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Excitation Energy Transfer in Photosynthetic Reaction Centres
Ptáček, Michal ; Mančal, Tomáš (advisor) ; Dostál, Jakub (referee)
The photosynthetic reaction centres have uppermost importance in photosynthesis. They represent the actual place where the energy carried by photons is turned into charge-separated states which then enable to establish the electrochemical H+ transmembrane gradient used by ATP synthases. The photosynthetic light- harvesting complexes gather the energy of light radiation and direct it in the form of electronic excitation energy into the reaction centres. The efficiency of this process is exceptionally high, close to unity, what is capturing the interest of researchers for decades. The development of experimental techniques has led to better understanding of this process down to atomic scale. Nowadays, this insight along with the theoretical basis stemming from quantum mechanics can be used to perform accurate computer simulations which can determine properties of the whole molecular aggregates independently of experiments. This thesis provides an introduction into the field of theoretical photosynthesis research, and it summarises the progress made in past two decades. The detailed theoretical approaches are being put into perspective of the reaction centres of photosynthetic purple bacterium Rhodobacter sphaeroides which is a valuable model organism. Both experimental and theoretical results of...
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Quantum mechanical study of the electron hoping processes of conjugated systems.
Fatková, Kateřina ; Pospíšil, Miroslav (advisor) ; Pittner, Jiří (referee)
This thesis uses previously proposed methodology for simulations of all-trans- polyenes with conjugated systems. Dynamic properties, especially the mean lifeti- mes of the excited states, of these molecules were systematically simulated. Obta- ined data shows that the method is still too time-consuming for polyene molecules with more than 20 carbon atoms, including most carotenoids. Thus, a study of active space reduction was performed with the model tetradecaheptaene molecule with regards to excited state mean lifetimes. A new, less time-consuming method would need further simulation studies. Moreover, static spectra of the these mo- lecules were studied as well, yielding a comparison of different DFT and ab-initio approaches. 1
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Electron-phonon Coupling in Finite Multi-chromophoric Systems
Herman, Daniel ; Mančal, Tomáš (advisor) ; Profant, Václav (referee)
Quantum systems in nature interact with other quantum systems, and these are examples of open quantum systems. In this work, we provide an introduction to the theory of open quantum system with a particular focus on the dynamics of molecular systems embedded in the protein environment, such as those found in photosynthetic antennas. We devote some time to the techniques of constructing equations of motion for the dynamics of a selected quantum system under the interaction with the bath, where we restrict ourselves to a finite number of degrees of freedom. We compare the exact calculation of the whole finite system with the results of approximate equations derived from an ansatz for the time evolution for the degrees of freedom of the bath part. We also reformulate the exact equations into a time non-local master equation using projection operator techniques, and we study the quality of results obtained with the modified quantum master equation. The time evolution of studied systems is also compared to the time evolution obtained by Schrödiger and Liouville-von Neumann equations. 1
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Short-lived Delocalization and Absorption by Light
Vokrouhlický, David ; Mančal, Tomáš (advisor) ; Veis, Libor (referee)
Coherent exciton delocalization improves the light harvesting function of photosyn- thetic antennae by creating conditions for very fast excitation transfer in space. This thesis focuses on two different effects creating coherence - short-lived excitation by light and weak coupling between pigments that is present in the system on longer timescales. The evolution and relaxation of simple systems - the dimer and trimer - are calculated. The core of this thesis are newly developed numerical methods for distinguishing and quantifying the effect of the two types of coherence throughout evolution, which are applied to the aforementioned systems. 1
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Study text on selected topic of Quantum mechanics course
Kyšková, Jana ; Koupilová, Zdeňka (advisor) ; Kapsa, Vojtěch (referee)
The objective of this bachelor thesis is to prepare a study text on selected topics of quantum mechanics, which would be appropriate for the se- cond year students of education of Physics at FMP CU attending the Quantum mechanics course. This thesis consists of two topics - Multiparticle Systems and Chemical Bond. The study text should help students understand the mathema- tical methods used in the field of multiparticle systems, and solve elementary problems. The text also extends secondary-school chemistry knowledge about atom orbitals and chemical bond and provides an explanation of the structure of simple molecules using the valence bond theory. The thesis is based on author's own experience of the Quantum mechanics course, the main sources are the fore- ign textbooks of quantum mechanics and author's own notes from lectures held on FMP CU. 1
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Báze vlnových balíků v popisu rezonančního rozptylu
Lukeš, Petr ; Kolorenč, Přemysl (advisor) ; Houfek, Karel (referee)
Title: Wave-packet basis in the description of the resonance scattering Author: Petr Lukeš Institute: Institute of Theoretical physics Supervisor: RNDr. Přemysl Kolorenč, Ph.D., Institute of Theoretical Physics Abstract: A common approach towards the solution of problems of particle scattering problems is the approximation of the wavefunctions with some set of square integrable functions. A new type of such basis is assessed in this work. The vectors of the basis are obtained by integration of eigenvectors of free Hamiltonian over finite intervals of energies. This basis is called the wave- packet basis. This basis is used to compute values of resonance width and resonant energy for two simple cases and the results are compared to benchmark data known from other works. The results serve to evaluate the properties of this basis. Also this work contains a proposal of how could this basis be applied in computations of quantum scattering. Keywords: potential scattering, wave-packet basis, resonance width, resonant energy.
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Quantum mechanical study of the electron hoping processes of pigments from photosystems. Simulation of absorption and emission photoelectron spectra.
Cajzl, Radim ; Burda, Jaroslav (advisor) ; Slavíček, Petr (referee)
Title: Quantum mechanical study of the electron hoping processes of pig- ments from photosystems. Simulation of absorption and emission photoelectron spectra. Author: Bc. Radim Cajzl Department: Department of Chemical Physics and Optics Supervisor: prof. RNDr. Ing. Jaroslav Burda, DrSc., Department of Chemical Physics and Optics Abstract: The aim of this thesis is to develop a methodology for simulation of dynamical properties of carotenoids by OMx method combined with surface electron hopping. We use linear conjugated polyenes: ethene, butadiene, hexa- triene up to polyenes with 22 carbon atoms as model systems. First, the spectra are calculated with sufficiently good agreement with the experimental data by both correct order of excited states and small deviation from experimental data. These results are used for electron surface hopping for calculation of mean lifetimes of excited states of studied polyenes. Calculated lifetimes are of the same order as experimental data for butadiene, hexatriene and octatetraene. Calculated lifetimes for poleynes with 20 resp. 22 carbon atoms agree well with chemically analogous carotenoids. Keywords: quantum mechanics, photoelectron spectra, pigments of photosys- tems, elecrton transitions, molecular and electronic dynamics
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Studies of Lanthanide Complexes by a Combination of Spectroscopic Methods
Krupová, Monika ; Bouř, Petr (advisor) ; Kapitán, Josef (referee)
Studies of Lanthanide Complexes by a Combination of Spectroscopic Methods Monika Krupová (Department of Physical and Macromoecular Chemistry, Faculty of Science, Charles University in Prague) Since conventional structural analysis offers rather limited means for the chirality detection, a series of lanthanide tris-(β-diketonates) are investigated as effective receptors for a better chirality sensing in biomolecular substrates. These lanthanide complexes containing β-diketonate ligands are electrically neutral; they can further coordinate with various small organic molecules such as chiral alcohols, amino alcohols or amino acids in organic solvents and produce a strong chiral signal. Previously, a resonance in Raman scattering was observed in the studied systems due to the correspondence of europium electronic transition energy to the laser excitation wavelength, about a 100-fold signal enhancement if compared to non-resonant vibrational ROA was observed. This enabled shorter detection times as well as lower sample concentrations. In the current work, interaction of the Eu(FOD) complex with (R)- and (S)- enantiomer of 1-phenylethanol in n-hexane was studied using IR spectroscopy, Raman spectroscopy and Raman optical activity (ROA), UV-Vis spectroscopy and ultraviolet circular dichroism (UVCD). Only...
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Quantum computing in many-body physics
Brandejs, Jan ; Cejnar, Pavel (advisor) ; Knapp, František (referee)
Název práce: Kvantové výpočty v mnohočásticové fyzice Autor: Jan Brandejs Katedra: Ústav částicové a jaderné fyziky Vedoucí bakalářské práce: prof. RNDr. Pavel Cejnar, Dr., DSc., Ústav částicové a jaderné fyziky Abstrakt: Při simulaci mnohočásticových kvantových systém· obvykle dochází k exponenciální explozi výpočetní složitosti. Kvantové počítače umožňují ten- to problém principiálně vyřešit. Díky práci R. Feynmanna je známo, že axiomy teorie složitosti vychází z fyzikálních zákon·. Situace se změní, zavedeme-li do výpočetního procesu mimo klasické fyziky i kvantovou teorii. Ukazuje se, že pro efektivní simulaci kvantového systému je vhodné použít jiný, lépe kontrolovatelný kvantový systém. Realizace výpočtu s využitím q-bit· a kvantového paralelismu pak ve vybraných případech vede k zásadní redukci složitosti. Kvantové počítače potenciálně umožňují realizaci výpočt· a simulací, které jsou s klasickými počíta- či prakticky neproveditelné. Zejména na poli kvantové chemie vyvstává možnost přímočaré aplikace. Tato práce je zaměřena na použití kvantových počítač· pro mnohočásticové problémy a obsahuje analýzu složitosti kvantové simulace atomo- vých jader. Klíčová slova: kvantový počítač, kvantová simulace, mnohočásticová fyzika
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