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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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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.
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Measurement of the Basic Material Characteristics forTransmission of Chain Filter
Melich, Radek
Observing the Sun with birefringent filters is done mainly with filters tuned constantly on some interesting spectral wavelength. However, a new problem that solves tuning of these filters by a temperature change, meets a problem of a insufficient accuracy of dispersion dependences which are used for calculation of transmission at the exact wavelength and the exact temperature. Designing a filter that reaches an extreme small value in its FWHM (e.g. 0.05 nm) it is then very important to determine birefringent dependency with a sufficient accuracy. The paper shows the technique of getting such dependencies, then it mentions a mathematical process suitable for getting the transmission of Solc filter and finally it compares data got from an experiment with computed data.
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