The ironmaking process involves the removal of oxygen atoms from the iron oxides to produce iron. Currently, the coal/coke-based blast furnace process dominates the industry with a 71% share of global steel production, making it responsible for 25% of total global industrial CO2 emissions. Several processes have been commercialized to reduce these CO2 emissions such as the direct reduction process which utilizes natural gas for energy and reducing agent. In the last few decades, H2 has been identified as an alternative reducing agent in place of coal and reformed natural gas for decarbonizing the ironmaking process.To commercialize the H2 direct reduction (H2DR) process, it is necessary to study this process on a laboratory, pilot, and industrial scale to identify and address the roadblocks in the path of commercialization. Based on the literature review performed in this dissertation, four knowledge gaps were identified, and hypotheses were formulated to address the same. First, a numerical model was developed for a single iron ore pellet reduction process with a dynamic porosity function, and it was validated using experiments. Second, the equation of the radius of pellet was derived as a function of the degree of reduction using experimental data to account for the shrinking and swelling. Third, a numerical model was developed for a pilot scale H2DR reactor and was validated for average metallization of the pellets at the reactor outlet and the internal temperature profile in the reduction zone. Fourth, the numerical model for the pilot scale H2DR reactor showed a gradient of metallization at the outlet boundary which was validated by experimental metallization analysis of 31 randomly selected pellet samples one by one. At the end of the dissertation, the pilot scale model of the H2DR reactor was scaled up to an industrial scale with a DRI production capacity of 2.38 million tons/year approximately. The mass balance obtained from the industrial scale model was used to perform the techno-economic analysis to determine the economic implications of shifting from a 100% natural gas operation to a 100% H2 operation on an industrial scale.

Amino acids and related targets are typically produced by well-characterized heterotrophs including Corynebacterium glutamicum and Escherichia coli. Recent efforts have sought to supplant these sugar-intensive processes through the metabolic engineering of cyanobacteria, which instead can directly utilize atmospheric carbon dioxide (CO2) and sunlight. One of the most promising among recently discovered photoautotrophic strains is Synechococcus elongatus UTEX 2973 (hereafter UTEX 2973), which has been reported to have doubling times as low as 1.5 hours. While encouraging, there are still major challenges preventing the widespread industrial acceptance of engineered cyanobacteria, chief among them is the scarcity of genetic tools and parts with which to engineer production strains. Here, UTEX 2973 was engineered to overproduce L-lysine through the heterologous expression of feedback-resistant copies of aspartokinase lysC and the L-lysine exporter ybjE from Escherichia coli, as aided by the characterization of novel combinations of genetic parts and expression sites. At maximum, using a plasmid-based expression system, a L-lysine titer of 556 ± 62.3 mg/L was attained after 120 hours, surpassing a prior report of photoautotrophic L-lysine bioproduction. Modular extension of the pathway then led to the novel photosynthetic production of the corresponding diamine cadaverine (55.3 ± 6.7 mg/L by 96 hours) and dicarboxylate glutarate (67.5 ± 2.2 mg/L by 96 hours). Lastly, mass transfer experiments were carried out to determine if the solubility of CO2 in and its rate of mass transfer to BG-11 media could be improved by supplementing it with various amines, including cadaverine. Ultimately, however, cyanobacteria grown in the presence of all tested amines was worse than in BG-11 alone, demonstrating the need for additional tolerance engineering to successfully implement this strategy.

Cyanobacteria contribute to more than a quarter of the primary carbon fixation worldwide. They have evolved a CO2 concentrating mechanism (CCM) to enhance photosynthesis because inorganic carbon species are limited in the aqueous environment. Bicarbonate transporters SbtA and BicA are active components of CCM, and the determination of their structures is important to investigate the bicarbonate transport mechanisms. E. coli was selected as the expression host for these bicarbonate transporters, and optimization of expression and protein purification conditions was performed. Single particle electron cryomicroscopy (cryo-EM) or protein crystallography was carried out for each transporter. In this work, SbtA, BicA and SbtB, a regulator protein of SbtA, were heterologously expressed in E. coli and purified for structural studies. SbtB was highly expressed and two different crystal structures of SbtB were resolved at 2.01 Å and 1.8 Å, showing a trimer and dimer in the asymmetric unit, respectively. The yields of SbtA and BicA after purification reached 0.1 ± 0.04 and 6.5 ± 1.0 mg per liter culture, respectively. Single particle analysis showed a trimeric conformation of purified SbtA and promising interaction between SbtA and SbtB, where the bound SbtB was also possibly trimeric. For some crystallization experiments of these transporters, lipidic cubic phase (LCP) was used. In the case of LCP, often times the crystals grown are generally too tiny to withstand radiation damage from the X-ray beam during an X-ray diffraction experiment. As an alternative approach for this research, the microcrystal electron diffraction (MicroED) method was applied to the LCP-laden crystals because it is a powerful cryo-EM method for high-resolution structure determination from protein microcrystals. The new technique is termed as LCP-MicroED, however, prior to applying LCP-MicroED to the bicarbonate transporters, methods needed to be developed for LCP-MicroED. Therefore the model protein Proteinase K was used and its structure was determined to 2.0 Å by MicroED. Additionally, electron diffraction data from cholesterol and human A2A adenosine receptor crystals were collected at 1.0 Å and 4.5 Å using LCP-MicroED, respectively. Other applications of MicroED to different samples are also discussed.

Oxygen transfer reactions are central to many catalytic processes, including those underlying automotive exhaust emissions control and clean energy conversion. The catalysts used in these applications typically consist of metal nanoparticles dispersed on reducible oxides (e.g., Pt/CeO2), since reducible oxides can transfer their lattice oxygen to reactive adsorbates at the metal-support interface. There are many outstanding questions regarding the atomic and nanoscale spatial variation of the Pt/CeO2 interface, Pt metal particle, and adjacent CeO2 oxide surface during catalysis. To this end, a range of techniques centered around aberration-corrected environmental transmission electron microscopy (ETEM) were developed and employed to visualize and characterize the atomic-scale structural behavior of CeO2-supported Pt catalysts under reaction conditions (in situ) and/or during catalysis (operando). A model of the operando ETEM reactor was developed to simulate the gas and temperature profiles during conditions of catalysis. Most importantly, the model provides a tool for relating the reactant conversion measured with spectroscopy to the reaction rate of the catalyst that is imaged on the TEM grid. As a result, this work has produced a truly operando TEM methodology, since the structure observed during an experiment can be directly linked to quantitative chemical kinetics of the same catalyst. This operando ETEM approach was leveraged to investigate structure-activity relationships for CO oxidation over Pt/CeO2 catalysts. Correlating atomic-level imaging with catalytic turnover frequency reveals a direct relationship between activity and dynamic structural behavior that (a) destabilizes the supported Pt particle, (b) marks an enhanced rate of oxygen vacancy creation and annihilation, and (c) leads to increased strain and reduction in the surface of the CeO2 support. To further investigate the structural meta-stability (i.e., fluxionality) of 1 – 2 nm CeO2-supported Pt nanoparticles, time-resolved in situ AC-ETEM was employed to visualize the catalyst’s dynamical behavior with high spatiotemporal resolution. Observations are made under conditions relevant to the CO oxidation and water-gas shift (WGS) reactions. Finally, deep learning-based convolutional neural networks were leveraged to develop novel denoising techniques for ultra-low signal-to-noise images of catalytic nanoparticles.

The list of applications of plasmonic nanoparticles in the fields of energy research, sensing, and diagnostics and therapeutics is continuously growing. Processes for the synthesis of the nanoparticles for such applications should incorporate provision to easily functionalize the particle formed and should ideally not use toxic reagents or create toxic by-products. The traditional methods of synthesizing nanoparticles generally are energy inefficient, requires stringent conditions such as high temperature, pressure or extreme pH and often produces toxic by-products. Although there exist a few solution-based methods to solve this problem, there is one avenue which has recently gained attention for nanoparticle synthesis: using biomolecules to facilitate nanomaterials synthesis. Using biomolecules for synthesis can provide a template to guide the nucleation process and helps to keep conditions biocompatible while also combining the step of functionalization of the nanoparticle with its synthesis through the biomolecule itself. The dissertation focuses on studying the bio-templated synthesis of two such noble metal nanoparticle which have biomedical applications: gold and platinum. In chapter 2, Gold Nanoparticles (GNP), with long-term stability, were synthesized using Maltose Binding Protein (MBP) as templating agent. The site of gold interaction on MBP was identified by X-ray crystallography. A novel gold binding peptide, AT1 (YPFGGSGGSGM), was designed based on the orientation of the residues in the gold binding site, identified through crystallography. This designed peptide was also shown to have stabilized and affected the growth rate of GNP formation, in similar manner to MBP. Further in chapter 3, a nanosensor was formulated using a variation of this GNP-MBP system, to detect and measure ionizing radiation dose for cancer radiation therapy. Upon exposure to therapeutic levels of ionizing radiation, the MBP‐based sensor system formed gold nanoparticles with a dose‐dependent color that could be used to predict the amount of delivered X‐ray dose. In chapter 4, a similar system of protein templated synthesis was introduced for platinum nanoparticle (PtNP). Here, GroEL, a large homo-tetradecamer chaperone from E.coli, was used as templating and stabilizing agent for reduction of K2PtCl4 ions to form PtNP. To understand how GroEL interacts with the PtNPs and thereby stabilizes them, single-particle cryo-electron microscopy technique was used to model the complex in solution. A 3.8-Å resolution 3D cryo-EM map of GroEL depicting the location of PtNP inside its central cylindrical cavity was obtained. Fitting a GroEL model to the map revealed Arginine-268 from two adjacent subunits of GroEL interacting with the PtNP surface. Finally in chapter 5, a solution to the potential issues of single particle data processing on protein nanoparticle complexes, specifically with 2D classification, was developed by creating masking algorithms.