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Characterization of surface and mechanical properties of microbial cells
Khýrová, Markéta ; Lukeš,, Jaroslav (referee) ; Plichta, Tomáš (advisor)
The subject of this diploma thesis is the characterization of bacterial strains capable of polyhydroxyalkanoates (PHA) production in terms of morphology and mechanical properties. With this aim, an atomic force microscope (AFM) was used together with a nanoindentation instrument to perform microcompression tests on selected microorganisms. The model bacterial strains, Cupriavidus necator and Rhodospirillum rubrum, were tested in their PHA-producing form and in their mutant non-producing variant, in order to study the effect of PHA amount on bacterial morphology and mechanical properties. In the experimental part of this work, the preparation of native bacterial samples for both techniques were first optimised. Glass substrates were treated with plasma and the cells were subsequently fixed with poly-L-lysine. In addition, sample preparation including fluorescent staining was optimized for the microcompression tests in order to easily detect cells and determine their size. Finally, the impact of different measurement parameters and mathematical models for calculating Young's modulus on the AFM data were evaluated. The results revealed the effect of PHA on bacterial cell morphology and showed that PHA producers exhibit higher Young´s modulus on average compared to their mutant. It was also shown experimentally that microcompression tests provide significantly higher Young's modulus values than those obtained by AFM.
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Controlled modification of tips usable for selected measurement modes of atomic force microscopy
Lišková, Kateřina ; Szabová, Jana (referee) ; Smilek, Jiří (advisor)
This master's thesis deals with the modification of tips commonly used in atomic force microscopy and their following utilization for determining the mechanical properties of selected hydrogel systems at the local level. For targeted modification, a method of micro-particle fixation on a cantilever was chosen, which was successfully modified using melamine resin particles. Initially, the mechanical properties of a selected representative of physically cross-linked hydrogels (agarose polysaccharide) were measured, which were evaluated based on the Young's modulus of elasticity, adhesive force, and work. The obtained results were compared with values measured using two commercially available cantilevers differing in both shape and basic parameters such as spring constant and resonance frequency. Subsequently, the influence of the setpoint force applied to the sample by the cantilever was verified. The usability of modified cantilevers was also tested on a selected representative of ionically cross-linked hydrogels (sodium alginate cross-linked with multivalent ions). Within the experimental part of the master's thesis, it was verified that the use of cantilevers with a higher contact area leads to more reliable results in terms of reliability and reproducibility, considering that the final value of the Young's modulus includes not only the contribution of the polymer chain but also the pores. When determining mechanical values, it is important to specify not only the cantilever used and its properties but also all other experimental parameters, the change of which may affect the final values of the Young's modulus determined at the micro level by atomic force microscopy.
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Preparation and characterization of nanostructured III-V semiconductor materials
Maniš, Jaroslav ; Kostelník,, Petr (referee) ; Hospodková,, Alice (referee) ; Šikola, Tomáš (advisor)
Předkládaná dizertační práce se zabývá výrobou a analýzou gallium nitridových (GaN) nanostruktur ve třech odlišných formách. V prvním případě byl zkoumám trojdimenzionální GaN ve formě nanokrystalů rostených na grafenu. Nanokrystaly byly připraveny s využitím techniky droplet epitaxy, která mimo jiné umožňuje růst nanostruktur za nízké teploty substrátu (T = 200°C). Studium se zaměřovalo jak na charakterizaci kvality připravených nanokrystalů, tak na statistický popis růstu. V dalším kroku byly připravené struktury využity pro výrobu fotodektoru citlivého na ultrafialové světlo. Výroba fotodektoru a jeho úspěšné použití slouží jako základ pro navazující výzkum. Ve druhém případě byly studovány dvoudimenzionální GaN nanostruktury, které byly rovněž připraveny za nízké teploty křemíkového substrátu. Následná analýza se soustředila na popis krystalové struktury a prvkovou analýzu, neboť byly takovéto struktury pozorovány vůbec poprvé. Další rozvoj možností přípravy těchto nanostruktur je předmětem navazujícího výzkumu. Ve třetím případě byly zkoumány jednodimenzionální GaN nanodráty připravené na safírovém substrátu. Účelem tohoto projektu bylo získání datasetu pro ověření teoretického modelu, který popisuje růst horizontálních nanodrátů. Na základě sběru a analýzy dat se podařilo modelovat růstovou dynamiku GaN nanodrátů, která byly v souladu s teoretickým modelem.
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Utilization of various methods of porosimetry in investigation of internal structure of biopolymer hydrogels
Zahrádka, Jan ; Pekař, Miloslav (referee) ; Sedláček, Petr (advisor)
The main aim of the thesis was to select, optimize and test suitable methods for studying inner structure of hydrogel materials. The study of the size of pores with potential use in fundamental and applied research of these materials is the central focus of the thesis. Firstly, a literature search was done in order to collect basic information about usefulness of the individual methods. On the basis of this literature search, the experimental part of the work was divided into several steps. First, selected methods of conventional porosimetry (mercury intrusion porosimetry, BET analysis and DSC thermoporometry) were applied on reference porous materials and the results obtained by the individual methods were compared. The methods optimized with the use of these reference materials were then utilized in the analysis of porosity of model hydrogels based on polyvinyl alcohol. Based on the results of this analysis, the usability and benefits of the individual methods were discussed with respect to the sample preparation, time and financial demands, and also from the viewpoint of compliance of the determined pore sizes with the range of sizes declared for the physical PVA gels.
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The Use of AFM Measurement Method in Crystalline Silicon Solar Cells Technology
Mojrová, Barbora ; Boušek, Jaroslav (referee) ; Hégr, Ondřej (advisor)
This thesis deals with the use of Atomic Force Microscopy (AFM) and Kelvin Probe Force Microscopy (KPFM) in solar cells production. Both techniques measure surface properties using interactions between surface and tip that progressively scans entire surface of the sample. Atomic force microscopy allows three dimensional imaging of surface structure. Kelvin probe force microscopy is used to measure the contact potential difference on the sample surface. There are described experimental measurements of monocrystalline and multicrystalline substrates after various etching processes using AFM. By using KPFM the contact potential difference was measured on dielectric layers PSG, SiOX, SiNX and Al2O3 and on selective emitter structures. All experiments described in this work were carried out at the Solartec Ltd. workplace and they completely correspond with the actual technology of crystalline solar cells production.
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Atomic force microscopy of soft materials
Šudáková, Anna ; Havlíková, Martina (referee) ; Smilek, Jiří (advisor)
This bachelor thesis focuses on atomic force microscopy (AFM), mainly on studying the measurement procedure and optimalization of measurement conditions with future perspective on imaging hydrogels and measuring mechanical properties (such as adhesion or stiffness) of hydrogels and semi-rigid materials at the microlevel. Atomic force microscopy is gaining significant importance in research due to its versatility, when it can provide topographical image of conductive and non-conductive samples while measuring mechanical properties of the samples, such as adhesion, elasticity or stiffness. Advantage of AFM method is that it can provide mechanical properties of the samples not only on macro levels as we are used to, for example, from rheology, but also on local level. Optimalization was performed on standard sample, one micrometre polystyrene nanoparticles , when the individual modes were measured, such as non-contact (AC Mode Imaging) mode and quantitative mode (QITM Advanced Imaging). This was followed by the measurement of a PVA foils, the measurement was performed because they are xerogels and will be studied more in the future. They were made with polyvinyl alcohol and chitosan. The internal environment of the hydrogels has been modified by adjusting the pH (NaOH) or by changing the ionic strength (NaCl). Furthermore, the effect of freezing on the PVA foils was observed, it is one of the possible ways of preparation of physically linked hydrogels. This work also examines the effect of porosity on concentration of physically linked thermoreversible agarose gels.
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The utilization of atomic force microscopy for study on hydrogels
Lišková, Kateřina ; Kalina, Michal (referee) ; Smilek, Jiří (advisor)
The presented bachelor thesis deals with the study of atomic force microscopy (AFM), especially the optimization of the measuring procedure for imaging the surface of variously crosslinked hydrogels in the hydrated state. The most attention was given to the physically crosslinked polysaccharide hydrogel (termoreversible agarose) in hydrated state, where the surface of the samples with mass concentration of 4, 2, 1, 0,75 and 0,5 % was measured. Subsequently, the surface of the ionically crosslinked 2 % alginate gel with calcium ions was measured. Based on a literature research, measurements were performed in water using the method of quantitative imaging (QITM Advanced Imaging), which is especially suitable for soft samples with uneven surfaces. Multiple cantilever were tested for measurement, finally the SNL-10 cantilever was selected, which showed versatility for imaging samples in any measuring environment, especially aqueous. The pore sizes of the agarose hydrogels were monitored by image analysis ImageJ. For the measurement of hydrogels in the swollen state, the procedure of measuring their surface using atomic force microscopy has been optimized, but for different types of hydrogels, individual optimization of both preparation and instrument setup will be required.
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Utilzation of physico-chemical analyses in study on microbial stress-response
Slaninová, Eva ; Pekař, Miloslav (referee) ; Sedláček, Petr (advisor)
This diploma thesis deals with the utilization of physico-chemical analysis in study on microbial stress–response. The main content of this work was to propose and optimize techniques and methods which are generally used in different industries. Two bacterial strains, Cupriavidus necator H16 and its mutant strain Cupriavidus necator PHB-4 producing polyhydroxyalkanoates (PHA) under certain conditions, were used as model microorganisms. Initially, microscopic teques such as transmission electron microscopy (TEM), cryo scanning electron microscopy (cryo SEM) and atomic force microscopy (AFM) were proposed and tested for the characteriozation of morphological differences of bacteria. Furthermore, viscoelastic properties of bacteria were determined and compared by the oscillatory tests of the rheology method considering another type of samples. Thermal analysis methods, differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) in particular, focused on water transport and behavior of intracellular water influenced by presence of the granules of PHB in bacteria. The last technique, utilized in the study, was dynamic and electrophoretic light dispersion during pH changes for characterization of the surface properties of bacteria such as size, zeta potential and the isoelectric point.
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Adhesion characterization of thin plasma-polymer films
Pálesch, Erik ; Klapetek, Petr (referee) ; Čech, Vladimír (advisor)
The diploma thesis deals with characterization of adhesion of plasma polymer films deposited on silicon wafers. The samples included organosilicon thin films based on tetravinylsilane monomer prepared by plasma-enhanced chemical vapour deposition. Scratch test was used to characterize film adhesion employing nanoindentation measurements. Adhesion of plasma polymer films of different mechanical properties and film thickness was analyzed by normal and lateral forces, friction coefficient, and scratch images obtained by scanning probe microscope working in atomic force microscopy mode.
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Study of biological samples using atomic force microscopy
Khýrová, Markéta ; Smilek, Jiří (referee) ; Slaninová, Eva (advisor)
The purpose of this bachelor thesis was to study Gram-negative bacteria with the ability to accumulate polyhydroxyalkanoates using atomic force microscopy. During the experimental part were studied bacterial strains Cupriavidus necator H16 and its mutant strain Cupriavidus necator PHB-4, Rhodospirillum rubrum, and Halomonas halophila. The main aim was to optimise this microscopy method to study either bacteria in the air or bacteria in liquid medium under physiological conditions. The optimisation was done considering the procedure's simplicity, time demands, and reproducibility. 10× diluted bacterial suspense was dried on a glass surface for measurements in the air. Scanning was performed using TESPA-V2 tip with lowered Spring constant in QITM mode. Various procedures for immobilising bacteria on a glass substrate using Poly-L-lysine and Poly(ethyleneimine) were tested for measurements in liquid. The method using Poly-L-lysine was chosen as the most sufficient way of immobilisation. The tips MLCT – A or SNL – B with the spring constant around 0,1 N/m were applied for measurements in liquid using QITM mode. Finally, an attempt was made to obtain information about the adhesion and Young's modulus of dried and live bacteria concerning the high difference of polyhydroxybutyrate content between the bacterial strains Cupriavidus necator H16 and Cupriavidus necator PHB-4.
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