• Structural and Dynamic Profiles of the WT hFEN1 in solution

      Almulhim, Fatimah F. (2020-06) [Thesis]
      Advisor: Jaremko, Mariusz
      Committee members: Falqui, Andrea; Saikaly, Pascal
      Genomic DNA is under constant assault by environmental factors that introduce a variety of DNA lesions. Cells evolved several DNA repair and recombination mechanisms to remove these damages and ensure the integrity of the DNA material. A variety of specific proteins, called nucleases, processes toxic DNA structures that deviate from the heritable duplex DNA as common pathway intermediates. DNA-induced protein ordering is a common feature in all DNA repair nucleases. Still, the conformational requirement of the DNA and the protein and how they control the catalytic selectivity of the nuclease remain largely unknown. This study focus on the bases of catalytic activity of a protein belongs to the 5’ nuclease super-family called the human Flap endonuclease 1 (FEN1); it removes excess 5’ flaps that are generated during DNA replication. hFEN1 mutations and over-expression had been linked to a variety of cancers. This thesis aims to study the structural and dynamic properties of free hFEN1 and the catalytic activity of DNA-bound hFEN1 in solution utilizing the modern high-resolution multidimensional Nuclear Magnetic Resonance (NMR) spectroscopy. It was possible to depict the secondary structure and backbone conformation in solution of wild type (WT) hFEN1 by the usage of the improved list of assigned resonances, derived from the NMR 2D and 3D ¹⁵N-detected experiments and compared to the assignment with the previously published resonance assignment (BMRB id: 27160). I was successfully assigned the new spectrum and enhanced it by assigning seven more residues. Moreover, we tested the interaction of 1:10 ratio of hFEN1-Ca2+ with DNA by the ¹³C-detected 2D CACO experiment. The results indicate hFEN1:DNA interaction. Furthermore, parts of hFEN1 get more ordered/structured once DNA appears, thus we recorded the protein flexibly by 2D ¹H-¹⁵N TROSY-HSQC using the relaxation rate parameters: longitudinal R1, transverse R2 complemented with ¹⁵N-{¹H} NOEs (heteronuclear Overhauser enhancement). It was found that the overall molecular architecture is rigid, and the highest flexibility lies in the α2-α3 loop and arch (α4-α5) regions. Further analysis is needed to understand more profoundly the activity of hFEN1 in an atomic level by inducing mutations and testing the protein in various environmental conditions.
    • An Experimental and Theoretical Investigation of Pressure-Induced Wetting Transitions

      Ahmad, Zain (2020-05) [Thesis]
      Advisor: Mishra, Himanshu
      Committee members: Nunes, Suzana; Farooq, Aamir; Ghaffour, Noreddine
      A number of industries suffer from inefficient use of energy resources due to frictional drag manifesting at solid-liquid interfaces. A simple method to reduce frictional drag under laminar flow conditions is to entrap air at the liquid-solid interface – in wetting state known as Cassie state. Over time, however, the entrapped air can be lost, and the Cassie state transitions to the fully-filled or the Wenzel state, thereby increasing the frictional drag dramatically. In particular, many practical applications expose surfaces to elevated pressures, and it is thus crucial to investigate pressure-induced Cassie-to-Wenzel transitions in gas-entrapping microtextured surfaces. However, there is a dearth of experimental techniques that can provide high-resolution optical images during wetting transitions at elevated pressures. In this thesis, we address this challenge designing and developing an inexpensive and robust pressure device that can act as an accessory for confocal laser scanning microscopy (CLSM). Equipped with this platform, we set out to visualize Cassie-to-Wenzel transitions in FDTS-coated circular doubly reentrant cavities (DRCs) and simple cavities. We demonstrate that on immersion in water, DRCs stabilize water-air interface, such that on the application of the external pressure as water penetrates into the DRCs, the liquid meniscus at the inlet remains pinned. In stark contrast, in SCs the water meniscus does not get pinned at the inlet, and it keeps on advancing with the increasing pressure along the cavity walls. Since localized laser heating in CLSM can influence wetting transitions, we utilized another custom-built pressure cell connected with upright optical microscopy as a complementary platform. We investigated the following wetting transitions: (i) breakthrough pressures (BtPs), defined as the pressure at which the liquid-vapor meniscus touches the cavity floor, by gradually ramping the external pressure, and (ii) wetting transitions at fixed pressures below the BtP. To understand the physical mechanisms underlying our experimental results, we utilized the Fick’s diffusion model and found that the consideration of air diffusion into water under elevated pressures is crucial. To conclude, we hope that the experimental and theoretical results presented here would advance the rational development of robust gas-entrapping microtextured surfaces for a myriad of applications
    • Conservation and Regulation of the Essential Epigenetic Regulator UHRF1 Across Vertebrata Orthologs

      Aljahani, Abrar (2020-05) [Thesis]
      Advisor: Fischle, Wolfgang
      Committee members: Arold, Stefan T.; Aranda, Manuel
      UHRF1 is a critical epigenetic regulator which serves as a molecular model for understanding the crosstalk between histone modification and DNA methylation. It is integrated in the process of DNA maintenance methylation through its histone ubiquitylation activity, ultimately functioning as a recruiter of DNA methyltransferase 1 (DNMT1). As the faithful propagation of DNA methylation patterns during cell division is a common molecular phenomenon among vertebrates, understanding the underlying conserved mechanism of UHRF1 for executing such a key process is important. Here, I present a broad-range evolutionary comparison of UHRF1 binding behavior and enzymatic activity of six species spanning across the vertebrata subphylum. According to their distinct binding modes to differentially methylated histone H3, a pattern is emerging which separates between mammalian and nonmammalian orthologs. H. sapiens, P. troglodytes and M. musculus UHRF1 orthologs utilize the functionality of both TTD and PHD domains to interact with histone H3 peptides, while G. gallus, X. laevis, and D. rerio employ either TTD or PHD. Further, UHRF1 allosteric regulation by 16:0 PI5P is a unique case to primate orthologs where H3K9me3 peptide binding is enhanced upon hUHRF1 and pUHRF1 interacting with 16:0 PI5P. This is due to their closed and autoinhibited conformation wherein TTD is blocked by the PBR region in linker 4. 16:0 PI5P outcompetes TTD for PBR binding resulting in a release of TTD blockage, hence, enhanced H3K9me3 binding. However, owing to the lack of phosphatidylinositol binding specificity and reduced sequence conservation of linker 4, the regulatory impact of 16:0 PI5P in avian and lower vertebrate orthologs could not be detected. Additionally, all UHRF1 orthologs exert their ubiquitylation enzymatic activity on histone H3 substrates, supporting the notion that the overall functionality of UHRF1 orthologs is conserved, despite their divergent molecular approaches. Taken together, my findings suggest that UHRF1 orthologs adopt distinct conformational states with a differential response to the allosteric regulators 16:0 PI5P and hemi-methylated DNA.
    • Assessing sharks and rays in shallow coastal habitats using baited underwater video and aerial surveys in the Red Sea

      Mcivor, Ashlie (2020-05) [Thesis]
      Advisor: Berumen, Michael Lee
      Committee members: Jones, Burton; Coker, Darren; Spaet , Julia
      Years of unregulated fishing activity have resulted in low abundances of elasmobranch species in the Saudi Arabian Red Sea. Coastal populations of sharks and rays in the region remain largely understudied and may be at risk from large-scale coastal development projects. Here we aim to address this pressing need for information by using fish market, unmanned aerial vehicle and baited remote underwater video surveys to quantify the abundance and diversity of sharks and rays in coastal habitats in the Saudi Arabian central Red Sea. Our analysis showed that the majority of observed individuals were batoids, specifically blue-spotted ribbontail stingrays (Taeniura lymma) and reticulate whiprays (Himantura sp.). Aerial surveys observed a catch per unit effort two orders of magnitude greater than underwater video surveys, yet did not detect any shark species. In contrast, baited camera surveys observed both lemon sharks (Negaprion acutidens) and tawny nurse sharks (Nebrius ferrugineus), but in very low quantities (one individual of each species). The combination of survey techniques revealed a higher diversity of elasmobranch presence than using either method alone, however many species of elasmobranch known to exist in the Red Sea were not detected. Our results suggest that aerial surveys are a more accurate tool for elasmobranch abundance estimates in low densities over mangrove-associated habitats. The importance of inshore habitats, particularly for batoids, calls for a deeper understanding of habitat use in order to protect these environments in the face of unregulated fishing, mangrove removal, and anticipated developments along the coastline of the Saudi Arabian Red Sea.
    • A Computational Study of Ammonia Combustion

      Khamedov, Ruslan (2020-05) [Thesis]
      Advisor: Im, Hong G.
      Committee members: Roberts, William Lafayette; Knio, Omar; Parsani, Matteo
      The utilization of ammonia as a fuel is a pragmatic approach to pave the way towards a low-carbon economy. Ammonia compromises almost 18 % of hydrogen by mass and accepted as one of the hydrogen combustion enablers with existing infrastructure for transportation and storage. From an environmental and sustainability standpoint, ammonia combustion is an attractive energy source with zero carbon dioxide emissions. However, from a practical point of view, the direct combustion of ammonia is not feasible due to the low reactive nature of ammonia. Due to the low combustion intensity, and the higher nitrogen oxide emission, ammonia was not fully investigated and there is still a lack of fundamental knowledge of ammonia combustion. In this thesis, the computational study of ammonia premixed flame characteristics under various hydrogen addition ratios and moderate or intense low oxygen dilution (MILD) conditions were investigated. Particularly, the heat release characteristics and dominant reaction pathways were analyzed. The analysis revealed that the peak of heat release for ammonia flame occurs near burned gas, which raises a question regarding the physics of this. Further analysis identified the dominant reaction pathways and the intermediate species (NH2 and OH), which are mainly produced in the downstream and back diffused to the leading edge and produce some heat in the low-temperature zone. To overcome low reactivity and poor combustion performance of pure ammonia mixture, the onboard ammonia decomposition to hydrogen and nitrogen followed by blending ammonia with hydrogen is a feasible approach to improve ammonia combustion intensity. With increasing hydrogen amount in the mixture, the enhancement of heat release occurs due to both transport and chemical effect of hydrogen. Another approach to mitigate the low reactive nature of ammonia may be eliminated by applying the promising combustion concept known as MILD combustion. The heat release characteristics and flame marker of ammonia turbulent premixed MILD combustion were investigated. The high fidelity numerical simulation was performed to answer fundamental questions of ammonia turbulent premixed combustion characteristics.
    • SeedQuant: A Deep Learning-based Census Tool for Seed Germination of Root Parasitic Plants

      Ramazanova, Merey (2020-04-30) [Thesis]
      Advisor: Ghanem,Bernard
      Committee members: Wonka, Peter; Thabet, Ali Kassem
      Witchweeds and broomrapes are root parasitic weeds that represent one of the main threats to global food security. By drastically reducing host crops' yield, the parasites are often responsible for enormous economic losses estimated in billions of dollars annually. Parasitic plants rely on a chemical cue in the rhizosphere, indicating the presence of a host plant in proximity. Using this host dependency, research in parasitic plants focuses on understanding the necessary triggers for parasitic seeds germination, to either reduce their germination in presence of crops or provoke germination without hosts (i.e. suicidal germination). For this purpose, a number of synthetic analogs and inhibitors have been developed and their biological activities studied on parasitic plants around the world using various protocols. Current studies are using germination-based bioassays, where pre-conditioned parasitic seeds are placed in the presence of a chemical or plant root exudates, from which the germination ratio is assessed. Although these protocols are very sensitive at the chemical level, the germination rate recording is time consuming, represents a challenging task for researchers, and could easily be sped up leveraging automated seeds detection algorithms. In order to accelerate such protocols, we propose an automatic seed censing tool using computer vision latest development. We use a deep learning approach for object detection with the algorithm Faster R-CNN to count and discriminate germinated from non-germinated seeds. Our method has shown an accuracy of 95% in counting seeds on completely new images, and reduces the counting time by a signi cant margin, from 5 min to a fraction of second per image. We believe our proposed software \SeedQuant" will be of great help for lab bioassays to perform large scale chemicals screening for parasitic seeds applications.
    • Evaluating the Application of Allele Frequency in the Saudi Population Variant Detection

      Alsaedi, Sakhaa (2020-04-26) [Thesis]
      Advisor: Hoehndorf, Robert
      Committee members: Gao, Xin; Gojobori, Takashi
      Human Mendelian disease in Saudi Arabia is both significant and challenging. Next-generation sequencing (NGS) has resulted in important discoveries of the genetic variants responsible for inherited disease. However, the success of clinical genomics using NGS requires accurate and consistent identification of rare genome variants. Rarity is one very important criterion for pathogenicity. Here we describe a model to detect variants by analyzing allele frequencies of a Saudi population. This work will enhance the opportunity to improve variant calling workflow to gain robust frequency estimates in order to better detect rare and unusual variants which are frequently associated with inherited disease.
    • Applications of Graph Convolutional Networks and DeepGNC's in Point Cloud Part Segmentation and Upsampling

      Abualshour, Abdulellah (2020-04-18) [Thesis]
      Advisor: Ghanem,Bernard
      Committee members: Hadwiger, Markus; Wonka, Peter
      Graph convolutional networks (GCNs) showed promising results in learning from point cloud data. Applications of GCNs include point cloud classi cation, point cloud segmentation, point cloud upsampling, and more. Recently, the introduction of Deep Graph Convolutional Networks (DeepGCNs) allowed GCNs to go deeper, and thus resulted in better graph learning while avoiding the vanishing gradient problem in GCNs. By adapting impactful methods from convolutional neural networks (CNNs) such as residual connections, dense connections, and dilated convolutions, DeepGCNs allowed GCNs to learn better from non-Euclidean data. In addition, deep learning methods proved very e ective in the task of point cloud upsampling. Unlike traditional optimization-based methods, deep learning-based methods to point cloud upsampling does not rely on priors nor hand-crafted features to learn how to upsample point clouds. In this thesis, I discuss the impact and show the performance results of DeepGCNs in the task of point cloud part segmentation on PartNet dataset. I also illustrate the signi cance of using GCNs as upsampling modules in the task of point cloud upsampling by introducing two novel upsampling modules: Multi-branch GCN and Clone GCN. I show quantitatively and qualitatively the performance results of our novel and versatile upsampling modules when evaluated on a new proposed standardized dataset: PU600, which is the largest and most diverse point cloud upsampling dataset currently in the literature.
    • Image Embedding into Generative Adversarial Networks

      Abdal, Rameen (2020-04-14) [Thesis]
      Advisor: Wonka, Peter
      Committee members: Hadwiger, Markus; Ghanem, Bernard
      We propose an e cient algorithm to embed a given image into the latent space of StyleGAN. This embedding enables semantic image editing operations that can be applied to existing photographs. Taking the StyleGAN trained on the FFHQ dataset as an example, we show results for image morphing, style transfer, and expression transfer. Studying the results of the embedding algorithm provides valuable insights into the structure of the StyleGAN latent space. We propose a set of experiments to test what class of images can be embedded, how they are embedded, what latent space is suitable for embedding, and if the embedding is semantically meaningful.
    • Crosstalk Cancellation in Structured Light Free Space Optical Communication

      Briantcev, Dmitrii (2020-04) [Thesis]
      Advisor: Alouini, Mohamed-Slim
      Committee members: Ooi, Boon S.; Park, Ki-Hong
      Free-space optics (FSO) is an unlicensed communication technology that uses the free space as a propagation medium to connect two communicating terminal wire- lessly [1]. It is an attractive solution to the last-mile connectivity problems in commu- nication networks, mainly when installing optical fibers is expensive or unavailable. A possible idea to increase the throughput of wireless optical links in free space is to use spatial multiplexing (SMM) [2]. Optical beam distortion due to propagation through a turbulent channel is one of the main factors limiting performance of such a system. Therefore, overcoming the effect of turbulence is a major problem for structured light optical communication in free space. Usually, this problem is approached by using adaptive optics systems and various methods of digital signal processing (DSP) on the receiver side [3–5]. Recently, an idea of optical channel pre-compensation to mit- igate inter-modal crosstalk was proposed [6] and experimentally validated [7]. Such a method, if implemented, will allow the use of entirely passive receivers or, in the case of full-duplex transmission, increase throughput. Here, the performance of a zero-forcing precoding technique to mitigate the effects of an optical turbulence in a Laguerre Gaussian mode based SMM FSO is investigated. Equally, details on a close to reality simulation of the atmospheric turbulence and beam propagation are provided.
    • Modeling and Assessment of Dynamic Charging for Electric Vehicles in Metropolitan Cities

      Nguyen, Duc Minh (2020-04) [Thesis]
      Advisor: Alouini, Mohamed-Slim
      Committee members: Shihada, Basem; Amin, Osama
      Electric vehicles (EVs) have emerged to be the future of transportation as the world observes its rising demand and usage across continents. However, currently, one of the biggest bottlenecks of EVs is the battery. Small batteries limit the EVs driving range, while big batteries are expensive and not environmentally friendly. One potential solution to this challenge is the deployment of charging roads, i.e., dynamic wireless charging systems installed under the roads that enable EVs to be charged while driving. In this thesis, we establish a framework using stochastic geometry to study the performance of deploying charging roads in metropolitan cities. We first present the course of actions that a driver may take when driving from a random source to a random destination, and then analyze the distribution of the distance to the nearest charging road and the probability that the trip passes through at least one charging road. These probability distributions assist not only urban planners and policy makers in designing deployment plans of dynamic wireless charging systems, but also drivers and automobile manufacturers in choosing the best driving routes given the road conditions and level of energy of EVs.
    • Contributions to the semi-classical signal analysis method: The arterial stiffness assessment case study

      Piliouras, Evangelos (2020-04) [Thesis]
      Advisor: Laleg-Kirati, Taous-Meriem
      Committee members: Feron, Eric; De Wolf, Stefaan; Al Attar, Talal
      Semi-classical signal analysis (SCSA) is a signal representation framework based on quantum mechanics principles and the inverse scattering transform. The signal of interest is decom- posed in a linear combination of the Schrodinger operator squared eigenfunctions, influenced by the semi-classical parameter. The framework has been utilized in several applications, in virtue of the adaptivity and localization of its components. In this thesis, we expand two direc- tions. From the theoretical perspective, up to date, the semi-classical parameter was selected in an error minimization context or a representation sparsity requirement. The framework is reinforced by providing the interval of this parameter, where a proper representation can be obtained. The lower bound is inspired by the semi-classical approximation and the sampling theorem, while the upper bound is based on the quantum perturbation theory. Such an interval defines the sampling theorem of the framework. Based on existing properties, we propose a non-uniform sampling of the semi-classical parameter, which can significantly increase the speed of convergence with minimal accuracy error. An immediate representation is also in- vestigated by providing an alternative convergence criterion drawn from signal features. Such criterion paves the way to a calculus-based parameter definition and extension to a filtering scenario. The semi-classical parameter exerts a strong influence on the SCSA components. Each component can be viewed as a soliton, a wave whose amplitude determines its width and velocity. In parallel, there exist arterial dynamics models where the solitons are solu- tions of the describing equations. We therefore propose that the soliton propagation velocity extracted from the algorithm is correlated with the pulse wave velocity, which is the blood pressure propagation velocity in the systolic phase. The velocity in the carotid-femoral seg- ment is considered the golden-standard to indicate cardiovascular risk. We therefore turn our attention to validate such a model and utilize it for arterial stiffness assessment. The model was validated based on an in-silico database fostering more than 3000 subjects. This SCSA-based model is proposed to be integrated into existing methods, where its calibration can yield single-point continuous velocity measurements.
    • INDEX MODULATION USING RECONFIGURABLE ARRAYS

      Celis Sierra, Sebastian (2020-04) [Thesis]
      Advisor: Salama, Khaled N.
      Committee members: Bagci, Hakan; Shihada, Basem
      Communication systems have remained almost unchanged since the invention of the superheterodyne receiver in 1918 by the US engineer Edwin Armstrong. With the introduction of multiple-input-multiple-output (MIMO) technologies, Index Modulation appears to be the promising technology to revolutionize the traditional radio-frequency (RF) chain. Index modulation is a high-spectrum, energy-efficient, simple digital communication technique that uses the states of the building blocks of a communication system. In this study, we have focused on the use of radiation patterns scattered by antenna arrays or a metasurface as indices that are encoded as data bits. Initially, we explore sets of 𝑁tx transmitting point source antennas located on the XY plane; we assume that every antenna has phase tunability capability. The phase, the position in space, and the size of the array determine the shape of the far-field radiation pattern. Following the antenna excitation, a set of 𝑁rx receiver antennas spread at specific locations of the spherical space measures the incoming power signal, allowing the sampling of the radiation pattern that is demodulated into information bits.This work is focused on the characterization of the measured radiation patterns under different system and channel variables and their direct effect on the Bit Error Rate.
    • A First Principle Investigation of Band Alignment in Emerging III-Nitride Semiconductors

      Al Sulami, Ahmad (2020-04) [Thesis]
      Advisor: Li, Xiaohang
      Committee members: Salama, Khaled N.; Schwingenschoegl, Udo
      For more than seventy years, semiconductor devices have functioned as the cornerstone for technological advancement, and as the defining transition into the information age. The III-Nitride family of semiconductors, in particular, underwent an impressive maturation over the past thirty years, which allowed for efficient light- emitting devices, photo-detectors, and power electronic devices. As researchers try to push the limits of semiconductor devices, and in particular, as they aim to design ultraviolet light emitters and high threshold power devices, the search for new materials with high band gaps, high breakdown voltages, unique optical properties, and variable lattice parameters is becoming a priority. Two interesting candidates that can help in achieving the aforementioned goals are the wurtzite BAlN and BGaN alloy systems, which are currently understudied due to difficulties associated with their growth in epitaxial settings. In our research, we will investigate the band alignment between BAlN and BGaN alloys, and other wurtzite III-Nitride semiconductors from first principle simulations. Through an understanding of band alignment types and a quantification of the band offset values, researchers will be able to foresee the applicability of a particular interface. As an example, a type-I band alignment with a high conduction band offset and a low valence band offset is a potential electron blocking layer to be implemented in standard LED designs. This first principle investigation will be aided by simulations using Density Functional Theory (DFT) as implemented in the Vienna Ab Initio Simulation Package (VASP) environment. In addition, we will detail an experiment from the literature that uses X- ray Photoelectron Spectroscopy on multiple samples to infer and quantify the band alignment between different materials of interest to us. We aim in this study to anticipate the band alignment in interfaces involving materials at the cutting edge of research. Our hope is to set a theoretical ground for future experimental studies on this same matter in parallel to the current efforts to improve the quality and stability of wurtzite BAlN and BGaN alloy crystals.
    • Asymptotic Sum Rate Analysis Over Double Scattering Channels With MMSE Estimation and MRT Precoding

      Ye, Jia (2020-04) [Thesis]
      Advisor: Alouini, Mohamed-Slim
      Committee members: Alouini, Mohamed-Slim; Ooi, Boon S.; Kammoun, Abla
      This thesis investigates the performance of a multi-user multiple-input single- output (MISO) system considering maximum ratio transmission (MRT) downlink precoding. The transmitted signal from the base station (BS) to each user is as- sumed to experience the double scattering channel. We adopt the minimum-mean- square-error (MMSE) channel estimator for the proposed model. Within this setting, we are interested in deriving tight approximations of the ergodic rate assuming the number of BS antennas, users, and scatterers grow large with the same pace. Under the special multi-keyhole channels, these deterministic equivalents are expressed in more simplified closed-form expressions. The simplified expressions reveal that unlike the standard Rayleigh channel in which the SINR grows as as O(N/k), the SINR associated with a multi-keyhole channel scales as O(S/N). This particularly shows that the K reaped gains of the large-scale MIMO over double scattering channels do not linearly increase with the number of antennas and are limited by the number of scatterers. We further show that the derived asymptotic results match the simulation results closely under moderate system dimensions and provide some useful insights into the interplay between N, K and S.
    • Exploring the Role of Glutamate Signaling in the Regulation of the Aiptasia-Symbiodiniaceae Symbiosis

      Konciute, Migle (2020-04) [Thesis]
      Advisor: Aranda, Manuel
      Committee members: Lauersen, Kyle J.; Morán, Xosé Anxelu G.
      The symbiotic relationship between cnidarians and their photosynthetic dinoflagellate symbionts underpins the success of coral reef communities in oligotrophic, tropical seas. Despite several decades of study, the cellular and molecular mechanisms that regulate the symbiotic relationship between the dinoflagellate algae and the coral hosts are still not clear. One of the hypotheses on the metabolic interactions between the host and the symbiont suggests that ammonium assimilation by the host can be the underlying mechanism of this endosymbiosis regulation. An essential intermediate of the ammonium assimilation pathway is glutamate, which is also known for its glutamatergic signaling function. Interestingly, recent transcriptomic level and DNA methylation studies on sea anemone Aiptasia showed differences in metabotropic glutamate signaling components when comparing symbiotic and non-symbiotic animals. The changes in this process on transcriptional and epigenetic levels indicate the importance of glutamate signaling in regard to cnidarian symbiosis. In this study, I tested glutamatergic signaling effect on symbiosis in sea anemone Aiptasia using a broad-spectrum glutamate receptor inhibitor 7- CKA and glutamate. Significantly decreased cell density was observed in animals with inhibitor treatment suggesting a possible correlation between glutamate signaling and the establishment or maintenance of symbiosis. Using RNA-Seq, I was able to obtain transcriptional profiles of the animals under inhibitor and glutamate treatment. Differential gene expression and gene ontology analyses indicated changes in amino acid metabolism, lipid metabolism and such signaling pathways as MAPK, NF-kappa B and phospholipase C. Although amino acid and lipid metabolism could be a result of the reduced symbiotic state of inhibitor treated Aiptasia, the signaling pathways which are related to apoptosis and immune response provide an exciting venue for direct regulatory interaction between symbiosis and glutamatergic signaling. However, as these signaling pathways mainly act via signal transduction through protein phosphorylation, further studies looking at changes on a post-translational level might provide further insight into the mechanisms underlying the observed phenotype.
    • Impedimetric Plant Biosensor Based on Minimally Invasive and Compliant Microneedle Electrodes

      Bu Khamsin, Abdullah (2020-04) [Thesis]
      Advisor: Kosel, Jürgen
      Committee members: Kosel, Jürgen; Salama, Khaled N.; Blilou, Ikram
      There is a rising need for inline sensors for continuous and non-destructive monitoring of crops status. As growth in agricultural productivity stagnates, farmers are increasingly adopting soil-implanted sensors that allow them to optimize their yields. In existing literature, plant bio-impedance has been shown to change accordingly with various biotic and abiotic stress factors, and thereby may constitute a marker of interest. Yet, to date, there is no widespread adoption of bio-impedance for plant health monitoring due to the low sensitivity of planar electrodes. This thesis is dedicated to the development of a plant impedimetric biosensor that utilizes micro-needles electrodes for enhanced sensitivity. The micro-needles have been designed to pierce the upper waxy layer (cuticle) of plants to measure impedance from the underlying layers. Moreover, a micromolding process has been utilized to fabricate the micro-needles at scale without sacrificing fidelity. The molds were fabricated using dip-in laser lithography to benefit from the high resolution and flexibility of the technique. Standard metal sputtering processes were then used to confer conductivity onto the micro-needles. Several micro-needle aspect ratios and geometries were explored and adapted for use on Barley (Hordeum vulgare L,) and Date Palm (Phoenix dactylifera). In order to assess the performance of the sensors, the impedance of several plant specimens was monitored using the developed sensors alongside planar electrodes. The impedance measured by the sensors was lower than that reported by planar electrodes at low frequencies, indicating successful bypassing of the cuticle, as desired. No adverse effects were observed on the plant tissue post micro-needle attachment for seven days. Furthermore, a cyclical diurnal pattern of impedance was observed in both plants that was entrained by light. Finally, the micromolding technique developed in this thesis can help produce high- fidelity 3D electrodes for bio-impedance monitoring. Once the mold is fabricated, the electrodes can be produced at scale without the need of clean-room equipment. Furthermore, the fabricated sensors can monitor bio-impedance of plant specimens for extended durations of time and may offer a platform that can be functionalized to selectively quantify specific phytohormones of interest.
    • Optimal Control Strategies for the Alignment Problem of Optical Communication Systems

      Cai, Wenqi (2020-04) [Thesis]
      Advisor: Laleg, Taous-Meriem
      Committee members: Laleg, Taous-Meriem; Ooi, Boon S.; Feron, Eric
      In this work, we propose three control strategies from different perspectives to solve the alignment problem for different optical wireless communication (OWC) systems. • Experimental modeling based strategy: we model and analyze the vibration effects on the stationary OWC system (e.g. urban free-space optical (FSO) communication system in our case). The proposed Bifurcated-Gaussian (B-G) distribution model of the receiver optical power is derived under different vibra- tion levels and link distances using the nonlinear iteration method. Besides, the UFSO channel under the effects of both vibration and atmospheric turbulence is also explored under three atmospheric turbulence conditions. Our proposed B-G distribution model helps to easily evaluate the link performance of UFSO systems and paves the way for constructing completed auxiliary control subsys- tems for robust UFSO links. • Extremum seeking control based strategy: we propose an extremum seeking control (ESC) based strategy for the mobile OWC system. Our proposed ap- proach consists of coarse alignment and fine alignment. The coarse alignment using feedback proportional-derivative (PD) control is responsible for tracking and following the receiver. For fine alignment, the perturbation-based extremum seeking control (ESC) is adopted for a continuous search for the optimal posi- tion, where the received optical power is maximum in the presence of distur- bance. The proposed approach is simple, effective, and easy to implement. • Time scale theory based strategy: we design a time scale based Kalman filter for the intermittent OWC system. First, the algorithm of Kalman filter on time scales is presented, followed by several numerical examples for interpretation and analysis. The design of Kalman filter on time scales for our simulated vibrating OWC system is then discussed, whose results are analyzed thoroughly and further validated by a reference system. The proposed strategy has great potential for solving the problem of observer design in the case of intermittent received signals (non-uniform measurements) and paves the way for further controller design. The three proposed control strategies directly or indirectly solve the beam align- ment problem for optical communication systems, supporting the development of robust optical communication link.
    • Harvesting Mechanical Vibrations using a Frequency Up-converter

      Fakeih, Esraa (2020-04) [Thesis]
      Advisor: Salama, Khaled N.
      Committee members: Younis, Mohammad I.; Ahmed, Shehab
      With the rise of wireless sensor networks and the internet of things, many sensors are being developed to help us monitor our environment. Sensor applications from marine animal tracking to implantable healthcare monitoring require small and non-invasive methods of powering, for which purpose traditional batteries are considered too bulky and unreasonable. If appropriately designed, energy harvesting devices can be a viable solution. Solar and wind energy are good candidates of power but require constant exposure to their sources, which may not be feasible for in-vivo and underwater applications. Mechanical energy, however, is available underwater (the motion of the waves) and inside our bodies (the beating of the heart). These vibrations are normally low in frequency and amplitude, thus resulting in a low voltage once converted into electrical signals using conventional mechanical harvesters. These mechanical harvesters also suffer from narrow bandwidth, which limits their efficient operation to a small range of frequencies. Thus, there is a need for a mechanical energy harvester to convert mechanical energy into electrical energy with enhanced output voltage and for a wide range of frequencies. In this thesis, a new mechanical harvester is introduced, and two different methods of rectifying it are investigated. The designed harvester enhances the output voltage and extends the bandwidth of operation using a mechanical frequency up-convertor. This is implemented using magnetic forces to convert low-frequency vibrations to high-frequency pulses with the help of a piezoelectric material to generate high output voltage. The results show a 48.9% increase in the output voltage at 12.2Hz at an acceleration of 1.0g, and a bandwidth increase from 0.23Hz to 11.4Hz. For the rectification, mechanical rectifiers are discussed, which would obviate the need for electrical rectification, thus preventing the losses normally caused by the threshold voltage of electronics. Two designs of mechanical rectifiers are investigated and implemented on the frequency up-converter: a static rectifier and a rotating rectifier. The results show a voltage rectification, which required a sacrifice in the bandwidth and boosted voltage.
    • Percolation Theory-Analysis of Malware Epidemics in Large-Scale Wireless Networks

      Zhaikhan, Ainur (2020-04) [Thesis]
      Advisor: Alouini, Mohamed-Slim
      Committee members: Shihada, Basem; Amin, Osama
      The foreseen massive deployment of the internet of things (IoT) is expected to suffer from high security risks. This mainly results from the difficulty to monitor and cure the IoT devices in such large-scale deployment. In this thesis, we propose a spatial random deployment of special nodes (firewalls) which can detect and cure infected nodes within certain radius. An important concern is to add sufficient number of firewalls to make an epidemics finite and, hence, prevent malware outbreak over the whole network. The problem will be analyzed using percolation theory. Namely, we derive an upperbound for the critical intensity of spatial firewalls which guarantees prevention of large-scale network epidemics, regardless of the intensity of regular nodes. Using tools from percolation theory, we analyze the proposed solution and show the conditions required to ensure its efficiency.