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  • Mechanistic Investigation into the Conversion of Methanol to Hydrocarbons by Zeolite Catalysts

    Liu, Zhaohui (2018-10)
    Catalytic conversion of methanol to hydrocarbons (MTH) provides an alternative route to the production of fuels and important industrial chemicals that are currently mainly produced from the refinery of petroleum. The ability to control the product distribution of MTH according to the demands of specific applications is of crucial importance, which relies on the thorough understanding of the reaction pathways and mechanisms. Despite the significant research efforts devoted to zeolite-catalyzed MTH, it remains a challenge to establish a firm correlation between the physicochemical properties of zeolites and their catalytic activity and selectivity. In this dissertation, we designed a series of experiments to gain fundamental understanding of how the structural and compositional parameters of zeolites influence their catalytic performances in MTH. We investigated different types of zeolites, covering large-pore Beta, medium-pore ZSM-5, and small-pore DDR zeolites, and tune their crystallite size/diffusion length, hierarchical (mesoporous) structure, and Si/Al ratio (density of acid sites) by controlled synthesis or post-synthesis treatments. The influence of mesoporosity of a zeolite catalyst on its catalytic performance for MTH, with zeolite Beta, was first investigated. The shorter diffusion length associated with the hierarchical structure results in a lower ethylene selectivity but higher selectivity towards C4-C7 aliphatics. Then we investigated the correlation between the Al content and the ethylene selectivity by ZSM-5 zeolites with similar crystal sizes but varied Si/Al ratios. We realized that ethylene selectivity is promoted with the increase of aluminum content in the framework. These two observations can be explained by the same mechanistic reason: the ethylene selectivity is associated with the propagation degree of the aromatics catalytic cycle and essentially determined by the number of the acid sites that methylbenzenes would encounter before they exit the zeolite crystallite. Last we explored how to maximize the propylene selectivity by tuning the physicochemical properties of DDR zeolites. Due to the confined pore space in DDR, the propagation of olefins-based catalytic cycle can be preferentially promoted in a tunable manner, which cannot be realized with zeolites having larger pores. Thus, the propylene selectivity increases with increasing the Si/Al ratio and decreasing the crystallite size.
  • Urban Image Analysis with Convolutional Sparse Coding

    Affara, Lama (2018-09-18)
    Urban image analysis is one of the most important problems lying at the intersection of computer graphics and computer vision research. In addition, Convolutional Sparse Coding (CSC) is a well-established image representation model especially suited for image restoration tasks. This dissertation handles urban image analysis using an asset extraction framework, studies CSC for the reconstruction of both urban and general images using supervised data, and proposes a better computational approach to CSC. Our asset extraction framework uses object proposals which are currently used for increasing the computational efficiency of object detection. In this dissertation, we propose a novel adaptive pipeline for interleaving object proposals with object classification and use it as a formulation for asset detection. We first preprocess the images using a novel and efficient rectification technique. We then employ a particle filter approach to keep track of three priors, which guide proposed samples and get updated using classifier output. Tests performed on over 1000 urban images demonstrate that our rectification method is faster than existing methods without loss in quality, and that our interleaved proposal method outperforms current state-of-the-art. We further demonstrate that other methods can be improved by incorporating our interleaved proposals. We also extend the applicability of the CSC model by proposing a supervised approach to the problem, which aims at learning discriminative dictionaries instead of purely reconstructive ones. We incorporate a supervised regularization term into the traditional unsupervised CSC objective to encourage the final dictionary elements to be discriminative. Experimental results show that using supervised convolutional learning results in two key advantages. First, we learn more semantically relevant filters in the dictionary and second, we achieve improved image reconstruction on unseen data. We finally present two computational contributions to the state of the art in CSC. First, we significantly speed up the computation by proposing a new optimization framework that tackles the problem in the dual domain. Second, we extend the original formulation to higher dimensions in order to process a wider range of inputs, such as RGB images and videos. Our results show up to 20 times speedup compared to current state-of-the-art CSC solvers.
  • Three-dimensional Modeling and Simulation of a Tuning Fork

    Larisch, Lukas (2018-09-16)
    The mathematical characterization of the sound of a musical instrument still follows Schumann’s laws [1]. According to this theory, the resonances of the instrument body, “the formants”, filter the oscillations of the sound generator (e.g., strings) and produce the characteristic “timbre” of an instrument. This is a strong simplification of the actual situation. It applies to a point source and does not distinguish between a loudspeaker and a three-dimensional instrument. In this work we investigate Finite-Element-based numerical simulations of eigenfrequencies and eigenmodes of a tuning fork in order to capture the oscillation behavior of its eigenfrequencies. We model the tuning fork as an elastic solid body and solve an eigenvalue equation derived from a system of coupled equations from linear elasticity theory on an unstructured three-dimensional grid. The eigenvalue problem is solved using the preconditioned inverse iteration (PINVIT) method with an efficient geometric multigrid (GMG) preconditioner. The latter allows us to resolve the tuning fork with a high resolution grid, which is required to capture fine modes of the simulated eigenfrequencies. To verify our results, we compare them with measurement data obtained from an experimental modal analyses of a real reference tuning fork. It turns out that our model is sufficient to capture the first eight eigenmodes of a reference tuning fork, whose identification and reproduction by simulation is novel to the knowledge of the author.
  • Polynuclear Rare-earth (RE) based Metal-Organic Frameworks (MOFs): From Topological Exploration to Preparation of Tailor-made MOFs

    Assen, Ayalew H. (2018-09)
    Metal-organic frameworks (MOFs) have emerged as a unique class of solid-state materials, exemplifying the power of combining organic and inorganic chemistries to address the enduring challenge pertaining to designing solid state materials with desired attributes. Notably, a myriad of MOFs were constructed in the last two decades. In particular, the use of well-defined polyatomic clusters as molecular building blocks (MBBs) permitted access to the looked-for geometrical features, incorporated in preselected building units prior to the assembly process, guiding the assembly of a targeted network. Nevertheless, the diverse coordination modes and geometries of rareearth (RE) elements requires the introduction of a sophisticated controlled approach for their use as polynuclear cluster MBBs. Subsequently, our group has introduced the use of 2-fluorobenzoic acid (2-FBA) modulator that consistently allows the in situ control and formation of multi-nuclear RE MBBs. The presented work in this thesis demonstrates the use of elaborate RE MBBs and their successful deployment in reticular chemistry for the construction of particular MOF platforms expressing unique properties in term of gas separations. Accordingly, the RE hexanuclear clusters were used to construct fcu- and fluMOF platforms with controlled pore-aperture sizes. Markedly, the isolated RE-MOFs, REfum-fcu-MOF and RE-bqdc-flu-MOF, showed unprecedented paraffin/isoparaffin molecular sieving. Further tuning of the windows of RE-fcu-MOFs afforded the assembly of a MOF suitable for propylene/propane separation. The exceptional thermal and chemical stability and high adsorption selectivity of some of these MOFs prompted us to explore the fcu-MOF platform for selective removal of H2S/CO2 from CH4 and for sensing of toxic gases, namely H2S and NH3. Additionally, the research presented in this dissertation highlights the topological exploration for the formation of new MOFs: i) highly-connected polyatomic RE-MOFs in combination with tetrahedrally oriented tetracarboxylate ligands afforded the formation MOFs with new underlying topologies, namely kna-, kel- and kem-MOFs; ii) mixed-metal approach (RE plus other elements) was employed to fabricate MOFs containing in situ formed metalo-linker MBBs that are difficult to be pre-assembled by organic synthesis; iii) supermolecular building layer (SBL) approach was extended from the prevalent sql to the less explored double sql layer for the rational design of pillared MOFs.
  • Experimental study on the viscosity effects on the bubbly flow dynamics inside a large Hele-Shaw cell

    Al Brahim, Ahmed (2018-09)
    We study experimentally the gravity-driven bubbly flow inside a large Hele-Shaw cell. The bubbles and foam were created by a series of upside-down overturns of the half-filled cell about its horizontal axis. When the liquid flows down it entraps a large number of bubbles, which remain stable as the liquid contains surfactant molecules. The total number and sizes of these bubbles slowly asymptote to a steady state after dozens of overturns. It takes longer to reach this asymptote when the viscosity of the liquid is larger. The bubbles also become more monodisperse with more cell over-turns. The number and distribution of the bubbles in turn affects the average motion of the liquid phase, which is characterized by the downwards motion of the liquid center of mass. We use high-resolution 6k video-camera to track the trajectories of thousands of bubbles. This required the development of software codes to identify individual bubbles and follow them between video frames. Successful thresholding algorithm required a machine-learning component, which was integrated into the program. This program also needed to account for possible splitting or coalescence of adjacent bubbles. The program can also find the velocities along the trajectories. In this way we can find the vertical velocity of bubbles as a function of their sizes. The smaller bubbles are sometimes observed to move downwards against their buoyancy. This occurs when the viscous stress from the surrounding liquid phase overcomes the upwards buoyancy force. Bubbles with similar sizes were often found to be stacking together and having worm-like rising movement that is faster than their individual rising velocity. The occurrence of the bubble stacking was dependent on the distance between the bubbles, their sizes and their wakes. Clusters of tiny bubbles that are much smaller than the gap of the Hele-Shaw cell were observed to form layers which can severely hinder the overall liquid motion.
  • Weekly variation of viruses and heterotrophic nanoflagellates and their potential impact on bacterioplankton in a Red Sea shallow ecosystem

    Sabbagh, Eman I. (2018-09)
    Heterotrophic bacterioplankton plays a pivotal role in marine food webs and biogeochemical cycling. However, their temporal dynamics and underlying factors are still poorly understood in many regions, including the tropical waters of the Red Sea. The main goal of the MS project was to describe the seasonality and assess the impact of top-down controls (viruses and heterotrophic nanoflagellates) in parallel to bottom-up controls (substrate availability) on coastal bacterioplankton on a weekly basis. To that end, we monitored the abundance of the different planktonic groups by flow cytometry together with a set of environmental variables including temperature, salinity, dissolved organic carbon (DOC) and nitrogen (DON) and chlorophyll a concentration. We analyzed a weekly dataset collected over 2017 at the surface water of KAUST Harbor. The abundance of heterotrophic bacteria ranged from 1.55 to 4.97 x 105 cells ml-1, with that of autotrophic bacteria 4 to 14 fold less on average and presents 1 x 104 to 1.19x105 cells ml-1, while viruses ranged from 1.30 x 106 to 1.59 x 107 particles ml-1, and heterotrophic nanoflagellates (HNF) ranged from 8.62 x 10 to 1.63 x 103 cells ml-1. We distinguished between five groups of heterotrophic bacteria depending on the relative nucleic acid content, membrane state and cell-specific metabolic activity, two groups of Synechococcus, as well as three groups of viruses based on relative nucleic acid content. We found unexpected inverse relationship between viruses and HNFs. Based on a strong negative correlation, the results suggest that viruses controlled heterotrophic bacteria during summer until early winter period. HNFs showed a selective grazing behavior based their apparent preference to prey on both high (HNA) and low nucleic acid bacteria (LNA). Our results demonstrates that top-down control are key agents of heterotrophic bacterioplankton mortality and more important than bottom-up control in governing heterotrophic bacterioplankton abundances in the coastal tropical waters of the Red Sea.
  • 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.
  • Titanium Neopentyl supported on KCC-1 and Al-modified KCC-1 and its Catalytic Application for Ethylene polymerization

    Alrais, Lujain M. (2018-08)
    A new generation of Titanium based catalysts for ethylene polymerization has been developed through the Surface Organometallic Chemistry (SOMC) methodology using a novel type of silica support having a 3D fibrous morphology, KCC-1. The first type of Tibased catalyst was obtained by reacting isolated silanol surface groups, ≡SiOH of KCC-1 (dehydroxylated at 700 ⁰C under high vacuum, 10-5 bar) with titanium (IV) tetraneopentyl, Ti(CH2tBu)4 to produce [(≡SiO)Ti(CH2tBu)3]. The second type of Ti-based catalyst was generated by using an Al-modified KCC-1. The peculiarity of this support is due to the presence of tetra-coordinated aluminum-bound hydroxyl group, [(≡Si-O-Si≡)(≡SiO)2Al- OH] that can be used as a Lewis Acid anchor sites and generate new catalytic properties. The well-defined [(≡Si-O-Si≡)(≡SiO)2Al-OH] was obtained by reacting diisopropylaluminum hydride with KCC treated at 700 °C followed by a thermal treatment at 400 °C and oxidation with N2O. IR spectra of pyridine adsorbed on the Al sites show that these were strong Lewis acid sites (constituting 80% of the total Al sites). Thus, the highly electrophilic support surface was used to create a single well-defined surface organo-titanium fragment [(≡Si–O–Si≡)(≡Si–O–)2Al–O–Ti(CH2tBu)3] by the reaction of the surface [(≡Si–O–Si≡)(≡Si–O)2Al–OH]) groups with Ti(CH2-tBu)4 at room temperature for 4 h in dry pentane. The performance of each Ti-supported catalyst assessed for ethylene polymerization. It was found that Al-modified support (highly electrophilic) provide better activity compared to the unmodified one. Indeed, the productivity of the catalyst [(≡Si–O– Si≡)(≡Si–O–)2Al–O–Ti(CH2tBu)3] was found to be 67.8 g of PE/ 1mmol Ti/ 1h with molecular weight of 3208408 g/mol; polydispersity was found to be 2.3, and (HDPE) high-density polyethylene was obtained. In contrast, [(≡SiO)Ti(CH2tBu)3] (unmodified one) produces lower molecular weight polymer 989843 g/mol, higher polydispersity (PD) 6.7 and low-density polyethylene (LDPE) productivity was found to be 14.670 g PE/1mmol Ti /1h. These results demonstrate that modification of the oxide ligands on silica through a generation of Al Lewis acid site opens up new catalytic properties, markedly enhancing the catalytic performance of supported organotitanium species. We also demonstrate how the silica mesostructure (2D vs 3D ) affects the catalytic activity in ethylene polymerization. While SBA15 (2D) could limit the accessibility of the active sites resulting in lower yield. In contrast, KCC-1 (3D) are more active in ethylene polymerization, because the active sites reside on the external surface are fully accessible to the substrate.
  • Autoignition chemistry of liquid and gaseous fuels in non-premixed systems

    Alfazazi, Adamu (2018-08)
    Heat-release in CI engines occurs in the presence of concentration and temperature gradients. Recognizing the need for a validation of chemical kinetic models in transport-affected systems, this study employs non-premixed systems to better understand complex couplings between low/high temperature oxidation kinetics and diffusive transport. This dissertation is divided into two sections. In the first section, a two-stage Lagrangian model compares model prediction of ignition delay time and experimental data from the KAUST ignition quality tester, and ignition data for liquid sprays in constant volume combustion chambers. The TSL employed in this study utilizes detailed chemical kinetics while also simulating basic mixing processes. The TSL model was found to be efficient in simulating IQT in long ignition delay time fuels; it was also effective in CVCC experiments with high injection pressures, where physical processes contributed little to ignition delay time. In section two, an atmospheric pressure counterflow burner was developed and fully validated. The counterflow burner was employed to examine the effects of molecular structure on low/high temperature reactivity of various fuels in transport-affected systems. These effects were investigated through measurement of conditions of extinction and ignition of various fuel/oxidizer mixtures. Data generated were used to validate various chemical kinetic models in diffusion flames. Where necessary, suggestions were made for improving these models. For hot flames studies, tested fuels included C3-C4 alcohols and six FACE gasoline fuels. Results for alcohols indicated that the substituted alcohols were less reactive than the normal alcohols. The ignition temperature of FACE gasoline was found to be nearly identical, while there was a slight difference in their extinction limits. Predictions by Sarathy et al. (2014) alcohol combustion model, and by the gasoline surrogate model (Sarathy et al., 2015), agreed with the experimental data. For cool diffusion flames studies, tested fuels included butane isomers, naphtha, gasolines and their surrogates. Results revealed that the addition of ozone successfully established cool flames in the fuels at low and moderate strain rates. Numerical simulations were performed to replicate the extinction limits of the cool flames of butane isomers. The model captured experimental trends for both fuels; but over-predicted their extinction limits.
  • Reconfigurable Electronics Platform: Concept, Mechanics, Materials and Process

    Damdam, Asrar N. (2018-08)
    Electronic platforms that are able to re-shape and assume different geometries are attractive for the advancing biomedical technologies, where the re-shaping feature increases the adaptability and compliance of the electronic platform to the human body. In this thesis, we present a serpentine-honeycomb reconfigurable electronic platform that has the ability to reconfigure into five different geometries: quatrefoil, ellipse, diamond, star and one irregular geometry. We show the fabrication processes of the serpentine-honeycomb reconfigurable platform in a micro-scale, using amorphous silicon, and in a macro-scale using polydimethylsiloxane (PDMS). The chosen materials are biocompatible, where the silicon was selected due to its superior electrical properties while the PDMS was selected due to its unique mechanical properties. We study the tensile strain for both fabricated-versions of the design and we demonstrate their reconfiguring capabilities. The resulting reconfiguring capabilities of the serpentine-honeycomb reconfigurable platform broaden the innovation opportunity for wearable electronics, implantable electronics and soft robotics.
  • 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.
  • Experimental Investigation on The Influence of Liquid Fuels Composition on The Operational Characteristics of The Liquid Fueled Resonant Pulse Combustor

    Qatomah, Mohammad (2018-07)
    In this study, the response of a liquid-fueled resonant pulse combustor to changes in liquid fuel composition was investigated. Experiments were performed with gasoline- ethanol, gasoline-diesel, and gasoline-heptane mixtures selected to produce meaningful variations in the ignition delay time. A review of ignition quality tester (IQT) data provided an expected increase in the overall delay for gasoline-ethanol mixtures with increasing ethanol concentrations, and a decrease for gasoline-diesel mixtures with increasing diesel concentrations in the mixture. By taking the phase of the ion signal as an indicator of heat release timing, the experimental results showed an agreement of gasoline-ethanol cases with the IQT data with a near linear increase with increasing ethanol concentrations. However, for gasoline-diesel, there exit no linear relation with the IQT data. For the case of gasoline-heptane mixtures, the results showed a linear decrease in delay with increasing heptane concentrations. Furthermore, it was shown that small changes in the physical properties of the fuel can significantly in sequence the cold-start operation of the combustor and alter the coupling between the unsteady heat release and resonant acoustic pressure wave during resonant operation. Dynamic combustion chamber pressure, stagnation temperature and pressure are recorded after a fixed warm-up time to characterize the performance and operation of the device. Results are interpreted in the context of fuel sensitivity and performance optimization of a resonant pulse combustor for pressure gain turbine applications.
  • 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.
  • Investigation of the Effect of Operational Parameters on the Fouling Development and Control in an Algal Membrane Photobioreactor for the Treatment of Simulated Secondary Wastewater

    Lamprea Cala, Andres (2018-07)
    The release of water effluents rich in nutrients such as nitrogen and phosphorus without adequate treatment represents environmental and human health concerns. Growing concerns about these impacts have resulted in increasingly stringent water quality regulations that encouraged the adoption of advanced treatment processes. Microalgae-based advanced wastewater treatment has gained momentum owing to its well-known advantages for advanced wastewater treatment, including the recovering of nutrients for the production of fertilizers, biofuels and fine chemical from microalgal biomass. Nevertheless, the progressive membrane fouling and permeate flux declining hamper the large-scale commercialization of membrane photobioreactors (MPBRs) in the wastewater sector. In order to get a further understanding of the fouling mechanisms and antifouling control strategies, this study investigated the effect of the hydraulic retention time on the fouling development, and the effect of different physical fouling control strategies in the fouling mitigation. A synthetic secondary effluent was continuously fed to three MPBRs operated at different HRTs (12, 24 and 36 hours). Different fouling behaviors were found as the HRT changed, which was confirmed by continuously monitoring the transmembrane pressure (TMP) and by measurements in the biomass and its algal organic matter (AOM) properties. Lowering the HRT resulted in higher fouling rates due to changes in the biomass and AOM properties. Higher HRTs led to lower fouling rates and to a lower organic rejection across the membrane. The retention of small-MW organics in SMPBR12h was found to exacerbate the fouling resistance, whereas the accumulation of large-MW biopolymers enhanced the rejection of organics, despite of not imparting significant resistance in SMPBR24h. In order to assess the impact of different physical fouling control strategies, namely relaxation, backwash and air scouring, OCT in-situ monitoring was employed in MPBR12h to provide real-time information of the fouling layer properties (thickness and relative roughness) and its interaction with the membrane surface. Different fouling mechanisms were observed under different fouling control strategies. MPBRRLX and MPBRBW presented similar fouling rates despite of the lower permeate productivities of the latter. The lowest fouling rates were observed in MPBRSC, where stronger interactions between the membrane and small-MW organics and particles was observed.
  • Mechanism Design for Virtual Power Plant with Independent Distributed Generators

    Kulmukhanova, Alfiya (2018-07)
    We discuss a model of a virtual power plant (VPP) that provides market access to privately-owned distributed generations (DGs). The VPP serves passive loads, processes bids from generators, and trades in the wholesale market. The generators can be renewable or thermal, and they act strategically to maximize their own profit. The VPP establishes the rules of the internal market to minimize the cost of energy and the cost of balancing while ensuring generator participation and load balancing. We derive a heuristic mechanism for internal market and propose a dynamic programming approach for minimizing the VPP cost. We present illustrative simulations for both single and multistage market bidding and then compare the resulting performance to the centralized VPP model, where the DGs are assumed to be owned by the VPP. We show that the proposed design incentivizes the DG agents to behave the same as in the centralized case, but the optimal cost paid by VPP is higher due to the payments to the DG owners.
  • Indoor Localization Using Three dimensional Multi-PDs Receiver Based on RSS

    Liu, Yinghao (2018-07)
    In modern life, there are many applications where positioning plays an important role. People have developed the global positioning system (GPS) to locate world wide position with error in decameter scales, which brings people much convenience. However, the accuracy of GPS is too low for indoor localization. The signals will drop down due to the signal attenuation caused by construction materials. With the well-developed GPS being indispensable for outdoor activities, many researchers have been also devoted to seeking an indoor positioning system to realize indoor localization with acceptable error. Indoor localization can be very useful in different situations, like locating, tracking, navigation and identification. For example, in the mall, locating the exact goods for customers can provide much convenience and benefits. Locating and tracking in the airport can greatly help passengers save their time and energy in reaching the destination. In another general scenario of identification, the population of observed targets is usually larger than just one. Hence, only with small error, indoor localization system (ILS) can be able to identify the targets despite the neighbors. Due to the emerging and urging demands of increasing the accuracy of indoor localization, we propose a novel design of three dimensional (3-D). optical receiver for visible light communication (VLC) indoor positioning system. First, we model the optical wireless channel. Then we utilize modified triangulation method to obtain more robust receiver position by using at least two light-emitting diodes (LEDs) and one receiver consisting of nine photodetectors (PDs). Finally, the improved algorithm is implemented and the results are shown under our three dimensional multiple photodetectors (multi-PDs) structure receiver. In the simulation, we take the parameters of Lambertian radiation pattern, LEDs and PDs as those shown in [1] . To be noticed, our design of multi-PDs receiver is fully expanded into three dimensions compared with the pyramid receiver (PR), which allows indoor positioning with our receiver structure to be more robust to the higher or corner positions. The details will be explained in the following sections. Based on Multiple-Photodiodebased Indoor Positioning algorithm [1], the indoor positioning algorithm is improved by redefining the optimization problem of obtaining the direction from receiver to LED and using weighted triangulation method to locate receiver position. We admit the solution under the redefined problem is not optimal to the actual problem. Yet, our given solution is better to that in [1] due to the existence of noise, which is reasonable and has been verified.
  • 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.
  • Entropy Stability of Finite Difference Schemes for the Compressible Navier-Stokes Equations

    AlSayyari, Mohammed (2018-07)
    In this thesis, we study the entropy stability of the compressible Navier-Stokes model along with a modification of the model. We use the discretization of the inviscid terms with the Ismail-Roe entropy conservative flux. Then, we study entropy stability of the augmentation of viscous, heat and mass diffusion finite difference approximations to the entropy conservative flux. Additionally, we look at different choices of the diffusion coefficient that arise from combining the viscous, heat and mass diffusion terms. Lastly, we present numerical results of the discretizations comparing the effects of the viscous terms on the oscillations near the shock and show that they preserve entropy stability.

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