|
|
Design of optomechanical module for chemical mapping using Laser-Induced Breakdown Spectroscopy
Švábíková, Anna ; Samek, Ota (referee) ; Pořízka, Pavel (advisor)
Tato diplomová práce se zabývá návrhem optomechanického modulu pro chemické mapování metodou spektroskopie laserem buzeného plazmatu (LIBS). Cílem je vyvinout modul, který bude umožňovat analýzu spektrálních čar zinku v ultrafialové (UV) oblasti. V práci jsou popsány teoretické základy metody LIBS a následně je provedena rešerše zaměřená na problematiku dálkové LIBS analýzy. V diplomové práci jsou prezentovány možné optické návrhy fokusační a sběrné optiky, z nichž jsou vybrané následně otestovány. Výsledkem práce je konstrukční návrh modulu.
|
|
|
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.
|
|
|
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.
|
|
|
Raman microspectroscopy of living cells and biological tissues
Moudříková, Šárka ; Mojzeš, Peter (advisor) ; Matthäus, Christian (referee) ; Samek, Ota (referee)
Title: Raman microspectroscopy of living cells and biological tissues Author: Šárka Moudříková Department / Institute: Institute of Physics of Charles University Supervisor of the doctoral thesis: doc. RNDr. Peter Mojzeš, CSc., Institute of Physics of Charles University Abstract: Raman microscopy combines Raman spectroscopy with optical confocal microscopy and thus provides information on chemical composition of a sample with a µm3 resolution. In this thesis, Raman microscopy has been used to study microalgae-unicellular photosynthetic organisms that are greatly relevant for the Earth's environment as well as for biotechnological applications. Raman microscopy of photosynthetic organisms struggles with a highly intensive background of the spectra, which is formed by fluorescence of cellular photosynthetic apparatus. In this thesis, we have developed a fast and reliable photobleaching method that suppresses the unwanted background; this method has enabled us to study intracellular distribution of algal biomolecules such as proteins, starch, lipids and polyphosphate. We have investigated an evolution of these structures during a cell cycle of a model microalga Desmodesmus quadricauda. Next, we have developed a method for quantitative analysis of polyphosphate in a cellular culture of a microalga Chlorella...
|
|
| |
|
|
Structure investigation of hydrogels using a cryo-SEM
Adámková, Kateřina ; Hrubanová, Kamila ; Samek, Ota ; Trudičová, M. ; Sedláček, P. ; Krzyžánek, Vladislav
Hydrogels can be characterized as elastic hydrophilic polymer chains connected in network\nwhich are able to swell notably when exposed to aqueous media by absorbing considerable\namounts of water. Besides being a constituent of living organisms, nowadays, there are\nvarious fields hydrated polymers (e.g. polyvinyl alcohol, collagen, and starch) can be utilized\n– in both biological and non-biological form. Classic examples of such applications are\nhuman health and cosmetics (contact lenses, wound healing dressings and artificial\nreplacement tissues – skin, arterial grafts, cornea and spinal disc replacement), pharmacy\n(drug delivery systems), bioengineering, food industry, agriculture etc. Also, hydrogels\ncan reversibly change their shape when being exposed to a temperature change.
|
|
|
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.
|
|
|
Principal component analysis of Raman spectroscopy data for determination of biofilm forming bacteria and yeasts
Šiler, Martin ; Samek, Ota ; Bernatová, Silvie ; Mlynariková, K. ; Ježek, Jan ; Šerý, Mojmír ; Krzyžánek, Vladislav ; Hrubanová, Kamila ; Holá, M. ; Růžička, F. ; Zemánek, Pavel
Many microorganisms (e.g., bacteria, yeast, and algae) are known to form a multi-layered structure composed of cells and extracellular matrix on various types of surfaces. Such a formation is known as the biofilm. Special attention is now paid to bacterial biofilms that are formed on the surface of medical implants, surgical fixations, and artificial tissue/vascular\nreplacements. Cells contained within such a biofilm are well protected against antibiotics and phagocytosis and, thus, effectively resist antimicrobial attack.\nA method for in vitro identification of individual bacterial cells as well as yeast colonies is presented. Figure 1 shows an an example of the biofilm formed by Staphylococcus epidermidis bacteria and Candida parapsilosis yeasts known for forming biofilms. The\npresented method is based on analysis of spectral “Raman fingerprints” obtained from the single cell or whole colony, see figure 2(top). Here, Raman spectra might be taken from the biofilm-forming cells without the influence of an extracellular matrix or directly form the bacterial/yeast colony.
|
|
|
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.
|
|
|
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.
|
guest ::
