An Electronic Structure Approach to Charge Transfer and Transport in Molecular Building Blocks for Organic Optoelectronics.

A fundamental understanding of charge separation in organic materials is necessary for the rational design of optoelectronic devices suited for renewable energy applications and requires a combination of theoretical, computational, and experimental methods. Density functional theory (DFT) and time-dependent (TD)DFT are cost effective ab-initio approaches for calculating fundamental properties of large molecular systems, however conventional DFT methods have been known to fail in accurately characterizing frontier orbital gaps and charge transfer states in molecular systems. In this dissertation, these shortcomings are addressed by implementing an optimally-tuned range-separated hybrid (OT-RSH) functional approach within DFT and TDDFT. The first part of this thesis presents the way in which RSH-DFT addresses the shortcomings in conventional DFT. Environmentally-corrected RSH-DFT frontier orbital energies are shown to correspond to thin film measurements for a set of organic semiconducting molecules. Likewise, the improved RSH-TDDFT description of charge transfer excitations is benchmarked using a model ethene dimer and silsesquioxane molecules. In the second part of this thesis, RSH-DFT is applied to chromophore-functionalized silsesquioxanes, which are currently investigated as candidates for building blocks in optoelectronic applications. RSH-DFT provides insight into the nature of absorptive and emissive states in silsesquioxanes. While absorption primarily involves transitions localized on one chromophore, charge transfer between chromophores and between chromophore and silsesquioxane cage have been identified. The RSH-DFT approach, including a protocol accounting for complex environmental effects on charge transfer energies, was tested and validated against experimental measurements. The third part of this thesis addresses quantum transport through nano-scale junctions. The ability to quantify a molecular junction via spectroscopic methods is crucial to their technological design and development. Time dependent perturbation theory, employed by non-equilibrium Green’s function formalism, is utilized to study the effect of quantum coherences on electron transport and the effect of symmetry breaking on the electronic spectra of model molecular junctions. The fourth part of this thesis presents the design of a physical chemistry course based on a pedagogical approach called Writing-to-Teach. The nature of inaccuracies expressed in student-generated explanations of quantum chemistry topics, and the ability of a peer review process to engage these inaccuracies, is explored within this context.PHDChemistryUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/111460/1/hlphill_1.pd

Manx: Close air support aircraft preliminary design

The Manx is a twin engine, twin tailed, single seat close air support design proposal for the 1991 Team Student Design Competition. It blends advanced technologies into a lightweight, high performance design with the following features: High sensitivity (rugged, easily maintained, with night/adverse weather capability); Highly maneuverable (negative static margin, forward swept wing, canard, and advanced avionics result in enhanced aircraft agility); and Highly versatile (design flexibility allows the Manx to contribute to a truly integrated ground team capable of rapid deployment from forward sites)

Eigenvector Centrality Distribution for Characterization of Protein Allosteric Pathways

Determining the principal energy pathways for allosteric communication in biomolecules, that occur as a result of thermal motion, remains challenging due to the intrinsic complexity of the systems involved. Graph theory provides an approach for making sense of such complexity, where allosteric proteins can be represented as networks of amino acids. In this work, we establish the eigenvector centrality metric in terms of the mutual information, as a mean of elucidating the allosteric mechanism that regulates the enzymatic activity of proteins. Moreover, we propose a strategy to characterize the range of the physical interactions that underlie the allosteric process. In particular, the well known enzyme, imidazol glycerol phosphate synthase (IGPS), is utilized to test the proposed methodology. The eigenvector centrality measurement successfully describes the allosteric pathways of IGPS, and allows to pinpoint key amino acids in terms of their relevance in the momentum transfer process. The resulting insight can be utilized for refining the control of IGPS activity, widening the scope for its engineering. Furthermore, we propose a new centrality metric quantifying the relevance of the surroundings of each residue. In addition, the proposed technique is validated against experimental solution NMR measurements yielding fully consistent results. Overall, the methodologies proposed in the present work constitute a powerful and cost effective strategy to gain insight on the allosteric mechanism of proteins

A Ratio of Spore to Viable Organisms: A Case Study of the JPL-SAF Cleanroom

Spacecraft surfaces that are destined to land on potential life-harboring celestial bodies are required to be rigorously cleaned and continuously monitored for spore bioburden as a proxy for spacecraft cleanliness. The NASA standard assay (NSA), used for spacecraft bioburden estimates, specifically measures spores that are cultivable, aerobic, resistant to heat shock, and grow at 30 C in a nutrient-rich medium. Since the vast majority of microorganisms cannot be cultivated using the NSA, it is necessary to utilize state-of-the art molecular techniques to better understand the presence of all viable microorganisms, not just those measured with the NSA. In this study, the nutrient-deprived low biomass cleanrooms, where spacecraft are assembled, were used as a surrogate for spacecraft surfaces to measure the ratio of NSA spores in relation to the total viable microorganism population in order to make comparisons with the 2006 Space Studies Board (SSB) estimate of 1 spore per approximately 50,000 viable organisms. Ninety-eight surface wipe samples were collected from the Spacecraft Assembly Facility (SAF) cleanroom at the Jet Propulsion Laboratory (JPL) over a 6-month period. The samples were processed and analyzed using classical microbiology along with molecular methodology. Traditional microbiology plating methods were used to determine the cultivable bacterial, fungal, and spore populations. Molecular assays were used to determine the total organisms (TO, dead and live) and the viable organisms (VO, live). The TO was measured using adenosine triphosphate (ATP) and quantitative polymerase chain reaction (qPCR) assays. The VO was measured using internal ATP, propidium monoazide (PMA)-qPCR, and flow cytometry (after staining for viable microorganisms) assays. Based on the results, it was possible to establish a ratio between spore counts and VO for each viability assay. The ATP-based spore to VO ratio ranged from 149-746, and the bacterial PMA-qPCR assay-based ratio ranged from 314-1,491 VO, per spore. The most conservative estimate came from fluorescent-assisted cell sorting (FACS), which estimated the ratio to be 12,091 VO per 1 NSA spore. Since archaeal (less than 1%) and fungal (approximately 2%) populations were negligible, the spore to VO ratios were based on bacterial population estimates. The most conservative ratio from this study can be used as a replacement for the SSB estimate on nutrient-deprived (oligotrophic) desiccated spacecraft surfaces, to estimate the VO from NSA measurements without utilizing state-of-the art molecular methods that are costly and require more biomass than is typically found on spacecraft surfaces

Molecular mechanisms and environmental adaptations of flagellar loss and biofilm growth of Rhodanobacter under environmental stress

Biofilms aid bacterial adhesion to surfaces via direct and indirect mechanisms, and formation of biofilms is considered as an important strategy for adaptation and survival in suboptimal environmental conditions. However, the molecular underpinnings of biofilm formation in subsurface sediment/groundwater ecosystems where microorganisms often experience fluctuations in nutrient input, pH, and nitrate or metal concentrations are underexplored. We examined biofilm formation under different nutrient, pH, metal, and nitrate regimens of 16 Rhodanobacter strains isolated from subsurface groundwater wells spanning diverse levels of pH (3.5 to 5) and nitrates (13.7 to 146 mM). Eight Rhodanobacter strains demonstrated significant biofilm growth under low pH, suggesting adaptations for survival and growth at low pH. Biofilms were intensified under aluminum stress, particularly in strains possessing fewer genetic traits associated with biofilm formation, findings warranting further investigation. Through random barcode transposon-site sequencing (RB-TnSeq), proteomics, use of specific mutants, and transmission electron microscopy analysis, we discovered flagellar loss under aluminum stress, indicating a potential relationship between motility, metal tolerance, and biofilm growth. Comparative genomic analyses revealed the absence of flagella and chemotaxis genes and the presence of a putative type VI secretion system in the highly biofilm-forming strain FW021-MT20. In this study we identified genetic determinants associated with biofilm growth under metal stress in a predominant environmental genus, Rhodanobacter, and identified traits aiding survival and adaptation to contaminated subsurface environments

The early-stage comprehensive costs of routine PrEP implementation and scale-up in Zambia

Pre-exposure prophylaxis (PrEP) is an effective HIV prevention option, but cost-effectiveness is sensitive to implementation and program costs. Studies indicate that, in addition to direct delivery cost, PrEP provision requires substantial demand creation and client support to encourage PrEP initiation and persistence. We estimated the cost of providing PrEP in Zambia through different PrEP delivery models. Taking a guidelines-based approach for visits, labs and drugs, we estimated the annual cost of providing PrEP per client for five delivery models: one focused on key populations (men-who-have-sex-with-men (MSM) and female sex workers (FSW), one on adolescent girls and young women (AGYW), and three integrated programs (operated within HIV counselling and testing services at primary healthcare centres). Program start-up and support costs were based on program expenditure data and number of PrEP sites and clients in 2018. PrEP clinic visit costs were based on micro-costing at two PrEP delivery sites (2018 USD). Costs are presented in 2018 prices and inflated to 2021 prices. The annual cost/PrEP client varied by service delivery model, from $394 (AGYW) to$655 (integrated model). Cost differences were driven largely by client volume, which impacted the relative costs of program support and technical assistance assigned to each PrEP client. Direct service delivery costs ranged narrowly from $205-212/PrEP-client and were a key component in the cost of PrEP, representing 35–65% of total costs. The results show that, even when integrated into full service delivery models, accessing vulnerable, marginalised populations at substantial risk of HIV infection is likely to cost more than previously estimated due to the programmatic costs involved in community sensitization and client support. Improved data on individual client resource usage and outcomes is required to get a better understanding of the true resource utilization, expected outcomes and annual costs of different PrEP service delivery programs in Zambia

Initial implementation of PrEP in Zambia: health policy development and service delivery scale-up

INTRODUCTION: Daily pre-exposure prophylaxis (PrEP) for HIV prevention is highly effective, but not yet widely deployed in sub-Saharan Africa. We describe how Zambia developed PrEP health policy and then successfully implemented national PrEP service delivery. POLICY DEVELOPMENT: Zambia introduced PrEP as a key strategy for HIV prevention in 2016, and established a National PrEP Task Force to lead policy advocacy and development. The Task Force was composed of government representatives, regulatory agencies, international donors, implementation partners and civil society organisations. Following an implementation pilot, PrEP was rolled out nationally using risk-based criteria alongside a national HIV prevention campaign. NATIONAL SCALE-UP: In the first year of implementation, ending September 2018, 3626 persons initiated PrEP. By September 2019, the number of people starting PrEP increased by over sixfold to 23 327 persons at 728 sites across all ten Zambian provinces. In the first 2 years, 26 953 clients initiated PrEP in Zambia, of whom 31% were from key and priority populations. Continuation remains low at 25% and 11% at 6 and 12 months, respectively. LESSONS LEARNT: Risk-based criteria for PrEP ensures access to those most in need of HIV prevention. Healthcare worker training in PrEP service delivery and health needs of key and priority populations is crucial. PrEP expansion into primary healthcare clinics and community education is required to reach full potential. Additional work is needed to understand and address low PrEP continuation. Finally, a task force of key stakeholders can rapidly develop and implement health policy, which may serve as a model for countries seeking to implement PrEP