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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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Identification of the Protein Tunnels Using Molecular Dynamics
Kohout, Petr ; Martínek, Tomáš (referee) ; Musil, Miloš (advisor)
This thesis focuses on the analysis of protein structures. The aim is to design Caver Web 2.0 -- a new version of the web application that integrates additional scientific tools and allows users to go through a complicated workflow to provide relevant results without the need for a deeper knowledge of the integrated tools. Everything will be delivered through a simple and interactive user interface. The application extends the original Caver Web 1.0 application with new features. Caver Web 1.0 is a web server suitable for identifying protein tunnels and channels for which it allows to run ligand transport analyses. The program is characterized by an intuitive and user-friendly interface with minimum required input from the user. The server is suitable for researchers without advanced bioinformatics or technical knowledge. Its current version is well established and highly used in the scientific community (35,000 completed calculations in two years of operation). The most significant limitation of the current version is the ability to analyze only static structure, which often provides an incomplete biological picture. Therefore, it was decided to extend the tool to calculate molecular dynamics to provide a comprehensive picture of protein structure changes.
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Influence of Solvent on Deformation Behavior of Hydrogels
Kulovaná, Eva ; Bartlová, Milada (referee) ; Mráček, Aleš (referee) ; Žídek, Jan (advisor)
The thesis deals with molecular dynamic simulation of the influence of water on the deformation of hydrogels. Hydrogels are model materials formed from macromolecular networks solvated with water. It was found that water can form bridges between macromolecules that take the form of temporary ionic crosslinks. These bridges affect the behavior of the network during deformation. Water bridges are water molecules that have a limited radius of motion in the space between two macromolecules. The concentration of the water bridges was regulated by a partial charge on the macromolecular chain in the organic network. Bridges are a type of interaction that is relatively strong but significantly delocalized. It is not possible to dissociate the water bridge, after dissociation it will be re-created in another place in a short time. The influence of water bridges was compared with other types of network crosslinks, especially covalent and physical bonds. Covalent crosslinks are modeled as a simple binding interaction between two macromolecules. They are undissociable and are local throughout the simulation. Physical bonds are modeled as micelles, where hydrophobic groups form the core and hydrophilic groups form the micelle shell. Physical bonds have the nature of dissociable bonds that are local. Different types of crosslinks have different effects on deformation properties. The deformation of a network containing a combination of two types of crosslinks was simulated: (i) physically-covalent, (ii) ionically-covalent, and (iii) physically-ionic networks and (iv) ternary physically-covalent-ion networks. For individual and combined networks, the behavior depending on simple networks was verified. The number of water bridges was fundamentally affected by the primary structure of the chains. When the PEG chain was replaced with hydrophobic polyoxymethylene (POM) or polyoxytrimethylene (POTM), their solvation and mechanical behavior deteriorated.
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Deformation mechanisms in crystals by means of molecular dynamics
Lamberský, Vojtěch ; Grepl, Robert (referee) ; Černý, Miroslav (advisor)
This work deals with molecular dynamics modeling of processes in condensed matter on atomic level. The physical principles used to predict motion of atom or molecule groups are described in the retrieval part. Then follows a description of the EAM method, ways how to parallelize computing on many processors and how perform calculation optimizing. Finally, we perform a theoretical tensile strength computation using Lammps program.
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Accuracy evaluation of neural network potentials for simulations of platinum nanocluster at hydroxylated silica interfaces
Pokorná, Kristýna ; Erlebach, Andreas (advisor) ; Vázquez Melis, Héctor (referee)
Supported platinum nanoparticles are important heterogeneous catalysts in many industrial processes, but their activity is strongly affected by particle diffusion and sintering mechanisms which lead to deactivation of the catalyst. To stabilise Pt nanoparticles, it is necessary to understand the reactive interactions of Pt with its support material, e.g., hydroxylated silica and defect-containing zeolites. Realistic simulations of such catalysts at the relevant timescales can be achieved with Neural Network Potentials (NNP) which retain ab initio accuracy at about 103 times lower computational costs compared to density functional theory (DFT) calculations. However, NNPs have only limited transferability to systems not included in the training database. Therefore, in this work recently developed SchNet NNPs were thoroughly tested. These NNPs were trained on a diverse set of Pt and defect-containing zeolites and hydroxylated silica surfaces. Firstly, the DFT database was extended by an active learning approach to accurately model the surfaces of α-quartz, MWW as well as the 2D zeolite layer IPC-1P (hydrolysis product of UTL). The NNPs trained on the new DFT database were then tested using MD simulations of systems unseen during the training procedure. These systems include a silanol nest containing...
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Developing biomolecular interactions models for molecular simulations: Critical evaluation of force field parametrizations
Tempra, Carmelo ; Jungwirth, Pavel (advisor) ; Vácha, Robert (referee) ; Vega de las Heras, Carlos (referee)
Force field molecular dynamics methods are nowadays commonly used to study molecular interactions in many scientific fields. The accuracy of force fields has been improving over the years, allowing for a meaningful physical description of molecular phenomena. However, force fields have limitations. In this dissertation, I explored some of these limitations resulting from the parametrization strategy of force fields and the extent to which non-classical behavior, such as nuclear quantum effects, can be incorporated into classical force field molecular dynamics. In the first part, I investigated to what extent nuclear quantum effects can be accounted for within a classical force field for water. This allowed us to model the differences between bulk light vs. heavy water. The developed model was then used to describe solvent isotope effects on biomolecules, such as amino acids, proteins, and biomembranes, and to seek an explanation why heavy water (unlike light water) tastes sweet. In the second part, I pointed out the drawbacks of using certain training datasets in comparison to others when optimizing a force field, using aqueous calcium chloride as an example. In the third part, I demonstrated the importance of using an accurate water model during the optimization of force fields for phospholipids to adequately capture...
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Computer simulations of protein structures using coarse-grained models
Halda, Miloš ; Nová, Lucie (advisor) ; Limpouchová, Zuzana (referee)
The main part of this bachelor's thesis is an operational software for coarse- grained protein simulations, suitable for testing of new potential functions. The program is using a pivot-based proposal of new states and Monte Carlo evaluation of the proposed state. The program also allows to use a simulated annealing technique with the linear temperature decrease. Mean estimation and error estimation using the Block Method are implemented for evaluation of the simulations. The software was tested on a several proteins. The simulations provided expected results for shorter chains (88 and less aminoacids), but simulations of longer chains (111 and more aminoacids) have shown the software limitations. Several options for the software improvement regarding the new state proposal for simulations of longer chains were discussed. 1
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The Interaction of Graphene Oxide with Humic Acids, a Computational Study
FERLIN, Stefan
This study was focused on the interactions of Graphene oxide with humic acids in aqueous solutions. Additionally, to this work, Graphene oxide and water interactions with and without the addition of ions were studied. The behavior of a fulvic acid in the presence of Graphene oxide has been investigated as well. The study was performed using computer simulations that were achieved by Molecular Dynamics simulations. These simulations provided useful data on a nanometer scale.
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Mechanistic Insights into Reactive Zeolite-Water Interactions
Benešová, Tereza ; Heard, Christopher James (advisor) ; Maldonado Dominguez, Carlos Mauricio (referee)
Title: Mechanistic Insights into Reactive Zeolite-Water Interactions Author: Tereza Benešová Department: Department of Physical and Macromolecular Chemistry Supervisor: Christopher Heard, PhD. Abstract: An in silico investigation of zeolite-water interactions was undertaken using a combined static and dynamic approach within density functional theory. Two periodic models of zeolite chabazite were used, purely siliceous and aluminosilicate in order to explain the different behaviour of water near Si-O-Si and Al-O-Si bridges. One or two water molecules per supercell of the model were used, corresponding to experimental conditions of steaming. Under such conditions, water can interact with zeolites by non-reactive adsorption but also by reactive interactions such as hydrolysis and oxygen exchange between water and the framework. The main goal of the study was to explain oxygen exchange at an atomistic level. The viable mechanisms of oxygen exchange were established. These mechanisms are different for Si-O-Si and Al-O-Si bridges but for both of them oxygen exchange is initiated by partial hydrolysis of the framework. After this hydrolysis, oxygen exchange heals the framework while incorporating into it the oxygen that originated from the water. Both established mechanisms are competitive with non-exchange...
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