• Wavelength Dependence of Underwater Turbulence Characterized Using Laser-Based White Light

      Alkhazragi, Omar (2019-04) [Thesis]
      Advisor: Ooi, Boon S.
      Committee members: Alouini, Mohamed-Slim; Shihada, Basem; Ng, Tien Khee
      The means of communication in oceanic environments is currently dominated by sonar. Although it is reliable for long-distance transmission, the vision of internet of underwater things (IoUT) requires an alternate means for high-data-rate transmission. It is also envisaged that a networked underwater and above-water objects, such as sensor nodes, and autonomous underwater vehicles will benefit seafloor exploration. The use of laser-based optical communication is poised to realize this dream while working hand-in-hand with acoustic and radio-frequency technologies from the littoral zone to deep blue sea. While blue and green lasers are typically utilized depending on the optical properties of the water, laser-based white light is attractive in a number of aspects. In this thesis, we proposed and realized the use of white light to model the channel and to provide the immediate decision for the preferred system configuration, which is critical for developing reliable communication links, particularly, in the presence of turbulence, which makes the alignment of underwater wireless optical communication (UWOC) links challenging. Temperature and salinity changes are among factors that change the refraction index, giving rise to beam wander. This thesis explores the dependence of underwater turbulence on the wavelength. After comparing the performance of red, green, and blue lasers, an ultra-fast comprehensive method that utilizes a white-light source that can produce a wide range of wavelengths is implemented. Experimental results show an 80%-decrease in the scintillation index as the wavelength is increased from 480 to 680 nm in weak turbulence caused by a 0.02-℃/cm temperature gradient with a 40-ppt salt concentration, which emulates conditions found in the Red Sea. The effect of turbulence on the bit error ratio (BER) is also investigated experimentally. Temperature gradients increased the BER especially for shorter wavelengths. The results along long-transmission distances were verified using Monte Carlo simulations. The correlation matrix between wavelengths was studied, which is important for designing multiple-input multiple-output systems. The results obtained show that as the difference in the wavelengths increases, the correlation decreases. Based on the interplay among scintillations, scattering, absorption, and the correlation between different wavelengths, it is possible to design a more reliable UWOC link.
    • Object Detection Using Multiple Level Annotations

      Xu, Mengmeng (2019-04) [Thesis]
      Advisor: Ghanem, Bernard
      Committee members: Al-Naffouri, Tareq Y.; Thabet, Ali Kassem
      Object detection is a fundamental problem in computer vision. Impressive results have been achieved on large-scale detection benchmarks by fully-supervised object detection (FSOD) methods. However, FSOD approaches require tremendous instance-level annotations, which are time-consuming to collect. In contrast, weakly supervised object detection (WSOD) exploits easily-collected image-level labels while it suffers from relatively inferior detection performance. This thesis studies hybrid learning methods on the object detection problems. We intend to train an object detector from a dataset where both instance-level and image-level labels are employed. Extensive experiments on the challenging PASCAL VOC 2007 and 2012 benchmarks strongly demonstrate the effectiveness of our method, which gives a trade-off between collecting fewer annotations and building a more accurate object detector. Our method is also a strong baseline bridging the wide gap between FSOD and WSOD performances. Based on the hybrid learning framework, we further study the problem of object detection from a novel perspective in which the annotation budget constraints are taken into consideration. When provided with a fixed budget, we propose a strategy for building a diverse and informative dataset that can be used to optimally train a robust detector. We investigate both optimization and learning-based methods to sample which images to annotate and which level of annotations (strongly or weakly supervised) to annotate them with. By combining an optimal image/annotation selection scheme with the hybrid supervised learning, we show that one can achieve the performance of a strongly supervised detector on PASCAL-VOC 2007 while saving 12:8% of its original annotation budget. Furthermore, when 100% of the budget is used, it surpasses this performance by 2:0 mAP percentage points.
    • Numerical study of linear and nonlinear problems using two-fluid plasma model in one dimension

      Mantravadi, Bhargav (2019-04) [Thesis]
      Advisor: Samtaney, Ravi
      Committee members: Farooq, Aamir; Wu, Ying
      The ideal two-fluid plasma model is a more generalized plasma model compared to the ideal MHD and it couples the ion and electron Euler equations via Maxwell's equations. Two-fluid plasma model is essential when the ion and electron fluids are at different temperatures. In this work, a fundamental investigation on the effect of non-dimensional light speed, ion-to-electron mass ratio and plasma beta on the plasma dynamics in the Brio-Wu shock tube Riemann problem is presented. A one dimensional finite volume code is developed based on the macroscopic governing equations, with second order accuracy in space and time. The source terms are treated implicitly and the homogeneous flux terms are treated explicitly. The credibility of the numerical results is assessed by performing several linear and nonlinear tests. Realistic light speed results in increasing the stiffness of the equations and severe time step restriction, which poses a challenge to the numerical simulations. In the context of the Brio-Wu shock tube problem, it is observed that the light speed is not important with respect to the hydrodynamics. However, light speed does affect the magnitude of the self generated electric field. Mass ratio affects the electron plasma dynamics. The speed of the fast moving electron plasma waves changes with the mass ratio. The results obtained using a mass ratio of 500 are in close agreement with that of realistic mass ratio of 1836. Increasing plasma beta suppresses the amplitude of the fast moving electron plasma waves.
    • Standardized short-term bleaching assays resolve differences in coral thermotolerance across microhabitat reef sites

      Perna, Gabriela (2019-04) [Thesis]
      Advisor: Voolstra, Christian R.
      Committee members: Aranda, Manuel; Tester, Mark A.
      Coral bleaching is now the main driver of reef degradation. The common notion is that most corals bleach and suffer mortality at just 1-2°C above their mean summer maximum temperatures, but some species and genotypes resist or recover better than others. Here we conducted a series of 18-hour short-term heat stress assays side-by-side with a long-term heat stress experiment to assess the ability of both approaches to resolve putative differences in coral thermotolerance and provide a measure of in situ reef temperature thresholds. Using a suite of measures (photosynthetic performance, coral whitening, chlorophyll a, host protein, algal symbiont counts, and algal type association), we assessed bleaching sensitivity/resilience of Stylophora pistillata colonies from the exposed and protected sides of a near-shore coral reef in the central Red Sea. As suggested by the differential mortality during a previous bleaching event, coral colonies from the protected site exhibited less impacted physiological performance in comparison to their exposed site counterparts, and these differences were resolved using both experimental setups. Notably, the long-term experiment provided better resolution with regard to the different measures collected, but at the price of portability, cost, and duration of the experiment. Variability in resilience to ocean warming is critical to reef persistence, yet we lack standardized diagnostics to rapidly assess bleaching severity or resilience across different corals and locations. Using a newly developed portable experimental system termed CBASS (the Coral Bleaching Automated Stress System), we demonstrate that mobile, short-term heat stress assays can resolve fine-scale differences in coral thermotolerance across reef sites. Based on our results, photosynthetic efficiency measured by non-invasive PAM fluorometry provides a rapid and representative proxy of coral resilience. Our system holds the potential to be employed for large-scale determination of in situ bleaching temperature thresholds across reef sites and species. Such data can then be used to identify resistant genotypes (and reefs) for downstream experimental examination and to complement existing remote-sensing approaches.
    • High-Performance Polyimide Gas Separation Membranes Based on Triptycene Dianhydrides and Di-Hydroxy-Diamino-Triptycene Monomers.

      Alqahtani, Abdulaziz Q. (2019-04) [Thesis]
      Advisor: Pinnau, Ingo
      Committee members: Lai, Zhiping; Han, Yu
      Distillation technology involves capital- and energy-intensive processes for light olefin/paraffin separation. Global demand for propylene has already exceeded 110 million tons per year. Therefore, distillation processes used for the separation of C3H6/C3H8 should be replaced or debottlenecked with more efficient and cost-effective technology. In the last three decades, membrane-based gas separation processes have successfully emerged, thus competing with conventional separation processes. Membranes potentially offer lower capital investment and operation cost than distillation columns. In this study, the use of advanced membrane materials for C3H6/C3H8 separation was investigated. Three novel triptycene-based polyimides were synthesized by Dr. Bader Ghanem from one diamine monomer, namely 2,6-dihydroxy-3,7-diaminotriptycene (DTA1-OH), and three dianhydride monomers, (i) non-substituted triptycene tetracarboxylic dianhydride (TDA), (ii) 9,10-dimethyltriptycene tetracarboxylic dianhydride (TDA1) and (iii) 9,10-iso-propyltriptycene tetracarboxylic dianhydride (TDAi3). It is important to note that polyimide membranes based on triptycene dianhydrides and triptycene diamines have never been reported in the literature before. Pure-gas permeability coefficients of He, H2, N2, O2, CO2, CH4, C3H6, and C3H8 were determined at 2 bar and 35 °C. Furthermore, C3H6 and C3H8 gas sorption isotherms were measured by gravimetric techniques, and experimental data were collected up to 7 bar at 35 °C. TDA-DAT1-OH, TDA1-DAT1-OH, TDAi3-DAT1-OH exhibited C3H6 permeability of 12.1, 16.6, and 5.64 Barrer with pure-gas C3H6/C3H8 selectivity of 35.7, 29.6, and 32.8 respectively. These properties exceeded the 2003 pure-gas upper bound for C3H6/C3H8. The BET surface area increased in the order of TDA-DAT1-OH (437 m2/g) < TDAi3-DAT1-OH (467 m2/g) < TDA1-DAT1-OH (557 m2/g). The frecational free volume (FFV) increased in the order of TDAi3-DAT1-OH (0.25) < TDA-DAT1-OH (0.28) < TDA1-DAT1-OH (0.30). TDA1-DAT1-OH (109 μm) showed less and slower physical aging than TDA-DAT1-OH (94 μm) after 60 days, where the O2 and CO2 permeability of both polyimides decreased by about 40% and 69%, respectively. After 30 days, TDAi3-DAT1-OH displayed the highest selectivity gain relative to its counterparts and exceeded the 2008 upper bound for CO2/CH4. TDA1-DAT1-OH exhibited 7-fold higher C3H6 permeability coupled with almost 3-fold higher C3H6/C3H8 selectivity relative to a previously reported commercial polyphenylene oxide (PPO) membrane.
    • Applications in computational structural biology: the generation of a protein modelling pipeline and the structural analysis of patient-derived mutations

      Guzmán-Vega, Francisco J. (2019-04) [Thesis]
      Advisor: Arold, Stefan T.
      Committee members: Gao, Xin; Jaremko, Łukasz
      Besides helping us advance the understanding of the physicochemical principles governing the three-dimensional folding of proteins and their mechanisms of action, the ability to build, evaluate, and optimize reliable 3D protein models has provided valuable tools for the development of different applications in the fields of biotechnology, medicine, and synthetic biology. The development of automated algorithms has made many of the current methodologies for protein modelling and visualization available to researchers from all backgrounds, without the need to be familiarized with the inner workings of their statistical and biophysical principles. However, there is still a lack in some areas where the learning curves are too steep for the methods to be widely used by the average non-programmer molecular biologist, or the implementation of the methods lacks key features to improve the interpretability and impact of their results. Throughout this work, I will focus on two different applications in the field of structural biology where computational methods provide useful tools to aid in synthetic biology or medical research. The first application is the implementation of a pipeline to build models of protein complexes by joining structured domains with disordered linkers, in individual or multiple chains, and with the possibility of building symmetric structures. Its capabilities and performance for the generation of complex constructs are evaluated, and possible areas of improvement described. The second application, but not less important, involves the structural analysis of patient-derived protein mutants using protein modelling techniques and visualization tools, to elucidate the potential molecular basis for the patient’s phenotype. The methodology for these analyses is described, along with the results and observations from 22 such cases in 13 different proteins. Finally, the need for a dedicated pipeline for the structure-based prediction of the effect of different types of mutations on the stability and function of proteins, complementary to available sequence-based approaches, is highlighted.
    • Synthesis, Characterization and Reactivity of Manganese PN3 Pincer Complexes

      Mal, Razan (2019-04) [Thesis]
      Advisor: Huang, Kuo-Wei
      Committee members: Lai, Zhiping; Rueping, Magnus
      Manganese is amongst the most abundant transition metals on earth. Playing several roles in enzymatic function, manganese is largely considered biocompatible and, in comparison to most transition metals, it is relatively inexpensive. It is surprising then, that manganese remains poorly explored in the field of pincer-based homogenous catalysis. PN3(P) pincer ligands have proved to impart different kinetic and thermodynamic properties to the complexes they are a part of when compared to analogous complexes of ligands with CH2 spacers. In part I of this work, we present unexpected results from a thorough investigation of the coordination chemistry between a PN3 phenanthroline-based ligand and several manganese salts that suggest that the coordination environment may promote a disproportionation reaction. We also present an efficient route towards dichloride substituted PN3 manganese complexes. In Part II, we investigate the reactivity of manganese(II) pincer compounds in ester reduction reactions and probe the promising results afforded by reduction through borohydride.
    • Activity Assessment of a Halophilic γ-carbonic Anhydrase from the Red Sea Brine Pool Discovery Deep

      Vancea, Alexandra (2019-04) [Thesis]
      Advisor: Rueping, Magnus
      Committee members: Arold, Stefan T.; Al-Babili, Salim
      Carbonic anhydrases catalyze a central reaction in life – the inter-conversion between carbon dioxide and water. Consequently, there is an increasing interest in research in using carbonic anhydrases for industrial applications such as biofuel production and carbon capture, since current approaches for CO2 capturing are expensive, harsh and energy demanding. The proof of principle for using carbonic anhydrase in these applications for carbon fixation has been validated. However, the current known and tested carbonic anhydrases are not tolerating the harsh industrial conditions. An ideal carbonic anhydrase should display thermo-, salt, and solvent stability and exhibit a decent reactivity. Herein we present the characterization and activity assessment of a halophilic γ-carbonic anhydrase from the Red Sea brine pool Discovery Deep. Protein X-ray structure exhibited the molecular structure and allowed the successful engineering of a small, active mutant library. Stopped-flow measurements gave insights into the activity and evaluated the engineering principles.
    • Functional diversity of herbivorous fishes in coral reefs in central Red Sea

      Pombo-Ayora, Lucía (2019-04) [Thesis]
      Advisor: Berumen, Michael L.
      Committee members: Moran, Xose Anxelu G.; Tester, Mark A.
      In this research, I explore the changes in the functional diversity of herbivorous fishes in zones of coral reefs with different benthic composition: a zone dominated by corals, a zone dominated by algae and a transition zone in between the previous two. I choose to use functional traits which explain the feeding mechanics of this group of fish, as well their feeding rates and their previously established functional groups to understand how different assemblages of this fishes could affect their environment in different ways. I found clear differences in the functional diversity by calculating five indexes, functional dispersion (FDis), functional richness (FRic), functional divergence (FDiv), functional evenness (FEve) and functional specialization (FSpe). Each zone showed different species composition with different abundances; both parameters contribute to obtaining different values of the indexes. The coral-dominated zone showed the biggest multidimensional functional trait space (MFTS) with a value of FRic equals to 1 which means that its assemblage occupies 100% of the MFTS, while the transition zone assemblage occupied 83% and the algae-dominated zone occupied 16% of it. Thanks to this index I identified three functionally redundant species in the coral-dominated and the transition zones. The algae-dominated zone showed the lower FDis explained by the high abundance of grazers individuals. FDiv did not vary significantly between the three zones. FEve was higher in the algae-dominated zone; the index value decreased in the transition and coral-dominated zones, a similar tendency was shown by FSpe. Finally, to explore the importance of including functional diversity I made a comparison between the taxonomic and functional β-diversity. This research showed close relations of herbivorous fishes with their environment, but I could not establish if the benthic composition shapes the herbivorous fish assemblage or the other way around. This research can be a baseline to start working in functional diversity in the Red Sea coral reefs, can help to understand what to expect in the evaluation of reefs in different health state and to identify which herbivorous fish species or groups are more vulnerable and more important according to their function for coral reefs.
    • Evaluation of Forward Osmosis Spacer Performance for Produced Water Treatment

      AlQattan, Jawad (2019-04) [Thesis]
      Advisor: Ghaffour, NorEddine
      Committee members: Pinnau, Ingo; Leiknes, TorOve
      Forward osmosis (FO) is one of the emerging membrane technologies in a field of water treatment. The potential advantages of a FO process are lower energy consumption, and higher fouling reversibility compared to other membrane-based desalting technologies, e.g., reverse osmosis and nanofiltration, due to low working pressure. Despite high fouling reversibility, membrane fouling can be still a major obstacle in the FO process. Thus, the employment of spacers can help in enhancing water flux and minimizing membrane fouling. However, the current design of spacers has a potential problem related to spacer fouling, thereby deteriorating the FO process. Therefore, the spacers were examined with the different designs (i.e., hole-type and twisted spacers) fabricated via a 3D-printer for the treatment of shale gas produced water (SGPW). To evaluate the performance of the spacers, either synthetic SGPW or Milli-Q water as feed solution (FS) and different concentration of sodium chloride as a draw solution (DS) were employed. Water flux, reverse solute flux (RSF) and reverse solute flux selectivity (RSFS) were firstly measured with increasing DS concentration with Milli-Q water as FS and a 1-hole spacer exhibited the highest water flux. When increasing FS concentration to 0.3 M NaCl, hole-type spacers exhibited higher water flux than twisted spacers. Therefore, 0-hole and hole-type spacers were selected for SGPW treatment. During SGPW treatment, severe flux decline was observed with all experiments due to the formation of BaSO4 scaling. Flux decline of 1- hole spacers was slightly severer than 0-hole. This might be because scales were broken by high shear force and more covered the membrane surface as shown in SEM images. However, interestingly, hole-type spacers showed no change of pressure drop during SGPW treatment while the pressure drop of the 0-hole spacer increased. Holes of spacers can prevent the accumulation of foulants on the spacer surface, thereby resulting in no change of pressure drop. Physical cleaning with no spacer and the 0-hole spacer showed less than 95% cleaning efficiency while hole-type spacers could enhance the cleaning efficiency and achieve 100%. This might be because the micro-jet induced by holes of the spacer can more readily destroy and remove foulants on the surface.
    • Development of Low-dimensional Metal Oxide Transistors for Biochemical Sensing Applications

      Alghamdi, Wejdan S. (2019-03-11) [Thesis]
      Advisor: Anthopoulos, Thomas D.
      Committee members: McCulloch, Iain; Inal, Sahika
      In the last two decades, there has been considerable development for biosensor devices as the need to more efficient sensing systems is increasing for monitoring the progress of medicine and help with the early diagnosis of the pathogens and treatment of diseases that would reduce the cost of patient care. DNA sensors, in particular, have attracted attention due to their abundance of practical applications in clinical diagnoses and genetic information which increase the demand for DNA probes. On the other hand, the development of the oxide semiconductors thin film transistors (TFT) devices have been greatly increased, owing to their superior electrical properties, lower cost and large coverage areas. Building a bridge across biological elements and electronic interface using advanced (TFT) platforms are based on materials design and device architecture. Here, a solution-processed multi-layer metal oxide (TFT) is explored as a novel DNA sensor. The device engineering combines the novel hetero-structure metal oxide channel that can sustain a 2-dimensional electron gas (2DEG) which leads to a higher mobility and surface functionalization capacity to create an ultrasensitive, highly stable, and versatile DNA sensor. The prototype solid-state TFT sensor features a sub-10 nm-thick metal oxide heterojunction channel of a In2O3 and a top ZnO layer. The devices developed here rely on a pyrene-based molecule as the receptor unit that is known to intercalate into double stranded DNA with a very high-affinity constant and at very low concentration.
    • Investigation of Zinc Interactions to Human Serum Albumin and Their Modulation by Fatty Acids

      Al-Harthi, Samah (2019-03) [Thesis]
      Advisor: Jaremko, Lukasz
      Committee members: Jaremko, Mariusz; Gao, Xin
      Zinc is an essential metal ion for the activity of multiple enzymes and transcription factors. Among many other transporting proteins human serum albumin (HSA) is the main carrier of Zn(II) in the blood plasma. HSA displays multiple ligand binding sites with extraordinary binding capacity for a wide range of ions and molecules including fatty acids. Hence, HSA controls the availability and distribution of those molecules throughout the body. Previous studies have established that the existence of one zinc site with high affinity (MBS-A) that is modulated by the presence of fatty acids. Therefore, the fatty acid concentration in the blood influences zinc distribution which may result in a significant effect on both normal physiological processes and a range of diseases. Based on the current knowledge of HSA's structure and its coordination chemistry with zinc ion, here, we attempted to investigate zinc interactions and coordination with HSA and the effect of different fatty acids on the protein structure, stability and on Zn(II) binding. By NMR titration, we examine the Zn(II) binding to HSA and the spectra show distinct movements of some resonances showing a conformational change has occurred as a result of Zn(II) binding. Isothermal calorimetry titrations study was performed to evaluate zinc binding affinity to HSA in the absence and presence of fatty acids. Free HSA results indicates the existence of one high affinity site and multiple low affinity sites. Upon the binding of fatty acids to HSA, three distinct behaviors of Zn(II) affinity was observed ranging from no effect to moderate to significant depending on the FAs. By the use of circular dichroism, we investigate secondary and tertiary structure of HSA in the presence and absence of FAs and Zn(II). We found albumin is predominately α-helical and the overall conformation of the protein remains unchanged even after interacting with FAs and Zn(II) with some exception. The structural stability of HSA was evaluated by obtaining the denaturation temperature in the presence and absence of fatty acid and we found the thermal denaturation of HSA increases with the increase of amount of fatty acids.
    • Tunable Twisting Motion of Organic Linkers via Concentration and Hydrogen-bond Formation

      Alturki, Abdullah (2019-01) [Thesis]
      Advisor: Mohammed, Omar F.
      Committee members: Huang, Kuo-Wei; Bakr, Osman
      Benzothiazole dibenzoic acid derivative (BTDB) is well-known organic linkers utilized for the syntheses of various metal organic frameworks, and demonstrates interesting photophysical properties upon concentration variations in solution. The presence of two carboxylic acid functional groups at each side of the rod-like molecule, facilitates dimerization and oligomerization equilibria. Interestingly, dimers and oligomers have completely different emission behaviors from the monomer of the same species. At a low range of concentration, 0.1 – 64 μM, dimerization process is dominant, and that the equilibrium constant of dimer formation found to be 18,000 M-1. On the other hand, in the 64 – 1000 μM concentration range, oligomerization takes over, and that it results in the formation of a small linear chain of 8 molecules, or 4 dimers, with a high equilibrium constant of 1.2 × 1013 M-3. Various experimental measurements and theoretical calculations have suggested hydrogen-bond formation is the main driving force for the dimerization and oligomerization in the nano- and micro- molar regime, and that structure rigidity of a species is a key factor in controlling its photophysical properties, such as emission quantum yield and excited state lifetime.
    • Bose-Einstein Condensation of Light in Disordered Nano Cavities at Room Temperature

      Erglis, Andris (2019-01) [Thesis]
      Advisor: Fratalocchi, Andrea
      Committee members: Li, Xiaohang; Manchon, Aurelien
      Bose-Einstein Condensation is a macroscopic occupation of bosons in the lowest energy state. For atoms, extremely low temperatures are required to observe this phenomenon. For photons, condensation has been demonstrated at room temperature, requiring a large number of particles (N 77000) and very complicated setup. Here we study the possibility of observing BEC of light at room temperature with a much lower number of particles by leveraging disorder in a dielectric material. There is no constraint in the number of photons in the system like in the previous research. We investigate what happens to photons once they are put inside a cavity with a disorder. The analysis is carried out by using time-dependent quantum Langevin equations, complemented by a thermodynamic analysis on quantum photons. Both approaches give the same expression for the critical temperature of condensation. We demonstrate that photons in a disordered cavity with arbitrary initial statistical distribution reach thermal equilibrium and undergo a Bose-Einstein Condensation if the temperature is su ciently reduced. In our model we demonstrate that the temperature is related to the losses of the system. At this state, photons follow Boltzmann distribution. It is demonstrated that by only varying the strength of disorder, it is possible to change the critical temperature of the phase transition, thus making condensation possible at room temperature. This work opens up the possibility to create new types of light condensate by using disorder.
    • Modeling and Analysis of Hybrid Aerial-Terrestrial Networks: A Stochastic Geometry Approach

      Alshaikh, Khlod K. (2018-12) [Thesis]
      Advisors: Alouini, Mohamed-Slim; Al-Naffouri, Tareq Y.
      Committee members: Amin, Osama; Elsawy, Hesham; Dahrouj, Hayssam; Kouzayha, Nour
      The ever-increasing demand for better mobile experiences is propelling the research communities to look ahead at how future networks can be geared up to meet such demands. It is likely that the next-generation of wireless communications will be revolutionary, outpacing the current systems capabilities in terms connectivity, reliability and intelligence. These trends and predictions will cause a revolutionary change in the wireless communications. In this context, the concept of Ultra-Dense Network (UDN) is poised to be the cornerstone of the development of fifth generation(5G) systems, whereby a massive number of base stations (BSs) are deployed for enhancing the network performance metrics. Though such densification might be economically viable in urban areas, it is mostly unfavorable in rural ones due to the sheer complexity and the various factors involved the planning and installation processes; all of which trigger the need for cost-effective, flexible and easily-implementable solutions. As a result, unmanned aerial vehicles (UAVs) emerge as a promising alternative solution for enhancing wireless coverage. Due to their mobility capabilities, UAVs are of particular importance in events of (i) terrestrial-based cellular systems dilapidation, (ii) infrastructure absence in remote and suburban areas, or (iii) limited-duration events or activities wherein there is a short-term need for supplementary network resources to handle the overload. While a growing body literature works towards characterizing and providing insights into the performance of UAVs-only networks (serving the first two purposes), understanding the performance of such networks when coupled with existing terrestrial BSs remains a challenging, yet interesting, open research venue. Towards this direction, this thesis provides a rigorous analysis of the downlink coverage probability of hybrid aerial-terrestrial networks using tools from Stochastic Geometry. The thesis presents a mathematical model that characterizes the coverage probability metric under different network environments. The proposed model is validated against intensive simulations so as to substantiate the analytical results. The developed work is essential to understanding the premises of one possible solution to the UDNs of tomorrow, capture its key performance metrics and, most importantly, to uncover key design insights and reveal new directions for the wireless communication industry.
    • A Biocomputational Study of Water-Nucleobase Stacking Contacts in Functional RNAs

      Kalra, Kanav (2018-12) [Thesis]
      Advisor: Cavallo, Luigi
      Committee members: Khashab, Niveen M.; Zhang, Xiangliang
      Recent structural studies evidenced the presence of a recurring well-known interaction between an oxygen atom and an aromatic nucleobase ring in structural motifs of nucleic acids. In particular, this type of interaction is observed between the O4' atom of the (deoxy)ribose moiety and the aromatic nucleobase in Z-DNA molecules and in a variety of structural RNA molecules. In this thesis, we comprehensively examine the hitherto undetected stacking interactions between an oxygen atom of a water (Ow) molecule and the aromatic nucleobase ring, using structural bioinformatics along with quantum mechanics. On the basis of the structural analysis of the high-resolution X-ray structures, we found out that the stacking distance between the Ow atom and the nucleobase plane varies between 3.1 and 4.0 Å. Further, the contact between the Ow-nucleobase plane can be categorized either as a lonepair-π type, where the Ow atom interacts directly with the aromatic surface of the nucleobase, or as an OH-π interaction, where one of the hydrogen atoms of the Ow points towards the nucleobase. Our quantum chemical analysis evidenced that the OH-π interaction is clearly favored in terms of energetics when compared to the lonepair-π, except for the uracil, where the lonepair-π kind of interaction seems to be energetically more stable, as also supported by electrostatic potential map calculations.
    • The Effect of Increasing Temperature on Greenhouse Gas Emissions by Halophila stipulacea in the Red Sea

      Burkholz, Celina (2018-12) [Thesis]
      Advisor: Duarte, Carlos M.
      Committee members: Moran, Xose Anxelu G.; Daffonchio, Daniele
      Seagrass ecosystems are intense carbon sinks, but they can also emit greenhouse gases (GHG), such as carbon dioxide (CO2) and methane (CH4), to the atmosphere. Yet, GHG emissions by seagrasses are not considered when estimating global CH4 production rates by natural sources, although these estimations will help predict future scenarios and potential changes in CH4 emissions. In addition, the effect of warming on GHG emissions by seagrasses has not yet been reported. The present study aims to assess the CO2 and CH4 production rates by vegetated and adjacent bare sediment of a monospecific seagrass meadow (Halophila stipulacea) located in the central Red Sea. We measured CH4 and CO2 fluxes and their isotopic signatures by cavity ringdown spectroscopy on chambers containing vegetated and bare sediment. The fluxes were measured at temperatures from 25 °C (winter seawater temperature) to 37 °C to cover the natural thermal range and future seawater temperatures in the Red Sea. Additional parameters analyzed included changes in the sediment microbial community composition, sediment organic matter, organic carbon, nitrogen, and phosphorus concentration. We detected up to 100-fold higher CH4 (up tp 571.65 µmol CH4 m−2 d−1) and up to six-fold higher CO2 (up to 13,930.18 µmol CO2 m−2 d−1) fluxes in vegetated sediment compared to bare sediment, and an increase in CH4 and CO2 production with increasing temperature. In contrast, CH4 and CO2 production rates decreased in communities that were maintained at 25 °C, while communities that were exposed to prolonged darkness showed a decrease in CH4 and an increase in CO2 production rates. However, only minor changes were seen in the microbial community composition with increasing temperatures. These results show that GHG emissions by seagrasses might be affected by natural temperature extremes and warming due to climate change in the Red Sea. The findings will have critical implications for the estimation of natural GHG sources, especially when predicting future changes in the global CH4 budget.
    • Preparation of modified DNA molecules for multi-Spectroscopy Application

      zhang, xinyu (2018-11-29) [Thesis]
      Advisor: Di Fabrizio, Enzo M.
      Committee members: Laquai, Frédéric; Adamo, Antonio
      Hot Electron Nanoscopy and Spectroscopy (HENs) is a current-sensing AFM technique recently developed in our lab, which have proven a new kind of response on conduction at the nanometer scale, casting a new light for the comprehension of electronic states in nanomaterials. Direct imaging of DNA structure has long been investigated, with the development of HENs technology, more structural information about DNA could be revealed by simultaneous measurements of height, phase, Raman signal, and conductivity. With the aim of applying it for the first time on biological molecules, customized double-stranded DNA sequences, including thiol-modified oligonucleotides are designed to create preferential conductive paths through the basis as a benchmark system for the technique on biomolecules. This work aims to a final goal to characterize hot-electron current between gold tip and thiol modified DNA which ideally is covalently bonded to the gold surface and optimized for the application. In this work, high density of DNA absorbed by SERS active gold surface with atomic flat islands has been prepared for HENs application. The samples have been characterized by AFM, SKPM and Raman Spectroscopy, as non-destructive and controlled interactive image analysis. High-resolution images of DNA have been acquired, S-S and Au-S bonding of DNA anchored on SERS active gold substrate are also visible with Surface-enhanced Raman and Tip-enhanced Raman signals. A submolecular feature has also been found in both topographical and electrical results. Herein, we report the synthesis and characterization steps to obtain the optimized operation standard.
    • Prediction of Active and Inactive Chemical Compounds from High-Throughput Assays

      Islam, Elaf J. (2018-11-28) [Thesis]
      Advisor: Bajic, Vladimir B.
      Committee members: Laleg-Kirati, Taous-Meriem; Moshkov, Mikhail
      This study considers chemical compounds that can exert their activity by interacting with a target protein or other molecular receptors. Our aim is to develop machine learning models that can predict if a chemical compound will be active in a particular test/assay. We will use data from assays that are present in the PubChem knowledgebase, specifically in its segment called BioAssays which reports the results of many high-throughput screening experiments. PubChem BioAssays is a valuable resource that contains information from a large number of experiments. In one assay, sometimes many hundreds or even many thousands of chemicals are tested. Data from these experimental assays contain information about chemicals that are active as well as chemicals that are not active in the assay. These represent an interesting resource of experimental data that are well suited for classification purposes. We will approach the problem by evaluating different ways that chemical compounds can be numerically described by means of so-called fingerprints, and then apply different machine learning (ML) and deep learning (DL) models to classify active and inactive chemicals for a number of assays. In this study, we will make comprehensive comparisons of the types of ML/DL models and types of fingerprint features that describe chemicals, and evaluate combinations of models and fingerprints that work best for the problem in question. Our focus is on finding those combinations which are useful for distinguishing active from inactive compounds in single PubChem assays. We will evaluate the methods across 10 assays and will examine the effects of 11 types of fingerprints. For example, PubChem fingerprints and MACCS keys fingerprints. For the evaluation, up to now we performed 88 experiments for each dataset and 968 in total for all 10 PubChem assays. These experiments involved approximately 6,000 interactions between chemicals and their targets. The implementation of this project has been done using MATLAB. Based on these and additional experiments, we will be in a position to propose which combination of fingerprints and ML/DL models works best in the above mentioned task. Such modeling will be useful to predict activity for chemicals that are not yet tested.
    • Visualization and Simulation of Variants in Personal Genomes With an Application to Premarital Testing (VSIM)

      Althagafi, Azza Th. (2018-11-28) [Thesis]
      Advisor: Hoehndorf, Robert
      Committee members: Moshkov, Mikhail; Gojobori, Takashi
      Interpretation and simulation of the large-scale genomics data are very challenging, and currently, many web tools have been developed to analyze genomic variation which supports automated visualization of a variety of high throughput genomics data. We have developed VSIM an automated and easy to use web application for interpretation and visualization of a variety of genomics data, it identifies the candidate diseases variants by referencing to four databases Clinvar, GWAS, DIDA, and PharmGKB, and predicted the pathogenic variants. Moreover, it investigates the attitude towards premarital genetic screening by simulating a population of children and analyze the diseases they might be carrying, based on the genetic factors of their parents taking into consideration the recombination hotspots. VSIM supports output formats based on Ideograms that are easy to interpret and understand, which makes it a biologist-friendly powerful tool for data visualization, and interpretation of personal genomic data. Our results show that VSIM can efficiently identify the causative variants by referencing well-known databases for variants in whole genomes associated with different kind of diseases. Moreover, it can be used for premarital genetic screening by simulating a population of offspring and analyze the disorders they might be carrying. The output format provides a better understanding of such large genomics data. VSIM thus helps biologists and marriage counsellor to visualize a variety of genomic variants associated with diseases seamlessly.