• Single molecule analysis of the diffusion and conformational dynamics

      Abadi, Maram (2018-07)
      Spatial and temporal dynamics of polymer chains play critical roles in their rheological properties, which have a significant influence on polymer processing and fabrication of polymer-based (nano) materials. Many theoretical and experimental studies have aimed at understanding polymer dynamics at the molecular level that give rise to its bulk phase properties. While much progress has been made in the field over the past ~60 years, many aspects of polymers are still not understood, especially in complicated systems such as entangled fluids and polymers of different topologies. In addition, the physical properties of biological macromolecules, i.e. DNA, are expected to affect the spatial organization of chromosome in a cell, which has the potential impact on a broad epigenetics research. Here, we propose new methods for simultaneous visualization of diffusive motion and conformational dynamics of individual polymer chains, two most important factors that characterize polymer dynamics, based on a new single-molecule tracking technique, cumulative-area (CA) tracking method. We demonstrate the applicability of the CA tracking to the quantitative characterization of the motion and relaxation of individual topological polymer molecules under entangled conditions, which is possible only by using the newly-developed CA tracking, using fluorescently-labeled linear and cyclic dsDNA as model systems. We further extend the technique to multi-color CA tracking that allows for the direct visualization and characterization of motion and conformation of interacting molecules. We also develop a new imaging method based on recently developed 3D super-resolution fluorescence microscopy technique, which allows direct visualization of nanoscale motion and conformation of the single molecules that is not possible by any other methods. Using these techniques, we investigate spatial and temporal dynamics of polymers at the single-molecule level, with special emphasis on the effect of topological forms of the molecules and the confined geometry on their spatiotemporal dynamics. Our results demonstrate that the new methods developed in this thesis provide an experimental platform to address key questions in the entangled topological polymer dynamics. The research will provide a platform for developing new polymer-based materials and open the possibility of studying spatial organization of DNA in a confined geometry from physics point of view.
    • Diversity, ecology, and biotechnological potential of microorganisms naturally associated with plants in arid lands

      Mosqueira Santillán, María José (2018-07)
      Plants naturally host complex microbial communities in which the plant and the symbiotic partners act as an integrated metaorganism. These communities include beneficial (i.e. plant growth promoting, PGP) microorganisms which provide fundamental ecological services able to enhance host plant fitness and stress tolerance. PGP microorganisms represent a potential bioresource for agricultural applications, especially for desert farming under the harsh environmental conditions occurring in hot/arid regions (i.e. drought and salinity). In this context, understanding the ecological aspects of the associated microorganisms is crucial to take advantage of their ecological services. Here, hot/desert ecosystems were selected and two contrasting plant categories were used as models: (i) wild plants (i.e. speargrasses) growing in hot-desert sand dunes and (ii) the main crop cultivated in desert ecosystems, the date palm. By using highthroughput DNA sequencing and microscopy, the ecology and functionality of the microbial communities associated with these plants were characterized. Additionally, the PGP services of bacteria isolated from date palm were explored. I found that the harsh conditions of the desert strongly affect the selection and assembly of microbial communities associated with three different speargrass species, determining a plant species-independent core microbiome always present among the three plant species and carrying important PGP traits. On the contrary, in agroecosystems where desert farming practices are used, the plant species, i.e. date palm exerts a stronger selective pressure than the environmental and edaphic factors favoring the recruitment of conserved microbial assemblages, independent of the differences in the soil and environmental conditions among the studied oases. Such selective pressure also favors the recruitment of conserved PGP microorganisms (i.e. Pseudomonas sp. bacterial strains) able to protect their host from salinity stress through the induction of root architectural changes regulated by the modification of the root system auxin homeostasis. Overall, we found that deserts are unique ecosystems that challenge the paradigm of microbial community assembly, as it was defined from studies in non-arid ecosystems. The understanding of the ecological features regulating the ecological properties of such unique microbial community assembly will be a key-step to improve the chances of successful application of ‘PGP microorganisms’ in arid agroecosystems.
    • Ecology of the Mangrove Microbiome

      Booth, Jenny (2018-07)
      Plants and animals have evolved unique morpho-physiological adaptions to cope with the harsh and steep environmental gradients that characterise the mangrove ecosystem. However, the capacity of these two main components of the system to thrive, and the extraordinary productivity of mangrove forests in extreme conditions, has been overlooked in terms of the role of the microbiome. By combining approaches that included molecular microbial ecology, biogeochemical analyses, microscopy, raman spectroscopy and microsensor measurements, this thesis aimed to investigate the potential role of bacterial symbiosis in the adaptation of mangrove crabs to their environment and subsequently how these different animals modify their environment. Finally, with a field-based approach monitoring microbial communities, sediment metabolism and plant performance, the thesis aimed to investigate the plant/animal/bacterial dynamics in relation to seasonal environmental changes to contribute to understand the mangrove plant productivity paradox of high productivity under conditions of limited nutrents. Crab species were associated with distinct gill-bacteria communities, that produced carotenoids, according with their level of terrestrial adaptation. These carotenoids may be involved in protecting the gills from oxidative stress during air exposure. The main groups of ecosystem engineering crabs in mangroves had significant but diverse effects on the sediment environment and microbiome predominantly related to their ecology (i.e. filter feeder vs herbivore). Burrows increase aerobic microbial activity in the immediate burrow wall with a cascade effect on sediment microbial communities and nutrient distribution observed consistently across mangroves in different locations and with diverse environmental conditions. Microorganisms play an important role in adapting crabs on their evolutionary path to land and could contribute to the success of their colonization. At high population densities, of more than 50 individuals per square meter in some mangroves, these crabs deeply impact the functioning of the mangrove ecosystem, affecting microbial networks and nutrient recycling in the sediment, which may ameliorate conditions for plant growth. The microbiome is an understudied component of mangroves that lies at the basis of the functioning of these systems, influencing the success of the animal inhabitants (ecosystem engineers) that deeply modify the sediment microbiome, therefore influencing ecosystem functioning and resilience and, potentially, the success of the plants themselves (ecosystem architects).
    • Scalable Discovery and Analytics on Web Linked Data

      Abdelaziz, Ibrahim (2018-07)
      Resource Description Framework (RDF) provides a simple way for expressing facts across the web, leading to Web linked data. Several distributed and federated RDF systems have emerged to handle the massive amounts of RDF data available nowadays. Distributed systems are optimized to query massive datasets that appear as a single graph, while federated systems are designed to query hundreds of decentralized and interlinked graphs. This thesis starts with a comprehensive experimental study of the state-of-the-art RDF systems. It identifies a set of research problems for improving the state-of-the-art, including: supporting the emerging RDF analytics required by many modern applications, querying linked data at scale, and enabling discovery on linked data. Addressing these problems is the focus of this thesis. First, we propose Spartex; a versatile framework for complex RDF analytics. Spartex extends SPARQL to seamlessly combine generic graph algorithms with SPARQL queries. Spartex implements a generic SPARQL operator as a vertex-centric program that interprets SPARQL queries and executes them efficiently using a built-in optimizer. We demonstrate that Spartex scales to datasets with billions of edges, and is at least as fast as the state-of-the-art specialized RDF engines. For analytical tasks, Spartex is an order of magnitude faster than existing alternatives. To address the scalability limitation of federated RDF engines, we propose Lusail; a scalable system for querying geo-distributed RDF graphs. Lusail follows a two-tier strategy: (i) locality-aware decomposition of the query into subqueries to maximize the computations at the endpoints and minimize intermediary results, and (ii) selectivity-aware execution to reduce network latency and increase parallelism. Our experiments on billions of triples show that Lusail outperforms existing systems by orders of magnitude in scalability and response time. Finally, enabling discovery on linked data is challenging due to the prior knowledge required to formulate SPARQL queries. To address these challenges; we develop novel techniques to (i) predict semantically equivalent SPARQL queries from a set of keywords by leveraging word embeddings, and (ii) generate fine-grained and non-blocking query plans to get fast and early results.
    • MOFs exploration: from synthesis and thin film fabrication to separation and sensing applications

      Chernikova, Valeriya (2018-05)
      The never-ending quest to design and produce bespoke materials optimized for specific purposes has recently led to the discovery of a rapidly expanding subclass of porous materials known as Metal-Organic Frameworks (MOFs). The potential of MOFs appears to be immense due to the accessibility of a nearly-infinite number of both organic and inorganic components – building blocks that can be easily self-assembled in extended networks. Taking advantage of modular composition, high surface areas, adjustable pore sizes, and tunable surface properties, MOFs are emerging as one of the most promising materials for energy and environmental applications. The main objective of this thesis is to explore different aspects concerning MOF materials, building on the knowledge from several subtypes of MOFs developed primarily in Prof. Eddaoudi’s group. In particular, this dissertation expands the diversity within and utility of the following MOF subtypes: MOFs comprised of sql supermolecular building layers (SBL), MOFs based on fluorometalates, and zeolite-like MOFs (ZMOFs). Whenever feasible, emphasis was placed on the synthesis and application of MOFs as supported thin films, particularly as the sensitive element of capacitive gas sensors or as a selective layer of composite membranes for gas separation. Some of the highlights from the results obtained in the course of this study include: - Introduction of MOFs to the field of reverse selective (CO2/H2) membranes for hydrogen purification. Notably, despite the challenges associated with the preparation of continuous “defect-free” MOF membranes, three different types of adsorption-driven MOF membranes have been synthesized and have shown a preferential permeation of CO2 over H2. In addition, the diffusion driven butane isomers separation was realized in ana-ZMOF membrane, being close to or even overperforming benchmark materials reported in the literature for the separation of both gas pairs. - Identification of an appropriate MOF compatible with the developed capacitive-based sensor system and capable of the detection of sulfur dioxide in ppb level. - Discovery of a ZMOF material with a new unprecedented zeolitic topology and its ability to separate propylene from propane upon the difference in diffusion of the adsorbates.
    • Paving the Way for Efficient Content Delivery in Mobile Networks

      Lau, Chun Pong (2018-07-10)
      The flexibility of future mobile networks exploiting modern technologies such as cloud-optimized radio access and software-defined networks opens a gateway to deploying dynamic strategies for live and on-demand content delivery. Traditional live broadcasting systems are spectral inefficient. It takes up a lot more radio spectrum than that of mobile networks, to cover the same size of an area. Furthermore, content caching at base stations reduces network traffic in core networks. However, numerous duplicated copies of contents are still transmitted in the unicast fashion in radio access networks. It consumes valuable radio spectrum and unnecessary energy. Finally, due to the present of numerous mobile receivers with a wide diversity of wireless channels in a base station coverage area, it is a challenge to select a proper modulation scheme for video broadcasting to optimize the quality of services for users. In this thesis, the challenges and the problems in the current strategies for content delivery are addressed. A holistic novel solution is proposed that considers user preferences, user mobility, device-to-device communication, physical-layer resource allocation, and video quality prediction. First, a system-level scheduling framework is introduced to increase the spectral efficiency on broadcasting live contents onto mobile networks. It considers the audience preferences for allocating radio resources spatially and temporally. Second, to reduce the redundant transmissions in radio access networks, a content distribution system that exploits user mobility is proposed that utilizes the urban-scale user mobility and broadcasting nature of wireless communication for delay-tolerant large size content. Third, to further reduce the energy consumption in network infrastructure, a content distribution system that relies on both user mobility, and device-to-device communication is proposed. It leverages the mobile users as content carriers to offload the heavy mobile traffic from network-level onto device-level. Fourth, to mitigate the multi-user channel diversity problem, a cross-layer approach is deployed to increase the video quality for users especially for those who have a low signal-to-noise ratio signal. Finally, data mining techniques are employed to predict video qualities of wireless transmissions over mobile networks. The holistic solution has been empirically developed and evaluated. It achieves high spectral and energy efficiency and mitigates the video quality degradation in mobile networks.
    • Solution Processing of Small Molecule Organic Semiconductors: From In situ Investigation to the Scalable Manufacturing of Field Effect Transistors

      Niazi, Muhammad Rizwan (2018-05)
      Solution-processed organic field effect transistors (OFETs) have emerged in recent years as promising contenders to be part of electronic and optoelectronic circuits owing to their compatibility with low-cost high throughput roll-to-roll manufacturing technology. The stringent performance requirements for OFETs in terms of carrier mobility, switching speed, turn-on voltage and uniformity over large areas require the performance of single crystal-based OFETs, but these suffer from major scale-up challenges. To achieve device performance approaching that of single crystals with scalable, high throughput and industry-compatible solution coating of OFETs requires understanding and ultimately controlling the crystallization of organic semiconductors (OSCs), and producing very low defect-density thin films. In this thesis, we develop an understanding of the process-structure-property-performance relationship in OSCs that bring fresh insights into the nature of solution crystallization and lead to novel ways to control OSC crystallization, and finally help achieve fabrication of high-performance OFETs by scalable, high throughput and industry-compatible blade coating method. We probe the solution crystallization of OSCs by employing a suite of ex & in situ characterization techniques. This leads us to an important finding that OSC molecules aggregate to form a dense amorphous intermediate state and nucleation happens from this intermediate state during blade coating under a wide window of coating conditions. This phenomenon resembles the so-called two-step nucleation model. Two-step nucleation mediates the crystallization of a wide range of natural and synthetic products ranging from soft materials, such as proteins, biominerals, colloids and pharmaceutical molecules, to inorganic compounds. We go on to show that this nucleation mechanism is generally applicable to achieve formation of high-quality polycrystalline films in a variety of small molecule OSCs and their polymer blends. This phenomenon results in highly textured and well-connected domains, which exhibit reduced interfacial and bulk trap-state densities, helping raise the carrier mobility by one to two orders of magnitude in OFETs in comparison to direct nucleation. We extend the understanding developed for solution crystallization of various acenes and thiophene-based small molecule OSCs to the high-performance benzothieno-benzothiophene (BTBT) based small molecule OSCs. On this end, we develop protocols to fabricate high-quality thin films of BTBT based OSCs by blade coating at industrially compatible coating speeds (>100 mms-1). These films show massive single-domains with very few apparent defects when crystallized via multiple liquid-crystalline phases in two-step nucleation conditions, resulting in an average carrier mobility of ~10 cm2V-1s-1. To sum up, this thesis develops an understanding of OSC solution crystallization and efficient protocols to control polycrystalline thin film quality for high-performance OFETs. These protocols involve a combination of two-step nucleation pathway, solvent mixtures, polymer blends and device-manufacturing conditions. Our efforts enable to realize high-performance OFETs based on high-quality polycrystalline OSC thin films at industry-compatible conditions.
    • Polyethylene-based Polymers: Synthesis and Characteriization and Self Assembly

      Alshumrani, Reem (2018-05)
      In the first Chapter, Polyhomologation, a powerful technique to synthesize well-defined, perfectly linear, polyethylenes with controllable molecular weight, topology and low polydispersity, is presented in the first Chapter. In this Chapter is also discussed the combination of polyhomologation with other polymerization techniques such as Ring Opening Polymerization, ROP, Atom Transfer Radical Polymerization, ATRP, as well as with chlorosilane linking chemistry towards well-defined polyethylene-based macromolecular architectures. In the second Chapter, α,ω-dihydroxy-polyethylene was synthesized by the polyhomologation of dimethylsulfoxonium methylide with 9-thexyl-9-BBN (9-BNN: 9-borabicyclo[3.3.1]nonane), a novel difunctional initiator produced from 9-BBN and 2,3-dimethylbut-2-ene with two active and one blocked sites, followed by hydrolysis/oxidation. The terminal hydroxy groups were used either directly as initiators, in the presence of 1-tertbutyl-2,2,4,4,4-pentakis(dimethylamino)-2λ5,4λ5-catenadi(phosphazene) (t-BuP2), for the ring opening polymerization of ε-caprolactone, ε-CL, in order to afford polycaprolactone-b-polyethylene-b-polycaprolactone (PCL-b-PE-b-PCL) or after transformation to ATRP initiating sites in order to polymerize styrene and produce polystyrene-b-polyethylene-b-polystyrene (PSt-b-PE-b-PSt) triblock copolymers. Molecular characterization by 11B, 13C and 1H NMR as well as FTIR, and high-temperature GPC (HT-GPC) confirmed the well-defined nature of the synthesized new difunctional initiator and triblock copolymers. Differential scanning calorimetry was used to determine the melting points and degree of crystallinity of PE and PCL. In the third Chapter, a novel triallylborane initiator was synthesized and used to afford α-allyl-ω-hydroxy-polyethylene by polyhomologation of dimethylsulfoxonium methylide. The α-allyl-ω-hydroxy-polyethylene was then used as a macroinitiator (OH group) for the ROP of ε-CL and LLA to afford well-defined triblock terpolymer of polylactide-b-polyethylene-b-polycaprolactone (PLLA-b-PE-b-PCL). The characterization of all intermediate and final products by 1H NMR, FTIR, and HT-GPC, verified the well-defined nature of the triblock terpolymer. In the fourth Chapter, polyethylene (PE)-based 3- and 4-miktoarm star [PE(PCL)2, PE(PCL)3], as well as H-type [(PCL)2PE(PCL)2] block copolymers (PCL: polycaprolactone), were synthesized by combining polyhomologation, chlorosilane chemistry, and Ring Opening Polymerization (ROP). For the synthesis of miktoarm stars, a hydroxyl-terminated PE-OH, prepared by polyhomologation of dimethylsulfoxonium methylide with a monofunctional boron initiator, reacted with either chloromethyl(methyl)dimethoxysilane or chloromethyltrimethoxysilane. After the hydrolysis of the methoxysilane groups, the produced difunctional or trifunctional macroinitiators were used for the ROP of ε-caprolactone, in the presence of 1-tert-butyl-2,2,4,4,4-pentakis(dimethylamino)-2λ5,4λ5-catenadi(phosphazene)(t-BuP2). The H-type block copolymers were synthesized using the same strategy but with a difunctional polyhomologation initiator. All intermediates and final products were characterized by HT-GPC, 1H NMR, and FTIR analysis. The thermal properties of the PE precursors and final products were studied by DSC and TGA. In the fifth Chapter, the self-assembly properties of the amphiphilic linear block copolymer PE-b-PCL and 3-miktoarm star copolymers (PE-b-PCL2) were studied in THF, a selective solvent for PCL, by Dynamic Light Scattering (DLS), Transmission Electron Microscopy (TEM) and Atomic Force Microscope (AFM). All the above findings presented in this dissertation emphasize the utility of polyhomologation for the synthesis of well-defined polyethylene-based complex macromolecular architectures, which is practically impossible through another kind of polymerization, including the catalytic polymerization of ethylene. In the sixth Chapter, the summary of the thesis and some consideration on the subjects of future work are given.
    • Numerically investigating the effects of gasoline surrogate physical and chemical properties in a gasoline compression ignition (GCI) engine

      Atef, Nour (2018-06)
      Gasoline compression ignition (GCI) engines show promise in meeting stringent new environmental regulations, as they are characterized by high efficiency and low emissions. Simulations using chemical kinetic models provide an important platform for investigating the behaviors of the fuels inside these engines. However, because real fuels are complex, simulations require surrogate mixtures of small numbers of species that can replicate the properties of real fuels. Accordingly, the development of high fidelity, well-validated kinetic models for surrogates is critical in order to accurately replicate the combustion chemistry of different fuels under engine-related conditions. This work focuses on the development of combustion kinetic models to better understand gasoline fuel combustion in GCI engines. An updated iso-octane detailed kinetic model was developed based on new thermodynamic group values and recently evaluated rate coefficients from literature. The model was validated against a wide range of experimental data and conditions. The iso-octane model was further used in 0D simulations for a homogeneous charge compression ignition (HCCI) engine. The results showed that the low-temperature heat release in engines increases with engine boosting when the addition of alky radicals to molecular oxygen is more favored. Ethanol addition was also found to act as a radical sink which inhibits the radical pool formation and results in lower reactivity. Although detailed models provide clarification of the combustion chemistry, their high computational cost impedes their utilization in 3-D engine simulations. Hence, a reduced model for toluene primary reference fuels was developed and validated against ignition delay time and flame speed experiments from literature. The model was then used in numerically investigating the effects of the fuel’s physical properties using hollow-cone and multi-hole injectors in a partially premixed compression ignition (PPCI) engine. It was concluded that the effects of physical properties are evident in multi-hole injection cases, which is attributable to the differences in mixture stratification. Finally, reduced models for multi-components surrogates for three full-blend fuels (light naphtha-Haltermann straight-run naphtha and GCI fuels) were developed. The models were validated against ignition delay time experiments from the literature and tested in 3D engine simulations.
    • CRISPR/Cas9-mediated Viral Interference in Plants

      Tashkandi, Manal (2018-05)
      In prokaryotes, CRISPR/Cas9 system provides molecular immunity to bacteria and archaea against invading phages, conjugative plasmids and nucleic acids. CRISPR/Cas9 system has been adapted for targeted genome editing across diverse eukaryotic species for a variety of applications in basic and applied research. In this dissertation, I propose to adapt the CRISPR/Cas9 system to function as molecular immunity machinery against plant DNA viruses. Therefore, to test whether the CRISPR/Cas9 system is portable to plants, I produced plants stably over-expressing Cas9 and sgRNAs against single or multiple DNA viruses in Nicotiana benthamiana (N. benthamiana) and tomato (Solanum lycopersicum) plants. sgRNAs targeting the Cas9 endonuclease against different coding and non-coding viral sequences were tested in virus- interference experiments. I explored the possibility of generating robust interference against single and multiple DNA viruses. Subsequently, I studied the possibility of virus evasion of the CRISPR/Cas9 machinery and evolution of the virus escapees. Finally, I produced N. benthamaiana and tomato plants stably expressing the CRISPR/Cas9 machinery for developing durable virus resistance. Furthermore, developing effective viral-interference system in plants will help to understand the molecular underpinning of virus biology and host-defense mechanisms against plant viruses. In conclusion, my research project attempted to establish the efficacy and extend the utility of CRISPR/Cas9 system for viral interference in plants which promise exciting applications including producing engineered plants resistant to multiple viral infection.
    • Underwater Wireless Optical Communications Systems: from System-Level Demonstrations to Channel Modeling

      Oubei, Hassan M. (2018-06)
      Approximately, two-thirds of earth's surface is covered by water. There is a growing interest from the military and commercial communities in having, an efficient, secure and high bandwidth underwater wireless communication (UWC) system for tactical underwater applications such as oceanography studies and offshore oil exploration. The existing acoustic and radio frequency (RF) technologies are severely limited in bandwidth because of the strong frequency dependent attenuation of sound in seawater and the high conductivity of seawater at radio frequencies, respectively. Recently, underwater wireless optical communication (UWOC) has been proposed as the best alternative or complementary solution to meet this challenge. Taking advantage of the low absorption window of seawater in blue-green (400-550 nm) regime of the electromagnetic spectrum, UWOC is expected to establish secure, efficient and high data rate communication links over short and moderate distances (< 100 m) for versatile applications such as underwater oil pipe inspection, remotely operated vehicle (ROV) and sensor networks. UWOC uses the latest gallium nitrite (GaN) visible light-emitting diode (LED) and laser diode (LD) transmitters. Although some research on LED lased UWOC is being conducted, both the military and academic 5 research communities are favoring the use of laser beams, which potentially could enhance the available bandwidth by up to three orders of magnitude. However, the underwater wireless channel is optically very challenging and difficult to predict. The propagation of laser beams in seawater is significantly affected by the harsh marine environments and suffers from severe attenuation which is a combined effect of absorption and scattering, optical turbulence, and multipath effects at high transmission rates. These limitations distort the intensity and phase structure of the optical beam leading to a decrease in signal-to-noise ratio (SNR) which ultimately degrades the performance of UWOC links by increasing the probability of error. In this dissertation, we seek to experimentally demonstrate the feasibility of short range (≤ 20 m) UWOC systems over various underwater channel water types using different modulation schemes as well as to model and describe the statistical properties of turbulence-induced fading in underwater wireless optical channels using laser beam intensity fluctuations measurements.
    • Interface Effects Enabling New Applications of Two-Dimensional Materials

      Sattar, Shahid (2018-05)
      Interface effects in two-dimensional (2D) materials play a critical role for the electronic properties and device characteristics. Here we use first-principles calculations to investigate interface effects in 2D materials enabling new applications. We first show that graphene in contact with monolayer and bilayer PtSe2 experiences weak van der Waals interaction. Analysis of the work functions and band bending at the interface reveals that graphene forms an n-type Schottky contact with monolayer PtSe2 and a p-type Schottky contact with bilayer PtSe2, whereas a small biaxial tensile strain makes the contact Ohmic in the latter case as required for transistor operation. For silicene, which is a 2D Dirac relative of graphene, structural buckling complicates the experimental synthesis and strong interaction with the substrate perturbs the characteristic linear dispersion. To remove this obstacle, we propose solid argon as a possible substrate for realizing quasi-freestanding silicene and argue that a weak van der Waals interaction and small binding energy indicate the possibility to separate silicene from the substrate. For the silicene-PtSe2 interface, we demonstrate much stronger interlayer interaction than previously reported for silicene on other semiconducting substrates. Due to the inversion symmetry breaking and proximity to PtSe2, a band gap opening and spin splittings in the valence and conduction bands of silicene are observed. It is also shown that the strong interlayer interaction can be effectively reduced by intercalating NH3 molecules between silicene and PtSe2, and a small NH3 discussion barrier makes intercalation a viable experimental approach. Silicene/germanene are categorized as key materials for the field of valleytronics due to stronger spin-orbit coupling as compared to graphene. However, no viable route exists so far to experimental realization. We propose F-doped WS2 as substrate that avoids detrimental effects and at the same time induces the required valley polarization. The behavior is explained by proximity effects on silicene/germanene due to the underlying substrate. Broken inversion symmetry in the presence of WS2 opens a substantial band gap in silicene/germanene. F doping of WS2 results in spin polarization, which, in conjunction with proximity-enhanced spin orbit coupling, creates sizable spin-valley polarization. For heterostructures of silicene and hexagonal boron nitride, we show that the stacking is fundamental for the details of the dispersion relation in the vicinity of the Fermi energy (gapped, non-gapped, linear, parabolic) despite small differences in the total energy. We also demonstrate that the tightbinding model of bilayer graphene is able to capture most of these features and we identify the limitations of the model.
    • Parameterization analysis and inversion for orthorhombic media

      Masmoudi, Nabil (2018-05)
      Accounting for azimuthal anisotropy is necessary for the processing and inversion of wide-azimuth and wide-aperture seismic data because wave speeds naturally depend on the wave propagation direction. Orthorhombic anisotropy is considered the most effective anisotropic model that approximates the azimuthal anisotropy we observe in seismic data. In the framework of full wave form inversion (FWI), the large number of parameters describing orthorhombic media exerts a considerable trade-off and increases the non-linearity of the inversion problem. Choosing a suitable parameterization for the model, and identifying which parameters in that parameterization could be well resolved, are essential to a successful inversion. In this thesis, I derive the radiation patterns for different acoustic orthorhombic parameterization. Analyzing the angular dependence of the scattering of the parameters of different parameterizations starting with the conventionally used notation, I assess the potential trade-off between the parameters and the resolution in describing the data and inverting for the parameters. In order to build practical inversion strategies, I suggest new parameters (called deviation parameters) for a new parameterization style in orthorhombic media. The novel parameters denoted ∈d, ƞd and δd are dimensionless and represent a measure of deviation between the vertical planes in orthorhombic anisotropy. The main feature of the deviation parameters consists of keeping the scattering of the vertical transversely isotropic (VTI) parameters stationary with azimuth. Using these scattering features, we can condition FWI to invert for the parameters which the data are sensitive to, at different stages, scales, and locations in the model. With this parameterization, the data are mainly sensitive to the scattering of 3 parameters (out of six that describe an acoustic orthorhombic medium): the horizontal velocity in the x1 direction, ∈1 which provides scattering mainly near the zero offset in the x1-x3 vertical plane, and ∈d, which is the ratio of the horizontal velocity squared in the x1 and x2 direction. Since, with this parameterization, the radiation pattern for the horizontal velocity is azimuth independent, we can perform an initial VTI inversion for two parameters (velocity and ∈1), then use ∈d to fit the azimuth variation in the data. This can be done at the reservoir level or any region of the model.
    • Decision and Inhibitory Trees for Decision Tables with Many-Valued Decisions

      Azad, Mohammad (2018-06-06)
      Decision trees are one of the most commonly used tools in decision analysis, knowledge representation, machine learning, etc., for its simplicity and interpretability. We consider an extension of dynamic programming approach to process the whole set of decision trees for the given decision table which was previously only attainable by brute-force algorithms. We study decision tables with many-valued decisions (each row may contain multiple decisions) because they are more reasonable models of data in many cases. To address this problem in a broad sense, we consider not only decision trees but also inhibitory trees where terminal nodes are labeled with “̸= decision”. Inhibitory trees can sometimes describe more knowledge from datasets than decision trees. As for cost functions, we consider depth or average depth to minimize time complexity of trees, and the number of nodes or the number of the terminal, or nonterminal nodes to minimize the space complexity of trees. We investigate the multi-stage optimization of trees relative to some cost functions, and also the possibility to describe the whole set of strictly optimal trees. Furthermore, we study the bi-criteria optimization cost vs. cost and cost vs. uncertainty for decision trees, and cost vs. cost and cost vs. completeness for inhibitory trees. The most interesting application of the developed technique is the creation of multi-pruning and restricted multi-pruning approaches which are useful for knowledge representation and prediction. The experimental results show that decision trees constructed by these approaches can often outperform the decision trees constructed by the CART algorithm. Another application includes the comparison of 12 greedy heuristics for single- and bi-criteria optimization (cost vs. cost) of trees. We also study the three approaches (decision tables with many-valued decisions, decision tables with most common decisions, and decision tables with generalized decisions) to handle inconsistency of decision tables. We also analyze the time complexity of decision and inhibitory trees over arbitrary sets of attributes represented by information systems in the frameworks of local (when we can use in trees only attributes from problem description) and global (when we can use in trees arbitrary attributes from the information system) approaches.
    • Numerical Computation of Detonation Stability

      Kabanov, Dmitry (2018-06-03)
      Detonation is a supersonic mode of combustion that is modeled by a system of conservation laws of compressible fluid mechanics coupled with the equations describing thermodynamic and chemical properties of the fluid. Mathematically, these governing equations admit steady-state travelling-wave solutions consisting of a leading shock wave followed by a reaction zone. However, such solutions are often unstable to perturbations and rarely observed in laboratory experiments. The goal of this work is to study the stability of travelling-wave solutions of detonation models by the following novel approach. We linearize the governing equations about a base travelling-wave solution and solve the resultant linearized problem using high-order numerical methods. The results of these computations are postprocessed using dynamic mode decomposition to extract growth rates and frequencies of the perturbations and predict stability of travelling-wave solutions to infinitesimal perturbations. We apply this approach to two models based on the reactive Euler equations for perfect gases. For the first model with a one-step reaction mechanism, we find agreement of our results with the results of normal-mode analysis. For the second model with a two-step mechanism, we find that both types of admissible travelling-wave solutions exhibit the same stability spectra. Then we investigate the Fickett’s detonation analogue coupled with a particular reaction-rate expression. In addition to the linear stability analysis of this model, we demonstrate that it exhibits rich nonlinear dynamics with multiple bifurcations and chaotic behavior.
    • Genome-scale Evaluation of the Biotechnological Potential of Red Sea Bacilli Strains

      Othoum, Ghofran K. (2018-02)
      The increasing spectrum of multidrug-resistant bacteria has caused a major global public health concern, necessitating the discovery of novel antimicrobial agents. Additionally, recent advancements in the use of microbial cells for the scalable production of industrial enzymes has encouraged the screening of new environments for efficient microbial cell factories. The unique ecological niche of the Red Sea points to the promising metabolic and biosynthetic potential of its microbial system. Here, ten sequenced Bacilli strains, that are isolated from microbial mat and mangrove mud samples from the Red Sea, were evaluated for their use as platforms for protein production and biosynthesis of bioactive compounds. Two of the species (B.paralicheniformis Bac48 and B. litoralis Bac94) were found to secrete twice as much protein as Bacillus subtilis 168, and B. litoralis Bac94 had complete Tat and Sec protein secretion systems. Additionally, four Red Sea Species (B. paralicheniformis Bac48, Virgibacillus sp. Bac330, B. vallismortis Bac111, B. amyloliquefaciens Bac57) showed capabilities for genetic transformation and possessed competence genes. More specifically, the distinctive biosynthetic potential evident in the genomes of B. paralicheniformis Bac48 and B. paralicheniformis Bac84 was assessed and compared to nine available complete genomes of B. licheniformis and three genomes of B. paralicheniformis. A uniquely-structured trans-acyltransferase (trans-AT) polyketide synthase/nonribosomal peptide synthetase (PKS/NRPS) cluster in strains of this species was identified in the genome of B. paralicheniformis 48. In total, the two B. paralicheniformis Red Sea strains were found to be more enriched in modular clusters compared to B. licheniformis strains and B. paralicheniformis strains from other environments. These findings provided more insights into the potential of B. paralicheniformis 48 as a microbial cell factory and encouraged further focus on the strain’s metabolism at the system level. Accordingly, a draft metabolic model for B. paralicheniformis Bac48 (iPARA1056) was reconstructed, refined, and validated using growth rate and growth phenotypes under different substrates, generated using high-throughput Phenotype Microarray technology. The presented studies indicate that several of the isolated strains represent promising chassis for the development of cell factories for enzyme production and also point to the richness of their genomes with specific modules of secondary metabolism that have likely evolved in Red Sea Bacilli due to environmental adaptation.
    • Versatile High-Performance Regenerated Cellulose Membranes Prepared using Trimethylsilyl Cellulose as a Precursor

      Puspasari, Tiara (2018-05)
      Cellulose has emerged as an indispensable membrane material due to its abundant availability, low cost, fascinating physiochemical properties and environment benignancy. However, it is believed that the potential of this polymer is not fully explored yet due to its insolubility in the common organic solvents, encouraging the use of derivatization-regeneration method as a viable alternative to the direct dissolution in exotic or reactive solvents. In this work, we use trimethylsilyl cellulose (TMSC), a highly soluble cellulose derivative, as a precursor for the fabrication of cellulose thin film composite membranes. TMSC is an attractive precursor to assemble thin cellulose films with good deposition behavior and film morphology; cumbersome solvents used in the one step cellulose processing are avoided. This derivative is prepared from cellulose by the known silylation reaction. The complete transformation of TMSC back into cellulose after the membrane formation is carried out by vapor-phase acid treatment, which is simple, scalable and reproducible. This process along with the initial TMSC concentration determines the membrane sieving characteristics. Unlike the typical regenerated cellulose membranes with meso- or macropores, membranes regenerated from TMSC display micropores suitable for the selective separation of nanomolecules in aqueous and organic solvent nanofiltration. The membranes introduced in this thesis represent the first polymeric membranes ever reported for highly selective separation of similarly sized small organic molecules based on charge and size differences with outstanding fluxes. Owing to its strong hydrophilic and amorphous character, the membranes also demonstrate excellent air-dehumidification performance as compared to previously reported thin film composite membranes. Moreover, the use of TMSC enables the creation of the previously unfeasible cellulose–polydimethylsiloxane (PDMS) and cellulose–polyethyleneimine (PEI) blend membranes with a good compatibility. The cellulose–PDMS membranes demonstrate attractive performance in ethanol-water pervaporation as compared to the commercial PDMS membrane, and allow nanofiltration of a wide range of solvents with different polarity. The cellulose-PEI membranes exhibit anomalous performance improvement in nanofiltration as compared to the corresponding pure membranes. This study has opened up many great opportunities for cellulose to continuously contribute to sustainable and economical membrane processes.
    • Hyperbranched Polyethylenebased Macromolecular Architectures: Synthesis, Characterization, and Selfassembly

      Al-Sulami, Ahlam (2018-05)
      "Chain walking” catalytic polymerization CWCP is a powerful tool for the one-pot synthesis of a unique class of hyperbranched polyethylene HBPE-based macromolecules with a controllable molecular weight, topology, and composition. This dissertation focuses on new synthetic routes to prepare HBPE-based macromolecular architectures by combining the CWCP technique with ring opening polymerization ROP, atom–transfer radical polymerization ATRP, and “click” chemistry. Taking advantage of end-functionalized HBPE, and a new ethynyl-soketal star-shape agent, we were able to synthesize different types of the HBPE-based architectures including hyperbranched-on-hyperbranched core-shell nanostructure, and miktoarm-star-HBPE-based block copolymers. The first part of the dissertation provides a general introduction to the synthesis of polyethylene types with controllable structures. Well-defined polyethylene with different macromolecule architectures were synthesized either for academic or industrial purposes. In the second part, the HBPE with different topologies was synthesized by CWCP, using a α-diimine Pd (II) catalyst. The effect of the temperature and pressure on the catalyst activity and polymer properties, including branch content, molecular weight, distribution, and thermal properties were studied. Two series of samples were synthesized: a) serial samples (A) under pressures of 1, 5, and 27 atm at 5˚C, and b) serial samples (B) at temperatures of 5, 15, and 35 ˚C under 5 atm. Proton nuclear magnetic resonance spectroscopy, 1H NMR, and gel permeation chromatography, GPC, analysis were used to calculate the branching content, molecular weight, and distribution, whereas differential scanning calorimetry, DSC, was used to record the melting and glass transition temperatures as well as the degree of the crystallinity. Well-defined HBPE-based core diblock copolymers with predictable amphiphilic properties are studied in the third part of the project. Hyperbranched polyethylene-b-poly(N-isopropylacrylamide), HBPE-b-PNIPAM, and hyperbranched polyethylene-b-poly(solketal acrylate), HBPE-b-PSA, were successfully synthesized by combining CWCP and ATRP. The synthetic methodology includes the following steps; a) synthesis of multifunction hyperbranched polyethylene initiators HBPE-MI by direct copolymerization of ethylene with 2-(2-bromoisobutyryloxy)ethyl acrylate BIEA in the presence of a α-diimine Pd(II) catalyst, and b) HBPE-MI with α-bromoester groups used as initiation sites for ATRP. Proton nuclear magnetic resonance spectroscopy, 1H NMR, gel permeation chromatography,GPC, and Fourier transform infrared, FT-IR, spectroscopy, were used for determining the molecular and composition structures. Also, differential scanning calorimetry, DSC, and thermogravimetric analysis, TGA, were used to record the melting temperature and to study the thermal stability, respectively. In the fourth part, a well-defined 3-miktoarm star copolymer 3μ-HBPE(PCL)2 (HBPE: hyperbranched polyethylene, PCL: poly(ε-caprolactone) was synthesized by combining CWCP, ring opening polymerization, ROP, and “click” chemistry. The synthetic methodology includes the following steps: a) synthesis of azido-functionalized hyperbranched polyethylene HBPE-N3 by CWCP of ethylene with the α-diimine Pd(II) catalyst, followed by quenching with an excess of 4-vinylbenzyl chloride and transformation of –Cl to the azido group with sodium azide, b) synthesis of in-chain ethynyl-functionalized poly(ε-caprolactone), (PCL)2-C≡CH by ROP of ε-CL with ethynylfunctionalized solketal [3-(prop-2-yn-1-yloxy) propane-1,2-diol] as a bifunctional initiator, in the presence of P2-t-Bu phosphazene super base, and c) “clicking” HBPE-N3 and (PCL)2-C≡CH using the copper(I)-catalyzed alkyne–azide cycloaddition CuAAC. Proton nuclear magnetic resonance spectroscopy, 1H NMR, gel permeation chromatography, GPC, and Fourier transform infrared, FT-IR, spectroscopy, were used to determine the molecular and composition structures. Also, the differential scanning calorimetry, DSC, was used to record the melting point temperature. The fifth part illustrates the self-assembly behavior of the HBPE-based block copolymers of poly(N-isopropylacrylamide), NIPAM, and poly(ε-caprolactone), PCL, at room temperature in water and a petroleum ether-selective solvent for NIPAM and PCL respectively. The synthesized copolymers HBPE-b-NIPAM and 3μ-HBPE(PCL)2 revealed either core-shell nanostructure in vesicles or worms and worm-likes branches, as confirmed by combining the analysis of dynamic light scattering, DLS, transmission electron microscopy, TEM, and atomic force spectroscopy, AFM. All the findings presented in this dissertation emphasize the utility of "living" CWCP to synthesize end-functionalized HBPE, and new star-linkage HBPE-based complex architectures. The summary and future works concerning predictable properties and applications are discussed in the sixth part.
    • Optical and Temporal Carrier Dynamics Investigations of III-Nitrides for Semiconductor Lighting

      Ajia, Idris A. (2018-05-22)
      III-nitride semiconductors suffer significant efficiency limitations; ‘efficiency’ being an umbrella term that covers an extensive list of challenges that must be overcome if they are to fulfil their vast potential. To this end, it is imperative to understand the underlying phenomena behind such limitations. In this dissertation, I combine powerful optical and structural characterization techniques to investigate the effect of different defects on the carrier dynamics in III-nitride materials for light emitting devices. The results presented herein will enhance the current understanding of the carrier mechanisms in such devices, which will lead to device efficiency improvements. In the first part of this dissertation, the effects of some important types of crystal defects present in III-nitride structures are investigated. Here, two types of defects are studied in two different III-nitride-based light emitting structures. The first defects of interest are V-pit defects in InGaN/GaN multiple quantum well (MQW) blue LEDs, where their contribution to the high-efficiency of such LEDs is discussed. In addition, the effect of these defects on the efficiency droop phenomenon in these LEDs is elucidated. Secondly, the optical effects of grain boundary defects in AlN-rich AlGaN/AlGaN MQWs is studied. In this study, it is shown that grain boundary defects may result in abnormal carrier localization behavior in these deep ultraviolet (UV) structures. While both defects are treated individually, it is evident from these studies that threading dislocation (TD) defects are an underlying contributor to the more undesirable outcomes of the said defects. In the second part, the dissertation reports on the carrier dynamics of III-nitride LED structures grown on emerging substrates—as possible efficiency enhancing techniques—aimed at mitigating the effects of TD defects. Thus, the carrier dynamics of GaN/AlGaN UV MQWs grown, for the first time, on (2̅01) – oriented β-Ga2O3 is studied. It is shown to be a candidate substrate for highly efficient vertical UV devices. Finally, results from the carrier dynamics investigation of an AlGaN/AlGaN MQW LED structure homoepitaxially grown on AlN substrate are discussed, where it is shown that its high-efficiency is sustained at high temperatures through the thermal redistribution of carriers to highly efficient recombination sites.
    • Exploiting Data Sparsity In Covariance Matrix Computations on Heterogeneous Systems

      Charara, Ali (2018-05-24)
      Covariance matrices are ubiquitous in computational sciences, typically describing the correlation of elements of large multivariate spatial data sets. For example, covari- ance matrices are employed in climate/weather modeling for the maximum likelihood estimation to improve prediction, as well as in computational ground-based astronomy to enhance the observed image quality by filtering out noise produced by the adap- tive optics instruments and atmospheric turbulence. The structure of these covariance matrices is dense, symmetric, positive-definite, and often data-sparse, therefore, hier- archically of low-rank. This thesis investigates the performance limit of dense matrix computations (e.g., Cholesky factorization) on covariance matrix problems as the number of unknowns grows, and in the context of the aforementioned applications. We employ recursive formulations of some of the basic linear algebra subroutines (BLAS) to accelerate the covariance matrix computation further, while reducing data traffic across the memory subsystems layers. However, dealing with large data sets (i.e., covariance matrices of billions in size) can rapidly become prohibitive in memory footprint and algorithmic complexity. Most importantly, this thesis investigates the tile low-rank data format (TLR), a new compressed data structure and layout, which is valuable in exploiting data sparsity by approximating the operator. The TLR com- pressed data structure allows approximating the original problem up to user-defined numerical accuracy. This comes at the expense of dealing with tasks with much lower arithmetic intensities than traditional dense computations. In fact, this thesis con- solidates the two trends of dense and data-sparse linear algebra for HPC. Not only does the thesis leverage recursive formulations for dense Cholesky-based matrix al- gorithms, but it also implements a novel TLR-Cholesky factorization using batched linear algebra operations to increase hardware occupancy and reduce the overhead of the API. Performance reported of the dense and TLR-Cholesky shows many-fold speedups against state-of-the-art implementations on various systems equipped with GPUs. Additionally, the TLR implementation gives the user flexibility to select the desired accuracy. This trade-off between performance and accuracy is, currently, a well-established leading trend in the convergence of the third and fourth paradigm, i.e., HPC and Big Data, when moving forward with exascale software roadmap.