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Item Mechanistic implications from 'in operando' optical and electrochemical studies of bio-related fuel chemistry in solid oxide fuel cells(Montana State University - Bozeman, College of Letters & Science, 2015) Kirtley, John David; Chairperson, Graduate Committee: Robert Walker; Bryan C. Eigenbrodt and Robert A. Walker were co-authors of the article, 'In situ optical studies of oxidation kinetics of NI/YSZ cermet anodes' in the journal 'ECS transactions' which is contained within this thesis.; David M. Halat, Melissa M. McIntyre, Bryan C. Eigenbrodt and Robert A. Walker were co-authors of the article, 'High temperature 'spectrochronopotentiometry': correlating electrochemical performance with in situ raman spectroscopy in solid oxide fuel cells' in the journal 'Analytical chemistry' which is contained within this thesis.; Melissa M. McIntyre, David M. Halat and Robert A. Walker were co-authors of the article, 'Insights into SOFC NI/YSZ anode degradation using in situ spectrochronopotentiometry' submitted to the journal 'ECS transactions' which is contained within this thesis.; Anand Singh, David Halat, Thomas Oswell, Josephine M. Hill and Robert A. Walker were co-authors of the article, 'In situ raman studies of carbon removal from high temperature NI-YSZ cermet anodes by gas phase reforming agents' submitted to the journal 'Journal of physical chemistry C' which is contained within this thesis.; Daniel A. Steinhurst, Jeffrey C. Owrutsky, Michael B. Pomfret and Robert A. Walker were co-authors of the article, 'In situ optical studies of methane and simulated biogas oxidation on high temperature solid oxide fuel cells' in the journal 'Physical chemistry chemical physics' which is contained within this thesis.; Daniel A. Steinhurst, Jeffrey C. Owrutsky, Michael B. Pomfret and Robert A. Walker were co-authors of the article, 'Towards a working mechanism of fuel oxidation in SOFCS: in situ optical studies of simulated biogas and methane' submitted to the journal 'Journal of physical chemistry C' which is contained within this thesis.Solid oxide fuel cells using bio-renewable fuels promise efficient, sustainable, and clean electricity production, and are becoming more attractive sources of electrical power as global consumption of non-renewables accelerates. The excellent efficiencies of solid oxide fuel cells as solid state electrochemical devices arise mainly from the direct conversion of chemical to electrical energy--through oxygen reduction at the cathode, oxide diffusion through the electrolyte, and fuel oxidation at the anode. Some of these processes possess high activation energies, requiring high operational temperatures (generally > 650 °C). These conditions can hasten deleterious carbon accumulation and anode deterioration. These high operating temperatures also pose significant challenges in directly observing chemical reactions responsible for electrochemical oxidation and materials degradation. Yet, these observations are needed to understand fundamental mechanisms responsible for these processes--an understanding necessary to improve the performance, durability and versatility of SOFCs, especially as these devices are required to operate with complex fuels and fuel mixtures. In this work, solid oxide fuel cells constructed with traditional Ni/yttrium stabilized zirconia ceramic-metallic (or cermet) anodes are studied in operando and in situ with several novel optical techniques (Raman vibrational spectroscopy, near infrared thermal imaging and fourier-transform infrared emission spectroscopy) and electrochemical measurements that provide vital insights into mechanisms surrounding bio-related fuel electrochemistry. The first study demonstrated that Ni oxidation is slower than reduction at the anode. The second study quantified electrochemically accessible anode carbon accumulation under methane fuel, while detailing deleterious mechanisms and microstructural changes that accompany cell polarization in the absence of gas phase fuels. The third study explored the kinetics of carbon removal from Ni-based anodes by CO 2, H 2O, and O 2 and detailed mechanistically why they may be different. The fourth study revealed mechanisms associated with carbon formation and current generation from biogas and methane as a function of operational condition. Collectively, these studies have begun to provide the direct, molecularly specific information necessary to empirically evaluate mechanistic descriptions of biorelated fuel electrochemistry and anode degradation.Item Characterization of the [FeFe]-hydrogenase : toward understanding and implementing biohydrogen production(Montana State University - Bozeman, College of Letters & Science, 2014) Swanson, Kevin Daniel; Chairperson, Graduate Committee: John W. PetersHydrogen may provide an avenue for a clean renewable fuel source, yet the methods to produce hydrogen are either extremely energy intensive, rely on fossil fuels, or require expensive noble metal catalysts. Biology may hold the keys necessary to unlocking new technologies that could change how hydrogen is produced. Microbial processes also produce hydrogen and harbor enzymes that carryout the reversible reduction of protons to hydrogen gas. These enzymes are capable of producing hydrogen at high rates comparable to platinum catalysts, but biological hydrogen catalysts can produce hydrogen using abundant elements carbon, oxygen, nitrogen, sulfur, iron, nickel and selenium. Biological hydrogen catalysts are termed hydrogenases, and though hydrogenases use abundant elements they are extraordinarily complex. This has made it difficult to construct model complexes using inorganic synthesis that can replicate the activities of their biological counterparts. One way to circumvent this problem is to use microbial hydrogen production and let microbes produce and maintain these enzymes inside a cell. Microbial hydrogen production also has the added benefit that hydrogen production could be engineered to connect with other metabolic processes such as photosynthesis and fermentation. Engineering microbes for hydrogen production could eventually allow for the production of hydrogen using inexpensive energy inputs such as solar energy or waste materials. Yet, there are many barriers that need to be overcome in order to engineer a robust microbial organism. One of the primary difficulties of developing this technology has been the oxygen sensitivity of hydrogenases. Hydrogenases when exposed to atmospheric concentrations of oxygen either completely inactivate or their rates are significantly slowed. To engineer a hydrogenase that is more amenable for microbial hydrogen production, the optimization of expressing and purifying hydrogenase enzymes has been developed. Methodologies have been developed to characterize how oxygen inactivates hydrogenase enzymes, and a new methodology has been explored to help find novel hydrogenase gene sequences that may help in engineering oxygen tolerant enzymes.Item Investigation into the metabolic control of lipid accumulation in the marine diatom Phaeodactylum tricornutum(Montana State University - Bozeman, College of Letters & Science, 2013) Valenzuela, Jacob Joseph; Co-chairpersons, Graduate Committee: Brian Bothner and Matthew Fields; R.P. Carlson, R. Gerlach, K.E. Cooksey, B.M. Peyton, B. Bothner, and M.W. Fields were co-authors of the article, 'Nutrient level control of cell growth and bio-oil accumulation in Phaeodactylum tricornutum' in the journal 'Applied microbiology and biotechnology' which is contained within this thesis.; A. Mazurie, R.P. Carlson, R. Gerlach, K.E. Cooksey, B.M. Peyton, and M.W. Fields were co-authors of the article, 'Potential role of multiple carbon fixation pathways during lipid accumulation in Phaeodactylum tricornutum' in the journal 'Biotechnology for biofuels' which is contained within this thesis.The uncontrolled consumption of fossil fuels over the last two centuries has resulted in unprecedented rates of CO 2 (greenhouse gas) accumulation in the atmosphere, which caused an increased average global temperature and climate shifts. Replacing current fuel demands with a renewable and carbon neutral biofuel can alleviate some of the negative consequences of fossil fuel emissions. Algal biofuel can be that renewable energy source. Microalgae are unicellular photosynthetic organisms that can grow on CO 2 as the sole source of carbon by harvesting light energy. Under nutrient limited conditions microalgae will store carbon as oil or triacylglycerides (TAGs). Algal bio-oil can be harvested and converted to biodiesel, which can be put into any current diesel engine without modification. The objective of this dissertation is to characterize bio-oil accumulation in the marine diatom, Phaeodactylum tricornutum by transcriptomic profiling and to investigate metabolic control points during light and dark photoperiods. Extensive growth analysis in tandem with RNA sequencing provided insight into the metabolism of TAG accumulation in microalgae. Phosphate and nitrate depletion initiated lipid accumulation independently, but nitrate depletion resulted in greater lipid yields. Nutrient depletion caused cell cycle arrest, which is controlled by the differential expression diatom specific cyclins. During times of decreased inorganic carbon levels P. tricornutum will employ carbon-concentrating mechanisms to maintain carbon flow for photosynthesis during the light cycle. During the dark period up-expression of CCM genes is still maintained for replenishing carbon intermediates of the TCA and urea cycle. Acetyl-CoA carboxylase is the rate-limiting step in fatty acid biosynthesis, but during the light period it is not highly over-expressed. However, central carbon metabolism pathways are highly expressed throughout growth and during the light and dark cycle. It was postulated that elevated concentrations of precursor carbon pools are driving lipid accumulation without a highly expressed acetyl-CoA carboxylase. Thus, enhancement of lipid accumulation is controlled by upstream carbon flow from pathways like the urea and TCA cycle to fatty acid biosynthesis.Item Insights into key barriers in the implementation of renewable biofuel technologies(Montana State University - Bozeman, College of Letters & Science, 2013) Therien, Jesse Beau; Chairperson, Graduate Committee: John W. Peters; Keith E. Cooksey, Matthew C. Posewitz, and John W. Peters were co-authors of the article, 'Extended hydrogen production by alginate-immobilized, sulfur-deprived Chlamydomonas reinhardtii' submitted to the journal 'International journal of hydrogen energy' which is contained within this thesis.; Oleg A. Zadvornyy and John W. Peters were co-authors of the article, 'Phototroph co-culturing for the optimal production of biofuels' submitted to the journal 'Biotechnology for biofuels' which is contained within this thesis.; Trinity L. Hamilton, Donald A. Bryant, Zhenfeng Liu, Seth M. Noone, Paul W. King, and John W. Peters were co-authors of the article, 'Genome of Clostridium pasteurianum, transcriptional analysis and structural determinants of its hydrogenases' submitted to the journal 'Journal of bacteriology' which is contained within this thesis.Bioenergy can be defined as renewable energy derived from biological sources. As world energy consumption increases and fossil fuel supplies are depleted, national and international energy requirements will become more diverse and more complicated. Clearly, the niche that alternative and renewable energy sources occupy in the energy portfolio will continue to increase over time. Currently, bioenergy in the form of biofuel production including alcohols, lipids, and hydrogen represent working technologies that are in large part only economically limited where large scale production is currently too costly to compete with fossil fuels. As a result, there has been a significant investment in basic science research to make these technologies more robust and more amenable to scale up. This includes large scale cultures of model biofuel producing organisms, consortia of organisms, and even mimetic systems in which components derived from biological sources are incorporated into materials. The success of future biofuel technologies is dependent on advancing these technologies by overcoming some of the key barriers that decrease the practicality of wide scale implementation. A key to the large scale production of biofuels in the form of alcohols, lipids, or hydrogen is to develop mechanisms to limit the costs associated with culturing organisms and harvesting fuels. A technique used to facilitate the production of bio-hydrogen from eukaryotic algae is described and shows promise as a way to reduce costs associated with handling microorganisms used in bioreactors. Immobilization the hydrogen producing alga Chlamydomonas reinhardtii in calcium alginate facilitates manipulation of culture conditions during biofuel production and their subsequent harvest. The design of tailored microbial consortia or co-culturing multiple organisms provides a means of simplifying and reducing costs of media components required for biofuel production by providing key media components metabolically. Finally, genomic and gene expression studies have provided clues into structural determinants responsible for superior hydrogen production by certain enzymes that can be incorporated into model hydrogen producing organisms or merged into biomaterials. Together, these studies have contributed to the progression and knowledge of bioenergy promoting an increasing and long lasting presence of renewable fuels in the global energy portfolio.