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Fabrication and study of epitaxial NiO thin films and their antiferromagnetic domain structure
Opršal, Jakub ; Caha, Ondřej (referee) ; Staňo, Michal (advisor)
Antiferomagnetické materiály získaly v posledních letech velkou pozornost díky svému uplatnění ve spintronice. NiO je dobře známý antiferomagnet a jeho Néelova teplota je nad pokojovou teplotou. Díky tomu je ideálním systémem pro studium antiferomagnetických domén. Pomocí reaktivního magnetronového naprašování jsme připravili tenké epitaxní vrstvy NiO na substrátech MgO (001) a safír (0001). Studovali jsme vliv jak substrátu tak depozičních parametrů na výslednou krystalovou a magnetickou strukturu. Použili jsme zobrazování pomocí magneto-optického dvojlomu, které slouží jako přístupnější alternativa k lineárnímu rentgenovému dichroismu pro pozorování T domén. Sestavili jsme laserovou soustavu a pomocí ní provedli experimenty zaměřené na optickou kontrolu antiferomagnetických domén.
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The Effect of Potassium Oxide K2O on the Purity of C3A
Jančíková, Andrea ; Ravaszová, Simona ; Dvořák, Karel ; Křištof, Michal
The article is devoted to the study of the preparation and stabilization of pure cubic phase of tricalcium aluminate C₃A. The findings from the literature and several experimental trials have been summarized. Based on these findings, the synthesis of C₃A was realized, and high purity of this mineral was achieved. Furthermore, the influence of foreign ions, mainly in the form of potassium oxide K₂O combined with Na₂O in the form of sodium oxide on the crystal structure was investigated. The transformation of the cubic phase of C₃A into an orthorhombic phase was observed when the amount of these ions in the structure was changed.
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Growth of metastable fcc Fe thin films on Cu/Si(100) substrates
Horký, Michal ; Cháb, Vladimír (referee) ; Urbánek, Michal (advisor)
This diploma thesis deals with the preparation of epitaxially grown metastable paramagnetic Fe films alloyed by Ni on Cu/Si(100) substrates at RT. Molecular beam epitaxy of Cu(100) buffer layer was performed on H-Si(100) native SiO2 free samples treated by etching in HF or thermal treatment. The epitaxially grown Cu layers with thickness ranging from 50 up to 130 nm serves as suitable substrate for the deposition of 44-ML-thick paramagnetic Fe78Ni22. The film growth was taking place in CO atmosphere and as well as Ni it led to paramagnetic film stabilization. The structural and magnetic ion-beam-induced transformation of desired Fe-Ni structure was performed and propeties of irradiated films were characterized afterwards by MOKE. Then some specific patterns on Si(100) by e-beam litography were fabricated and they served as suitable matrix for Cu(100) buffer layer and paramagnetic Fe. Prepared Si(100), globally and locally deposited metal films were examined by LEED, XPS, AFM, AES, SEM a STM. The recorded results showed the possibility of paramagnetic films preparation on H-Si(100) where it was possible to make ferromagnetic patterns on paramagnetic background by irradiation of specific ion dose.
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Study of organic molecular compound by x-ray radiation
Stejkora, Jakub ; Richtera, Lukáš (referee) ; Salyk, Ota (advisor)
Derivates of diketopyrrolopyrrole are coloured pigments with potential use in field of organic semiconductor structures. Their electrical attributes such as conductivity, photocon- ductivity and electroluminescence relate to their crystal structures, that determine charge transport path through the compound. The work deals with determination of these structures by using x-ray diffractometry. The diffractogram based on known crystalografic structure of diketo-dipyridyl-pyrrolo-pyrrole is modeled by available software and measured diffractogram is used for structure re-modeling. This method is used for other related derivates with unknown crystal structure.
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Novel Molecular Materials for Optics - Synthesis and Characterization of 5-aminotetrazole Salts
Pospíšil, Stanislav ; Zábranský, Martin (advisor) ; Tyrpekl, Václav (referee)
Title: Novel Molecular Materials for Optics - Synthesis and Characterization of 5-aminotetrazole Salts Author: Stanislav Pospíöil Department: Department of Inorganic Chemistry Supervisor: Mgr. Martin Zábransk˝, Ph.D., Department of Inorganic Chemistry Advisors: Prof. RNDr. Ivan N mec, Ph.D., RNDr. Irena Matulková, Ph.D., De- partment of Inorganic Chemistry Abstract: Nonlinear optics is currently an important field for the development of areas such as laser physics or telecommunications, and its understanding is essen- tial for development of new technologies. Its development can also be aided by the investigation of various crystalline materials, such as salts containing cations and anions derived from polarizable organic molecules, exhibiting essential properties for nonlinear optics. This bachelor thesis is focused on preparation of crystalline forms of these compounds. These are salts of simple, nitrogen-rich bases with 5- aminotetrazole. Bigunidium 5-aminotetrazolate, guanidinium 5-aminotetrazolate and aminoguanidium 5-aminotetrazolate were prepared and further characteri- zed. The structures of the latter salts were solved from X-ray di raction data. The methods of spectral vibrational analysis supplemented with nuclear magne- tic resonance and powder di raction were applied to these prepared compounds....
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Development of pharmacophore-guided molecular docking protocol for design of SARS-CoV-2 main protease inhibitors
Klenor, Mikuláš ; Lepšík, Martin (advisor) ; Riedlová, Kamila (referee)
Covid-19 is a highly contagious potentially life-threatening disease caused by the SARS-CoV-2 coronavirus. The virus is responsible for a global pandemic and has claimed over 6 million human lives between years 2020 and 2022. To limit the spread of SARS-CoV-2, numerous vaccines have been developed and applied. For already infected individuals, antiviral drugs are applied. An important validated target is the main protease of SARS-CoV-2 (Mpro ). Although thousands of inhibitors have been prepared and one is used in clinical practice (sold under the name of Paxlovid), improved computational protocols to design new active compounds are needed. The computational approach used here is based on pharmacophores. By curating and inspecting 298 structures of Mpro /inhibitors complexes retrieved from the Protein Data Bank (PDB), we have generated six distinct pharmacophores featuring different binding modes. With their aid, we have carried out molecular docking, whose effectiveness was evaluated by measuring root-mean-square deviation (RMSD) of the generated poses with respect to the native conformations. The routine captured 177 out of 213 ligands naturally binding to the active site of the protein with 127 (72% of the captured) generated with RMSD within 2 Å relative to the native conformation....
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Preparation and characterization of crystalline materials - salts of N-guanylglycinium and guanidinium
Skopalík, Jiří ; Matulková, Irena (advisor) ; Zákutná, Dominika (referee)
The scope of this bachelor thesis is the preparation and study of new salts, which can be obtained from systems N-guanylglycine - inorganic acid and guanidine - amidosulfuric acid, as new materials with potential for applications in nonlinear optics. Prepared crystalline salts of N-guanylglycinium - i.e. chloride, two hydrogenphosphites and sulfate dihydrate along with guanidinium amidosulfate were characterized by methods of vibrational spectroscopy (infrared and Raman) and X-ray diffraction (single crystal and powder methods). To estimate the nonlinear optical properties and for the interpretation of the vibrational manifestations of N-guanylglycinium cation, quantum-chemical calculations were performed. Finally, for two non-centrosymmetric N-guanylglycinium hydrogenphosphites, the efficiency of second harmonic generation was determined for powder samples.
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Molecular Crystals for Nonlinear Optics - Salts of Nitrogen-containing Bases with Selenious Acid and Hypophosphorous Acid
Němcová, Tereza ; Matulková, Irena (advisor) ; Tyrpekl, Václav (referee)
In this bachelor thesis, systems of selenious acid and hypophosphorous acid with six organic bases (2-aminopyrimidine, 3-amino-1,2,4-triazole, 4-amino-1,2,4-triazole, 3,5-diamino-1,2,4-triazole, 2-aminoguanidine and biguanide) were studied as the source of new materials for nonlinear optics. The six prepared crystalline compounds were identified and characterized by vibrational spectroscopy and X-ray diffraction. Unfortunately, all prepared salts contain a centre of symmetry in their structures, and therefore none of them are suitable for nonlinear optics especially the second harmonic generation.
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Parasite cystatins as inhibitors of cysteine proteases: structural aspects of functional specificity and their evolution
Buša, Michal ; Mareš, Michael (advisor) ; Hudeček, Jiří (referee) ; Kukačka, Zdeněk (referee)
Members of the cystatin family are important inhibitors of cathepsin-type cysteine proteases and are involved in a number of pathologies. Parasite cystatins are attractive target molecules for parasite control, but our knowledge about them is still limited. This work is focused on cystatins of two blood-feeding parasites: the common tick (Ixodes ricinus) as the main vector of Lyme disease and tick-borne encephalitis, and the liver fluke (Fasciola hepatica), the causative agent of fasciolosis. Four novel cystatins were functionally and structurally characterized to determine the structural determinants of their inhibitory specificity and describe them in the context of evolution and physiological role of cystatins. The cystatin FhCyLS-2 from F. hepatica has broad inhibitory specificity and is suggested to play a dual role in the regulation of proteolytic systems in host tissue and the parasite gut. FhCyLS-2 combines the characteristics of two cystatin subfamilies in a unique way and is a model representative of a novel evolutionary group of cystatins identified in several orders of parasitic flukes. Ricistatin and iristatin are salivary cystatins of I. ricinus with immunomodulatory effects on the host caused by an exceptionally narrow inhibitory specificity. It was explained by structural modifications of...
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Structure and Function of the C-terminal Domain of the HsdR Subunit from the Type I Restriction-Modification System EcoR124
GRINKEVICH, Pavel
The Type I restriction-modification enzyme EcoR124 is a pentameric complex consisting of one specificity subunit, two methylation subunits and two motor subunits (HsdR) that can recognize specific DNA sequences and perform double-stranded DNA cleavage and modification. The HsdR subunit is responsible for ATP-dependent DNA translocation and DNA cleavage. Even though the first crystal structure of HsdR was obtained ten years ago, a large part of the C-terminus has not been resolved in any HsdR structures to date. This dissertation aims to elucidate its role within the HsdR subunit and the whole pentameric complex by solving the structure of the C-terminus by means of X-ray diffraction crystallography and explore its function using biochemical, microbiological, bioinformatical and computational methods.
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