VictorJuiz/thesis huggingface dataset:
Direct measurement of eddy viscosity and analysis of non-boussinesq effects in wall-bounded turbulent flows

This work presents studies of momentum mixing by turbulence in a channel flow, a separated boundary layer flow, and a separated boundary layer with sweep using direct numerical simulation (DNS) and the macroscopic forcing method (MFM, Mani and Park, Physical Review Fluids, 2021, p.054607) to quantify the non-Boussinesq effects of momentum mixing from turbulent eddies. The key goal of our investigation is to develop a quantitative understanding of the anisotropy and nonlocality of the eddy viscosity operator in wall-bounded turbulent flows. These studies provide important perspectives on the macroscopic behavior of turbulence in diverse flow setups, and they supply valuable data for enhancing turbulence closure models. Furthermore, they encourage a reevaluation of previous works in turbulence modeling and provide a foundation for enhancing the effectiveness of current RANS models.

Keywords: Engineering.
Mechanical Engineering.
Advisor: Mani Ali (Professor of mechanical engineering)
Alonso Juan José
McKeon Beverley J.
A discrete adjoint framework for turbulent hypersonic flows in thermochemical nonequilibrium

Hypersonic vehicle design and analysis continues to challenge the aerospace community. These systems operate in a unique flow environment characterized by thermochemical nonequilibrium effects, adding constraints and complexity not observed in other flow regimes. Numerical simulations must resolve these high-temperature, atomic-scale physical phenomena to accurately predict vehicle performance parameters such as lift, drag, control authority, and surface heat transfer. As a result, expensive CFD simulation models are substituted with low-fidelity correlation-based models in the design process. This yields, at best conservative vehicle configurations and, at worst, failed designs. Consequently, despite the rapid growth of computational power, hypersonic vehicle design has stagnated without the proper methods to efficiently incorporate CFD into the design process. This dissertation presents, to the author's knowledge, the first discrete adjoint framework for the efficient computation of aerothermodynamic sensitivities of turbulent hypersonic flows in thermochemical nonequilibrium to reintegrate high-fidelity simulations into the preliminary design phases for hypersonic vehicle systems

Keywords: Engineering.
Aeronautics and Astronautics.
Advisor: Alonso Juan José
Hara Ken
Lele Sanjiva K. (Sanjiva Keshava)
Dissecting the function of astrocytic synaptic cell adhesion molecules

Information is transmitted through synapses in the nervous system. Efforts have been made to visualize synaptic connectivity and understand synapse formation. While essential synaptic molecules have mainly been studied in neurons, astrocytes also play a role in synapse interactions. Astrocytes express synaptic cell adhesion molecules (CAMs) like neuroligins (Nlgns), which could regulate astrocyte-neuron interactions. A recent study suggested that loss of astrocytic Nlgn2 affects astrocyte size and excitatory synaptogenesis, which conflicts with previous studies reporting that constitutive deletion of Nlgns does not affect synapse number. To investigate the role of astrocytic Nlgns, we genetically deleted Nlgns 1-3 in astrocytes and observed no impairment in synaptic protein expression or synapse number. Electrophysiological measurements and 3D astrocyte reconstruction showed no impact on synaptic function or astrocyte volume, respectively. Therefore, astrocytic Nlgns are not crucial for synaptogenesis or astrocyte morphogenesis. Further, monosynaptic rabies virus (RV) tracing methods have been developed to identify the molecules involved in synapse development. However, synapse number as measured by RV tracing does not always align with that as reported by traditional immunohistochemistry techniques. This discrepancy may be due to synaptic activity influencing RV tracing. Thus, we investigated whether RV tracing methods simply require structural synapses or if synaptic transmission is also necessary for neuronal labeling with RV. By eliminating evoked transmission, we found that spontaneous release is sufficient for RV spread. Loss of both evoked and spontaneous synaptic transmission halted retrograde labeling entirely. Our studies improve the understanding of astrocyte-mediated synapse maintenance and the techniques used to study them, supporting further research on the molecular and cellular aspects of synapses

Keywords: Medicine.
Advisor: Südhof Thomas C.
Chen Lu (Professor of neurosurgery)
Kaltschmidt Julia
Luo Liqun
Dissecting the Parasympathetic Neural Circuits of the Heart

The autonomic nervous system carefully balances its sympathetic “fight or flight” and parasympathetic “rest and digest” divisions to mediate critical cardiopulmonary functions. Dysfunction between and within these divisions causes a broad range of disease, including heart failure, asthma, and chronic obstructive pulmonary disease (COPD). Here we examine postganglionic parasympathetic or intrinsic neurons, which are exceedingly rare and fragile and housed within the organ they innervate. Recent work has shown that activation of a major subset of cardiac intrinsic neurons by nucleus ambiguus cardiovascular (ACV) neurons evokes bradycardia, whereas activation of another subset of cardiac intrinsic neurons and lung intrinsic neurons that are jointly innervated by nucleus ambiguus cardiopulmonary (ACP) neurons evokes simultaneous bradycardia and bronchoconstriction1, demonstrating their role in controlling and coordinating critical cardiac and cardiopulmonary responses. Despite their functional importance, the molecular diversity and organization of these neural circuits, especially those under parasympathetic control, remain largely unknown. To characterize the anatomical, cellular, molecular, and functional properties of intrinsic lung and cardiac neurons, we use single-cell RNA- sequencing, immunohistochemistry, and single-molecule fluorescent in situ hybridization (smFISH). We reveal molecularly distinct populations of lung and cardiac intrinsic neurons and offer optimized protocols for procuring and analyzing these rare and fragile neurons. These studies aim to elucidate the characteristics and roles of intrinsic lung and cardiac neurons in mediating precise cardiopulmonary regulation and interrogate their interactions with neighboring neuronal populations.

Keywords:  Department of Biology
parasympathetic
cardiopulmonary
Neural circuits
intrinsic cardiac neurons
Text
Thesis
Advisor: Krasnow Mark
Bergmann Dominique
Distributed and certifiable optimization for multi-robot systems

This thesis addresses two key challenges in applying optimization methods to multi-robot systems. First, the need for distributed optimization arises in unstructured and remote environments in which centralized coordination is impractical or infeasible. Second, the nonconvexity of many relevant problems necessitates certifiable optimization, which provides provable bounds on the quality of a solution. We present new techniques for both distributed optimization and certifiable optimization, as well as a unified framework for distributed and certifiable multi-robot optimization. Several tools presented in this thesis enable robots to achieve system-wide coordination through pairwise communication. The ability to cooperatively solve optimization problems through distributed robot-to-robot communication is a crucial component of multi-robot autonomy. We introduce a communication-efficient general-purpose distributed optimization method, Separable Optimization Variable ADMM, and demonstrate its scalability and robustness. Additionally, an optimization-based approach to distributed estimation replicates the performance of the centralized Kalman Filter. We prove that our Distributed Rolling-Window Tracking algorithm maintains consistent estimates without communicating covariance matrices as alternative methods require. Our approach to certifiable optimization considers a broad class of synchronization problems that admit a semidefinite relaxation. We present a novel reformulation of the distance-based localization problem, showing for the first time that it belongs to this same class of certifiable optimization problems. Compared to other distance-based localization algorithms, our method recovers good solutions over a range of problem instantiations. Finally, we present a new approach to distributed certifiable optimization. Our technique for solving a decomposition of a sparse semidefinite program introduces a novel "dualized agreement" constraint. This formulation allows networked robots to iteratively solve for their individual components in a large semidefinite program. Together, these contributions provide a general framework for fully distributed and provably optimal multi-robot coordination.

Keywords: Engineering.
Mechanical Engineering.
Advisor: Kennedy Monroe
Schwager Mac
Pilanci Mert
Distributional robustness and minimax optimality in selected problems

This thesis offers a comprehensive exploration of distributional uncertainties and their implications on machine learning and statistical estimation, providing insights and solutions that are both theoretically sound and practically impactful. We study a diverse array of problem settings, including non-parametric regression, multivariate extreme values theory, and data analytics scenarios involving missing data.

Keywords: Engineering.
Management Science and Engineering.
Advisor: Blanchet Jose H.
Glynn Peter W.
Pelger Markus
Divergence in ecological and sexual traits shapes the evolution of swordtail fish and their naturally occurring hybrids

In this thesis, I explore the consequences of hybridization, or genetic exchange between species, with a focus on divergent traits that have evolved between species. I performed these studies leveraging a system where natural hybridization is ongoing between species that vary in their sexual displays and ecology: the swordtail fishes \emph{Xiphophorus malinche} and \emph{X. birchmanni}. In my first chapter, I provide an introduction to the genomic consequences of hybridization, highlighting open questions around predicting the effects of different and interacting selective forces on hybrid genomes. In my second chapter, I explore the genetic basis of a sexually-selected ornament, called the sword. In my third and fourth chapters, I focused on divergence between species in thermal tolerance and offspring size. These two traits can be viewed as models of evolved differences between these species in response to the environment and allow me to explore the interplay between ecological adaptations in species and their breakdown in hybrids.

Keywords: Humanities and Sciences.
Biology.
Advisor: Schumer Molly
Exposito-Alonso Moises
Fraser Hunter
Gifford Casey
Diversity and Community Dynamics of Ammonia-Oxidizing Microorganisms in Monterey Bay Aquarium Biofilters

In aquaria, biofilters are used to prevent the accumulation of ammonia by fostering communities of nitrifying microbes, including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB). Previous studies have shown that aquarium biofilters are usually dominated by AOA rather than AOB, but have not yet fully characterized the microbial communities living in those biofilters. In this study, we analyze the microbial communities within the Fluidized Bed (FB) biofilter systems at the Monterey Bay Aquarium (MBA) and investigate how those communities change over time and are influenced by the microbial community of Monterey Bay, which directly supplies seawater to the aquarium. We focus on the dynamics of nitrifier communities, AOA in particular, to investigate which microbes are most important to the biofilter’s function. Using high throughput sequencing of the archaeal and bacterial 16S rRNA gene, we investigated the microbial communities in water and sand samples for the FB systems at MBA over a 3 month period, during the establishment of a new FB. FB samples were compared to microbial communities associated with Filter 1 (F1), the biofilter treating incoming water from Monterey Bay. Further analysis of AOA abundance was conducted using quantitative PCR (qPCR). We found that the FBs had a distinct microbial community from F1 and that the microbial communities in FB sand samples were more stable over time than those in the FB water samples. When it comes to nitrifiers, the FBs were dominated by AOA and NOB, and their populations remained stable over time in sand samples. Of the AOA in the FBs, 99% came from a single operational taxonomic unit (OTU2) with close phylogenetic affiliation to AOA from Monterey Bay. Overall, this study supports previous findings about AOA dominance in aquarium biofilters, and represents the first in-depth characterization of the microbial community in a MBA biofilter.

Keywords: nitrifiers
archaea
aquarium biofilter
ammonia oxidation
Bacteria
Monterey Bay Aquarium
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Thesis
Advisor: Francis Chris
Tolar Bradley
Diversity, learning, and knowledge : a study across institutions

My dissertation, titled 'Diversity, Learning, and Knowledge: A Study Across Institutions', delves into the intricate dynamics of diversity within the realms of educational institutions and the Internet. This research underscores the multifaceted nature of diversity and is segmented into three chapters. The first chapter investigates student interactions within the framework of India's extensive affirmative action program, revealing the persistent nature of caste-based segregation in higher education and the positive influence of classmate diversity in reducing such segregation. The second chapter, set within the same affirmative action context, examines the impact of faculty diversity on student learning. Contrary to common criticisms of affirmative action, the findings suggest that faculty hired under reservation categories, despite having lower qualifications, do not compromise on (and in fact provide slightly better) quality of instruction. The third chapter transitions to the digital realm, introducing a novel metric to quantify 'information completeness' on the Internet. By analyzing 6.5 trillion search results, I highlight the challenges posed by consistent consumption of ranked information and its implications for open-mindedness and informed decision-making. Collectively, this dissertation underscores the importance of fostering diversity in both traditional and digital spaces, emphasizing its potential to enhance learning, promote intellectual growth, and contribute to a more inclusive and harmonious global community.

Keywords: Education.
Advisor: Domingue Ben
Haber Nick
Loyalka Prashant
The domestic politics of defense in the U.S. Congress

The US defense budget is one of the few pieces of legislation that regularly passes the US Congress, but current scholarship in American politics and US foreign policy struggle to explain precisely why this happens. Existing theories of Congressional behavior that explain other issue areas— like the influence of a member's districts or his or her personal history— have a history of null results when applied to defense votes. My dissertation addresses the question of why the US defense budget is so popular in Congress, and how this varies across members and time. I decompose support for the defense budget into a member's engagement, or work on this issue, and their voting record, and show that existing theories explain well members' engagement— members with military industry in their district tend to work on defense issues more than other members— but does not explain a members' vote pattern. This is largely because of the large number of unengaged congressmembers who vote in favor of defense bills despite not having these characteristics. I suggest that this occurs because members of Congress are concerned about the domestic political consequences of being labeled soft on defense, and engage in strategic voting in support of defense, particularly in times of national threat. I use survey experiments and 80 years of Congressional behavior to support this claim. My final paper compares two instances in which soft on defense criticism were used to change the politics of missile defense and demonstrates how a perception of threat in Congress is a precondition for this effect

Keywords: Humanities and Sciences.
Political Science.
Advisor: Sagan Scott Douglas
Grimmer Justin
Schultz Kenneth A.
"The drama of our world : spectator and subject in medieval Kashmir and early modern Europe

Is all the world a stage? How do we as subjects and spectators perceive the world? How do we take pleasure in watching plays? At surface level, one might not think that thinkers from two cultures as removed from each other as the long tenth century in Kashmir and the long seventeenth century in France and England might have much to say to each other on these abstract questions. And yet, in examining the thought of philosophers, playwrights, and literary critics from the long seventeenth century in France and England and the long tenth century in Kashmir, this dissertation argues otherwise. On questions of epistemology and metaphysics on the one hand and dramatic theory and poetics on the other, they shared surprisingly many common perspectives, including the critical intuition of the interdependence of these disciplines. These common threads enable us to create a conversation between them as equals at a table, precisely the kind made impossible by colonization and its legacy. In a broad sense, then, the goals of this intervention are threefold: historical (to change the narrative about where certain ideas originated), political (to make room at this conversational table), and intellectual (to ensure that these ideas do not remain the property of a certain civilization but as shared cultural property). In doing so, this dissertation offers a methodological model that can be useful for creating conversations among cultures from across the world, not despite but because of their radical alterity and seeming irrelevance to our modern world

Keywords: Humanities and Sciences.
Comparative Literature.
Advisor: Greene Roland
Landy Joshua
Edelstein Dan
Fisher Elaine M.
Drip or drop : evidence on state dependence and consumption constraints from TV streaming

I study how state dependence affects consumer choices when consumption is constrained by product release strategies. Using a unique dataset of automatically-logged user-level TV streaming data, I show that constraints on users' consumption imposed by the availability of episodes affect consumption choices and that these choices lead to state dependence within and across shows. This implies that show-level policies will affect aggregate consumption outcomes. However, because consumers communicate about TV shows, user-level experimentation with episode release timing is practically infeasible. Instead, I estimate a structural model of TV watching that includes state dependence and consumption constraints via episode availability. This enables the evaluation of counterfactual episode release policies. I allow state dependence to spill over to other shows and to affect subsequent choices, thereby linking release policy and total viewership outcomes. I find evidence for state dependence and imperfect spillovers across shows. Counterfactual simulations highlight the importance of episode release timing. as an input to overall watching behavior for streaming platforms. This work has implications for product availability strategies and policies which encourage varying patterns of consumption in any setting where consumption is constrained or may be state-dependent

Keywords: Business.
Advisor: Narayanan Sridhar
Kim Yewon (Assistant professor of marketing) 
Lattin James M.
Dynamic wavefront shaping with high-quality-factor resonant metasurfaces

Wavefront shaping and control is essential for advancing optical technologies spanning communication, computation, and sensing. Metasurfaces promise to miniaturize future optical components, by shaping light with subwavelength nanostructures that precisely control the wave's amplitude, polarization, and phase. However, most current metasurface designs are static, unable to flexibly tune their responses to environmental or operational cues once fabricated. This thesis presents the design, fabrication, and characterization of dynamic metasurfaces that efficiently modulate their behavior based on the integration of high quality factor (high-Q) resonances. Through demonstrating a variety of devices, including lenses and beam steerers, both theoretically and experimentally this work will clearly lay out high-Q wavefront shaping metasurfaces as a promising route to achieving active devices utilizing many possible modulation mechanisms to realize a variety of transfer functions and novel design schemes

Keywords: Engineering.
Materials Science and Engineering.
Advisor: Dionne Jennifer Anne
Brongersma Mark L.
Lindenberg Aaron Michael
Dynamics in thin films measured with reflection-mode ultrafast infrared spectroscopy

Significant insights can be gained by studying the behavior of molecules in thin films. Many important processes in energy generation, chemical synthesis, gas capture, and tribology occur at interfaces. The properties of a chemical system near a surface are often different from those of the bulk material. Therefore, understanding interactions at surfaces is of great interest. In thin films, most or all of the molecules are close to the interface, providing a unique opportunity to measure the effect of the surface. In addition, thin films have many applications including solar cells, chemical sensors, and microelectronics components. In this work, two ultrafast infrared spectroscopy techniques, two-dimensional infrared spectroscopy and polarization-selective pump-probe spectroscopy, were applied to thin films to measure their molecular dynamics on the picosecond time scale. Spectroscopy experiments on thin films are challenging because of the small number of molecules present in the samples. To make the experiments feasible, the signal was enhanced by using a reflection-mode geometry instead of the standard transmission geometry. The chemical systems studied in this work were a two-dimensional perovskite and room temperature ionic liquids (RTILs). The perovskite experiments showed that the lattice undergoes rapid structural fluctuations, which may be relevant to perovskites' effectiveness at stabilizing charge carriers. The RTIL experiments showed that the effect of the interface propagates for tens of nanometers into the liquid, which is a notably large distance compared to the corresponding length scale in conventional liquids like water.

Keywords: Humanities and Sciences.
Chemistry.
Advisor: Fayer Michael
Dai Hongjie
Moerner William