VictorJuiz/thesis huggingface dataset:
Controlling and Imaging Molecular Motion at the Surface of a Gate-Tunable Graphene Device

The ability to control nanoscale molecular motion with device-scale electric fields opens many exciting possibilities for nanotechnology. Collective motion of molecules can be used to assemble new nanostructures, induce mass and charge transport, transform device properties by surface modifications, and can potentially be used as a tool for constructing nanoscale machines. As components for electromechanical devices approach the nanometer length scale, how they interact with local electric fields and currents becomes increasingly important. This dissertation focuses on exploring how macroscopic electric fields and currents can manipulate and probe the collective motion of adsorbed molecules on gate-tunable devices./nThe movement of F4TCNQ molecules on a graphene field-effect transistor was controlled by the application of a gate voltage and source-drain current, and concurrently imaged using a scanning tunneling microscope. Various field-induced molecular phenomena were investigated on the device, including gate-tunable surface molecular concentrations, gate-tunable molecular phase transitions, gate-dependent molecular diffusion, molecule density-dependent current transport, and current-induced electromigration. These phenomena provide insight into how nanoscale molecular motion can be controlled by external electric fields, and how force and momentum are transmitted between electrons and adsorbates under non-equilibrium conditions.

Advisor: Crommie, Michael F
Social Dance after Social Practice: Between the Stage and the Museum

This dissertation examines dance practices by choreographers and visual artists from the late 20th century whose work incorporates a range of (often marginalized) communities in order to address the social issues of their time. I argue that these participatory and collective dances by Anna Halprin, Adrian Piper, and Bill T. Jones are overlooked in the nascent genealogy of social practice that has yet to consider dance as either a medium or conceptual frame. Conversely, I contend that the frame of social practice addresses a gap in dance studies that has yet to contend with the ethics, power dynamics, and history of community-based and community-sourced dance practices. Through the conscious deployment of bodies in space, social practice often appears as staged encounters, and performance studies scholars, such as Shannon Jackson, have analyzed it as such. Yet, I argue social practice is also inherently choreographic. By bringing a dance framework to social practice—and an art historical framework to dance studies—I demonstrate the synergy between social practice and the ethos of Black social dance: improvisation, community, and collectivity. Such connections and influences prompt the need to elaborate new frames and categories around what I call “social practice dance.”

Advisor: Jackson, Shannon
Three Hommages for String Quartet

Composed in 2019 and revised and expanded in 2022, Three Hommages is a work for string quartet. It was premiered by Tana Quartet in Berkeley, California. The work is in four movements, all of which revolve around the ideas connected to musical time and synchronization. The music score serves as the main body of this dissertation with the written component provided as analytical supporting material.Two composers and a novelist are the main influences for this work: Witold Lutosławski and Conlon Nancarrow’s compositions, especially those composed for the string quartet medium- are primary influences. Both composers tried using different methods to create an out-of-sync feeling. Nancarrow, just like in Three Hommages, uses the time signature 1/4 in his String Quartet No. 3, and uses different subdivisions to create four different tempi for the four instruments. Lutosławski on the other hand, uses four different systems for all instruments in his String Quartet. Most of the time, the performers play their parts independent from each other, with different synchronization points in which they come together. In addition to these two composers, Three Hommages takes its literal inspiration from a Turkish novel, Saatleri Ayarlama Enstitusu by Ahmed Hamdi Tanpinar. This novel is about a fictional institute responsible for synchronizing all the public clocks in a city. The first and third movements of Three Hommages are exactly about going from an out- of-sync to an in-sync state, whereas the second and final movements do the opposite, in which all the instruments start in-sync and slowly go out-of -sync. The process of going to in-sync is planned very thoroughly, and the method devised in this work is analyzed in depth in this text. The reverse process is composed freely, since going from order to chaos is a natural process.

Advisor: Campion, Edmund
The Varangian Guard in Literature

The Varangian Guard was a mercenary unit of many cultures, including Norse, that served the Byzantine Army from 988 to 1204. The 11th century is considered the heyday of Norse presence in the Guard, but few facts of their service have survived to today. The present dissertation argues that the Varangians as we know them are largely detached from their murky history, and are instead defined by their fictionalized depictions in literature, particularly the Old Norse sagas. In this context, these mercenaries are identifiable by Varangian symbols of great honor, immense wealth, and martial prowess, established through repetition in the Scandinavian corpus. However, the roles these characters play in their respective texts are highly individualized and heavily dependent on the surrounding narrative. As a result, they are malleable figures that fascinate due to their elite status and accomplishments, but adapt easily to reflect and explore the values of different time periods, settings, and formats of storytelling due to the lack of concrete history attached to them./nThe first two chapters center on Varangians abroad, who are predominantly inspired by the most influential literary Varangian, Haraldr Sigurðarson. Chapter one looks at Haraldr himself and the construction of his early years in the poetry and kings' sagas. Chapter two deals with the further development of the Haraldr model into new genres via Bolli Bollason and Þorsteinn drómundr. The third chapter delves into Varangian veterans at home in the North: Bolli, Halldórr Snorrason, Gríss Sæmingsson, and Þorkell Þjóstarsson. These figures are much more diverse in their depictions, drawing heavily on the context of their respective sagas to provide commentary on contemporary rather than historical issues, from political tensions to combat trauma. The fourth chapter approaches two modern works featuring Varangians, the graphic novel Northlanders (2008-2011) and the video game Horizon Zero Dawn (2017), and how these mercenaries are still being leveraged to tell relevant stories in today's world.

Advisor: Wellendorf, Jonas
Computation of in vivo myocardial deformation from planar imaging

Cardiovascular disease has remained the leading cause of death worldwide. In addition, the 2015 Annual Data Report from the US Renal Data System shows that sudden cardiac death and arrhythmias are the leading cause of mortality for patients on routine hemodialysis for end-stage renal disease (ESRD). In this study, we aim to augment cardiac magnetic resonance (CMR) images obtained for such patients through a registration framework developed for analyzing two-dimensional (2D) CMR image sequences. The framework consolidates existing tools, such as segmentation and the large deformation diffeomorphic metric mapping (LDDMM) algorithm, and provides a systematic process to define the circumferential and radial directions in general left ventricle geometries, to quantify its myocardial strain throughout the cardiac cycle. While CMR image sequences are used in this work, the framework is designed to be agnostic to the imaging modality. In conjunction with this framework, validation tests were developed using synthetic deformation data generated through solid mechanics simulations. This was done for three analytical shapes: a box, thick-walled cylinder, and a thick-walled ellipsoid, all in three dimensions. This synthetic data was then used to provide a 2D input to the registration framework, which allowed a direct comparison of the deformation computed from the solid mechanics simulation and the registration framework. All of this was developed to use data that is generally readily accessible in clinical settings, as well as to provide a template for designing validation tests for myocardial strain computations.

Advisor: Shadden, Shawn C
Investigating the effects of context on semantic representations in the brain and mapping social representations in the brain

Context is an important part of understanding the meaning of natural language, but most neuroimaging studies of meaning use isolated words and isolated sentences with little context. Because the brain may process natural language differently from how it processes simplified stimuli, it is unclear whether prior results on word meaning generalize to natural language. In Chapter 1, I present a neuroimaging experiment that examines whether the results of neuroimaging studies that use stimuli with little context generalize to natural language. Results show that context both affects the quality of neuroimaging data and changes where and how semantic information is represented in the brain. This suggests that findings from studies using stimuli with little context do not generalize to natural language./nIn Chapters 2 and 3, I present two neuroimaging experiments that map representations of social information in the brain. Relationships are an integral part of life, and people store extensive knowledge about themselves, other individuals, and their dynamics to maintain these relationships. Many prior neuroimaging studies have investigated where different types of social information are represented in the brain. However, because of methodological limitations in these studies, the representation of social information in the brain remains unclear. In Chapter 2, I present a neuroimaging experiment that simultaneously maps the representation of five types of social information that have been investigated in prior studies. Results show that only three of these five types of social information are represented in the brain, and that individual brain regions each represent one type of social information. In Chapter 3, I present a neuroimaging experiment that maps the representation of the self and six different types of other people. Preliminary results from this experiment suggest that the brain represents the self and different types of others in distinct brain regions. These data also reveal three possible axes along which the brain may organize information about the self and others.

Advisor: Gallant, Jack L.
Molecular determinants of flavivirus non-structural protein 1

Flaviviruses are arthropod-borne, positive-sense RNA viruses of significant medical and public health importance. While safe and effective vaccines have been developed against some members of the Flavivirus genus, limited progress has been made against others, such as dengue (DENV), West Nile (WNV), and Zika (ZIKV) viruses – which cause distinct human diseases and affect different tissues. Importantly, there are currently no flavivirus-specific therapeutics. Flaviviruses encode a secreted non-structural protein 1 (NS1) that directly interacts with endothelial cells, resulting in barrier dysfunction. The clinical manifestations of these interactions are thought to include DENV NS1-induced vascular leak in the lungs, WNV NS1 enhancing viral infection of the brain, and ZIKV NS1 causing hyperpermeability in placental tissues. We previously found that flavivirus NS1 binds to endothelial cells and disrupts barrier functions in a tissue-specific manner consistent with the disease tropism of the respective viruses. Understanding the underlying molecular mechanism of tissue-specific NS1-endothelial cell interactions will help guide better interventions to prevent and control flaviviral diseases. To elucidate the distinct role(s) that the domains of NS1 (β-roll, wing, and β-ladder) play in NS1 interactions with endothelial cells, we constructed flavivirus NS1 chimeras that exchanged the wing and β-ladder domains in a pair-wise manner between DENV, WNV, and ZIKV NS1. We found that both the NS1 wing and β-ladder domains conferred NS1 tissue-specific endothelial dysfunction, with the wing conferring cell binding and the β-ladder involved in inducing endothelial hyperpermeability as measured by transendothelial electrical resistance assay. Then, we utilized the DENV-WNV NS1 chimera and identified residues 91 to 93 (GDI) of DENV NS1 as a molecular motif determining binding specificity. Using a mouse model of localized leak, we corroborated that the NS1 wing domain and GDI molecular determinant motif triggered NS1-induced vascular leak in vivo. Further, we report other molecular determinants of interest, including a highly conserved motif in the NS1 wing domain that mediates pan-flavivirus NS1 binding to pulmonary endothelial cells and identified the wing domain to mediate interactions with endothelial cell surface glycans. Finally, we explored the protective effects of the iminosugar UV-4B against DENV NS1-induced endothelial dysfunctions by inhibiting proper host-dependent glycosylation processing of NS1. Taken together, these findings contribute to improved understanding of flavivirus NS1 and the molecular details conferring its tissue-specific functional patterns, that could help guide future vaccine design and therapeutic developments.

Advisor: Harris, Eva
Amphibian Conservation in Working and Natural Landscapes: Investigating the Impacts of Disease, Bioacoustics, and Natural History

Amphibians are among the world’s most endangered vertebrates, especially in the tropics. Land-use change remains the most significant driver of amphibian declines worldwide; natural history information on most tropical species is severely lacking, rendering conservation strategies difficult. Human actions have become one of the dominant forces driving the outcomes of a classic question in ecology: Why are species found where they are? Some frog species are tolerant to habitat disturbance, inhabiting urban areas or various types of agriculture, while others are only found in relatively untouched habitats like primary forests. Still other species are so understudied that we are unable to assess their distributions. This dissertation investigates the role of natural history traits in disturbance tolerance, as well as in the discovery of undescribed frog species and behaviors in Ecuador. Chapter 1 introduces these concepts in more detail. Chapter 2 investigates the effect of land management and species traits on pathogen prevalence, specifically the aquatic fungus Batrachochytrium dendrobatidis (Bd)—another major driver of global amphibian loss. At the community level, body size and lifetime aquatic index (level of water dependence for breeding) were the strongest predictors of Bd infection. The results introduce nuance to the theory that amphibian populations experience higher disease risk in natural habitats. In Chapter 3, I investigate how land-use change influences sound propagation, which has direct implications for amphibian communication. If the change in vegetation causes a habitat to become acoustically inhospitable, frogs with certain call properties would be rendered unable to attract mates. I found that species with high-pitched calls in some families (Hylidae and Strabomantidae) were more likely to be found in disturbed habitats—as hypothesized—but, unexpectedly, species with high-pitched calls in Centrolenidae were more likely to be found in undisturbed habitats. This work highlights the need to consider the acoustic environment when assessing a species’ vulnerability to habitat disturbance. In Chapter 4, I describe the call and visual signaling behavior of Sachatamia orejuela, an elusive glassfrog species that occupies a noisy acoustic niche. Documenting these new natural history traits provides a fascinating example of behavioral convergent evolution and further evidence that signals are shaped by their environment. Finally, Chapter 5 describes two new glassfrog species that are phenotypically very similar to other glassfrog species but are genetically and acoustically distinct. We recommend that both be listed as Endangered, given the rate of deforestation in their only known habitat. Chapter 6 discusses conservation challenges in the Ecuadorian Andes, especially for amphibians.

Advisor: Kremen, Claire
Long-range ferroic ordering in two-dimensional van der Waals materials

The recent discoveries of ferroic properties, such as ferromagnetism and ferroelectricity, in two-dimensional van der Waals (2D vdW) materials have generated a surge of interest in the exploration of fundamental interaction in reduced dimensions and functional device applications./nOn one hand, ferromagnetism in 2D vdW crystals enables better understanding of fundamental interactions in ultra-thin condensed matter systems. However, existing material candidates face limitations, such as the lack of room-temperature magnetic ordering. Here we report the room-temperature ferromagnetism in Co-doped graphene-like ZnO, a novel chemically stable 2D material, down to single-atom thickness. Through magneto-optic Kerr effect and superconducting quantum interference device measurements, we identify the spontaneous magnetization in such systems at room temperature and above. X-ray characterization shows that the Co atoms form Co2+ states in graphitic ZnO. By varying the Co doping level, we observe an exotic manipulation among paramagnetic, ferromagnetic, and disordered phases. Our development of Co-doped 2D ZnO opens an appealing path to 2D ferromagnetism persisting at room temperature with unique controllability./nOn the other hand, the stabilization of 2D ferroelectricity overcomes the thickness limit. In contrast with conventional 3D ferroelectrics, 2D ferroelectrics show great advantages, including but not limited to, high mobility, perfect interface, allowing for non-destructive reading, being fatigueless. In this dissertation, we report the physical vapor deposition (PVD) of 2D vdW SnSe directly onto the silicon substrate. The synthesis process occurs at relatively low temperatures; the deposition temperature is 250 ℃. By varying the time of synthesis, we are able to manipulate the thickness of SnSe single crystals, which spans in a large range from 6 nm to the bulk. Out-of-plane ferroelectricity is detected in SnSe at room temperature (300 K) by means of piezoresponse force microscopy (PFM). More importantly, the ferroelectric switching voltage scales linearly with the sample thickness. A 6-nm-thick SnSe sheet displays sub-0.3 V switching, which is substantially smaller than those of previously reported 2D ferroelectrics and hafnium oxides. Moreover, the ferroelectric mechanisms are unraveled by transmission electron microscopy (TEM); AA stacking of vdW layers and interlayer sliding give rise to the vertical ferroelectric polarization. The ferroelectric dipole, as a new degree of freedom, can effectively manipulate the optical and electrical behaviors in SnSe. These results indicate that 2D SnSe is a promising candidate for future energy-efficient and non-volatile electronics or optoelectronics, which is highly compatible with the emergent complementary metal oxide semiconductor (CMOS) technologies.

Advisor: Yao, Jie
Exploratory and Explanatory Tools for ML Application Development

While Deep Learning ("DL") techniques have enabled groundbreaking advances in many domains, non-expert DL users encounter significant usability challenges when attempting to develop, debug, and interpret DL applications. This work describes how techniques from program analysis and DL interpretability are drawn upon to build novel, interactive tools that support users in important stages of DL development. Key interactions of these tools facilitate pattern discovery through exploration and provide explanations that reveal underlying structure. At early stages, ACUMEN helps users find suitable templates to start their DL projects through exploring and annotating an interactive visualization of code embeddings and extracted attributes. UMLAUT helps users find and fix silent errors in DL programs during model training with an interface unifying visualizations, code, and error explanations. IMACS helps users explore and compare influential concepts extracted from image classification models during model evaluation. User studies reveal how these systems address usability gaps at different stages of the DL development process, as well as how these interaction techniques can generalize to other scenarios.

Advisor: Hartmann, Bjoern
Network Optimization Algorithms and Applications to Molecular Biology

In this thesis, I pursue several problems in molecular biology through abstraction into network optimization algorithms./nIn the first chapter of this thesis I consider our first flavor of network problems - sub-network optimization within a known dynamic network. In these instances, I introduce the notion of Condition and Time Conditioned networks, in which a network may dynamically change over time (i.e. vertices or edges). In our first set of problems, the goal becomes to find a global sub-network of minimum cost, which satisfies all local connectivity demands across conditions. In the second set of problems, I consider optimizing a singular walk demand beginning at source node $a$ in timepoint $t_1$ and ending at a destination node $b$ at a later timepoint $t_2$, while maintaining a notion of consistency over time. Lastly, I utilize these frameworks to investigate signal transduction in Th17 cells with the purpose of finding novel downstream proteins of interest involved in IL23 receptor signalling./nIn the second chapter of this thesis, I consider the problem of lineage tracing in CRISPR/Cas9 models - given a set of terminal nodes or cells generated via CRISPR/Cas9 lineage tracing, what is the most likely tree that best represents the ground truth generative process. In particular, I begin by introducing two methods towards this analysis - a greedy approach, and an exact integer linear programming approach. I then test these methods via simulation and via ground truth trees generated in vitro. Lastly, I take a step back and consider the theoretical guarantees of our framework. That is, I explore the relationship between the number of characters/cut sites in our model against variables such as minimum cell division times, number of cells, and cutting rates. In particular I derive upper bounds for the number of characters required for exact reconstruction given perfect knowledge about the experimental setup./nIn the third and final chapter of this thesis, I consider a network flow abstraction for estimating metabolic activity within cells. Given the relationship between metabolism and immunological function, our goal becomes to discover tissue specific metabolic programs within Th17 cells. To achieve this goal, I leverage a Flux Balance Analysis approach to estimate network wide metabolic flux within Th17 cells collected from mice across various tissues, whereby I discover a novel gut specific metabolic target of interest responsible for regulating effector-like function and homeostasis.

Advisor: Yosef, Nir