VictorJuiz/thesis huggingface dataset:
Linear and nonlinear processes in hypersonic boundary layer transition to turbulence [electronic resource]

The design of vehicles which travel at hypersonic speeds is strongly determined by drag characteristics and heat transfer. A portion of this drag and heating is due to the boundary layer where viscosity and thermal conductivity are most important. The level of drag and heating depends on whether the boundary layer is laminar or turbulent with the latter leading to higher levels of drag and heating. In addition, as high speed boundary layers transition from laminar to turbulent flow, an overshoot of the heat transfer beyond that of turbulent flow has been observed in experiments. In low disturbance environments, transition to turbulence follows the path of receptivity, linear growth, nonlinear interaction, and finally breakdown to turbulence. The linear growth of disturbances can be determined by linear stability theory. An analysis of the predicted growth rates and integrated growth of linear disturbances for hypersonic boundary layers including thermal and chemical non-equilibrium is undertaken. The sensitivity to different chemical assumptions, transport models and thermal boundary conditions is investigated. A disturbance energy norm is proposed and its corresponding balance equation is derived. This energy norm is then to determine the effect of different terms of the linear stability equations and to compute transient growth for hypersonic laminar boundary layers. DNS (Direct Numerical Simulation) is used to simulate the nonlinear breakdown to turbulence for a variety of transition scenarios for both zero pressure gradient and adverse pressure gradient high-speed flat plate boundary layers in order to investigate the mechanism for the overshoot of heat transfer in transitional hypersonic boundary layers. The initial disturbances are excited through suction and blowing at the wall and their frequencies are chosen based on linear stability theory. Different transition mechanisms are investigated including a pair of oblique waves and 2D and 3D instabilities at higher frequencies which are unique to high speed boundary layers. Oblique breakdown shows a clear overshoot in heat transfer and skin friction and leads to a fully turbulent boundary layer. The alternative scenarios also lead to transition but further downstream and without large overshoots in heat transfer. A detailed analysis of the transitional and turbulent regions is undertaken.

Keywords: Aeronautics and Astronautics
Advisor: Lele Sanjiva K. (Sanjiva Keshava)
Iaccarino Gianluca advisor. Thesis advisor
MacCormack R. W. (Robert William)
Linking orogenic deformation, exhumation, and basin evolution in the Patagonian Andes and Magallanes Basin, southernmost South America [electronic resource]

Convergent orogenic belts evolve through the interactions among topographic growth by crustal thickening and magmatic arc emplacement, lithospheric deformation, and mass redistribution by surface processes. While feedbacks among these processes are becoming well-understood for orogenic systems within cratonal or continental lithosphere, mountain belts that evolve in predecessor backarc and rift settings appear to exhibit fundamental differences in structural style and basin physiography. This dissertation investigates the thermotectonic evolution of the Patagonian Andes and Magallanes retroforeland basin of southernmost South America and demonstrates that inherited tectonic history can profoundly affect the style of subsequent crustal deformation, spatio-temporal distribution of rock unroofing, and many aspects of foreland basin character. Geologic mapping across the Patagonian fold-thrust belt and subsurface foreland basin stratigraphy documents ~32-40 km (19-23%) of retroarc crustal shortening and inversion of rift-related structures. This work identifies an important shift from thin-skinned thrusting across the Late Cretaceous thrust belt to early Miocene deep-seated thrusting and uplift of the Cretaceous foreland depocenter. Apatite and zircon (U-Th)/He results from across the sub-Andean orogen show that the locus of deep crustal exhumation has migrated eastward from the batholith since ca. 30 Ma. Deep exhumation has been focused on the retroarc (leeward) side of the Patagonian Andes since ca. 22-18 Ma, coeval with structural uplift and unroofing of the fine-grained siliciclastic strata in the sub-Andean thrust sheets. Detrital thermochronology and thermal modeling results indicate that (1) sedimentary burial of the Paleocene basin-fill was much deeper than previously thought, and (2) sediment recycling of Mesozoic basement zircons in Upper Cretaceous foredeep deposits was an important sediment source for the Oligocene-Miocene depocenter. Finally, elasto-plastic modeling of lithospheric deflection in the Upper Cretaceous Magallanes Basin suggests that plastic yielding during plate bending appears to be an important mechanism of lithospheric deformation in successor foreland basins. These findings have important implications for interpreting tectonic histories from basin stratigraphy and dispersal patterns compared to foreland basins that develop on cratonal lithosphere.

Keywords: Geological and Environmental Sciences.
Advisor: Graham S. A. (Stephan Alan)
Dumitru Trevor (Trevor Alan) advisor. Thesis advisor
Grove Marty
Hilley George E. advisor. Thesis advisor
Linking the computational structure of variance adaptation to biophysical mechanisms [electronic resource]

Neurons have a limited dynamic range. To more efficiently encode the large range of natural inputs, neural circuits adapt by dynamically changing their output range as a function of the input statistics. Variance adaptation provides an informative example of this process, whereby neurons change their response characteristics as a function of variance of their input. When their input distribution changes, sensory systems shift and scale their response curves to efficiently cover the new range of input values and they focus on different segments of the frequency spectrum, for example by choosing to average out the noise in a low signal-to-noise ratio environment by low-pass filtering their input and sacrificing resolution. In multiple sensory systems, adaptation to the variance of a sensory input changes the sensitivity, kinetics and average response over timescales ranging from < 100 ms to tens of seconds. Here we present a simple biophysically relevant model of retinal contrast adaptation that accurately captures both the membrane potential response and all adaptive properties. The adaptive component of this model is a first-order kinetic process of the type used to describe ion channel gating and synaptic transmission. We conclude that all adaptive dynamics can be accounted for by depletion of a signaling mechanism, and that contrast adaptation can be explained as adaptation to the mean of a thresholded signal. A diverse set of adaptive properties that implement theoretical principles of efficient coding can be generated by a single type of molecule or synapse with just a few microscopic states. The LNK model helps to highlight important aspects of adaptation by letting us focus on individual computational blocks separately. By using the LNK model, we investigate the source of the adaptive process in On-Off retinal ganglion cells, which show strong changes in their kinetics as a function of contrast. By analyzing properties of the LNK model, we conclude that most of the adaptive effect is due to differences in the threshold of the two pathways, with a smaller contribution from different adaptive kinetics. Adaptive temporal decorrelation in the retina arises due to differential thresholding in two parallel neural pathways.

Keywords: Electrical Engineering
Advisor: Baccus Stephen A. primary advisor. Thesis advisor
Boahen Kwabena (Kwabena Adu) advisor. Thesis advisor
Shenoy Krishna V. (Krishna Vaughn) advisor. Thesis advisor
Literature and its rivals (1500-1660) [electronic resource]

I observe three closely related functions of speech in the early modern period, communication, persuasion, and expression; and postulate theories about each in order to understand the mechanisms of discursive suppression. Drawing on a wide range of literary and cultural texts, including the works of Shakespeare, Sidney, and Milton, I argue that there was a rivalry between literary authors and religious authority over certain valued modes of speech. In the chapter on communication, I devise a normative taxonomy of speech that reflects religious orthodoxy; then, I reconstruct models of persuasion based on several recurring figures (speech as a food, drug, child, and messenger, to name a few); and last, I look at two concepts: expression, or speech that reflects a self capable of ordering things independently, in the burgeoning essay; and suppression, or speech that wishes to promote a divine order, in the form of Le Catalógue Des Livres Censurez, the first modern index of prohibited books.

Keywords: Comparative Literature
Advisor: Greene Roland
Alduy Cécile advisor. Thesis advisor
Gumbrecht Hans Ulrich advisor. Thesis advisor
The liturgy of the holy sepulchre and the templar rite [electronic resource] : edition and analysis of the Jerusalem ordinal (Rome, Bib. Vat., Barb. lat. 659) with a comparative study of the acre breviary (Paris, Bib. Nat., Ms. Latin 10478)

This dissertation consists of an edition and analysis of the twelfth-century ordinal of the Church of the Holy Sepulchre in Jerusalem. In my thesis I explore the historical events surrounding the formation of the Crusader's Holy Sepulchre liturgy and discuss the rite's most salient aspects. This is realized by analyzing the liturgy of the temporale and sanctorale sections in combination with their associated processions. I also include in the discussion a thirteenth-century breviary written in Acre for the Knights Templar chapel. This breviary follows the use of the Holy Sepulchre and permits among other things, a discussion of how the rite changed through time.

Keywords: Music
Advisor: Mahrt William P.
Berger Karol
Burgtorf Jochen
Rodin Jesse advisor. Thesis advisor
The living rock [electronic resource] : natural, human, and sacred histories of the earth, 1680-1740

The dissertation charts the birth of earth history as a new field of knowledge in the early Enlightenment. In early modern Europe, the earth was a simultaneous subject for natural, sacred, and human history. The capacious, contentious new field of inquiry which arose around this unstable object 'Earth' in the late seventeenth century was characterized by exuberant syncretism and fierce debate. Savants across the Republic of Letters drew on multiple areas of learning and culture--including antiquarianism, the life sciences, political economy, and Protestant and Catholic theology and faith--in order to better understand the planet's past and future, its fertility and vitality, and national and human origins. Eventually, the earth's history became the subject of a field of specifically natural--rather than sacred or humanistic--knowledge. This controversial and surprising development was a function of the emergence of a multi-confessional and international conversation about the earth; increasingly sharp distinctions between disciplines, pursuits and professions in the Enlightenment; and transformations in the very meaning of 'Nature' and 'history.'.

Keywords: History.
Advisor: Findlen Paula primary advisor. Thesis advisor
Riskin Jessica primary advisor. Thesis advisor
Como David R.
Proctor Robert
The logic of redistributive non-democracies [electronic resource]

The "redistributive hypothesis" holds democracy to be the fundamental cause of redistribution from rich to poor. It is based on the following intuition. In contrast to autocracy, under which political power is concentrated among economic elites, democracy empowers all citizens equally by creating a mechanism through which the majority can vote for egalitarian economic policies. This argument traces its intellectual roots at least to Tocqueville, has been formalized through political economy models (Romer 1975; Roberts 1977; Meltzer and Richard 1981) and recently has been expanded to underpin an important set of theories about the economic origins of democracy and dictatorship (Boix 2001, 2003; Acemoglu and Robinson 2000, 2001, 2006). I argue that the prevailing view underestimates the ability of non-democratic regimes to redistribute to the poor and explore alternative mechanisms for redistribution in non-democratic contexts. I use original datasets from archival sources for in-depth case studies, statistical analyses at the cross-national level, and formal models to make my case. My findings offer new insights on the causes of economic redistribution, advance the systematic study of autocracy and contribute to an emerging literature on the autocratic roots of social policy in developing nations.

Keywords: Political Science.
Advisor: Haber Stephen H.
Rodden Jonathan advisor. Thesis advisor
Wright Gavin advisor. Thesis advisor
Logical spreadsheets [electronic resource]

Computerized spreadsheets are tremendously popular and useful. Despite their success, computerized spreadsheet systems today have significant and unnecessary restrictions that limit their usefulness. One significant restriction is that the formulas used to specify calculations must be functions. Another unnecessary restriction is that propagation can only occur in one direction. We can lift these restrictions, allowing for many-to-many logical constraints and multidirectional propagation. We call such a spreadsheet a logical spreadsheet. We allow for inconsistency between the constraints of the spreadsheet. To allow for the consequences of the spreadsheet to be shown, we create a new paraconsistent entailment relation and show how it can be computed. We discuss the issues involved in updating a logical spreadsheet, and design a family of domain-independent update operators for updating logical spreadsheets. To allow for domain-dependent behavior, we design a logic called Markov Change Logic that can be used to express update policies for spreadsheets. The design of Markov Change Logic is motivated in part by an analysis of dynamic database constraints, in which we prove that all database constraints can be reduced to Markov dynamic constraints if the schema may be reformulated. We describe the implementation of a logical spreadsheet engine called Webcell which can be used to turn Web pages into logical spreadsheets, and discuss its application to the Stanford Computer Science Master's Program Sheets.

Advisor: Genesereth Michael R.
Garcia-Molina Hector advisor. Thesis advisor
Chaudhri Vinay K.
Long baseline atom interferometry [electronic resource]

Due to its impressive sensitivity, long baseline atom interferometry is an exciting tool for tests of fundamental physics. We are currently constructing a 10-meter scale apparatus to test the Weak Equivalence Principle (WEP) using co-located Rb85 and Rb87 atom interferometers. This apparatus aims to improve the current limit on WEP violation 100-fold, which illustrates the power of this technique. This scientific goal sets stringent requirements on the kinematic preparation of the atomic test masses, the interferometer laser wavefront and stability, as well as the electromagnetic and gravitational field homogeneity of the interferometer region. The efforts to control these sources of systematic error are discussed. Additionally, applications of long baseline atom interferometry to space-based sensors for geodesy and gravitational wave detection are presented.

Keywords: Physics
Advisor: Kasevich Mark A. primary advisor. Thesis advisor
Mabuchi Hideo primary advisor. Thesis advisor
Manoharan Harindran C. (Harindran Chelvasekaran)
Low-dimensional neural features reflect central features of muscle activation [electronic resource]

Any time we move, our brains solve the difficult problem of translating our motor intentions to muscle commands. Understanding how this computation takes place, and in particular, what role the motor cortex plays in movement generation, has been a central issue in systems neuroscience that remains unresolved. In this thesis, we took an unconventional approach to the analysis of cortical neural activity and its relationship to executed movements. We used dimensionality reduction to extract the salient patterns of neural population activity, and related those to the muscle activity patterns generated during arm reaches to a grid of targets. We found that salient neural activity patterns appeared to tightly reflect muscle activity patterns with a biologically-plausible lag. We also applied our analyses to movements that were planned before being executed, and found that a muscle-framework view of the cortical activity was consistent with previously-described predictions of movement kinematics based on the state of the cortical population activity. Overall, our results elucidate remarkable simplicity of the motor-cortical activity at the population level, despite the complexity and heterogeneity of individual cell's activities.

Keywords: Electrical Engineering
Advisor: Shenoy Krishna V. (Krishna Vaughn) primary advisor. Thesis advisor
Newsome William T. advisor. Thesis advisor
Ng Andrew Y.
Low-noise current readout for in vivo fluorescence detection [electronic resource]

Post-treatment follow-up protocols for cancer patients often call for periodic hospital visits for magnetic resonance (MR), positron electron tomography (PET) or computer tomography (CT) scanning. Continuous monitoring through an implantable device would provide doctors and patients with important information between visits. With continuous monitoring, disease progression can be tracked in real-time, therapeutic regimens can be evaluated and adjusted as needed, and abnormal activity can be detected and acted on in a timely fashion. Optical molecular imaging based on fluorescence detection can provide a quantitative measure of many cellular and molecular processes of interest. Fluorescence detection is emerging as a powerful preclinical research tool, and is an attractive candidate for continuous in vivo cancer monitoring. However, in vivo fluorescence imaging is presently possible only with bulky instrumentation that does not permit monitoring of freely-moving subjects. In order to make a fluorescence detection system implantable, and thus portable, a vertical-cavity surface-emitting laser (VCSEL), a detector and a readout circuit for measuring photocurrents need to be integrated in one package. In this work, the design, implementation and testing of a current measuring circuit for fluorescence imaging is presented. The readout architecture is based on current integration using a capacitive transimpedance amplifier (CTIA), followed by analog-to-digital (A/D) conversion based on sigma-delta modulation. Unlike conventional approaches of measuring the voltage signal at the end of the current integration period, the [Sigma][Delta] modulator oversamples the output of the CTIA directly while current integration takes place. Thus, the input to the [Sigma][Delta] modulator is a voltage ramp, and the digital filter at the output of the [Sigma][Delta] modulator implements a line-fitting operation. This technique offers an improvement in the estimation of the CTIA output slope, and removes the limitation introduced in existing architectures by the sample-and-hold (S/H) stage preceding the A/D converter. The tradeoffs among noise power, integration time and oversampling ratio are examined in detail, and a method for extending the dynamic range (DR) of the system by a factor of five, even when voltage saturation occurs, is described. As an experimental demonstration, a prototype readout circuit was integrated in a 0.18-[Mu]m CMOS technology and then interfaced to a fluorescence detector. In vitro fluorescence measurements were performed, and an implantable solution made possible with miniaturized packaging of the two chips was demonstrated. This miniature package was implanted in live animals, which enabled in vivo fluorescence detection in freely-moving mice.

Keywords: Electrical Engineering
Advisor: Wooley Bruce A.
Barkin David
Shenoy Krishna V. (Krishna Vaughn) advisor. Thesis advisor
Low-powder and high-rate wireless transmission systems for neural implants [electronic resource]

Neural recording systems are fundamental to the advancement of brain-machine interfaces that can significantly improve the quality of lives of patients with neurological diseases, such as spinal cord injuries or quadriplegia. This thesis presents two newly developed wireless neural recording systems that are able to provide a high degree of usability and neural decoding accuracy. They are capable of simultaneously transmitting 32 to 96 channels of neural signals detected by an implanted neural sensor array. This work was carried out within the framework of the Hermes project and its technical design challenges will be addressed. The Hermes project is aimed at primarily developing hardware and software tools that extract neural information from the motor cortex. Those tools can enable practical prosthetic devices used to significantly ameliorate the life of patients with neurological impairments that directly affect motor functions. The first developed system, HermesD, is a 32-channel broadband transmission system using an FSK modulated carrier at 24 Mbit/s in the 3.7-4.1 GHz band. The link range extends beyond 20 m and the total power consumption is 142 mW. The HermesD system uses only COTS components and can be easily replicated. HermesD is fully operational and is currently used to transmit broadband neural data for neuroscience research in the Neural Prosthetic Systems Laboratory (NPSL) at Stanford University. HermesD is also planned as the base platform for future human trials to take place in the same laboratory. The second system that represents the next Hermes generation, HermesE, uses a novel UWB transmitter architecture implemented in a custom IC in the 65-nm CMOS technology. The transmitted signal bandwidth covers the 3.6 to 7.5 GHz frequency range. The time domain waveform is digitally programmable, allowing a very flexible control of the output spectrum to avoid interference and to allow multi-band operation. The UWB transmitter chip is part of a 96-channel broadband recording system delivering 40 Mbit/s. Its power consumption is 230 uW for a communication range of about 5 m. The antenna subsystems for these wireless recording devices presented a design challenge given the requirements for small size, large bandwidth and high efficiency. While HermesD has an operating FBW of 10%, HermesE is much more demanding in this respect, with 70% FBW, requiring unconventional antenna structures. The design techniques and performance of the antennas required to meet the specifications of both systems are also addressed in this work.

Keywords: Electrical Engineering
Advisor: Meng Teresa H. primary advisor. Thesis advisor
Leeson David B.
Shenoy Krishna V. (Krishna Vaughn) advisor. Thesis advisor