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Bonding and non-bonding interaction potentials for simulations of coarse-grained protein models
Pavlíková, Markéta ; Nová, Lucie (advisor) ; Bačová, Petra (referee)
Protein folding involves the transformation of an amino acid chain to a unique 3D structure. The conformation of a protein is determined by its amino acid sequence. Understanding the process of protein folding and dynamics is crucial since protein function is closely related to its structure and dynamics. These processes can be investigated by means of molecular simulations. Coarse- grained models, which are used in molecular simulations, provide a favorable trade-off between computational efficiency and accuracy. To employ such mod- els, a reasonable force field is necessary. The force field includes both bonding and non-bonding interaction potentials, which are derived either from atomistic simulations or from known, experimentally determined protein structures. We derived such potentials using dataset of more than 4,500 structures from PDB database. 1
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Computer Simulation Methods of Soft Matter
Kazakov, Aleksandr ; Uhlík, Filip (advisor) ; Bačová, Petra (referee) ; Jirsák, Jan (referee)
iii CHARLES UNIVERSITY Faculty of Science Department of Physical and Macromolecular Chemistry Doctoral Thesis Computer Simulation Methods of Soft Matter by MS. Aleksandr D. KAZAKOV Abstract This thesis is dedicated to the theoretical study of hydrogels under different con- ditions, and implementing new simulation approaches: for polymer- and carbon- based systems. The hydrogel was modeled with presence of multivalent ions at good solvent conditions and with presence of monovalent ions at different salt concentrations and different pH pK values at poor solvent conditions. The competition between elec- trostatic repulsion with short-range hydrophobic interactions in case of pH-respon- sive polyelectrolyte lead to first-order transition in the system. The study has shown how to utilize and to tune the transition with respect to parameters. A novel hybrid MC-SCF method was implemented, which combines a mean- field representation by the machinery of Scheutjens - Fleer self-consistent field and a coarse-grained model driven by the Monte Carlo method. The study provides a comparison of the novel method with pure coarse-grained and mean-field methods. The family of fullerenes with an even number of carbon atoms n = 20-80 was calculated using the DFT method and subsequently trained using a convolutional neural network...
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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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Facebook and the elections. The analysis of a self-presentation of the Czech political parties before the elections to the Chamber of Deputies of the Parliament of the Czech Republic in 2010
Báčová, Petra ; Marcelli, Miroslav (advisor) ; Nováková, Martina (referee)
The elections to the Chamber of Deputies of the Parliament of the Czech Republic on 28th and 29th May 2010 was called Facebook elections. The reason for such title was the scale of usage of Facebook by the political parties for their campaigns. The thesis Facebook and the elections. The analysis of a self-presentation of the Czech political parties before the elections to the Chamber of Deputies of the Parliament of the Czech Republic in 2010 focuses on a semiotic analysis of Facebook accounts of some political parties and their chairmen. During the monitored period Facebook presentations were presented by the Civic Democratic Party, the Czech Social Democratic Party, TOP 09, the Public Affairs party, Christian Democratic Union - Czechoslovak People's Party and the Greens. The Communist Party of Bohemia and Moravia was not officially registered on Facebook. We also analyzed Facebook pages of Mirek Topolanek (ODS), Petr Necas (ODS), Jiri Paroubek (CSSD), Karel Schwarzenberg (TOP 09), Radek John (VV), Cyril Svoboda (KDU-CSL) and Ondrej Liska (SZ). We call Facebook a viral social network. We analyzed it as a cyberspace with an ambivalent structure which influences the mean of a communication process before elections. Rhizomatic map of Facebook is comparable with a topology of a virtual cafe. We also...
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Dieudonné as an example of new antisemitism in France
Bačová, Petra ; Matějka, Ondřej (advisor) ; Tomalová, Eliška (referee)
This bachelor thesis is aimed at specific character of the new anti-Semitism in France and concrete elements that differ the new wave from the old one. This topic is very up to date in today's France because of significant increase of anti-Semitic crimes and growing numbres of jews emigrating to Israel. Three main differences which I explore in my thesis are : connection between new anti-Semitism and moslim immigrants, overlapping anti-Semitism with anti-Zionism and shift of anti-Semitism on the political spetrum. Second part of my thesis is study of artistic production of Dieudonné M'bala M'bala, french entertainer known for his controversial statements. In his political and artistic career I am trying to find aspects of new anti-Semitism mentioned in the first part.
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Facebook and the elections. The analysis of a self-presentation of the Czech political parties before the elections to the Chamber of Deputies of the Parliament of the Czech Republic in 2010
Báčová, Petra ; Marcelli, Miroslav (advisor) ; Nováková, Martina (referee)
The elections to the Chamber of Deputies of the Parliament of the Czech Republic on 28th and 29th May 2010 was called Facebook elections. The reason for such title was the scale of usage of Facebook by the political parties for their campaigns. The thesis Facebook and the elections. The analysis of a self-presentation of the Czech political parties before the elections to the Chamber of Deputies of the Parliament of the Czech Republic in 2010 focuses on a semiotic analysis of Facebook accounts of some political parties and their chairmen. During the monitored period Facebook presentations were presented by the Civic Democratic Party, the Czech Social Democratic Party, TOP 09, the Public Affairs party, Christian Democratic Union - Czechoslovak People's Party and the Greens. The Communist Party of Bohemia and Moravia was not officially registered on Facebook. We also analyzed Facebook pages of Mirek Topolanek (ODS), Petr Necas (ODS), Jiri Paroubek (CSSD), Karel Schwarzenberg (TOP 09), Radek John (VV), Cyril Svoboda (KDU-CSL) and Ondrej Liska (SZ). We call Facebook a viral social network. We analyzed it as a cyberspace with an ambivalent structure which influences the mean of a communication process before elections. Rhizomatic map of Facebook is comparable with a topology of a virtual cafe. We also...
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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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