|
Methods computer simulation
SUCHAN, Petr
This text includes analyses of fundamental techniques that are often used for creating mathematic models in the computer physics. The text is divided into four basic chapters. The first chapter brings the definition of computer models and of computer simulation. The following chapter deals with particle, linking and hybrid techniques of the computer modeling. In the end the text describes the most used methods of the computer simulation, i.e. the method of molecular dynamics and the Monte Carlo method.
|
|
Atomistické simulace uspořádávání v niklových slitinách pod vlivem mechanického napětí
Buršík, Jiří
Systems containing up to six alloing elements typical of advanced Ni-based superalloys were modelled.their ordering was simulated at atomic level using a Monte Carlo approach with púeriodic boundary conditions and Kawasaki dynamics.molecular dynamics routines were embedded into standard kinetic Ising model to account for relaxing of local atomic positions.Straining computer experiments show that elastic parameters and bulk modulus undergo comparatively large changes at the beginning of ordering process.
|
|
Modelling of Phase Composition of Heat Resistant Steels and their Welds
Dvořáček, Ondřej ; Foret, Rudolf (referee) ; Jan, Vít (advisor)
This work deals with the effects of high temperature exposition of low alloyed creep resistant steels on their structural stability and structural stability of their weld joint. The theoretical part of this work gives an overview of creep resistant steels considering their chemical and phase composition and their connection to high temperature mechanical properties. The CALPHAD method is presented as generally accepted approach for equilibrated calculations and Thermo-Calc and DICTRA software packages are introduced as CALPHAD applications. Thermo-Calc software is used for calculation of phase composition of the examined materials and for calculation of the phase diagrams. Software DICTRA is used for simulations of diffusion controlled phase reactions in the analysed weld. Experimentally one weld joint of the steels 15 128 and 15 313 has been studied after four different annealing procedures. The experimental results include chemical profiles across the welds, microhardness profiles and metallographic analysis of significant regions of the welds. These experimental results are compared with the simulation results. The comparison shows a reasonable agreement between experimental and simulation data.
|
|
Computational modelling of mechanical tests of isolated cells
Sůkal, Petr ; Fuis, Vladimír (referee) ; Burša, Jiří (advisor)
The master’s thesis deals with computational modelling of mechanical testing of isolated cells, particularly of single-axle tensile test. The aim is to imitate the real deformed shape known from experiments. At first, the structure of each cell component is described and analyzed according to their significance for mechanical behavior. The outline of basic mechanical tests used for cell testing is discussed next. A structural computational model comprising all components significant for mechanical purposes is created for the modelling. Those components are nucleus, cytoplasm, cell membrane and cytoskeleton. Due to the problems with convergence the model was divided into two parts. The first one treats separately the shape of cytoskeleton and the second one treats the shape of communicating components (nucleus, cytoplasm and cell membrane). Both of those partial models succeed in reaching the deformations according to the experiments.
|
|
Experimental determination of stress-strain dependence of non-standard materials
Vavřík, Daniel ; Drdácký, Miloš
The subject of this work is experimental determination of mechanical properties for different types of animal hairs. Mortars reinforced by thin fibres have promising properties for application in cultural heritage protection. Theoretical research is based on mathematical modeling of composite materials with inorganic (brittle) matrix and differential types of reinforcement fibres - natural as well as man made polymeric fibres. For these models, knowledge of mechanical properties of the fibres is needed. Optical method developed especially from this purpose will be introduced in this paper.
|
|
Computer simulations of plasma discharge for biomedical and environmental applications
ERHART, Jaroslav
This diploma thesis is aimed to the possibilities of using low-temperature plasma in various fields of science, research and production with the main focus is given to applications in medicine and environmental applications. In the practical part is presented design a computer model for simulation of the plasma behavior in the above areas. This model is a hybrid type and as a working gas is used oxygen.
|
| |
|
Biodegradation of environmental pollutants - Structural characterization of a new type of haloalkane DbeA
PAPEŽ, Martin
The aim of this work is the crystallization of model protein Xylanase and a new haloalkane dehalogenase DbeA and description of DbeA structure using modeling programs. For this purpose, the crystallization methods based on sitting and hanging drop vapor diffusion, crystallization under oil and crystallization in capillaries were applied. The structure was solved using programs WinCoot and VMD. The results will be used for further research of structure-functional relationships of haloalkane dehalogenases.
|
|
Modeling and simulation of a hybrid micro grid in PSCAD environment
Moravčík, Martin ; Mastný, Petr (referee) ; Drápela, Jiří (advisor)
In the opening part of this master´s thesis there is given concept, description, usage and advantages of micro hybrid grids in comparison to micro grids and there are evolution steps towards hybrid grid. There is also a mention about economics of operation of these grids. In the second part of this thesis there are descriptions of devices that are suitable for usage in micro hybrid grids with emphasis on generators and accumulation possibilities. In the next part of this thesis there is given an approach and description for modeling of various components of hybrid grids in PSCAD environment. In the next part of this thesis there are given simulation results that were conducted on created model. Especially power balance in 24 hour operation of the grid with method for determining suitable size of accumulation and installed capacity of photovoltaics. And next there are showed responses from change of power from photovoltaics, next there is a transition to islanded mode and last there is showed the behavior of converter when the limits of accumulation are reached. In the final part of this thesis there are conclusions, fulfillment of goals of this thesis and possibilities of further study.
|
|
Modeling Substrate-Enzyme Interactions in Fungal Hydrolases
KULIK, Natallia
Computational tools play an important role in the description of biological systems. Scientists describe and study structure, conformational changes and interactions between molecules in silico, often as a cheaper and faster alternative for biosynthesis. The simulated dynamic behavior in time of a molecular system is a straight forward source of information about substrate-enzyme interactions at the atomic level, and a powerful tool for the identification of molecular properties important in enzymatic reactions. Our study is focused on the computational investigation of structure and substrate specificity of hydrolases important in biotransformation. The computational work was performed in close collaboration with biochemists-experimentalists from Charles University and the Microbiological Institute of the Academy of Sciences of the Czech Republic. Hydrolases have great a potential in the chemoenzymatic synthesis of modified carbohydrates with regulated properties. Carbohydrates, as substrates of hydrolases, are important in normal functionality of many organisms. They have a dual role in immune response regulation: some carbohydrates (like GlcNAc and ManNAc) participate in activation and some (like GalNAc) in suppressing immunity; glycosidase deficiency is associated with a number of lysosomal disorders. We used homology modeling, computational docking and molecular dynamics simulation (MD) methods for the complex study of fungal hydrolases: alpha-galactosidase/alpha-N-acetylgalactosaminidase from Aspergillus niger; beta-N-acetylhexosaminidases (HEX) (from Aspergillus oryzae and Penicillium oxalicum); nitrilase from Aspergillus niger. Our structural study unambigously demonstrates that the enzyme encoded by genes variant A (aglA) from A. niger is able to accept alpha-N-acetylgalactosamine as its substrate and explains structural features responsible for its specificity. Homology models of HEXs from P. oxalicum and A. oryzae were built and compared. Homology models were used to study the role of protein glycosylation, disulfide bonds, dimer formation and interaction with natural and modified substrates. Model of nitrilase from Aspergillus niger helped to analyze multimer formation.
|
guest ::
