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MAT TRIAD 2019: Book of Abstracts
Bok, J. ; Hartman, David ; Hladík, M. ; Rozložník, Miroslav
This volume contains the Book of abstracts of the 8th International Conference on Matrix Analysis and its Applications, MAT TRIAD 2019. The MATTRIAD conferences represent a platform for researchers in a variety of aspects of matrix analysis and its interdisciplinary applications to meet and share interests and ideas. The conference topics include matrix and operator theory and computation, spectral problems, applications of linear algebra in statistics, statistical models, matrices and graphs as well as combinatorial matrix theory and others. The goal of this event is to encourage further growth of matrix analysis research including its possible extension to other fields and domains.
Stuctural Aspects of Graph Homomorphisms
Bok, Jan ; Nešetřil, Jaroslav (advisor) ; Hubička, Jan (referee)
This thesis is about graph-indexed random walks, Lipschitz mappings and graph homo- morphisms. It discusses connections between these notions, surveys the existing results, and shows new results. Graph homomorphism is an adjacency-preserving mapping between two graphs. Our main objects of study are graph homomorphisms to an infinite path. We are interested in two parameters: maximum range and average range. The average range of a graph is the expected size of the image of a uniformly picked random homomorphism to an infinite path. We obtain formulas for several graph classes and investigate main conjectures on this parameter. For maximum range parameter we show a general formula and an algorithm to compute it for general graphs. Besides that, we study the problem of extending a prescribed partial graph homomorphism to a full graph homomorphism. We show that this problem is polynomial in some cases. 1
Cooperative interval games
Bok, Jan ; Hladík, Milan (advisor) ; Valla, Tomáš (referee)
In this thesis, we study cooperative interval games, a generalized model of cooperative games in which worth of every coalition corresponds with a closed interval representing all possible outcomes of their cooperation. We give a brief introduction into classical cooperative games, interval analysis and finally introduction to cooperative interval games with focus on selections, that is on all possible outcomes of interval game with no additional uncertainty. We introduce new selection-based classes of interval games and prove their characterizations and relation to existing classes. We show a new results regarding core and imputations. We introduce a definition of strong imputation and core and examine a problem of equality of two different versions of core -- the main stability solution of cooperative interval games. Finally, we make some new remarks on Shapley value of interval games.
Molecular dynamics simulations of membrane proteins
Španěl, David ; Barvík, Ivan (advisor) ; Bok, Jiří (referee)
Basic facts about the structure of biomolecules and algorithms applied in molecular dynamics (MD) simulations were recapitulated in the theoretical part of this thesis. A program for MD simulations of a periodic box with water molecules represented by various models (SPC, TIPS, TIP3P) was developed for active mastery of basic algorithms applied in MD simulations. MD simulation methodology was subsequently applied to the structure of the membrane protein A2AGPCR anchored in the phospholipid bilayer and surrounded by water molecules (approx. 120,000 atoms altogether). The purpose of these MD simulations was to compare binding of the natural agonist (adenosine) and its synthetic analog NECA into the binding pocket situated on the extracellular side of A2AGPCR. For these MD simulations were used software package NAMD and computer cluster Gram (in which each node is equipped with 16 CPU cores and 4 GPU) in supercomputing MetaCentrum. Powered by TCPDF (
Molecular dynamics simulations of biomolecules
Naništa, Ján ; Barvík, Ivan (advisor) ; Bok, Jiří (referee)
This study deals with classical molecular dynamics simulations of time evolution of a biomolecular system. The simulated system consists of the D3 GPCR membrane receptor for dopamine surrounded by a cell membrane and covered with water molecules and ions. The aim was to analyze the ability of Eticlopride to bind into the active site of the GPCR receptor.
Molecular dynamics simulations of biomolecular complexes consisting of proteins and nucleic acids
Melcr, Josef ; Barvík, Ivan (advisor) ; Bok, Jiří (referee)
Literature search on the Elongation factor Tu (EF-Tu), which is involved in the process of translation of genetic information, was performed. Further, computational methods as molecular dynamics (MD) and Monte Carlo (MC) were studied. Then, computer programs for MD and MC simulations of a Lennard-Jones gas were developed. MD simulations were further applied to EF-Tu using the NAMD and ACEMD software packages. Multiprocessor PC clusters and programmable NVIDIA GPUs were used. MD simulations of EF-Tu uncovered binding of monovalent ions in nearby of the EF-Tu active site. The impact of Na$^+$ binding on evolutionarily conserved residues (His85, Val20, Ile61, Asp21, Tyr47, Asp87, etc.) was studied in detail.
Phyllotactic Model Linking Nano and Macro World
Horáček, Miroslav ; Meluzín, Petr ; Krátký, Stanislav ; Urbánek, Michal ; Bok, Jan ; Kolařík, Vladimír
Recently, the arrangement of diffraction primitives according to a phyllotactic model was presented. This arrangement was used to benchmarking purposes of the e-beam writer nano patterning. The phyllotactic arrangement has several interesting properties. One of them is related with the coherence between the nanoor microscopic domain of individual optical primitives and the properties of visually perceived images crated by these structures in the macro domain. This paper presents theoretical analysis of the phyllotactic arrangement in the referred context. Different approaches enabling the creation of diffractive optically variable images are proposed. The practical part of the presented work deals with the nano patterning of such structures using two different types of the e-beam pattern generators. One of them is a system with a variable shaped beam of electrons, while the other one is a system with a Gaussian-shaped beam. E-beam writing strategies and the use of inherent spiral patterns for exposure ordering and partitioning are also discussed.
Large-area gray-scale structures in e-beam writer versus area current homogeneity and deflection uniformity
Kolařík, Vladimír ; Horáček, Miroslav ; Matějka, Milan ; Krátký, Stanislav ; Bok, Jan
The high stability and good current homogeneity in the spot of the e-beam writer is crucial to the exposure quality, particularly in the case of large-area structures when gray-scale lithography is used. Even though the deflection field distortion is calibrated regularly and beam focus and beam astigmatism is dynamically corrected over the entire deflection field,\nwe can observe disturbances in the exposed relief for both nowadays types of e-beam writers, the shaped e-beam writing system and the Gaussian e-beam writing system. A stable and homogeneous angular current density distribution in the spot is important especially in the case of shaped e-beam lithography systems. A non-homogeneity of the spot over deflection field is seen alongside the field boundaries of both lithography systems.
Laboratory wind turbine control system
Borski, Roman ; Bok, Jaromír (referee) ; Šlezingr, Jan (advisor)
This thesis is about creating measure and control system for wind turbine DS 300. This system purpose is data collection of wind turbine, especially measurement of supplied power and their archivation. Next is to expend control functions, which are supported by transducer, that is provided by the wind turbine manufacturer, especially for remote shut-down function of wind turbine. Created control system is based on CompactRIO platform, whose software is created in LabVIEW.
Project for an automouse source of electrical energy
Vinkler, Stanislav ; Bok, Jaromír (referee) ; Matoušek, Antonín (advisor)
Purpose of the thesis is enlarged the theory about potential utilization of an autonomous (autonomic) electric power supply used for a family house. Forepart will dealt with description of the resources in accordance with conversion of different kinds of energy to electric power. There will be always given the principle of the power generation as well as a list of main components of the system for each single source. Second part will be focused on generator output assessment of the autonomous source to ensure the power supply for the model family house. There will be my own design of the autonomous sources namely a project of a small hydropower plants and a project of a cogeneration unit in the third section of the thesis. The last part is aimed at the techno-economical evaluation of the engineered sources.

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See also: similar author names
1 Bok, J.
6 Bok, Jan
1 Bok, Jaromír