Theses and Dissertations
As a condition of graduation, KAUST requires master's students who complete a thesis to deposit it in the KAUST digital archive. Similarly, doctoral students must submit an electronic copy of their dissertation to the KAUST digital archive.
KAUST student authors retain copyright to their theses or dissertations. However, the university retains a non-exclusive license to make copies of dissertations or theses as needed for the academic or archival purposes of the institution. This includes providing open access to the work on the Internet.
Collections in this community
Study of III-nitride Nanowire Growth and Devices on Unconventional Substrates(2019-10) [Dissertation]
Advisor: Ooi, Boon S.
Committee members: Ooi, Boon S.; Ohkawa, Kazuhiro; Alshareef, Husam N.; Tchernycheva, MariaIII-Nitride materials, which consist of AlN, GaN, InN, and their alloys have become the cornerstone of the third generation compound semiconductor. Planar IIINitride materials are commonly grown on sapphire substrates which impose several limitations such as challenging scalability, rigid substrate, and thermal and lattice mismatch between substrate and material. Semiconductor nanowires can help circumvent this problem because of their inherent capability to relieve strain and grow threading dislocation-free without strict lattice matching requirements, enabling growth on unconventional substrates. This thesis aims to investigate the microscopic characteristics of the nanowires and expand on the possibility of using transparent amorphous substrate for III-nitride nanowire devices. In this work, we performed material growth, characterization, and device fabrication of III-nitride nanowires grown using molecular beam epitaxy on unconventional substrates. We rst studied the structural imperfections within quantum-disks-in-nanowire structure grown on silicon and discovered how growth condition could a ect the macroscopic photoluminescence behavior of nanowires ensemble. To expand our work on unconventional substrates, we also used an amorphous silica-based substrate as a more economical substrate for our nanowire growth. One of the limitations of growing nanowires on an insulating substrate is the added fabrication complexity required to fabricate a working device. Therefore, we attempted to overcome this limitation by investigating various possible GaN nanowire nucleation layers, which exhibits both transparency and conductivity. We employed various nucleation layers, including a thin TiN/Ti layer, indium tin oxide (ITO), and Ti3C2 MXene. The structural, electrical, and optical characterizations of nanowires grown on di erent nucleation layers are discussed. From our work, we have established several key processes for transparent nanowire device applications. A nanowire LED emitting at 590 nm utilizing TiN/Ti interlayer is presented. We have also established the growth process for n-doped GaN nanowires grown on ITO and Ti3C2 MXene with transmittance above 40 % in the visible wavelength, which is useful for practical applications. This work paves the way for future devices utilizing low-cost substrates, enabling further cost reduction in III-nitride device fabrication.
Biofouling in anaerobic membrane bioreactors: To control or not to?(2019-10) [Dissertation]
Advisor: Hong, Peiying
Committee members: Nunes, Suzana; Moran, Anxelu; Smith, AdamAnaerobic membrane bioreactor (AnMBR) serves as a more sustainable form of wastewater treatment. However, biofouling is particularly detrimental to the performanceof AnMBRs. This dissertation focuses on understanding more about the biofouling in nMBR, and to devise strategies to control or make use of these biofoulant layers. First, we aim to investigate the microbial community structure of sludge and biofilm from 13 different AnMBRs. Our findings indicate 20 sludge core genera and 12 biofilm core genera (occurrence ≥ 90% samples) could potentially account for the AnMBR performance. Sloan neutral model analysis indicates the anaerobic microbial consortium between sludge and biofilm is largely affected by stochastic dispersal and migration processes (i.e., neutral assembly), suggesting that the majority of these core genera are not selectively enriched for biofilm formation. Therefore, the second part of this dissertation aims to minimize the growth of the overall bacterial cells attached on the membranes. For this, membranes embedded with zinc oxide (ZnO) and copper oxide (CuO) nanoparticles were examined for their antifouling efficacies. Our findings indicate both CuO and ZnO nanoparticles embedded membranes could delay biofouling formation without significantly triggering the overall expression/abundance of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in biofilm. Furthermore, CuO and ZnO nanoparticles could inhibit the expression of quorum sensing associated genes, resulting in lower quorum sensing signal molecules production. Despite the positive results demonstrated from this study as well as those from others, we recognize that no control strategies are likely to achieve total prevention of anaerobic biofouling. Therefore, the last part of this dissertation focuses on exploring the effects of different foulant layers on antibiotic-resistant bacteria (ARB) and ARGs removal. Our findings suggest both ARB and ARGs could be absorbed by membrane foulant. Transmembrane pressures and the foulant layer synergistically affected ARB removal, but the foulant layer is the main factor that contributed to ARG removal through adsorption. Overall, the collective findings could bring new insights to the anaerobic membrane biofouling phenomenon, and offer pragmatic approaches to minimize biofouling without compromising the post-AnMBR effluent quality.
Characterization of a Novel Nuclear Specific Dicer-isoform in Human Cells(2019-09) [Thesis]
Advisor: Orlando, Valerio
Committee members: Froekjaer Jensen, Christian; Al-Babili, SalimFor more than a decade, studies focused on RNA interference (RNAi) pathway as a pivotal gene regulatory mechanism. RNAi components are attracting considerable interest due to the recent evidence demonstrating that they play a role not only in post-transcriptional regulation but also in transcriptional level. The involvement of RNAi components in heterochromatin formation and RNA Pol II processivity and alternative splicing in different organisms has been shown. Dicer protein, a highly conserved protein among kingdoms, is one of the main effectors in this pathway. There is a considerable amount of literature on Dicer’s role in the cytoplasm; however, there is still vast ambiguity concerning nuclear Dicer. More recent evidence reveals the existence of Dicer1 variants that are differentially expressed in some cancer cells. Our experiments set out to investigate one of these variants that we hypothesise is responsible for the nuclear function. We undertook genomic and biochemical approaches applied to HAP 1 cells as a model system to characterise Dicer1-s, taking advantage of a custom-made antibody in our research group. Here, as anticipated, our experiments proved that Dicer1-s is enriched in the nuclear compartment compared to full-length Dicer1, indicating that it might be a putative contributor to nuclear gene regulation activity. Unfortunately, it was not possible to establish a mutant cell line to investigate the significant nuclear function of Dicer1-s, due to the need for further optimisation of the methods used. Exploitation of previously optimised gene knock-out tools might accelerate shedding light on protein, DNA, and RNA partners, disclosing the exact nuclear mechanisms that might exhibit similar activity.
Compliant Electronics for Unusual Environments(2019-09) [Dissertation]
Advisor: Hussain, Muhammad Mustafa
Committee members: Hussain, Muhammad Mustafa; Ooi, Boon S.; Bakr, Osman; Ma, Zhenqiang (Jack)Compliant electronics are an emerging class of electronics which offer physical flexibility in their structure. Such mechanical flexibility opens up opportunities for wide ranging applications. Nonetheless, compliant electronics which can be functional in unusual environments are yet to be explored. Unusual environment can constitute a harsh environment where temperature and/or pressure is much higher or lower than the usual room temperature and/or pressure. Unusual environment can be an aquatic environment, such as ocean/sea/river/pond, industrial processing related liquid and bodily fluid environment, external or internal for implantable electronics. Finally, unusual environment can also be conditions when extreme physical deformation is anomalously applied to compliant electronics in order to understand their performance and reliability under such extraordinary mechanical deformations. Therefore, in this thesis, three different aspects of compliant electronics are thoroughly studied, addressing challenges of material selection/optimization for unusual environment applications, focusing on electrical performance and mechanical flexible behavior. In the first part, performance of silicon-based high-performance complementary metal oxide semiconductor (CMOS) devices are studied under severe mechanical deformation. Next, a high-volume manufacturing compatible solution is offered to reduce the usage of toxic chemicals in semiconductor device fabrication. To accomplish this, Germanium Dioxide (GeO2) is simultaneously used as transient material and dielectric layer to realize a dissolvable/bioresorbable transient electronic system which can be potentially used for implantable electronics. Finally, wide bandgap semiconductor Gallium Nitride is studied to understand its mechanical flexibility under high temperature conditions. In summary, this research contributes to the advancement of material selection, optimization and process development towards achieving compliant and transient devices for novel applications in unusual environments.
Skeletonization of Data for Seismic Inversion, Seismic Imaging and GPS Marker Detection(2019-09) [Dissertation]
Advisor: Schuster, Gerard T.
Committee members: Sun, Shuyu; Zhang, Xiangliang; Lin, YouzuoThis thesis develops four skeletonization methods for seismic inversion, seismic imaging, and GPS marker detection to improve both their computational efficiency and accuracy. The first two improve the accuracy of the final inverted images by novel skeletonized inversion methods. The third one improves the quality of seismic imaging by employing skeletonized preconditional operators. The fourth one uses skeletonized data for machine learning (ML) identification of GPS markers in drone photos. Three papers are published in top applied-geophysics journals, one paper is submitted and under review, while the fifth paper is now online at ArcXiv. It will soon be submitted to the journal Remote Sensing. 1. To obtain a good starting model for anisotropic full waveform inversion (FWI), the simultaneous inversion of anisotropic parameters vp0 and ε is initially performed using the wave-equation traveltime inversion (WT) method. Then a transmission+reflection wave-equation traveltime and waveform inversion (WTW) method is presented for a vertical transverse isotropic (VTI) medium where both traveltimes and waveforms are inverted for the velocity model. 2. To mitigate the amplitude mismatch problem, multiscale phase inversion (MPI) is presented where the magnitude spectra of the predicted data are replaced by those of the observed data. Moreover, the data are integrated N times in the time domain to boost the low-frequency components. In this case, the skeletonized data are traces with the substituted magnitude spectra so that only the recorded phase data need to be inverted. 3. I have developed a velocity-independent workflow for reconstructing a high-quality zero-offset reflection section from prestack data with a deblurring filter. In this case the Hessian inverse is approximated by its skeletonized representation, also known as the deblurring operator. 4. The GPS markers are only about 0.5×0.5 m2 in size and are difficult to detect manually in the drone images. The marker has a unique hourglass shape and its color is dark. To take advantage of these features, superpixels are used as the skeletonized representations of the targets. Then a superpixel-based classification method is applied to the aerial images.
Reversible Formic Acid Dehydrogenation to Hydrogen and CO2 Catalyzed by Ruthenium and Rhodium Complexes(2019-09) [Dissertation]
Advisor: Huang, Kuo-Wei
Committee members: Han, Yu; Lai, Zhiping; Zheng, JunrongFormic acid (FA) has been considered as one of the most promising materials for hydrogen storage today. The catalytic decarboxylation of formic acid ideally leads to the formation of CO2 and H2, and such CO2/H2 mixtures can be successfully applied in fuel cells. A large number of transition-metal based homogeneous catalysts with high activity and selectivity have been reported for the formic acid decarboxylation. In this presentation, we report ruthenium and rhodium complexes containing an N, N′-diimine ligand for the selective decomposition of formic acid to H2 and CO2 in water in the absence of any organic additives. Among them, the Ru complex could provide a TOF (turnover frequency) of 12 000 h–1 and a TON (turnover number) of 350 000 at 90 °C in the HCOOH/HCOONa aqueous solution. In addition to that, efficient production of high-pressure H2 and CO2 (24.0 MPa (3480 psi)) was achieved through the decomposition of formic acid with no formation of CO by this Ru complex. Moreover, well-defined ruthenium (II) PN3P pincer complexes were also developed for the reversible reaction-hydrogenation of carbon dioxide. Excellent product selectivity and catalytic activity with TOF and TON up to 13,000 h-1 and 33,000, respectively, in a THF/H2O biphasic system were achieved. Notably, effective conversion of carbon dioxide from the air into formate was conducted in the presence of an amine, allowing easy product separation and catalyst recycling.
Novel Surface Wave Imaging Methods(2019-09) [Dissertation]
Advisor: Schuster, Gerard T.
Committee members: Peter, Daniel; Santamarina, Carlos; Bruhn, Ronald L.I develop four novel surface-wave inversion and migration methods for reconstructing the low- and high-wavenumber components of the near-surface S-wave velocity models. 1. 3D Wave Equation Dispersion Inversion. To invert for the 3D background S-wave velocity model (low-wavenumber component), I first propose the 3D wave-equation dispersion inversion (WD) of surface waves. The results from the synthetic and field data examples show a noticeable improvement in the accuracy of the 3D tomogram compared to 2D tomographic inversion if there are significant 3D lateral velocity variations. 2. 3D Wave Equation Dispersion Inversion for Data Recorded on Rough Topography. Ignoring topography in the 3D WD method can lead to significant errors in the inverted model. To mitigate these problems, I present a 3D topographic WD (TWD) method that takes into account the topographic effects in surface-wave propagation modeled by a 3D spectral element solver. Numerical tests on both synthetic and field data demonstrate that 3D TWD can accurately invert for the S-velocity model from surface-wave data recorded on irregular topography. 3. Multiscale and layer-stripping WD. The iterative WD method can suffer from the local minimum problem when inverting seismic data from complex Earth models. To mitigate this problem, I develop a multiscale, layer-stripping method to improve the robustness and convergence rate of WD. I verify the efficacy of our new method using field Rayleigh-wave data. 4. Natural Migration of SurfaceWaves. The reflectivity images (high-wavenumber component) of the S-wave velocity model can be calculated by the natural migration (NM) method. However, its effectiveness is demonstrated only with ambient noise data. I now explore its application to data generated by controlled sources. Results with synthetic data and field data recorded over known faults validate the effectiveness of this method. Migrating the surface waves in recorded 2D and 3D data sets accurately reveals the locations of known faults.
Analyzing and Manipulating Wave Propagation in Complex Structures(2019-08-29) [Dissertation]
Advisor: Wu, Ying
Committee members: Keyes, David E.; Schuster, Gerard T.; Assouar, BadreddineThe focus of this dissertation is analyzing and manipulating acoustic wave propagation in metamaterials, which can be used to assist the design of acoustic devices. Metamaterials are artificial materials, which are arranged in certain patterns at a scale smaller than the wavelength and can exhibit properties beyond those naturally occurring materials. With metamaterials, novel phenomena, such as focusing, super absorption, cloaking and localization of ultrasound, are theoretically proposed and experimentally verified. In recent years, a planar version of metamaterials, often called meta-surfaces, has attracted a great deal of attention. Meta-surfaces can control and manipulate the amplitude, phase, and directions of waves. In this dissertation, we conducted a systematic study by deriving the effective medium theories (EMTs), and developing the theoretical and numerical models for our proposed designed metamaterial. Very recently, acoustic meta-surfaces have been used in the design of acoustic lenses, which can achieve various functionalities such as focusing and collimation. In the designs of acoustic lenses, impedance is an important issue because it is usually difficult to make the impedance of the lens equal to that of the environment, and mismatched impedance is detrimental to the performance of the acoustic lens. We developed an EMT based on a coupled-mode theory and transfer matrix method to characterize the propagation behavior and, based on these models, we report two designs of acoustic lenses in water and air, respectively. They are rigid thin plates decorated with periodically distributed sub-wavelength slits. The building block of the acoustic lens in water is constructed from coiling-up spaces, and that of the acoustic lens in air is made of layered structures. We demonstrate that the impedances of the lenses are indeed matched to those of the background media. With these impedance-matched acoustic lenses, we demonstrate acoustic focusing and collimation, and redirection of transmitted acoustic energy by finite-element simulations. In the framework of the hidden source of the volume principle, an EMT for a coupled resonator structure is derived, which shows that coupled resonators are characterized by a negative value of the effective bulk modulus near the resonance frequency and induce flat bands that give rise to the confinement of the incoming wave inside the resonators. The leakage of sound waves in a resonance-based rainbow trapping device prevents the sound wave from being trapped at a specific location. Based on our EMT, we report a sound trapping device design based on coupled Helmholtz resonators, loaded to an air waveguide, to effectively tackle the wave leakage issue. We show that a coupled resonators structure can generate dips in the transmission spectrum by an analytical model derived from Newton’s second law and a numerical analysis based on the finite-element method. We compute the transmission spectra and band diagram from the effective medium theory, which are consistent with the simulation results. Trapping and the high absorption of sound wave energy are demonstrated with our designed device.
Asynchronous Task-Based Parallelism in Seismic Imaging and Reservoir Modeling Simulations(2019-08-26) [Dissertation]
Advisor: Keyes, David E.
Committee members: Knio, Omar M.; Hadwiger, Markus; Ltaief, Hatem; Badia, RosaThe components of high-performance systems continue to become more complex on the road to exascale. This complexity is exposed at the level of: multi/many-core CPUs, accelerators (GPUs), interconnects (horizontal communication), and memory hierarchies (vertical communication). A crucial task is designing an algorithm and a programming model that scale to the same order of the HPC system size at multiple levels. This trend in HPC architecture more critically affects memory-intensive appli- cations than compute-bound applications. Accomplishing this task involves adopting less synchronous forms of the mathematical algorithm, reducing synchronization in the computational implementation, introducing more SIMT-style concurrency at the finest level of system hierarchy, and increasing arithmetic intensity as the bottleneck shifts from number of floating-point operations to number of memory accesses. This dissertation addresses these challenges in scientific simulation focusing in the dominant kernels of a memory-bound application: sparse solvers in implicit model- ing, and I/O in explicit reverse time migration in seismic imaging. We introduce asynchronous task-based parallelism into iterative algebraic preconditioners. We also introduce a task-based framework that hides the latency of I/O with computation. This dissertation targets two main applications in the oil and gas industry: reservoir simulation and seismic imaging simulation. It presents results on multi- and many- core systems and GPUs on four Top500 supercomputers: Summit, TSUBAME 3.0, Shaheen II, and Makman-2. We introduce an asynchronous implementation of four major memory-bound kernels: Algebraic multigrid (MPI+OmpSs), tridiagonal solve (MPI+OpenMP), Additive Schwarz Preconditioned Inexact Newton (MPI+MPI), and Reverse Time Migration (StarPU/StarPU+MPI and CUDA).
Automatic Protein Function Annotation Through Text Mining(2019-08-25) [Thesis]
Advisor: Hoehndorf, Robert
Committee members: Moshkov, Mikhail; Bajic, Vladimir B.The knowledge of a protein’s function is essential to many studies in molecular biology, genetic experiments and protein-protein interactions. The Gene Ontology (GO) captures gene products' functions in classes and establishes relationship between them. Manually annotating proteins with GO functions from the bio-medical litera- ture is a tedious process which calls for automation. We develop a novel, dictionary- based method to annotate proteins with functions from text. We extract text-based features from words matched against a dictionary of GO. Since classes are included upon any word match with their class description, the number of negative samples outnumbers the positive ones. To mitigate this imbalance, we apply strict rules before weakly labeling the dataset according to the curated annotations. Furthermore, we discard samples of low statistical evidence and train a logistic regression classifier. The results of a 5-fold cross-validation show a high precision of 91% and 96% accu- racy in the best performing fold. The worst fold showed a precision of 80% and an accuracy of 95%. We conclude by explaining how this method can be used for similar annotation problems.
Facade Segmentation in the Wild(2019-08-19) [Thesis]
Advisor: Wonka, Peter
Committee members: Alouini, Mohamed-Slim; Thabet, Ali KassemFacade parsing is a fundamental problem in urban modeling that forms the back- bone of a variety of tasks including procedural modeling, architectural analysis, urban reconstruction and quite often relies on semantic segmentation as the first step. With the shift to deep learning based approaches, existing small-scale datasets are the bot- tleneck for making further progress in fa ̧cade segmentation and consequently fa ̧cade parsing. In this thesis, we propose a new fa ̧cade image dataset for semantic segmenta- tion called PSV-22, which is the largest such dataset. We show that PSV-22 captures semantics of fa ̧cades better than existing datasets. Additionally, we propose three architectural modifications to current state of the art deep-learning based semantic segmentation architectures and show that these modifications improve performance on our dataset and already existing datasets. Our modifications are generalizable to a large variety of semantic segmentation nets, but are fa ̧cade-specific and employ heuris- tics which arise from the regular grid-like nature of fac ̧ades. Furthermore, results show that our proposed architecture modifications improve the performance compared to baseline models as well as specialized segmentation approaches on fa ̧cade datasets and are either close in, or improve performance on existing datasets. We show that deep models trained on existing data have a substantial performance reduction on our data, whereas models trained only on our data actually improve when evaluated on existing datasets. We intend to release the dataset publically in the future.
Development of Solution Processed Co-planar Nanogap Capacitors and Diodes for RF Applications Enabled Via Adhesion Lithography(2019-08-18) [Thesis]
Advisor: Anthopoulos, Thomas D.
Committee members: Laquai, Frédéric; McCulloch, IainFabrication process of capacitors and Schottky diodes with nanogap electrodes is explained in this Thesis. The Schottky diode is made with IGZO in the nanogap, whereas the capacitor is made with ZrO2 in the nanogap which acts as the dielectric. Moreover, the electric characterization of both the diode and capacitor was obtained for different frequencies and different diameters. The end result showed that as the frequency increases the diode performance increases, but the capacitance of the capacitors decreases. Also, the barrier height and concentration were obtained using the Mott-Schottky plot for different frequencies. The 10MHz had the highest carrier concentration (5.9E+18cm-3) and barrier height (1V).
Closing the Lab-to-Fab Gap with Inkjet-Printed Organic Photovoltaics(2019-08-08) [Thesis]
Advisor: Baran, Derya
Committee members: Inal, Sahika; Shamim, AtifInkjet printing promises to be an invaluable technique for processing organic solar cells with key advantages such as low material consumption, freedom of design and compatibility with different types of flexible substrates making it suitable for large-area production. However, one concern about inkjet printed organic solar cells is the common use of chlorinated solvents during the ink formulation process. While chlorinated solvents suit the inkjet printing process due to their high boiling points, suitable viscosity, and excellent solubility of organic donor and acceptor compounds, they still pose some risks for both human health and the environment, excluding them from being the ultimate choice for large-area production. As a step towards commercialization of OPV, we demonstrated the possibility to close the laboratory to fabrication gap, through the engineering of environmentally friendly inks, using a blend of non-halogenated benzene derivatives solvents optimized to meet the viscosity and surface tension requirements for the inkjet printing process. Starting from using the non-fullerene acceptor O-IDTBR combined with the commercially available donor polymer P3HT we obtained solar cell device with efficiency up to 4.73% - the best efficiency achieved by the P3HT:O-IDTBR system processed with all non-halogenated solvents via inkjet printing. We also delivered highly transparent active layer with device power conversion efficiency of up to 10% with a highly efficient blend of polymer donor PTB7-Th in combination with the ultranarrow band gap NFA IEICO-4F, using hydrocarbons solvent. Lastly, we demonstrated both high efficiency, transparency, and stability by presenting a novel approach based on NFAs consisting of lowering the donor:acceptor ratio in the photoactive layer ink formulations, resulting in more stable devices with comparable power conversion efficiencies to those achieved by lab methods. This breakthrough in ink engineering paves the way in closing the lab-to-fab gap in organic photovoltaic using the low-cost, high throughput inkjet printing technology while considering both environmental and health-conscious mass production and device stability of organic photovoltaics.
Expression of EZH1-Polycomb Repressive Complex 2 and MALAT1 lncRNA and their Combined Role in Epigenetic Adaptive Response(2019-08-04) [Thesis]
Advisor: Orlando, Valerio
Committee members: Orlando, Valerio; Arold, Stefan T.; Al-Babili, SalimLiving cells maintain stable transcriptional programs while exhibiting plasticity that allows them to respond to environmental stimuli. The Polycomb repressive complex 2 (PRC2) is a key regulator of chromatin structure that maintains gene silencing through the methylation of histone H3 on lysine 27 (H3K27me), establishing chromatin-based memory. Two variants of PRC2 are present in mammalian cells, PRC2-EZH2 which is predominantly present in differentiating cells, and PRC2-EZH1 that predominates in post-mitotic tissues. PRC2-EZH1α/β pathway is involved in the response of muscle cells to oxidative stress. Atrophied muscle cells respond to oxidative stress by enabling the nuclear translocation of EED and its assembly with EZH1α and SUZ12. Here we prove that the metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) long noncoding RNA (lncRNA) is required for the assembly of PRC2-EZH1 components. The absence of MALAT1 significantly decreased the association between EED and EZH1α proteins. Biochemical analysis shows that the presence of MALAT1 increases the enzymatic activity of PRC2-EZH1 in vitro. In addition, we show that the simultaneous expression of PRC2 core components is necessary for their solubility. The successful expression of PRC2 proteins enables the execution of several downstream experiments, which will further explain the nature of the interplay between MALAT1 and PRC2.
Study of ultraviolet AlGaN nanowires light-emitting diodes(2019-08) [Dissertation]
Advisor: Ooi, Boon S.
Committee members: Ooi, Boon S.; Ohkawa, Kazuhiro; Schwingenschlögl, Udo; Mi,ZetianUltraviolet (UV) group III-Nitride-based light emitters have been used in various applications such as water purification, medicine, lighting and chemical detection. Despite attractive properties such as bandgap tunability in the whole UV range (UV-C to UV-A), high chemical stability and relative low cost, the low quantum efficiency hamper the full utilization. In fact, external quantum efficiencies of UV devices are below 10 % for emission wavelength shorter than 350 nm. This thesis aims to show alternative solutions to such problems by employing nanowires (NWs) structures, and target the eventual application of reliable and high power NWs-based light-emitting devices, enabling large-scale production using the established silicon foundry processes. Here, we present the improvement of injection current and optical power of AlGaN NWs LEDs by involving a metal bilayer thin film with a dual purpose: eliminate the potential barrier for carrier transport, and inhibit the formation of silicide. We then study the AlGaN/GaN UV LED design to optimize the device structure and improve the LED performance. We compared multiple devices having different active region and graded layers’ thicknesses. Improvement on the output power was achieved for larger p-AlGaN graded layer and thinner p-GaN contact layer structure due to the better hole injection and lower p-GaN absorption. The junction temperature of AlGaN-based NWs LEDs on metal bi-layer and silicon is also presented as a crucial parameter affecting the device efficiency, chromaticity and reliability. In this regard, by using the forward-voltage and peak-shift method we extracted the junction temperature values and confirmed the better heat dissipation in NWs grown on metal substrate. Finally, the origin of single and ensemble NWs current injection and injection efficiency are studied by treating the AlGaN NWs with KOH solution. Measurements based on conductive atomic force microscopy enabled a fast feedback cycle without fabricating the device. Despite the NWs technology is still at its infancy compared to the matured planar, we believe that this research effort will give important insight in advancing the AlGaN NWs devices for future industrial employment.
Design and Real-time Implementation of Model-free Control for Solar Collector(2019-08) [Thesis]
Advisor: Laleg-Kirati, Taous-Meriem
Committee members: Ahmed, Shehab; Kammoun,Alba; Diagne, MamadouThis work addresses the design and real-time implementation of adaptive control strategies on the parabolic solar collector to enhance the production efficiency under varying working conditions. For example, the unpredictable variations of the solar irradiance and thermal losses, these factors can be a major problem in the control design. The control objective is to force the outlet temperature of the collector fluid, to track a predefined reference temperature regardless of the environmental changes. In this work, two control strategies have been designed and analyzed. First, an intelligent proportional-integral feedback control, which combines the proportionalintegral feedback control with an ultra-local model is proposed. This strategy uses a transfer function model that has been derived and identified from real-time data and used to test the controller performance. Second, an adaptive nonlinear control using Lyapunov stability theory combined with the phenomenological representation of the system is introduced. This strategy uses a bilinear model derived from the heat transfer equation. Both control strategies showed good performance in the simulations with respect to the convergence time and tracking accuracy. Besides, the conventional proportional-integral controller has been successfully implemented in the real system.
Optimizing a Selective Whole Genome Amplification (SWGA) Strategy for Clinical Malaria Infections(2019-08) [Thesis]
Advisor: Pain, Arnab
Committee members: Habuchi, Satoshi; Blilou, IkramPlasmodium is a genus well known for causing malaria, a life-threatening infection for many people where malaria is endemic. The blood-borne disease is transmitted by the female Anopheles mosquito. Till date, eight parasite species have been reported to cause malaria in humans that include P. falciparum, P. vivax, P. malariae, P. ovale curtisi, P. ovale wallikeri, P. cynomolgi, P. knowlesi and more recently P. simium. Amongst them, the most genetically understood species is P. falciparum, causing most of the deaths in children from malaria. Understanding genome variation at the population level of all malaria species is of utmost importance, including clinical cases with very low parasitemia. To achieve this purpose, we need sufficient amounts of parasite DNA material from the pool of host DNA, which always is overrepresented in clinical infections. We utilized a strategy of selective whole genome amplification (SWGA) technology on P. malariae and P. ovale curtisi (two neglected human infecting malaria parasites that often cause mild yet clinically relevant infections with low parasitemia) to efficiently enrich their genomic DNA for high-quality whole genome sequencing. Previous studies on SWGA applied on P. falciparum and P. vivax showed that SWGA could efficiently enrich the amount of starting DNA material from inadequate amounts of parasites directly from clinical samples without separating the host DNA using specifically designed primer sets. We have successfully designed multiple sets of primers and tested the efficiency of five best primer sets using polymerase chain reaction to enrich the genomes of P. malariae and P. ovale curtisi. The efficiency of primers in enriching the genome was tested on two clinical samples for each of P. malariae and P. ovale curtisi. We were able to enrich the genome of P. malariae with an average of 19-fold (19X) enrichment across both samples. For P. ovale curtisi, we could achieve an enrichment of 3 folds only. Nevertheless, we still obtained a sufficient amount of gDNA to prepare Illumina sequencing libraries and call for SNPs and Indels in a biologically reproducible manner at genome-scale.
Designing Surfaces for Enhanced Water Condensation and Evaporation(2019-08) [Dissertation]
Advisor: Wang, Peng
Committee members: Nunes, Suzana Pereira; Lai, Zhiping; Wang, ZuankaiWith the increasing pressure of providing reliable potable water in a sustainable way, it is important to understand water phase change phenomena (condensation and evaporation) as the water phase change is involved in many processes such as membrane distillation and solar still which can be a feasible choice of supplementing the present potable water access. In the present thesis, we first elucidate the role of wettability of water condensation substrate by combining the droplet growth dynamics and droplet population evolution. The results show that wettability has a negligible effect on water condensation rate in an atmospheric environment. After confirming the role of substrate wettability, we provide a quantitative analysis of the effect of substrate geometry on water condensation in the atmospheric environment. The analysis can help to predict the efficiency of water condensation rate with a given substrate of a certain geometry with the aid of computational simulation tools. The results show that water condensation can be increased by 40% by rationally designing the geometry of the condensation surface. However, the condensation rate in the atmospheric environment is relatively slow due to the presence of non-condensable gas. In order to increase the condensation rate, a relatively pure vapor environment is desired, in which condensed water will be the major heat transfer barrier. Coalescence induced jumping of condensed droplets on superhydrophobic surfaces is an interesting phenomenon to help faster removal of condensed droplets. However, it is still not clear how to optimize the overall heat transfer efficiency by condensation on such surfaces. We observed an interesting phenomenon on a superhydrophobic nano-cones array, on which water preferentially condenses within larger cavities among the nanocones. Droplets growing form larger cavities have larger growth rate. This finding can possibly provide a solution to optimizing heat transfer efficiency. Finally, a nylon-carbon black composite is prepared by electrospinning to enhance water evaporation under solar radiation. The composite shows an interesting light absorption property. In a wet state, the composite can absorb around 94% of the incident sunlight. The composite also shows strong mechanical and chemical stability. Thus, the composite is considered to be a practical candidate to be applied in the solar distillation process.
Leader-Follower Approach with an On-board Localization Scheme for Underwater Swarm Applications(2019-08) [Thesis]
Advisor: Shamma, Jeff S.
Committee members: Shamma, Jeff S.; Ooi, Boon S.; Jones, BurtonA striking feature of swarm robotics is its ability to solve complex tasks through simple local interactions between robots. Those interactions require a good infrastructure in communication and localization. However, in underwater environments, the severe attenuation of radio waves complicates communication and localization of di erent vehicles. Existing literature on underwater swarms use centralized network topology which require physical vicinity to the central node to ensure reliability. We are interested in building a decentralized underwater swarm with a decentralized network topology that only requires neighbour communication and self-localization. We develop a simple leader-follower interaction rule where the follower estimates the leader's position and acts upon that estimation. The leader shines a 450 nm di racted blue laser that the follower uses to continuously align its light sensors to the light source. Furthermore, the leader's laser can be modulated for explicit communication purposes. The proposed leader-follower approach produces satisfactory results in surge and sway axes, however, it is not robust against illumination changes in the environment. We then proceed to solve the self-localization problem, by fusing Inertial Measurement Unit (IMU) values with the thrust to estimate a robot's position. In an Ardusub Simulation in the loop (SITL), the particle lter showed a slightly better performance than the Extended Kalman Filter (EKF) in the surge axis. However, both lters are prone to drifting after a while. We have observed that IMU values need to be ltered properly or another reliable sensor must be used alternatively.
The role of NAC transcription factors in responses of plants to heat and salt stresses(2019-08) [Dissertation]
Advisor: Tester, Mark
Committee members: Blilou, Ikram; Pain, Arnab; Balazadeh, SalmaSoil salinity and heat stress are two major abiotic stresses affecting plant growth and yield. Transcription factors (TFs) are key regulators in stress responses. They link stress sensing with many tolerance mechanisms by translating stress signals into changes in gene expression that ultimately contribute to stress tolerance. The NAC (NAM, ATAF and CUC) TF family have been found to be involved in responses to biotic and abiotic stresses. In this PhD project, the role of NAC TFs in response to heat and salt stress was studied in the model system Arabidopsis thaliana (Arabidopsis), and in two agriculturally relevant species, Solanum lycopersicum (tomato) and Chenopodium quinoa (quinoa). Plants have the ability to acquire thermotolerance if they are pre-exposed to a mild, non-lethal high temperature. The maintenance of acquired thermotolerance for several days is known as thermomemory. Here we investigated the role of NAC TFs in thermotolerance. The expression profiles of 104 Arabidopsis NAC TFs were measured and compared between primed and unprimed plants. Some NACs with a distinctive expression pattern in response to thermopriming were selected for further phenotypic analysis. Knock-out (KO) mutants of the ATAF1 gene showed an enhanced thermomemory phenotype compared with wild type plants (WT) and from this work, the functions of the ATAF1 gene were studied further. RNAseq co-expression analyses of ATAF1 overexpressor and ataf1 KO plants found that ANAC055 expression was co-regulated with that of ATAF1. JUBGBRUNNEN1 (JUB1) is another NAC TF involved in responses to heat, drought and salinity. In this study, the role of AtJUB1 overexpression in salinity was investigated in tomato plants. AtJUB1 overexpression resulted in higher proline levels and improved maintenance of water content and biomass in AtJUB1-overexpressing plants grown hydroponically under salinity compared with WT plants. Quinoa has recently gained much attention because of its high nutritional value and high tolerance to several stresses including drought and salinity. NAC TFs are hypothesized to play a major role in quinoa’s tolerance to abiotic stresses. In this study, the NAC TFs family were identified and investigated in the genome of quinoa. 107 NAC TF genes were identified and their transcriptional responses to different stresses including salt, drought and heat were investigated.