VictorJuiz/thesis huggingface dataset:
Adjoint sensitivity analysis for nanophotonic structures [electronic resource]

We present a local optimization method for design of dispersive and nondispersive dielectric structures for applications in nanophotonics, based on adjoint solutions of Maxwell's equations. The sensitivity of a merit function (e.g. total absorption) is sought with respect to design parameters (e.g. shape and size of scattering structures). We use adjoint design sensitivity analysis to obtain this sensitivity in a computationally efficient manner. By discretizing Maxwell's equations as a linear FDTD system with matrix elements that vary smoothly with design parameters, the entire numerical system is made differentiable. The derivative of the merit function with respect to all design parameters may be derived using the chain rule, and calculated efficiently using a solution to the adjoint FDTD system. Next we formulate the adjoint problem as a partial differential equation and solve it with the finite element method. This more accurate method is applied to metals. An ``optimization force'' may be calculated for all design parameters, or visualized at points along material interfaces to lend insight into design rules. We apply this method to the design of waveguide mode converters and resonant metallic nano-apertures.

Keywords: Applied Physics.
Advisor: Hesselink Lambertus primary advisor. Thesis advisor
Byer R. L. (Robert L.)
Fan Shanhui
Advanced optimization in image-guided radiation therapy [electronic resource]

Radiotherapy is an image-guided intervention, and medical imaging is involved in every key step of the treatment process, ranging from patient staging, simulation, treatment planning, and radiation delivery, to patient follow-up. Image guided-radiation therapy (IGRT) is the most sophisticated method of radiation treatment to address the issue of tumor movement during treatment. IGRT uses advanced imaging technology such as cone-beam CT (CBCT) using on-board imager (OBI) to provide high-resolution, three-dimensional images to pinpoint tumor sites, adjust patient positioning when necessary, and complete a treatment within the standard treatment time slot. Combined with modern technologies in planning and delivering such as intensity-modulated radiation therapy (IMRT) and volumetric modulated arc therapy (VMAT), IGRT improves the accuracy of tumor localization while reducing the radiation exposure of healthy tissues. For radiotherapy, repeated CBCT scan of the patient is often required, but excessive radiation exposure is directly related to the risk of polymorphism of genes involved in DNA damage and repair. Hence, we first demonstrate algorithms CBCT for dose reduction. With a low-dose CBCT protocol, the radiation exposure can be mitigated while signal-to-noise ration (SNR) of the measurement is also lowered. It is shown that the high-quality medical image can be reconstructed from noisy CBCT projections by solving an large-scale optimization problem with reasonable preconditioning techniques. In the presence of patient's movement, CBCT projections are highly undersampled, and the precondition in the full-scan case is no longer available. Instead, a first-order method with linearization is adopted for the reconstruction. To further accelerate the convergence speed, we demonstrate a scaling technique in Fourier space. For inverse planning of IGRT, two issues are introduced: beam direction selection and beamlet based optimization. We present an iterative framework suited to modern IMRT/VMAT.

Keywords: Electrical Engineering.
Advisor: Xing Lei primary advisor. Thesis advisor
Boyd Stephen P. advisor. Thesis advisor
Pauly John (John M.) advisor. Thesis advisor
The aesthetics of habitability [electronic resource] : Edward C. Wortz, NASA, and the art of light and space, 1966-1973

This dissertation explores four American artists working at the intersection of sculpture, architecture, and design in the late 1960s and early 1970s as they shaped the discourse of "habitability, " a spatial term developed by the National Aeronautics and Space Administration (NASA). While NASA initially used habitability to describe the physiological suitability of hostile environments (e.g., outer space) for human exploration, this study shows how these artists revised the meaning of this term in order to accommodate a variety of architectural, environmental, psychological, and social interpretations. Over the course of four chapters, I examine the artistic practices and theories of four Los Angeles-based artists—James Turrell, Robert Irwin, and Larry Bell, all members of a 1960s "Light and Space" sculptural movement; and Sheila Levrant de Bretteville, a feminist graphic designer and co-founder of the Woman's Building, an independent feminist art and education center—as they directly engaged with the concept of habitability (and in turn, NASA's research) between 1966 and 1973. I consider these four artists and their responses to habitability—which ranged from their enthusiastic collaboration with social scientists and engineers, to their careful parsing of the philosophical and epistemological foundations of the discourse, to their explicit critique on the basis of difference and gender—by way of their work with two additional figures who simultaneously developed habitability in empirical and aesthetic contexts: Edward C. Wortz (1930--2004), a perceptual psychologist who worked in the aerospace industry at the height of the 1960s "Space Race"; and his wife, Melinda (Farris) Wortz (1940--2002), who wrote extensively about these artists as an art historian, critic, and curator. The first comprehensive examination of the Wortz archives, this study addresses the intersection of art and science during the Cold War. I combine formal analysis of the artwork occasioned by these collaborations (minimal abstract sculpture, installations of projected light, experimental architecture, and radical interior and graphic design) with inquiry into the social history of both postwar American art and scientific research.

Keywords: Art and Art History.
Advisor: Lee Pamela M. primary advisor. Thesis advisor
Maxmin Jody advisor. Thesis advisor
Turner Fred advisor. Thesis advisor
Wolf Bryan Jay advisor. Thesis advisor
Zervigón Andrés Mario advisor. Thesis advisor
Affective norms, deviance, and moral judgment [electronic resource]

The present research provides support for Affective Norm Theory (ANT), a new theory proposing that cultural context and situational norms interact to define both what is considered an appropriate affective display, and how observers respond to affective norm violations, or instances where the affect a person displays is inconsistent with both situational norms and observer expectations. A series of studies supports the hypotheses put forward by ANT: that in European American cultural contexts, (H1) observers notice affective deviance and (H2) negatively evaluate individuals who display deviant affect, that (H3) one reason affective displays are so powerful is because observers can use deviant displays to draw inferences about moral values, and that (H4) observers narrow the range of affective expressions they find appropriate in response to a stimulus when they interpret it as having moral content. Discussion focuses on the role of beliefs about the meaning of affective displays, individual difference measures, and the importance of gender and cultural context in defining and understanding affective norms and expectations.

Keywords: Psychology.
Advisor: Monin Benoît
Gross James
Tsai Jeanne Ling advisor. Thesis advisor
Algebraic order and the BKT transition in an exciton-polariton gas [electronic resource]

Below a critical temperature, three-dimensional bosonic gases form a Bose-Einstein-condensate which exhibits spatial coherence. In two-dimensional (2D) systems, true long range order is impossible at non-zero temperatures since long-range fluctuations which increase the entropy and destroy the coherence can easily be excited. However it has been predicted by the Berezinskii-Kosterlitz-Thouless (BKT) theory that such a 2D condensate can exhibit quasi-long-range order which is characterized by a power-law decay of the spatial correlation function. This thesis presents the first observation of the coherence decay in a 2D exciton-polariton condensate with a power-law whose exponent (less than 1/4) behaves as predicted by the theory. Exciton-polaritons are quasi-particles which can be described as the quantum mechanical superposition of an exciton in a quantum well and a photon trapped in a semiconductor cavity. Due to their bosonic properties and small effective mass, they already condense at a temperature of a few kelvin, compared to a few hundred nanokelvin in the atomic case. Exciton-polaritons are created by optical excitation of the sample, and they continuously decay through the leakage of photons out of the sample. These leaking photons preserve the coherence properties of the decaying exciton-polaritons, and their coherence can be determined through interference measurements.

Keywords: Applied Physics.
Advisor: Yamamoto Yoshihisa primary advisor. Thesis advisor
Mabuchi Hideo advisor. Thesis advisor
Miller D. A. B. advisor. Thesis advisor
The algorithmic mind [electronic resource] : a study of inference in action

What is the nature of human inference? How does it work, why does it work that way, and how might we like it to work? I advance a framework for answering these questions in tandem, with a rich interplay between normative and descriptive considerations. Specifically, I explore a view of inference based on the idea of probabilistic sampling, which is supported by behavioral psychological data and appears to be neurally plausible, and which also engenders a philosophically novel and appealing view of subjective probability. I then discuss this view in the context of the Bayesian program in cognitive psychology, proposing a methodology of boundedly rational analysis, which particularly exemplifies the normative/descriptive interplay. By taking resource bounds seriously, we can improve and augment the more standard rational analysis strategy. This helps us focus efforts to understand how minds in fact infer, and in turn allows sharpening normative questions about how minds ought to infer. Against this background I explore the phenomenon of metareasoning, which arises naturally when discussing bounded but representationally sophisticated agents, but which has not been explored in the context of probabilistic approaches to the mind. I propose an analysis of metareasoning in terms of the value of information, and explore the consequences of this view for how we should think about inference. The focus of this dissertation is on implemented (or at least implementable) models of agents, and the role of inference in guiding and supporting intelligent action for real, resource-bounded agents. Consequently, a number of the suggestions and claims made are supported by simulation studies.

Keywords: Philosophy.
Advisor: Benthem Johan van
Bratman Michael advisor. Thesis advisor
Goodman Noah (Noah D.) advisor. Thesis advisor
Skyrms Brian advisor. Thesis advisor
Algorithms for the alignment of biological sequences [electronic resource]

High throughput sequencing of biological sequences has become a core component of many experiments in biology. An important step in the analysis of these biological sequences is alignment to a reference genome. Alignment algorithms have existed for several decades and have evolved as sequencing technologies have progressed. The recent trend in sequencing is to generate longer reads at high throughput. This thesis introduces two new methods designed for this new type of data. The first method is for DNA sequences. By taking advantage of the longer reads, we develop a method that is several times faster than current approaches while improving the accuracy. We also propose a novel approach to reduce the memory requirement. This method is compared with popular approaches in both alignment accuracy and also the accuracy of the resulting variants called. The second method is for mRNA sequences. It leverages our approach to aligning DNA reads to align long mRNA reads. The unavoidable introns in mRNA sequences split a read into shorter sub-sequences, which makes alignment more difficult. We describe a method to align these intron junctions, resulting an method that is both faster and more accurate than current approaches. Our method is compared to a number of popular approaches based on both alignment accuracy and junction detection accuracy. Overall, the data generated by new sequencing platforms warrant development of new methods as significant improvement in speed and accuracy can be gained.

Keywords: Electrical Engineering.
Advisor: Wong Wing Hung primary advisor. Thesis advisor
Dill David L. advisor. Thesis advisor
Montanari Andrea advisor. Thesis advisor
Weissman Tsachy advisor. Thesis advisor
Amateurism and College Athletics

This paper explores the concept of amateurism as it relates to college sports. The history of amateurism in sports will be reviewed with consideration of how that history has been revised to support the modern-day, $16 billion college-sports enterprise. The National College Athletic Association’s (NCAA) history will be summarized, and its role as the head of a cartel of colleges engaged in a sports-entertainment business will be discussed. After the economics of this cartel is examined, it will be argued that NCAA member schools enjoy monopolistic and monopsonistic powers that give them impressive market power. The NCAA’s amateurism rules serve to protect the integrity of the cartel and allow colleges to extract rents from studentathletes, especially Division I football and men’s basketball players. Too often with this current system, athletic scholarships fail to translate into a college education. Additionally, the injury risks inherent to college sports seem undermanaged and undercompensated. The paper will conclude with possible alternatives to amateurism in college sports.

Keywords:  Department of Economics
Stanford Department of Economics
amateur athlete
college sports
revenue-generating sports
NCAA
cartel economics
monopsonistic cartel
athletic scholarship
college-sports-related injuries
Thesis
Advisor: Cogan John F.
Ambient pressure XPS studies on electrochemical reactions [electronic resource]

Capable of converting electricity into chemicals and chemicals into energy, heterogeneous electrocatalysis is a promising field in the development of clean, renewable energy. At the present time, further development in catalyst design and optimization is necessary to achieve the efficiencies necessary for electrocatalysis to be cost effective. In order to achieve rational catalytic design, it is paramount to understand the fundamental principles governing each electrocatalytic process, and that requires the utilization of spectroscopic techniques capable of probing the system in operando, i.e. as the chemical reaction is taking place. Among the many in operando techniques, Ambient Pressure X-ray Photoelectron Spectroscopy stands out for the interrogation of electrocatalytic processes due to its ability to probe a catalyst in a surface- and chemically-sensitive manner. This thesis shows the design of an APXPS-compatible electrochemical cell and its use to investigate three key electrochemical processes pertinent to the field of renewable energy. First, we investigated the oxygen reduction reaction (ORR), the rate-limiting step for the electrochemical combination of hydrogen and oxygen in a fuel cell device, on both pure platinum and platinum alloy catalysts. Second, we researched the electrolysis of water through the oxygen evolution reaction (OER) on an iridium oxide catalyst. Third, we investigated the electrochemical production of hydrogen from protons through the hydrogen evolution reaction (HER) on amorphous molybdenum nanoparticles. We conclude that APXPS electrochemistry is a powerful tool for understanding electrocatalytic processes, allowing for the elucidation of reaction mechanisms through intermediates that can only be observed in operando, such as the identification of non-hydrated hydroxide on platinum during ORR or the identification of the oxidation state of iridium oxide during OER. Furthermore, APXPS electrochemistry allows us to follow the activation processes undergone by catalysts under realistic reaction conditions, such as the dealloying process of Pt-Y nanoparticles or the transformation of MoSx into a predominantly MoS2 phase. This powerful technique can be extended to even more catalytic systems, and we believe that in the near future it will become a standard characterization tool for heterogeneous catalysis.

Keywords: Chemistry.
Advisor: Nilsson Anders
Chidsey Christopher E. D. (Christopher Elisha Dunn)
Jaramillo Thomas Francisco advisor. Thesis advisor
An 'Epochal' Agreement? Aftermath and Implications of the US-India Civil Nuclear Agreement on Indian Nuclear Policy and the Nonproliferation Regime

In 2005, a small group of American and Indian diplomats engineered a landmark agreement that released India from decades of restrictions imposed on its nuclear weapons program after its 1974 and 1998 tests. Before and after the Deal passed Congress, there was an active debate among critics and supporters who predicted its effects. This thesis provides the first comprehensive analysis and evaluation of the outcome. It incorporates the available scholarly evidence as well as interviews from prominent policymakers and scholars in both the Obama and Bush Administrations.
This survey of the aftermath of the US-India Deal reveals a mixed outcome. While it appeared to make India’s nuclear policies more responsible on the international stage, India has engaged in hedging in order to maintain relations with the United States while ensuring a steady supply of oil from Iran. Many developing countries believed that the US had undermined its own commitments to preventing the spread of nuclear weapons, but in the end, they did not actively oppose the Agreement. More significantly, despite the opaque nature of the Indian and Pakistani nuclear arsenals, it is clear that Pakistan in particular has chosen to produce even more weapons in the aftermath of the US-India deal, leaving South Asia less stable. Regarding precedent-setting, the US-India Deal allowed the US to break longstanding international rules given its position as the global power. China would have more difficulty taking the same route. However, the Deal did not set a precedent because China did not follow the same path to break and then remake the rules. Thus, while American actions were legitimate in a system fashioned by the United States, China used the conclusion of the India Deal as an opportunity to pursue an alternative policy and to circumvent the export controls entirely.

Keywords: Political Science
International Security Studies
CISAC
US-India Civil Nuclear Deal
US
India
Nuclear Nonproliferation
Policy
Bush
Obama
Center for International Security and Cooperation
Thesis
Advisor: Sagan Scott D.
An Examination of Subtype B HIV-1 Genetic Infection Tropism Prediction

HIV usually makes use of either the CCR5 or CXCR4 co-receptors to gain entry into cells. Which coreceptor the virus uses (the tropism) determines the efficacy of different cell entry-inhibiting antiretroviral drugs, and is therefore important medical information. HIV tropism may be accurately assessed with sensitive recombinant virus phenotyping tests such as the Trofile assay, but these tests are often prohibitively expensive. Viral genome sequencing and interpretation of genotype using free online software programs such as Web PSSM and Geno2Pheno offer a low-cost alternative by predicting tropism from the V3 loop sequence in the HIV env gene. However, these programs' predictions are insensitive to minority viral variants and may be less accurate than the commercial recombinant virus phenotypic assays.
We sequenced proviral subtype B HIV-1 DNA from peripheral blood mononuclear cell (PBMC) samples obtained from patients under drug-induced viral suppression and viral RNA from plasma samples obtained from the same patients after viral re-emergence. Predictions of re-emergent viral tropism were made by Geno2Pheno and Web PSSM assessment of the proviral DNA V3 loop sequences. Trofile tests were performed on plasma samples to provide a gold-standard re-emergent virus phenotype. Through statistical and qualitative analysis of these paired prediction and tropism data, we tested the hypothesis that the tropism of virus re-emerging into the blood following drug interruption can be accurately predicted by Geno2Pheno and Web PSSM analysis of proviral DNA.
We show here that proviral DNA sequence analysis was able to predict re-emergent plasma virus tropism with 83.3% success, and exclusive R5 tropism with 87.0% success. Generalized linear modeling showed a highly significant relationship between prediction-tropism discordance and lower DNA-RNA sequence similarity. Qualitative analysis of clone env sequences demonstrated sequence interpretation accuracy by both Geno2Pheno and Web PSSM. Together, these results suggest that proviral PBMC DNA consensus sequences may fail to predict the re-emergent plasma virus tropism in more than 10% of cases. Differences between proviral DNA-based tropism predictions and re-emergent plasma virus phenotype may result from the selection of minority variants and the evolution of plasma virus.

Keywords:  Department of Biology
HIV
HIV coreceptor
viral tropism
tropism prediction
CCR5
CXCR4
antiretroviral therapy
Biology
Infectious Disease
Thesis
Advisor: Katzenstein David
Shen Kang
Analysis and design of high density RRAM arrays [electronic resource]

Among the emerging nonvolatile memory technologies that could potentially replace flash memory, RRAM (resistance change random access memory) is particularly appealing thanks to its small size, short switching time, low operation voltage, and good compatibility with the standard CMOS process. However, for RRAM to be a cost-competitive candidate for high-density and high-capacity commercial products, some architectural-level challenges must be tackled. In this dissertation, research results that advance the design of high-density RRAM arrays are presented. After a brief review of the RRAM device and array fundamentals, a complete analysis of cross-point arrays in read operations is presented. The analysis concludes with a proposal for a new bias scheme that increases the read margin of the cross-point RRAM array. A compact, one-transistor-four-RRAM (1T4R) array architecture, with corresponding read/write and decoding schemes, that achieves high RRAM density is then introduced. Circuit simulation results that validate this new architecture and a proof-of-concept test chip with fully integrated RRAM devices are described. For this test chip, a particular sequence to form the cross-point RRAM array is presented. Measurement results of successful array operations demonstrate the feasibility of high-capacity integration of the proposed architecture. The research then focuses on the scaling effects of on-chip interconnects on RRAM array performance. Due to the continuously shrinking process feature size, the voltage drop along the interconnect gradually reduces the voltage available to operate the RRAM device. To more efficiently analyze this effect for an arbitrary array size, a compact array model is developed. Simulations using this model are shown to quantitatively illustrate the maximum achievable array size in the future. Interconnect electromigration and parasitic capacitance effects are then considered at the end.

Keywords: Electrical Engineering.
Advisor: Wong S. Simon primary advisor. Thesis advisor
Lee Thomas H.
Nishi Yoshio