• Development of bismuth (oxy)sulfide-based materials for photocatalytic applications

      BaQais, Amal (2019-01-07)
      Technologies based on alternative and sustainable energy sources present a vital solution in the present and for the future. These technologies are strongly driven by the increased global energy demand and need to reduce environmental issues created by fossil fuel. Solar energy is an abundant, clean and free-access resource, but it requires harvesting and storage for a sustainable future. Direct conversion and storage of solar energy using heterogeneous photocatalysts have been identified as parts of a promising paradigm for generating green fuels from sunlight and water. This thesis focused on developing semiconductor absorbers in a visible light region for photocatalytic hydrogen production reaction. In addition, theoretical studies are combined with experimental results for a deep understanding of the intrinsic optoelectronic properties of the obtained materials. The study presents a novel family of oxysulfide BiAgOS, produced by applying a full substitution strategy of Cu by Ag in BiCuOS. I was interested to address how the total substitution of Cu by Ag in a BiCuOS system affects its crystal structure, optical and electronic properties using experimental characterizations and theoretical calculations. Single-phase bismuth silver oxysulfide BiAgOS was prepared via a hydrothermal method. Rietveld refinement of the powder confirmed that BiAgOS is an isostructural BiCuOS. The diffraction peak positions of BiAgOS, relative to those of BiCuOS, were shifted toward lower angles, indicating an increase in the cell parameters. BiCuOS and BiAgOS were found to have indirect bandgaps of 1.1 and 1.5 eV, respectively. The difference in the bandgap results from the difference in the valence band compositions. The hybrid level of the S and Ag orbitals in BiAgOS is located at a more positive potential than that of S and Cu, leading to a widened bandgap. Both materials possess high dielectric constants and low electron and hole effective masses, making them interesting for photoconversion applications. BiAgOS has a potential for photocatalytic hydrogen evolution reaction in the presence of sacrificial reagents; however, it is inactive toward water oxidation. BiCuOS and BiAgOS can be considered interesting starting compositions for the development of new semiconductors for PV or Z-scheme photocatalytic applications. The second study investigates the synthesis and characterization of NaBiS2, this contains Bi3+, which belongs to the p-block electronic configuration Bi3+ 6s26p0, and NaLaS2, which contains La3+ with electronic configuration 6s05d0. Solid-state reactions from oxide precursor starting materials were applied for synthesis the materials. The sulfurization process was conducted by pressurizing a saturated vapor of CS2. The obtained black material of NaBiS2 has an indirect transition with high absorption coefficients in the visible region of the spectrum and the absorption edge is determined at 1.21 eV. However, NaBiS2 did not show photocatalytic activity toward hydrogen production. NaLaS2 is characterized by an indirect transition with a bandgap in the UV region at 3.15 eV and can drive the photocatalytic hydrogen evolution reaction in Na2S/Na2SO3 solution. Utilizing the solid solution NaLa1-xBixS2 strategy, the absorption properties and band edge position for photocatalytic hydrogen evolution reaction were optimized. The results indicated that the bismuth content is critical parameter for maintaining the photocatalytic activity. The incorporation of low Bi content up to 6% in NaLaS2 leads to extending the photon absorption from the UV to the visible region and enhancing the photocatalytic activity of hydrogen production. In contrast, all the solid solutions that have Bi content of more than 12% present absorption edges close to that of pure NaBiS2, and they are inactive for photocatalytic hydrogen production. Combining the experimental measurements with density functional theory calculations, such behavior can be explained by the degree of overlapping of Bi and La states on the conduction band minimum (CBM). Finally, self-assembly of Bi2S3 nanorods were grown on FG or FTO substrates. Bi2S3 thin films were prepared by sulfurization of Bi metal layer using the hydrothermal method. The results show that Bi2S3 has absorption up to 1.3 eV and has a moderate absorption coefficient in the visible region. The ultraviolet photoelectron spectroscopy and photoelectron spectroscopy in air results showed that the conduction band minimum of Bi2S3 is located slightly above the hydrogen redox potential. However, Pt/Bi2S3 did not evolve a detectable amount of hydrogen, suggesting the presence of surface states that can hinder the hydrogen reduction reaction.
    • Ultrafast Spectroscopy of Polymer: Non-fullerene Small Molecule Acceptor Bulk Heterojunction Organic Solar Cells

      Alamoudi, Maha A (2019-01-07)
      Organic photovoltaics has emerged as a promising technology for electricity generation. The essential component in an organic solar cell is the bulk heterojunction absorber layer, typically a blend of an electron donor and an electron acceptor. Efforts have been made to design new materials such as donor polymers and novel acceptors to improve the power conversion efficiencies. New fullerene free acceptors providing low cost synthesis routes and tenability of their optoelectronic and electrochemical properties have been designed. Despite the efforts, still not much is known about the photopysical processes in these blends that limit the performance. In this respect, time-resolved spectroscopy such as transient absorption and time-resolved photoluminescence, can provide in-depth insight into the various (photo) physical processes in bulk heterojunction solar cell. In this thesis, PCE10 was used as donor and paired with different non fullerene acceptors. In the first part of this thesis the impact of the core structure (cyclopenta-[2, 1-b:3, 4-b’]dithiophene (CDT) versus indacenodithiophene (IDTT)) of malononitrile (BM)-terminated acceptors, abbreviated as CDTBM and IDTTBM, on the photophysical characteristics of BHJ solar cells is reported. The IDTT-based acceptor achieves power conversion efficiencies of 8.4%, higher than the CDT-based acceptor (5.6%), due to concurrent increase in short-circuit current and open-circuit voltage. Using (ultra)fast transient spectroscopy we demonstrate that reduced geminate recombination in PCE10: IDTTBM blends is the reason for the difference in short-circuit currents. External quantum efficiency measurements indicate that the higher energy of interfacial charge-transfer states observed for the IDTT-based acceptor blends is the origin of the higher open-circuit voltage. In the second part of this thesis, I report the impact of acceptor side chains on the photo-physical processes of BHJ solar cells using three different IDT-based acceptors, namely O-IDTBR, EH-IDTBR and O-IDTBCN blended with PCE10. Power conversion efficiencies as high as 10 % were achieved. The transient absorption spectroscopy experiments provide insight into sub-picosecond exciton dissociation and charge generation which is followed by nanosecond triplet state formation in PCE10:O-DTBR and PCE10:EH-IDTBR blends, while in O-IDTBCN triplets are not observed. Time delayed collection field experiments (TDCF) were performed to address the charge carrier generation and examine its dependence on the electric field.
    • Molecular Basis for p85 Dimerization and Allosteric Ligand Recognition

      Aljedani, Safia (2018-12)
      The phosphatidylinositol-3-kinase α (PI3Kα) is a heterodimeric enzyme that is composed of a p85α regulatory subunit and a p110α catalytic subunit. PI3Kα plays a critical role in cell survival, growth and differentiation, and is the most frequently mutated pathway in human cancers. The PI3Kα pathway is also targeted by many viruses, such as the human immunodeficiency virus (HIV-1), the herpes simplex virus 1 (HSV-1) or the influenza A virus, to create favourable conditions for viral replication. The regulatory p85α stabilizes the catalytic p110α, but keeps it in an inhibited state. Various ligands can bind to p85α and allosterically activate p110α, but the mechanisms are still ill-defined. Intriguingly, p85α also binds to, and activates, the PTEN phosphatase, which is the antagonist of p110α. Previous studies indicated that only p85α monomers bind to the catalytic p110α subunit, whereas only p85α dimers bind to PTEN. These findings suggest that the balance of p85α monomers and dimers regulates the PI3Kα pathway, and that interrupting this equilibrium could lead to disease development. However, the molecular mechanism for p85α dimerization is controversial, and it is unknown why PTEN only binds to p85α dimers, whereas p110α only binds to p85α monomers. Here we set out to elucidate these questions, and to gain further understanding of how p85α ligands influence p85α dimerization and promote activation of p110α. We first established a comprehensive library of p85α fragments and protocols for their production and purification. By combining biophysical and structural methods such as small angle X-ray scattering, X-ray crystallography, nuclear magnetic resonance, microscale thermophoresis, and chemical crosslinking, we investigated the contributions of all p85α domains to dimerization and ligand binding. Contrarily to the prevailing thought in the field, we find that p85α dimerization and ligand recognition involves multiple domains, including those that directly bind to and inhibit p110α. This finding allows us to suggest a molecular mechanism that links p85α dimerization and allosteric p110α activation through ligands.
    • Rational Design of Photothermal Material for Clean Water Generation Driven by Solar Energy

      Shi, Le (2018-11)
      An ancient technology of solar-driven water evaporation and distillation has recently been revived due to the concept of interfacial solar evaporation and the development of photothermal materials. There have been many research interests in improving solar light harvesting and solar-to-water evaporation efficiency within these systems, including new photothermal materials search, structural engineering, and thermal management. The application horizon of both solar-driven water evaporation and distillation has been broadly expanded beyond their conventional domain, including now wastewater treatment, seawater desalination, steam sterilization, electric generation, and chemicals/fuels productions. This dissertation focused on designing of photothermal materials and their applications to clean water production. More specifically: (1) a bi-layered porous rGO membrane with a polystyrene (PS) foam as the heat insulator was designed and proved to be effective for reducing heat conduction to the bulk water and to improve the solar-to-water evaporation efficiency, (2) a tandem-structured SiC-C ceramic monolith was prepared and demonstrated to be mechanically and chemically stable to withstand physical or chemical cleaning during long-term use in real seawater and wastewater, (3) in order to simultaneously treat the contaminated water and get clean distillate water, multi-functional SiC foam modified with mesoporous Au/TiO2 nanocomposites has been prepared, which was demonstrated to possess both photocatalytic reduction and oxidation abilities for complex wastewater treatment, and (4) when the water source was contaminated by VOCs, another efficient multi-functional photothermal material was designed with a honeycomb ceramic plate as the matrix material, and a CuFeMnO4 nanocomposite coating layer acting as both photothermal material and Fenton agent for VOCs removal. Therefore, the light absorption property of photothermal material could be improved by using a porous structure, tandem-structure, porous foam or 3D structure. The solar-to-water evaporation efficiency was improved by including a heat insulator and the reduction of the water channels’ dimension. The ceramic-based material showed potential for long-term use with high mechanical strength to endure physical cleaning. Multi-functional photothermal materials were successfully developed for complex wastewater treatment and clean water generation.
    • Spatio-Temporal Data Analysis by Transformed Gaussian Processes

      Yan, Yuan (2018-12-06)
      In the analysis of spatio-temporal data, statistical inference based on the Gaussian assumption is ubiquitous due to its many attractive properties. However, data collected from different fields of science rarely meet the assumption of Gaussianity. One option is to apply a monotonic transformation to the data such that the transformed data have a distribution that is close to Gaussian. In this thesis, we focus on a flexible two-parameter family of transformations, the Tukey g-and-h (TGH) transformation. This family has the desirable properties that the two parameters g ∈ R and h ≥ 0 involved control skewness and tail-heaviness of the distribution, respectively. Applying the TGH transformation to a standard normal distribution results in the univariate TGH distribution. Extensions to the multivariate case and to a spatial process were developed recently. In this thesis, motivated by the need to exploit wind as renewable energy, we tackle the challenges of modeling big spatio-temporal data that are non-Gaussian by applying the TGH transformation to different types of Gaussian processes: spatial (random field), temporal (time series), spatio-temporal, and their multivariate extensions. We explore various aspects of spatio-temporal data modeling techniques using transformed Gaussian processes with the TGH transformation. First, we use the TGH transformation to generate non-Gaussian spatial data with the Matérn covariance function, and study the effect of non-Gaussianity on Gaussian likelihood inference for the parameters in the Matérn covariance via a sophisticatedly designed simulation study. Second, we build two autoregressive time series models using the TGH transformation. One model is applied to a dataset of observational wind speeds and shows advantaged in accurate forecasting; the other model is used to fit wind speed data from a climate model on gridded locations covering Saudi Arabia and to Gaussianize the data for each location. Third, we develop a parsimonious spatio-temporal model for time series data on a spatial grid and utilize the aforementioned Gaussianized climate model wind speed data to fit the latent Gaussian spatio-temporal process. Finally, we discuss issues under a unified framework of modeling multivariate trans-Gaussian processes and adopt one of the TGH autoregressive models to build a stochastic generator for global wind speed.
    • Drinking Water Microbial Communities

      El-Chakhtoura, Joline (2018-11)
      Water crises are predicted to be amongst the risks of highest concern for the next ten years, due to availability, accessibility, quality and management issues. Knowledge of the microbial communities indigenous to drinking water is essential for treatment and distribution process control, risk assessment and infrastructure design. Drinking water distribution systems (DWDSs) ideally should deliver to the consumer water of the same microbial quality as that leaving a treatment plant (“biologically stable” according to WHO). At the start of this Ph.D. program water microbiology comprised conventional culturedependent methods, and no studies were available on microbial communities from source to tap. A method combining 16S rRNA gene pyrosequencing with flow cytometry was developed to accurately detect, characterize, and enumerate the microorganisms found in a water sample. Studies were conducted in seven fullscale Dutch DWDSs which transport low-AOC water without disinfectant residuals, produced from fresh water applying conventional treatment. Full-scale studies were also conducted at the desalination plant and DWDS of KAUST, Saudi Arabia where drinking water is produced from seawater applying RO membrane treatment and then transported with chlorine residual. Furthermore, biological stability was evaluated in a wastewater reuse application in the Netherlands. When low-AOC water was distributed without disinfectant residuals, greater bacterial richness was detected in the networks, however, temporal and spatial variations in the bacterial community were insignificant and a substantial fraction of the microbiome was still shared between the treated and transported water. This shared fraction was lower in the system transporting water with chlorine residual, where the eukaryotic community changed with residence time. The core microbiome was characterized and dominant members varied between the two systems. Biofilm and deposit-associated communities were found to drive tap water microbiology regardless of water source and treatment scheme. Network flushing was found to be a simple method to assess water microbiology. Biological stability was not associated with safety. The biological stability concept needs to be revised and quantified. Further research is needed to understand microbial functions and processes, how water communities affect the human microbiome, and what the “drinking” water microbiome is like in undeveloped countries.
    • Communication Reducing Approaches and Shared-Memory Optimizations for the Hierarchical Fast Multipole Method on Distributed and Many-core Systems

      Abduljabbar, Mustafa (2018-12-06)
      We present algorithms and implementations that overcome obstacles in the migration of the Fast Multipole Method (FMM), one of the most important algorithms in computational science and engineering, to exascale computing. Emerging architectural approaches to exascale computing are all characterized by data movement rates that are slow relative to the demand of aggregate floating point capability, resulting in performance that is bandwidth limited. Practical parallel applications of FMM are impeded in their scaling by irregularity of domains and dominance of collective tree communication, which is known not to scale well. We introduce novel ideas that improve partitioning of the N-body problem with boundary distribution through a sampling-based mechanism that hybridizes two well-known partitioning techniques, Hashed Octree (HOT) and Orthogonal Recursive Bisection (ORB). To reduce communication cost, we employ two methodologies. First, we directly utilize features available in parallel runtime systems to enable asynchronous computing and overlap it with communication. Second, we present Hierarchical Sparse Data Exchange (HSDX), a new all-to-all algorithm that inherently relieves communication by relaying sparse data in a few steps of neighbor exchanges. HSDX exhibits superior scalability and improves relative performance compared to the default MPI alltoall and other relevant literature implementations. We test this algorithm alongside others on a Cray XC40 tightly coupled with the Aries network and on Intel Many Integrated Core Architecture (MIC) represented by Intel Knights Corner (KNC) and Intel Knights Landing (KNL) as modern shared-memory CPU environments. Tests include comparisons of thoroughly tuned handwritten versus auto-vectorization of FMM Particle-to-Particle (P2P) and Multipole-to-Local (M2L) kernels. Scalability of task-based parallelism is assessed with FMM’s tree traversal kernel using different threading libraries. The MIC tests show large performance gains after adopting the prescribed techniques, which are inevitable in a world that is moving towards many-core parallelism.
    • Molecular Diversity, Phylogeny, and Biogeographic Patterns of Crustacean Copepods Associated with Scleractinian Corals of the Indo-Pacific

      Mudrova, Sofya (2018-11)
      Biodiversity of coral reefs is higher than in any other marine ecosystem, and significant research has focused on studying coral taxonomy, physiology, ecology, and coral-associated fauna. Yet little is known about symbiotic copepods, abundant and numerous microscopic crustaceans inhabiting almost every living coral colony. In this thesis, I investigate the genetic diversity of different groups of copepods associated with reef-building corals in distinct parts of the Indo-Pacific; determine species boundaries; and reveal patterns of biogeography, endemism, and host-specificity in these symbiotic systems. A non-destructive method of DNA extraction allowed me to use an integrated approach to conduct a diversity assessment of different groups of copepods and to determine species boundaries using molecular and taxonomical methods. Overall, for this thesis, I processed and analyzed 1850 copepod specimens, representing 269 MOTUs collected from 125 colonies of 43 species of scleractinian corals from 11 locations in the Indo-Pacific. The genetic assessment of the most abundant copepod morphotypes associated with hermatypic corals in Lizard Island (Great Barrier Reef) revealed a large number of species previously unknown for this region. Analyses of diversity and patterns of biogeographical distribution of copepods associated with Galaxea corals throughout the Indo-Pacific showed that the species diversity of this group is high and appears to be regionally specific, an uncommon pattern in most coral reef-associated invertebrates. Results for the symbiotic copepod fauna of Red Sea pocilloporid corals, a family of corals with a high level of morphological variability within and among its members, showed that the majority of the discovered poecilostomatoid copepods belong to the genus Spaniomolgus, which demonstrated a significant genetic diversity of morphologically-similar species. Assessment of the diversity of copepods associated with the Red Sea mushroom corals revealed several undescribed species and showed no evidence of specificity to the hosts neither on species nor on the family level, which contradicts a modern assumption of high host-specificity of copepods. Overall, this dissertation is a first study of genetic diversity of copepods associated with invertebrates, and it provides substantial insight into the diversity of coral-associated microcrustaceans and insight to patterns of their host-specificity as well as distribution around the Indo-Pacific.
    • Using single molecule fluorescence to study substrate recognition by a structure-specific 5’ nuclease

      Rashid, Fahad (2018-12)
      Nucleases are integral to all DNA processing pathways. The exact nature of substrate recognition and enzymatic specificity in structure-specific nucleases that are involved in DNA replication, repair and recombination has been under intensive debate. The nucleases that rely on the contours of their substrates, such as 5’ nucleases, hold a distinctive place in this debate. How this seemingly blind recognition takes place with immense discrimination is a thought-provoking question. Pertinent to this question is the observation that even minor variations in the substrate provoke extreme catalytic variance. Increasing structural evidence from 5’ nucleases and other structure-specific nuclease families suggest a common theme of substrate recognition involving distortion of the substrate to orient it for catalysis and protein ordering to assemble active sites. Using three single-molecule (sm)FRET approaches of temporal resolution from milliseconds to sub-milliseconds, along with various supporting techniques, I decoded a highly sophisticated mechanism that show how DNA bending and protein ordering control the catalytic selectivity in the prototypic system human Flap Endonuclease 1 (FEN1). Our results are consistent with a mutual induced-fit mechanism, with the protein bending the DNA and the DNA inducing a protein-conformational change, as opposed to functional or conformational selection mechanism. Furthermore, we show that FEN1 incision on the cognate substrate occurs with high efficiency and without missed opportunity. However, when FEN1 encounters substrates that vary in their physical attributes to the cognate substrate, cleavage happens after multiple trials During the course of my work on FEN1, I found a novel photophysical phenomena of protein-induced fluorescence quenching (PIFQ) of cyanine dyes, which is the opposite phenomenon of the well-known protein-induced fluorescence enhancement (PIFE). Our observation and characterization of PIFQ led us to further investigate the general mechanism of fluorescence modulation and how the initial fluorescence state of the DNA-dye complex plays a fundamental role in setting up the stage for the subsequent modulation by protein binding. Within this paradigm, we propose that enhancement and quenching of fluorescence upon protein binding are simply two different faces of the same process. Our observations and correlations eliminate the current inconvenient arbitrary nature of fluorescence modulation experimental design.
    • Stimuli Responsive Self-Assembled Hybrid Organic-Inorganic Materials

      Al-Rehili, Safaa (2018-11)
      Because of the latest developments in nanotechnology and the need to have new functions, a high demand for innovative materials is created. The technological requirements for new applications cannot be fulfilled by most of the well-developed materials like metals, plastics, or ceramics. Therefore, composite materials that can exhibit better properties in contrast to their single counterpart represents a valuable and interesting alternative for the development of new and more performing functional materials. In the past few years, one of the most rapidly developing fields in materials chemistry is research and development of innovative hybrid materials and nanocomposites having exceptional properties. A significant reason for this is that this group of materials closes the gaps between different scientific fields and brings together the ideal properties of the different disciplines into a single system. Conventional materials like polymers or minerals can be mixed with substances of a different kind, like biological molecules and different chemical functional groups to create unique functional materials with the help of a building block method. Inorganic and organic chemistry, physical and biological sciences are integrated in the search for new recipes in a purely interdisciplinary way to generate unique materials. Compounds that are created frequently have interesting new properties for forthcoming functional materials and technological applications. Natural materials frequently function as a model for these systems and various examples of biomimetic methods can be obtained while generating these hybrid materials. The research and development of these materials is driven by the needs of future technologies. The research carried out in this thesis is entirely based on hybrid organic-inorganic materials; hence, it consists of soft organic/bioorganic section that makes it possible to generate multifunctional materials, whereas the hard inorganic section functions as a rigid and stable platform for developing nanocarriers and imaging agents. A key domain in materials chemistry is the creation of smart materials that have the ability to respond to environmental changes or be triggered on demand. These materials have led to the creation of new technologies, like electroactive materials, electrochromic materials, biohybrid materials, sensors and membranes, etc. The required functionality can be provided by the organic or inorganic components, or from both. In this dissertation, the synthesis, methodology, and creation of three unique organic-inorganic hybrid stimuli responsive systems having targeted features for specific applications are examined. The first example is represented by supramolecular microtoroids created by spontaneous self-assembly of amphiphilic molecules and a hydrophilic polymer (chitosan), in the presence of iron (III) chloride. Light irradiation is the stimulus responsible for assembly/disassembly of this new supramolecular entities. The basis of the photo-response of the microtoroids is the photoreaction of the anthracene derivatives. In order to make these materials bio applicable, the microtoroid size was controlled and narrowed down to nanometers, which has led to our second system called metal organic complexes (MOCs). In this system, chitosan was replaced by PNIPAM polymer at optimized concentrations. The reversible thermo-response of MOCs comes from the phase transition ability of PNIPAM. The third hybrid material is the core-shell system consisting of mesoporous organosilica coated with iron oxide nanoparticles, used for cargo delivery and cell imaging. The magnetic-response of the core-shell system results from the strong magnetic properties of iron oxide nanoparticles, while the presence of PMOs increased its biocompatibility. Our research on such organic-inorganic hybrid materials represents a promising development in the field of materials chemistry. Due to the possibility of mixing various properties in a single material, a variety of combinations regarding possible materials and applications have emerged.
    • The Role of Chromatin Associated Proteins in Plant Innate Immunity and Jasmonic Acid Signaling

      Jarad, Mai (2018-11)
      Pathogen-associated molecular pattern (PAMP) recognition occurs by plasma membrane located receptors that induce among other processes nuclear gene expression. The plant FLS2-BAK1 receptor complex binds the bacterial PAMP, flg22 and induces a series of defense responses. The resulting signal transduction events occur through the activation of two MAPK signaling cascades, which trigger a rapid and strong activation of MPK3, MPK4 and MPK6. Cellular responses to pathogens are regulated by the activated MAPKs, which lead to the eventual phosphorylation of cytoplasmic and nuclear substrates. These MAPK substrates in turn respond to phosphorylation by reprogramming the expression of defense genes. A large scale phosphoproteomics screen of nuclear proteins in wild type and mpk mutant plants in response to flg22 revealed several novel putative targets of MAP kinases. This thesis is aimed at identifying the role of two of these chromatin associated proteins in plant immunity and their signaling mechanisms. The chromatin associated proteins we chose to study here are LITTLE NUCLEI/CROWDED NUCLEI (LINC/CRWN), LINC1 and the AT-HOOK MOTIF CONTANING NUCLEAR LOCALIZED 13 (AHL13) proteins. We demonstrate that these two chromatin associated proteins play a positive regulatory role in jasmonic acid signaling and immunity. Knock out mutants for both genes exhibit impairment in early and late innate immune reposes to both PAMP and hemibiotrophic pathogen strains. We also demonstrate that these mutants are compromised in regulating the expression of genes involved in jasmonic acid (JA) signaling and responses and genes involved in the biosynthesis both the indole and aliphatic glucosinolate (GS) pathways. Moreover, Pst DC3000 hrcC triggers JA and JAIle accumulation in these mutants, whereas salicylic acid (SA) levels are unchanged. We were also able to identify and validate two novel MAPK targeted phosphosites in AHL13 that affect the protein stability of AHL13 and we establish its role as a MPK6 substrate that affects jasmonic acid biosynthesis and PTI responses. Together this work identifies two novel signaling components involved in the regulation of jasmonic acid homeostasis and immunity.
    • Bioinspired solvent resistant nanofiltration membranes

      Pérez-Manríquez, Liliana (2018-11)
      In the last decades, there has been a trend towards bio-inspired approaches for the formation of nanocoatings as well as to accomplish energy-intensive industrial separations in a more sustainable fashion. Solvent Resistant Nanofiltration (SRNF) is a pressure driven technology where the operation conditions are moderate and additional waste streams are minimized, making this a favorable energy efficient approach for challenging molecular separations such as purification of active pharmaceutical ingredients, production of specialty chemicals and in the petrochemical industry just to mention a few examples, where this technology can be currently applied. The overall performance of SRNF membranes is determined by solute/solvent interactions with the membrane top layer. Therefore, the modification of the membrane surface becomes crucial to obtain high-performance SRNF membranes, as well as exploring novel and green approaches to improve the separation properties of SRNF membranes, without sacrificing their permeation properties. One alternative for the fabrication of the thin-films in SRNF membranes proposed in this work is the use of biopolyphenolic molecules. Among the many classes of phenolic biomolecules, plant phenols are capable of binding and cross-linking due to their strong interfacial activity. Here, the successful optimization of the interfacial polymerization reaction for the manufacture of SRNF membranes is demonstrated by replacing the common toxic amines used for this method with natural occurring bio-polyphenols such as dopamine, tannic acid, morin hydrate and catechin. These bio-polyphenols can be found in mussels, date fruits, guava fruits and green tea respectively and they were used to form a selective thin film on top of a crosslinked polyacrylonitrile or a cellulose support. These membranes have shown an exceptional performance and resistance towards harsh solvent environments. Due to the incorporation of natural compounds for the manufacture, they provide a cost-effective alternative for industrial separations due to the ease of chemical modification and preparation, which is potentially easy to scale up at low cost taking advantage of the natural compounds for their manufacture.
    • Catalysis by design: Well-Defined Aluminum tetra-coordinated Surface Ligand for Catalytic applications

      werghi, baraa (2018-11)
      The main target of this thesis is the design of a new aluminum-based surface ligand with low coordination and expected high acidity. These new supports will serve for the immobilization of different organometallic complexes with the surface organometallic chemistry (SOMC). The resulting molecular like species will be used for various catalytic applications including alkane metathesis, olefin metathesis and polymerization. The first chapter is an introduction to the field of catalysis, more specifically, surface organometallic with a summary of its concept and the main examples cited for the immobilization of transition metal complexes on different oxide surfaces (silica, silica-alumina and alumina). This chapter presents, as well, an overview of the use of the aluminum alkyls compounds and their immobilization on a surface for the generation of various aluminum based surfaces. The Second chapter details the reaction involving the grafting of the monomeric triisobutylaluminum on SBA-15700. The final structures and the mechanism involved were determined by various characterization techniques including FT-IR, 1H and 13C solid-state NMR, and DFT calculations. The reaction leads mainly to a bipodal [(≡Si-O-Si≡)(≡SiO)2AliBu] species with 3 differents types of alumium coordinations (AlIV, AlV and AlVI) along with 37% [≡Si-H] and 63% [≡Si-ibu]. The Third chapter describes the reaction of a highly dehydroxylated SBA-15 with a trimeric di-isobutyl aluminum hydride, [i-Bu2AlH]3 is investigated by both experiments and DFT calculations. The mechanism involves very different pathway comparing to the TIBA case where only AlIV-isobutyl were generated. Further β-H elimination leads to an well-defined AlIV hydride analog [(≡Si-O-Si≡)(≡SiO)2Al-H]. The later shows good activity in ethylene polymerization reaction with the formation of HDPE. The Fourth Chapter deals with the immobilization of the 2nd generation Hoveyda-Grubbs (HGII) catalyst onto well-ordered 2D hexagonal (SBA15), and 3D fibrous (KCC-1) mesostructure silica containing tetra-coordinated [Al-H] sites. The resulting catalysts show high activity in the non-functionalized olefin metathesis of propene. The results clarified that the supported catalyst prepared using KCC-1 shows better performance than the one prepared using SBA-15 due to the diffusion effect; and exhibits much higher activity than the HG-II itself, in homogeneous phase. The Fifth chapter of this thesis presents the formation of tetra-coordinated [(≡Si–O–Si≡)(≡Si– O)2Al–OH], through [Al-H] oxidation using N2O. The synthesis was detailed and the grafted species were fully characterized. This new site will serve as anchoring site for the immobilization of the tungsten based complexes. Its activity was evaluated in the propane metathesis reactions, where a TON of 800 was obtaine, which is the highest value obtained for a SOMC monometallic catalyst. Finally, the last chapter will present the thesis conclusion including most of the ongoing applications related to the use of those new surfaces.
    • Reticular Chemistry for the Rational Design of Intricate Metal-Organic Frameworks

      Jiang, Hao (2018-11)
      The rational design and construction of Metal-Organic Frameworks (MOFs) with intricate structural complexity are of prime importance in reticular chemistry. However, the design of intricate structures that can practically be synthesized is very difficult, and the suitable targeted intricate nets are still unexplored. Evidently, it is of great value to build the fundamental theory for the design of intricate structures. This dissertation is focused on the exploration of cutting-edge design methodologies in reticular chemistry. This research shows the design and synthesis of several MOF platforms (hex, fcu, gea and the) based on rare earth polynuclear clusters. Furthermore, this research unveils the latest addition, named merged nets approach, to the design toolbox in reticular chemistry for the rational design and construction of intricate mixed-linker MOFs. In essence, a valuable net for design enclosing two edges is rationally generated by merging two edge-transitive nets, spn and hxg. The resultant merged net, named sph net, offers potential for the deliberate design and construction of highly symmetric isoreticular intricate mixed-linker MOFs, sph-MOF-1 to 4, which represent the first examples of MOFs where the underlying net is merged from two 3-periodic edge-transitive nets. Furthermore, the underlying principle of the merged net approach, the fundamental merged net equation, and two key parameters are disclosed. Also, we discovered three analysis methods to check and validate corresponding signature nets in an edge-transitive net. Based on these analysis methods, a signature map of all edge-transitive nets was established. This map showing the systematic relationship among edge-transitive nets will help the material chemist to comprehend more about the underlying nets in reticular chemistry. Based on the revealed map, we systematically described the nine types of merging combination and 140 merged nets based on two edge-transitive nets. Among these enumerated nets, only 18 of them was shown on the RCSR database before. These enumerated merged nets significantly increased the designable targets in reticular chemistry. Using an example of enumerated sub net, we show how this approach can be utilized to design and synthesis mixed-linker porous materials based on the intricate sub-MOF platform, which presents one of the most intricate MOF structures synthesized by design.
    • Multilayer Dielectrics and Semiconductor Channels for Thin Film Transistor Applications

      Alshammari, Fwzah (2018-11-13)
      Emerging transparent conducting and semiconducting oxide (TCO) and (TSO) materials have achieved success in display markets. Due to their excellent electrical performance, TSOs have been chosen to enhance the performance of traditional displays and to evaluate their application in future transparent and flexible displays. This dissertation is devoted to the study ZnO-based thin film transistors (TFTs) using multilayer dielectrics and channel layers. Using multilayers to engineer transistor parameters is a new approach. By changing the thickness, composition, and sequence of the layers, transistor performance can be optimized. In one example, Al2O3/Ta2O5 bilayer gate dielectrics, grown by atomic layer deposition at low temperature were developed. The approach combined high dielectric constant of Ta2O5 and the excellent interface quality of Al2O3/ZnO, resulting in enhanced device performance. Using zinc oxide (ZnO)/hafnium oxide (HfO2) multilayer stack as a TFT channel with tunable layer thicknesses resulted in significant improvement in TFT stability. Atomic layer deposited SnO2 was developed as a gate electrode to replace ITO in thin film transistors and circuits. The SnO2 films deposited at 200 °C show low electrical resistivity of ~3.1×10-3 Ohm-cm with the high transparency of ~93%. TFT fabricated with SnO2 gate show excellent transistor properties. Using results from the above experiments, we have developed a novel process in which thin film transistors (TFTs) are fabricated using one binary oxide for all transistor layers (gate, source/drain, semiconductor channel, and dielectric). In our new process, by simply changing the flow ratio of two chemical precursors, C8H24HfN4 and (C2H5)2Zn, in an ALD system, the electronic properties of the binary oxide HZO were controlled from conducting, to semiconducting, to insulating. A complete study of HZO thin films deposited by (ALD) was performed. The use of the multi-layer (HfO2/ZnO) channel layer plays a key role in improving the bias stability of the devices. The low processing temperature of all materials at 160 °C is an advantage for the fabrication of fully transparent and flexible devices. After precise device engineering, including growth temperature, gate dielectric, electrodes (S/D&G) and semiconductor thickness, TFT with excellent device performance are obtained.
    • Proximity Mechanisms in Graphene: Insights from Density Functional Theory

      Alattas, Maha H. (2018-11-27)
      One of the challenges in graphene fabrication is the production of large scale, high quality sheets. To study a possible approach to achieve quasi-freestanding graphene on a substrate by the intercalation of alkali metal atoms, Cs intercalation between graphene and Ni(111) is investigated. It is known that direct contact between graphene and Ni(111) perturbs the Dirac states. Cs intercalation restores the linear dispersion characteristic of Dirac fermions, which agrees with experiments, but the Dirac cone is shifted to lower energy, i.e., the graphene sheet is n-doped. Cs decouples the graphene sheet, while the spin polarization of Ni(111) does not extend through the intercalated atoms to the graphene sheet, for which we find virtually spin-degeneracy. In order to employ graphene in electronic applications, one requires a finite band gap. We engineer a band gap in metallic bilayer graphene by substitutional B and/or N doping. Specifically, the introduction of B-N pairs into bilayer graphene can be used to create a band gap that is stable against thermal fluctuations at room temperature. Introduction of B-N pairs into B and/or N doped bilayer graphene likewise hardly modifies the band dispersions, however, the size of the band gap is effectively tuned. We also study the influence of terrace edges on the electronic properties of graphene, considering bare edges and H, F, Cl, NH2 terminations. Periodic structural reconstruction is observed for the Cl and NH2 edge terminations due to interaction between the terminating atoms/groups. We observe that Cl edge termination p-dopes the terraces, while NH2 edge termination results in n-doping.
    • Side Chain Modification of Conjugated Polymers for Bioelectronics and Biological Applications

      du, weiyuan (2018-09)
      Organic bioelectronics is the convergence of organic electronics and biology. Motivated by the unique combination of both electronic and ionic conductivity, organic semiconducting materials have been applied in OECTs for sensing applications to translate bio-logical signals into a quantitative electrical reading. Due to their carbon-based structure and flexibility, CPs can achieve improved biocompatibility compared to inorganic devices as they are intrinsically “softer”, avoiding mechanical mismatch and the need for surface compatibilizing layers. These promising materials have broad potential to be used in applications such as biosensors, drug delivery, and neural interfaces. In the second chapter, a series of lysine-functionalized DPP3T semiconducting polymers, outline their synthesis, and demonstrate that these particular polymers allow neuron cells to adhere and grow, in comparison to unfunctionalized polymers, where cells quickly die. Through covalent attachment of small lysine units, the conjugated polymer backbone and cells can directly electrically communicate, favorable for neural signals recording/stimulating. In the third chapter, NDI-based semiconducting polymers are selected for lysinefunctionalization, giving protein-like surfaces for neurons to attach, grow and form a network without the need of an intermediate PDL coating. Most importantly, this careful choice of NDI backbone allows lysinated-NDI polymers to operate in OECTs with an outstanding normalized transconductance value of 0.25 S/cm. In the fourth chapter, a new technique is presented to biofunctionalize thin film surface of polymers. Two methods including CuAAC and thiol-ene click are demonstrated to be applicable to biofunctionalize surface. In particular, both of them can achieve biocompatible surface by attaching biomolecules at high density while maintaining electrically conductive film. In the final chapter, three series of NDI-T2 are presented synthesized via Stille coupling reaction using different Pd catalysts. Following electrochemical and device characterization, the study of the influence of spacers between backbone and EG chain for performance in OFET and OECT operations is carried out. It is clearly evidenced that electron mobility increases by a factor of 10 with gradual increased spacers for all polymers in OFETs devices. For OECTs, within three series, pNDI-Cx-T2 stands out, especially pNDI-C4-T2 giving the highest reported transconductance at 0.479 S/cm and a low threshold voltage of 0.18 V.
    • Enzymatic and biological studies on the Arabidopsis enzyme DWARF27 and its homolog DWARF27-like 1

      Abuauf, Haneen W. (2018-10)
      Strigolactones (SLs) are a novel class of phytohormones that shape shoot and root architecture. Carlactone, the precursor of SLs, is synthesized from all-trans-β-carotene by the sequential action of three enzymes: the all-trans/9-cis-β-carotene isomerase DWARF27 (D27) that reversibly converts all-trans-β-carotene into 9-cis-β-carotene (shown only for the rice D27) and the carotenoid cleavage dioxygenases 7 and 8 (CCD7 and CCD8). Genomes of higher plants encode two D27 homologs (D27-like 1 and D27-like 2) with unknown function. Rice and Arabidopsis d27 mutants show less pronounced high tillering/more branching phenotype, compared to ccd7 or ccd8 mutants. This difference might be the result of functional redundancy caused by the presence of D27-like 1 and D27-like 2. In this study, we investigated the enzymatic and biological activity of the Arabidopsis D27 and the rice and Arabidopsis D27-like 1, using both in vivo and in vitro studies. Our results show that AtD27 is a true ortholog of the rice D27. Like SLs, the biosynthesis of ABA requires an all-trans/9-cis-isomerization reaction. However, the enzyme postulated for this activity is still elusive. Our enzymatic activity tests exclude a direct involvement of AtD27 in ABA biosynthesis. Nevertheless, Atd27 mutant shows low level of ABA, and analysis of AtD27 promoter::GUS lines generated in this study shows an induction upon treatment with Auxin and ABA, indicating a role of AtD27 in ABA biosynthesis. Arabidopsis ad rice D27-like 1 enzymes catalyze a novel isomerization reaction converting different β-carotene cis-isomers into each other. Constitutive overexpression of AtD27-like 1 in Atd27 mutant restored the wild type branching phenotype, suggesting that AtD27-like 1 may be involved in the SL biosynthesis pathway. To further elucidate the biological function of AtD27-like 1, we generated CRISPR-Cas9knockout lines, which will be analyzed in future work.
    • Coral-Associated Bacterial Community Dynamics in Healthy, Bleached, and Disease States

      Hadaidi, Ghaida A. (2018-11)
      Coral reefs are the proverbial rainforests of the ocean, but these spectacular structures are under threat from globally rising sea surface temperatures and ocean acidification. The Red Sea and the Persian/Arabian Gulf (PAG) display unusually high sea surface temperatures, and therefore, provide a model for studying environmental change. Corals are so-called holobionts consisting of the coral host, photosynthetic algae (Symbiodiniaceae), along with other microorganisms, such as bacteria, archaea, fungi, and viruses. While the importance of bacteria to coral holobiont functioning is acknowledged, little is known about changes in the microbial communities under natural environmental stressors in the Red Sea and the PAG. Accordingly, I investigated microbial community and mucus differences in bleached, healthy, and diseased corals. Analysis of the composition of mucus-associated microbial communities of bleached and healthy Porites lobata colonies from the Red Sea and the PAG were stable, although some regional differences were present. In a distinct study investigating coral disease, a broad range of corals in the Red Sea were shown to be infected with black band disease (BBD). Investigating the microbial community associated with BBD revealed the presence of the three main indicators for BBD (cyanobacteria, sulfate-reducing bacteria (SRB), and sulfide-oxidizing bacteria (SOB). Last, I investigated the chemical composition (carbohydrates) of the surface mucus layer of a range of Red Sea corals. Given that coral mucus represents a first line of defense, I was interested to examine whether mucus carbohydrate composition would point to a role of adaptation to the extreme environment of the Red Sea. This analysis showed that mucus consists of conserved sugars that are globally conserved. In summary, this thesis characterizes the microbial communities associated with a range of coral species in different health states (bleached, healthy, and diseased). The microbial community patterns I characterized support the notion that bacteria contribute to coral holobiont health and possibly adaptation to extreme environmental conditions in the Red Sea and PAG.
    • Cylindrical Magnetic Nanowires Towards Three Dimensional Data Storage

      Mohammed, Hanan (2018-12)
      The past few decades have witnessed a race towards developing smaller, faster, cheaper and ultra high capacity data storage technologies. In particular, this race has been accelerated due to the emergence of the internet, consumer electronics, big data, cloud based storage and computing technologies. The enormous increase in data is paving the path to a data capacity gap wherein more data than can be stored is generated and existing storage technologies would be unable to bridge this data gap. A novel approach could be to shift away from current two dimensional architectures and onto three dimensional architectures wherein data can be stored vertically aligned on a substrate, thereby decreasing the device footprint. This thesis explores a data storage concept based on vertically aligned cylindrical magnetic nanowires which are promising candidates due to their low fabrication cost, lack of moving parts as well as predicted high operational speed. In the proposed concept, data is stored in magnetic nanowires in the form of magnetic domains or bits which can be moved along the nanowire to write/read heads situated at the bottom/top of the nanowire using spin polarized current. Cylindrical nanowires generally exhibit a single magnetic domain state i.e. a single bit, thus for these cylindrical nanowire to exhibit high density data storage, it is crucial to pack multiple domains within a nanowire. This dissertation demonstrates that by introducing compositional variation i.e. multiple segments along the nanowire, using materials with differing values of magnetization such as cobalt and nickel, it is possible to incorporate multiple domains in a nanowire. Since the fabrication of cylindrical nanowires is a batch process, examining the properties of a single nanowire is a challenging task. This dissertation deals with the fabrication, characterization and manipulation of magnetic domains in individual nanowires. The various properties of are investigated using electrical measurements, magnetic microscopy techniques and micromagnetic simulations. In addition to packing multiple domains in a cylindrical nanowire, this dissertation reports the current assisted motion of domain walls along multisegmented Co/Ni nanowires, which is a fundamental step towards achieving a high density cylindrical nanowire-based data storage device.