UC Merced

Computational combustion plays a major role in engineering applications. However, solving the large systems of differential equations that model combustive processes is challenging. One of the major computational difficulties with the numerical modeling of combustion lies in the widely varying time scales present in the model equations that describe chemical interactions of species with the fluid and thermodynamic transport phenomena. The resulting dramatic stiffness ofthe equations demands the development of more efficient temporal integrators to enable efficient and accurate combustion simulation.

Traditionally, the stiffness of computational combustion models has been addressed using implicit methods. However, the performance of the implicit schemes depends highly on the availability of an efficient preconditioner to alleviate stiffness constraints. Additionally, due to the complexity of the coupling between chemistry, fluid, and transport phenomena, splitting is often used to simplify the time integration of the model equations. Splitting, in turn, reduces the accuracy of theapproximation. While constructing a preconditioner for a portion of the source terms, such as chemical reactions, is feasible, this task becomes more complicated if one considers the full source term of the equations.

Exponential integrators have recently emerged as an efficient alternative to implicit methods for solving large-scale stiff systems, particularly when no effective preconditioner is available. In this thesis, we explore whether exponential methods can be used for combustion simulations and study the computational advantages of such schemes.

We first explore how to tackle the stiff nature of chemical kinetics in a model that forgoes transport phenomena to isolate the chemical kinetics terms and forms the core of various more complex combustion models. A novel time adaptive exponential integrator is presented and then applied to this zero-dimensional (Zero-D) combustion problem. We demonstrate that the new method can perform comparably to well-established implicit-Krylov time integration methods. We study the performance of the exponential integration methods and demonstrate how theyare affected by the spectrum of the problem.

We then extend the chemical kinetics core to include transport phenomena and develop an exponential integration-based numerical approach to the propagating flame front model in one dimension. In addition to the embedded homogeneousreactor problem, advection and diffusion terms are added, and continuity is considered, which generates a highly coupled system of PDEs. In these problems, operator splitting is typically used to separate the stiff chemical reaction source terms from the much slower transport phenomena. Effectively, this reduces the equations to a Zero-D problem and a transport problem, which needs to be solved at each time step. While effective, this introduces unfavorable splitting errors; we demonstrate that this split can be avoided when using an exponential time integration scheme. We study the performance of the new exponential integration approach for the model using several different chemical mechanisms and compare the performance of the new integrators to the state-of-the-art NGA code, which uses implicit methods.

Our computational models and numerical experiments indicate that exponential methods offer a promising approach to modeling combustion and highlight directions for further studies that can help to develop more efficient time integra-tors for computational combustion problems.

Decarbonization roadmaps have been accepted among common strategies for mitigating greenhouse gas emissions. However, these plans tend not to employ any detailed environmental evaluation, particularly life cycle assessment, in their creation. The consequence of omitting LCA is that plans can only measure the impacts during operation and thus overlook the other sections' impacts; therefore, the climate change mitigation accomplishment that was set for the plan is unattainable from the beginning. LCA input data should be performed on a wide range of data, such as geospatial, engineering, and chemical data. For decarbonization roadmaps that are planned for the future, the data should also be projected, which raises the level of uncertainty in input data. This dissertation introduces and demonstrates approaches for overcoming challenges in implementing LCA for the energy transition in 4 chapters. First, a methodological framework for conducting geospatial LCA to manage uncertainty in emerging energy technology LCAs is introduced. Next, the climate change impacts are calculated for a piezoelectric energy harvesting generator as an emerging technology that includes both uncertainty and variability parameters. The third study measures the impacts of energy system processes that were not included in the most recent state decarbonization plan for California. California's decarbonization plan did not account 378.19 million metric tons (MMT) of CO2eq of greenhouse emissions that will be released on a life cycle basis if the plan is implemented. Lastly, the global warming potential of thousands of natural gas well pads across New Mexico were determined, focusing on direct land use change (DLUC) impacts such as losses in organic carbon in plants, soil organic carbon, and cuts in net primary productivity along with the effects of changes in surface albedo on global warming potential of well pads. The results show that greenhouse gas emissions resulting from DLUC may contribute up to 25 % of total emissions in constructing some well pads, an impact that has been ignored in many studies until now. Overall, all the outcomes of these studies demonstrate that conducting advanced geospatial LCA and proper interpretation of uncertainties in the system is necessary to genuinely achieve the decarbonization plans' goals.

To address growing rental costs and a lack of affordable housing in metropolitan areas across the United States, city governments are partnering with affordable housing developers to create income-based housing for low-income families and individuals; however, proposed developments often meet a mix of community opposition and support. While current research focuses on how Not in my Backyard (NIMBY) arguments affect the location and development of affordable housing complexes, little research centers the experiences of potential affordable housing recipients – individuals often associated with racist and classist stereotypes through NIMBY rhetoric. This study utilizes experimental survey data to demonstrate the implications of NIMBY and Yes in my Backyard (YIMBY) community rhetoric on the mental health of potential affordable housing recipients. Participants were randomly assigned to one of three vignettes that mirrored a neutral factsheet, NIMBY arguments, or YIMBY sentiments. I discover that the self esteem of individuals in the control and YIMBY group increased while the change in self-esteem among NIMBY group participants was insignificant. Findings indicate that neutral and supportive rhetoric surrounding affordable housing development can have a positive effect on potential recipients’ self-esteem. This study contributes to the present literature on both the effect of positive rhetoric on mental health and affordable housing.

Over two dozen cave shrines are known from the Mimbres Mogollon region, more than have been reported from any other cultural region in the United States Southwest and Northwest Mexico (SW/NW). Despite some variation, the archaeological record of these sites is remarkably consistent and readily allows for their identification as shrines due to the presence of ethnographically recognizable offertory materials such as prayer sticks (pahos), cane cigarettes, and painted wood objects (“tablitas”). It remains difficult to determine, however, whether this phenomenon represents a stronger interest in cave ritual among the Mimbres or is simply the product of more thorough cave survey in that region, especially the work of Harriet and C. Burton Cosgrove in the 1920s and Walter Hough in 1905. Neighboring regions show related patterns but fewer cave shrines. A synthesis of available data, including the few available 14C dates, suggests that cave ritual did indeed reach unprecedented levels during the Mimbres Classic (ca. 1000–1130 CE). Herein I synthesize a wide range of data in order to place Mimbres cave ritual in its spatial and temporal context. Available evidence suggests that this intensification in cave ritual was driven simultaneously by population expansion, and by social, political, and environmental factors.

Hematopoiesis depends on complex interactions between hematopoietic stem cells (HSCs) and the bone marrow (BM) microenvironment. However, alterations in this regulated system can lead to malignant transformation and hematopoietic diseases. Acute myeloid leukemia (AML) is characterized by uncontrolled growth of leukemic blasts in the BM and is the most common acute leukemia in adults. Tumor survival after cytotoxic treatment of AML patients remains a major therapeutic challenge, contributing to disease relapse. Fine-tuning the cytotoxic conditioning regimen to discover the most effective treatment plan has the potential to significantly improve outcomes in AML patients, thereby reducing the risk of relapse. The mechanism by which conditioning achieves therapeutic outcomes is through BM ablation. Additionally, conditioning can impact different compartments of the BM microenvironment. In this study, we investigated the impact of busulfan conditioning on the BM niche, focusing on how the intensity of cytotoxic conditioning regimens and animal age influence this dynamic process. We later expanded our findings to an AML mouse model to evaluate the BM niche around resistant tumor cells after cytotoxic therapy.

By examining the impact of varying dosages and recipient age factors on treatment response as well as BM microenvironment adjacent to the residual tumor cells after therapy, we sought to optimize chemotherapy regimens and establish the groundwork for tailoring treatment strategies to AML cancer patients.

Critical pedagogy surrounding Spanish as a heritage language (SHL) has focused on the student’s attitudes regarding their language and culture, specifically as it relates to Spanish and Latinxs in the United States. These heritage language (HL) learners, who were exposed to Spanish in the home, enroll in Spanish classes to further a sense of identity and recover, develop, and foster their first language. Research in linguistics and pedagogy has explored writing through different genres in the HL as it is the skill with which the learners have the least experience and is perceived as the most difficult to learn the heritage language by the students themselves according to preliminary surveys. However, few have examined SHL speakers’ writing in both English and Spanish in the US context. Additionally, studies have had a disciplinary focus, while this project engages applied linguistics, writing studies and Chicanx/Latinx studies. Looking at English and Spanish writing concurrently creates a space for HL speakers that would not be included in Spanish-only focused studies. This bilingual and bicultural research space not only invites the student to write about their attitudes regarding culture and identity, but it also generates possibilities for the use of features of language that have been previously unexplored in this context: namely using figurative language like metaphors in both languages. This study pairs genre theory from systemic functional linguistics (SFL) and conceptual metaphor theory to examine the use of figurative language reported here as initial findings, in 192 SHL speakers through the students’ written texts (86 in English and 106 in Spanish). The exploration of students’ work through various genres provides differing spaces to explore their ideas about language and identity, and the focus on metaphor provides insights into both their cognitive and affective experiences. Preliminary findings demonstrate students’ use of metaphors to conceptualize their identity and cultural experience as well as to explain their language learning experiences. Using a holistic approach that incorporates the use of conceptual metaphors in the bilingual heritage context has yet to be studied, even though it has the potential to give instructors important insights into how students feel about their identity and cultural development. This study provides context-specific, culturally relevant insights and structured guidance on how to further enhance students’ social, emotional, and academic engagement in language development with particular benefit to multilingual speakers. This project presents a qualitative and quantitative case-study to produce a theoretical pedagogical framework that maps the affective experiences of Hispanic students through their cognitive achievements. By focusing on cognitive and affective understandings, we can approach new ideas, reform current instruction, and contribute to critical heritage pedagogy. This project will follow an integrative vision of the study through a presentation of the relevant literature and theoretical frameworks of metaphor and genre theories. It continues with a discussion of the current research methodology, dissertation framework, Spanish, English, and genre chapter analysis. It ends with findings, pedagogical implications, and a summary presenting this work in conjunction with its broader significance.

This dissertation examines the visible and invisible labor of Black and Black-biracial women faculty in California Community Colleges, introducing the theory of daughtering as a method to understand patterns of care-giving and its resulting burnout. Using a mixed method approach that includes institutional ethnography, autotheory, oral history and literary analysis, the research reveals that the current context of equity and social justice movements within the community college system has created a different set of labor demands on Black and Black-biracial women faculty. This reframes the perception of care/work provided by these faculty and relies on their cultural knowledge to lead equity solutions related to student care. Institutional resistance to change and existing systems of social coordination leave faculty feeling powerless and siloed into positions that require emotional labor. These positions have a deleterious effect on well-being and persistence. Daughtering as theory gives insight to internalized perception of self and serving-ness that Black and Black-biracial women faculty bring to their positions and how this identity results in specific methods of performing care/work. This research also presents the concept of visionary daughtering as a method of transforming care/work into autonomous power and reclamation of voice to stay alive within academia.

With increasing levels of intelligence and automation mobile robots are now an enabling technology for autonomous patrolling of indoor and outdoor environments. Patrolling is a repetitive and potentially dangerous task whose execution costs can be mitigated by deploying surveillance robots in the area of interest. Because these systems are designed to be autonomous, the high-level planning of the surveillance activities emerges as one of the most critical challenges to achieving good performance and, ultimately, detecting and preventing malicious activities in the environment. Issues like how to plan efficient paths, where and when to schedule surveillance actions, and how to coordinate with teammates have been tackled by models encoding some environment representation and assumptions on agents capabilities and behaviors. This dissertation itself addresses some of the challenges in computing patrolling schedules for an agent, or team of agents, working against an intruder with limited observablility of the environment. First, we present an overview of related literature associated with the specific types of problems discussed throughout. This includes: techniques for single agent instances, techniques for multi-robot instances, machine learning for patrolling, and common metrics used for gauging a defender’s performance. It is, then, divided into several chapters which each address different aspects of the aforementioned challenges.

RNA viruses are ubiquitous across diverse environmental ecosystems and are associated with a wide array of eukaryotic hosts. Ranging from their essential role in biogeochemical cycling to their pathogenic implications in causing animal and plant diseases, extensive insight into the RNA virome has been developed in association with eukaryotic supergroups Opisthokonta and Chloroplastida. Considering the diversity that spans the eukaryotic Tree of Life, animals, plants, and fungi capture only a small proportion of diversity otherwise characterized by unicellular eukaryotes. In this dissertation, studies expand the known diversity of protist-associated RNA viruses, and provide atomistic insight into the binding dynamics that constitute the effort to prevent early HIV-1 infection.

Chapter 1 provides a review on the ubiquity of environmental protists, RNA viruses, and their interplay across diverse ecosystems. This work aims to highlight the current strategies and efforts to broaden understanding of the protist-associated RNA virome, and provide perspective as to future developments. The article puts into perspective the global distribution of unicellular eukaryotes and their diverse roles spanning from biogeochemical cycling to sustaining marine species biodiversity. This review highlights advancements in Next-Generation Sequencing (NGS) technologies, open-source bioinformatic programs, and provides perspective on how these tools will contribute to expansion of the global RNA virome.

Chapter 2 explores the abundance and roles of environmental Riboviria associated with unicellular eukaryotic hosts. Based on 302 metatranscriptomes derived from soil and fresh-water protists (amoeba, ciliates, foraminifera, and euglenoids), discovery of novel RNA viruses was performed based on detection of the RNA-dependent RNA polymerase (RdRp) hallmark gene. This study applied a bioinformatic strategy which included identification of viral genomes using geNomad, detection of RdRp-encoding viruses using profile hidden Markov models (HMM), and maximum-likelihood phylogenetic tree construction. While results confirmed the presence of protist-associated Riboviria, analysis of newly identified members were not indicative of general auxiliary metabolic function. Instead, RNA viruses were largely associated with functions related to viral replication.

Chapter 3 explores the efficacy of the antiviral lectin Griffithsin against early HIV infection. Based on the crystal structure of Griffithsin complexed with mannose glycans (PDB: 2GUD), classical molecular dynamics (MD) was applied to investigate the impact of mutating conserved residues within Griffithsin’s carbohydrate binding sites. Assessment of induced mutations were performed using programs such as Groningen Machine for Chemical Simulations (GROMACS),PyMOL, Avogadro, and Automated Topology Builder (ATB). Results reflected the delocalization of bound mannose glycans in mutant isoforms and validated MD as a robust method to study protein-ligand binding dynamics.

Coccidioidomycosis, also known as Valley fever, is primarily a respiratory disease caused by the fungal pathogen Coccidioides. The fungus predominantly inhabits the soil of the Southwestern United States, but the area of endemicity is expected to expand with global warming. Inhalation of the fungal spores leads 40% of patients to experience flu-like symptoms. Similarities in symptomology and fibrosis in chest x-ray often lead to misdiagnosis of Valley fever as bacterial pneumonia. Patients undergo several rounds of antibiotic treatment prior to accurate diagnosis, resulting in a perturbed microbiome and contributing to antibiotic resistance. The effect that a perturbed microbiota has on Coccidioides is unexplored; however, a soil B. subtilis-like species inhibits the growth of Coccidioides. We show that, in vitro, the intestinal and tracheal microbiomes can inhibit Coccidioides growth on select agar. Results also indicate that perturbing an established microbiome with an antibiotic disk cocktail eliminates the inhibitory effects of the microbiome and creates a niche for Coccidioides growth. Sequencing data revealed that the predominant genus responsible for the inhibition may belong to the Lactobacillus and Staphylococcus genus; with the addition of Bifidobacterium and Achromobacter found in the whole lung extracts. These bacteria with inhibitory potential could serve therapeutic purposes for this infection. Currently, fluconazole and amphotericin B are the primary antifungals used to treat coccidioidomycosis; however, these treatments have adverse side effects. Although most patients recover, 1% can develop disseminated disease leading to lifelong treatment as these antifungals are suppressive, not lethal to the fungus. In addition to these potential probiotic therapies, through our compound screens, we have found that avocado tree extracts could also have antifungal properties against Coccidioides. Together, probiotics and avocado compound extracts could potentially serve as supplemental therapies to the current antifungal drugs.