VictorJuiz/thesis huggingface dataset:
New chemistries and applications in molecular layer deposition

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.

Keywords: Chemistry.
Advisor: Bent Stacey 
Chidsey Christopher E. D. (Christopher Elisha Dunn)
Waymouth Robert M.
New directions in uncertainty quantification using task-based programming

Many problems of interest in modern computational science and engineering involve multiple interacting physical processes. To properly simulate such problems computational scientists must combine multiple physics solvers in a tightly-coupled environment. Mainstream low-level HPC programming frameworks are a poor match for the complexities of such applications, especially given the need to adapt to rapidly-changing hardware platforms, that are becoming increasingly heterogeneous. Moreover, the predictive power of such complex applications is hindered by their large number of uncertain inputs, making Uncertainty Quantification (UQ) a critical feature of any multi-physics solver. However, the current practice of UQ involves a high degree of manual effort, and current tools do not take full advantage of the available parallelism. We believe that Task-Based Programming, a distributed programming approach that has gained popularity in recent years, can significantly improve multiple aspects of building multi-physics applications. Task-based systems, with their higher level of abstraction, are simpler to program than traditional HPC frameworks like MPI, and the final code is easier to tune, port and maintain. Additionally, such systems have the potential to significantly improve the time required to perform UQ studies, not just by improving how efficiently ensembles can be executed, but also by automating many aspects of UQ that are currently performed by hand, and possibly even enable new UQ algorithms. In this dissertation we report on our experience developing Soleil-X, a multi-physics solver supporting coupled simulations of fluid, particles and radiation, in the Legion task-based programming system. We discuss how to design and optimize such an application, and evaluate our solver's scalability on Sierra, a leadership-class supercomputer. We implement UQ support for Soleil-X and use it to prototype a framework for automatically constructing an optimal low-fidelity model for use in UQ studies. We apply this framework on a medium-size simulation and compare its performance against human experts. Finally, we discuss the problem of optimizing the execution of UQ ensembles

Advisor: Aiken Alexander
Hanrahan P. M. (Patrick Matthew) 
Ré Christopher
The new Japanese love novel

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.

Keywords: East Asian Languages and Cultures.
Advisor: Reichert Jim (James Robert) 
Levy Indra A. 
Matsumoto Yoshiko
A new model for the structure and composition of the inversin compartment

Primary cilia in many cell types contain a peri-axonemal sub-compartment called the inversin compartment. Four proteins have been found to assemble within the inversin compartment: INVS, ANKS6, NEK8, and NPHP3. The function of the inversin compartment is unknown but appears to be critical for normal development including left-right asymmetry and renal tissue homeostasis. Here we combine super-resolution imaging of human RPE1 cells, a classic model for studying primary cilia in vitro, with a genetic dissection of the protein-protein relationships important for compartment assembly to develop a new structural model. We propose that INVS is the core structural determinant of a compartment composed of novel fibril-like substructures which we identify here by 3D single-molecule super-resolution imaging. We find that NEK8 and ANKS6 depend on INVS for localization to the compartment, but NEK8-ANKS6 density within the compartment is intrinsically regulated by NEK8. Together NEK8 and ANKS6 are required downstream of INVS to localize and concentrate NPHP3 within the compartment. These results provide a more detailed structure for the inversin compartment and introduce a new example of a membrane-less compartment organized by protein-protein interactions

Advisor: Jackson Peter K. (Peter Kent)
Cimprich Karlene
Graves Edward (Edward Elliot)
Meyer Tobias
Nonlocal light-mediated interactions for fast scrambling

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.

Keywords: Physics.
Advisor: Schleier-Smith Monika
Hayden Patrick
Lev Benjamin L.
Nonverbal cues in avatar-mediated virtual environments

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.

Keywords: Communication.
Advisor: Bailenson Jeremy 
Hancock Jeff 
Reeves Byron
Zaki Jamil
A novel chromatin opening element for resisting transgene silencing in mammalian cells

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.

Keywords: Bioengineering.
Advisor: Smolke Christina D. 
Bintu Lacramioara 
Kay Mark Allan
Nuclear architecture dynamics in tadpole tail regeneration

Mammals possess very limited regeneration capabilities, where the few examples of scarless healing tend to be restricted to early development. In light of this, it is of great interest to study animals that can faithfully regrow complete appendages, and uncover the biological properties that facilitate regeneration. Xenopus tropicalis is an excellent vertebrate model of regeneration, as tadpoles rapidly regenerate amputated tails, a process that has an interesting developmental history that may be widely informative as to why mammals selectively heal through scarring as they age. Though we have some understanding of what processes are required for tail regeneration, we have yet to systematically chronicle the molecular and regulatory events that must set up an apparently coordinated response. In this dissertation, I address two primary questions in the field of regeneration—what molecular events occur in the first 24 hours to set up a potent regenerative bud, and how is this process regulated? In Chapter 2, I chronicle the transcriptional history of tadpole tail regeneration, focusing primarily within the first 24 hours post amputation. In Chapter 3, I describe a novel nuclear morphology I identified in the tadpole tail, detail how nuclei change shape as an early regeneration response, and investigate the relationship between nuclear shape and chromatin state. Finally, in Chapter 4, I address several future directions with respect to this thesis.

Keywords: genetics) degree supervisor.
Genetics.
Advisor: Bergmann Dominique 
Kundaje Anshul
Villeneuve Anne
Numerical simulation and design of multifunctional structural batteries

Multifunctional materials have been widely used in electrical applications because it has been demonstrated that high-strength composites can be integrated with active live battery material. This allows high strength and high energy density storage structures that can meet the transportation requirements on mobility and energy density. However, the design of multifunctional material requires fundamental understanding of the mechanical behavior of the integrated structural battery systems under various loading and environmental conditions. Characterization of this new class of multifunctional material becomes challenging without an adequate simulation model to guide the tests and to validate the results. The primary objective of this investigation is to develop the mechanical simulation and design of multifunctional battery systems, in particular Multifunctional Energy Storage Composites (MESC). It consists of multiple thin battery layers, polymer reinforcements, and carbon fiber composites. The combination of them poses significant challenges in simulation and modeling. To tackle these issues, homogenization techniques were adopted to characterize the multi-layer structure of the battery material with physics-based constitutive equations. Non-linear deformation theories are used to handle the interface between the battery layers. Second, mechanical and failure modes among battery materials, polymer reinforcements and composite-polymer interfaces were characterized by developing appropriate models and experiments. The numerical model of MESC has been implemented in a commercial finite element code. A comparison of the structural response and the failure modes between numerical simulation results and experimental test data will be presented. The results of the study have demonstrated that the prediction of elastic and damage responses of MESC at various loading conditions agree with the experimental results. With appropriate material property parameters determined from model calibration, this multi-physics model can be used as a necessary tool to understand and to govern the design of MESC for many applications.

Keywords: Aeronautics and Astronautics.
Advisor: Chang Fu-Kuo 
Hong Guosong 
Senesky Debbie
Nutrition for national defense : American food science in World War II and the Cold War

"Nutrition for National Defense: American Food Science in World War II and the Cold War" tells the story of how home economists, doctors, food technologists, military strategists, and corporate researchers linked the emerging science of nutrition to the needs of a country at war. In the late 1930's, nutrition experts offered tools to identify and solve new nutrition problems. The still-young discipline of nutrition was catapulted onto the national stage during World War II, when both German and American experts declared that the fate of their nations hinged on the vitamin content of their bread. In the fraught context of the Cold War, the American government sponsored nutrition research both to fashion soldiers' bodies to the needs of war and to direct international politics. Throughout both conflicts, American nutritionists promised that better eating would form the foundation of a strong military, a strong nation, and a strong, democratic world. Nutrition also gave the government a new tool with which to see, assess, and hierarchize citizens. Because hunger anywhere was considered a threat to the nation, the link between nutrition and national defense changed assumptions about the government's responsibility to keep people nourished. The potential malnourishment of different groups—soldiers, war workers, white middle-class consumers, and poor people in the Third World and at home—elicited different responses from the government, from gentle to coercive. Nutrition became a site of conflict and contestation around the rights and privileges of citizens and the duties of the state.

Keywords: History.
Advisor: Schiebinger Londa L. 
Burns Jennifer
Proctor Robert
observ - getting the news, first

Observ is an online application designed for local journalists, to help them find public records that are relevant to their beat. With observ, the user can research a database of public records of local municipalities and subscribe to a query of their liking. They will then be notified every hour, day or week if there are new documents in the database that match their query.

Keywords:  Department of Communication
observ
Department of Communication
Stanford
MA Journalism
programming
Stanford Journalism School
Journalism
public records
local journalism
Thesis
Advisor: Tumgoren Serdar
Zacharia Janine