VictorJuiz/thesis huggingface dataset:
Theory, design, and demonstration of a new microwave-based undulator [electronic resource]

Synchrotron Light Sources and Free Electron Lasers (FEL) oﬀer great applications in the ﬁelds of metallurgy, biology, chemistry, and archeology etc., by providing a radiation probe for extremely small structures (like molecules, DNAs) and small durations (like timescale of chemical reactions). In these experimental facilities, electrons are accelerated to relativistic energies and then passed through an undulator or wiggler to generate the radiation. The undulator, which is the backbone of such a light source, is conventionally a series of permanent magnets with a strong magnetic ﬁeld, constant in time but alternating in space. These undulators, however, provide limited control over the properties of the generated radiation. Moreover, it is very challenging to scale the magnetic undulators down to smaller undulating periods -- a useful feature to generate shorter wavelength radiation by spending lesser energy in the acceleration of the electrons. Such scaling will also require strict limits on the maximum electron beam aperture, ﬁeld strength, and consequently the radiation brightness. To overcome these shortcomings of the magnetic undulator technology, we have designed a novel short-period microwave undulator and have demonstrated its successful operation at NLCTA, SLAC. This microwave undulator is essentially a Thomson scattering device that has yielded tunable spontaneous emission and seeded coherent radiation. It is about 1 m long axisymmetric, corrugated, copper cavity, resonant at 11.424 GHz with an undulator period of 1.39 cm. The undulator deﬂection parameter (K) of this microwave undulator is tunable and has achieved a value as high as 0.7 (the equivalent ﬁeld strength is 0.55 Tesla). Given the availability of a high power rf source, K = 1 could also be achieved without breakdowns due to high surface ﬁelds in the undulator cavity. Moreover, the design of this undulator is conveniently scalable to smaller undulator periods as the required size of the electron beam aperture does not reduce as sharply as it does for the magnetic undulators. The undulator ends were designed to have tapered ﬁeld to minimize transverse drift and kick induced in the electron beam. For future generation light sources, this device promises shorter undulator period, large aperture, and fast dynamic control. We have also presented a new Finite Element Method (FEM) based implementation that can eﬃciently calculate electromagnetic ﬁelds in general axisymmetric cavities.

Keywords: Electrical Engineering.
Advisor: Tantawi Sami primary advisor. Thesis advisor
Lee Thomas H.
Pianetta Piero advisor. Thesis advisor
A theory of countryside biogeography [electronic resource]

Humans are the dominant influence affecting patterns of life on the planet. Our demand for food, fuel, and fiber create the countless countryside ecosystems that collectively constitute the majority of the biosphere. Countryside biogeography studies the distribution of biological variation over space and time in human-dominated ecosystems. It explicitly considers all ecosystem components, including: minimally-altered habitats; novel ecosystems; domestic and feral plants and animals; human populations; and the services provided by nature to people, including quality of life. Countryside biogeography also deliberately focuses on forecasting changes in biodiversity and biodiversity-driven ecosystem services under a variety of possible futures. As such, one of the primary aims of countryside biogeography is to understand what kinds of ecosystems will exist in the coming decades and which might merit the most protection through human intervention.

Keywords: Biology.
Advisor: Daily Gretchen C.
Ehrlich Paul
Fukami Tadashi
Hadly Elizabeth Anne
Thermodynamic and kinetic studies of hydrogenenation reaction in magnesium/palladium nanostructures [electronic resource]

The factors affecting the formation rate and stability of metal hydride thin films, so crucial for hydrogen storage applications, are not well understood. The low equilibrium hydrogen pressure, hence high stability, of metal hydride inhibits easy charging/discharging for fuel cell applications. The significant increase of equilibrium hydrogen pressure observed in Mg/Pd thin films is encouraging, but has been mistakenly attributed to mechanical and not chemical factors. Our experiments prove that mechanical strain is present only in the Pd layer and cannot significantly affect the hydride stability. However, a simple thermodynamic analysis suggests that an intermixing layer of Mg and Pd will destabilize the hydride enough to account for the observed increase in equilibrium hydrogen pressure. We used TEM and XPS to look for this layer and found it, as expected. We show that the equilibrium pressure increase can be further enhanced by increasing the amount of intermixing. Having determined the effect of intermixing on the hydride thermodynamics, it is still unclear how the diffusion of hydrogen and propagation of the hydride phase boundary occurs in the metal hydride. We next characterize hydride formation from isolated points of nucleation in a simple morphology in order to develop design rules for more complicated hydrogen storage structures. In order to physically control the nucleation, we only permit hydrogen to enter the magnesium through sparsely distributed Pd ``nanoportals.'' Because the Pd nanoportals are far apart, we are able to study hydride nucleation one site at a time. We are able to measure the nucleation time constant and the diffusion constants of hydrogen in the hydride by fitting data to a modified Avrami model. We observe that the morphology of grown hydride and the growth rate of hydride are prominently affected by the crystal structure of the magnesium film. However, continuous oxidation of the Mg film pinches off the Pd portals and slows the hydride formation. Better control of the sample structure and chemical state is needed to extract the kinetic parameters correctly and understand the reaction kinetics. By doing so, we hope to provide new ideas and design rules for future storage materials.

Keywords: Materials Science and Engineering.
Advisor: Clemens B. M. (Bruce M.) primary advisor. Thesis advisor
Cui Yi
Salleo Alberto
Thunderstorm-induced enhancements in the E-region ionosphere [electronic resource]

The purpose of this study is to understand the coupling between convective phenomena in the lower atmosphere and the Sporadic-E anomaly observed in the E-region of the ionosphere. The ionosphere is a region of partially ionized air in the upper atmosphere created by solar radiation. It has often been observed that Sporadic-E, an anomalous ionization enhancement occurring in the E-region of the ionosphere, often disrupts satellite-earth communications at the MF, HF and even in the VHF frequency bands and that this anomaly is thought to be fairly prevalent during thunderstorm activity. However, very little is known about the mechanisms behind Sporadic-E formation, though multiple theories that attempt to explain the physics behind this phenomenon are topics of ongoing research. This study attempts to explore the theory of indirect enhancement of the E-region ionosphere through the launching of atmospheric gravity waves (AGWs) and the subsequent formation of traveling ionospheric disturbances (TIDs) through two observational experiments. In the first experiment, two dual-band GPS receivers were used to measure fluctuations in total electron content during thunderstorms. This experiment was aimed at providing insights into whether or not thunderstorms were always associated with AGWs and TIDs. As part of the second experiment, a stellar radio source was observed within a range of output radio frequencies from the Long Wavelength Array (LWA) at Datil, NM, during both stormy and fair weather days. Preferential blockage of the lower stellar frequencies could then be used to suggest that the E-region has been enhanced to 'cutoff' the low frequency stellar radiation. Although the experiments themselves were conducted successfully on multiple occasions, there is insufficient data for conclusions regarding the correlation between thunderstorms and the formation of Sporadic-E. Nonetheless, some encouraging conclusions and recommendations are discussed and the study is hoped to serve as a stepping stone for future research.

Keywords: Aeronautics and Astronautics.
Advisor: Close Sigrid
Timing of discrete musical air-gestures [electronic resource]

Motion sensing technologies enable musical interfaces where a performer can control sound by moving their body ``in the air, '' without manipulating or contacting a physical object. These interfaces work well when the movement and resulting sound are smooth and continuous. However, it has proven difficult to design a system which triggers discrete sounds with precision that feels natural to the performer and allows them to play complex rhythmic music. This thesis presents a study into "air-drumming" gestures. Participants performed drumming-like gestures in time to simple recorded rhythmic drum sounds. These movements are recorded and then examined to look for aspects of the movement that correspond to the timing of the drum sounds. The goal of this research is to understand what we do with our bodies when we gesture in the air to trigger a sound, with the hope that the results can be used to design more accurate and responsive air-gesture-controlled instruments. It is assumed that when we gesture in the air to generate a sound, we do something with our bodies to create a sensation of a moment in time and that we intend the sound to occur at this time. Eight movement features are extracted from the movement data, and it is hypothesized that one or more of these movement features correspond to this body sensation. Four of the movement features are based on tracking the location of the hand and wrist. Hits are moments where the hand or wrist suddenly change direction at the end of a strike gesture, and a novel algorithm for detecting hits is presented. And acceleration peaks are peaks in the magnitude acceleration of the hand or wrist as they suddenly decelerate at the end of the gesture . The remaining four movement features are based on the angles of the elbow and wrist joints. Extrema in joint angle are detected, as are sudden peaks in angular acceleration of the joint. The timing of these movement events is analyzed with respect to the timing of the drum sounds. Analysis is also performed comparing how the timing of movement events changes when speed at which notes are repeated changes. In general it is found that features based on acceleration peaks occur earlier, closer to the audio event, and with less noise, and that these features vary less with respect to note speed. It is also shown that timing differences between hand and wrist features can be used to study individual differences and group performers according to movement style.

Keywords: Music.
Advisor: Chafe Chris primary advisor. Thesis advisor
Berger Jonathan
Fujioka Takako
To stake a claim [electronic resource] : the making of rabbinic agricultural spaces in the Roman contryside

This dissertation argues that the prescriptions for Jewish practice and the boundaries of Jewish space in the Late Antique countryside may be considered a call by the rabbis for the transformation of a landscape filled with many different neighbors, from non-rabbinic Jews to Roman conquerors. The rabbinic sources set forth the vision for an idealized Jewish landscape filled with rabbinic Jews who manage their estates in accordance with God's will. In modern scholarship, agricultural rituals and spaces in the Mishnah and the Tosefta are often set aside in favor of consideration of urban life and society. By interrogating the importance of these spaces and their rituals, this dissertation shows that the authors of Jewish literature adopt Roman ideals of rural life but subvert those ideals to impose a specifically Jewish vernacular upon the landscape. The commitment to Biblical laws of agriculture, even in light of profound changes to the landscape wrought by Roman imperial domination, serves to challenge that domination through the assertion of distinctly Jewish agricultural spaces. In this dissertation, the halakhic reasoning and argumentation found in early rabbinic literature is analyzed through textual, literary, and spatial analysis to reveal the cultural and spatial ideals of the creators of these texts. These legal texts describe a world filled with outsiders, from Roman conquerors to Jews with different interpretations of scripture and practice: the laws of Jewish farming serve to differentiate normative Jewish practice and social structures from those others. It is the spatial aspect of agricultural life, from its fences to its regimented rows of crops that serve to physically and visually mark a Jewish space as distinct. This dissertation offers tools for spatial analysis of legal texts in rabbinic Judaism specifically and imperial spaces more broadly.

Keywords: Religious Studies.
Advisor: Fonrobert Charlotte Elisheva primary advisor. Thesis advisor
Bashir Shahzad
Klein Gil P. advisor. Thesis advisor
Parker Grant Richard
Weitzman Steven
To Starve a Fever or Feed a Cold? How Food Intake Modifies an Immune Response

In many organisms, including humans and mice, diet-restriction is one of the most common immune responses. In mice, long-term diet restriction has been shown to decrease the age-associated reduction in immune function, effectively increasing the capacity of the immune response. Despite this, long-term diet restriction decreased mouse survival from Influenza infections. In Drosophila, anorexia can alter both host tolerance and resistance in response to microbial infection, and can be beneficial or detrimental to host survival rates, depending upon the pathogen. This suggests that diet has the ability to modulate expression of genes of the innate immune system. Although anorexia is a commonly-induced immune response, its mechanism of action is unclear. Further research into the mechanism and effects of infection-induced diet restriction on the immune system is necessary because previous research has focused mostly on long-term diet restriction. We seek to determine how infection-induced anorexia, and subsequently diet restriction, alters gene expression profiles in order to modulate an immune response.
The effectiveness of an immune response is shaped by the genes that are activated to fight the infection and their degree of activation at different times during the infection. Diet restricted flies that are infected with Listeria monocytogenes show decreased survival when compared to non-diet restricted flies. We hypothesized that diet-restriction could affect survival
of infected flies by changing the dynamics of the immune response.
Recent work from our lab has shown that many immune responsive genes, including antimicrobial peptide (AMP) genes, are expressed at levels directly dependent upon microbe number in the fly. Analyzing complete gene expression profiles for immune genes allows us to more precisely describe changes in gene induction by measuring not only maximal induction levels but the rate of gene induction. Here we show that for several AMP genes, diet restriction causes gene induction at a lower microbe concentration, thereby increasing the sensitivity of the fly to infection and reducing survival. We conclude that diet is an important factor during infection that can cause shifts in the expression of many immune genes, a fact that was
previously unnoticed due to the way in which gene expression was measured.

Keywords:  Department of Biology
diet restriction
AMPs
gene expression profiles
immunity
Drosophila
anorexia
Biology
Thesis
Advisor: Schneider David
Mudgett Mary Beth
Topics in matrix inference [electronic resource]

Two topics in matrix inference are considered: matrix denoising and matrix organization. In matrix denoising, one attempts to recover an unknown matrix $X$ from a single noisy observation $Y=X+Z$, where $Z$ is a noise matrix with independent, identically distributed entries. It is shown that random matrix theory delivers simple, convincing answers to a range of fundamental questions, such as the minimax risk of matrix denoising by singular value soft thresholding, the location of the optimal singular value threshold and the shape of the optimal singular value shrinker. In matrix organization, one attempts to recover the latent structure of the row set of the column set of a matrix, such that matrix entries can be reliably predicted from close-by entries. We propose a self-contained framework for matrix organization and subsequent sampling, approximation and compression.

Keywords: Statistics.
Advisor: Coifman Ronald R. (Ronald Raphaël) primary advisor. Thesis advisor
Donoho David Leigh primary advisor. Thesis advisor
Johnstone I. M.
Topics in quantum information and string theory [electronic resource]

There are many aspects of the Ads/CFT correspondence that end up having rather direct applications to condensed matter physics. While some of these applications are rather straightforward and expected from parallel results in the condensed matter literature, some of the results are rather interesting and new, and sometimes derive from entirely unexpected aspects of the gravitational theory proposed to be dual to the condensed matter eld theory. In this thesis, I will explore several such examples that I have had the honor to study. This thesis is based on the papers [75], [2], [3] and [4] written with Xi Dong, Sarah Harrison, Shamit Kachru, Eva Silverstein, Subir Sachdev, and Gonzalo Torroba, or some subset thereof. It should not be cited without also referencing those papers.

Keywords: Physics.
Advisor: Silverstein Eva
Hartnoll Sean advisor. Thesis advisor
Kachru Shamit
Torque spectroscopy of DNA [electronic resource]

Cellular processes such as transcription and replication are regulated by torque in supercoiled DNA. Torque affects the kinetics of DNA-associated enzymes and can favor localized unwinding and other structural transitions of the double helix. High-resolution methods for direct measurement and control of DNA torque are needed in order to understand the sequence-dependent energetics and dynamics of torsionally strained DNA. I have developed a single-molecule magnetic tweezers method for torque measurement and feedback, enabling investigations of DNA under biologically relevant mechanical perturbations. My colleagues and I characterized the overall response of DNA to torque, the sequence-dependent energetics of strand separation and Z-DNA formation, and the physical properties of DNA mismatches. We analyzed the results using an equilibrium model for cooperative structural transitions that quantitatively describes our observations. I have further explored the dynamics of strand separation, and showed how my measurements can be explained using a drag-limited model in which the observed single-molecule dynamics depend only on parameters measured in equilibrium. The results contribute to our understanding of non-canonical DNA conformations, provide general lessons for studying transition dynamics in tethered systems, and enable future studies of mechanochemistry in molecular machines at the heart of biology.

Advisor: Bryant Zev David primary advisor. Thesis advisor
Kirkegaard Karla advisor. Thesis advisor
Puglisi Joseph D. advisor. Thesis advisor
Toxoplasma gondii reduces innate fear to predator urine by altering the brain of its rodent host [electronic resource]

The protozoan parasite Toxoplasma gondii is known to dampen fear responses to cat urine in infected rodent hosts. Such manipulation is likely advantageous to the parasite in the wild, possibly increasing predation by the definitive host of Toxoplasma, the cat. Here we report that in infected rats, Toxoplasma modifies limbic structures responsive to appetitive, sexual stimuli, converting ensembles of neural activity in regions of sexual attraction to respond to cat urine. Understanding how Toxoplasma is inspiring these behavioral changes in the host brain requires knowledge of the precise anatomical location of the parasite in the host brain. For this reason, we used a genetically-engineered Toxoplasma in a mouse that allowed us to track, at single-neuron resolution, the location of the parasite and the location of any neuron it invaded or tried to invade ("Toxoplasma-interacted neurons"). We report high individual variation in loss-of-aversion to cat urine in infected mice and that numbers of Toxoplasma-interacted neurons in the total brain did not explain this variation. However, variation in number of Toxoplasma-interacted neurons in the corpus striatum predicted response to the dopamine D2 receptor antagonist haloperidol, providing evidence that Toxoplasma is interacting with dopamine in the infected host brain.

Keywords: Neuroscience.
Advisor: Sapolsky Robert M. primary advisor. Thesis advisor
Boothroyd John C. advisor. Thesis advisor
Fernald Russell D. advisor. Thesis advisor
Hestrin Shaul
Transmit array concepts for improved safety in magnetic resonance imaging [electronic resource]

Magnetic resonance imaging (MRI) is a powerful medical imaging modality that can generate high-resolution diagnostic images with excellent soft-tissue contrast. Unlike x-ray and CT, MRI does not use any ionizing radiation and consequently is considered a safe imaging modality for most patients. However, for patients with implanted medical devices, MRI presents significant safety hazards. The transmit radiofrequency (RF) fields used in MRI can induce current in elongated conductors, such as neurostimulator and cardiac pacemaker leads, potentially causing dangerous heating of surrounding tissues. This safety hazard prevents many patients with implanted medical devices from receiving MRI exams, and it also presents challenges for MRI-guided interventional procedures. Much of the RF safety work to date has focused on modifying implanted devices to be safer in the MRI environment. This dissertation presents a different approach to the RF safety problem. Instead of modifying devices for the MRI environment, this work explores how transmit array technology can be used to make the MRI environment itself safer for existing devices by controlling the induced RF current levels that are responsible for heating. A novel toroidal transmit-receive coil for safely visualizing conductive interventional guidewires is presented. This coil transforms conductive guidewires and catheters into controllable elements of a transmit array and allows device visualization using only milliwatts of transmit power. Successful device visualization is demonstrated at 1.5T and 3T. Fluoroptic temperature probe measurements indicate that the low power levels required for device visualization are orders of magnitude below the levels that induce heating in a tissue-mimicking phantom. It is then shown that an array of independently-controllable transmit coils (parallel transmit) can be used to induce minimal RF current in elongated conductors, thereby reducing the RF heating risk, while still allowing visualization of the surrounding volume. Feasibility is demonstrated on a four-channel parallel transmit system at 1.5T, and the current reduction performance is quantified with current sensor measurements and image-based current estimates. Fluoroptic temperature probe measurements confirm that the reduction in current results in the reduction of wire tip heating.

Keywords: Electrical Engineering.
Advisor: Pauly John (John M.) primary advisor. Thesis advisor
Scott Greig Cameron
Nishimura Dwight George advisor. Thesis advisor