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Contribution to the tectonic interpretation of the seismicity pattern of Banda Arc, SE Asia
Matějková, Radka ; Špičák, Aleš (advisor) ; Zahradník, Jiří (referee)
i Abstract Contribution to the tectonic interpretation of the seismicity pattern of the Banda Arc, Southeast Asia Tectonic structure of the Banda Arc in Southeast Asia is regarded as an extremely complicated unit as it is situated at the intersection of four lithospheric plates: Eurasian, Indo-Australian, Pacific, and Philippine. The present-day tectonic regime is arc-continent collision. The seismotectonic pattern of the Banda Arc region was studied using global seismological data. Relocated EHB hypocentral determinations for the period 1964 - 2004 and fault plane solutions of Harvard CMT data for the period 1976 - 2004 have been used. The analysis of spatial distribution of earthquake foci and the analysis of focal mechanisms enabled to distinguish the foci belonging to the Wadati-Benioff zone of the subducting plate from those occurring in the overriding plate. The analysis discriminated two opposite dipping subduction zones - southern Banda subduction and northern Seram subduction. The following specific phenomena were observed in the Wadati-Benioff zone: (i) unusual lateral bent of the Wadati-Benioff zone of the southern Banda subduction, (ii) intermediate- depth (100 - 220 km), vertically situated domain of the highest seismicity within the Wadati-Benioff zone of the southern Banda subduction, (iii)...
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Seismic Site Effects (Data Analysis and Modelling)
Caserta, Arrigo ; Zahradník, Jiří (advisor) ; Růžek, Bohuslav (referee) ; Burjánek, Jan (referee)
A comprehensive study of the soil shaking under the seismic wave-field ex- citation is presented. It includes theoretical, geological, geotechnical, data analysis and numerical simulations aspects. The aim is to quantify the main parameters allowing the estimate of the soil shaking in urban areas for better mitigating seismic risk due to future earthquakes. The city of Rome has been chosen as a case study because of its high density of popula- tion and large concentration of historical monuments with high earthquake vulnerability. This study improves significantly the knowledge concerning the detailed near-surface geology of the chosen study area of Rome, ful- fills the absence both of knowledge concerning its geotechnical properties and earthquake data recordings in the city. Among others, it allows for a better explanation of the spatial damage pattern observed in the city due to earthquakes in the past. The main innovations include the construction and long-term operation a seismic array in the city, analysis of the natural seismic noise, and instrumental recordings of the 2009 L'Aquila earthquake sequence. The 3D array (including a borehole sensor at 70-m depth) is the first one in Italy planned, realized and operated within an urban area, and the first one that recorded a significant earthquake in...
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Bacterial REP elements
Staněk, Tadeáš ; Nunvář, Jaroslav (advisor) ; Zahradník, Jiří (referee)
Insertion sequences are the smallest type of mobile genetic element. They are formed from specific repetitive elements, between which gene for transposition is placed. That is an enzyme used for their genome propagation. REP elements are short repetitive sequences abundantly represented in many bacterial classes. They are placed in noncoding regions of genome. They have a palindromic structure, thanks to that their sides are complementary. ssRNA and ssDNA forms of REP can form a stem-loop structure. In the host genome, there are hundreds of these elements. REPs are usually grouped in higher structural units: REPIN, which has structure REP-spacer-REP, or BIME with iREP-spacer-iREP structure. These structures are associated with RAYT, tyrosine nuclease related to IS200/IS605 transposase family. The RAYT is a domesticated enzyme propagating REP elements through the genome. The presence of REP elements has an influence on transcription and translation of neighbouring genes. In addition, REPs interact with proteins important for cell physiology. This thesis is focused on the dissemination of REP elements, their characteristics, function in cells, and cooperation with RAYT nucleases. This thesis also summarizes the findings of RAYT and their similarities and differences from other families of...
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Targeted modifications of the protein-protein interactions: Ternary complex of interferon-γ as a model system
Zahradník, Jiří
A key prerequisite for a deeper understanding of biological processes at molecular level is a detailed description of the three-dimensional structure of interaction partners and their complexes. We adopted the IFN-γ complex as our model system. Even though IFN-γ is one of the key modulators of the immunity response, which has been studied intensively for more than 60 years, the structure of the accessory receptor chain and the understanding of the IFN-γ complex is still lacking. In this work we firstly discussed the binary system between IFN-γ and its high affinity receptor R1 which is structurally known. Using a new innovative methodology we focused on the modulation of the affinity between IFN-γ and its receptor R1. Our approach was based on the modulation of protein - protein stability by mutating cavities in the proteins' structure and increasing the affinity about seven-fold. Secondly, we crystallized and solved the structure of the IFN-γ receptor 2, the accessory receptor molecule. Our analysis of variable residues on the surface of the structures of type II family receptors, to which receptor 2 belongs, revealed the putative binding site for IFN-γ. In the third part of our work, we crystallized IFN-γ from olive flounder Paralichthys olivaceus and solved its structure at 2.3 Å resolution (PDB...
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Vulnerabilities assessment for industrial protocols
Zahradník, Jiří ; Fujdiak, Radek (referee) ; Blažek, Petr (advisor)
Thesis deals with testing of selected vulnerabilities from the IEC 61850 standard and following design of mitigation measures for selected vulnerabilities. Author simulated vulnerabilities of the GOOSE protocol, NTP attack and attack ona MMS client. Those attacks were GOOSE stNum, GOOSE semantic, GOOSE test bit,GOOSE replay, GOOSE flood, NTP spoofing and MMS password capture. Attacks on protocols GOOSE and MMS were successful, attack on NTP was only partially successful since the device confirmed receiving spoofed time, however it did not change it’s inner clock. Author then designed possible mitigation measures. Tool for automatic testing of selected vulnerabilities, parser for the GOOSE protocol and lightweight multiplatform parser for configuration files were created as well.The outcome of this thesis allows the implementation of lager scale tool for penetration testing of industrial networks as well as it allows implementation of discussed mitigation measures.
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Development of effective code for earthquake dynamic source simulations
Premus, Jan ; Gallovič, František (advisor) ; Zahradník, Jiří (referee)
Title: Development of effective code for earthquake dynamic source simulations Author: Bc. Jan Premus Department: Department of Geophysics Supervisor: doc. RNDr. František Gallovič, Ph.D, Department of Geophysics Abstract: Dynamic rupture modeling coupled with strong motion data fitting offers an insight into physical mechanisms behind earthquake sources [Gallovic et al., 2019]. Running a large number of dynamic model simulations is required due to the nonlinearity of the inverse problem. The goal of this Thesis is a development of an efficient forward solver for the dynamic inversions. The fi- nite difference staggered grid code FD3D by Madariaga and Olsen [1998] served as a basis for the development, offering sufficient speed, but rather low accu- racy. Traction at split node implementation of the fault boundary condition and perfectly matched layers as the absorbing boundary condition were required to obtain desirable accuracy. In addition to the slip weakening friction law, fast ve- locity weakening friction law has been implemented, increasing the applicability of the code. We test the new code FD3D TSN using USGS/SCEC benchmarks TPV5 (slip-weakening friction) and TPV104 (fast rate weakening friction) [Harris et al., 2018], showing very good agreement with results calculated by advanced numerical...
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Targeted modifications of the protein-protein interactions: Ternary complex of interferon-γ as a model system
Zahradník, Jiří
A key prerequisite for a deeper understanding of biological processes at molecular level is a detailed description of the three-dimensional structure of interaction partners and their complexes. We adopted the IFN-γ complex as our model system. Even though IFN-γ is one of the key modulators of the immunity response, which has been studied intensively for more than 60 years, the structure of the accessory receptor chain and the understanding of the IFN-γ complex is still lacking. In this work we firstly discussed the binary system between IFN-γ and its high affinity receptor R1 which is structurally known. Using a new innovative methodology we focused on the modulation of the affinity between IFN-γ and its receptor R1. Our approach was based on the modulation of protein - protein stability by mutating cavities in the proteins' structure and increasing the affinity about seven-fold. Secondly, we crystallized and solved the structure of the IFN-γ receptor 2, the accessory receptor molecule. Our analysis of variable residues on the surface of the structures of type II family receptors, to which receptor 2 belongs, revealed the putative binding site for IFN-γ. In the third part of our work, we crystallized IFN-γ from olive flounder Paralichthys olivaceus and solved its structure at 2.3 Å resolution (PDB...
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Targeted modifications of the protein-protein interactions: Ternary complex of interferon-γ as a model system
Zahradník, Jiří ; Schneider, Bohdan (advisor) ; Obšilová, Veronika (referee) ; Vaněk, Ondřej (referee)
A key prerequisite for a deeper understanding of biological processes at molecular level is a detailed description of the three-dimensional structure of interaction partners and their complexes. We adopted the IFN-γ complex as our model system. Even though IFN-γ is one of the key modulators of the immunity response, which has been studied intensively for more than 60 years, the structure of the accessory receptor chain and the understanding of the IFN-γ complex is still lacking. In this work we firstly discussed the binary system between IFN-γ and its high affinity receptor R1 which is structurally known. Using a new innovative methodology we focused on the modulation of the affinity between IFN-γ and its receptor R1. Our approach was based on the modulation of protein - protein stability by mutating cavities in the proteins' structure and increasing the affinity about seven-fold. Secondly, we crystallized and solved the structure of the IFN-γ receptor 2, the accessory receptor molecule. Our analysis of variable residues on the surface of the structures of type II family receptors, to which receptor 2 belongs, revealed the putative binding site for IFN-γ. In the third part of our work, we crystallized IFN-γ from olive flounder Paralichthys olivaceus and solved its structure at 2.3 Å resolution (PDB...
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Automated determination of earthquake source parameters
Vackář, Jiří ; Zahradník, Jiří (advisor) ; Evangelidis, Christos (referee) ; Fischer, Tomáš (referee)
Title: Automated determination of earthquake source parameters Author: Jiří Vackář Department: Department of Geophysics Supervisor: prof. RNDr. Jiří Zahradník, DrSc., Department of Geophysics Abstract: The thesis deals with methods for automated inversion of seismic source parameters. We studied the influence of structure model used and show an ex- ample how the existing model can be improved. We have developed a new, fully automated tool for the centroid moment tensor (CMT) inversion in a Bayesian framework. It includes automated data retrieval from ArcLink server or local data storage. Step-like disturbances are detected using modeling of the distur- bance according to instrument parameters and such components are automati- cally excluded from further processing. Frequency ranges for the filtration and time windows for the inversion are determined automatically due to epicentral distance. Full-waveform inversion is performed in a space-time grid around a provided hypocenter. A data covariance matrix calculated from pre-event noise yields an automated weighting of the station recordings according to their noise levels and also serves as an automated frequency filter suppressing noisy frequency ranges. The method is tested on synthetic and observed data. It is applied on a dataset from the Swiss seismic...
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