|
|
Bonding and non-bonding interaction potentials for simulations of coarse-grained protein models
Pavlíková, Markéta ; Nová, Lucie (advisor) ; Bačová, Petra (referee)
Protein folding involves the transformation of an amino acid chain to a unique 3D structure. The conformation of a protein is determined by its amino acid sequence. Understanding the process of protein folding and dynamics is crucial since protein function is closely related to its structure and dynamics. These processes can be investigated by means of molecular simulations. Coarse- grained models, which are used in molecular simulations, provide a favorable trade-off between computational efficiency and accuracy. To employ such mod- els, a reasonable force field is necessary. The force field includes both bonding and non-bonding interaction potentials, which are derived either from atomistic simulations or from known, experimentally determined protein structures. We derived such potentials using dataset of more than 4,500 structures from PDB database. 1
|
|
|
Study of self-assembly and degree of ionization of block copolymers using transmission electron microscopy and molecular simulations
Illés, Peter ; Nová, Lucie (advisor) ; Štěpánek, Miroslav (referee)
Responsive systems, such as block copolymers with solvent-affine blocks, can undergo self-assembly into structures like micelles or vesicles. These assem- blies are highly sensitive to slight changes in external conditions, like pH or temperature, leading to the formation or dissolution of micelles. When one of the polymer blocks is a weak polyelectrolyte, its degree of ionization depends not only on the external conditions but also on the association state. This study focuses on investigating the size and degree of ionization of micellar struc- tures formed by polymer chains containing thermoresponsive and pH-responsive blocks. The investigation combines high-resolution transmission electron mi- croscopy and Hamiltonian Monte Carlo simulations to provide a comprehensive understanding of these micellar structures. 1
|
|
|
Application of Electronic Continuum Correction to Molecular Simulations of Nano/Bio Interfaces
BIRIUKOV, Denys
Nowadays it is almost impossible to imagine our life without nanotechnologies. They are present in smartphones and many other gadgets we use every day, while advanced nanoparticle-based devises are currently indispensable in medicine, engineering, and science. In the case of biomedical applications, the knowledge how a specific nanomaterial behaves and changes its properties in complex physiological medium is essential to guarantee the accomplishment of all specific goals facing a scientist or engineer. Some of physical and chemical processes occurring when a nanodevice enters biological environment are yet very difficult to fully detail without accurate computer simulations, so special attention needs to be focused on theoretical studies of nano-bio interactions. In this thesis, molecular simulations were used to investigate the interactions between different nanomaterials (titanium dioxide, silicon dioxide, and gold) and aqueous solutions, which contain ions, organic molecules, and amino acids. The importance of this scope and particularly selected for this study materials and compounds is given in Introduction. To model nano/bio interfaces, we adopted and integrated recent theoretical approaches, which together with basic principles of molecular simulations are described in Methods. Obtained results are divided in four parts and address several important issues that are vital in deciphering molecular mechanisms, through which nanoparticles identify and bind various biomolecules. The simulation data are thoroughly discussed, compared to experiments, and used to explain some of experimental observations. Additionally, outcomes of this thesis serve as a springboard for further theoretical studies aimed to advance our understanding of nano-bio interactions.
|
|
|
2D structures based on metal phosphonates; relationships between arrangement and properties studied by molecular simulations methods
Škoda, Jakub ; Pospíšil, Miroslav (advisor) ; Čapková, Pavla (referee) ; Praus, Petr (referee)
This work deals with the structural analysis of layered zirconium sulfophenylphosphonates and their intercalates with the use of the classical molecular simulation methods. The inner composition of both fully and partially sulfonated layers was determined in agreement with available experimental data, especially chemical analysis, thermogravimetric measurements and X-ray diffraction. The calculations revealed the positions of the water molecules in the planes of sulfo groups which strongly affect the resultant diffraction pattern. Within the zirconium sulfophenylphosphonate layered structure, the arrangements of intercalated species based on optically active dipyridylamine molecules and cations of sodium, copper and iron were solved with the respect to the agreement with experimental results and values of potential energy. In case of the dipyridylamine molecules and its derivatives, the resultant disordered partially row arrangements of the organic molecules in the interlayer were showed to influence the dipole moment of the intercalate. From this point of view, nitro-derivative has been picked out as the most suitable for potential applications. Regarding the intercalated cations, sodium cations take up the space of water molecules next to the sulfo groups while copper and iron cations are distributed in a...
|
|
|
2D structures based on metal phosphonates; relationships between arrangement and properties studied by molecular simulations methods
Škoda, Jakub ; Pospíšil, Miroslav (advisor) ; Čapková, Pavla (referee) ; Praus, Petr (referee)
This work deals with the structural analysis of layered zirconium sulfophenylphosphonates and their intercalates with the use of the classical molecular simulation methods. The inner composition of both fully and partially sulfonated layers was determined in agreement with available experimental data, especially chemical analysis, thermogravimetric measurements and X-ray diffraction. The calculations revealed the positions of the water molecules in the planes of sulfo groups which strongly affect the resultant diffraction pattern. Within the zirconium sulfophenylphosphonate layered structure, the arrangements of intercalated species based on optically active dipyridylamine molecules and cations of sodium, copper and iron were solved with the respect to the agreement with experimental results and values of potential energy. In case of the dipyridylamine molecules and its derivatives, the resultant disordered partially row arrangements of the organic molecules in the interlayer were showed to influence the dipole moment of the intercalate. From this point of view, nitro-derivative has been picked out as the most suitable for potential applications. Regarding the intercalated cations, sodium cations take up the space of water molecules next to the sulfo groups while copper and iron cations are distributed in a...
|
|
|
Molecular simulations of interactions among CdS nanoparticles and montmorillonite
Pšenička, Milan ; Pospíšil, Miroslav (advisor) ; Malý, Marek (referee)
This thesis investigate the structure of cadmium sulfide (CdS) nanoparticles and its stabilization by a surfactant - cetyltrimethylamonnium cation CTA+ and further describe interactions among stabilized CdS nanoparticles and the surface of the layered clay mineral - montmorillonite with using the molecular simulation methods. Initial models of the CdS nanoparticles were build for both crystal structures (Greenockit (G) and Hawleyit (H)). The preferred orientations of the molecules of CTA+ for both crystal types of CdS nanoparticles were found with respect to minimum energy. Prefered orientation is monolayer for Greenockite and bilayer for Hawleyite. Models with the preferred orientation of the molecules of CTA+ were placed on the surface of montmorillonite and after optimization, adsorption energy of CdS nanoparticles with its envelope and montmorillonite surface was calculated. All results and used procedures were compiled in the form of practice for the subject Computational experiments in the theory of molecules I - NBCM100 taught at MFF UK in Prague.
|
|
|
Application of Molecular Simulations in Complex Structural Analysis of Layered Materials
Veteška, Marek ; Pospíšil, Miroslav (advisor) ; Demel, Jan (referee) ; Tokarský, Jonáš (referee)
Title: Application of Molecular Simulations in Complex Structural Analysis of Layered Materials Author: RNDr. Marek Veteška Department: Department of Chemical Physics and Optics Supervisor: RNDr. Miroslav Pospíšil, Ph.D., Dept. of Chemical Physics and Optics Abstract: Techniques of molecular simulations were used together with experimental measurements (X-ray diffraction, thermogravimetry, infrared spectroscopy, elemental analysis and others) to clarify the structure properties of various types of layered materials. The structure of Zn-Al-layered double hydroxide intercalated by pyrenetetra- sulfonate acid was solved. Depending on the relative humidity, the samples showed different arrangements with three planes of water molecules and with either one or two planes of pyrenetetrasulfonate anions. At the same time considerable variability of anions arrangement was demonstrated. The adsorption behavior of natural montmorillonite and montmorillonite modified by tetramethylammonium cations in relation to aniline and phe- nol was explored. Adsorption features differed according to both the type of adsorbed molecules and the type of adsorbents. An important role was played by the plane of water molecules right above the surface which medi- ated adsorption of anilines. The water plane area was reduced by...
|
|
| |
|
| |
|
| |
guest ::
