|
|
Interaction of Cytochromes P450 with Flavodoxin: a theoretical study
Culka, Martin ; Martínek, Václav (advisor) ; Chmelík, Josef (referee)
Cytochromes P450 are diverse group of heme enzymes found in most species on Earth. In humans they are involved in metabolism of foreign compounds or steroids, bacteria employ cytochromes P450 for utilization of various hydrophobic substrates. General reaction catalyzed by cytochromes P450 is monooxygenation, when one atom of oxygen molecule is introduced into the substrate, while the other is reduced producing water. NADPH:cytochrome P450 oxidoreductase or cytochrome b5 usually serves as an electron donor providing electrons needed for activation of oxygen in eukaryotic organisms, in bacteria small FeS proteins or flavoproteins are these electron donors. It was shown earlier that bacterial electron donor flavodoxin could also interact with human cytochromes P450 in vitro. This thesis employs molecular modeling techniques to support a hypothesis that flavodoxin is responsible for reduction of human (1A2, 2A6, 2A13, 2C9, 2C19, 3A4) and bacterial (101A1 a 176A1) cytochromes P450 heterologously expressed in Escherichia coli. An initial guess of possible mutual orientations of cytochrome P450 and flavodoxin was predicted using information-driven protein-protein docking. The stability of these complexes was examined by directed dissociation method. The most stable orientation for each cytochrome P450 was further...
|
|
|
Laboratory astrochemistry and applications of computer simulations
Roučka, Štěpán ; Hrach, Rudolf (advisor) ; Bonaventura, Zdeněk (referee) ; Novák, Stanislav (referee)
This work is focused on laboratory studies of ion chemistry at conditions relevant for astrophysics. The three main outcomes of the thesis are: (1) The experimental study of the reaction rate coefficient of the associative detachment reaction H- + H -> H2 + e-; measurement of the thermal rate coefficient at the temperatures in the range 10-135 K is described. (2) The design of a novel apparatus for detecting the electrons produced in the RF trap and measuring their energy; numerical simulations and preliminary experimental results are presented. (3) The development of a model of the electron cooling in the afterglow plasma and the application of the model in the analysis of the H3+ recombination measurements.
|
|
|
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.
|
|
| |
|
|
Computer modeling of plasma-material interactions: particle flow
ČERNÁ, Veronika
Bachelor thesis deals with computer modeling of the interaction of plasma with the surface of the solid material, primarily by determining the flow of electrically charged particles to the surface. The main emphasis lays on study of this phenomenon using COMSOL Multiphysics. After introductory chapter, in which is briefly characterized the fourth state of matter plasma, there is a chapter introducing the basic techniques of computer modeling. The third chapter presents software for technical calculations, the use of which is practically demonstrated in the next chapter by the example of the continuous modeling. The last part of the thesis forms a sample output of the model. Conclusion is the evaluation of the whole bachelor thesis and the possibilities of its further use.
|
|
|
Loop antennas for medical applications
Zejda, Luboš ; Puskely, Jan (referee) ; Raida, Zbyněk (advisor)
This thesis is focused on the design of loop antennas for medical applications. The main goal of this thesis is to verify the functionality of published designs of broadband loop antennas, and to compare them with each other. Compared antennas are modified for available substrate and a specified frequency. Antenna with best parameters is selected, manufactured and its characteristics are compared with simulations. Design and simulation software used is CST Microwave Studio.
|
|
| |
|
|
Design and Optimization of Electromagnetic Band Gap Structures
Kovács, Peter ; Škvor,, Zbyněk (referee) ; Dědková, Jarmila (referee) ; Lukeš, Zbyněk (advisor)
Dizertační práce pojednává o návrhu a optimalizaci periodických struktur s elektromagnetickým zádržným pásmem (EBG – electromagnetic band gap) pro potlačení povrchových vln šířících se na elektricky tlustých dielektrických substrátech. Nepředvídatelné chování elektromagnetických vlastností těchto struktur v závislosti na parametrech elementární buňky činí jejích syntézi značně komplikovanou. Bez patřičného postupu je návrh EBG struktur metodou pokusu a omylu. V první části práce jsou shrnuty základní poznatky o šíření elektromagnetických vln v tzv. metamateriálech. Následně je diskutován správný způsob výpočtu disperzního diagramu ve vybraných komerčních programech. Jádrem dizertace je automatizovaný návrh a optimalizace EBG struktur využitím různých globálních optimalizačních algoritmů. Praktický význam vypracované metodiky je předveden na návrhových příkladech periodických struktur s redukovanými rozměry, dvoupásmovými EBG vlastnostmi, simultánním EBG a AMC (artificial magnetic conductor – umělý magnetický vodič) chováním a tzv. superstrátu. Poslední kapitola je věnována experimentálnímu ověření počítačových modelů.
|
|
| |
|
|
Computer modeling of laser beam
Mittner, Ondřej ; Wilfert, Otakar (referee) ; Raida, Zbyněk (advisor)
This bachelor’s thesis theoretically describes Gaussian beam, its characteristics and its passing through optical elements. The main attention is focused on creating of computer models of Gaussian beam in COMSOL Multiphysics application, detailed description of these models, presentation of achieved results and comparing these results with theoretic presumptions.
|
guest ::
