Recent Submissions

  • BranchNet: Tree Modeling with Hierarchical Graph Networks

    Zhang, Jiayao (2021-07-04) [Thesis]
    Advisor: Michels, Dominik L.
    Committee members: Wonka, Peter; Elhoseiny, Mohamed H.
    Research on modeling trees and plants has attracted a great deal of attention in recent years. Early procedural tree modeling can be divided into four main categories: rule-based algorithms, repetitive patterns, cellular automata, and particle systems. These methods offer a very high level of realism; however, creating millions of varied tree datasets manually is not logistically possible, even for professional 3D modeling artists. Trees created using these previous methods are typically static and the controllability of these procedural tree models is low. Deep generative models are capable of generating any type of shape automatically, making it possible to create 3D models at large scale. In this paper, we introduce a novel deep generative model that generates 3D (botanical) tree models, which are not only edible, but also have diverse shapes. Our proposed network, denoted BranchNet, trains the tree branch structures on a hierarchical Variational Autoencoder (VAE) that learns new generative model structures. By directly encoding shapes into a hierarchy graph, BranchNet can generate diverse, novel, and realistic tree structures. To assist the creation of tree models, we create a domain-specific language with a GUI for modeling 3D shape structures, in which the continuous parameters can be manually edited in order to produce new tree shapes. The trees are interpretable and the GUI can be edited to capture the subset of shape variability.
  • Produced Water Pretreatment Prior to Filtration with Forward Osmosis and Membrane Distillation Integrated System

    Alqulayti, Abdullah (2021-07) [Thesis]
    Advisor: Ghaffour, NorEddine
    Committee members: Saikaly, Pascal; Fortunato, Luca; Saqib Nawaz, Muhammad
    The simultaneous treatment of different produced water streams with the forward osmosis membrane distillation hybrid system (FO-MD) has been suggested recently. This work investigates the need for pretreatment of produced water prior to filtration with FO-MD in order to reduce the level of fouling and scaling in the system. The desalter effluent (DE) stream was selected as FO feed solution, and the water oil separator (WO) stream was used as FO draw solution/MD feed solution, and a significant flux decline was observed in FO and MD within the first 5 hours of operations. SEM and EDX analysis indicated that the formation of scale layer on both membranes was the main reason for the sharp flux decline. Silica was the major contributor to the scaling of the support layer of the FO membrane. While the scaling layer on MD membrane consisted mainly of CaSO4 crystals with some deposition of Silica. Therefore, electrocoagulation (EC) was selected for the pretreatment of produced water to target the removal of Ca, SiO2 and SO4 ions in order to reduce the likelihood of inorganic fouling in FO-MD. The different parameters of EC, namely, the current density, electrolysis time, and initial pH were tested at a wide range of values of 7-70 mA/cm2 , 10-60 minutes, 5-9, respectively. calcium and sulfate ions were not effectively removed at the relatively high applied current density of 70 mA/cm2 , while high removal of silica was achieved even at low applied current densities. The optimum conditions of EC for silica removal were found to be 7 mA/cm2 for the current density and 10 minutes for the electrolysis time which resulted in a 97% removal of silica. it was found that due to pretreatment, the average FO and MD fluxes increased by 49% (9.93 LMH) and 39% (8.55 LMH), respectively. Therefore, even though EC did not show promising results in terms of the removal of calcium and sulfate, efficient silica removal was achieved with minimum energy requirements which suggests that it could have a potential to be integrated with the FO-MD hybrid system for the treatment and reclamation of produced water.
  • Improving Formation Pressure Integrity Tests with Field-Wise Test Data Analysis and Hydraulic Impedance Testing

    Abilov, Elmir (2021-07) [Thesis]
    Advisor: Patzek, Tadeusz
    Committee members: Finkbeiner, Thomas; Ahmed, Shehab
    Drilling operations without issues and non-productive time are highly desired by operators. Circulation loss is one of the common issues faced during drilling when a formation is fractured by mud weight or by Equivalent Circulating Density (ECD) exceeding the formation fracture gradient. This makes it necessary to obtain information about in-situ stress and rock strength. Formation Pressure Integrity Tests (FPITs) determine directly the fracture pressure of the formation or test the formation for a safe drilling mud weight window and kick tolerance. Although FPIT is a routine test conducted before drilling each hole section, previous studies and field experience have demonstrated several problems and a lack of unique operational procedures for these tests. This study examines some of the main issues faced during operation and interpretation of FPITs and possible solutions to eliminate them. We generated a unique database of FPITs which includes all necessary technical and non-technical details about each test and analyzed the discrepancy between surface and downhole pressure data generated while conducting FPITs. We also analyzed pressure build-up behavior versus pumped fluid volume and its similarities with Casing Integrity Tests (CIT). Furthermore, we investigated pressure loss rates after shut-in, and the application of hydraulic impedance testing to improve test quality. Our analysis of the discrepancy trends indicated that Reservoir Drilling Fluid (RDF) causes more pressure transmission losses than Oil-Based Mud (OBM). We examined more than 50 tests based on pressure build-up behavior versus pumped fluid volume and obtained an empirical equation that only requires the measured depth to give an estimation for the pressure build-up rate. In addition, comparing CIT with FPIT based on pressure build-up rate shows similarities between the tests, and CIT build-up rate values can potentially be used as an initial assumption for FPIT build-up rate. Our findings reveal that pressure loss rate after pump-off is less than 6 psi/min in more than 65% of the Formation Integrity Tests (FITs). We also suggest to use Hydraulic Impedance Testing (HIT) method together with formation strength tests to give a qualitative indication of fracture initiation and a quantitative estimation of fracture dimensions.
  • Characterization of a Red Multimode Vertical-Cavity Surface-Emitting Laser for Intrinsic Parameters

    Wagstaff, Jonathan (2021-07) [Thesis]
    Advisor: Ooi, Boon S.
    Committee members: Salama, Khaled N.; Schwingenschlögl, Udo; Ng, Tien Khee
    Compared to single-mode VCSELs, multimode VCSELs have not received much attention in models and characterizations for functional parameters, despite making up the majority of commercially available VCSELs [1]. In particular, the extraction of the linewidth enhancement factor for multimode VCSELs has been overlooked, likely due to difficulties in measurement. Additionally, multimode models for VCSELs have, until recently, omitted spectral characteristics such as linewidth [2]. This is the first work to report a measured linewidth enhancement factor value (lower bound) for a multimode VCSEL. A characterization for the functional parameters of a red multimode vertical-cavity surface-emitting laser (VCSEL) is shown herein. The extracted values form a complete working set of parameters for the laser rate equations. The techniques employed for extracting values include frequency responses, power versus current fittings, and optical spectral measurements. From the frequency responses at various bias currents, the relaxation oscillation frequency and damping factor are found. The power versus current curve is fitted to find parameters including the modal spontaneous emission rate and carrier density at threshold. The spectral measurements are used for evaluating the linewidth enhancement factor (LEF) also known as the alpha factor or Henry factor. These 5 methods have been applied previously to characterizing single-mode VCSELs [3]–[5]. The experimentally extracted parameters herein are important for creating accurate models and simulations for multimode VCSELs. Improved multimode VCSEL models are necessary for improving optical communication, especially for short-range optical interconnects [2]. The measured parameters for the characterized VCSEL are comparable to similar single-mode VCSELs characterized in other works. This is promising because multi-mode VCSELs have higher output power than their single-mode counterparts, thus these results may aid in improving short-range optical interconnects.
  • Evaluation of Different Forward Osmosis Membrane Cleaning Strategies for Produced Water Streams Treatment

    Alamoudi, Talal (2021-07) [Thesis]
    Advisor: Ghaffour, NorEddine
    Committee members: Pinnau, Ingo; Vrouwenvelder, Johannes S.; Saqib Nawaz, Muhammad
    Forward osmosis (FO) as a novel membrane separation technology has recently been investigated in various water treatment applications. The natural mass transfer process between two solutions driven by the osmotic pressure difference leads to many operational advantages in the FO process, such as low energy consumption and minimal fouling problems. It makes FO a feasible technology for the treatment of produced water (PW). Although previously, the treatment of PW using FO has been investigated, osmotic backwashing (OB) is not systematically examined for water flux recovery of the PW fouled FO membranes. Moreover, the cleaning of FO membranes used for the simultaneous treatment of different PW streams was never previously attempted. In this study, OB was thoroughly investigated for the cleaning of PW-fouled FO membranes. Also, FO membrane chemical cleaning using SDS and NaOH solutions was examined too. To investigate OB, the cleaning efficiency of a 60 min OB cleaning protocol was examined under different FO operating modes in (5 x 20 h) experiments using synthetic desalter effluent as FO feed solution (FS) and 1.2 M NaCl solution or water-oil separator outlet (WO) as draw solutions (DS). The AL-FS (active layer facing FS) mode outcompeted the AL-DS (active layer facing DS) mode, achieving a flux of 12.9 LMH and 80.1% water reclamation when using WO as a DS. Therefore, this FO configuration 5 was selected when evaluating the cleaning protocols. Moreover, after evaluating different OB methods, the 30 min OB protocol achieved the highest system efficiency rate of 95% and was studied for the treatment of real PW streams. The SDS and NaOH chemical cleaning methods achieved flux recovery rates of 99% and 98% by the end of the third treatment cycle, respectively, outperforming the 89% flux recovery rate of the optimized OB protocol. Although the investigated cleaning methods were able to restore the system performance, a substantial increase in RSF was observed due to mainly irreversible colloidal fouling. This study demonstrates the feasibility of OB and chemical cleaning in restoring FO system performance for the simultaneous treatment of PW streams
  • Is Post Transplantation Performance Driven by the Variability of the Habitat of Origin?

    Golding, Victoria C. (2021-07) [Thesis]
    Advisor: Aranda, Manuel
    Committee members: Peixoto, Raquel; Schmidt-Roach, Sebastian
    As rising sea temperatures and increases in the frequency, duration, and intensity of marine heatwaves threaten coral survival at a global scale, research on the capacity of corals to acclimatize and adapt to changing environments has become a high priority. Understanding how environmental parameters shape coral thermal performance across habitats is crucial to identify populations with high vulnerability or high thermal tolerance to future ocean warming. In recent studies, corals from high temperature variable environments (HVE) have shown increased thermal tolerance compared to corals from low temperature variable environments (LVE). Here, I investigate if these phenotypes are shaped by acclimatization, habitat-specific adaptation, or a combination of both, in the branching coral, Acropora hemprichii, by reciprocally transplanting individuals between a back (HVE) and front reef (LVE). After ten months of acclimatization, comparisons of photosynthetic efficiency (photosystem II), mortality, and bleaching recovery was assessed for > 2 months between coral ramets following a natural bleaching event in the central Red Sea. In tandem, coral bleaching severity and recovery in each reef environment was assessed to genus level by photographic surveys of fixed belt transects. Bleaching between reef sites was compared against bleaching in treatments to differentiate the role of habitat specific adaptation and acclimatization in the corals. This study aims to elucidate the evolutionary mechanisms driving coral habitat-specific thermal stress tolerances, which may inform coral reef management and restoration efforts.
  • New Algorithms to Solve the Positioning Problem of Outdoor Localization Using Constrained and Unconstrained Optimization Techniques

    Alsaif, Muhanned (2021-07) [Thesis]
    Advisor: Al-Naffouri, Tareq Y.
    Committee members: Feron, Eric; Wittum, Gabriel
    The demand for outdoor precise location is increasing with the development of new applications such as autonomous vehicles, exploration robots and wireless sensor networks. Global Navigation Satellite System (GNSS) is the go-to system for outdoor localization. This thesis focuses on developing new methods for GNSS single-point positioning (SPP) model, where no access to a reference station or precise GNSS parameters is needed. We investigated the limitations of the standard method, least- squares adjustment (LSA), and we derived the Cramer-Rao bounds for the SPP estimation problem. We also investigated different techniques to formulate the positioning problem with the goal to increase the accuracy. A new method is developed by reformulating the problem as difference-of-convex program (DC program) and utilizing convex-concave procedure (CCCP) to solve the positioning problem without linearizing the observation equations. In addition, we examined the potential of multiple-receiver systems in increasing the accuracy. We formulated the multiple- receiver SPP estimation problem, and we proposed to configure the multiple receivers in a fixed equilateral triangle to exploit the symmetry and the geometrical constraints of the configuration. We extended the use of LSA in multiple-receiver system. We also developed a modification of LSA algorithm, named least-squares adjustment extension (LSAE), that utilizes attitude information and the constraints of the multiple-receiver system. In addition, we developed a new algorithm to optimizes the SPP estimates over the equilateral triangles Riemannian manifold, which enforces the geometrical constraints of the multiple-receiver system. Furthermore, we derived the constrained and the unconstrained Cramer-Rao bounds (CRB and CCRB) for the multiple-receiver SPP problem. Moreover, we investigated the influence of both attitude information and the equilateral triangle baseline length on the algorithms’ performances and the derived CCRB. Finally, we carried out a numerical analysis by implementing the algorithms and the bounds in MATLAB, where we tested the algorithms on simulated GNSS scenarios. The proposed multiple-receiver methods provide more precise estimates for the SPP problem in comparison to the single receiver methods.
  • Environmental origin and compartmentalization of bacterial communities associated with Avicennia marina mangroves on the Red Sea coast

    Escobar prieto, Juan david (2021-07) [Thesis]
    Advisor: Daffonchio, Daniele
    Committee members: Marasco, Ramona; Soares, Alexandre; Pain, Arnab
    Mangrove forests are highly productive ecosystems widespread in tropical and subtropical coastlines, with a coverage of 75% of the world’s tropical shorelines. Mangrove plants developed specific physiological and morphological adaptation to thrive in such unique environments. Together with plant adaptations, mangroves develop a tight partnership with microorganisms, mainly bacteria and fungi, that form the so-called mangrove-microbiome. Plant-associated microorganisms are generally recruited by the root system (root tissues and rhizosphere) and the colonization process starts with the release of root-related exudates detected by the surrounding edaphic microorganisms that are attracted in the rhizosphere zone. Then, root surface selects those microorganisms that can enter the tissues as endophytes. The microorganisms recruited belowground can migrate through the plant tissues by using the plant vessels and may colonize the aboveground compartments of the plant. Here, I aimed to evaluate the environmental origin and compartmentalization of the mangrove microbiome. To do this, I sampled bulk sediments, sea water, and mangrove plant compartments (root rhizosphere and endosphere, pneumatophores, shoot, leaves, flowers and propagules) of 20 gray mangrove trees (Avicennia marina L.) across two sites on the Red Sea coast of the King Abdullah University of Science and Technology (KAUST), Saudi Arabia. By high-throughput sequencing of the bacterial 16S rRNA gene, I showed that the bacterial assembly in A. marina plant compartments follows a clear niche partition process in which bacterial communities are actively recruited from the surrounding ecosystem (sediment and sea water) by the root system, and further distributed across the different plant organ and compartments. Moreover, the composition of microbiome detected had many similitudes with others previously described around the world, suggesting that certain bacteria represent a mangrove “core microbiome”. The conservation of microbiome composition, mainly driven by environmental and host selection, that beneficial bacteria provide to the plant and contribute to its growth and fitness by several mechanisms. Thus, the characterization and identification of mangrove microbiome can meliorate our knowledge regarding plant–microbe interactions, as well as put the bases for the development of Nature-based Solution (NBS) to enhance reforestation and rehabilitation of mangrove ecosystems
  • A Synergy of Spatiotemporal Transcriptomic Techniques for Non-Model Organism Studies: Something Old, Something New, Something Borrowed, Something Ocean Blue

    Watson, Kelly (2021-07) [Thesis]
    Advisor: Aranda, Manuel
    Committee members: Peixoto, Raquel; Frøkjær-Jensen, Christian
    In situ hybridization (ISH) has played a crucial role in developing a spatial transcriptomic understanding of emerging model organisms in the past, but advancing high-throughput RNA-sequencing (RNA-seq) technology has pushed this method into the shadows, leading to a loss of data resolution. This shift in research towards the exclusive use of RNA-seq neglects essential considerations for transcriptomic studies including the spatial and temporal expression of transcripts, available budget, experimental design needs, and validation of data. A synergy of spatiotemporal transcriptomic techniques is needed, using the bulk and unbiased analysis of RNA-seq and the visual validation and spatiotemporal resolution of ISH. Integration of this synergistic approach can improve our molecular understanding of non-model organisms and establish the background data needed for advancing research techniques. A prime example lies within an emerging model of the marine science and symbiosis fields, where I present a case study on a threatened coral reef keystone – the cnidarian-dinoflagellate symbiosis. Establishing a whole-mount ISH protocol for the emerging cnidarian model Aiptasia (sea anemone) will help future studies reveal the gene regulation underpinning the establishment, persistence, and breakdown of this complex symbiotic relationship.
  • Impact of Different Cleaning Methods on Biofilm Removal in Membrane Distillation

    Amin, Najat A. (2021-07) [Thesis]
    Advisor: Ghaffour, NorEddine
    Committee members: Vrouwenvelder, Johannes S.; Alpatova, Alla
    Membrane distillation (MD) is an emerging thermal separation technology which proved its efficiency in desalination of highly saline waters, including seawater, brines and impaired process waters. In a long-term prospective, MD can reinforce sustainability of the clean water production and mitigate the water-energy stress caused by lacking suitable freshwater recourses. However, just like in any other membrane separation process, MD membrane is susceptible to biofouling which presents a significant challenge by substantially reducing its performance and deteriorating permeate quality. This study evaluated different cleaning methods aimed at controlling biofilm development on a surface of hydrophobic MD membrane in a direct contact MD (DCMD) process fed by the Red Sea water. This was achieved by applying physical (hydraulic) cleaning and chemical cleanings with a range of chemicals utilized in membrane separation processes including citric acid (mineral acid), ethylenediaminetetraacetic acid (EDTA, metal-chelating agent) and sodium hypochlorite (NaOCl, oxidant). Flux recovery and changes in biofilm morphology, including its thickness and structure as well as microbial and extracellular polymeric substances (EPS) contents before and after cleanings have been analyzed to elucidate cleaning mechanisms and suggest effective strategies of biofilm removal. The results showed that 0.3% EDTA exhibited the best cleaning performance resulting in the highest permeate flux recovery (93%), followed by 0.3% NaOCl (89%), 3% citric acid (76%), and hydraulic (66%) cleanings. Application of EDTA and NaOCl has also resulted in the lowest number of bacterial cells and substantial reduction of the peak intensities caused by protein-like compounds and tyrosine-containing proteins present on the membrane surface after its treamtent. The observed trends are in a good correlation with the optical coherence tomography (OCT) observations which revealed substation changes in biofilm morphology leading to a significant reduction of biofilm thickness which followed the order of hydraulic cleaning < citric acid cleaning < NaOCl cleaning < EDTA cleaning. This study suggests that selection of an appropriate cleaning type and formulation is critical for achieving sustainable MD plant operations, both technically and economically.
  • Bottled Drinking Water: Assessment of Physical-Chemical and Microbiological Parameters and Biological Stability of 19 Different Brands Available in Saudi Arabia

    Nadreen, Yasmeen (2021-07) [Thesis]
    Advisor: Vrouwenvelder, Johannes S.
    Committee members: Gonzalez-Gil, Graciela; Saikaly, Pascal
    Bottled drinking water is a common form of water consumption that has grown in popularity and dependency. With countless types and brands available, there are factors to consider regarding the variations in mineral content and microbiological quality, and environmental consequences associated with importing natural bottled waters. Saudi Arabia is the largest desalinated water producer, and although there are scarce natural water resources, consuming locally produced water can alleviate environmental pressures, so long as local bottled water is of good quality and provides the basic function of drinking water. The objective of this study is to scrutinize the variations in bottled waters available in the Saudi market and compare local and imported waters regarding water quality and compliance with health regulations. Surveying local bottled waters revealed that over 60% were imported, adding to the environmental significance. Results from inductively coupled plasma-atomic emission spectroscopy, ion chromatography, and pH meters indicate most bottled waters were compliant with health standards. Flow Cytometry (FCM) was used to determine microbial cell densities. Purified waters, on average, contained significantly lower concentrations than other water types, while mineral waters contained the most cells per milliliter. Microbiological stability was examined through incubating samples at 30°C to promote microbial growth, and results were analyzed using an online FCM system. Purified waters had the least amount of growth and to a lesser degree than mineral and sparkling, which varied in microbial growth responses. DNA extractions and microbial community analyses were performed on select mineral waters before and after incubation. Results showed microbial genera found were similar between samples from the same country and some were unique. All samples exhibited some change in microbial community composition after incubation, signifying that certain communities thrived more than others. Proteobacteria was the most common abundant phylum among samples. Although analysis was restricted to the genera level, there were no health concern associated with types of bacteria discovered. In conclusion, local purified waters had greater microbiological quality and stability than imported waters, and mineral compositions were within the healthy range. Reducing reliance on foreign natural waters may help alleviate environmental consequences and improve local economy
  • Understanding the Genetic Basis for piRNA Silencing in the Soma and Germline of Caenorhabditis elegans

    Peng, Yuli (2021-07) [Thesis]
    Advisor: Frøkjær-Jensen, Christian
    Committee members: Lauersen, Kyle J.; Krattinger, Simon G.
    C. elegans is a commonly used genetic model organism due to the ease of genetic screens, transgenesis, and microscopy. Here, I describe methods that improve transgenesis in C. elegans and the development of a genetic screen to identify genes involved in the piRNA pathway. Transgenesis is commonly used for most laboratories that utilize C. elegans and improvements are therefore likely to facilitate research across many research areas. In the first chapter, I characterized a pan-muscular promoter that drives fluorophore expression to help identify C. elegans transgenesis. This promoter is an improved co-injection marker as it drives bright fluorescence with low toxicity and high efficiency. In the second chapter, I study piRNAs which are a large class of non-coding RNA that play important roles in protecting the genome from transposable elements in most animals. The study of piRNAs has mostly focused on their function in the germline, but recent evidence suggests functions in somatic cells such as neurons. To identify genes involved in the piRNA pathway in C. elegans, I performed a chemical genetic screen. I identified one mutant with a somatic phenotype and six mutants with a germline phenotype. I have focused on the germline and sequenced two strains and identified candidate genes involved in the piRNA pathway. Future work will focus on validating and identifying the remaining mutants.
  • A Multi-platform Comparison of Phenology for Semi-automated Classification of Crops

    Kanee, Sarah (2021-07) [Thesis]
    Advisor: McCabe, Matthew
    Committee members: Johansen, Kasper; Blilou, Ikram
    Remote sensing has enabled unprecedented earth observation from space and has proven to be an invaluable tool for agricultural applications and crop management practices. Here we detect seasonal metrics indicating the start of the season (SOS), the end of the season (EOS) and maximum greenness (MAX) based on vegetation spectral signatures and the normalized difference vegetation index (NDVI) for a time series of Landsat-8, Sentinel-2 and PlanetScope imagery of potato, wheat, watermelon, olive and peach/apricot fields. Seasonal metrics were extracted from NDVI curves and the effect of different spatial and temporal resolutions was assessed. It was found that Landsat-8 overestimated SOS and EOS and underestimated MAX due to its low temporal resolution, while Sentinel-2 offered the most reliable results overall and was used to classify the fields in Aljawf. Planet data reported the most precise SOS and EOS, but proved challenging for the framework because it is not a radiometrically normalized product, contained clouds in its imagery, and was difficult to process because of its large volume. The results demonstrate that a balance between the spatial and temporal resolution of a satellite is important for crop monitoring and classification and that ultimately, monitoring vegetation dynamics via remote sensing enables efficient and data-driven management of agricultural system
  • Geometry-based self-assembly of DNA origami-protein hybrid nanostructures

    Al-Zarah, Hajar A. (2021-07) [Thesis]
    Advisor: Habuchi, Satoshi
    Committee members: Liberale, Carlo; Frokjaer-Jensen, Christian
    Biological nanomaterials are defined as materials with sizes within the nanoscale range of 1 - 100 nm. The fundamental functionalities and biocompatibility of these materials can be tailored for biotechnology applications. In 1983, Ned Seeman successfully developed the first customized DNA nanostructures, Holliday junctions. Since then, the field has continued to expand rapidly and various 2D and 3D nanostructures has been designed. Although the high predictability of DNA base-pairing is essential for the design of complex DNA nanostructures, it greatly limits its functional versatility; therefore, proteins are conjugated with DNA nanostructures to compensate for that. DNA origami-protein hybrid nanostructures were introduced in 2012. However, the structural units based on DNA origami-protein hybrid nanostructures are still limited, and the majority are constructed by covalent or sequence-specific non-covalent interactions. Here we utilize the inherent, non-sequence-specific interaction between DNA and histones to present sequence-independent self-assembled DNA origami-protein hybrid nanostructures. We demonstrated using various molecular biology and imaging techniques that ssDNAs and histone proteins self-assemble into structurally well-defined complexes. We successfully assembled DNA origami–histone hybrid nanostructures using two different shapes of DNA origami: rectangular (PF-3), and rectangular with central aperture (PF-2) nanostructures. We observed precise localization of nucleosome-like histone-ssDNA nanostructures at the edge (PF-3) or the center (PF-2) of the DNA origami. In addition, we demonstrated that this DNA origami-histone interaction results in the assembly of larger DNA origami complexes, including a head-to-head type dimer and a cross-shape complex. Our results suggest the successful self-assembly of the DNA origami–histone hybrid nanostructures provide a principal structural unit for constructing higher-order nanostructures. Given the reversible nature of the geometry-based noncovalent interaction between the DNA origami and the nucleosome-like histone-ssDNA nanostructures, the self-assembly/disassembly of DNA-histones hybrid nanostructures may open new opportunities to construct stimuli-responsive DNA-protein hybrid nanostructures.
  • Developing Production Methods for Different Microbial Strains and Beneficial Testing on Crop Species

    Alghanmi, Linah Y. (2021-07) [Thesis]
    Advisor: Hirt, Heribert
    Committee members: Blilou, Ikram; Chodasiewicz, Monika
    Microorganisms will play a significant role in the agricultural revolution in the coming decades and help meet the growing population's needs. Hence, understanding the impact of beneficial bacteria on crop development is key to the future of developing microbial products. The ability of PGPB to increase crop yields has been recently investigated in agriculture, as PGPB can support and protect plants under different stresses. Since PGPB interactions occur naturally, finding a method to apply beneficial bacteria while maintaining their efficiency and quality is a topic of interest. PGPB have been used as microbial inoculants, biofertilizers, and also as seed coatings. Preservation of microorganisms through desiccation has been used as the preferred method for long-term storage of microbial culture. The use of dry powders is favored over liquid cultures due to their ease of transportation and better quality control. For microbial preservation, freeze-drying has been defined as the most convenient and satisfactory preservation method for long-term storage. Freeze-drying is generally preferred over other drying techniques as it gives a high-quality dehydrated product. However, to reach a high-quality product, many parameters need to be monitored, such as bacterial cell concentration, growth medium, lyophilization buffer, rehydration, and duration of freeze-drying. In this research, SA190 was freeze-dried with 10% sucrose mixed with 5% trehalose as lyophilization buffer. Pseudomonas argentinensis SA190 was isolated from the root nodules of the desert plant Indigofera argentae in Saudi Arabia, specifically Jizan. The SA190 freeze-dried product was examined by several tests to assess the product viability and quality, such as accelerated test and water stability test. For future work, the effect of freeze-dried SA190 on plant growth and crop yield will be investigated. Moreover, optimization of the freeze-drying process, formulation, and packaging for commercial will be considered. In addition, bacterial strains isolated in DARWIN21 project with promising effects on plant growth, will be subjected to freeze-drying process.
  • Molecular Insights into the A. thaliana CDC48-NPL4-UFD1 Complex

    Zahodnik-Huntington, Brandon D. (2021-07) [Thesis]
    Advisor: Arold, Stefan T.
    Committee members: Hamdan, Samir; Blilou, Ikram
    The maintenance of protein homeostasis as a response to changing external conditions is crucial for cellular survival and proper function. Since plants cannot adapt by changing location, their need for a rapid intracellular response is accentuated. The AAA ATPase CDC48 maintains protein homeostasis in conjunction with NPL4 and UFD1 by coupling ATP hydrolysis with mechanical force to extract and unfold ubiquitylated proteins from organelle membranes, chromatin, or protein complexes. Our bioinformatic analysis revealed considerable domain and binding motif differences in A. thaliana NPL4 compared to its orthologs in animals and fungi. Using ITC, MST, and SEC-MALS, we found that NPL4 and UFD1 did not heterodimerize, NPL4 bound to CDC48A in the absence of UFD1, and the complex was not stable in vitro. Additionally, we provided the first medium-high-resolution reconstructions of CDC48A in both an AMP-PNP bound and apo state, using cryo-EM. AMP-PNP bound CDC48A was reconstructed in both a tense (3.3 Å) and relaxed (3.5 Å) conformation with the N domain was positioned above or coplanar with the D1 ring, respectively. Our heterogeneity analysis using CryoDRGN revealed continuous flexibility of the N domains between the two conformations. The apo state was reconstructed as a single conformation at 4.4 Å resolution. A cryo-EM reconstruction of the complex was also obtained at a resolution of ~6 Å, which showed expected cofactor stoichiometry and binding positions. Through our efforts, we have observed differences in the interaction between A. thaliana CDC48A and its cofactors UFD1 and NPL4 that may correspond to functional differences between kingdoms.
  • Application of Physics-Informed Neural Networks to Solve 2-D Single-phase Flow in Heterogeneous Porous Media

    Alhubail, Ali (2021-07) [Thesis]
    Advisor: Hoteit, Hussein
    Committee members: Sun, Shuyu; Ahmed, Shehab
    Neural networks have recently seen tremendous advancements in applicability in many areas, one of which is their utilization in solving physical problems governed by partial differential equations and the constraints of these equations. Physics-informed neural networks is the name given to such neural networks. They are different from typical neural networks in that they include loss terms that represent the physics of the problem. These terms often include partial derivatives of the neural network outputs with respect to its inputs, and these derivatives are found through the use of automatic differentiation. The purpose of this thesis is to showcase the ability of physics-informed neural networks to solve basic fluid flow problems in homogeneous and heterogeneous porous media. This is done through the utilization of the pressure equation under a set of assumptions as well as the inclusion of Dirichlet and Neumann boundary conditions. The goal is to create a surrogate model that allows for finding the pressure and velocity profiles everywhere inside the domain of interest. In the homogeneous case, minimization of the loss function that included the boundary conditions term and the partial differential equation term allowed for producing results that show good agreement with the results from a numerical simulator. However, in the case of heterogeneous media where there are sharp discontinuities in hydraulic conductivity inside the domain, the model failed to produce accurate results. To resolve this issue, extended physics-informed neural networks were used. This method involves the decomposition of the domain into multiple homogeneous sub-domains. Each sub-domain has its own physics informed neural network structure, equation parameters, and equation constraints. To allow the sub-domains to communicate, interface conditions are placed on the interfaces that separate the different sub-domains. The results from this method matched well with the results of the simulator. In both the homogeneous and heterogeneous cases, neural networks with only one hidden layer with thirty nodes were used. Even with this simple structure for the neural networks, the computations are expensive and a large number of training iterations is required to converge.
  • Modeling free space optical communication channels for future generation systems deployment

    Alqurashi, Fahad (2021-07) [Thesis]
    Advisor: Alouini, Mohamed-Slim
    Committee members: Ooi, Boon S.; Shihada, Basem
    The COVID-19 global pandemic forced long lock-downs and physical distancing in different world regions. As a consequence, many jobs, services, and courses switched to online mode. This sudden turn of events created a dramatic increase in internet bandwidth demand, which has reached crisis point—even in developed countries—and widened the gap between those living in cities and far-flung regions. Installing new optical fibers to extend the capacity can be expensive. Radiofrequency (RF) is cur- rently the technology of choice to satisfy the bandwidth demand in under-connected regions, but is bandwidth-limited and strictly regulated. Connecting the unconnected via laser beams propagating in the atmosphere can be an efficient solution to provide fiber-like connectivity, while also being economically profitable. Free-space optics (FSO) is an unlicensed technology that uses infrared links to connect two communi- cating terminals. FSO systems can be running quickly compared to RF ones. FSO is also seen as a potential solution to provide high-speed connectivity between satellites and ground stations, and fly unmanned aerial vehicles (UAVs) and ground terminals. However, FSO is subject to various channel-related challenges, including atmospheric attenuation, turbulence, and pointing errors. In this thesis, we develop an FSO chan- nel simulation tool that considers the various effects that could potentially occur in terrestrial and vertical channels. We extend our study to cover structured light beams, which have been intensively considered in the last decade, as an extra degree of freedom for FSO. Finally, we consider realistic meteorological data from different regions in the Kingdom of Saudi Arabia to identify the best locations to deploy FSO systems.
  • Carbonate Acidizing: Modeling and Uncertainty Propagation Analysis

    Sahu, Qasim (2021-07) [Thesis]
    Advisor: Hoteit, Hussein
    Committee members: Alafifi, Abdulkader Musa; Vahrenkamp, Volker C.
    Reservoir stimulation is a common technique used to improve the productivity of carbonate reservoirs. One of the effective stimulation methods is carbonate acidizing. This process involves injecting a reactive fluid to dissolve the rock mineral, creating a conductive path for hydrocarbon flow. With the development of tight and unconventional reservoirs, stimulation has become more critical for optimal economic production. This study aims to simulate the dissolution of carbonate in matrix acidizing. A reactive transport model is implemented in a finite – element solver to simulate the initiation and propagation of the dissolution channel in the carbonate rock in a two – dimensional domain. We investigate the effect of varying the injection rate on the dissolution channel and the efficiency of the acidizing fluid. Next, we use polynomial chaos expansion to conduct uncertainty propagation analysis. These uncertainties may have a major impact on the predictability of the simulation model. We utilize the surrogate model and Sobol indices to identify the most significant parameter in the model. The analysis provides an assessment of how the uncertainty can propagate to the model’s response. Also, we utilize the surrogate model to calculate the univariate effect. The results showed that the dissolution channel and pore volume to breakthrough depends on the injection rate. Furthermore, the surrogate model reproduces the simulation model results for the 5 dissolution channel, the pore volume to breakthrough, and the effective permeability. The global sensitivity analysis shows that the acid capacity number is the most significant parameter for the pore volume to breakthrough with the highest Sobol index value. For effective permeability, the initial mean porosity is the primary source of uncertainty. The marginal effect calculated for the individual parameter correlates with the results from Sobol indices.
  • Shock Fitting For Converging Cylidrical Shocks In Hydrodynamics And Ideal Magnetohydrodynamics

    Arshad, Talha (2021-07) [Thesis]
    Advisor: Samtaney, Ravi
    Committee members: Farooq, Aamir; Parsani, Matteo; Bakhsh, Abeer
    Converging shocks have long been a topic of interest in theoretical fluid mechanics, and are of prime importance in inertial confinement fusion. However, tracking converging shocks in numerical schemes poses several challenges. Numerical schemes based on shock capturing inherently diffuse out shocks to multiple grid cells, making it hard to track the shock. Converging shocks are significantly harder to track, as this numerical smearing is much more significant when converging shocks approach the axis of convergence. To mitigate this problem, we transform the conservation laws to a non-inertial frame of reference in which the accelerating shock is stationary. A system of equations is derived based on the transformed conservation laws coupled to the shock speed obtained from jump conditions and a characteristic-based derivation of a relation governing shock acceleration. We solve these equations using a finite volume method. Our numerical results compare favorably with the analytical value of Guderley exponent for self-similarly converging cylindrical hydrodynamic shocks. Results for fast magnetosonic shock in MHD are also presented and compared with results from geometrical shock dynamics (GSD). Results from our shock fitting method, developed without any approximation to the original ideal magnetohydrodynamics equations, provide further credibility to GSD applied to converging fast magnetosonic shocks. This sort of shock fitting is a precursor to future multidimensional stability analysis of imploding shocks.

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