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Search results for: 2D molecular descriptors
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Molecular Pain
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MOLECULAR BIOLOGY
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MOLECULAR ENDOCRINOLOGY
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MOLECULAR PSYCHIATRY
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MOLECULAR INTERVENTIONS
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Molecular Imaging
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Molecular Neurodegeneration
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MOLECULAR BREEDING
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Molecular Biomedicine
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Molecular Plant
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MOLECULAR CELL
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MOLECULAR THERAPY
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MOLECULAR VISION
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Processing and Maturation of Cathepsin C Zymogen: A Biochemical and Molecular Modeling Analysis
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Coordination polymers and molecular structures among complexes of mercury(II) halides with selected 1-benzoylthioureas
PublicationSix new 1-benzoyl-3-phenylthiourea and 1-benzoyl-3-(2-methylphenyl)thiourea complexes of mercury( II) were obtained in the reactions of the ligands with HgX2 in methanol (X = Cl, Br, I). Their structures, determined by single-crystal X-ray diffraction analysis, exhibit different stoichiometries and molecular organization. Coordination centers adopt more or less distorted tetrahedral geometry (five structures) or distorted trigonal...
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New Peptide Based Fluconazole Conjugates with Expanded Molecular Targets
PublicationInfections of Candida spp. etiology are frequently treated with azole drugs. Among azoles, the most widely used in the clinical scenario remains fluconazole (FLC). Promising results in treatment of dangerous, systemic Candida infections demonstrate the advantages of combined therapies carried out with combinations of at least two different antifungal agents. Here, we report five conjugates composed of covalently linked FLC and...
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Study of the Interactions between Neurophysin II and Dipeptide Ligand by Means of Molecular Dynamics
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Depression as is Seen by Molecular Spectroscopy. Phospholipid- Protein Balance in Affective Disorders and Dementia
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Interactions of N-alkyl-N-methylmorpholinium based ionic liquids with acetonitrile studied by density and velocity of sound measurements and molecular dynamics simulations
PublicationMorpholinium-based ionic liquids (ILs) and their mixtures with polar co-solvents are an interesting class of emerging electrolytes in electrochemistry that is relatively poorly studied. In this work, densities and sound velocities of four ILs, N-ethyl-N-methylmorpholinium tetrafluoroborate, N-butyl-N-methylmorpholinium tetrafluoroborate, N-octyl-N-methylmorpho-linium tetrafluoroborate and N-decyl-N-methylmorpholinium tetrafluoroborate...
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Thermodynamic Studies of Interactions between Sertraline Hydrochloride and Randomly Methylated β-Cyclodextrin Molecules Supported by Circular Dichroism Spectroscopy and Molecular Docking Results
PublicationThe interaction between sertraline hydrochloride (SRT) and randomly methylated β-cyclodextrin (RM β CD) molecules have been investigated at 298.15 K under atmospheric pressure. The method used—Isothermal Titration Calorimetry (ITC) enabled to determine values of the thermodynamic functions like the enthalpy (DH), the entropy (DS) and the Gibbs free energy (DG) of binding for the examined system. Moreover, the stoichiometry coefficient...
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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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In silico modelling for predicting the cationic hydrophobicity and cytotoxicity of ionic liquids towards the Leukemia rat cell line, Vibrio fischeri and Scenedesmus vacuolatus based on molecular interaction potentials of ions
PublicationIn this study we present prediction models for estimating in silico the cationic hydrophobicity and the cytotoxicity (log [1/EC50]) of ionic liquids (ILs) towards the Leukemia rat cell line (IPC-81), the marine bacterium Vibrio fischeri and the limnic green algae Scenedesmus vacuolatus using linear free energy relationship (LFER) descriptors computed by COSMO calculations. The LFER descriptors used for the prediction model (i.e....
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Synthesis, Molecular Structure, Metabolic Stability and QSAR Studies of a Novel Series of Anticancer N-Acylbenzenesulfonamides
PublicationA series of novel N-acyl-4-chloro-5-methyl-2-(R1-methylthio)benzenesulfonamides 18–47 have been synthesized by the reaction of N-[4-chloro-5-methyl-2-(R1-methylthio) benzenesulfonyl]cyanamide potassium salts with appropriate carboxylic acids. Some of them showed anticancer activity toward the human cancer cell lines MCF-7, HCT-116 and HeLa, with the growth percentages (GPs) in the range from 7% to 46%. Quantitative structure-activity relationship...
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Computationally Effcient Solution of a 2D Diffusive Wave Equation Used for Flood Inundation Problems
PublicationThis paper presents a study dealing with increasing the computational efficiency in modeling floodplain inundation using a two-dimensional diffusive wave equation. To this end, the domain decomposition technique was used. The resulting one-dimensional diffusion equations were approximated in space with the modified finite element scheme, whereas time integration was carried out using the implicit two-level scheme. The proposed...
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Preparation of Internal Standards for 2D-UPLC-MS/MS Quantification of Noncanonical DNA Bases
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2D Viscous Flutter Analysis of a 11th Standard Configuration Using Ansys Cfx 14
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Portable parallel simulator using MPI for 2D and 3D domains: design and performance testing
PublicationW artykule prezentujemy szczegóły projektowo-implementacyjne naszego modularnego kodu symulacyjnego z wykorzystaniem MPI, w tym nakładaniem obliczeń i komunikacji. Podkreślamy modularność naszej implementacji pozwalającą na łatwą adaptację kodu dla innych zasotosowań. Prezentujemy związek pomiędzy przyspieszeniem obliczeń, rozmiarem i kształtami trójwymiarowych domen z różnymi stosunkami liczby węzłów aktualizowanych przez procesor...
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Effect of steel fibres on concrete behavior in 2D and 3D simulations using lattice model.
PublicationW artykule przedstawiono wyniki numerycznej symulacji betonu zbrojonego włóknami stalowymi. Beton został opisany w skali mezo jako materiał 3-fazowy przy zastosowaniu modelu sieciowego. Obliczenia wykonano dla rozciągania jednoosiowego. Porównano ze sobą wyniki dwu- i trójwymiarowe.
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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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An insight into the mixed quantum mechanical-molecular dynamics simulation of a ZnII-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding investigations
PublicationAn important aspect of research pertaining to Curcumin (HCur) is the need to arrest its degradation in aqueous solution and in biological milieu. This may be achieved through complex formation with metal ions. For this reason, a complex of HCur was prepared with ZnII, that is not likely to be active in redox pathways, minimizing further complications. The complex is monomeric, tetrahedral, with one HCur, an acetate and a molecule...
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Low-energy electron scattering from molecular hydrogen: Excitation of the X1Σg+ to b3Σu+ transition
PublicationWe present time-of-flight differential cross-section measurements and convergent close-coupling calculations of differential cross sections for the electron-impact excitation of the X 1 g + → b 3 u + transition in molecular hydrogen. A part of this work was recently published [M. Zawadzki et al., Phys. Rev. A 97, 050702(R) (2018)]. In this work, agreement between theory and experiment is excellent overall, and marks a transition...
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Hopping or Tunneling? Tailoring the Electron Transport Mechanisms through Hydrogen Bonding Geometry in the Boron-Doped Diamond Molecular Junctions
PublicationMechanisms of charge transport in molecular junctions involving hydrogen bonds are complex and remain mostly unclear. This study is focused on the elucidation of the electron transfer in a molecular device consisting of two boron-doped diamond interfaces bound with an aromatic linker and a hydrogen bonding surrogating molecule. The projected local density of states (PLODS) analysis coupled with transmission spectra and current−voltage...
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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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Cellular and molecular basis of thyroid autoimmunity
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Fifth Workshop on Atomic and Molecular Physics
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Molecular Analysis of Retrogradation of Corn Starches
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Molecular Modeling of Meta II Rhodopsin
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Probing Radiation Damage at the Molecular Level
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Generating molecular entities as structured data
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The molecular entities in linked data dataset
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Molecular Origin of Anticooperativity in Hydrophobic Association
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Molecular Dynamics Studies on Amyloidogenic Proteins
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Molecular Dynamics Studies on Amyloidogenic Proteins
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An ancestral molecular response to nanomaterial particulates
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ELECTRON ATTACHMENT TO HETEROGENEOUS MOLECULAR CLUSTERS
PublicationHeterogeneous clusters are unique model species enabling studies of bulk and surface processes by vacuum restricted methods. This is of particular importance for the reactions of low-energy electrons which have extremely short penetration depth in bulk environments. This contribution overviews our recent experiments with low-energy electrons and clusters prepared by different techniques. First, the deposition of molecules on argon...
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Molecular structure and electrochemical properties of alkyldithiocarbamates.
PublicationZastosowano klasyczne metody elektroanalityczne do badania właściwości redoks ditiokarbaminianów litu w środowisku dimetylosulfotlenku. Użyto elektrody z platyny i węgla szklistego. Badane związki zsyntezowano z N,N'-dimetyloetylenodiaminy, do której podstawiono jedną lub dwie grupy ditiokarbonylowe na drodze reakcji z CS2 w środowisku alkalicznym. Stwierdzono, że elektrochemiczne utlenianie ditiokarbaminianów przebiega z udziałem...
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Molecular modelling of a psychrophilic β-galactosidase
PublicationAntarktyczny szczep, gram-ujemnych bakterii, wyizolowanych z przewodu pokarmowego kryla z gatunku Thyssanoessa macrura, sklasyfikowany na podstawie analizy sekwencji nukleotydowej geny 16S rDNA jako Pseudoalteromonas sp. 22b jest producentem wewnątrzkomórkowej zimnolubnej beta-galaktozydazy. Ponieważ enzym ten wykazuje wysoką aktywność katalityczną w zakresie temperatur od 0 do 30 stC, stanowi on atrakcyjny biokatalizator, użyteczny...
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Molecular dynamics study of the influence of calcium ions on the conformation of gelsolin S2 domain
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Endothelial dysfunction due to eNOS uncoupling: molecular mechanisms as potential therapeutic targets
PublicationNitric oxide (NO) is one of the most important molecules released by endothelial cells, and its antiatherogenic properties support cardiovascular homeostasis. Diminished NO bioavailability is a common hallmark of endothelial dysfunction underlying the patho‑ genesis of the cardiovascular disease. Vascular NO is synthesized by endothelial nitric oxide synthase (eNOS) from the substrate L‑arginine (L‑Arg), with tetrahydrobiopterin...
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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,...