VictorJuiz/thesis huggingface dataset:
Convex optimization for Monte Carlo [electronic resource] : stochastic optimization for importance sampling
Keywords: Computational and Mathematical Engineering.

In Monte Carlo simulations it is often essential that a method is accompanied by an appropriate variance reduction method. Reducing the variance of a Monte Carlo method is, at least conceptually, an optimization problem, and mathematical optimization has indeed been used as a theoretical and conceptual tool in this pursuit. However, traditional Monte Carlo methods have only used numerical optimization sparingly, and convex optimization even less. Numerical optimization is study of algorithms for finding a solution to an optimization problem, as opposed to the study of analytical solutions of an optimization problem. Convex optimization is the study of convex optimization problems, a subclass of optimization problems for which efficient algorithms for finding the global optimum exists. In this work we present a framework for using convex optimization for Monte Carlo. More specifically, we present a framework for using stochastic convex optimization for adaptive importance sampling, self-normalized importance sampling, and what-if simulations. The main idea is to perform importance sampling and numerical optimization simultaneously. In particular, the numerical optimization does not rely on blackbox optimization solvers, and this allows the computational cost of each iteration to remain cheap. Because the optimization is performed on a convex problem, we can establish convergence and optimality.
Correlated X-ray Scattering of Metallic Nanoparticles at the Stanford Synchrotron Radiation Lightsource
Keywords:  Department of Physics
Correlated X-ray Scattering
x-ray scattering
nanoparticles
Thesis

This thesis reports on the results of a new method for interpreting x-ray scattering data as applied to silver and platinum nanoparticles. Correlated X-ray Scattering (CXS) is the subject of much interest due to the possibilities of imaging un-crystallized proteins. CXS can also give much more detailed information about the structure of nanoparticles than more traditional solution scattering x-ray techniques, and could thus be immensely helpful in industrial/technical studies. With their femtosecond pulses of high intensity x-rays, x-ray Free Electron Lasers (XFEL) are the obvious choice for CXS studies due to the large numbers of photons and short exposure times necessary for this technique. For applications, however, it is important to figure out when it is possible to use the much more common and cheaper, albeit less powerful, synchrotron x-ray sources. This experiment attempts to use the method of difference correlations on data from solutions of platinum and silver nanoparticles to see if meaningful and interesting data can be extracted using CXS with synchrotron radiation. It is shown that with proper filtering techniques it is possible to extract a CXS signal from nanoparticle data. From this signal the finer details of the internal structure of these nanoparticles were determined, including observation of twinning structures. Although it requires specific and careful sample preparation to a very high concentration, CXS is an extremely promising x-ray scattering technique with a wide variety of possible applications.
Coupling electrochemistry and desorption electrospray ionization mass spectrometry to observe transient electrochemical intermediates [electronic resource]
Keywords: Chemistry.

The observation of electrochemical reaction species directly after electrochemical generation has been a goal of electrochemists for years, and is a problem that has been approached using many different analytical techniques. The challenge in acquiring faster response times exists in transferring electrochemically generated species quickly from solution to the gas phase for MS detection. The development of DESI allows for analyses to be made on surfaces under atmospheric pressure and at room temperature with a sampling time on the order of milliseconds. In collaboration with Prof. Hao Chen, we present a new DESI-ECMS technique for the mass spectrometric detection of fleeting reaction intermediates in electrochemical reactions utilizing a "waterwheel" working electrode setup is presented here. This setup takes inspiration from DESI-MS to sample directly from the surface of a working electrode for in situ electrochemical mass spectrometric analysis in seeking shorter analysis timescales. A number of systems is presented here verifying the viability of the waterwheel for DESI-ECMS analysis to observe fleeting electrochemical intermediates.
Coupling isotachophoresis to reaction and separation assays [electronic resource]
Keywords: Mechanical Engineering.

Molecular diagnostics are rapidly growing with applications in disease detection, genetic profiling, forensic investigation, and various research purposes. These techniques include PCR, sequencing, antibodies, and hybridization assays, and offer exquisite sensitivity and multiplexity. However, widespread adoption of molecular diagnostics is constrained by a number of key challenges. Assay times often take 16 hours or more, due to slow second order hybridization kinetics as well as time-consuming sample preparation methods. Furthermore, sample preparation itself is laborious, requiring manual intervention by highly-skilled personnel at several steps in the workflow. This dissertation discusses approaches that leverage isotachophoresis (ITP) and its coupling to at least one other assay step with an aim to significantly reduce analysis times and complexity of molecular detection assays. ITP is an electrokinetic technique which uses a heterogeneous buffer system to preconcentrate and separate ions based on their electrophoretic mobilities. In the first part of this dissertation, we present a simple analytical model to describe accumulation and reaction rates in ITP. This model is useful in the design of ITP experiments, and enables a user to make informed decisions regarding optimal sample placement in ITP assay design. In the second part of this dissertation, we describe a novel approach that leverages ITP to accelerate chemical reactions and also use an ionic spacer to separate reaction products. We first demonstrate this approach using synthetic DNA targets, and show high-sensitivity detection in a 10 min assay. We then extend this technique and use high-mobility probes to recruit typically non-focusing species (such as proteins) into ITP. We demonstrate this assay using C-reactive Protein (CRP) in buffer as well as in diluted serum. We also present a numerical and analytical model to describe ITP assays that involve non-focusing targets recruited into ITP. The last part of this dissertation shows how ITP purification can simplify sample preparation protocols and integrate with downstream analysis methods. We first show size-based RNA fractionation using ITP in a 10 min assay. We use a commercial electrophoresis system to analyze resulting sample fractions. Finally, we show how ITP purification can extend the applicability of recombinase polymerase amplification (RPA) to whole blood samples. We demonstrate lysis, purification, and detection of inactivated Listeria Monocytogenes cells from whole blood using ITP and RPA.
Covariance estimation and graphical models for infinite collections of random variables [electronic resource]
Keywords: Mathematics.

Estimating correlations for a large collection of random variables is an important part of an enormous number of modern applications of data science, statistics, and mathematics. In particular, it is often necessary to work with either an infinite collection of variables (such as in a spatial-temporal field) or to approximate a large high-dimensional finite stochastic system with an infinite-dimensional system. Two of the most common techniques used for high dimensional covariance estimation are Markov random fields, also known as graphical models, and positive definite functions, also known as covariance functions, but neither of these approaches has been adequately explored for use with infinite collections of random variables. In particular, the theory of Markov random fields is highly dependent on the finiteness of the graphs used to represent the random variables, and while covariance functions can be used for high-dimensional covariance estimation in certain contexts, they generalize poorly to non-spatiotemporal collections of random variables and have other drawbacks (e.g., they may induce poorly conditioned covariance matrices). This dissertation attempts to expand the mathematical theory of Markov random fields to enable infinite dimensional applications, and explores the relationship between graphical approaches to covariance estimation and positive definite functions.
Creativity Machines: How Video Game Hardware Characteristics Influence Software Variety
Keywords: Brandon Evans
Stanford University
Program in Science Technology and Society
STS
Honors Thesis
Video Game
Software Variety
Thesis

In writing this thesis, I explored the following research questions: What is the relationship between a console’s design characteristics and the types of video games developers tend to create for it? Do increases in hardware capabilities (i.e., processing power and storage capacity) correspond to increases in the creativity of video game developers, as reflected by increased software variety? Is there a relationship between increased software variety and console sales? Most specifically, this thesis evaluated the hypothesis that unconventional hardware corresponds to increased developer creativity. I found that ‘unconventional’ consoles (i.e., consoles that upended preexisting hardware paradigms in one or more ways) corresponded to increased genre variety, but processing power and media storage capacity had little correlation to genre variety. I also identified a correlation between genre variety and console unit sales: consoles with greater genre variety tended to outsell consoles with lower genre variety.
Creatures of two worlds [electronic resource] : small robots and hybrid aerial-terrestrial locomotion
Keywords: Mechanical Engineering.

This thesis is about the design and analysis of small, mobile robots that operate in various combinations of air and surface locomotion. Our goal is to create robots that traverse unstructured environments with speed and efficiency. Our analysis focuses on the physics of the transitions between states that make this kind of locomotion possible. Throughout the work, we will find connections with the natural world, where operation in multiple modes and at small scales defines the operational life of many animals. We note how advances in processors, sensors, and actuators have made it easier to create robots which explore these spaces, and look forward to the potential future growth of inexpensive, active platforms.
Cross-cultural understanding [electronic resource] : an examination on its measurement, teachability, and application
Keywords: Psychology.

Markus and Kitayama's seminal work (1991) on the independent and interdependent self-way has greatly benefited psychologists in understanding and interpreting cultural differences observed in the East and the West in the past decades. But it is unclear how much insight lay people have about this framework. How well do people from independent and interdependent cultures understand each other? I studied this question with two cultures that had been used frequently in past research: The mainstream American culture (an example of independent culture) and the traditional Chinese culture (an example of interdependent culture). I developed a scale that measured independent/interdependent cultural understanding, and used it to examine and compare Chinese and American people's understanding of each other (Study 1). I found that, in general, American participants were more "accurate" in their cross-cultural understanding than Chinese participants, and while Americans tended to stereotype the Chinese culture, the Chinese were more likely to project their own cultural values on Americans. I then looked at whether we could teach people about the independent/interdependent framework to help them gain insight into the other culture (Study 2). I found that learning about the framework led American participants to exaggerate the difference between Chinese and American culture. Lastly, I selected one cross-cultural setting to examine whether greater insight would lead to better cross-cultural interaction (Study 3), and found that cultural insight did not readily translate into culturally appropriate behaviors. Taken together, these studies begin to look at lay people's understanding of culture and of other cultures. It creates a space for research and discussion of how psychologists can best help people to understand and appreciate other cultures and "culture" itself as a construct that shapes and is shaped by every one of us.
Cross-species immune system atlas [electronic resource]
Keywords: Microbiology and Immunology.

Animal models are an integral part of the drug development and evaluation process. However, they are unsurprisingly imperfect reflections of humans. With the rise of targeted and biological therapeutics, it is increasingly important that we understand the molecular differences in immunological behavior of humans and model organisms. Thus, we profiled a large number of healthy humans, along with the model organisms most similar to humans: rhesus and cynomolgus macaques and African green monkeys, and the most widely used mammalian model: mice. Immune cell signaling responses to a panel of 15 stimuli were measured using CyTOF mass cytometry to read out universal signaling and phenotyping panels. We found numerous instances of different immune signaling events occurring between species with likely effects on evaluation of therapeutics. We frame these differences in the context of the immune system as a modular network.
Crystal structure determinations of xenon nanoparticles and X-ray induced transient lattice contraction in the solid-to-plasma transition [electronic resource]
Keywords: Applied Physics.

With the advent of free-electron lasers, the electronic and mechanical properties of single nanoparticles can be studied with intense, femtosecond x-ray bursts. X-ray coherent diffractive imaging techniques on single, non-periodic structures under the `diffraction-before-destruction' principle proves atomic resolution is within reach, but before the full potential of free-electron lasers is realized, a complete understanding of x-ray--matter interaction is of utmost importance. Xenon nanoclusters in the gas phase are ideal model systems for investigating light--matter interactions and x-ray induced electronic and structural effects. The experiments presented in this work were performed on such systems at the Coherent X-ray Imaging (CXI) Instrument of the Linac Coherent Light Source (LCLS). So far, serial femtosecond crystallography (SFX) experiments at the LCLS have been limited to particles larger than 100 nm, but in this study these techniques are extended to investigate nanoparticles 10--30 nm in diameter. In a first experiment, xenon nanoparticles were illuminated with hard x-ray flashes. When properly oriented in the ~100 nm FEL focus, Bragg scattering from the xenon crystals was recorded on a high resolution x-ray pixel array detector. Crystallite size, determined from Bragg peak shape, conform well to known scaling parameters. Structural determinations highlight the `crystal structure problem' for rare gas clusters, and suggest complex growth dynamics. Namely, the xenon cluster crystal structure is highly dependent on particle size, with more observed crystal faults as the particle size is increased. The data suggests a hexagonal close-packed (hcp) structure emerges from stacking faults in the face-centered cubic (fcc) structure of large clusters. All matter irradiated by intense FEL pulses is ionized within femtoseconds. The nanoplasma formation process is crucial for understanding x-ray--matter interactions. In a second experiment, the novel twin bunch operating mode for producing two hard x-ray pulses at the LCLS is utilized to investigate nanoplasma dynamics in 70 nm Xe clusters. An initial hard x-ray pump pulse (~15 fs, 1/3 mJ) isochorically heats the nanocluster and a second hard x-ray probe pulse (~15 fs, 2/3 mJ), delayed by up to 80 fs, probes the state of the nanoplasma. In addition to electronic and structural damage, time-resolved signals show an unexpected lattice contraction as the nanoplasma evolves. This contraction is attributed to the strongly enhanced electron mobility, resulting in a drastic change in bond character.
Crystallography of Prussian blue analogues and its effect on electrochemistry [electronic resource]
Keywords: Materials Science and Engineering.

Rechargeable batteries have revolutionized portable electronics and electric vehicles. Soon, they may also play an instrumental role in the integration of intermittent solar and wind resources by providing cost-effective grid-scale energy. Prussian Blue analogue (PBA) materials have demonstrated exceptional electrochemical properties that make them suitable for a variety of battery applications. However, little is understood about the specific mechanisms that enable these unique properties. In my work, I have demonstrated how the unique crystal structure of PBAs directly affects and enhances their electrochemical properties. In the first part of my dissertation, I showed that a wide variety of divalent and trivalent cations in aqueous solution can be electrochemically inserted and extracted with high speed and reversibility. I used synchrotron X-ray diffraction (XRD) to establish a novel vacancy-mediated pathway for multivalent ion conduction that could be valuable in the future development of multivalent-ion batteries. In the second part of my dissertation, I presented a PBA cathode material (manganese hexacyanomanganate) that exhibits promise as a high-capacity sodium-ion cathode in organic electrolyte. This system possessed the highest sodium-ion capacity (209 mAh/g) ever recorded, and I used synchrotron XRD to understand the structural distortions that enable this unusually high capacity. In the third part of my dissertation, I developed a framework to understand high-capacity PBA cathodes in aqueous systems. Using in situ synchrotron XRD and soft X-ray absorption spectroscopy, I investigated the complex interactions between the electronic structures of metal ions, the crystal structure, and electrochemical properties in this system. These experiments demonstrated fundamental kinetic limitations associated with electronic structure that may affect the future development of high-capacity PBA electrodes.
Cultivating the next generation [electronic resource] : three studies of college access among the children of immigrants
Keywords: Education.

Ensuring smooth transitions to college may be difficult for the children of immigrants since their families are likely unfamiliar with the U.S. system of higher education, which is horizontally stratified and requires a number of steps before admission. Bridging social science literature on immigrant assimilation, cultural, social, and human capital, and college choice, I study the pathway to college among immigrant youth, focusing on heterogeneity by generation and legal status and how community and state contexts moderate educational outcomes. In the first paper, I explore inequalities in college knowledge using data from the High School Longitudinal Study of 2009. Specifically, I examine whether 11th graders can accurately estimate tuition and fees at two- and four-year institutions and the expected earnings of various levels of educational attainment. The second paper builds on the first by testing for heterogeneous treatment effects of social interactions in high school using the Education Longitudinal Study of 2002. If there are differences in college knowledge, it is possible that discussing college with teachers, counselors, or college representatives has disproportionate impacts for the children of immigrants. Since 2001, 27 states have passed policies that limit or facilitate college access for undocumented students. Some states have banned them from receiving in-state resident tuition, while others allow it and provide financial aid. The final paper uses survey data from the Current Population Survey and administrative data from California and Texas to determine whether these policy regimes affect college choice and preparation for likely-undocumented Mexican and Hispanic youth. The findings from this dissertation may prove useful to practitioners and policymakers interested in improving the knowledge acquisition, academic preparation, and enrollment decisions of the children of immigrants, a group comprising nearly a quarter of schoolchildren today.
Cultivating Upstanding Democratic Citizens in the English Classroom: Reader-Response and Teaching the Conflicts Pedagogies
Keywords: English Education
Literature
moral imagination
Graduate School of Education
high school English
Breakthrough
Louise Rosenblatt
dialogic
student uptake
student discussion
multicultural literature
democracy
textual engagement
teaching the lenses
education
teaching the conflicts
reader-response
Thesis

In Stealth Democracy, Elizabeth Theiss-Morse and John R. Hibbing demonstrate that the majority of American citizens are unable to properly engage in conflict because they do not take the perspective of others seriously. Louise Rosenblatt’s vision for the English classroom in Literature as Exploration seeks to address these democratic problems, arguing that students must develop (1) critical thinking skills, where students can reflect on their own positions, and (2) a robust moral imagination, where students can imagine the perspective of someone different from them. This thesis examines and assesses two pedagogical candidates for fulfilling that Rosenblatt’s vision. The first is a variation of “reader-response theory” that aims to address the criticisms against traditional reader-response for being too self-focused and atheoretical. The second is Gerald Graff’s “teaching the conflicts,” which aims to prepare students for conflict by exposing students to conflicts surrounding literature and having students read opposing critical essays about a text. To conduct this study, I taught two 9th Literature classes for four weeks during a summer program, and I taught one class (n = 12) using a critical and multicultural variation of reader-response, and the other (n = 14) using teaching the conflicts. In analyzing the classroom discourse, I found traces of Rosenblatt’s vision fulfilled. While students in reader-response did less well with textual engagement than teaching the conflicts, it did better than its critics claim and facilitated impressive and meaningful personal discussions among students. Students in teaching the conflicts had fewer opportunities for personal engagement than reader-response, but they excelled in cultivating rigorous textual discussion and cultivating critical thinking skills. Both pedagogies are also educationally worthwhile insofar as they facilitate impressive student-to-student discussion.