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Modelling of Pulse Propagation in Nonlinear Photonic Structures
Sterkhova, Anna ; Richter, Ivan (referee) ; Samek, Ota (referee) ; Petráček, Jiří (advisor)
V současnosti jsme svědky stále zvyšujících se nároku na rychlost přenosu a zpracování signálu a kapacitu pamet’ových zařízení. Proto se pozornost výzkumných pracovníku zaměřuje k plně optickým zařízením, která by mohla splnit zmíněné požadavky. Jednou z intenzívně zkoumaných možností je využití mikroprstencových optických rezonátoru. Při výzkumu je nutné využít numerických metod, které simulují šíření optického záření v dané struktuře. K tomuto účelu existuje celá rada metod, které se liší v efektivitě výpočtu, použitých aproximacích, i možnostech použití. Cílem této práce bylo vyvinout dvě jednoduché a praktické numerické metody pro modelování šíření pulzního záření v nelineárních vlnovodných strukturách. Přítom bylo požadováno, aby, na rozdíl od obecně známé a často využívané metody konečných diferencí v časové oblasti (FD-TD), bylo možné metody snadno aplikovat při studiu nelineárních struktur založených na mikroprstencových rezonátorech. Proto vyvinuté metody používají některé aproximace, zejména aproximaci pomalu proměnné obálky. Výhodou metod je vysoká rychlost a skromné požadavky na výpočetní zdroje. Obě metody vycházejí ze zkutečnosti, že naprostá většina nelineárních struktur založených na mikroprstencových rezonátorech se skládá ze dvou základních prvku: obyčejných vlnovodu a vlnovodných vazebních clenu. První metoda řeší vázané parciální diferenciální rovnice, které popisují šíření obálky pulzu ve struktuře. Přitom je použito tzv. „up-wind“ schéma vhodné pro parciální diferenciální rovnice popisující šíření vln. Druhá metoda vychází z první; rozdíl je v popisu vazby mezi dvěma vlnovody. Pokud se v první metodě uvažuje realistická vazba rozložená na určité délce, pak druhá metoda je založena na představě vazby nacházející se v jednom místě. Díky tomu je možné integrovat příslušné rovnice a dosáhnout výrazného urychlení výpočtu. Kvazianalytický charakter druhé metody umožňuje dále snadnou klasifikaci různých typu ustálených řešení. Vzhledem k těmto vlastnostem byla druhá metoda využita k výzkumu samovolné generace optických pulzu ve strukturách skládajících se z vázaných prstencových rezonátoru. Obě metody, které byly vyvinuty během této práce, představují rychlé a fyzikálně názorné alternativy k metodě FD-TD, a tak lze očekávat, že mohou hrát důležitou roli při výzkumu nelineárních vlnovodných struktur.
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Raman spectroscopy as a tool for analysis of microbial cells
Pokorný, Petr ; Enev, Vojtěch (referee) ; Samek, Ota (advisor)
This bachelor thesis is focused on the use of Raman spectroscopy for analysis of ectoine and hydroxyectoine presence in bacterial strain Halomonas elongata. Theoretical part compile characteristics of extremophiles with closer look on halophilic organisms and one of their main osmolytes, ectoines. Following by description of Raman spectroscopy method and its uses. Experimental part deals with cultivation of bacteria on different combinations of substrate and salt concentration in order to reach optimal production of PHA and for achieving the highest possible yield of biomass to be analysed by Raman spektroskopy. As the best substrate for PHA production turned out to be glukose along with salt concentration 30 g/l NaCl, where percentage representation of PHB makes 30,5229 %. As an ideal substrate for the highest yield of biomass proved to be sacharose. Bacteria that grew on sacharose with three different salt concentrations, 40, 70 and 100 g/l NaCl was measured along with Halomonas salina and Halomonas organivorans for comparison. Raman spectroscopy unfortunately turned out to be inadequate for measurement of this type of sample, thus we were not able to measure ectoine of hydroxyectoine presence in cells.
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Diagnostics of Ti:Sa laser pulses for plasma generation
Weiss, Jiří ; Samek, Ota (referee) ; Kaiser, Jozef (advisor)
This diploma thesis is focused on investigation of temporal characteristics of laser pulses generated by oscillator with Ti:Sapphire active laser medium. In terms of properties of laserinduced plasmas the beam quality is crucial, in particular laser pulse contrast ratio. A new prototype of third order autocorrelator was designed. Pulse contrast ratio measurement is based on sum frequency generation between pulse of fundamental wavelength and its frequency doubled replica. Dynamic range of presented autocorrelator is estimated to be up to 8×10^12 which is more than currently available commercial devices can offer.
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Production and characterization of biosurfactants
Kratochvílová, Olga ; Samek, Ota (referee) ; Obruča, Stanislav (advisor)
This diploma thesis deals with the microbial production of biosurfactants of selected bacterial strains. In order to test the biosurfactant production ability, screening methods were chosen to be able to review the potential of the selected strains to produce biosurfactants. With the scope of the work, 11 bacterial strains, which are used as polyhydroxyalkanoate (PHA) producers, have been tested. The ability to produce biosurfactants was tested in all strains both in complex inoculation and mineral production media. The presence of biosurfactants in Pseudomonas putida was detected on the basis of the results obtained after cultivation in inoculation and production media. The bacteria Pseudomonas fulva was put under more deep study to support their production by cultivation in different types of production media supplemented by different sources of carbon and nitrogen, and the effect of cultivation time was tested as well. Biosurfactants produced by these bacteria were subsequently identified by Fourier transform infrared spectroscopy (FTIR) on the basis of which the substances were identified as rhamnolipids. According to thin-layer chromatography result (TLC), Pseudomonas putida produces a mixture of mono- and dirhamnolipids, with monorhamnolipids being more dominant in our samples.
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Analytical methods for qualitative and quantitative determination of PHA in cyanobacteria
Černayová, Diana ; Samek, Ota (referee) ; Sedláček, Petr (advisor)
The diploma thesis is confused to verify the applicability of selected physicochemical and spectroscopic methods for characterization of cyanobacteria, with special emphasis on possibilities of qualitative and quantitative analysis of polyhydroxyalkanoates (specifically polyhydroxybutyrate (PHB)) accumulated in cyanobacterial cells. The sample basis of the work was formed by cultures of cyanobacterial strains of Synechocystis sp. PCC 6803 and Synechocystis salina CCALA 192. The cultures were were cultivated in several ways to cover the widest possible range of physiological conditions and PHB contents, in particular using an autotrophic way of cultivation on shakers and multicultural culture method in a basic culture medium,and in media enriched with 2% salt (NaCl ) as well as mixotrophic culture media with different types of the carbon substrate. After few weeks of cultivation, cyanobacterial cultures were obtained and complexly analyzed by following techniques- cell suspensions were analyzed by flow cytometry and UV-VIS spectrometry (transmission and diffusion transmission mode), dry cell biomass was characterised by gas chromatography to obtain a exact amount of PHB, and then FT-IR spectrometry and thermogravimetric analysis. The work aimed to assess whether any of these methods can be a quick and affordable alternative to the determination of PHB content to the most commonly used method of gas chromatography, but also to assess what additional information about the physiological state of cyanobacterial cells can provide test methods. The highest correlation on PHB content was determined for the parameters determined by infrared spectroscopy, in which specific peaks from the characteristic wavelengths for polyhydroxybutyrate were important. Weak correlations on PHB content were achieved in thermogravimetric analysis and cytometry, using the hydrophobic fluorescent probe BODIPY 439/503, which bound to lipophilic parts of cells. In addition to the determination of PHB, it was possible to determine pigments present in cyanobacteria (such as chlorophyll, phycocyanin and carotenoids) by flow cytometry and UV-VIS diffusion transmission spectrometry. In the end, results from all used techniques were compared by PCA analysis to determine the similarity of all analyzed samples.
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Raman spectroscopy of prokaryotic cells
Večeríková, Paula ; Bernatová,, Silvie (referee) ; Samek, Ota (advisor)
The presented bachelor‘s thesis deals with the Raman spectroscopy of bacterial cells. This method proves to be very suitable for monitoring the culture conditions of these bacterial strains because it is essentially non-destructive and fast compared to gas chromatography. Due to it‘s non-destructive nature, it is possible to further cultivate the measured cells. This analytical method can also be used to sort and select individual cells with increased ability to produce PHB. This would enable the possibility to select the generation of so-called PHB superproducers. Polyhydroxybutyrate (PHB) belongs to the group of polyhydroxyalkanoates (PHA), which serve as a substitute for plastics made in the petrochemical industry, whose consumption is increasing, especially during a pandemic. Current biodegradable substitutes are based on starch, which, in turn, depletes nutritional material for humans and animals. This bachelor thesis can serve as a basis outline for reducing the cost of PHB production, because Raman spectroscopy can be used in cell culture as a sensor of PHB content in response to a bacterial strain. In the experimental part of the work, the Raman spectra of selected bacteria were measured, where the result showed the greatest response to PHB in Chelatococcus shambunathi and the lowest in the thermophilic isolate BZ (Paenibacillus sp.). Quantitative information on the content of PHA in bacteria was obtained by gas chromatography, where the highest content was the bacteria- Chelatococcus shambunathi and the lowest Termobacillus composti. The subject of the second part was the separation of a mixture of PHA-producing and non-PHA-producing bacterial cultures. The result clearly proves that the mixture is separable based on the intensity of the selected sorting parameter.
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Modification of the focusing part of the table-top setup for Laser Induced Breakdown Spectroscopy (LIBS)
Borovský, Ján ; Prochazka, David (referee) ; Samek, Ota (advisor)
This bacheolor thesis solves functional modifications of the foccusing part of the table-top setup for laser induced breakdown spectroscopy LIBS. Main requirements for modified draft includes increasing view field of the navigation camera, increasing the setup’s aperture and prevention of the camera destruction by radiation of plasma. These requirements were fulfilled in new draft of optical stand including possible solution as enlarging focusing lens, new dielectric mirror and mechanical iris shutter. Some elements of proposed solution will be used in suggestion of Tescan company‘s new interaction chambers for LIBS analysis.
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Optical micromanipulation and Raman spectroscopy of cells in microfluidic systems
Klementová, Tereza ; Samek, Ota (referee) ; Mravec, Filip (advisor)
This diploma thesis deals with optimization of analysis process and measuring antibiotics induced changes in E. coli cells via Raman spectroscopy, LTRS and microfluidic systems. Optical micromanipulation by a laser beam allows noncontact and noninvasive manipulation of objects on scale 10^-5–10^-8 m, for example bacterial cells. Microfluidic device consists of microchannels and microchambers in transparent polymer and it is used for isolation, observation and cultivation of bacterial cells. Combination of these methods gives an effective tool for observation, manipulation and analysis of microorganisms. E. coli is a microorganism potentially pathogenic for humans and faster detection of its sensitivity to antibiotic treatment would make the whole process of diagnostics and treatment easier. We performed laser tweezer-Raman spectroscopy and conventional Raman spectroscopy of bacterial cells and cells under antibiotic stress and collected Raman spectra and characteristic areas were compared with literature to establish the reliability and usefulness of this method.
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Evolutionary engineering of cyanobacteria with respect to PHA accumulation
Vašířová, Kristýna ; Slaninová, Eva (referee) ; Samek, Ota (advisor)
The aim of this diploma thesis was to subject selected cyanobacterial strains to adaptive evolution and subsequently investigate the properties of the resulting adapted strains, especially their changes related to polyhydroxyalkanoates (PHA) accumulation. The theoretical part of the work describes in more detail the issue of cyanobacteria, PHA and their interconnection in the field of evolutionary engineering. Cyanobacterial strains Synechocystis sp 6803 and. Synechocystis salina CCALA 192 were used for evolutionary experiments. Selection pressures of hydrogen peroxide and copper. were applied to selected representatives. The resulting cultures and their ability to accumulate PHA were subsequently assessed by gas chromatography. Both of these selection pressures proved to be unsuitable, as strong growth inhibition was observed after their application to cultures, which did not allow the application of evolutionary engineering methods. In the second half of the experimental part, the provided adapted strains to 6% NaCl were monitored. Adaptation has been shown to have a positive effect on microorganisms, as they have a higher biomass content, better stress resistance and a slight increase in PHA accumulation.
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