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Molekulové simulace nukleace ledu
Pluhařová, Eva ; Jungwirth, Pavel (advisor) ; Kolafa, Jiří (referee)
Title: Molecular simulations of ice nucleation Author: Eva Pluhařová Department: Department of Physical and Macromolecular Chemistry Faculty of Science UK Advisor: doc. Mgr. Pavel Jungwirth, DSc., IOCB AS CR, v.v.i. Advisor's e-mail address: pavel.jungwirth@uochb.cas.cz Abstract: By means of molecular dynamics simulations we have systematically investigated homogeneous ice nucleation in neat and surface contaminated water. As models of the adsorbates we have assumed pentanol and pentanoic acid. In neat water nucleation preferentially starts in the subsurface region, which accommodates better than the bulk the volume increase associated with freezing. Homogeneous ice nucleation is affected more by alcohol than by acid. Water slabs covered by a disordered layer of pentanol exhibit negligible preference for subsurface nucleation and longer nucleation times in comparison with neat water, while nucleation times are almost unaffected by the presence of pentanoic acid and the subsurface preference is only slightly decreased. We tried to rationalize the differences between the effects of different compounds by their ability to orient water molecules and to change their mobility. The fact that adsorbates differ in the influence on homogeneous ice nucleation has important implications for the microphysics of...
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Computer modeling of ion protein interactions: Allo steric effects of phenolic ligands and ions on insulin hexamer struct ure
Palivec, Vladimír ; Jungwirth, Pavel (advisor) ; Fišer, Jiří (referee)
Title: Computer modeling of ion protein interactions: Allosteric effects of phenolic ligands and ions on insulin hexamer structure Author: Vladimír Palivec Department: Department of Physical and Macromolecular Chemistry Faculty of Science UK Advisor: prof. RNDr. Pavel Jungwirth, DSc., IOCB AS CR, v.v.i. Advisor's email address: pavel.jungwirth@uochb.cas.cz Abstract: Insulin hexamer is an allosteric protein capable of undergoing conformational changes between three states: T6, T3R3, and R6. Transitions between them, as well as the formation of insulin hexamers, are mediated through binding of phenolic ligands or ions. This thesis presents a molecular dynamics study of allosteric behavior of insulin using empirical force fields. Two effects are closely inspected - cation (Zn2+ , Ca2+ , K+ , and Na+ ) binding to the insulin hexamers and a possible binding of two neurotransmitters - dopamine and serotonin to the phenolic pocket. The results show that high charge density cations (Zn2+ and Ca2+ ) are mostly localized in the B13 glutamate cavity, slow- down diffusion, while preventing other cations from entering. In contrast, low charge density cations (Na+ and K+ ) do not have this effect. Concerning neurotransmitters, dopamine does not bind to the phenolic pocket whereas serotonin binds in a similar way like...
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Molekulové simulace nukleace ledu
Pluhařová, Eva ; Kolafa, Jiří (referee) ; Jungwirth, Pavel (advisor)
Title: Molecular simulations of ice nucleation Author: Eva Pluhařová Department: Department of Physical and Macromolecular Chemistry Faculty of Science UK Advisor: doc. Mgr. Pavel Jungwirth, DSc., IOCB AS CR, v.v.i. Advisor's e-mail address: pavel.jungwirth@uochb.cas.cz Abstract: By means of molecular dynamics simulations we have systematically investigated homogeneous ice nucleation in neat and surface contaminated water. As models of the adsorbates we have assumed pentanol and pentanoic acid. In neat water nucleation preferentially starts in the subsurface region, which accommodates better than the bulk the volume increase associated with freezing. Homogeneous ice nucleation is affected more by alcohol than by acid. Water slabs covered by a disordered layer of pentanol exhibit negligible preference for subsurface nucleation and longer nucleation times in comparison with neat water, while nucleation times are almost unaffected by the presence of pentanoic acid and the subsurface preference is only slightly decreased. We tried to rationalize the differences between the effects of different compounds by their ability to orient water molecules and to change their mobility. The fact that adsorbates differ in the influence on homogeneous ice nucleation has important implications for the microphysics of...
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