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ION-BEAM-ASSISTED DEPOSITION OF TRANSPARENT CONDUCTIVE THIN FILMS : ON THE WAY TOWARD REPLACING INDIUM TIN OXIDE
No full textThesis (Ph.D.)--Michigan State University. Materials Science and Engineering - Doctor of Philosophy, 2024In light of the escalating costs of Indium Tin Oxide, the quest for its sustainable alternatives becomes imperative. This dissertation delves into the utilization of a single-beam ion source in conjunction with magnetron sputtering to manipulate film microstructures, aiming to enhance and fabricate transparent conductive electrodes. Through the assistance of the ion source, an extensive range of modulation in the magnetron voltage was achieved. This mechanism led to a low-voltage high-current magnetron discharge, facilitating a 'soft sputtering mode' conducive for thin film growth. Indium tin oxide (ITO) thin films were successfully deposited at room temperature by employing a combined single-beam ion source and magnetron sputtering, resulting in the creation of polycrystalline ITO thin films characterized by significantly reduced resistivity and surface roughness. Notably, the ion beam treatment played a pivotal role in the growth of a silver seed layer, approximately 1 nm in thickness, enhancing the subsequent silver film's wettability. This, in turn, led to the creation of a continuous silver film of approximately 6 nm, boasting a resistivity of 11.4 \u3bc\u3a9.cm. To enhance stability of resulting silver ultra-thin films, an approach involving a cap layer of aluminum on silver was introduced. The resulting film, composed of a 1 nm buffer layer of ion beam-treated silver, a layer of pure silver sputter-deposited, and a 0.2 nm nominal thick cap layer of aluminum, significantly bolstered the film's stability without a marked compromise on its optical and electrical properties. Further, thermal treatment of the duplex film led to an enhancement in its electrical conductivity and optical transmittance owing to an improvement in crystallinity. The annealed aluminum/silver duplex structure exhibited low electrical resistance and high optical transmittance, comparable to simulated results, positioning it among the top films reported. The stabilized ultra-thin silver films were then leveraged to craft highly transparent and conductive electrodes on glass substrates in a sandwich structure with optimized layers of indium tin oxide (ITO). Notably, exceptional thermal stability was achieved, and annealing at 200\ub0C in vacuum and air enhanced the film's optical and electrical performance. The resultant electrodes showcased outstanding transparency, conductivity, and thermal stability, positioning them favorably for architectural glass coatings and optoelectronic applications such as photovoltaics and displays. Further computational works were conducted to study the optical performances of six different sandwich structures on glass, comprising typical transparent conductive oxides with an ultra-thin layer of silver at 6 nm and 7 nm in the middle. The simulation finds Glass/TiO2/Ag/AZO, Glass/TiO2/Ag/SnO2 and Glass/SnO2/Ag/SnO2 structures exhibiting high optical performances, comparable to ITO in solar-cell and display applications, theoretically. This dissertation also shows some other examples of optimizing the optical performance of the structures for specific applications. Furthermore, a case study was conducted to explore the use of tantalum-doped tin oxide (TTO) as a viable alternative to ITO. Employing a room temperature treatment facilitated by a single beam ion source, highly transparent and conductive TTO films were produced. Specifically, the TTO thin film achieved a resistivity as low as 9.3 m\u3a9.cm and an average transmittance of 79% in the 400 nm to 1200 nm range. In contrast, without ion beam assistance, the minimum resistivity achieved was 15.9 m\u3a9.cm, accompanied by an average transmittance of 78% within the same wavelength range.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references
FROM DATA TO DYNAMICS : DATA INTEGRATION TO ESTIMATE AVIAN POPULATION AND COMMUNITY DYNAMICS
No full textThesis (Ph.D.)--Michigan State University. Integrative Biology - Doctor of Philosophy, 2023In this dissertation, I assess data collection methods for avian surveys and develop and apply integrated models to estimate demographic rates and trends for bird species of conservation concern. The work in this dissertation advances the capacity of science to inform management decisions for bird conservation through evaluation and improvement of data collection and analysis methods, and further demonstrates the application of new modeling techniques to understand ecological phenomena. I focus on survey methods and modeling approaches for shorebird and waterbird species\u2014migratory birds that experience numerous challenges and population-level threats due to their long-distance migrations, reliance on water bodies and coastal habitats, and sensitivity to anthropogenic-induced climate change. In Chapter One, I review data collection issues associated with aerial surveys, a common survey method to estimate waterbird population abundance, and provide evidence-based solutions for overcoming issues such as, non-detection, counting error, and species misidentification. The challenges associated with aerial survey data are highlighted using a case study featuring waterbirds in the Gulf of Mexico. In the remaining chapters, I use integrated modeling methods to combine multiple data types into unified analyses of target species to simultaneously estimate demographic rates and inform management needs of migratory species in decline. In Chapter Two, I develop an integrated population model of black terns (Chlidonias niger) in the Upper Midwestern United States and combine it with a Bayesian population viability analysis to predict the effects of various management strategies on population persistence. The results reveal that current conservation efforts, taking place almost exclusively during the breeding season, are unlikely to reverse the black tern declines observed over the last decade. My assessments indicate that to be effective, black tern conservation must also include interventions targeting adult survival during nonbreeding periods of the annual cycle. In Chapter Three, I estimate demographic rates, including the effects of environmental drivers, for three species of Arctic-breeding shorebirds using single-species integrated population models. I assess species\u2019 demographic rate correlations (i.e., population synchrony), which indicate that breeding season dynamics are relatively synchronous for the three species while nonbreeding season dynamics vary asynchronously. The disparities observed in shorebird species dynamics suggest that differential responses to environmental conditions, such as differences in responses to climactic variation and distinct nonbreeding season conditions arising from different migratory pathways and nonbreeding season ranges, could be driving shorebird population dynamics. The results from chapters two and three highlight the importance of enhancing management efforts for migratory species during migration and nonbreeding periods, which constitute a much larger, and generally riskier, proportion of the avian annual cycle compared to the breeding season. In Chapter Four, I extend the integrated population model from a single-species context to a multi-species framework to estimate demographic rates at both the species- and community-levels for a community of eight Arctic-breeding shorebirds, including species for which few data exist. The application and extension of integrated models to sparse and disparate community-level datasets allows researchers to estimate species\u2019 demographic rates and trends in cases when traditional, independent analyses of such data are not likely to yield robust inferences. My dissertation demonstrates how the continued assessment and improvement of data collection techniques and integrated modeling approaches can provide conservation scientists with accurate and precise estimates of population and community dynamics that can be used to inform biodiversity monitoring and conservation initiatives for birds and other taxa.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references
DETERMINING SURFACTANT PRESENCE IN EMULSION POYMER SAMPLES USING SINGLE-QUADRUPOLE MASS DETECTION
No full textThesis (M.S.)--Michigan State University. Clinical Laboratory Sciences - Master of Science, 2024Surfactant analysis is generally performed using liquid chromatography (LC) and a tandem triple-quadrupole mass spectrometer (MS-MS). This method provides the sensitivity and specificity required to resolve this type of molecule in a mixture. A less equipped laboratory may not have this option. Here we show a method developed to detect residual quantities of the surfactant Reasoap SR-10 in emulsion polymer samples. This was achieved using an Acclaim Surfactant Plus column from Thermo Scientific installed on a Waters 2695 liquid chromatograph connected to a Waters QDa single quadrupole mass detector set for single ion recording at m/z = 557, utilizing electrospray ionization. While specificity was achieved, the method had challenges with consistent sensitivity, precision and recovery which will lead to more effort in method refinement, namely sample preparation. Even though for now it is better classified as a qualitative method, a fully successful method would be a benefit for our laboratory. This would prevent causing delays for needed information and higher costs due to utilizing a reference laboratory, creating efficiencies for in-house product troubleshooting as well as research and development.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references
METABOLIC MODELING : INTEGRATION WITH MULTI-OMIC DATASETS, STATISTICAL EVALUATION, AND APPLICATION TO OUR UNDERSTANDING OF PHOTOSYNTHETIC CARBON ASSIMILATION
No full textThesis (Ph.D.)--Michigan State University. Biochemistry and Molecular Biology - Doctor of Philosophy, 2024Many biotechnological efforts in plants have been proposed to address issues around climate change, sustainability, and food security. These include the modification of the oilseed crop Camelina sativa to improve the efficiency with which it produces oil from captured carbon, to the suppression of photorespiration and enhancement of yield in crops by engineering a Carbon Concentrating Mechanism into them. However, research and development efforts to use biotechnological interventions to improve plants and microbes have been hampered by their extreme complexity. Many of these bioengineering efforts seek to modify the rates of in vivo biochemical reactions \u2013 referred to hereafter as fluxes \u2013 in order to improve the efficiency or yield with which a desired product(s) is produced. Therefore, these efforts require the characterization and modification of the organism\u2019s metabolic activity. As in other areas of engineering, these processes can be aided by the use of quantitative modeling. In the case of metabolic modeling, multiple approaches already exist. These include the use of simplified compartmental models (Chapter 2) and enzyme-based modeling (Chapter 4), as well as constraint-based approaches such as the linear-optimization-based Flux Balance Analysis (Chapter 3) and the nonlinear regression based Metabolic Flux Analysis (Chapter 2). Although these methods are rarely used in tandem, they are mathematically interrelated and can be used to validate and/or corroborate one another\u2019s findings. Indeed, previous literature in the area of metabolic modeling has frequently paid short shrift to the importance of validation and model selection in this area of study, calling into question the biological relevance and accuracy of many modeling studies. I begin with a discussion of challenges and prospects for future development in the statistical evaluation of metabolic models (Chapter 1), emphasizing the need for cross-comparison of multiple techniques, which I put into practice in later chapters. Emphasis is put on the need for careful validation of 13C-Metabolic Flux Analysis findings using multiple lines of evidence and on the usefulness of validating Flux Balance Analysis flux predictions using estimates from 13C-Metabolic Flux Analysis. I apply these methodological insights to studies of Camelina sativa and its relative Arabidopsis thaliana. I start with a 13C-Metabolic Flux Analysis study of the metabolism of photosynthesizing leaves of Camelina sativa (Chapter 2). By modeling the stable isotopic labeling levels of Calvin-Benson intermediates with a series of polyexponential models, I corroborate the study\u2019s 13C-Metabolic Flux Analysis findings, resulting in a more detailed model of C. sativa\u2019s leaf metabolism and resolving a decades-old mystery in the labeling of these metabolites. Following this, I present a novel method of incorporating multi-omic datasets into FBA predictions of metabolic fluxes in the closely related organism A. thaliana (Chapter 3). I demonstrate that this new method successfully improves agreement between FBA and 13C-MFA flux maps of A. thaliana, setting the stage for improved FBA and metabolic engineering insight into the related C. sativa.Finally, I turn my attention to reaction-diffusion modeling. In Chapter 4, I apply enzyme-based and spatial modeling techniques to understand the net CO2 fixation and light-use efficiency implications of incorporating a biophysical Carbon Concentrating Mechanism into a C3 plant. After some concluding remarks in Chapter 5, I present two additional studies that are related either to the quantitative modeling of plants or metabolic networks, but which are not directly related to the rest of the investigations in this thesis. First, I investigate the extent to which the kinds of tissue-specific gene expression patterns utilized in Chapter 3 are conserved across all flowering plants, providing evidence that such an approach may be broadly usable in plant metabolic modeling. Finally, I present interactive educational materials that teach the underlying theory for all of the metabolic modeling approaches used in the above studies. I implemented these materials into an intensive workshop series put on at Michigan State University and demonstrate that participants\u2019 self-assessed confidence in the techniques taught increased significantly.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references
"We're Not Here to Teach You How to be Gay" Recommendations for the Use of Emotionally Focused Therapy with LGBTQ + Romantic Relationships : A Critical Phenomenological Analysis
No full textThesis (Ph.D.)--Michigan State University. Human Development and Family Studies - Doctor of Philosophy, 2024The systemic oppression of lesbian, gay, bisexual, transgender, queer/questioning plus (LGBTQ +) communities significantly contributes to higher rates of both physical and mental health concerns. Moreover, this systemic oppression negatively impacts LGBTQ + romantic relationships, resulting in increased rates of intimate partner violence, lower levels of trust, and relationship instability. Research indicates that LGBTQ + individuals are more likely to seek therapy compared to their heterosexual, cisgender peers despite a reported lack of comfort and competency reported by therapists working with this population. Additionally, very few evidence-based few models of romantic relationship therapy have been applied to and/or developed with/for LGBTQ + relationships. The dearth of therapeutic approaches, such as Emotionally Focused Therapy (EFT), specifically tailored and adapted to meet the unique therapeutic preferences, needs, and lived experiences of LGBTQ + relationships as well as the lack of integration of client voices and identities into therapeutic interventions jeopardizes the quality, rigor, and the ability of relationship therapy to adequately address the concerns brought forth by LGBTQ + communities. Therefore, this study offers important empirical insight into how an evidence-based model of therapy, namely EFT, can be modified to account for LGBTQ + client therapeutic preferences, needs, identities, and lived experiences. The purpose of this qualitative, phenomenological study was to explore the recommendations made by LGBTQ + EFT clients for adapting EFT to account for their unique therapeutic preferences, needs, identities, and lived experiences. The sample included 35 EFT clients who identified as members of LGBTQ + communities and who had attended at least six sessions of EFT. Data were collected across eight focus groups using theater testing. A rigorous thematic analysis approach was used to label, analyze, and consolidate patterns of meaning following the tenants of Braun and Clarke (2006; 2019). Data analysis resulted in seven primary themes: (1) the universality of emotion, EFT, and the withdraw/pursue cycle, (2) client enthusiasm for EFT, (3) the impact of marginalization, (4) the importance of finding an LGBTQ + affirming therapist, (5) the integration of discrimination in relationship therapy, (6) the discussion of identity as othering, (7) client recommendations for EFT, and (8) working with therapists holding marginalized identities. Results illustrated the effectiveness of EFT, as well as how the lived experiences of the LGBTQ + communities impact the content and process of EFT. Although the aim of the study was to obtain recommendations for adapting EFT, participants also broadly discussed their experience of EFT overall, the impacts of marginalization, and the importance of working with relational therapists who understood the unique lived experiences of LGBTQ + clients. Several implications for both future research and clinical practice were identified. The qualitative findings from this study can inform how EFT is applied when working with members of the LGBTQ + communities as well as further research examining the effectiveness of an adapted EFT. The results are applicable not only for EFT therapists, but also any therapists using an evidence-based relational therapy model with people who identify as a member of the LGBTQ + communities.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references
EXPLORING THE POTENTIAL OF 20S PROTEASOME MODULATION AS A NOVEL THERAPEUTIC STRATEGY FOR THE TREATMENT OF NEURODEGENERATIVE DISEASES AND CANCERS
No full textThesis (Ph.D.)--Michigan State University. Chemistry - Doctor of Philosophy, 2024The accumulation of intrinsically disordered proteins (IDPs) and the associated disruption of cellular proteostasis is implicated in the progression of a number of neurodegenerative diseases and cancers. Due to the highly disordered nature of IDPs, they are considered \u201cundruggable\u201d targets because of their lack of typical drug binding pockets. The work in this dissertation focuses on the exploration of an alternative approach to pharmacologically regulate these \u201cundruggable\u201d proteins through proteasome-mediated degradation. The 20S proteasome is a large protein degradation complex responsible for maintaining low cellular levels of IDPs. Our approach uses small molecule enhancers of proteolytic activity of the 20S proteasome to enhance the degradation of IDPs, thereby preventing their accumulation and associated toxicity. To demonstrate the potential use of small molecule 20S activation as a novel therapeutic approach for the treatment of neurodegenerative diseases, we studied the effects of a 20S proteasome activator toward an IDP target associated with the progression of amyotrophic lateral sclerosis (ALS). Recently, 30 to 60 percent of familial ALS cases have been linked to a gene mutation that results in the production of five highly disordered dipeptide repeat (DPR) proteins. The accumulation and aggregation of DPRs have shown to disrupt cellular proteostasis, leading to uncontrolled protein levels, resulting in neuron death and further disease progression. In a recent collaborative study, we have demonstrated that 20S proteasome activator, TCH-165, enhances the degradation of DPR proteins. The enhanced degradation of DPR proteins led to the restoration of cellular proteostasis and provided protection against DPR induced neurotoxicity in ALS disease models. We then aimed to explore the potential use of small molecule 20S activation as a novel therapeutic strategy for cancer treatment. The overexpression of the highly disordered transcription factor, c-MYC, has been found in more than 70 percent of all human cancers. Dysregulation of c-MYC protein levels and its accumulation has shown to induce its oncogenic transcriptional activity, resulting in the transcription of a number of genes that promote tumor growth and cancer cell proliferation. In a recent study, we demonstrated the ability of TCH-165 to reduce cellular c-MYC protein levels. The enhanced degradation of c-MYC prevented its oncogenic effects, inhibiting cancer cell proliferation and reducing tumor growth in vivo. To further explore this therapeutic strategy, a novel class of 20S proteasome activators was identified and synthetically modified to generate a series of analogues. Through investigation of the biological activities of this new class of 20S proteasome activators, a new component of the therapeutic mechanism was discovered. These findings provide evidence that activation of the 20S proteasome can be tuned to selectively target IDPs based on their amino acid sequence. This suggests the exciting possibility that a small molecule 20S proteasome activator could be designed to selectively target a specific IDP for a more targeted disease treatment. In all, this work suggests that small molecule activation of the 20S proteasome may offer a potential novel therapeutic strategy for the treatment of neurodegenerative diseases and cancers in which intrinsically disordered protein accumulation plays a significant role in disease progression.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references
Mass Timber Curriculum Development for Engineering Students Using DACUM and Delphi Methodologies
No full textThesis (M.S.)--Michigan State University. Civil Engineering - Master of Science, 2024Mass timber is an emerging construction technology growing in popularity in the United States. One obstacle in the gradual adoption of mass timber construction is the limited availability of qualified engineers and designers. While successful efforts have been made to address research topics related to mass timber design and to identify common barriers and challenges to the adoption of mass timber as a construction material, little research has been conducted to identify desired student outcomes for undergraduate civil or structural engineering students working with mass timber after graduation. This thesis describes the development of an industry-guided educational resource for curriculum development in order to improve alignment between undergraduate student outcomes and employer requirements related to mass timber design. A \u201cDeveloping A Curriculum\u201d (DACUM) chart was produced by a panel of qualified industry professionals to identify the tasks, duties, general knowledge, skills, and worker characteristics required of successful entry-level structural engineers working with mass timber. A second panel of qualified subject matter experts was assembled for implementation of the Delphi Survey Methodology, in which experts were instructed to draw upon their opinions and perspectives honed through years of industry experience to rank their level of agreement with each item and propose changes to the chart. Findings reflect a prioritization of competencies related to design of mass timber elements and structures, understanding of material characteristics, navigation of available design resources, contributions to project deliverables, and support of sustainability goals. The finalized DACUM chart provides clarity on curriculum needs to ensure graduating engineers are well-prepared to work with mass timber elements as the industry continues to grow in popularity. The chart can be used as a resource to guide the development of mass timber engineering educational materials, including learning modules, virtual tours, and student assignments to be presented independently or implemented with existing engineering coursework.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references
Topological Data Analysis Driven Feature Generation in Machine Learning Models
No full textThesis (Ph.D.)--Michigan State University. Computational Mathematics, Science and Engineering - Doctor of Philosophy, 2024Topological data analysis (TDA) is an emerging field in data science, with origins inalgebraic topology. I focus on two main disciplines of topological data analysis, mapper and persistent homology. Mapper is an algorithm to construct a graph that is similar to a Reeb graph, allowing for the abstraction of shape from data. Persistent homology is way to measure features in a dataset, and returns a set of points (a persistence diagram) that represents the structure of the dataset. While both mapper and persistent homology are effective tools in their own right, a significant area of research includes using features created from these topological tools in machine learning algorithms. In this dissertation, I focus on advancing both theoretical and computational methods that allow the use of topological data analysis in machine learning algorithms. I have developed an extension to the mapper algorithm, named predictive mapper, that uses the eigenvectors of the graph Laplacian of the geometric realization of a mapper graph, allowing features to be created from a linear combination of the eigenvector values for use in machine learning. I have also contributed to teaspoon, an open source package for topological signal processing by including new datasets and expanded functionality for featurization methods. Lastly, I have started the development of ceREEBerus, a python package for working with Reeb graphs while implementing a standardized software development framework for the Munch Lab.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references
EFFECT OF ADOLESCENT COCAINE USE : CONTEXT-INDUCED DRUG SEEKING BEHAVIORS AND HIPPOCAMPAL NEUROPLASTICITY
No full textThesis (M.A.)--Michigan State University. Psychology - Master of Arts, 2024The health and economic costs associated with substance use disorders (SUDs) are immense, with a rise in overdose deaths related to stimulant or stimulant and opiate use from 2016-2021 (NIDA). Drug use during adolescence increases the risk for development of SUDs, with the severity of diagnosis associated with worse outcomes later in life. Recent reports of increased stimulant use among 15\u201323-year-olds and the number of overdose deaths associated with cocaine use highlight the need to understand both the behavioral and underlying molecular changes associated with craving and relapse in this age group.We developed an abbreviated cocaine self-administration (Coc-SA) procedure which allowed us to examine relapse during adolescence and found that the magnitude of contextual cocaine-seeking is the same for adolescent and adult cocaine-exposed rats after 1 day of abstinence. However, adolescent rats had significantly higher seeking after 15 days of abstinence (incubation of craving). The current proposal aims to examine whether changes in plasticity, specifically activation of NMDA and AMPA receptor subunits, occur during abstinence periods that precede relapse. Adolescent and adult rats received Coc-SA in a distinct context (2h sessions, 2x/day, minimum 10 sessions), followed by extinction training (EXT) in a second distinct context (2h session, 2x/day, minimum 8 session). Adolescent and adult rats were split into three separate Relapse Test groups: No Test (30min in homecage), Test in the EXT context (EXT), Test in the Cocaine-paired context after 1 day (T1), or 15 days (T15) of abstinence. Tissue samples from the dorsal hippocampus were collected 30min after Relapse Tests. We found increased cocaine-seeking behavior in adolescent and adult rats after 15 days of abstinence, however we did not observe Age or Relapse Test-dependent changes in NMDA or AMPA subunit activation associated with craving and relapse.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references
INSIGHTS INTO HUMAN HEALTH THROUGH COMPUTATIONAL MODELING : TARGETING TUBERCULOSIS AND UNDERSTANDING PFAS TOXICITY
No full textThesis (Ph.D.)--Michigan State University. Chemistry - Doctor of Philosophy, 2024Computational modeling approaches have been instrumental to biological and biochemical researchfor over 50 years, providing insight that can impact advances in human, animal, and environmental health. The use of in silico methods in drug discovery can reduce financial cost and time required for the development of new drugs by providing molecular-level insight and information about structure-activity relationships. Computational chemistry approaches can provide compound identification, optimization and screening towards the development of more potent and novel molecules. Computational biophysical methods are not only useful in drug discovery, but they are also useful in environmental science as well, in areas such as determining the toxicity of pollutants. The validation of computational protocols is an important step in computational modeling. SAMPL blind challenges provide host-guest systems with known binding affinities and physical properties to benchmark developed methods and protocols against experiment. A benchmark for the protocols used throughout the dissertation has been provided. Per- and polyfluoroalkyl substances (PFAS) are man-made molecules that have very interesting chemical features. These compounds are both water and oil-resistant therefore, they have been utilized in many industrial processes and household products, including fast food packaging, firefighting foams, dental floss, water-resistant garments, batteries, and non-stick cookware. However, research conducted in recent years has shown that some PFAS can cause significant health problems thyroid problems, cholesterol and lipid issues, and cancer in living organisms upon consistent exposure and bioaccumulation. Several of the chapters in this dissertation highlight investigations of three different protein targets of PFAS: \u2022 human Peroxisome proliferator receptor gamma - retinoid x receptor alpha /DNA (PPAR?- RXR?/DNA) is an important protein for regulation of glucose metabolism and fat cell differentiation, \u2022 human thyroglobulin protein (hTG) which is responsible for producing the thyroid hormones, \u2022 rainbow trout estrogen receptor ? and ? (ER?, ER?) controlling the reproduction. The goal of each of the studies was to gain a molecular-level understanding of the impact of selected common and alternative PFAS on the proteins. In considering specific disease, tuberculosis (TB) is a persistent disease largely observed in rural parts of the world. While there are available treatment regimens for both drug-susceptible as well as drug-resistant TB, these treatment protocols require use of many different drugs and take from six months to up to two years. Therefore, there is a need for the development of better treatment strategies. A chapter in this dissertation highlights how computational chemistry approaches have been used in studies to develop compounds targeting the treatment of Tuberculosis via two different protein targets, mycobacterium membrane protein large 3 (mmpL3) and DosS in collaboration with medicinal chemists. Homology modeling, binding energy estimations, as well as conformational dynamics of these proteins were investigated.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references