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Search results for: APPARENT MOLAR VOLUME APPARENT MOLAR COMPRESSIBILITY MOLECULAR DYNAMICS AMINO ACID IONIC LIQUIDS MORPHOLINIUM IONIC LIQUIDS WATER
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Molecular Dynamics Studies on Amyloidogenic Proteins
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Gluten-Free Bread with Cricket Powder—Mechanical Properties and Molecular Water Dynamics in Dough and Ready Product
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Separation of nicotinic acid and its structural isomers using 1-ethyl-3-methylimidazolium ionic liquid as a buffer additive by capillary electrophoresis
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Structure of the interlayer between Au thin film and Si-substrate: Molecular Dynamics simulations
PublicationInteraction between 2, 3, 5 and 7 atomic layers of gold and a (111) silicon surface was investigated with the molecular dynamics simulation method. The simulation of the diffusion interaction between gold and silicon in the temperature range 425-925 K has been carried out. The peculiarities of the concentration changes of the interacting components and the atomic density at the boundary...
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Molecular and structural basis of inner core lipopolysaccharide alterations in Escherichia coli: incorporation of glucuronic acid and phosphoethanolamine in the heptose region.
PublicationIt is well established that lipopolysaccharide (LPS) often carries nonstoichiometric substitutions in lipid A and in the inner core. In this work, the molecular basis of inner core alterations and their physiological significance are addressed. A new inner core modification of LPS is described, which arises due to the addition of glucuronic acid on the third heptose with a concomitant loss of phosphate on the second heptose. This...
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The Influence of Water and Mineral Oil on Pressure Losses in Hydraulic Motor
PublicationIn this paper, pressure losses in hydraulic motor supplied with water and mineral oil (two liquids that have significantly different viscosity and lubricating properties) are described and compared. The experimental tests were conducted using a hydraulic satellite motor that is dedicated to working with different liquids, including water. The methodology of measuring the pressure drop in internal channels of this motor is also...
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Effect of heat treatment on the diffusion intermixing and structure of the Cu thin film on Si (111) substrate: a molecular dynamics simulation study
PublicationThis work is devoted to the study of the diffusion process at the interface between copper films with a thickness of 2, 3, 4, 7 and 10 atomic monolayers and silicon substrate by molecular dynamics simulation method. For this purpose, the variation of the concentration of copper and silicon along the perpendicular direction to the interface was investigated. An analysis of the density profile along this direction made it possible...
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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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Betaine and L-carnitine ester bromides: Synthesis and comparative study of their thermal behaviour and surface activity
PublicationSix esters of both betaine and L-carnitine bromides, featuring alkyl groups ranging from C8 to C18 in length, have been synthesized. The thermal behaviour of these twelve bio-based salts has been analyzed and compared by thermal gravimetric analysis and differential scanning calorimetry. The L-carnitine alkyl ester bromides melted below 100 C and can hence be considered ionic liquids (ILs) with full rights. Conversely, the betaine...
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Solubility enhancement of metronidazole using natural deep eutectic solvents: Physicochemical and thermodynamic studies
PublicationThis research aimed to explore the utility of natural deep eutectic solvents (NADES) as the co-solvents for slightly water-soluble metronidazole (MNZ). After testing 70 wt% (percentage by weight) aqueous mixtures of seven NADESs, it was found that MNZ had the highest solubility in water solutions of NADES composed of choline chloride (ChCl) and citric acid (CA). The solubility of MNZ (expressed as 103 mol fraction) increased with...
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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublicationEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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Formation of Protein Networks between Mucins: Molecular Dynamics Study Based on the Interaction Energy of the System
PublicationMolecular dynamics simulations have been performed for a model aqueous solution of mucin. As mucin is a central part of lubricin, a key component of synovial fluid, we investigate its ability to form cross-linked networks. Such network formation could be of major importance for the viscoelastic properties of the soft-matter system and crucial for understanding the lubrication mechanism in articular cartilage. Thus,the inter- and...
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Ionic conductivity behavior by activated hopping conductivity (AHC) of barium aluminoborosilicate glass–ceramic system designed for SOFC sealing
PublicationNon-conducting BaO-B2O3-Al2O3-SiO2 parent glasses designed for solid oxide fuel cell (SOFC) sealing applications were prepared using the melt-quenching technique. The glass formation region was determined according to phase equilibrium relations and was found to be in the composition range 70BaO-(x)Al2O3-(10−x)B2O3-20SiO2 where 3.0 < x < 6.0 wt%. The conductivity values obtained conductivity ranged from 10−5 to 10−10 S/cm at temperatures...
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Water Reuse_2022
e-Learning CoursesLectures on the subject of Water Reuse
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Water Reuse_2023
e-Learning CoursesLectures on the subject of Water Reuse
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Water Reuse_2024
e-Learning CoursesLectures on the subject of Water Reuse
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Correction to: Plasma free amino acid profiling as metabolomic diagnostic and prognostic biomarker in paediatric cancer patients: a follow-up study
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Simultaneous voltammetric determination of Cd2+, Pb2+, and Cu2+ ions captured by Fe3O4@SiO2 core-shell nanostructures of various outer amino chain length
PublicationIn the present study, we examined a novel functionalised magnetic nanoparticles Fe3O4@SiO2-Nn as a nano adsorbent for binding of Cd2+, Pb2+, Cu2+ ions in an aqueous solution. First, we obtained the nanoparticles functionalised with various carbon chains containing different number of amino groups: (3-amino)propyltriethoxysilane (Fe3O4@SiO2-N1), N-(2-aminoethyl)-3-aminopropyltrimethoxysilane (Fe3O4@SiO2-N2) and N1-(3-trimethoxysilylpropyl)diethylenetriamine...
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VEHICLE DYNAMICS (2024)
e-Learning Courses(W) Vehicle dynamics (W-Lecture) - DAPE - WIMiO The course entitled "Vehicle dynamcs" (VD) is conducted for the DAPE WIMiO Students. The VD course is to discuss the following problems: - major problems of vehicle dynamics from the application point of view, - definition of working environment, - types of vehicles, - parameters and characteristics of vehicles, - assessment of performance of vehicles towards design, -...
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SEM micrographs of NH4VO3 crystals - molar concetration factor after annealing
Open Research DataThe DataSet contains the scanning electron microscopy (SEM) micrographs of NH4VO3 nano_crystals obtained by the LPE-IonEx method with different morphology after annealing at 400C under argon atmosphere (with a heating rate of 10 C/min).
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Towards the Application of Structure-Property Relationship Modeling in Materials Science: Predicting the Seebeck Coefficient for Ionic Liquid/Redox Couple Systems
PublicationThis work focuses on determining the influence of both ionic liquid (IL) type and redox couple concentration on Seebeck coefficient values of such a system. The quantitative structure property relationship (QSPR) and read-across techniques are proposed as methods to identify structural features of ILs (mixed with LiI/I2 redox couple), which have the most influence on the Seebeck coefficient (Se) values of the system. ILs consisting...
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Obtaining ionic forces by the total-energy tight-binding method
PublicationZastosowanie metody ciasnego wiązania w sformułowaniu nieortogonalnym do obliczania sił atomowych w symulacji metodą dynamiki molekularnej pozwala na stworzenie modelu charakteryzującego się lepszą przenośnością, w porównaniu z potencjałami empirycznymi, którymi posługuje się tradycyjna dynamika molekularna. W niniejszej pracy przedstawiono szczegółowo sposób obliczenia pochodnych elementów macierzy Hamiltona i macierzy nakładania...
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Moderately Reactive Molecules Forming Stable Ionic Compounds with Superhalogens
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Chemical interaction between perovskite La0.6Sr0.4FeO3 and Super-Ionic Zr0.84Y0.16Ox
PublicationW pracy przedstawiono wyniki badań interakcji chemicznej pomiędzy materiałem perowskitowym LSF a materiałem superjonowym YSZ. Materiał superjonowy został wytworzony w niskiej temperaturze z użyciem prekusora polimerowego i zawiesiny proszku ceramicznego.W badaniach korzystano z spektroskopii rentgenowskiej.
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Ionic transport in silica xerogels investigated by dynamic current voltagecharacteristics.
PublicationPodano wstępne rezultaty badania transportu ujemnych jonów w kserożelach Si02 w warunkach wysokiego gradientu temperatury w próbce, wywołanego jej ekstremalnie niską przewodnością cieplną. Uzyskane charakterystyki pozostają w zgodzie z przewidywaniami teoretycznymi. Na ich podstawie określono znak jonów, ich ruchliwość i energię aktywacji.
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Simulation of solid state ionic conductors I-V characteristics
PublicationW pracy przedstawiono sumulacje charakterystyk prądowo-napięciowych czujników elktrokatalitycznych. Zastosowano metode różnić skończonych.
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Ionic hydration behavior derived from infrared spectra in HDO
PublicationNa podstawie widm HDO w zakresie podczerwieni scharakteryzowano hydratacjejonów o różnym charakterze. Zastosowana analiza danych widmowych opierała się na metodzie widm różnicowych. Wyniki prowadzą do wniosku, że kationy i aniony wywierają jakościowo bardzo różny wpływ na strukturę wody. Energia wiązań wodorowych cząsteczek wody oddziaływającej z anionem zmienia się proporcjonalnie z siłą polaryzującą anionów. W przeciwieństwie...
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Taurine as a water structure breaker and protein stabilizer
PublicationThe enhancing effect on the water structure has been confirmed for most of the osmolytes exhibiting both stabilizing and destabilizing properties in regard to proteins. The presented work concerns osmolytes, which should be classified as “structure breaking” solutes: taurine and N,N,N-trimethyltaurine (TMT). Here, we combine FTIR spectroscopy, DSC calorimetry and DFT calculations to gain an insight into the interactions between...
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Molecular dynamics simulations of the affinity of chitin and chitosan for collagen: the effect of pH and the presence of sodium and calcium cations
PublicationChitosan and chitin are promising biopolymers used in many areas including biomedical applications, such as tissue engineering and viscosupplementation. Chitosan shares similar properties with hyaluronan, a natural component of synovial fluid, making it a good candidate for joint disease treatment. The structural and energetic consequences of intermolecular interactions are crucial for understanding the biolubrication phenomenon...
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Molecular biology
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Molecular biology
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Fabrication of ILs-Assisted AgTaO3 Nanoparticles for the Water Splitting Reaction: The Effect of ILs on Morphology and Photoactivity
PublicationThe design of an active, stable and ecient photocatalyst that is able to be used for hydrogen production is of great interest nowadays. Therefore, four methods of AgTaO3 perovskite synthesis, such as hydrothermal, solvothermal, sol-gel and solid state reactions, were proposed in this study to identify the one with the highest hydrogen generation eciency by the water splitting reaction. The comprehensive results clearly show that...
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Physical crosslinking of hyaluronic acid in the presence of phospholipids in an aqueous nano-environment
PublicationHyaluronic acid and phospholipids are two components in the synovial joint cavity that contribute to joint lubrication synergistically. Molecular dynamics simulations were performed and hydrogen bonds in hyaluronic acid were analyzed to identify specific sites that are responsible for its physical cross-linking. Two molecular masses of hyaluronic acid, 10 kDa and 160 kDa, were considered. We use molecular dynamics simulations and...
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Molecular dynamics-based model of VEGF-A and its heparin interactions
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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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Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA
PublicationG-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully...
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“Dilute & Shoot” approach for rapid determination of trace amounts of nicotine in zero-level e-liquids by reversed phase liquid chromatography and hydrophilic interactions liquid chromatography coupled with tandem mass spectrometry-electrospray ionization
PublicationTwo analytical procedures are proposed where HILIC and RPLC techniques are coupled with tandem mass spectrometry detection for rapid determination of trace amounts of nicotine in zero-level liquids for electronic cigarettes. Samples are prepared on the basis of the approach “dilute & shoot” which makes this important step quick and not complicated. The chromatographic separation was carried out on a Zorbax XDB column (RPLC method)...
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The Impact of Sloshing Liquids on Ship Stability for Various Dimensions of Partly Filled Tanks
PublicationLiquid sloshing phenomenon taking place in partly filled ships' tanks directly affects the stability of a vessel. However, only static calculations are carried out onboard ships nowadays and static transfer of liquid weight is taken into account in the course of routine stability calculation. The paper is focused on a dynamic heeling moment due to liquid sloshing in tanks onboard ships. A number of numerical simulations of liquid...
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Mechanism of Binding of Antifungal Antibiotic Amphotericin B to Lipid Membranes: An Insight from Combined Single-Membrane Imaging, Microspectroscopy, and Molecular Dynamics
PublicationAmphotericin B is a lifesaving polyene antibiotic used in the treatment of systemic mycoses. Unfortunately, the pharmacological applicability of this drug is limited because of its severe toxic side effects. At the same time, the lack of a well-defined mechanism of selectivity hampers the efforts to rationally design safer derivatives. As the drug primarily targets the biomembranes of both fungi and humans, new insights into the...
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Effect of Cl/Ni molar ratio on the catalytic conversion of polypropylene into Cu–Ni/C composites and their application in catalyzing “Click” reaction
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Molecular dynamics simulation of polymerization of p-xylylene
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Solvation of alkaline earth metal ions in N,N-dimethylformamide and N,N-dimethylacetamide – A volumetric and acoustic study
PublicationDensities and sound velocities at temperatures (298.15, 303.15, 308.15, 313.15 and 318.15) K of magnesium(II), calcium(II) and strontium(II) rifluoromethanesulfonates (triflates), as well as barium(II) perchloratein N,N-dimethylformamide (dmf) and N,N-dimethylacetamide (dma) have been measured over the composition range studied. From these results, apparent molar volumes and apparent molar isentropic compressibilities at infinite...
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Water and chemical properties of hydrometeors over central european mountains
PublicationAtmospheric pollutants are transferred to the groundby the contribution of various types of hydrometeors. Because ofthe different techniques of measurement, comparative analysesbetween them are often neglected. Hence, the main goal is tocompare water volume and chemistry of different types ofhydrometeors and their role in both: water balance and pollutantsdeposition. The results of water input and atmospheric depositschemistry...
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Determination of methylcyclopentadienyl-manganese tricarbonyl in gasoline and water via ionic-liquid headspace single drop microextraction and electrothermal atomic absorption spectrometry
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Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
PublicationExascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified...
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Rengel Cane Sia Doctoral Candidate
PeopleI'm Rengel, born and raised in the Philippines. As an undergraduate I did kinetic modeling on Copper-catalyzed atom transfer radical addition (ATRA). Then I was inspired to do both theoretical and experimental studies, which led me to propose my master's thesis on Synthesis, Computational, Electrochemical, and Photoconductivity Studies on Naphthalene and its derivatives. This led to a master's degree in Chemistry in the Mindanao...
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Identification of 1H‐indene‐(1, 3, 5, 6)‐tetrol derivatives as potent pancreatic lipase inhibitors using molecular docking and molecular dynamics approach
PublicationPancreatic lipase is a potential therapeutic target to treat diet-induced obesity in humans, as obesity-related diseases continue to be a global problem. Despite intensive research on finding potential inhibitors, very few compounds have been introduced to clinical studies. In this work, new chemical scaffold 1H-indene-(1,3,5,6)-tetrol was proposed using knowledge-based approach, and 36 inhibitors were derived by modifying its...
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Molecular dynamics simulations of the growth of poly(chloro-para-xylylene) films
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Facile formation of self-organized TiO2 nanotubes in electrolyte containing ionic liquid - ethylammonium nitrate and their remarkable photocatalytic properties
PublicationThe oriented TiO2 nanotube arrays (NTs) are identified as a stable, active and recyclable photocatalytic surface. However, their photoactivity is strictly depended on morphology (especially length), which could be controlled by anodic oxidation parameters, including electrolyte properties. To control the morphology, were successfully synthesized a series of NTs by a novel approach where ionic liquid (IL), ethylammonium nitrate...
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Jan Franz dr hab.
People