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Wyświetlanie 1-3 z 3
Tytuł:
Linear computational cost implicit solver for parabolic problems
Autorzy:
Gurgul, Grzegorz
Łoś, Marcin
Paszynski, Maciej
Calo, Victor
Powiązania:
https://bibliotekanauki.pl/articles/1839258.pdf
Data publikacji:
2020
Wydawca:
Akademia Górniczo-Hutnicza im. Stanisława Staszica w Krakowie. Wydawnictwo AGH
Tematy:
isogeometric analysis
implicit dynamics
linear computational cost
direct solvers
Opis:
In this paper, we use the alternating direction method for isogeometric finite elements to simulate transient problems. Namely, we focus on a parabolic problem and use B-spline basis functions in space and an implicit time-marching method to fully discretize the problem. We introduce intermediate time-steps and separate our differential operator into a summation of the blocks that act along a particular coordinate axis in the intermediate time-steps. We show that the resulting stiffness matrix can be represented as a multiplication of two (in 2D) or three (in 3D) multi-diagonal matrices, each one with B-spline basis functions along the particular axis of the spatial system of coordinates. As a result of these algebraic transformations, we get a system of linear equations that can be factorized in a linear O(N) computational cost at every time-step of the implicit method. We use our method to simulate the heat transfer problem. We demonstrate theoretically and verify numerically that our implicit method is unconditionally stable for heat transfer problems (i.e., parabolic). We conclude our presentation with a discussion on the limitations of the method.
Źródło:
Computer Science; 2020, 21 (3); 335-352
1508-2806
2300-7036
Pojawia się w:
Computer Science
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Three-dimensional simulations of the airborne COVID-19 pathogens using the advection-diffusion model and alternating-directions implicit solver
Autorzy:
Łoś, Marcin
Woźniak, Maciej
Muga, Ignacio
Paszynski, Maciej
Powiązania:
https://bibliotekanauki.pl/articles/2086863.pdf
Data publikacji:
2021
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
COVID-19
pathogen spread
isogeometric analysis
implicit dynamics
advection-diffusion
parallel alternating directions solver
rozprzestrzenianie się patogenu
analiza izogeometryczna
dynamika ukryta
adwekcja-dyfuzja
rozwiązywanie równoległych zmiennych kierunków
Opis:
In times of the COVID-19, reliable tools to simulate the airborne pathogens causing the infection are extremely important to enable the testing of various preventive methods. Advection-diffusion simulations can model the propagation of pathogens in the air. We can represent the concentration of pathogens in the air by “contamination” propagating from the source, by the mechanisms of advection (representing air movement) and diffusion (representing the spontaneous propagation of pathogen particles in the air). The three-dimensional time-dependent advection-diffusion equation is difficult to simulate due to the high computational cost and instabilities of the numerical methods. In this paper, we present alternating directions implicit isogeometric analysis simulations of the three-dimensional advection-diffusion equations. We introduce three intermediate time steps, where in the differential operator, we separate the derivatives concerning particular spatial directions. We provide a mathematical analysis of the numerical stability of the method. We show well-posedness of each time step formulation, under the assumption of a particular time step size. We utilize the tensor products of one-dimensional B-spline basis functions over the three-dimensional cube shape domain for the spatial discretization. The alternating direction solver is implemented in C++ and parallelized using the GALOIS framework for multi-core processors. We run the simulations within 120 minutes on a laptop equipped with i7 6700 Q processor 2.6 GHz (8 cores with HT) and 16 GB of RAM.
Źródło:
Bulletin of the Polish Academy of Sciences. Technical Sciences; 2021, 69, 4; e137125, 1--8
0239-7528
Pojawia się w:
Bulletin of the Polish Academy of Sciences. Technical Sciences
Dostawca treści:
Biblioteka Nauki
Artykuł
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
Artykuł
    Wyświetlanie 1-3 z 3

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