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Wyszukujesz frazę "MD simulation" wg kryterium: Temat

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    Wyświetlanie 1-6 z 6
    Tytuł:
    How to stimulate polymeric surfaces biocompatibility and hydroxyapatite formation: experiments supported by MD simulations
    Autorzy:
    Gołda-Cępa, Monika
    Chytrosz, Paulina
    Riedlova, Kamila
    Kulig, Waldemar
    Ćwiklik, Łukasz
    Kotarba, Andrzej
    Powiązania:
    https://bibliotekanauki.pl/articles/1844887.pdf
    Data publikacji:
    2020
    Wydawca:
    Akademia Górniczo-Hutnicza im. Stanisława Staszica w Krakowie. Polskie Towarzystwo Biominerałów
    Tematy:
    biocompatibility
    hydroxyapatite
    MD simulation
    biokompatybilność
    hydroksyapatyty
    symulacja
    Źródło:
    Engineering of Biomaterials; 2020, 23, 158 spec. iss.; 40
    1429-7248
    Pojawia się w:
    Engineering of Biomaterials
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    In silico assessment of the inhibitory effect of four flavonoids (chrysin, naringin, quercetin, kaempferol) on tyrosinase activity using the MD simulation approach
    Autorzy:
    Farasat, A.
    Ghorbani, M.
    Gheibi, N.
    Shariatifar, H.
    Powiązania:
    https://bibliotekanauki.pl/articles/2097135.pdf
    Data publikacji:
    2020
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    tyrosinase
    chrysin
    quercetin
    kaempferol
    naringin
    MD simulation
    Opis:
    Tyrosinase is a tetrameric enzyme that plays an important role in pigment production. Overproduction of melanin, which may lead to several skin disorders, is a result of tyrosinase activity. Hence, tyrosinase inhibitors are of key importance in the treatment of these disorders. In the present study, four flavonoid inhibitors, namely chrysin, naringin, quercetin, and kaempferol, were evaluated physiochemically, and the inhibitory effects of these compounds on tyrosinase activity were evaluated using the molecular dynamics (MD) simulation method. To create the best conformation of the enzyme-substrate/inhibitor, the docking process for enzyme-substrate, i.e., enzyme-chrysin, enzyme-quercetin, enzyme-naringin, and enzyme-kaempferol, was performed. The complexes with the best binding energies were selected as the models for the MD simulation process. Furthermore, the structural (RMSD, Rg, RMSF, and Distance) and the thermodynamics properties of the complexes were evaluated. Additionally, the PMF was conducted to calculate the binding free energies. The results showed that chrysin, quercetin and the substrate were at similar distances to the amino acids of the active site, but naringin and kaempferol were closer to the active site of the enzyme than the substrate. Moreover, the analysis of the binding energy revealed that the substrates, chrysin, kaempferol, quercetin, and naringin bound to the enzyme with binding energies of -7.8, -3.1, -7.1, -3.9, and -8.4 kcal/mol, respectively, which confirms that naringin has the highest inhibitory effect on tyrosinase among other inhibitors, which makes it an appropriate candidate as a whitening agent in skin disorders.
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2020, 101, 3; 193-204
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Multiscale water drop contact angles at selected silica surfaces
    Autorzy:
    Zhang, Chen
    Wang, Xuming
    Li, Lixia
    Jin, Jiaqi
    Polson, Randy
    Miller, Jan D.
    Powiązania:
    https://bibliotekanauki.pl/articles/2146924.pdf
    Data publikacji:
    2022
    Wydawca:
    Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
    Tematy:
    contact angle
    atomic force microscopy
    hollow tip
    submicron-drop
    wettability
    MD simulation
    Opis:
    In this study, multiscale advancing contact angles for glycerol/water drops at silica surfaces are reported for millidrops, submicron-drops, and nanodrops. Selected silica surfaces were muscovite, silicon, and talc. The contact angles for millidrops (1–2 mm) were determined by the traditional sessile drop technique. For submicron-drops (0.1–1.0 μm), a hollow tip Atomic Force Microscope (AFM) procedure was used. The contact angles for nanodrops (~7 nm) were examined from Molecular Dynamics (MD) simulation. The results were compared to evaluate the effect of drop size on the contact angle. In the case of the hydrophobic talc surface, the 75° advancing contact angle did not vary significantly with drop size. For the hydrophilic muscovite surface, the water drop wet the surface and an advancing contact angle of about 10° was found for the millidrops and submicron-drops. However, for the MD simulated nanodrops, attachment and spreading of the ~7 nm drop created a 2D film of molecular dimensions, the contact angle of which was difficult to define and varied from 0° to 17°. Perhaps of equal interest from the MD simulation results was that the spreading of the glycerol/water nanodrop at the muscovite surface resulted in crystallographic directional transport of water molecules to the extremities of the 2D film. Such separation and segregation left the center of the film with an increased concentration of glycerol. Based on these results, the line tension, which has been found in other investigations to account for contact angle decrease with a decrease in drop size, does not seem to be a significant factor in this study.
    Źródło:
    Physicochemical Problems of Mineral Processing; 2022, 58, 5; art. no. 152154
    1643-1049
    2084-4735
    Pojawia się w:
    Physicochemical Problems of Mineral Processing
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Considering semi-crystallinity in molecular simulations of mechanical polymer properties – using nanoindentation of polyethylene as an example
    Autorzy:
    Fritz, Susanne
    Powiązania:
    https://bibliotekanauki.pl/articles/29520097.pdf
    Data publikacji:
    2021
    Wydawca:
    Akademia Górniczo-Hutnicza im. Stanisława Staszica w Krakowie. Wydawnictwo AGH
    Tematy:
    MD
    simulation
    polymer
    polyethylene
    semi-crystalline
    mechanical properties
    crystallization
    nanoindentation
    Opis:
    Molecular dynamic (MD) simulations have been used to investigate the response of semi-crystalline polymers in nanoindentation tests, using polyethylene (PE) as an example. To that purpose, semi-crystalline simulation boxes of linear PE with various chain lengths up to C2000 were created by homogeneous nucleation during the non-isothermal cooling of melts. The final crystallinity depended on the chain length and the cooling rate used and could be estimated using various parameters like density, fraction of bonds in trans conformation, and energy terms. The simulation boxes were transferred into surface models and subjected to nanoindentation tests using non equilibrium MD. This allowed the deformation behaviour of the material to be analysed directly. Strong dependencies on the crystallinity of the PE were found, which underlines the importance of considering crystallinity when investigating the mechanical properties of semi-crystalline polymers by means of simulations.
    Źródło:
    Computer Methods in Materials Science; 2021, 21, 1; 35-50
    2720-4081
    2720-3948
    Pojawia się w:
    Computer Methods in Materials Science
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Molecular order and dynamics of 5CB liquid crystals in confined space - computer simulation
    Autorzy:
    Gwizdała, W.
    Gburski, Z.
    Powiązania:
    https://bibliotekanauki.pl/articles/1940712.pdf
    Data publikacji:
    2015
    Wydawca:
    Politechnika Gdańska
    Tematy:
    liquid crystal
    5CB
    carbon nanostructure
    nanotube
    graphene
    computer simulation
    MD
    second rank order parameter
    Opis:
    We studied the dynamical and structural properties of an important nematic 4-n-pentyl-4’-cyanobiphenyl (5CB) mesogen placed near carbon allotropes (graphene, nanotube), using modeling and molecular dynamics simulations (MD). Every investigated nanosystem (a free cluster of 5CB, a 5CB cluster confined in a single-walled carbon nanotube, 5CB mesogens located between two graphene sheets, a 5CB thin layer on a single-walled carbon nanotube, a thin layer of a 5CB molecules near graphene plane) contains a liquid crystal cluster consisting of 5CB molecules (22–98 molecules). We also performed a computer experiment for a 5CB bulk sample (196 5CB mesogens) with periodic boundary conditions. The following observables were calculated for several temperatures: mean square displacement, radial distribution function and second rank order parameter of 5CB clusters. The obtained results from MD simulations were discussed and compared with the experimental data.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2015, 19, 1; 35-64
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Assessment of the possibilities of determining the characteristics of a pneumatic tyre with the use of an original road test system
    Ocena możliwości wyznaczania charakterystyk koła ogumionego za pomocą autorskiego systemu do badań drogowych
    Autorzy:
    Stańczyk, T.
    Stachowski, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/263602.pdf
    Data publikacji:
    2013
    Wydawca:
    Sieć Badawcza Łukasiewicz. Przemysłowy Instytut Motoryzacji
    Tematy:
    badania drogowe
    badania symulacyjne
    koło ogumione
    MD ADAMS
    opona
    znoszenie boczne
    pneumatic tyre
    road tests
    road wheel
    side slip
    simulation tests
    Opis:
    An original method of the carrying out of road test measurements, which enables the obtaining of side slip characteristics of pneumatic tyres in a simple way, has been presented. A unique measuring trailer built at the Chair of Automotive Vehicles and Transport of the Kielce University of Technology has be en demonstrated. The trailer design and the trailer actually built have been shown. The measurements carried out during road tests with the use of the trailer have been described and an example of the measurement results obtained has been presented in the form of a side slip characteristic curve of the tyre under tests. Furthermore, a model for investigating the dynamic characteristics of the towing vehicle and trailer system was formulated to assess the correctness of the method used. The necessary parameters and assumptions we re introduced and the number of degrees of freedom was determined for the model. The procedure to build the model with the use of the MD ADAMS software designed for analysing the dynamics of multi-mass systems has been described. The elements of the system under consideration, in particular the model solids and links between them, the system of external forces, and the pneumatic tyre model used, have been characterized. The simulation tests performed have been described. The simulation test results and the procedure of analysing them to determine the side force values for an argument applied in the form of a set of tyre slip angle values have been presented. The characteristic curve of the side slip of the pneumatic tyre as obtained from the tests has be en compared with the reference characteristic curve of the pneumatic tyre model used in the system under investigation. The results obtained from the work done have been recapitulated and assessed.
    W pracy zaprezentowano autorską metodologię wykonywania pomiarów drogowych, umożliwiających w prosty sposób pozyskiwanie charakterystyk bocznego znoszenia kół ogumionych. Przedstawiono oryginalną przyczepę pomiarową zbudowaną w Katedrze Pojazdów Samochodowych i Transportu Politechniki Świętokrzyskiej. Zaprezentowano przyczepę na etapie jej projektowania i w postaci zbudowanego urządzenia. Opisano pomiary drogowe wykonane z użyciem przyczepy i przedstawiono przykładowy wynik tych pomiarów w postaci charakterystyki bocznego znoszenia badanego koła. Następnie, w celu oceny poprawności zastosowanej metodologii, sformułowano model do badania dynamiki układu samochód . przyczepa. Wprowadzono niezbędne parametry i założenia oraz określono liczbę stopni swobody modelu. Opisano procedurę tworzenia modelu za pomocą oprogramowania do analizy dynamiki układów wielomasowych MD ADAMS. Scharakteryzowano elementy tworzące analizowany układ, bryły i więzy występujące pomiędzy nimi, siły zewnętrzne oraz użyty model koła ogumionego. Opisano przeprowadzone badania symulacyjne. Przedstawiono wyniki otrzymane podczas badań symulacyjnych i procedurę ich analizy w celu otrzymania wartości siły bocznej dla argumentu zadanego w postaci kąta znoszenia. Otrzymaną charakterystykę bocznego znoszenia porównano z charakterystyką wzorcową modelu koła ogumionego, zastosowanego w badanym układzie. Dokonano podsumowania i oceny otrzymanych wyników.
    Źródło:
    Archiwum Motoryzacji; 2013, 1; 65-83
    1234-754X
    2084-476X
    Pojawia się w:
    Archiwum Motoryzacji
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-6 z 6

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