ASU Electronic Theses and Dissertations
This collection includes most of the ASU Theses and Dissertations from 2011 to present. ASU Theses and Dissertations are available in downloadable PDF format; however, a small percentage of items are under embargo. Information about the dissertations/theses includes degree information, committee members, an abstract, supporting data or media.
In addition to the electronic theses found in the ASU Digital Repository, ASU Theses and Dissertations can be found in the ASU Library Catalog.
Dissertations and Theses granted by Arizona State University are archived and made available through a joint effort of the ASU Graduate College and the ASU Libraries. For more information or questions about this collection contact or visit the Digital Repository ETD Library Guide or contact the ASU Graduate College at gradformat@asu.edu.
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Description
Polydimethyl siloxane is a commonly used fabrication material for microfluidic devices. However, its hydrophobic nature and protein adsorption on the surface restricts its use for microfluidic applications. Also, it is critical to control the electroosmotic flow for electrophoretic and dielectrophoretic manipulations. Therefore, surface modification of PDMS is essential to make it well suited for bioanalytical applications. In this project, the role of polyethylene oxide copolymers F108 and PLL-PEG has been investigated to modify the surface properties of PDMS using physisorption method. Measuring electroosmotic flow and adsorption studies tested the quality and the long-term stability of the modified PDMS surface. Static and dynamic coating strategies were used to modify the PDMS surface. In static coating, the PDMS surface was incubated with the coating agent prior to the measurements. For dynamic coating, the coating agent was always present in the solution throughout the experiment. F108 and PLL-PEG were equally effective to prevent the protein adsorption under both strategies. However, dynamic coating was more time saving. Furthermore, effective reduction of EOF was observed with F108 coating agent under dynamic conditions and with PLL-PEG coating agent under static conditions. Moreover, PLL-PEG dynamic coatings exhibited reversal of EOF. These important findings could be used to manipulate EOF and suggest optimal coating agent and strategies for PDMS surface treatment by the physisorption method.
ContributorsManchanda, Shikha (Author) / Ros, Alexandra (Thesis advisor) / Hayes, Mark (Committee member) / Liu, Yan (Committee member) / Arizona State University (Publisher)
Created2012
Description
Most of the sunlight powering natural photosynthesis is absorbed by antenna arrays that transfer, and regulate the delivery of excitation energy to reaction centers in the chloroplast where photosynthesis takes place. Under intense sunlight the plants and certain organisms cannot fully utilize all of the sunlight received by antennas and excess redox species are formed which could potentially harm them. To prevent this, excess energy is dissipated by antennas before it reaches to the reaction centers to initiate electron transfer needed in the next steps of photosynthesis. This phenomenon is called non-photochemical quenching (NPQ). The mechanism of NPQ is not fully understood, but the process is believed to be initiated by a drop in the pH in thylakoid lumen in cells. This causes changes in otherwise nonresponsive energy acceptors which accept the excess energy, preventing oversensitization of the reaction center. To mimic this phenomenon and get insight into the mechanism of NPQ, a novel pH sensitive dye 3'6'-indolinorhodamine was designed and synthesized which in a neutral solution stays in a closed (colorless) form and does not absorb light while at low pH it opens (colored) and absorbs light. The absorption of the dye overlaps porphyrin emission, thus making energy transfer from the porphyrin to the dye thermodynamically possible. Several self-regulating molecular model systems were designed and synthesized consisting of this dye and zinc porphyrins organized on a hexaphenylbenzene framework to functionally mimic the role of the antenna in NPQ. When a dye-zinc porphyrin dyad is dissolved in an organic solvent, the zinc porphyrin antenna absorbs and emits light by normal photophysical processes. Time resolved fluorescence experiments using the single-photon-timing method with excitation at 425 nm and emission at 600 nm yielded a lifetime of 2.09 ns for the porphyrin first excited singlet state. When acetic acid is added to the solution of the dyad, the pH sensitive dye opens and quenches the zinc porphyrin emission decreasing the lifetime of the porphyrin first excited singlet state to 23 ps, and converting the excitation energy to heat. Under similar experimental conditions in a neutral solution, a model hexad containing the dye and five zinc porphyrins organized on a hexaphenylbenzene core decays exponentially with a time constant of 2.1 ns, which is essentially the same lifetime as observed for related monomeric zinc porphyrins. When a solution of the hexad is acidified, the dye opens and quenches all porphyrin first excited singlet states to <40 ps. This converts the excitation energy to heat and renders the porphyrins kinetically incompetent to readily donate electrons by photoinduced electron transfer, thereby mimicking the role of the antenna in photosynthetic photoprotection.
ContributorsBhushan, Kul (Author) / Gust, Devens (Thesis advisor) / Moore, Ana (Committee member) / Hayes, Mark (Committee member) / Arizona State University (Publisher)
Created2012
Description
Mass spectrometric analysis requires that atoms from the sample be ionized in the gas phase. Secondary ion mass spectrometry achieves this by sputtering samples with an energetic primary ion beam. Several investigations of the sputtering and ionization process have been conducted. Oxygen is commonly used in secondary ion mass spectrometry (SIMS) to increase ion yields, but also can complicate the interpretation of SIMS analyses. An 18O implant in silicon has been used to quantify the oxygen concentration at the surface of sputtered silicon in order to study the dependence on oxygen of several sputtering and depth profile phenomena. The ion yield dependence of trace elements in silicon on the surface oxygen concentration is a function of the ionization potential of the element. The ion yield is high and unaffected by oxygen for elements with low ionization potential and ranges over several orders of magnitude for elements with high ionization potential. Depth resolution in sputter profiles has been shown to be degraded by the presence of oxygen, the mechanism of this effect has been investigated using an 18O implant to quantify oxygen levels and it is shown that the process does not appear to be a consequence of surface oxide formation. Molecular ions are a source of mass interference in SIMS analysis, and multiply charged atomic ion signals might be interference-free due to the possible instability of multiply-charged molecular ions. Sputtered SiH2+, AlH2+, BeH2+, Mo22+ and Mg22+ ions have been observed and appear surprisingly stable. The formation mechanism of some of these species has been explored.
ContributorsSobers, Richard Carlisle, Jr (Author) / Williams, Peter (Thesis advisor) / Hayes, Mark (Committee member) / Petuskey, William (Committee member) / Arizona State University (Publisher)
Created2012
Description
N-nitrosodimethylamine (NDMA) is a probable human carcinogen that has been detected in various environments including the atmosphere, clouds, surface waters, and drinking water. NDMA can form through natural reactions in the aqueous phase of the atmosphere and it can form as a disinfection byproduct in water treatment. Due to its carcinogenic nature, it is important to understand the mechanism of formation of NDMA in both engineered processes such as water treatment and in natural processes in fogs and clouds. NDMA might form through the reaction of chloramines with amines in both cases. This work analyzes polydiallyldimethyl ammonium chloride (PolyDADMAC), which is the most commonly used polymer at drinking water treatment plants and has the potential to form NDMA if free polymer is present during the chloramination (disinfection) process. The composition of industrial polyDADMAC solutions is not well understood and is difficult to analyze. This work uses 1H and 13C nuclear magnetic resonance (NMR) to analyze the polymer solution composition. Both 1H and 13C NMR allow investigation of the presence of trace impurities in the solution, gather structural information such as chain length, and inform on reaction mechanisms. The primary impurities of concern for NDMA formation were identified as dimethylamine (DMA) and short-chain oligomers of the polyDADMAC. 13C NMR was further used to confirm that NDMA likely forms from polyDADMAC via a Hofmann elimination.
Chloramines might also form in fogs and clouds although to date the potential for chloramines to form NDMA in atmospheric fog and cloud droplets has not been investigated. This work uses computational modeling to determine that at reported atmospheric conditions, the chloramine pathway contributes to less than 0.01% NDMA formation. The numerical modeling identified a need for more atmospheric HOCl measurements. This work proposes a concept of using HOCl to react to form chloramine, which can react to form NDMA as a way to quantify atmospheric HOCl.
ContributorsDonovan, Samantha Jo (Author) / Herckes, Pierre (Thesis advisor) / Westerhoff, Paul (Committee member) / Hayes, Mark (Committee member) / Arizona State University (Publisher)
Created2022
Description
This work focuses on a novel approach to combine electrical current with cyanobacterial technology, called microbial electrophotosynthesis (MEPS). It involves using genetically modified PSII-less Synechocystis PCC 6803 cells to avoid photoinhibition, a problem that hinders green energy. In the work, a cathodic electron delivery system is employed for growth and synthesis. Photoinhibition leads to the dissipation energy and lower yield, and is a major obstacle to preventing green energy from competing with fossil fuels. However, the urgent need for alternative energy sources is driven by soaring energy consumption and rising atmospheric carbon dioxide levels. When developed, MEPS can contribute to a carbon capture technology while helping with energy demands. It is thought that if PSII electron flux can be replaced with an alternative source photosynthesis could be enhanced for more effective production. MEPS has the potential to address these challenges by serving as a carbon capture technology while meeting energy demands. The idea is to replace PSII electron flux with an alternative source, which can be enhanced for higher yields in light intensities not tolerated with PSII. This research specifically focuses on creating the initiation of electron flux between the cathode and the MEPS cells while controlling and measuring the system in real time.
The successful proof-of-concept work shows that MEPS can indeed generate high-light-dependent current at intensities up to 2050 µmol photons m^‒2 s^‒1, delivering 113 µmol electrons h^‒1 mg-chl^‒1. The results were further developed to characterize redox tuning for electron delivery of flux to the photosynthetic electron transport chain and redox-based kinetic analysis to model the limitations of the MEPS system.
ContributorsLewis, Christine Michelle (Author) / Torres, César I (Thesis advisor) / Fromme, Petra (Thesis advisor) / Woodbury, Neal (Committee member) / Hayes, Mark (Committee member) / Arizona State University (Publisher)
Created2023
Description
The physiological phenomenon of sensing temperature is detected by transient
receptor (TRP) ion channels, which are pore forming proteins that reside in the
membrane bilayer. The cold and hot sensing TRP channels named TRPV1 and TRPM8
respectively, can be modulated by diverse stimuli and are finely tuned by proteins and
lipids. PIRT (phosphoinositide interacting regulator of TRP channels) is a small
membrane protein that modifies TRPV1 responses to heat and TRPM8 responses to cold.
In this dissertation, the first direct measurements between PIRT and TRPM8 are
quantified with nuclear magnetic resonance and microscale thermophoresis. Using
Rosetta computational biology, TRPM8 is modeled with a regulatory, and functionally
essential, lipid named PIP2. Furthermore, a PIRT ligand screen identified several novel
small molecular binders for PIRT as well a protein named calmodulin. The ligand
screening results implicate PIRT in diverse physiological functions. Additionally, sparse
NMR data and state of the art Rosetta protocols were used to experimentally guide PIRT
structure predictions. Finally, the mechanism of thermosensing from the evolutionarily
conserved sensing domain of TRPV1 was investigated using NMR. The body of work
presented herein advances the understanding of thermosensing and TRP channel function
with TRP channel regulatory implications for PIRT.
receptor (TRP) ion channels, which are pore forming proteins that reside in the
membrane bilayer. The cold and hot sensing TRP channels named TRPV1 and TRPM8
respectively, can be modulated by diverse stimuli and are finely tuned by proteins and
lipids. PIRT (phosphoinositide interacting regulator of TRP channels) is a small
membrane protein that modifies TRPV1 responses to heat and TRPM8 responses to cold.
In this dissertation, the first direct measurements between PIRT and TRPM8 are
quantified with nuclear magnetic resonance and microscale thermophoresis. Using
Rosetta computational biology, TRPM8 is modeled with a regulatory, and functionally
essential, lipid named PIP2. Furthermore, a PIRT ligand screen identified several novel
small molecular binders for PIRT as well a protein named calmodulin. The ligand
screening results implicate PIRT in diverse physiological functions. Additionally, sparse
NMR data and state of the art Rosetta protocols were used to experimentally guide PIRT
structure predictions. Finally, the mechanism of thermosensing from the evolutionarily
conserved sensing domain of TRPV1 was investigated using NMR. The body of work
presented herein advances the understanding of thermosensing and TRP channel function
with TRP channel regulatory implications for PIRT.
ContributorsSisco, Nicholas John (Author) / Van Horn, Wade D (Thesis advisor) / Mills, Jeremy H (Committee member) / Wang, Xu (Committee member) / Yarger, Jeff L (Committee member) / Arizona State University (Publisher)
Created2018
Description
Massive glycerol cluster ions with many charges (~ 106 Da, ~ ±100 charges) have been generated by electrospray to bombard biomolecules and biological sample surfaces. The low impact energy per nucleon facilitates intact sputtering and ionization of biomolecules which can be subsequently imaged. Various lipids, peptides and proteins have been studied. The primary cluster ion source has been coupled with an ion-microscope imaging mass spectrometer (TRIFT-1, Physical Electronics). A lateral resolution of ~3µm has been demonstrated, which is acceptable for sub-cellular imaging of animal cells (e.g. single cancer cell imaging in early diagnosis). Since the available amount of target molecules per pixel is limited in biological samples, the measurement of useful ion yields (ratio of detected molecular ion counts to the sample molecules sputtered) is important to determine whether enough ion counts per pixel can be obtained. The useful ion yields of several lipids and peptides are in the 1-3×10-5 range. A 3×3 µm2lipid bilayer can produce ~260 counts/pixel for a meaningful 3×3 µm2 pixel ion image. This method can probably be used in cell imaging in the future, when there is a change in the lipid contents of the cell membrane (e.g. cancer cells vs. normal cells).
ContributorsZhang, Jitao (Author) / Williams, Peter (Thesis advisor) / Hayes, Mark (Committee member) / Nelson, Randall (Committee member) / Arizona State University (Publisher)
Created2015
Description
Nature is a master at organizing biomolecules in all intracellular processes, and researchers have conducted extensive research to understand the way enzymes interact with each other through spatial and orientation positioning, substrate channeling, compartmentalization, and more.
DNA nanostructures of high programmability and complexity provide excellent scaffolds to arrange multiple molecular/macromolecular components at nanometer scale to construct interactive biomolecular complexes and networks. Due to the sequence specificity at different positions of the DNA origami nanostructures, spatially addressable molecular pegboard with a resolution of several nm (less than 10 nm) can be achieved. So far, DNA nanostructures can be used to build nanodevices ranging from in vitro small molecule biosensing to sophisticated in vivo therapeutic drug delivery systems and multi-enzyme networks.
This thesis focuses on how to use DNA nanostructures as programmable biomolecular scaffolds to arranges enzymatic systems. Presented here are a series of studies toward this goal. First, we survey approaches used to generate protein-DNA conjugates and the use of structural DNA nanotechnology to engineer rationally designed nanostructures. Second, novel strategies for positioning enzymes on DNA nanoscaffolds has been developed and optimized, including site-specific/ non site-specific protein-DNA conjugation, purification and characterization. Third, an artificial swinging arm enzyme-DNA complex has been developed to mimic substrate channeling process. Finally, we extended to build a artificial 2D multi-enzyme network.
DNA nanostructures of high programmability and complexity provide excellent scaffolds to arrange multiple molecular/macromolecular components at nanometer scale to construct interactive biomolecular complexes and networks. Due to the sequence specificity at different positions of the DNA origami nanostructures, spatially addressable molecular pegboard with a resolution of several nm (less than 10 nm) can be achieved. So far, DNA nanostructures can be used to build nanodevices ranging from in vitro small molecule biosensing to sophisticated in vivo therapeutic drug delivery systems and multi-enzyme networks.
This thesis focuses on how to use DNA nanostructures as programmable biomolecular scaffolds to arranges enzymatic systems. Presented here are a series of studies toward this goal. First, we survey approaches used to generate protein-DNA conjugates and the use of structural DNA nanotechnology to engineer rationally designed nanostructures. Second, novel strategies for positioning enzymes on DNA nanoscaffolds has been developed and optimized, including site-specific/ non site-specific protein-DNA conjugation, purification and characterization. Third, an artificial swinging arm enzyme-DNA complex has been developed to mimic substrate channeling process. Finally, we extended to build a artificial 2D multi-enzyme network.
ContributorsYang, Yuhe Renee (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Chen, Julian (Committee member) / Hayes, Mark (Committee member) / Arizona State University (Publisher)
Created2016
Description
Efficient separation techniques for organelles and bacteria in the micron- and sub-micron range are required for various analytical challenges. Mitochondria have a wide size range resulting from the sub-populations, some of which may be associated with diseases or aging. However, traditional methods can often not resolve within-species size variations. Strategies to separate mitochondrial sub-populations by size are thus needed to study the importance of this organelle in cellular functions. Additionally, challenges also exist in distinguishing the sub-populations of bio-species which differ in the surface charge while possessing similar size, such as Salmonella typhimurium (Salmonella). The surface charge of Salmonella wild-type is altered upon environmental stimulations, influencing the bacterial survival and virulence within the host tissue. Therefore, it is important to explore methods to identify the sub-populations of Salmonella.
This work exploits insulator-based dielectrophoresis (iDEP) for the manipulation of mitochondria and Salmonella. The iDEP migration and trapping of mitochondria were investigated under both DC and low-frequency AC conditions, establishing that mitochondria exhibit negative DEP. Also, the first realization of size-based iDEP sorting experiments of mitochondria were demonstrated. As for Salmonella, the preliminary study revealed positive DEP behavior. Distinct trapping potential thresholds were found for the sub-populations with different surface charges.
Further, DEP was integrated with a non-intuitive migration mechanism termed absolute negative mobility (ANM), inducing a deterministic trapping component which allows the directed transport of µm- and sub-µm sized (bio)particles in microfluidic devices with a nonlinear post array under the periodic action of electrokinetic and dielectrophoretic forces. Regimes were revealed both numerically and experimentally in which larger particles migrate against the average applied force, whereas smaller particles show normal response. Moreover, this deterministic ANM (dANM) was characterized with polystyrene beads demonstrating improved migration speed at least two orders of magnitude higher compared to previous ANM systems with similar sized colloids. In addition, dANM was induced for mitochondria with an AC-overlaid waveform representing the first demonstration of ANM migration with biological species. Thus, it is envisioned that the efficient size selectivity of this novel migration mechanism can be employed in nanotechnology, organelle sub-population studies or fractionating protein nanocrystals.
This work exploits insulator-based dielectrophoresis (iDEP) for the manipulation of mitochondria and Salmonella. The iDEP migration and trapping of mitochondria were investigated under both DC and low-frequency AC conditions, establishing that mitochondria exhibit negative DEP. Also, the first realization of size-based iDEP sorting experiments of mitochondria were demonstrated. As for Salmonella, the preliminary study revealed positive DEP behavior. Distinct trapping potential thresholds were found for the sub-populations with different surface charges.
Further, DEP was integrated with a non-intuitive migration mechanism termed absolute negative mobility (ANM), inducing a deterministic trapping component which allows the directed transport of µm- and sub-µm sized (bio)particles in microfluidic devices with a nonlinear post array under the periodic action of electrokinetic and dielectrophoretic forces. Regimes were revealed both numerically and experimentally in which larger particles migrate against the average applied force, whereas smaller particles show normal response. Moreover, this deterministic ANM (dANM) was characterized with polystyrene beads demonstrating improved migration speed at least two orders of magnitude higher compared to previous ANM systems with similar sized colloids. In addition, dANM was induced for mitochondria with an AC-overlaid waveform representing the first demonstration of ANM migration with biological species. Thus, it is envisioned that the efficient size selectivity of this novel migration mechanism can be employed in nanotechnology, organelle sub-population studies or fractionating protein nanocrystals.
ContributorsLuo, Jinghui (Author) / Ros, Alexandra (Thesis advisor) / Hayes, Mark (Committee member) / Borges, Chad (Committee member) / Arizona State University (Publisher)
Created2015
Description
X-ray crystallography is the most widely used method to determine the structure of proteins, providing an understanding of their functions in all aspects of life to advance applications in fields such as drug development and renewable energy. New techniques, namely serial femtosecond crystallography (SFX), have unlocked the ability to unravel the structures of complex proteins with vital biological functions. A key step and major bottleneck of structure determination is protein crystallization, which is very arduous due to the complexity of proteins and their natural environments. Furthermore, crystal characteristics govern data quality, thus need to be optimized to attain the most accurate reconstruction of the protein structure. Crystal size is one such characteristic in which narrowed distributions with a small modal size can significantly reduce the amount of protein needed for SFX. A novel microfluidic sorting platform was developed to isolate viable ~200 nm – ~600 nm photosystem I (PSI) membrane protein crystals from ~200 nm – ~20 μm crystal samples using dielectrophoresis, as confirmed by fluorescence microscopy, second-order nonlinear imaging of chiral crystals (SONICC), and dynamic light scattering. The platform was scaled-up to rapidly provide 100s of microliters of sorted crystals necessary for SFX, in which similar crystal size distributions were attained. Transmission electron microscopy was used to view the PSI crystal lattice, which remained well-ordered postsorting, and SFX diffraction data was obtained, confirming a high-quality, viable crystal sample. Simulations indicated sorted samples provided accurate, complete SFX datasets with 3500-fold less protein than unsorted samples. Microfluidic devices were also developed for versatile, rapid protein crystallization screening using nanovolumes of sample. Concentration gradients of protein and precipitant were generated to crystallize PSI, phycocyanin, and lysozyme using modified counterdiffusion. Additionally, a passive mixer was created to generate unique solution concentrations within isolated nanowells to crystallize phycocyanin and lysozyme. Crystal imaging with brightfield microscopy, UV fluorescence, and SONICC coupled with numerical modeling allowed quantification of crystal growth conditions for efficient phase diagram development. The developed microfluidic tools demonstrated the capability of improving samples for protein crystallography, offering a foundation for continued development of platforms to aid protein structure determination.
ContributorsAbdallah, Bahige G (Author) / Ros, Alexandra (Thesis advisor) / Buttry, Daniel (Committee member) / Hayes, Mark (Committee member) / Arizona State University (Publisher)
Created2016