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Structural analysis of extrinsic proteins from the oxygen-evolving complex of photosystem II from higher plants
KOHOUTOVÁ, Jaroslava
All life on earth depends mainly on the presence of oxygen. Largest producers of oxygen are green plants, cyanobacteria and algae. Oxygen is released from the oxygenevolving complex of photosystem II during photosynthesis and it is used in cellular respiration of all life complexes. The oxygen-evolving complex of photosystem II has the same function in each photosynthetic organism, but it has a different composition and organization of extrinsic proteins; only PsbO protein is ubiquitous in all known oxyphototrophs. Until now only low resolution electron microscopy structural models of plant PSII and crystal structures of cyanobacterial PSII are available. Higher plant extrinsic proteins (PsbP, PsbQ and PsbR) are structurally unrelated, non-homologues to the cyanobacterial extrinsic proteins (PsbO, PsbU and PsbV) and this is the reason why it is not possible to predict arrangement of these proteins on the lumenal site of higher plant PSII. Recently, models differ mainly in the structure of the oxygen-evolving complex, which could be resolved by determination of the exact binding sites for extrinsic proteins. An other question evolves: if the difference in the oxygen-evolving complex composition is the result of evolution or adaptation of photosynthetic organisms to their environment. Structural knowledge of extrinsic proteins that could help to resolve the location and subsequently the function of extrinsic proteins is still incomplete. From this case,structural analysis, interactions and probably arrangement of proteins PsbP and PsbQ was studied and is described in detail in this thesis.
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Vliv tlaku v jednofázové kondenzaci
Wedekind, J. ; Hyvärinen, A-P. ; Brus, David ; Reguera, D.
The pressure-efect of a chemically inert carrier-gas on the nucleation rate is one of the biggest puzzles in the research of gas-liquid nucleation. Different experiments may show a positive effect a negative effect, or no effect at all, at the same experiment can show both trends for the same substance depending on temperature or for different substances at the same temperature. We show how this ambiguous pressure effect naturally arises from the competition of nonisothermal effects and pressure volume work. We are able to apparently contradictory experimental results and quantify the variation of the nucleation ability in the presence of an ambient gas. Molecular dynamics simulations confirm these predictions very well.
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Parallel programming in molecular dynamics simulations
Pelikán, Vladimír ; Hora, Petr ; Machová, Anna
Molecular dynamics simulation is a well-established technique for modeling complex many-particle systems in diverse areas of physics and chemistry. The computational requirements of simulations of large systems are enormous. They make the use of high-performance parallel computers indispensable and have led to the development of a broad range of advanced algorithms for these machines. We have developed a classical molecular dynamics code in MPI based on Newtonian dynamics.
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