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Effect of steric constraint and surface interactions on the behavior of block copolymers (Computer study)
Blovský, Tomáš ; Limpouchová, Zuzana (advisor) ; Lísal, Martin (referee)
In this thesis, the influence of spatial confinement and interactions with solid surfaces on the conformational behavior of symmetric diblock amphiphilic copolymers A5B5 is stud- ied using dissipative particle dynamics (DPD). In the first two chapters, the motivation for studying such systems and the description of the simulation method are given. In the remaining chapters, the effect of spatial confinement on the association behavior of diblock copolymers is studied, as well as the effect of interactions between the solvophobic block B and the solid wall. The results are compared with simulations without spatial confinement. DPD simulations showed that the attractive interaction between block B and the wall significantly changes the association behavior of block copolymers in a se- lective solvent, whereas the purely steric effect is negligible in spatially confined systems with a non-interacting wall. Keywords: block copolymers, surface interactions, steric constraint, computer simula- tion, complex solution, dissipative particle dynamics
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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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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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Computer simulations of conformational behavior of block copolymers in selective solvents
Šindelka, Karel ; Limpouchová, Zuzana (advisor) ; Kuldová, Jitka (referee)
The presented bachelor thesis deals with the study of the conformational be- haviour of diblock copolymers in the selective solvent. The polymer solution was modelled using a coarse-grained model and is simulated using dissipative particle dynamics (DPD). An original C-code for DPD simulations together with a new software package for processing of simulation data was developed. Functionality of the code and software were tested for two systems. The first system corre- sponded to a linear homopolymer in a solvent and the scaling laws for homopoly- mer in dilute solution were reproduced. The second system represented diblock copolymers in selective solvents and micellar behaviour simulated with the de- veloped code agreed with simulations by Sheng et al. Then, the self-assembly of long copolymer chains in selective solvents that mimics a block copolymer of poly(methacrylic acid) and poly(ethylene oxide) in aqueous solution at pH 1 was studied for different polymer concentrations. The simulation results provided valuable insight into the studied system and serve as a good starting point for DPD simulations of this system with added surfactants and at different values of pH, where the electrostatic interactions become important.
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Conformational behavior of dendritic branched polymers in aqueous solutions (Dissipative particle dynamics)
Suchá, Lucie ; Limpouchová, Zuzana (advisor) ; Posel, Zbyšek (referee)
Bakalářská práce se věnuje studiu konformačního chování polymerních den- drimer· ve vodných roztocích. Polymerní roztoky byly simulovány pomocí di- sipativní částicové dynamiky. Všechny simulace byly provedeny pomocí pro- gramu DL−MESO. Pro generování vstupních soubor· a zpracování výsledk· simulací byly napsány vlastní programy. Správná funkce programu a správné nastavení simulačních parametr· bylo ověřeno pomocí parametrické studie nekonečně zředěných roztok· homopolymerních dendrimer· v dobrém roz- pouštědle. 'kálovací exponent gyračního poloměru získaný pomocí simulací je v souladu s publikovanými daty. Dále bylo porovnáváno konformační chování homopolymerního a kopolymerního dendrimeru. Klíčová slova: Počítačové simulace, disipativní částicová dynamika, dendri- mer, konformační chování, vodné roztoky, větvený polymer
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Linear semiflexible polyelectrolytes in solutions
Bačová, Petra ; Limpouchová, Zuzana (advisor) ; Lísal, Martin (referee)
Title: Linear semiflexible polyelectrolytes in solutions Author: Petra Bačová Department: Faculty of Science, Charles University in Prague Supervisor: Doc. Ing. Zuzana Limpouchová, CSc. Supervisor's e-mail address: zl@vivien.natur.cuni.cz Consultant: Mgr. Peter Košovan, PhD. Abstract: In this thesis I used the Molecular dynamics simulations for study of charged polymers (polyelectrolytes) and their behaviour in solutions. Wide range of polyelectrolytes are se- miflexible and in contrast to neutral polymers it is possible to influence their stiffness by changing the properties of solution as for example ionic strength. The chain flexibility may be characterized by the persistence length. Thesis explains how to express the persistence length from orientational correlation function which shows the double exponential decay. Two contributions to chain stiffness are discussed and the interest is concentrated around electrostatic persistence length which seems to be scale dependent. An effect of added salt on the chain conformation is studied. Salt is treated implicitly within the Debye-Hückel approximation. The results are confronted with OSF theory and the conclusions of vari- ational calculations of Maghi and Netz. The presented thesis describes the conformational behaviour of polyelectrolytes in salty solutions,...
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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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Conformational behavior of branched polymers
Wang, Xiu ; Limpouchová, Zuzana (advisor) ; Cifra, Peter (referee) ; Kolafa, Jiří (referee)
This PhD thesis is devoted to the study of the conformational behavior of branched polymers in confined volumes. This behavior depends not only on polymer architecture and composition but also on steric confinement and on interaction of polymer segments with the confining wall. Better understanding of complex entropy-to-enthalpy interplay can elucidate the mechanism of the chromatographic separation at the microscopic level. An unambiguous size-exclusion chromatography (SEC) analysis of mixtures containing different polymer architectures is difficult because the sizes of polymer coils, which determine the separation, depend not only on molar mass but also on the polymer architecture. Modern chromatographic methods combine the SEC with the interaction chromatography (IC). They exploit the fact that polymer interactions with pore walls, which are the prerequisite for efficient IC separation, depend strongly on polymer architecture. The knowledge of the conformational behavior of linear and branched polymers in confined volumes and of their interactions with confining medium enables to find optimum conditions either for enhancing or for suppressing the role of individual factors that influence the separation. We have shown that the complex entropy-to-enthalpy interplay in polymer solutions in confined...
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