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Molecular Simulations of Surfaces of Aqueous Solutions
Vácha, Robert ; Jungwirth, Pavel (vedoucí práce) ; Kolafa, Jiří (oponent) ; Barvík, Ivan (oponent)
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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Molekulárně-dynamické simulace komplexů sestávajících z proteinů a nukleových kyselin
Zíma, Vlastimil ; Barvík, Ivan (vedoucí práce) ; Jungwirth, Pavel (oponent)
V rámci diplomová práce byly prostudovány algoritmy numerické integrace. Poté byla provedena důkladná studie aktivních míst polymeras virů HCV a HIV v komplexech s přirozeným substrátem a komplexem, ve kterém byl přistupující nukleosidtrifosfát nahrazen inhibitorem (S)-HMPMGpp resp. (S)-HMPMApp. Následně byla použita metoda ABF pro získání profilů volné energie pro přechod vody a methanu přes rozhraní vody a vakua. Stejná metoda byla na závěr použita pro získání profilu volné energie pro průchod vody, methanu a guanosinu skrz lipidovou dvouvrstvu.
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Molekulárně-dynamické simulace komplexů nukleových kyselin enzymu RNase H
Bartek, Tomáš ; Burda, Jaroslav (oponent) ; Barvík, Ivan (vedoucí práce)
The aim of this diploma thesis was to study interactions between human Rase H enzyme and a natural and modified substrate using molecular dynamics simulations (altogether 9 MD runs ere produced). Conformational preferences of internucleotide linkages (undergoing contacts with the RNase H enzyme) were studied using several versions of the AMBER force field. Either one or two copies of RNase H were included into the simulated system. As the most important DNA-binding residues were recognized Trp93 and Ser101 in the first DNA binding site and Thr49 and Arg47 in the second DNA binding site. Further, the AMBER force field was re-parameterized slightly using ab initio calculations to produce force constants for the modified phosphonate internucleotide linkage. Biologically active version of the modified internucleotide linkage C3-O3-P-C-O5-C5 was able to bind Arg47 using two hydrogen bonds within the 10 ns MD run (even more effciently than in the case of MD runs with natural internucleotide linkages). On the other hand, the biologically inactive C3-O3-C-P-O5-C5 internucleotide linkage lose contacts with Arg47 quickly.
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Nucleosid fosfonové kyseliny a odvozené oligonukleotidy: Strukturní diversita vs biologické vlastnosti
Rosenberg, Ivan ; Barvík, I. ; Buděšínský, Miloš ; Kočalka, Petr ; Králíková, Šárka ; Liboska, Radek ; Pačes, Ondřej ; Páv, Ondřej ; Petrová, Magdalena ; Pohl, Radek ; Pressová, Martina ; Rejman, Dominik ; Votruba, Ivan ; Točík, Zdeněk
Článek se zabývá biologickými a fyzikálně-chemickými vlastnostmi izopolárních, izosterních a neizosterních nukleosidfosfonových kyselin a příslušných oligonukleotidů.
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