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Design of a measurement circuit for electrochemical cells cycling in SEM chamber
Tran, Quoc Bao ; Trochta, David (referee) ; Klvač, Ondřej (advisor)
This diploma thesis deals with the design of a measurement circuit consisting of two separate modules for measuring electric current in the order of nanoamperes (nA) for the in-situ analysis of lithium-ion cells in microscopic dimensions. The aim of this thesis is to build a prototype measurement circuit to solve the electromagnetic interference (EMI) problems associated with in-situ analysis and to perform subsequent testing of this circuit or modules. The diploma thesis is divided into two parts, namely a theoretical and an experimental part. In the theoretical part, research on electrochemical cells is described, where the focus is directed towards lithium-ion cells. The principle of the function of these cells is described and research on their degradation mechanisms has also been carried out. Furthermore, the testing methods of lithium-ion cells such as GCPL, OCV and CV have been described. In the theoretical part, the in-situ experiments already performed at Thermo Fisher Scientific Brno are described. One experiment consisted of assembling an electrochemical cell on a MEMS chip and the other experiment was performed using a micromanipulator as a current collector. Measured data were affected by electromagnetic interference. The practical part discusses the design of a measurement circuit that would theoretically solve the problems of measuring very small currents from an EMI perspective. It also describes how the measurement circuit was tested.
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Utilization of advanced techniques of electron microscopy in altrastructural analysis of microbial cells and microbial biotechnology products
Havlíčková, Anna ; Sedláček, Petr (referee) ; Krzyžánek,, Vladislav (advisor)
In the theoretical part, this thesis deals with direct and indirect mechanisms of plant growth-promoting rhizobacteria, which is followed by a section on the selected model organism Azotobacter vinelandii. The second part of the theoretical section deals with electron microscopy starting with the possible interactions of the electron beam with the sample, through types of electron microscopes to various methods of preparing biological samples. The experimental part discusses the cultivation of selected bacterial cultures, the gelation of the cell cultures using chosen cross-linking agents (calcium chloride, malic acid, glucono--lactone with calcium carbonate) and, above all, various methods of preparation and analysis of pure and encapsulated cultures by the means of electron microscopy. In particular, cryogenic scanning electron microscopy and scanning transmission electron microscopy imaging were selected. Using both techniques, poly-3-hydroxybutyrate granules, which were confirmed to be elastic even at cryogenic temperatures, were observed inside the bacteria. Furthermore, it was found that cross-linking of extracellular alginate occurs even in samples without the addition of cross-linking agents. However, the hydrogel network present in these samples was significantly thinner than in samples with the addition of all cross-linking agents used. In this work, the density of the hydrogel network cross-linked with glucono--lactone was also compared. When using this agent with the addition of calcium carbonate, a significantly denser hydrogel network was observed in comparison with using the agent alone. Last but not least, when comparing the obtained results with the literature, it was found that the A. vinelandii bacteria form capsules, during the formation of the capsules the shape of the cells changes from an oval to a spherical bacterium and also the size of the given cell is reduced. From the resulting images, it was found that these capsules are made up of two layers, to which literature refers as electron-transparent intine and electron-dense exine.
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Design of a nitrogen Dewar vessel for electron microscopes
Brauner, Tomáš ; Voňka,, Jakub (referee) ; Urban, Pavel (advisor)
Observation of biological samples in electron microscopes in a state closest to the native state requires reaching cryogenic temperatures, most often with the use of liquid nitrogen (LN2). For this purpose a Dewar vessel with cooled copper thumb for cooling the sample holder and anticontamination shield inside the vacuum chamber of the scanning electron microscope (SEM) and focused ion beam (FIB) source was designed. Characteristics of the designed LN2 Dewar vessel were validated by measuring executed on the real functional sample. The reached temperature at the tip of the thumb under estimated heat load 2 W was 90,8 K. Corresponding refilling interval of LN2 is about 11 h. Experimentally measured data correlate with theoretically calculated characteristics. The designed Dewar vessel with a cooled thumb fulfills the required properties specified in the thesis assignment with a margin.
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Regenerace smyslových orgánů u raků
KOR, Golara
The antennae are a crucial sensory organ in crayfish that plays vital roles in their survival, communication, and orientation within their environment. They are equipped with sensory hairs that enable crayfish to detect various stimuli. Crayfish possess the unique ability to regenerate their antennae. Hemocytes are specialized cells within crayfish and play a crucial role in their immune system and contribute to the process of regeneration. We applied cryo-scanning and Transmission electron microscopies to study sensory organ morphology and regeneration in crayfish. In Chapter 2, cryo-scanning electron microscopy was used to identify potential differences in antennal morphology in six different crayfish species including marbled crayfish Procambarus virginalis, Mexican dwarf crayfish Cambarellus patzcuarensis, red swamp crayfish Procambarus clarkii, signal crayfish Pacifastacus leniusculus, common yabby Cherax destructor, and spiny-cheek crayfish Faxonius limosus. We observed significant differences among the six crayfish species in the ratios of antenna length, segment length and width to carapace length, and the number of segments. Examination of ultrastructural features unveiled differences in the distribution patterns of sensory hairs along the antenna and the morphology of the antennal surface. The varying morphology of antennae among studied species possibly indicates an adaptation to the specific conditions of their respective habitats. Furthermore, the outcomes demonstrated that a combination of variations in both antennal morphological characteristics and biometric measurements could effectively help us to distinguish the different studied crayfish species. In Chapter 3, the ultrastructural behaviour of hemocytes during coagulation and phagocytosis in the initial phases of injury in marbled crayfish was explored using transmission electron microscopy. During the coagulation process, hemocytes experienced marked transformations in morphology. The cytoplasmic granules exhibited a change from electron-dense to electron-lucent forms with the progress of coagulation. The transformed granules containing amorphous, electron-lucent material were observed to combine and release their contents into the extracellular space as part of the coagulation process. Additionally, it was observed that the nucleus contents also play a role in the coagulation process. Furthermore, the amputation of the leg led to substantial muscle degeneration, and phagocytic hemocytes start to take up the necrotic tissues. Besides, we observed the digested remains from phagocytized necrotic tissues merged into granules and other cellular components, thereby enhancing the granularity of the hemocytes and altering their cellular morphology. However, it is essential to note that hemocyte degranulation during coagulation could potentially reduce their granularity. Since morphological features are critical for classifying hemocytes, these morphological changes during coagulation and phagocytosis must be considered significant factors. The degenerated material that stored inside phagocytic hemocytes may have application in immunological and regeneration processes. In Chapter 4, we employed transmission electron microscopy to explore the ultrastructural aspects of potential immune cell involvement in nerve regeneration within crayfish antennae post-amputation. The findings indicated that, during nerve regeneration, all three forms of hemocytes were present. However, the granules within semi-granulocytes and granulocytes mainly contributed to the generation of new organelles such as mitochondria, the Golgi apparatus, and nerve fibers in the regenerated nerves of crayfish antennae. We revealed the transformation of granules of hemocytes into diverse organelles during the process of nerve regeneration at the ultrastructural level. In conclusion, these granules function as compact repositories of adaptable materials carried by immune cells, capable of transformatio
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Precise Image Registration Used for Correction of Geometrical Image Distortion
Zemčíková, Petra ; Odstrčilík, Jan (referee) ; Mézl, Martin (advisor)
Cílem předkládané diplomové práce je pomocí lícování obrazů přesně popsat distorzní pole pro následné odstranění geometrické distorze. Snímky zkreslené geometrickou distorzí pochází z prozařovacího elektronového mikroskopu. První část práce se zabývá zejména teorií spojenou s elektronovou mikroskopií, vznikem geometrické distorze a samotnou obrazovou registrací s důrazem na intenzitní flexibilní metody lícování. Ve druhé části je pak představena vytvořená metoda pro modelování geometrické distorze a lícování obrazů postižených slabou geometrickou distorzí. Vyvinutá metoda je následně otestována na testovacích i reálných datech a srovnána s existujícími popsanými metodami pro obrazovou registraci (například open-source softwarem Elastix).
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Image composition
Smital, Petr ; Petyovský, Petr (referee) ; Richter, Miloslav (advisor)
This thesis deals with methods of improving the quality of image output of an electron microscope by composing consecutive frames. The thesis contains a brief description of an electron microscope and the problems that deteriorate its image quality, and three basic mathematical algorithms that can be used to remove them. These are the simple averaging method, the method of least squares and the method of vector space. For all of the methods, the thesis describes ways of their implementation, the possibilities of their use and their mutual comparison. This thesis also deals with the problem of so-called superresolution, i.e. exceeding the physical resolution of a sensor using the methods mentioned above, and the problem of electron beam centring.
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Analysis of the impact of the conic aperture placement in the supersonic flow in the differentially pumped chamber
Rous, Miroslav ; Bílek, Michal (referee) ; Maxa, Jiří (advisor)
The thesis is focused on the medium dynamics simulation in the environmental scanning electron microscope. Specifically, it researches (examines) the conical aperture location effect in the differential pumped chamber and the width of the pumping channel in this chamber. The theoretical part deals with the environmental scanning microscope generally and other tools used in this thesis, e.g. ANSYS Fluen software, fluid turbulence, medium free path of molecules and electrons scattering. In the practical part, the work is focused on data processing from the ANSYS Fluent program and on their evaluation.
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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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Parasitic aberrations of the hexapole corrector of spherical aberration - analysis and corrections
Sopoušek, Jan ; Lencová, Bohumila (referee) ; Radlička, Tomáš (advisor)
Jednou z možností korekce sférické vady v elektronové mikroskopii je hexapólový korektor. Ačkoliv samotný princip korekce je poměrně dobře v literatuře popsán, jen relativně málo je věnováno samotnému seřízení hexapólového korektoru, jež je stěžejní pro správnou funkčnost. Práce je věnována analytickému rozboru vad seřízení a jejich vlivu na rozlišení obrazu za použití metody eikonálu a aberačních integrálů. Je ukázáno, že nejdůležitější roli v parazitických aberací hrají výchylky a náklon hexapólů. V závěru je pak popsáno, jakým způsobem je třeba hexapólový korektor seřídit pro odstranění parazitických vad.
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Analysis of the shape of the intake ports of the current concept differentially pumped chamber
Bílek, Michal ; Vyroubal, Petr (referee) ; Maxa, Jiří (advisor)
This master´s thesis discusses the analysis of the shape of the intake ports of differentially pumped chamber for the current concept. The first part is an introduction to the microscopy issue, then it is focused on ESEM microscopes and it also includes a describtion of the Flow dynamics and a mathematical describtion. In the following chapters the software Solid Works, where the model of differentially pumped chamber is created, and the software Ansys Fluent, which is used for analysis, are described. The second part concerns the proposed concepts and the results of their simulations. At the end of the work the results are analyzed and evaluated.
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