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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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Design, Fabrication and Testing of Environmental Chamber for Atomic Force Microscope and for Electronic Measurements of Nanosensors
Cahlík, Aleš ; Mach, Jindřich (referee) ; Bartošík, Miroslav (advisor)
This thesis deals with the concept of the chamber for atomic force microscope device NTegra Prima or alternatively for stand-alone measurements of nanosensors. The chamber will be used for defined modification of ambient conditions in space around measured sample. In first part, the theoretical principles of influence of ambient conditions on AFM methods are discussed. In the second chapter, the principles of graphene sensors measurements are showed. Further the reasons and requirements for designing this chamber are introduced. Main part deals with description of design. At the end the results of stress analysis and wall deflection of evacuated chamber are presented.
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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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|
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Design, Fabrication and Testing of Environmental Chamber for Atomic Force Microscope and for Electronic Measurements of Nanosensors
Cahlík, Aleš ; Mach, Jindřich (referee) ; Bartošík, Miroslav (advisor)
This thesis deals with the concept of the chamber for atomic force microscope device NTegra Prima or alternatively for stand-alone measurements of nanosensors. The chamber will be used for defined modification of ambient conditions in space around measured sample. In first part, the theoretical principles of influence of ambient conditions on AFM methods are discussed. In the second chapter, the principles of graphene sensors measurements are showed. Further the reasons and requirements for designing this chamber are introduced. Main part deals with description of design. At the end the results of stress analysis and wall deflection of evacuated chamber are presented.
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