VictorJuiz/thesis huggingface dataset:
Multiscale geomechanical and geochemical studies of unconventional shale reservoirs
Keywords: Geophysics.

With the advancement of horizontal drilling and hydraulic fracturing, unconventional shale reservoirs are now capable of being drilled faster and produced economically at commercial rates. Although these shale resources are massive in size and globally abundant, they are still being produced with low recovery factors (less than 5\% for shale oil and less than 20\% for shale gas). This low recovery could be attributed to an incomplete understanding of the complex intrinsic properties of shale rocks. In this thesis, I focused on investigating the main factors that control pore volume (porosity) and pore-size distribution of different shale reservoirs and how this variability in pore space can be related to measured permeability and well production. I present in this thesis a laboratory workflow highlighting a series of fluid penetration and permeability measurements performed on multiple shale reservoir samples. My approach looks at characterizing and imaging the nanoscale porosity first to better understand the pore space distribution and building upwards in scale through the permeability measurements. Next, I apply my previous findings towards a specific geochemical application setting involving the hydraulic fracturing fluid composition and its effect on the shale permeability. Lastly, understanding how porosity is distributed across the shale matrix and altered during hydraulic fracturing and throughout production is crucial to identify beforehand as it will have a potential impact on enhancing the recovery factors of producing shales.
Multi-scale soft matter physics of biological systems with applications in models of human disease
Keywords: Chemical Engineering.

Biological systems are regulated by active forces that must be coordinated over a vast hierarchy of scales in length and time. However, developing a physical understanding of how these forces are integrated across scales to give rise to the emergent collective behavior of organisms remains a formidable task. In this thesis, I explore how theoretical polymer physics models can be integrated with multi-scale experimental characterization techniques to develop a physical description of biological systems that spans disparate length and time scales.
Musculoskeletal simulation and optimization for predicting human movement
Keywords: Bioengineering.

Human movement requires complex coordination between the muscular, skeletal, and neural systems. When these systems are impaired, gait pathologies can occur. Previous research has studied how neuromuscular and skeletal deficits result in abnormal, inefficient, gait patterns. However, while these studies have suggested relationships between musculoskeletal parameters and observed gait, they have been limited in understanding the cause-effect relationship between these variables. Other previous work has focused on developing devices to augment human performance, both for individuals with and without impairments, but results have been mixed, likely due to the complex human dynamics and human-device interactions. This thesis describes two musculoskeletal simulation and optimization frameworks that were developed to explore if simulations can be used to 1) probe the cause-effect relationship between muscle deficits and commonly observed pathological gait patterns and 2) help design assistive devices. For each study, the frameworks generated predictive simulations, or simulations in which movement trajectories were created without tracking any experimental data. In the first study, the framework could generate realistic simulations of walking. Plantarflexor muscle weakness or contracture, commonly observed in individuals with stroke or cerebral palsy, was then added to the model, and the model adopted gait patterns that are seen in pathologic gait. In the second study, the framework could generate realistic simulations of a standing long jump. Potential active and passive assistive devices were then added to the model, and the framework tuned the devices to increase jump distance. This work shows how simulation frameworks can be used to predict how movement would change under various conditions, leading to a deeper understanding of mechanisms behind gait pathologies and a framework to aid in designing devices to augment human performance.
Musical modernism and the search for second-person lyric
Keywords: Music.

Why and how did lyric persist in the seemingly hostile conditions of musical modernism? Although modernist music is often accused of turning its back on human relationality, certain canonical works hinge on lyric moments in which one senses a voice trying to initiate second-person address. By putting lyric in the mouths of those who lack agency and voice, these moments simultaneously respond to anxieties about lyric's viability in modernity that had already begun in Schubert's time and express a hope that lyric, in its very thinglike gratuitousness, might be able to open communicative space when other modes fail. Contextualizing the modernist lyric of Schoenberg's Pierrot lunaire (1912), Berg's Wozzeck (1914--22), and Britten's Peter Grimes (1942--45) in the shifts in lyric reception around the turn of the century, I show how these works pleaded for a revision—not only of lyric form or style, but of the ethical ideals that underpinned contemporary lyric reception. Modernist lyric sought to escape the idealization of the integrated self, I argue, instead seek-ing to understand the self as always already given over to second-person relation. Yet this idea, which is latent in the rhetorical figure of apostrophe that Jonathan Culler places at the core of Romantic lyric, was in a certain sense nothing new. By mediating between schools of thought that view Schoenberg as either the last gasp of Romanticism or the pioneer of a New Music divorced from its past, my approach offers a new angle from which we might see the ethical significance of Schoenberg's legacy. While Adorno perhaps felt only despair about lyric's ethical or redemptive powers in modernity, a despair encapsulated in his famous statement that "to write poetry after Auschwitz is barbaric, " the works I study invite some-thing like hope—not in the sense of an expectation of a divinely mediated redemption, but an awakening to the un-idealized truth that lyric always retains: that I am not you, and yet I must relate to you. They show how, by opening a momentary, fragile, but real common space, lyric can create the preconditions of repair for those suffering from trauma and moral injury—precisely because it accomplishes and means nothing but is devoted only to the possibility of relationality itself.
Nanoengineering and knockoffs for an electronic molecular fingerprinting platform
Keywords: Electrical Engineering.

To diagnose complex diseases and perform advanced drug screening and chemical monitoring, we need sensors capable of broadband, multi-analyte detection. This is achieved either by multiplexing affinity probes to capture different target analytes, or through mass or vibrational spectroscopy. While affinity-based techniques currently dominate and are capable of high specificity and sensitivity, probe multiplexing can be time consuming, expensive, and difficult to execute reliably outside of a laboratory environment. On the other hand, spectroscopic chemical detection is label- and affinity-free, but often requires costly and bulky instrumentation. In this thesis, we describe an affinity-free sensor for measuring vibrational signatures of analytes in liquid samples, which can be implemented on a scalable and fully-electronic platform. This relies on resonant electrochemical charge transfer at room temperature, which is made possible by nanoscale interface engineering and low-noise potentiostatic feedback. We describe advances in the knowledge and technology required to realize key aspects of this platform, including the nanoscale sensor site, electrochemical measurement system, and signal analysis framework. Together, these pave the way for continued development of a practical electronic platform for molecular fingerprinting platform in complex samples.
Nanophotonics for polarization control and thermal management
Keywords: Electrical Engineering.

Polarization is one of the most fundamental degree of freedoms of photons. Techniques to control polarization are therefore of crucial importance from a fundamental perspective and find applications in many areas such as optical communications, sensing, and imaging. An important task in the control of polarization is to achieve polarization conversion, where one seeks to generate a target output polarization for a given input polarization. In the first part of this dissertation, we show that a photonic crystal slab with a mirror underneath can provide complete conversion between linear polarizations in a reflection process. Moreover, such an effect is topological since the complex reflection coefficients have a nonzero winding number in the wavevector space. We next show that such a structure can also achieve arbitrary polarization conversion. For a given incident light with any fixed polarization, one can generate arbitrary polarization in the reflected light, by varying the direction of the incident light. Photons are also important heat carriers. The ability to control thermal radiation and radiative heat transfer is of fundamental importance for a wide range of energy applications. In the second part of this dissertation, we use nanophotonic structures and principles to control thermal radiation and heat flow, which can provide thermal capabilities that are unavailable from conventional structures. In the first exmaple, we demonstrate narrowband thermal radiation with unity emissivity peak in the near-infrared range by critically coupling a flat tungsten surface with guided resonances of a dielectric photonic crystal slab. The frequency and linewidth of the emissivity peak are highly tunable. In the second example, we propose a scheme for achieving thermal switch in near-field radiative heat transfer. We present a practical implementation consisting of three nanospheres that are aligned in a straight line. Exploiting the thermal dependent resonances of the nanospheres, we show that the heat transfer between the two side spheres can be turned `on' and `off' by varing the temperature of the center sphere.
Network-based methods for the elucidation of disease and drug mechanisms
Keywords: Biomedical Informatics.

Complex, chronic diseases represent some of the most common diseases known to man, yet often little is understood regarding the underlying biological mechanisms, leading to challenges in their prevention and treatment. Characterizing complex disease can be daunting, as combinations of perturbations in a delicate web of genetic and environmental interactions may lead to a similar disease phenotype. These intricacies provide an opportunity for computational approaches, in particular network-based approaches, which have the ability to capture and model large, complex biological systems. I have leveraged the power and versatility of these approaches and developed novel network-based methods for phenotype classification and drug discovery. I applied my methods to inflammatory bowel disease (IBD), a chronic, heterogeneous disease which has significant unmet need in subtyping patients, predicting treatment response, and optimizing treatment regimens. I first discovered new candidate genes implicated in IBD by traversing a network consisting of IBD related genes and Mendelian phenotypes. Next, I developed a new supervised, individualized pathway-based classification method, and demonstrated its superiority over existing gene-based and pathway-based methods for distinguishing the two common subtypes of IBD. I showed that pathway-based methods can extract robust features for disease differentiation as well as provide mechanistic biological insight into disease subtypes. Finally, I developed a network-based method for drug repurposing which predicts personalized drug treatments for individual patients. Through these works, I demonstrate the potential of network-based bioinformatics tools in furthering patient care by advancing our understanding of disease and drug mechanisms
New chemistries and applications in molecular layer deposition
Keywords: Chemistry.

Recent advancements in nanotechnologies have highlighted the need for thin film deposition capabilities that allow for fine thickness and compositional control. One technique that could help meet these needs is molecular layer deposition (MLD). MLD is a vapor-to-surface organic deposition method that utilizes sequential, self-limiting surface reactions, whereby thin film polymers can be grown. Since its inception, there has been significant progress in MLD synthesis capability, but certain challenges remain. Due to its vapor-phase nature, MLD is unable to utilize solvents and catalysts available to solution phase chemistry. This constraint has limited the variety of polymers that can be grown by MLD, including those formed by carbon-carbon bond synthesis. Another challenge for MLD is to enable area selective (AS) deposition, a process of significant interest in the semiconductor industry because of its potential to reduce fabrication processing steps and facilitate the scale-down of device feature sizes. The first portion of this work discusses a technique allowing for enhanced selectivity in AS-MLD. To achieve these highly selective depositions, a self-assembled monolayer (SAM) layer is used to act as a resist towards MLD. A chemical lift-off step is also employed, which is shown to significantly increase the overall selectivity of the AS-MLD process. Next, a new method for MLD of a silicon oxycarbide (SiOC) material is introduced. SiOC films are typically made with highly oxidizing reactants at elevated temperatures, causing film degradation during the deposition. The new MLD process, however, utilizes mild reactants at room temperature, thereby eliminating degradation problems, resulting in well defined SiOC films. The SiOC films crosslink during the deposition forming a robust film with exceptional thermal stability. The films show a low dielectric (k) constant, supporting their potential use in semiconductor devices where thermally resistant coatings with low-k properties are needed. Lastly, the development of a new MLD polymer is introduced. By utilizing UV light for radical polymerization, direct formation of carbon-carbon bonds is enabled in a photoactivated MLD (pMLD) synthesis. An alternating hydrocarbon-fluorocarbon copolymer, grown via pMLD using iodo-ene coupling, polymerizes by new carbon-carbon bond formation. The fluoropolymer exhibits high thermal stability and chemical resistance as well as the ability to be patterned using a photomask. The pMLD film also shows the ability to be used as a resist for selective deposition. The continued development of thin film techniques such as MLD is essential for progress to be made in nanoscale technologies and could have significant impact towards increasing energy efficiency, providing clean air and water, and improving healthcare. The focus of this work, therefore, is to advance the capabilities of MLD, allowing for new materials and applications.
The new Japanese love novel
Keywords: East Asian Languages and Cultures.

My dissertation confronts the contemporary genre of Japanese love novels. Specifically, I consider four postwar women writers and demonstrate the collective power of their works to reimagine the idea and ideals of love. The protagonists in these works find romance transient and unfulfilling, reject marriage and negate the romantic love ideology that positions marriage as the desirable culmination of heterosexual love. Methodologically, I study how a text's material form influences its interpretation and shapes its audience. Three of the texts I analyze began as serializations in newspapers, weekly magazines or even fashion magazines. Thus, when examined as part of their initial publication venue, these texts illuminate some of the mechanisms of literary production. They challenge the notion of single authorship, as serialized texts are the common enterprise of an author and the periodical's editor. Readers' responses also illustrate how reading a serialization and reading the same texts in a single volume constitute fundamentally different experiences, that require different temporal engagements with the text. Another material element that I investigate in detail is the obi, or book-belt, which is a narrow slip of paper wrapped around the cover of Japanese books. The obi is essentially an advertisement designed to attract consumers' attention. It is a creature of the bookstore and would not be found on the same book in a library. Thus, one methodological contribution of my research is to consider the bookstore -- as opposed to the library -- as a forum for literary engagement. I show how the genre of a work emerges as text, material form, consumers, and publishers converse within this forum. The first chapter analyzes Setouchi Harumi's early work "Kashin" (The Floral Core, 1957), which unapologetically narrates the adulterous relationship of a married woman and which drew considerable backlash from critics upon its publication. Although it is now advertised as "love literature, " I argue that the work is in fact a late example of nikutai bungaku (literature of the flesh) that never received the appreciation it deserves. The second chapter traces the publication history of Tanabe Seiko's novel Iiyoru (Seduction, 1973) and its transformation from a work of soft-pornography serialized in a weekly magazine for men to a work advertised as a "love novel" and praised for its feminist message. The next chapter examines Hayashi Mariko's novel Anego (Big Sis, 2003) as an expression of postfeminist dilemmas, reflected in the character's longing for emotional and financial dependence, despite her status as self-reliant working woman. The last chapter studies Yuikawa Kei's love novel Katagoshi no koibito (Sweetheart Over the Shoulder, 2001). This work presents the fragility of romance and the stability of female friendship, which, as I demonstrate, is a theme inherited from the older and established genre of girls' novels.
Nonlocal light-mediated interactions for fast scrambling
Keywords: Physics.

Quantum entanglement is essential to the description of diverse physical phenomena occurring in condensed matter, cold atomic, high-energy, and gravitational systems, and is known to play a crucial role in quantum computing algorithms exhibiting a speedup over the best known classical algorithms. The Fast Scrambling Conjecture places a fundamental bound on the growth rate of many-body entanglement in arbitrary quantum systems. Quantum systems that saturate this bound, such as black holes, are called Fast Scramblers and generate entanglement at the fastest rate possible; such systems may be regarded as nature's fastest information processors. Can such an ultimate processor be built in the laboratory? In this thesis I present minimal ingredients for experimental access to fast scrambling dynamics and present concrete, realistic proposals for engineering fast scramblers in the laboratory using nonlocal cavity-mediated interactions available in near-term cavity QED experiments. The high degree of tunability of these optically-controlled interactions enables experimental simulation of entirely novel classes of exotic nonlocal spin models with unconventional properties. Theoretical analysis of these spin models reveals a rich set of many-body phenomena, including a novel form of integrability in one family of spin models and the emergence of treelike geometries in another. I report on experimental demonstrations paving the way toward simulating these spin models, including the first direct imaging of nonlocal spin-exchange dynamics. Finally, I present the first experimental proposals for measuring Out-of-Time-Ordered Correlators to diagnose quantum information scrambling in experimental systems; these proposals have since been realized in the laboratory by several experimental groups. These building blocks lay the groundwork for experimental access to fast scrambling and the controlled production of increasingly complex forms of entanglement, which we expect to continue to play a key role in our understanding of problems arising in fields ranging from quantum information processing to condensed matter to quantum gravity.
Nonverbal cues in avatar-mediated virtual environments
Keywords: Communication.

This research focuses on the individual and joint contributions of two nonverbal channels (i.e., face and body) in avatar mediated-virtual environments. A total of 140 dyads (280 participants) were randomly assigned to communicate with each other via avatar-mediated platforms that varied in their capacity to deliver nonverbal cues (i.e., avatars that displayed both face and body cues, only face cues, only body cues, or avatars that were static). Dyads that were able to see their partner's facial movements being mapped on to their avatars reported higher levels of interpersonal attraction and were able to form more accurate impressions about their partners. Furthermore, dyads that had access to their partner's facial movements described their interaction experiences more positively, although this was only true when they could also see their partner's bodily gestures. Dyads that could only see their partner's bodily movements, but not their facial movements, described their experiences more negatively compared to those who interacted with a static avatar that did not portray any nonverbal cues. Behaviorally, dyads that were able to see their partner's bodily movements moved their bodies more, although this trend was only significant when they were also able to see their partner's facial movements. In contrast, the extent to which dyads exhibited facial movement was not influenced by the visibility of their partner's facial movements or bodily gestures. The current study also found that dyads showed higher levels of bodily and facial nonverbal synchrony when their partner's bodily movements and facial movements were available, respectively. Finally, the present study employed two machining learning algorithms to explore whether nonverbal cues that were automatically tracked during dyadic interactions would be able to predict interpersonal attraction through an inductive process. Results showed that (1) these classifiers could predict high and low interpersonal attraction individuals at an accuracy rate that was approximately 14-17% higher than the majority class baseline and that (2) the main features that predicted interpersonal attraction were related to synchrony of smiling behavior.
A novel chromatin opening element for resisting transgene silencing in mammalian cells
Keywords: Bioengineering.

Long-term stable expression of transgenes in mammalian cells is important in gene therapy, recombinant protein production, genetic reprogramming and mammalian synthetic biology. However, transgenes are susceptible to time-dependent epigenetic silencing, as well as position effect variegation, making reproducible stable expression challenging. To counteract this problem, genetic engineers have discovered and characterized various chromatin insulator sequences that promote consistent long-term expression; however, these elements are also often cumbersome to use due to length and copy requirements, and have varying effect depending on cell type and genetic context. A more recent development in the field was the discovery and validation of a Ubiquitous Chromatin Opening Element (UCOE), a sequence from the human genome, which drastically outperforms traditional chromatin insulators due to its activating features. In order to discover more UCOEs, we developed a bioinformatics algorithm based on the epigenetic features of the published UCOE and screened the resulting candidates to discover a novel UCOE that is shorter in length and more modular. We show that our novel UCOE prevents time-dependent silencing and significantly stabilizes gene expression in a variety of genetic contexts.