cells that carry the p.G2019S mutation (LRRK2-G2019S-iPSCs) in the Leucine-Rich Repeat Kinase-2 (LRRK2) gene, the most common PD-related mutation; pluripotent lines that cells that carry a full SNCA gene triplication on one allele; and control pluripotent lines. We demonstrate that these PD autosomal dominant mutant LRRK2-G2019S-iPSCs, SNCA-triplication-iPSCs and Control-iPSCs were able to differentiate into dopaminergic neurons and showed increased expression of key oxidative stress response genes and alpha-synuclein protein. Moreover, LRRK2-G2019S iPSC derived dopaminergic neurons, specifically, were more sensitive to caspase-3 activation caused by exposure to hydrogen peroxide, MG-132, and 6-hydroxydopamine, compared to control dopaminergic neurons. While, SNCA-triplication iPSC derived dopaminergic neurons formed early ubiquitin positive puncta and were more sensitive to peak toxicity hydrogen peroxide induced cell stress. These findings suggest that LRRK2-G2019S and SNCA-triplication iPSC derived dopaminergic neurons exhibit early phenotypes linked to PD. Due to the high penetrance of the LRRK2 mutation, the expression of wild type protein in the SNCA-triplication line, and the clinical resemblance of patients afflicted with these disorders to sporadic PD patients, these neurons may provide a valuable platform for identification of novel pharmacological agents and diagnostics for modeling and alleviation of a subset of disease phenotypes.

Keywords: Bioengineering.
Advisor: Reijo Pera Renee primary advisor. Thesis advisor
Palmer Theo advisor. Thesis advisor
Puglisi Joseph D. advisor. Thesis advisor