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Study of interactions of organic matter and its components via molecular dynamics
BARVÍKOVÁ, Hana
Humic acids and humates are principal components of humic substances major organic constituents of soil, peat, coal and water around the world. I was involved in research into molecular dynamics simulations of interactions of quartz surfaces with aqueous solutions of ions and small organic molecules representing basic building blocks of larger biomolecules and functional groups of organic matter. We studied interactions of molecules with surfaces for a set of surface charge densities corresponding to the experimentally or environmentally relevant ranges of pH values employing molecular mechanics, molecular dynamics and ab initio techniques. Simulated quartz surfaces covered the range of surface charge densities 0.00, -0.03, -0.06 and -0.12 C-m-2, approximately corresponding to pH values 4.5, 7.5, 9.5 and 11. As model molecules, benzoic acid, phenol, o-salicylic acid and their conjugated bases were chosen. My task was to prepare topologies and parametric models of selected organic matter basic building blocks organic molecules. I focused on studying interactions of these molecules in an aqueous environment with mineral surface quartz. The aim was to process simulation results and analyse conformations of the adsorption complexes and their thermodynamic properties such as interaction energies, free energies and adsorption geometries.
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Interaction between TiAl melt and coated oxide refractories
Dočekalová, Kateřina ; Dlouhý, Antonín ; Zemčík, L. ; Fiala, J.
The present study focuses on reactions between ceramic crucibles and molten TiAl intermetallics. Coating strategies are investigated that exhibit a potential in slowing down the decomposition of the crucible wall. Uncoated crucibles (system TiAl melt - Al2O3 crucible) and crucibles with the coat (system TiAl melt - CaO coat - Al2O3 crucible) were used in melting and casting experiments. The reference state of the coated crucible before the melting trial was also investigated. Results of the SEM, EDAX and X-ray diffraction analysis contributed to the identification of the reaction zone and its chemical composition. The melt contamination with oxide inclusions results from the erosion process in which individual components of the melt diffuse along grain boundaries of the refractory and activate chemical reactions that decompose the crucible wall. Assessment of thermodynamic parameters associated with the chemical reactions helped in identifying the nature of the erosion process.
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Study of plasma-solid interaction at medium pressures
Roučka, Štěpán ; Hrach, Rudolf (advisor) ; Novotný, Dušan (referee)
The thesis is aimed at particle simulation of plasma at medium pressures. Main results concern modelling of collisions in particle-in-cell algorithm. Dierent methods of modelling of collisions are discussed and their accuracy and eciency are investigated. Furthermore a new modication of particle-in-cell algorithm for modelling at medium pressures was proposed. Numerical benchmarks in the nal chapter show advantages of the new algorithm.
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The role of acetylation in the RNA recognition motif of SRSF5 protein
Icha, Jaroslav ; Staněk, David (advisor) ; Šenigl, Filip (referee)
Acetylation is emerging as an important posttranslational modification, which is found in thousands of proteins in eukaryotes, as well as prokaryotes. Global proteomic studies implicated acetylation in regulation of various processes like metabolism, gene expression, cell cycle or aging to name a few. In this work I set out to investigate the role of acetylation of a splicing regulatory protein SRSF5 by creating mutations in its acetylation site. I tested the hypothesis that acetylation influences SRSF5 interaction with RNA. I expressed acetylation-mimicking (Q) or non-acetylable (R) mutant of SRSF5 in HeLa cells and measured their interaction with RNA by RNA immunoprecipitation or in vitro by fluorescence anisotropy. Both approaches agreed that mutants interact with RNA less than the wild type protein and Q mutant bound RNA weaker than R mutant. I did not detect further difference in localization or dynamics among the proteins in vivo, which suggests that difference caused by weakened interaction of mutants with RNA was outweighed by other factors influencing SRSF5 behaviour, probably protein-protein interactions. I also found out that mutant SRSF5 proteins do not have a dominant effect on splicing of fibronectin alternative EDB exon. The data obtained give an indirect evidence for the hypothesis that...
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Media content organization and solutions in JavaFX
Smíšek, Matěj ; Pavlíčková, Jarmila (advisor) ; Tran, Lam (referee)
The bachelor thesis looks into changes in television and movie audience behavior. Increas-ing amount of TV shows and movies in user media library brings new needs those files properly organize a record which one has been already watched by user. Software solution must abide audience custom and allow smooth transition from slowly degrading television audience to new, more interactive one. Current offer on market of media organization software is broad, but it is important to focus in detail on functions of those applications and verify if they truly meet all set requirements, or if they are robust application software, which can be not very user-friendly for common user. Custom solution in Java using brand new user interface library JavaFX 8, which goal is to bring basic framework of possibilities of solving media organization for future programmers.
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