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Wyświetlanie 1-10 z 47
Tytuł:
Water film structure during rupture as revealed by MDS image analysis
Autorzy:
Truong, N. T.
Dang, L. X.
Lin, C.-L.
Wang, X.
Miller, J. D.
Tematy:
image processing
molecular dynamics simulation
film stability
molecular porosity
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Wydawca:
Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
Powiązania:
https://bibliotekanauki.pl/articles/110251.pdf  Link otwiera się w nowym oknie
Opis:
The structure of thin water films during the rupture process was investigated by a new approach, which combines molecular dynamics simulation (MDS) with image processing analysis. The analysis procedure was developed to convert MDS trajectories to readable 3D images. The water films were studied at different thicknesses by MDS to determine the critical thickness at which the film ruptures. The potential energy of each specific film thickness during the simulation time was analyzed, and the results showed that the potential energy of stable films remained unchanged while the potential energy kept decreasing for films which ruptured during the simulation time. By applying the new procedure, the molecular porosity, which is defined as the void fraction between the volume of molecular pores in the water film and the total volume of the water film, was calculated. The results of molecular porosity for different film thicknesses during the simulation time suggested a critical molecular porosity as 49%. In other words, stable films have a molecular porosity of less than 49%. If a water film has a molecular porosity greater than 49%, rupture occurs during the simulation.
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
The effect of the Glu342Lys mutation in α1-antitrypsin on its structure, studied by molecular modelling methods.
Autorzy:
Jezierski, Grzegorz
Pasenkiewicz-Gierula, Marta
Tematy:
serpins
protein structure
energy minimisation
molecular dynamics simulation
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Wydawca:
Polskie Towarzystwo Biochemiczne
Powiązania:
https://bibliotekanauki.pl/articles/1044164.pdf  Link otwiera się w nowym oknie
Opis:
The structure of native α1-antitrypsin, the most abundant protease inhibitor in human plasma, is characterised primarily by a reactive loop containing the centre of proteinase inhibition, and a β-sheet composed of five strands. Mobility of the reactive loop is confined as a result of electrostatic interactions between side chains of Glu342 and Lys290, both located at the junction of the reactive loop and the β structure. The most common mutation in the protein, resulting in its inactivation, is Glu342→Lys, named the Z mutation. The main goal of this work was to investigate the influence of the Z mutation on the structure of α1-antitrypsin. Commonly used molecular modelling methods have been applied in a comparative study of two protein models: the wild type and the Z mutant. The results indicate that the Z mutation introduces local instabilities in the region of the reactive loop. Moreover, even parts of the protein located far apart from the mutation region are affected. The Z mutation causes a relative change in the total energy of about 3%. Relatively small root mean square differences between the optimised structures of the wild type and the Z mutant, together with detailed analysis of 'conformational searching' process, lead to the hypothesis that the Z mutation principally induces a change in the dynamics of α1-antitrypsin.
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Flotation and molecular dynamics simulation of muscovite with mixed anionic/cationic collectors
Autorzy:
Bai, Yang
Li, Caixia
An, Hongyun
Wang, Guoliang
Zhao, Xin
Zhang, Jinqi
Tematy:
muscovite
mixed anionic/cationic collectors
flotation
molecular dynamics simulation
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Wydawca:
Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
Powiązania:
https://bibliotekanauki.pl/articles/110125.pdf  Link otwiera się w nowym oknie
Opis:
In this study, three kinds of anionic collectors (sodium oleate (NaOl), sodium dodecyl sulfonate (SDS) and naphthenic acid (NA)) were used in combination with dodecylamine (DDA) to investigate the flotation behavior of muscovite under the action of different mixed anionic/cationic collectors, and their mechanisms for adsorption on the muscovite (001) Surface were clarified using molecular dynamics simulations. The flotation results indicated that different mixed anionic/cationic collectors could improve the recovery of muscovite to varying degrees, but the optimum molar ratio of anionic collectors to DDA and the optimum mixed collector dosage were different. Molecular dynamics simulations showed that the mixed anionic/cationic collectors could significantly increase the hydrophobicity of the muscovite, as evidenced by the decrease in the calculated water molecule density on the muscovite surface and the diffusion coefficient of water molecules at the solid/liquid interface. The interaction between the amino group and the polar group of anionic collectors reduced the electrostatic repulsion between DDA cations and theoretically increased the adsorption capacity of the mixed anionic/cationic collectors on the muscovite surface. Moreover, DDA/NA and DDA/NaOl could improve the calculated carbon atom density on the muscovite surface, which enhanced the hydrophobic association between nonpolar carbon chains, thus further achieving an enhanced flotation performance.
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular dynamics study of the fracture of single layer buckled silicon monosulfide and germanium selenide
Autorzy:
Le, M.-Q
Tematy:
2D materials
fracture
molecular dynamics simulation
mechanical properties
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Wydawca:
Instytut Podstawowych Problemów Techniki PAN
Powiązania:
https://bibliotekanauki.pl/articles/38629974.pdf  Link otwiera się w nowym oknie
Opis:
Molecular dynamics simulations were conducted with the Stillinger–Weber potential at room temperature to study the mechanical properties and find the mode-I critical stress intensity factor of buckled two-dimensional (2D) hexagonal silicon mono-sulfide (SiS) and germanium selenide (GeSe) sheets. Uniaxial tensile tests were simulated for pristine and pre-cracked sheets. 2D Young’s modulus of SiS and GeSe are estimated at 38.3 and 26.0 N/m, respectively. Their 2D fracture strength is about 3.1–3.5 N/m. By using the initial crack length with the corresponding fracture stress, their mode-I critical stress intensity factor is estimated in the range from 0.19 through 0.22 MPapm. These values differ within 5% from those obtained by the surface energy and are very small compared to the reported fracture toughness of single-crystalline monolayer graphene.
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Determining the effects of pseudouridine incorporation on human tRNAs
Autorzy:
Dahate, Priyanka
Indyka, Paulina
Rawski, Michał
Biela, Anna
Nowak, Jakub
Moafinejad, Seyed Naeim
Dobosz, Dominika
Chramiec-Głąbik, Andrzej
Bujnicki, Janusz M
Lin, Ting-Yu
Jeżowski, Jakub
Wien, Frank
Biela, Artur
Arluison, Veronique
Mehta, Rahul
Mukherjee, Sunandan
Glatt, Sebastian
Maiti, Satyabrata
Opis:
Transfer RNAs (tRNAs) are ubiquitous non-coding RNA molecules required to translate mRNA-encoded sequence information into nascent polypeptide chains. Their relatively small size and heterogenous patterns of their RNA modifications have impeded the systematic structural characterization of individual tRNAs. Here, we use single-particle cryo-EM to determine the structures of four human tRNAs before and after incorporation of pseudouridines (Ψ). Following post-transcriptional modifications by distinct combinations of human pseudouridine synthases, we find that tRNAs become stabilized and undergo specific local structural changes. We establish interactions between the D- and T-arms as the key linchpin in the tertiary structure of tRNAs. Our structures of human tRNAs highlight the vast potential of cryo-EM combined with biophysical measurements and computational simulations for structure-function analyses of tRNAs and other small, folded RNA domains.
Dostawca treści:
Repozytorium Uniwersytetu Jagiellońskiego
Artykuł
Tytuł:
The cavitation nuclei transient characteristics of Lennard-Jones fluid in cavitation inception
Autorzy:
Fu, Q.
Zhang, B.
Zhao, Y.
Zhu, R.
Liu, G.
Li, M.
Tematy:
cavitation nuclei
molecular dynamics simulation
Lennard-Jones fluid
cavitation inception
nucleation
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Wydawca:
Politechnika Gdańska. Wydział Inżynierii Mechanicznej i Okrętownictwa
Powiązania:
https://bibliotekanauki.pl/articles/259255.pdf  Link otwiera się w nowym oknie
Opis:
In the field of ocean engineering, cavitation is widespread, for the study of cavitation nuclei transient characteristics in cavitation inception, we applied theoretical analysis and molecular dynamics (MD) simulation to study Lennard-Jones (L-J) fluid with different initial cavitation nuclei under the NVT-constant ensemble in this manuscript. The results showed that in cavitation inception, due to the decrease of liquid local pressure, the liquid molecules would enter the cavitation nuclei, which contributed to the growth of cavitation nuclei. By using molecular potential energy, it was found that the molecular potential energy was higher in cavitation nuclei part, while the liquid molecular potential energy changes greatly at the beginning of the cavitation nuclei growth. The density of the liquid and the surface layer changes more obvious, but density of vapor in the bubble changes inconspicuously. With the growth of cavitation nuclei, the RDF peak intensity increased, the peak width narrowed and the first valley moved inner. When cavitation nuclei initial size reduced, the peak intensity reduced, the corresponding rbin increased. With the decrease of the initial cavitation nuclei, the system pressure and total energy achieved a balance longer, and correspondingly, they were smaller. In addition, at the beginning of the cavitation nuclei growth, the total energy and system pressure changed greatly.
Dostawca treści:
Biblioteka Nauki
Artykuł
Wyświetlanie 1-10 z 47

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