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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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Image Super-Resolution Using Deep Learning
Mojžiš, Tomáš ; Beran, Vítězslav (referee) ; Španěl, Michal (advisor)
The aim of this thesis is to create a deep neural net capable of super-resolution on images acquired by electron microscopes. The thesis consists of two parts - finding appropriate data and creating a dataset for the super-resolution task and designing a neural net architecture capable of solving the super-resolution task. Within the thesis, two datasets comprised of images acquired by electron microscopes were created. The datasets differ in the approach to data augmentation. They allow to train a neural network which fulfills the super-resolution task. To solve this task, two U-Net based and one GAN based architecture were trained. The resolution of images was upscaled by a factor of two and four. The best artificially upscaled images were created by neural network Real-ESRGAN. The values of metrics were not higher than the tested interpolation method, but the images seem more visually pleasing especially when they were upscaled four times. Thanks to this thesis, two datasets were created allowing to train other possible neural network architectures to improve the quality of the artificially upscaled images. The neural networks trained in this thesis can be utilized in the process of acquiring higher quality data from low resolution electron microscope images.
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Characterization of cheese analogues produced with addition of nut oil
Mitra, Michal ; Diviš, Pavel (referee) ; Vítová, Eva (advisor)
This thesis deals with the production and characterization of cheese analogues, i.e. products where some of the dairy components are partially or completely replaced by a non-dairy component. Model samples – Eidam type cheese and analogue with the addition of pistachio oil, were produced by a conventional technological process at MENDELU in Brno. Free and bound fatty acids, volatile substances and sensory quality were selected and monitored as the main characterizing parameters of the sample quality. The aim was to characterize the differences between the samples caused by the addition of nut oil in the monitored parameters. The HS-SPME-GC-MS method was used for the identification and semi-quantification of volatiles. The extraction of fats from the samples was performed with a mixture of solvents (diethyl ether, petroleum ether), fatty acids were converted to methyl esters by acid esterification with methanolic solution of boron trifluoride as a catalyst and subsequently identified and quantified by GC-FID. Descriptive scales and comparisons with standard were used to sensory evaluate the appearance, color, texture, odor, taste, and overall acceptability of the samples. The structure was monitored by electron microscopy. The results show that the addition of pistachio oil affects the sensory properties, the maturation process (higher content of volatile substances), the nutritional value (increased content of unsaturated fatty acids) and the stability of the product.
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Analysis of the gas flow when pumping vacuum for newly designed scintillation detector
Poruban, Milan ; Vaculík, Sebastian (referee) ; Maxa, Jiří (advisor)
The aim of this thesis is to study the issue of eniveromental scanning electron microscopy and pumping gas to create vacuum in the newly designed scintillation detector. Further, creating a model of recently proposed scintillation detector and simulating and analyzing pumping gas in differentially pumped chamber of detector. The theoretical part deals with electron microscopy, electron sources, electron optics and secondary electrons detectors. It is also presented which signals are generated by the electron beam on the surface of a solid. Further fluid flow issues and equations describing the flow in the solved chamber are dismantled. Furthermore, the impact of gaseous environment on the trajectory of primary electrons, because there are collisions of primary beam with atoms and molecules of gas. The following section discusses creating, quality and importance of the network in mathematical modelling. A method of a final volume used to calculate the differential equations describing the flow of gas at the premises of the detector is described . The practical part consists in creating a model of scintillation detector and analyzing the gas flow in drawing a vacuum in the newly designed scintillation detector. At the end the simulation results of gas flow are compared for different variants of apertures and various pressures on the neck of a scintillation detector designed for optimum performance of the detector. The outcome of this thesis is model of newly designed scintillation detector with optimized shapes of apertures according to functional requirements.
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Evaluation of gas flow in the scintillation detector at different profiles and sizes of holes in the screens that have shaped the network
Truhlář, Michal ; Špinka, Jiří (referee) ; Maxa, Jiří (advisor)
This work deals with the flow of gas in the scintillation detector. Thesis describes the function of an electron microscope, the composition, distribution and development of microscopes from the earliest to modern. The work also includes familiarization with SolidWorks 3D modeling in which is the electron microscope modeled and Cosmos FloWorks in which they are carried out simulations of gas flow. The paper is focused on the flow of gas in various shapes of the screen and various pressures in chamber of specimen. The results of the analysis of both apertures variants are compared with the request to minimize the pressures in the trajectory of the secondary electrons of well as in the chamber of specimen.
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Complementary analysis of procaryotic cells by electron microscopy and Raman spectroscopy
Ikrényiová, Terézia ; Sedláček, Petr (referee) ; Hrubanová, Kamila (advisor)
This master thesis deals with conventional methods of bacterial cell analysis, polyhydroxyalkanoates, Raman spectroscopy and electron microscopy in the theoretical part. The production of polyhydroxybutyrate by selected thermophilic bacteria and their analysis by gas chromatography, cryogenic scanning electron microscopy and Raman spectroscopy is described in the experimental part. The chosen sample was analyzed by a transmission electron microscope. Comparing the results from previous mentioned methods it was found that the bacteria Schlegelella thermodepolymerans accumulated the highest amount of PHB. The lowest amount of PHB was obtained by bacteria Rubrobacter xylanophilus. The assumption that the PHB granules formed so-called needle-like plastic deformations during freeze-fracturing was affirmed by cryo-SEM photos analysis. Moreover, it was found that the bacterial cell characterization deduced from microscopic observation of samples corresponded to the description in the literature. TEM provided better resolution photos and in consequence the cells and PHB are more visible. The thesis is also focused on chemical fingerprint analysis of cells by Raman spectroscopy. Several biomolecules were identified by measured Raman spectra for the particular samples.
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