VictorJuiz/thesis huggingface dataset:
Particle accelerator on a chip fabrication and characterization of a three-dimensional photonic crystal accelerator [electronic resource]

Charged particles are currently accelerated by microwave radiation generated in large klystrons. This is very reminiscent of vacuum tube diodes on which early computers relied. Can particle accelerator technology follow the shift that drove the semiconductor industry from vacuum tubes to solid state devices? Can particle accelerators benefit from the high energy density provided by lasers at optical and infrared wavelengths? Can dielectric materials replace the metallic waveguides allowing us to utilize the high peak powers available in lasers today? In making this jump from microwave to infrared wavelengths, a decrease of 10,000 times in wavelength, entirely new fabrication technologies are needed. And entirely new physics must be applied in transitioning from metals to dielectrics. This thesis focuses on the fabrication and characterization of a three-dimensional photonic crystal designed for accelerating electrons. We present the design for a woodpile structure with a waveguide or defect that supports an accelerating mode. This mode has a speed-of-light phase velocity and longitudinal electric field. It has an estimated accelerating gradient of 351 MV/m. The 17 layer woodpile structure was fabricated at the Stanford Nanofabrication facility using semiconductor processing techniques. The structure was fabricated in a layer-by-layer approach resulting in two half-structures which were then aligned and bonded together. Three versions of structures were fabricated with operating wavelengths of 3.45, 3.95, and 4.94 [micrometers]. Optical characterization of these structures was performed using Fourier transform infrared spectroscopy. Simulations show good agreement with the measurements when the structure parameters are modeled appropriately. Finally, an optical parametric oscillator was built for studying the defect modes in the structure.

Keywords: Applied Physics.
Advisor: Byer R. L. (Robert L.)
Chao Alex
Ruth Ronald D. advisor. Thesis advisor
Particle populations and high energy emission in pulsar wind nebulae [electronic resource]

Energetic particles streaming out from rapidly spinning neutron stars radiate across the electromagnetic spectrum, creating a pulsar wind nebula (PWN). Many PWNe are spatially resolved in the radio, X-ray, and even gamma-ray wavebands, and thereby provide an excellent laboratory to study not only pulsar winds and dynamics, but also shock processes, magnetic field evolution, and particle transport. Single-zone spectral energy distribution (SED) models have long been used to study the global properties of PWNe, but to fully take advantage of high spatial resolution data one must move beyond these simple models. Supported by multiple X-ray PWN observations, we describe multi-zone time-dependent SED model fitting, with particular emphasis on the spatial variations within nebulae. The SED model constrains the wind velocity profile, magnetic field profile, age and spin-down history of the central pulsar, and the PWN injection spectrum. These constraints are of great value to the study of the gamma-ray pulsar population, and to investigations of particle acceleration and the cosmic ray spectrum. The large size of many PWNe in the very high energy gamma-ray (TeV) regime is indicative of significant particle transport over the pulsar lifetime, and in the case study of HESS J1825-137 we find that rapid diffusion of high energy particles is required to match the multi-wavelength data.

Keywords: Physics
Advisor: Romani Roger W. (Roger William) primary advisor. Thesis advisor
Funk Stefan
Michelson Peter F.
The payoff to skill and earnings inequality in the third industrial revolution [electronic resource]

This dissertation develops a new approach to analyzing changes in wage inequality in the United States, based on a comprehensive framework of nonmanual workplace skill, including cognitive, creative, technical and social types of skill, measured at the occupational level. By applying this framework to the individual-level 1983-2010 Current Population Surveys, we are able to adjudicate between competing accounts of the changing market structure, returns to skill, and wage inequality. We find substantial heterogeneity in the payoff to different types of skill. The most important trend under this multidimensional model is a precipitous increase in the payoff to analytical skill that involves synthesis, critical thinking, and abstract reasoning. This multidimensional approach is also helpful in expanding our knowledge on gender and racial gaps in skill and earnings. As we apply this model to different gender and racial groups separately, we find sizeable gender and racial disparities in terms of employment distribution and wage returns across different types of skill. We argue that this multidimensional framework of skill can better gauge the relationship between skill-biased trends and earnings inequality. These trends are driven more by institutional, social, and cultural changes than by narrowly defined technological change.

Keywords: Sociology.
Advisor: Grusky David B. primary advisor. Thesis advisor
England Paula advisor. Thesis advisor
Walder Andrew G. (Andrew George)
Peptide-MHC heterodimers reveal differential contribution of weak self-peptides to positive and negative selection [electronic resource]

T cell central tolerance depends on the T cell receptor's affinity for self peptide/major histocompatibility complex, but how this affinity translates into the decision to mature or apoptose is unclear. In this body of work, we show that the OT-I TCR's affinity for its endogenous positively-selecting ligands, catnb/H-2Kb and cappa1/H-2Kb, is significantly lower than its previously reported affinity for artificial positively-selecting peptide/H-2Kbs. To understand how these extremely weak ligands produce signals in maturing thymocytes, we generated soluble monomeric and dimeric peptide/H-2Kb ligands. Monomeric agonist ovalbumin (ova)/Kb elicited no detectable signaling in OT-I thymocytes, but heterodimers of ova/Kb paired with an endogenous peptide/Kb induced very efficient deletion, for both positively-selecting and nonselecting endogenous peptides but not for an engineered 'null' partner peptide. In contrast, dimer-induced positive selection was much more sensitive to the identity of the partner peptide, because while catnb/Kb-catnb/Kb homodimers induced efficient positive selection, heterodimers of catnb/Kb paired with a nonselecting peptide/Kb could not induce selection, even though both ligands have measurable affinities for the OT-I TCR. Thus, both positive and negative selection can be driven by dimeric but not monomeric ligands, but positive selection has much more stringent requirements for the partner self-pMHC.

Keywords: Microbiology and Immunology
Advisor: Davis Mark M. primary advisor. Thesis advisor
Chien Yueh-Hsiu advisor. Thesis advisor
Garcia K. Christopher advisor. Thesis advisor
Nolan Garry P. advisor. Thesis advisor
The performance of analysis [electronic resource] : habit and conversion in seventeenth-century French thought

My dissertation examines a cognitive model for conversion, "the performance of analysis", which was prevalent in seventeenth-century French thought. According to the model, an actor seeking conversion should begin by acting as if he or she were already what he or she wants to become, imitating the actions of one already embodying the hypothetical state; habituation then actualizes that which begins as an imaginary hypothesis into a concrete reality. I argue that this model for conversion was correlated to mathematical practice in the period, and I trace its manifestations in Descartes, Pascal, Rotrou, Molière, and La Rochefoucauld.

Keywords: Comparative Literature
Advisor: Greene Roland
Gumbrecht Hans Ulrich primary advisor. Thesis advisor
Edelstein Dan advisor. Thesis advisor
A phase portrait approach to vehicle stabilization and envelope control [electronic resource]

Loss of control accidents, which lead to thousands of deaths every year in America alone, are often caused by a miscalculated action of the driver or a sudden change in the road surface. Recent years have seen several technologies arise in an attempt to decrease accident rates, one of which is Electronic Stability Control. While ESC is effective at stabilizing the vehicle, it functions without full knowledge of the vehicle states or tire-road coefficient of friction. As more sensors become available and control objectives become more complicated, car designers will need to implement a more holistic control scheme like aircraft envelope control, which integrates multiple sensors and actuators to keep the vehicle within a safe operating regime. This dissertation outlines two initial building blocks for a full vehicle control system. The first, called Vehicle Envelope Control, stabilizes the car by keeping it within a safe region of the yaw rate-sideslip state space. An analysis of the yaw acceleration isoclines in the yaw rate-sideslip phase plane allows for determination of an envelope boundary that is consistent with the natural system dynamics. The chosen boundary is defined by the yaw acceleration nullcline at the maximum steering angle that results in open loop stable dynamics, and the lines of maximum rear slip angle, which prevent rear tire saturation. The envelope boundaries are enforced by an attractive controller defined by the distance of the vehicle states from the safe boundary. An inner boundary proportional controller provides a soft landing at the yaw rate boundaries by limiting the driver's steering angle to the maximum stable steering angle as the vehicle approaches the boundary. To prove the effectiveness of the controller, Stanford's steer-by-wire vehicle, P1, performs several maneuvers during which the controller must activate to stabilize the car. The second building block for the full-vehicle control system involves determining and implementing the mechanical changes necessary to enhance estimation of tire-road coefficient of friction and peak lateral tire force. The ability to estimate friction reliably allows for real-time updates to the envelope boundaries, relaxing them as the friction increases, and constraining them as the friction decreases. Isolating the aligning moment, the portion of steer-axis reaction torque from lateral tire forces, gives information on friction; however, there are typically several other torques felt about the steering axis that must be estimated and subtracted out before the aligning moment can be determined. The suggested suspension design eliminates contributions from these other torques, so that the aligning moment is measured directly.

Keywords: Mechanical Engineering
Advisor: Gerdes J. Christian primary advisor. Thesis advisor
Cutkosky Mark R. advisor. Thesis advisor
Rock Stephen M. advisor. Thesis advisor
Photoacoustic imaging using capacitive micromachined ultrasonic transducers [electronic resource]

One of the primary goals of a medical imaging procedure is to spatially localize disease in an individual. This dissertation focuses on photoacoustic imaging, which is a relatively new medical imaging modality that shows great promise for disease diagnosis - especially cancer detection. In photoacoustic imaging, short laser pulses absorbed by molecules in tissue induce ultrasonic pressure waves which are then detected to form an image. In this work, using a custom built mechanically scanned single-transducer photoacoustic imaging system, we extend photoacoustic imaging into the molecular imaging domain. In this first such demonstration, we show how an exogenous contrast agent that binds preferentially to an angiogenesis biomarker enables an early cancer diagnosis in living subjects. To accelerate the goal of taking photoacoustic imaging from the lab to the clinic, this thesis introduces capacitive micromachined ultrasonic transducer (CMUT) arrays as an enabling technology platform. CMUT technology allows the fabrication of highly sensitive, wide bandwidth, 2D transducer arrays that can be tightly integrated with electronics. This thesis shows the first results of true 3D volumetric photoacoustic imaging using CMUTs. Deep tissue photoacoustic imaging up to a depth of ~5 cm and preliminary results from real-time photoacoustic imaging are also shown. Finally, in this work, we describe a new CMUT microfabrication process called the Thick-BOX process. The Thick-BOX process promises a simpler fabrication process that produces more reliable and robust CMUTs. Experimental fabrication results of low frequency CMUT devices are presented as a proof-of-concept verification for this fabrication process.

Keywords: Electrical Engineering
Advisor: Gambhir Sanjiv Sam primary advisor. Thesis advisor
Khuri-Yakub Butrus T.
Howe Roger Thomas advisor. Thesis advisor
Photon shot noise limits on optical detection of neuronal spikes and estimation of spike timing [electronic resource]

Optical approaches for tracking neural dynamics are of widespread interest, but a theoretical framework quantifying the physical limits of these techniques has been lacking. We formulate such a framework by using signal detection and estimation theory to obtain physical bounds on the detection of neural spikes and the estimation of their occurrence times set by photon statistics (shot noise). These bounds are succinctly expressed via a discriminability index that depends on the kinetics of the optical indicator and the relative fluxes of signal and background photons. This approach facilitates quantitative evaluations of different indicators, detector technologies, and data analyses. We compare various types of Ca-2+ indicators and show that background photons are a chief impediment to voltage sensing. Thus, voltage indicators that change color in response to membrane depolarization may offer a key advantage over those that change intensity. We also identify the regimes in which commonplace ratiometric analysis of signals from fluorescence resonance energy transfer (FRET) indicators is sub-optimal and describe new, optimal filtering techniques. Overall, our treatment offers a valuable guide to experimental design, by showing how different optical factors interact to affect signal quality, and provides measures of confidence to assess optically extracted traces of neural activity.

Keywords: Applied Physics
Advisor: Schnitzer Mark Jacob
El Gamal Abbas A. advisor. Thesis advisor
Mabuchi Hideo advisor. Thesis advisor
Photovoltaic retinal prosthesis [electronic resource]

Degenerative retinal diseases are among the leading causes of vision loss in the developed world. In these diseases, the "image capturing" photoreceptor layer slowly dies while the "image processing" inner retinal layers are preserved to large extent. One approach to restore vision of patients suffering from the selective photoreceptor loss is to deliver information to the visual system by patterned electrical stimulation of the remaining retinal circuitry. Several retinal prosthetic systems have achieved promising results in clinical studies, with the most successful prostheses allowing blind people to read large letters. However, the current retinal prosthetic designs require a trans-scleral cable to deliver power or data to the retinal stimulating array. We designed a photovoltaic prosthetic system with a silicon photodiode array placed behind the retina, in which each pixel of the array photovoltaically converts patterned pulsed near-infrared light projected from video goggles into pulses of bi-phasic electric current to stimulate the nearby retinal neurons. The light-powered 30-µm thick photodiode array does not require any wired power connections, which greatly simplifies the surgical procedure and reduces chances of infection. Several arrays could be juxtaposed to tile a larger area on the retina and thereby expand the visual field. The local return electrodes in each pixel help to reduce the spatial spread of electric current, thereby reducing the cross-talk between pixels and improving the spatial resolution of the implant. Each pixel contains three photodiodes connected in series to increase charge injection levels. Deep reactive-ion etched trenches are used to isolate the three photodiodes in each pixel. Trenches between the pixels are open to allow perfusion of nutrient, which is essential for in-vitro electrophysiological experiments, and may also help with the in-vivo integration of the implant with the retina. We fabricated 1 and 2 mm wide arrays of photodiode for implantation in small and large animals. Three sizes of pixels (280 µm, 140 µm and 70 µm) were fabricated to explore the resolution that could be achieved by the implant. The development of the fabrication process for the silicon photodiode array is presented, which involves eight mask layers, including deep isolation trench etch, n+ region predeposition, p+ region ion implantation, first via etching, first metal deposition and liftoff, second via etching, polysilicon etching in selected trenches, second metal deposition and liftoff. A detailed optoelectronic characterization of the fabricated photodiode array is also presented. The initial electrophysiological results of retinal stimulation in-vitro and in-vivo show that the fabricated devices are able to reliably elicit retinal responses at safe near-infrared light irradiances, with good acceptance of the photodiode array in the subretinal space.

Keywords: Electrical Engineering
Advisor: Harris J. S. (James Stewart)
Kamins Theodore I.
Palanker Daniel advisor. Thesis advisor
Phylogenetic patterns and ecological determinants of adaptive radiation [electronic resource]

It is well recognized that much of the biodiversity on Earth is the result of adaptive radiation, which is the process by which one biological lineage gives rise to many descendant lineages, all adapted to the various ecological roles they fill. However, it remains unclear why some lineages diversify greatly by adaptive radiation while others diversify little or not at all. The classic view is that "ecological opportunity" (where organisms find themselves in an area with abundant or under-utilized resources) allows the lineage to interact with the environment in novel ways and this promotes adaptive radiation. Here I utilize three taxonomically disparate systems (microbes, plants, and fishes) to examine patterns of diversification and identify possible ecological factors that promote or suppress adaptive radiation. In a laboratory experiment with bacteria and phage, I show that the prior evolutionary history of immigrants may determine their subsequent diversification dynamics after arrival to a new habitat. In another study, using molecular phylogenetics to investigate the rate of diversification of an adaptive radiation of flowering plants in Hawaii, I show that this radiation is among the most rapid yet studied in plants, on a per-unit-area basis, and suggest that the relative scale of habitable area available for the organisms under study is necessary to understand both the rate and the extent of diversification. Lastly, I utilize a radiation of marine fishes along the west coast of North America and show that morphological adaptations can facilitate habitat shifts leading to further evolutionary diversification not only in terrestrial and freshwater systems, but in marine systems as well, confirming the idea that general evolutionary principles apply across systems. One common theme that emerges from these studies is that the "ecological opportunity" hypothesis is supported, but that it may not fully explain diversification patterns. Overall, these studies suggest that explicit consideration of the prior evolution of immigrants, the relative scale of habitable area, and adaptive morphological shifts to novel habitats are necessary to fully understand patterns and drivers of adaptive radiation.

Keywords: Biology.
Advisor: Fukami Tadashi
Dirzo Rodolfo advisor. Thesis advisor
Hadly Elizabeth Anne
Watt Ward B. advisor. Thesis advisor
Physical constraints on the size and shape of microalgae [electronic resource]

Scaling laws provide a link between biology and physics. They provide a means by which patterns in biology can be quantified and an explanation from physics can be correlated with such patterns. In this thesis, I use scaling laws to look for connections between biology and physics in two systems, diatom frustules and coralline algal reproduction. In Part I, I investigate diatom sinking speeds, a system for which a biologically derived scaling law has been known for some time, but is yet to be explained by a physically derived correlate (Chapter 1). Once I solve this discrepancy between the physical and biological scaling laws, I then spend the rest of the Part I deriving several other related scaling laws, from physical (Chapters 2 and 4) and biological (Chapter 3) perspectives. Part II works with an entirely new system for which few scaling laws have been derived, the spores of red algae and their attachment ability. This second part of my thesis works primarily from a biological perspective, as I empirically derive scaling laws and try to make sense of a new system.

Keywords: Biological Sciences
Advisor: Denny Mark W.
Connor Judith
Monismith Stephen Gene advisor. Thesis advisor
Somero George N. advisor. Thesis advisor
Physical modeling of the harpsichord plectrum-string interaction [electronic resource]

The harpsichord is a plucked string keyboard instrument which was prominent during the 16th through 18th centuries. In this thesis, we set out to physically model the complex interaction between the harpsichord plectrum and string during the plucking event. The modeling efforts are aided by various experimental work, and the model is later extended with additional digital filters with a focus on sound synthesis.

Keywords: Physics
Advisor: Doniach S. primary advisor. Thesis advisor
Rossing Thomas D.
Chafe Chris advisor. Thesis advisor
Smith Julius O. (Julius Orion) advisor. Thesis advisor
The physics of target-site search and DNA supercoiling in the cell [electronic resource]

Protein-DNA interactions within the confines of the crowded cellular space control critical biological processes such as genome regulation, replication, and compaction. In turn, protein activity on the genome is susceptible to the structure and dynamics of the DNA itself, a complex relationship whose study falls within the realm of polymer physics. Using analytical theory and numerical simulations, we present a systematic study of the relationship between DNA structure and dynamics and cellular processes mediated by DNA-binding proteins, in particular those involving a search for a target-site on the chromosome. We build a theoretical description of the transport of DNA-binding proteins along linear DNA modeled as a wormlike chain and delineate the resulting dynamic strategies employed by the cell in order to maximize translocation speed and efficiency. We extend this model to address the otherwise imperceptible molecular events present during effective protein diffusion along a stretched DNA strand during single-molecule experiments. In an effort to address the genome's higher-order structural effects, we explore the structure and dynamics of supercoiled DNA both as a free molecule in solution and under confinement in the cell, as in the case of Caulobacter crescentus. Our investigation of supercoiled DNA in confinement highlights dynamic consequences of vital importance to the cell's genome regulatory strategies. Finally, we synthesize our study of DNA-binding protein transport with our investigation of supercoiling dynamics to address the effect of DNA superstructure on the target-site search process, and we identify the search enhancement wrought by supercoiling of the chromosome.

Keywords: Chemical Engineering
Advisor: Spakowitz Andrew James primary advisor. Thesis advisor
Bryant Zev David advisor. Thesis advisor
Shaqfeh Eric S. G. (Eric Stefan Garrido) advisor. Thesis advisor