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Search results for: SODIUM DODECYL SULFATE SODIUM 1-ALKYLSULFONATES CRITICAL MICELLE CONCENTRATION MICELLAR AGGREGATION NUMBER THERMODYNAMIC PARAMETERS FLUORESCENCE SPECTROSCOPY CONDUCTIVITY MOLECULAR DYNAMICS
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Negative Ion Formation in Sodium Chloride TrimerAn ab Initio Study
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Free volume in physical absorption of carbon dioxide in ionic liquids: Molecular dynamics supported modeling
PublicationUnderstanding the mechanisms underlying the carbon dioxide (CO2) absorption in ionic liquids (ILs) is the key to their efficient utilization in industrial flue gas treatment. One of the parameters considered substantially important in the process is the Free Volume. In this study, the Fractional Free Volume (FFV) of 73 ILs was calculated using Molecular Dynamics (MD). A quantitative Structure-Property Relationship (QSPR) study...
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The Influence of Sulfate on Anaerobic Ammonium Oxidation in a Sequencing Batch Reactor
PublicationAnaerobic ammonia-oxidizing bacteria have a more comprehensive metabolism than expected - there may be other electron acceptors that oxidize ammonium nitrogen under anaerobic conditions, in addition to the well-known nitrite nitrogen, one of which is sulfate in the sulfammox process. Sulfate-containing compounds are part of the medium for the anammox process, but their concentrations are not particularly high (0.2 g MgSO4 ∙ 7H2O/dm3...
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Molecular dynamics and verisimilitude - to what extent can one trust a computational simulation?
PublicationFor the last several tens of years, computer simulations have become of undeniable importance. Molecular Dynamics (MD) simulation techniques are used to examine the phenomena which occur at the level that cannot be observed directly. Thus, they can be successfully exploited in many different scientific fields such as: materials science, applied mathematics and theoretical physics, biochemistry, biophysics or drug design. Despite...
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Spectroscopic and theoretical investigation into substituent- and aggregation-related dual fluorescence effects in the selected 2-amino-1,3,4-thiadiazoles
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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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Phenazine - 2,6-dihydroxybenzoic acid (1/1)
PublicationOtrzymano krystaliczny kompleks fenazyny z kwasem 2,6-dihydroksybenzoesowym o stechiometrii 1:1. Badania struktury kompleksu za pomocą metod rentgenograficznych wykazały, że powiązane wiązaniami wodorowymi typu OH...N cząsteczki fenazyny układają się w stosy, które stabilizowane są poprzez oddziaływania typu π-π pierścieni aromatycznych. Cząsteczki kwasu zajmują przestrzenie kanałów tworzonych pomiędzy kolumnami pierścieni aromatycznych...
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Molecular Strategy for Survival at a Critical High Temperature in Eschierichia coli
PublicationThe molecular mechanism supporting survival at a critical high temperature (CHT) in Escherichia coli was investigated. Genome-wide screening with a single-gene knockout library provided a list of genes indispensable for growth at 47°C, called thermotolerant genes. Genes for which expression was affected by exposure to CHT were identified by DNA chip analysis. Unexpectedly, the former contents did not overlap with the latter except...
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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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Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublicationReverse transcriptase (RT) inhibitors are currently used to treat human immunodeficiency virus (HIV)-1 infections. In this work, novel triethylamine derivatives were designed and studied by rigid and flexible docking and molecular dynamics (MD) approaches. An apo form of HIV-1 RT was also studied by MD simulation to analyze comparative response of protein in ligand-bound and ligand-unbound forms. Among newly designed HIV-1 RT inhibitors,...
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Analysis the Parameters of the Adaptive Controller for Quality Control of Dissolved Oxygen Concentration
PublicationThe wastewater treatment plant can be considered a dynamic large scale complex system, in which the most important control parameter is the dissolved oxygen concentration in the aerobic zone. The air is supplied to this zone by the aeration system. In the paper, both the sequencing batch reactor and the aeration system are modelled and used as plant of control performed by the cascade nonlinear adaptive control system extended...
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Conductivity and viscosity changes of imidazolium ionic liquids induced by H2O and CO2
PublicationSeveral solutions of ionic liquids based on 1-ethyl-3-methylimidazolium cation saturated and unsaturated with carbon dioxide were prepared and characterized by electrochemical impedance spectroscopy. The in fluence of ILs saturation on its electrical conductivity was determined. Additionally, the in fluence of the water presence and variations of temperature on electrical properties of ionic liquids were investigated. Changes of...
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The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublicationAmphotericin B (AmB) is an effective but toxic antifungal drug, known to increase the permeability of the cell membrane, presumably by assembling into transmembrane pores in a sterol-dependent manner. The aggregation of AmB molecules in a phospholipid bilayer is, thus, crucial for the drug’s activity. To provide an insight into the molecular nature of this process, here, we report an atomistic molecular dynamics simulation study...
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<p>Analysis of toxicity and anticancer activity of micelles of sodium alginate-curcumin</p>
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Correlations of structural, thermal and electrical properties of sodium doped complex borophosphosilicate glass
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Extraordinary Adsorption of Methyl Blue onto Sodium-Doped Graphitic Carbon Nitride
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Renal regulation of sodium, potassium and chloride balance in single- and twin-pregnant goats
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Advances in Atomic and Molecular Spectroscopy
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Long range molecular dynamics study of regulation of eukaryotic glucosamine-6-phosphate synthase activity by UDP-GlcNAc
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase catalyses the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5' diphospho N-acetyl-D-glucosamine (UDPGlcNAc), is an essential substrate for assembly of bacterialand fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which makes it a potential target...
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Micellar Route of the Synthesis of Alkyl Xylosides: An Unexpected Effect of Amphiphilic Imidazolium Ionic Liquids
PublicationThis manuscript presents results from the investigation on the synthesis of alkyl xylosides by the novel, very efficient and promising protocol of the Fischer synthesis from unprotected xylose and aliphatic alcohol. The use of 1-alkyl-3-methylimidazolium hydrogen sulfate ionic liquids as the catalysts with dual functionality (surfactant + acid catalyst) and micellar reaction system are the main novelty of described method. It has...
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The Product of Matrix Metalloproteinase Cleavage of Doxorubicin Conjugate for Anticancer Drug Delivery: Calorimetric, Spectroscopic, and Molecular Dynamics Studies on Peptide–Doxorubicin Binding to DNA
PublicationMatrix metalloproteinases (MMPs) are extracellular matrix degradation factors, promoting cancer progression. Hence, they could provide an enzyme-assisted delivery of doxorubicin (DOX) in cancer treatment. In the current study, the intercalation process of DOX and tetrapeptide-DOX, the product of the MMPs' cleavage of carrier-linked DOX, into dsDNA was investigated using stationary and time-resolved fluorescence spectroscopy, UV-Vis...
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Effect of Nanohydroxyapatite on Silk Fibroin–Chitosan Interactions—Molecular Dynamics Study
PublicationFibroin–chitosan composites, especially those containing nanohydroxyapatite, show potential for bone tissue regeneration. The physicochemical properties of these biocomposites depend on the compatibility between their components. In this study, the intermolecular interactions of fibroin and chitosan were analyzed using a molecular dynamics approach. Two types of systems were investigated: one containing acetic acid and the other...
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Thermodynamic study of binary mixtures of toluene with ionic liquids, 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide, 1-hexyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide and 1-butylpyridinium bis(trifluoromethylsulfonyl)imide
PublicationDensities, refractive indices and viscosities at 293.15, 298.15, 303.15, 308.15 and 313.15 K of binary mixtures of toluene with 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide, 1-hexyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide and 1-butylpyridinium bis(trifluoromethylsulfonyl)imide have been measured over the miscible region at p = 0.1 MPa. From the experimental data, values of excess molar volume,...
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Sample Concentration of Charged Small Molecules and Peptides in Capillary Electrophoresis by Micelle to Cyclodextrin Stacking
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Raman spectroscopy analysis of molecular configuration forms of the macular xanthophylls
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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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Micelle-bound conformations of neurohypophyseal hormone analogues modified with a Cα-disubstituted residue: NMR and molecular modelling studies
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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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Hydration of amino acids: FTIR spectra and molecular dynamics studies
PublicationThe hydration of selected amino acids, alanine, glycine, proline, valine, isoleucine and phenylalanine, has been studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H2O. The difference spectra procedure and the chemometric method have been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. To support interpretation of obtained spectral results,...
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Effect of Temperature and Nanoparticle Concentration on Free Convective Heat Transfer of Nanofluids
PublicationA theoretical analysis of the influence of temperature and nanoparticle concentration on free convection heat transfer from a horizontal tube immersed in an unbounded nanofluid was presented. The Nusselt (Nu) number and heat transfer coefficient were parameters of the intensity of the convective heat transfer. For free convection, the Nu number was a function of the Rayleigh (Ra) number and Prandtl (Pr) number. The Rayleigh (Ra)...
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Fuzzy Collision Threat Parameters Area (FCTPA) - a new display proposal
PublicationW rozdziale przedstawiono nową metodę wizualizacji umożliwiającą nawigatorom oszacowanie sytuacji zbliżenia dwóch statków i w razie konieczności - wybór manewru antykolizyjnego. Metoda ta jest oparta na metodzie CTPA i oferuje następujące, nowe w stosunku do CTPA elementy: rozmyte sektory zabronionych prędkości i kursów oraz możliwość zastosowania dowolnej domeny statku. Metoda jest wystarczająco szybka do zastosowania w dowolnym...
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Viscoelastic properties of oil-in-water emulsions stabilized by acylpropyleneglycol emulsifiers obtained with sodium soaps
PublicationZbadano właściwości reologiczne emulsji typu O/W, stabilizowanych emulgatorami acylopropylenoglikolowymi. Do badań wykorzystano reometr o kontrolowanym naprężeniu ścinającym. Wykonano testy oscylacyjne tzw. ''dużej deformacji próbki'' oraz analizy typu ''pełzanie i powrót''. Stwierdzono, że właściwości lepkosprężyste emulsji determinowane były składem stosowanego emulgatora. Wszystkie badane układy emulsyjne charakteryzowały się...
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Simultaneous Removal of Heavy Metals from Wastewater Using Modified Sodium Montmorillonite Nanoclay
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Novel design of sodium alginate based absorbable stent for the use in urethral stricture disease
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Spectroscopic studies on physicochemical properties of selected unsymmetrical bisacridine derivatives and NMR analysis of their interactions with the model sequence Pu22 aided by molecular dynamics
PublicationIn recent years, new promising acridine derivatives have appeared, belonging to the unsymmetrical bisacridines (UAs) family with high anticancer activity. Both their physicochemical properties and their mechanism of action at the molecular level have not been thoroughly analyzed so far. Four derivatives were selected for the study, termed as: C-2028, C-2041, C-2045 and C-2053. The first aim of this work was to determine the protonation...
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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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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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Solvent Exchange around Aqueous Zn(II) from Ab Initio Molecular Dynamics Simulations
PublicationHydrated zinc(II) cations, due to their importance in biological systems, are the subject of ongoing research concerning their hydration shell structure and dynamics. Here, ab initio molecular dynamics (AIMD) simulations are used to study solvent exchange events around aqueous Zn2+, for which observation in detail is possible owing to the considerable length of the generated trajectory. While the hexacoordinated Zn(H2O)62+ is the...
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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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Spectroscopic properties of Rhodamine B entrapped in hybrid porous nanolayers at high dye concentration
PublicationThe preparation procedure and characterization of Rhodamine B entrapped in zirconia, silica and mixed silica–zirconia nanolayers is described. The nanolayers were produced by the sol–gel spin-coating technique. The pronounced effect of the dye concentration on the absorption and fluorescence spectra as well as on time-resolved fluorescence spectra was found. The results show that the aggregation of Rhodamine B is stronger in silica...
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Layer-by-layer polymer deposited fabrics with superior flame retardancy and electrical conductivity
PublicationSmart and multifunctional textiles and fabrics are progressively developing, such that multifunctional fabrics are becoming more widespread. We elaborated herein multi-layered flax fabrics with superior flame retardancy and conductivity, which revealed fireproof feature while keeping conductivity during burning. The flax fabric was reinforced by layer-by-layer (LbL) deposition of sodium polyacrylate (SPA), polyethylenimine (PEI),...
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Molecular dynamics of fentanyl bound to μ-opioid receptor
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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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Detection of Denatonium Benzoate (Bitrex) Remnants in Noncommercial Alcoholic Beverages by Raman Spectroscopy
PublicationIllegal alcoholic beverages are often introduced into market using cheap technical alcohol, which is contaminated by denatonium benzoate (Bitrex) of very small concentration. Bitrex is the most bitter chemical compound and has to be removed before alcohol consumption. The home-made methods utilize sodium hypochlorite to disintegrate particles of denatonium benzoate in alcohol and to remove bitter taste before trading. In this experimental...
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PM10 concentration and microbiological assessment of air in relation to the number of acute cases of type 1 diabetes mellitus in the Lubelskie Voivodeship. Preliminary report
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Problem of aggregation in dye-DNA interaction, calorimetry studies
PublicationNucleic acids are the biological target for many antimicrobial, antitumor and antiviral drugs. Ligand-DNA interactions can be classified into two major categories: 1. covalent binding, which can provide to intermolecular adducts, 2. physico-chemical interactions, which can be divided into intercalation (e.g. adriamycin) or groove binding (e.g. dystamycin). There are several methods to investigate interactions between drug and DNA....
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Electron impact fragmentation of pyrrole molecules studied by fluorescence emission spectroscopy
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The thermodynamic critical field and specific heat of superconducting state in phosphorene under strain
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Determination of Biogenic Amines in Wine Using Micellar Electrokinetic Chromatography
PublicationProduction on a large-scale of fermented alcoholic drinks made from different kinds of fruits is carried out in homes. Although wine laws regulating home production exist, they do not include upper concentration limits of biogenic amines. Therefore, a quick and inexpensive way to determine BAs in wine is crucial. A new analytical method based on micellar electrokinetic chromatography has been developed for the separation of the...
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Molecular Dynamics Studies on Amyloidogenic Proteins
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