VictorJuiz/thesis huggingface dataset:
Applications of atomic layer deposition for next-generation nanoscale devices

Atomic Layer Deposition (ALD) is a thin film deposition technique that has gained prominence in recent years due to its ability to synthesize highly conformal and uniform films, with precise thickness control and for a wide range of materials. This work explores how the unique properties of ALD films can be leveraged through novel nanofabrication processes to enable higher performance devices. First, a comprehensive characterization of the etch rates of 9 oxide ALD films in 20 wet chemicals and vapor etchants is presented, as knowing the films' etch rates and their compatibility with commonly used processing chemicals is crucially important when integrating them into nanofabrication processes. Second, a new process is described that, by taking advantage of ALD films' excellent properties as etch stop layers for vapor releases, allows the simultaneous release of suspended structures of varying sizes and arbitrary shapes with high accuracy. This so-called "sandbox" process can be incorporated into the fabrication of many kinds of devices, and has been successfully employed for aluminum nitride piezoelectric resonators, resulting in a record high figure of merit. Finally, the development of thermal accelerometers featuring ultrathin suspended platinum thermistors with thicknesses down to 8 nm is presented. Using plasma-enhanced ALD of platinum for the first time in a thermal accelerometer enables a 100x reduction in beam cross-section compared to previous work. Plasma treatments and nucleation layer dependencies of ALD platinum are investigated to further enhance material properties. Novel fabrication processes allow large cavity sizes of up to 500 μm depth and 4000 μm length, resulting in unprecedentedly high aspect ratios exceeding 100,000:1, which confer many benefits such as increased heating efficiency and decreased thermal time constants.

Keywords: Mechanical Engineering.
Advisor: Prinz F. B. 
Howe Roger Thomas 
Kenny Thomas William
Applications of convex optimization in metabolic network analysis

Twenty years ago, the first genome-scale metabolic network reconstruction of the cellular metabolism of an organism was published, shortly after the first genome was sequenced. From that time on, the ever-increasing advances in the high-throughput omics technologies have allowed for the comprehensive reconstructions of exponentially growing sizes. However, the vast amount of data can be a two-edged sword which makes many essential tasks computationally intractable. To overcome the demands of systems biology, even while they are outpacing Moore's law, faster computational techniques are needed to enable the current methods to scale up to match the progress of data generation in a prospective manner. In this dissertation, we go over several different areas of systems biology from flux coupling analysis to context-specific reconstruction and propose efficient computational methods for several tasks separately. Then we work towards a more holistic approach and discuss the idea of a canonical metabolic network reduction to reduce the number of reactions for any general task. In analogy to the concept of lossless compression in information theory, we will show that the well-known emergent redundancies of flux distributions are the key concept. Additionally, we will derive the minimum reduced metabolic network and prove a converse that any further reduction loses some information on the elementary modes.

Keywords: Electrical Engineering.
Advisor: Boyd Stephen P. 
Tse David 
Ye Yinyu
Applications of Lagrangian field theory in the computational modeling of beam-wave interactions

Modeling the non-linear interaction between intense charged particle beams and electromagnetic fields in beam-based radiation sources, from klystrons to free electron lasers, has historically been addressed using semi-analytical simulation tools. Through recent advances in manufacturing and materials science, we can now realize structures and interaction topologies which are vastly more complex than in current devices -- unintuitive configurations with the potential to overcome traditional limits in interaction efficiency and output power. These device concepts lie beyond the assumptions of semi-analytical models, however. Their multi-scale nature, spanning time scales from picoseconds to milliseconds, also renders them computationally intractable to model with more general, transient solvers (particle-in-cell codes). To address this issue, we have developed a steady-state solver which applies abstract concepts from Lagrangian mechanics, classical and quantum field theory and differential geometry to the concrete challenge of full-wave electromagnetic finite element analysis. Through this unique field theory perspective, we overcome several open problems in beam-wave modeling, from the interpolation of the current density from particle trajectories (where we demonstrate an 80 fold improvement in accuracy over existing state of the art approaches), to the revival of the traditional nodal finite element framework for the solution of electromagnetic fields. This approach is also computationally efficient, converging to the steady-state solution in less than ten iterations compared to the thousands to billions of time steps required by a transient solver.

Keywords: Electrical Engineering.
Advisor: Tantawi Sami 
Fan Shanhui
Pianetta Piero 
Raubenheimer Tor O.
Applications of metallic nanoparticles for in-situ combustion : delivery and enhanced performance

The advantage of using nanoparticles to influence reaction kinetics in hydrocarbon reservoirs is two-fold: nanoparticles are better catalysts for oxidation reactions because of their large surface-area-to-volume ratio and have increased transportability through porous media because of their small size. In-situ combustion (ISC) is a thermal recovery method used to access light and heavy crude oil deposits by physically and chemically altering the oil in place. Success, among a host of factors, depends on the nature of oxidation and non-oxidative reactions and the combustion fuel. Metal nanocatalysts, specifically, can improve the process by providing a way to alter those critical parameters beneficially. This work explains why and how specific metal nanoparticles enhance heavy-oil ISC and develops a new method for the emplacement of those nanoparticles in porous media. The effects of seven different transition metal nanoparticles on Colombian, Venezuelan, and Mexican crude oil samples were investigated. Experiments were used to measure the change in burning characteristics with additives at two different length scales. At the small-scale, select nanoparticles decrease the apparent activation energy for combustion, change the limiting gateway reaction, make combustion fuel more reactive, increase fuel quality, and alter low-temperature oxidation products. During reactive flow, the improvements as mentioned above are critical to helping sustain combustion when excessive fuel deposition causes premature quenching. For ISC candidates that burn well, increased efficiency leads to greater oil production. Considering these benefits, emplacement of nanoparticles into the hydrocarbon system needs to be handled appropriately. The most critical feature of any transport mechanism is its ability to maximize catalytic surface area; however, due, in large part, to a lack of understanding of the fundamental science governing delivery and emplacement of nanoparticles on or near solid-liquid and liquid-liquid interfaces, this is a nontrivial undertaking. Therefore, a new method is developed in order to achieve the result mentioned above. The mechanism decreases particle interactions with other elements in the reservoir by encapsulating nanoparticles in the dispersed phase of an oil-in-water emulsion. The hydrophilic-lipophilic difference, a semi-empirical formulation, provides the means to calculate the temperature (phase inversion temperature) that the emulsion destabilizes and releases nanocatalysts in the pore space. Direct visualization and injection experiments confirm delivery efficacy and show that the technique delivers a relatively equitable distribution of nanoparticles to the porous medium.

Keywords: Energy Resources Engineering.
Advisor: Kovscek Anthony R. (Anthony Robert) 
Castanier Louis M.
Horne Roland N.
Applying genome editing and genomics for novel cellular tracking and measurement

The three projects comprising this thesis explore and apply genetic diversity to various biological processes. In the first project, I engineer updatable and diverse CRISPR-based sequence barcodes for lineage tracing applications. I demonstrate the potential of such CRISPR-based barcoding methods by illustrating the agreement between the fully known lineage of C. elegans and that obtained using dynamic sequence barcodes, delve into the challenge presented by sequence dropouts through a simulation-based approach, and underscore the technique's promise by establishing its information content. In the second project, I add a new tool to the CRISPR/Cas9 toolbox by exploring the genetic diversity of CRISPR systems and discovering IgnaviCas9, a Cas9 from a hyperthermophilic Ignavibacterium. IgnaviCas9 expands the temperature range at which targeted nucleic acid cleavage is possible, thus speeding the development of new biotechnological techniques. I demonstrate one such application by using IgnaviCas9 to deplete undesired amplicons during the amplification step of library preparation in sequencing workflows. In the final project, I enable the examination of how genetic diversity is created during the processes of sperm development. I apply microfluidic methods to capture and amplify DNA from single sperm cells. I then perform whole genome sequencing to understand selection processes during spermatogenesis.

Keywords: Bioengineering.
Advisor: Quake Stephen Ronald 
Bassik Michael 
Qi Lei (Professor of Bioengineering)
Arachne : improving latency and efficiency through core aware thread management

Arachne is a new user-level implementation of threads that provides both low latency and high throughput for applications with extremely short-lived threads (only a few microseconds). Arachne is core-aware: each application determines how many cores it needs, based on its load; it always knows exactly which cores it has been allocated, and it controls the placement of its threads on those cores. A central core arbiter allocates cores between applications. Adding Arachne to memcached improved SLO-compliant throughput by 37%, reduced tail latency by more than 10x, and allowed memcached to coexist with background applications with almost no performance impact. Adding Arachne to the RAMCloud storage system increased its write throughput by more than 2.5x. The Arachne threading library is optimized to minimize cache misses; it can initiate a new user thread on a different core (with load balancing) in 320 ns. Arachne is implemented entirely at user level on Linux; no kernel modifications are needed.

Advisor: Ousterhout John K. 
Bailis Peter 
Zaharia Matei
An archaeology of europeanization : transnationalism, heritage, and communities in post-communist Albania

Albania, a European Union (EU) candidate country since 2014, has struggled with a turbulent post-communist period (1991-present) defined by civil unrest, political corruption, a struggling economy, and extremes in socio-economic inequalities (Elbasani & Šabić 2018; Abrahams 2015; Vickers & Pettifer 2013). The built environment of the entire Albanian landscape has held no exception to such social and political mayhem. Albania's heritage landscape in particular has been subject to diverging episodes of destruction and material manipulation, each dependent on current political needs and visions to enforce a national narrative of prosperity and democratic success. This dissertation is particularly concerned with Albania's process of Europeanization and cultural heritage's role within it. In this dissertation I argue that the Albanian government has been negotiating its cultural heritage, from its archaeological sites to its memorials and museums, in a dramatic and tumultuous process of heritage erasure, promulgation, and reconfiguration; yet, it is doing so not only as part of a need to create a new Albanian narrative, but as a response to growing international pressures to shape its socio-political system into one that is democratic to Western standards, economically thriving, and socially stable with tight political borders that protect Europe from a growing immigration crisis. Yet, as Albania's heritage landscape is altered, the communities that are connected to that landscape are impinged upon as well. While this dissertation explores how the Albanian government manages its material past within its ever-present Europeanization process, it also investigates the social consequences of such a heritage negotiation at the whim of international agendas and global tensions. Examining diverse types of heritage, including museums, memorials, religious buildings, and archaeological sites, as well as investigating heritage from several periods of Albania's past, be it the remains of its Roman or communist periods, this research underscores Albania's struggle with managing a past that has been largely defined by foreign occupations. Based upon more than 24 months of ethnographic fieldwork, my research shows that the valorization of cultural heritage in Albania comes almost exclusively from the outside, from international agencies and nation-states that the Albanian government holds in its highest esteem and may even seek to emulate. Ultimately, this dissertation argues that in order for Albania to shed a past of foreign dependencies, Albania will need to own its past.

Keywords: Anthropology.
Advisor: Meskell Lynn 
Hodder Ian 
Hodges Richard 
Seetah Krish
Architectural Energetics for Byzantine Chancel Screen Construction: The Case of the Marzamemi II "Church Wreck"

The present work introduces the first architectural energetics analysis of a Byzantine chancel screen from the Marzamemi II shipwreck. Emerging technologies in digital modeling present new opportunities for research in architecture, archaeology, and classical studies. The burgeoning technological resources of today's world, coupled with new 3D digital modeling programs, have the potential to ease the research of archaeological sites and artifacts. For this thesis I digitally recreated an “ideal” version of a Byzantine chancel screen (a religious architectural artifact) from the fragments recovered at the Marzamemi II shipwreck. This reconstruction represents the state of the artifact when it was loaded onto the ship after leaving the quarry approximately 1500 years ago.
Over the course of the 2018 field season, I took measurements, created sketches, and used digital Artec models of conserved and recently recovered architectural artifacts to begin re-creating their original shape prior to the wreck of the ship. These calculations can help the researchers at the Marzamemi Maritime Heritage Project to better understand the possibility of standardization within the recovered architectural elements. Following the 2018 field season, I used 3D models of the recovered chancel screen fragments to digitally produce the “ideal” chancel screen. During this time, I also explored the architectural energetics of the chancel screen in regards to religious symbolism, Byzantine economics, and labor estimates for the carving of one screen.

Keywords:  Department of Civil and Environmental Engineering
chancel screens
Marzamemi
architectural energetics
Stanford University
School of Engineering
Byzantine empire
Architectural Design
religious architecture
Thesis
Advisor: Barton John
Armenia across borders : heritage revitalization from the Soviet era to the present

Armenia, a small landlocked country in the South Caucasus, is densely packed with an estimated 33,000 cultural heritage sites ranging from a prehistoric wine production center to hundreds of medieval churches. Since the beginning of the Armenian Soviet Socialist Republic (1922-1991), these sites, and in particular, medieval religious complexes, have been the target of heritage revitalization projects meant to not only return heritage to a previous state or to prevent further decay but also to make heritage usable, in a sense, to revive heritage. This dissertation ethnographically explores heritage revitalization projects from the Soviet era to the present. Drawing upon extensive fieldwork in Yerevan and the villages of Areni and Tatev, this dissertation reveals how for the past eighty years, heritage mediators have enacted a multitude of heritage revitalization projects at sites with little to no contestation, promulgating seemingly similar identity-building narratives while also pursuing alternative social, political, and economic agendas. Ultimately, this dissertation, while focusing on the history of heritage revitalization programs in a South Caucasus nation, broadens anthropological research in the former Soviet Union, and encourages a reconceptualization of what happens to heritage in transitional phases of statehood. This dissertation reveals that in Armenia, heritage can be simultaneously used for dissonant purposes without causing contestations or frictions.

Keywords: Anthropology.
Advisor: Meskell Lynn 
Hodder Ian 
Watenpaugh Heghnar Zeitlian
Arrest and Identity in East Baton Rouge Parish, Louisiana

For her capstone project, Elise Gonzalez complied research data comparing arrest trends and prison demography in East Baton Rouge (EBR) Parish to their national correlates and developed a web application that makes this information more accessible to the public. Her research sought to explain the level of representation of various demographic groups in the arrested population in EBR Parish, the likelihood of arrest for people with various identities and combinations of identities in EBR Parish, all the while comparing these rates to national correlates. Utilizing census data and local and national arrest records, Elise discussed ways EBR Parish mirrors the United States correctional system, generally, in its overrepresentation and incarceration centered around young men of color. The web application developed serves as a public education tool showcasing the above findings and is meant to shine a light on the impact of identity on arrest probability, as well as increase public awareness of the conditions inside the EBR Parish Prison.

Keywords: Mass incarceration
Statistics
Louisiana > East Baton Rouge Parish
Text
Report
Thesis
Assessing the Role of Aurora A Kinase in Prostate Cancer Progression

Neuroendocrine prostate cancer (NEPC) is an aggressive, untreatable form of prostate cancer that emerges after multiple rounds of conventional prostate cancer therapies. Unlike most prostate cancers, NEPCs share histological features with lung small cell carcinomas, express markers of neuroendocrine cells, and are resistant to the hormone depletion therapies that are commonly used to treat prostate cancer. Aurora A Kinase (AURKA), an oncogenic protein that regulates the G2/M checkpoint, centrosome maturation, and neurite extension, is specifically upregulated in NEPC compared to normal prostate cancer, and AURKA expression in prostate cancer is closely correlated with worse clinical outcomes; however, this protein's role, if any, in NEPC has not yet been defined. We show that AURKA plays a functional role in prostate cancer progression using lentiviral integration techniques to ectopically express AURKA in non-neuroendocrine prostate cancer cell lines. In vitro, AURKA upregulation leads to the development of properties of NEPC, including proliferation and survival in low-androgen conditions. In addition, we found that low androgen conditions cause post-transcriptional downregulation of AURKA. These experiments reveal that AURKA is a potential mediator for resistance to androgen deprivation therapy in advanced prostate cancers, and is a potential druggable target for new advanced prostate cancer therapies.

Keywords:  Department of Biology
Aurora A Kinase
Prostate Cancer
Molecular Biology
Biology
Thesis
Advisor: Stoyanova Tanya
Skotheim Jan
Pitteri Sharon
Assessing the role of zinc in Parkin activity

Neurodegeneration, the progressive loss of structure and function of neurons in the human brain, results in several disorders such as Alzheimer disease, Parkinson disease, amyotropic lateral sclerosis, and Huntington disease. Among older adults, Parkinson disorder (PD) ranks as the second most common age-related neurodegenerative disorder. PD is caused by the loss of dopaminergic neurons, key cells in the motor system. The four main symptoms of PD are tremors, bradykinesia, rigidity, and impaired balance. To this date there are only medications that target specific symptoms -- none target the underlying pathophysiology. Most PD cases, ~90%, are sporadic with a typical age of onset at 60. However, certain forms of PD have been linked to genetic causes. One of the most studied familial forms of PD is autosomal recessive juvenile parkinsonism (ARJP). Approximately 50% of all forms of ARJP are linked to the mutations of the PARK2 gene, which produces the protein parkin. Parkin is an E3 ligase, which plays an important role in targeting protein substrates for degradation or modification through ubiquitin tagging. Parkin belongs to a class of RING (Really Interesting New Gene) proteins designated in the RBR (RING-between-RING) family of E3 ligases. RING domains are rich in cysteines and have a strong affinity for binding zinc ions. Recent studies of the RING domains in parkin suggest that binding of zinc may play an important role in maintaining stability and solubility, which in turn may regulate protein function. The goal of my project is to determine a mechanism of Parkin activity independent of PINK1. My results suggest that autoubiquitination of Parkin is affected by zinc and that regulation occurs within the picomolar range of free zinc concentrations in PINK1 independent assays. Additionally, E1-ubiquitin conjugation is affected by zinc and the inhibition of conjugation occurs in the nanomolar zinc levels. As an initial test of this hypothesis I examined Parkin's effects on mitophagy when the intracellular zinc concentration was changed or by mutation of a zinc binding site in Parkin. External zinc was applied in in vitro assays with a chelator to regulate levels. Using site directed mutagenesis I tested whether known zinc sites were required for the zinc mediated inhibition of Parkin.

Advisor: Wang Xinnan
Clandinin Thomas R. (Thomas Robert)
Garner Craig 
Reimer Richard J. 
Weis William I.