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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.
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První experimenty s distribuovaným Bayesovským rozhodováním
Šmídl, Václav ; Andrýsek, Josef
Decision-making under uncertainty is a natural part of everyday life of every human being. In societal science, various aspects of decision-making were studied, mostly in the area of psychology. In technical science, the process was formalized using probability theory yielding so called Bayesian theory of decision making. However, one of the key assumptions of this theory is that the decision-maker is the only entity that intentionally influences the system. This assumption is certainly violated in more complicated systems, such as human society or distributed control. Recently, a series of papers attempts to offer an extension of the Bayesian theory for many decision-makers, i.e. decentralized stochastic control. Since there are no proofs of optimality of the proposed Bayesian distributed decision making available in the literature, we study this approach via experimental simulation studies.
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Preparation of a presentation for popularisation of computer physics - area of computer simulations
HARVALÍK, Jaroslav
The purpose of the submitted paper is to make the computerized physics more popular among the potential university/college students, namely in the areas of the simulation. Simultaneously, that work is intended to act as explanatory notes of the additional presenation which is composed under the same purpose as the above mentioned paper. It contains the basical terms of the computerized physics. Moreover, the overview of programs for creation of models and simulations as well as resulting examples have been included. Finally, the areas of the computerized simulations are listed, accompanied by the synoptic examples.
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Mathematical Modelling and Simulation of TBR Behavior, Part III, Final Research Report, Task B and C, Project FT-TA/039,2006.
Šimíčková, M. ; Tukač, V. ; Chyba, V. ; Lederer, J. ; Kolena, J. ; Kubička, D. ; Hanika, Jiří ; Jiřičný, Vladimír ; Staněk, Vladimír
Mathematical modelling of hydrogenation, one particle model, particles column model, model of catalytic bed in TBR.
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Housing Financing in the Czech Republic
STŘELEČKOVÁ, Lucie
This bachelor thesis is dealing with the different ways, how to finance housing needs in the Czech Republic within one particular financial group. By this group was chosen Česká spořitelna, inc., because it is one of the biggest and most important banks at czech financial market, which offer and provide many products taking care of this problem. One of the possibilities how to obtain some financial resources to solve the housing situation, is establishing of building savings, or more precise bridge loans from these savings. As another choice people can take mortgage credits, loans from national housing developement fund, consumer lendings and a lot more products provided by another different financial groups. In literary background research were presented main possibilities of financing housing needs (loans provided by the building savings and mortgage credits ) and these specifical possibilities were explained. Laws, conditioning the ways of financing these housing needs, were shown there and then other possibilities were characterized. In practical part there is short characteristics of Česká spořitelna, inc. and also description of the offered products. There were made some simulations and tests on these products. Target was to get the most information about these produtcs at model created situation and find out all the advantages and disadvantages of the products and thanks to that be able to recommend suitable product to different clients
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Aging assessment of heterogeneous weld on the basis of instrumented indentation
Dlouhý, Ivo ; Hadraba, Hynek ; Stodola, M. ; Čupera, Pavel ; Al Khaddour, Samer
Sets of data for development of computing procedures of tensile loading curves from indentation curves have been summarised. The data obtained have been supplied also in digital form (tables) representing indentation curves for different loads by ball indentation technique and, in addition, tensile loading curves of the same microstructures obtained at room temperature. The paper focuses interest on the effect of simulated ageing on fracture behaviour of sub weld deposit regions, and, in addition, empirical analyses of indentation curves obtained from the interface between 22K low carbon steel and weld deposit.
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The preprocessor for system LISA
Hora, Petr ; Šiňor, M.
In this contribution we pay attention to the propagation of the stress waves in an arbitrary complex inhomogeneous media. For the system of elastodynamic wave equations we have adopted the method of solution based on the local interaction simulation approach (LISA) and the sharp interface model (SIM) introduced for 1D, 2D and 3D cases in [1-3].
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Ab initio calculations of theoretical strength and phase stability in copper
Černý, M. ; Šob, Mojmír ; Šandera, P.
Simulation of tensile test of copper cryslat along <001> is performed using ab initio full-potential linear augmented plane waves (FLAPW) method. Both the local density approximation (LDA) and generalized gradient approximation (GGA) are used to evaluate exchange-correlation contribution to the total energy. Equilibrium lattice parameter and Young modulus are computed ro assess reliability of our results by comparing them with experiment. Stability conditions for uniaxially loaded system are presented and analyzed. Finally, the ideal strength (IS) is calculated.
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