abstract: As the detection of planets become commonplace around our neighboring stars, scientists can now begin exploring their possible properties and habitability. Using statistical analysis I determine a true range of elemental compositions amongst local stars and how this variation could affect possible planetary systems. Through calculating and analyzing the variation in elemental abundances of nearby stars, the actual range in stellar abundances can be determined using statistical methods. This research emphasizes the diversity of stellar elemental abundances and how that could affect the environment from which planets form. An intrinsic variation has been found to exist for almost all of the elements studied by most abundance-finding groups. Specifically, this research determines abundances for a set of 458 F, G, and K stars from spectroscopic planet hunting surveys for 27 elements, including: C, O, Na, Mg, Al, Si, S, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Y, Zr, Mo, Ba, La, Ce, Nd, Eu, and Hf. Abundances of the elements in many known exosolar planet host stars are calculated for the purpose investigating new ways to visualize how stellar abundances could affect planetary systems, planetary formation, and mineralogy. I explore the Mg/Si and C/O ratios as well as place these abundances on ternary diagrams with Fe. Lastly, I emphasize the unusual stellar abundance of τ Ceti. τ Ceti is measured to have 5 planets of Super-Earth masses orbiting in near habitable zone distances. Spectroscopic analysis finds that the Mg/Si ratio is extremely high (~2) for this star, which could lead to alterations in planetary properties. τ Ceti's low metallicity and oxygen abundance account for a change in the location of the traditional habitable zone, which helps clarify a new definition of habitable planets. / Dissertation/Thesis / Ph.D. Astrophysics 2014

Este trabalho apresenta o estudo de algumas moléculas do meio interestelar úteis para o levantamento do conteúdo de matéria orgânica do universo e para as condições pré-bióticas na Terra e em outros ambientes no universo. Utilizamos como objeto-teste a Nebulosa Cabeça de Cavalo, devido à sua geometria simples, à sua distância moderada até nós, ao seu campo de radiação ultravioleta bem conhecido resultante da iluminação por uma estrela próxima, $\\sigma$ Orionis, e por ter sido extensivamente estudada por diversos trabalhos. Desse modo, podemos investigar com segurança diversos processos físicos e químicos no meio interestelar. O principal instrumento utilizado neste trabalho foi o código PDR Meudon devido ao fato de que é amplamente utilizado por ser um dos programas de análise de dados de projetos recentes de astronomia, como o projeto Herschel, e por ser público. O código pode ser utilizado para modelizar com confiabilidade a Nebulosa Cabeça de Cavalo, visto que ela mesma é uma PDR (região de fotodissociação) prototípica. Atualizamos o setor de química do código para testar diversos cenários de formação de moléculas. Consideramos o impacto nas abundâncias derivadas das moléculas de várias suposições em relação ao estado do gás (modelos isocórico, isotérmico e isobárico), decidindo em favor de um modelo isobárico. Verificou-se o papel dos raios cósmicos e de vários conjuntos de dados das reações químicas. Obtivemos as abundâncias de várias moléculas, incluindo algumas de potencial importância pré-biótica: CN e seus íons, HCN, HNC, nitrilas e seus íons, hidretos de nitrogênio, benzeno. Investigamos o papel dos ânions e dos PAHs. Finalmente, exploramos canais de produção para heterocíclicos nitrogenados com relevância em astrobiologia: pirrol e piridina. As presentes simulações apresentaram como a exploração de uma pequena gama de possíveis canais de produção de heterocíclicos já resultou em abundâncias significativas para ao menos uma espécie de heterocíclicos nitrogenados, a piridina. Dessa forma, excursões sistemáticas pelos diversos canais de produção deverão revelar mais espécies para serem alvos de buscas. / This work presents the study of some molecules of the interstellar medium that are useful for the bookkeeping of the molecular content of the universe and for prebiotic conditions on Earth and in other environments in the universe. The Horsehead Nebula was chosen as test object, due to its simple geometry, its moderate distance to us, its well-known ultraviolet radiation field resulting from the star $\\sigma$ Orionis, and due the fact that it has been extensively studied in several works. In this way, we can safely investigate several physical and chemical processes on the interstellar medium. The main tool used in the present work was the Meudon PDR code due the fact that it is widely used as one of the legacy data analysis programs of current astronomy projects, e.g. the Herschel project, and it is public. The code can reliably model the Horsehead Nebula, since this nebula is a prototypic PDR (photodissociation region). We updated the chemical sector of the code in order to test several scenarios for molecule production. We considered the impact on the derived molecule abundances of several assumptions relative to the gas state (isochoric, isothermal and isobaric models), and the isobaric model was found to be the most plausible. We checked the role of cosmic rays and several datasets of chemical reactions. We derived the abundances of several molecules, including some of potential prebiotic importance: CN and their ions, HCN, HNC, nitriles and their ions, nitrogen hydrides, and benzene. We investigated the role of anions and PAHs. Finally, we explored production channels for astrobiologically relevant nitrogenated heterocycles: pyrrole and pyridine. This presents simulations show us how the exploration of a small quantities of possibles path of prodution of heterocycles resulted already in significants abundances at least one n-heterocycle specie, the pyridine. Thereby, systemact tours for the many productions paths should show more species to be targe of searches.

abstract: Universal biology is an important astrobiological concept, specifically for the search for life beyond Earth. Over 1.2 million species have been identified on Earth, yet all life partakes in certain processes, such as homeostasis and replication. Furthermore, several aspects of biochemistry on Earth are thought to be universal, such as the use of organic macromolecules like proteins and nucleic acids. The presence of many biochemical features in empirical data, however, has never been thoroughly investigated. Moreover, the ability to generalize universal features of Earth biology to other worlds suffers from the epistemic problem of induction. Systems biology approaches offer means to quantify abstract patterns in living systems which can more readily be extended beyond Earth’s familiar planetary context. In particular, scaling laws, which characterize how a system responds to changes in size, have met with prior success in investigating universal biology. This thesis rigorously tests the hypothesis that biochemistry is universal across life on Earth. The study collects enzyme data for annotated archaeal, bacterial, and eukaryotic genomes, in addition to metagenomes. This approach allows one to quantitatively define a biochemical system and sample across known biochemical diversity, while simultaneously exploring enzyme class scaling at both the level of both individual organisms and ecosystems. Using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Joint Genome Institute’s Integrated Microbial Genomes and Microbiomes (JGI IMG/M) database, this thesis performs the largest comparative analysis of microbial enzyme content and biochemistry to date. In doing so, this thesis quantitatively explores the distribution of enzyme classes on Earth and adds constraints to notions of universal biochemistry on Earth. / Dissertation/Thesis / Masters Thesis Geological Sciences 2020

For this research project we designed an instrument to detect bacteria via biomolecular fluorescence. We introduce the current understanding of astrobiology, our knowledge of life beyond Earth, and the commonality of Earth life as it pertains to the search for life on Mars. We proposed a novel technique for searching for direct evidence of life on the surface of Mars using fluorescence. We use the arid region of the Mojave Desert as an analog of Mars. Results indicate the fluorescence of the biotic component of desert soils is approximately as strong as the fluorescence of the mineral component. Fluorescence laboratory measurements using the portable instrument reveal microbial concentration in the Mojave Desert soil is 107 bacteria per gram of soil. Soil microbial concentrations over a 50 meter area in the Mojave Desert, determined in situ via fluorescence, show that the number varies from 104 to 107 cells per gram of soil. We then designed an instrument for detection of biomolecular fluorescence, and considered also fluorescence from polycyclic aromatic hydrocarbons and minerals on the Martian surface. The majority of the instrument is designed from Mars surface operation flight qualified components, drastically reducing development costs. The basic design adapts the ChemCam instrument package on-board Mars Science Laboratory rover Curiosity to detect organics via fluorescence. By placing frequency multipliers in front of the 1064 nm laser, wavelengths suitable for fluorescence excitation (266 nm, 355 nm, and 532 nm) will be achieved. The emission system is modified by the addition of band pass filters in front of the existing spectrometers to block out the excitation energy. Biomolecules and polycyclic aromatic hydrocarbons are highly fluorescent at wavelengths in the ultra violet (266 nm, 355 nm), but not as much in the visible 532 nm range. Preliminary results show minerals discovered, such as perchlorate, fluoresce highest when excited by 355 nm. Overall, we conclude the fluorescent instrument described is suitable to detect soil microbes, organics, biomolecules, and some minerals via fluorescence, offering a high scientific return for minimal cost with non-contact applications in extreme environments on Earth and on future missions to Mars.

Given the role of HCN as a reactant in RNA building block production (e.g. nucleobases, ribose, and 2-aminooxazole), we propose that an atmosphere rich in hydrogen cyanide (HCN) is a distinguishing feature of what we term biogenic worlds. These are worlds that can produce key biomolecules for the emergence of life in situ rather than requiring they be delivered, e.g., by meteorites. To attack the question of whether early Earth was biogenic, we develop a series of new capabilities including the calculation of missing/unknown HCN reaction rate coefficients, the simulation of HCN chemistry in planetary atmospheres, and the coupling of atmospheric HCN chemistry and rain-out to the production and evolution of RNA building blocks in warm little ponds (WLPs). We make a major leap in understanding the origin of RNA on a biogenic early Earth by building a comprehensive model that couples terrestrial geochemistry, radiative transfer, atmospheric photochemistry, lightning chemistry, and aqueous pond chemistry. We begin by developing an accurate and feasible method to calculate missing reaction rate coefficients related to HCN chemistry in planetary atmospheres. We use density functional theory simulations to solve the transition states for various reactions, and use the simulated energies and partition functions to calculate the corresponding rate coefficients using the principles of statistical mechanics. We initially explore and calculate rate coefficients for a total of 110 reactions present in reducing atmospheres dominated by N2, CH4, and H2, including 48 reactions that were previously unknown in the literature. Our rate coefficients are most commonly within a factor of two of experimental values, and generally always within an order of magnitude of these values. This accuracy is consistent with the typical uncertainties assigned in large-scale kinetic data evaluations. Next, we develop a consistent reduced atmospheric hybrid chemical network (CRAHCN) containing experimental values when available (32%) and our calculated rate coefficients otherwise (68%). To validate our chemistry, we couple CRAHCN to a 1D disequilibrium chemical kinetic model (ChemKM) to compute HCN production in the reducing atmosphere of Saturn's moon Titan. Our calculated atmospheric HCN profile agrees very well with the measurements performed by instruments aboard the Cassini spacecraft, suggesting our chemical network is accurate for modeling HCN production in reducing environments. We also perform sensitivity analyses on this chemistry and find HCN production and destruction on Titan can be understood in terms of only 19 dominant reactions. The process begins with UV photodissociation of N2 and CH4 in the upper atmosphere, and galactic cosmic ray dissociation of these species in the lower atmosphere. The dissociation radicals then proceed to react along four main channels to produce HCN. It is of particular excitement that one of these channels was newly discovered in this work. Moving forward to modeling early Earth, we expand upon CRAHCN by exploring and calculating rate coefficients related to HCN and H2CO chemistry in atmospheres with oxidizing conditions. We calculate the rate coefficients for 126 new reactions, including 45 reactions that were first discovered in this work. We find the accuracy of our method continues to produce most commonly factor of two agreement with respect to experimental values. Next, we develop the oxygen extension to CRAHCN (CRAHCN-O), containing a total of 259 reactions for computing HCN and H2CO production in atmospheres dominated by N2, CO2, H2, CH4, and H2O. Again, experimental rate coefficients are used when available (43%), and our calculated values are used otherwise (57%). We then build a comprehensive model with a unique coupling of early Earth geochemistry, radiative transfer, atmospheric UV and lightning chemistry, and aqueous chemistry in WLPs. We calculate self-consistent pressure-temperature profiles using a 1D radiative transfer code called petitRADTRANS, and couple these to CRAHCN-O and ChemKM to simulate HCN and H2CO production on early Earth. We model two epochs, at 4.4 and 4.0 billion years ago (bya), which differ in atmospheric composition, luminosity, UV intensity, radical production from lightning, and impact bombardment rate. The respective reducing and oxidizing atmospheric compositions of the 4.4 and 4.0 bya epochs are mainly driven by the balance of H2 impact degassing and CO2 outgassing from volcanoes. We then couple the rain-out of HCN with a comprehensive WLP model to compute the in situ production of RNA building blocks for each epoch. HCN pond concentrations are multiplied by experimental yields to calculate biomolecule production, and there are various biomolecule sinks present including UV photodissociation, hydrolysis and seepage. At 4.4 bya, we find that HCN rain-out leads to peak adenine production of 2.8μM (378 ppb) for maximum lightning conditions. These concentrations are comparable to the peak adenine concentrations delivered by carbon-rich meteorites (10.6μM); however, the concentrations from in situ production persist for > 100 million years in contrast to ~days for meteoritic concentrations. Guanine, cytosine, uracil and thymine concentrations from in situ production at this time peak in the 0.19–3.2μM range, and ribose and 2-aminooxazole peak in the nM range. We note that cytosine and thymine are not present in meteorites, suggesting this biogenic pathway may be one of the only plausible origins of these RNA and DNA building blocks. We find that the high mixing ratio of HCN near the surface of our 4.4 bya model is mainly driven by lightning chemistry rather than UV chemistry. Our results show that HCN production at the surface is linearly dependent on lightning flash density. This result supports a lightning-based Miller-Urey scenario for the origin of RNA building blocks. At 4.0 bya, HCN production and rain-out is 2–3 orders of magnitude less abundant than it is at 4.4 bya, leading to negligible concentrations of RNA building blocks in WLPs during this late oxidizing phase. Similar to HCN production in Titan's atmosphere, HCN production in early Earth's atmosphere is strongly correlated with CH4 content. Reducing (H2-dominant) conditions sustain CH4 levels at a roughly constant ppm-level over 100 million years, which is favourable for HCN production. In oxidizing conditions, CH4 is readily oxidized into CO2, leading to less HCN. These results suggest that early Earth was biogenic at 4.4 bya, and remained so for at least ~100 million years, but was over by 4.0 bya due to oxidation of the atmosphere. This thesis provides a firm theoretical foundation for an origin of RNA in WLPs on a biogenic early Earth within about 200 million years after the Moon-forming impact and the cooling of the magma ocean. / Thesis / Doctor of Philosophy (PhD)

No / The Raman and mass spectra of 1,4-diphenylbuta-1,3-diene and several of its monomethyl and dimethyl homologues are reported and discussed, with a view to developing a spectroscopic protocol for detecting the presence and position of a methyl group in these compounds. Raman spectroscopy and mass spectrometry are shown to provide complementary information, by which the four available monomethyl homologues may be readily distinguished from each other and 1,4-diphenylbuta-1,3-diene itself. The utility of these 1,4-diarylbutadienes as model compounds for carotenoids and related materials, which may serve as indicators of extinct or extant extraterrestrial life, is considered.

No / Recent studies relating to the analytical chemical characterization of terrestrial extremophiles reveal the presence of biomolecules that have been synthesized for the survival of the colonies in response to the extreme environmental conditions, where otherwise life could not exist. This is a vital part of the planned space missions now being undertaken to planets and their satellites in the search for extinct or extant life signatures in our Solar System. Extremophiles have existed on the Earth for some 3.8 Gyr and their interrogation indicates their strategic survival methods which can be associated and compared with extraterrestrial scenarios on Mars, Titan, Enceladus and Europa.

Life would not exist in the absence of catalysis. The “RNA World” model for the origin of life hinges on the capabilities of ribonucleic acid to encode information and perform catalysis (i.e. self-replication). Previously, functional nucleic acids such as ribozymes and deoxyribozymes (DNAzymes) have been isolated using the process of in vitro selection. This method is typically performed by isolating a catalytically active molecule from a large random library, with the assumption being that active molecules are already present in the pool and this method filters them from inactive molecules. However, in vitro selection has never been used to show that a molecule can be evolved from an inactive to an active catalyst. Here we show that the properties of DNA can be exploited to act as a proxy system for the origins of biotic chemistry by isolating a functional catalyst from a previously non-catalytic sequence. This project employs a novel perspective; rather than a random library, a known, non-functional sequence is utilized. Using in vitro selection, this known sequence is gradually evolved into a functional catalyst by solely allowing the existence of sequences that acquire mutations which enhance their function. Deep sequencing analysis of DNA pools along the evolution trajectory has identified individual mutations as the progressive drivers of molecular evolution. Evolving a catalyst from a non-catalyst gives insight into the comprehension of how life originated. This project demonstrates that an enzyme can indeed arise from a sequence of a functional polymer via permissive molecular evolution, a mechanism that may have been exploited by nature for the creation of the enormous repertoire of enzymes in the biological world today. / Thesis / Master of Science (MSc)

The search for life beyond Earth is the driving force behind several future missions to Mars. An essential task in the lead-up to these missions is a critical assessment of the habitability for, and feasibility of, life. However, little research has been conducted on this issue, and our understanding of the plausibility for life on Mars remains unconstrained. Owing to the anoxic and iron-rich nature of Mars, microbial iron reduction (MIR) represents a compelling candidate metabolism to operate in the Martian subsurface, past and present. The objectives of this thesis are to address the feasibility of MIR on Mars by i) better defining the habitability of MIR on Earth, and ii) assessing the range and availability of organic electron donors in the subsurface of Earth and Mars. Samples collected from Mars-relevant environments on Earth were used to initiate MIR enrichment cultures at 4°C, 15°C and 30°C. Results indicate MIR is widespread in riverbed and subglacial sediments but not sediments from desert or recent volcanic plains. The iron-reducing microorganisms in subglacial enrichments are at least psychrotolerant and in some cases psychrophilc. Culture-independent methods highlighted the changes in diversity between temperature conditions for subglacial sediments, and indicated that members of the prolific MIR Geobacteraceae family are common. The genera Geobacter and Desulfosporosinus are responsible for MIR in the majority of enrichments. Long-term anoxia and the availability of redox constituents are the major factors controlling MIR in these environments. A MIR enrichment culture was unable to use shales and kerogens as the sole source of electron donors for MIR, despite the presence of known electron donors. Furthermore, MIR was inhibited by the presence of certain kerogens. The causes of inhibition are unknown, and are likely to be a combination of chemical and physical factors. Experiments were conducted to assess the ability of three pure strains and a MIR enrichment to use non-proteinogenic amino acids common to carbonaceous meteorites as electron donors for MIR. Results demonstrate that γ-aminobutyric acid served as an electron donor for the enrichment culture, but no other amino acids supported MIR by this or other iron-reducing cultures. The D-form of chiral amino acids was found to exert a strong inhibitory effect, which decreased in line with concentration. Theoretical calculations using published meteoritic accretion rates onto the surface of Mars indicate that the build up inhibitory amino acids may place important constrains on habitability over geologic time scales. Contamination of a pure strain of Geobacter metallireducens with a strain of Clostridium revealed a syntrophic relationship between these microorganisms. Anaerobic heterotrophs are likely to play an important role in maintaining an available supply of electron donors for MIR and similar chemoorganic metabolisms operating in the subsurface. This research indicates that MIR remains a feasible metabolism to operate on Mars providing a readily available redox couple is present. However, given the observed inhibition in the presence of bulk carbonaceous material and certain amino acids found in meteorites, the use of extraterrestrial carbonaceous material in the Martian subsurface for microbial iron reduction is questionable, and should be the focus of future research.

Exoplanets are now known to be ubiquitous throughout the Galaxy. From the Kepler survey, we expect nearly every main-sequence star to form planetary systems during its formation phase. However, the detection limits of Kepler are confined to planets with short orbital periods, comparable to those in the inner solar system. Thanks to the long observational time baseline of the McDonald Observatory Radial Velocity (RV) Survey, we can identify gas giant planets in the outer regions of extrasolar planetary systems. The statistics of such planets are not well known, and are important for understanding the physics behind planet formation and migration. In this dissertation, I detail the discovery of five giant exoplanets on long-period orbits–so-called “Jupiter analogs.” For two systems of giant planets discovered through our survey, pairs of planets follow closely-packed orbits, creating the possibility for dynamical instability. I therefore examine the orbital resonances that allow these planets to avoid gravitational disruption. Because we see an abundance of small, potentially habitable exoplanets in the Kepler data set, current and upcoming exoplanet surveys concentrate on finding Earth-mass planets orbiting stars near enough to facilitate detailed follow-up observations. Particularly attractive targets are cool, low-mass “M dwarf” stars. Their low masses (and thus higher RV amplitudes from exoplanets) and close-in habitable zones allow for relatively quick detection of low-mass planets in the habitable zone. However, the RV signals of such planets will be obscured by stellar magnetic activity, which is poorly understood for M stars. In an effort to improve the planet detection capabilities of our M dwarf planet survey, I have conducted a detailed investigation of the magnetic behavior of our target stars. I show that, while stellar activity does not appear to systematically influence RV measurements above a precision level of ∼ 5 m/s, activity cycles can occasionally produce RV signals in excess of 10 m/s. Additionally, I show that long-term, solar-type stellar activity cycles are common amongst our M dwarf targets, although they are significantly less frequent than for FGK stars. In the case of GJ 328, I have discovered a magnetic activity cycle that appears in the RV data, causing the giant planet around the star to appear to be on a more circular orbit than indicated by the activity-corrected data. Such corrections are essential for the discovery of Earthlike exoplanets. / text