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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.
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Influence of Solvent on Deformation Behavior of Hydrogels
Kulovaná, Eva ; Bartlová, Milada (referee) ; Mráček, Aleš (referee) ; Žídek, Jan (advisor)
The thesis deals with molecular dynamic simulation of the influence of water on the deformation of hydrogels. Hydrogels are model materials formed from macromolecular networks solvated with water. It was found that water can form bridges between macromolecules that take the form of temporary ionic crosslinks. These bridges affect the behavior of the network during deformation. Water bridges are water molecules that have a limited radius of motion in the space between two macromolecules. The concentration of the water bridges was regulated by a partial charge on the macromolecular chain in the organic network. Bridges are a type of interaction that is relatively strong but significantly delocalized. It is not possible to dissociate the water bridge, after dissociation it will be re-created in another place in a short time. The influence of water bridges was compared with other types of network crosslinks, especially covalent and physical bonds. Covalent crosslinks are modeled as a simple binding interaction between two macromolecules. They are undissociable and are local throughout the simulation. Physical bonds are modeled as micelles, where hydrophobic groups form the core and hydrophilic groups form the micelle shell. Physical bonds have the nature of dissociable bonds that are local. Different types of crosslinks have different effects on deformation properties. The deformation of a network containing a combination of two types of crosslinks was simulated: (i) physically-covalent, (ii) ionically-covalent, and (iii) physically-ionic networks and (iv) ternary physically-covalent-ion networks. For individual and combined networks, the behavior depending on simple networks was verified. The number of water bridges was fundamentally affected by the primary structure of the chains. When the PEG chain was replaced with hydrophobic polyoxymethylene (POM) or polyoxytrimethylene (POTM), their solvation and mechanical behavior deteriorated.
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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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Computer simulations of protein structures using coarse-grained models
Halda, Miloš ; Nová, Lucie (advisor) ; Limpouchová, Zuzana (referee)
The main part of this bachelor's thesis is an operational software for coarse- grained protein simulations, suitable for testing of new potential functions. The program is using a pivot-based proposal of new states and Monte Carlo evaluation of the proposed state. The program also allows to use a simulated annealing technique with the linear temperature decrease. Mean estimation and error estimation using the Block Method are implemented for evaluation of the simulations. The software was tested on a several proteins. The simulations provided expected results for shorter chains (88 and less aminoacids), but simulations of longer chains (111 and more aminoacids) have shown the software limitations. Several options for the software improvement regarding the new state proposal for simulations of longer chains were discussed. 1
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Mechanistic Insights into Reactive Zeolite-Water Interactions
Benešová, Tereza ; Heard, Christopher James (advisor) ; Maldonado Dominguez, Carlos Mauricio (referee)
Title: Mechanistic Insights into Reactive Zeolite-Water Interactions Author: Tereza Benešová Department: Department of Physical and Macromolecular Chemistry Supervisor: Christopher Heard, PhD. Abstract: An in silico investigation of zeolite-water interactions was undertaken using a combined static and dynamic approach within density functional theory. Two periodic models of zeolite chabazite were used, purely siliceous and aluminosilicate in order to explain the different behaviour of water near Si-O-Si and Al-O-Si bridges. One or two water molecules per supercell of the model were used, corresponding to experimental conditions of steaming. Under such conditions, water can interact with zeolites by non-reactive adsorption but also by reactive interactions such as hydrolysis and oxygen exchange between water and the framework. The main goal of the study was to explain oxygen exchange at an atomistic level. The viable mechanisms of oxygen exchange were established. These mechanisms are different for Si-O-Si and Al-O-Si bridges but for both of them oxygen exchange is initiated by partial hydrolysis of the framework. After this hydrolysis, oxygen exchange heals the framework while incorporating into it the oxygen that originated from the water. Both established mechanisms are competitive with non-exchange...
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The study of the association behavior of the amphiphilic copolymers in solutions containing low molar compounds by means of computer simulations.
Šindelka, Karel ; Limpouchová, Zuzana (advisor) ; Slavíček, Petr (referee) ; Vondrášek, Jiří (referee)
Title: The study of the association behaviour of the amphiphilic copolymers in solutions containing low molar compounds by means of computer simulations. Author: Mgr. Karel Šindelka Department: Faculty of Science, Charles University Supervisor: Doc. Ing. Zuzana Limpouchová, Csc. Abstract This doctoral thesis focuses on the study of electrostatic self- and co-assembly in complex polymer solutions containing polyelectrolyte (PE) block copolymers together with surfactants, neutral homopolymers, or oppositely charged PEs using the dissipative particle dynamics (DPD). It was shown that the electro- static self-assembly depends not only on the cooperative interactions of oppo- sitely charged PE chains, but also on the amphiphilicity of PE species or on the polymer block compatibility, among other properties. PEs with incompatible blocks create well-defined core-shell structures, while large ill-defined crew-cut aggregates form from PEs with compatible blocks In non-stoichiometric mixtures of PEs with incompatible blocks, co-assembled nanoparticles are smaller than in stoichiometric mixtures and are charged. The destabilization of larger aggregates depends on how the PE charge surplus is introduced: the effect is strongest when the density of the surplus PE charge on the PE chains is increased and weakest when the...
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Molecules in Cell Membranes
Timr, Štěpán ; Jungwirth, Pavel (advisor) ; Böckman, Rainer (referee) ; Ettrich, Rüdiger (referee)
Biological membranes are actively involved in a multitude of processes in living cells; therefore, a detailed characterization of their structure, dynamics, and function is essential for an understanding of living organisms at the molecular level. In this work, we made use of the high spatial and temporal resolution offered by computer simulations to investigate the behavior of several molecular species which associate with cellular membranes. Using a combination of classical molecular dynamics simulations and ab initio electronic structure calculations, we were able to characterize nonlinear optical properties of membrane- embedded fluorescent probes and thus contribute to establishing two-photon polarization microscopy as a tool of structural biology. Moreover, our molecular dynamics simulations provided an atomistic picture of the reversible membrane binding of recoverin, a neuronal calcium-sensing protein involved in vision adaptation, and they also yielded an important insight into the mechanism of its calcium-induced myristoyl switch. In addition, we examined the biological role of cholesterol oxidation and compared two methods of representing transmembrane voltage in molecular dynamics simulations.
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Design, parameterization and verification of a coarse-grained model of DNA
Dršata, Tomáš ; Lankaš, Filip (advisor) ; Jurečka, Petr (referee)
Structure and mechanical properties of DNA play a key role in its biological functioning. A lot of well-established conclusions about the DNA structure and its sequence-dependent variabil- ity came from various experimental and computational studies of the Dickerson-Drew dodecamer (DD), a prototypic B-DNA molecule of the sequence (5')CGCGAATTCGCG(3'). In this study we present a detailed analysis of structural and mechan- ical properties of DD based on extensive atomistic molecular dynamics (MD) simulations with explicit representation of wa- ter and ionic environment. We analyze three simulated systems covering different ionic conditions and water models. Two MD trajectories are reported for the first time, one of them being 2.4 µs long. An extensive comparsion with one recent NMR struc- ture and four recent X-ray structures is made. It is found that the end basepairs can adopt two different pairing motifs dur- ing the simulation: the canonical Watson-Crick pair or a non- canonical trans Watson-Crick/Sugar Edge pair. These states can significantly influence the structure of DD even at the third step from the end. A clear relationship is found between the BI/BII backbone substates and the basepair step conformation. A model of rigid bases is used to study mechanical properties of the DNA. The non-local...
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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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Development and applications of molecular dynamics for chiral systems
Kessler, Jiří ; Bouř, Petr (advisor) ; Fanfrlík, Jindřich (referee)
The Thesis deals with MD simulations of solutions of chiral solutes in chiral solvents. These solutions consist of 2,2,2-trifluoro-1-phenylethanol, 1-phenylethanol and 1-phenyl- ethanamine.The differences in NMR properties between different combnations of solvent and solute absolute configuration were modeled. Indeed, differences in radial distribution functions and conformer abundances of solute calculated by the WHAM method were found. These results correlated with experimental differences in NMR shifts. Additionally, a method of cluster preselection was developed. It significantly decreased the amount of clusters needed for computations of NMR shieldings and hence the computer time. Keywords: chirality, molecular dynamic, nuclear magnetic resonance
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