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The modification of the graphene structures by low energy ions (E
Maniš, Jaroslav ; Čermák,, Jan (referee) ; Mach, Jindřich (advisor)
Diploma thesis deals with the influence of low energy ions on graphene structures. Graphene structures were modified by nitrogen and argon ions of energies lower than 100 eV. Modified structures were analysed by Raman spectroscopy and x-ray photoelectron spectroscopy. The influence of the dose of ions on quality of graphene were investigated as well. In addition, this diploma thesis includes the literature search which focuses on modification of graphene by charged particles.
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Fabrication of Nanostructures Using Focused Ion Beam
Bartoš, Radko ; Tomanec, Ondřej (referee) ; Kolíbal, Miroslav (advisor)
This bachelor´s thesis deals with the ion-beam milling. Focused ion beam instrument is presented, as well as possibilities of initial setup conditions, which finally result in different nanostuctures´ shapes. In the thesis the methodology of fabrication and analysis of the nanostructures is described. Ideal ion beam setup conditions were deduced so that the nanostructures are of requested shape.
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Developing biomolecular interactions models for molecular simulations: Critical evaluation of force field parametrizations
Tempra, Carmelo ; Jungwirth, Pavel (advisor) ; Vácha, Robert (referee) ; Vega de las Heras, Carlos (referee)
Force field molecular dynamics methods are nowadays commonly used to study molecular interactions in many scientific fields. The accuracy of force fields has been improving over the years, allowing for a meaningful physical description of molecular phenomena. However, force fields have limitations. In this dissertation, I explored some of these limitations resulting from the parametrization strategy of force fields and the extent to which non-classical behavior, such as nuclear quantum effects, can be incorporated into classical force field molecular dynamics. In the first part, I investigated to what extent nuclear quantum effects can be accounted for within a classical force field for water. This allowed us to model the differences between bulk light vs. heavy water. The developed model was then used to describe solvent isotope effects on biomolecules, such as amino acids, proteins, and biomembranes, and to seek an explanation why heavy water (unlike light water) tastes sweet. In the second part, I pointed out the drawbacks of using certain training datasets in comparison to others when optimizing a force field, using aqueous calcium chloride as an example. In the third part, I demonstrated the importance of using an accurate water model during the optimization of force fields for phospholipids to adequately capture...
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Application of Electronic Continuum Correction to Molecular Simulations of Nano/Bio Interfaces
BIRIUKOV, Denys
Nowadays it is almost impossible to imagine our life without nanotechnologies. They are present in smartphones and many other gadgets we use every day, while advanced nanoparticle-based devises are currently indispensable in medicine, engineering, and science. In the case of biomedical applications, the knowledge how a specific nanomaterial behaves and changes its properties in complex physiological medium is essential to guarantee the accomplishment of all specific goals facing a scientist or engineer. Some of physical and chemical processes occurring when a nanodevice enters biological environment are yet very difficult to fully detail without accurate computer simulations, so special attention needs to be focused on theoretical studies of nano-bio interactions. In this thesis, molecular simulations were used to investigate the interactions between different nanomaterials (titanium dioxide, silicon dioxide, and gold) and aqueous solutions, which contain ions, organic molecules, and amino acids. The importance of this scope and particularly selected for this study materials and compounds is given in Introduction. To model nano/bio interfaces, we adopted and integrated recent theoretical approaches, which together with basic principles of molecular simulations are described in Methods. Obtained results are divided in four parts and address several important issues that are vital in deciphering molecular mechanisms, through which nanoparticles identify and bind various biomolecules. The simulation data are thoroughly discussed, compared to experiments, and used to explain some of experimental observations. Additionally, outcomes of this thesis serve as a springboard for further theoretical studies aimed to advance our understanding of nano-bio interactions.
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High sensitivity analysis and detection of ions
Vanko, Erik ; Plašil, Radek (advisor) ; Dohnal, Petr (referee)
This paper investigates response of the MCP (MicroChannel Plate) detector and the counting efficiency of pulses produced by ions of different masses found in the used mass spectrum starting from 2 Da up to 30 Da. Tests were performed on an apparatus with a cryogenic 22- pole RF ion trap which is used to measure ion interactions. After the ions are released from the trap, they are detected by the MCP detector. Upon detection, the measured signal is processed by a discriminator which has a threshold of 10 mV. The consequence of the chosen discriminator threshold is a loss of pulses with an amplitude of less than 10 mV. From the measured data, we compared the relative losses of pulses for the chosen ions. At the same time we estimated the upper limit of the loss of pulses. The obtained results will be used to evaluate the measurements on the apparatus with the ion trap.
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Sputtering of dust grains and its consequences for space processes.
Vyšinka, Marek ; Šafránková, Jana (advisor) ; Stöckel, Jan (referee) ; Wild, Jan (referee)
Title: Sputtering of dust grains and its consequences for space processes Author: Marek Vyšinka Department: Department of Surface and Plasma Science Supervisor: prof. RNDr. Jana Šafránková, DrSc., Department of Surface and Plasma Science Abstract: A great part of matter in a space has a form of dust grains, tiny pieces of rocks with the dimensions of hundreds nanometers to hundreds micrometers. In this environment dust grains undergo collisions with energetic particles (electron, ions, UV photons) that leads to their charging and modification. The presented thesis studies ion-dust interactions and is focussed on dust grain modification through ion implantation and its destruction via sputtering process. Two compu- ter models are presented - first for computing the ion implantation profile in the grain and second, for the shape of the sputtered grain lying on the surface of a bigger object. The resulting shape of the grain is compared with that obtained experimentally. Important results of the thesis are measured sputtering yields for spherical SiO2 grains at several surface potentials obtained by simultaneous ion and electron bombardments. Keywords: ions, dust grains, sputtering, sputtering yield, implantation profile 1
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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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Modeling interactions of proteins with ions and membranes
Kadlec, Jan ; Jungwirth, Pavel (advisor) ; Kolafa, Jiří (referee)
The protein recoverin, localized in the eye in the rod outer segment of the retina, is a neuronal calcium sensor involved in vision adaptation. Recoverin reversibly associates with cellular membranes via its calcium-activated myristoyl switch. This reversible interaction is vastly dependent on the concentration of calcium ions in the cytosol and on conformation of recoverin. By using methods of molecular dynamics simulations and free energy calculations this work presents a detailed analysis of the energetics of myristoyl insertion into a lipid bilayer and interactions of non-myristoylated recoverin with the membrane. These results are in a perfect agreement with experimental data. The thesis provides a piece of puzzle to the so far unexplored mechanism of myristamide insertion into the membrane and also to recoverin conformational change. It gives an important insight into binding of recoverin to a membrane, which has a significant biological role.
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Sputtering of dust grains and its consequences for space processes.
Vyšinka, Marek ; Šafránková, Jana (advisor)
Title: Sputtering of dust grains and its consequences for space processes Author: Marek Vyšinka Department: Department of Surface and Plasma Science Supervisor: prof. RNDr. Jana Šafránková, DrSc., Department of Surface and Plasma Science Abstract: A great part of matter in a space has a form of dust grains, tiny pieces of rocks with the dimensions of hundreds nanometers to hundreds micrometers. In this environment dust grains undergo collisions with energetic particles (electron, ions, UV photons) that leads to their charging and modification. The presented thesis studies ion-dust interactions and is focussed on dust grain modification through ion implantation and its destruction via sputtering process. Two compu- ter models are presented - first for computing the ion implantation profile in the grain and second, for the shape of the sputtered grain lying on the surface of a bigger object. The resulting shape of the grain is compared with that obtained experimentally. Important results of the thesis are measured sputtering yields for spherical SiO2 grains at several surface potentials obtained by simultaneous ion and electron bombardments. Keywords: ions, dust grains, sputtering, sputtering yield, implantation profile 1
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