In this project, the potential of ferrous iron precipitation as an alternative for ground improvement applications is investigated. This study analyzes the potential of naturally occurring iron oxidation, which uses Fe2+ as an electron donor to produce Fe3+ precipitate. The goal of this study was to stimulate or accelerate the naturally occurring iron oxidation and precipitation process, to form a ferruginous crust in the subsurface, that would reduce hydraulic conductivity or increase soil strength. Iron precipitation can occur through aerobic or anaerobic iron oxidizers. Initial experimental test results in falcon tubes and a literature review showed that to obtain significant oxidation of ferrous iron and consequent precipitation of iron minerals required a buffer to prevent acidification. Experimental studies in which aerobic and anaerobic iron precipitation is stimulated in sand columns under various boundary conditions also leads to an optimization of conditions for mineralization. Mineralized zones are evaluated via permeability loss tests, extent of iron oxidized and characterization tests which show that the crust has the most concentration of precipitated iron, which can be used in targeting pollution mitigation, erosion control, etc. The results show a significant loss of permeability- by a factor of two, in high concentration of iron with a balanced buffer control. In this study, the knowledge on ground stabilization by studying the naturally occurring mechanism of iron precipitation, leading to possible industrially relevant geotechnical applications are successfully investigated.

Factors affecting biofilm development, specifically the materials of the pipe, were investigated. Two laboratory scale bioreactor systems were constructed to study biofilm formations: a pipe loop bioreactor with continuous flow at 10.1 liters per minute (LPM), and a tank bioreactor under stagnant conditions with a minimal flow of 0.0095 LPM. The continuous flow bioreactors were constructed using cross-linked polyethylene (PEX), copper, and galvanized steel pipes. The tank bioreactors consisted of glass chambers containing coupons made from the pipe materials, as well as glass microscope slides. Municipality tap water was used in the experimentation, with no nutrients added. Legionella pneumophila was spiked into all the pipe loop bioreactors, and only in one tank bioreactor. Detection of heterotrophic bacteria, coliforms and Legionella using tryptic soy agar (TSA), Brilliance, and buffered yeast charcoal extract (BYCE), respectively. Over ten weeks, biofilms were developed on PEX, copper, and steel, in the pipe loop bioreactors and the tank bioreactors. Heterotrophic bacteria were detected in all systems; however, no coliforms were detected, and Legionella pneumophila was only detected on a coupon in the copper pipe loop bioreactor, as measured by bacterial concentration on test materials. In the tank bioreactors, biofilms developed the most rapidly on PEX, followed by galvanized steel, and finally copper. Out of the four materials, copper had the lowest bacterial growth, which can be ascribed to the bactericidal impact of copper ions on the bacterial cells attaching to the copper surface. After biofilm aging, higher bacterial colonization on copper and accumulation of dead bacterial layer on the surface may act as a protective barrier against copper ions. Bacterial densities in the biofilm reached a high concentration of 1.40 x 105 CFU/cm2 on the PEX pipe loop bioreactor, and 1.05 x 104 CFU/cm2in the PEX coupon in the tank bioreactors. Comparing the turbulent conditions in the pipe loop bioreactors to the stagnant conditions in the tank bioreactor, showed that biofilms formed more rapidly under stagnant conditions, but in larger quantities under turbulent conditions.

Corrosion is one of the key failure modes for stainless steel (SS) piping assets handling water resources managed by utility companies. During downtime, the costs start to incur as the field engineer procures its replacement parts. The parts may or may not be in stock depending on how old, complex, and common the part model is. As a result, water utility companies and its resilience to operate amid part failure are a strong function of the supply chain for replacement piping. Metal additive manufacturing (AM) has been widely recognized for its ability to (a) deliver small production scales, (b) address complex part geometries, (c) offer large elemental metal and alloy selections, (d) provide superior material properties. The key motive is to harvest the short lead time of metal AM to explore its use for replacement parts for legacy piping assets in utility-scale water management facilities. In this paper, the goal was to demonstrate 3D printing of stainless steel (SS) 316L parts using selective laser melting (SLM) technology. The corrosion resistance of 3D printed SS 316L was investigated using (a) Chronoamperometry (b) Cyclic Potentiodynamic Polarization (CPP) and Electrochemical Impedance Spectroscopy (EIS) and its improved resistance from wrought (conventional) part was also studied. Then the weldability of 3D printed SS 316L to wrought SS 316L was illustrated and finally, the mechanical strength of the weld and the effect of corrosion on weld strength was investigated using uniaxial tensile testing. The results show that 3D printed part compared to the wrought part has a) lower mass loss before and after corrosion, (b) higher pitting potential, and (c) higher charge transfer resistance. The tensile testing of welded dog bone specimens indicates that the 3D printed parts despite being less ductile were observed to have higher weld strength compared to the wrought part. On this basis, metal AM holds great value to be explored further for replacement piping parts owing to their better corrosion resistance and mechanical performance.

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.

Optimizing cathodes for microbial fuel cells is important to maximize energy harvested from wastewater. Cathodes were made by modifying a recipe from previous literature and testing the current of the cathode using linear sweep voltammetry. The cathodes contained an Fe-N-C catalyst combined with a Polytetrafluoroethylene binder. Optimizing the power resulting from the microbial fuel cells will help MFCs be an alternative energy source to fossil fuels. The new cathodes did improve in current production from −16 𝐴/𝑚 to −37 𝐴/𝑚 at -0.4 V. When fitted using a Butler-Volmer model, the cathode linear-sweep voltammograms did not follow the expected exponential trend. These results show a need for more research on the cathodes and the Butler-Volmer model, and they also show that the cathode is ready for further and longer application in a microbial fuel cell.

Biofuels are a carbon-neutral energy source proving to be a sustainable alternative to greenhouse gas-emitting fossil fuels that are accelerating the detrimental effects of anthropogenic climate change. A developing system aimed at more efficiently producing biofuels is called Microbial Electro-Photosynthesis (MEPS). In MEPS, a Synechocystis sp. PCC 6803 mutant lacking photosystem II (PSII) receives electrons by a hydroduroquinone (DQH2) mediator from a more efficient water-splitting electrochemical cell, rather than splitting water itself using PSII. However, growth of the Synechocystis cells prior to use in MEPS requires an organic carbon source, leading to internally-stored electron sources, namely glycogen, that compete with preferred DQH2 mediator-delivered electrons. In this study, the effects of organic carbon source (pyruvate, acetate, glucose, and no carbon source) and light condition (light or dark) on the physiology and P700+ reduction kinetics of photoheterotrophically grown Synechocystis mutants were studied with the hope of identifying a maintenance culturing method that allowed for both cell viability and mitigated glycogen storage. While no significant decreases in internal electron-sources were found with these methods, it was observed that Synechocystis cells fed pyruvate in the light had most successfully reduced competition between internal electron sources and preferred DQH2-delivered electrons. This study suggests that these experiments be re-run after removing exogenous carbon sources and that the nutrients available to the cells and their effects on pyruvate and acetate uptake be further investigated.

Exoelectrogenic microorganisms can grow by transferring electrons from their internal metabolism to extracellular substrates in a process known as extracellular electron transfer (EET). This dissertation explores the mechanisms of EET by both chemotrophic and phototrophic organisms and constructs a novel supramolecular structure that can be used as a model for microbial, long-range electron transfer. Geobacter sulfurreducens has been hypothesized to secrete and use riboflavin as a soluble, extracellular redox shuttle in conjunction with multi-heme, outer membrane, c-type cytochromes, but the required proteins and their properties have not been defined. To address the mechanism of extracellular electron transfer by G. sulfurreducens, the first part of this work explores the interaction between an outer membrane, octaheme, c-type cytochrome OmcZs from G. sulfurreducens and riboflavin. Interrogation via multiple physical techniques shows that OmcZs transfers electrons to riboflavin. By analogy to other characterized systems, riboflavin then likely interacts with extracellular acceptors directly. The second part of this work addresses the mechanisms of EET by the model cyanobacterium Synechocystis sp. PCC 6803. It has been hypothesized that Synechocystis employs conductive pili for production of extracellular current. However, the results herein show that a strain that does not have pili produces extracellular photocurrent in a direct electrochemical cell at a level similar to that by wild type cells. Furthermore, conductive atomic force microscopy (AFM) imaging is used to show that pili produced by the wild type organism are not conductive. Thus, an alternative EET mechanism must be operable. In the third part of this work, a supramolecular structure comprised of peptide and cytochromes designed to serve as a model for long-range electron transfer through cytochrome rich environments is described. The c-type cytochromes in this synthetic nanowire retain their redox activity after assembly and have suitable characteristics for long-range electron transfer. Taken together, the results of this dissertation not only inform on natural microbial mechanisms for EET but also provide a starting point to develop novel, synthetic systems.

Reactive inkjet printing (RIJP) is a direct-write deposition technique that synthesizes and patterns functional materials simultaneously. It is a route to cheap fabrication of highly conductive features on a versatile range of substrates. Silver reactive inks have become a staple of conductive inkjet printing for application in printed and flexible electronics, photovoltaic metallization, and more. However, the high cost of silver makes these less effective for disposable and low-cost applications.

This work aimed to develop a particle-free formulation for a nickel reactive ink capable of metallizing highly pure nickel at temperatures under 100 °C to facilitate printing on substrates like paper or plastic. Nickel offers a significantly cheaper alternative to silver at slightly reduced bulk conductivity.

To meet these aims, three archetypes of inks were formulated. First were a set of glycerol-based inks temperature ink containing nickel acetate, hydrazine, and ammonia in a mixture of water and glycerol. This ink reduced between 115 – 200 °C to produce slightly oxidized deposits of nickel with carbon content around 10 wt %.

The high temperature was addressed in a second series, which replaced glycerol with lower boiling glycols and added sodium hydroxide as a strong base to enhance thermodynamics and kinetics of reduction. These inks reduced between 60 and 100 °C but sodium salts contaminated the final deposits.

In a third set of inks, sodium hydroxide was replaced with tetramethylammonium hydroxide (TMAH), a strong organic base, to address contamination. These inks also reduced between 60 and 100 °C. Pipetting or printing onto gold coated substrates produce metallic flakes coated in a clear, thick residue. EDS measured carbon and oxygen content up to 70 wt % of deposits. The residue was hypothesized to be a non-volatile byproduct of TMAH and acetate.

Recommendations are provided to address the residue. Ultimately the formulated reactive inks did not meet design targets. However, this thesis sets the framework to design an optimal nickel reactive ink in future work.

Carbon dioxide (CO2) levels in the atmosphere have reached unprecedented levels due to increasing anthropogenic emissions and increasing energy demand. CO2 capture and utilization can aid in stabilizing atmospheric CO2 levels and producing carbon-neutral fuels. Utilizing hollow fiber membranes (HFMs) for microalgal cultivation accomplishes that via bubbleless gas-transfer, preventing CO2 loss to the atmosphere. Various lengths and geometries of HFMs were used to deliver CO2 to a sodium carbonate solution. A model was developed to calculate CO2 flux, mass-transfer coefficient (KL), and volumetric mass-transfer coefficient (KLa) based on carbonate equilibrium and the alkalinity of the solution. The model was also applied to a sparging system, whose performance was compared with that of the HFMs. Typically, HFMs are operated in closed-end mode or open-end mode. The former is characterized by a high transfer efficiency, while the latter provides the advantage of a high transfer rate. HFMs were evaluated for both modes of operation and a varying inlet CO2 concentration to determine the effect of inert gas and water vapor accumulation on transfer rates. For pure CO2, a closed-end module operated as efficiently as an open-end module. Closed-end modules perform significantly worse when CO2-enriched air was supplied. This was shown by the KLa values calculated using the model. Finally, a mass-balance model was constructed for the lumen of the membranes in order to provide insight into the gas-concentration profiles inside the fiber lumen. For dilute CO2 inlet streams, accumulation of inert gases -- nitrogen (N2), oxygen (O2), and water vapor (H2O) -- significantly affected module performance by reducing the average CO2 partial pressure in the membrane and diminishing the amount of interfacial mass-transfer area available for CO2 transfer.

Microbial fuel cells(MFC) use micro-organisms called anode-respiring bacteria(ARB) to convert chemical energy into electrical energy. This process can not only treat wastewater but can also produce useful byproduct hydrogen peroxide(H2O2). Process variables like anode potential and pH play important role in the MFC operation and the focus of this dissertation are pH and potential control problems.

Most of the adaptive pH control solutions use signal-based-norms as cost functions, but their strong dependency on excitation signal properties makes them sensitive to noise, disturbances, and modeling errors. System-based-norm( H-infinity) cost functions provide a viable alternative for the adaptation as they are less susceptible to the signal properties. Two variants of adaptive pH control algorithms that use approximate H-infinity frequency loop-shaping (FLS) cost metrics are proposed in this dissertation.

A pH neutralization process with high retention time is studied using lab scale experiments and the experimental setup is used as a basis to develop a first-principles model. The analysis of such a model shows that only the gain of the process varies significantly with operating conditions and with buffering capacity. Consequently, the adaptation of the controller gain (single parameter) is sufficient to compensate for the variation in process gain and the focus of the proposed algorithms is the adaptation of the PI controller gain. Computer simulations and lab-scale experiments are used to study tracking, disturbance rejection and adaptation performance of these algorithms under different excitation conditions. Results show the proposed algorithm produces optimum that is less dependent on the excitation as compared to a commonly used L2 cost function based algorithm and tracks set-points reasonably well under practical conditions. The proposed direct pH control algorithm is integrated with the combined activated sludge anaerobic digestion model (CASADM) of an MFC and it is shown pH control improves its performance.

Analytical grade potentiostats are commonly used in MFC potential control, but, their high cost (>$6000) and large size, make them nonviable for the field usage. This dissertation proposes an alternate low-cost($200) portable potentiostat solution. This potentiostat is tested using a ferricyanide reactor and results show it produces performance close to an analytical grade potentiostat.