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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  • Towards Rational Design of Biosynthesis Pathways

    Alazmi, Meshari (2018-11-19)
    Recent advances in genome editing and metabolic engineering enabled a precise construction of de novo biosynthesis pathways for high-value natural products. One important design decision to make for the engineering of heterologous biosynthesis systems is concerned with which foreign metabolic genes to introduce into a given host organism. Although this decision must be made based on multifaceted factors, a major one is the suitability of pathways for the endogenous metabolism of a host organism, in part because the efficacy of heterologous biosynthesis is affected by competing endogenous pathways. To address this point, we developed an open-access web server called MRE (metabolic route explorer) that systematically searches for promising heterologous pathways by considering competing endogenous reactions in a given host organism. MRE utilizes reaction Gibbs free energy information. However, 25% of the reactions do not have accurate estimations or cannot be estimated. To address this issue, we developed a method called FC (fingerprint contribution) to provide a more accurate and complete estimation of the reaction free energy. To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. For a given pair of starting and desired compounds in a given chassis organism, MRE ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/. Accurate and wide-ranging prediction of thermodynamic parameters for biochemical reactions can facilitate deeper insights into the workings and the design of metabolic systems. Here, we introduce a machine learning method, referred to as fingerprint contribution (FC), with chemical fingerprint-based features for the prediction of the Gibbs free energy of biochemical reactions. From a large pool of 2D fingerprint-based features, this method systematically selects a small number of relevant ones and uses them to construct a regularized linear model. FC is freely available for download at http://sfb.kaust.edu.sa/Pages/Software.aspx.
  • Interfacial Dynamics and Contact Passivation in Perovskite Solar Cells

    de Bastiani, Michele; Aydin, Erkan; Allen, Thomas; Walter, Daniel; Fell, Andreas; Peng, Jun; Gasparini, Nicola; Troughton, Joel; Baran, Derya; Weber, Klaus; White, Thomas P.; De Wolf, Stefaan (Wiley, 2018-11-15)
    Charge accumulation at the electron and hole transport layers generates anomalous electrical behavior in perovskite solar cells (PSCs). Hysteresis in the current–voltage characteristic and recombination at the interfaces are the clearest manifestations of this phenomenon, which compromises device performance and stability. Here, the underlying charge-carrier dynamics of a variety of PSCs are investigated by analyzing their transient photocurrent response. Towards shorter time scales, PSCs often show increasingly severe hysteretic responses. This phenomenon is correlated with the presence of interfacial accumulated charges that hinders the photogenerated carrier extraction process. However, introducing passivating contacts improves the carrier-injection properties and the devices become completely hysteresis free. These results underline the importance of contact passivation for PSCs and the need to further develop new passivating interlayers that simultaneously eliminate charge-carrier recombination and provide selective transport for each carrier type at the PSC's contacts.
  • Ten States of Nonvolatile Memory through Engineering Ferromagnetic Remanent Magnetization

    Zhong, Hai; Wen, Yan; Zhao, Yuelei; Zhang, Qiang; Huang, Qikun; Chen, Yanxue; Cai, Jianwang; Zhang, Xixiang; Li, Run-Wei; Bai, Lihui; Kang, Shishou; Yan, Shishen; Tian, Yufeng (Wiley, 2018-11-15)
    Emerging nonvolatile multilevel memory devices have been regarded as a promising solution to meet the increasing demand of high-density memory with low-power consumption. In particular, decimal system of the new computers instead of binary system could be developed if ten nonvolatile states are realized. Here, a general remanent magnetism engineering method is proposed for realizing multiple reliable magnetic and resistance states, not depending on a specific material or device structure. Especially, as a proof-of-concept demonstration, ten states of nonvolatile memory based on the manipulation of ferromagnetic remanent magnetization have been revealed in both Co/Pt magnetic multilayers with strong perpendicular magnetic anisotropy and MgO-based magnetic tunneling junctions at room temperature. Considering ferromagnets have been one of the key factors that enabled the information revolution from its inception, this state-of-the-art remanent magnetism engineering approach has a very broad application prospect in the field of spintronics.
  • A Comparative Study of Interdigitated Electrode and Quartz Crystal Microbalance Transduction Techniques for Metal–Organic Framework-Based Acetone Sensors

    Chappanda, Karumbaiah N.; Tchalala, Mohammed; Shekhah, Osama; Surya, Sandeep G.; Eddaoudi, Mohamed; Salama, Khaled N. (MDPI AG, 2018-11-14)
    We present a comparative study of two types of sensor with different transduction techniques but coated with the same sensing material to determine the effect of the transduction mechanism on the sensing performance of sensing a target analyte. For this purpose, interdigitated electrode (IDE)-based capacitors and quartz crystal microbalance (QCM)-based resonators were coated with a zeolitic⁻imidazolate framework (ZIF-8) metal⁻organic framework thin films as the sensing material and applied to the sensing of the volatile organic compound acetone. Cyclic immersion in methanolic precursor solutions technique was used for depositing the ZIF-8 thin films. The sensors were exposed to various acetone concentrations ranging from 5.3 to 26.5 vol % in N₂ and characterized/compared for their sensitivity, hysteresis, long-term and short-term stability, selectivity, detection limit, and effect of temperature. Furthermore, the IDE substrates were used for resistive transduction and compared using capacitive transduction.
  • Speed breeding in growth chambers and glasshouses for crop breeding and model plant research

    Ghosh, Sreya; Watson, Amy; Gonzalez-Navarro, Oscar E.; Ramirez-Gonzalez, Ricardo H.; Yanes, Luis; Mendoza-Suárez, Marcela; Simmonds, James; Wells, Rachel; Rayner, Tracey; Green, Phon; Hafeez, Amber; Hayta, Sadiye; Melton, Rachel E.; Steed, Andrew; Sarkar, Abhimanyu; Carter, Jeremy; Perkins, Lionel; Lord, John; Tester, Mark A.; Osbourn, Anne; Moscou, Matthew J.; Nicholson, Paul; Harwood, Wendy; Martin, Cathie; Domoney, Claire; Uauy, Cristobal; Hazard, Brittany; Wulff, Brande B. H.; Hickey, Lee T. (Springer Nature America, Inc, 2018-11-14)
    ‘Speed breeding’ (SB) shortens the breeding cycle and accelerates crop research through rapid generation advancement. SB can be carried out in numerous ways, one of which involves extending the duration of plants’ daily exposure to light, combined with early seed harvest, to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral crops. In this protocol, we present glasshouse and growth chamber–based SB approaches with supporting data from experimentation with several crops. We describe the conditions that promote the rapid growth of bread wheat, durum wheat, barley, oat, various Brassica species, chickpea, pea, grass pea, quinoa and Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale up plant numbers for single-seed descent (SSD). In addition, instructions are provided on how to perform SB on a small scale in a benchtop growth cabinet, enabling optimization of parameters at a low cost.

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