Recent Submissions

  • iSCAN: A Point-of-Care SARS-CoV-2 Diagnostic Test

    Mahas, Ahmed; Marsic, Tin; Ali, Zahir; Aman, Rashid; Gundra, Sivakrishna Rao; Ghouniemy, Ahmed; Hassan, Norhan; Mahfouz, Magdy M. (2021-11-22) [Poster]
    Type VI CRISPR-Cas systems have been repurposed for various applications such as gene knock-down, viral interference, and molecular diagnostics. However, the identification and characterization of thermophilic orthologues will expand and unlock the potential of diverse biotechnological applications. In this work, we identified and characterized a novel, thermostable orthologue of the Cas13a family, from the thermophilic organism Thermoclostridium caenicola (TccCas13a). We show that TccCas13a has a close phylogenetic relation to HheCas13a and shares several properties such as thermostability and inability .
  • Quick and Easy Assembly of a One-step qRT-PCR Kit for COVID-19 Diagnostics Using In-House Enzymes

    Takahashi, Masateru; Tehseen, Muhammad; Salunke, Rahul; Takahashi, Etsuko; Mfarrej, Sara; Sobhy, Mohamed A.; Alhamlan, Fatimah S.; Hala, Sharif; Mandujano, Gerardo R.; Al-Qahtani, Ahmed A.; Alofi, Fadwa S.; Alsomali, Afrah; Hashem, Anwar M.; Khogeer, Asim; Almontashiri, Naif A. M.; Lee, Jae Man; Mon, Hiroaki; Sakashita, Kosuke; Li, Mo; Kusakabe, Takahiro; Pain, Arnab; Hamdan, Samir (2021-11-22) [Poster]
    One-step qRT-PCR is the most widely applied method for COVID-19 diagnostics. Notwithstanding the facts that one-step qRT-PCR is well-suited for the diagnosis of COVID-19 and that there are many commercially available one-step qRT- PCR kits in the market, their high cost and unavailability due to airport closures and shipment restriction became a major bottleneck that had driven the desire to produce the key components of such kits locally. Here, we provide a simple, economical, and powerful one-step qRT-PCR kit based on patent-free, specifically-tailored versions of Moloney Murine Leukemia Virus Reverse Transcriptase and Thermus aquaticus DNA polymerase and termed the R3T (Rapid Research Response Team) One-step qRT-PCR. We also demonstrate the robustness of our enzyme production strategies and provide the optimal reaction conditions for their efficient augmentation in a one-step approach. Our kit was routinely able to reliably detect as low as 10 copies of the synthetic RNAs of the SARS-CoV-2. More importantly, our kit successfully detected COVID-19 in clinical samples of broad viral titers with similar reliability and selectivity as that of the Invitrogen SuperScript III Platinum One-step qRT-PCR and TaqPath 1-Step RT-qPCR kits. Overall, our kit has shown robust performance in both laboratory settings and the Saudi Ministry of Health-approved testing facility.
  • Saudi Arabian SARS-CoV-2 genome analysis reveals the functional impact of N protein mutations on differential host-virus interactions

    Shuaib, Muhammad (2021-11-22) [Poster]
    Monitoring SARS-CoV-2 spread and evolution through genome sequencing is essential in handling the COVID-19 pandemic. The availability of patient hospital records is crucial for linking the genomic sequence information to virus function during the course of infections. Here, we sequenced 892 SARS-CoV-2 genomes collected from patients in Saudi Arabia from March to August 2020. From the assembled sequences, we estimate the SARS-CoV-2 effective population size and infection rate and outline the epidemiological dynamics of transmission events during this period in Saudi Arabia. We show that two consecutive mutations (R203K/G204R) in the SARS-CoV-2 nucleocapsid (N) protein are associated with higher viral loads in COVID-19 patients. Our comparative biochemical analysis reveals that the mutant N protein displays enhanced viral RNA binding and differential interaction with key host proteins. We found increased interaction of GSK3A kinase simultaneously with hyper-phosphorylation of the adjacent serine site (S206) in the mutant N protein. Furthermore, analysis of the host cell transcriptome suggests that the mutant N protein results in dysregulated interferon response genes. Here, we provide crucial information in linking the R203K/G204R mutations in the N protein as a major modulator of host-virus interactions and increased viral load and underline the potential of the nucleocapsid protein as a drug target during infection.
  • Host-Directed editing of SARS-CoV-2 genome: From perspective of host APOBEC and ZAP

    Sadykov, Mukhtar; Mourier, Tobias; Guan, Qingtian; Pain, Arnab (2021-11-22) [Poster]
    RNA viruses use CpG reduction to evade the host cell defense, but the driving mechanism is still largely unknown. To address this, we used a rapidly growing genomic dataset of SARS-CoV-2 with relevant metadata information. Remarkably, by simply ordering SARS-CoV-2 genomes by their date of collection, we find a progressive increase of C-to-U substitutions resulting in CpG loss over just a few months. This is consistent with APOBEC-mediated RNA editing resulting in CpG reduction, thus allowing the virus to escape ZAP-mediated RNA degradation. Our results thus link the dynamics of target sequences in the viral genome for two known host molecular defense mechanisms, mediated by the APOBEC and ZAP proteins.
  • MesoCraft – 3D Modeling Software for Creating Mesoscale Atomistic Models

    Strnad, Ondrej (2021-11-22) [Poster]
    MesoCraft is a new 3D modeling tool implementing visual programming approach. It provides the user with the capabilities of loading, rendering and manipulating several modalities (protein data, volumetric data, meshes) and overlaying them inside one rendering view. The modeling algorithm is based on statistical and rule based modeling approaches that are rapid to author, fast to construct, and easy to revise. Biological information can be incorporated by interactively defining the rules that spatially characterize the biological entity, such as mutual interactions among macromolecules, and their distances and orientations relative to other structures. These rules are defined through an intuitive 3D interactive visualization as a visual programming feedback loop.
  • Tracking COVID-19 through mutation fingerprints, worldwide.

    Alam, Intikhab; Uludağ, Mahmut; Radovanovic, Aleksandar; Incitti, Roberto; Kamau, Allan A.; Alarawi, Mohammed; Gojobori, Takashi (2021-11-22) [Poster]
    The SARS-CoV-2 virus causing the COVID-19 pandemic, has been sequenced in patients over 4.5 million times with over 2 million genomes belong to Delta while 1 million genomes belong to Alpha variant. This increase in the sequencing efforts is due to WHO call on stepping up sequencing to actively track the rise of mutations or variants of concern related to increased infectivity and evasion of antibodies. Here, we present a daily updated geographic sequencing effort and genomic 'mutation fingerprints' based COVID-19 virus mutation tracking system (CovMT) that processes publicly available genome data from GISAID. The CovMT interactive resource is available online for scientists, general public and public health authorities at
  • Bouncing with filaments

    Yang, Zi Qiang; Al Julaih, Ali; Thoroddsen, Sigurdur T (2021-11-21) [Poster]
  • Role of sodium dodecyl sulfate surfactant at the Interface of the Decane + Brine in the Presence of CO2, CH4, and Their Mixture

    Choudhary, Nilesh; Kumar Narayanan Nair, Arun (2021-11-11) [Poster]
    Role of Sodium Dodecyl Sulfate Surfactant at the Interface of the Decane + Brine System in the Presence of CO2, CH4, and Their Mixture/nNilesh Choudhary1,2, Arun Kumar Narayanan Nair2, Shuyu Sun2/n1. Indian Institute of Technology Tirupati, Tirupati, India, and 2. King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia/nIntroduction /nThe emission of anthropogenic CO2 is one of the major causes of global climatic changes. Carbon capture and storage technology might be beneficial for mitigating these emissions. Various adsorbents (e.g., carbon nanotubes and clays) have been extensively utilized for carbon dioxide capture. In enhanced oil recovery (EOR) operations, the oil recovery could also be combined with carbon dioxide storage. The water-alternating-gas (WAG) approach has been utilized for mobility control during CO2 -EOR operations. The WAG cycles consist of injecting water (or surfactant) and CO2 alternatively into the reservoirs. Lowering the interfacial tension (IFT) of the oil + water system leads to an increase in the capillary number which may help to recover more oil. In general, the presence of surfactant/CO2 decreased this IFT. In addition, the captured CO2 contains impurities (e.g., CH4) that may have an important influence on the EOR operations./nSimulation Method/nMD simulations of Decane + water + surfactant and Decane + brine + surfactant two-phase systems in the presence of CH4 and CO2 at 323 and 443 K, and pressure up to 100 MPa were carried out using the GROMACS package. The salt (NaCl) concentration is 2.7 mol/kg and the amounts of surfactant adsorbed at the interface are 0.008 and 0.016 SDS/Å2. Each system was equilibrated for 5 ns in the NPT ensemble (only Lz varied) and we ran a 5 ns production under NVE conditions./nConclusions/n•The addition of CH4, CO2, and the presence of SDS surfactant at the interface reduced the IFTs of the Decane + water and Decane + brine (NaCl) systems./n•The effect of CO2 is more because the interface was highly enriched with CO2 molecules than with CH4 molecules./n•The interfacial thickness between water and Decane/CH4/CO2 molecules increases with increasing surfactant concentration and decreases with salt./nReferences/n1.Choudhary, N., Nair, A. K. N., & Sun, S. (2021). Interfacial Behavior of the Decane + Brine + Surfactant System in the Presence of Carbon Dioxide, Methane, and Their Mixture. Soft Matter (accepted), N., Nair, A. K. N., Ruslan, M. F. A. C., & Sun, S. (2019). Bulk and interfacial properties of Decane in the presence of carbon dioxide, methane, and their mixture. Scientific reports, 9(1), 1-10., N., Ruslan, M. F. A. C., Nair, A. K. N., & Sun, S. (2021). Bulk and interfacial properties of alkanes in the presence of carbon dioxide, methane, and their mixture. Ind. Eng. Chem. Res., 60(1), 729-738., N., Ruslan, M. F. A. C., Nair, A. K. N., Qiao, R., & Sun, S. (2021). Bulk and Interfacial Properties of the Decane+ Brine System in the Presence of Carbon Dioxide, Methane, and Their Mixture. Ind. Eng. Chem. Res., 60(30), 11525-11534. thank the support of this work by the KAUST under Award No. OSR-2019-CRG8-4074 and HPC:-SHAHEEN/IBEX/n
  • Co-optimization of CO2 Storage and Enhanced Gas Recovery Using Carbonated Water and Supercritical CO2

    Omar, Abdirizak; Addassi, Mouadh; Vahrenkamp, Volker; Hoteit, Hussein (2021-11-11) [Poster]
    Co-optimization of CO2 Storage and Enhanced Gas Recovery Using Carbonated Water and Supercritical CO2/nCO2-based enhanced gas recovery (EGR) is an appealing method with the dual benefit of improving recovery frommature gas reservoirs and storing CO2in the subsurface, thereby reducing net emissions. However, CO2 injection for EGR has the drawback of excessive mixing with the methane gas, therefore, reducing the quality of gas produced and leading to an early breakthrough of CO2. Although this issue has been identified as a major obstacle in CO2-based EGR, few strategies have been suggested to mitigate this problem. We propose a novel hybrid EGR method that involves the injection of a slug of carbonated water before beginning CO2 injection. While still ensuring CO2 storage, carbonated water hinders CO2 -methane mixing and reduces CO2 mobility, therefore delaying breakthrough. We use reservoir simulation to assess the feasibility and benefit of the proposed method. Through a structured design of experiments (DoE) frame-work, we perform sensitivity analysis, uncertainty assessment, and optimization to identify the ideal operation and transition conditions. Results show that the proposed method only requires a small amount of carbonated water injected up to 3% pore volumes. This EGR scheme is mainly influenced by the heterogeneity of the reservoir, slug volume injected, and production rates. Through Monte Carlo simulations, we demonstrate that high recovery factors and storage ratios can be achieved while keeping recycled CO2 ratios low./n
  • Assessment of CO2 Geological Storage near Riyadh, Saudi Arabia

    Corrales, Miguel; Mantilla, Sofia; Tasianas, Alexandros; Hoteit, Hussein (2021-11-11) [Poster]
    Assessment of CO2 Geological Storage near Riyadh, Saudi Arabia/nThe Kingdom of Saudi Arabia (KSA) signed the Paris Agreement on climate change and committed to reducing its greenhouse gas emissions. KSA has also launched the Circular Carbon Economy (CCE), a comprehensive framework to address the dual challenge of energy and the environment. Current CO2 emissions from KSA are 600 mty (million tons per year), from which 415mty are from stationary industrial sources. CO2 capture and storage (CCS) offers a safe and effective means to reduce CO2 emissions, at scale, without compromising the role of hydrocarbons in fueling the local and global economies. To determine the storage potential near to the Riyadh area we built a geological model focused on the Unayzah formation using published data. Also, we performed compositional simulations to evaluate the capacity of the reservoir, the fluid flow in the highly-heterogenous reservoir, the contribution of the trapping mechanicians, and the leakage potential of the Khuff formation. Preliminary results showed the potential to store 300 mt of CO2 at a rate of 6 mty. The total storage capacity is, however, much larger and its assessment is ongoing.
  • Pressure Transient Analysis in Stress Sensitive Face-Damaged Fractured Wells

    Figueroa-Hernandez, Ruben; Hoteit, Hussein (2021-11-11) [Poster]
    Pressure Transient Analysis in Stress Sensitive Face-Damaged Fractured Wells/nHydraulic fractures are created to produce and make low permeability reservoirs economically profitable. Fracturesare also caused unintentionally by the uncontrolled injection in secondary recovery or CO2 geological storageprojects. The fractures act as high conductivity conduits that increase the flow capacity. The fracture conductivityis strictly related to its geometry and hydraulic properties. However, these tend to degrade as pressure decreases,causing a reduction in the well performance. During proppant placement or CO2 injection, pore-clogging andmineral precipitation reduce the permeability near the wellbore region. This work focuses on modeling fractureclosure in damaged fractured wells using PTA approach to identify fracture closure effects using pressure data./n
  • 4D Pore-Scale Assessment of Rock-to-Rock Spontaneous Imbibition

    Alaamri, Jamal; Chandra, Viswasanthi; Hoteit, Hussein (2021-11-11) [Poster]
  • Elastic response of porous medium to accumulated slip on complex fault network. A case study from fault map to porous medium permeability alteration

    Yalcin, Bora (2021-11-11) [Poster]
    ELASTIC RESPONSE OF POROUS ROCKS TO ACCUMULATED SLIP ON COMPLEX FAULT NETWORK/nBy coupling triangular dislocation theory and linearized poro-elastic equations we achieved to quantify the change in porosity with respect to accumulated slip on faults. Our numerical experiments show that the rock types (initial porosity and permeability) control the overall rate of change in the permeability. Young’s and Shear Modulus of rock-types controls the amount of porous medium deformation. Roughness amplifies and scatters the deformed space along the fault direction in porous medium. We scaled up the benchmark results to faults in the reservoir with different lengths, orientations and locations. The results show that accumulated slip can change the porous medium permeability significantly, creating anisotropy based on combination of shear sense and fault network. We suggest geoscientists to use the provided workflow and the code to improve the permeability distribution model in fractured porous medium./n
  • A 6M Digital Twin for Reservoirs

    Zhang, Tao (2021-11-11) [Poster]
  • Inverse Problems In Geosciences

    Luiken, Nick (2021-11-03) [Poster]
    Inverse problems in geosciences The Deep Imaging Group (DIG) research activities lie at the intersection between geoscience andinverse problems. We aim to leverage recent advances from the inverse problem communityas well as to develop novel methods ourselves for solving geoscientific problems. Our researchis highly interdisciplinary, combining ideas from applied mathematics, machine learning, imagingsciences, and computer science. In this poster I will showcase a few topics of our ongoing andfuture research. In inverse problems we wish to infer the properties of hidden objects from measured data and anunderlying physical model by solving an optimization problem. Although, generally speaking, genâ erating data from a known model is a wellâ posed problem, inverse problems are illâ posed, meaningthat at least one of the three following conditions is violated: 1. A solution exists,2. The solution is unique,3. The solution is stable with respect to perturbations in the data. This is due to either incomplete and corrupted data or the nonâ invertibility of the model. To solvesuch problems, we have to rely on prior knowledge about the solution. Incorporating the priorknowledge into the optimization problem is called regularization. Active research in the field ofinverse problems is mostly focused on designing new regularizers and algorithms that can solvethe resulting optimization problem in a computationally and memory efficient way. In this poster we showcase two recent works of our group: Multiâ Dimensional Deconvolution: a process that is ubiquitous in exploration geophysics andother fields like ultrasound imaging. We show that this problem can be stably solved byincorporating regularization based on information about some physical properties of thesolution;SR3: a novel algorithm that can be used with a widely used class of regularizers that promotesparsity. We present novel insight into the convergence rate of the algorithm and propose animplementation suitable for largeâ scale problems.
  • Hybrid Polypepti(O)Des Based Unimolecular Micelles

    Mahi, Basma (2021-11-03) [Poster]
    Hybrid Polypepti(o)des Based Unimolecular Micelles Introduction Arborescent polymers have a tree-like architecture resulting from successive grafting reactions, leading to useful properties for multiple applications. In particular, amphiphilic dendritic polymers display micelle-like properties with good colloidal stability and tailorable characteristics, making them good candidates as drug carriers. Unlike other dendritic systems, arborescent polymers can be synthesized with high molecular weight and low polydispersity index (PDI < 1.1) in a few steps 1-3. In the example provided here, the arborescent polypeptides derived from biocompatible and degradable poly(γ-benzyl-L-glutamate)-co-L-glutamic acid 1-tert-butyl ester PBG-co-PGlu(OtBu) segments serve as hydrophobic core for the unimolecular micelles, while polysarcosine (Psar) segments form a hydrophilic corona. Living ring-opening polymerization (ROP) was applied to synthesize the linear polymers. All generations of arborescent systems were produced by peptides coupling reaction (grafting onto method). Two different grafting modes were studied during the coating process (end grafted and randomly grafted method). The resulting unimolecular micelles were characterized by nuclear magnetic resonance (NMR), dynamic light scattering (DLS), atomic force microscopy (AFM), and transmission electron microscopy (TEM). Conclusions ⠢Arborescent unimolecular micelles were synthesized and characterized successfully ⠢The shielding effect was significant for the hydrophobic core in 1H NMR spectroscopy ⠢Two grafting modes were successfully applied for coating the hydrophobic core PBG-co-PGlu(OtBu) by Psar corona ⠢End-grafted unimolecular arborescent illustrated well-defined core-shell structure in contrast to its analog randomly-grafted unimolecular arborescent
  • Data-Driven Rock-Physics Inversion Of Seismic Pre-Stack Data For Co2 Monitoring

    Corrales, Miguel; Ravasi, Matteo; Hoteit, Hussein (2021-11-03) [Poster]
    Data-driven Rock-Physics inversion of seismic pre-stack data for CO2 monitoring Due to the high global energy demand, CCS and CCUS projects became targets to mitigate net CO2 emissions. In this context, we are facing the need to characterize and monitor the CO2 plume in saline aquifers. Our study aims to obtain the petrophysical properties of a reservoir before and during carbon dioxide injection. To achieve this, we propose a data-driven approach to rock physics inversion that uses a rock-physics model with optimal basis functions to invert band-limited seismic data for rock properties directly. Our new approach promises to be more robust and efficient than the traditional two-step-inversion process from the seismic gather to elastic parameters and then petrophysical properties. We have presented a fast and accurate methodology to invert pre-stack seismic data for petrophysical properties directly. Some of the distinguishing features of our methodology are: Direct recovering of petrophysical properties. Valid for strong contrasts and high angles. Reduced need for regularization parameters. Computational cost reduced. However, being this a data-driven approach, the optimal basis functions are expected to perform poorly when used to extrapolate to unseen geological settings.
  • Multiple Spark Plugs Coupled With Pressure Sensors: A New Approach For Knock Mechanism From Si Engines

    Shi, Hao; Uddeen, Kalim; Tang, Qinglong; Magnotti, Gaetano (2021-11-03) [Poster]

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