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Generation of computer program for specific-heat analysis
Majer, Peter ; Ježek, Lukáš (referee) ; Javorský, Pavel (advisor)
This work is about to design and implement the speci c-heat analysis application. The application consists of two parts: the rst one provides for data manipulation, the second one plots a graph. The data manipulation part resembles a spreadsheet program - each column in a dataset stands for one measurement. Columns containing a temperature data could be used for a speci c-heat calculation. This calculation is based on this model functions: conduction electrons consideration, phonon contribution and Schottky contribution. It is also possible to arrange your own formulas by using basic mathematical operations (namely summation, substraction, multiplication and division). Fitting data to the selected model is also possible. Levenberg-Marquardt and simplex method are being used for it. Hamiltonian matrix used for energy levels calculations of magnetic ions in crystalline electric elds could also be calculated. The application is written in C# programming language.
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Study of conditions of crystallization and of thermodynamic properties of selected intermetallic compounds of lanthanides
Štěpánová, Karla ; Svoboda, Pavel (advisor) ; Javorský, Pavel (referee)
In this diploma work, I present the results of structural and thermodynamic studies of selected RNi4Si (R - La, Pr, Nd, Sm, Gd, Er, Ho, Dy) compounds. Contrary to its parent compound RNi5, these compounds do not crystallize in the hexagonal structure (CaCu5-type, space group P6/mmm). Instead of this, the orthorhombic structure with the space group Cmmm was found. The phase transition temperatures were determined from the zero-field specific heat measurement. Apart of PrNi4Si all compounds order ferromagnetically below the transition temperature. The phase transition temperature dependence of these compounds is in very good agreement with the de Gennes factor. Specific heat was analysed using a sum of the electronic, phonon and magnetic contribution. The significant magnetic contribution was fully described by the Schottky formula for n-level system. The magnetic entropy was calculated and is approaching the expected free ion entropy. Specific heat measurement of NdNi4Si compound showed structure transition at higher temperatures. Anisotropic properties cannot be studied on a polycrystalline sample and further studies must be carried out on the single-crystal. Trials to prepare single-crystals confirmed an incongruency of these samples. The mozaicity of measured samples is very high having the hexagonal...
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Linear semiflexible polyelectrolytes in solutions
Bačová, Petra ; Limpouchová, Zuzana (advisor) ; Lísal, Martin (referee)
Title: Linear semiflexible polyelectrolytes in solutions Author: Petra Bačová Department: Faculty of Science, Charles University in Prague Supervisor: Doc. Ing. Zuzana Limpouchová, CSc. Supervisor's e-mail address: zl@vivien.natur.cuni.cz Consultant: Mgr. Peter Košovan, PhD. Abstract: In this thesis I used the Molecular dynamics simulations for study of charged polymers (polyelectrolytes) and their behaviour in solutions. Wide range of polyelectrolytes are se- miflexible and in contrast to neutral polymers it is possible to influence their stiffness by changing the properties of solution as for example ionic strength. The chain flexibility may be characterized by the persistence length. Thesis explains how to express the persistence length from orientational correlation function which shows the double exponential decay. Two contributions to chain stiffness are discussed and the interest is concentrated around electrostatic persistence length which seems to be scale dependent. An effect of added salt on the chain conformation is studied. Salt is treated implicitly within the Debye-Hückel approximation. The results are confronted with OSF theory and the conclusions of vari- ational calculations of Maghi and Netz. The presented thesis describes the conformational behaviour of polyelectrolytes in salty solutions,...
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The Study of hydration models on platinum complexes important in anticancer cure
Bradáč, Ondřej
In this work, there are studied some biologically important platinum complexes, cisplatin analogues, with central platinum atom in state Pt(II), or Pt(IV). I concentrated on the hydration processes of the examined complexes. Thermodynamical and kinetical aspects of reactions were studied and NPA charge analyses were carried out, too. All computations were performed on DFT level with B3LYP functional. All reactions were considered in vacuum. Supermolecular approach was used for energy calculations.
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Raman optical activity and conformational flexibility of peptides in solution
Hrudíková, Jana ; Baumruk, Vladimír (advisor) ; Kapitán, Josef (referee)
Title: Raman optical activity and conformational flexibility of peptides in solution Author: Jana Hrudíková Department: Institute of Physics of Charles University Supervisor: Doc. RNDr. Vladimír Baumruk, DrSc. Supervisor's e-mail address: baumruk@karlov.mff.cuni.cz Abstract: Molecular flexibility can significantly modify Raman and ROA spectral intensities, band positions and the ROA signs. Taking into account dynamic aspects of behavior of studied molecules in solution via conformational averaging therefore seems to be crucial for spectral interpretation. The first of studied models, histidine, plays an important role in metallo-enzymatic reactions and peptide folding, due to its imidazole ring. ROA spectra of His at different pH, His complexed with Cu2+ and dipeptides His- Gly and Gly-His were recorded on the spectrometer built at the Institute of Physics of the Charles University as a first step of the subsequent study. The second studied system, a cyclic hexapeptide c-(Phe-D-Pro-Gly-Arg-Gly-Asp), serves as a convenient model for β- hairpin and anti-parallel β-sheet. It was previously studied by means of VCD and IR. From molecular dynamics simulations 10 peptide geometries were selected for spectral modeling. The Raman and ROA spectra were calculated ab initio. For a model fragment Phe-D-Pro, which...
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MD simulations of complexes between nucleic acids and RNase H
Bartek, Tomáš ; Burda, Jaroslav (referee) ; Barvík, Ivan (advisor)
The aim of this diploma thesis was to study interactions between human Rase H enzyme and a natural and modified substrate using molecular dynamics simulations (altogether 9 MD runs ere produced). Conformational preferences of internucleotide linkages (undergoing contacts with the RNase H enzyme) were studied using several versions of the AMBER force field. Either one or two copies of RNase H were included into the simulated system. As the most important DNA-binding residues were recognized Trp93 and Ser101 in the first DNA binding site and Thr49 and Arg47 in the second DNA binding site. Further, the AMBER force field was re-parameterized slightly using ab initio calculations to produce force constants for the modified phosphonate internucleotide linkage. Biologically active version of the modified internucleotide linkage C3-O3-P-C-O5-C5 was able to bind Arg47 using two hydrogen bonds within the 10 ns MD run (even more effciently than in the case of MD runs with natural internucleotide linkages). On the other hand, the biologically inactive C3-O3-C-P-O5-C5 internucleotide linkage lose contacts with Arg47 quickly.
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The Study of hydration models on platinum complexes important in anticancer cure
Bradáč, Ondřej ; Burda, Jaroslav (advisor) ; Záliš, Stanislav (referee)
In this work, there are studied some biologically important platinum complexes, cisplatin analogues, with central platinum atom in state Pt(II), or Pt(IV). I concentrated on the hydration processes of the examined complexes. Thermodynamical and kinetical aspects of reactions were studied and NPA charge analyses were carried out, too. All computations were performed on DFT level with B3LYP functional. All reactions were considered in vacuum. Supermolecular approach was used for energy calculations.
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Hydraulic calculation of sewage system in Lipůvka
Balas, Jan ; Raček, Jakub (referee) ; Hluštík, Petr (advisor)
Diploma thesis is focused on hydraulic assessment of Lipůvka´s sewer system, done by dynamic rainfall-runoff simulation model. Because of this fact, chapter about mathematical models is included. Commonly used programs to this actions are listed as well. Next part of the thesis describes monitoring campaign, which was done in Lipůvka and results are used to calibrate the simulation model. Hydraulic assessment of sewer system by this calibrated model was done.
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Establishing Mutual Links among Brain Structures
Klimeš, Petr ; Hlinka,, Jaroslav (referee) ; Krajča,, Vladimír (referee) ; Halámek, Josef (advisor)
The Human brain consists of mutually connected neuronal populations that build anatomically and functionally separated structures. To understand human brain activity and connectivity, it is crucial to describe how these structures are connected and how information is spread. Commonly used methods often work with data from scalp EEG, with a limited number of contacts, and are incapable of observing dynamic changes during cognitive processes or different behavioural states. In addition, connectivity studies almost never analyse pathological parts of the brain, which can have a crucial impact on pathology research and treatment. The aim of this work is connectivity analysis and its evolution in time during cognitive tasks using data from intracranial EEG. Physiological processes in cognitive stimulation and the local connectivity of pathology in the epileptic brain during wake and sleep were analysed. The results provide new insight into human brain physiology research. This was achieved by an innovative approach which combines connectivity methods with EEG spectral power calculation. The second part of this work focuses on seizure onset zone (SOZ) connectivity in the epileptic brain. The results describe the functional isolation of the SOZ from the surrounding tissue, which may contribute to clinical research and epilepsy treatment.
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