VictorJuiz/thesis huggingface dataset:
Computational aeroacoustics of complex flows at low Mach number [electronic resource]

Designing quiet mechanical systems requires an understanding of the physics of sound generation. Among various sources of noise, aerodynamic sound is the most difficult component to mitigate. In practical applications, aerodynamic sound is generated by complex flow phenomena such as turbulent wakes and boundary layers, separation, and interaction of turbulent flow with irregular solid bodies. In addition, sound waves experience multiple reflections from solid bodies before they propagate to an observer. Prediction of an acoustic field in such configurations requires a general aeroacoustic framework to operate in complex configurations. A general computational aeroacoustics method is developed to evaluate noise generated by low Mach number flow in complex configurations. This method is a hybrid approach which uses Lighthill's acoustic analogy in conjunction with source-data from an incompressible calculation. Flow-generated sound sources are computed by using either direct numerical simulation (DNS) or large eddy simulation (LES); scattering of sound waves are computed using a boundary element method (BEM). In this approach, commonly-made assumptions about the geometry of scattering objects or frequency content of sound are not present, thus it can be applied to a wider range of aeroacoustic problems, where sound is generated by interaction of complex flows with solid surfaces. This new computational technique is applied to a variety of aeroacoustic problems ranging from sound generated by laminar and turbulent vortex shedding from cylinders to realistic configurations such as noise emitted from a rear-view side mirror and a hydrofoil. The purpose of each test case, in addition to validation of the method, is to explore various physical and technical aspects of the problem of sound generation by unsteady flows. Through these test cases, it is demonstrated that the predicted sound field by this technique is accurate in the frequency range in which the sound sources are resolved by the computational mesh. It is also shown that in computation of sound, acoustic analogies are less sensitive to numerical errors than direct computations. Finally, a discussion on the efficacy of LES and the effect of sub-grid scale dynamics on predicted sound is presented.

Keywords: Mechanical Engineering
Advisor: Moin Parviz primary advisor. Thesis advisor
Lele Sanjiva K. (Sanjiva Keshava)
Wang Meng advisor. Thesis advisor
Computational investigation of the SN2 reactivity of halogenated pollutants [electronic resource]

The SN2 displacement reaction, in which a halide is displaced from a molecule by a nucleophile represents an important mechanism by which halogenated pollutants can be removed from the environment. Experimental SN2 transformation rates for halogenated pollutants vary widely and depend on both compound structure and whether the reaction takes place via abiotic or biological processes. I used computational methods to examine SN2 reactivity for a comprehensive set of halogenated compounds in order to develop structure-activity relationships, and to improve our understanding of the fundamental factors that govern reactivity of halogenated pollutants in the natural environment. I used a quantum chemistry method (Gaussian 98) to calculate activation energies and establish an order of reactivity for a comprehensive set of over 70 halogenated compounds. Examination of transition state structures and comparison to experimental and calculated measures of substrate electron affinity yielded valuable information about the nature of substituent effects. I employed a molecular docking algorithm (AUTODOCK) to study the effect of halogenated pollutant structure on enzyme-substrate interactions within the confined active sites of two haloalkane dehalogenase enzymes, and to understand the implications on catalysis by these enzymes. Output from both computational methods was then used in combination with experimentally derived properties to perform a statistical quantitative structure activity relationship (QSAR) analysis to develop models of reactivity. I identified the dominant structural effects on SN2 reactivity of halogenated pollutants, provided mechanistic insights about the origin of these effects, and demonstrated the importance of accounting for solvent and enzyme interactions in explaining observed transformation rates. My research provides a more complete picture of SN2 reactivity of halogenated pollutants based on sets of energies derived independently of experimental data. I have demonstrated that robust models can be developed from theoretical results that can account for the observed variability in experimental data as well as provide a means for estimation of SN2 transformation rates for untested compounds.

Advisor: Reinhard Martin
Hildemann Lynn M. (Lynn Mary) advisor. Thesis advisor
Leckie Jim
Computational modeling of structural heterogeneity in folded proteins [electronic resource]

Proteins are biomolecules that play a key role in a wide diversity of vital functions, such as metabolism and signal transmission. Each protein is a linear chain of amino acids that folds into a flexible three-dimensional structure. Protein's flexibility is widely believed to be essential for its function. Motion of a protein occurs at timescales that span several orders of magnitude. Thermal fluctuations, which occur in picoseconds, are small-amplitude, uncorrelated, harmonic motions of the individual atoms. In contrast, conformational deformations closely related to the protein's function occur in microseconds to milliseconds. These slow deformations are usually large-scale, correlated, anharmonic motions that correspond to transitions between meta-stable states, such as binding and non-binding states. In this dissertation we are mainly interested in modeling structural heterogeneity associated with such slow deformations. This dissertation presents new computational methods to study the flexibility of folded protein in the context of three important biological problems: (a) Loop sampling, (b) Interpretation of electron density maps, and (c) Determination of allosteric pathways. Computational modeling of structural heterogeneity in the folded state of a protein is a challenging problem, mainly because of the high-dimensionality of the protein's conformation space and the very small relative volume of its feasible motion space. Although our methods are specific to each of the three problems, they share the same sample and select approach: they combine efficient sampling algorithms that allow us to represent structural heterogeneity in a folded protein by a collection of sampled conformations and selection algorithms that allow us to reliably pick the sampled conformations that provide a solution to the problem. This dissertation demonstrates the power of geometric computation and efficient sampling to model structural heterogeneity in the folded protein.

Keywords: Mechanical Engineering
Advisor: Delp Scott primary advisor. Thesis advisor
Latombe Jean-Claude primary advisor. Thesis advisor
Batzoglou Serafim advisor. Thesis advisor
Computational recognition of protein-coding genes using multiple genomic alignments [electronic resource]

In this thesis, I describe three main contributions I have made toward creating more accurate systems for the computational recognition of protein-coding genes. First, I present N-SCAN, a gene predictor based on a hidden Markov model that uses Bayesian networks to model multiple alignments. I also describe CONTRAST, a discriminative gene predictor based on a conditional random field and a set of support vector machines for recognizing coding region boundaries. Both N-SCAN and CONTRAST represented substantial improvements over the state-of-the-art at the time they were introduced. Additionally, I give an algorithm for training conditional random fields that maximizes an approximation to labelwise accuracy, as opposed to the usual maximum likelihood approach. This algorithm proved key to CONTRAST's success.

Advisor: Batzoglou Serafim primary advisor. Thesis advisor
Ng Andrew Y.
Sidow Arend advisor. Thesis advisor
Concentration polarization at microfluidic-nanofluidic interfaces [electronic resource]

Nanofluidic devices have the potential to offer unique functionality by exploiting length scales comparable to the Debye length or the size of individual biomolecules. Integration of nanofluidics with microfluidics also has potential benefits as a system can thereby draw from the benefits of both technologies. To leverage these functionalities, the physics associated with interfacing microchannels and nanochannels needs to be understood rigorously. In particular, when current is applied across a microchannel-nanochannel interface, surface charge effects inside the nanochannel often lead to an imbalance of fluxes of positive and negative species. This, in turn, creates a region of high ionic strength on one side of the nanochannel and low ionic strength on the other side, a phenomena known as concentration polarization (CP). Prior work on the physics of microchannel-nanochannel interfaces has neglected several key issues which we will address in this work. We review an analytical model of propagating CP and present experimental and computational validation of this model. In particular, our results show that enrichment and depletion regions propagate as 'shockwaves' of concentration which can profoundly change the flow and electric field conditions in a microfluidic system. Additionally, we present new analytical model which predicts the behavior of analyte ions in a microchannel-nanochannel system with CP. This work shows that CP can restrict the transport of analyte ions such that they cannot reach all regions of a microfluidic-nanofluidic system. The effects of CP, therefore, must be considered in the design of microfluidic-nanofluidic systems for biological or chemical analysis. Finally we present the first simultaneous visualization of nanochannel ionic strength and conductance. Our experiments show that, for some cases, the propagating CP model is a fair predictor of trends in nanochannel concentration. However, in some cases, the concentration inside the nanochannel reaches a temporary 'meso' state before transitioning to a final, significantly different concentration which is not described by theory. The latter shows that there is yet much room for further studies of this phenomenon.

Keywords: Mechanical Engineering
Advisor: Santiago Juan G. primary advisor. Thesis advisor
Eaton John K. advisor. Thesis advisor
Howe Roger Thomas advisor. Thesis advisor
Constructing agency [electronic resource] : the role of language

Speakers of the world's languages differ in how they typically describe the same events. For example, to describe the same physical event in some languages it would be natural to say "He broke the vase" while in others one would say "The vase broke itself." Do such patterns in language matter for how people construe and remember the same events? Do patterns in language shape whether we construe someone as being an agent, whether we attend to and remember who was involved, and how much we blame and punish those involved? Evidence from several populations - speakers of English, Spanish, and Japanese; adults and children -- suggests that the answer to these questions is "Yes". There are cross-linguistic differences in eye-witness memory for the same events, and language influences judgments of blame and punishment. The effects of language appear to be strong: Patterns in one's linguistic environment affect thinking even when people are not required to use language in a task and even when other rich sources of non-linguistic information are available.

Keywords: Psychology
Advisor: Boroditsky Lera primary advisor. Thesis advisor
Clark Herbert H. advisor. Thesis advisor
McClelland James L. advisor. Thesis advisor
Constructing genealogies in early modern England and the Mediterranean [electronic resource]

My dissertation uncovers how and why authors in early modern English and Mediterranean literature construct explanations of their own or their societies' origins. The framework for my analysis is the notion of "genealogies"--a term that may signify bloodlines, imperial lineages, religious genealogies, imagined genealogies of heroic conquerors, or literary genealogies of authors. I further argue that competing Muslim and Christian claims to the same genealogies complicate (or even render unsustainable) many of the assumed distinctions between "East" and "West" that have endured from the Renaissance to the present day. Chapter one discusses how both Leo Africanus and his _Descrizione dell'Africa_ both reify Muslim and Christian geographical distinctions while simultaneously challenging them. I conclude the chapter with a discussion of the afterlife of Africanus' work through a European "isnad" in Luis del Mármol Carvajal's _Descripción general de Africa_. Mármol unwittingly adapts Africanus' hybrid literary genealogy in a hostile manner unintended by Africanus and, in effect, writes Africanus out of his own history. Chapter two deals with ideologies of empire, comparing consanguineal and heroic genealogies in Ludovico Ariosto's _Orlando furioso_ and Edmund Spenser's _Faerie Queene_. I address why Ariosto makes Ruggiero (the "ancestor" of Ariosto's patrons) Muslim and how Spenser manipulates genealogies to provide a solution for the aging, heirless Queen Elizabeth by collapsing time and place within his poem. Chapter three notes two competing genealogies of English kingship in Shakespeare's Henriad--Christian divine right and heroic Greco-Roman genealogies. Fluellen's comparison of Henry V with Alexander "the Pig, " even as it relies upon Plutarch's paralleled lives of Alexander and Julius Caesar, demonstrates that if Shakespeare's handling of Henry V's "Turkishness" is subversive, it is because it is emulative, not slanderous. Finally, to make a larger point about mixed blood and religion in seventeenth-century Spain, I take Cervantes' suggestion literally, that his readers imagine Sidi Hamete Benengeli as the "true author" of _Don Quijote_ and explore how, similar to Mármol's appropriation of Leo Africanus' open-ended genealogy, Avellaneda, the author of an apocryphal sequel, engages in unauthorized continuation Sidi Hamete's "verdadera historia.".

Keywords: Comparative Literature.
Advisor: Greene Roland
Barletta Vincent advisor. Thesis advisor
Gumbrecht Hans Ulrich advisor. Thesis advisor
Parker Patricia
Construction of Time-and-Angle-Resolved Photoelectron Spectroscopy on Correlated Materials

Angle-Resolved Photoelectron Spectroscopy (ARPES) has been a major experimental technique in studying the electronic band structure of condensed matter systems. The traditional ARPES system resolves binding energies and in-plane electron momenta of electronic systems. It is of great scientific interest to further resolve the information of electron dynamics. In this thesis, I give a brief review of the theoretical and experimental backgrounds of the Femtosecond Time-Resolved ARPES technique. I report the construction of such a system, which consists of an ultrafast 1.5 eV pump beam and 6 eV probe beam, and a Scienta SES200 electron analyzer. An optical autocorrelator verifies that the duration of the pump laser pulse is 75 fs; An ARPES experiment on an Sb sample demonstrates that the angular resolution of the electron analyzer is less than 0:34 [degrees] and that the energy resolution is less than 50 meV.

Keywords: Physics
Angle-Resolved Photoelectron Spectroscopy
ARPES
Femtosecond Time-Resolved ARPES
Thesis
Advisor: Shen Zhi-Xun
Osheroff Douglas
Contentious politics in liquefied natural gas facility siting [electronic resource]

The siting of locally unwanted land uses (LULUs) -- hazardous waste facilities, landfills, prisons, power plants, etc. -- has proved to be a difficult task. Recent attempts to site liquefied natural gas (LNG) terminals in the U.S. have been no exception. These terminals receive LNG produced overseas and regasify it for distribution. Since 2000, more than 50 such terminals have been proposed but only five are currently operational. Like most LULU siting efforts, LNG proposals have drawn attention -- and sparked protest -- from local citizens. The siting of an LNG terminal presents many issues around which a community can mobilize. As a result, attempts to site these facilities create an ideal laboratory for better understanding the factors and processes that drive variations in community mobilization efforts in the context of LULUs. Why do some communities respond quickly and forcefully to a siting announcement, while others remain passive? Why do some community groups turn to more disruptive activities, such as protests and demonstrations, while others rely on more familiar forms of political participation, such as public hearings and letter writing? Using theories from the study of facility siting and social movements, I explore these issues through two in-depth studies of attempts to site LNG facilities in California. I then test the findings from the two in-depth case studies with eleven additional case studies of randomly selected LNG proposals around the country. These additional case studies include a review of relevant newspaper articles, regulatory documentation and five to ten interviews in each field site. Findings from these cases indicate five different types of community response: acceptance, local opposition, administrative opposition, unexpected opposition and well-resourced opposition. My analysis also suggests that high resource communities mobilize regardless of threat or opportunity. However, for low to medium resource communities, higher levels of threat and political opportunity matter for mobilization. Finally, the results show that mobilization is sufficient but not necessary for project failure. This work provides important insights both for researchers on facility siting -- in terms of the importance of combinations of key causal factors -- and for planners embroiled in such conflicts -- in terms of key policy levers affecting mobilization outcomes.

Advisor: McAdam Doug primary advisor. Thesis advisor
Ortolano Leonard primary advisor. Thesis advisor
McDermott Monica
The contribution of myelin lipids to the failure of central nervous system axon regeneration [electronic resource]

CNS myelin is strongly inhibitory to growing axons and is presently thought to be a major contributor to CNS axon regenerative failure. Although a number of proteins present in myelin, including Nogo, MAG and OMgp, have been identified as myelin-associated inhibitors, studies of mice lacking these genes suggest that additional inhibitors present in CNS myelin remain to be identified. Here, I have investigated the hypothesis that myelin lipids contribute to CNS regenerative failure. I identified sulfatide, a major constituent of CNS myelin, as a novel myelin-associated inhibitor of neurite outgrowth. Sulfatide, but not galactocerebroside or ceramide, strongly inhibited the neurite outgrowth of retinal ganglion cells (RGCs) when used as a purified lipid substrate. The mechanism involved in sulfatide-mediated inhibition shared features with other known inhibitors, as the stabilization of GTP-bound Rho was required for inhibition. Myelin in which sulfatide was lacking or blocked using specific antibodies was significantly less inhibitory to RGC neurite outgrowth in vitro than was wild type myelin, indicating that sulfatide is a major component of CNS myelin's inhibitory activity. Mice unable to make sulfatide did not regenerate RGC axons more robustly after optic nerve crush than wild type littermates under normal conditions, but did exhibit a small but significant enhancement in the extent of zymosan-induced regeneration. These results demonstrate that specific lipids can powerfully inhibit axon growth, identify sulfatide as a novel myelin-associated axon growth inhibitor, and provide evidence that sulfatide inhibition contributes to axon regenerative failure in vivo.

Keywords: Developmental Biology.
Advisor: Barres Ben
Fuller Margaret
Luo Liqun
McConnell Susan K. advisor. Thesis advisor
Contributions to high-dimensional principal component analysis [electronic resource]

Principal component analysis is a widely used dimension reduction method, but difficulties can arise when it is applied to very high dimensional data. In this thesis, motivated by examples in chemometrics, signal processing, econometrics, etc., we investigate two aspects of high-dimensional principal component analysis for a class of "low-rank signal plus noise'' models under Gaussian assumption. In the first part, we study rates of convergence for the distributions of extreme sample eigenvalues to their Tracy-Widom limits, when there is no signal in the observations and the sample size and the dimensionality of the feature space grow to infinity proportionally. By careful choice of the rescaling constants, we improve the rate to the second order for the largest eigenvalue. An analogous result is established for the smallest eigenvalue. Numerical experiments show that the asymptotic distributions are informative even when the sample size or the feature dimenionality is as small as 2. In the second part, we consider recovery of principal subspaces under the assumption that the principal axes have a sparse representation. We find that a new iterative thresholding approach recovers the leading principal subspace consistently, and even achieves near optimal rate of convergence, in a wide range of high-dimensional settings. Both statistical and computational properties of the approach are studied. Its competitive performance is demonstrated on a collection of simulated examples.

Keywords: Statistics
Advisor: Johnstone Iain primary advisor. Thesis advisor
Diaconis Persi advisor. Thesis advisor
Tibshirani Robert advisor. Thesis advisor
Control of dynamic maneuvers for bipedal robots [electronic resource]

There are many topographies in both the natural and man-made worlds which pose difficulties to machines: rubble fields, collapsed structures, ecologically sensitive areas, and even generally rugged terrain. If mechanical systems could negotiate such environments, the benefit to society would be great, with applications in search and rescue, ecologically friendly harvesting industries, and infantry support. The focus of this thesis is on gait control for bipedal robots. Before developing control algorithms, two areas of a bipedal robotic system are considered: leg design and control architecture. Noting the success of biologic systems in navigating difficult terrains, inspirations are taken from nature in both of these areas. A dynamic simulation method appropriate for systems with varying topology, such as legged robots, is also developed. In order to test the leg design, control architecture, and dynamic simulator, the relatively simple task of monopod hopping is studied. Stable results are achieved in both simulation and hardware, and the leg design, control architecture, and dynamic simulator are validated. Four bipedal maneuvers are then considered: steady-state running, accelerating, decelerating, and turning. Stable simulated results are demonstrated for all of these maneuvers. An experimental biped is also created. When the torso pitch is partially constrained, stable experimental steady-state running is achieved. When the torso pitch is unconstrained, five steps are achieved before falling. This work contains significant contributions in the areas of control architecture, leg design, and dynamic simulation methods for multi-topology systems. Novel control algorithms are presented for monopod hopping and steady-state running. Finally, control algorithms are presented for accelerating, decelerating, and turning, which have not been previously studied in bipedal robots.

Keywords: Mechanical Engineering
Advisor: Waldron Kenneth J. primary advisor. Thesis advisor
Gerdes J. Christian advisor. Thesis advisor
Roth Bernard advisor. Thesis advisor