VictorJuiz/thesis huggingface dataset:
Semiconductor crystal islands for three-dimensional integration [electronic resource]

The critical operation needed to achieve 3-dimensional integrated circuits (3DICs) is obtaining single-crystal, device-quality semiconductor material on upper circuit layers without damaging circuits below (400°C temperature limit). Simulation shows that microsecond pulse 532 nm Nd:YAG laser can melt and crystallize amorphous Si or Ge layers without excessively heating the circuit layers underneath. However, experimental results of unseeded (graphoepitaxy) and seeded (RMG) crystallization of Si and Ge indicate that much longer pulse lengths are required for high-quality single-crystal formation, rendering the approach not 3DIC compatible. A more straightforward approach is to directly attach high-quality crystal islands for upper-layer device fabrication. A variety of viable low-temperature ([less than or equal to]400°C) bonding methods have been investigated: fusion bonding (SiO2-SiO2, Si-SiO2, Ge-SiO2), thermo-compressive bonding (Cu-Cu, Ti-Ti), as well as Al-Ge eutectic bonding. The unique advantages of AlGe technique for 3DICs are reported for the first time. They include superior bond strength, low void density, non-stringent roughness requirement, use of thin films and CMOS friendly materials. Finally, we present a completed 3DIC compatible process of obtaining single crystal Si or Ge islands for upper layer device fabrication via SmartCut® and CMP finish.

Keywords: Electrical Engineering
Advisor: Brongersma Mark L. primary advisor. Thesis advisor
Pease R. (R. Fabian W.) primary advisor. Thesis advisor
Kamins Theodore I.
Nishi Yoshio
Semi-supervised learning on graphs [electronic resource] : a statistical approach

Data on graphs are growing tremendously in size and prevalence these days; consider the World Wide Web graph or the Facebook social network. In semi-supervised learning on graphs, features observed at one node are used to estimate missing values at other nodes. Many prediction methods have been proposed in the machine learning community over the past few years. In this thesis we show that several such proposals are equivalent to kriging predictors based on a fixed covariance matrix driven by the link structure of the graph. We then propose a data-driven estimator of the correlation structure that exploits patterns among the observed response values. We also show how we can scale some of the algorithms to large graphs. Finally, we investigate the fundamental smoothness assumption underlying many prediction methods by exploring some normality properties arising from empirical data analysis.

Keywords: Statistics
Advisor: Owen Art B. primary advisor. Thesis advisor
Tibshirani Robert advisor. Thesis advisor
Wong Wing Tak Jack Wong advisor. Thesis advisor
Sequential methods for rare event simulation [electronic resource] : theory and applications

We consider rare events modeled as a Markov Chain hitting a certain rare set. A sequential importance sampling with resampling (SISR) method is introduced to provide a versatile approach for computing such probabilities of rare events. The method uses resampling to track the zero-variance importance measure associated with the event of interest. A general methodology for choosing the importance measure and resampling scheme to come up with an efficient estimator of the probability of occurrence of the rare event is developed and the distinction between light-tailed and heavy-tailed problems is highlighted. Applications include classic tail probabilities for sums of independent light-tailed or heavy-tailed random variables. Markovian extensions and simultaneous simulation are also given. The heuristics and the methodology can also be applied to more complex Monte Carlo problems that arise in recent works on the dynamic portfolio credit risk model.

Keywords: Statistics
Advisor: Lai T. L. primary advisor. Thesis advisor
Giesecke Kay advisor. Thesis advisor
Siegmund David
Sex-specific structure and function of the olfactory system in Drosophila melanogaster [electronic resource]

For my graduate work, I have chosen to investigate sex-specific patterning and function of the olfactory system in the fruit fly, Drosophila melanogaster, by addressing three questions: 1) What is the developmental genetic regulation of the sexual dimorphism in numbers of olfactory sensilla? 2) Do olfactory receptor neurons (ORNs) expressing Or47b (Or47b-ORNs) stimulate courtship in males and females? 3) Which genes are regulated by male-specific fruitless isoforms (FRUM) in olfactory and other peripheral sensory neurons? In Drosophila, terminal sexual differentiation is orchestrated by the activity of the transcription factors fruitless (fru) and doublesex (dsx). I have shown that the action of dsx alone is necessary and sufficient to specify sex-appropriate numbers of olfactory sensilla (the peripheral sensory unit). The dsx locus encodes sex-specific isoforms that differentially organize the developing antenna to specify sex-appropriate numbers of different types of olfactory sensilla. The female-specific DSX isoform promotes female-appropriate numbers of basiconic sensilla and depresses the number of trichoid sensilla on the antenna. Male-specific DSX promotes male-appropriate numbers of trichoid sensilla but appears to have little effect on determining numbers of basiconic sensilla. Inferred from the expression pattern of dsx, the DSX proteins do not show significant overlap with olfactory sensilla precursors. These data and other lines of evidence suggest that it is likely that dsx controls numbers of olfactory sensilla cell non-autonomously. One subtype of sexually dimorphic trichoid sensilla is innervated by ORNs that express the receptor Or47b and respond to a pheromone produced by males and females. I asked whether these ORNs promote male courtship and female receptivity. I have shown that Or47b-ORNs may promote courtship in males, but they appear to play no detectable role in stimulating female receptivity. Finally, in an effort to elucidate how sexual dimorphism is built into the developing olfactory system, I have collaborated with David Mellert (a former graduate student) to identify genes that are regulated by male-specific fru isoforms in peripheral sensory neurons of the olfactory and gustatory systems, as well as in mechanosensory neurons of the genitalia. We used laser capture microdissection to collect fru-expressing neurons in the antennae, prothoracic forelegs, and genitalia from fru+ and fru-null males. By comparing the whole-genome expression profiles of these samples, we were able to identify candidate targets of FRUM regulation in these tissues. For the antenna, this yielded a promising list of ~100 candidates that are in the process of being validated. Moreover, we found essentially no overlap in the candidate lists for different tissues, suggesting that FRUM regulates different genes in different tissues.

Keywords: Neurosciences.
Advisor: Baker Bruce Stewart
Clandinin Thomas R. (Thomas Robert)
Fernald Russell D. advisor. Thesis advisor
Lipsick Joseph Steven
Luo Liqun
Shear adhesion, friction, and wear of multi-point micro- and nano-scale contacts [electronic resource]

Adhesion, friction, and wear are the principal failure mechanisms that have limited the use of contacting and sliding surfaces in commercial MEMS applications. As the size of mechanical structures reaches the micro- and nano-scales, surface forces such as van der Waals, capillary, and electrostatic forces dominate the interactions between contacting surfaces. At these scales, the magnitude of the friction force is very sensitive to the complicated interaction between the surface properties, material properties, contact conditions, and environmental conditions. This work investigates the role of the contact conditions on the friction forces and wear rate of a MEMS probe array of small-scale tips in contact with a flat sliding surface. The friction measurement experiment involves a laterally unconstrained slider that sits on top of a MEMS probe array. As the array is laterally actuated, solely friction forces at the tips govern the motion of the slider. MEMS probe arrays enable precise control over the shape and the total number of contact points between the two surfaces. The results show that the friction forces are very sensitive to small changes in the contact or environment conditions. But for a given, well-controlled set of conditions, the friction forces scale linearly with the normal force. However, the friction coefficient is strongly dependent on the total number of contact points and the local conditions around those contact points. Factors such as humidity or adsorbed water on the surfaces further increase the linear relationship between the friction forces and the number of contacts. In addition, the wear rate of the tips is linearly related to the normal force acting at each tip. Factors such as the presence of water on the surface and a stiff vertical contact also lead to high wear rates. This work concludes with a set of recommendations to minimize the detrimental effects of friction and wear at the micro- and nano-scales.

Keywords: Mechanical Engineering
Advisor: Kenny Thomas William primary advisor. Thesis advisor
Hartwell Peter George
Howe Roger Thomas advisor. Thesis advisor
Shocks to the system [electronic resource] : the politics of decision making in San Francisco public schools

I trace the history of two education policies in San Francisco that flared into public controversy during the onset of a major crisis. The first controversy, which transpired in the wake of the 1906 Earthquake, involved the San Francisco Board of Education's attempt to segregate Japanese students. The second was the drive for school construction during the Great Depression. School officials and other political actors resiliently pursued their agendas even when faced with the turmoil caused by the crises. Politics did not subside; in fact, politics gave meaning to chaos. Two generalizations help to explain this finding. First, political actors searched for opportunities in crisis. When crises radically altered the physical and material infrastructure of the school department, people seized whatever resources they could to achieve their goals. Second, crises forced political actors to adjust their rhetoric by adapting their language to fit the circumstances. Prior to the earthquake and depression, political actors attempted to sway the public in their favor by defining the core values involved in segregation and school construction. The crises generated a new set of values. Political actors adjusted their rhetoric by integrating new values into the old political discourse.

Keywords: Education.
Advisor: Labaree David F.
Williamson-Lott Joy Ann
Wineburg Samuel S. advisor. Thesis advisor
Sieves and lenses [electronic resource] : essays on the role of categories in social valuation

Systems of classification are pervasive and consequential in economic life, as they are in the social world more generally. Membership in socially defined categories, such as industries or genres, constitutes a core part of an organization's identity, and, as such, profoundly impacts how the organization, its products and actions are evaluated. This dissertation includes three essays that analyze the ways in which similar actions in market settings are interpreted and assessed quite differently depending on the categorical identity of the performer. The first essay introduces the idea that categories of organizations (e.g., industries) differ in status and that status differences at the category level influence the social standing of individual members of the category. The second essay tests and finds support for the idea that category status impacts the way in which an organization's actions are perceived and evaluated. In particular, I find that earnings restatements from members of high-status categories are viewed less negatively than those from lower-status categories. Finally, the third essay, co-authored with Ming Leung, provides evidence of an audience-driven penalty for multiple-category membership in markets.

Keywords: Sociology.
Advisor: Hannan Michael
Sorensen Jesper B.
Correll Shelley Joyce advisor. Thesis advisor
Silicon based photonic crystal light sources [electronic resource]

Efficient light generation on silicon is desirable for a variety of applications because of its low fabrication cost relative to III/V semiconductors and because it will enable monolithic integration with electronic components on the same Si platform. We studied silicon-rich silicon nitride with emission in the visible and erbium-doped silicon nitride (Er:SiNx) with emission at 1540 nm. Both of these materials are compatible with the mainstream complementary metal-oxide semiconductor (CMOS) processing technology. This thesis discuses our results on using photonic crystal (PC) cavities to enhance luminescence from these materials. Nano-resonators modify the optical density of states (DOS) to enhance the emission in a fundamentally different way than what is accessible through materials engineering. Specifically, photon emission rate can be enhanced at a particular wavelength because the optical DOS is higher at the cavity resonance, which in turn improves efficiency and allows faster modulation rates. We have demonstrated up to 11-fold enhancement at photonic crystal resonance relative to smooth film at 730 nm and over 20-fold enhancement at 1540 nm. Time resolved measurements on erbium-doped sample confirmed significant enhancement of spontaneous emission rate. In addition, we have observed cavity line-width narrowing with increasing pump power in the erbium-doped sample, resulting from decrease in ground-state absorption by erbium ions as more of them are excited. We achieved excitation of up to 31% of Er ions at cryogenic temperature. This is an important step toward realizing a laser or amplifier based on Er:SiNx in the future.

Keywords: Electrical Engineering
Advisor: Vuckovic Jelena primary advisor. Thesis advisor
Miller D. A. B. advisor. Thesis advisor
Nishi Yoshio
Silicon-based photonic, plasmonic, and optomechanic devices [electronic resource]

The integration of optical devices and electronic devices on the same platform is currently a gateway into many research and practical applications. Because silicon and silicon compatible materials have dominated electronic development, optical devices must also conform to the silicon platform. One of the greatest challenges in building such an integrated opto-electronic system is the development of an efficient Si-compatible light emitter. In this thesis, we develop several Si-based nano-photonic devices for the control of light at the nano-scales. However, several Si-compatible materials and light emitters have low index of refraction, and high degrees of confinement using only index contrast and total internal reflection is difficult. We design high quality (Q-) factor photonic crystal nanobeam cavities for a variety of materials with low index, such as silicon dioxide, silicon rich oxide, and silicon nitride, all with high Q sand low mode volumes. We employ these cavity designs to a variety of active materials, including Si-nanocrystal doped silicon oxide, Er-doped amorphous silicon nitride, and InAs quantum quantum dots in GaAs. By placing emitters in these ultrasmall, high-Q cavities, we demonstrate that the cavity enhances emission and absorption processes, such as free carrier absorption, gain, and lasing. We also design plasmonic cavity and grating structures, which have lower Q compared to photonic crystal cavities due to metal ohmic losses, but have low mode volumes that break the diffraction limit. We propose and study a planar distributed Bragg reflector plasmonic cavity analogous to the nanobeam photonic cavity. We also demonstrate the enhancement of emission from silicon nanocrystals coupled to wide area plasmonic grating modes and Er-doped silicon nitride coupled to metal-insulator-metal modes confined between two metal layers. We demonstrate the control of emission wavelength by changing the device dimensions in both cases, and in the case of the Er material, observe an order of magnitude increase in collected emission compared to a sample with only one side contacting the metal. Finally, we demonstrate resonant actuation of a mechanical mode with optical gradient forces in a Si nanobeam cavity. The optical cavity enhances the optomechanical coupling between the optical mode and the mechanical vibration, and enables detectable mechanical motions with small optical powers driving an optical cavity mode.

Keywords: Electrical Engineering
Advisor: Vuckovic Jelena primary advisor. Thesis advisor
Fan Shanhui
Miller D. A. B. advisor. Thesis advisor
Single-Molecule AFM Cantilever for THz Force Detection

Increasing the resonance frequency of an Atomic Force Microscope (AFM) cantilever is necessary to effectively probe short-range chemical forces. Current AFM cantilevers have frequencies of about 100−200 kHz, limiting the minimum force-gradient that can be measured to the order of 10 pN/nm. This study demonstrates the ability of Inelastic Tunneling Spectroscopy (IETS) to probe THz vibrational modes of a single CO molecule attached to the tip of a low-temperature Scanning Tunneling Microscope (STM). Using molecular manipulation, a CO molecule is transferred to the end of the STM tip and lock-in techniques are used to measure 𝑑2𝐼/𝑑𝑉2 tunneling spectra. Shifts in the frequency of specific vibrational modes of the CO molecule are analyzed as a function of the tip-to-sample distance. This shows that a single molecule can be used as an AFM cantilever for force spectroscopy with the ability to measure small force-gradients to the order of 10−6 pN/nm. IETS with a CO terminated STM tip is also performed over adsorbed CO molecules on a Cu(111) surface revealing a novel vibrational mode due to coupling between the two CO molecules. In future, the small force-gradients detected by STM-IETS can be used to resolve single atoms within a molecule to reveal additional molecular structure.

Keywords: Physics
Atomic Force Microscope (AFM)
Inelastic Tunneling Spectroscopy (IETS)
Thesis
Advisor: Manoharan Harindran C. (Harindran Chelvasekaran) "Hari"
Moler Kathryn
Single-molecule studies of nucleic acid folding [electronic resource]

Nucleic acids--DNA and RNA--are critical to life, involved in the storage and decoding of genetic information in the cell as well as the regulation and catalysis of specific biological processes. The function of a nucleic acid molecule is determined in large part by the structure it adopts, which in turn depends on its sequence. The mechanisms of sequence-directed nucleic acid folding remain incompletely understood, particularly for large RNA molecules. The work presented in this thesis uses single-molecule optical-trapping techniques to study nucleic acid folding, where reversible folding is induced and measured in individual molecules through the application of force. In Chapter 2 we demonstrate direct measurement of the full folding energy landscapes of DNA hairpins, which comprise a model system for studying nucleic acid secondary structure, and show how such landscapes are sensitive to sequence. In Chapter 3 we study the electrostatics of DNA hairpin folding by measuring trends in folding energies under different ionic conditions and comparing these trends with those predicted by Poisson-Boltzmann theory. Finally, in Chapter 4 we examine folding of the TPP riboswitch aptamer, an RNA molecule with complex secondary structure that also adopts tertiary structure upon binding a small-molecule ligand. We measured the folding energy landscape of the aptamer and perturbations of this landscape resulting from mutations and ligand binding, and propose a kinetic model to describe the coupling between aptamer folding and ligand binding. Taken together, the results presented here demonstrate the usefulness of the energy landscape framework for characterizing nucleic acid folding in conjunction with single-molecule measurements.

Keywords: Biophysics.
Advisor: Block Steven M. primary advisor. Thesis advisor
Herschlag Daniel advisor. Thesis advisor
Pande Vijay advisor. Thesis advisor
Single-walled carbon nanotubes (SWNTs) as near infrared fluorescent imaging agents in biological systems [electronic resource]

The near infrared range has long been known to be advantageous for biological imaging and sensing applications. In particular, the second near infrared window (1000 nm -- 1400 nm, NIR II) is characterized by low endogenous autofluorescence and deep tissue penetration due to reduced tissue scatter. To address the dearth of fluorophores in this window, this work focuses on utilizing the intrinsic near infrared photoluminescence of semiconducting single walled carbon nanotubes (SWNTs) to take advantage of this unique spectral region. First, SWNTs are made bio-inert and applied as fluorescent probes for highly specific cellular targeting using antibodies such as Rituxan and Herceptin. These probes were then used for the first whole animal fluorescent imaging using SWNTs in vivo following tail vein injection, including the observation of high SWNT accumulation in tumors. By implementing a surfactant exchange method to improve the fluorescence yield of SWNTs solubilized by phospholipid-polyethylene glycol, high magnification intravital microscopy of tumor vessels beneath thick skin was achieved. Further improvements were made to improve the fluorescence yield of the SWNT probes by utilizing a density gradient separation method which removed poorly fluorescent short tubes and nanotube bundles. Another separation method, ion-exchange chromatography was applied to isolate single chirality SWNTs and perform multicolor NIR imaging in vitro and in vivo. Finally, these bright, biocompatible nanotube fluorophores were used to achieve video rate imaging of mice in vivo during tail vein injection for dynamic contrast enhanced imaging through principal component analysis. The emission in the NIR II region allowed crisp anatomical resolution, confirmed by mock tissue phantom studies and Monte Carlo simulation.

Keywords: Chemistry
Advisor: Dai Hongjie
Chidsey Christopher E. D. (Christopher Elisha Dunn)
Zare Richard N. advisor. Thesis advisor
Spectroscopic and theoretical studies of copper-oxygen intermediates in enzyme model complexes and zeolites [electronic resource] : electronic structure contributions to reactivity

Copper-oxygen species catalyze a wide range of biologically and catalytically relevant reactions. In this dissertation a combined spectroscopic and theoretical approach is used to define the geometric and electronic structure of two copper-oxygen intermediates proposed to be activated for H-atom abstraction: an end-on bound mononuclear cupric-superoxo and a zeolitic site activated for methane monooxygenation.

Keywords: Chemistry
Advisor: Solomon Edward I. primary advisor. Thesis advisor
Hodgson K. O. (Keith O.)
Stack T. (T. Daniel P.)