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Molecular simulation of Lennard-Jones fluid as a task for physical chemistry laboratory
Krieger, Jakub ; Košovan, Peter (advisor) ; Kolafa, Jiří (referee)
Molecular simulations are capable of reproducing and predicting the behavior of real systems using a simplified model. Over the past 70 years, thanks to the rapid development of computers, this method has become an important part of various scientific fields. Thanks to their speed and low cost, molecular simulations can work hand in hand with a real experiment and in some cases even replace it. The didactics of this progressive method are in its beginnings at the Faculty of Science of Charles University, and its teaching is limited to master's and higher studies. In this work, we created and tested a task for physical chemistry laboratory, which can serve as a first introduction to molecular simulations for undergraduate chemistry students. The task, written in the interactive Jupyter Notebook environment, was designed based on modern pedagogical approaches of inquiry based learning, supplemented by a high level of scaffolding due to the complexity of the teaching content. The choice of simulating the model of supercritical argon described by the Lennard-Jones potential was based on the requirement for conceptual simplicity and the possibility of connection with already known concepts. Testing of the task on 12 students made it possible to create a time schedule, correct errors, identify the most common...
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Modeling of biologically relevant lipid multilayers in the context of drug delivery
Saija, Maria Chiara ; Cwiklik, Lukasz (advisor) ; Szczęsna-Iskander, Dorota (referee) ; Heyda, Jan (referee)
Understanding the topical drug delivery at basic physico-chemical and biophysical levels is still challenging. One of the main reasons is the specificity of the processes involved, depending on the delivery target. The tear film lipid layer plays a vital role in ocular health and serves as a target for topical ophthalmic drug delivery. This doctoral thesis investigates two topics related to topical eye delivery, including a case study of drug delivery systems and their major components in the tear film lipid layer, and the effect of a lipid modification on a lipid-associate peptide as a potential drug. This research is conducted by using molecular dynamics simulations, which are comple- mented by various experimental techniques. The research about the drug delivery systems is threefold: the first objective is to study the impact of commonly used preservatives on the tear film lipid layer; the second one is to explore the influence of the latanoprost drug on the tear lipids; the third one is to investigate different drug delivery systems containing latanoprost drug and their interaction with the lipid layer in the tears. These studies are conducted by combining molecular dynamics simulations and the experiments involving the Langmuir-type lipids film. The key findings of this research have practical...
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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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