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Optical responses of biomolecules on regular metal plasmonic nanostructures
Šubr, Martin ; Procházka, Marek (advisor) ; Michl, Martin (referee) ; Valenta, Jan (referee)
Title: Optical Responses of Biomolecules on Regular Metal Plasmonic Nanostructures Author: Martin Šubr Department: Institute of Physics of Charles University Supervisor of the doctoral thesis: prof. RNDr. Marek Procházka, Dr., Institute of Physics of Charles University Abstract: Adsorption of molecules on metal plasmonic nanostructures leads to significant enhancement of many optical processes, such as Raman scattering (surface-enhanced Raman scattering - SERS) or fluorescence (surface-enhanced fluorescence - SEF). Two groups of substrates were tested within this thesis: (i) Silver nanorods prepared by oblique angle vapor deposition, and (ii) silver and gold nanoislands growing on magnetron-sputtered polytetrafluoroethylene film. Step-by- step optimization process was performed on the nanoislands in order to obtain optimum SERS sensitivity and reproducibility. Detailed SERS intensity profiles were obtained using gradient nanostructures with the localized surface plasmon resonance (LSPR) condition varying across the sample and three different excitation wavelengths. It was also found that spectral position and height of the LSPR band can be controlled simultaneously using mixed gold/silver nanoislands. Detailed investigation of polarization- and angular- dependences of anisotropic silver nanorods was...
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Dynamic light scattering in the world of biomolecules
Križanová, Katarína ; Hofbauerová, Kateřina (advisor) ; Bednárová, Lucie (referee)
Title: Dynamic light scattering in the world of biomolecules Author: Katarína Križanová Department: Institute of Physics of Charles University Supervisor: RNDr. Kateřina Hofbauerová, Ph.D., Institute of Physics of Charles University Abstract: Dynamic light scattering (DLS) represents a non-destructive method which can determine the hydrodynamic radius of particles in a sample by laser scattering. Consequently, their real sizes can be calculated or, in the case of proteins, molecular masses can be estimated. DLS is nowadays widely used for the study of biomolecules and their reactions, as is documented in the thesis in a brief review. Our experimental work was focused on the measurement of proteins by DLS - lysozyme was used as a model protein. The laboratory protocol for sample preparation and DLS measurement was successfully optimized. In the framework of methodology optimization, the ability of correct detection of small particles was tested using sucrose. We came to the lowest limit of particle dimensions measurable by DLS using sucrose. We were able to observe the linear dependence of the measured hydrodynamic radius on sucrose concentration in the solution and we were also able to determine the hydrodynamic radius of sucrose correctly, in agreement with literature. We practically demonstrated the...
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Molecular modeling of biomolecules - surface interactions
KROUTIL, Ondřej
Interactions between (bio)molecules, ions and solid surfaces play crucial role in many biological processes as well as in many scientific applications and understanding of this phenomenon on molecular level is a challenging task for today science. Computer simulations can provide detailed view on atomic level if carefully prepared and evaluated models are used. In this thesis, interactions of several types of (bio)molecules with inorganic surfaces are studied by classical and ab initio molecular dynamics. Chemisorbed biomolecules, namely DNA and oligopeptide, covalently attached to graphene and mercury surface, respectively, were studied to make link with DNA chip design and experimental label-free electrochemical measurements, respectively. Quartz (101) surface model applicable to wide range of pH conditions was developed and evaluated against experimental X-ray data. Physisorption of the nucleobases on quartz (101) surface and oxalate dianion on rutile (110) was examined and discussed.
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Designing and testing of new metal nanosubstrates for biomolecular sensors based on surface-enhanced Raman scattering (SERS) spectroscopy
Peksa, Vlastimil ; Procházka, Marek (advisor) ; Matějka, Pavel (referee) ; Richter, Ivan (referee)
Title: Designing and testing of new metal nanosubstrates for biomolecular sensors based on surface-enhanced Raman scattering (SERS) spectroscopy Author: Vlastimil Peksa Department: Institute of Physics of Charles University Supervisor: doc. RNDr. Marek Procházka, Ph.D., Institute of Physics of Charles University Abstract: This experimental methodical work was aimed at the optimization of selected gold and silver substrates and their use in construction of SERS-based biosensors, including following practical application. Several types of substrates, fabricated via a combination of bottom-up techniques on solid surfaces, were tested. The properties of these substrates were examined with probe molecules, namely methylene blue, porphyrins and tryptophan, on a confocal Raman microspectrometer. Obtained findings about the influence of analyte application, objective focusing and internal intensity standard were exploited for optimization of measurement procedures with regard to sensitivity, accuracy and reproducibility. A method for quantitative detection of food dye azorubine (E 122) in commercially available drinks was developed, based on these findings. Its results have shown its potential as a pre-scan method for field application and preliminary testing. Keywords: Metal nanosubstrates, biomolecules,...
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SERS spectroscopy of model biomolecules for SERS biosensing
Šubr, Martin ; Procházka, Marek (advisor) ; Michl, Martin (referee)
Title: SERS spectroscopy of model biomolecules for SERS biosensing Author: Martin Šubr Department: Institute of Physics of Charles University Supervisor: doc. RNDr. Marek Procházka, Dr., Institute of Physics of Charles University Abstract: The main requirement for surface enhanced Raman scattering (SERS)-based biomolecular sensing is high sensitivity and spectral reproducibility. For this purpose, ordered silver and gold nanostructures fabricated by magnetron sputtering and lithography methods at cooperating institutes were tested in this work. Reproducible SERS spectra of employed model biomolecules (amino acids, lysozyme and albumin) were obtained on ordered silver surfaces at concentrations 10-4 M - 10-6 M and as low as ≈ 10-7 M in the case of porphyrins. SERS spectra of certain biomolecules were also compared to spectra measured on silver colloid. The limit of detection provided by hydroxylamine-reduced silver colloid, using KCl as an aggregating agent, is substantially lower (on the order of 10-8 M for cysteine), but with lower spectral reproducibility. The main drawback of SERS spectra measured on silver surfaces was the occurrence of spurious bands resulting from the preparation procedure. In the case of sputter-deposited silver surfaces, it was found that keeping the substrates several hours in...
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The Study of Transient Species and Precursors of Biomolecules using Spectroscopic Techniques
Ferus, Martin ; Civiš, Svatopluk (advisor) ; Šponerová, Judit E. (referee) ; Wild, Jan (referee)
The presented thesis is focused on a spectroscopic study of unstable radicals, ions and molecules in a positive column glow discharge and laser plasma. The research of these fragments is supplemented by a study of biomolecules formation from these species and influence of catalysts. Molecular dynamics of radicals, ions and unstable molecules has been studied using a time resolved Fourier transform infrared spectroscopy. Time resolved spectra of CH4, HCONH2, BrCN, CH3CN, CF3Br, (CF3)2CHBr positive column glow discharges have been measured and simulated using a kinetic model including molecular dynamics, collisions and chemical and radiation transfer processes. The model has been compared with our experimental results and time resolved spectra were described in details. Fit to a complex reaction mechanism has been used to estimate a rate constant of a HCN conversion to HNC by a collision with H radical. The study of precursors of biomolecules was focused on chemical consequences of a laser induced dielectric breakdown in formamide vapor and gaseous carbon monooxide with 18 O labeled water. Dissociation products have been detected using the Fourier transform absorption spectroscopy. The experimental results have been explained by a help of a chemical laser spark dynamics model. Additionally, our the...
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Solvent Influence on Photochemistry of Small Biomolecules in Clusters
Profant, V. ; Dian, J. ; Fárník, Michal ; Poterya, Viktoriya
We present a photolysis study of pyrrole, imidazole and pyrazole clusters in comparison to the photolysis of the isolated molecules. Size distributions of different mean cluster sizes have been prepared and characterized in supersonic expansions. The clusters were photolyzed at 243 and 193 nm and the kinetic energy distributions (KEDs) of the H-fragments were measured. The KEDs of all systems exhibit a bimodal character with slow and fast H-fragment peaks similar to the spectra of the corresponding single molecules. However, with the increasing clusters size the slow component gains on intensity in comparison to the fast component. A similar effect is observed with increasing the excitation energy from 243 to 193 nm.
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