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- Genre: Doctoral Dissertation
Description
The accurate and fast determination of carbon dioxide (CO2) levels is critical for many health and environmental applications. For example, the analysis of CO2 levels in exhaled breath allows for the evaluation of systemic metabolism, perfusion, and ventilation, and provides the doctors and patients with a non-invasive and simple method to predict the presence and severity of asthma, and Chronic Obstructive Pulmonary Disease (COPD). Similarly, the monitoring of CO2 levels in the atmosphere allows for assessment of indoor air quality (IAQ) as the indoor CO2 levels have been proved to be associated with increased prevalence of certain mucous membrane and respiratory sick building syndrome (SBS) symptoms. A pocket-sized CO2 analyzer has been developed for real-time analysis of breath CO2 and environmental CO2. This CO2 analyzer is designed to comprise two key components including a fluidic system for efficient gas sample delivery and a colorimetric detection unit integrated into the fluidic system. The CO2 levels in the gas samples are determined by a disposable colorimetric sensor chip. The sensor chip is a novel composite based sensor that has been optimized to provide fast and reversible response to CO2 over a wide concentration range, covering the needs of both environmental and health applications. The sensor is immune to the presence of various interfering gases in ambient or expired air. The performance of the sensor in real-time breath-by-breath analysis has also been validated by a commercial CO2 detector. Furthermore, a 3D model was created to simulate fluid dynamics of breath and chemical reactions for CO2 assessment to achieve overall understanding of the breath CO2 detection process and further optimization of the device.
ContributorsZhao, Di (Author) / Forzani, Erica S (Thesis advisor) / Lin, Jerry Ys (Committee member) / Torres, Cesar (Committee member) / Tsow, Tsing (Committee member) / Xian, Xiaojun (Committee member) / Arizona State University (Publisher)
Created2014
Description
Metabolic engineering is an extremely useful tool enabling the biosynthetic production of commodity chemicals (typically derived from petroleum) from renewable resources. In this work, a pathway for the biosynthesis of styrene (a plastics monomer) has been engineered in Escherichia coli from glucose by utilizing the pathway for the naturally occurring amino acid phenylalanine, the precursor to styrene. Styrene production was accomplished using an E. coli phenylalanine overproducer, E. coli NST74, and over-expression of PAL2 from Arabidopsis thaliana and FDC1 from Saccharomyces cerevisiae. The styrene pathway was then extended by just one enzyme to either (S)-styrene oxide (StyAB from Pseudomonas putida S12) or (R)-1,2-phenylethanediol (NahAaAbAcAd from Pseudomonas sp. NCIB 9816-4) which are both used in pharmaceutical production. Overall, these pathways suffered from limitations due to product toxicity as well as limited precursor availability. In an effort to overcome the toxicity threshold, the styrene pathway was transferred to a yeast host with a higher toxicity limit. First, Saccharomyces cerevisiae BY4741 was engineered to overproduce phenylalanine. Next, PAL2 (the only enzyme needed to complete the styrene pathway) was then expressed in the BY4741 phenylalanine overproducer. Further strain improvements included the deletion of the phenylpyruvate decarboxylase (ARO10) and expression of a feedback-resistant choristmate mutase (ARO4K229L). These works have successfully demonstrated the possibility of utilizing microorganisms as cellular factories for the production styrene, (S)-styrene oxide, and (R)-1,2-phenylethanediol.
ContributorsMcKenna, Rebekah (Author) / Nielsen, David R (Thesis advisor) / Torres, Cesar (Committee member) / Caplan, Michael (Committee member) / Jarboe, Laura (Committee member) / Haynes, Karmella (Committee member) / Arizona State University (Publisher)
Created2014
Description
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.
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.
ContributorsJoshi, Rakesh (Author) / Tsakalis, Konstantinos (Thesis advisor) / Rodriguez, Armando (Committee member) / Torres, Cesar (Committee member) / Spanias, Andreas (Committee member) / Arizona State University (Publisher)
Created2018
Description
This dissertation focuses on the biosynthetic production of aromatic fine chemicals in engineered Escherichia coli from renewable resources. The discussed metabolic pathways take advantage of key metabolites in the shikimic acid pathway, which is responsible for the production of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. For the first time, the renewable production of benzaldehyde and benzyl alcohol has been achieved in recombinant E. coli with a maximum titer of 114 mg/L of benzyl alcohol. Further strain development to knockout endogenous alcohol dehydrogenase has reduced the in vivo degradation of benzaldehyde by 9-fold, representing an improved host for the future production of benzaldehyde as a sole product. In addition, a novel alternative pathway for the production of protocatechuate (PCA) and catechol from the endogenous metabolite chorismate is demonstrated. Titers for PCA and catechol were achieved at 454 mg/L and 630 mg/L, respectively. To explore potential routes for improved aromatic product yields, an in silico model using elementary mode analysis was developed. From the model, stoichiometric optimums maximizing both product-to-substrate and biomass-to-substrate yields were discovered in a co-fed model using glycerol and D-xylose as the carbon substrates for the biosynthetic production of catechol. Overall, the work presented in this dissertation highlights contributions to the field of metabolic engineering through novel pathway design for the biosynthesis of industrially relevant aromatic fine chemicals and the use of in silico modelling to identify novel approaches to increasing aromatic product yields.
ContributorsPugh, Shawn (Author) / Nielsen, David (Thesis advisor) / Dai, Lenore (Committee member) / Torres, Cesar (Committee member) / Lind, Mary Laura (Committee member) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2016
Description
Of the potential technologies for pre-combustion capture, membranes offer the advantages of being temperature resistant, able to handle large flow rates, and having a relatively small footprint. A significant amount of research has centered on the use of polymeric and microporous inorganic membranes to separate CO2. These membranes, however, have limitations at high temperature resulting in poor permeation performance. To address these limitations, the use of a dense dual-phase membrane has been studied. These membranes are composed of conductive solid and conductive liquid phases that have the ability to selectively permeate CO2 by forming carbonate ions that diffuse through the membrane at high temperature. The driving force for transport through the membrane is a CO2 partial pressure gradient. The membrane provides a theoretically infinite selectivity. To address stability of the ceramic-carbonate dual-phase membrane for CO2 capture at high temperature, the ceramic phase of the membrane was studied and replaced with materials previously shown to be stable in harsh conditions. The permeation properties and stability of La0.6Sr0.4Co0.8Fe0.2O3-δ (LSCF)-carbonate, La0.85Ce0.1Ga0.3Fe0.65Al0.05O3-δ (LCGFA)-carbonate, and Ce0.8Sm0.2O1.9 (SDC)-carbonate membranes were examined under a wide range of experimental conditions at high temperature. LSCF-carbonate membranes were shown to be unstable without the presence of O2 due to reaction of CO2 with the ceramic phase. In the presence of O2, however, the membranes showed stable permeation behavior for more than one month at 900oC. LCGFA-carbonate membranes showed great chemical and permeation stability in the presence of various conditions including exposure to CH4 and H2, however, the permeation performance was quite low when compared to membranes in the literature. Finally, SDC-carbonate membranes showed great chemical and permeation stability both in a CO2:N2 environment for more than two weeks at 900oC as well as more than one month of exposure to simulated syngas conditions at 700oC. Ceramic phase chemical stability increased in the order of LSCF < LCGFA < SDC while permeation performance increased in the order of LCGFA < LSCF < SDC.
ContributorsNorton, Tyler (Author) / Lin, Jerry Y.S. (Thesis advisor) / Alford, Terry (Committee member) / Lind, Mary Laura (Committee member) / Smith, David (Committee member) / Torres, Cesar (Committee member) / Arizona State University (Publisher)
Created2013
Description
Polymers have played a pivotal role in building modern society. Polymers can be classified as synthetic and natural polymers. Accumulation of both synthetic and natural polymer waste leads to environmental pollution. This dissertation aims at developing one-pot bioprocesses for a breakdown of natural polymers like cellulose, and hemicellulose and synthetic polymers like polyethylene terephthalate (PET). First, a one-pot process was developed for hemicellulose breakdown. A signal peptide library of native SEC pathway signal peptides was developed for efficient secretion of endoxylanse enzyme. Furthermore, in situ, the process was successfully created for hemicellulose to xylose with the highest reported xylose titer of 7.1 g/L. In addition, E. coli: B. subtilis coculture bioprocess was developed to produce succinate, ethanol, and lactate from hemicellulose in one pot process.
Second, a one-pot process was developed for cellulose breakdown. In vitro enzyme assays were used to select SEC pathway signal peptides for endoglucanase and glucosidase secretion. Then, the breakdown of carboxymethyl cellulose (CMC), a cellulose derivative, was conducted in in situ conditions. U-13C fingerprinting study showed carbon enrichment from CMC when cultures were cofed with CMC and [U-13C] glucose. Further, Whatman filter paper sheets showed a change in shape in recombinant cocultures. SEM images showed continuous orientation in the case of two enzymes confirmed by fast Fourier transform (FFT), suggesting higher crystallinity of residues. Similarly, in microcrystalline cellulose breakdown in in situ conditions, a 72% reduction of avicel cellulose was achieved in a one pot bioprocess. SEM images revealed valleys and crevices on residues of coculture compared to smoother surfaces in monoculture residues pressing the importance of the synergistic activity of enzymes.
Finally, one pot deconstruction process was developed for synthetic polymer PET. First, the PET hydrolase secretion strain was developed by selecting a signal peptide library. The first bis(2-hydroxyethyl) terephthalate (BHET) consolidated bioprocess was developed, which produced a terephthalic acid titer of 7.4 g/L. PET breakdown was successfully demonstrated in in vitro conditions with a TPA titer of 4 g/L. Furthermore, PET breakdown was successfully demonstrated in in situ conditions. Consolidated bioprocesses can be an invaluable approach to waste utilization and making cost-effective processes.
ContributorsMhatre, Apurv (Author) / Varman, Arul (Thesis advisor) / Nielsen, David (Committee member) / Misra, Rajeev (Committee member) / Nannenga, Brent (Committee member) / Torres, Cesar (Committee member) / Arizona State University (Publisher)
Created2023
Improving cyanobacterial hydrogen production through bioprospecting of natural microbial communities
Description
Some cyanobacteria can generate hydrogen (H2) under certain physiological conditions and are considered potential agents for biohydrogen production. However, they also present low amounts of H2 production, a reaction reversal towards H2 consumption, and O2 sensitivity. Most attempts to improve H2 production have involved genetic or metabolic engineering approaches. I used a bio-prospecting approach instead to find novel strains that are naturally more apt for biohydrogen production. A set of 36, phylogenetically diverse strains isolated from terrestrial, freshwater and marine environments were probed for their potential to produce H2 from excess reductant. Two distinct patterns in H2 production were detected. Strains displaying Pattern 1, as previously known from Synechocystis sp. PCC 6803, produced H2 only temporarily, reverting to H2 consumption within a short time and after reaching only moderately high H2 concentrations. By contrast, Pattern 2 cyanobacteria, in the genera Lyngbya and Microcoleus, displayed high production rates, did not reverse the direction of the reaction and reached much higher steady-state H2 concentrations. L. aestuarii BL J, an isolate from marine intertidal mats, had the fastest production rates and reached the highest steady-state concentrations, 15-fold higher than that observed in Synechocystis sp. PCC 6803. Because all Pattern 2 strains originated in intertidal microbial mats that become anoxic in dark, it was hypothesized that their strong hydrogenogenic capacity may have evolved to aid in fermentation of the photosynthate. When forced to ferment, these cyanobacteria display similarly desirable characteristics of physiological H2 production. Again, L. aestuarii BL J had the fastest specific rates and attained the highest H2 concentrations during fermentation, which proceeded via a mixed-acid pathway to yield acetate, ethanol, lactate, H2, CO2 and pyruvate. The genome of L. aestuarii BL J was sequenced and bioinformatically compared to other cyanobacterial genomes to ascertain any potential genetic or structural basis for powerful H2 production. The association hcp exclusively in Pattern 2 strains suggests its possible role in increased H2 production. This study demonstrates the value of bioprospecting approaches to biotechnology, pointing to the strain L. aestuarii BL J as a source of useful genetic information or as a potential platform for biohydrogen production.
ContributorsKothari, Ankita (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Vermaas, Willem F J (Committee member) / Rittmann, Bruce (Committee member) / Torres, Cesar (Committee member) / Arizona State University (Publisher)
Created2013
Description
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.
ContributorsThirumurthy, Miyuki (Author) / Jones, Anne K (Thesis advisor) / Redding, Kevin (Committee member) / Torres, Cesar (Committee member) / Arizona State University (Publisher)
Created2019
Description
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.
ContributorsThaker, Amar Nilkamal (Author) / Nannenga, Brent L (Thesis advisor) / Acharya, Abhinav (Committee member) / Torres, Cesar (Committee member) / Mills, Jeremy (Committee member) / Rege, Kaushal (Committee member) / Arizona State University (Publisher)
Created2020
Description
Electrolytes play a critical role in electrochemical devices and applications, and therefore design and development of electrolytes with tailored properties are much desired to accommodate variety of operation requirements. Extreme temperatures are considered as one of the challenging environmental conditions, especially for devices rely on liquid state electrolytes, rendering failure of operations once the electrolyte systems undergo phase transitions. This work focuses on development of low-temperature iodide-containing liquid electrolyte systems, specifically designed for the molecular electronic transducer (MET) sensors in space applications. Utilizing ionic liquids, molecular liquids, and salts, multiple low-temperature liquid electrolytes were designed with enhancements in thermal, transport, and electrochemical properties. Effects of intermolecular interactions were further investigated, revealing correlations between optimization of microscopic dynamics and improvements of macroscopic characteristics. As a result, three low-temperature electrolyte systems were reported utilizing ethylammonium/water, gamma-butyrolactone/propylene carbonate, and butyronitrile as solvent with ionic liquid, 1-butyl-3-methylimidazolium iodide, and lithium iodide salt. Consequently, the liquidus range of these systems have been extended to -108 ˚C, -120 ˚C, and -152 ˚C, respectively, marking the lowest liquidus temperature of liquid electrolytes to the author’s best knowledge. Moreover, transport properties of designed systems were characterized from 25 to -75 ˚C. Effects of selected cosolvent/solvent on evolutions of transport properties were observed, revealing interplay between two governing mechanisms, ion disassociation and ion mobility, and their dominance at different temperatures. Experimental spectroscopy characterization techniques validated the hypothesized intermolecular interactions between solvent-cation and solvent-anion, complimented by computational simulation results on the complex dynamics between constituent ions and molecules. To support MET sensing technology, the essential iodide/triiodide redox were investigated in developed electrolytes. Effects of different molecular solvents on electrochemical kinetics were elucidated, and steady performances were validated under a properly controlled electrochemical window. Optimized electrolytes were tested in the MET sensor prototypes and showcased adequate functionality from calibration. The MET sensor prototype has also successfully detected real-time earthquake with low noise floor during long term testing at ASU seismology facility. The presented work demonstrates a facile design strategy for task-specific electrolyte development, which is anticipated to be further expanded to high temperatures for broader applications in the future.
ContributorsLin, Wendy Jessica (Author) / Dai, Lenore L (Thesis advisor) / Wiegart, Yu-chen Karen (Committee member) / Emady, Heather (Committee member) / Lind Thomas, MaryLaura (Committee member) / Torres, Cesar (Committee member) / Arizona State University (Publisher)
Created2022