Počítačové modelování membránových proteinů

The present work deals with the application of steered molecular dynamics simulations on medically interesting biomolecular systems. At first, methods for determi- ning the free energy profile were tested on the (Ala)10 model system. Then we focused on determining the free energy profile for binding of a ligand to the adenosine A2A GPC receptor. We further studied the free energy profile associated with ion passage through the Gramicidin A ion channel. Finally, we applied this methodology to the TRPM2 ion channel. 1Předkládaná práce se zabývá aplikací řízených molekulárně dynamických simulací na medicínsky zajímavé biomolekulární systémy. Nejprve byly otestovány metody určení profilu volné energie na modelovém systému (Ala)10. Potom jsme se zaměřili na určení profilu volné energie při vazbě ligandu do vazebného místa adenosinového A2A GPC receptoru. Dále jsme určovali profil volné energie spojený s tranzitem iontů přes modelový systém Gramicidinu A. A nakonec jsme tuto metodiku aplikovali na iontový kanál TRPM2. 1Fyzikální ústav UKInstitute of Physics of Charles UniversityFaculty of Mathematics and PhysicsMatematicko-fyzikální fakult

Unravelling the basic concepts and intents of misbehavior in post-truth society

Objective: To explore the definitions and connections between the terms misinformation, disinformation, fake news, rumors, hoaxes, propaganda and related forms of misbehavior in the online environment. Anotherobjective is to infer the intent of the authors, where relevant.Design/Methodology/Approach: A conceptual analysis of three hundred fifty articles or monographies from all types of disciplines with a priority of the articles focused on terminological analysis was being utilized. A conceptual map of the terminology that is relevant to the post-truth era was created. In the case of the lack of agreement, the etymology of the terms, utilizing dictionaries, terminological databases and encyclopedias,was favored.Results/Discussion: The approach made possible to delimit the borders between the core terms of posttruth society and to classify them according to the intents of the authors: power (influence), money, fun, sexual harassment, hate/discord, ignorance, passion and socialization. These features were identified to be able to differentiate the concepts: falsity (misleadingness, deceptiveness, lack of verification), accuracy, completeness, currency, medium, intent and analyzable unit. The conceptual map, summarizing and visualizing our findings is attached in the article.Conclusions: We argued that disinformation and misinformation are different terms with different authors and intents in the online environment. Likewise, fake news was delimitated as species of disinformation, which is limited by the medium and financial intent. The intent of hoaxers is rather the amusement of the authors or to spread discord between different groups of society. The intent and analyzable units as statement, claim, article, message, event, story and narrative that were identified in the literature, are crucial for the understanding and communication between social (human) scientists and computer scientists in order to better detect and mitigate various types of false information.Originality/Value: The study provides a theoretical background for detecting, analyzing and mitigating false information and misbehavior

Investigation of dislocation structure evolution in advanced magnesium alloys

: This thesis deals with evolution of dislocation structures in mag- nesium alloys containing long-period stacking ordered phase (LPSO). Before de- formation the samples were studied by optical light microscopy, in the process of deformation by neutron diffraction. Obtained diffraction profiles were of two types, axial and radial diffraction profiles (created by planes oriented in the di- rection of deformation and orthogonally to the direction of deformation). Profiles were evaluated by Convolutional Multiple Whole Profile method and by Hexbur- ger program. This work is focused on the role of LPSO phase in the evolution of dislocation density and population of dislocations in slip systems depending on the composition of alloys and on the volume fraction of LPSO phase.

Computational Modeling of Membrane Proteins

The present work deals with the application of steered molecular dynamics simulations on medically interesting biomolecular systems. At first, methods for determi- ning the free energy profile were tested on the (Ala)10 model system. Then we focused on determining the free energy profile for binding of a ligand to the adenosine A2A GPC receptor. We further studied the free energy profile associated with ion passage through the Gramicidin A ion channel. Finally, we applied this methodology to the TRPM2 ion channel.

Studium vývoje dislokační struktury v pokročilých hořčíkových slitinách

: This thesis deals with evolution of dislocation structures in mag- nesium alloys containing long-period stacking ordered phase (LPSO). Before de- formation the samples were studied by optical light microscopy, in the process of deformation by neutron diffraction. Obtained diffraction profiles were of two types, axial and radial diffraction profiles (created by planes oriented in the di- rection of deformation and orthogonally to the direction of deformation). Profiles were evaluated by Convolutional Multiple Whole Profile method and by Hexbur- ger program. This work is focused on the role of LPSO phase in the evolution of dislocation density and population of dislocations in slip systems depending on the composition of alloys and on the volume fraction of LPSO phase. 1: Předkládaná práce se zabývá vývojem dislokačných struktur v hořčíkových slitinách obsahujících fáze uspořádány na dlouhé vzdálenosti, takz- vané LPSO fáze. Vzorky byly studovány pomocí optické světelné mikroskopie ve stavu před deformací. Během deformace byly studovány pomocí neutronové dif- rakce. Získané difrakční profily byly dvou typů, axiální a radiální difrakční profily (vytvořené rovinami orientovanými ve směru a kolmo na směr deformace). Pro- fily byly vyhodnoceny pomocí metody CMWP (Convolutional Multiple Whole Profile method) a pomocí programu Hexburger. Práce je zaměřena na roli LPSO fázi při vývoji dislokačnej hustoty a populace dislokací v skluzových systémech v závislosti na složení slitin a na objemovém zlomku LPSO fázi. 1Department of Physics of MaterialsKatedra fyziky materiálůMatematicko-fyzikální fakultaFaculty of Mathematics and Physic

Influence of Volume Fraction of Long-Period Stacking Ordered Structure Phase on the Deformation Processes during Cyclic Deformation of Mg-Y-Zn Alloys

Deformation mechanisms in extruded Mg-Y-Zn alloys with different volume fractions of the long-period stacking ordered (LPSO) structure have been investigated during cyclic loading, i.e., compression followed by unloading and reverse tensile loading. Electron backscattered diffraction (EBSD) and in situ neutron diffraction (ND) techniques are used to determine strain path dependence of the deformation mechanisms. The twinning-detwinning mechanism operated in the α-Mg phase is of key importance for the subsequent hardening behavior of alloys with complex microstructures, consisting of α-Mg and LPSO phases. Besides the detailed analysis of the lattice strain development as a function of the applied stress, the dislocation density evolution in particular alloys is determined.This research was funded by the Czech Science Foundation under grant 20-07384Y (D.D., G.F., K.F.); by Spanish Ministry of Economy and Competitiveness under project number MAT2016-78850-R; and by the Operational Programme Research, Development and Education, The Ministry of Education, Youth and Sports (OP RDE, MEYS) under the grant CZ.02.1.01/0.0/0.0/16_013/0001794.Peer reviewe