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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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Encapsulation of Amikacin into Microparticles Based on Low-Molecular-Weight Poly(lactic acid) and Poly(lactic acid-co-polyethylene glycol)
PublicationThe aim of this study was to fabricate novel microparticles (MPs) for efficient and long-term delivery of amikacin (AMI). The emulsification method proposed for encapsulating AMI employed low-molecular-weight poly(lactic acid) (PLA) and poly(lactic acid-co-polyethylene glycol) (PLA−PEG), both supplemented with poly(vinyl alcohol) (PVA). The diameters of the particles obtained were determined as less than 30 μm. Based on an in-vitro...
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Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes
PublicationGlycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes...
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Grzegorz Boczkaj dr hab. inż.
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Hydrogen degradation of structural steels in technical hydrocarbon liquids
PublicationDla stali stopowych przeprowadzono badania absorpcji wodoru, mechaniczno-korozyjne przy stałej małej prędkości odkształcania, przy stałym obciążeniu i przy obciążeniu cyklicznie-zmiennym. Środowiskiem było paliwo kotłowe, przepracowany olej mineralny oraz gliceryna. Stwierdzono, iż pochłonięty wodór nie powoduje przedwczesnego zniszczenia stali poddanych działaniu stałego obciążenia ponizej granicy plastyczności oraz, że zaabsorbowany...
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Estimation of flow for tissue perfusion of nutrient liquids in bioreactor.
PublicationPrzedstawione zostały problemy związane z wyznaczaniem pola prędkości w warstwie przyściennej opływanej tkanki miękkiej w bioreaktorze. Warunki brzegowe na powierzchni miękkiej tkanki o właściwościach porowatych zostały w niniejszej pracy sformułowane.
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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
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The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
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Closer look into the structures of tetrabutylammonium bromide–glycerol-based deep eutectic solvents and their mixtures with water
PublicationIn recent years, deep eutectic solvents (DES) and it’s mixture with water have become more and more attention as green solvents used in chemistry. However, there are only a few theoretical studies on the mechanisms of pure DES and DES-water complex formation. Therefore, the structural properties of tetrabutylammonium bromide–glycerol-based deep eutectic solvents and their mixtures with water have been investigated by means of Molecular...
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Effect of multi-walled carbon nanotubes properties on the photocatalytic activity of bismuth-based composites synthesised via an imidazolium ionic liquid
PublicationThe use of various types of multi-walled carbon nanotubes in the synthesis of bismuth oxybromide semiconductors via imidazolium ionic liquid was studied in detail. The effect of the MWCNT shape, specific surface area, and various diameters on the morphology, surface properties and photoactivity of the Bi-based composites has been investigated for the first time. So far, the literature has only shown the enhancement of photocatalytic...
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Triticale extrudates – Changes of macrostructure, mechanical properties and molecular water dynamics during hydration
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MEL zeolite nanosheet membranes for water purification: insights from molecular dynamics simulations
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Excess Gibbs energies and excess molar volumes for binary mixtures: (2-pyr-rolidone+water), (2-pyrrolidone+methanol), and (2-pyrrolidone+ethanol) at the temperature 313.15K
PublicationZmierzono całkowite prężności pary oraz zmiany objętości mieszania dla tytułowych układów dwuskładnikowych w temperaturze 313.15K. Rezultaty zostały porównane z wynikami uzyskanymi poprzednio dla pozostałych amidów N-metylofor-mamidu, N,N-dimetyloformamidu oraz N-metyloacetamidu.
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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublicationEmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the...
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Optimization of hydrodynamic vortex separator for removal of sand particles from storm water by computational fluid dynamics
PublicationStorm water treatment has been gradually acknowledged for the removal of pollutants from urban areas using the hydro cyclone separation technique. The separation efficiency of the hydrodynamic vortex separator (HDVS) is a complex phenomenon. With the aim enhance the separation potency of HDVS for storm runoff to get rid of sand particles, the HDVS with different structural configurations was studied by computational fluid dynamics....
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Mixed ionic-electronic conductivity and structural properties of strontium-borate glass containing nanocrystallites of Bi2 VO5.5
PublicationSamples of strontium borate glass containing bismuth vanadate nanocrystallites were prepared. Nanocomposites containing up to 45mol% of the Bi2VO5.5 phase exhibit electrical properties closer to the strontium-borate glass than to the ferroelectric Bi2VO5.5 ceramic. The glass matrix still may contain some part of bismuth and vanadium ions even after crystallization process and there is too little of crystalline phase to observe...
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Molecular level interpretation of excess infrared spectroscopy
PublicationInfrared (IR) spectroscopy is an invaluable tool in studying intermolecular interactions in solvent mixtures. The deviation of the IR spectrum of a mixture from the spectra of its pure components is a sensitive measure of the non-ideality of solutions and the modulation of intermolecular interactions introduced by mutual influence of the components. Excess IR spectroscopy, based on the established notion of excess thermodynamic...
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Ordered TiO2 nanotubes with improved photoactivity through self-organizing anodization with the addition of an ionic liquid: effects of the preparation conditions
PublicationModifying the geometric and surface parameters of oriented TiO2 nanotubes (NTs) is beneficial to the utilization of solar energy for chemical reactions, and this performance may be further improved. Thus, the effects of adding an ionic liquid (IL), 1-butylpiridinium chloride [BPy][Cl], and the effects of the water content and preparation conditions on the surface morphological, physicochemical, photocatalytic and photoelectrochemical...
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Molecular Dynamics simulations of thermal conductivity of penta-graphene
PublicationThe thermal conductivity of penta-graphene (PG), a new two dimensional carbon allotrope and its dependence on temperature, strain, and direction are studied in this paper. The thermal conductivity of PG is investigated using a non-equilibrium molecular dynamics simulation (NEMD) with the Two Region Method by applying the optimized Tersoff interatomic potential. Our study shows that the thermal conductivity of PG (determined for...
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Hydration of N-Hydroxyurea from Ab Initio Molecular Dynamics Simulations
PublicationN-Hydroxyurea (HU) is an important chemotherapeutic agent used as a first-line treatment in conditions such as sickle cell disease and β-thalassemia, among others. To date, its properties as a hydrated molecule in the blood plasma or cytoplasm are dramatically understudied, although they may be crucial to the binding of HU to the radical catalytic site of ribonucleotide reductase, its molecular target. The purpose of this work...
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Usuwanie lotnych związków organicznych z fazy gazowej z zastosowaniem cieczy jonowych
PublicationUżycie cieczy jonowej do usuwania LZO jest limitowane przez rozpuszczalność usuwanych związków. Dane literaturowe sugerują, że ciecze jonowe jako faza membranowa mogą być z powodzeniem stosowane do selektywnej separacji węglowodorów aromatycznych z mieszanin węglowodorów aromatycznych i alifatycznych. Przedmiotem pracy było kompleksowe opisanie procesu separacji LZO z fazy gazowej z uwzględnieniem czynników wpływających na efektywność...
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Solvation and partial molar volumes of some transition metal cations in N,N-dimethylacetamide, triethylphosphate and acetonitrile.
PublicationW oparciu o precyzyjne pomiary gęstości roztworów nadchloranów metali przejściowych szeregu Mn(II)-Zn(II) w DMA, TEP i AN wyznaczono pozorne molowe oraz graniczne wartości cząstkowych molowych objętości sole w temperaturach 293, 298 i 303,15 K. Wyznaczone wartości rozdzielono na udziały jonowe. Przeanalizowano czynniki decydujące o wielkości cząstkowych molowych objętości solwatowanych kationów.
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Structure of liquid gold from tight-binding driven molecular-dynamics
PublicationPraca przedstawia wyniki symulacji ciekłego złota w nadkomórce periodycznej przy użyciu stworzonego przez autorów programu komputerowego, za pomocą połączonych metod dynamiki molekularnej (MD) i ciasnego wiązania (TB). Omówiono strukturę tak symulowanej cieczy, porównując ją z dostępnymi danymi doświadczalnymi oraz wynikami innych symulacji, pod kątem radialnej i kątowej funkcji rozkładu i elektronowej gęstości stanów.A tight-binding...
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Interfacial water controls the process of adsorption of hyperactive antifreeze proteins onto the ice surface
PublicationA mechanism of interactions between the ice-binding surface of a hyperactive antifreeze protein molecule and the ice surface is proposed, involving the influence of water present between the two surfaces on the behavior of the approaching molecule. It is demonstrated that the interfacial water, even before its full solidification, can act as a factor that pushes away or pulls nearer the protein molecule to ensure its proper positioning....
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Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules
PublicationSingle-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution...
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Volumes of N,N-dimethylacetamide solvated metal cations. Variation within the manganese(II) to zinc(II) series
PublicationDensities and apparent molar volumes for Mn(ClO4)2,Co(ClO4)2 , Ni(ClO4)2,Cu(ClO4)2 , and Zn(ClO4)2 in N, N -dimethylacetamide (DMA) solutions at T = 298.15 K are reported. Densities and apparent molar volumes of tetrabutylammonium tetraphenylborate...
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Application of ionic liquid-based microwave-assisted extraction of malachite green and crystal violet from water samples
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Encapsulation of an anticancer drug Isatin inside a host nano-vehicle SWCNT: a molecular dynamics simulation
PublicationThe use of carbon nanotubes as anticancer drug delivery cargo systems is a promising modality as they are able to perforate cellular membranes and transport the carried therapeutic molecules into the cellular components. Our work describes the encapsulation process of a common anticancer drug, Isatin (1H-indole-2,3-dione) as a guest molecule, in a capped single-walled carbon nanotube (SWCNT) host with chirality of (10,10). The...
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Sławomir Milewski prof. dr hab. inż.
PeopleSławomir Milewski, born in 1955 in Puck, Poland, graduated in 1979 in Chemistry from the Faculty of Chemistry, Gdańsk University of Technology (GUT). In 1984 was employed at the Department of Pharmaceutical Technology and Biochemistry. In 1985 he got his PhD, in 1994 became a DSc (habilitation) and in 2002 got the professorship in chemical sciences. Currently he is a full professor and Head of the Department of Pharmaceutical Technology...
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Complexation of amino acids derivatives in water by calix[4]arene phosphonic acids
PublicationSeries of the calix[4]arene phosphonic acids with various substituents at the lower rim was synthesized. Complexing properties of these receptors towards methyl esters of six amino acids strongly depended on the calix[4]arene conformation flexibility. The complex formation processes were monitored using 1H NMR spectroscopy (deuterated phosphate buffer at pD 7.3, 22 oC) and association constant values were evaluated. Inherently...
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Electrochemical investigations on corosivity of de-icing liquids for railway infrastructure
PublicationThe paper presents the results of electrochemical tests of the de-icing fluid for railway infrastructure. DC and AC electrochemical tests were performed to determine the corrosion rates of structural steel, cast iron and aluminium in the newly produced fluid. The results were compared with the corrosion rates of the same materials in the fluid without corrosion inhibitors. The obtained test results indicate a low corrosion risk...
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WATER SCIENCE AND TECHNOLOGY
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Collagen type II–hyaluronan interactions – the effect of proline hydroxylation: a molecular dynamics study
PublicationHyaluronan–collagen composites have been employed in numerous biomedical applications. Understanding the interactions between hyaluronan and collagen is particularly important in the context of joint cartilage function and the treatment of joint diseases. Many factors affect the affinity of collagen for hyaluronan. One of the important factors is the ratio of 3- or 4-hydroxy proline to proline residues. This article presents...
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Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublicationIterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using...
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Mechanical Properties of Twisted Carbon Nanotube Bundles with Carbon Linkers from Molecular Dynamics Simulations
PublicationThe manufacturing of high-modulus, high-strength fibers is of paramount importance for real-world, high-end applications. In this respect, carbon nanotubes represent the ideal candidates for realizing such fibers. However, their remarkable mechanical performance is difficult to bring up to the macroscale, due to the low load transfer within the fiber. A strategy to increase such load transfer is the introduction of chemical linkers...
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Paweł Możejko dr hab.
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Transdermal transport of collagen and hyaluronic acid using water in oil microemulsion
PublicationCollagen and hyaluronic acid (HA) are biopolymers that affect the appearance and condition of the skin. Delivery of these compounds into the skin is highly challenging since have a number of disadvantageous properties, such as high molecular weight and hydrophilicity. Here, we evaluated the transdermal penetration of low and high molecular weight collagen and HA from microemulsions. A number of microemulsion formulations, differing...
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Solvation numbers of manganese(II) and zinc(II) perchlorates in methanol obtained from volumetric and compressibility properties
PublicationZmierzono gęstości roztworów nadchloranów manganu(II) i cynku(II) w metanolu w temperaturach: 283.15, 288.15, 293.15, 298.15, 303.15, 308.15, 313.15 K. Ponadto wyznaczono szybkości rozchodzenia się dźwięku w badanych roztworach w 298.15 K. Uzyskane wielkości pozwoliły na obliczenie pozornych objętości molowych oraz pozornych molowych ściśliwości adiabatycznych elektrolitów w metanolu. Oszacowane wielkości graniczne wykorzystane...
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Limiting partial molar volumes and expansibilities of ammonium perchlorate, tetraalkylammonium perchlorates, and tetrabutylammonium tetraphenylborate in N,N-dimethylformamide
PublicationWyniki pomiarów gęstości i szybkości rozchodzenia się dźwięku w roztworach nadchloranu amonu, nadchloranów alkiloamoniowych i tetrafenyloboranu tetrabutylomoniowego w N,N-dimetyloformamidzie wyznaczono wartości graniczne cząstkowych molowych objętości i rozszerzalności. Dokonano rozdziału tych wartości na udziały jonowe. Przeanalizowano wpływ temperatury oraz długości łańcucha na te wielkości.
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Ionic liquid as morphology-directing agent of two-dimensional Bi2WO6: New insight into photocatalytic and antibacterial activity
PublicationAn efficient and durable utilization of light to drive photocatalytic reactions still requires the overcoming of barriers. Herein, two-dimensional (2D) ultrathin IL_Bi2WO6 (IL_BWO) photocatalysts were prepared for the first time via ionic liquid-assisted hydrothermal route by adjusting the amount of tetrabutylammonium chloride [TBA][Cl], synthesis temperature and duration. IL played the role of morphology-directing agent given...
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Molecular dynamics of fentanyl bound to μ-opioid receptor
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Measurements of the Hydraulic Fluids Compressibility
PublicationPerformance of the hydrostatic high-pressure drive systems is affected by the changes of working fluid’s volume. Presence of air bubbles in the fluid cause this problem to be even more serious. To study this phenomenon precise measurements of fluid’s bulk modulus are necessary. Differ-ent measurement methods are applied, but they are either limited to low pressure range or give inaccurate results. To solve the problem the new...
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Wetting processes in supported ionic liquid membranes technology
PublicationCiecz jonowe znajdują szerokie zastosowanie w technologii membran ciekłych, szczególnie w procesach separacji i oczyszczania gazów. Praca opisuje zdolność cieczy jonowych do zwilżania komercyjnie dostępnych porowatych nośników stosowanych w technologii membran ciekłych. Wyznaczenie charakterystyki nośników pozwoliło na wskazanie czynników mających wpływ na procesy zwilżania. Do wyznaczenia kątów zwilżania zastosowano metodą siedzącej...
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Ionic conductivity of bismuth silicate and bismuth germanate glasses.
PublicationPrzedstawiono wyniki badań przewodnictwa d.c i a.c. szkieł BixGe1-xO2-0.5x (gdzie x=0.13, 0.23, 0.33, 0.47) i BixSi1-xO2-0.5x (gdzie x=0.47, 0.57, 0.67). Wyniki sugerują, że przewodnictwo elektryczne jest zdeterminowane ruchem jonów tlenu. Znaczący wzrost przewodnictwa elektrycznego przy x> 0.33 został wytłumaczony na podstawie faz perkolacyjnego modelu ruchu jonów w podsieci BiO5-6.
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Cytochrome P450 izoenzymes involved in metabolism of antitumor 9-amino-1-nitroacridine derivatives, C-857, C-1748
PublicationPraca jest częścią szerszych badań zmierzających do poznania molekularnego mechanizmu metabolicznej transformacji przeciwnowotworowych pochodnych 9-amino-1-nitroakrydyny. W naszym zespole wyselekcjonowano pochodną nowej generacji, która w porównaniu z poprzednimi wykazała znacznie obniżoną toksyczność ogólną. W wyniku przeprowadzonych badań wykazaliśmy, że nowa pochodna jest znacznie mniej podatna na metabolizm katalizowany przez...
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Room temperature ionic liquid-based dispersive liquid–liquid microextraction of uranium in water samples before spectrophotometric determination
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How acidic amino acid residues facilitate DNA target site selection
PublicationDespite the negative charge of the DNA backbone, acidic residues (Asp/Glu) commonly participate in the base readout, with a strong preference for cytosine. In fact, in the solved DNA/protein structures, cytosine is recognized almost exclusively by Asp/Glu through a direct hydrogen bond, while at the same time, adenine, regardless of its amino group, shows no propensity for Asp/Glu. Here, we analyzed the contribution of Asp/Glu...
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The effect of imidazolium ionic liquid on the morphology of Pt nanoparticles deposited on the surface of SrTiO3 and photoactivity of Pt–SrTiO3 composite in the H2 generation reaction
PublicationPhotocatalytic water splitting has great potential in solar-hydrogen production as a low-cost and environmentally friendly method. Different unique techniques used to obtain photocatalysts with various modifications to improve H2 generation have been introduced. In the present work, SrTiO3 was successfully synthesized via the solvothermal method in the presence of ionic liquid (IL) - 1-butyl-3-methylimidazolium bromide ([BMIM][Br])...
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Application of Headspace Solid-phase Microextraction with Poly(1-vinyl-3- Hexylimidazolium Chloride) Polymeric Ionic Liquid Coating using GC - MS to Determine Volatile Fatty Acids in Dairy Wastewater
PublicationVolatile fatty acids were determined in this study using headspace solid-phase microextraction (HS-SPME) with a poly(1-vinyl-3-hexylimidazolium chloride) polymeric ionic liquid coated fiber followed by gas chromatography - mass spectrometry. Experimental parameters such as extraction time and temperature, sample volume as well as desorption time and temperature were optimized. Detection limits of the method were in the range of...
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Green adsorbents and solvents in food analysis
PublicationGreen analytical chemistry aims to minimize the negative impact of analytical procedures on the environment and human health. This can be achieved through the use of non-toxic and environmentally friendly reagents. Classical green solvents include water, ethanol, acetone, and supercritical fluids. Water has been used for the extraction of water-soluble compounds (sugars, amino acids). Ethanol and acetone have been used for the...
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Molecular Dynamics Studies on Amyloidogenic Proteins
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