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DFT calculations of graphene regarding to biosenzoric applications
Špaček, Ondřej ; Friák, Martin (referee) ; Bartošík, Miroslav (advisor)
This diploma thesis is focused on calculation of both structure and electronic properties of the graphene after the adsorption of atomic and molecular oxygen and urea using the Density Functional Theory (DFT). The influence of van der Waals interactions on the structure and adsorption energy is studied, as well as influence of the thermal corrections, the charge density spatial distribution and the electronic doping of graphene after the adsorption of the adsorbant on the graphene.
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Double-gate biosensor of glucose based on functionalized graphene
Malatinová, Michaela ; Pavlásková, Lucie (referee) ; Bartošík, Miroslav (advisor)
V tejto bakalárskej práci bola skúmaná funkcionalizácia grafénu s sukcinimidyl ester pyrenbutanovou kyselinou a enzýmom glukóza oxidáza pre detekciu glukózy biosenzorom. Funkcionalizovaný grafén bol implementovaný ako kanál v poľom riadenom tranzistore pre výrobu biodetekčného zariadenia. Proces funkcionalizácie potvrdila Ramanova spektroskopia a mikroskopia atomárných síl. Charakterizácia senzoru a jeho kvalít bola sledovaná pomocou transferových kriviek a časovej odozvy senzoru. Posun Diracovho bodu a jeho poloha boli analyzované v závislosti na rôznych koncentráciach glukózy s ohľadom na efektivitu funkcionalizácie. Výber hradlovej elektródy v grafénovom poľom riadenom tranzistore bol skúmaný vzhľadom na jeho možný dopad na výsledky merania.
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Photocontrolled Biomolecules
Planer, Jakub ; Bartošík, Miroslav (referee) ; Vácha,, Robert (referee) ; Kulhánek, Petr (advisor)
This work is focused on molecular dynamics simulations of artificial photosensitive ion channel and AFM probe. To assemble this ion channel, DFT methods were employed for reparametrization of the GAFF force field describing the bridged azobenzene, which was used as a light controlled molecular switch. We proved by molecular dynamics simulations that newly developed parameters correctly describe behavior of assembled model of ion channel in a lipid bilayer. We also constructed a model of AFM probe and observed formation of water meniscus between the AFM probe and surface, both made of -quartz, by employing molecular dynamics simulations. A contribution of this work is the set of new parameters extending GAFF force field for description of the bridged azobenzene. We also verified functionality of ion channel model and model of AFM probe, which can be used for the further water meniscus studies.
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Selective hydrogenation/Oxidation of CVD graphene using AFM
Přikryl, Vojtěch ; Švarc, Vojtěch (referee) ; Bartošík, Miroslav (advisor)
Graphene is a perspective material for utilization in electronics due to its high charge carrier mobility. However, in order to be applicable in practice the bandgap opening is necessary. One way of achieving this is modification of graphene by hydrogenation or oxidation. This work concerns the possibility of using AFM for local hydrogenation/oxidation of graphene depending on the bias voltage between the tip and the sample. The presence of hydrogenation/oxidation was examined by Kelvin probe force microscopy and Raman spectroscopy. The possibility of oxidation was proved but hydrogenation was not proved.
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UHV-EC transfer system for electrochemical surface science studies
Jakub, Zdeněk ; Vanýsek, Petr (referee) ; Bartošík, Miroslav (advisor)
This thesis deals with the combined ultra-high vacuum (UHV) and electrochemical (EC) studies of selected iron oxide surfaces, namely Fe3O4(001) and -Fe2O3(012). The state-of- the-art knowledge regarding these surfaces is briefly reviewed, and importance of understanding these materials in the electrochemical environment is discussed. The design of the transfer system between UHV and EC environment is presented; individual features of the system are thoroughly discussed and the system is used for testing the stability of the Fe3O4(001) (2×2)R45° surface reconstruction in ambient conditions. The experimental results presented in this thesis show that the Fe3O4(001) (2×2)R45° reconstruction, utilized as an adatom array for single atom catalysis studies, survives both exposure to air and to liquid water, if the exposure is achieved in well-controlled fashion. Further, this thesis presents the first-ever atomic scale scanning tunneling microscopy (STM) study of the -Fe2O3(012) surface, which is important for photoelectrochemical water splitting. STM images of two surface reconstructions of the -Fe2O3(012) surface known to date are presented. A bulk terminated model of the (1×1) reconstruction is confirmed and a novel surface structure model for the (2×1) reconstructed surface is proposed. Adsorption studies of H2O and O2 on the (2×1) reconstructed surface are documented by timelapse STM.
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Preparation of 2D materials in an ultrahigh vacuum electron microscope
Dymáček, Michal ; Bartošík, Miroslav (referee) ; Kolíbal, Miroslav (advisor)
This thesis is devoted to preparation of multilayer graphene and h-BN by CVD method. In the theoretical part of this thesis, both materials are introduced, as well as the CVD method and SEM. In the experimental part, the equipment and samples are described, as well as the computer codes, that were made within this work and used for analysis of taken images, and experiments, that were carried out. Utilizing in-situ analysis in ultra-high vacuum scanning electron microscope, the goal was to answer a question how is the multilayer graphene formed on the surface. Also, the first experiments of preparation of h-BN in this aparature were carried out.
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