THE KAUST Repository is an initiative of the University Library to expand the impact of conference papers, technical reports, peer-reviewed articles, preprints, theses, images, data sets, and other research-related works of King Abdullah University of Science and Technology (KAUST). 

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  • Computation of Electromagnetic Fields Scattered From Objects With Uncertain Shapes Using Multilevel Monte Carlo Method

    Litvinenko, Alexander; Yucel, Abdulkadir; Bagci, Hakan; Oppelstrup, Jesper; Tempone, Raul; Michielssen, Eric (2019-02-14)
    Computational tools for characterizing electromagnetic scattering from objects with uncertain shapes are needed in various applications ranging from remote sensing at microwave frequencies to Raman spectroscopy at optical frequencies. Often, such computational tools use the Monte Carlo (MC) method to sample a parametric space describing geometric uncertainties. For each sample, which corresponds to a realization of the geometry, a deterministic electromagnetic solver computes the scattered fields. However, for an accurate statistical characterization the number of MC samples has to be large. In this work, to address this challenge, the continuation multilevel Monte Carlo (CMLMC) method is used together with a surface integral equation solver. The CMLMC method optimally balances statistical errors due to sampling of the parametric space, and numerical errors due to the discretization of the geometry using a hierarchy of discretizations, from coarse to fine. The number of realizations of finer discretizations can be kept low, with most samples computed on coarser discretizations to minimize computational cost. Consequently, the total execution time is significantly reduced, in comparison to the standard MC scheme.
  • MXene-Derived Ferroelectric Crystals

    Tu, Shao Bo; Ming, Fangwang; Zhang, Junwei; Zhang, Xixiang; Alshareef, Husam N. (Wiley, 2019-02-14)
    This study demonstrates the first synthesis of MXene-derived ferroelectric crystals. Specifically, high-aspect-ratio potassium niobate (KNbO3 ) ferroelectric crystals is successfully synthesized using 2D Nb2 C, MXene, and potassium hydroxide (KOH) as the niobium and potassium source, respectively. Material analysis confirms that a KNbO3 orthorhombic phase with Amm2 symmetry is obtained. Additionally, ferroelectricity in KNbO3 is confirmed using standard ferroelectric, dielectric, and piezoresponse force microscopy measurements. The KNbO3 crystals exhibit a saturated polarization of ≈21 µC cm-2 , a remnant polarization of ≈17 µC cm-2 , and a coercive field of ≈50 kV cm-1 . This discovery illustrates that the 2D nature of MXenes can be exploited to grow ferroelectric crystals.
  • Advanced Hepatitis C Virus Replication PDE Models within a Realistic Intracellular Geometric Environment

    Knodel, Markus; Targett-Adams, Paul; Grillo, Alfio; Herrmann, Eva; Wittum, Gabriel (MDPI AG, 2019-02-13)
    The hepatitis C virus (HCV) RNA replication cycle is a dynamic intracellular process occurring in three-dimensional space (3D), which is difficult both to capture experimentally and to visualize conceptually. HCV-generated replication factories are housed within virus-induced intracellular structures termed membranous webs (MW), which are derived from the Endoplasmatic Reticulum (ER). Recently, we published 3D spatiotemporal resolved diffusion–reaction models of the HCV RNA replication cycle by means of surface partial differential equation (sPDE) descriptions. We distinguished between the basic components of the HCV RNA replication cycle, namely HCV RNA, non-structural viral proteins (NSPs), and a host factor. In particular, we evaluated the sPDE models upon realistic reconstructed intracellular compartments (ER/MW). In this paper, we propose a significant extension of the model based upon two additional parameters: different aggregate states of HCV RNA and NSPs, and population dynamics inspired diffusion and reaction coefficients instead of multilinear ones. The combination of both aspects enables realistic modeling of viral replication at all scales. Specifically, we describe a replication complex state consisting of HCV RNA together with a defined amount of NSPs. As a result of the combination of spatial resolution and different aggregate states, the new model mimics a cis requirement for HCV RNA replication. We used heuristic parameters for our simulations, which were run only on a subsection of the ER. Nevertheless, this was sufficient to allow the fitting of core aspects of virus reproduction, at least qualitatively. Our findings should help stimulate new model approaches and experimental directions for virology.
  • Beyond the visual: using metabarcoding to characterize the hidden reef cryptobiome

    Carvalho, Susana; Aylagas, Eva; Villalobos, Rodrigo; Kattan, Yasser; Berumen, Michael L.; Pearman, John K. (The Royal Society, 2019-02-13)
    In an era of coral reef degradation, our knowledge of ecological patterns in reefs is biased towards large conspicuous organisms. The majority of biodiversity, however, inhabits small cryptic spaces within the framework of the reef. To assess this biodiverse community, which we term the ‘reef cryptobiome’, we deployed 87 autonomous reef monitoring structures (ARMS), on 22 reefs across 16 degrees latitude of the Red Sea. Combining ARMS with metabarcoding of the mitochondrial cytochrome oxidase I gene, we reveal a rich community, including the identification of 14 metazoan phyla within 10 416 operational taxonomic units (OTUs). While mobile and sessile subsets were similarly structured along the basin, the main environmental driver was different (particulate organic matter and sea surface temperature, respectively). Distribution patterns of OTUs showed that only 1.5% were present in all reefs, while over half were present in a single reef. On both local and regional scales, the majority of OTUs were rare. The high heterogeneity in community patterns of the reef cryptobiome has implications for reef conservation. Understanding the biodiversity patterns of this critical component of reef functioning will enable a sound knowledge of how coral reefs will respond to future anthropogenic impacts.
  • Plant Genome Engineering for Targeted Improvement of Crop Traits

    Sedeek, Khalid E. M.; Mahas, Ahmed; Mahfouz, Magdy M. (Frontiers Media SA, 2019-02-12)
    To improve food security, plant biology research aims to improve crop yield and tolerance to biotic and abiotic stress, as well as increasing the nutrient contents of food. Conventional breeding systems have allowed breeders to produce improved varieties of many crops; for example, hybrid grain crops show dramatic improvements in yield. However, many challenges remain and emerging technologies have the potential to address many of these challenges. For example, site-specific nucleases such as TALENs and CRISPR/Cas systems, which enable high-efficiency genome engineering across eukaryotic species, have revolutionized biological research and its applications in crop plants. These nucleases have been used in diverse plant species to generate a wide variety of site-specific genome modifications through strategies that include targeted mutagenesis and editing for various agricultural biotechnology applications. Moreover, CRISPR/Cas genome-wide screens make it possible to discover novel traits, expand the range of traits, and accelerate trait development in target crops that are key for food security. Here, we discuss the development and use of various site-specific nuclease systems for different plant genome-engineering applications. We highlight the existing opportunities to harness these technologies for targeted improvement of traits to enhance crop productivity and resilience to climate change. These cutting-edge genome-editing technologies are thus poised to reshape the future of agriculture and food security.

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