VictorJuiz/thesis huggingface dataset:
The development of high-temperature stable amorphous metal alloy gates for the reduction of threshold voltage variability in short channel CMOS devices [electronic resource]

Polycrystalline metal gates have replaced polycrystalline silicon gates in complementary metal oxide semiconductor (CMOS) devices for high speed performance applications. This is because the decreased capacitance caused by the gate electrode depletion layer in polycrystalline silicon gates was a pressing concern for device performance and continued scaling. Metal gates do not have this depletion issue; however, work function tuning is an issue. Consequently, a focus in the metal gate area is placed on work function engineering and the effect of processing conditions on the effective work function. The first project in this thesis studies the effect oxygen on the work function of tungsten electrodes. It is found that the presence of the meta-stable A15 phase is correlated with oxygen concentration. It is hypothesized that the observed variation in work function is due to the incorporation of oxygen from the growth environment into the W layer at the SiO2/W interface. This work shows that stochastic fluctuations in processing conditions could also cause wafer-to-wafer variability, even in long channel devices. Another concern with metal gates is that due to their polycrystalline nature, device variability could become a problem as the gate dimensions are scaled down and become comparable to the grain size since work function can vary significantly with varying grain orientation. The main project in this thesis is to develop amorphous metal gates that have the potential to reduce work function variability with respect to polycrystalline gates in nano-scale MOS devices. Thus, high temperature stable amorphous Ta40W40Si10C10 gates were developed and it is also shown that when Ta40W40Si10C10 gate electrodes are integrated in long channel transistor devices, the effective channel mobility appears to be enhanced with respect to crystalline gates.

Keywords: Materials Science and Engineering
Advisor: Clemens B. M. (Bruce M.) primary advisor. Thesis advisor
Nishi Yoshio
Deal Michael
McIntyre Paul Cameron advisor. Thesis advisor
The development of miniaturized microscopes for in vivo neuronal imaging in freely moving mice [electronic resource]

A central goal in neuroscience is to explain animal behavior in terms of causal cellular processes. It has been a longstanding challenge, however, to simultaneously track behavior and the cellular dynamics driving it. In this thesis, I discuss how a series of one- and two-photon fluorescence microscopes, based on gradient refractive index (GRIN) lenses, were developed to meet this challenge. The predominant difficulty in the design of these microscopes was how to take a traditional bench top microscope and shrink it to a size small enough for a mouse to easily carry on its head, a limit of 3 grams. We chose mice as our design target due to the wide availability of genetically modified mouse models for the study of cognitive functions, animal behaviors, and disorders of the nervous system. The earlier devices, relying on fiber optics to bring light to and from the animal, met with limited success but still provided useful insight in the development of the surgical techniques and analytical tools necessary for later successful experiments. In contrast, our latest system fully integrates the entire light pathway onto the head of mouse, eliminating many of the remaining roadblocks to truly freely-moving imaging. This device has enabled novel observations of both microcirculatory and neuronal calcium dynamics in the cerebellum of freely-moving mice at frame rates up to 100 Hz. As the genetic toolbox for mice continues to mature, these miniaturized microscopes will facilitate a wide set of future studies of how cellular function in the brain varies across different behavioral and physiological states.

Keywords: Mechanical Engineering
Advisor: Kenny Thomas William primary advisor. Thesis advisor
Schnitzer Mark Jacob
El Gamal Abbas A. advisor. Thesis advisor
Development of stable metal oxide electrodes for the conversion of electricity to chemical fuels [electronic resource]

The conversion of renewable sources of electricity to molecular fuels is widely viewed as an important component of our future energy economy. To accomplish this, stable electrodes are necessary to perform electrochemical reactions of interest for extended periods of operation with high efficiency. In the first part of this thesis, a method to immobilize homogeneous catalysts to a metal oxide electrode through click chemistry on an attached p-azidophenyl phosphonic acid linker is presented. This strategy allows for a convergent approach to surface modification that results in stable attachments while allowing for facile charge transfer between the electrode and the immobilized catalyst. The deposition of p-azidophenyl phosphonic acid to the metal oxide surface and subsequent click with molecules of interest was investigated with Fourier transform infrared spectroscopy, electrochemistry and X-ray photoelectron spectroscopy. The electrochemical oxidation of water to supply the electrons need for fuel synthesis remains a challenge due to the lack of materials which can both efficiently remove four electrons and withstand the harsh oxidative conditions of the reaction. A novel type of dimensionally stable anode utilizing silicon as the base substrate and also as an in-situ photon collector has been developed. It uses a thin amount of titanium dioxide as a protective layer deposited by atomic layer deposition. A thin layer of physical vapor deposited iridium is used as the water oxidation catalyst. Results shown include water oxidation efficiency in both light and dark conditions and over a range of pH values with an emphasis on the operational stability and durability of the anodes.

Keywords: Chemistry
Advisor: Chidsey Christopher E. D. (Christopher Elisha Dunn)
Stack T. (T. Daniel P.)
Waymouth Robert M. advisor. Thesis advisor
Development of techniques for live cell RNA imaging [electronic resource]

The development of live cell RNA imaging techniques will lead to the unraveling of many important biological processes. To achieve this goal, there have been three different strategies developed. They are the development of small molecule probes, nucleic acid probes, and green fluorescent protein (GFP) probes. In the following thesis, the pros and cons of each approach are discussed, followed by a proposal to resolve the limitations. In the small molecule case, a probe was developed that utilized a quenched sulforhodamine dye. It was designed so that its structure can be rationally modified from the initial lead compound. An aptamer sequence that activates the sulforhodamine probe with micro molar affinity was found by in vitro Systematic Evolution of Ligands by Exponential Enrichment (SELEX), followed by fluorescence screening in E.coli. The rational modification of the structure of the initial sulforhodamine probe resulted in an overall 33-fold increase in binding affinity compared to the initial lead compound. Instead of the chemical modification of the lead compound, the small molecule's cell permeability and binding affinity to the target could be improved by linking to cell penetrating peptides (CPP). A CPP is a short peptide sequence composed of poly arginine amino acids which shows excellent cell uptake and affinity to RNA. However, the use of the CPP-linked dye in live cell imaging has been limited by strong signals in the endosome region. An attempt was made to overcome this difficulty by linking a quencher molecule to the dye-CPP via a disulfide bond, which only breaks when it enters the cytosol. For the nucleic acid probe, the major problem was its low cell permeability and low signal-to-background ratio due to the low copy number of mRNA targets within the cell. We made mutant Hammerhead ribozymes and embedded them in a non-coding region of the GFP expression vector that can be transfected to mammalian cells. This modified Hammerhead ribozyme acts as a logic gate, and the signal is amplified by the expression of GFP in the presence of the target mRNA. In vitro and in vivo results are discussed. Finally, a fragmented GFP system, the fluorescence of which could be recovered by binding to a specific RNA tag, was developed. The major problem for the GFP-mediated RNA imaging system was the low signal-to-background ratio from the GFP probe that is not bound to the RNA tag. To find the non-fluorescent GFP, the GFP was truncated from the C-terminus such that it loses its fluorescence with minimum loss of amino acids. An RNA sequence that has high affinity to this GFP was found by in vitro SELEX. The subsequent E.coli screening found an RNA sequence that reactivates the fluorescence of the GFP probe.

Keywords: Chemistry
Advisor: Rao Jianghong primary advisor. Thesis advisor
Huestis Wray advisor. Thesis advisor
Moerner W. E. (William Esco)
The development of techniques for three-dimensional super-resolution fluorescence microscopy and their application to biological systems [electronic resource]

Fluorescence microscopy is one of the most widely used tools in cell biology due its intrinsically high detection sensitivity coupled with the ability to genetically label proteins and other cellular structures with fluorescent tags. However, the resolution of fluorescence microscopy has historically been limited to about 200 nm laterally and 800 nm axially because of the diffraction limit of visible light. In the past five years, imaging below the diffraction limit ("super-resolution imaging") by localizing single fluorophores, one at a time (1-3), has opened a wide a variety of new biological systems for study. This Dissertation is a collection of both techniques for two and three dimensional super-resolution imaging as well as applications in bacterial and yeast imaging. References 1. Betzig E, et al (2006) Imaging intracellular fluorescent proteins at nanometer resolution. Science 313: 1642-1645. 2. Hess ST, Girirajan TPK & Mason MD (2006) Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys J 91: 4258-4272. 3. Rust MJ, Bates M & Zhuang X (2006) Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 3: 793-795.

Keywords: Chemistry
Advisor: Moerner W. E. (William Esco)
Boxer Steven G. (Steven George)
Fayer Michael D. advisor. Thesis advisor
Device technology for nanoscale III-V compound semiconductor field effect transistors [electronic resource]

As silicon CMOS technology reaches its fundamental scaling limits, alternative materials such as high mobility III-V compounds have proven to be strong contenders for extending high performance logic. However, most promising demonstrations of III-V FET/HEMTs have micron-scale source/drain spacing despite gate lengths on the nanometer scale. III-V semiconductor devices have historically relied on alloyed ohmic contacts which require large spacings to prevent shorting between the source and drain after alloying, where contacts can diffuse up to hundreds of nanometers. This severely limits the scalability of III-V logic technology. Non-alloyed contacts offer a practical route to greatly reduce the III-V device footprint for application in future technology nodes. In this dissertation, I demonstrate a route to non-alloyed contacts by shifting the pinned III-V Fermi level to reduce the metal/n-GaAs and metal/n-InGaAs Schottky barrier heights. The Fermi level is controlled by the insertion of thin dielectrics in a metal-insulator-semiconductor (MIS) contact structure. The MIS contact is studied across a wide range of metal and dielectric materials, and found to have great flexibility in the material selection. I will also discuss the use of bi-layer high-[kappa] dielectrics, and report results which show that despite an overall thicker dielectric, there is an additional reduction in the barrier height and contact resistance beyond that of a single dielectric MIS. This MIS contact is then integrated in an InGaAs MOSFET as a non-alloyed source/drain contact, though it can also be applied to Schottky Barrier FETs. I will conclude by discussing possible physical mechanisms of the observed barrier height reductions, by examining the effects of fixed charge and electronic dipoles.

Keywords: Electrical Engineering
Advisor: Saraswat Krishna primary advisor. Thesis advisor
Wong Hon-Sum Philip
Nishi Yoshio
A diagrammatic kinetic theory for describing long timescale correlations in dense, simple liquids in the overdamped limit [electronic resource]

Starting from an exact diagrammatic theory for density correlations in dense, atomic fluids, we derive a set of graphical approximations to this theory that are consistent with a set of physical assumptions that define an overdamped limit of the dynamics of the system. The results of a simple one loop approximation to this theory are then compared with data from molecular dynamics simulations for a number of correlation functions of a simple Lennard-Jones fluid at a single, high density and a range of temperatures. For correlation functions that have most of their decay over times for which the overdamped theory is valid, the one loop approximation gives accurate results, except for coherent correlation functions at small wavevector, for which the overdamped theory is not expected to be accurate. Although the temperature range we studied included only temperatures at or above the liquid's triple point, it is our hope that the overdamped theory can ultimately be used to characterize the dynamics of supercooled liquids. This will certainly require going beyond the one loop approximation.

Keywords: Chemistry
Advisor: Andersen Hans
Pande Vijay primary advisor. Thesis advisor
Moerner W. E. (William Esco)
Dictating forms [electronic resource] : authoritarian power in the Latina/o novel

In "Dictating Forms: Authoritarian Power in the Latina/o Novel, " I identify an emerging corpus of literature by contemporary Latina and Latino writers who, I contend, are using the resources of the novel to articulate intersecting connections between authoritarianism, imperialism, and racism in the Américas. Reading narrative forms as abstractions of social relations, I argue that this new generation of writers is extending the formal and geo-political contours of the Latin American dictatorship novel. The Latin American dictatorship novel represents authoritarian regimes headed by dictators, caudillos, or military juntas in Latin America. Major studies of the tradition theorize the seminal novels published by the 1970s Boom generation while scholarship on contemporary post-dictatorship literary production concentrates heavily on the Southern Cone and Hispaniola. My dissertation extends this body of scholarly work by focusing on U.S. based writers including Junot Díaz ("The Brief Wondrous Life of Oscar Wao"), Salvador Plascencia ("The People of Paper"), Edwidge Danticat ("The Farming of Bones"), and Héctor Tobar ("The Tattooed Soldier"). I demonstrate how representations of overlapping geographies and histories in these novels reveal continuities between dictatorial structures of power in the Caribbean, Mexico, Central America, and the United States. I further illuminate how particular formal devices such as parodic characterization, generic mixture, footnotes, rumor, and metafiction represent imaginary contestations of socio-political domination. By drawing on their community's experiences of dictatorship and their own experiences as racialized minorities in the United States, these writers are generating a transAmerican counter-dictatorial imaginary, thereby developing a new idiom for depicting and theorizing power in Latino and Diasporic Caribbean literature.

Advisor: Moya Paula M. L. primary advisor. Thesis advisor
Elam Michele advisor. Thesis advisor
Saldívar José David advisor. Thesis advisor
Saldívar Ramón advisor. Thesis advisor
The digital patient [electronic resource] : machine learning techniques for analyzing electronic health record data

The current unprecedented rate of digitization of longitudinal health data --- continuous device monitoring data, laboratory measurements, medication orders, treatment reports, reports of physician assessments --- allows visibility into patient health at increasing levels of detail. A clearer lens into this data could help improve decision making both for individual physicians on the front lines of care, and for policy makers setting national direction. However, this type of data is high-dimensional (an infant with no prior clinical history can have more than 1000 different measurements in the ICU), highly unstructured (the measurements occur irregularly, and different numbers and types of measurements are taken for different patients) and heterogeneous (from ultrasound assessments to lab tests to continuous monitor data). Furthermore, the data is often sparse, systematically not present, and the underlying system is non-stationary. Extracting the full value of the existing data requires novel approaches. In this thesis, we develop novel methods to show how longitudinal health data contained in Electronic Health Records (EHRs) can be harnessed for making novel clinical discoveries. For this, one requires access to patient outcome data --- which patient has which complications. We present a method for automated extraction of patient outcomes from EHR data; our method shows how natural languages cues from the physicians notes can be combined with clinical events that occur during a patient's length of stay in the hospital to extract significantly higher quality annotations than previous state-of-the-art systems. We develop novel methods for exploratory analysis and structure discovery in bedside monitor data. This data forms the bulk of the data collected on any patient yet, it is not utilized in any substantive way post collection. We present methods to discover recurring shape and dynamic signatures in this data. While we primarily focus on clinical time series, our methods also generalize to other continuous-valued time series data. Our analysis of the bedside monitor data led us to a novel use of this data for risk prediction in infants. Using features automatically extracted from physiologic signals collected in the first 3 hours of life, we develop Physiscore, a tool that predicts infants at risk for major complications downstream. Physiscore is both fully automated and significantly more accurate than the current standard of care. It can be used for resource optimization within a NICU, managing infant transport to a higher level of care and parental counseling. Overall, this thesis illustrates how the use of machine learning for analyzing these large scale digital patient data repositories can yield new clinical discoveries and potentially useful tools for improving patient care.

Advisor: Koller Daphne primary advisor. Thesis advisor
Penn Anna Asher advisor. Thesis advisor
Thrun Sebastian
Directors’ and Officers’ Insurance: Ordinary Corporate Expense or Valuable Signaling Device?

After many years in which directors have used directors’ and officers’ (D&O) coverage to shield themselves from personal responsibility for corporate failure, directors at Enron and WorldCom have been forced to pay $31 million out of their own pockets to settle securities class action lawsuits stemming from two of the largest corporate governance scandals in U.S. history. These settlements have brought the question of director's liability to the foreground, generating interest in the extent to which a firm’s D&O liability coverage reveals valuable information regarding its quality of corporate governance. Since insurers are expected to perform a thorough examination of the directors for whom insurance protection is sought, there is reason to believe that poor governance increases litigation risk and thus the size of the insurance premium. Using a sample of D&O premiums gathered from the proxy statements of firms cross-listed in the U.S. and Canada, I find a significant negative relationship between D&O premiums and variables that proxy for the quality of firms’ governance structures. This association is robust to a number of alternate specifications. As further evidence that the D&O premium reflects the quality of a firm’s corporate governance, the proxies for weak governance are positively related to excess CEO compensation. Overall, these results suggest that the D&O premium can be a useful measure of the quality of a firm’s governance.

Keywords:  Department of Economics
Stanford Department of Economics
corporate governance
D&amp;O insurance
premium
litigation risk
Thesis
Advisor: Klausner Michael
The discontinuous enrichment method (DEM) for multi-scale transport problems [electronic resource]

A discontinuous enrichment method (DEM) for the efficient finite element solution of advection-dominated transport problems in fluid mechanics whose solutions are known to possess multi-scale features is developed. Attention is focused specifically on the two-dimensional (2D) advection-diffusion equation, the usual scalar model for the Navier-Stokes equations. Following the basic DEM methodology [1], the usual Galerkin polynomial approximation is locally enriched by the free-space solutions to the governing homogeneous partial differential equation (PDE). For the constant-coefficient advection-diffusion equation, several families of free-space solutions are derived. These include a family of exponential functions that exhibit a steep gradient in some flow direction, and a family of discontinuous polynomials. A parametrization of the former class of functions with respect to an angle parameter is developed, so as to enable the systematic design and implementation of DEM elements of arbitrary orders. It is shown that the original constant-coefficient methodology has a natural extension to variable-coefficient advection-diffusion problems. For variable-coefficient transport problems, the approximation properties of DEM can be improved by augmenting locally the enrichment space with a "higher-order" enrichment function that solves the governing PDE with the advection field a(x) linearized to second order. A space of Lagrange multipliers, introduced at the element interfaces to enforce a weak continuity of the solution and related to the normal derivatives of the enrichment functions, is developed. The construction of several low and higher-order DEM elements fitting this paradigm is discussed in detail. Numerical results for several constant as well as variable-coefficient advection-diffusion benchmark problems reveal that these DEM elements outperform their standard Galerkin and stabilized Galerkin counterparts of comparable computational complexity by a large margin, especially when the flow is advection-dominated.

Advisor: Farhat Charbel primary advisor. Thesis advisor
Barone Matthew F. (Matthew Franklin) advisor. Thesis advisor
Papanicolaou George advisor. Thesis advisor