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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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Analysis of the transport properties of graphene nanostructures
Novák, Martin ; Bartošík, Miroslav (referee) ; Lišková, Zuzana (advisor)
Graphene transport properties are analysed in this thesis. They are strongly dependent on doping with charge carriers. The number of charge carriers can be influenced by electric field, substrate or surface adsorbates. The graphene field-effect transistor (FET) has been prepared. Graphene made by chemical vapor deposition (CVD) has been con tacted through gold structures made by electron beam lithography (EBL). Dependences on electrode configuration, gate voltage and used substrate are observed.
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Selective hydrogenation of graphene prepared by chemical vapour deposition
Kovařík, Štěpán ; Nováček, Zdeněk (referee) ; Bartošík, Miroslav (advisor)
Controlled bandgap opening is one of the skills necessary for the application of graphene in electronics. The graphene hydrogenation is one of the possible ways to open the bandgap. In this work we deal with local hydrogenation of graphene prepared by chemical vapour deposition on a Si/SiO2 substrate. The hydrogenation was performed by atomic source of hydrogen and polymethyl methacrylate pattern was used for localization of hydrogenated structures on graphene. The pattern was prepared by electron beam lithography. The presence of structures formed by hydrogenated graphene was investigated by Raman spectroscopy, Kelvin probe force microscopy and PeakForce tunneling atomic force microscopy. All three methods have confirmed the local hydrogenation of graphene.
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