UC Davis

Understanding the fate and transport of nitrogen through the vadose zone is vital to reduce nitrate leaching, protecting groundwater quality, and enhancing resource use efficiency. Currently, there is limited data on the continuous monitoring of nitrate transport through the deep vadose zone. The lack of high-quality data makes it difficult to evaluate the effectiveness of conservation practices aimed at reducing nitrate leaching. The vadose-zone monitoring system (VMS) serves as an innovative technology for near real-time monitoring of nitrate and other contaminants as they travel through the shallow and deep vadose zone to groundwater. The objective of this study was to evaluate the performance of the VMS technology at three sites using bromide (Br-) as a tracer and the unsaturated flow model HYDRUS 1D to understand underlying vadose zone water flow and solute transport processes. Site 1 was a field crop site near Esparto, CA, with a heavy Capay-clay soil and a groundwater depth of approximately 10 m. Site 2 was an almond orchard near Modesto, CA, with a moderately homogenous sandy loam in the top 2 m and a sandy clay loam down to 6 m and a water table at approximately 8 m. Site 3 was a citrus orchard near Orange Cove, CA, with a sandy loam soil at the shallow depths (0-2 meters) followed by sandy clay loam down to 7 m and a groundwater depth of approximately 25 m. The VMS was installed at all sites to collect soil pore water samples at approximately 1 m intervals to about 7 m depth. To test the system performance, approximately 380 L of a 500 ppm Br- solution was applied as a conservative tracer at the three sites. The applied tracer was either percolated by rain, irrigation, or a combination of the two. The site HYDRUS models demonstrated a complete breakthrough of Br- at each vadose sampling port depth. Measured pore-water from the VMS exhibited similar solute breakthroughs with varying time and concentrations. The bromide tracer results confirm that the VMS is capable of monitoring flow and transport processes in the deep vadose zone.

Little is known about the proteins involved in gamete plasma membrane interaction during mammalian fertilization, and even less is known about the molecules involved in livestock species, such as the pig. Affinity chromatography of porcine sperm and oocyte plasma membrane proteins followed by mass spectrometry to identify eluted proteins detected apolipoprotein E (APOE) and a 167 amino acid Jacalin-type lectin domain-containing protein (A0A287AVU8) as potential proteins involved in this interaction (Vazquez Morales, 2023). To further explore the potential involvement of porcine APOE and A0A287AVU8 in fertilization, this study utilized an antibody inhibition technique. APOE antibodies were incubated with oocytes and A0A287AVU8 antibody were incubated with sperm for 10 minutes each prior to gamete co-incubation with the final dilution of antibody during sperm-oocyte interaction being 5 ng/µl. Each of the three replicates contained approximately 50 oocytes per treatment. A reduced ratio of fertilization (P < 0.05) was observed following the inclusion of the first APOE antibody (amino acid peptide residues 101-200) compared to the control (no antibodies). A trend toward reduced fertilization (P = 0.10) was observed with a second APOE antibody (amino acid peptide residues 151-250). Isotype control rabbit IgG did not alter fertilization. No effect on fertilization ratio was observed following incubation with rabbit anti-A0A287AVU8 IgG (P > 0.05), compared to the control (rabbit IgG), or sodium azide-containing rabbit IgG. These results suggest that APOE on the oocyte surface may contribute to effective sperm-oocyte interaction during porcine fertilization. This might be a specific receptor-ligand interaction or a more general “sticky” interaction involving APOE. Alexa Fluor 594-conjugated secondary antibody successfully localized APOE on the plasma membrane of the oocyte, and A0A287AVU8 on the sperm’s acrosome and tail, intensively staining the extremity of the latter. These findings contribute to the overall understanding of porcine fertilization.

A fabrication process for a p-i-n germanium photodiode design was developed for epitaxiallygrown germanium wafers. Devices fabricated were tested for DC large-signal I-V characteristics and AC temporal responses. The germanium wafers were in-situ doped with the p-i-nstructure to minimize dark current generated by lattice defects. With higher atomic mass, germanium provides stronger stopping power for high-energy photons in the hard X-ray regime above 20 keV. The fabrication process developed was able to achieve 86.7% yield with a 2-day lead time. The p-i-n devices fabricated were measured to have an average turn-on voltage of 1.6 V, an average dark current of 3.9 mA with ambient illumination. The average breakdown voltage was measured to be -11.85 V. At -40 V applied bias, the fabricated germanium diodes were able to generate a maximum signal level 229% of that generated by commercially available AXUV silicon-based detectors. The average 87% rise time of fabricated germanium devices was 150 nanoseconds and the average 13% fall time was 128 nanoseconds. The germanium devices achieved an average frametime of 278 ns. The signal-to-noise ratio measured was 20.9 with ≪ 10% illuminated area at -40 V bias. In general, the fabrication process was successful in fabricating germanium p-i-n photodidoes with satisfactory temporal and DC characteristics. The devices were also able to demonstrate the superior performance expected from germanium-based devices.

Previous studies in second language teaching have called attention to the importance and benefits of including reading, especially graded readers (i.e., books adapted to the proficiency level of the students), in the L2 curriculum (Martinez, 2017; Rodrigo, 2018). On one hand, previous scholars have found the following benefits from graded readers: (1) an increase in reading comprehension (Beglar et al. 2012; Suk, 2016), (2) a reduction of anxiety towards reading (Martinez, 2017; Rodrigo, 2011), (3) a fostering of cultural knowledge (Hill 2013), and (4) an increase in vocabulary learning (Horst, 2009; Suk, 2016), to name a few. On the other hand, most of the research on graded readers has been conducted in English as a second language classes and little is known about the experience of L2 Spanish elementary proficiency learners at university settings (Nation & Waring, 2020). To fill this gap, this dissertation provides information on the implementation of a Reading Program using graded readers in an ongoing first-year Spanish program at the university level. Two different studies have been conducted. The first one explores the implementation of the Reading Program, the creation of in-house graded readers and present students' reactions and opinions on the reading program in general and the graded readers in particular. Through focus groups before the implementation of the reading program and a student questionnaire at the end, this study highlights the importance of matching the proficiency level of the graded readers with the students’ level and the importance of creating stories with familiar settings and relatable protagonists to increase students’ enjoyment. The second study focuses on vocabulary acquisition and the effects of post-reading fill-in-the-blanks activities and evaluates the reliability of the Technique Feature Analysis (TFA) framework on measuring the effectiveness of these activities. 260 students participated in this

study and were divided into 4 groups (i.e., a control group and three experimental group), they have to complete a vocabulary test before and at the end of the Reading Program. Results in this study emphasized the importance of complementing reading with word focused activities in order to increase vocabulary acquisition, highlighted the fill-in-the-blanks with the translation of the target words in English as the most powerful one, and advocate for the use of the TFA framework in order to choose the most appropriate activities.

We analyze geometric aspects of clustering procedures based on low-dimensional embeddings. In particular, we are interested in understanding the occurrence of the so-called orthogonal cone structure (OCS) that can be observed empirically in various low-dimensional embeddings, including kernel PCA, spectral clustering, Isomap, and clustering based on the Hodge Laplacian. Inspired by recent work on the OCS based on graph Laplacians, we study OCS in the context of weighted Laplacian and kernel PCA. This involves the development of a notion of a well-separated mixture model and other characteristics of the methodology. These characteristics are then used to quantify the OCS. We illustrate this for weighted Laplacian and kernel PCA in both the population setting and the sample setting.

A century of concerted effort brought new levels of physical understanding and engineering capability to quantum physics that promise major advances in fundamental theory and technology applications. A case in point, quantum computation has the potential to become one of humanity’s most innovative and disruptive technologies. Advances there are pushing physics to probe quantum phenomena in systems that are increasingly complex, and in more detailed ways than ever before. It is now clearer than ever that further progress will require constructively working with noise, error, and environmental interactions. A key part of this is to understand the properties of time series of quantum states emitted by a quantum system—the main subject of this work.

This dissertation sets out to study time-series of quantum states emitted by a quantum system. The fundamental objects in this are Quantum-State Stochastic Processes (QSSPs)—sequences of stochastically generated quantum states. In particular, the focus is on the interaction of a classical observer—via quantum measurement—with these objects, and the informational and statistical characterization of the classical stochastic processes that result from that interaction.

As a classical observer uses a measurement protocol to observe a Quantum-State Stochastic Process, the outcomes form a time series. Individual time series are realizations of a stochastic process over the measurements’ classical outcomes. This dissertation studies the dependence of that stochastic process of measurement outcomes on both the QSSP and the measurement protocol. In particular, it demonstrates that regardless of the measurement protocol—and for several specific protocols explicitly discussed in this work—the output classical stochastic process is generically highly complex in two specific senses: (i) it is generically unpredictable, to a degree that depends on the measurement choice, and (ii) achieving optimal prediction for these stochastic processes will generically require an infinite amount of memory.

Inspired by the study of classical stochastic processes, this dissertation uses and adapts the theory of computational mechanics and hidden Markov models to understand and categorize these measured stochastic processes. Specifically, we identify the mechanism underlying their complicatednessas generator nonunifilarity—the degeneracy between sequences of generator states and sequences v of measurement outcomes. This makes it possible to quantitatively explore the influence that measurement choice has on a quantum process’ degrees of randomness and structural complexity using recently introduced methods from ergodic theory. This dissertation provides the explicit metrics and associated algorithms for that quantification. It demonstrates that under certain conditions, dependence of these metrics on the choice of measurements is smooth. In addition, these metrics are used to design informationally-optimal measurements of time-series of quantum states. Most approaches to quantum stochastic dynamics focus on the evolution of the quantum state of a particular system—for example, quantum collision models. In contrast, the results here lay the groundwork for the study of time series of quantum states emitted by a quantum system, which have so far been largely unexplored. Additionally, they provide a first description of what classical interaction with these time series yields.

The work contained within this dissertation aims to investigate the role and mechanisms of CaV1.2 and KV2.1 ion channel cluster formation in the membrane of arterial smooth muscle cells. Clustering of ion channels selective for these ions have long been a commonly observed phenotype, yet the mechanisms of cluster formation are still unknown. Overall, this dissertation provides a model by which ion channel clusters form stochastically via a self-assembly process in the membrane based on three mechanistic probabilities: nucleation, growth, and removal. Additionally, we focused on clustering and interactions of two key ion channels, KV2.1 and CaV1.2, in smooth muscle physiology selective for potassium (K+) and calcium (Ca2+) respectively. The opening of these channels play key roles in arterial physiology, counterbalancing each other to affect arterial diameter. The key findings from this work help to elucidate the mechanisms involved in the trafficking of ion channels, maintenance of clusters in the plasma membrane and provide potential reasoning for sex-based differences in smooth muscle physiology. Using a multiscale experimental and computational approach, we describe a key interaction between CaV1.2 and KV2.1 in arterial smooth muscle. This model proposes that KV2.1 clustering state is not a determinate of channel conduction in mesenteric smooth muscle. Additionally, KV2.1 macro-clusters serve as a sex-specific site for increased CaV1.2 clustering and decreasing KV2.1 macro-clustering decreases CaV1.2 channel clustering. This sex-based interaction ultimately plays a key role in Ca2+ dynamics and smooth muscle physiology.

The allylation reaction is an ambiphilic reaction depending on the nature of the allylic substituent. Depending on the allylic substituent the allyl can either be nucleophilic or electrophilic. This dissertation describes the nucleophilic crotylation of a-chiral alkoxy imines in high diastereoselectivity and the electrophilic enantioselective allylation of a prochiral heterocyclic sulfonimidamide in high enantioselectivity and yield. Chapter 1 describes the Lewis acid promoted addition of prochiral E and Z allyl nucleophiles to chiral a-alkoxy N-tosyl imines is described. Alkene geometry is selectively transferred to the newly formed carbon-carbon bond, resulting in stereochemical control of carbons 2 and 3, resulting in 2-alkoxy-3-N-tosyl-4-alkyl-5-hexene products. A computational analysis to elucidate the high selectivity is also presented. This methodology was employed in the synthesis of two naturally occurring isomers of clausenamide. Chapter 2 describes the enantioselective allylation of prochiral sulfonimidamides via a Tsuji-Trost Asymmetric Allylation reaction. Sulfonimidamides undergo prototropic tautomerization in solution. In the case where both nitrogen substituents of a disubstituted sulfonimidamide are the same, the two tautomers are also enantiomers, allowing deprotonation to generate a prochiral anion. Herein we report the first transition metal catalyzed approach to the desymmetrization of sulfonimidamides relying on commercially available palladium catalysts and ligands. The reaction leads to functionalized, enantioenriched products in high yields.

Abstract This thesis is a translation of The Dream of Tibet (Ro’ya-ye Tabbat) by Fariba Vafi (b.1963/ Tabriz, Iran), a post-revolutionary Iranian novelist. Written in forty-five chapters and narrated in the second person, The Dream of Tibet is part of Vafi’s four-decade writing career and is reflective of the so-called adabiyat-e apartemani or apartment literature that arose in the 1990s in Iran. The novel depicts complicated romantic stories and reflects trends among post-revolutionary Iranian women writers, showcasing themes such as infidelity in relationships, the weakening of the institution of marriage, and disenchantment with the traditional roles of women. In this story, the women characters emerge as the survivors in the new social order, seeking independence and expressing their displeasure against society. Key Words: Fariba Vafi, The Dream of Tibet, Translation, adabiyat-e apartemani

Natural gas demand response (GDR) is an emerging technology that has garnered significant attention in recent years due to its potential as a tool for grid management. Despite the growing interest in GDR, a careful examination of the literature suggests that there is still much to learn about the full potential of this technology, particularly with regards to demand-side management which is the response from the customer or user side. In this thesis, we aim to address this critical research gap by proposing various actions and strategies to optimize the utilization of natural gas during Gas Demand Response events, with the goal of encouraging customers to participate in these programs.This study focuses specifically on the use of multi-source residential heating, with natural gas serving as the primary source. To calculate consumption during periods of high demand, we utilized a simulation model using Open Studio and Energy Plus software, which is funded by the Department of Energy and managed by the National Renewable Energy Laboratory. The simulation model enabled the determination of the heating energy requirements for a typical residential apartment over the course of an entire year, with the ability to break down the demand for each hour based on location and weather conditions. The generated energy requirement was utilized by an optimization tool to decide which source of energy the customer should use based on different incentive and pricing programs. Both the model and the optimization tools allowed us to test different possible solutions and modifications to quantify the energy savings, particularly during Gas Demand Response events. Through this research, we seek to contribute to the growing body of literature on GDR and advance the understanding of demand response from the demand side. By proposing various strategies to optimize natural gas utilization during Gas Demand Response events, we hope to encourage greater participation in demand response programs and promote the adoption of GDR as a reliable and sustainable solution to grid management challenges. The simulation model represents a valuable tool for testing proposed solutions and modifications, and our findings can inform the development of effective demand response strategies that enhance the overall potential of GDR as a tool for grid management.