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    Wyświetlanie 1-8 z 8
    Tytuł:
    Preferential solvation of amides by methanol - a comparison of molecular dynamics calculations with the experimental data
    Autorzy:
    Zielkiewicz, J.
    Powiązania:
    https://bibliotekanauki.pl/articles/1965827.pdf
    Data publikacji:
    2001
    Wydawca:
    Politechnika Gdańska
    Tematy:
    amides
    alcohols
    preferential solvation
    Kirkwood-Buff integrals
    molecular dynamics simulations
    Opis:
    Using the Kirkwood-Buff theory of solutions, the preferential solvation of the N-methylacet-amide (NMA), N-methylformamide, (NMF), and N,N-dimethylformamide, (DMF), molecule has been investigated in the binary {amide+methanol} mixtures at 313.15 K. Moreover, for the {amide+methanol} mixtures, where amide = NMF, DMF, and NMA, the molecular dynamics calculations at xamide=0.518 were performed. From the obtained molecule-molecule radial distribution functions, (rdf), and atom-atom rdf, it was possible to estimate the local mole fractions around the amide molecule, the orientation effects of molecules within the solvation shell, and a possibility of the formation of complexes. The general picture obtained from analysis of the molecular dynamics results is consistent with the deductions derived from thermodynamic data.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 3; 317-329
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    The structure of Pb-PbO-SiO2 glass via molecular dynamics simulation
    Autorzy:
    Rybicki, J.
    Witkowska, A.
    Bergmański, G.
    Mancini, G.
    Feliziani, S.
    Powiązania:
    https://bibliotekanauki.pl/articles/1954650.pdf
    Data publikacji:
    2022-01-20
    Wydawca:
    Politechnika Gdańska
    Tematy:
    lead-silicate glasses
    oxide glasses
    medium-range order
    ring analysis
    molecular dynamics simulations
    Opis:
    The paper is dedicated to a molecular dynamics (MD) study of the structure of partially reduced lead-silicate glass of composition 1Pb 1PbO 1SiO2. The simulations have been performed in the constant volume regime, using a two-body potential (Born-Mayer repulsive forces, and Coulomb forces due to full ionic charges). The system was initially prepared as a well equilibrated hot melt, and then slowly cooled down to 300K. The information on short-range correlations were obtained in a conventional way (from pair and angular distribution functions), while the medium-range order was studied via cation-anion ring analysis. In the paper, the short- and medium-range order in the simulated system is discussed and compared with the structure of a glassy completely reduced system, i.e. 2Pb 1SiO2 and unreduced one, i.e. 2PbO 1SiO2 glass.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2003, 7, 2; 243-256
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Probing of Cu2+ ions binding to A β (5−16) peptide using ITC measurements and MD simulations
    Autorzy:
    Makowska, J.
    Żmudzińska, W.
    Wyrzykowski, D.
    Brzozowski, K.
    Zblewska, H.
    Chmurzyński, L.
    Powiązania:
    https://bibliotekanauki.pl/articles/1938620.pdf
    Data publikacji:
    2016
    Wydawca:
    Politechnika Gdańska
    Tematy:
    A β (5 − 16) fragments
    metal-peptide binding
    isothermal titration calorimetry
    molecular dynamics simulations
    Opis:
    It is shown that probably three residues: His6, His14 and His16 in the original sequence A β (1−42) serve as metal-binding sites for Cu2+ions. On the other hand, there is a possibility that only one of them plays a crucial role in the formation of the{A β (1-42)-Cu2+} complex. The isothermal titration calorimetry (ITC) measurements supported by molecular dynamic simulation (MD) with the NMR-derived restrains were used to investigate the interactions of Cu2+ with A β(5-16), a fragment of the A β(1-42) protein, with the following sequence: Ac-Arg-His-Asp-Ser-Gly-Tyr-Glu-Val-His-His-Gln-Lys-NH2, termed HZ1. The conditional thermodynamic parameters suggest that the formation of the Cu2+-HZ1 complex is both an enthalpy and entropy driven process under the experimental conditions. The studies presented here (after comparison with our previous results) show that the affinity of peptides to copper metal ions depends on two factors: the primary structure (amino acid composition) and the shape of the peptide conformation adopted.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2016, 20, 4; 409-416
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    The intercalation of imidazoacridinones into DNA induces conformational changes in their side chain.
    Autorzy:
    Mazerski, Jan
    Muchewicz, Karolina
    Powiązania:
    https://bibliotekanauki.pl/articles/1044393.pdf
    Data publikacji:
    2000
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    molecular dynamics simulations
    conformational changes
    structure of intercalation complex
    C-1311
    antitumor drugs
    imidazoacridinones
    Opis:
    Imidazoacridinones (IAs) are a new group of highly active antitumor compounds. The intercalation of the IA molecule into DNA is the preliminary step in the mode of action of these compounds. There are no experimental data about the structure of an intercalation complex formed by imidazoacridinones. Therefore the design of new potentially better compounds of this group should employ the molecular modelling techniques. The results of molecular dynamics simulations performed for four IA analogues are presented. Each of the compounds was studied in two systems: i) in water, and ii) in the intercalation complex with dodecamer duplex d(GCGCGCGCGCGC)2. Significant differences in the conformation of the side chain in the two environments were observed for all studied IAs. These changes were induced by electrostatic as well as van der Waals interactions between the intercalator and DNA. Moreover, the results showed that the geometry of the intercalation complex depends on: i) the chemical constitution of the side chain, and ii) the substituent in position 8 of the ring system.
    Źródło:
    Acta Biochimica Polonica; 2000, 47, 1; 65-78
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    The role of side chains in the interaction of new antitumor pyrimidoacridinetriones with DNA: Molecular dynamics simulations.
    Autorzy:
    Mazerski, Jan
    Antonini, Ippolito
    Martelli, Sante
    Powiązania:
    https://bibliotekanauki.pl/articles/1044390.pdf
    Data publikacji:
    2000
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    molecular dynamics simulations
    structure of intercalation complex
    pyrimidoacridinetrione antitumor agents
    role of side chain(s)
    Opis:
    Pyrimidoacridinetriones (PATs) are a new group of highly active antitumor compounds. It seems reasonable to assume that, like for some other acridine derivatives, intercalation into DNA is a necessary, however not a sufficient condition for antitumor activity of these compounds. Rational design of new compounds of this chemotype requires knowledge about the structure of the intercalation complex, as well as about interactions responsible for its stability. Computer simulation techniques such as molecular dynamics (MD) may provide valuable information about these problems. The results of MD simulations performed for three rationally selected PATs are presented in this paper. The compounds differ in the number and position of side chains. Each of the compounds was simulated in two systems: i) in water, and ii) in the intercalation complex with the dodecamer duplex d(GCGCGCGCGCGC)2. The orientation of the side chain in relation to the ring system is determined by the position of its attachment. Orientation of the ring system inside the intercalation cavity depends on the number and position of side chain(s). The conformations of the side chain(s) of all PATs studied in the intercalation complex were found to be very similar to those observed in water.
    Źródło:
    Acta Biochimica Polonica; 2000, 47, 1; 47-57
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Flows in microchannels
    Autorzy:
    Kucaba-Piętal, A.
    Walenta, Z.
    Peradzyński, Z.
    Powiązania:
    https://bibliotekanauki.pl/articles/1955808.pdf
    Data publikacji:
    2001
    Wydawca:
    Politechnika Gdańska
    Tematy:
    microchannel flow
    microflows
    micropolar fluid
    molecular dynamics simulations
    direct Monte Carlo simulation
    direct Monte Carlo methods
    Opis:
    The aim of this paper is to present a survey of the results for the flows of simple gases and liquids with substructure through narrow channels, obtained with the Direct Monte-Carlo and Molecular Dynamics Simulation methods.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 2; 179-189
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Synergistic mechanism of dodecylamine/octanol mixtures enhancing lepidolite flotation from the self-aggregation behaviors at the air/liquid interface
    Autorzy:
    Bai, Yang
    Xu, Mengxu
    Wen, Weixiang
    Zhu, Shifei
    Mo, Weichen
    Yan, Pingke
    Powiązania:
    https://bibliotekanauki.pl/articles/27323641.pdf
    Data publikacji:
    2023
    Wydawca:
    Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
    Tematy:
    DDA/OCT mixtures
    self-aggregation behaviors
    flotation foam
    molecular dynamics simulations
    surface tension
    air interface
    liquid interface
    Opis:
    Surface tension measurements and molecular dynamics (MD) simulations were used to explore the flotation foam properties and self-aggregation behaviors of dodecylamine (DDA)/octanol (OCT) mixtures formed with different mole ratios at the air/liquid interface. Based on the surface and thermodynamic parameters, the DDA/OCT mixtures exhibited greater interfacial activities and adsorption capacities than their individual components. The MD simulations showed that DDA and OCT were aggregated through hydrogen bonding, coulombic forces and hydrophobic association. OCT was inserted into the DDA adsorption layer, causing the alkyl chains of both DDA and OCT to extend from water to air at varying heights and angles. The addition of OCT improved the hydration of the amino groups and reduced the overall number of hydrogen bonds. The stability of the flotation foam decreased, and the high viscosity and difficult defoaming of the DDA flotation foam were significantly improved. When the DDA/OCT mole ratio was 2:1, the included angle formed between the alkyl chains and the interface was maximized, leading to enhanced compatibility among the alkyl chains, and the hydrogen bond energy was relatively large, which showed a strong synergistic effect. The MD simulation findings were consistent with the results obtained from the lepidolite flotation and surface tension experiments conducted in this study; our results could provide a theoretical foundation for the selection of superior mixed collectors and frothers.
    Źródło:
    Physicochemical Problems of Mineral Processing; 2023, 59, 6; art. no. 176510
    1643-1049
    2084-4735
    Pojawia się w:
    Physicochemical Problems of Mineral Processing
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Dopant ions size impact on structural properties of ordered poly(3,4-ethylenedioxythiophene) systems
    Wpływ wielkości jonów domieszkujących na właściwości strukturalne uporządkowanych układów poli(3,4-etylenodioksytiofenu)
    Autorzy:
    Śniechowski, Maciej
    Kozik, Tomasz A.
    Łużny, Wojciech
    Powiązania:
    https://bibliotekanauki.pl/articles/947384.pdf
    Data publikacji:
    2020
    Wydawca:
    Sieć Badawcza Łukasiewicz - Instytut Chemii Przemysłowej
    Tematy:
    self-organization
    molecular dynamics simulations
    conductive polymers
    X-ray diffraction
    crystal structure
    samoorganizacja
    symulacja dynamiki molekularnej
    polimery przewodzące
    dyfrakcja promieniowania rentgenowskiego
    struktura krystaliczna
    Opis:
    The purpose of this work was to determine whether the structures of ordered part of novel poly(3,4-ethylenedioxythiophene) PEDOT : OTf (doped with trifluoromethanesulfonate anions) and PEDOT : HSulf (doped with hydrogensulfate anions) systems could really be simply the layered structure of PEDOT : Tos (doped with tosylate anions) with the counter ion changed to the appropriate one. Insight into this problem could be provided by molecular dynamics simulations but also by swarm intelligence optimization, developed earlier for the purpose of investigating the other structures.
    Zbadano zdolność struktury uporządkowanej części nowych układów domieszkowanych poli(3,4-etylenodioksytiofenu) (PEDOT) [PEDOT : OTf (domieszkowane anionami trifluorometanosulfonianowymi) i PEDOT : HSulf (domieszkowane anionami wodorosiarczanowymi)] do powielania znanej z literatury warstwowej struktury PEDOT : Tos (domieszkowane anionami tosylanowymi) z jonem domieszki zmienionym na odpowiedni. Poszukiwania nowych struktur wspomagano symulacjami dynamiki molekularnej, a także z zastosowaniem optymalizacji opartej na algorytmach inteligencji stadnej.
    Źródło:
    Polimery; 2020, 65, 9; 639-643
    0032-2725
    Pojawia się w:
    Polimery
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-8 z 8

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