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Evolution of protein-RNA and protein-cofactor interactions
Sanchez Rocha, Alma Carolina ; Hlouchová, Klára (advisor) ; Lepšík, Martin (referee) ; Berka, Karel (referee)
Genetický kód je překládán do bílkovin s využitím abecedy 20 proteinogenních aminokyselin. Přes současnou dominanci kanonicke abecedy je pravděpodobné, že primordiální proteiny byly složeny pouze z části tohoto aminokyselinového repertoáru. V této práci jsme prozkoumali soubor peptidů a proteinů s cílem objasnit, jak vyvíjející se repertoár aminokyselin ovlivnil jejich fyzikálně-chemické a biologické vlastnosti a sklon k interakci s evolučně konzervovanými molekulami, jako jsou kofaktory a RNA. V první části jsme prozkoumali soubor nejkonzervovanejších protoribozomálních peptidů s cilem odhalit jejich strukturní a funkční charakteristiky. Pomocí experimentálních a bioinformatických analýz jsme potvrdili převážně nestrukturovanou povahu těchto peptidů a odhalili jejich úlohu při stabilizaci peptidyltransferázového centra a ochraně RNA před degradací. Tyto procesy odráží nejstarší pochody koevoluce RNA a peptidů jež předcházely zrodu posledního univerzálního společného předka (LUCA z angl. Last Universal Common Ancestor). Dále jsme se zaměřili na pre-ribozomálni peptidy s potenciálním prebiotickým významem. Pomocí bioinformatických metod jsme prozkoumali strukturní charakteristiky kompletních knihoven peptidů zahrnujících kanonické a prebioticky přípustné nestandardní aminokyseliny. Predikce...
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Computer network design for a metal stamping plant
Daněk, Michal ; Martin,, BERKA (referee) ; Ondrák, Viktor (advisor)
The bachelor thesis focuses on the design of a computer network for a metal stamping plant. The first part of the thesis contains theoretical background. The second part contains an analysis of the current state of the network in the company. These first two parts were then used as a basis for the design of the new computer network, which is included in the third and final part along with an economic evaluation.
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Precision forging
Berka, Martin ; Peterková, Eva (referee) ; Lidmila, Zdeněk (advisor)
This bachelor´s thesis deals with the technology of precision forging. The thesis describes basic distribution of the forging according to the nature of the material flow and his procedure. After the introductory part this thesis deals with the analysis of the methods of the drop forging with fin groove. The next section contains a description, parameters and methods of precision forging. Technical a economical evaluation of the component technology is as a conclusion of the thesis.
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The influence of geometry and cutting tool parameters on residual stress during machining of the pressure containers
Berka, Martin ; Kouřil, Karel (referee) ; Strejček, Jan (advisor)
This thesis deals with the influence of changes in cutting parameters and tool geometry on residual stress inside the material. I examine the influence by deep drilling. Changing the cutting parameters concerns the alteration of the tool feed and the pressure of the coolant during the process. The influence of tool geometry is studied by using two different single edge cannon drills. The research was realized in cooperation with Bosch Diesel Ltd. The theoretical part includes a description of the injection system, in which a high-pressure container is contained. The high-pressure container was used to evaluate the influence of the cutting parameters and tool geometry on residual stress. Furthermore, the theoretical part deals with the deep drilling technology used and the theory of residual stresses. The practical part shows the measurement parameters and the corresponding results. In the conclusion of this thesis, a technical-economic evaluation of the measurement is conducted.
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Planning the construction contract by the contractor
Dáňa, Tomáš ; Berka, Jan (referee) ; Nový, Martin (advisor)
The diploma thesis deals with the process of planning the costs of a contract for construction. The thesis describes the pricing, contract for construction, construction time models, and allocation of costs during the construction. It introduces a particular contract for construction, which is analysed mainly with regard to the allocation of costs during the construction. The thesis introduces also alternative solutions for the allocation of costs during the construction. The purpose of the thesis is to compare the alternative solutions with the reality, and analyse the allocation of costs during the construction.
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Sports Centre
Maděránek, Martin ; Berka, Pavel (referee) ; Donaťáková, Dagmar (advisor)
Solution of the thesis is sportcentrum near Brno Dam. The building is brick, two-storey, basement, covered flat roof. On the first floor is a sports-recreation rooms and a restaurant, on the second floor facilities for staff.
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Tail units design of VUT 100 aircraft made out composite
Berka, Martin ; Cejpek, Jakub (referee) ; Mališ, Michal (advisor)
This Master´s thesis describes the design of composite horizontal tail of VUT 100 aircraft. Load calculation and selection of the critical load cases is performed. Internal structure of stabilizer and right elevator is designed. Construction materials are chosen and the structure of the composite materials is proposed. FEM models of stabilizer and the right elevator are created in MSC Patran system and consequently the strength test of the models for the selected load cases is executed using MSC Nastran software and COMPOST.
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Topics in Yield Curve Modeling
Kučera, Adam ; Kočenda, Evžen (advisor) ; Horváth, Roman (referee) ; Mandel, Martin (referee) ; Berka, Martin (referee)
The aim of the thesis is to examine the interaction of macroeconomic and fi- nancial factors through the lens of yield curve dynamics. The thesis consists of three essays that jointly demonstrate the complexity of information incorporated in the yield curve and the importance of attributing yield curve movements to those factors correctly. The first essay uses news-based approach to identify triggers of the U.S. Treasury yield curve movements and demonstrates shifts in the importance of various causes of the movements. The second essay further evaluates the transmission of fiscal policy shocks to the U.S. Treasury yield curve. The first and the second essay together contribute to the literature by showing that the factors beyond the U.S. economic conditions and monetary policy have been becoming an increasingly important cause of the U.S. yield curve movements. These factors include changes in portfolio allocation, cross-border flight to quality and changes in fiscal policy. The third essay proposes a novel method to apply the up-to-date yield curve models to a government bond yield curve in an economy with a relatively shallow government bond market, using the case of the Czech government bond yield curve. This enables decomposing the yield curve and interpreting its movements while accounting for...
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Profiling translation of conceptual schemas to XML schemas
Berka, Lukáš ; Nečaský, Martin (advisor) ; Holubová, Irena (referee)
In the present work we analyze the algorithm that was introduced in [4]. The algorithm performs a translation of a conceptual schema to an XML schema expressed in the XML Schema language. We look for limitations of the algorithm and try to discover parameters that can be potentially used to influence its behavior. We propose solutions to the most serious limitations. Also, we introduce a concept of a translation profiling. The concept is based on a configuration that contains a set of parameters. We modify the algorithm to use the user requirements specified in the configuration. Thanks to the improvements, the new algorithm works with the concept of XML Namespaces, uses XML Schema designs and also, focuses on an elimination of redundancy. The elimination of redundancy in an output of the algorithm is an important part of this work and we create a formal model that helps us to solve this task.
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Computational Studies of Interactions of Small Molecules with their Biological Targets
Nekardová, Michaela ; Hobza, Pavel (advisor) ; Berka, Karel (referee) ; Kabeláč, Martin (referee)
The thesis specializes in the computational description of pharmaceutically important compounds. A substantial number of pharmaceutical drugs are small molecules that are bound to an active site of an enzyme by the "lock (binding site) and key (drug)" model through non-covalent interactions. The association of enzymes with drugs cause an increase or decrease in the activity of enzymes. The main topic is focused on the computational elucidation of the structural basis for the interactions of the purine-like compounds with the enzyme cyclin- dependent kinase 2 that belongs to the protein-kinase enzyme family. These enzymes play an important role in the cell cycle regulation; their increased activity significantly contributes to the loss of control over cell proliferation, which is one of the primary causes of cancer cell formation. The study describes the binding motifs of roscovitine, which shows an inhibitory effect on the function of cyclin-dependent kinases, and its analogues containing bioisosteric central heterocycles in the complex with cyclin-dependent kinase 2. The binding affinity between the cyclin-dependent kinase 2 enzyme and the inhibitors was quantified as calculated binding scores and evaluated in relation to the conformation of the optimized structures. The hybrid model combining the...
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