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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublicationCRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...
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Optimized photodegradation of palm oil agroindustry waste effluent using multivalent manganese–modified black titanium dioxide
PublicationThis article presents a methodological approach to use manganese (Mn3+Mn7+)-modified black titanium dioxide (Mn/BTiO2) as a photocatalyst to optimize and improve visible-light-driven photodegradation of treated agro-industrial effluent (TPOME). A modified wet chemical process was used to prepare BTiO2. The BTiO2 was then wet impregnated with Mn and calcined at 300 °C for 1 h to produce Mn/BTiO2. The activity of Mn/BTiO2 was investigated...
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Fabrication and photoactivity of ionic liquid–TiO2 structures for efficient visible-light-induced photocatalytic decomposition of organic pollutants in aqueous phase
PublicationTo investigate the effect of the ionic liquid (IL) chain length on the surface properties and photoactivity of TiO2, a series of TiO2 microspheres have been synthesized via a solvothermal method assisted by 1-methyl-3-octadecylimidazolium chloride ([ODMIM][Cl]) and 1-methyl-3-tetradecylimidazolium chloride ([TDMIM][Cl]). All as-prepared samples were characterized by X-ray powder diffraction (XRD), X-ray photoelectron spectroscopy...
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Variable-Fidelity Simulation Models and Sparse Gradient Updates for Cost-Efficient Optimization of Compact Antenna Input Characteristics
PublicationDesign of antennas for the Internet of Things (IoT) applications requires taking into account several performance figures, both electrical (e.g., impedance matching) and field (gain, radiation pattern), but also physical constraints, primarily concerning size limitation. Fulfillment of stringent specifications necessitates the development of topologically complex structures described by a large number of geometry parameters that...
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Material Design and Optimisation of Electrochemical Li-Ion Storage Properties of Ternary Silicon Oxycarbide/Graphite/Tin Nanocomposites
PublicationIn this work, we present the characterization and electrochemical performance of various ternary silicon oxycarbide/graphite/tin (SiOC/C/Sn) nanocomposites as anodes for lithium-ion batteries. In binary SiOC/Sn composites, tin nanoparticles may be produced in situ via carbothermal reduction of SnO2 to metallic Sn, which consumes free carbon from the SiOC ceramic phase, thereby limiting the carbon content in the final ceramic nanocomposite....
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Expedited Variable-Resolution Surrogate Modeling of Miniaturized Microwave Passives in Confined Domains
PublicationDesign of miniaturized microwave components is largely based on computational models, primarily, full-wave electromagnetic (EM) simulations. EM analysis is capable of giving an accurate account for cross-coupling effects, substrate and radiation losses, or interactions with environmental components (e.g., connectors). Unfortunately, direct execution of EM-based design tasks such as parametric optimization or uncertainty quantification,...
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Cu( II ) ions removal from wastewater using starch nanoparticles ( SNPs ): An Eco‐sustainable approach
PublicationThe complex structured starch particles were reduced to the nanoscale size range through hydrolysis utilizing low concentration acid assisted with ultrasound irradiation. The synthesized starch nanoparticles (SNPs) were characterized by TEM, FTIR, and XRD techniques. The synthesized SNPs possessed surface activated entities, as many cationic functional groups were confirmed through the FTIR spectrum. Also, these SNPs were effectively...
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Formaldehyde detection with chemical gas sensors based on WO3 nanowires decorated with metal nanoparticles under dark conditions and UV light irradiation
PublicationWe report results of formaldehyde gas (CH2O) detection under dark conditions and UV light irradiation with pristine tungsten trioxide nanowires (WO3 NWs) and metal nanoparticles decorated WO3 NWs gas sensing layers. The resistive layers were deposited by one step aerosol assisted chemical vapor deposition (AACVD) on commercial alumina substrates with 10-pair interdigitated platinum electrodes. The elaborated gas sensors, based...
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Melanoma skin cancer detection using mask-RCNN with modified GRU model
PublicationIntroduction: Melanoma Skin Cancer (MSC) is a type of cancer in the human body; therefore, early disease diagnosis is essential for reducing the mortality rate. However, dermoscopic image analysis poses challenges due to factors such as color illumination, light reflections, and the varying sizes and shapes of lesions. To overcome these challenges, an automated framework is proposed in this manuscript. Methods: Initially, dermoscopic...
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An Empirical Study on the Impact of Gender on Mobile Applications Usability
PublicationIn the area of broadband wireless Internet, mobile applications have already replaced their desktop equivalents and are recognized as valuable tools for any size of businesses and for private use. With the emergence of millions of apps, the quality of their interaction with the user remains an open question for software vendors. While female and male requirements and preferences are not always similar, to the best of our knowledge,...
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Variable Data Structures and Customized Deep Learning Surrogates for Computationally Efficient and Reliable Characterization of Buried Objects
PublicationIn this study, in order to characterize the buried object via deep-learning-based surrogate modeling approach, 3-D full-wave electromagnetic simulations of a GPR model has been used. The task is to predict simultaneously and independent of each characteristic parameters of a buried object of several radii at different positions (depth and lateral position) in various dispersive subsurface media. This study has analyzed variable...
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Effect of Thermal Treatment of Birch Wood by Saturated Water Vapor on Granulometric Composition of Chips from Sawing and Milling Processes from the Point of View of Its Processing to Composites
PublicationThe goal of this work is to investigate the impact of thermal modification of birch wood with saturated steam on the particle size distribution of the sawing and milling process. Birch wood (Betula pendula Roth) is an excellent source to produce plywood boards. Wastes from mechanical processing of birch wood are suitable to produce composite materials. Granulometric analyses of chips from sawing processes on the PRW 15M frame saw,...
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Intracranial hemorrhage detection in 3D computed tomography images using a bi-directional long short-term memory network-based modified genetic algorithm
PublicationIntroduction: Intracranial hemorrhage detection in 3D Computed Tomography (CT) brain images has gained more attention in the research community. The major issue to deal with the 3D CT brain images is scarce and hard to obtain the labelled data with better recognition results. Methods: To overcome the aforementioned problem, a new model has been implemented in this research manuscript. After acquiring the images from the Radiological...
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Buckling analysis of piezo-magnetoelectric nanoplates in hygrothermal environment based on a novel one variable plate theory combining with higher-order nonlocal strain gradient theory
PublicationIn the present investigation, a new first-order shear deformation theory (OVFSDT) on the basis of the in-plane stability of the piezo-magnetoelectric composite nanoplate (PMEN) has been developed, and its precision has been evaluated. The OVFSDT has many advantages compared to the conventional first-order shear deformation theory (FSDT) such as needless of shear correction factors, containing less number of unknowns than the existing...
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Detection of Bioactive Compounds in Organically and Conventionally Grown Asparagus Spears
PublicationIn the recent reports, there are contradictory conclusions about the nutritional and health properties of organic and conventionally growing vegetables. We hypothesized that organic cultivation system results in higher quality of asparagus (Asparagus officinalis L.) because of organic manure and effective organisms. Therefore, new analytical methods were applied in order to find the differences in bioactive compounds between the...
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Mathematical Modeling of Ice Dynamics as a Decision Support Tool in River Engineering
PublicationThe prediction of winter flooding is a complicated task since it is affected by many meteorological and hydraulic factors. Typically, information on river ice conditions is based on historical observations, which are usually incomplete. Recently, data have been supplemented by information extracted from satellite images. All the above mentioned factors provide a good background of the characteristics of ice processes, but are not...
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Derivation of motor mean phase currents in PMSM drives operating with low switching-to-fundamental frequency ratio
PublicationPulse width modulation (PWM) of inverter output voltage causes the waveforms of motor phase cur-rents to consist of distinctive ripples. In order to provide suitable feedback for the motor current con-trollers, the mean value must be extracted from the currents’ waveforms in every PWM cycle. A com-mon solution to derive the mean phase currents is to sample their value at the midpoint of a symmetrical PWM cycle. Using an assumption...
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Tool Wear Monitoring Using Improved Dragonfly Optimization Algorithm and Deep Belief Network
PublicationIn recent decades, tool wear monitoring has played a crucial role in the improvement of industrial production quality and efficiency. In the machining process, it is important to predict both tool cost and life, and to reduce the equipment downtime. The conventional methods need enormous quantities of human resources and expert skills to achieve precise tool wear information. To automatically identify the tool wear types, deep...
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Green chromatography
PublicationAnalysis of organic compounds in samples characterized by different composition of the matrix is very important in many areas. A vast majority of organic compound determinations are performed using gas or liquid chromatographic methods. It is thus very important that these methods have negligible environmental impact. Chromatographic techniques have the potential to be greener at all steps of the analysis, from sample collection...
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Exploring the Solubility Limits of Edaravone in Neat Solvents and Binary Mixtures: Experimental and Machine Learning Study
PublicationThis study explores the edaravone solubility space encompassing both neat and binary dissolution media. Efforts were made to reveal the inherent concentration limits of common pure and mixed solvents. For this purpose, the published solubility data of the title drug were scrupulously inspected and cured, which made the dataset consistent and coherent. However, the lack of some important types of solvents in the collection called...
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Membrane-SPME the best 'green' sample preparation technique for the gas chromatographic determination polar organic pollutants in polar media
PublicationOne of the most popular technique for sample preparation, which fulfill requirements of green analytical chemistry, is solid phase microextraction (SPME). Because of the undoubted advantages of SPME technique, solvent-free character of the extraction process and the enormous potential in analytical practice, a series of studies has been undertaken to develop new technical solutions, where improving the sensitivity and the extraction...
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Challenges in determination of pesticides from various chemical groups in fruits and vegetables applying QuEChERS method
PublicationPesticides are a large group of compounds with different physical and chemical properties, which place some of them among the most toxic, environmentally stable, and mobile substances. Nevertheless, their number, use, and application are continuously expanding. A consequence of their use is the possible presence of residues in treated food products. To protect consumers from exposure to unacceptable levels of pesticides Maximum...
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Deep Eutectic Solvents: Properties and Applications in CO2 Separation
PublicationNowadays, many researchers are focused on finding a solution to the problem of global warming. Carbon dioxide is considered to be responsible for the “greenhouse” effect. The largest global emission of industrial CO2 comes from fossil fuel combustion, which makes power plants the perfect point source targets for immediate CO2 emission reductions. A state-of-the-art method for capturing carbon dioxide is chemical absorption using...
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Influence of temperature and anion type on thermophysical properties of aqueous solutions of morpholine based amino acid ionic liquids
PublicationDensities and sound velocities of aqueous solutions of N-butyl-N-methylmorpholine based amino acid ionic liquids (AAILs), including N-acetyl-L-alanine, N-acetyl-Lvalinate, N-acetyl-L-leucinate, and N-acetyl-L-izoleucinate anions were measured at a temperature from 293.15 to 313.15 K at 5 K intervals and atmospheric pressure. These data were used to calculate the apparent molar volumes and the apparent molar compressibilities in...
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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublicationLow solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the...
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Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE
PublicationThe current surge in bacterial multi-drug resistance (MDR) is one of the largest challenges to public health, threatening to render ineffective many therapies we rely on for treatment of serious infections. Understanding different factors that contribute to MDR is hence crucial from the global “one health” perspective. In this contribution, we focus on the prototypical broad-selectivity proton-coupled antiporter EmrE, one of the...
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BODIPY‐Perylene Charge Transfer Compounds; Sensitizers for Triplet‐Triplet Annihilation Up‐conversion
PublicationBODIPY heterochromophores, asymmetrically substituted with perylene and/or iodine at the 2 and 6 positions were prepared and investigated as sensitizers for triplet-triplet annihilation up conversion (TTA-UC). Single-crystal X-ray crystallographic analyses show that the torsion angle between BODIPY and perylene units lie between 73.54 and 74.51, though they are not orthogonal. Both compounds show intense, charge transfer absorption...
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A rapid and sensitive method for the quantitative analysis of ibuprofen and its metabolites in equine urine samples by gas chromatography-tandem mass spectrometry
PublicationIbuprofen is widely used in human and veterinary medicine for the treatment of chronic pain as well as rheumatic and musculoskeletal disorders. However, t he anal- gesic and anti-inflammatory properties of Ibuprofen have contributed to frequent drug abuse in equestr ian s ports. A sensitive and rapid gas chromatography with tandem mass spectrometry based method with a simple liquid-liquid extraction and deriva- tization requiring...
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Impact of Tetrazolium Ionic Liquid Thermal Decomposition in Solvothermal Reaction on the Remarkable Photocatalytic Properties of TiO2 Particles
PublicationIonic liquids (ILs) could serve as a structuring agent, a solvent, or a source of dopant during solvothermal synthesis of semiconductors particles. To understand the role of IL during formation of TiO2 particles, it is necessary to study the stability of this IL in solvothermal synthesis conditions, as well as studying the surface properties of formed TiO2 particles. In view of this, the effect of the 2,3,5-triphenyltetrazolium...
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Up-to-date strategies and future trends towards the extraction and purification of Capsaicin: A comprehensive review
PublicationBackground According to the current need of manufacturing healthier products, food companies are seeking specific biomolecules that may offer additional added value (i.e., biological activities) to the new food formulations. Capsaicin, as the pungent ingredient of chili peppers, has become so far one of the target biomolecules explored since the 1950s. There is evidence demonstrating that capsaicin exhibits important biological...
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Thermal Instability of Choline Chloride-Based Deep Eutectic Solvents and Its Influence on Their Toxicity─Important Limitations of DESs as Sustainable Materials
PublicationDeep eutectic solvents (DESs) have become a hot topic in many branches of science due to their remarkable properties. They have been studied in a wide variety of applications. In particular, choline chloride (ChCl)-based DESs are one of the most commonly used representatives of these fluids. Nevertheless, in order to apply DESs in some fields, it is essential to guarantee their stability, reusability, and biocompatibility. In this...
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Electrochemistry from first-principles in the grand canonical ensemble
PublicationProgress in electrochemical technologies, such as automotive batteries, supercapacitors, and fuel cells, depends greatly on developing improved charged interfaces between electrodes and electrolytes. The rational development of such interfaces can benefit from the atomistic understanding of the materials involved by first-principles quantum mechanical simulations with Density Functional Theory (DFT). However, such simulations are...
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Ionic liquids-based microextraction techniques
PublicationIn recent years, the development of highly efficient analytical techniques is of great importance, however, the direct analysis of complex sample matrix is still impossible in many cases. Therefore, the step of sample preparation is commonly involved in an analytical procedure. Over the years, it has been realized that the major source of inaccuracy and imprecision on general analysis results from the operations associated to sample...
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TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field
PublicationWe present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression...
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Enhanced capacitance of composite TiO2 nanotube / boron-doped diamond electrodes studied by impedance spectroscopy
PublicationWe report on the novel composite nanostructures based on boron-doped diamond thin film grown on top of TiO2 nanotubes. The nanostructures made of BDD-modified titania nanotubes showed an increase in activity and performance when used as electrodes in electrochemical environments. The BDD thin films (~200-500 nm) were deposited using microwave plasma assisted chemical vapor deposition (MW PA CVD) onto anodically fabricated TiO2...
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Opto-Electrochemical Sensing Device Based on Long-Period Grating Coated with Boron-Doped Diamond Thin Film
PublicationThe fabrication process of thin boron-doped nanocrystalline diamond (B-NCD) microelectrodes on fused silica single mode optical fiber cladding has been investigated. The B-NCD films were deposited on the fibers using Microwave Plasma Assisted Chemical Vapor Deposition (MW PA CVD) at glass substrate temperature of 475 ºC. We have obtained homogenous, continuous and polycrystalline surface morphology with high sp3 content in B-NCD...
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Diamond-based protective layer for optical biosensors
PublicationOptical biosensors have become a powerful alternative to the conventional ways of measurement owing to their great properties, such as high sensitivity, high dynamic range, cost effectiveness and small size. Choice of an optical biosensor's materials is an important factor and impacts the quality of the obtained spectra. Examined biological objects are placed on a cover layer which may react with samples in a chemical, biological...
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Nano-particle doped hydroxyapatite material evaluation using Spectroscopic Polarization Sensitive Optical Coherence Tomography
PublicationBio-ceramics such as hydroxyapatite (HAp) are widely used materials in medical applications, especially as an interface between implants and living tissues. There are many ways of creating structures from HAp like electrochemical assisted deposition, biomimetic, electrophoresis, pulsed laser deposition or sol-gel processing. Our research is based on analyzing the parameters of the sol-gel method for creating thin layers of HAp....
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Nanocrystalline diamond microelectrode on fused silica optical fibers for electrochemical and optical sensing
PublicationFabrication process of thin boron-doped nanocrystalline diamond (B-NCD) microelectrode on fused silica single mode optical fiber has been investigated. The B-NCD films were deposited on the fibers using Microwave Plasma Assisted Chemical Vapor Deposition (MW PA CVD) at glass substrate temperature of 475 ºC. We have obtained homogenous, continuous and polycrystalline surface morphology with the mean grain size in the range of 100-250...
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Synthesis, characterization and application of cross-linked functional terpolymer through epoxy group as sorbent for extraction of cadmium from waters and foods: Multivariate optimization
PublicationThe purpose of this study was to develop a selective sorbent for cadmium ions (Cd(II)) enrichment in orbital shaker assisted solid phase microextraction (OS-SPME) from different aqueous and food samples. A maleic anhydride-styrene-glycidyl methacrylate (MA-St-GMA) terpolymer was synthesized and characterized in detail. Experimental variables of sample preparation step were optimized using a central composite design (CCD). The final...
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Photocatalytic activity of zinc oxide nanorods incorporated graphitic carbon nitride catalyst
PublicationBackground Photocatalysts are user-friendly and serve as compatible materials for degrading industrial dye pollutants. This study utilizes zinc oxide/graphitic carbon nitride (ZnO/g-C3N4) nanocomposites against degrading methylene blue (MB). Methods The hydrothermal method assisted sonication technique was used to fabricate the ZnO/g-C3N4 composite with varying ratios of ZnO/g-C3N4 (1:0.25, 1:0.50, 1:1). The synthesized materials...
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Machine-Learning-Based Global Optimization of Microwave Passives with Variable-Fidelity EM Models and Response Features
PublicationMaximizing microwave passive component performance demands precise parameter tuning, particularly as modern circuits grow increasingly intricate. Yet, achieving this often requires a comprehensive approach due to their complex geometries and miniaturized structures. However, the computational burden of optimizing these components via full-wave electromagnetic (EM) simulations is substantial. EM analysis remains crucial for circuit...
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Management of ground tire rubber waste by incorporation into polyurethane-based composite foams
PublicationRapid economic growth implicated the developing multiple industry sectors, including the automotive branch, increasing waste generation since recycling and utilization methods have not been established simultaneously. A very severe threat is the generation of enormous amounts of post-consumer tires considered burdensome waste, e.g., due to the substantial emissions of volatile organic compounds (VOCs). Therefore, it is essential...
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Topological-numerical analysis of a two-dimensional discrete neuron model
PublicationWe conduct computer-assisted analysis of a two-dimensional model of a neuron introduced by Chialvo in 1995 [Chaos, Solitons Fractals 5, 461–479]. We apply the method of rigorous analysis of global dynamics based on a set-oriented topological approach, introduced by Arai et al. in 2009 [SIAM J. Appl. Dyn. Syst. 8, 757–789] and improved and expanded afterward. Additionally, we introduce a new algorithm to analyze the return times...
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Salt melt synthesis of curved nitrogen-doped carbon nanostructures: ORR kinetics boost
PublicationImplementing metal-free electrocatalysts for the oxygen reduction reaction (ORR) and revealing crucial chemical or topographical parameters driving their activity are vital for the development of power cells. The carbon-based catalysts are very often synthesized through carbonization of biopolymers, in particular, those one containing nitrogen groups such as chitosan. Unfortunately, the resulting carbonaceous materials usually...
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Deposition of phosphate coatings on titanium within scaffold structure
PublicationPurpose: Existing knowledge about the appearance, thickness, and chemical composition of phosphate coatings on titanium inside porous structures is insufficient. Such knowledge is important for the design and fabrication of porous implants. Methods: Metallic scaffolds were fabricated by selective laser melting of 316L stainless steel powder. Phosphate coatings were deposited on Ti sensors placed either outside the scaffolds or...
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UV-Vis-Induced Degradation of Phenol over Magnetic Photocatalysts Modified with Pt, Pd, Cu and Au Nanoparticles
PublicationThe combination of TiO2 photocatalyst and magnetic oxide nanoparticles enhances the separation and recoverable properties of nanosized TiO2 photocatalyst. Metal-modified (Me = Pd, Au, Pt, Cu) TiO2/SiO2@Fe3O4 nanocomposites were prepared by an ultrasonic-assisted sol-gel method. All prepared samples were characterized by X-ray powder diffraction (XRD) analysis, Brunauer-Emmett-Teller (BET) method, X-ray photoelectron spectroscopy...
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Shape-dependent enhanced photocatalytic effect under visible light of Ag3PO4 particles
PublicationSilver phosphate (Ag3PO4) could be considered as visible light induced photocatalyst for pollutants degradation, due to its narrow band gap (∼2.4 eV). However, Ag3PO4 photoactivity depends on surface properties and synthesis route. In this study, differently shaped Ag3PO4 photocatalysts have been synthesized through the precipitation, ion exchange, soft-chemical or hydrothermal method. To correlate surface properties with photoactivity all...
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Low-Cost Yield-Driven Design of Antenna Structures Using Response-Variability Essential Directions and Parameter Space Reduction
PublicationQuantifying the effects of fabrication tolerances and uncertainties of other types is fundamental to improve antenna design immunity to limited accuracy of manufacturing procedures and technological spread of material parameters. This is of paramount importance especially for antenna design in the industrial context. Degradation of electrical and field properties due to geometry parameter deviations often manifests itself as, e.g.,...
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On Fast Multi-objective Optimization of Antenna Structures Using Pareto Front Triangulation and Inverse Surrogates
PublicationDesign of contemporary antenna systems is a challenging endeavor, where conceptual developments and initial parametric studies, interleaved with topology evolution, are followed by a meticulous adjustment of the structure dimensions. The latter is necessary to boost the antenna performance as much as possible, and often requires handling several and often conflicting objectives, pertinent to both electrical and field properties...