VictorJuiz/thesis huggingface dataset:
Inverse control by mirroring joint dynamics within the olivo-cerebellar complex [electronic resource]

In this dissertation, I revisit Kawato's proposal, that the cerebellum predictively modulates descending motor commands, to achieve smooth and coordinated motion, by acquiring an inverse model of the biomechanical plant, and extend it by describing a novel and precise mapping between a cerebellar multizonal microcomplex and a joint's inverse model. This mapping renders two novel predictions: First, inferior olive's oscillations mirror the biomechanical joint's oscillations. Second, deep cerebellar neurons implement a gain factor, set by Purkinje cell inhibition, on inferior olive's signals to mirror the spinal cord's gain. I use biophysical modeling to show that oscillations within the inferior olive match the range of natural frequencies and damping ratios of biophysical joints, and that deep cerebellar neurons enable a multiplicative interaction between the Purkinje and the olivary pathways. Furthermore, I determine the effects of current injection into the inferior olive and the deep cerebellar nuclei and use these results within a control theory model to predict that experimentally disturbing the inferior olive will introduce motor output ringing, while disturbing the deep nuclei will also scale motor output. In both cases, manipulating the inverse model implemented by microzonal microcomplex will unmask the joint's natural dynamics as observed by motor ringing at the joint's natural frequency.

Keywords: Bioengineering.
Advisor: Boahen Kwabena (Kwabena Adu) primary advisor. Thesis advisor
Schnitzer Mark Jacob
Delp Scott advisor. Thesis advisor
Ionics at nanoscale [electronic resource] : application to fuel cells

The overall efficiency of energy conversion devices such as batteries, fuel cells, and biological cells is often limited by charge transfer reactions at electrode-electrolyte interfaces. Because interfaces are the site of nearly all chemical (and electrochemical) reactions, understanding and improving their characteristics and structures can lead to significant reductions in both catalytic and interfacial losses. To this end, nano electrochemistry may offer us ways to understand details of charge transfer reaction at nanoscale resolution and open opportunities to engineer the interface with better kinetics. This work presents the results of three studies aimed at lowering the elec- trochemical reaction losses in both ceramic fuel cells and biological systems. The first part of work discusses a study of oxide ion incorporation and transport at the cathode of solid oxide fuel cells (SOFC). SOFCs are an attractive clean en- ergy technology because of the low to zero emissions from their operation and their potentially high efficiency. For wider applications, it is desirable to lower the oper- ation temperature of SOFCs, but this causes significant increase of interfacial loss due to sluggish kinetics of oxygen reduction reaction at the cathode. In this study, I demonstrated both spectroscpic (AC impedance spectroscopy) and spectrometric (Nano secondary ion mass spectrometry) evidence that oxygen incorporation from the cathode into the electrolyte is significantly enhanced at grain boundaries of the electrolyte. The second part of work discusses a study focused on proton transport in proton- conducting ceramic fuel cells. Acceptor-doped perovskites have attracted recent at- tention as potential electrolyte materials for the next generation protonic devices, including fuel cells, because of their high ionic conductivity at intermediate temper- atures. The chemical instability of most of proton-conducting ceramics in acidic gas environments such as carbon dioxide, however, compromises their practical use. I discuss the evidence of proton conduction in nanoscale yttria-stabilized zirconia, well known oxide ion conductor; this points to its possible usage as a chemical barrier layer for proton-conducting ceramics. The third part of work presents a study of the possibility of extracting electricity from plant cell and the economic feasibility. Plants have developed sophisticated solar energy capture mechanisms that may be adapted to be less expensive or to perform better than current photovoltaic solar energy collectors. I discuss direct extraction of photosynthetic electrons from a single plant cell done by inserting nanoscale electrodes into their chloroplasts in vivo; these results may represent an initial step in generating high efficiency bioelectricity.

Keywords: Mechanical Engineering
Advisor: Prinz F. B. primary advisor. Thesis advisor
Gür Turgut M.
Kenny Thomas William advisor. Thesis advisor
Justification of induction by inference to lesser coincidence [electronic resource]

I begin by identifying David Hume's problem of induction. Hume argues that induction cannot be justified by a priori reasoning, because the failure of induction does not imply contradiction, or by a posteriori reasoning, because reasoning that the unobserved will resemble the observed based on observation would be circular. Hume concludes that induction cannot be justified by any reasoning. The principle that nature is uniform cannot be established without assuming that nature is uniform. But many paradigmatic instances of induction can be justified in terms of something weaker than the principle that nature is uniform, namely a form of reasoning I call "inference to lesser coincidence". This form of reasoning is meant to incorporate traditional formulations of the justification of induction expressed in terms of inference to the best explanation, statistical sampling, and Bayesian reasoning. My version of the argument is as follows: The conditional, time-invariant proposition that vast regularities in progress are likely to continue somewhat further is either true or false. If false, then the regularities we have observed are colossally coincidental. If true, they are far less coincidental. Therefore the proposition is probably true. If, in fact, vast regularities in progress are likely to continue, this has application to specific cases, such as the possibility that the Sun will rise again. I respond to three objections, which claim that time-restricted laws lessen the coincidence of observed regularities without making it likely that the Sun will rise again, that the "sample" of observed events might be biased, and that a zero prior probability assignment for dependence might be justified. I conclude by discussing the meaning of 'cause'.

Keywords: Philosophy
Advisor: De Pierris Graciela Teresa primary advisor. Thesis advisor
Perry John primary advisor. Thesis advisor
Crimmins Mark advisor. Thesis advisor
Ryckman Thomas advisor. Thesis advisor
Kalendergeschichte and fait divers, the poetics of circumscribed space [electronic resource]

This study analyzes the poetics of two small literary forms: the German Kalendergeschichte and the French fait divers. Intimately connected with more prominent genres like the novella, the aphorism, or the Poème en Prose, these ephemeral forms distinguish themselves through their specific material history, originating as publishing exigencies—stopgaps or infill for blank space. In the German case, on calendar pages. In the French, on the white space in between newspaper headlines. It is the play with and within these very concrete, material and traditional constraints that constitutes their literary appeal. Poets from Heinrich von Kleist to Charles Baudelaire, and E.T.A. Hoffmann to Stéphane Mallarmé all influenced the development of both genres significantly. But it was two outstanding authors in particular, Johann Peter Hebel and Félix Fénéon, that eventually made the pragmatic restrictions of the Kalendergeschichte and the fait divers the source of a genuine—and genuinely new—poetics. James Joyce, Franz Kafka, and Bertolt Brecht integrated these formal innovations into their own oeuvre. Thinkers like Martin Heidegger, Maurice Merlau-Ponty, or Roland Barthes reflected on their poetico-philosophic power. The study covers the general history of both genres, a close reading of the specific formal changes brought about by Hebel and Fénéon respectively, as well as a broad view of the historico-cultural context that produced them. Whereas the first part is focused on the Kalendergeschichte and Johann Peter Hebel's Der Rheinländische Hausfreund, the second part traces the fait divers and Félix Fénéon's Nouvelles en trois lignes in particular.

Keywords: Comparative Literature
Advisor: Greene Roland
Gumbrecht Hans Ulrich primary advisor. Thesis advisor
Cohen Margaret advisor. Thesis advisor
Kinetics of crude-oil combustion in porous media interpreted using isoconversional methods [electronic resource]

One method to access unconventional, heavy-oil and natural bitumen resources as well as waterflood residual oil is to apply in situ combustion (ISC) to oxidize in place a small fraction of the hydrocarbon thereby providing heat to reduce oil viscosity and pressure that enhances recovery. ISC is also attractive because it provides the opportunity to upgrade oil in-situ by increasing the API gravity and decreasing, for instance, sulfur content. Experimental analysis of crude-oil oxidation kinetics provides parameters, such as activation energy, for modeling and optimization of ISC processes. The complex nature of petroleum as a multi-component mixture and multi-step character of oxidation reactions complicates substantially the kinetic analysis of crude-oil. Isoconversional techniques provide model-free methods for estimating activation energy and naturally deconvolve multi-step reactions. In addition, isoconversional methods are also useful as a screening tool to recognize the burning characteristics of different oils. By using experimentally determined combustion kinetics of different oil samples along with combustion tube results, we show that isoconversional analysis of ramped temperature oxidation data is useful to predict combustion-front propagation. It also provides new insight into the nature of the reactions occurring during ISC. Ramped temperature oxidation (RTO) tests with effluent gas analysis are conducted to probe ISC reaction kinetics along with isothermal coke formation experiments. The role of oxygen during coke formation reactions (i.e., fuel formation for ISC) is investigated using X-ray photoelectron spectroscopy (XPS) of intermediate reaction products. The XPS data is analyzed along with companion RTO experiments to obtain a simplified multi-step reaction scheme. Synthetic cases illustrate the connection between a proposed reaction scheme for oil/matrix pairs and one-dimensional combustion front propagation. Analysis of experimental results illustrate that the reaction scheme is capable of reproducing experimental results including the basic trends in oxygen consumption and carbon oxides production for RTO experiments as a function of heating rate for both good and poor ISC candidates. The combination of XPS and RTO studies indicates that the quality (or reactivity) of coke formed during the process is a function of oxygen presence/absence.

Keywords: Energy Resources Engineering
Advisor: Kovscek Anthony R. (Anthony Robert) primary advisor. Thesis advisor
Castanier Louis M. advisor. Thesis advisor
Gerritsen Margot (Margot G.) advisor. Thesis advisor
A lattice model of the translational dynamics of nonrotating rigid rods [electronic resource]

We present a lattice model of oriented, nonrotating, rigid rods in three dimensions with random walk dynamics and an algorithm to simulate the model. We use the ideas of the Doi-Edwards (DE) theory, which was originally developed for a system of rods that both translate and rotate in continuous space, to predict the dependence of the translational diffusion constant of the rods in the perpendicular direction, on the (dimensionless) concentration in the semidilute regime. We find that the transnational perpendicular diffusion constant is proportional to the inverse square of the concentration. The theory is based on a `tube model' for the constraints imposed on the motion of a rod by the surrounding rods. Simulations of the model confirm that the scaling predicted by DE ideas and that the nature of the agreement is similar to that for the rotational diffusion constant in the original DE theory. We formulate a quantitative theory for the prefactor in the scaling relationship using only DE ideas, but it predicts a proportionality constant that is much too small. To explain this discrepancy, we modify the DE approach to obtain a more accurate estimate of the average tube radius, and we take into account two effects, called `leakage' and `drift', that are caused by perpendicular motions of rods that are ignored by the original DE theory. The theory of leakage takes into account the fact that the ends of a rod are less effective than the middle of the rod for blocking the motion of nearby rods. The theory of drift takes into account that the tube that any one rod is in can move in the perpendicular direction without changing its structure as a result of the perpendicular motion of the rods that form the tube. With these changes, the theory predicts a prefactor that is in much better agreement with the simulations. The simulations find that, as the concentration is increased, the approach to the limit of DE scaling is slow, and the -2 power in the DE scaling law is never quite achieved even at the highest concentration simulated. We propose a new scaling relationship that explains the deviations from the DE scaling relationship. Finally, we study the self and total density-density space time correlation functions for this model and propose a simple theory for the short time behavior of these functions based on a one-dimensional two-component lattice gas model.

Keywords: Chemistry
Advisor: Andersen Hans
Pande Vijay primary advisor. Thesis advisor
Pecora Robert
Learning to drive [electronic resource] : perception for autonomous cars

Every year, 1.2 million people die in automobile accidents and up to 50 million are injured. Many of these deaths are due to driver error and other preventable causes. Autonomous or highly aware cars have the potential to positively impact tens of millions of people. Building an autonomous car is not easy. Although the absolute number of traffic fatalities is tragically large, the failure rate of human driving is actually very small. A human driver makes a fatal mistake once in about 88 million miles. As a co-founding member of the Stanford Racing Team, we have built several relevant prototypes of autonomous cars. These include Stanley, the winner of the 2005 DARPA Grand Challenge and Junior, the car that took second place in the 2007 Urban Challenge. These prototypes demonstrate that autonomous vehicles can be successful in challenging environments. Nevertheless, reliable, cost-effective perception under uncertainty is a major challenge to the deployment of robotic cars in practice. This dissertation presents selected perception technologies for autonomous driving in the context of Stanford's autonomous cars. We consider speed selection in response to terrain conditions, smooth road finding, improved visual feature optimization, and cost effective car detection. Our work does not rely on manual engineering or even supervised machine learning. Rather, the car learns on its own, training itself without human teaching or labeling. We show this "self-supervised" learning often meets or exceeds traditional methods. Furthermore, we feel self-supervised learning is the only approach with the potential to provide the very low failure rates necessary to improve on human driving performance.

Advisor: Thrun Sebastian
Li Fei Fei
Ng Andrew Hock-soon
Learning to see the world [electronic resource] : Pasternak and Rilke, 1911-1931

"Learning to See the World: Pasternak and Rilke 1911-1931" investigates the relationship between Boris Pasternak and Rainer Maria Rilke through an innovative approach to the question of poetic influence. Rather than concentrating on intertextual dialog or formal similarities in their works, this dissertation tracks fundamental changes in poetic perception introduced by Rilke, and argues that Pasternak used a Rilkean perspective to construct his own poetic universe. Although the two poets' common approach to the question of seeing -- that is, perception -- can be identified with the help of a phenomenological paradigm formulated by Edmund Husserl, their common approach to the subsequent creation of their self-contained poetic worlds is best understood in categories suggested by Martin Heidegger. The trajectory of Pasternak's development, traced in select examples from his earliest poems and translations from Rilke to Safe Conduct, includes several crucial stages. It begins with Pasternak's experimentation with new forms of representing his unique artistic vision early in his career; culminates in his synthesizing this vision into a coherent whole in his mature works; and comes to a conclusion in attempts by Pasternak to reconstruct and protect the world's unity, which was shaken by the violence of the Russian Civil War, and crumbled under the pressures of the communist authoritarian regime. By tracing this trajectory, I show how Pasternak's distinct vision of the world and its representation in his writings were shaped in dialogue with Rilke, in spite of, and indeed because of radical differences in their poetics.

Keywords: Slavic Languages and Literatures
Advisor: Greenleaf Monika
Gumbrecht Hans Ulrich advisor. Thesis advisor
Safran Gabriella
Let Them Eat Yellow Cake Understanding the History of France’s Sensitive Nuclear Export Policy

Between 1957 and 1981, France was a liberal supplier of sensitive nuclear technology, material and equipment. During these years, France signed a total of nine contracts for sensitive nuclear assistance, six of which contributed to covert nuclear weapon programs. However, in the early 1980s, France stopped exporting sensitive nuclear technology and formally defined its nuclear export policy. This thesis attempts to understand why France exported sensitive nuclear technology to non-nuclear weapon states for over two decades and why France then halted its sensitive export activity and became a more responsible nuclear supplier in the early 1980s. It concludes that in the absence of a definitive national nonproliferation and nuclear export policy, economic interests and pressure from the domestic bureaucracy – namely, the French Atomic Energy Agency and its subsidiary firms – drove France’s nuclear export policy. However, in 1974, a new leader came to power in Paris, President Valéry Giscard d’Estaing, whose conception of France’s strategic interests differed drastically from his Gaullist predecessors. In the interest of preventing the further spread of nuclear weapons and fostering a closer French-US relationship, President Giscard established a new executive council charged with upholding a responsible export policy. Through this institution, in the late 1970s, the President enacted several policies that effectively reined in France’s liberal export activity. Situated in the broader context of global nuclear trade, the findings of this thesis offer insights into the motivations of nuclear suppliers in the international system and contain lessons on how to promote policies that constrain the spread of proliferation-prone technology.

Keywords: Center for International Security and Cooperation
CISAC
Stanford University
France
nuclear weapons
non-nuclear weapons states
policy
Thesis
Advisor: Sagan Scott
May Michael
Light activated reassembly of split green fluorescent protein (GFP) [electronic resource]

Green fluorescent protein (GFP) is an incredibly useful tool to image protein expression, location, and interactions because the chromophore forms from within the protein without need for additional enzymes or external cofactors. Split GFPs are fragments of GFP that often require fused interacting proteins in order to interact, fold, and form the chromophore and are therefore used to image protein-protein interactions specifically. In this thesis a split GFP that does not require fused interacting proteins is used to make semi-synthetic proteins. The reassembly of this particular split GFP is light mediated, and the underlying mechanism and kinetics of this reassembly process are discussed in detail. Truncated Green Fluorescent Protein with the 11th [beta]-strand removed is potentially interesting for bioconjugation, imaging, and the preparation of semi-synthetic proteins with novel spectroscopic or functional properties. Surprisingly, the truncated GFP generated by removing the 11th strand, once refolded, does not reassemble with a synthetic peptide corresponding to strand 11, but does reassemble following light activation. The chromophore in this refolded truncated GFP is found to be in the trans configuration. Upon exposure to light a photostationary state is formed between the trans and cis conformations of the chromophore, and only truncated GFP with the cis configuration of the chromophore binds the peptide. As described above, GFPs and split GFPs are typically used to observe protein-protein interactions, but this unique light-driven reassembly of split GFP is potentially useful for controlling protein-protein interactions.

Keywords: Chemistry
Advisor: Boxer Steven G. (Steven George)
Chidsey Christopher E. D. (Christopher Elisha Dunn)
Rao Jianghong advisor. Thesis advisor
Limit theorems for Ginzburg-Landau [grad phi] random surfaces [electronic resource]

We study the massless field on lattice approximations of planar domains with smooth boundary, with uniformly convex, nearest neighbor, gradient interaction. This is the so-called Ginzburg-Landau (GL) interface model. It is a general model for a (2+1)-dimensional effective interface in which h represents the height. Our main results are two new limit theorems for functionals of h: (CLT) linear functionals of the height converge to the continuum Gaussian free field and the macroscopic level sets converge to variants of the Schramm-Loewner evolution (SLE). The main step in the proof of both results is a new estimate which describes how the boundary data of the field affects its law in the bulk. Along the way, we also give a new construction of the shift ergodic GL Gibbs (Funaki-Spohn) states. For the CLT, we take our boundary conditions to be a continuous perturbation of a macroscopic tilt. We prove that the fluctuations of linear functionals of h about the tilt converge in the limit to a Gaussian free field on D, the standard Gaussian with respect to a weighted Dirichlet inner product whose weights we will identify explicitly. The limiting result for the level sets resolves a conjecture of Sheffield that SLE(4), a conformally invariant random curve, is the universal limit of the chordal zero-height contours of random surfaces with isotropic, uniformly convex potentials.

Keywords: Mathematics
Advisor: Dembo Amir primary advisor. Thesis advisor
Diaconis Persi advisor. Thesis advisor
Ryzhik Leonid advisor. Thesis advisor