|
|
Molecular dynamics as a tool to study biological systems
SOVOVÁ, Žofie
Molecular dynamics simulations are a theoretical method enabling to trace the movement of atoms within a system. The system studied is usually treated on the atomistic level, however its overall properties can be also described satisfactory if several atoms are handled as one particle (coarse-grained molecular dynamics). This thesis presents molecular modeling and (coarse-grained) molecular dynamics as tools for the description of different biologically relevant systems. The coarse-grained force field parameters had to be developed prior to characterization of the thylakoid membrane from cyanobacterium Synechocystis PCC6803. Two different compositions of the membrane were studied in order to reveal differences in their behavior. The PsbI subunit of photosystem II was embedded into the thylakoid membrane and its behavior, both as an isolated protein and as a cluster of several units, was described. The last system examined was the C-type lectin-like domain of NKR-P1, a surface receptor of natural killer cells. Attention was payed to its structural characterization.
|
|
|
Computer simulation of interactions of molecules with mineral surfaces
BARVÍKOVÁ, Hana
This thesis is focused on molecular dynamics, modelling interactions and their simulation. One of the tasks was to familiarize with GROMACS, a molecular dynamics simulation software. This work also introduces the basics of molecular dynamics and modelling interactions of organic molecules with mineral surfaces. The aim of the thesis was to solve model tasks in GROMACS and analyze the output results. The thesis describes some of the most important file formats and utilities that are needed for working with GROMACS and the use of both the formats and the utilities. In this program, I built up several systems consisting of combinations of organic molecules such as benzoic acid, phenol, salicylic acid and their conjugate bases with mineral surfaces (quartz crystal) of different surface charge density. Furthermore I analyzed the results of these simulations, behaviour of the structures and adsorption geometries and interaction energies within these systems. The thesis might also serve as a quick introduction and familiarization with GROMACS with emphasis on simulations and analysis of systems with planar interfaces. Within the MetaCentrum Project I worked on the Hermes Computer Cluster belonging to the Faculty of Science at the University of South Bohemia.
|
|
|
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.
|
|
|
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.
|
|
| |
|
| |
|
| |
|
| |
|
|
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.
|
|
| |
guest ::
