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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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Molecular modeling of lipid membranes with fluorescent probes
Dékány Fraňová, Miroslava ; Pospíšil, Miroslav (advisor) ; Vácha, Robert (referee) ; Barvík, Ivan (referee)
Title: Molecular modeling of lipid membranes with fluorescent probes Author: RNDr. Miroslava Dékány Fraňová Department / Institute: Department of Chemical Physics and Optics MFF UK Supervisor of the doctoral thesis: RNDr. Miroslav Pospíšil, Ph.D., Department of Chemical Physics and Optics, MFF UK Abstract: We studied biological membranes with fluorescent probes. First part of the work describes the properties of lipid bilayer consisting of DPPC (dipalmitoylphosphatidylcholine) and various cholesterol concentrations (5 mol % and 20 mol %). The properties are studied via the free probe - DPH (diphenylhexatriene) which is in various concentrations randomly immersed into both layers of the membrane. Second part of this work studies the properties of DOPC (dioleoylphosphatidylcholine) membrane via pyrene probes attached to 4th , 6th , 8th , and 10th carbon atom in both acyl chains of the host lipid and compares how the membrane properties differ based on the various pyrene positions. Here we focused also on dimerization rate of pyrene probes based on their position and the relationship with lateral pressure profile. Keywords: molecular simulation, membrane, fluorescent probes, lipids, lateral pressure profile
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The effect of peptides derived from protein transmembrane domains on membranes
Olšinová, Marie ; Cebecauer, Marek (advisor) ; Obšil, Tomáš (referee) ; Vácha, Robert (referee)
Rich structure of cell membranes raises broad number of questions regarding the mechanisms driving and regulating processes taking place on membranes. The thesis presents four articles investigating organization of lipid membranes and peptide-lipid interactions. The experiments were performed on model lipid membranes. These simplified systems that partially mimic cell membranes enable to study protein-lipid interactions at the molecular level and membrane physico-chemical properties in a controlled way. Advanced fluorescence techniques such as FCS, TDFS, FLIM and anisotropy were used for the system characterization. First publication describes newly designed fluorescence dyes based on boron dipyrromethene structure, the so- called molecular rotors, which are reported to be viscosity-sensitive probes. Detailed analysis of fluorescence lifetime of excited state of the molecular rotors inserted into lipid membranes showed diverse incorporation of dyes into membranes and their reorientation in membranes of different rigidity. The second part investigates existence of lipid nanodomains in membranes caused by the presence of a cross-linker. Even though standard fluorescence microscopy techniques do not allow direct visualization of the nanodomains, we were able to detect these structures by employment of...
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Investor jako Homo Oeconomicus nebo Human; Jaké jsou zdroje odchylek od racionality na finančních trzích?
Vacha, Robert ; Chytilová, Helena (advisor) ; Prokop, Jaromír (referee)
The thesis deals with the differences among phenomena of Homo Oeconomicus and Human and their presence in the financial markets. Furthermore, it aims at revealing differences of behavior in alignment with the phenomena among groups of people involved and not involved in the financial markets. To do so we use an experiment with its assessment based on the Anchoring Index. For the purpose of the research of behavior in alignment with the Prospect theory, the thesis defines new index of assessment of human behavior the Human Index upon which it draws conclusions about the two groups. The results show no significant difference in propensity to bias and marginal difference in behavior in alignment with the prospect theory where the group involved in the financial markets reveals less Human behavior. Altogether, the findings are no remarkable difference in behavior among the two groups, i.e. both the group of people involved in the financial markets as well as those not involved are Human at very similar levels.
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Molecular modeling of lipid membranes with fluorescent probes
Dékány Fraňová, Miroslava ; Pospíšil, Miroslav (advisor) ; Vácha, Robert (referee) ; Barvík, Ivan (referee)
Title: Molecular modeling of lipid membranes with fluorescent probes Author: RNDr. Miroslava Dékány Fraňová Department / Institute: Department of Chemical Physics and Optics MFF UK Supervisor of the doctoral thesis: RNDr. Miroslav Pospíšil, Ph.D., Department of Chemical Physics and Optics, MFF UK Abstract: We studied biological membranes with fluorescent probes. First part of the work describes the properties of lipid bilayer consisting of DPPC (dipalmitoylphosphatidylcholine) and various cholesterol concentrations (5 mol % and 20 mol %). The properties are studied via the free probe - DPH (diphenylhexatriene) which is in various concentrations randomly immersed into both layers of the membrane. Second part of this work studies the properties of DOPC (dioleoylphosphatidylcholine) membrane via pyrene probes attached to 4th , 6th , 8th , and 10th carbon atom in both acyl chains of the host lipid and compares how the membrane properties differ based on the various pyrene positions. Here we focused also on dimerization rate of pyrene probes based on their position and the relationship with lateral pressure profile. Keywords: molecular simulation, membrane, fluorescent probes, lipids, lateral pressure profile
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Molecular Simulations of Surfaces of Aqueous Solutions
Vácha, Robert ; Jungwirth, Pavel (advisor) ; Kolafa, Jiří (referee) ; Barvík, Ivan (referee)
This thesis consists of 18 papers, in which we investigated the behavior of molecules and ions at aqueous interfaces by means of molecular dynamics (MD) simulations. We started our simulations with the surface of neat water, where we investigated the behavior of hydronium and hydroxide ions, i.e., the products of autolysis of water that are of 10�7M concentration in pure water. The results, ranging from ab initio high level calculations on water clusters and ab initio dynamics on small systems to statistically converged classical molecular dynamics simulations are mutually consistent47,48,50. The observed surface adsorption of hydronium is also consistent with the surface selective spectroscopy experiments (VSFG, SHG, PES)45,51,55{59, surface tension measurements60, and with _-potential measurements of acidic solutions62,63. The spectroscopy and surface tension experiments are also in agreement with the weak surface repulsion/non-accumulation of hydroxide observed in our simulations. However, there are macroscopic measurements, such as higher pH electrophoretic mobility measurements, titration of oil emulsions, and thin _lm stability experiments that indicate a negative charge on air/water and oil/water interfaces 61{71. Even though these experiments do not directly reveal the chemical nature or...
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Anticipated knowledge from the ecology in textbooks of grammary school
VÁCHA, Robert
This bachelor thesis is divided on a theoretical and practical part. In the theoretical part it describes the general educational program - its definition and content. Especially it focuses on the educational field Biology and on a cross-cutting theme Nature environmental education. In the thesis is defined a notion textbook, there are described functions of a textbook in learning process and ways of analyzing textbooks. The theoretical part also deals with didactic tests. The practical part is devoted to analysis and comparison of selected series of textbooks. It presents a design of a simple test in the research of knowledge from the ecology at basic school students and it evaluates the results of the experimental pilot survey.
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