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    Wyświetlanie 1-9 z 9
    Tytuł:
    A method of integration of molecular dynamics and continuum mechanics for solids
    Autorzy:
    Kaczmarek, J.
    Powiązania:
    https://bibliotekanauki.pl/articles/1963003.pdf
    Data publikacji:
    2002
    Wydawca:
    Politechnika Gdańska
    Tematy:
    continuum mechanics
    molecular dynamics
    multiscale modelling
    Opis:
    In this paper a formal system called collection of dynamical systems with dimensional reduction is considered. This is a multiscale method of mathematical description which allows to consider molecular dynamics and continuum mechanics within one theoretical framework. Transition between molecular dynamics and continuum mechanics is realized by means of the dimensional reduction procedure. In order to realize such a procedure the formulation of continuum mechanics is modified. This modification consists in incorporation scale of averaging for properties of processes considered during modelling into this formulation. As a result we introduce finite-dimensional fields on continuum only. All fundamental terms of continuum mechanics are now joined with an elementary dynamical system. In such a case continuum mechanics can be obtained by means of the dimensional reduction procedure applied to the elementary dynamical system. A numerical example of vibrating chain of material points is realized in order to show how in practice the dimensional reduction can be carried out. In this example decomposition of processes into slowly and quickly varying parts is accomplished. To this end a finite element representation of averaged fields is applied. Solutions of equations of the elementary dynamical system and the dimensionally reduced dynamical system are compared.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2002, 6, 2; 253-271
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    A molecular dynamics study of the influence of chemical reduction on the structure of amorphous Germania
    Autorzy:
    Witkowska, A.
    Murawski, L.
    Bergmański, G.
    Powiązania:
    https://bibliotekanauki.pl/articles/1963001.pdf
    Data publikacji:
    2002
    Wydawca:
    Politechnika Gdańska
    Tematy:
    oxide glasses
    hydrogen reduction
    molecular dynamics
    structural modelling
    Opis:
    The contribution is dedicated to the molecular dynamics (MD) study of the structure of reduced germania glass of composition 1Ge 1GeO2. The work is inspired by a recent report on the formation of Ge clusters in hydrogen reduced germanate glasses containing oxides of heavy metals. The MD simulations have been performed in the microcanonical (NVE) ensemble, using a simple two-body Born-Mayer-Huggins interaction potential. A tendency of germanium atoms to agglomeration into clusters, observed in the present calculations, is compared with an analogous tendency of Bi and Pb atoms, observed previously in the xBi (1-x)GeO2 and xPb (1-x)GeO2 systems. The differences in the short and medium-range order in GeO2 system between the 1Ge 1GeO2 and GeO2 glasses are discussed.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2002, 6, 2; 273-281
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    A new program package for structural analysis of computer simulated solids
    Autorzy:
    Bergmański, G.
    Rybicki, J.
    Mancini, G.
    Powiązania:
    https://bibliotekanauki.pl/articles/1954546.pdf
    Data publikacji:
    2000
    Wydawca:
    Politechnika Gdańska
    Tematy:
    ring analysis
    structure of matter
    molecular dynamics
    computer modelling
    Opis:
    The opportunity to gain detailed information on representative set of rings and chains of atoms is of great importance in the analysis of medium-range order in the computer simulated structures of solids. A new program package (ANELLI) for ring and chain analysis of computer simulated atomic structures is presented. The paper includes detailed description of input and output files. The package presentation is followed by exemplary results obtained using our programs.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2000, 4, 4; 555-573
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    A new program package for structural analysis of computer simulated solids
    Autorzy:
    Bergmański, G.
    Rybicki, J.
    Mancini, G.
    Powiązania:
    https://bibliotekanauki.pl/articles/1954549.pdf
    Data publikacji:
    2000
    Wydawca:
    Politechnika Gdańska
    Tematy:
    ring analysis
    structure of matter
    molecular dynamics
    computer modelling
    Opis:
    The opportunity to gain detailed information on representative set of rings and chains of atoms is of great importance in the analysis of medium-range order in the computer simulated structures of solids. A new program package (ANELLI) for ring and chain analysis of computer simulated atomic structures is presented. The paper includes detailed description of input and output files. The package presentation is followed by exemplary results obtained using our programs.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2000, 4, 4; 555-573
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Targets for majority of drugs: G protein-coupled receptors - their structure and interaction with bioligands
    Autorzy:
    Ciarkowski, J.
    Czaplewski, C.
    Pasenkiewicz-Gierula, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/1953953.pdf
    Data publikacji:
    1998
    Wydawca:
    Politechnika Gdańska
    Tematy:
    G protein-coupled receptor
    molecular modelling
    GPCR/bioligand interaction
    molecular dynamics
    membrane
    Opis:
    G protein-coupled receptors (GPCRs) are the most frequent targets for many drugs. They form the largest superfamily of integral membrane proteins, of which more than 1000 members have the following common features: (i) All GPCRs form 7 hydrophobic a-helices of length ~38A (25 amino acids, 7 turns) along a single chain. The consecutive helices alternatively cross the membrane, starting from the extracellular side, so that they form a heptahelical transmembrane domain interwoven with 6 loops, of which the even ones plus the N-terminus create the receptor's extracellular domain while the odd ones plus the C-terminus form its intracellular domain. (ii) All GPCRs are stimulated by diverse extracellular (primary) signals. (iii) Stimulated GPCRs convey the primary signals via their transmembrane and intracellular domains to the cytosolic peripheral heterotrimeric GTP-binding proteins (G proteins), mediating the signal's further transduction to various cellular second messenger systems. A current status of structural studies on GPCRs, consisting of low ~7.5A resolution experimental structures and supplementary molecular modeling, is outlined. Subsequently, some results of authors' own work on studying essential interactions of the V2 vasopressin renal receptor (V2R) with its agonist [Arg8]Vasopressin (AVP) and selected antagonists are presented, as well as their possible impact on the biological signal transduction is discussed. Finally, perspectives for future developments are sketched.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 1998, 2, 4; 583-599
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Modelling drug-receptor interactions in an average binding site for NK2
    Autorzy:
    Alagona, G.
    Ghio, C.
    Monti, S.
    Powiązania:
    https://bibliotekanauki.pl/articles/1953954.pdf
    Data publikacji:
    1998
    Wydawca:
    Politechnika Gdańska
    Tematy:
    receptor modelling
    docking
    non covalent interactions
    molecular mechanics
    molecular dynamics
    substituent effects
    Opis:
    A tentative procedure applied to the search for a new antagonist of neurokinin A (NKA) is presented. In parallel a tentative 3-D model of the NK2 receptor was created, using bacteriorhodopsin (BRD) as a template. The residue substitutions were performed in BRD to obtain the sequence for NK2R_H and the seven a-helical segments were optimized forcing the a-helical backbone to match the corresponding aligned parts of BRD, while the arrangements of the side chains were model built based on available site-directed mutagenesis studies. Constrained MM and molecular dynamics simulations were carried out H-bonding a low energy conformer of the known drugs to residues in the receptor site, allowing both the receptor site and drugs to relax. The Connolly surface for each ligand allowed to determine an "average" binding site in which all the low energy conformers of known and prospective drugs were docked and classified according to a statistical index. The whole procedure was repeated exploiting the lately published structure of an actual G protein coupled receptor as a better template, thus producing a cavity in the binding site to directly dock the drugs. Corollary validations of the force fields used are also mentioned. In addition intra- and intermolecular interactions suitable to produce more active drugs were evaluated.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 1998, 2, 4; 563-581
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Prediction of turbomachinery flow physics from CFD - review of recent computations of APPACET test cases
    Autorzy:
    Gregory-Smith, D. G.
    Crossland, S. C.
    Powiązania:
    https://bibliotekanauki.pl/articles/1967658.pdf
    Data publikacji:
    2001
    Wydawca:
    Politechnika Gdańska
    Tematy:
    turbomachinery
    CFD
    computational fluid dynamics CFD
    turbulence modelling
    grid dependence
    unsteady interaction
    Opis:
    In order to maintain a competitive edge, the turbomachinery industry has to rely increasingly on design and analysis methods based on numerical simulation of flow. The European funded APPACET was set up to study the application of turbulence modelling and the simulation of unsteady interactions to provide guidelines for the application of CFD to design. This paper shows the results of computations of four of the test cases studied by the project. The importance of grid refinement has been clearly demonstrated, but no evidence was found that one family of turbulence models could be definitely better than the other. Compared to steady results, unsteady time-averaged solutions have not shown any major improvement in accuracy. However unsteady flow phenomena generating losses within each blade row have been captured and partly explained.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 4; 407-431
    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:
    Computational fluid dynamics methods in turbomachinery
    Autorzy:
    Chmielniak, T. J.
    Powiązania:
    https://bibliotekanauki.pl/articles/1953985.pdf
    Data publikacji:
    1998
    Wydawca:
    Politechnika Gdańska
    Tematy:
    computational fluid dynamics CFD
    CFD
    turbomachinery
    numerical methods
    modelling
    steady flow
    unsteady flow
    multiphase flow
    multicomponent flow
    blade cooling
    Opis:
    This paper aims to present a general view of flow problems in turbomachinery and the current levels of numerical methods for solving these problems. The flow models used for modelling phenomena in blade cascades are presented. Models of turbulence are discussed. A variety of examples of turbomachinery problems, such as steady, unsteady, multiphase and multicomponent flows, and also blade cooling are described. The actual research fields of computational fluid mechanics are presented.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 1998, 2, 2; 205-213
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-9 z 9

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