Theses and Dissertations
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Novel Materials Based on Poly(2-Oxazoline): Synthesis, Molecular Characterization, and Application in Drug Delivery(2023-06-01) [Dissertation]
Advisor: Hadjichristidis, Nikos
Committee members: Nunes, Suzana Pereira; Khashab, Niveen M.; Avgeropoulos, ApostolosPoly(2-oxazolines) (POxs) are a class of polymers that have gained significant interest in biomedical applications. POxs are mainly synthesized using living cationic ring-opening polymerization (CROP) under microwave irradiation. POxs are considered pseudo-polypeptides because they are similar to polypeptides. Nevertheless, they are more chemically stable than polypeptides due to the presence of tertiary amides. POxs The major goal of this research is to synthesize and characterize a novel well-defined amphiphilic block copolymer based on POxs. These amphiphilic block copolymers can comprise core cross-linked star polymers (CCS) or linear block copolymers. This research demonstrates and describes the synthesis of poly(2-methyl-2-oxazoline-b-poly(2,2'-(1,4-phenylene)bis-2-oxazoline)-co-(2-n-2-butyl-2-oxazoline)(PMeOx-b-P(PhenBisOx-co-ButOx) amphiphilic core cross-linked star polymers (CCS) based on POxs. The CCS polymers are synthesized via sequential CROP in two steps by synthesizing Poly(2-methyl-2-oxazoline) (PMeOx) as the living arms followed by cross-linking of the core 2, 2’-(1,4-phenylene)bis-2-oxazoline (PhenBisOx) as the cross-linker and 2-n-butyl-2-oxazoline (ButOx) as a hydrophobic monomer to form the core of the CCS polymers. In addition, this research will clarify the other kinds of amphiphilic copolymers based on aggregation-induced emission (AIE) fluorophores, tetraphenylethylene (TPE) as an initiator that have been synthesized by a combination of cationic and anionic ROP. First, the difunctional initiator TPE-(OH)2 was synthesized via McMurry coupling reaction. Then, two kinds of triblock copolymers, TPE-poly(2-methyl-2-oxazoline)-b-poly(ε-caprolactone) (TPE-(PMeOx-b-PCL)2) and TPE-poly(ε-caprolactone)-b-poly(2-methyl-2-oxazoline) (TPE-(PCL-b-PMeOx)2), were synthesized by altering the sequence of polymerization. The resulting polymers, CCS polymers and the triblock copolymers were loaded with the anticancer drug doxorubicin (DOX) and their in vitro properties, cytotoxicity, and drug release at different pH were studied. Furthermore, the resulting polymers were characterized by size exclusion chromatography (SEC), nuclear magnetic resonance (NMR), dynamic light scattering (DLS), and transmission electron microscopy (TEM). All results in this research showed that the amphiphilic block copolymers, the CCS polymers and the triblock copolymers could be suitable carriers for drug delivery systems.
Comprehensive Kinetic Study of Oxidative Coupling of Methane (OCM) over La2O3-based catalysts(2022-12) [Dissertation]
Advisor: Sarathy, Mani
Committee members: Gascon, Jorge; Farooq, Aamir; Chin, Ya-Huei (Cathy)Oxidative coupling of methane (OCM) represents a potentially viable method to convert methane directly into more desirable products such as ethane, and ethylene. In this dissertation, a comprehensive kinetic study of oxidative coupling of methane was performed over La2O3-based catalysts. An accurate and reliable gas-phase model is critical for the entire mechanism. The gas-phase kinetics was first studied using a jet-stirred reactor without catalyst. Both experiments and simulations were conducted under various operating conditions using different gas-phase models. Quantities of interest and rate of production analyses on hydrocarbon products were also performed to evaluate the models. NUIGMech1.1 was selected as the most comprehensive model to describe the OCM gas-phase kinetics and used for the next study. Next, microkinetic analysis on La2O3-based catalysts with different dopants was performed. The Ce addition has the greatest boost over the performance. The kinetics at low conversion regimes were analyzed and correlated to the catalysts’ properties. The activation energy for methane hydrogen abstraction was estimated, with the formation rate of primary products, which suggested that the initiation reaction steps were similar for La2O3-based catalyst. A homogeneous-heterogeneous kinetic model for La2O3/CeO2 catalyst was then constructed. By applying in situ XRD, the doping of CeO2 not only enhanced catalytic performance but also improved catalyst stability from CO2 and H2O. A wide range of operating conditions was investigated experimentally and numerically, where a packed bed reactor model was constructed based on the dimensions of experimental setup and catalyst characterization. The rate of production (ROP) was also performed to identify the important reactions and prove the necessity of surface reactions for the OCM process. Laser-induced fluorescence was implemented to directly observe the presence of formaldehyde. The last section includes the implementation of in situ laser diagnosis techniques at the near-surface region to solve the existing challenges. Raman scattering was implemented to quantitate the concentration profiles of major stable species near the surface and measure the in situ local temperatures at different heights above the catalyst surface, to study the kinetics transiting from the surface edge to the near-surface gas phase and provide a new perspective in OCM kinetic studies.
Ultraviolet micro light-emitting diode and color-conversion for white-light communication(2022-11-29) [Thesis]
Advisor: Ooi, Boon S.
Committee members: Ohkawa, Kazuhiro; Ng, Tien Khee; Mohammed, Omar F.Visible-light communication (VLC) has several advantages over the commonly used radio frequency (RF) spectrum, including high bandwidth and low crosstalk. These features have become of more significance, especially as the proliferation of wireless devices increases and causes spectrum crowding. The white light in VLC systems is typically obtained from blue/violet light-emitting diodes (LEDs) and phosphors partially converting blue light into longer wavelength colors spanning the visible-light band. One phosphor that is frequently used is cerium-doped yttrium aluminum garnet (YAG). However, YAG suffers from a low color-rendering index (CRI) and high correlated color temperature (CCT). Lead halide perovskites provide an alternative to YAG and have been extensively utilized for optoelectronic devices owing to their tunable bandgap and high photoluminescence quantum yield (PLQY). However, their drawbacks, e.g., lead toxicity and instability, hinder their widespread application. Herein, in order to take advantage of a high-performance lead-free tin-based halide perovskite phosphor that has a high absolute PLQY of near unity and a wide spectral emission ranging from 500 to 700 nm, we fabricated ultraviolet (UV) micro light-emitting diodes (micro-LEDs) with a peak wavelength at 365 nm to match the peak of the photoluminescence excitation (PLE) spectra of the material to obtain strong yellow-spectrum emission. Together with a blue LED, white light was obtained with a CRI of 84.9 and 4115-K CCT. Despite the long PL lifetime of the perovskite material, which is in the order of μs, a net data rate of 1.5 Mb/s was achieved using orthogonal frequency-division multiplexing (OFDM) with adaptive bit and power loading to take advantage of the exceptionally high PLQY of the phosphor to improve the data throughput of the VLC system using higher modulation orders. Furthermore, through improvements to the nanostructure of lead-free tin-based halide perovskite phosphor and the use of excitation sources with a higher power, the data rate is expected to be even higher. The lead-free nature of this material, along with its wide spectrum and high conversion efficiency, makes it a promising alternative to conventional toxic perovskite-based phosphors. As the first demonstration of VLC links using lead-free perovskite, this study paves the way for safer, more sustainable VLC systems.
A 5D Magnetic Tracking System for Placement Verification of Umbilical Catheters and Endotracheal Tubes in Neonates(2022-11-25) [Dissertation]
Advisor: Kosel, Jürgen
Committee members: Salama, Khaled N.; Inal, Sahika; Carrara, SandroThe use of subcutaneous medical devices has advanced the field of clinical medicine and surgery. However, localizing devices internally requires imaging techniques such as x-ray or ultrasound. A novel 5D magnetic tracking system for subcutaneous medical catheters is presented, providing the capability for precise device localization in an extremely compact and portable pocket-size format. It is entirely benign, avoids x-rays, and can be used to immediately confirm the proper instrument placement. The magnetic tracking system has been implemented on umbilical catheters and endotracheal tubes and is characterized by bench-test, cadaveric and in-vivo studies. The systems consist of a magnetic tip fixed to the distal end of the subcutaneous device, as well as a Magnetic Sensing Device that utilizes magnetic field sensors to localize the magnetic tip. Various Magnetic Sensing Devices have been developed, each with a specific use case in mind within the clinical environment. The magnetic tip is made from a soft, flexible, and lightweight magnetic composite material that is capable of sustaining a high magnetic remanence field whilst also being non-cytotoxic. The bench tests show high localization accuracy for a distance up to 4 cm. The accuracy is slightly reduced during cadaveric and in-vivo tests, due to external factors impacting the application, such as the dermal surface topography and the method of establishing the reference frame before radiographic imaging. A bias circuit has been developed and implemented to increase the operational depth of the magnetic tracking system and prevents sensor saturation at close distances. The magnetic tracking system has shown to be robust in performance and functionality in real-world clinical applications, and with its intuitive approach and portability, it has the potential to make real-time subcutaneous device tracking widely accessible.
Novel Linear and Star Poly(vinylidene fluoride)-Based Polymers: Synthesis, Characterization and Applications(2022-11-24) [Dissertation]
Advisor: Hadjichristidis, Nikos
Committee members: Nunes, Suzana Pereira; Cavallo, Luigi; Ameduri, BrunoPoly(vinylidene fluoride) PVDF is a semi-crystalline fluoropolymer that attracted researchers' attention more than a decade ago due to its remarkable properties, such as mechanical strength, thermal stability, chemical resistance, good processability, and excellent aging resistance. Due to these excellent properties, PVDF is applied in many applications such as membranes and filtration, biomedical applications, drug delivery, batteries, energy generation, energy storage, sensors, actuators, and energy harvesting applications. The dissertation was inspired by PVDF’s outstanding properties and applications. First of all, the effect of chain topology of on the crystallization and polymorphism between linear and star PVDF homopolymers were studied. Well-defined linear and stars PVDF homopolymers architectures were synthesized by reversible addition−fragmentation chain transfer (RAFT) polymerization. The non-isothermal crystallization study showed an increase in the amount of ferroelectric β-phase with respect to the paraelectric α-phase as the number of arms in the PVDF stars increases. This finding is explained by the increased topological complexity in the stars of several arms, which leads to the preferential formation of the less thermodynamically stable ferroelectric β-phase. Moreover, the isothermal crystallization kinetics of the PVDF stars was faster than the linear PVDF as a result of their speedier nucleation. Secondly, we report the synthesis of poly(n-isopropylacrylamide)-b-poly(vinylidene fluoride) (PNIPAM-b-PVDF), amphiphilic block copolymers with linear and star architectures by RAFT sequential living polymerization. Due to the presence of a lower critical solution temperature (LCST) for PNIPAM (coil-globule transition around 32 °C), the synthesized PNIPAM-b-PVDF block copolymers have thermo-responsive behavior, therefore, potential application in the fabrication of thermo-responsive membranes. All fabricated membranes by nonsolvent-induced phase separation (NIPS) method exhibited thermo-responsive behavior with water permeability and PEG rejection experiments. Moreover, the several heating-cooling cycles showed that the thermal-responsive behavior of these membranes are reversible and stable. Finally, a suggested potential future work is given to synthesize other PVDF-based block copolymers via sequential living polymerizations.
Commercial chemical vapor-deposited hexagonal boron nitride: how far is it from mechanically exfoliated-like quality?(2022-11-10) [Thesis]
Advisor: Lanza, Mario
Committee members: Zhang, Xixiang; Li, Xiaohang; Anthopoulos, Thomas D.Two-dimensional (2D) layered hexagonal boron nitride (h-BN) has become a very popular material in nanoelectronics in recent years because of its extraordinary chemical stability and thermal conductivity . Recently, h-BN is also commonly used as a dielectric material , and research in this area is still in its early stages. The commonly used methods for fabricating h-BN include mechanical exfoliation and chemical vapor deposition (CVD). CVD is a recognized industry-compatible method for producing large-area h-BN. However, studies have shown that multilayer h-BN grown by CVD is polycrystalline and contains multiple local defects . These defects and inhomogeneity cannot be avoided and lead to small amounts of atom-wide amorphous regions that have weak dielectric strength . Although the general characteristics of h-BN prepared by these two fabrication methods can be learned from different works in the literature, it is difficult to study the quality of h-BN without systematically comparing the differences between the two growth methods under the same experimental conditions and with large number of samples. This also makes it difficult for researchers to choose the best-quality h-BN. In this work, the morphological characteristics and electrical properties of mechanically exfoliated h-BN and CVD-grown h-BN from different sources have been compared under different conditions. Commercially available h-BN flakes mechanically exfoliated from NIMS h-BN bulk crystal show no leakage current at electrical fields up to 25.9 MV/cm, and above this applied electrical force, the size of the conductive spots is extremely small (1.99 ± 1.81 nm2). On the contrary, “monolayer” CVD-grown h-BN samples from Graphene Supermarket were shown to be amorphous in ~20% of their area, which makes them appear discontinuous from an electrical point of view, plus they contain large thickness fluctuations up to 6 layers. Moreover, in nanoelectronic measurements collected with a conductive atomic force microscope (CAFM) working in vacuum, mechanically exfoliated h-BN showed better electrical homogeneity and presented later dielectric breakdown compared to the h-BN samples fabricated by the CVD method.
Nesting Ecology and Conservation of Sea Turtles in the Saudi Arabian Red Sea(2022-11) [Dissertation]
Advisor: Berumen, Michael L.
Committee members: Jones, Burton; Alafifi, Abdulkader Musa; Brainard, Russell E.In the Saudi Arabian Red Sea, two of the seven species of sea turtles are known to nest and forage along the coast, the hawksbill turtle (Eretmochelys imbricata) and the green turtle (Chelonia mydas). As a result of some life history characteristics, sea turtles are particularly vulnerable to anthropogenic impacts. Under Saudi Arabia’s Vision 2030 and the recent opening of its borders to recreational tourists, the country aims to develop several large-scale projects along the Red Sea coast, locally known as “giga-projects”. Thus, imminent pressures from coastal development highlight the urgency needed for multi-country cooperation in protecting sea turtles in the region. This dissertation aims to establish some baseline data and protocols for future work to meet the data needs of the relevant conservation authorities in Saudi Arabia. In particular, this thesis contributes new and important information to some of the identified knowledge gaps for the Red Sea region, including sea turtle habitat use, threat assessment (plastic and heavy metal pollution), and evaluating hatching success. I used satellite telemetry to understand foraging home ranges of hawksbill and green turtles, post-nesting migrations, and inter-nesting habitat use of green turtles. Additionally, I used photo identification to understand the abundance and behavior of turtles at a Rabigh fringing reef, in the central Red Sea. I assessed two anthropogenic contaminants as a threat to Red Sea turtles: heavy metal contamination and plastic ingestion. Heavy metal concentrations in the sand were evaluated at the largest green turtle rookery in Saudi Arabia, Ras Baridi, which is located next to a cement factory. I also assessed the concentration of heavy metals in the tissues of dead hatchlings found at Ras Baridi. Additionally, I studied plastic ingestion in ten deceased turtles found along the Saudi Arabian Red Sea. In my last data chapter, I assessed the hatching success of green turtle nests, and investigated clutch relocation as a possible method of increasing success. The final chapter summarizes the results from this research in the context of the 2004 PERSGA Marine Turtle Conservation Plan, and provides possible conservation strategy recommendations to protect Red Sea turtles
Visualization of the combustion process using a narrow throat pre-chamber geometry for a heavy-duty engine(2022-11) [Dissertation]
Advisor: Turner, James W. G.
Committee members: Magnotti, Gaetano; Finkbeiner, Thomas; Armas, OctavioLean combustion is one of the most applied methods to increase engine efficiency and maintain a good trade-off with engine emissions. The pre-chamber combustion (PCC) is one of the most promising combustion concepts to extend the lean operating limits of the engine. The Narrow throat pre-chamber has shown long lean limit extension than other ignition sources. The pre-chamber combustion and main-chamber combustion were studied in a Heavy-Duty optical engine using methane fuel to determine the generalities of the combustion process in the two volumes: pre- and main chamber. The combustion process was recorded using three collection systems: (a) Natural Flame Luminosity (NFL), (b) OH* Chemiluminescence, and (c) CH* Chemiluminescence. Additionally, the effect of three pre-chamber geometrical parameters, volume, nozzle area and throat diameter, on the pre-chamber combustion was also addressed in this research. The generalities of the pre-chamber combustion inside the pre-chamber exhibited a flame propagation nature for the combustion process, with high propagation velocities inside the throat. The main chamber process for the reference narrow throat pre-chamber exhibited defined jets from six of the twelve jets corresponding to the bottom row of nozzles for the reference pre-chamber. Regarding the geometrical parameters, the throat area to nozzle area ratio determines the propagation mode for the main chamber, evolving from only six jets and ultra-low throat intensity for ultra-low ratios to, twelves jethe ts with same penetration and high throat intensity for ratios above one.
Effects of Common Osmolytes on Electrostatic and Hydrophobic Surface Forces(2022-11) [Thesis]
Advisor: Mishra, Himanshu
Committee members: Nunes, Suzana Pereira; Fatayer, Shadi P.Surface forces due to electrostatics and hydrophobic interactions in aquatic media are implicated in numerous phenomena in natural and applied contexts, such as protein folding, ATP synthesis, flocculation, froth flotation, food and beverage industry, and separation and purification processes. Although the effects of hard ions like K+ and Cl- on such surface forces have been extensively studied and well understood, the effects of common osmolytes such as urea, TMAO, betaine, sarcosine, and glycine on electrostatics and the hydrophobic interaction are not entirely clear. In the recent years, direct surface force measurements are being utilized to probe these effects. The expectation is that these findings will bring us one step closer to understanding the balance of surface and molecular forces in extremophiles, e.g., Escherichia coli, Sepia officinalis, and Dasyatis americana. In this thesis, we have utilized Atomic Force Microscopy (AFM) and complimentary techniques to directly quantify the effects of common osmolytes on (i) electrostatic interactions between the charged silica surfaces; and (ii) hydrophobic interactions between perfluorinated surfaces. Urea, TMAO, betaine, sarcosine, and glycine enhanced the magnitude of electrostatic interaction. We provide some clues towards mechanistic insight. For hydrophobic surfaces, urea increased adhesion when perfluorinated surfaces were brought into contact, whereas TMAO, betaine, and sarcosine reduced it in the following order: TMAO > betaine > sarcosine. Advancing/receding contact angles were measured to check whether the osmolytes adsorbed onto the hydrophobic surfaces. Contact angle hysteresis data revealed that the adsorption was not significant, and these findings were corroborated via Quartz Crystal Microbalance with Dissipation experiments. Taken together, our findings advance the current understanding of osmolytes’ effects on electrostatic and hydrophobic interactions.
Comprehensive assessment of PM10 and PM2.5 pollution in the west side of Saudi Arabia using CMAQ and WRF-Chem models(2022-11) [Thesis]
Advisor: Stenchikov, Georgiy L.
Committee members: Jones, Burton; Sun, ShuyuThis work is aimed to study the capabilities of CMAQ and WRF-Chem models for predicting the PM10 and PM2.5 pollution in the west side of Saudi Arabia. To do this fairly, one-month simulations (April, 2021) are done in both models using same initial and boundary conditions, meteorology and anthropogenic emissions. Unique configurations in both models allow to compare differences in the chemical processes and natural emissions estimation of each model. Simulated PM (PM10 and PM2.5) surface concentrations and AOD are compared with available observations to assess models’ performance. Moreover, CMAQ is used to study a real air pollution episode generated by a fire in the Rabigh Electricity Power Station between April 8 and April 11, 2021.
The Microbiome After Bail-out: Testing Individual Polyps from Pocillopora verrucosa as Models for Coral Microbiology Studies(2022-11) [Thesis]
Advisor: Peixoto, Raquel S
Committee members: Habuchi, Satoshi; Lastra, Manuel I. ArandaCoral reefs are among the most biodiverse ecosystems in the world, being essential for marine life. The engineers of these ecosystems, reef-building corals, live in association with a great diversity of microorganisms, which can affect their host’s health in beneficial or detrimental manners. Corals are currently threatened by climate change and other environmental stressors, that lead to the phenomenon of coral bleaching, in which these animals lose their endosymbiotic algae. Even though the stressors that cause coral bleaching are known, the exact cellular and molecular mechanisms that provoke this process are still undiscovered. The lack of information regarding micro-scale processes that happen in unhealthy corals could be resolved with more efforts in developing micro-scale studying models. The use of individual polyps that bail-out of the coral skeleton induced by acute stress has been suggested as a model to study these processes. However, little is known about how these polyps change after bailing-out of a colony, which could become a problem once reliable models should be consistent and well understood. Thus, investigating these changes and optimizing a methodology to minimize them is crucial to establish these polyps as models to study corals. Herein, we investigated microbiological changes of isolated polyps by performing an experiment to study shifts in their microbiome after the separation from the colony. Before the experiment, different methods to isolate polyps were tested to find the one that granted the highest survival. After finding that salinity-induced separation was the most efficient, this method was used to study the microbiome of coral polyps. We found that while no significant changes in the microbiome could be observed immediately after the separation of polyps from their colony compared to coral fragments, this pattern changed after two weeks. We propose that the maintenance of polyps without fixation to a substrate might be the cause for such changes, and that polyps able to attach to a substrate and regrow as a colony might still recover a microbiome composition closer to coral fragments. Finally, a new microfluidic device for fixation and maintenance of coral polyps was developed and tested for use in future experiments.
Towards the Direct Synthesis of Gasoline-Range Hydrocarbons from Carbon Dioxide(2022-11) [Thesis]
Advisor: Gascon, Jorge
Committee members: Ruiz-Martinez, Javier; Cavallo, LuigiThe emergence of climate change led to major mitigation drives towards circular carbon economy and carbon neutrality. More specifically, an environmentally sustainable approach – stemming from reacting CO2 with green H2 – can be tailored to produce gasoline-range hydrocarbons. This would lead to further diversification from conventional energy, while also offering a valuable recycle route for CO2 emissions. This thesis successfully applied advanced chemical engineering concepts – via multifunctional heterogeneous catalysis – to directly convert CO2 into hydrocarbons, in the same reactor. The approach combined two catalysts: an In/Co bimetallic catalyst, which converted CO2 into methanol, and a Pt/Zn modified zeolite beta (BEA) catalyst, which converted methanol into hydrocarbons. High-throughput synthesis and catalytic reaction units were utilized to create and test 22 different catalysts – varying In-Co-Pt-Zn/BEA compositions and synthesis methods – in a total of 32 catalytic configurations. These catalysts were analyzed via techniques including XRD, WDXRF, BET, TGA, ICP-OES, pyridine-IR, TEM, and HAADF-STEM EDX, for further characterization and optimization. Results include the discovery of optimum catalytic configurations that led to methanol and isoparaffin selectivities upward of 70% and 60%, respectively – with minimal deactivation rates, at 300 ℃, 50 bar, and with H2/CO2 volumetric ratio of 4:1.
Effect of heat stress on in vitro pollen germination and pollen tube elongation of Chenopodium quinoa and wild relatives(2022-11) [Thesis]
Advisor: Tester, Mark A.
Committee members: Blilou, Ikram; Chodasiewicz, MonikaClimate change is one of the biggest challenges facing agriculture today. Transient or prolonged heat stress can be detrimental to plant reproductive development. The male gametophyte, pollen, is particularly sensitive to heat stress, resulting in sterile pollen (pre-anthesis) or deformed/stunted pollen tubes (post-anthesis). Quinoa (Chenopodium quinoa Willd.) has recently seen a rise in global interest due to its nutritional qualities, but global expansion of quinoa is partially hindered by its susceptibility to heat. It has been hypothesized that introgression of heat tolerance traits from wild relatives that occupy warmer environments can increase thermotolerance in quinoa. The goal of this research was to investigate the effect of heat stress on mature pollen grains from quinoa and its wild relatives, C. berlandieri and C. hircinum. To answer this question, several experiments were performed: 1. The nuclear number of the pollen of wild relatives was assessed to determine whether mature pollen grains were released at the trinucleate stage. All pollen was found to be trinucleate. 2. Pollen germination medium was optimized for four accessions: C. quinoa (QQ74; PI 614886), C. berlandieri var. zschackei (CB; BYU14118), and C. hircinum (CHA; Hircinum-069 and CHC; BYU17105). Optimal sucrose and PEG concentrations were determined to be: 5% sucrose/20% PEG for QQ74 and CB; 20% sucrose/0% PEG for CHA; and 10% sucrose/20% PEG for CHC. 3. Temperature optima for pollen germination for QQ74 was 32°C-36°C; CB was 30°C-34°C; CHA was 36°C; and CHC was 32°C -34°C. Overall, pollen from wild relatives was not found to be more heat-tolerant than pollen from domesticated quinoa. 4. Pollen tube elongation over time was observed for all four accessions at 34°C and 38°C, with CHA and QQ74 having the lowest decrease in rate at 38°C (35 and 45%, respectively). This study provides a new method for pollen collection for quinoa and its wild relatives, further optimizes the pollen germination media for QQ74, introduces pollen germination media for three wild accessions, and investigates the effect of heat stress on mature pollen grains. These observations can be employed in future studies investigating heat stress response of pollen in quinoa and its wild relatives.
Microstructural Analysis and Engineering of III-Nitride-Based Heterostructures for Optoelectronic Devices(2022-11) [Dissertation]
Advisor: Ohkawa, Kazuhiro
Committee members: Ooi, Boon S.; Roqan, Iman S.; Sakai, AkiraAfter the invention of the high-efficiency blue light-emitting diode (LED) at the end of the twentieth century, a new generation of light-emitting devices based on III-nitrides emerged, showcasing the capabilities of this semiconductor family. Despite the current limitations in the fabrication of III-nitrides, their optical and electronic properties still place them as some of the most promising semiconductors to continue the development of optoelectronic devices. To take full advantage of the versatility offered by these materials, the fabrication of novel III-nitride-based devices demands rigorous control of all of its stages. From the initial deposition of the materials, which involves controlling the composition and size of often complex heterostructures, up to the microfabrication processing used to create a final device, any deficiency occurring will negatively impact the performance of the device. Most of the time, these deficiencies reflect in microscopic defects, hindering their detection and identification of their origin. Without such knowledge, the deficiencies cannot be fixed, stalling the improvement of the device fabrication process and, consequently, its performance. This dissertation presents a variety of methodological approaches to characterize, from a microstructural point of view, different properties of novel III-nitride-based heterostructures and devices. The characterizations include studying the structure, interface, composition, and crystalline defects of different heterostructures and evaluating the microfabrication quality of microscopic LEDs. The results of the different characterizations contributed to developing novel LED and photocatalytic devices, for example, a single-quantum-well InGaN-based red LED with a high color purity, a monolithic phosphor-free white LED, microscopic green LEDs with a size smaller than 5×5 μm$^2$, and metal oxide/GaN-based photocatalysts with improved resilience to photocorrosion. The analyses and results presented in this dissertation strongly relied on the analytical capabilities offered by transmission electron microscopy, which proved to be a convenient and versatile tool for the characterization of many aspects related to the fabrication of III-nitride-based optoelectronic devices.
Nutrition and organism flows through tropical marine ecosystems(2022-11) [Dissertation]
Advisor: Jones, Burton
Committee members: Berumen, Michael L.; McCabe, Matthew; Ellis, JoanneIn tropical seascapes, coral reefs often exist in proximity to marine vegetated habitats such as seagrass, mangroves, and macroalgae. This habitat mosaic offers the possibility for connection and exchange of both organisms and nutrition between habitats, mediated by biological and physical processes. This dissertation examines flows of organisms and nutrition between coral reefs and tropical vegetated habitats in the central Red Sea through 3 different mechanisms: 1) Use of multiple habitat types by tropical marine fishes, 2) Transport of algal material to coral reefs via the foraging behavior and movements of herbivorous fishes, and 3) Physical flow of water between coastal habitats. The results of this thesis suggest that coastal tropical habitats maintain a variety of ecological links at different spatial and temporal scales. A large fraction (36%) of fish species found on coral reefs are also found in at least one marine vegetated habitat in the central Red Sea, with many species mainly living in vegetated habitats as juveniles. This demonstrates the value of mangrove, seagrass, and macroalgae habitats to coral reef fishes, and suggests that many species make ontogenetic migrations between reef and non-reef habitats through their lives. Two species of herbivorous reef fishes (Naso elegans and N. unicornis) were found on coral reefs with algae in their guts which likely originated from nearby Sargassum-dominated macroalgae canopies, representing a fish-mediated, cross-habitat flux of nutrition from macroalgae habitats to coral reefs. Finally, we used a combination of remote sensing, a dye tracer study, and in-water measurements to observe water movement from shallow seagrass and mangrove habitats to nearby lagoon and coral reef habitats. Water exiting seagrass and mangrove habitats had altered concentrations of various nutrients (such as increased particulate organic carbon or decreased dissolved nutrients), suggesting that Red Sea mangroves and seagrasses change nutrient concentrations in water and the movement of water from these habitats to coral reefs could supply reefs with an allochthonous source of nutrition. These various linkages, controlled by a range of physical and biological processes, highlight the interconnected nature of tropical coastal ecosystems, and thereby the need to conserve whole habitat mosaics in the pursuit to protect coral reefs and maintain healthy and functioning coastal ecosystems.
The Red Sea Coral Reef Cryptobiome: How do Nearby Benthic Communities Influence the Biodiversity of the Reef's Hidden Majority?(2022-11) [Thesis]
Advisor: Berumen, Michael L.
Committee members: Hong, Pei-Ying; Carvalho, SusanaMost of the reef's biodiversity remains undiscovered due to its complex tridimensional structure and the small size of the organisms that compose most of its biodiversity. To better understand the biodiversity of the major biological component of the reef environment (the cryptobiome), artificial cubic-like tools called Autonomous Reef Monitoring Structures (ARMS) were created to mimic the tridimensional nature of coral reefs. Here, I deployed 16 ARMS within four distinct benthic habitats on Tahla reef in the Red Sea (Saudi Arabia) to investigate how changes in reef habitats reflect changes in associated biodiversity of the cryptobiome. The following habitat types were selected after reef surveys and based on benthic coverage prevalence: i) Algae Pavement; ii) Rubble; iii) Plating corals; and iv) Branching corals. Habitats were located at the same depth contour (~10m), under similar exposure conditions and separated by at least 35m. The rugosity of the habitats was estimated based on the chain method, whereas monthly measurements of the physicochemical characteristics of the water were assessed by water collections (nutrients and chlorophyll a) and Conductivity-Temperature-Depth (CTD) instrument deployments (temperature, salinity). A fixed quadrat of approximately 15m2 was marked within each habitat type and four ARMS were deployed randomly within it. Units were retrieved after a period of approximately seven months for analysis of pioneer eukaryotic assemblages through traditional taxonomy identification of organisms larger than 2000μm, and through molecular metabarcoding using COI and 18S markers for the remaining ARMS fractions: sessile, 500μm-2000μm, and 106μm-500μm. To compare two distinct current methodologies to assess cryptobenthic taxa, water collections next to each ARMS unit were conducted right before retrieval. These samples were used to investigate the environmental DNA using the same COI and 18S markers. The biodiversity of the pioneer cryptobiome assemblage was analyzed through a combination of univariate and multivariate statistical methods. Overall, the habitats that showed greatest significantly distinct cryptobenthic community composition were Algae Pavement and Plating Corals, the ARMS and eDNA were defined as complementary techniques to assess the cryptofauna, and the use of a multi-marker approach increased the resolution of the cryptofauna characterization across different reef habitats.
Hybrid Arborescent Polypept(o)ides for Biomedical Applications(2022-11) [Dissertation]
Advisor: Hadjichristidis, Nikos
Committee members: Khashab, Niveen M.; Nunes, Suzana Pereira; Gauthier, MarioThis work reports a novel biocompatible and biodegradable arborescent amphiphilic polypept(o)ides-based polymer poly(γ-benzyl L-glutamate)-co-poly(γ-tert-butyl L-glutamate)-g-polysarcosine (P(BG-co-Glu(OtBu))-g-PSar) as a smart dual-responsive targeting drug vehicle. The synthesis pathway in this work highlighted the grafting reaction improvement of the polypeptides core and using polysarcosine (PSar) corona as a coating agent. The responsiveness of the polymer is caused by the pH sensitivity of the polypeptides and the reducible linker introduced between the core and corona. While adding the tripeptides arginine, glycine, and aspartate (RGD) as a ligand on the unimolecular micelles’ surface increases the targeting ability of the polymer. During the building of the arborescent, the coupling sites were controlled by using γ-tert-butyl L-glutamate (Glu(OtBu)-NCA) as a second monomer besides γ-benzyl L-glutamate (BG-NCA) since the deprotection conditions are different for Bz and tBu groups. Knowing the coupling sites provides accuracy in calculating the molecular weight (MW) of graft polymers since it facilitates the determination of the grafting yield (Gy). The arborescent unimolecular micelles were formulated by coating the hydrophobic core with PSar hydrophilic corona. The distribution of the coupling sites on the substrates in the last generation yielded end-grafted and randomly-grafted unimolecular micelles. A comparison between those micelles by DLS, TEM, and AFM revealed that the end-grafted micelles showed more uniformity in terms of morphology and size distribution. Also, the surface modification achieved via RGD addition increased the shape uniformity and contributed to avoiding the particles’ aggregation. The sizes and shapes of end-grafted unimolecular micelles match the drug delivery systems (DDSs) requirements. Doxorubicin (DOX) was encapsulated physically into the unimolecular micelles to study the drug loading capacity (DLC) and drug loading efficiency (DLE). The maximum DLC and DLE were 14% and 28% w/w, respectively. The drug release profiles were investigated in healthy- and cancer-mimicking media. The results showed that in cancer-mimicking microenvironment (low pH and high glutathione (GSH) content), the drug diffused out the micelles faster. In addition, a slower drug release was noticed for RGD decorated unimolecular micelles. Finally, the biocompatibility, cytotoxicity, and cellular uptake of the unimolecular micelles were studied. The obtained results were promising as the arborescent unimolecular micelles showed excellent biocompatibility; meanwhile, the DOX-loaded unimolecular micelles have good cytotoxicity compared to free DOX. RGD targeting ligand contributes to increasing the cellular uptake and supports the sustained release.
Terrain-Based UAV Positioning: Tractable Models, Generalized Algorithms, and Analytical Results(2022-11) [Thesis]
Advisor: Alouini, Mohamed-Slim
Committee members: Gao, Xin; Eltawil, Ahmed; Trichili, AbderrahmenDeploying unmanned aerial vehicle (UAV) networks to provide coverage for outdoor users has attracted great attention during the last decade. Terrain information requires extensive attention in outdoor UAV networks, and it is one of the most important factors affecting coverage performance. Providing tractable models and common methods is necessary to generalize the terrain-based outdoor UAV positioning strategies. In this thesis, we demonstrate that UAVs can provide stable coverage for regularly moving users based on the existing local terrain reconstruction methods with UAV sampling. Next, a coarse-grained UAV deployment can be performed with a simple set of parameters that characterize the terrain features. A stochastic geometry framework can provide general analytical results for the above coarse-grained UAV networks. In addition, the UAV can avoid building blockage without prior terrain information through real-time linear-trajectory search. We proposed four algorithms related to the combinations of collecting prior terrain information and using real-time search, and then their performances are evaluated and compared in different scenarios. By adjusting the height of the UAV based on terrain information collected before networking, the performance is significantly enhanced compared to the one when no terrain information is available. The algorithm based on real-time search further improves the coverage performance by avoiding the shadow of buildings. During the execution of the real-time search algorithm, the search distance is reduced using the collected terrain information.
Machine learning in hardware via trained metasurface encoders: theory, design and applications(2022-11) [Dissertation]
Advisor: Fratalocchi, Andrea
Committee members: Moshkov, Mikhail; Ooi, Boon S.; Kivshar, YuriThe development of modern Machine Learning (ML) frameworks trained on large datasets established a rapid increase in the performance of cognitive computing algorithms for a wide range of applications. However, due to the processing capacity restrictions of electronics, scaling up the existing state-of-the-art is currently meeting a bottleneck. Recently, flat-optics arose as a promising alternative to conventional electronics due to intrinsic parallelism, tuneability, and high-speed of optical computations. Finding scalable, highly effective designs that can tolerate fabrication defects brought on by nanoscale manufacturing processes and the demanding design specifications of the end task is one of the main hurdles of flat optics. In this study, we address this problem by introducing an end-to-end optimization methodology that is robust to fabrication intolerance and performance losses due to material absorption and can simultaneously optimize in tens of millions of degrees of freedom. The core of this technology is universal approximators, a single surface of optical nanoresonators mathematically equivalent to a single layer of an artificial neural network (ANN). For these structures, we provide theoretical guarantees for universal approximation, an ability to approximate arbitrary defined material's transfer function. We validate this framework's capability by creating several optical components achieving near unity efficiencies for vectorial light processing with broadband spectral responses and pre-defined wavefront characteristics. In addition, leveraging the high-dimensional capabilities of that system, we present a novel concept of spectral-informed imaging, which does not require the use of spectral analyzers or complex mechanical filters but uses an artificial-intelligence engineered, "hardware" flat-optics surface that processes spectral encoding at the speed of light inside silicon (Si) metasurface.
Cellulose acetate membranes for organic solvent nanofiltration(2022-11) [Thesis]
Advisor: Szekely, Gyorgy
Committee members: Saikaly, Pascal; Lauersen, Kyle J.Organic solvent nanofiltration (OSN) is a membrane-based sustainable alternative to conventional separation techniques because it is non-thermal and energy-efficient. The fabrication of membranes usually includes fossil-based polymers and toxic solvents that present significant challenges. For example, its declining availability, concerns about its degradability and cross-contamination that involve toxicity risks. Nowadays, there is an increasing interest in the development of more sustainable membranes that maintain an optimum performance even in harsh solvents. The aim of my thesis research is to develop stable OSN membranes from cellulose acetate and explore the use of deacetylation reactions. The effect of the degree of acetylation on the membrane performance and stability in different organic solvents was investigated. The chemical composition and morphology were investigated using Fourier Transform Infrared (FTIR), Scanning Electron Microscope (SEM), and Atomic Force Microscopy (AFM). It was found that cellulose acetate membranes with less than 22% acetylation present a satisfactory solvent resistance and rejection in harsh solvents, such as DMF and acetone. In the performance tests were identified two main trends: one for polar protic solvents and one for polar aprotic solvents. This was attributed to their capacity to interact with the membrane via H-bond formation. The molecular weight cutoff (MWCO) was in the range of 735–325 g mol–1 in aprotic solvents and higher than 885 g mol–1 for polar protic solvents. The results found in this research can be translated into a reduce in costs, waste generated, energy required, and time employed in the fabrication of membranes. Also, it opens potential areas in the industry as it can be implemented in harsh solvent environments.