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Theoretical Investigation of ethanol dehydration catalyzed by acid sites in zeolites
Vacek, Jaroslav ; Nachtigall, Petr (advisor) ; Uhlík, Filip (referee)
Zeolites are a group of aluminosilicate minerals with catalytic properties. They may be used for many industrial applications such as catalytic cracking of oil. Zeolites are also capable of converting ethanol to diethylether and ethylen. This reaction is known as dehydration of ethanol. The reaction is potentially interesting as a way of converting ethanol to more valuable molecules. An experimental study (Shashikant A. Kadam, Mariya V. Shamzhy, 2018) has proven that diethylether is the preferred product when the temperatures are low and the partial pressure of ethanol is high. Ethylen is more significant product with higher temperature and lower partial pressure of ethanol. Aim of this thesis is to determine the mechanism of dehydration of ethanol. Furthermore it was attempted to explain the behavior of the reaction under different circumstances. The research was done in silico using the methods of computational chemistry. Such methods give information on the geometry and the energy of systems of molecules. Thus computational chemistry can be used to investigate the relational path and activation energy of the studied reaction. This thesis is a theoretical study of dehydration of ethanol catalysed by a zeolite.
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A new method for the solution of the Schrödinger equation
Kocák, Jakub ; Uhlík, Filip (advisor) ; Demel, Ondřej (referee)
Title: A new method for the solution of the Schrödinger equation Author: Jakub Kocák Department: Department of Physical and Macromolecular Chemistry Supervisor: doc. RNDr. Filip Uhlík, Ph.D. Abstract: In this thesis we study method for the solution of time-independent Schrö- dinger equation for ground state. The wave function, interpreted as probability density, is represented by samples. In each iteration we applied approximant of imaginary time propagator. Acting of the operator is implemented by Monte Carlo simulation. Part of the thesis is dedicated to methods of energy calculation from samples of wave function: method based on estimation of value of wave function, method of convolution with heat kernel, method of averaged energy weighed by wave function and exponential de- cay method. The method for the solution was used to find ground state and energy for 6-dimensional harmonic oscillator, anharmonic 3-dimensional octic oscillator and hydrogen atom. Keywords: imaginary time propagation, Monte Carlo method, variational principle, ground state 1
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Theoretical studies of catalysts for Suzuki-Miyaura reaction
Měrka, Pavel ; Uhlík, Filip (advisor) ; Srnec, Martin (referee)
This thesis is focused on theoretical study of Suzuki-Miyaura cross- coupling reaction catalyzed by palladium complex with phosphinopherrocene li- gand. The aim of this work is to provide basic image of the catalytic cycle with newly prepared coordination compounds of palladium. Bromobenzene and phe- nyltriolborate were chosen as the model reagent. DFT method M06-2X was used for characterization of molecular goemetries of intermediates and most important transition states for all parts of catalytic cycle.
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Simulations of Polymers with Brownian Dynamics
Hájková, Alexandra ; Uhlík, Filip (advisor) ; Posel, Zbyšek (referee)
Title: Simulations of Polymers with Brownian Dynamics Author: Alexandra Hájková Supervisor: RNDr. Filip Uhlík, Ph.D. Department of Physical and Macromolecular Chemistry Abstract: This work presents Brownian Dynamics simulations of macromolecules. A com- mon approaches to hydrodynamic interactions employes the Rotne-Prager-Yamakawa (RPY) tensor. In such cases simple simulation step takes time proportional to O(N3) when Cholesky decomposition of RPY tensor is used. This makes the simulation too much time-consuming. This work proposes a new method for approximation of hydrodynamic interactions with a Toeplitz matrix. Decomposition of this matrix can be performed in O(N2) time, which considerably speeds up the simulations. In this work the new method was implemented, thoroughly tested, compared to a reference RPY approximation and applied to linear, cyclic and star macromolecules. Keywords: Brownian dynamics, macromolecules, hydrodynamic interactions, Rotne-Prager- Yamakawa tensor, Toeplitz matrix, Cholesky decomposition 1
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Quantum variational Monte Carlo method
Kocák, Jakub ; Uhlík, Filip (advisor) ; Srnec, Martin (referee)
Title: Quantum Variational Monte Carlo method Author: Jakub Kocák Department: Department of Physical and Macromolecular Chemistry Supervisor: RNDr. Filip Uhlík, Ph.D. Abstract: In this thesis, we study variational Monte Carlo method in quantum- mechanical systems. We analysed choice of trial wave function and afterwards we optimized selected function for helium singlet and triplet state. In the first chapter, we discuss basic notions of quantum mechanics and general properties of wave function and properties of ground state of the system. In the second chapter, we consider computational algorithms used to calculate integrals, to estimate errors and for optimization. In the third chapter, we present results of optimization and properties of optimized trial wave function. Keywords: variational principle, Monte Carlo method, ground state, helium 1
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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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Multireference CC calculations using optimized virtual orbitals
Lang, Jakub ; Pittner, Jiří (advisor) ; Uhlík, Filip (referee)
i Abstract The aim of this work is to test the performance of multireference methods using the truncated virtual orbital space as a result when OVOS method is employed. As a guess function, the OVOS wave function is used for the calculations of the two-determinantal state of a quasi-degenerate system. The resulting energies are investigated for different truncation of the virtual orbital space.
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Počítačové modelování větvených polymerů
Preisler, Zdeněk ; Uhlík, Filip (advisor) ; Netopilík, Miloš (referee)
In this work we study properties of branched polymers in a good solvent. We focus on problematic related to the size exclusion chromatography and predicting elution behavior of randomly branched polymers. We developed a software for generating self-avoiding walks (SAW) of any given non-looping architecture on a cubic lattice using Monte Carlo (MC) simulation and vali- date its reliability by presenting the scaling of different architectures: linear, 3-arm star and 6-arm star and asymmetric star. We calculate distribu- tion coefficients and calibration curves for size exclusion chromatography for various architectures to validate that the hydrodynamic radius is more suitable for predicting elution volume than the radius of gyration. Then we propose a new method for, although approximate, a very fast estimation of radius of gyration and hydrodynamic radius for different architecture using a graph method. It is done by comparing MC results with results obtained from graph theory. Then we introduce a correction to graph-theory results to fit the MC. At the end we present depletion layer calculation from MC and self-consistent field (SCF) method for polymers and their comparison. We show how calculation of depletion layer using SCF can be improved to get significantly better agreement with MC results. v
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