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Utilization of pulse labelling techniques for studying the dynamics of proteins and protein complexes
Polák, Marek ; Novák, Petr (advisor) ; Obšil, Tomáš (referee) ; Vrbacký, Marek (referee)
(In English) Mass spectrometry (MS) techniques are routinely used to probe the structure and dynamics of proteins and protein complexes. Although MS techniques lack the high resolution of data provided by X-ray crystallography, NMR, or cryo-EM, they excel in providing insights into analyte dynamics, structure, and interactions with other components, such as ligands. This doctoral thesis presents a contribution to the field of structural biology employing and extending covalent labelling approaches, namely Fast Photochemical oxidation of Proteins (FPOP) and oxidation by singlet oxygen (1 O2). These approaches were followed to study the structure, dynamics, and interaction of proteins, nucleic acids, and protein-DNA complexes in solution. Initially, FPOP was used to investigate the interaction interface of FOXO4 and DAF16-DNA response element and to show the possibilities of analyzing such a complex using both 'bottom- up' and 'top-down' approaches. Furthermore, an isotope depletion strategy combined with multiCASI-ECD proved effective in delivering structural information with the highest possible resolution for mapping protein-DNA interfaces. This research showcases how information derived from structural proteomic methods can guide the construction of in-silico models for protein-DNA complexes with...
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Draft of educational materials for the subject basics of radiopharmacy for higher vocational medical schools with certified pharmaceutical assistant study program
Novák, Pavel ; Hanušová, Jaroslava (advisor) ; Váchová, Alena (referee)
The thesis addresses the topic of nuclear medicine and radiopharmacy, focusing on creating suitable educational materials in this field for the "Certified Pharmaceutical Assistant" study program. The theoretical part includes a description of the pharmaceutical assistant's role and basic information about nuclear medicine. These insights lead into the key chapter of this work, namely radiopharmacy and the preparation of radiopharmaceuticals. The empirical part of the thesis consists of two questionnaire surveys. The first section of the empirical part consists of a questionnaire aimed at teachers who teach subjects focused on radiopharmacy for the "Certified Pharmaceutical Assistant" study program. The second section of the empirical part consists of a questionnaire among students in their final year of the mentioned program. Both questionnaires aim to gather information on the pedagogical reality of subjects focused on radiopharmacy and simultaneously collect suggestions for improving teaching for future students. It was found that only 28,6 % of the surveyed teachers use teaching methods other than just frontal teaching. Furthermore, it was discovered that none of the 56 surveyed students plan to work in a radiopharmaceutical preparation laboratory. Based on these findings, 13 educational...
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Commercial center Miris Garden in Croatia
Uherková, Jana ; Vintr, Jan (referee) ; Novák, Petr (advisor)
The subject of the bachelor thesis is the preparation of project documentation for building permits and documentation for construction implementation, based on the assignment provided in the 3rd year during the winter semester in the subject BGA 032 – Architectural Studio IV. The study focuses on the design of a new commercial center placed in the area of a newly planned holiday resort in Croatia. The addressed plot is located in the Croatian Dalmatia region, near the village of Stari Grad-Paklenica. Currently, the whole area is unused, undeveloped, and overgrown with wild vegetation. The architectural concept aims to create a building that responds to the sloping terrain of the plot and provides its future visitors with a sense and atmosphere of Croatian architecture. This is achieved through the use of stone cladding and wooden shading elements, which are typical materials for this region. The irregularly shaped building consists of two above-ground floors. The first floor is used for dining, commerce, and sports, while the second floor accommodates dining, services, administration, and entertainment. In contrast to the first floor, the second floor is more shallow, creating a walkable terrace from which individual units are accessible. The terrace also features outdoor seating for gastronomic establishments, complemented by wooden pergolas with sliding fabric shading. One of the dominant elements of the complex is the outdoor staircase connecting both floors. It is not only a guiding element but also reveals views of the sea and the setting sun. The design also emphasizes public spaces. In the front area of the commercial center on the northeast side, the space is divided into green islands with seating. These green islands, along with a water feature, complete the square in front of the commercial center facing the sea. The area also includes wooden pergolas with sliding fabric shading, resembling waves of the sea, providing a unique atmosphere.
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Commercial center Miris Garden in Croatia
Hlavinková, Kateřina ; Bažant, Lukáš (referee) ; Novák, Petr (advisor)
The subject of the bachelor thesis is the preparation of project documentation for building permits and part of the documentation for the implementation of construction based on the assignment, which was provided in the course AG032 - Architectural Design Studio IV in the winter semester of the third year on the topic of public buildings. The study focuses on the design of a new commercial centre to a planned resort in Croatia. It is a three-storey building that is partially embedded in the ground. Its shape and location respects the building plot and its surroundings as much as possible. The building is composed of three functional units. The main one is a commercial centre with several shops, restaurants, a bar, a bistro and many other facilities. The ellipse building which will be primarily used for rest and relaxation. The last unit is the administration building, this is used only for the resort staff. All these parts are connected by the main corridor of the commercial centre, which is a distinctive wooden walkway, it is located on the southern part of the building and offers a beautiful view of the sea from all the establishments and the walkway itself.
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Malá Amerika in Brno
Kalmykova, Valeriia ; Bažant, Lukáš (referee) ; Novák, Petr (advisor)
This bachelor thesis focuses on the design proposal for a new multifunctional building called "Malá Amerika" in Brno, based on an architectural study conducted within the course BGA021 - Architectural Design Studio 2 - Public Buildings. The aim of this thesis was to prepare project documentation comprising documentation for building permits, construction documentation, and architectural detail design. The proposed building is in Brno near the historical industrial structure "Malá Amerika" and the Titania buildings, within the area bounded by the streets Úzká and Nové sady. The multifunctional building "Malá Amerika" includes offices, art galleries, a library, a restaurant, cafes, rooftop terraces, and spaces for events. The new construction respects the existing urban and architectural structure of the surrounding development. It consists of five standalone buildings interconnected by an underground parking lot. The massing is composed of several blocks at different height levels connected by accessible terraces. Streets and squares with many interesting perspectives emerge between the individual buildings. The building is connected to "Malá Amerika" by an accessible terrace and designed not to obstruct the historical structure. Towards the Titania buildings, the volumes of the individual building components increase. The project's intention was to create a multifunctional building that would not only be an introverted structure benefiting solely from its perfect location and existing urban infrastructure but also feature ground floors full of commerce and services accessible to passersby even after working hours.
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Commercial center Miris Garden in Croatia
Olšáková, Linda ; Vintr, Jan (referee) ; Novák, Petr (advisor)
The subject of the bachelor thesis is the creation of project documentation for building permits and parts of the documentation for construction implementation based on a previously developed study within the course BGA032 Architectural Design Studio 4 in the winter semester of the 3rd year, focusing on public buildings. The project theme involves the new construction of a commercial center consisting of five independent two-story structures. The chosen site is located in Croatia, in the village of Starigrad in the Zadar County. The nearby surroundings are undeveloped, and the commercial center is part of a planned vacation resort. The architectural concept aims for the most efficient use of the existing sloping terrain. Therefore, the center is composed of five standalone buildings, partially embedded into the terrain, following its funnel-like shape. Four buildings have a simple cubic shape, while the fifth has an arched ground plan. The intention is to create shopping streets with shop windows of retail spaces and restaurants facing them. The facades, designed with imitation of exposed concrete, incorporate shading using rotating wooden elements and individual fixed wooden panels. Outdoor spaces are protected by adjustable fabric shading. The commercial center houses rentable spaces for retail and services, restaurant areas, an entrance hall with a reception, and private administrative spaces including necessary facilities.
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Commercial center Miris Garden in Croatia
Žilková, Monika ; Doležal, Ondřej (referee) ; Novák, Petr (advisor)
The subject of the bachelor thesis is preparation of project documentation for building permits and part of the documentation for the implementation of construction based on the assignment, which was provided in the course BGA032 - Architectural Design Studio 4. The topic of the study is a design of a new building of the commercial center Miris Garden in Croatia near the town Starigrad. The building is to form the main point of the newly built resort on the sloping coast of the Adriatic Sea. The commercial center is to fulfill a commercial function (with several smaller shops and gastro businesses) and in part of the building also an administrative function, where offices are available for the management of the center and for tenants. The three buildings forming a unified whole are designed in the shape of two central hexagons, creating a space imitating a shopping street. It then culminates in a square with a view of the sea. The center has a total of three floors, which, however, are fitted into the terrain in such a way that when viewed towards the sea it looks like a single-storey building, so it does not disturb the views of the surrounding villas. The new building will be located in an open landscape, so its construction and operation will not disturb any nearby residents in any way.
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Gallery of Modern Art in Brno
Knipiglová, Nina ; Doležal, Ondřej (referee) ; Novák, Petr (advisor)
The bachelor's thesis focuses on the design of a modern art gallery located in the city district of Brno-Center. The plot, with an elevation ranging from 205.200 to 207.100 meters above sea level, features an irregular layout. While the central location is advantageous, nearby roadways contribute to the noise in the local environment. The structure, consisting of five floors with two underground and three above-ground levels, is designed in accordance with the city's plan for mixed-use areas, taking into consideration the planned circular park. The main entrance is located on the first floor on the western side, featuring a large entrance hall, a café, a library, and office spaces. The second and third floors are designated for exhibition spaces, supplemented by rentable studio areas. The underground sections include double-decker garages and supply rooms. The design concept responds to the surroundings; the building's break follows the street line in the Kolište section, and the northern façade is parallel to the city hall. The building's façade is visually divided. The first above-ground floor is glazed with white plaster, while the other above-ground levels are covered with aluminum panels. The objective of the project is to integrate into the urban environment and provide a space that supports cultural and social activities in Brno-Center.
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Estimation ff the Global Root Mean Square Error of Geoid Height Calculated by Integral Transforms
Belinger, Jiří ; Pitoňák, Martin ; Trnka, Petr ; Novák, Pavel ; Šprlák, Michal
Integral transformations of the gravitational field gradients are defined over the entire solid angle on the surface of the sphere. Despite the indisputable progress in satellite gravimetry and gradiometry, gravity field focused satellite missions allow accurate determination of the gravity field with a spatial resolution of 100 km, i.e. only in its long-wavelength part. However, there is also a need for high-resolution gravity field models at regional, national or continental scales, especially concerning the determination of the quasi-geoid or geoid. On the other hand, potential weakness of ground-based data is the long-wavelength gravity field accuracy and limited availability due to several constraints (e.g. deserts, lakes and large rivers, forests, or lack of goodwill between neighboring countries to share sensitive data). The ideal scenario combines ground and satellite data that complement each other. In this paper, relations defining the estimation of the global root mean square errors of geoid heights using integral transformations will be derived and presented. For practical calculation, knowledge about the accuracy of measured terrestrial data and formal errors of global satellite models of the Earth's gravity field will be utilized.
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A New Software For the Calculation of Far–Zone Effects For Spherical Integral
Trnka, Petr ; Pitoňák, Martin ; Belinger, Jiří ; Novák, Pavel ; Šprlák, Michal
Integral transformations are a useful mathematical apparatus for modelling the gravitational field. They represent the mathematical basis for the formulation of integral estimators of gravity field values, including error propagation. One of the basic assumptions of integral transformations is global data coverage. However, the availability of ground measurements is frequently limited. In practice, the global integral is divided into two complementary regions, namely the near and far zones. Non-negligible systematic effects of data in the far zone require accurate evaluation.
For this purpose, a new software library is being created in the MATLAB environment to calculate far-zone effects in integral transformations for gravitational potential gradients up to the third order.
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