• NANOBOTS Smart Systems to Improve Therapeutics Delivery

      Alsaiari, Shahad (2018-10)
      With the remarkable advancement in the nanoparticles (NPs)-based drug delivery systems (DDS) over the past several decades, the pharmacological properties associated with conventional free drugs delivery are improved. In this thesis, we report potential candidates for the next-generation NP-based DDS. While natural DDS are promising as they possess exceptional delivery mechanisms and selective targeting, synthetic DDS are more favorable for their low immunogenicity. Our developed natural DDS called magnetotactic bacterial cages (MBC), which is based on magnetotactic bacteria (MTB) as a guidable delivery vehicle for DNA functionalized gold nanoparticles (AuNPs). Loading DNA functionalized AuNPs in MTB aided in increasing the maximum-tolerated dose of DNA functionalized AuNPs and tackled issues related to DNA functionalized AuNPs stability and systemic delivery. Natural DDS hold great advantages; however, it is difficult to make complete prediction about their immunogenicity and toxicity on the basis of preclinical trials. Thus, we assessed the efficacy of synthetic NP-based DDS. Using inorganic platforms, we were able to develop the first visual monitoring system of bacteria-NPs interaction. The system offers simultaneous sensing and inhibition of bacteria in infected cells. The system is comprised of Au nanoclusters @lysozyme (AuNC@lys) colloids MSN loaded with antibacterial agents. The applicability of the inorganic DDS in the biomedical field has been limited by the high bioaccumulation risks. Hybrid materials combine the advantages of organic, inorganic and natural carriers, offering opportunities for enhanced stability, manipulating release behavior and combine two or more functions in a single platform. To further enhance the properties our inorganic DDS, we incorporated light-responsive organic ligands to silicabased NPs. Plasmid DNA was loaded on the light-responsive bridged silsesquioxane nanocomposites (BS NPs). Light irradiation was performed to reverse the surface charge of NPs via a photoreaction of the organic fragments (silsesquioxane) within the NPs, that resulted in the release of plasmid DNA in HeLa cancer cells. Finally, we assessed a new class of organic-inorganic DDS composed of inorganic metal ions and organic linkers, zeolite imidazolate frameworks-8 (ZIF-8). These NPs showed exceptional ability to entrap large cargo due to their tunable porosity and structural flexibility.
    • Investigating the Role of Salinity in the Thermotolerance of Corals

      Gegner, Hagen (2018-11)
      Coral reefs are in global decline due to ocean warming and ocean acidification. While these stressors are commonly studied in climate change predictions, salinity, although being an important environmental factor, is not well understood. The response of the coral holobiont (the association of the coral host, its algal endosymbiont and a suit of other microbes) to changes in salinity and the contribution of each holobiont compartment underlying the necessary osmoadaptation remain especially elusive. Interestingly, we find some of the most thermotolerant corals in some of the most saline seas, e.g. the Red Sea and the Persian Arabian Gulf. This observation sparked the hypothesis of a link between osmoadaptation and coral thermotolerance. Here, we set out to elucidate the putative effects of high salinity on conveying thermotolerance and thereby a possible link to bleaching in the context of the coral holobiont. For this, we conducted a series of heat stress experiments at different salinities in the coral model Aiptasia and subsequently validated our findings in corals from the central Red Sea. We confirm a role of osmoadaptation in increased thermotolerance and reduced bleaching in Aiptasia and Red Sea corals. This salinity-conveyed thermotolerance was characterized by a reduction in algal endosymbiont loss, photosystem damage and leakage of damaging reactive oxygen species (ROS) in high salinity. Further analysis of the osmoadaptation response using targeted GC-MS uncovered high levels of the sugar floridoside at high salinity only in holobionts that show the salinity-conveyed thermotolerance. The increase of floridoside, an osmolyte capable of scavenging ROS, and the concurrent reduction of ROS argues for a mechanistic link of increased thermotolerance and reduced bleaching in high salinities. In addition, the restructuring of the microbiome at high salinity that aligned with the difference in thermotolerance in Aiptasia may be indicative of a microbial contribution towards a more beneficial holobiont composition. Hence, emphasizing the potential cumulative contribution of each holobiont compartment during stress-resilience, as well as highlighting the overall role of osmoadaptation in the thermotolerance of corals.
    • Towards Rational Design of Biosynthesis Pathways

      Alazmi, Meshari (2018-11-19)
      Recent advances in genome editing and metabolic engineering enabled a precise construction of de novo biosynthesis pathways for high-value natural products. One important design decision to make for the engineering of heterologous biosynthesis systems is concerned with which foreign metabolic genes to introduce into a given host organism. Although this decision must be made based on multifaceted factors, a major one is the suitability of pathways for the endogenous metabolism of a host organism, in part because the efficacy of heterologous biosynthesis is affected by competing endogenous pathways. To address this point, we developed an open-access web server called MRE (metabolic route explorer) that systematically searches for promising heterologous pathways by considering competing endogenous reactions in a given host organism. MRE utilizes reaction Gibbs free energy information. However, 25% of the reactions do not have accurate estimations or cannot be estimated. To address this issue, we developed a method called FC (fingerprint contribution) to provide a more accurate and complete estimation of the reaction free energy. To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. For a given pair of starting and desired compounds in a given chassis organism, MRE ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/. Accurate and wide-ranging prediction of thermodynamic parameters for biochemical reactions can facilitate deeper insights into the workings and the design of metabolic systems. Here, we introduce a machine learning method, referred to as fingerprint contribution (FC), with chemical fingerprint-based features for the prediction of the Gibbs free energy of biochemical reactions. From a large pool of 2D fingerprint-based features, this method systematically selects a small number of relevant ones and uses them to construct a regularized linear model. FC is freely available for download at http://sfb.kaust.edu.sa/Pages/Software.aspx.
    • Spatio-Temporal Characterization of Ligand-Receptor Interactions in Haematopoietic Stem Cell Rolling during Homing

      Al Alwan, Bader (2018-11)
      Researches on Hematopoietic Stem Cell (HSC) have been expanding that leads to an increase in our understanding of HSC normal behaviors and abnormal alterations. One of the most important issues in the research on HSCs is to understand the mechanism of the homing process of these cells to settle in their niche in the bone marrow and establish the production of various blood cell types after bone marrow transplantation. The cells first must come in contact with the endothelial cells. This contact is known as adhesion and occurs through a multi-step paradigm ending with transmigration to the bone marrow niche. The initial step of the homing, tethering and rolling of HSC, is mediated by P- and E-Selectins present on endothelial cell surface through their interactions with the ligands expressed on the surface of HSC. Thus, understanding the adhesion process and its contribution for efficient HSCs homing will have great impact on HSC therapy. The selectin – ligands interaction has been intensively studied using in vivo and in vitro approaches. However, the molecular mechanism involved by HSCs at single molecule level is poorly understood. Here in this study, a novel experimental method to unravel the molecular mechanisms of the Selectin-ligands interactions in vitro at the single molecule level is developed by combining microfluidics, epi-fluorescence microscopy and live cells. In this work, the new single-molecule imaging technique enabled us to directly visualize the nanoscale spatiotemporal dynamics of the membrane protein-ligand interactions under conditions of shear stress acting on the cells at the molecular level in real time. Using this method, we revealed that selectin ligands on membrane-tethers and slings show unique spatiotemporal dynamics that is distinct from those on the cell body. We demonstrated that the membrane tethers are formed from single microvilli on the cells, which provides a mechanism to spatially localize selectin ligands, PSGL-1 and CD44 on the tethers and slings. We also demonstrated that the selectin ligands show fast diffusional motion along the tethers and slings compared with that on the cell body due to the detachment of cell membranes from actin cytoskeleton during the formation of the tethers. Our results suggest that the spatial confinement of the selectin ligands together with the fast scanning of a large area by the selectin ligands increase the efficiency of selectin-ligands interaction during the rolling, resulting in slow and stable rolling of the cell on selectin. Our findings contribute significantly to molecular level understanding of the initial step of HSCs. This single-molecule imaging technique that we developed in this study will find wide applications in the molecular-level studies on cell-cell interactions including cancer cell metastasis.
    • Rational Design of (Reduced) Graphene Oxide Materials and Their Applications

      Alazmi, Amira (2018-11)
      The Graphene term has become synonymous with layered carbon sheets having thicknesses ranging from the monolayer to stacks of about ten layers. For bulk volume production, graphite chemical exfoliation is the preferred solution. For this reason, much interest has congregated around different processes to oxidize and peel off graphite to obtain graphene oxide (GO) and its counterpart, reduced GO (rGO). The community at-large has quickly adopted those processes and has been intensively using the resulting (r)GO as active materials for a myriad of applications. Yet, partially given the absence of comparative studies in synthesis methodologies, a lack of understanding persists on how to best tailor these carbon materials for a given application. In this dissertation, the effect of using different chemical oxidation-reduction strategies for graphite, namely the impact on the structure and chemistry of GOs and rGOs is systematically discussed. Added to this, it is demonstrated that the drying step of the powdered materials cannot be neglected. Its influence is demonstrated in studies such as the optimization of capacitance of rGOs touted as electrochemical energy storage materials (Chapter 4). It is concluded that, in order to maximize the performance of GO and rGO materials for any particular application, there must be a judicious choice of their synthesis steps. Obvious as it may be for anyone working in Chemistry, this point has been surprisingly overlooked for too long by the vast majority of those working with these carbon materials.
    • Contributions Towards Modern MIMO and Passive Radars

      Jardak, Seifallah (2018-11)
      The topic of multiple input multiple output (MIMO) radar recently gained considerable interest because it can transmit partially correlated or fully independent waveforms. The inherited waveform diversity helps MIMO radars identify more targets and adds flexibility to the beampattern design. The realized advantages come at the expense of enhanced processing requirements and increased system complexity. In this regards, a closed-form method is derived to generate practical finite-alphabet waveforms with specific correlation properties to match the desired beampattern. Next, the performance of adaptive estimation techniques is examined. Indeed, target localization or reflection coefficient estimation usually involves optimizing a given cost-function over a grid of points. The estimation performance is directly affected by the grid resolution. In this work, the cost function of Capon and amplitude and phase estimation (APES) adaptive beamformers are reformulated. The new cost functions can be evaluated using the two-dimensional fast-Fourier-transform (2D-FFT) which reduces the estimation runtime. Generalized expressions of the Cram´er-Rao lower bound are computed to assess the performance of our estimators. Afterward, a novel estimation algorithm based on the monopulse technique is proposed. In comparison with adaptive methods, monopulse requires less number of received pulses. Hence, it is widely used for fast target localization and tracking purposes. This work suggests an approach that localizes two point targets present in the hemisphere using one set of four antennas. To separate targets sharing the same elevation or azimuth angles, a second set of antennas is required. Two solutions are suggested to combine the outputs from the antenna sets and improve the overall detection performance. The last part of the dissertation focuses on the application and implementation side of radars rather than the theoretical aspects. It describes the realized hardware and software design of a compact portable 24 GHz frequency-modulated-continuous-wave (FMCW) radar. The prototype can assist the visually impaired during their outdoor journeys and prevents collisions with their surrounding environment. Moreover, the device performs diverse tasks such as range-direction mapping, velocity estimation, presence detection, and vital sign monitoring. The experimental result section demonstrates the device’s capabilities in different use-cases.
    • Robotic Manipulation and Control for Mobile Autonomous Platforms: Design and Implementation

      Shaqura, Mohammad (2018-08)
      This thesis presents contributions to applied robotic control and manipulation in the areas of motion algorithm design, hardware, and software robotic system design. Mobile robotic systems are widely used in several applications. Control of such systems poses many challenges caused by system modeling uncertainty. Complex physics phenomena and environmental effects are usually neglected to simplify analysis and control design. In motion planning, this thesis introduces an algorithm for navigation learning in mobile robots that aims to reduce the effect of modeling uncertainties on control performance. Starting from an initial feasible state and input trajectories, the objective is to reduce navigation time through iterative trials. A nominal model of the actual system and the experimental system output are used to update the control input in every iteration for incremental improvement. The navigation problem is formulated as an optimal control problem that is solved after each trial to generate a vector of input deviations for the next trial. The formulation of the approach, simulation, and experimental results shows the effectiveness of the presented method. The design part focuses on developing hardware and software systems for manipulation and aerial robots. A software tool for automated generation of multirotor simulation models is developed utilizing CAD software API and Matlab. In the area of human-robot interaction, a human-supervised UAV inspection system has been developed and tested. The UAV is guided by a human operator using a handheld laser pointing device that is designed and fabricated in-house. In the field of robotic manipulation, a novel gripper mechanism is designed and implemented. The proposed mechanism targets applications where a grasped object lies in areas with limited surrounding clearance and where external torques affect the grasped object. This design was implemented on a mobile manipulation platform and tested during an international robotics competition.
    • Full-Dimension Massive MIMO Technology for Fifth Generation Cellular Networks

      Nadeem, Qurrat-Ul-Ain (2018-11)
      Full dimension (FD) multiple-input multiple-output (MIMO) technology has recently attracted substantial research attention in the 3rd Generation Partnership Project (3GPP) as a promising technique for the next-generation of wireless communication networks. FD-MIMO scenarios utilize a planar two-dimensional (2D) active antenna system (AAS) that not only allows a large number of antenna elements to be placed within feasible base station (BS) form factors, but also provides the ability of elevation beamforming. This dissertation presents the elevation beamforming analysis for cellular networks utilizing FD massive MIMO antenna arrays. In particular, two architectures are proposed for the AAS - the uniform linear array (ULA) and the uniform circular array (UCA) of antenna ports, where each port is mapped to a group of vertically arranged antenna elements with a corresponding downtilt weight vector. To support FD-MIMO techniques, this dissertation presents two di erent 3D ray-tracing channel modeling approaches, the ITU based `antenna port approach' and the 3GPP technical report (TR) 36.873 based `antenna element approach'. The spatial correlation functions (SCF)s for both FD-MIMO arrays are characterized based on the antenna port approach. The resulting expressions depend on the underlying angular distributions and antenna patterns through the Fourier series coe cients of the power spectra and are therefore valid for any 3D propagation environment. Simulation results investigate the performance patterns of the two arrays as a function of several channel and array parameters. The SCF for the ULA of antenna ports is then characterized in terms of the downtilt weight vectors, based on the more recent antenna element approach. The derived SCFs are used to form the Rayleigh correlated 3D channel model. All these aspects are put together to provide a mathematical framework for the design of elevation beamforming schemes in single-cell and multi-cell scenarios. Finally, this dissertation proposes to use the double scattering channel to model limited scattering in realistic propagation environments and derives deterministic equivalents of the signal-to-interference-plus-noise ratio (SINR) and ergodic rate with regularized zeroforcing (RZF) precoding. The performance of a massive MIMO system is shown to be limited by the number of scatterers. To this end, this dissertation points out future research directions.
    • Modeling, Analysis, and Design of 5G Networks using Stochastic Geometry

      Ali, Konpal (2018-11)
      Improving spectral-utilization is a core focus to cater the ever-increasing demand in data rate and system capacity required for the development of 5G. This dissertation focuses on three spectrum-reuse technologies that are envisioned to play an important role in 5G networks: device-to-device (D2D), full-duplex (FD), and nonorthogonal multiple access (NOMA). D2D allows proximal user-equipments (UEs) to bypass the cellular base-station and communicate with their intended receiver directly. In underlay D2D, the D2D UEs utilize the same spectral resources as the cellular UEs. FD communication allows a transmit-receive pair to transmit simultaneously on the same frequency channel. Due to the overwhelming self-interference encountered, FD was not possible until very recently courtesy of advances in transceiver design. NOMA allows multiple receivers (transmitters) to communicate with one transmitter (receiver) in one time-frequency resource-block by multiplexing in the power domain. Successive-interference cancellation is used for NOMA decoding. Each of these techniques significantly improves spectral efficiency and consequently data rate and throughput; however, the price paid is increased interference. Since each of these technologies allow multiple transmissions within a cell on a time-frequency resource-block, they result in interference within the cell (i.e., intracell interference). Additionally, due to the increased communication, they increase network interference from outside the cell under consideration as well (i.e., increased intercell interference). Real networks are becoming very dense; as a result, the impact of intercell interference coming from the entire network is significant. As such, using models that consider a single-cell/few-cell scenarios result in misleading conclusions. Hence, accurate modeling requires considering a large network. In this context, stochastic geometry is a powerful tool for analyzing random patterns of points such as those found in wireless networks. In this dissertation, stochastic geometry is used to model and analyze the different technologies that are to be deployed in 5G networks. This gives us insight into the network performance, showing us the impacts of deploying a certain technology into real 5G networks. Additionally, it allows us to propose schemes for integrating such technologies, mode-selection, parameter-selection, and resource-allocation that enhance the parameters of interest in the network such as data rate, coverage, and secure communication.
    • Electrical Impedance Characterization for Damage Detection in Carbon Fiber-Reinforced Polymer (CFRP) Laminated Composites

      Almuhammadi, Khaled H. (2018-10)
      The use of modern carbon fiber-reinforced polymer (CFRP) composite materials is becoming increasingly widespread recently. However, the failure modes of such composite structures are extremely complex and, unlike metals, they may suffer significant degradation with barely visible surface damage. Since the damage may cause serious decrease in material strength and lead to catastrophic failure, the development of reliable structural health monitoring techniques is indispensable and has a tremendous impact on the life-cycle cost spent for inspection and repair. Such techniques that are based on the change in the electrical properties of materials are promising and viable approach for maintaining the structural integrity. They are low-cost, fast, effective, and have high potential to be applicable on real structures where they can be monitored online and real-time. The topic of this PhD dissertation is mainly focused on a number of key developments and milestones towards monitoring damage in CFRP laminated composites and making electrical-based methods practical on real structures. One of the major components of these methods is the electrode, which is the interface between the external hardware and the monitored structure. We develop a novel method for surface preparation of composite laminates for better electrode quality using pulsed laser irradiation. Further, we provide a new insight on the anisotropic behavior of the contact impedance for the electrodes on CFRP laminated composites. Another major component for achieving reliable monitoring techniques is the in-depth understanding of impedance response of these materials when subjected to an alternating electrical excitation, information that is only partially available in the literature. For more efficient electrical signal-based inspections, we investigate the electrical impedance spectroscopy response at various frequencies of laminates chosen to be representative of classical layups employed in composite structures. Finally, we use different electrodes configurations on CFRP plates applied to one side mimicking the case of real structures that is undergoing a quasi-static indentation representative of the impact load. We investigate the coupling between the electrical measurements and the type of mechanical degradation using an in-house built electro-mechanical system that measures the change in impedance and phase angle in-situ and real-time.
    • Statistical Analysis and Bayesian Methods for Fatigue Life Prediction and Inverse Problems in Linear Time Dependent PDEs with Uncertainties

      Sawlan, Zaid A (2018-11-10)
      This work employs statistical and Bayesian techniques to analyze mathematical forward models with several sources of uncertainty. The forward models usually arise from phenomenological and physical phenomena and are expressed through regression-based models or partial differential equations (PDEs) associated with uncertain parameters and input data. One of the critical challenges in real-world applications is to quantify uncertainties of the unknown parameters using observations. To this purpose, methods based on the likelihood function, and Bayesian techniques constitute the two main statistical inferential approaches considered here. Two problems are studied in this thesis. The first problem is the prediction of fatigue life of metallic specimens. The second part is related to inverse problems in linear PDEs. Both problems require the inference of unknown parameters given certain measurements. We first estimate the parameters by means of the maximum likelihood approach. Next, we seek a more comprehensive Bayesian inference using analytical asymptotic approximations or computational techniques. In the fatigue life prediction, there are several plausible probabilistic stress-lifetime (S-N) models. These models are calibrated given uniaxial fatigue experiments. To generate accurate fatigue life predictions, competing S-N models are ranked according to several classical information-based measures. A different set of predictive information criteria is then used to compare the candidate Bayesian models. Moreover, we propose a spatial stochastic model to generalize S-N models to fatigue crack initiation in general geometries. The model is based on a spatial Poisson process with an intensity function that combines the S-N curves with an averaged effective stress that is computed from the solution of the linear elasticity equations.
    • Multi-scale Inference of Lithospheric Seismic Structure in Saudi Arabia

      Tang, Zheng (2018-11)
      The complex geology of the Arabian plate together with the sparse nature of previous datasets have prevented a detailed characterization of the lithospheric structure and its spatial relationship to surface geology. With newly acquired large amount of seismic data, we investigate the crustal and upper-mantle velocity structure and develop highresolution 3-D shear-wave velocity models for Saudi Arabia using receiver functions and surface wave dispersion velocities. Our datasets, including teleseismic data for obtaining receiver functions and regional earthquake data for measuring Rayleigh-wave dispersion curves, are recorded by Saudi National Seismic Network (SNSN) stations operated by the Saudi Geological Survey (SGS). Our results reveal significant lateral variations in shearwave speeds of the crust and upper mantle, bulk Vp/Vs ratio, crustal thickness, and Lithosphere-Asthenosphere Boundary (LAB) depth beneath Saudi Arabia. Particularly, we notice interesting mantle-lid velocity and temperature patterns in which slow shearvelocities and high temperatures are observed below the southern and northern tips of the Arabian shield, compared with the values obtained for the central shield. Also, we detect high crustal bulk Vp/Vs ratios in Harrat Lunayyir and a few crustal low shear-velocity anomalies below the Cenozoic lava fields in the Arabian shield. In addition, a rather thin lithosphere and an upper-mantle low shear-velocity zone below western Arabia are imaged. We discuss our results and how they are related to previous geochemical observations, the origin of the Cenozoic volcanism, the influence of the Red Sea rift and the Afar plume on the volcanism, as well as possible plumbing system of magmas underneath western Arabia.
    • Wave-Equation Elastic Least-Squares Migration and Migration Velocity Analysis

      Feng, Zongcai (2018-11)
      This thesis develops novel wave-equation based seismic imaging and inversion methods that invert for the high- and low-wavenumber components of P- and Svelocity models. To invert for the P- and S-wave velocity perturbations (highwavenumber component), I first propose a linearized elastic waveform inversion method denoted as elastic least-squares reverse time migration (LSRTM). Elastic LSRTM solves the linearized elastic-wave equation for forward modeling and the adjoint equations for backpropagating the residual wavefield. Both synthetic- and field-data results prove that this method can accurately reconstruct the P- and S-wave velocity perturbations. Compared with the elastic reverse time migration (RTM) method, the elastic LSRTM images have fewer artifacts, higher resolution and better amplitude balancing. In addition, elastic LSRTM mitigates the coupling effect between elastic parameters, and so gives accurate relative information about the P- and S-wave velocity distributions. Elastic LSRTM method suffers from a slow convergence rate because of blurring effects and crosstalk artifacts. To mitigate these problems, I propose a multiparameter deblurring filter that approximates the multiparameter inverse Hessian. This method significantly improves the quality for multiparameter migration images. Numerical tests show that the multiparameter deblurring filter can compute elastic migration images similar in quality to the ones inverted by elastic LSRTM at a much lower cost. It can also be used as a preconditioner to accelerate the convergence rate in multiparameter inversion. In general, the proposed method can also be applied to elastic full waveform inversion (FWI) or any multiparameter migration/inversion operator. One of most crucial problems for elastic inversion is the accurate estimation of the background P- and S-wave velocity models (low-wavenumber component). To accurately estimate the velocity models, I propose a joint PP and PS wave-equation migration velocity analysis method using plane-wave common image gathers (CIGs) with depth consistency. Both the moveout residuals of CIGs and relative depth shifts between PP and PS images are transformed into weighted image perturbations for updating the velocity models. Numerical tests with synthetic and multicomponent field data demonstrate that this method can accurately invert for P- and S-wave velocity models.
    • Rare Events Simulations with Applications to the Performance Evaluation of Wireless Communication Systems

      Ben Rached, Nadhir (2018-10-08)
      The probability that a sum of random variables (RVs) exceeds (respectively falls below) a given threshold, is often encountered in the performance analysis of wireless communication systems. Generally, a closed-form expression of the sum distribution does not exist and a naive Monte Carlo (MC) simulation is computationally expensive when dealing with rare events. An alternative approach is represented by the use of variance reduction techniques, known for their efficiency in requiring less computations for achieving the same accuracy requirement. For the right-tail region, we develop a unified hazard rate twisting importance sampling (IS) technique that presents the advantage of being logarithmic efficient for arbitrary distributions under the independence assumption. A further improvement of this technique is then developed wherein the twisting is applied only to the components having more impacts on the probability of interest than others. Another challenging problem is when the components are correlated and distributed according to the Log-normal distribution. In this setting, we develop a generalized hybrid IS scheme based on a mean shifting and covariance matrix scaling techniques and we prove that the logarithmic efficiency holds again for two particular instances. We also propose two unified IS approaches to estimate the left-tail of sums of independent positive RVs. The first applies to arbitrary distributions and enjoys the logarithmic efficiency criterion, whereas the second satisfies the bounded relative error criterion under a mild assumption but is only applicable to the case of independent and identically distributed RVs. The left-tail of correlated Log-normal variates is also considered. In fact, we construct an estimator combining an existing mean shifting IS approach with a control variate technique and prove that it possess the asymptotically vanishing relative error property. A further interesting problem is the left-tail estimation of sums of ordered RVs. Two estimators are presented. The first is based on IS and achieves the bounded relative error under a mild assumption. The second is based on conditional MC approach and achieves the bounded relative error property for the Generalized Gamma case and the logarithmic efficiency for the Log-normal case.
    • How Corals Got Bones - Comparative Genomics Reveals the Evolution of Coral Calcification

      Wang, Xin (2018-09)
      Scleractinian corals represent the foundation species of one of the most diverse and productive ecosystem on earth, coral reefs. Corals not only constitute the trophic basis of these ecosystems, but also provide essential habitats and shelter for a wide variety of marine species, many of which are commercially relevant. They also provide other important ecosystem services such as food provision, shoreline protection and opportunities for ecotourism. Despite the ecological importance of corals, very little is known about how their soft-bodied ancestor evolved the ability to form a calcified skeleton and became the ecosystem builders they are today. Corallimorpharia are closely related to reef-building corals but lack the ability to form calcified skeletons. Here we assembled and annotated two draft genomes of the corallimorpharians, Amplexidiscus fenestrafer and Discosoma sp., and further provided an online interface to facilitate the use of these resources. The two genomes can not only inform on the current evolutionary gap in genomic resources for the subclass of Hexacorallia but also provide important resources for comparative genomic studies aiming at understanding the evolution of coral specific traits. Our broad phylogenomic approach using whole genome data, including phylogenetic analyses of nuclear encoding genes as well as genome-wide presence/absence information and synteny conservation from six hexacorallian species, provides robust evidence that corallimorpharians are a monophyletic sister group of scleractinians, therefore rejecting the “naked coral” hypothesis. Being the closest non-calcifying relative of scleractinian corals, corallimorpharians appear to be the best candidates to understand the evolutionary origin of coral calcification. Molecular divergence analysis of scleractinian coral and Corallimorpharia genes suggests that the soft-bodied ancestor of corals evolved the ability to calcify within approximately 80 million years after the divergence of these two orders. To uncover the molecular basis of coral skeletal formation and growth, we integrate genomic and transcriptomic data as well as skeletal proteomic data, and show that gene and domain duplications have been the main evolutionary mechanisms underlying the evolution of calcification in scleractinian corals.
    • Mid-IR Laser Absorption Diagnostics for Shock Tube and Rapid Compression Machine Experiments

      Nasir, Ehson Fawad (2018-10)
      High-fidelity chemical kinetic models for low-temperature combustion processes require high-fidelity data from fundamental experiments conducted in idealized transient reactors, such as shock tubes and rapid compression machines (RCM). Non-intrusive laser absorption diagnostics, in particular quantum cascade lasers (QCL) in the mid-infrared wavelength region, provide a unique opportunity to obtain quantitative, time-resolved species concentration and temperature from these reactive systems. In this work, three novel laser absorption diagnostics in the mid-infrared wavelength region are presented for three different experimental applications. The first diagnostic was developed for measuring CO2 concentration using an external cavity QCL centered in the ν3 fundamental vibrational band of CO2. Absorption cross-sections were measured in a shock tube, at a fixed wavelength for the R(32) line centered at 2371.42 cm-1 (4.217 µm) over 700 – 2900 K and nominal pressures of 1, 5 and 10 bar. The diagnostic was used to measure rate coefficients for the reaction between carbon monoxide and hydroxyl radical over 700 – 1230 K and 1.2 – 9.8 bar using highly dilute mixtures. The second diagnostic was developed for measuring CO concentration using a pulsed QCL centered at 2046.28 cm-1 (4.887 µm) and an off-axis cavity implemented on the RCM. The duty cycle and pulse repetition rate of the laser were optimized for increased tuning range, high chirp rate and increased line-width to achieve effective laser-cavity coupling. A gain factor of 133 and time resolution of 10 μs were demonstrated. CO concentration-time profiles during the oxidation of highly dilute n-heptane/air mixtures were recorded and compared with chemical kinetic models. This represents the first application of a cavity-enhanced absorption diagnostic in an RCM. Finally, a calibration-free temperature diagnostic based on a pair of pulsed QCLs centered at 2196.66 cm-1 and 2046.28 cm-1 was implemented on the RCM. The down-chirp phenomenon resulted in large spectral tuning (∆v ~ 2.8 cm-1) within a single pulse of each laser at a high pulse repetition frequency (100 kHz). The diagnostic for was used to measure the temperature rise during first-stage ignition of n-pentane at nominal pressures of 10 and 15 bar for the first time.
    • 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.
    • 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.
    • 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.
    • 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.