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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.
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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...
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ANALYSIS OF IMPACT OF EXPERIMENT REALISATION ON MECHANICAL CHARACTERISTICS OF BIOMATERIALS
Slažanský, Martin ; Petruška, Jindřich (referee) ; Horný,, Lukáš (referee) ; Burša, Jiří (advisor)
Dizertační práce se zabývá věrohodností mechanického testování měkkých biologických tkání a predikčními schopnostmi různých modelů materiálů. Obě oblasti byly zkoumány užitím metody konečných prvků. První část práce je věnována úvodu do problému a popisu měkkých biologických tkání, které s problémem souvisí, a rešerši nynějšího způsobu jejich mechanického testování. Druhá část práce se zabývá hledáním optimálního nastavení experimentálního zařízení za použití počítačového modelování pomocí virtuální simulace mechanických testů. Výsledky analýzy potvrdily, že dvě úzké svorky po délce hrany, stejně jako běžně používané háčky, jsou použitelné pro dvouosé tahové zkoušky různých měkkých tkání za použití čtvercového vzorku. Použití svorek je proto časově úsporná, jednoduchá a spolehlivá alternativa, která není podřadná použití háčků. V práci byla rovněž provedena analýza, jejímž výsledkem jsou doporučení ohledně typu, počtu a velikosti uchycení pro různě velké vzorky. Třetí část práce zkoumá predikční schopnosti modelů materiálů měkkých tkání a závislosti těchto schopností. Lze shrnout, že výsledné mechanické chování proloženého modelu materiálu závisí na počátečních parametrech a že neexistují „ideální“ počáteční parametry při prokládání experimentálních dat. Navzdory absenci „ideálních“ počátečních parametrů je navržen v rámci možností nejefektivnější způsob aproximace experimentálních dat z mnoha jejich souborů. Dále je možné shrnout, že omezení hodnot parametrů modelu při prokládání experimentálních dat ústí v nepředvídatelný vliv na kvalitu aproximace. V závěrečné části práce byl analyzován předpoklad afinní a neafinní deformace modelů materiálů za účelem vysvětlení velkých rozporů mezi výsledky strukturně založených modelů a výsledky dvouosých testů při různých testovacích protokolech. Ačkoli byly zjištěny určité rozdíly mezi výsledky analyzovaných modelů, přece nebyly dostatečně významné, aby vysvětlily výše uvedené velké rozpory. V poslední části práce jsou zmíněny další možné oblasti výzkumu.
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Conformational behavior of branched polymers
Wang, Xiu ; Limpouchová, Zuzana (advisor) ; Cifra, Peter (referee) ; Kolafa, Jiří (referee)
This PhD thesis is devoted to the study of the conformational behavior of branched polymers in confined volumes. This behavior depends not only on polymer architecture and composition but also on steric confinement and on interaction of polymer segments with the confining wall. Better understanding of complex entropy-to-enthalpy interplay can elucidate the mechanism of the chromatographic separation at the microscopic level. An unambiguous size-exclusion chromatography (SEC) analysis of mixtures containing different polymer architectures is difficult because the sizes of polymer coils, which determine the separation, depend not only on molar mass but also on the polymer architecture. Modern chromatographic methods combine the SEC with the interaction chromatography (IC). They exploit the fact that polymer interactions with pore walls, which are the prerequisite for efficient IC separation, depend strongly on polymer architecture. The knowledge of the conformational behavior of linear and branched polymers in confined volumes and of their interactions with confining medium enables to find optimum conditions either for enhancing or for suppressing the role of individual factors that influence the separation. We have shown that the complex entropy-to-enthalpy interplay in polymer solutions in confined...
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Theoretical study of enzymes related to carcinogenesis: DNA polymerase β and cytochromes P450
Jeřábek, Petr ; Martínek, Václav (advisor) ; Entlicher, Gustav (referee) ; Ettrich, Rüdiger (referee)
Present doctoral thesis contributed to understanding of mechanistic principles of two enzymes participating in the process of carcinogenesis; DNA polymerase (pol ) and cytochromes P450 (CYP). Pol is part of the DNA base-excision repair mechanism (BER). The primary role of pol in, the BER mechanism, is inserting a new nucleotide into a DNA strand according to Watson-Crick base pairing rules. Pol plays an important role in the process of carcinogenesis, approximately 30 % of human tumors express pol mutants. The ability of pol to discriminate between "right" and "wrong" nucleotide during the insertion process is called fidelity. We employed computational methods to elucidate molecular basis of the fidelity of pol . First, the relative free energy calculation method LRA was employed to compare differences in free energies between the "right" and "wrong" nucleotide during its insertion into DNA. The results indicated a better stabilization of transition-state of the nucleophilic substitution catalyzed by pol in the case of the "right" versus "wrong" nucleotide. This difference resulted in an 80-fold contribution to its fidelity. Further, computational methods FEP and LIE were used to examine how mutations effect fidelity of pol . Results were than correlated with experimental data...
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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...
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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.
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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.
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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.
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