|
|
Molecular simulation study of aqueous solutions of alifatic alcohols
Peštuka, Martin ; Žídek, Jan (referee) ; Janeček, Jiří (advisor)
The aim of this bachelor thesis was to carry out set of molecular dynamic simulations of aqueous solutions of aliphatic alcohols in infinite attenuation. In order to work with molecular dynamic simulations it was necessary to become familiar with the program equipment to perform molecular dynamic simulations and analyze the results. Within the work the basic simulation boxes contained 300, 400, 500 and 1000 water molecules and one molecule of aliphatic alcohol. From the simulated trajectories we evaluated the volume change associated with the insertion of one particle of alcohol and the radial distribution functions around the molecule of solute. The results were compared with experimental data.
|
|
|
Analysis and Implementation of Virus Pattern Rules
Janeček, Jiří ; Schäfer, Jiří (referee) ; Janoušek, Vladimír (advisor)
This bachelor's thesis deals with analysis and implementation of rules for program, which routes virus samples for their later processing. The expert system is integrated in this program. It was created by using tool called CLIPS. This thesis also describes environment, where program is situated, and importance of component like this in system for virus sample processing. Analyzer has been implemented in C/C++ language.
|
|
|
Effect of metal ions on the rheological behaviour of polyelectrolyte solutions
Lišková, Kateřina ; Běťák, Jiří (referee) ; Janeček, Jiří (advisor)
This diploma thesis is focused on two parts. The first one deals with rheological behavior of sodium carboxymethylcellulose (CMC-Na) solutions in the presence of sodium and calcium ions. The solutions of various concentrations were prepared by solubilization in aqueous solutions of NaCl or CaCl2. The effect of monovalent and bivalent ions on apparent viscosity and viscoelastic properties of these solutions was studied. It was found that in the case of low concentrations of CMC-Na in the sample (up to 0.5% w/w) the elastic character increases. At the same time the stiffness of the sample is higher with higher concentration of calcium ion in the solution. This increase might indicate the formation of gel network. On the other hand the viscosity of these solutions decreases with higher concentration of calcium ions. In case of solutions with concentration higher than 1.5% w/w changes of viscosity did not happen by influence of addition ions. Rheological behavior was compared also with solutions prepared without adding an electrolyte as well as with acid form of carboxymethylcellulose (CMC-H). In terms of second part the molecular dynamic simulations of hyaluronan tetramer both sodium and calcium in aqueous medium were performed. Structure and arrangement of water molecules in the surrounding of hyaluronan chain were studied. Structure was described by formalism of radial distribution functions. In the case of system containing sodium ions only, the obtained results are in accordance with earlier published data. Presence of calcium ions does not cause qualitative changes during the radial distribution functions in comparison with the system with sodium ions.
|
|
|
Acidobasic behavior of carboxymethylcellulose solutions
Teslíková, Ivana ; Kislinger, Jiří (referee) ; Janeček, Jiří (advisor)
This work concerns with the study of acidobasic behavior of solutions of sodium salts of carboxymethylcellulose (CMC-Na). This behavior was investigated using acidimetric titrations of the salt solutions with potentiometric and conductometric indications. In order to determine the content of carboxylic groups in two different samples of CMC-Na (M1=90 kDa, DS1=0.7; M2=700 kDa, DS2=0.9), we employed the method of Ray von Wandruzska, originally proposed for the determination of the acidity of humic substances. The values of the degree of substitution (DS) obtained using this method correspond to the values declared by the producer. The small differences (of the order few percentage points) can be attributed to the humidity of the samples. The acidimetric titrations were performed also for solutions with different ionic strengths. There is an apparent effect of the ionic strength on the shape of titration curves; nevertheless these data were not used for any theoretical interpretation.
|
|
|
Determination of acidic groups in humic substances.
Kabeláčová, Kateřina ; Sedláček, Petr (referee) ; Janeček, Jiří (advisor)
Within this bachelor thesis we compared three method to determine the acidity of humic substances. We employed the baryta-method (which determines the total acidity), the Ca-acetate method (determines the content of carboxylic groups only) and the technique of Ray von Wandruszka. This method should provide the content of groups dissociable at pH>12. We used four different samples of humic acids isolated from two sources (lignite and peat). While the differences between results of baryta and Ca-acetate methods were expected and can be easily explained, the values of acidity obtained by the von Wandruszka method represent roughly one half of the results of Ca-acetate method and almost only ten percent of the baryta results. In the cases of baryta as well as von Wandruszka methods we observed a dependency of the results on the time-length of the analysis. In the theoretical part the characterisation, divided, creation, structure and properties of humic substances are summarized. In the end of theoretical part are described using method for analysis of humic acids.
|
|
|
Optimization of Structured Queries on Large Databases
Janeček, Jiří ; Šebek, Michal (referee) ; Burget, Radek (advisor)
This master's thesis deals with optimization of structured queries on large databases. Principles of these optimizations are used during creation of application, which allows finding over one specific large database. At the same time this thesis compares efficiency between the new designed SQL constructions and the not optimized SQL constructions.
|
|
|
Hydration of biomolecules
Flimel, Karol ; Janeček, Jiří (referee) ; Kučerík, Jiří (advisor)
The aim of this thesis was to apply methods of thermal analysis (differential scanning calorimetry and termogravimetry) to study kinetics of water evaporation from hyaluronan. This approach allowed to determine the changes of desorption energies in the course of evaporation and consequently helped to improve the understanding of the hyaluronan hydration. Thermoanalytical methods in combination with model-free kinetics previously suggested by Ozawa were used to determine kinetic parameters of studied processes. Results confirmed previous knowledge about the content of water located in primary hydration shell of hyaluronan, i.e. concentration range from 0.4 – 0.8 g of water per 1 g of hyaluronan. Further, it was found out that during the evaporation in this concentration range, the hyaluronan gel, stabilized probably by hydrogen bonds, is formed.
|
|
|
Uncoupling of DNA restriction and DNA translocation functions of the Type I restriction modification enzyme EcoR124I
Šišáková, Eva ; Weiserová, Marie (advisor) ; Janeček, Jiří (referee) ; Janščák, Pavel (referee)
v vuuuerJ Type I restriďion-modificationenzymeEcoRl24I is a multifunctional,hetero.oligomeric enzyme complex that cleaves DNA after extensiveATP hydrolysis coupled to processive DNA translocation.ATP hydrolysis and DNA translocationare conferredby superfamily2 (SF2) helicase motifs in the central domain of its HsdR subunit.The N-terminal domain carries a conservedregion with catalytic residuesreminiscentof the PD-@/D)xK catalytic motif of Type II restrictionenzymes. Single amino acid substitutionsin the motifs II and III reducedor removedDNA cleavage activiý of the enzymecomplexwithoutďfecting an assemblyof the complex and its DNA- binding properties.Using a combinationof bulk solution and single-moleculeassays,we investigatedthe influence of these mutationson the DNA translocationpropertiesof the enzyme,conferredby the helicase domain. Reduced ATPase activiý of the mutantswas detectedby steady-statestopped flow measurementswith the use of phosphate-binding protein.These results do not show a clear relationshipbetweenthe translocationratesand ATPase rates.Probably the broaderand bimodal distributionof hanslocationratesand the stalling eventsduring initiation revealedin single molecule experimentsall lead to a lower apparentATPase rates.We suggestanexistenceof possibleinterdomďninteractionsbetween the...
|
|
|
Optimization of Structured Queries on Large Databases
Janeček, Jiří ; Šebek, Michal (referee) ; Burget, Radek (advisor)
This master's thesis deals with optimization of structured queries on large databases. Principles of these optimizations are used during creation of application, which allows finding over one specific large database. At the same time this thesis compares efficiency between the new designed SQL constructions and the not optimized SQL constructions.
|
|
|
Restrikčně-modifikační enzymy Typu I - identifikace pomocí dvourozměrné elektroforesy a studium fosforylace podjednotek Hsd.
Cajthamlová, Kamila ; Weiserová, Marie (advisor) ; Janeček, Jiří (referee) ; Pospíšek, Martin (referee)
107 7. Závěr 1. Vytvořili jsme podmínky pro dělení a identifikaci všech tří podjednotek Hsd R-M enzymů Typu I EcoKI a EcoR124I na dvourozměrném gelu. Optimalizovali jsme podmínky dělení těchto enzymů v nerovnovážném gradientu pH (NEPHGE) v prvním rozměru 2D-PAGE na pozadí celkových proteinů buněčného extraktu. Tento systém nám v budoucnu umožní provést detailnější studie exprese a postranslační modifikace R-M enzymů Typu I v závislosti na různých fyziologických podmínkách a v souvislosti celkové buněčné proteinové exprese. 2. Využití tohoto systému v primárních pokusech odhalilo existenci dvou isoforem podjednotky HsdR systému EcoKI lišících se velikostí náboje. Usoudili jsme, že jedna z těchto isoforem by mohla být posttranslačně modifikována. 3. Sledování fosforylace zástupců tří skupin R-M enzymů Typu I EcoKI (skupina IA), EcoAI (skupina IB) a EcoR124I (skupina IC), na základě imunoprecipitačních analys kmenů E. coli produkujících tyto enzymy, prokázalo fosforylaci enzymu EcoKI na podjednotce HsdR. Podjednotky HsdM ani HsdS enzymu EcoKI fosforylovány nejsou. Žádná z podjednotek Hsd systémů EcoAI a EcoR124I také fosforylována nebyla. 4. Podjednotka HsdR enzymu EcoKI je fosforylována in vivo pokud je součástí komplexní REasy EcoKI. Samotná HsdR, bez současné exprese HsdM a HsdS, kdy se netvoří funkční...
|
guest ::
RSS feed.