VictorJuiz/thesis huggingface dataset:
Ge/SiGe electroabsorption modulators for Si-based photonic integrated chips [electronic resource]
Keywords: Electrical Engineering

In chapter 1, we explain how optical interconnects can drastically improve data transmission performance while reducing power use. This is critical to the economic and environmental sustainability of the projected growth of data transmission needed for the rapid expansion of communication, commerce, and computation. We explain the importance of Si-CMOS process compatibility and energy requirements for optical components, and describe our solution using the quantum-confined Stark effect in Ge/SiGe quantum wells. In chapter 2, we summarize our improvements to the Ge/SiGe material system, requisite to the success of the surface-normal and microdisk modulators described in chapters 3 and 4. These devices are capable of high-speed, efficient modulation and compact form factors necessary for CMOS process integration. The advances described in this thesis help pave the way for widespread adoption of Ge/SiGe electroabsorption modulators for Si-based photonic integrated chips.
Global identification and functional analysis of calcineurin substrates in yeast [electronic resource]
Keywords: Biology.

The regulation of the phosphoproteome by kinases and phosphatases is a critical component of complex signaling networks. Many tools for identification of kinase substrates cannot be applied to phosphatases, creating a disparity in kinase versus phosphatase substrate identification. In this work, we describe two complementary approaches for identifying phosphatase substrates, both using the calcium-dependent phosphatase calcineurin in S. cerevisiae as a model. First, mass spectrometry-based analysis of calcineurin-deficient and calcineurin-activated yeast, in silico screening to identify calcineurin-docking motifs, and biochemical verification led to the identification of 15 novel calcineurin substrates from a set of 29 novel interactors for calcineurin in yeast. This represents the first successful comprehensive identification of phosphatase substrates in any organism and significantly advances our understanding of calcium/calcineurin signaling. Substrate identification has suggested new roles for calcium/calcineurin signaling in polarized growth, autophagy, and zinc homeostasis. Specific analysis suggests that calcineurin negatively regulates the kinase Elm1 in the alkaline pH stress response and early G1 of the cell cycle. Second, a protein microarray phosphatase assay was used to identify calcineurin substrates in vitro. This assay uses a mixture of purified yeast kinases to radiolabel phosphorylation sites that have been dephosphorylated by calcineurin. Our pilot screen identified approximately 90 potential calcineurin substrates with Hel2, Sgt1, and Skg1 being verified by secondary assays. The methodologies presented in this work may be generalizable to identify substrates for phosphatases in yeast and other organisms and help lead to a better understanding of complex signaling networks.
Graph colorings and graph limits [electronic resource]
Keywords: Mathematics

This thesis in two parts. The first part studies the monotonicity properties of chromatic polynomials. The second part studies the limiting behavior of certain exponential random graph models. \\ In the first part (chapter 2 and 3), a generalization of the birthday problem is studied and connections are shown to two conjectures about chromatic polynomials: the shameful conjecture due to D. Welsh and Brenti's conjecture about the log-concavity of chromatic polynomials. The probability of getting a proper coloring of a graph under a random coloring scheme is studied. The goal is to understand conditions under which a random coloring with q+1 colors has a higher probability of resulting into a proper coloring of the graph than a random coloring with q colors has? It is shown that one criteria guaranteeing that the above property is true is that q should be large enough in terms of the highest degree of the graph. Ideas from the work of A. Sokal and C. Borgs giving bounds on the roots of chromatic polynomials are used to prove this property. In fact, a much stronger property is proved. Further generalizations of this question are also studied and some useful examples and analyses are provided. \\ The second part (chapter 4) studies the limiting behavior of certain exponential random graph models (ERGMs) with some negative coefficients. This study is motivated by recent results of Diaconis and Chatterjee in which they show that ERGMs with positive coefficients have the same limiting behavior as Erdos Renyi random graph models. Using the theory developed in their work the limiting behavior of the Strauss model is studied. Methods from extremal graph theory such as Turan's theorem are used and proofs of their analogous statements in graph limit theory are also proved. Some more complicated models are studied through simulations and these results are also presented here.
Growth opportunities [electronic resource] : developing a culturally responsive pedagogy in a school context
Keywords: Education.

Abstract Research offers data of the backgrounds and practices of individual teachers who enact a culturally responsive pedagogy and there is limited research investigating how teachers learn the dispositions and practices it involves. Because the major tenets of a culturally responsive pedagogy involve ways of being in the world, the development the pedagogy, like many aspects of teaching, happens over time. This dissertation asks if teachers can develop a culturally responsive pedagogy in a school context. If so what resources would a school need for learning and what conditions would make those resources useful and utilized? I conducted a case study of one high performing high school serving low-income students of color to address this question. Data were collected over one and half years among seven focal teachers, the faculty, and administrators at "Serramonte Prep", a new small high school in a medium sized urban area. Data includes observations of teachers practice, collaborative work, school events, documents and interview data. Data are analyzed through a conceptual framework grounded in a sociocultural theory of learning and a theory of culturally responsive pedagogy largely based on Geneva Gay's (2000) conceptualization. Personalization structures, common assessments, targeted professional development and shared curriculum are identified as substantive resources for the development of culturally responsive pedagogy. Conditions that facilitate opportunities to learn from these resources include a close focus on the student, involved expertise, joint work with colleagues and an expanded role of the classroom teacher. Moreover, findings also suggest teachers' professional preparation and background influence their capacity to benefit from participation in school resources, and the development of an ethic of deep care is particularly difficult to develop in the context alone. They also indicate that school resources are not available to all teachers and therefore limit their use.
Heating and acceleration of intracluster medium protons by turbulence
Keywords:  Department of Physics
galaxies
clusters
acceleration of particles
x-rays
Thesis

We investigate the possibility of nonthermal inverse bremsstrahlung radiation as a source of hard X-ray emissions from the intracluster medium of galaxy clusters. In particular, using a numerical algorithm that simultaneously solves the coupled Fokker-Planck equations of protons and electrons subject to Coulomb collisions and stochastic acceleration, we determine whether it is possible to accelerate background protons without excessive heating. Under a simplified but generic acceleration model adopted in Petrosian & East (2008), the time evolution of both proton and electron spectra are computed. We find that nonthermal protons necessary for the inverse bremsstrahlung process to produce hard X-ray photons can emerge only with excessive heating of the entire plasma, unless the acceleration parameters, the duration of the acceleration, and/or the initial distributions are significantly fine-tuned. These results severely constraint the feasibility of nonthermal inverse bremsstrahlung process producing hard X-ray emissions. In Appendix A, we also derive and present a formula for the energy loss rate by the proton-proton interaction, which becomes the dominant energy loss process for protons of kinetic energy higher than 320 MeV.
Helioseismic detections of sunspot regions [electronic resource]
Keywords: Physics

Sunspots are regions where strong magnetic fields emerge from the solar interior and where major eruptive events occur. Sunspot studies are needed to understand the generation and emergence of magnetic fields in the photosphere and monitor the solar magnetic activity. In this thesis, local helioseismology methods are used to detect and study sunspot regions on the far-side of the Sun, the photosphere, and the deep convection zone, before these magnetic regions become visible on the solar disc. One of the successes of helioseismology is the imaging of solar far-side magnetic regions. Helioseismic holography and time-distance technique are capable of detecting sunspot regions on the far side of the sun and provide useful warnings for space weather forecasts. These techniques employ acoustic waves that travel to the far side and return to the front side after multiple bounces in the photosphere. We explore the possibility of far-side imaging by the time-distance technique using three-skip acoustic signals. This method is first validated with use of numerical simulation data and then it is used to detect sunspot regions on the solar far side using SOHO/MDI observations. It is shown that if these maps are combined with maps of existing methods, the appearance of spurious signals is reduced. Sunspot observations in the photosphere show that the acoustic power inside a sunspot region is significantly reduced compared to the quiet Sun. The power deficit is due to three main groups of physical mechanisms: absorption, emissivity reduction, and local suppression. These effects are separated with a measurement scheme that utilizes one- and double-skip waves in sunspots and quiet-sun regions. Using a large sample of sunspots observed with SOHO/MDI, the coefficients of each mechanism are measured as functions of travel distance and their relative contribution to the total power reduction is determined as well. The methods and the results of this study will be utilized for the detection of emerging sunspot regions in the convection zone. Helioseismic methods can be used to detect and study the properties of sunspot regions not only on the solar far side and the photosphere but also in the deep solar interior. We develop a measurement procedure which is capable of detecting emerging sunspot regions at depths around 60,000 km and 1-2 days before the detected magnetic structures emerge to the surface. The detection is based on measurements of the acoustic phase travel-time perturbations with the time-distance helioseismology technique using SOHO/MDI, SDO/HMI, and GONG datasets. The travel-time anomalies are related with cross-covariance frequency perturbations that depend strongly on the acoustic frequency. The implications of these measurements to studies of magnetic flux emergence in the solar convection zone and the potential applications to space weather forecasts are discussed.
Heterogeneous integration by parallel insertion of chiplets into wafer [electronic resource]
Keywords: Electrical Engineering

The HIPPI process (Heterogeneous Integration by Palletized Parallel Insertion) embeds CMOS chiplets into MEMS wafers, to bypass the monolithic integration challenges of combining MEMS functionality with CMOS circuitry. Dry alignment is provided by passive guide tabs, which are created through polysilicon refill of front-side etched trenches. The guide tabs are compatible with further processing on the wafer. Precision chiplets are created by through-wafer etching. After chiplet drop-in, optical detection provides feedback of chiplet jamming, and horizontal driving of the chiplets finishes the zero insertion force assembly process. We demonstrate less than 2.5[mu]m of chiplet to substrate alignment error. Theoretical scaling of alignment accuracy reaches numbers comparable to photolithography, allowing high density interconnects for heterogeneous integration without precision manipulators.
Hidden diversity in corals and their endosymbionts [electronic resource]
Keywords: Biology.

Understanding the ecological and evolutionary processes that are responsible for the origin, distribution and maintenance of biodiversity is integral to interpreting the dynamics of natural systems and has important implications for a large number of disciplines including epidemiology, agriculture and biodiversity conservation. In this dissertation, I use genetic data to explore the evolutionary histories of two members of the coral holobiont, the coral host and its photosynthetic endosymbionts, which together form the structural foundation of the ocean's most diverse ecosystems. First, I focus on the coral host and explore the evolutionary histories of four closely related species within the abundant and diverse genus, Acropora. In Chapter 1, I utilize multi-locus population genetics to quantitatively test several alternative hypotheses for the high levels of shared genetic variability among species, and I demonstrate that these evolutionary patterns can largely be explained through a combination of a) morphologically cryptic species complexes and b) historical and/or contemporary genetic exchange among species (introgression). Then, in Chapter 2, I explore the geographic distribution of these morphologically cryptic species complexes and examine the consistency of introgression across space. I show that a) there are a handful of geographically widespread, morphologically cryptic species within each species complex, b) there is considerable overlap in the geographic ranges of the cryptic species and c) patterns of introgression are consistent throughout sympatric distributions. Second, I examine the evolutionary diversity of the photosynthetic dinoflagellates that form symbioses with these corals (Symbiodinium), a partnership that is integral for the health of coral reefs. I explore diversity within this group at two distinct taxonomic levels. In Chapter 3, I investigate patterns of nucleotide substitution among deeply divergent clades of Symbiodinium to highlight specific genes and functional groups that may be involved in adaptation of clade D Symbiodinium to high temperature environments, including a fatty acid desaturase, several chaperones and genes involved in photosynthesis and the thylakoid membrane. Then, in Chapter 4, I utilize high throughput transcriptome sequence data to provide an initial look at population-level diversity within two divergent subclades of Symbiodinium. My results illustrate unexpectedly high levels of polymorphism within each of these subclades, and demonstrate that the distribution of these polymorphisms, within and between corals, suggests that they primarily originate from intragenomic variation in multi-copy gene families. Combined, this work illustrates the evolutionary complexity of reef corals and their endosymbionts. A thorough understanding of these complexities is necessary in order to properly address questions regarding the ecological function and resilience of these economically important ecosystem builders.
High fidelity simulations of reactive liquid-fuel jets [electronic resource]
Keywords: Mechanical Engineering

Most of the propulsion combustion engines, due to weight and volume restrictions, rely on liquid phase combustion processes. The multi-physics aspect of liquid phase combustion introduced by the fuel evaporation along with combustion in a highly-turbulent environment makes experimental investigation of such a system a very challenging endeavor. This lack of high fidelity experimental data explaining complex interaction between different physical mechanisms motivates the need for detailed simulations in order to improve our understanding and thereby advance model development. Traditionally in turbulent combustion research, focus is directed towards understanding the fully burning state. However our understanding of the transition from an unburnt state to a fully burning state is relatively underdeveloped and therefore is the focus of the present work. While most of the industrial combustion devices rely on either an external ignition source or auto-ignition to start combustion, this work will solely focus on understanding and modeling auto-ignition in liquid hydrocarbon fuel jets. To study the phenomena of auto-ignition we have performed three-dimensional high fidelity simulations of reacting n-heptane liquid-fuel temporal jet in Diesel engine type conditions. In these simulations the continuous phase is described using an Eulerian representation whereas Lagrangian particle tracking is used to model the dispersed phase. The chemical kinetics are described using a reduced n-heptane chemical mechanism with 42 species and 304 reactions. The results from the simulations are used to characterize auto-ignition in turbulent spray flames. Auto-ignition kernels are first seen in fuel-lean mixture fraction regions. The role of scalar dissipation rate on auto-ignition is highlighted. Auto-ignition is observed only in the regions of low scalar dissipation rate. Subsequent to formation of auto-ignition kernels, reaction fronts propagate towards the fuel-rich regions and establish regions of increased reaction rate. Dominance of partially premixed mode of burning is also noted. Finally, the flamelet combustion models are analyzed using the simulation database. The a-priori tests highlight the deficiencies of premixed progress variable based model in reproducing auto-ignition. The a-priori tests also reveal the superior performance of non-premixed progress variable model in capturing the auto-ignition behavior.
High resolution breast MRI [electronic resource]
Keywords: Bioengineering.

Breast cancer is the second leading cause of female cancer death in the United States with an average lifetime risk of 1 in 8. Early detection of the disease and subsequent treatment increase the chance of survival. X-ray mammography is the standard imaging technique for breast cancer screening, but it is difficult to identify malignant lesions in women with dense breasts using x-ray mammography. Dynamic-contrast-enhanced (DCE) magnetic resonance imaging (MRI) has provided high sensitivity for breast cancer diagnosis due to its excellent soft tissue contrast, but there have been varied reports on its specificity. A recent study with a small surface coil has shown that high spatial and temporal resolution breast DCE MRI can improve sensitivity and specificity of ductal carcinoma in situ diagnosis by visualizing smaller scale features such as ductal and periductal enhancement. However, a small surface coil is not suitable for screening or bilateral staging exams where volumetric coverage of both breasts is necessary. Conversely, many commercially-available breast coils offer volumetric coverage of the breasts, but the large coil elements limit the signal-to- noise ratio (SNR) and thus the ability to increase spatial and temporal resolution with high parallel imaging acceleration factors. To address these concerns, we have designed and developed a custom-fitted 18-channel, bilateral breast radiofrequency (RF) coil array for providing high-resolution images in clinically-feasible scan times. The purpose of this work was three-fold: outline the construction process of a high- SNR custom-fitted array, benchmark its performance compared to a commercial design, and evaluate its utility for high-resolution clinical breast MRI. By placing a chain of overlapping small coil elements close to the tissue, we were able to obtain high SNR over the entire breast volume for medium-sized women. To reduce the overall exam time, we laid the coil elements in a geometry that facilitated bidirectional parallel imaging. Comparing the custom-fitted array to a commercially-available 8-channel breast array, the results show 3.6 times higher average SNR and superior parallel imaging quality for the custom-fitted array in volunteers. Using parallel imaging and taking advantage of the SNR benefits from the 18-channel coil array, we clinically demonstrated a 10-fold improvement in spatial resolution over the current Stanford Hospital protocol. We have conducted a clinical study comparing the diagnostic quality of high-resolution scans with the 18-channel array versus lower resolution scans in patients with suspicious lesions on mammography. The initial findings show that the improved resolution enables better depiction of overall lesion morphology and tissue interfaces. In summary, we have presented a method for constructing an 18-channel custom-fitted breast RF array and demonstrated its SNR and parallel imaging benefits. In a clinical setting, our initial findings show improved morphology characterization in high-resolution exams with the 18-channel array.
High-k dielectric layers and their application in organic electronics [electronic resource]
Keywords: Materials Science and Engineering

Solution processed organic field effect transistor (OFETs) have being proposed for low-cost electronic applications such as sensors, RFID tags, and electronic paper. In order to achieve high performance, the effects of microstructure on charge transport as well as the design of new organic semiconductors have been investigated. Equally important, however, is the influence of the gate dielectric interface on the properties of organic semiconductors for various applications. In the first chapter, the functionality of a dual gate transistor as a chemical sensor will be demonstrated. The top high-[kappa] dielectric, Al2O3, is deposited on a conventional single gate OTFT to build the sensing element. When polar molecules of interest attach to the top high-k dielectric, an electric field is induced on the top surface of semiconductor, affecting the response of the transistor thereby providing a sensing mechanism. As a result, such top dielectric sensing architecture produces a high-sensitivity response and mitigates the poor ambient stability of organic semiconductors. The second chapter of this dissertation will focus on room-temperature, solution-based fabrication of high-[kappa] ZrO2 thin films for low-voltage-operated OFETs. An alternative UV curing method for the densification of Zr-based gel films, which allows for low-temperature processing, is compared to the conventional thermal annealing method. Electrical and microstructural analysis shows that UV-curing induces the decomposition of organic-metal bonds and causes the densification of the metal oxide film, just as the conventional thermal annealing of gel films does, resulting in a high-[kappa] dielectric layer from Zr-based solutions. Using this dielectric layer with an octadecylphosphonic acid self-assembled monolayer, solution-processed polymer OFETs with PBTTT-C-14 as the organic semiconductor function well at low voltage (below -3 V). The effect of SAM on the morphology and microstructure of the organic semiconductor deposited on the ZrO2 dielectrics is investigated. We also demonstrate a solution-processed OFETs fabricated on a flexible substrate at low temperature (T< 70°C). In third chapter, the third part of the presentation will focus on dielectric surface modification effects on an ambipolar organic semiconductor in order to control on-set voltage by introducing known amounts of deep trap states. Self-assembled monolayers with different head group were used to modify the charge transport properties of an ambipolar organic semiconductor, poly(3,6-bis-selenophene-2-octyl-1-dodecyl-diketopyrrolopyrrole- co-benzothiadiazole (PSeDPPBT). To further investigate the origin of the surface modification effect, micro- and electronic structure of PSeDPPBT were characterized with grazing incident x-ray diffraction and temperature dependent charge transport measurements.