Recent Submissions

  • Free Space Optics for 5G Backhaul Networks and Beyond

    Alheadary, Wael (2018-08)
    The exponential increase of mobile users and the demand for high-speed data services has resulted in signi cant congestions in cellular backhaul capacity. As a solution to satisfy the tra c requirements of the existing 4G network, the 5G net- work has emerged as an enabling technology and a fundamental building block of next-generation communication networks. An essential requirement in 5G backhaul networks is their unparalleled capacity to handle heavy tra c between a large number of devices and the core network. Microwave and optic ber technologies have been considered as feasible solutions for next-generation backhaul networks. However, such technologies are not cost e ective to deploy, especially for the backhaul in high-density urban or rugged areas, such as those surrounded by mountains and solid rocks. Addi- tionally, microwave technology faces alarmingly challenging issues, including limited data rates, scarcity of licensed spectrum, advanced interference management, and rough weather conditions (i.e., rain, which is the main weather condition that a ects microwave signals the most). The focus of this work is to investigate the feasibility of using free-space-optical (FSO) technology in the 5G cellular backhaul network. FSO is a cost-e ective and wide-bandwidth solution as compared to traditional backhaul solutions. However, FSO links are sensitive to atmospheric turbulence-induced fad- ing, path loss, and pointing errors. Increasing the reliability of FSO systems while still exploiting their high data rate communications is a key requirement in the de- ployment of an FSO backhaul network. Overall, the theoretical models proposed in this work will be shown to enhance FSO link performance. In the experimental direction, we begin by designing an integrated mobile FSO system. To the best of our knowledge, no work in the literature has addressed the atmospheric path loss characterization of mobile FSO channels in a coastal envi- ronment. Therefore, we investigate the impact of weather e ects in Thuwal, Saudi Arabia, over FSO links using outdoor and indoor setups. For the indoor experiments, results are reported based on a glass climate chamber in which we could precisely control the temperature and humidity.
  • 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.
  • 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).
  • 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.
  • 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.
  • Molecular Fingerprinting to Understand Diazotrophic Microbe Distribution in Oligotrophic Oceans

    MOHAMED, ROSLINDA (2018-07)
    In oligotrophic systems, where primary production is low and nitrogen is in short supply, nitrogen fixation process is intense. Although a few diazotrophs (eg. Trichodesmium) have been widely-studied, the rest of the diazotrophic community is still poorly understood. Furthermore, the global distribution of diazotrophs are yet to be clearly resolved. This dissertation assessed the distribution of diazotrophs in oligotrophic systems, particularly in the tropical and subtropical oceans, using genomics tools including next-generation sequencing. We first tested out a pair of nifH-specific primer that previously performed well in silico, but found that its application on seawater samples was biased towards paralogous, non-functional nitrogenase nifH genes. Instead, we found that the use of a nested PCR method using different primers sets to be more effective in amplifying functional nifH genes. Trichodesmium sp., UCYN-A and Pseudomonas sp. forms the core of the diazotrophic communities in oligotrophic oceans. Temperature is the primary driver of the abundances and distributions of these organisms in the Pacific, Atlantic and Indian Oceans, as well as in the oligotrophic Red Sea. Trichodesmium tends to dominate warm, surface waters, while UCYN-A prefers cooler environments and dwell in sub-surface waters in the Red Sea. Due to the dominance of Pseudomonas in the large-sized fraction samples, they are believed to be part of the Trichodesmium-associated consortia, although this requires further investigations. We also found non-cyanobacterial species of diazotrophs to be dominant previously-described hotspots of nitrogen fixation, and found evidence for the widespread of alternative nitrogenases (Cluster II). Using the Red Sea as an exemplar for future warming ocean, we found patterns of niche partitioning in the Red Sea diazotrophs, based on their distribution along seasons, latitude and depth. Our one-year observation of Red Sea Trichodesmium population witnessed the collapse of the population at temperatures above 32°C. This dissertation not only improve our understanding of the effects of future rising temperature on the natural populations of diazotrophs, but it also helps to establish a baseline understanding of the structure, spatial and temporal dynamics of Red Sea diazotrophs, which has not been discussed elsewhere.
  • Real-Time and Ultra-High De finition Video Transmission in Underwater Wireless Optical Networks

    Al-Halafi, Abdullah (2018-07)
    Oceans form about three quarters of our planet Earth, and house immense resources that are critical for future generations. Exploring and monitoring such resources is becoming essential to protect the effected ones by the irresponsible human behavior, and to discover new ones. The limitations of depths mandate the search for alternatives and where human divers become endangered. Using remotely operated vehicles is commonly used for marine explorations, while tethered to ships. To be fully autonomous and to avoid damaging the fragile marine environment, they must be equipped with wireless communication solutions that enable real-time control and feedback on their maneuvering and mobility. Also, the ultimate tool to monitor, inspect and repair underwater structures is to use video streaming to mimic the reality of those unseen parts of the world. Existing underwater communications do not provide the necessary features to transmit video from the deep. Acoustic waves as well as the radio frequency waves are either limited in bandwidths or strongly attenuated by the water medium. On the other hand, wireless optical communication is an emerging technology that provides high transmission speeds and can enable video streaming underwater. This motivates bringing wireless optical technologies for real-time video streaming underwater to a practical implementation by undertaking theoretical and experimental studies of systems and techniques that can provide optimized solutions within our proposed framework. We present our video transmission architecture that facilitates programmable system configurations. Software defined platforms provide us with the means of configuring several setups to test our approach. In order to fully utilize the available optical spectrum, we have additionally implemented several modulation techniques in various laboratory scenarios. Real-time and ultra-high definition video has been successfully demonstrated. The overall system performance and throughput analysis have been provided. A thorough investigation of the system performance under various underwater channel conditions was undertaken. Also, as the delay resulting from queuing, when video packets are waiting for service, is key in time critical applications, we derive the mathematical model and investigate the delay effects and the packet dropping probability on the overall system performance when our setup is extended to a multi-channel configuration.
  • First principles based fuel design: investigating fuel properties and combustion chemistry

    Ahmed, Ahfaz (2018-07)
    Advanced combustion engine concepts require fuels which are meticulously designed to harness full potential of novel engine technologies. To develop such fuels, better understanding of fuel properties and their effect on combustion parameters is needed. The investigations reported in this work establishes relationships between several fuel properties and combustion parameters at engine relevant conditions. Further, these findings along with conclusions from other studies are utilized to synthesize fuels and surrogate fuels with tailored combustion properties. This approach of designing fuels relies on constrained non-linear optimization of several combustion properties simultaneously to design surrogate fuels for transportation fuels to enable combustion simulations. This scheme of fuel design has been devised and presented as Fuel Design Tool in Ahmed et al. Fuel 2015. Detailed investigations have been made to understand the effect of fuel properties on the ignition of fuels in Rapid compression machines utilizing a custom built multi-zone model. The study was further extended to explore fuel effects on engine combustion utilizing experiments and modelling to gather understanding of instances of engine knocking and pollutant formation. Bio-blended fuels allow mitigation of harmful pollutants and also enables engines to operate at higher efficiency. Ignition characteristics of two high octane bio-blended gasolines were studied experimentally in rapid compression machine and shock tube and detailed chemical kinetic analysis was conducted to understand how the presence of biofuels (i.e., ethanol) in gasoline influences the evolution of important radicals controlling ignition. Another set of biofuels namely methyl acetate and ethyl acetate were studied employing fundamental experimental and computational methods. The investigation involved development and analysis of combustion chemistry models, speciation studies in jet stirred reactors, ignition delay measurements and determination of laminar burning velocities. These fuels are found suited for high performance advanced spark ignition engines and the developed model and analysis will lead to optimization of combustion performance. The developed fuel design tool along with enhanced understanding of combustion chemistry and fuel properties enables a complete toolkit ready to be utilized to develop fuels with better suited properties for the advanced combustion modes.
  • On the role of thermal fluctuations in fluid mixing

    Narayanan, Kiran (2018-07)
    Fluid mixing that is induced by hydrodynamic instability is ubiquitous in nature; the material interface between two fluids when perturbed even slightly, changes shape under the influence of hydrodynamic forces, and an additional zone called the mixing layer where the two fluids mix, develops and grows in size. This dissertation reports a study on the role of thermal fluctuations in fluid mixing at the interface separating two perfectly miscible fluids of different densities. Mixing under the influence of two types of instabilities is studied; the Rayleigh-Taylor (RTI) and Richtmyer-Meshkov (RMI) instabilities. The study was conducted using numerical simulations after verification of the simulation methodology. Specifically, fluctuating hydrodynamic simulations were used; the fluctuating compressible Navier-Stokes equations were the physical model of the system, and they were solved using numerical methods that were developed and implemented in-house. Our results indicate that thermal fluctuations can trigger the onset of RTI at an initially unperturbed fluid-fluid interface, which subsequently leads to mixing of multi-mode character. In addition we find that for both RMI and RTI, whether or not thermal fluctuations quantitatively affect the mixing behavior, depends on the magnitude of the dimensionless Boltzmann number of the hydrodynamic system in question, and not solely on its size. When the Boltzmann number is much smaller than unity, the quantitative effect of thermal fluctuations on the mixing behavior is negligible. Under this circumstance, we show that mixing behavior is the average of the outcome from several stochastic instances, with the ensemble of stochastic instances providing the bounds on mixing-related metrics such as the mixing width. Most macroscopic hydrodynamic systems fall in this category. However, when the system is such that the Boltzmann number is of order unity, we show that thermal fluctuations can significantly affect the mixing behavior; the ensemble-averaged solution shows a departure from the deterministic solution. We conclude that for such systems, it is important to account for thermal fluctuations in order to correctly capture their physical behavior.
  • Exploration of Low-Cost, Natural Biocidal Strategies to Inactivate New Delhi Metallo-beta-lactamase (NDM)-Positive Escherichia coli PI-7, an Emerging Wastewater-Contaminant

    Aljassim, Nada I. (2018-07)
    Conventional wastewater treatment plants are able to reduce contaminant loads within regulations but do not take into account emerging contaminants. Antibiotic resistance genes and antibiotic resistant bacteria have been shown to survive wastewater treatment and remain detectable in effluents. The safety of treated wastewaters is crucial, otherwise unregulated and unmitigated emerging contaminants pose risks to public health and impede wastewater reuse. This dissertation aimed to further understanding of emerging microbial threats, and tested two natural and low-cost tools for their mitigation: sunlight, and bacteriophages. A wastewater bacterial isolate, named E. coli PI-7, which is highly antibiotic resistant, carries the novel antibiotic resistance gene New Delhi metallo-beta-lactamase NDM-1 gene, and displays pathogenic traits, was chosen to model responses to the treatments. Results found that solar irradiation was able to achieve a 5-log reduction in E. coli PI-7 numbers within 12 hours of exposure. However, the results also emphasized the risks from emerging microbial contaminants since E. coli PI-7, when compared with a non-pathogenic strain E. coli DSM1103 that has less antibiotic resistance, showed longer survival under solar irradiation. In certain instances, E. coli PI-7 persisted for over 6 hours before starting to inactivate, exhibited complex stress resistance gene responses, and activated many of its concerning pathogenicity and antibiotic resistance traits. However, upon solar irradiation, gene expression results obtained from both E. coli strains also showed increased susceptibility to bacteriophages. Hence, bacteriophages were coupled with solar irradiation as an additional mitigation strategy. Results using the coupled treatment found reduced cell-wall and extracellular matrix production in E. coli PI-7. DNA repair and other cellular defense functions like oxidative stress responses were also impeded, rendering E. coli PI-7 more susceptible to both stressors and successfully hastening the onset of its inactivation. Overall, the dissertation is built upon the need to develop strategies to further mitigate risks associated with emerging microbial contaminants. Solar irradiation and bacteriophages demonstrate potential as natural and low-cost mitigation strategies. Sunlight was able to achieve significant log-reductions in tested E. coli numbers within a day’s exposure. Bacteriophages were able to overwhelm E. coli PI-7’s capacity to resist solar inactivation while not affecting the indigenous microbiota.
  • Potential of Bacterial Volatile Organic Compounds for Biocontrol of Fungal Phytopathogens and Plant Growth Promotion Under Abiotic Stress

    Soussi, Asma (2018-07)
    Bacterial volatile organic compounds (VOCs) are signal molecules that may have beneficial roles in the soil-plant-microbiome ecosystem. In this Ph.D. thesis, I aimed to assess and characterize the role of bacterial VOCs in plant tolerance to drought and in the biocontrol of fungal pathogens. I started by studying two root endophytic bacteria isolated from pepper plants cultivated under desert farming conditions. They showed an enhancement of pepper tolerance to drought stress and an amelioration of its physiological status. Moreover, they induced the expression of a vacuolar pyrophosphatase proton pump (V-PPase), implicated in the regulation of the vacuolar osmotic pressure, facilitating water uptake. Besides, the exposure of Arabidopsis thaliana plants, grown under salinity stress, to the volatile 2,3-butanediol, described for its plant growth promotion (PGP) potential, enhanced the plants tolerance to salinity, proving the potential involvement of this volatile in the osmotic stress resistance mechanism. Then, I studied VOCs released by three bacteria associated to healthy rice plants. Their released VOCs mixtures modified the color pattern of Magnaporthe oryzae, the agent of the rice blast disease, and protected rice from the pathogen infection. A significant reduction of melanin production, sporulation and appressoria formation was measured in presence of the bacterial VOCs, without major effects on mycelial proliferation. 1-butanol-3-methyl, one of the nine VOCs co-produced by the studied bacteria, proved its potential of reducing M. oryzae melanin in vitro. In vivo tests confirmed the infection inhibition effects mediated by the rice-bacterial VOCs, with a reduction of 94% of the disease incidence. Lastly, I compared the genomes of the five bacteria considered in the previous experimental studies. The PGP traits and the VOCs pathways identified from the genome analyses confirmed the effects observed with the in vitro and in vivo assays, revealing a complex mode of promotion and protection offered by the studied plant-associated bacteria. In conclusion, plant-associated bacterial VOCs can play potentially important roles in modulating plant drought tolerance and reducing fungal virulence. Such biological resources represent novel tools to counteract the deleterious effects of abiotic and biotic stresses and have the potential to be exploited for sustainable approaches in agriculture.
  • 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.
  • 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.
  • 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.
  • Premixed and Partial Premixed Turbulent Flames at High Reynolds Number

    Luca, Stefano (2018-06)
    Methane/air premixed and partially premixed turbulent flames at high Reynolds number are characterized using Direct Numerical Simulations (DNS) with detailed chemistry in a spatially evolving slot Bunsen configuration. Two sets of simulations are performed. A first set of simulations with fully premixed inlet conditions is considered in order to assess the effect of turbulence on the flame. Four simulations are performed at increasing Reynolds number and up to 22400, defined based on the bulk velocity, slot width, and the reactants' properties, and 22 billion grid points, making it one of the largest simulations in turbulent combustion. The simulations feature finite rate chemistry with a 16 species mechanism. To perform these simulations, few preliminary steps were required: (i) two skeletal mechanisms were developed reducing GRI-3.0; (ii) a convergence study is performed to select the proper spatial and temporal discretization and (iii) simulations of fully developed turbulent channel flows are preformed to generate the inlet conditions of the jet. The study covers different aspects of flame-turbulence interaction. It is found that the thickness of the reaction zone is similar to that of a laminar flame, while the preheat zone has a lower mean temperature gradient, indicating flame thickening. The characteristic length scales of turbulence are investigated and the effect of the Reynolds number on these quantities is assessed. The tangential rate of strain is responsible for the production of flame surface in the mean and surface destruction is due to the curvature term. A second set of simulations with inhomogeneous inlet conditions is performed to study how partial premixing and turbulence interact with the flame and with each other. The jet Reynolds number is 5600, and a 33 species mechanism is used. The effect of the inlet fluctuations is reflected on heat release rate fluctuations, however the conditional mean is not affected. The flames show thickening of the preheat zone, and for the lowest level of mixing a slight thickening of the reaction zone is observed. The effect of partially mixed mixture on the NOx formation is analyzed and no major impact was found.
  • 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.
  • 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.
  • A Study of Schrödinger–Type Equations Appearing in Bohmian Mechanics and in the Theory of Bose–Einstein Condensates

    Sierra Nunez, Jesus Alfredo (2018-05-16)
    The Schrödinger equations have had a profound impact on a wide range of fields of modern science, including quantum mechanics, superfluidity, geometrical optics, Bose-Einstein condensates, and the analysis of dispersive phenomena in the theory of PDE. The main purpose of this thesis is to explore two Schrödinger-type equations appearing in the so-called Bohmian formulation of quantum mechanics and in the study of exciton-polariton condensates. For the first topic, the linear Schrödinger equation is the starting point in the formulation of a phase-space model proposed in [1] for the Bohmian interpretation of quantum mechanics. We analyze this model, a nonlinear Vlasov-type equation, as a Hamiltonian system defined on an appropriate Poisson manifold built on Wasserstein spaces, the aim being to establish its existence theory. For this purpose, we employ results from the theory of PDE, optimal transportation, differential geometry and algebraic topology. The second topic of the thesis is the study of a nonlinear Schrödinger equation, called the complex Gross-Pitaevskii equation, appearing in the context of Bose-Einstein condensation of exciton-polaritons. This model can be roughly described as a driven-damped Gross-Pitaevskii equation which shares some similarities with the complex Ginzburg-Landau equation. The difficulties in the analysis of this equation stem from the fact that, unlike the complex Ginzburg-Landau equation, the complex Gross-Pitaevskii equation does not include a viscous dissipation term. Our approach to this equation will be in the framework of numerical computations, using two main tools: collocation methods and numerical continuation for the stationary solutions and a time-splitting spectral method for the dynamics. After performing a linear stability analysis on the computed stationary solutions, we are led to postulate the existence of radially symmetric stationary ground state solutions only for certain values of the parameters in the equation; these parameters represent the “strength” of the driving and damping terms. Moreover, numerical continuation allows us to show, for fixed parameters, the ground and some of the excited state solutions of this equation. Finally, for the values of the parameters that do not produce a stable radially symmetric solution, our dynamical computations show the emergence of rotating vortex lattices.

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