Now showing items 1-20 of 19470

• #### Towards Rational Design of Biosynthesis Pathways

(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.
• #### Physical-Layer Security for Mixed <formula>\n <tex>$\eta-\mu$</tex>\n </formula> and <formula>\n <tex>$\mathcal{M}$</tex>\n </formula>-Distribution Dual-Hop RF/FSO Systems

(Institute of Electrical and Electronics Engineers (IEEE), 2018-11-16)
In this correspondence, we investigate the physical-layer security of a mixed radio frequency/free space optical (RF/FSO) dual-hop communication system for both fixed and variable gain relaying schemes. More specifically, we only assume that the eavesdropping happens at the RF link because the optical link has high security. We assume that all RF channels suffer from <formula><tex>$\eta-\mu$</tex></formula> fading, while the FSO link experiences <formula><tex>$\mathcal{M}$</tex></formula>-distributed fading. Then, we derive some analytical results for the average secrecy rate (ASR) and secrecy outage probability (SOP).
• #### A Robust and Cost-Efficient Scheme for Accurate Conformational Energies of Organic Molecules

(Wiley, 2018-11-16)
Several standard semiempirical methods as well as the MMFF94 force field approximation have been tested in reproducing 8 DLPNO-CCSD(T)/cc-pVTZ level conformational energies and spatial structures for 37 organic molecules representing pharmaceuticals, drugs, catalysts, synthetic precursors, industry-related chemicals (37conf8 database). All contemporary semiempirical methods surpass their standard counterparts resulting in more reliable conformational energies and spatial structures, even though at significantly higher computational costs. However, even these methods show unexpected failures in reproducing energy differences between several conformers of the crown ether 1,4,7,10,13,16-hexaoxacyclooctadecane (18-crown-6). Inexpensive force field MMFF94 approximation groups with contemporary semiempirical methods in reproducing the correct order of conformational energies and spatial structures, although the performance in predicting absolute conformational energies compares to standard semiempirical methods. Based on these findings, we suggest a two-step strategy for reliable yet feasible conformational search and sampling in realistic-size flexible organic molecules: i) geometry optimization/preselection of relevant conformers using the MMFF94 force field; ii) single-point energy evaluations using a contemporary semiempirical method. We expect that developed database 37conf8 is going to be useful for development of semiempirical methods.
• #### Revealing the effects of matrix behavior on low-velocity impact response of continuous fiber-reinforced thermoplastic laminates

(Elsevier BV, 2018-11-16)
Matrix behavior is expected to widely influence the impact response of composites, but detailed conclusions in the case of thermoplastic laminates are still needed. In this paper, we investigated the effect of using either ductile homopolymer PP or less-ductile impact copolymer PP matrices on the low-velocity impact responses of continuous glass fiber-reinforced polypropylene (PP) laminate. These PP types represent two variants in the same family of thermoplastic matrix. A thorough experimental campaign was first performed to provide the tensile properties (for PP and glass/PP) and fracture toughness (Mode-I and Mode-II, glass/PP only) of the employed materials. Then, low-velocity impact tests where the energy levels are ranging from 12 to 30 J were performed. Using ductile PP in glass/PP laminates reduces the energy dissipated during impact as well as the impact damage area. The effect of selected stacking sequences on the resistance to impact was also studied as a way to reveal the difference between ductile and less-ductile glass/PP. Stacking sequence with thin plies shows better impact properties than other sequences regardless of the matrix ductility, which can be explained by micromechanics for both grades of material. Finally, as quasi-static indentation (QSI) is usually used to quickly access the resistance of laminates towards out-of-plane impact, we systematically compared our impact results with QSI results. We found that the prospective use of QSI in forecasting impact properties and damage is very limited in glass/PP composite due to strain-rate sensitivity.
• #### ZIF-67 as silver-bullet in Adsorptive Propane/Propylene Separation

(Elsevier BV, 2018-11-16)
The cobalt-based ZIF-67 has been evaluated for the adsorptive propylene/propane separation in a fixed bed. Characterization techniques and dynamic measurements have been performed over ZIF-67 to evaluate its potential in this defiant process. Cobalt promotes a more rigid framework than zinc in the isostructural ZIF-8. Although the adsorption affinity of ZIF-67 for both hydrocarbons is similar, the lower flexibility of the framework makes ZIF-67 behaving with a clear preference towards propane. This inverse selectivity promotes the enrichment in propylene content upon breakthrough, and may simplify the separation scheme. Therefore, ZIF-67 adsorptive separation is presented as an alternative to energy-demanding distillation.
• #### Interfacial Dynamics and Contact Passivation in Perovskite Solar Cells

(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

(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.
• #### Hydrocarbon recovery using ultra-microporous fluorinated MOF platform with and without uncoordinated metal sites: I- Structure properties relationships for C2H2/C2H4 and CO2/C2H2 separation

(Elsevier BV, 2018-11-15)
In this work, the reticular chemistry approach was implemented on a very stable ultra-microporous fluorinated MFFIVE-1-Ni MOFs to unveil the effect of subtle changes of the structure-employment of different fluorinated inorganic block on the adsorption of C2H2, C2H4 and CO2. A series of variable temperature single C2H2, C2H4 and CO2 adsorption isotherms and mixed gas adsorption column breakthrough experiments for different C2H2/C2H4 and CO2/C2H2 gas pair systems were carried out on the two isoreticular NbOFFIVE-1-Ni and AlFFIVE-1-Ni, containing respectively [NbOF5]2- and [AlF5]2- inorganic building blocks. The introduction of potential open metal site in a very confined pores led to favoring interaction of C2H2 but lowering the interaction with CO2, which resulted in enhancement of C2H2/C2H4 selectivity at low C2H2 concentration but a decrease in CO2/C2+ selectivity. The comparison of the C2H2/C2H4 and CO2/C2H2 separation performances with the structures of the MFFIVE-1-Ni MOFs provides useful information to shed light on the relationship between the structural features of this MOF platform and C2H2/C2H4 and CO2/C2H2 separation properties. This is a critical step in the wanted rational discovery/design of materials with enhanced performances for C2H2 recovery from C2H4 and CO2 at different concentration and having different level of input energy for recycling.
• #### Linearly Decoupled Energy-Stable Numerical Methods for Multicomponent Two-Phase Compressible Flow

(Society for Industrial & Applied Mathematics (SIAM), 2018-11-15)
In this paper, for the first time we propose two linear, decoupled, energy-stable numerical schemes for multicomponent two-phase compressible flow with a realistic equation of state (e.g., Peng--Robinson equation of state). The methods are constructed based on the scalar auxiliary variable (SAV) approaches for Helmholtz free energy and the intermediate velocities that are designed to decouple the tight relationship between velocity and molar densities. The intermediate velocities are also involved in the discrete momentum equation to ensure consistency with the mass balance equations. Moreover, we propose a componentwise SAV approach for a multicomponent fluid, which requires solving a sequence of linear, separate mass balance equations. The fully discrete schemes are also constructed based on the finite difference/volume methods with the upwind scheme on staggered grids. We prove that the semidiscrete and fully discrete schemes preserve the unconditional energy-dissipation feature. Numerical results are presented to verify the effectiveness of the proposed methods.
• #### A Comparative Study of Interdigitated Electrode and Quartz Crystal Microbalance Transduction Techniques for Metal–Organic Framework-Based Acetone Sensors

(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

(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.
• #### Cascadable Microelectromechanical Resonator Logic Gate

(IOP Publishing, 2018-11-14)
Micro/nano-electromechanical resonator-based logic elements have emerged recently as an attractive potential alternative to semiconductor electronics. The next step for this technology platform to make it into practical applications and to build complex computing operations beyond the fundamental logic gates is to develop cascadable logic units. Such units should produce outputs that can be used as inputs for the next logic units. Despite the recent developments in electromechanical computing, this requirement has remained elusive. Here, we demonstrate for the first time a conceptual framework for cascadable logic units. Cascadability is experimentally demonstrated through two case studies; one by cascading two OR logic gates. The other case is the universal NOR logic gate realized by cascading an OR and a NOT gate. The logic operations are performed by on-demand activation and deactivation of the second mode of vibration of a clamped-clamped microbeam resonator. We show that the demonstrated approach significantly lowers the complexity and number of microresonator-based logic functions compared to the CMOS-based counterparts, which improves energy efficiency. This can potentially lead toward the realization of a novel technology platform for an alternative computing paradigm.
• #### TGF-b2, catalase activity, H2O2 output and metastatic potential of diverse types of tumour

(Cold Spring Harbor Laboratory, 2018-11-14)
Theileria annulata is a protozoan parasite that infects and transforms bovine macrophages causing a myeloid-leukaemia-like disease called tropical theileriosis. TGF-b2 is highly expressed in many cancer cells and is significantly increased in Theileria-transformed macrophages, as are levels of Reactive Oxygen Species (ROS), notably H2O2. Here, we describe the interplay between TGF-b2 and ROS in cellular transformation. We show that TGF-b2 drives expression of catalase to reduce the amount of H2O2 produced by T. annulata-transformed bovine macrophages, as well as by human lung (A549) and colon cancer (HT-29) cell lines. Theileria-transformed macrophages attenuated for dissemination express less catalase and produce more H2O2, but regain both virulent migratory and matrigel traversal phenotypes when stimulated with TGF-b2, or catalase that reduce H2O2 output. Increased H2O2 output therefore, underpins the aggressive dissemination phenotype of diverse tumour cell types, but in contrast, too much H2O2 can dampen dissemination.
• #### C-Terminal Residue of Ultrashort Peptides Impacts on Molecular Self-Assembly, Hydrogelation, and Interaction with Small-Molecule Drugs

(Springer Nature America, Inc, 2018-11-14)
Single molecular changes on a tripeptide can have dramatic effects on their self-assembly and hydrogelation. Herein, we explore C-terminal residue variation on two consistent ultrashort peptide backbones, i.e. acetylated-Leu-Ile-Val-Ala-Gly-Xaa and acetylated-Ile-Val-Xaa (Xaa = His, Arg, Asn). The objective of this study is to identify candidates that can form hydrogels for small-molecule drug (SMD) delivery. Haemolysis and cytotoxicity (with human adipose-derived mesenchymal stem cells) assays showed that the new soluble peptides (Xaa = His, Arg) are cytocompatible. Gelation studies showed that all but acetylated-Ile-Val-Arg could gel under physiological conditions. Longer peptidic backbones drive self-assembly more effectively as reflected in field emission scanning electron microscopy (FESEM) and circular dichroism spectroscopy studies. Rheological studies revealed that the resultant hydrogels have varying stiffness and yield stress, depending on the backbone and C-terminal residue. Visible spectroscopy-based elution studies with SMDs (naltrexone, methotrexate, doxorubicin) showed that besides the C-terminal residue, the shape of the SMD also determines the rate and extent of SMD elution. Based on the elution assays, infrared spectroscopy, and FESEM, we propose models for the peptide fibril-SMD interaction. Our findings highlight the importance of matching the molecular properties of the self-assembling peptide and SMD in order to achieve the desired SMD release profile.
• #### Reduced ion migration and enhanced photoresponse in cuboid crystals of methylammonium lead iodide perovskite

(IOP Publishing, 2018-11-10)
The optoelectronic and photocatalytic properties of a number of semiconductor materials, including halide perovskites, have recently been found to be facet-dependent. While methylammonium lead iodide (CH3NH3PbI3) perovskite – an important material for energy applications – has shown facet-dependent electronic properties as well, most studies on CH3NH3PbI3 perovskite were performed on rhombo-dodecahedral (or rhombic) single crystals with the (200) and (112) facets exposed. In contrast, less is known about the electronic properties, including mixed conductivity behavior and possible in-plane anisotropy, of the (002) facet. Thus, we report a facile method for the growth of cuboid crystals of CH3NH3PbI3 perovskite with the (002) and (110) facets exposed. Two-terminal devices fabricated on the (002) facet demonstrate significantly improved charge transport and optoelectronic characteristics compared to those on the (200) facet of typical rhombic crystals, including: reduced ion migration, low dark current, and temporally-stable high photocurrents. These desirable characteristics of cuboid crystals are linked to their favorable growth conditions and preferred facet orientations. Our results provide a guidance for utilizing facets and crystal growth to achieve more efficient in-plane halide perovskite devices.
• #### Interaction of amylin species with transition metals and membranes

(Elsevier BV, 2018-11-10)
Islet Amyloid Polypeptide (IAPP), also known as amylin, is a 37-amino-acid peptide hormone that is secreted by pancreatic islet β-cells. Amylin is complementary to insulin in regulating and maintaining blood glucose levels in the human body. The misfolding and aggregation of amylin is primarily associated with type 2 diabetes mellitus, which is classified as an amyloid disease. Recently, the interactions between amylin and specific metal ions, e.g., copper(II), zinc(II), and iron(II), were found to impact its performance and aggregation processes. Therefore, the focus in this review will be on how the chemistry and structural properties of amylin are affected by these interactions. In addition, the impact of amylin and other amyloidogenic peptides interacting with metal ions on the cell membranes is discussed. In particular, recent studies on the interactions of amylin with copper, zinc, iron, nickel, gold, ruthenium, and vanadium are discussed.
• #### Statistical Analysis and Bayesian Methods for Fatigue Life Prediction and Inverse Problems in Linear Time Dependent PDEs with Uncertainties

(2018-11-10)
This work employs statistical and Bayesian techniques to analyze mathematical forward models with several sources of uncertainty. The forward models usually arise from phenomenological and physical phenomena and are expressed through regression-based models or partial differential equations (PDEs) associated with uncertain parameters and input data. One of the critical challenges in real-world applications is to quantify uncertainties of the unknown parameters using observations. To this purpose, methods based on the likelihood function, and Bayesian techniques constitute the two main statistical inferential approaches considered here. Two problems are studied in this thesis. The first problem is the prediction of fatigue life of metallic specimens. The second part is related to inverse problems in linear PDEs. Both problems require the inference of unknown parameters given certain measurements. We first estimate the parameters by means of the maximum likelihood approach. Next, we seek a more comprehensive Bayesian inference using analytical asymptotic approximations or computational techniques. In the fatigue life prediction, there are several plausible probabilistic stress-lifetime (S-N) models. These models are calibrated given uniaxial fatigue experiments. To generate accurate fatigue life predictions, competing S-N models are ranked according to several classical information-based measures. A different set of predictive information criteria is then used to compare the candidate Bayesian models. Moreover, we propose a spatial stochastic model to generalize S-N models to fatigue crack initiation in general geometries. The model is based on a spatial Poisson process with an intensity function that combines the S-N curves with an averaged effective stress that is computed from the solution of the linear elasticity equations.
• #### Theileria\n highjacks JNK2 into a complex with the macroschizont GPI-anchored surface protein p104

(Wiley, 2018-11-09)
Constitutive JNK activity characterizes bovine T and B cells infected with Theileria parva, and B cells and macrophages infected with T. annulata. Here, we show that T. annulata infection of macrophages manipulates JNK activation by recruiting JNK2 and not JNK1 to the parasite surface, whereas JNK1 is found predominantly in the host cell nucleus. At the parasite's surface JNK2 forms a complex with p104 a GPI-anchored T. annulata plasma membrane protein. Sequestration of JNK2 depended on PKA-mediated phosphorylation of a JNK-binding motif common to T. parva and a cell penetrating peptide harbouring the conserved p104 JNK-binding motif competitively ablated binding, whereupon liberated JNK2 became ubiquitinated and degraded. Cytosolic sequestration of JNK2 suppressed small mitochondrial ARF-mediated autophagy, whereas it sustained nuclear JNK1 levels, c-Jun phosphorylation and matrigel traversal. Therefore, T. annulata sequestration of JNK2 contributes to both survival and dissemination of Theileria-transformed macrophages.
• #### Charge and Triplet Exciton Generation in Neat PC70\nBM Films and Hybrid CuSCN:PC70\nBM Solar Cells

(Wiley, 2018-11-09)
Organic solar cells that use only fullerenes as the photoactive material exhibit poor exciton-to-charge conversion efficiencies, resulting in low internal quantum efficiencies (IQE). However, the IQE can be greatly improved, when copper(I) thiocyanate (CuSCN) is used as a carrier-selective interlayer between the phenyl-C70-butyric acid methyl ester (PC70BM) layer and the anode. Efficiencies of ≈5.4% have recently been reported for optimized CuSCN:PC70BM (1:3)-mesostructured heterojunctions, yet the reasons causing the efficiency boost remain unclear. Here, transient absorption (TA) spectroscopy is used to demonstrate that CuSCN does not only act as a carrier-selective electrode layer, but also facilitates fullerene exciton dissociation and hole transfer at the interface with PC70BM. While intrinsic charge generation in neat PC70BM films proceeds with low yield, hybrid films exhibit much improved exciton dissociation due to the presence of abundant interfaces. Triplet generation with a rate proportional to the product of singlet and charge concentrations is observed in neat PC70BM films, implying a charge–singlet spin exchange mechanism, while in hybrid films, this mechanism is absent and triplet formation is a consequence of nongeminate recombination of free charges. At low carrier concentrations, the fraction of charges outweighs the population of triplets, leading to respectable device efficiencies under one sun illumination.
• #### Optimization Strategy of Sustainable Concentrated Photovoltaic Thermal (CPVT) System for Cooling

(Springer Singapore, 2018-11-09)
Renewable energy resources are susceptible to intermittent power supply, and their standalone operation has prime importance for steady power supply. Solar energy resources have high global availability and potential among all energy sources. Most of areas with high solar energy potential have either dry hot or tropical climate. A major portion of primary energy supply for such area is utilized in their cooling energy needs. In this chapter, a sustainable approach for cooling needs has been proposed using solar energy-based highly efficient concentrated photovoltaic (CPV). A combined cooling system, based upon mechanical vapour compression (MVC), and adsorption chillers have been considered. The MVC chiller utilizes the produced electricity by the third -generation multi-junction solar cells (MJCs). However, adsorption chiller is operated with thermal energy recovered from the cooling of CPV system, which also increases the system efficiency as high as 71%. To handle intermittency, hydrogen production is used primary energy storage system, along with the hot water storage. The complete system configuration is then optimized for standalone operation with optimum components size and minimum cost, using micro-genetic algorithm according to proposed optimization strategy.