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    Wyświetlanie 1-6 z 6
    Tytuł:
    Comparison of Wear Resistance in Polycrystalline and Monocrystalline Iron
    Autorzy:
    Liu, Zhiming
    Zhang, Qiang
    Liu, Fangying
    Zhang, Hezhe
    Powiązania:
    https://bibliotekanauki.pl/articles/2203723.pdf
    Data publikacji:
    2023
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    molecular dynamics
    polycrystalline
    centro symmetric analysis
    abrasive wear
    Opis:
    In the present research, we used molecular dynamics simulation to determine the effect of cutting parameters on micro-grain boundary structures and Burgers vector distribution in single crystal iron and polycrystalline iron materials. The result showed that the destruction of the lattice in polycrystalline iron caused by the cutting tool was restricted to the contact surface area. In addition, in the precision machining process, a higher refining grain was observed on the iron surface. During the cutting process of single crystal iron, large-scale slip occurred along the <111> crystal direction on the {110} crystal plane. And the slip presented an annular shape.
    Źródło:
    Archives of Metallurgy and Materials; 2023, 68, 1; 15--20
    1733-3490
    Pojawia się w:
    Archives of Metallurgy and Materials
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Nanovortex evolution in entrance part of the 2D open type long nanocavity
    Autorzy:
    Kordos, A.
    Kucaba-Piętal, A.
    Powiązania:
    https://bibliotekanauki.pl/articles/200327.pdf
    Data publikacji:
    2018
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    nanofluidics
    molecular dynamics
    nanocavity
    nanovortices
    nanodevices
    dynamika molekularna
    nanowgłębienia
    nanowiry
    nanourządzenia
    Opis:
    Non-equilibrium molecular dynamics method (NEMD) is applied to investigate a formation process of water nanovortex in 7 nm wide nanocavity (aspect ratio of which was equal to 3.6). The flow in the nanocavity was induced by Poiseuille 2D water nanoflow in a main nanochannel, to which the nanocavity is situated perpendicularly. The wall of main channel and the nanocavity is made from quartz. Flow is induced by applying constant force to molecules inside the main channel. Based on NEMD simulation data, the sequence of images representing water velocity vector fields was obtained at constant time intervals equal to 1 ns, which shows vortex formation mechanism. Flow field images analysis indicates that the shape and centre position of the nanovortex vary slightly each nanosecond, nevertheless, the structure remains stable in the flow field at the entrance to the nanocavity.
    Źródło:
    Bulletin of the Polish Academy of Sciences. Technical Sciences; 2018, 66, 2; 119-125
    0239-7528
    Pojawia się w:
    Bulletin of the Polish Academy of Sciences. Technical Sciences
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Design, molecular docking, drug-likeness, and molecular dynamics studies of 1,2,4-trioxane derivatives as novel Plasmodium falciparum falcipain-2 (FP-2) inhibitors
    Autorzy:
    Ghosh, S.
    Chetia, D.
    Gogoi, N.
    Rudrapal, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/2096418.pdf
    Data publikacji:
    2021
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    1
    2
    4-trioxane
    Plasmodium falciparum
    drug resistance
    molecular docking
    molecular dynamics
    falcipain 2 inhibitors
    Opis:
    Despite significant progress made in drug discovery and development over the past few decades, malaria remains a life-threatening infectious disease across the globe. Because of the widespread emergence of drug-resistant strains of Plasmodium falciparum, the clinical utility of existing drug therapies including Artemisinin-based Combination Therapies (ACTs) in the treatment of malaria has been increasingly limited. It has become a serious health concern which, therefore, necessitates the development of novel drug molecules and/or alternative therapies to combat, particularly resistant P. falciparum. The objective of the present study was to develop 1,2,4-trioxane derivatives as novel antimalarial agents that would be effective against resistant P. falciparum. In our study, 15 new trioxane derivatives were designed by molecular modification of the 1,2,4-trioxane scaffold as possible antimalarial agents. Molecular modeling studies of trioxane derivatives were performed based on the CADD approach using Biovia Discovery Studio (DS) 2018 software. The protein-ligand docking study was performed against P. falciparum falcipain 2 (FP-2) using the simulation-based docking protocol LibDock by the flexible docking method. The assessment of drug-likeness, ADMET properties, and toxicity was also performed. Furthermore, the compounds CC3 and CC7, which showed the best binding affinity against the target P. falciparum FP-2, were investigated by molecular dynamics (MD) simulation studies followed by the calculation of MM-PBSA binding free energy of protein-ligand complexes using DS 2020. Results of the docking study showed that among the 15 compounds, three trioxane derivatives were found to possess promising binding affinity with LibDock scores ranging from 117.16 to 116.90. Drug-likeness, ADMET, and toxicity properties were found to be satisfactory for all the compounds. Among the 15 compounds, two compounds, namely CC3 and CC7, showed the highest binding affinity against FP-2 with LibDock score of 117.166 and 117.200, respectively. The Libdock score of the co-crystal inhibitor was 114.474. MD studies along with MM-PBSA calculations of binding energies further confirmed the antimalarial potential of the compounds CC3 and CC7, with the formation of well-defined and stable receptor-ligand interactions against the P. falciparum FP-2 enzyme. Additionally, the selectivity of trioxane hits identified as potential inhibitors of P. falciparum cysteine protease FP-2 was determined on human cysteine proteases such as cathepsins (Cat K and Cat L), which are host homologous. Finally, it was concluded that the newly designed 1,2,4-trioxane derivatives can be further studied for in vitro and in vivo antimalarial activities for their possible development as potent antimalarial agents effective against resistant P. falciparum
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2021, 102, 3; 257-275
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    In silico prediction and characterization of three-dimensional structure of actin-1 of Arabidopsis thaliana
    Autorzy:
    Sahu, M.
    Dehury, B.
    Sarmah, R.
    Sahoo, S.
    Sahu, J.
    Sarma, K.
    Sen, P.
    Modi, M.K.
    Barooah, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/80321.pdf
    Data publikacji:
    2013
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    actin-1
    protein sequence
    Arabidopsis thaliana
    comparative modelling
    three-dimensional structure
    molecular dynamics simulation
    Opis:
    Actin-1 is a ubiquitous protein belonging to the reproductive class of Actin family in Arabidopsis thaliana . This protein is involved in the formation of filaments that are major components of the cytoskeleton. Despite the importance of this protein, very little information is available regarding its structure and function in plants. In this study, analysis of the protein sequence was done and comparative model of Actin-1 was constructed (UNIPROT ID: P0CJ46) from Arabidopsis thaliana using the crystal structure of Dictyostelium discoideum actin (PDB ID: 1NLV-A) as template employing Modeller version 9.9. The stable structure was generated by 5 nanosecond molecular dynamics simulation steps using GROMOS43A1 96 force field that characterized its structural and dynamic feature. The biochemical function of the final simulated structure was also investigated using PROFUNC. The molecular simulation study suggested that the modeled Actin-1 protein retain its stable conformation in aqueous solution. The predicted binding sites in the modeled Actin-1 protein are very informative for further protein-ligand interaction study.
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 4
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Grain Boundary Relaxation in Bi-Crystals: Mechanical Spectroscopy and Molecular Dynamics Simulations
    Relaksacja granic ziaren w bikryształach: spektroskopia mechaniczna i symulacje metodą dynamiki molekularnej
    Autorzy:
    Maier, A.-K.
    Mari, D.
    Tkalcec, I.
    Schaller, R.
    Powiązania:
    https://bibliotekanauki.pl/articles/353074.pdf
    Data publikacji:
    2015
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    internal friction grain boundaries
    gold alloys
    molecular dynamics
    granice wewnętrzne tarcia ziarna
    stop złota
    dynamika molekularna
    Opis:
    Different Au-Ag-Cu samples have been studied by mechanical spectroscopy. Both polycrystals and bi-crystals show a relaxation peak at 800 K, accompanied by an elastic modulus change. Since this peak is absent in single crystals it is related to the presence of grain boundaries. Molecular dynamics simulations reveal two microscopic mechanisms, when a shear stress is applied onto a Σ5 grain boundary: at 700 K, the boundary migrates perpendicularly to the boundary plane under an external stress. At 1000 K, only sliding at the boundary is observed. These two mechanisms acting in different temperature intervals are used to model the mechanic response of a polycrystal under an applied stress. The models yield expressions for the relaxation strength Δ and for the relaxation time τ as a function of the grain size. A comparison with the mechanical spectroscopy measurements of polycrystals and the bi-crystals show that the grain boundary sliding model reproduces correctly the characteristics of the grain boundary peak.
    Różne próbki ze stopów Au-Ag-Cu badano metodą spektroskopii mechanicznej. Zarówno w polikryształach, jak i bikryształach występuje pik relaksacyjny w temperaturze 800 K, któremu towarzyszy zmiana modułu sprężystości. Ponieważ pik ten nie występuje w monokryształach to jego występowanie wiązane jest z obecnością granic ziaren. Symulacje dynamiki molekularnej ujawniają dwa mikroskopowe mechanizmy, gdy naprężenie ścinające jest przyłożone do granicy ziarna Σ5: w temperaturze 700 K, granica przemieszcza się prostopadle do płaszczyzny granicznej pod wpływem zewnętrznego naprężenia. W 1000 K, obserwuje się tylko poślizg po granicy. Te dwa mechanizmy działające w różnych zakresach temperatur są używane do modelowania mechanicznej reakcji polikryształu na przyłożone naprężenie. Modele podają wyrażenie na stopień relaksacji Δ i czas relaksacji τ w funkcji wielkości ziaren. Porównanie z wynikami badań polikryształów i bikryształów uzyskanych metodą spektroskopii mechanicznej pokazuje, że model poślizgu granicy ziarna poprawnie odtwarza charakterystykę piku pochodzącego od granic ziaren.
    Źródło:
    Archives of Metallurgy and Materials; 2015, 60, 1; 377-380
    1733-3490
    Pojawia się w:
    Archives of Metallurgy and Materials
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Estimation of phonon relaxation time for silicon by means of using the velocity autocorrelation function of atoms in molecular dynamics
    Autorzy:
    Andriyevsky, Bohdan
    Maliński, M.
    Buryło, Ł.
    Stadnyk, V. Y.
    Romanuk, M. O.
    Piekarski, J.
    Andriyevska, L.
    Powiązania:
    https://bibliotekanauki.pl/articles/201222.pdf
    Data publikacji:
    2019
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    silicon
    molecular dynamics
    relaxation time of the velocity autocorrelation function
    coefficient of thermal diffusivity
    krzem
    dynamika molekularna
    Opis:
    Results of the ab initio molecular dynamics calculations of silicon crystals are presented by means of analysis of the velocity autocorrelation function and determination of mean phonon relaxation time. The mean phonon relaxation time is crucial for prediction of the phonon-associated coefficient of thermal conductivity of materials. A clear correlation between the velocity autocorrelation function relaxation time and the coefficient of thermal diffusivity has been found. The analysis of the results obtained has indicated a decrease of the velocity autocorrelation function relaxation time t with increase of temperature. The method proposed may be used to estimate the coefficient of ther-mal diffusivity and thermal conductivity of the materials based on silicon and of other wide-bandgap semiconductors. The correlation between kinetic energy fluctuations and relaxation time of the velocity autocorrelation function has been calculated with the relatively high coefficient of determination R2 = 0.9396. The correlation obtained and the corresponding approach substantiate the use of kinetic energy fluctuations for the calculation of values related to heat conductivity in silicon-based semiconductors (coefficients of thermal conductivity and diffusivity).
    Źródło:
    Bulletin of the Polish Academy of Sciences. Technical Sciences; 2019, 67, 3; 651-656
    0239-7528
    Pojawia się w:
    Bulletin of the Polish Academy of Sciences. Technical Sciences
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-6 z 6

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