Search results for: Computational Chemistry
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Weighted Ensemble with one-class Classification and Over-sampling and Instance selection (WECOI): An approach for learning from imbalanced data streams
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Optimal shape design of multi-element trawl-doors using local surrogate models
PublicationTrawl-doors have a large influence on the fuel consumption of fishing vessels. Design and optimiza-tion of trawl-doors using computational models are a key factor in minimizing the fuel consump-tion. This paper presents an optimization algorithm for the shape design of trawl-door shapes using computational fluid dynamic (CFD) models. Accurate CFD models are computationally expensive. Therefore, the direct use of traditional optimization...
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Aerodynamic shape optimization by variable-fidelity computational fluid dynamics models: a review of recent progress
PublicationA brief review of some recent variable-fidelity aerodynamic shape optimization methods is presented.We discuss three techniques that—by exploiting information embedded in low-fidelity computationalfluid dynamics (CFD) models—are able to yield a satisfactory design at a low computational cost, usu-ally corresponding to a few evaluations of the original, high-fidelity CFD model to be optimized. Thespecific techniques considered here...
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Quadratic Cohen representations in spectral analysis of serration process in Al–Mg alloys
PublicationImportant from mechanical point of view the Portevin–Le Chatelier serration phenomenon is being characterized by a complicated spectral profile. As a typical example of nonstationary processes it demands a special treatment allowing to follow the evolution of energy of stress fluctuations as a function of strain. The authors suggest the utilization of a compact system of quadratic transformations, known as Cohen class, as a technique...
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Negative Poisson’s ratio from pentagons: A new auxetic structure combining three different auxetic mechanisms
PublicationA novel class of two-dimensional auxetic structures based on the pentagon motif is proposed. Their mechanical properties are investigated by combining molecular mechanics simulations with a simple three-parameter mechanical model which assumes perfectly elastic behavior. It is predicted that the proposed structures – termed as double re-entrant honeycomb – may possess unique mechanical characteristics, which include complete and...
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Personalized prediction of the secondary oocytes number after ovarian stimulation: A machine learning model based on clinical and genetic data
PublicationControlled ovarian stimulation is tailored to the patient based on clinical parameters but estimating the number of retrieved metaphase II (MII) oocytes is a challenge. Here, we have developed a model that takes advantage of the patient’s genetic and clinical characteristics simultaneously for predicting the stimulation outcome. Sequence variants in reproduction-related genes identified by next-generation sequencing were matched...
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Frequency bands selection of the Portevin-LeChatelier
PublicationEfekt Portevina-LeChateliera ujawnia się w postaci skokowych zmian naprężenia w trakcie procesu odkształcenia próbek pewnych stopów. Zjawisko PLC występuje w kilku odmianach charakteryzujących się istotnymi różnicami zarówno w przestrzennym rozkładzie pasm odkształcenia jak też przebiegu krzywej naprężeniowej. Przebiegi odpowiadające różnym odmianom serration charakteryzują się odmiennymi właściwościami rozkładu energetycznego...
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Generalized Einstein relation in disordered organic semiconductors: Influence of the acoustic phonons–charge carriers scattering
PublicationIn this work, we analyze the generalized Einstein relation for disordered organic semiconductors with a non-equilibrium Druyvesteyn-type distribution function. The Druyvesteyn behavior of hot electrons in a solid state is associated with the acoustic phonons–charge carriers scattering. Such a case has been experimentally demonstrated in electroluminescent inorganic rare–earth–doped zinc chalcogenides. Therefore, we can assume that,...
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Two-step mechanism of J-domain action in driving Hsp70 function
PublicationJ-domain proteins (JDPs), obligatory Hsp70 cochaperones, play critical roles in protein homeostasis. They promote key allosteric transitions that stabilize Hsp70 interaction with substrate polypeptides upon hydrolysis of its bound ATP. Although a recent crystal structure revealed the physical mode of interaction between a J-domain and an Hsp70, the structural and dynamic consequences of J-domain action once bound and how Hsp70s...
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Structure and properties of liquid Al–Cu alloys: Empirical potentials compared
PublicationWe report on the structure and mass transport properties of liquid Al–Cu alloys predicted by two recently-developed empirical many-body potentials: MEAM (Jelinek et al., 2012) and EAM-ADP (Apostol and Mishin, 2011), and by the well-known Gupta potential. Total and partial pair correlation functions, angular distribution functions, densities, coordination numbers and self-diffusion coefficients are compared with published experimental...
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Applying molecular dynamics simulation to take the fracture fingerprint of polycrystalline SiC nanosheets
PublicationGraphene-like nanosheets are the key elements of advanced materials and systems. The mechanical behavior of the structurally perfect 2D nanostructures is well documented, but that of polycrystalline ones is less understood. Herein, we applied molecular dynamics simulation (MDS) to take the fracture fingerprint of polycrystalline SiC nanosheets (PSiCNS), where monocrystalline SiC nanosheets (MSiCNS) was the reference nanosheet....
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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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Multi-agent large-scale parallel crowd simulation with NVRAM-based distributed cache
PublicationThis paper presents the architecture, main components and performance results for a parallel and modu-lar agent-based environment aimed at crowd simulation. The environment allows to simulate thousandsor more agents on maps of square kilometers or more, features a modular design and incorporates non-volatile RAM (NVRAM) with a fail-safe mode that can be activated to allow to continue computationsfrom a recently analyzed state in...
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Why do G-quadruplexes dimerize through the 5’-ends? Driving forces for G4 DNA dimerization examined in atomic detail
PublicationG-quadruplexes (G4) are secondary structures formed by guanine-rich nucleic acid sequences and shown to exist in living cells where they participate in regulation of gene expression and chromosome maintenance. G-quadruplexes with solvent-exposed guanine tetrads show the tendency to associate together through cofacial stacking, which may be important for packaging of G4-forming sequences and allows for the design of higher-order...
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Efficient knowledge-based optimization of expensive computational models using adaptive response correction
PublicationComputer simulation has become an indispensable tool in engineering design as they allow an accurate evaluation of the system performance. This is critical in order to carry out the design process in a reliable manner without costly prototyping and physical measurements. However, high-fidelity computer simulations are computationally expensive. This turns to be a fundamental bottleneck when it comes to design automation using numerical...
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A Multi-Fidelity Surrogate-Model-Assisted Evolutionary Algorithm for Computationally Expensive Optimization Problems
PublicationIntegrating data-driven surrogate models and simulation models of different accuracies (or fideli-ties) in a single algorithm to address computationally expensive global optimization problems has recently attracted considerable attention. However, handling discrepancies between simulation models with multiple fidelities in global optimization is a major challenge. To address it, the two major contributions of this paper include:...
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In-depth characterization of icosahedral ordering in liquid copper
PublicationThe presence of icosahedral ordering in liquid copper at temperatures close to the melting point is now well-established both experimentally and through computer simulation. However, a more elaborate analysis of local icosahedral and icosahedron-like structures, together with a system for classifying such structures based on some measure of "icosahedrity", has so far been conspicuously absent in the literature. Similarly, the dynamics...
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Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions
PublicationAbility to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in...
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GPU-Accelerated LOBPCG Method with Inexact Null-Space Filtering for Solving Generalized Eigenvalue Problems in Computational Electromagnetics Analysis with Higher-Order FEM
PublicationThis paper presents a GPU-accelerated implementation of the Locally Optimal Block Preconditioned Conjugate Gradient (LOBPCG) method with an inexact nullspace filtering approach to find eigenvalues in electromagnetics analysis with higherorder FEM. The performance of the proposed approach is verified using the Kepler (Tesla K40c) graphics accelerator, and is compared to the performance of the implementation based on functions from...
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Generating optimal paths in dynamic environments using RiverFormation Dynamics algorithm
PublicationThe paper presents a comparison of four optimisation algorithms implemented for the purpose of finding the shortest path in static and dynamic environments with obstacles. Two classical graph algorithms –the Dijkstra complete algorithm and A* heuristic algorithm – were compared with metaheuristic River Formation Dynamics swarm algorithm and its newly introduced modified version. Moreover, another swarm algorithm has been compared...
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Generalization of Phylogenetic Matching Metrics with Experimental Tests of Practical Advantages
PublicationThe ability to quantify a dissimilarity of different phylogenetic trees is required in various types of phylogenetic studies, for example, such metrics are used to assess the quality of phylogeny construction methods and to define optimization criteria in supertree building algorithms. In this article, starting from the already described concept of matching metrics, we define three new metrics for rooted phylogenetic trees. One...
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Characteristics, Chemical Modification Processes as well as the Application of Silica and its Modified Forms
PublicationThe variety of chemical modifications of the surface of silica and its modified forms cause thesematerials to find a consistently wider scope of application. In the publication, the characteristicsof silica, silica gel, aerogel and xerogel are presented. The obtainment, application and propertiesof these materials are discussed. Methods of chemical modifications of surface structures withthe use of different chemical compounds...
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New clicked full agonists of the estrogen receptor β
PublicationA click chemistry approach was used to synthesize a series of 1,4-diaryl-substituted 1,2,3-triazoles designed to behave as estrogen receptor (ER) ligands. We studied their affinities for both receptors α and β, their agonist activities in a cell-based luciferase reporter assay and their effect on the proliferation of the hormone-dependent MCF-7 cell line. We found two compounds (3a and 3c) that behave as selective full agonists...
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Komitet Chemii Analitycznej PAN i jego działalność : Historia i dzień dzisiejszy
PublicationIn the contemporary society analytical chemistry as a scientific discipline and its practical application, termed often ;analysis'', has many important aims, and its role still increases. The Committee, formed in 1955 as a Commission, during several decades has coordinated and supported the activity of Polish analytical chemists on the national and international fields. Its present role includes organization of conferences and...
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SYNTHETIZED MEMBRANES FOR ULTRASOUND-ASSISTED SOLVENT EXTRACTION OF POROUS MEMBRANE PACKED SOLID SAMPLES.
PublicationMembranes are becoming more and more popular in analytical chemistry, which is why they are used, among others, in extraction processes. Therefore, this work focuses on the process of synthesis PVDF membranes and its optimization. The obtained membranes were used as bags for the phthalate extraction in disposable diapers for babies. Extraction was accomplished by method ultrasound-assisted solvent extraction of porous PVDF membrane...
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Towards sugar-derived polyamides as environmentally friendly materials
PublicationAs part of our ongoing study investigating isohexide-based polyamides, we have synthesized isosorbide(bis(propan-1-amine)) (DAPIS) and studied its reactivity in the polymerization towards fully biobased polyamides. Polycondensation of nylon salts with various contributions of DAPIS afforded a family of homo- and copolyamides, which were characterized using complementary spectroscopic techniques. The chemical structure of the materials...
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Natural Deep Eutectic Solvents as Agents for Improving Solubility, Stability and Delivery of Curcumin
PublicationPurpose Study on curcumin dissolved in natural deep eutectic solvents (NADES) was aimed at exploiting their beneficial properties as drug carriers. Methods The concentration of dissolved curcumin in NADES was measured. Simulated gastrointestinal fluids were used to determine the concentration of curcumin and quantum chemistry computations were performed for clarifying the origin of curcumin solubility enhancement in NADES. Results NADES...
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The chemistry, properties and performance of flame-retardant rubber composites: Collecting, analyzing, categorizing, machine learning modeling, and visualizing
PublicationRubbers combine the flexibility with mechanical strength, supporting myriad applications, but suffer from inherent flammability. Formulation and production of flame-retardant rubber composites (FRRCs) have intensively been practiced over years, but not comprehensively reviewed. This necessity has outlined collecting, analyzing, screening, classifying, and interpreting the literature with the aim of classifying the FRRCs. We quantified...
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Evaluation of Green Sample Preparation Techniques for Organic Compounds
PublicationNowadays, Green Analytical Chemistry (GAC) idea is of high importance, with impact on the rapid growth in the sample preparation area with special emphasis on sample preparation simplification, miniaturization and automation. Due to the fact that GAC is of high importance today, this study is focused on the evaluation of green sample preparation techniques for organic compounds. It is well known that sample preparation is considered...
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Binary-Encounter Model for Direct Ionization of Molecules by Positron-Impact
PublicationWe introduce two models for the computation of direct ionization cross sections by positron impact over a wide range of collision energies. The models are based on the binary-encounter-Bethe model and take into account an extension of the Wannier theory. The cross sections computed with these models show good agreement with experimental data. The extensions improve the agreement between theory and experiment for collision energies...
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A competition between two- and three-body dissociation channels in photo-double-ionization of tetrahydro-2H-pyran and 3,4-dihydro-2H-pyran molecules
PublicationVarious molecules possess structures consisting of the heterocyclic rings containing oxygen atoms. These substances often play a significant role in many different fields of chemistry, medicine, and biology. Due to a specific atomic composition and bond arrangement, many of these molecules retain unique electronic properties, which may be probed by diverse spectroscopic techniques, including those utilizing synchrotron radiation....
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Potential energy surfaces of the low-lying electronic states of the Li+LiCs system
PublicationAb initio quantum chemistry calculations are performed for the mixed alkali triatomic system. Global minima of the ground and first excited doublet states of the trimer are found and Born-Oppenheimer potential energy surfaces of the Li atom interacting with the LiCs molecule were calculated for these states. The lithium atom is placed at various distances and bond angles from the lithium-caesium dimer. Three-body nonadditive forces...
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Environmental impact and industrial development of biorenewable resources for polyurethanes
PublicationPolyurethanes are among the most developed types of polymers. They are produced from the three primary components, i.e., polyols, low-molecular-weight glycols used as chain extenders, and diisocyanates. Until recently, all these substrates have been obtained via petrochemical processes. A decrease in petroleum-based resources and new ecological trends in chemistry, chemical technology, and materials engineering have generated increasing...
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Are stabilizing osmolytes preferentially excluded from the protein surface? FTIR and MD studies
PublicationInteractions between osmolytes and hen egg white lysozyme in aqueous solutions were studied by means of FTIR spectroscopy and molecular dynamics. A combination of difference spectra method and chemometric analysis of spectroscopic data was used to determine the number of osmolyte molecules interacting with the protein, and the preferential interaction coefficient in presented systems. Both osmolytes – L-proline and trimethylamine-N-oxide...
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Antioxidants: a premature scientific hypothesis that reshuffled the traditional food pyramid
PublicationAntioxidants present in substantial amounts in foods, plant-based products in particular, have been suggested as chemopreventive agents that can curb the development of undesirable health effects caused by oxidative stress simply by enriching diet in such compounds. This idea has been enthusiastically accepted by consumers, as well as food and pharmaceutical industry, and created great demand for products containing antioxidant...
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Multicriteria Decision Analysis and Grouping of Analytical Procedures for Phthalates Determination in Disposable Baby Diapers
PublicationThis study presents the application of one of the tools from the multicriteria decision analysis set (MCDA), the Technique for Order Preference by Similarity to Ideal Solution (TOPSIS). Selected green analytical chemistry metrics were used to rank analytical procedures for the phthalate determination in disposable baby diapers. Nine analytical procedures were assessed in order to find one that has the lowest environmental impact...
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Green Chromatography: State-of-the-art, Opportunities and Future Perspectives
PublicationIt is well known that chromatographic procedures could have a significant impact on the environment if laboratory practice is not in line with the principles of green analytical chemistry (GAC). However, chromatographic techniques have the potential to be greener in all steps of the analysis. The approaches used to make chromatographic separations greener differ depending on the type of chromatographic method. This chapter considers...
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Band engineering of BiOBr based materials for photocatalytic wastewater treatment via advanced oxidation processes (AOPs) – A review
PublicationSemiconductor based photocatalysts have been an efficient technology for water and wastewater remediation, addressing the concepts of green chemistry and sustainable development. Owing to narrow and suitable band structure, BiOBr is a promising candidate for efficient wastewater treatment via photocatalysis. Enhancement of photocatalytic properties can be obtained by various techniques like doping, element rich strategy, facet...
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Występowanie bakterii siarkowych a jakość wód podziemnych ujęcia Osowa
PublicationAbstrakt. Microorganisms that live in groundwater should be considered not only from the sanitary-hygienic point of view but also in terms of adverse changes in groundwater chemistry in the aquifer layer and its negative influence on the installed devices. For these reasons, it is important to correct approach to the problem of bacterial contamination of groundwater. The paper presents selected results of physicochemical and bacteriological...
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Fabrication, structural and electrical properties of Sr(V,Nb)O 3-δ perovskite materials
PublicationThe SrV1-xNbxO3-δ materials with different niobium content in perovskite B-sublattice were prepared by a solid-state reaction process. The microstructure and phase compositions of obtained samples were analyzed by the X-ray diffraction technique (XRD) and scanning electron microscopy (SEM). The electrical conductivity of samples was measured by a DC 4-wire method in range of 100–600 °C in different gas conditions. The oxidation...
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Synthesis and properties of carboxy derivative of Epidian 6 monomethacrylate (in English)
PublicationWe present the synthesis of an oligomer with carboxy and methacrylic groups based on Epidian 6. The effect of the catalyst nature and amount, solvent nature and process temperature on the rate of the reaction between Epidian6 monomethacrylate and adipic acid was examined at 313, 323 and 333 K in the presence of 4-dimethylaminopyridine, 1,4-diazobicyclo[2.2.2]octane, and benzyltriammonium chloride. The synthesized oligomer was characterized...
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Comparative Analysis of Laboratory-Made and Industrial-Made Sewage Sludge Ash: Implications for Effective Management Strategy Development
Publicationfirst_pageDownload PDFsettingsOrder Article Reprints Open AccessArticle Comparative Analysis of Laboratory-Made and Industrial-Made Sewage Sludge Ash: Implications for Effective Management Strategy Development by Bartłomiej Michał Cieślik 1,*ORCID,Oskar Ronda 1ORCID,Elżbieta Grządka 2ORCID,Jolanta Orzeł 2 andJustyna Płotka-Wasylka 1 1 Department of Analytical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Gabriela...
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The role of the sawage treatment plant in the removal of genotoxic compounds from the environment
PublicationOne reason for increased incidence of various types of cancer are environmental pollutants particularly of anthropogenic origin. All human activities may pollute the environment, but some have significant impact, just to mention energy industry, mining, transportation, chemical and petrochemical industries and housing. Environmental pollutants are a large group of compounds in terms of their physicochemical properties, some of...
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A Green Chemistry "environmentally friendly" approach to the synthesis of chloro-intermediates of ephedrine/pseudoephedrine
PublicationMethylamphetamine is an addictive stimulant drug that strongly activates certain systems in the brain. It is closely related chemically to amphetamine, but the central nervous system effects of methamphetamine are greater. There is much interest in methylamphetamine among scientists and therefore the synthesizes of methylamphetamine and its metabolites are carried out on a large scale in chemical laboratories. Globally, ephedrine...
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Supramolecular deep eutectic solvents and their applications
PublicationIn recent years, the growing awareness of the harmfulness of chemicals to the environment has resulted in the development of green and sustainable technologies. The compromise between economy and environmental requirements is based on the development of new efficient and green solutions. Supramolecular deep eutectic solvents (SUPRADESs), a new deep eutectic solvent (DES) subclass characterized by inclusion properties, are a fresh...
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The Influence of Microstructure on the Passive Layer Chemistry and Corrosion Resistance for Some Titanium-Based Alloys
PublicationThe effect of microstructure and chemistry on the kinetics of passive layer growth and passivity breakdown of some Ti-based alloys, namely Ti-6Al-4V, Ti-6Al-7Nb and TC21 alloys, was studied. The rate of pitting corrosion was evaluated using cyclic polarization measurements. Chronoamperometry was applied to assess the passive layer growth kinetics and breakdown. Microstructure influence on the uniform corrosion rate of these alloys...
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Chemical Vapor Transport Route toward Black Phosphorus Nanobelts and Nanoribbons
PublicationChemical vapor transport (CVT) method is widely used for bulk black phosphorus (BP) fabrication. In this work, we demonstrate that CVT provides a route for the fabrication of BP nanoribbons and nanobelts. This method consists of a two-step procedure, including initial BP column growth using the CVT technique, followed by ultrasonic treatment and centrifugation. The obtained nanostructures preserve BP column dimensions, forming...
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Chemical Vapor Transport Route toward Black Phosphorus Nanobelts and Nanoribbons
PublicationChemical vapor transport (CVT) method is widely used for bulk black phosphorus (BP) fabrication. In this work, we demonstrate that CVT provides a route for the fabrication of BP nanoribbons and nanobelts. This method consists of a two-step procedure, including initial BP column growth using the CVT technique, followed by ultrasonic treatment and centrifugation. The obtained nanostructures preserve BP column dimensions, forming...
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State of the art and prospects of methods for determination of lipophilicity of chemical compounds
PublicationLipophilicity of the compounds is useful to (i) explain their distribution in biological systems, which is different in plant and in animal organisms, (ii) predict the possible pathways of pollutant transport in the environment, and (iii) support drug discovery process and select optimal composition in terms of bioactivity and bioavailability. The lipophilic properties can be determined by two main approaches, experimental, which...
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Predicting the viscosity and electrical conductivity of ionic liquids on the basis of theoretically calculated ionic volumes
PublicationSelected physical properties of the ionic liquids might be quantitatively predicted based on the volumes of the ions these systems are composed of. It is demonstrated that the ionic volumes calculated using relatively simple theoretical quantum chemistry methods can be utilised to estimate the viscosities and electrical conductivities of various commonly used ionic liquids. The fitting formulas of the exponential form are offered...