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Stress at the initial stage of growth for Lennard-Jones films

100%

Zientarski T. , Chocyk D.

2009

tom Vol. 39, nr 4

975-979

Molecular dynamics simulation was used to study the influence of a relative size of adsorbed and substrate atoms on the stress of growing films. Atoms in the system interact via the Lennard-Jones potential. The simulations were performed at a fixed value of systems temperature. The relative size of deposited atoms was changed in the range from 0.7 to 1.2, relatively to the size of substrate atoms. Proposed modeling allows to explain the behaviour of mean biaxial stress for systems with different sizes of adsorbed atoms and a substrate. For considered systems, significant changes in mean biaxial stress have only first three monolayers.

The effect of the Glu342Lys mutation in α1-antitrypsin on its structure, studied by molecular modelling methods.

100%

Jezierski G. , Pasenkiewicz-Gierula M.

Acta Biochimica Polonica

2001

tom 48

nr 1

65-75

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.

Molecular dynamics computer simulation of water flows in nanochannels

100%

Kucaba-Piętal A. , Walenta Z. A. , Peradzyński Z.

2009

tom Vol. 57, nr 1

55-61

The work presents the results of the simulations of water flows through narrow channels (Poiseuille flows) performed using the molecular dynamics method, for two different channel widths (equal to 5 and 10 diameters of the water molecule) and for two different materials of the channel walls (copper and quartz). In the simulations, physical properties of the materials and their electrostatic interactions were considered. The obtained results are compared with the analytical solutions for a micropolar fluid flow taking account of the experimentally obtained rheological constants of water.