• 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.
    • Insights into bacterial community changes following heat and salinity treatments in Aiptasia

      Randle, Janna L. (2018-11) [Thesis]
      Advisor: Voolstra, Christian R.
      Committee members: Aranda, Manuel; Hirt, Heribert
      Coral bleaching, i.e. the loss of photosynthetic algal symbionts, caused by ocean warming is now the main factor driving reef decline, but not all corals are affected equally. Corals from the Arabian Seas have unusually high temperature tolerances, and recently studies implicated salinity as one of the contributing factors. In particular, a recent heat stress experiment at different salinities using the model system Aiptasia and Red Sea corals, showed that cnidaria at large bleach less at heat stress under high salinities and that this is associated with an increase of the osmolyte, floridoside Here we were interested to assess microbial community changes under heat stress at different salinity levels and whether this could help to explain the increase in thermal tolerance of the metaorganism at high salinities. We determined microbial community composition via HiSeq 16S rRNA gene amplicon sequencing of two anemone strains that differ in their associated symbionts, namely H2-SSB01 (type B1) and CC7-SSA01 (type A4), after six days under ambient (25 °C) and heat stress (34 °C) temperatures at salinities of 36, 39, and 42. Both anemones harbored distinct microbial communities, irrespective of temperature or salinity, that were also different from the bacteria in surrounding seawater. Within both host-endosymbiont pairings, the bacterial community composition at low (36) and intermediate (39) salinities did not differ between ambient and heat stress, but was significantly different at high (42) salinities. Subsequent elucidation of bacterial indicator species revealed several taxa that could be associated with a response to temperature and salinity. Our results underline that microbial community composition adjusts under different environmental settings. Importantly, microbial community dynamics of H2-SSB01 aligned with observed differences in bleaching susceptibility and thermal tolerance, whereas the pattern remains unclear for CC7-SSA01, which harbors an intrinsically higher thermal tolerance. Such responses could argue for a contribution of the microbiome to the observed increase in temperature tolerance of the Aiptasia metaorganism at increased salinities. An alternative interpretation is that the microbiome changes denotes a parallel response to changing salinities.
    • 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.
    • Cycloalkane Metathesis using a Bi-metallic System: Understanding the Effect of Second metal in Metathesis Reaction

      Alshanqiti, Ahmed M. (2018-12) [Thesis]
      Advisor: Basset, Jean-Marie
      Committee members: Huang, Kuo-Wei; Saikaly, Pascal
      Over the past decades, since the discovery of a single–site silica-supported catalyst for the alkane metathesis reaction by our group, we have been extensively working on the development of supported catalytic systems for the improved alkane metathesis reaction. During these developments, we understand the reaction mechanism and reached a new perspective for the synthesis of various supported bimetallic systems via the surface organometallic chemistry (SOMC) approach. Recently, with this bi-metallic system, we got a very high TON (10000) in propane metathesis reaction. As these catalysts are very efficient for linear alkanes we thought to apply it for cyclo-alkanes specifically, for cyclo-octane metathesis expecting better activity. Besides, the value of the ring alkanes are higher than the linear alkanes. The current work demonstrates a combination of [(ΞSi−O−)W(Me)5] and [(ΞSi− O−)Ti(Np)3 pre-catalyst with several supports (SiO2-700, SBA-15 and MCM-41) for metathesis of cyclooctane. The catalysts have been synthesized and fully characterized by elemental analysis (EA), FT-IR and NMR spectroscopies. After fully characterization the bi-metallic catalyst was tested for metathesis of cyclooctane with highest ever TON 2500 as compared to that of mono-metallic catalyst where we got 430 TON. Which again corroborates our prediction that bimetallic catalysts are better catalysts than monometallic catalysts.
    • 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.
    • A Comparative Assessment of the Physiological Performance of Red Sea and non-Red Sea Symbiodiniaceae Strains in Acute Heat and Light-Stress Conditions

      Alshwairikh, Yara (2018-11) [Thesis]
      Advisor: Aranda, Manuel
      Committee members: Voolstra, Christian R.; Hirt, Heribert
      Corals reefs worldwide are facing many challenges due to global warming. Of these challenges, increasing sea temperatures represent a major threat. An increase of 1 °C above summer mean levels is greatly associated with coral bleaching, and massive coral bleaching is observed when accumulation of thermal-stress reaches 4 °C-weeks according to Degree Heating Weeks (DHW) measurements. The coral holobiont is an assemblage of many organisms including Symbiodiniaceae; a family of photosynthetic microalgae that form an endosymbiotic relationship with corals. Studies suggest that Symbiodiniaceae may drive the performance of the host, therefore, resilience of the coral host against thermal stress may be largely influenced by Symbiodiniaceae. The aim of this study was to compare the physiological performance under acute heat and light-stress conditions of several Symbiodiniaceae strains (clade A and B) isolated from different geographical locations with distinct thermal profiles (Red Sea, Hawaii, and North Carolina). Oxygen production, respiration rate, photosynthetic efficiency, and production of ROS were measured under conditions of acute heat and light-stress. The Red Sea strains (RS-B*, RS-B, and RS-A) exhibited a higher photosynthetic efficiency with increasing temperatures than the Hawaii and North Carolina strains (SSBO1, SSAO1, respectively). After heat-stress of 34 °C, RS-A was found to have the best thermotolerance with regard to ROS production. Oxygen production and respiration rate data showed high biological variation between culture replicates which prevented inter-strain comparisons and limited observation of consistent trends. The observed variability was largely due to the differential age of the cultures used, and the inability of the cell counting method to differentiate between live and dead cells. The results of this study indicate that Symbiodiniaceae strains originating from warmer geographic locations exhibit an overall better performance under acute heat-stress conditions. Variability in the physiological response of three samples from the same species (Breviolum minutum) exemplifies the large diversity in the family Symbiodiniaceae, and indicates the need to support genomic identification of Symbiodiniaceae isolates with physiological studies. Efforts to predict the future of coral reefs under current threats of climate change will only be productive if we have a comprehensive understanding of the complex interactions between corals and Symbiodiniaceae.
    • Cycloalkane Metathesis using a Bi-metallic System: Understanding the Effect of Second metal in Metathesis Reaction

      Alshanqiti, Ahmed M. (2018-09) [Thesis]
      Advisor: Basset, Jean-Marie
      Committee members: Huang, Kuo-Wei; Saikaly, Pascal
      Over the past decades, since the discovery of a single–site silica-supported catalyst for the alkane metathesis reaction by our group, we have been extensively working on the development of supported catalytic systems for the improved alkane metathesis reaction. During these developments, we understand the reaction mechanism and reached a new perspective for the synthesis of various supported bimetallic systems via the surface organometallic chemistry (SOMC) approach. Recently, with this bi-metallic system, we got a very high TON (10000) in propane metathesis reaction. As these catalysts are very efficient for linear alkanes we thought to apply it for cyclo-alkanes specifically, for cyclo-octane metathesis expecting better activity. Besides, the value of the ring alkanes are higher than the linear alkanes. The current work demonstrates a combination of [(ΞSi−O−)W(Me)5] and [(ΞSi− O−)Ti(Np)3 pre-catalyst with several supports (SiO2-700, SBA-15 and MCM-41) for metathesis of cyclooctane. The catalysts have been synthesized and fully characterized by elemental analysis (EA), FT-IR and NMR spectroscopies. After fully characterization the bi-metallic catalyst was tested for metathesis of cyclooctane with highest ever TON 2500 as compared to that of mono-metallic catalyst where we got 430 TON. Which again corroborates our prediction that bimetallic catalysts are better catalysts than monometallic catalysts.
    • Biological and Biochemical Properties of Two KDM1A Associated Alternatively Spliced SWIRM Domains

      Fadaili, Yara (2018-11) [Thesis]
      Advisor: Adamo, Antonio
      Committee members: Hamdan, Samir; Aranda, Manuel
      LSD1 is the first described histone demethylase which demethylates H3K4me1/2 (Shi et el., 2004), thus, causing transcriptional repression. Alternatively, LSD1 was demonstrated to have H3K9me1/2 demethylase activity when bound by androgen receptor, hence, causing transcriptional activation (Schule et al., 2005). LSD1 is commonly recruited by the so called CoREST core complex including: RCOR1, HDAC1 and HDAC2 among others and therefore is coupled with histone deacetylation and transcriptional repression (Foster et al., 2010). It is an important regulator of pluripotency in early development and it occupies, along with pluripotency factors NANOG and OCT4, the promoters of major lineage determining genes that are poised for activation in the pluripotent state, (Adamo et al., 2011). There are four described isoforms for LSD1: LSD1, LSD1-E2a, LSD1-8a and LSD1-E2a/E8a (Zibetti et al., 2010). While the Cterminus of LSD1 is extensively studied and the function of the isoforms LSD1-E8a and LSD1-E8aE2a is described, there is scarce knowledge on LSD1 N-terminus unstructured region and the SWIRM domain. In this project I examined the role of the differently spliced exon 2a on the function of the SWIRM domain through generation of eight constructs coding for the N-terminal portion of LSD1 SV1 and SV2 fused with a C- or N-terminus FLAG tag. I then performed an immunoprecipitation experiment followed by mass spectrometry and proteomics analysis that led to the identification of previously unknown binding partners to the LSD1 SWIRM domain: NONO and IGF2B3.
    • 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.
    • Sand temperature profiles at turtle nesting sites in the Red Sea: implications for hatchling sex ratios

      Tanabe, Lyndsey K. (2018-11) [Thesis]
      Advisor: Berumen, Michael L.
      Committee members: Jones, Burton; Hoteit, Ibrahim
      Climate change poses a serious threat to species that demonstrate temperature dependent sex determination (TDS), including marine turtles. Increased temperatures can result in highly female skewed sex ratios and decreased hatchling success. In situ sand temperature data was collected from the nesting depth of hawksbill and green turtles at five study sites along the coast of the Red Sea. The sand temperature profile at four of the sites exceeded the pivotal temperature of 29.2°C (commonly cited in literature) throughout the study duration, which suggests feminization of turtles could be occurring, but further studies need to identify the pivotal temperature in this region. The percentage of days exceeding the commonly cited maximum thermal threshold (33 and 35°C) was calculated for each site at 30 and 50 cm. Sand temperature recordings were as high as 36.0°C at 30 cm depth, and 35.3°C at 50 cm. This suggests that the turtle hatchlings in some areas of the Red Sea could already have high mortality rates due to high temperatures, unless they are locally adapted to these high temperatures. The Red Sea is home to five out of the seven extant species of marine turtles in the world, but not much is known about these populations. The Red Sea is an understudied region of the world, but it has the potential to provide insight on how species might adapt to future climate change due to its high and variable water temperatures (range of 20°C to 35°C) and high salinity (40 PSU). Sites with lower sand temperatures (and lower risk of feminization) may represent priority areas for conservation efforts, particularly in regions facing imminent coastal development.
    • Single-Copy Insertion of Split-GFP for the Restriction of Germline Expression in Caenorhabditis elegans

      Al Johani, Mohammed (2018-11) [Thesis]
      Advisor: Frøkjær-Jensen, Christian
      Committee members: Adamo, Antonio; Krattinger, Simon G.
      Gene regulation in C. elegans germ cells depend on transgenerational chromatin modification and small RNA pathways. Germline silencing mechanisms evolved to repress foreign DNA from compromising the transfer of genetic information to progeny. Effective genetic tools that circumvent the silencing machinery will facilitate studies using this model organism. Specifically, translation of heat-shock inducible transgenes is inhibited in the germline making it challenging to transiently express enzymes to modify the genome. Here, we describe a genetic screen design that can be used to identify pathways that prevent germline expression of heat-shock induced transgenes. We use split-GFP (GFP1-10 and GFP11) to confine a genetic screen to germ cells. Stable transgenic lines with germline expression of single-copy integrated GFP11 were produced using MosSCI. The insertion lines will be used in RNAi or chemical mutagenesis screens for the germline de-repression of GFP1-10 expressed under heat-shock promoters. The screen is likely to identify candidate RNAi or chromatin factors involved in repressing heat-shock expression in the germline, particularly from extrachromosomal arrays. Inducible high-level expression in the germline from extrachromosomal arrays would be a valuable tool for large-scale genome engineering.
    • How does light affect the heat stress response in Arabidopsis?

      Kim, Eunje (2018-11) [Thesis]
      Advisor: Tester, Mark A.
      Committee members: Hirt, Heribert; Voolstra, Christian R.
      Light and temperature are two of the most important environmental factors regulating plant development. Although heat stress has been well studied, little is known about the interaction between light and temperature. In this study, we performed phenotypic assays comparing seedling responses to heat under light and dark conditions. Seedlings exposed to heat in the dark show lower survival rates than seedlings stressed in the light. To identify transcriptional changes underlying light-dependent heat tolerance, we used RNA-sequencing. The light-dependent heat stress responses involved a plethora of genes which could be potential candidate genes for light-induced heat tolerance, including transcription factors (bHLH) and genes commonly associated with biotic stress. By using the latest high-throughput phenotyping facility, we found that the light-dependent heat tolerance is reflected more on the maintenance of photosynthetic capacity, rather than leaf temperature. These results provide insights into how light increases heat stress tolerance in Arabidopsis seedlings and suggest its underlying mechanisms.
    • Effect of Boron on Nickel and Cobalt Catalysts for the Dry Reforming of Methane

      Al Abdulghani, Abdullah (2018-11) [Thesis]
      Advisor: Cavallo, Luigi
      Committee members: Gascon, Jorge; Huang, Kuo-Wei
      The dry reforming of methane (DRM) has received critical attention because it converts two major greenhouse gases, methane and carbon dioxide, into molecular hydrogen and carbon monoxide, known as synthesis gas (syngas). Syngas is an important feedstock to produce various chemicals. A major drawback of the DRM process is the high deactivation rates of conventional nickel and cobalt catalysts. Experimental findings indicate that treating nickel and cobalt catalysts with boron reduces deactivation rates and enhances the catalytic activity. This study investigates the mechanism through which boron promotes catalytic stability using density functional theory calculations. First, the location of boron in nickel and cobalt catalysts is explored. Boron is found to be more stable occupying on-surface and substitutional sites in the catalysts. However, during DRM operation, carbon dioxide is able to oxidize on-surface and substitutional boron. The formed boron oxide units may react with each other and form diboron trioxide or react with hydrogen to form boric acid, and eventually leave the catalyst, which means they cannot have an effect on deactivation rates. This study argues that interstitial boron plays the major role since it is protected from getting oxidized by carbon dioxide. Geometric optimization indicates that interstitial boron leads to spontaneous surface reconstruction in both extended surfaces and nanoparticles. The effect of interstitial boron on the binding energies of methyl, hydrogen, carbon monoxide, and oxygen on extended surfaces and nanoparticles is studied and utilized using the Brønsted-Evans-Polanyi principle to give an insight about how boron reduces deactivation rates. Our analysis indicates that interstitial boron lowers the activation energies of methane and carbon dioxide. On (100) surfaces, boron lowers C–H activation energies in methane more than it lowers C=O activation energies in carbon dioxide, which means catalytic deactivation rates due to metal oxidation are lowered. On (111) surfaces, boron lowers carbon dioxide activation energies more than it lowers methane activation energies, which means catalytic deactivation rates due to coke formation are lowered. The computational study is consistent with experimental findings and gives an atomistic understanding of the beneficial role of boron on the DRM process catalyzed by nickel and cobalt.
    • Fine Jetting from Drops Impacting on a Superhydrophobic Surface

      Alhazmi, Mohammad A. (2018-10) [Thesis]
      Advisor: Thoroddsen, Sigurdur T
      Committee members: Johansson, Bengt; Ghaffour, NorEddine
      In this study, the associated dynamic of water droplets at low impact velocity on the Superhydrophobic surface have been investigated. The experiment is conducted on superhydrophobic surface (SH), (Contact Angel > 1500) while varying the impact velocity (V0). When the drop hits the surface, large oscillation starts, and the capillary waves travel up to the upper of the drop where a cylindrical cavity can be formed inside the drop. The cavity closes up in a self-similar way until collapse, followed by a violent singular jet which can reach up to 35 m/s. The study showed that during drop receding, the cavity can collapse in different scenarios based on the impact velocity and the surface wettability. More importantly, the collapse is observed for the first time at very high-speed video, up to 5 million fps. Furthermore, we correct the optical distortion of the cavity due to the curvature of the drop surface. This study classifies all of the 5 encountered behaviors of the cavity collapse. The jet formation and speed are strongly dependent on the specific cavity configuration. Very fast jetting behavior is observed when the collapse is pinch-off singularity which reaches zero value in the middle of the drop. Other behaviors of the collapse such the unsymmetrical closing of the cavity or bubble entrapment is discussed. The optical distortion factor is calculated through 3 different approaches. The first one is an experimental calibration technique where a small cylinder is inserted into the drop. While the other two approaches are indirect implantations of theoretical models presented in the literature to fit the instantaneous geometrical shape of the cavity inside the drop. The distortion factor (DF) gives in all cases a similar value. Therefore, the averaged distortion value is calculated, and it is a magnification of 33% increase of the actual size. The experiment results of the cavity radius are compared with power-laws and the modified Rayleigh-Plesset equation for free cylindrical flow and good agreement is shown.
    • 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.
    • 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.
    • 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.
    • Superwettable Membranes for Highly Efficient Separation of Oil-in-Water Emulsions

      Alduraiei, Fadhilah H. (2018-11) [Thesis]
      Advisor: Wang, Peng
      Committee members: Han, Yu; Thoroddsen, Sigurdur T; Alsharani, Farhan
      In this work, we report a facile and robust surface membrane modification method via a simple coating of PVDF membrane using tannic acid (TA) followed by oxidation with sodium periodate (NaIO4). The modified membranes were investigated by SEM, AFM, XPS, FTIR, and a water contact angle measurement. The Contact angle measurement shows that the TA modified membrane exhibits superhydrophilicity and underwater oleophobicity. Results from FTIR and XPS indicate that the carboxylic groups were formed on the surface of the TA modified membrane due to the oxidation of quinone by NaIO4, which is the key to superhydrophilicity of the TA modified membrane surface. In addition, the modified membrane was tested for oil-in-water emulsion separation. A high TOC rejection of 99% was achieved for different kinds of surfactant-stabilized oil-in-water emulsions as well as the surfactant-free oil/water mixture. The modified membrane not only showed a good water flux and oil/water separation performance but also exhibited excellent recyclability and chemical stability. Also, the developed method is versatile and can be applied to the different types of substrate material. This robust, simple, and green approach gives great potential to fabricate large-scale material surfaces for the industrial oily wastewater treatment.
    • Isobaric Combustion: A Potential Path to High Efficiency, in Combination with the Double Compression Expansion Engine (DCEE) Concept

      Babayev, Rafig (2018-11) [Thesis]
      Advisor: Johansson, Bengt
      Committee members: Farooq, Aamir; Knio, Omar
      The efficiency of an internal combustion engine is highly dependent on the peak pressure at which the engine operates. A new compound engine concept, the double compression expansion engine (DCEE), utilizes a two-stage compression and expansion cycle to reach ultrahigh efficiencies. This engine takes advantage of its high-integrity structure, which is adapted to high pressures, and the peak motored pressure reaches up to 300 bar. However, this makes the use of conventional combustion cycles, such as the Seiliger–Sabathe (mixed) or Otto (isochoric) cycles, not feasible as they involve a further pressure rise due to combustion. This study investigates the concept of isobaric combustion at relatively high peak pressures and compares this concept with traditional diesel combustion cycles in terms of efficiency and emissions. Multiple consecutive injections through a single injector are used for controlling the heat release rate profile to achieve isobaric heat addition. In this study, the intake pressure is varied to enable a comparison between the isobaric cases with different peak pressures, up to 150 bar, and the mixed cycle cases. Tests are performed at several different levels of EGR. The experiments are performed on a 12.8 L displacement 6-cylinder Volvo D13C500 engine utilizing a single cylinder with a standard 17-compression-ratio piston. In this study, the cylinder represents the high-pressure unit of the DCEE. The fuel used in all the experiments is a standard EU diesel. In each target condition, the different injection strategies are compared with the total amount of fuel kept relatively constant. The results prove that the isobaric combustion concept is feasible with a traditional injection system and can achieve gross indicated efficiencies close to or higher than those of a conventional diesel combustion cycle. Moreover, the results show that with an isobaric cycle, heat transfer losses can be reduced by over 20%. However, the exhaust energy is higher, which can eventually be recovered in the second stage of expansion. Thus, this cycle could be suitable for the DCEE concept. The CO, UHC and soot emission levels are proven to be fairly similar to those of the conventional diesel combustion. However, the NOx emissions are significantly lower for the isobaric combustion.
    • First assessment of viral diversity across corals from the central Red Sea suggests abundant association with Baculoviridae

      Ye, Jin (2018-11) [Thesis]
      Advisor: Voolstra, Christian R.
      Committee members: Moran, Xose Anxelu G.; Tegner, Jesper N.
      Coral reefs are among the most diverse marine ecosystems, but they are threatened by climate change. The foundation of reef ecosystems is the coral holobiont or metaorganism that consists of the coral animal host, photosynthetic microalgae, bacteria, and viruses (among other organisms). While microalgae provide the energy for corals to build the massive three-dimensional skeletons, bacteria support functions related to metabolism, immunity, and environmental adaptation. Conversely, the function of viruses is less well understood. Although viruses were previously associated with coral disease and bleaching, we are missing an overall understanding of the diversity and identity of viruses associated with corals, in particular for understudied areas such as the Red Sea. Here we characterized coral-associated viral community composition using a large metagenomic and metatransciptomic dataset covering > 1 billion sequences across > 100 coral samples collected from 14 different coral species in the central Red Sea. The viral sequence portion shows that coral species significantly differ from each other, but the most abundant viral families were consistently present. Notably, we found a pervasive abundance of Baculoviridae in metagenomes. In contrast, Polydnaviridae were the most abundant viruses in metatranscriptomes, highlighting that the combined approach of metagenomics and metatranscriptomics is informative with regard to deciphering viral diversity and activity. Our study provides a first comprehensive description of viruses associated with Red Sea corals. In line with previous studies, we confirm the presence of Baculoviridae, Polydnaviridae, Phycodnaviridae, Mimiviridae, and Herpesviridae, which may be considered viral families that are globally and commonly associated with corals. The reason for the pervasive abundance of Baculoviridae in Red Sea corals at present remains unknown, but it is tempting to speculate that the association is related to the uniquely warm and salty environment of the Red Sea.