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Wyniki wyszukiwania dla: 2D molecular descriptors
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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
PublikacjaChitosan 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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Density functional theory-based simulations of sum frequency generation spectra involving methyl stretching vibrations: effect of the molecular model on the deduced molecular orientation and comparison with an analytical approach
PublikacjaThe knowledge of the first hyperpolarizability tensor elements of molecular groups is crucial for a quantitative interpretation of the sum frequency generation (SFG) activity of thin organic films at interfaces. Here, the SFG response of the terminal methyl group of a dodecanethiol (DDT) monolayer has been interpreted on the basis of calculations performed at the density functional theory (DFT) level of approximation. In particular,...
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Hydration of N-Hydroxyurea from Ab Initio Molecular Dynamics Simulations
PublikacjaN-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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Assessment of the effect of vegetation on the transition of the flood wave using hydraulic 2D models
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High catalytic performance of 2D Ti3C2Tx MXene in α-pinene isomerization to camphene
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2D numerical simulation of tear film dynamics: Effects of shear-thinning properties
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Applying, Canceling and Identifying the Magnetic Field Received and Emitted by a 2D Plan System
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A Study of Cross-Linguistic Speech Emotion Recognition Based on 2D Feature Spaces
PublikacjaIn this research, a study of cross-linguistic speech emotion recognition is performed. For this purpose, emotional data of different languages (English, Lithuanian, German, Spanish, Serbian, and Polish) are collected, resulting in a cross-linguistic speech emotion dataset with the size of more than 10.000 emotional utterances. Despite the bi-modal character of the databases gathered, our focus is on the acoustic representation...
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Modelling and simulation of striated muscle and groups of muscles in arm-forearm system 2D
PublikacjaModel mięśnia szkieletowego poprzecznie prążkowanego został przedstawiony jako szeregowe połączenie aktywnych i pasywnych odcinków reologicznych. Zasymulowane zostały: skurcze pojedyncze, niecałkowity skurcz tężcowy, całkowity skurcz tężcowy. Model zespołu mięśni w układzie ramię-przedramię opisu-je zmianę kąta obrotu przedramienia względem nieruchomego ramienia. Pobudzając zginacze i prostowniki był zasymulowany obrót przedramienia.
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Reguły animacji tradycyjnej w komputerowych systemach animacji 2D i 3D
PublikacjaWykorzystywane obecnie reguły animacji sformułowane zostały ponad 70 lat temu. Artykuł zawiera ich opis i klasyfikację oraz sposoby zastosowania w technice komputerowej. Zaproponowano zestaw testów subiektywnych dotyczących oceny realizmu animacji stworzonych z wykorzystaniem reguł.
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Effect of aggregate structure on fracture process in concrete using 2D lattice model
PublikacjaArtykuł przedstawia symulacje rys w betonie przy zastosowaniu nowego modelu siatkowego. Zbadano wpływ rozkładu i wielkości kruszywa oraz wpływ strefy kontaktu na nośność i propagacje rys. Obliczenia były dwuwymiarowe.
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Shear zone formation in 2D random granular specimens within enhanced hypoplasticity.
PublikacjaW artykule przedstawiono wyniki numerycznej stochastycznej analizy wpływu rozkładu początkowego wskaźnika porowatości w materiałach granulowanych na powstawanie lokalizacji odkształceń. Obliczenia wykonano dla ściskania dwuosiowego stosując metodę elementów skończonych na bazie mikropolarnego, nielokalnego i gradientowego prawa hipoplastycznego.
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Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
PublikacjaIterative 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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Spectroscopic, molecular docking and molecular dynamic simulation studies on the complexes of β-lactoglobulin, safranal and oleuropein
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Solvent Exchange around Aqueous Zn(II) from Ab Initio Molecular Dynamics Simulations
PublikacjaHydrated 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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Prediction of Overall In Vitro Microsomal Stability of Drug Candidates Based on Molecular Modeling and Support Vector Machines. Case Study of Novel Arylpiperazines Derivatives
PublikacjaOther than efficacy of interaction with the molecular target, metabolic stability is the primary factor responsible for the failure or success of a compound in the drug development pipeline. The ideal drug candidate should be stable enough to reach its therapeutic site of action. Despite many recent excellent achievements in the field of computational methods supporting drug metabolism studies, a well-recognized procedure to model...
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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
PublikacjaSix 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
PublikacjaInfections 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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Kontrola parametrów obwodu wymuszającego w quasi-statycznych magnetycznych badaniach nieniszczących stali, cz. I: Model analityczny i 2D
PublikacjaW artykule zaprezentowane zostało dwuwymiarowe modelowanie Metodą Elementów Skończonych (MES) układu do badań nieniszczących (ang. non-destructive testing, w skrócie NDT), składającego się z elektromagnesu jarzmowego i płyty ferromagnetycznej magnesowanej w sposób quasi-statyczny. Wykazane zostały ograniczenia stosowalności opartych na równaniach Maxwella obliczeń analitycznych 1D, które przynoszą zadowalające wyniki jedynie w...
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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
PublikacjaMorpholinium-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
PublikacjaThe 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
PublikacjaHyaluronan–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
PublikacjaIn 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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Effect of Nanohydroxyapatite on Silk Fibroin–Chitosan Interactions—Molecular Dynamics Study
PublikacjaFibroin–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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Synthesis, Molecular Structure, Metabolic Stability and QSAR Studies of a Novel Series of Anticancer N-Acylbenzenesulfonamides
PublikacjaA 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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Low-energy electron scattering from molecular hydrogen: Excitation of the X1Σg+ to b3Σu+ transition
PublikacjaWe 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
PublikacjaMechanisms 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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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
PublikacjaAn 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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Structure of the interlayer between Au thin film and Si-substrate: Molecular Dynamics simulations
PublikacjaInteraction 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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Fifth Workshop on Atomic and Molecular Physics
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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 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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An ancestral molecular response to nanomaterial particulates
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Molecular Dynamics Studies on Amyloidogenic Proteins
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Cellular and molecular basis of thyroid autoimmunity
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ELECTRON ATTACHMENT TO HETEROGENEOUS MOLECULAR CLUSTERS
PublikacjaHeterogeneous 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.
PublikacjaZastosowano 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
PublikacjaAntarktyczny 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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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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Computationally Effcient Solution of a 2D Diffusive Wave Equation Used for Flood Inundation Problems
PublikacjaThis 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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Portable parallel simulator using MPI for 2D and 3D domains: design and performance testing
PublikacjaW 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...