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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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Influence of aminoacid side-chain ionization on protein structure
Tomanová, Ema ; Nová, Lucie (advisor) ; Muzdalo, Anja (referee)
Protein folding is governed by many different types of interactions. Aside from the formation of hydrophobic cores and hydrogen bonding, Coulombic forces are believed to play an important role in this process. Their importance arises mainly in partially unfolded states and pH sensitive regions where ionization of amino acid side chains may trigger conformational changes. Better understanding of the role of ionizable residues in folding thereby provides us with new opportunities in protein design and property-enhancing protein modifications.
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Study of self-assembly and degree of ionization of block copolymers using transmission electron microscopy and molecular simulations
Illés, Peter ; Nová, Lucie (advisor) ; Štěpánek, Miroslav (referee)
Responsive systems, such as block copolymers with solvent-affine blocks, can undergo self-assembly into structures like micelles or vesicles. These assem- blies are highly sensitive to slight changes in external conditions, like pH or temperature, leading to the formation or dissolution of micelles. When one of the polymer blocks is a weak polyelectrolyte, its degree of ionization depends not only on the external conditions but also on the association state. This study focuses on investigating the size and degree of ionization of micellar struc- tures formed by polymer chains containing thermoresponsive and pH-responsive blocks. The investigation combines high-resolution transmission electron mi- croscopy and Hamiltonian Monte Carlo simulations to provide a comprehensive understanding of these micellar structures. 1
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Computer simulations of protein structures using coarse-grained models
Halda, Miloš ; Nová, Lucie (advisor) ; Limpouchová, Zuzana (referee)
The main part of this bachelor's thesis is an operational software for coarse- grained protein simulations, suitable for testing of new potential functions. The program is using a pivot-based proposal of new states and Monte Carlo evaluation of the proposed state. The program also allows to use a simulated annealing technique with the linear temperature decrease. Mean estimation and error estimation using the Block Method are implemented for evaluation of the simulations. The software was tested on a several proteins. The simulations provided expected results for shorter chains (88 and less aminoacids), but simulations of longer chains (111 and more aminoacids) have shown the software limitations. Several options for the software improvement regarding the new state proposal for simulations of longer chains were discussed. 1
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Legal, Tax and Accounting Factors of Employee Welfare
NOVÁ, Lucie
The goal of this bachelor thesis is to analyse the influence that legal, tax, and accounting factors have that impact the employee welfare in a company. Certain influences are evaluated on how much they affect the employers and/or employees. Employee welfare is divided into three categories in this thesis - mandatory, stipulated, and voluntary. The applied research mainly focuses on the category of voluntary employee welfare. Two types of questionaires and semi-structured interviews with selected employers were used for the applied research. For social and demographic aspects that indicate which benefits are preferred research was carried out with employees, while among employers the legal and tax factors were the main focus. As part of the research, a comparison of employee welfare in two different companies was also conducted. Even though the two selected companies were vastly different in size and industry-specialisation, the differences regarding employee welfare were minimal.
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Sušice, the Gate of Šumava Mountains. Development and Promotion of Tourism in the Region of Sušice in years 1918-1938
NOVÁ, Lucie
This thesis deals with the topic of development and promotion of tourism in the region of Sušice in years 1918 - 1938. It expands the field of research of the author´s bachelor thesis Activities of the Club of Czech Tourist in years 1890 - 1914. Firstly, three big building projects of the Club are observed: construction of Klostermann´s chalet in Modrava and chalet in Prášily, as well as the re-erection of Svatobor´s view tower. The following part focuses on the development of the possibilities of transport in the region: trains, regular and occasional tourist buses and cars. Marked tourist paths for walking are also considered. Later it´s examined whether the centre of the region - the town Sušice - conforms to the typical depiction of a summer resort. Main steps making the locality more attractive for tourists are explored. The changes in numbers of visitors in Sušice from the second half of 1920s are outlined. In the next part the author analyses the vacationers from the summer 1930 in social and vocational terms. The last part compares guidebooks and other promotional materials and based on them enquires, whether the presentation of town Sušice in the interwar period diverges from the end of the 19th century. The topic of nationalism is omnipresent in the whole thesis.
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The function and forms of the Chodsko's traditional costume in the past and present
Nová, Lucie ; Štěpánová, Irena (advisor) ; Krupková, Jaroslava (referee)
In this thesis, I described the evolution of the traditional clothing from the half of the 19th century until the 21st century. It was my concern to achieve a work of not only descriptive content, which I found so frequent. I sought also for the occasions for wearing the traditional costume, on what occasion, the way the traditional costume changes when the original materials changes. I looked for the reasons why and with what functionality it is still worn by people living today. Among the historical evolution, I put emphasis also on the recent form and function of the traditional clothing.
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Activities of the Club of Czech Tourist in Sušice in years 1890-1914
NOVÁ, Lucie
This thesis deals with the activities of the Klub českých turistů (Club of Czech Tourist) between the years 1890 and 1914. Using literature it recapitulates the problem of establishing the tourist association including legislative, culturally-historical and socio-economical perquisites. Following three main cores of the work are based on the primary sources research. The first is the socio-professional analysis of the member base. The others are two most prominent projects of the club; building of the view tower on the hill Svatobor and publishing of written tour guide Průvodce po Šumavě. At the same time the thesis concerns technical conditions of these projects as well as response to them and their impact on public. The last completing part puts these two big projects into context of other less prominent activities of the club and briefly compares quantity of work of Sušice´s section of Klub českých turistů to other sections.
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The function and forms of the Chodsko's traditional costume in the past and present
Nová, Lucie ; Krupková, Jaroslava (referee) ; Štěpánová, Irena (advisor)
In this thesis, I described the evolution of the traditional clothing from the half of the 19th century until the 21st century. It was my concern to achieve a work of not only descriptive content, which I found so frequent. I sought also for the occasions for wearing the traditional costume, on what occasion, the way the traditional costume changes when the original materials changes. I looked for the reasons why and with what functionality it is still worn by people living today. Among the historical evolution, I put emphasis also on the recent form and function of the traditional clothing.
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