Temat: field modeling - Katalog OPAC zbiorów

Skocz do pozycji: 1.

Tytuł:: Parallel and distributed seismic wave-field modeling
Autorzy:: Danek, T.
Franczyk, A.
Powiązania:: https://bibliotekanauki.pl/articles/1964208.pdf
Data publikacji:: 2004
Wydawca:: Politechnika Gdańska
Tematy:: wave field modeling
PC clusters
finite difference method
Opis:: Elastic or acoustic wave-field modeling is an important part of seismic exploration. It can be used during the planning, processing and interpretation stages of seismic investigation. First attempts of using wave-field modeling were undertaken in the seventies by Alford, Kelly and others (Alford R M, Kelly K R and Boore D M 1974 Geophysics 39 (6) 834; Kelly K R, Ward R W, Treitel S and Alford R M 1976 Geophysics 41 2). These attempts were restricted by the limitations of computers at that time. Even now, computation for models of the standard exploration scale could last many hours, and many days in case of longer recording times. One of the best methods to overcome this disadvantage is parallelization of computations (Niccanna C and Bean C J 1997 Computers and Geosciences 23 (7) 771; Villareal A and Scales J A 1997 Computers in Physics 11 (4) 388). This paper presents the results of distributed parallelization of elastic and acoustic wave-field modeling based on a Parallel Virtual Machine.
Źródło:: TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2004, 8, 4; 573-581
1428-6394
Pojawia się w:: TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:: Biblioteka Nauki

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Skocz do pozycji: 2.

Tytuł:: Protein-protein docking refinement using restraint molecular dynamics simulations
Autorzy:: Zacharias, M.
Powiązania:: https://bibliotekanauki.pl/articles/1938618.pdf
Data publikacji:: 2016
Wydawca:: Politechnika Gdańska
Tematy:: protein-protein complex
docking prediction
force field modeling
implicit solvent modeling
Opis:: A realistic prediction of the structure of protein-protein complexes is of major importance to obtain three-dimensional models for the interaction of proteins to form complexes and assemblies. In addition to the systematic search for putative binding sites on the surface of two binding partners, the second step of a docking effort, the refinement of docked complexes, is a major bottleneck to obtain realistic interaction geometries. Typically, the first initial systematic search employs rigid partner structures or few flexible degrees of freedom, whereas the refinement step involves fully flexible partner structures. The possibility to refine docked complexes using restraint MD simulations combined with an implicit solvent (Generalized Born) mode l was explored on three example test complexes starting from unbound partner structures. Significant improvement, both in scoring and agreement with the native complex structure after refinement was observed for two test cases. No improvement was found for a test case of a complex with lower binding affinity. The method can be easily applied to any docked protein-protein complex, however, more general applicability requires further improvements in the scoring function.
Źródło:: TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2016, 20, 4; 353-360
1428-6394
Pojawia się w:: TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:: Biblioteka Nauki

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