VictorJuiz/thesis huggingface dataset:
High-level digital interfaces with low overhead [electronic resource]

The majority of today's digital designs are coded in hardware description languages (HDLs) such as Verilog, VHDL, BlueSpec, SystemC, etc. HDLs provide useful abstractions to facilitate the design of complex systems, and although they offer diverse syntaxes for expressing hardware, they actually share similar module interface semantics. These interfaces rely on hardwired, timing-dependent communication protocols, and offer poor design-time parameterization of internal control logic, both of which impede complex system design. In this thesis, we describe a high-level interface abstraction that improves upon the hardwired interfaces common to popular HDLs. These high-level interfaces create logically asynchronous connections between modules, allowing module timings to vary without breaking system functionality. This has a number of design advantages, including better design exploration and easier module reuse. Moreover, high-level interfaces abstract hardwired control logic as per-instance module elaboration parameters, further enabling module reuse. These generic, flexible interfaces are rarely used today because they lead to timing and area overheads compared to hardwired, customized designs. To address this, we present a reachability analysis framework that can be used to identify and remove overhead from high-level interfaces in gate-level netlists. This makes the synthesis results of high-level interfaces comparable to typical hardwired approaches. We use various examples from the Stanford Smart Memories project to demonstrate the use of high-level interfaces, and how they can be synthesized into efficient implementations. By building modules with high-level interfaces, system designers can both modify existing designs (e.g., pipeline long paths) and reuse modules to compose new working systems, without worrying about the timing of interface handshakes. Furthermore, reachability analysis ensures high-level interfaces do not add any logic overhead compared to a hardwired interface. Therefore, we believe high-level interfaces are a useful abstraction for extending HDLs as design complexities continue growing into the future.

Keywords: Electrical Engineering
Advisor: Horowitz Mark (Mark Alan) primary advisor. Thesis advisor
Kozyrakis Christoforos
Olukotun Oyekunle Ayinde advisor. Thesis advisor
High-order discontinuous Galerkin method with Lagrange multipliers for advection-diffusion problems [electronic resource]

A high-order discontinuous Galerkin method with Lagrange multipliers (DGLM) is proposed for solving the advection-diffusion equation on unstructured meshes. Following the same methodology as the discontinuous enrichment method (DEM), free-space solutions of the governing homogeneous partial differential equation are used in lieu of standard polynomials in order to finely capture features of the solution. Polynomial Lagrange multipliers are used to enforce weak continuity of the solution at the element interfaces. The design of arbitrary-order elements for homogeneous problems is discussed in detail and is supported by a mathematical analysis. For solving non-homogeneous advection-diffusion problems, a novel approach is proposed to decrease the computational cost. Adaptivity of the method is highlighted by the use of an a posteriori error estimate for automatic mesh refinement. The numerical results reveal that these DGLM elements outperform their standard Galerkin and stabilized Galerkin counterparts of comparable computational complexity.

Keywords: Aeronautics and Astronautics
Advisor: Farhat Charbel primary advisor. Thesis advisor
Jameson Antony
Lew Adrian advisor. Thesis advisor
High-order energy stable flux reconstruction schemes for fluid flow simulations on unstructured grids [electronic resource]

Nowadays, most commercial CFD software relies exclusively on low-order methods (methods for which the spatial order of accuracy is at most two) for the simulation of flows over complex geometries. Although these methods are extremely robust and efficient, they are often inadequate when simulations require a very high level of accuracy. As desired error tolerances continue to decrease, high-order methods for unstructured grids will continue to grow in popularity. In the context of fluid flow simulations, applications that require high levels of accuracy (which could therefore benefit greatly from the use of high-order methods) include Direct Numerical Simulations (DNS), Large-Eddy Simulations (LES), Computational Aero-Acoustics (CAA) and vortex dominated flows. In 2007, Huynh presented the Flux Reconstruction (FR) approach to high-order methods. The method is attractive because it is intuitive, straightforward to implement, unifying (in the sense that it can recover various well known high-order methods), computationally efficient (since it does not require the use of numerical integration), and easily parallelizable. However, there remained questions regarding the stability of FR schemes and their applicability to practical fluid flow problems. In this thesis, a new class of FR schemes is identified, and applied to solve the 3D Navier-Stokes equations on mixed unstructured grids. The new schemes are referred to as Energy Stable Flux Reconstruction (ESFR) schemes. Their implementation in 1D, on triangular and quadrilateral elements in 2D, and on prismatic and hexahedral elements in 3D is discussed. The stability and accuracy properties of ESFR schemes are studied thoroughly. An energy stability proof is used to show the linear stability of the schemes for all orders of accuracy, in 1D and on triangular elements in 2D. Various numerical experiments in the field of fluid dynamics are then used to demonstrate their effectiveness. The implementation of ESFR schemes on Graphics Processing Units (GPUs) is also discussed. Because of their high arithmetic intensity and their element-local nature, the schemes are well suited for new massively parallel hardware architectures such as GPUs. The efficient implementation of ESFR schemes on GPUs results in speedups of at least one order of magnitude relative to traditional high-order methods for unstructured grids running on conventional computer hardware.

Keywords: Aeronautics and Astronautics
Advisor: Jameson Antony
Lele Sanjiva K. (Sanjiva Keshava)
MacCormack R. W. (Robert William)
High-performance Ge/SiGe quantum well waveguide modulators for optical interconnect systems [electronic resource]

Optical interconnects have the potential to help create faster, more powerful computers that use far less energy than they currently do. However, to accomplish this goal, key material and device design breakthroughs must first occur. This Ph.D. dissertation focuses on developing the technology for one component of future optical interconnects, the optical modulator. Ge/SiGe quantum wells exhibit the quantum-confined Stark effect, the strongest high-speed electroabsorption modulation mechanism available in a CMOS-compatible material. We begin by examining the ultrafast carrier dynamics of these quantum wells as a way to understand the fundamental limitations to optical modulators which rely on this material. Using a pump-probe experimental setup, we measured the intervalley scattering time of electrons from the direct valley to the indirect L valley in the conduction band of the germanium wells to be ~185 fs. We also measured field screening in these quantum wells and modeled its recovery through diffusive conduction within 120 ps. This improved understanding of Ge/SiGe quantum wells allowed us to design a waveguide-integrated modulator that relies on selective area growth of this material in thick silicon-on-insulator waveguides. Selective area quantum well waveguide modulators offer the potential of high contrast ratios, low operating energies, and low loss. We developed a novel growth substrate fabrication process to enable high quality selective area growth of Ge/SiGe quantum wells with minimal sidewall growth. We then fabricated selective area modulators integrated with SOI waveguides, and present here preliminary results from these devices.

Keywords: Electrical Engineering
Advisor: Miller D. A. B. primary advisor. Thesis advisor
Harris J. S. (James Stewart)
Saraswat Krishna advisor. Thesis advisor
High-sensitivity thermally stable interferometric acoustic sensors and fiber-optic sensor networks for remote sensing applications [electronic resource]

Optical sensors and sensor networks have been the key devices in a number of applications, including remote sensing, underwater acoustic communications, oil exploration, surveillance, seismic surveying arrays, military sonar arrays and structural health monitoring for massive aerospace and wind-energy structures. These applications impose critical specifications both at device level and systems level. In the first part of this dissertation, a high-sensitivity, thermally stable, compact interferometric acoustic sensor with a large bandwidth and high dynamic range will be introduced. The device is based on a photonic-crystal fabricated on a compliant single-crystal silicon membrane, which is placed near the metalized end of a single-mode fiber to form a Fabry-Perot (FP) cavity. We demonstrated high reproducibility in operating wavelength (±1 nm) and fabricated ten FP sensors with measured displacement sensitivities within ±0.3 dB. The response was shown to be polarization independent and thermally stable. We showed that ±65 °C change in temperature can be tolerated before the FP resonance shifts by only 1 nm. An experimental sensor was shown to measure acoustic pressures down to a record low of 5.6 µPa/√Hz with a flat-band response greater than 8 kHz and a sensitivity extending down to at least 100 Hz. The dynamic range in pressure was greater than 100 dB. An electromechanical model of the device is presented as a tool for designing and optimizing this micro-physical structure. This analytical model enabled the analysis of the coupled design parameters on the device's sensitivity and noise. Results are shown to be in very good agreement with the experimentally measured quantities. In the second part of the dissertation, the design of a time-division-multiplexed optical sensor network architecture employing multiple low-gain erbium-doped fiber amplifiers will be introduced. Using this architecture, an experimental system will be demonstrated with ten acoustic sensors multiplexed and interrogated with a single laser source at a single wavelength. The signal-to-noise-ratio for each sensor response was measured to be within ±0.95 dB of the nominal value. System performance in terms of cross-talk and polarization dependence will also be discussed. Finally, a model identifying the noise contributions in this complex system will be introduced, which predicts that up to 350 sensors can be multiplexed with this new multiplexing architecture.

Keywords: Electrical Engineering
Advisor: Digonnet Michel J. F. primary advisor. Thesis advisor
Solgaard Olav primary advisor. Thesis advisor
Kino Gordon S. advisor. Thesis advisor
How metaphor shapes thought [electronic resource]

The way we talk about complex and abstract ideas is suffused with metaphor. In a series of behavioral experiments and computational simulations, I explore how these metaphors influence the way that we reason about complex issues. I find that even the subtlest instantiation of a metaphor (via a single word) can have a powerful influence on how people attempt to solve social problems like crime and how they gather information to make ''well-informed'' decisions. Interestingly, I find that the influence of the metaphorical framing effect is covert: people do not recognize metaphors as influential in their decisions; instead they point to more ''substantive'' (often numerical) information as the motivation for their problem-solving decision. I also investigate the underlying mechanisms and contextual factors that support and influence how this process unfolds. Metaphors in language appear to instantiate frame-consistent knowledge structures and invite structurally consistent inferences. Far from being mere rhetorical flourishes, metaphors have profound influences on how we conceptualize and act with respect to important societal issues.

Keywords: Psychology
Advisor: Boroditsky Lera primary advisor. Thesis advisor
McClelland James L. advisor. Thesis advisor
McClure Samuel M. advisor. Thesis advisor
How obesity and aging interact to create increased risk of osteoarthritis and disability [electronic resource]

Obesity, a condition characterized by excess adipose tissue, is becoming an important public health problem. Not only has the prevalence rate in adults risen steadily since the 1980's, obesity is a strong risk factor for the development of knee osteoarthritis (OA) and general mobility disability. There are currently no disease-modifying treatments for OA, so it is important to develop preventive strategies. However, we must first understand the mechanism of increased risk in the obese population. Knee cartilage and other joint structures respond both to mechanical loads during activities of daily living and to the biological environment within the joint, so the pathway to OA in the obese population therefore likely involves changes in both. The primary goal of this dissertation was to test the hypothesis that aging and obesity are linked to changes in gait mechanics and changes in the relationship between cartilage morphology and joint loads, and that these changes are consistent with increased knee OA risk. We also analyzed whether these changes are also observed in individuals with early asymptomatic knee joint degeneration. Finally, we tested the hypothesis that stair climbing requires adaptive changes that reflect a reduction in muscle strength in the aging obese population and indicate increased mobility disability risk. The results indicate that in obese, but not normal-weight individuals, age was associated with an increased adduction moment, which reflects increased loads on the medial compartment of the knee. Furthermore, the positive relationship between cartilage thickness and ambulatory load in young subjects was significantly weaker in middle-aged obese individuals. The increased OA risk in older obese individuals is therefore likely due to both an increase in ambulatory loads and to a change in the relationship between those ambulatory loads and cartilage properties due to the elevated pro-inflammatory cytokine levels characteristic of obesity. During stair climbing, middle-aged obese individuals also had lower peak knee flexion moments, indicative of quadriceps weakness due to aging and relative to their weight. Finally, the gait and stair climbing mechanics of individuals with early OA were not different from their age- and BMI-matched healthy counterparts, indicating that the gait alterations seen in healthy middle-aged obese individuals are the same as those in obese individuals who have already developed the disease, and are likely risk factors or early functional markers of OA.

Keywords: Mechanical Engineering
Advisor: Andriacchi Th. P. (Thomas P.) primary advisor. Thesis advisor
Delp Scott advisor. Thesis advisor
Levenston Marc Elliot advisor. Thesis advisor
Humboldt squid in the northern California current system [electronic resource]

Humboldt squid (Dosidicus gigas) are large (>1 m), short-lived (1-2 years), fast-growing (1 mm/d in adults), highly fecund (30 million eggs/female), generalist predators in the eastern Pacific Ocean that support the world's largest invertebrate fishery (FAO 2009). Life history and behavioral characteristics of the Humboldt squid have likely facilitated its range expansion into the northern California Current System. After an initial presence during the 1997/1998 El Niño, Humboldt squid were observed in variable numbers from 2002-2010. Seasonal feeding migrations likely bring them to the productive waters off the coast of Washington and British Columbia to forage before returning to warmer waters to spawn. I investigated the behavior and habitat of Humboldt squid in situ with both electronic tags deployed on individual animals and observations collected by remotely operated vehicles (ROVs) in Monterey Bay that recorded thousands of Humboldt squid from 1997-2010. Several tagged squid dove to depths >1.25 km, through the core of the oxygen minimum zone (OMZ), and I estimated they can sustain horizontal velocities of >35 km/day for over two weeks, with maximum velocities >50 km/day. Further, I integrated observations of Humboldt squid on each ROV dive with information on time-at-depth of the ROV, creating an "encounter rate" metric that can be used in ecosystem and fisheries models, similar to catch per unit effort (CPUE). I used this metric to investigate the seasonality of Humboldt squid presence in the Monterey Bay area in relation to upwelling and found that early evolution of the upwelling season may serve as an indicator for the annual magnitude of their presence. My work reveals capabilities and behaviors of Humboldt squid that will enhance our understanding of their impacts on the ecosystems and fisheries in the California Current System.

Keywords: Biological Sciences
Advisor: Gilly William primary advisor. Thesis advisor
Bograd Steven J.
Denny Mark W.
Field John C. advisor. Thesis advisor
Somero George N. advisor. Thesis advisor
Hydrogen interaction with nanostructured carbon - electronic and geometric structure changes and applications [electronic resource]

The hydrogenation of carbon nanostructures has been explored in this thesis work. The purpose of studying hydrogen interactions with carbon was twofold -- (a) to understand the electronic and structural changes in graphene induced by hydrogenation and (b) explore hydrogen storage possibilities in carbon materials. Since graphene is a semi metal with zero band gap at the Fermi level, there is a necessity to open a band gap for transistor applications. Several hypotheses have been suggested for opening a band gap, one of which is chemisorbing ad-atoms on graphene layer (like hydrogen). Hydrogenation of graphene grown on Pt(111) was studied using x-ray spectroscopy including x-ray photoelectron spectroscopy (XPS), x-ray absorption (XAS), x-ray emission (XES), resonant inelastic x-ray scattering (RIXS), which provides for an atom specific probe of the electronic structure and the chemical environment of the carbon atoms. Hydrogen adsorption is accompanied by delocalization of the [pi] band contrary to band opening behavior. Finite density of states (DOS) was observed at the Fermi level in the carbon projected DOS. The structural distortion caused by hydrogen adsorption is stabilized through pinning of the graphene to the substrate through the formation of local C-Pt bonds which does not result in band opening due to the delocalization of the [pi] band through substrate hybridization. Surface hydrogen adsorption on few layer graphene/Pt(111) induces changes in the bond symmetry of all the carbon atoms in the various graphene layers resulting in a "diamond like" structure. This propagation of the sp3 hybridization to underneath layers is again stabilized through hybridization between the carbon atoms in the interfacial layer and the substrate. Finally the carbon-Pt system was explored as a potential hydrogen storage candidate. The concept of "spillover" of H atoms from H2 molecules dissociated on the Pt catalyst was exploited towards reducing the kinetic barrier involved in the process of de-hydrogenation of carbon nanotube/Pt composites at near ambient conditions (~8.25 atm. of hydrogen gas at room temperature) yielding a hydrogen storage capacity of 1.6wt%.

Keywords: Materials Science and Engineering.
Advisor: Clemens B. M. (Bruce M.) primary advisor. Thesis advisor
Nilsson Anders
Mao Wendy (Wendy Li-wen) advisor. Thesis advisor
Hydroxylation of unactivated tertiary carbon-hydrogen bonds using high-valent ruthenium catalysts [electronic resource]

The prevalence of the hydroxyl group in organic molecules of synthetic and biological interest makes direct, selective hydroxylation of unactivated carbon-hydrogen (C—H) bonds in complex molecules a desirable goal. This approach to oxygen incorporation is further inspired by Nature, where enzymes mediate hydroxylation of complex substrates with exquisite selectivity. Chemists have designed catalysts for C—H hydroxylation, but further improvements in chemoselectivity, positional selectivity and turnover numbers are needed for C—H hydroxylation to become a widely-used tool for fine chemicals synthesis. Our approach to the problem of C—H hydroxylation involves the use of high-valent ruthenium oxo complexes. We have found that addition of pyridine to ruthenium tetroxide (RuO¬4, generated using ruthenium trichloride and potassium bromate) results in a notable improvement in the ability of RuO4 to catalyze C—H hydroxylation of functionalized substrates. This reaction proceeds with predictable selectivity in substrates with more than one tertiary C—H center. Incorporation of isotopically labeled oxygen into a substrate is possible using this methodology. However, the highly-oxidizing nature of RuO4 places some limits on the types of functionality that may be present in substrate molecules. Limitations of the ruthenium tetroxide/pyridine catalyst system have led us to examine ruthenium complexes with tunable ligands. The complex (Me3tacn)RuCl3 (Me3tacn = 1,4,7-trimethyl-1,4,7-triazacyclononane), in combination with silver perchlorate and ceric ammonium nitrate, catalyzes tertiary and benzylic C—H hydroxylation at room temperature with up to 80 turnovers. This catalyst system displays functional group compatibility and turnover numbers comparable with or superior to known catalysts for C—H hydroxylation. Mechanistic studies suggest that the reaction proceeds via hydrogen atom abstraction followed by fast, solvent-caged radical rebound. Efforts to tune the ligand to further increase turnover numbers and catalyst selectivity are described.

Keywords: Chemistry
Advisor: Du Bois Justin primary advisor. Thesis advisor
Stack T. (T. Daniel P.)
Waymouth Robert M. advisor. Thesis advisor
Hyperspectral and multivariate analyses of ultrafast experiments [electronic resource]

Ultrafast laser pulses can be used to initiate, probe, and control molecular dynamics. In a typical pump-probe experiment, spectra are collected as a function of delay between two laser pulses. In control experiments, an experimental search is conducted to identify spectrally ``shaped" laser pulses that can guide the system into a desired target state. In both pump-probe and control experiments, hundreds or thousands of repeated measurements are made. I will discuss how multivariate statistics can be fruitfully applied to such experiments. First I discuss the photo-initiated ring opening of 1,3-cyclohexadiene (CHD) to form 1,3,5-hexatriene (HT) in the gas phase. By applying simplex-based spectral unmixing to spectra collected during a standard pump-probe experiment, it is possible to determine the number of transient photoproducts and to track their evolution. Then for control experiments in methanol and a simulated control experiment in diatomic iodine, I discuss how standard statistical methods such as principal component analysis can reveal the pulse features responsible for control and hint at the underlying dynamics.

Keywords: Applied Physics
Advisor: Bucksbaum Philip H. primary advisor. Thesis advisor
Fayer Michael D. advisor. Thesis advisor
Kasevich Mark A. advisor. Thesis advisor