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    Wyświetlanie 1-5 z 5
    Tytuł:
    Conformational studies of tachykinin peptides using NMR spectroscopy
    Autorzy:
    Rodziewicz, S.
    Xiao-Fei, Qi.
    Rolka, K.
    Powiązania:
    https://bibliotekanauki.pl/articles/1954059.pdf
    Data publikacji:
    1998
    Wydawca:
    Politechnika Gdańska
    Tematy:
    conformational analysis
    tachykinin peptides
    NMR spectroscopy
    Scyliorhinin II
    molecular dynamics calculation methods
    DMSO
    Opis:
    Conformational analysis of two tachykinin family peptides: Scyliorhinin I (ScyI) and Scyliorhinin II (ScyII) was carried out by 1D- and 2D-NMR (DQF-COSY, TOCSY, HMQC, HMBC, NOESY and ROESY) and molecular dynamics calculation methods in water and DMSO. Scyliorhinin I is an equipotent agonist of NK-1 and NK-2 tachykinin receptors and Scyliorhinin II is a selective agonist of the NK-3 tachykinin receptor. In DMSO, two groups of conformations (major and minor) were obtained for both peptides based on the experimental data. The conformations proposed for ScyI represent a folded structure, which show certain similarities to the structures reported for other NK-1 and NK-2 tachykinin agonists. In water ScyII displays a flexible, extended structure, whereas in DMSO the structure is more compact and in the fragment from the centre to the C-terminus several beta -turns may be present.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 1998, 2, 1; 47-53
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    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:
    Molecular modelling in the rational design of some anti-tumor and antifungal agents
    Autorzy:
    Mazerski, J.
    Borowski, E.
    Powiązania:
    https://bibliotekanauki.pl/articles/1953949.pdf
    Data publikacji:
    1998
    Wydawca:
    Politechnika Gdańska
    Tematy:
    molecular modelling
    molecular mechanics
    molecular dynamics
    semiempirical methods
    antifungal agents
    anti-tumor agents
    rational design
    Opis:
    In this paper we present our approaches and results concerning application of molecular modelling techniques in the design of new chemotherapeutic agents for the control of eukariotic systems, comprising compounds for the treatment of systemic fungal infections and tumor deseases. In the case of anti-tumor agents we focused our attention on molecular properties of natural and synthetic anthraquinones. In the area of antifungal compounds we adopted two approaches. In one of them we examine molecular nature of undesirable properties of polyene macrolide antifungal antibiotic - amphotericin B using molecular modelling techniques. Another approach was aimed at the development of selective inactivator of glucosamine synthase, a novel target for antifungal compounds. In this problem we have used computational chemistry methods to identify structural features responsible for the selective inactivation of the target enzyme.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 1998, 2, 4; 511-550
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Quantum-classical calculations of the nanomechanical properties of metals
    Autorzy:
    Dziedzic, J.
    Powiązania:
    https://bibliotekanauki.pl/articles/1964138.pdf
    Data publikacji:
    2009
    Wydawca:
    Politechnika Gdańska
    Tematy:
    hybric methods
    cross-scaling
    tight-binding
    learn-on-the-fly
    nanoscale
    metals
    nanoindentation
    molecular-dynamics
    Sutton-Chen potential
    Opis:
    Molecular-dynamics (MD) simulations constitute an important tool in the study of nanoscale metallic systems, especially so in the face of the difficulties plaguing their experimental analysis. Main limitations of the MD method stem from the empirical nature of the potentials employed, their functional form which is postulated ad hoc, and its classical nature. The neglect of electronic effects and the unjustified utilization of the potential for system configurations significantly different from those, for which the potential was parametrized makes the results of strictly classical calculations dubious, at least for a certain class of systems. On the other hand, high computational complexity of quantum-based methods, where atomic interactions are described ab initio, prohibits their direct use in the study of systems larger than several tens of atoms. In the last decade, a growing popularity of so-called hybrid (or cross-scaling) methods can be observed, that is, methods which treat the most interesting part of the system with a quantum-based approach, while the remainder is treated classically. Physically sound handshaking between the two methodologies (quantum and classical) within a single simulation constitutes a serious challenge, the majority of difficulties concentrating around the interface between the fragments of the system treated with the two methods. The aforementioned interface is most easily constructed for covalently bonded systems, where the bonds cut by the isolation of the quantum-based region can be saturated by the introduction of specially crafted link-atoms. In metallic systems, however, due to electronic delocalization, this traditional approach cannot be employed. This paper describes a physically sound and adequately efficient computational technique, which allows for the inclusion of results of locally employed quantum-based computations within a molecular-dynamics simulation, for systems described by the many-body Sutton-Chen (SC) potential, used in the study of fcc metals. The proposed technique was developed taking as a point of departure the Learn-on-the-Fly (LOTF) formalism, a recent development itself. The original LOTF approach is only suitable for two- or three-body potentials and is serial in nature, whereas the proposed technique can be used with many-body potentials and is parallel-ready. An implementation of the proposed approach in the form of computer code, which allows for parallel hybrid computations for metallic systems is also described. Finally, results from a set of hybrid simulations of nanoindentation of a copper workmaterial with a hard indenter utilizing the aforementoned technique and computer code is presented, as evidence of its viability.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2009, 13, 3; 207-310
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    2D simulations of liquid percolation through model porous media: preliminary MD and DPD results
    Autorzy:
    Rychcik, M.
    Bośko, J.
    Rybicki, J.
    Alda, W.
    Dzwinel, W.
    Mancini, G.
    Fioretti, L.
    Powiązania:
    https://bibliotekanauki.pl/articles/1964080.pdf
    Data publikacji:
    2001
    Wydawca:
    Politechnika Gdańska
    Tematy:
    2D flow simulations
    particle methods
    molecular dynamics
    dissipative particle dynamics method
    Opis:
    In the paper we make a short overview of computer models based on particle approach, which can be suitable for the simulation of fluid flow through porous media. We concentrate on Molecular Dynamics (MD) and Dissipative Particle Dynamics (DPD) methods. We describe main features of our simulation programs, and present and discuss preliminary results of MD and DPD simulations of 2D fluid flow through a simple model rigid porous media. The paper aims at the evaluation of the applicability of MD and DPD methods for simulations of liquid flows in media of complicated geometry.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 1; 85-97
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-5 z 5

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