VictorJuiz/thesis huggingface dataset:
On the efficiency of the turbulent cascade

Turbulent flows are chaotic and highly fluctuating, with a large number of interacting scales of motion, which makes them difficult to predict. One approach (known as Large Eddy Simulation) is to resolve all scales of motion down to a cutoff scale of interest and to capture the effect of all omitted smaller scales by modeling the unclosed unresolved turbulent deviatoric stress. This stress appears in the energy equation of the resolved scales of motion in the scale-to-scale energy flux term. The energy flux term is a dot product of two symmetric tensors: the unresolved turbulent stress tensor and the resolved strain rate tensor. Thus, we may interpret it as mechanical work done by the large resolved scales of motion on the smaller unresolved ones. This work is not only a function of the magnitudes of these two tensors but also of the relative alignment of their eigenframes. For no work can be done when the direction of force (stress) is orthogonal to the displacement (strain). A new quantity that characterizes this alignment is the cascade efficiency. Although one of the defining characteristics of the turbulent cascade is the scale-to-scale energy transfer, this transfer is found to be on average inefficient in the inertial range (around 25\%) due to a poor alignment between the stress and strain rate tensors. Another finding is that the embedding dimension of the flow plays a strong role in setting the direction of the scale-to-scale energy flux, for when geometric alignments between the stress and strain rate tensors encountered in three-dimensional turbulence are projected onto a two-dimensional configuration, the direct energy cascade towards smaller scales of motion reverses to a two-dimensional inverse energy cascade towards larger scales. The efficiency proves to be an effective metric in revealing the broken time-reversal symmetry of the turbulent cascade, for it is seen that the geometry of the turbulent stress lags that of the strain rate in three-dimensional turbulence, which is the opposite of what is observed in two dimensions. However, the time lags required for peak alignment do not properly scale with filter size when considering Eulerian quantities lagged in-place or along particle trajectories. It is only when expressing the scale-to-scale energy flux in a fully Lagrangian manner based on the right Cauchy-Green strain rate tensor and the second Piola--Kirchhoff stress tensor, that the times required for peak efficiency along fluid eddies follow the expected 2/3 Kolmogorov scaling

Advisor: Ouellette Nicholas (Nicholas Testroet)
Fringer Oliver B. (Oliver Bartlett) 
Koseff Jeffrey Russell
On tuning and understanding electrocatalysts for hydrogen and carbon-based energy storage

The following thesis is a composition of published and soon-to-be published works. All works use density functional theory (DFT) calculations and descriptor-based mechanistic models to tune and screen catalytic materials for the hydrogen evolution reaction (HER) and the CO2 reduction reaction (CO2RR). In several works, experiments are included to substantiate predictions. The early sections focus on elucidating the role of key descriptors in the HER and CO2RR, specifically the H* and CO* adsorption state. It was found that nickel-gallium intermetallic systems can alter the CO* adsorption energy to achieve an early onset potential for C1 and C2 product distributions. With regards to system stability, CO* adsorption was found to induce surface refaceting towards stepped motifs on three commonly used metal catalysts, Cu, Ni, and Pt. In the latter sections, the thesis builds upon past mechanistic models to develop a multi-descriptor model that suggests new strategies to screen for better catalysts for CO2RR. It is found that not all steps may be necessarily electrochemical steps; some key intermediate steps may be surface driven, which dramatically simplifies the selectivity picture of products formed in CO2RR. As such, OH* and C* are noted as possible descriptors to use in conjunction with CO* to build potential-dependent selectivity maps that describe how the competition from the HER may affects product selectivity in CO2RR. Finally, the thesis dives into the mechanistic trends of HER, where kinetic scaling relations are calculated explicitly with a metal-water interface across multiple transition metals. It was found that the Volmer-Heyrovsky route can produce an optimal peak at ∆G_H* = ~0eV, where ∆G_H* is the free binding energy of hydrogen. The active species of H* has also been elucidated to be any adsorbed hydrogen, and not strictly H* adsorbed on weaker binding, atop sites. Tafel plots indicate that although electrochemical barriers vary with potential, the overall HER rate stays governed by the surface coverage of hydrogen. Lastly, we find that CO* and OH* adsorbate-adsorbate interactions can either hinder or promote HER by leaving only weaker binding sites to H*. Prior to presenting the findings, this thesis attempt at a short primer on the physical chemistry concepts behind computational catalysis, as well as the conceptual tools used in computational catalysis. The section is aimed at theoretical or experimental researchers with an interest in computational science and catalysis. This is in part because the technical jargon used herein may seem vague or less familiar to those not in the field of computational catalysis, such as the term 'free energetics', 'atomic orbitals', 'descriptor', 'scaling relations'. The reader is welcomed to bring themselves up to speed in the background and concepts section

Keywords: Materials Science and Engineering.
Advisor: Noerskov Jens
Reed Evan J. 
Cargnello Matteo
Online assignment mechanisms with applications in resource allocation

We study online assignment mechanisms in different contexts, namely online assignment mechanisms under fairness constraints and online bayesian selection problem under combinatorial constraints. In both cases, we design mechanisms that achieve a constant fraction of the optimum online policy in objective value. One common challenge we face in obtaining our results is generating a solution that satisfies all the structural constraints imposed by the problem. In doing so, we introduce several novel techniques for achieving and rounding our results

Keywords: Management Science and Engineering.
Advisor: Saberi Amin 
Ashlagi Itai 
Lo Irene (Management science professor)
Online linear programming : algorithm design and analysis

We discuss the problem of online linear programming (LP) in which the objective function and constraints are observed sequentially and not known a priori. We consider (i) stochastic input model where the columns of the constraint matrix along with the corresponding coefficients in the objective function are generated i.i.d. from an unknown distribution and revealed sequentially over time and (ii) random permutation model where the constraint matrix and the corresponding coefficients arrive in a randomly permuted order. Under the stochastic input model, we first establish convergence properties on the dual optimal solution to a large-scale LP problem and develop an adaptive learning algorithm that improves the previous algorithm performances by taking into account the past input data as well as decisions/actions already made. In the end, we present a fast algorithm for approximately solving a class of large-scale binary integer LPs. The algorithm is free of matrix multiplication and requires only one single pass over the inputs of the integer LP

Keywords: Management Science and Engineering.
Advisor: Giesecke Kay
Pelger Markus
Glynn Peter W.
Optical measurement of thermal diffusivity in strongly correlated materials

In this dissertation, we discuss the importance of thermal diffusivity in the study of the incoherent transport in strongly correlated systems. We introduce a non-contact optical thermal microscope with superior spatial and angular resolution that directly extract the thermal diffusivity of materials. We present measurements in various cuprate materials, both hole- and electron- doped, as representative strongly correlated systems, and discuss how various aspects of the thermal diffusivity, combined with electrical transport measurements, can provide insight to the transport of the so called bad metals. We also discuss the the role complex insulator plays in the understanding of incoherent transport and quantum chaos in strongly correlated materials

Keywords: Physics.
Advisor: Kapitulnik Aharon
Fisher Ian R. (Ian Randal)
Hartnoll Sean
Kivelson Steven
Optimal control of nanomechanical quantum memory coupled to superconducting qubit

Quantum memory coupled to a single non-linear element such as superconducting qubit can serve as a promising quantum information processing platform with advantages in lifetime and hardware-efficiency. However, naïve implementation of this quantum computing architecture requires two additional SWAP gates between the memory resonator and the processing qubit per each gate operation, which causes longer gate time and larger error. In this work we implement a power- and bandwidth-limited pulse optimization method on the hybrid system of nanomechanical resonators coupled to transmon qubit. We find the optimal pulse for generating entangled state of mechanical resonators as well as implementing phonon-phonon CNOT gate. We verify the pulse's robustness to experimental imperfections, such as decoherence, pulse distortion, and parasitic mechanical modes. Finally, we perform optimal control on more than two resonators and evaluate the prospects of achieving a scalable quantum computing architecture.

Keywords:  Department of Physics
Stanford LINQS
optimal control
nanomechanical quantum memory
superconducting qubit
GRAPE
quantum computing
Thesis
Advisor: Safavi-Naeini Amir
Hayden Patrick
Organizations and the contingent consequences of status competition

People compete to be esteemed and respected in nearly all group settings. Does intragroup status competition erode the ability for groups to achieve collective aims, or is competition for status part of the very fabric upon which collective action is produced? This dissertation aims to bridge an evolutionary perspective on status competition, in which social actors compete in rivalrous contests that are generally damaging to the group, and a cultural perspective, in which status competition is governed by widely shared norms and generally encourages collective action. It advances an organizational perspective to explain the contingent consequences of status competition, whereby the consequences of status competition depend on how the competition is organized. Drawing on a variety of approaches, including quasi-experimental methods, network analysis, and participant observation, I then develop and test three specific, "middle-range" theories that demonstrate the utility of this perspective. Results from these studies challenge conventional notions of status competition as a monolithic force, suggesting how organizational forces moderate their consequences. By identifying dimensions that govern whether status competition leads to beneficial or deleterious consequences for groups, this work also offers concrete suggestions for policymakers and practitioners seeking to harness the immense power of these competitions for collective good

Keywords: Sociology.
Advisor: Willer Robert Bartley
Bearman Peter S.
McFarland Daniel (Daniel A.) 
Powell Walter W.
Walder Andrew G. (Andrew George)
“Othering” and Integration: The Role of Ethnic Identity in the Assimilation of Second and Third-Generation Chinese Immigrants in Peru

In my thesis, I focus on the assimilation of second and third-generation Chinese immigrants in Peru. When considering structural factors of assimilation such as language abilities, intermarriage, socioeconomic status, and spatial concentration, Chinese Peruvians seem to be fairly well integrated into Peruvian society. However, during the interviews I conducted with Chinese descendants, most did not ethnically identify as Peruvian and did not see themselves as the typical Peruvian. In order to understand and measure assimilation, it is crucial that we not only consider structural factors but also social and cultural factors. In the case of Chinese descendants, there are both push and pull factors that inhibit their complete assimilation. They simultaneously are pushed away from Peruvian-ness by the racism and discrimination they face from Peruvians and also pulled towards Chinese-ness through language, cultural practices, and spaces that facilitate the Chinese community. While Chinese Peruvians should have organizations and locations to spend time with other community members, these settings can also serve as tools to increase Peruvian interest in Chinese culture and acceptance of Chinese populations.

Keywords: Immigration
Assimilation
Ethnic Studies
Race
Identity
Peru
Chinese
Chinese Peruvian
Racism
Discrimination
Stanford University
Center for Latin American Studies
Thesis
Advisor: Asad Asad L.
p21 Overexpression Delays Tumor Progression in Myc Driven Hepatocellular Carcinoma by Triggering Senescence

Hepatocellular carcinoma (HCC) is one of the most common causes of cancer death and it is becoming increasingly more prevalent. It is a particularly aggressive cancer with almost no effective therapeutic solutions. Activation of the Myc oncogene and the loss of p53 are two of the most common genetic drivers of human HCC. The cell cycle regulator p53 is a common tumor suppressor which controls cell cycle arrest, DNA repair and apoptosis. More specifically, p53 transactivates its downstream target gene p21, a cyclin dependent kinase inhibitor, that is able to arrest the cells in G1 phase, where they regress to G0 phase. This study utilized a mouse model of HCC in which the tetracycline regulatory system conditionally regulates the restricted concomitant overexpression of the Myc transgene and p21 (Cdkn1a) gene in hepatocytes. Tumor growth and overall survival were measured in the Myc/p21 model to quantify the impact of p21 overexpression. Immunostaining assays and Western blot were utilized to evaluate the gene expression of various available senescence markers such as p15, p16 and B-galactosidase. This study tests the hypothesis that concomitant induction of a growth promoting oncogene (Myc) and senescence causing cell-cycle inhibitor (p21) will result in a dominant negative tumor regression by the cell-cycle inhibitor p21. The results of this study support the hypothesis that co-expression of p21 and Myc in this mouse model delays tumor growth as a result of p21-induced senescence as characterized by a senescent associated secretory phenotype.

Keywords: Felsher, Dean
Cao, Zhongwei
hepatocellular carcinoma
Myc
p21
cell cycle
senescence
Thesis
"Pain has an element of blank:" Interpretations of and Judgments on Female Illness in the Nineteenth-Century British Gothic

Nineteenth-century gothic novels teem with female illness. From typhus to tuberculosis, madness to melancholy, ill women are abundant. And yet, mainstream feminist scholarship insists that these illnesses must be read as metaphor only. This thesis integrates traditional feminist theory with disability theory to create a more complete discourse. Examining Charlotte Brontë’s Jane Eyre and Bram Stoker’s Dracula, we consider illness as illness and disability as disability. We thus learn a great deal about not only the world in which these novels were created but also the continuing unspoken attachment of readers to the ideal heroine as necessarily able-bodied.

Keywords: Department of English
Disability Studies
Disability Theory
Feminist Critical Theory
Victorian Studies
Heroines
Female Illness
Mental Illness
Dracula
Jane Eyre
Charlotte Brontë
Bram Stoker
Gothic
Nineteenth-Century Novels
Monstrosity
Political Economy
Thesis
Advisor: Kantor Roanne
Quayson Ato
Painting daily life : spatial contexts, temporalities and experiences of architectural paintings at Çatalhöyük

Given their aesthetic, symbolic, and epistemological underpinnings, prehistoric inscribed or image-bearing artifacts such as architectural paintings have long been treated as a 'transcendent' category of archaeological finds, to be investigated in isolation from their broader contexts and even from their own materiality. This dissertation revisits one of the richest corpuses of architectural paintings in prehistoric Southwest Asia, uncovered at the Anatolian site of Çatalhöyük (c. 7100-5900 BC), with a specific focus on their spatial contexts, materialities, temporalities and daily experience. Through a diversified set of archaeological methods including spatial analysis, cross-sectional analysis, photogrammetry and virtual reconstruction, this research shows how deeply integrated paintings were within the practices and rhythms that constituted daily life at the Neolithic site. In terms of spatial patterning and contextual associations, this research reveals a widespread distribution of paintings throughout the site, but also higher densities of paintings in some buildings and some periods within the long occupation of the site. The contextual associations of paintings also change through time at the site, with a marked ritual association to funerary practices during the middle occupation and a new association with fire installations such as ovens and hearths since the late period. Significant changes through time also emerged from the analysis of plastering and painting practices, with peaks of multi-layered paintings in the early and middle periods and a generalized decrease in painting activity since the late period. In-depth examination of painted plasters also shows peculiar practices of painting preparation, application, repetition, and repair, practices that reveal the dynamic nature of painted surfaces and their frequent transformations. An experimental study of lighting conditions within Çatalhöyük houses suggests very low levels of illuminance, especially in the preferential locations of paintings, further downplaying an assumption of architectural paintings as durable surfaces mainly intended for visual display. These interconnected research threads compose an understanding of architectural paintings that significantly differs from the ocularcentric narrative of the disembodies image, one where the emphasis is on the act of painting itself and its associated practices, rather than on the paintings' visual content

Keywords: Anthropology.
Advisor: Hodder Ian 
Bauer Andrew M. 
Lercari Nicola
Panoptic imaging of distributed neuronal dynamics

Anatomical evidence suggests that planning and execution of adaptive behaviors in mammals may involve coordinated neuronal activity throughout the neocortex. To investigate this previously-unapproachable hypothesis, in collaboration with others, I developed a set of optical tools for probing fast neuronal activity across many cortical regions simultaneously. One of these methods—COSMOS—allows synchronous recording at 30 Hz from over a thousand near-cellular resolution neuronal sources distributed throughout the entire dorsal neocortex of awake mice. We applied these tools to make three discoveries. First, we found global cortical representations of goal-directed task engagement, with cell-type specific dynamics. Second, we identified neuronal population representations spanning dorsal neocortex that precisely encode ongoing and planned motor actions. Third, we discovered a localized neuronal rhythm underlying dissociation, a mysterious altered behavioral state in which normally-integrated cognitive processes—such as those linking the sense of self to body-position and action—become selectively disconnected. Together, these results illuminate how circuits throughout the brain of behaving mammals function as a coupled system—and the consequences that can arise when they decouple

Keywords: Electrical Engineering.
Advisor: Deisseroth Karl
Shenoy Krishna V. (Krishna Vaughn) 
Wetzstein Gordon
Parameterized topological data analysis

This dissertation investigates several ways in which topological data analysis can be made more digestible by structuring computations and models. First, we introduce a new method for computing algebraic invariants of diagrams of topological spaces using matrices associated with quiver representations. This computational framework allows for parallel algorithms to compute persistent and zigzag homology in the most general case, with arbitrary induced maps on homology. Next, we extend the classical techniques of acyclic carriers to the filtered setting and demonstrate how these tools can be used to construct interleavings to compare persistent homology of filtered spaces. We introduce a class of geometric complexes parameterized by a cover of a data set and use carriers to analyze the relationship between these complexes to the unparameterized geometric complexes. Finally, we investigate spaces of data generated from sampling small cubes of voxels (patches) from three-dimensional images through the use of a map that captures the direction of the largest variation

Advisor: Carlsson G. (Gunnar)
Taylor Jonathan E.
Kerckhoff Steve
Partisan Bias, Altruism, and Universalism: Evidence From a Controlled Experiment

The effect of partisan bias is not confined to the political arena but extends to consumer markets and labor markets. In order to better understand the relationship between affective polarization and economic behavior, I conduct a controlled experiment using a series of dictator games to measure partisan bias in altruism. I find that participants behave more altruistically toward members of their own party and that participants who report higher levels of partisanship display more partisan bias in altruistic behavior. This implies that self-reporting can be a useful tool for gauging differences in partisan bias. However, even participants who report low levels of partisanship display a significant level of partisan bias in altruistic behavior, perhaps because they are unaware of their partisanship or are unwilling to admit it. Therefore, screening for partisan behavior may be a more accurate gauge of partisanship than self-reporting. Additionally, I find that partisan bias in altruism is distinct from and stronger than bias based on shared home state. Finally, in testing a recently-developed questionnaire designed to measure universalism in altruism, I find discrepancies between the results of the universalism questionnaire and the results of the dictator games, raising questions about the validity of the questionnaire.

Keywords: Partisanship
intergroup bias
Altruism
Universalism
affective polarization
American politics
Experimental economics
behavioral economics
Stanford University
Mathematical and Computational Science
Text
Thesis
Advisor: Niederle Muriel