Now showing items 21-40 of 1067

    • De novo assembly of the Tamarindus indica genome as part of the Kingdom of Saudi Arabia Native Genome Project

      Navarrete Rodriguez, Maria Eugenia (2022-08-10) [Thesis]
      Advisor: Wing, Rod Anthony
      Committee members: Blilou, Ikram; Merzaban, Jasmeen
      The Kingdom of Saudi Arabia Native Genome project aims to generate genomic resources for all the plants, animals, and associated microbiome species in the Kingdom. Tamarindus indica was pointed out by the MEWA as an endangered native species in the KSA and forms part of the first 15 plant species to be studied in the NGP. A voucher tree was identified in the Rijal Almaa region, from which leaf samples were collected. HMW DNA was extracted from this tissue and sequenced using CCS with the Pac-Bio Sequel II platform. The raw data obtained from the sequencing was assembled using HIFIASM, contaminant contigs were removed, and the 15 largest contigs were selected as the primary T. indica assembly. The genome sequence of Sindora glabra was used as reference guide for primary scaffolding, and T. indica optical maps were used for super-scaffolding. Secondary scaffolding utilized Hi-C data to produce a chromosome level assembly of the T. indica genome. Transposable element analysis and a preliminary annotation were performed on the final assembly. This project represents the first step in studying T. indica for the NGP. The final assembly can be used as a foundation for more genetic studies on this species, as a possible reference for other legume species from the Detarioideae family, and for Neo-domestication and reforestation. The pipeline developed for this project can also be used as a template for sequencing and assembling the remaining species in the NGP.
    • Effect of Gallium and Platinum distribution encapsulated in Silicalite-1 (MFI) zeolite on controlled propane dehydrogenation reaction

      Almukhtar, Fadhil (2022-08-04) [Thesis]
      Advisor: Ruiz-Martinez, Javier
      Committee members: Huang, Kuo-Wei; Grande, Carlos A.
      The preparation method of the catalyst highly impacts its properties and activity. Optimizing the synthesis conditions mainly targets improving the catalyst performance and overcoming the bottlenecks such as sintering of metal active sites, deactivation, short catalyst lifetime and poor selectivity. In this study, we investigated the influence of the design and preparation method of Silicalite-1 bearing Pt and Ga active species on the properties and the performance of the catalysts for propane dehydrogenation reaction aiming to increase propylene yield. Various synthesis routes, leading to different Pt and Ga location and distances were tested: (1) supporting metals on the zeolite where both Pt and Ga are randomly distributed on the surface, (2) confining of Pt and Ga within the zeolite pores following in-situ approach with no control of their relative positions, and (3) core-shell design where one metal is confined within Silicalite-1 is covered by a Silicalite-1 layer including the second metal. The influence of structure, textural properties, location of Pt and Ga nanoparticles and their synergetic interaction to form Pt-Ga alloys were studied using several characterization techniques such as XRD, BET, TEM-EDX and NMR. Catalytic performance revealed that confining metals improved the selectivity and lifetime of the catalyst. Moreover, spatial separation of Pt and Ga through the core-shell design further boosted the reaction yield with conversions hitting the equilibrium limit. Ga/Pt ratio played a crucial role in tuning the catalyst performance. 0.26%Pt(core)-2.65%Ga(shell)@S-1 catalyst with Ga/Pt of 10 exhibited superior results of 70.5% conversion and 98% selectivity.
    • Dry Reforming of Methane by Ni-In-Ce Supported Catalysts

      Alharbi, Abdulrahman (2022-08) [Thesis]
      Advisor: Ruiz-Martinez, Javier
      Committee members: Grande, Carlos A.; Huang, Kuo-Wei
      In light of global warming’s environmental implications, research is shifted towards potential processes that can utilize CO2 and reduce its emissions in the industrial sector. One of the promising processes is dry reforming of methane (DRM), which is capable of utilizing CO2 and producing valuable syngas (H2 and CO). The main challenge of DRM is the deactivation of catalysts under the reaction temperatures (above 700 °C) due to sintering of the active metal and coke formation. Ni-based catalysts are the most widely investigated catalysts in literature for DRM due to their cost efficiency and availability. This study is an extension of the work done by Saudi Basic Industries Corporation (SABIC) devoted to investigating Ni-Ce-In system for DRM reaction. Five catalysts were synthesized by dry impregnation method according to SABIC synthesis procedure (Ni/Al2O3, Ni-In/Al2O3, Ni/CeO2/Al2O3, Ni/In-CeO2/Al2O3, and Ni-In/CeO2/Al2O3). The metallic loading targets were 7.5 wt.%, 10 wt.%, and 0.8 wt.% for nickel, cerium, and indium, respectively. The addition of indium in combination with cerium resulted in the highest catalytic activity. Additionally, the co-impregnation of indium and cerium resulted in enhancing the catalytic activity more than subsequential impregnation (Ni/In-CeO2/Al2O3 compared to Ni-In/CeO2/Al2O3). The addition of cerium or indium separately with nickel did not seem to affect activity since Ni/Al2O3, Ni-In/Al2O3, and Ni/CeO2/Al2O3 exhibited similar conversion values. All catalysts were stable for more than two days under DRM conditions without deactivating. Therefore, deactivation behaviors of the catalysts were not covered in this study.
    • Influence of A-site Cation Composition on Electronic Properties of Halide Tin Perovskites

      Tounesi, Roba S. (2022-08) [Thesis]
      Advisor: Baran, Derya
      Committee members: Bakr, Osman; Heeney, Martin
      Tin halide perovskites are gaining interest as a replacement for lead perovskites for various device applications. However, compared to lead-based perovskites, the understanding of their charge transport properties has received limited attention. In particular, the effect of A-site cation on electronic properties of tin perovskites warrants further attention to design efficient material systems for various applications beyond photovoltaics. In the presented work, leveraging the composition tunability of halide perovskites, we establish a relationship between the A-site composition and electronic properties in tin perovskites (ASnI3). The effect of prototypical A-site cations such as Formamidinium (FA), Methylammonium (MA), Cesium (Cs), and their binary combinations on structure, morphology, and electronic properties are explored. MACs combination offers the highest electrical conductivity owing to enhanced mobility compared to mono-cations MA and Cs, resulting in an impressive electrical conductivity of ∼ 143 Scm−1 and thermoelectric power factor of ∼ 149 μW m−1K−2. The library of properties generated for Sn perovskites in this work will be helpful for their further development as an electronic material.
    • Precise genomic deletions and insertions via paired prime editing for crop bioengineering

      Moreno-Ramírez, Jose Luis (2022-08) [Thesis]
      Advisor: Mahfouz, Magdy M.
      Committee members: Blilou, Ikram; Lauersen, Kyle J.
      CRISPR/Cas has been developed for targeted mutagenesis in diverse species, including plants. However, precise genome editing via homology-directed repair (HDR) is inefficient in plants, limiting our ability to make large deletions or insertions in the plant genomes. Prime editing increases the control over the desired editing and allows the precise introduction of all types of mutations, including insertion, deletions, and all possible base conversions, albeit at low efficiencies. Here, we designed a dual prime editing system to generate large deletions and precise insertions of sequences by repairing template complementarity. We coupled dual pegRNA with Cas9 nickase (nCas9) to generate deletions and insertions. In another modality, we used dual pegRNA with wild-type Cas9 to generate double-stranded breaks to improve the editing at the targeted sites. We tested dual pegRNAs to delete the last exon in OsCCD7, delete the microRNA targeted sequence in OsIPA, and insert the T7 promoter in the 3'UTR of OsALS. Our results showed a high frequency of targeted insertion of the T7 promoter sequence in the 3'UTR of OsALS with wtCas9 and nCas9. Sanger sequencing analysis showed partial deletions at the targeted locus. Further improvements in the designs of pegRNAs will increase the precise genome insertions and deletions in plants.
    • The Influence of Varying Si/Al Ratio (SAR) of Beta Zeolite in the Methanol to Hydrocarbons (MTH) Reaction

      Bokhari, Maram (2022-08) [Thesis]
      Advisor: Ruiz-Martinez, Javier
      Committee members: Grande, Carlos A.; Khashab, Niveen M.
      Excessive greenhouse gas emissions, like carbon dioxide, contribute to global warming and climate change. Methanol is hydrogenated from syngas and can react to produce hydrocarbons in a reaction known as methanol to hydrocarbons (MTH). Catalysts are vital in this reaction and are largely of zeolite origin. The zeolite typology, acidity, and reaction conditions donate the products produced and catalytic stability. Further, previous work shows increased catalytic stability and higher desired product selectivity when metal is incorporated onto the zeolite’s framework. We study the role of varying silica/alumina ratio (SAR) of beta zeolite via dealumination and incorporating titanium to understand their effect on product distribution, catalytic lifetime, and deactivation in the MTH reaction The samples maintained their structural integrity following the dealumination and metal incorporation. Techniques like XRD, N2 physisorption, ICP–OES, FTIR, and Raman spectroscopy are shown and discussed. They confirm the preservation of the zeolite structure following dealumination and metal incorporation. Pyridine-FTIR and ammonia TPD are used to understand the acidity character of the samples. Both show decreased acidity as the SAR increases. 27Al NMR and 1H NMR show the removal of extra framework 27Al as SAR increases and the presence of silanol nests in the dealuminated samples, respectively. A packed bed reactor in a PID setup with a UV-vis probe is used to test the catalytic activity and study the neutral and charged species formation, respectively. The catalytic activity results show a decrease in conversion as the SAR increases for the dealuminated samples. High propylene/ethylene ratio reaching up to 41.5 is observed for the 13M sample. Further, the UV-vis analysis shows the higher formation of bulkier hydrocarbons, like polyaromatics, as the reaction progresses. It is found that the parent sample deactivates quicker than the dealuminated samples as it presents stagnant UV-vis bands at the end of the reaction. The higher accumulation of polyaromatics and lower product formation of ethylene, in higher SARs, is related to the aromatic cycle hindrance and the dominance of the olefinic cycle products.
    • Xeno-pumice from Harrat Rahat: Understanding magma-crust interaction

      Garcia, Evelyn R. Garcia Paredes (2022-07-28) [Thesis]
      Advisor: Van der Zwan, Froukje M.
      Committee members: Jonsson, Sigurjon; Troll, Valentin R; van Buchem, Frans
      “Xeno-pumice” describes a pumice-like material, high in silica content and vesiculation, found as a xenolith in a more mafic rock. A xeno-pumice is an indicator of magma-crust interaction; however, the origin, nature, and processes behind this xenolith are still debated. Xeno-pumice has been described in a few places worldwide, including the Canary Islands in Spain, Indonesia, Iceland, the USA, Chile and Mexico. This thesis, for the first time, presents and analyzes the mineralogy, textural features, whole-rock geochemistry (major and trace element), and oxygen isotopes of xeno-pumice samples found in Harrat Rahat, Saudi Arabia. Harrat Rahat is a volcanic field whose last eruption was in 1256A.D. and reached the outskirts of Madinah, one of the main cities in Saudi Arabia. Harrat Rahat is characterized by a wide range of volcanic products: from basalts to trachyte. Previous studies suggested that this chemical variation has its source in the mantle and minor crustal contamination; however, the xeno-pumice samples found indicate magma-crust interaction. Thus, in this thesis, the crust-melt interaction hypothesis is addressed as a process that could modify the composition of the melt and thus the resulting volcanic products and eruptive style of the volcanic field. Indeed, the chemistry and oxygen isotope values of the studied volcanic rocks show a variation in composition, which is suggested to be the consequence of crust-melt interaction. The petrology, chemistry and oxygen isotope values suggest that the melt interacted with either the metamorphosed plutonic portion of the upper Arabian crust or with (meta-) sediments below Harrat Rahat. Finally, this thesis proved that magma-crust interaction occurred at Harrat Rahat, which has important implications for interpreting eruption mechanisms and mantle sources.
    • Evaluative screening of kinetic models for simulating the performances of oxidative coupling of methane catalysts

      Gobouri, Abdullah (2022-07-27) [Thesis]
      Advisor: Castaño, Pedro
      Committee members: Ruiz-Martinez, Javier; Hauser, Charlotte
      In this work, multiple kinetic models have been screened as potential candidates for simulating the performances of three oxidative coupling of methane (OCM) catalysts. Two of the proposed models were subjected to testing and optimization. The types of models screened covered both kinetic and microkinetic type models, i.e., radical omitting and radical considering. Some of the models only accounted for catalytic heterogeneous pathways, while others have expanded on the homogeneous gas-phase mechanism of the OCM reaction. The optimization process was carried out in MATLAB® R2020a using an error minimization tool. The range of experimental conditions examined was as follows: 740–800◦C, 100 kPa, 2–4 CH4/O2 ratio, 1–6 gcat h molC –1 spacetime. The results show successful optimization of both models as well as discrepancies in terms of their performances in predicting experimentally obtained values of CH4 and O2 conversions, as well as selectivities towards COx and C2+ products. While a kinetic model served as an easy option to optimize, it expressed limits in terms of achievable performance, mainly failing to simulate experimental runs conducted at low spacetimes. A microkinetic model on the other hand, managed to simulate all experimental conditions, with less accuracy towards COx species and much greater computational demand.
    • Establishment of 3D culture protocols for the maintenance and expansion of human pluripotent stem cell aggregates in a low scale platform and in the DASbox® Mini-Bioreactor System

      Hernandez-Bautista, Carlos Alberto (2022-07-27) [Thesis]
      Advisor: Adamo, Antonio
      Committee members: Merzaban, Jasmeen; Ibrahim, Leena Ali
      The human Embryonic Stem Cells (hESCs) and human induced Pluripotent Stem Cells (hiPSCs) have offered numerous advantages including but not limited to model diseases, high-throughput drug screening, and regenerative purposes. However, the employment of monolayer cultures has not been sufficient to mimic the in vivo stem cells niche. Thus, three-dimensional suspension cultures have helped us to advance our knowledge and ease the development of the human organs’ counterparts, commonly referred as organoids. Currently, the challenge is the generation of homogenous and reproducible human Pluripotent Stem Cell (hPSC) aggregates, the basic cellular unit to derive organoids. To date, the Ultra-Low Attachment (ULA) 6-well plates have been routinary used for the hPSC aggregates formation, which mainly relies on the inhibition of the Rho-associated kinase (ROCK) pathway resulting in the enhancement of cell survival coming from cryopreserved stocks or when passaging. However, little is known in this regard when analyzing the aggregate formation of hPSCs with two widely used compounds: RevitaCellTM Supplement and Y27632. Importantly, due to the high demand required from the regenerative medicine, I aimed to upscale the hPSC aggregates production in the DASbox® Mini-Bioreactor System. In this thesis, I established protocols for the hPSC aggregates formation by using two different types of media in two platforms being the ULA 6-well plates and the DASbox® Mini-Bioreactor System. In addition, I demonstrated that monolayer confluence cultures before single cell inoculations are paramount for the formation of bona fide hPSC aggregates in healthy and X aneuploid hiPSCs, precisely two hESCs and five hiPSCs.
    • Sars-Cov-2 Intra-Host Evolution in Immunocompromised Patients for the Emergence of Variants of Concerns, Including Omicron.

      Bantan, Azari I. (2022-07-21) [Thesis]
      Advisor: Gojobori, Takashi
      Committee members: Mineta, Katsuhiko; Pain, Arnab
      Unexpected high mutations detected in new emerging variants of concern (VOCs) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), especially in the case of omicron, raises concerns and efforts to understand their evolutionary trajectory. Several hypotheses have been discussed in literature to conceptualize the source of their emergence, including intra-host viral evolution in immunocompromised patients. These patients grant opportunities for the emergence of new variants through a persisting virus winning against host immunity, and selection for viral mutations driven by treatment interventions. VOCs have in common high mutation rate exceeding the average rate of 1-2 mutations per month. Not many studies have investigated the evolutionary rate of SARS-CoV-2 in immunocompromised candidates. Therefore, the purpose of this study is to reveal potential mechanisms underlying the emergence of VOCs by exploring substitution rate of SARS-CoV-2 genomes from surveyed COVID-19 immunocompromised patient’s studies. First, SARS-CoV-2 genome sequences were collected at sequential time series throughout host infection, which were reported in the previous studies. Filtration criteria was applied to reanalyze patients with prolonged infection documented for ≥ 2 months, and comprehensive sequenced samples for ≥ 6 time points. Then, phylogenetic analysis was conducted using Nextclade (, followed by mutation rate analysis using two substantial similar approaches to calculate the rate in i) substitutions per month and ii) substitutions per site (per year). The mutation tendency of SARS-CoV-2 in immunocompromised hosts was compared to reported VOCs, particularly to omicron. The highest observed mutation rate accounted for approximately 2.2 mutations per month, which is higher than the average rate. High mutation rate was due to prolonged infection and selection pressure by treatment interventions (i.e., convalescent plasma and antibodies). Here, higher rate of intra-host viral evolution in immunocompromised patients is detected, potentially leading to the emergence of VOC. Hence, this research highlights the need for sequencing efforts in high-risk individuals, updating treatment strategies along with further analysis on adaptive mutants pronounced due to intra-host evolution. Together, such findings provide an ultimate synergy for future public health guidelines and infection control measures.
    • De novo genome-scale prediction of protein-protein interaction networks using ontology-based background knowledge

      Niu, Kexin (2022-07-18) [Thesis]
      Advisor: Hoehndorf, Robert
      Committee members: Inal, Sahika; Moshkov, Mikhail
      Proteins and their function play one of the most essential roles in various biological processes. The study of PPI is of considerable importance. PPI network data are of great scientific value, however, they are incomplete and experimental identification is time and money consuming. Available computational methods perform well on model organisms’ PPI prediction but perform poorly for a novel organism. Due to the incompleteness of interaction data, it is challenging to train a model for a novel organism. Also, millions to billions of interactions need to be verified which is extremely compute-intensive. We aim to improve the performance of predicting whether a pair of proteins will interact, with only two sequences as input. And also efficiently predict a PPI network with a proteome of sequences as input. We hypothesize that information about cellular locations where proteins are active and proteins' 3D structures can help us to significantly improve predict performance. To overcome the lack of experimental data, we use predicted structures by AlphaFold2 and cellular locations by DeepGoPlus. We believe that proteins belonging to disjoint biological components have very little chance to interact. We manually choose several disjoint pairs and further confirmed it by experimental PPI. We generate new no-interaction pairs with disjoint classes to update the D-SCRIPT dataset. As result, the AUPR has improved by 10% compared to the D-SCRIPT dataset. Besides, we pre-filter the negatives instead of enumerating all the potential PPI for de-novo PPI network prediction. For E.coli, we can pass around a million negative interactions. To combine the structure and sequence information, we generate a graph for each protein. A graph convolution network using Self-Attention Graph Pooling in Siamese architecture is used to learn these graphs for PPI prediction. In this way, we can improve around 20% in AUPR compared to our baseline model D-SCRIPT.
    • Water Effect on the Methanol to Olefin Conversion over SSZ-13 Catalyst with an Operando Spectroscopy

      Alsindi, Mohammed (2022-07-18) [Thesis]
      Advisor: Ruiz-Martinez, Javier
      Committee members: Pinnau, Ingo; gomez-cabrero, David
      For more than 50 years, the methanol to olefins (MTO) reaction remains to be a hot topic within the catalysis community. The recent discoveries about it and the industrial implementation made it even receive more attention. The best way this process can be used is by hydrogenation of CO2 to make methanol and undergo after that the MTO reaction. This method will save energy, be more environmentally friendly, and be sustainable, but it requires advancement regarding carbon capture. The purpose of this paper is to understand the effect of water on SSZ-13 commercial zeolite when it is used for MTO reaction by a combination of gas chromatography (GC) analysis and operando UV – vis spectroscopy. It was observed that water with a ratio of 2:1 methanol to water would increase the lifetime of the catalyst from 3 h to 6.5 h, and the ratio of 1:1 would increase it to 9 h. However, a higher amount of water hadn’t been analyzed, but theoretically, it would cause dealumination to the zeolite invoking a different type of deactivation. This increase in catalyst lifetime was first due to the competitive adsorption between water and methanol; leading to a lower methanol reactivity toward methoxide formation. Second, because of the competition between water and propylene, it resulted in a longer induction period and a delay in the formation of hydrocarbon pool. Hence, less coke was formed from the reaction and more species were able to diffuse into the inner pores. Also, it was observed that ethylene selectivity increased with the addition of water to the feed. The UV-vis analysis proved the longer induction period and showed the formation of more species due to that. The deactivating materials were identified to be polyaromatic carbocation and phenanthrene, while the main activating species was methylated naphthalene carbocation. In addition, multiple characterization techniques, such as nitrogen physisorption, ammonia TPD, and SEM, were performed to understand the nature of the catalyst. It was found that it has weak and strong Bronsted acid sites, BET surface area of 665.7 m2/g, and crystal size of about 0.5 – 2 µm.
    • Benthic Habitat Mapping of Thuwal’s Reefs Using High-Resolution Acoustic Technologies and Imaging Data

      Watts, Marta A. Ezeta (2022-07-14) [Thesis]
      Advisor: Benzoni, Francesca
      Committee members: Berumen, Michael L.; Volker, Vahrenkamp
      Remote sensing studies based on satellite and aerial imagery have improved our understanding of the morphology and distribution of several shallow reefs along the Red Sea Arabian coast and of the benthic assemblages associated to them (Bruckner et al., 2011; Bruckner et al., 2012; Rowlands et al., 2016). However, data concerning the deeper benthic assemblages' composition and spatial distribution in the central Red Sea are still missing. Using high-resolution acoustic technology and an underwater remotely operated vehicle (ROV), we aim to map, describe, and classify the reefs found in Thuwal's coastal area, filling the information gap by producing the first benthic habitat map of this area and making progress towards the evaluation of shallow and upper mesophotic benthic resources in the Saudi Arabian Red Sea. High-resolution acoustic data was collected using a multibeam echosounder system, which generated a bathymetric model. Based on this, the seafloor features were classified into 12 morphotypes following a visual assessment. Based on the morphotypes classification, 28 sites were visually selected for ground-truthing data acquisition and characterization of the substrate and benthic assemblages using a remotely operated vehicle equipped with an ultra-short baseline (USBL) positioning system. With the information obtained from the bathymetry data and the ROV video transects, a Top-Down approach in which we analyzed, categorized, and classified the data was used to create Thuwal's reefs benthic habitat map in which 23 different benthic habitat types were identified. This research uncovered previously poorly studied reef morphologies in the Red Sea and their associated benthic assemblages. Moreover, this work will help improve the understanding of the spatial distribution of benthic communities located on Thuwal's reefs, giving a baseline with the potential to provide fundamental information that can be used for mapping, management, conservation, and future research at other Red Sea reef sites in Saudi Arabia.
    • Fast, Robust, Iterative Riemann Solvers for the Shallow Water and Euler Equations

      Muñoz-Moncayo, Carlos (2022-07-12) [Thesis]
      Advisor: Ketcheson, David I.
      Committee members: Tzavaras, Athanasios; Truscott, T. T.
      Riemann problems are of prime importance in computational fluid dynamics simulations using finite elements or finite volumes discretizations. In some applications, billions of Riemann problems might need to be solved in a single simulation, therefore it is important to have reliable and computationally efficient algorithms to do so. Given the nonlinearity of the flux function in most systems considered in practice, to obtain an exact solution for the Riemann problem explicitly is often not possible, and iterative solvers are required. However, because of issues found with existing iterative solvers like lack of convergence and high computational cost, their use is avoided and approximate solvers are preferred. In this thesis work, motivated by the advances in computer hardware and algorithms in the last years, we revisit the possibility of using iterative solvers to compute the exact solution for Riemann problems. In particular, we focus on the development, implementation, and performance comparison of iterative Riemann solvers for the shallow water and Euler equations. In a one-dimensional homogeneous framework for these systems, we consider several initial guesses and iterative methods for the computation of the Riemann solution. We find that efficient and reliable iterative solvers can be obtained by using recent estimates on the Riemann solution to modify and combine well-known methods. Finally, we consider the application of these solvers in finite volume simulations using the wave propagation algorithms implemented in Clawpack.
    • Estimation of Mercury Injection Capillary Pressure (MICP) from the Nuclear Magnetic Resonance (NMR) exponential decay with the Machine Learning (ML) Neural Network (NN) approach

      Ugolkov, Evgeny A. (2022-07-09) [Thesis]
      Advisor: Hoteit, Hussein
      Committee members: Santamarina, Carlos; Ahmed, Shehab
      Information about the capillary pressure has a wide range of applications in the petroleum industry, such as an estimation of irreducible water saturation, calculation of formation absolute permeability, determination of hydrocarbon-water contact and the thickness of the transition zone, evaluation of the seal capacity, and an estimation of relative permeability. All the listed parameters in the combination with petrophysical features, pressures, and fluid properties allow us to evaluate the economic viability of the well or the field overall. For this reason, capillary pressure curves are of great importance for petroleum engineers working on any stage of the field development: starting from exploration and finishing with production stages. Nowadays, capillary pressure experiments are provided either in the lab on the plugs of the rocks, either in the well on the certain stop points with the formation tester tools on the wire or tubes. Core extraction and formation testing are both laborious, expensive, and complicated processes since the newly-drilled well remain in the risky uncased condition during these operations, and for this reason, usually the listed works are provided in the exploration wells only. Afterward, the properties obtained from the exploration wells are assumed to be the same for the extraction or any other kinds of wells. Therefore, these days petroleum engineers have limited access to the capillary pressure curves: the modern tests are provided on the limited points of formation in the limited number of wells. An extension of capillary pressure measurements in the continuous mode for every well will dramatically expand the abilities of modern formation evaluation and significantly improve the field operation management by reducing the degree of uncertainty in the decision-making processes. This work is the first step toward continuous capillary pressure evaluation. Here we describe the procedure of finding the correlation between the results of the lab Nuclear Magnetic Resonance (NMR) experiment and lab Mercury Injection Capillary Pressure (MICP) measurements. Both experiments were provided on the 9 core plugs of the sandstone. Afterward, a Machine Learning (ML) algorithm was applied to generate additional samples of the porous media with different petrophysical properties representing the variations of the real cores of available sandstones. Overall, 405 additional digital rock models were generated. Thereafter, the digital simulations of MICP and NMR experiments were provided on the generated database of digital rocks. All the simulations were corrected for limited resolution of the CT scan. Based on the created database of experiments, we implemented a ML algorithm that found a correlation between the NMR echo data and MICP capillary pressure curves. Obtained correlation allows to calculate capillary pressure curve from the NMR echo data. Since NMR logging may be implemented in every well in the continuous mode, an extension of the created technique provides an opportunity for continuous estimation of capillary pressure for the whole logging interval. This extension is planned as future work.
    • An Experimental Investigation of Soot Formation in Laminar Inverse and Normal Diffusion Flames at Elevated Pressure

      Alsheikh, Ibrahim (2022-07-07) [Thesis]
      Advisor: Roberts, William L.
      Committee members: Sarathy, Mani; Hoteit, Hussein
      Hydrogen production from autothermal reforming (ATR) with Carbon Capture Utilization and Storage (CCUS) is gaining traction as prospect for a blue hydrogen economy. ATR is susceptible to catalyst poisoning and degradation from soot formation, which decrease H2 yield. In this work soot formation was examined thoroughly in conditions close to ATR, using an oxygen rich inverse diffusion flame (IDF) burner at elevated pressure. Normal diffusion flames (NDF) were also investigated against the same conditions to ultimately be compared alongside IDF. In NDF, soot formation and oxidation happen simultaneously, while in IDF soot oxidation is ignorable. Primary fuel was CO2 diluted methane, and the oxidizer stream has a 70%-by-mol O2 (30% N2) concentration. OH* chemiluminescence was used to find flame height against key parameters, PAH concentration and soot volume fraction were captured using Laser Induced Fluorescence (LIF) and Laser Induced Incandescence (LII) respectively. Key findings in this work were the dissimilarities between IDF and NDF against pressure and the effects of varying flame constituents on flame height in IDF.
    • Biophysical Characterization of the BIRD Complex and their Mode of Interaction

      Wang, Luyao (2022-07-06) [Thesis]
      Advisor: Arold, Stefan T.
      Committee members: Habuchi, Satoshi; Blilou, Ikram
      In Arabidopsis thaliana, the development and the defense system are precisely controlled by some proteins to allocate energy and resources as needed. JASMONATE-ZIM domain 3 protein is the repressor of the jasmonic acid defense pathway. JACKDAW (JKD), SHORTSHOOT (SHR), and SCARECROW (SCR) bind together to form the BIRD complex, which regulates root patterning. The transcription factor Teosinte branched1/Cycloidea/Proliferating cell factor 14 (TCP14) also regulates plant development. Recent data shows that JAZ3 and TCP14 interact with JKD and may form a ternary complex, which reveals the study of the five proteins mentioned above may help to understand how defense signals are interpreted during plant growth. The interactions of these five proteins provide a theoretical base to maximize plant fitness and increase crop yield. Using protein purification, microscale thermophoresis, isothermal titration calorimetry, negative staining, X-ray crystallography in this project, we identified JKD interacted with JAZ3, and JKD interacted with TCP14, but they could not form a ternary complex in vitro; SHR/SCR interacted with JAZ3. Those binding results suggests TCP14 and SHR/SCR may have very similar binding site of JKD, and JAZ3 may guide the degradation of the BIRD complex. In structural studies, we resolved the 2D class average that showed the outline of the BIRD complex and it potentially helped to identify how JKD bound to DNA. We also determined the crystal structure of the TCP14 domain, which was an intertwined dimer that possibly uses arginine residues in the N terminus to interact with DNA. These interaction and structure studies of the five proteins provide the basis to understand how defense signals affect plant development.
    • Predicting the future high-risk SARS-CoV-2 variants with deep learning

      Chen, NingNing (2022-07-04) [Thesis]
      Advisor: Gao, Xin
      Committee members: Gojobori, Takashi; Wang, Di
      SARS-CoV-2 has plagued the world since 2019 with continuously emergence of new variants, resulting in repeated waves of outbreak. Although the countermeasures like vaccination campaign has taken worldwide, the sophisticated virus mutated to escape immune system, threatening the public health. To win the race with the virus and ultimately end the pandemic, we have to take one step ahead to predict how the SARSCoV-2 might evolve and defeat it at the beginning of a new wave. Hence, we proposed a deep learning based framework to first build a deep learning model to shape the fitness landscape of the virus and then use genetic algorithm to predict the high-risk variants that might appear in the future. By combining pre-trained protein language model and structure modeling, the model is trained in a supervised way, predicting the viral transmissibility and antibodies escape ability to eight antibodies simultaneously. The prevenient virus evolution trajectory can be largely recovered by our model with high correlation to their sampling time. Novel mutations predicted by our model show high antibody escape through in silico simulation and overlapped with the mutations developed in prevenient infected patients. Overall, our scheme can provide insights into the evolution of SARS-CoV-2 and hopefully guide the development of vaccination and increase the preparedness.
    • E-selectin mediated signaling and chemosensitivity in AML cells

      Lopez Madrigal, Gloria (2022-07) [Thesis]
      Advisor: Merzaban, Jasmeen
      Committee members: Rosado, Alexandre S.; Gadhoum, Samah Z.
      E-selectin is an endothelial adhesion molecule important in the recruitment of leukocytes to the bone marrow and inflammatory tissues; moreover, it has also been implicated in cancer metastasis and as a critical mediator of chemoresistance. This study investigated the effects triggered by the binding of E-selectin on acute myeloid leukemia (AML) cell lines regarding the activation of significant signaling pathways and their impact on biological functions. We observed that upon treatment with a recombinant E-selectin construct on AML cells, there was an activation of the AKT/NF-κB pathways, which are known to be central regulators of many cellular processes, including survival and proliferation. We found that the E-selectin-mediated activation varied in rate and amplitude among AML cell lines spanning differentiation blockage at different stages. Furthermore, we found that E-selectin binding in HL-60 and KG1-a cells sensitized the cells to daunorubicin (DNR), a chemotherapy drug commonly used to treat AML. The observed chemosensitivity could be linked to the decrease of Aldo Keto Reductases (AKR) protein levels upon E-selectin treatment, which is known to metabolize DNR and reduce its cytotoxicity. Additionally, we explored the role of exosomes as a regulator of the generation of therapy resistance by examining the effects treatment with KG1-a derived exosomes, a cell line that exhibits higher chemoresistance compared to other AML cell lines, had on viability in HL-60 cells upon chemotherapy. We found that even in the absence of KG1-a cells, exosomes were sufficient to provide an increase in chemoresistance. Overall, these studies explore properties exerted by AML cells that could lead to further understanding of AML and thus the development of potential therapeutic targets to overcome challenges currently found in the treatment of this disease.
    • Synthesis, Modification, and Evaluation of MXene as a Novel Anode Electrode Material for Bio-electrochemical Systems

      KOLUBAH, PEWEE DATOO (2022-07) [Thesis]
      Advisor: Castaño, Pedro
      Committee members: Szekely, Gyorgy; Saikaly, Pascal
      Bioelectrochemical systems (BESs) show promising prospects for recovering energy and chemicals from industrial and municipal wastewater. Despite the advances in the development of this technology, there is still a significant need for efficient electrode materials with high conductivity, hydrophilicity, and good biocompatibility to boost their performance and increase productivity. In this work, metal nanoparticle-two-dimensional MXene (W2N-Ti3C2Tx and Fe-W2N-Ti3C2Tx) composite electrocatalysts were synthesized using a simple impregnation method and deposited on carbon cloth (CC) to be used as a cheap and high performing anode in BESs. The plain CC, Ti3C2Tx-CC, W2N-Ti3C2Tx-CC, and Fe-W2N-Ti3C2Tx-CC were characterized using several techniques including scanning electron microscopy, transmission electron microscopy, water contact angle, and atomic force microscopy. The prepared anodes were tested in a single chamber air cathode microbial fuel cell inoculated with industrial wastewater for power generation and wastewater treatment simultaneously. The obtained results show that carbon cloth modified with W2N-Ti3C2Tx and Fe-W2N-Ti3C2Tx exhibited improved power density of 548 mW m-2 and 327 mW/m-2 with 81% and 44%, coulombic efficiency, respectively. The obtained power densities were 6 and 3.7 times higher, respectively than that achieved for pure carbon cloth (88 mW m-2). This study demonstrates the potential of combining two-dimensional MXene with metal nanoparticles to form an active composite anode catalyst for enhancing power generation and wastewater treatment using microbial fuel cells.