VictorJuiz/thesis huggingface dataset:
Understanding and Improving Graph Algorithm Performance

Graph processing is experiencing a surge of renewed interest as applications in social networks and their analysis have grown in importance. Additionally, graph algorithms have found new applications in speech recognition and the sciences. In order to deliver the full potential of these emerging applications, graph processing must become substantially more efficient, as graph processing's communication-intensive nature often results in low arithmetic intensity that underutilizes available hardware platforms./nTo improve graph algorithm performance, this dissertation characterizes graph processing workloads on shared memory multiprocessors in order to understand graph algorithm performance. By querying performance counters to measure utilizations on real hardware, we find that contrary to prevailing wisdom, caches provide great benefit for graph processing and the systems are rarely memory bandwidth bound. Leveraging the insights of our workload characterization, we introduce the Graph Algorithm Iron Law (GAIL), a simple performance model that allows for reasoning about tradeoffs across layers by considering algorithmic efficiency, cache locality, and memory bandwidth utilization. We also provide the Graph Algorithm Platform (GAP) Benchmark Suite to help the community improve graph processing evaluations through standardization./nIn addition to understanding graph algorithm performance, we make contributions to improve graph algorithm performance. We present our direction-optimizing breadth-first search algorithm that is advantageous for low-diameter graphs, which are becoming increasingly relevant as social network analysis becomes more prevalent. Finally, we introduce propagation blocking, a technique to reduce memory communication on cache-based systems by blocking graph computations in order to improve spatial locality.

Advisor: Asanović, Krste
Patterson, David
New World Mennonite Low German: An Investigating of Changes in Progress

This dissertation explores dialect diversification in the long-distance New World Plautdietsch speech community. Plautdietsch dialects are traditionally classified as belonging to one of two types: either Chortitza or Molotschna. The traditional dialect classification has recently come under scrutiny because speakers rarely use features exclusive to either type. I propose that variation in vowel production is an alternative way of classifying dialect affiliation. In this project, I analyze both the production of vowels and the production of traditional dialect features used by native Plautdietsch speakers living in North America. This work finds that both the traditional dialect features and the innovations in the vowel system are linked to information about a community's migration history, but the two systems represent different aspects of a community's history.

Advisor: Holland, Gary
Molecular Design Principles for Electrochemical Materials

Electrochemical materials play an increasingly important role in our energy landscape, and understanding their behavior at a molecular level is critical for the design of next- generation electrochemical materials that will meet our energy needs. In this dissertation, I will share my work towards the molecular design of three different classes of electrochemical materials: nanocrystals, membranes, and redox mediators./nIn the first part of this dissertation, I describe my work with controlling nanocrystal (NC) surface chemistry. NCs are being actively studied due to their unique optical, thermal, electrochemical, and mechanical properties that make them uniquely suited as energy conversion and storage materials. For applications that involve electron transport to or from the NC, the insulating ligands that are commonly used to stabilize the NCs during their synthesis must be removed. I will describe my work studying and developing a new class of ligand stripping reactions that accomplishes this while preserving colloidal stability for the widest group of NC materials to date. The "naked" NC inks produced by my approach are expected to find use in a wide variety of energy conversion and storage applications./nIn the second part of this dissertation, I describe my work developing and study- ing size-sieving membranes for next-generation batteries. Many next-generation battery chemistries, including Li–O2, Li–S, and non-aqueous redox-flow batteries store charge with soluble active-species in non-aqueous electrolytes. Each of these chemistries requires the development of new membranes that are capable of blocking active-species crossover while allowing transport of the working-ion. I have established membranes based on polymers of intrinsic microporosity (PIMs) as a class of size-sieving membranes that accomplish this goal. In this dissertation, I outline my work applying these membranes to two different battery chemistries (Li–S and all-organic non-aqueous redox-flow batteries) and explore the impact of membrane reactivity and swelling on its active-species blocking-ability./nIn the third and final part of this dissertation, I describe my work with soluble redox-mediators that aid in the electrodeposition of insulating active-materials for next- generation batteries. Many next-generation battery chemistries, including Li–O2 and Li–S, rely on the electrodeposition of insulating active materials to store charge. This electrodeposition process is usually self-limiting, and leads to limits on battery capacity for a given surface area of current collector. In this dissertation, I describe how I circumvent this limit by designing redox-mediators that allow electron transfer and electrodeposition to be spatially decoupled, leading to the electrodeposition of thick deposits (rather than thin coatings) of the insulating active material.

Advisor: Helms, Brett
Yaghi, Omar
Phenomenology of creation of antihydrogen and measurement of antihydrogen properties

This dissertation focuses on three ideas useful to the nonneutral plasma experiment at/nUC Berkeley and the ALPHA experiment at CERN. While these may seem like disparate/nideas, in all cases, a careful mathematical treatment of the problems yield useful insights./nFirst, we present improvements to the analysis for diagnostics of temperature and den-/nsity of plasmas in Penning-Malmberg trap experiments. Our new methods are faster and/nmore accurate than previously used methods of analysis. This allows us to conduct these/ndiagnostics in real-time without any input from a human./nWe then theoretically consider the problem of enhanced cooling of an electron plasma/nfrom a coupling of the plasma to cavity modes. We make more rigorous the previous analysis/nthat was done on the topic, and then extend these results to a longitudinally dynamic plasma./nWe compare our theoretical results with experimental observations from the Berkeley plasma/ntrap and with simulations and find good agreement./nFinally, we consider analyses of ALPHA data to measure antihydrogen properties. We/nplace a statistically rigorous bound on the antihydrogen charge from ALPHA data. This/nimproves the previous bound on antihydrogen charge by a factor of 20, and assuming super-/nposition, improves the bound on the positron charge anomaly by a factor of 25. Finally, we/nconsider analyses for a future measurement of the gravitational mass of antihydrogen. We/nfind that with reasonable constraints, a measurement of the gravitational mass of antihydro-/ngen with a precision of 1% should be feasible.

Advisor: Wurtele, Jonathan S
Passive Focusing of Intense Ion Beams

The radial control of high current ion beams from induction accelerators or generated by short pulsed intense laser-plasma interactions is generally limited by Coulomb repulsion of the ion beam. In this dissertation, we investigate a novel focusing technique for the radial control of intense ion beams. The concept envisions using a stack of thin, closely spaced conducting foils to mitigate defocusing self-electric forces to enable self-magnetic forces to focus./nThe ion beam must be energetic enough to penetrate the stack of foils with limited beam degradation from scattering and energy loss. We study beam focusing and scattering and find constraints on the design and performance of such a passive lens./nWe further investigate the effects of secondary electrons generated by the impact of ions on foils and show the importance of secondary electrons whose velocity is higher than the ion beam velocity. In this case, current neutralization could exceed charge neutralization, i.e., the self-magnetic focusing would be reduced more than the self-electric defocusing, producing a net defocusing force on the ion beam./nA statistical envelope model is developed and its predictions are compared to those of the PIC simulation code WARP./nAn ion beam focused by the stack of thin foils may have potential applications to research fields requiring intense beams, e.g., nuclear fusion, tumor therapy or high energy density laboratory physics. We provide in the appendix an analysis of the expansion of a thin foil heated to the warm dense matter (WDM) regime which can be reached by such beams.

Advisor: Wurtele, Jonathan Syrkin
van Bibber, Karl Albert
Fluid Mechanics Problems Motivated by Gravure Printing of Electronics

During intaglio (gravure) printing, a blade wipes excess ink from the engraved plate with the object of leaving ink--filled cells defining the image to be printed. That objective is not completely attained. Capillarity draws some ink from the cell into a meniscus connecting the blade to the substrate, and the continuing motion of the engraved plate smears that ink over its surface. That smear behind the cell delivers a feature lacking in sharpness. Even though the smear formation occurs at micron scale, it affects the functionality at the scale of micron size printed electronics. By examining the limit of vanishing capillary number ($Ca$, based on substrate speed), we reduce the problem of determining smear volume to one of hydrostatics. Using numerical solutions of the corresponding free boundary problem for the Stokes equations of motion, we show that the hydrostatic theory provides an upper bound to smear volume for finite $Ca$; as $Ca$ is decreased, smear volume increases. The theory explains why polishing to reduce the tip radius of the blade is an effective way to control smearing. As the motion continues, smear volume under the meniscus is printed as a tail behind the cell extending back toward the blade. In the limit of vanishing $Ca$, an inner and outer analysis of the meniscus printing problem shows that the meniscus rotates around the pinned contact line at the trailing edge of the cell, and the volume under the meniscus is used to coat a film of thickness decreasing linearly in time forming a tail shape. The tail lengthens with decreasing $Ca$, owing to the concomitant increase in smear volume; the opposite is true as $Ca$ approaches $O(1)$. For small $Ca$, it is computationally expensive to use the Stokes solver to show that the physical mechanism of tail formation described by the analysis as $Ca \to 0$ is correct. Lubrication theory, on the other hand, predicts tail formation mechanism closely for contact angles over the blade close to $\uppi/2$, and this motivates us to use the lubrication model for smaller $Ca$. With the continuing motion of substrate, we show the transition from the tip region (squeeze film) to the Landau-Levich film in the form of a tail shape extending back toward the bulk meniscus (static), and this agrees with the physical picture described by the analysis as $Ca \to 0$. The results contribute to the control and understanding of smear formation mechanism during gravure printing of electronics.

Advisor: Morris, Stephen
Pedagogy, Display, and Sympathy at the French Jesuit Orphanage Workshops of Tushanwan in Early-twentieth Century Shanghai

This dissertation closely examines the art and craft workshops at the French-Jesuit-run orphanage of Tushanwan in the first decades of the twentieth-century. Founded in the 1860s, the workshops taught Chinese orphaned boys a wide range of vocational skills from painting to shoemaking in preparation for their entry into adulthood in a rapidly modernizing China. Using different art objects and projects created at the major workshops as my primary subjects of investigation, the dissertation analyzes the transmission, translation, and reinvention of modern Euro-American aesthetic ideologies and techniques at Tushanwan and their receptions. In the process, I question the nature and motivation of commercial workshops like Tushanwan beyond the monetary and reframe its practices and operations in terms of the religious, institutional, cultural, and historical legacies of the Jesuits in China. I also expand the global scope of popular late-nineteenth-century European aesthetic movements such as the Arts and Crafts by accounting for the reinterpretation of those ideologies within the local context. Through the works and practices from the workshops, I describe a collage of interactions between China and the world united by a sense of common spiritual identity that supposedly transcended national and state boundaries, but instead reified and maintained the heterogeneity of identities.

Advisor: Berger, Patricia
A study on the development and application of optically polarized materials: Spin hyperpolarization from the nitrogen vacancy center in diamond and hyperpolarized 129Xe NMR biosensors

Optically hyperpolarized electrons can be harnessed to transfer polarization to interacting nuclei. One example of this is the optically hyperpolarized spin state of nitrogen vacancy centers (NV- center) in diamond, which can act as sources of polarization for neighboring 13C nuclei. Spin-exchange optical pumping (SEOP) using circularly polarized light has been used for 129Xe hyperpolarization. Both hyperpolarization techniques provide a means of overcoming the fundamentally low sensitivity that has been a long-existing problem of NMR/MRI. Here, physical properties on polarization transfer from optically hyperpolarized NV- centers to 13C nuclei in diamond are studied as well as the development of several hyperpolarized 129Xe NMR/MRI biosensors./nOn the subject of NV- centers in diamond, I studied polarization transfer to nearby 13C in natural abundance 13C diamond. The bulk 13C spin polarization was estimated to be ~6 % at room temperature. Dynamic nuclear polarization and its mechanism were investigated for various diamonds with different 13C concentrations (10, 25, 100%). The diamond with 10% 13C enrichment showed similar polarization enhancement as the natural abundance sample and spin diffusion was considered to be the limiting factor in the polarization transfer mechanism. Optically detected magnetic resonance (ODMR) studies were also carried out on NV- centers in nanodiamond powders. Interestingly, we observed not only broad powder patterns stemming from Δm =1 transitions, but also sharp powder patterns from orientation independent overtone transitions (Δm =2) that were supported by simulation./nOn the subject of hyperpolarized 129Xe biosensors, I synthesized a multi-metal ion sensor using hyperpolarized 129Xe NMR, whose chemical shifts in a cryptophane cage gave distinct signals with regard to different metal ions. Also the metal ion concentration dependent signal intensity was found to have potential for quantification applications. A 129Xe NMR/MRI biosensor targeting a folate receptor was developed and its binding on the Hela cell, which overexpresses folate receptors, was investigated by confocal laser scanning microscopy, flow cytometry, and 129Xe hyper-CEST NMR/MRI technique. Furthermore, an estradiol-based biosensor was developed for 129Xe Hyper-CEST detection of the estrogen receptor in breast cancer and a new methodology to detect endocrine distruptors in environmental samples by using 129Xe hyper-CEST NMR was proposed. Lastly, I successfully synthesized a targeted, selective, and highly sensitive 129Xe NMR nanoscale biosensor using a spherical MS2 viral capsid, cryptophane cage, and DNA aptamer.

Advisor: Pines, Alexander
Environmental gas sensing with high surface area nanomaterials on a low-power microfabricated heater platform

Gas sensors can provide information about the presence of dangerous gases in industrial and residential sites, allowing for improved environmental protection and human health and safety. In order to enable ubiquitous wireless monitoring of combustible and toxic gases, sensor elements with low power consumption are required. Two common types of gas sensors, namely calorimetric and conductometric sensors, rely on heated sensor elements to activate the appropriate reactions with the gas of interest, resulting in high power requirements to maintain the necessary operating temperatures. Miniaturized gas sensors made with microfabricated heater platforms and nanoscale sensing materials can lead to low power sensor elements with high performance. The minimization of the power consumption cannot be at the expense of the sensor’s ability to detect dangerous combustible and toxic gases. The sensing performance is impacted by the properties of both the microheater and the sensing material, as well as the integration of the two elements, creating significant opportunity for research and development to improve the performance parameters, such as sensitivity, detectable concentration range, selectivity, response and recovery time, stability, size, manufacturability, and cost, as well as power consumption./nThe development approach described in the following thesis relies on an optimized microheater platform as well as novel sensing materials. The design, fabrication, and characterization of a low-power microheater platform is described, with polycrystalline silicon as the heater material for moderate temperature and polycrystalline silicon carbide for improved reliability at high temperature operation. A small, isolated heated area decreases the required power consumption and a closed membrane facilitates easier deposition of sensing materials. Sensing materials for combustible and toxic gas detection have been developed based on ultra high surface area aerogels. For combustible gas sensing, graphene or boron nitride aerogel acts as a scaffold for catalytic platinum or palladium nanoparticles. Bare graphene aerogel and graphene aerogel coated with single to few-layer molybdenum disulfide sheets are used for toxic gas detection./nThe microheater platform with fast response and recovery times provides opportunities for localized, in-situ synthesis of high surface area sensing materials. The use of the microheater platform for localized growth of a nanocrystalline tin oxide sensing film is described. The fast thermal response of the microheater leads to rapid heating of the precursor, creating a highly porous film that is proven beneficial for toxic gas sensing.

Advisor: Maboudian, Roya
Photochemical Reaction Dynamics Studied by Femtosecond Soft X-ray Transient Absorption Spectroscopy

The ability to discern and understand the time evolution of both molecular and electronic structure during a chemical reaction in real-time, and with atomic-scale sensitivity, is a primary goal of modern chemical dynamics research. In this dissertation, femtosecond extreme ultraviolet/soft x-ray transient absorption spectroscopy is developed on a table-top apparatus and applied to investigate the evolution of both vibrational and electronic degrees of freedom in molecules following photoexcitation or ionization. Several molecular systems are considered in detail. In the first study, the strong-field ionization of a heteronuclear diatomic molecule, IBr, and the ensuing vibrational wavepacket dynamics in the electronic ground state of the neutral molecule are characterized with atomic-site sensitivity. The element-specificity of the core-level transient absorption technique is further extended to investigate the multichannel ultraviolet photodissociation reaction of bromoiodomethane, CH2IBr. The core-to-valence absorption spectrum of the bromomethyl radical, CH2Br, which is formed via the major C-I photodissociation coordinate at 266 nm, is characterized for the first time. The measured C-I dissociation time (~50 fs) differs significantly from the C-Br dissociation time (~110 fs), which indicates that more than one excited-state surface is involved. In the third study, the evolution of the transient valence electronic structures in the transition state regions of both the methyl and allyl iodide photodissociation reactions are directly observed and characterized. As the C-I bond is breaking, new 4d(I) core-to-valence resonances localized on the I atom are observed and assigned to repulsive valence-excited transition-state regions. The transition-state resonances directly probe the evolving valence electronic structure during these fundamental bond-breaking reactions. Finally, a full-scale apparatus upgrade was undertaken to extend the femtosecond light source into the soft x-ray energy domain up to and beyond 300 eV. With this new setup, the first femtosecond soft x-ray transient absorption experiments at the carbon K-edge (~284 eV) are performed. In particular, the ultrafast electrocyclic ring-opening reaction of 1,3-cyclohexadiene is investigated and the evolution of the valence electronic structure during the ~180 fs ring-opening process is directly captured. The core-to-valence spectroscopic signatures of the elusive transient intermediate excited states, which lead to ring-opening, are characterized, in combination with time-dependent density functional theory calculations, to reveal overlap and mixing of the frontier valence orbital energy levels.

Advisor: Leone, Stephen R
Genetic determinants of phenotypic evolution in Saccharomyces yeast

Years of trait mapping studies have uncovered the genetic determinants underlying phenotypic evolution over both short and long timescales in a variety of organisms./nA more general understanding of the mechanisms through which evolution produces phenotypic novelty, however, still remains out of reach. Many outstanding questions remain, among them how coding sequence divergence and gene expression divergence respectively contribute to trait evolution, as well as what role rare and large effect genetic variants play in the genetic networks underlying evolving phenotypes. Using Saccharomyces yeast as a genetically tractable model system in which to probe these questions, we identify and dissect several examples of trait divergence within and between yeast species. We first investigate an instance of intraspecific variation among yeasts isolated from a single population, finding that large effect rare variants at hypermutable loci are drivers of many common morphological and growth phenotypes. Next, in a comparison of both recently-diverged and long-diverged species, we investigate the role that gene expression variation plays in phenotypic evolution. We find evidence in multiple gene networks for complex and coherent regulatory evolution, and in one instance we succeed in identifying the loci that effect this change, as well as several phenotypic novelties they produce. Collectively, these investigations will contribute to the growing body of literature that describe the genetic mechanisms that underlie phenotypic change and seek, eventually, to achieve a greater understanding of basic evolutionary principles.

Advisor: Brem, Rachel B
Taylor, John W