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Computer Simulation Methods of Soft Matter
Kazakov, Aleksandr ; Uhlík, Filip (advisor) ; Bačová, Petra (referee) ; Jirsák, Jan (referee)
iii CHARLES UNIVERSITY Faculty of Science Department of Physical and Macromolecular Chemistry Doctoral Thesis Computer Simulation Methods of Soft Matter by MS. Aleksandr D. KAZAKOV Abstract This thesis is dedicated to the theoretical study of hydrogels under different con- ditions, and implementing new simulation approaches: for polymer- and carbon- based systems. The hydrogel was modeled with presence of multivalent ions at good solvent conditions and with presence of monovalent ions at different salt concentrations and different pH pK values at poor solvent conditions. The competition between elec- trostatic repulsion with short-range hydrophobic interactions in case of pH-respon- sive polyelectrolyte lead to first-order transition in the system. The study has shown how to utilize and to tune the transition with respect to parameters. A novel hybrid MC-SCF method was implemented, which combines a mean- field representation by the machinery of Scheutjens - Fleer self-consistent field and a coarse-grained model driven by the Monte Carlo method. The study provides a comparison of the novel method with pure coarse-grained and mean-field methods. The family of fullerenes with an even number of carbon atoms n = 20-80 was calculated using the DFT method and subsequently trained using a convolutional neural network...
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Computer Modelling of Macromolecules
Khirnova, Oleksandra ; Uhlík, Filip (advisor) ; Jirsák, Jan (referee)
In the present work we study diffusion of linear and cyclic polymers. We run simulations using Brownian dynamics in θ-solvent and good solvent with several hydrodynamic models. Obtained results were compared with existing theories. In the present work we study diffusion of linear and cyclic polymers. We run simulations using Brownian dynamics in θ-solvent and good solvent with several hydrodynamic models. Obtained results were compared with existing theories. In the present work we study diffusion of linear and cyclic polymers. We run simulations using Brownian dynamics in θ-solvent and good solvent with several hydrodynamic models. Obtained results were compared with existing theories. In the present work we study diffusion of linear and cyclic polymers. We run simulations using Brownian dynamics in θ-solvent and good solvent with several hydrodynamic models. Obtained results were compared with existing theories. In the present work we study diffusion of linear and cyclic polymers. We run simulations using Brownian dynamics in θ-solvent and good solvent with several hydrodynamic models. Obtained results were compared with existing theories.
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On a molecular theory of water
Jirsák, Jan ; Nezbeda, Ivo (advisor) ; Hrubý, Jan (referee) ; Kolafa, Jiří (referee) ; Jungwirth, Pavel (referee)
/ Summary Water is the most important liquid on Earth, but despite an errormous cffort put into research, it is not yet fully understood. A number of thermodyna- mic anomalies have been identified in water (e.g. the maximum of density at 4"C) and their occurrence intuitively linked to a strong intermolecular associ- ative force, i.e., hydrogen bonding. Nevertheiess, so far no rigorous molecular theory has been formulated. The present work attempts to propose and apply a rigorous statistical- -mechanical approach to water. The approach is based on recent findings that the structure of associating fluids is determined rnainly by the short-range forces (both repulsive ancl attractive). This fact enables us to apply the per- turbation theory taking a short-range model as a reference. The properties of the short-range reference model are then estimated by means of a simple, so-called primitive, model. Primitive models are anaiytically constructed to reproduce the structure of the short-range reference model keeping the in- teractions simple enough for theory. The contribution of the primitive model evaluated by Wertheim's TPT2 is used as a reference term in the perturbation expansion. The equation of state is then completed by adding dispersion and dipole-dipole correction terms. Main results of the work are as...
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Computer study of protein folding using simplified models
Nierostek, Jakub ; Uhlík, Filip (advisor) ; Jirsák, Jan (referee)
The aim of this work is to design and describe a suitable coarse-grained protein model, on the basis of which protein-folding will be studied. The model will be implemented as a computer program, development of the model in time will be simulated by Hamiltonian Monte Carlo. Using computer simulations, not only the protein-folding itself will be investigated, but also the quantities that characterize the process and the similarity of the real and simulated protein's native conformation. Keywords: protein folding, computer simulation, Hamiltonian Monte Carlo, coarse-grained model 1
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On a molecular theory of water
Jirsák, Jan ; Nezbeda, Ivo (advisor) ; Hrubý, Jan (referee) ; Kolafa, Jiří (referee) ; Jungwirth, Pavel (referee)
/ Summary Water is the most important liquid on Earth, but despite an errormous cffort put into research, it is not yet fully understood. A number of thermodyna- mic anomalies have been identified in water (e.g. the maximum of density at 4"C) and their occurrence intuitively linked to a strong intermolecular associ- ative force, i.e., hydrogen bonding. Nevertheiess, so far no rigorous molecular theory has been formulated. The present work attempts to propose and apply a rigorous statistical- -mechanical approach to water. The approach is based on recent findings that the structure of associating fluids is determined rnainly by the short-range forces (both repulsive ancl attractive). This fact enables us to apply the per- turbation theory taking a short-range model as a reference. The properties of the short-range reference model are then estimated by means of a simple, so-called primitive, model. Primitive models are anaiytically constructed to reproduce the structure of the short-range reference model keeping the in- teractions simple enough for theory. The contribution of the primitive model evaluated by Wertheim's TPT2 is used as a reference term in the perturbation expansion. The equation of state is then completed by adding dispersion and dipole-dipole correction terms. Main results of the work are as...
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Computer Modelling of Macromolecules
Khirnova, Oleksandra ; Uhlík, Filip (advisor) ; Jirsák, Jan (referee)
In the present work we study diffusion of linear and cyclic polymers. We run simulations using Brownian dynamics in θ-solvent and good solvent with several hydrodynamic models. Obtained results were compared with existing theories. In the present work we study diffusion of linear and cyclic polymers. We run simulations using Brownian dynamics in θ-solvent and good solvent with several hydrodynamic models. Obtained results were compared with existing theories. In the present work we study diffusion of linear and cyclic polymers. We run simulations using Brownian dynamics in θ-solvent and good solvent with several hydrodynamic models. Obtained results were compared with existing theories. In the present work we study diffusion of linear and cyclic polymers. We run simulations using Brownian dynamics in θ-solvent and good solvent with several hydrodynamic models. Obtained results were compared with existing theories. In the present work we study diffusion of linear and cyclic polymers. We run simulations using Brownian dynamics in θ-solvent and good solvent with several hydrodynamic models. Obtained results were compared with existing theories.
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Molecular Simulation of Electrospinning.
Jirsák, Jan ; Moučka, F. ; Nezbeda, Ivo
Our recent attempts to apply standard molecular simulation techniques to the process of electrospinning are presented. We employ a molecular dynamics simulation to study phenomena involved in the electrospinning of polymer solutions, with particular attention to the formation of the Taylor cone and the development of a liquid jet. A molecular-based approach allows us to reveal the molecular structure and dynamics, which are inaccessible to continuum methods.
Fulltext: content.csg -  PDF
Plný tet: SKMBT_22317031713170 - PDF
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