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Photocontrolled Biomolecules
Planer, Jakub ; Bartošík, Miroslav (referee) ; Vácha,, Robert (referee) ; Kulhánek, Petr (advisor)
This work is focused on molecular dynamics simulations of artificial photosensitive ion channel and AFM probe. To assemble this ion channel, DFT methods were employed for reparametrization of the GAFF force field describing the bridged azobenzene, which was used as a light controlled molecular switch. We proved by molecular dynamics simulations that newly developed parameters correctly describe behavior of assembled model of ion channel in a lipid bilayer. We also constructed a model of AFM probe and observed formation of water meniscus between the AFM probe and surface, both made of -quartz, by employing molecular dynamics simulations. A contribution of this work is the set of new parameters extending GAFF force field for description of the bridged azobenzene. We also verified functionality of ion channel model and model of AFM probe, which can be used for the further water meniscus studies.
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Transition from regular to chaotic motion in black hole magnetospheres
Kopáček, Ondřej ; Karas, Vladimír (advisor) ; Kulhánek, Petr (referee) ; Rezzolla, Luciano (referee)
Cosmic black holes can act as agents of particle acceleration. We study properties of a system consisting of a rotating black hole immersed in a large-scale organized magnetic field. Electrically charged particles in the immediate neighborhood of the horizon are influenced by strong gravity acting together with magnetic and induced electric components. We relax several constraints which were often imposed in previous works: the magnetic field does not have to share a common symmetry axis with the spin of the black hole but they can be inclined with respect to each other, thus violating the axial symmetry. Also, the black hole does not have to remain at rest but it can instead perform fast translational motion together with rotation. We demonstrate that the generalization brings new effects. Starting from uniform electro-vacuum fields in the curved spacetime, we find separatrices and identify magnetic neutral points forming in certain circumstances. We suggest that these structures can represent signatures of magnetic reconnection triggered by frame-dragging effects in the ergosphere. We further investigate the motion of charged particles in these black hole magnetospheres. We concentrate on the transition from the regular motion to chaos, and in this context we explore the characteristics of chaos in...
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Role of Magnetosheath Parameters on Magnetopause Processes
Tkachenko, Oksana ; Šafránková, Jana (advisor) ; Kulhánek, Petr (referee) ; Šimůnek, Jiří (referee)
Title: Role of magnetosheath parameters on magnetopause processes Author: Oksana Tkachenko Department: Department of Surface and Plasma Science Supervisor: Prof. RNDr. Jana Šafránková, DrSc. e-mail address: Jana.Safrankova@mff.cuni.cz Abstract: The thesis addresses of two regions significant for the solar wind- magnetosphere coupling: the cusp in high geomagnetic latitudes and the low-latitude (LLBL) subsolar magnetopause. A penetration of plasma of a solar origin into the magnetosphere could be realized directly through magnetospheric cusps. The region adjacent to the magnetopause in the cusp vicinity is highly turbulent, occupied by the heated magnetosheath- -like plasma with a low drift velocity for which occurrence of vortices is a very common feature. In the first part of the thesis, we present a de- tailed analysis of a vortex-like structure created by a turbulent plasma flow around the magnetopause indentation above the cusp and using the data from Interball-1 and Magion-4; we find necessary conditions and a possible mechanisms to creation of such structures. The second part concerns the low-latitude boundary layer formation, its spatial structure and temporal changes based on THEMIS multipoint observations. In spite of its cru- cial role in transfer of mass, momentum, and energy from the...
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Turbulence in the solar wind from inertial to kinetic scales
Pitňa, Alexander ; Šafránková, Jana (advisor) ; Hellinger, Petr (referee) ; Kulhánek, Petr (referee)
Solar wind, a stream of supersonic plasma emanating from the solar corona, serves as an ideal laboratory for a study of high Reynolds number plasma flows. Turbulent processes that govern the dynamics of the so-called inertial range, i.e., the spatial scales smaller than energy injection scales but larger than the scales where the dissipation processes set in, have been studied for decades. At present, it is believed that the large-scale free energy in a form of kinetic and magnetic fluctuations is transferred via turbulent cascade into smaller scales, where kinetic effects become dominant and heating takes place. In order to understand dissipation processes, high-cadence measurements of solar wind parameters are necessary. The bright monitor of the solar wind (BMSW) instrument on board the Spektr-R spacecraft provides such data, and in tandem with high-cadence measurements of the magnetic field from the Wind spacecraft, we are able address the nature of the sub-ion scale fluctuations. The thesis focus on three interconnected topics, (a) what changes are induced by the passage of a collisionless IP shock in the framework of turbulence, (b) study of a decay of the turbulent energy downstream an IP shock, and (c) identifying the dominant mode of the sub-ion scale fluctuations.
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Magnetopause: location,shape and structure
Dušík, Štefan ; Šafránková, Jana (advisor) ; Kulhánek, Petr (referee) ; Šimůnek, Jiří (referee)
For studies of the solar wind-magnetosphere interaction, the magnetopause is a key region. Prediction of its location and knowledge of its structure in a broad range of upstream parameters are important for further progress on this eld. The present thesis deals with statistical investigations of the magnetopause location as well as case studies of the magnetopause and LLBL structure. Based on simultaneous Themis, Geotail, Interball and Magion measurements, we prepared a study of possible sources of the deviations from magnetopause models including low and high latitudes. We found a signicant deformation of the magnetopause surface in the cusp region at high latitudes and the dependence of the subsolar magnetopause position on the IMF cone angle. The analysis of several events using so called n-T plots brings new results connected with mechanisms of the LLBL formation. We found that during the northward pointing interplanetary magnetic eld, reconnection tailward of the cusp creates the outer part of the LLBL, whereas this sublayer is missing through southward magnetic eld.
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Shell-like structures in the ISM: Observation versus simulations
Sidorin, Vojtěch ; Palouš, Jan (advisor) ; Kulhánek, Petr (referee) ; Recchi, Simone (referee)
Title: Shell-like structures in the ISM: Observation versus simulations Author: Vojtěch Sidorin (vojtech.sidorin@gmail.com)1 Department: Astronomical Institute of Charles University2 Supervisor: Prof. RNDr. Jan Palouš, DrSc. (palous@asu.cas.cz), Astronomical Institute of the Czech Academy of Sciences3 Abstract: Shell-like structures are objects found in large numbers in the inter- stellar medium (ISM). They usually appear as bubbles or segments of bubbles and are believed to result from the deposition of mass and energy into the ISM by stars, gamma-ray bursts, or high-velocity clouds. Interstellar turbulence may play a role in their creation too. These structures influence the dynamics of the ISM and are also linked to star formation. In this thesis, I review our current knowledge of the ISM, interstellar turbulence, and shell-like structures in the ISM. Then I present the research into the GLIMPSE bubble N107 conducted in collaboration with my colleagues. N107 is a dusty shell-like structure found in our Galaxy. We explored its atomic, molecular, and radio-continuum components; derived its distance (3.6 kpc), size (radius of 12 pc), and expansion velocity (8 km s−1 ); and identified 49 associated molecular clumps. Using numerical simulations, we estimated the conditions under which N107 formed and concluded...
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Study of naphthalene access pathways to cytochrome P450 1A2.
Martinka, Jakub ; Jeřábek, Petr (advisor) ; Kulhánek, Petr (referee)
Cytochrome P450 1A2 is a human liver enzyme of a hemoprotein nature that belongs to the evolutionarily ancient group of cytochromes P450. Cytochrome P450 substrates include a wide range of drugs and most procarcinogens, making it a crucial enzyme for the study of carcinogenesis. The main reaction catalyzed by cytochrome P450 1A2 is monooxygenation, in which an oxygen atom is incorporated into a substrate molecule. This reaction takes place at an active site which, in the case of published structure of cytochrome P450 1A2, is buried in the core of the catalytic domain without an accessible tunnels. Molecular modeling techniques allow the study of dynamic phenomena in large systems and are therefore also suitable for simulations of the transport of substrate molecules to the active site. The tunnels are being made accessible due to structural fluctuations. In this work, molecular modeling techniques were used to study the pathways that the naphthalene molecule uses to enter the active site of cytochrome P450 1A2. A system consisting of cytochrome P450 1A2 anchored in a phospholipid membrane, water, ion and naphthalene molecules was simulated. The simulations yielded trajectories with a total length of 8 µs and the analysis identified seven tunnels that can be used to transport substrates....
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Magnetic reconnection in the solar wind
Enžl, Jakub ; Přech, Lubomír (advisor) ; Bárta, Miroslav (referee) ; Kulhánek, Petr (referee)
Magnetic reconnection is a fundamental process that changes magnetic field configuration and converts a magnetic energy to flow energy and plasma heating. It can be found in a plasma with frozen magnetic field lines at boundaries where different magnetic field topologies encounter each other and thin current sheets are created as it is typical in the solar wind. In the thesis, we have used spacecraft measurements of solar wind plasma and magnetic field to found magnetic reconnection exhausts. We analyze and compare them with theoretical predictions. The results of the statistical analysis oriented on re-distribution of the magnetic energy in reconnection showed that both a portion of the energy deposited into heat as well as the energy spent on an acceleration of the exhaust plasma increase with the magnetic shear angle in accord with the increase of the magnetic flux available for reconnection. Moreover, we identify unusual events in the solar wind; we found magnetic reconnection exhausts accompanied by one or two side jets and explained their possible causes.
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Turbulence in the solar wind from inertial to kinetic scales
Pitňa, Alexander ; Šafránková, Jana (advisor) ; Hellinger, Petr (referee) ; Kulhánek, Petr (referee)
Solar wind, a stream of supersonic plasma emanating from the solar corona, serves as an ideal laboratory for a study of high Reynolds number plasma flows. Turbulent processes that govern the dynamics of the so-called inertial range, i.e., the spatial scales smaller than energy injection scales but larger than the scales where the dissipation processes set in, have been studied for decades. At present, it is believed that the large-scale free energy in a form of kinetic and magnetic fluctuations is transferred via turbulent cascade into smaller scales, where kinetic effects become dominant and heating takes place. In order to understand dissipation processes, high-cadence measurements of solar wind parameters are necessary. The bright monitor of the solar wind (BMSW) instrument on board the Spektr-R spacecraft provides such data, and in tandem with high-cadence measurements of the magnetic field from the Wind spacecraft, we are able address the nature of the sub-ion scale fluctuations. The thesis focus on three interconnected topics, (a) what changes are induced by the passage of a collisionless IP shock in the framework of turbulence, (b) study of a decay of the turbulent energy downstream an IP shock, and (c) identifying the dominant mode of the sub-ion scale fluctuations.
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Modeling of an influence of a phospholipid membrane composition on the structure and dynamics of cytochromes P450s.
Gücklhorn, David ; Jeřábek, Petr (advisor) ; Kulhánek, Petr (referee)
Cytochrome P450 1A2 is one the most important enzymes that take part in phase I of biotransformation of xenobiotics in human body. This enzyme is anchored in membrane via transmembrane α-helix. Composition of the phospholipid membrane can affect structure and dynamics of this enzyme. In this thesis optimized full-length all-atom model of cytochrome P450 1A2 in POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membrane was created based on crystal structure of catalytic domain of this enzyme. Methods of molecular dynamics were used for creation and optimization of the model which contained parts with unknown structure. The optimized model was subjected to thorough analysis of its structure and dynamics and compared to a similar model with DLPC (1,2-dilauroyl-sn-glycero-3- phosphocholine) membrane. The results show that the composition of the membrane significantly affects dynamics of transmembrane domain and its contact with catalytic domain. Usage of the thicker POPC membrane resulted in smaller contact between both domains which caused partial emergence of the catalytic domain from membrane. Penetration of palmitoyl chain of POPC into tunnel 2f was observed in one the trajectories. Analysis of pathways to active site of cytochrome P450 1A2 and the influence of the membrane composition on...
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