|
| |
|
|
Conformational behavior of dendritic branched polymers in aqueous solutions (Dissipative particle dynamics)
Suchá, Lucie ; Limpouchová, Zuzana (advisor) ; Posel, Zbyšek (referee)
Bakalářská práce se věnuje studiu konformačního chování polymerních den- drimer· ve vodných roztocích. Polymerní roztoky byly simulovány pomocí di- sipativní částicové dynamiky. Všechny simulace byly provedeny pomocí pro- gramu DL−MESO. Pro generování vstupních soubor· a zpracování výsledk· simulací byly napsány vlastní programy. Správná funkce programu a správné nastavení simulačních parametr· bylo ověřeno pomocí parametrické studie nekonečně zředěných roztok· homopolymerních dendrimer· v dobrém roz- pouštědle. 'kálovací exponent gyračního poloměru získaný pomocí simulací je v souladu s publikovanými daty. Dále bylo porovnáváno konformační chování homopolymerního a kopolymerního dendrimeru. Klíčová slova: Počítačové simulace, disipativní částicová dynamika, dendri- mer, konformační chování, vodné roztoky, větvený polymer
|
|
|
Computer simulations of conformational behavior of block copolymers in selective solvents
Šindelka, Karel ; Limpouchová, Zuzana (advisor) ; Kuldová, Jitka (referee)
The presented bachelor thesis deals with the study of the conformational be- haviour of diblock copolymers in the selective solvent. The polymer solution was modelled using a coarse-grained model and is simulated using dissipative particle dynamics (DPD). An original C-code for DPD simulations together with a new software package for processing of simulation data was developed. Functionality of the code and software were tested for two systems. The first system corre- sponded to a linear homopolymer in a solvent and the scaling laws for homopoly- mer in dilute solution were reproduced. The second system represented diblock copolymers in selective solvents and micellar behaviour simulated with the de- veloped code agreed with simulations by Sheng et al. Then, the self-assembly of long copolymer chains in selective solvents that mimics a block copolymer of poly(methacrylic acid) and poly(ethylene oxide) in aqueous solution at pH 1 was studied for different polymer concentrations. The simulation results provided valuable insight into the studied system and serve as a good starting point for DPD simulations of this system with added surfactants and at different values of pH, where the electrostatic interactions become important.
|
|
| |
|
|
Excitation and Detection of Plasmon Polaritons
Šustr, Libor ; Schmidt, Eduard (referee) ; Kalousek, Radek (advisor)
The diploma thesis is aimed to excitation and detection of surface plasmon polaritons by visible light. First of all, we will briefly remind some basic principles like waves, electromagnetic wave, light on the interface and optical properties of metals. By using these principles we show presence of surface plasmon polaritons states. After the explanation of their properties there will be clearly visible reasons for aplications of the special excitationand detection methods. We will describe especially the prism coupling, periodic grating coupling and SNOM. Two last sections deal with computer simulations and experiments related to these methods. This means we can exemplify some knowledge presented in previous chapters. Results of simulations are compared with the experiment where we study the excitations of surface plasmon polaritons by periodic grating on aluminium surface.
|
|
|
Optimization of cooling of a family house by using a geothermal system
Buchta, Jan ; Formánek, Marian (referee) ; Šikula, Ondřej (advisor)
The master’s thesis deals with optimization of cooling system of family house using borehole heat exchanger as a single cooling source. In the experimental part of the thesis was carried out long-term mearurements. The main part of the master’s thesis is the development and verification mathematical and physical model of thermal behavior chilled room. The result are computer simulations and evaluation of individual scenarios and design requirements for a potential optimization of measurement and control system. The theoretical part generally deals with radiant cooling systems.
|
|
|
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.
|
|
|
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.
|
|
| |
|
| |
guest ::
