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Structure and selforganization of aggregates of photosynthetic molecules
Sláma, Vladislav ; Mančal, Tomáš (advisor) ; Duffy, Christopher (referee) ; Veis, Libor (referee)
In this work we demonstrate how quantum chemistry (QC) methods and molecular dynamics (MD) simulations can be used in combination with Frenkel exciton model (FEM) to obtain optical and excitation energy transfer properties of complex molecular systems from the molecular structure. The combination of QC and MD methods with FEM provides a powerful tool to study and explain molecular level processes, which are out of reach of the standard FEM parametrization. We use these methods to study and explain molecular mechanism of excitation energy transfer in rylene dyads, especially to explain observed fast excitation energy transfer in dyad with orthogonal arrangement of transition dipoles, where standard approach predicts no excitation energy transfer. On a fundamental level, we relate FEM to configuration interaction method of QC and propose extension of FEM, which accounts for interaction between excitonic manifolds. We investigate effects of this interaction on the optical properties. Inspired by the core features of FEM, we propose new concept of artificial light harvesting antenna based on fluorographene, with design principles inspired by natural light harvesting complexes. We use structure based methods to investigate its excitation transfer properties. We also introduce a new general method for treating...
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Theory of Relaxation and Energy Transfer in Open Quantum Systems
Olšina, Jan ; Mančal, Tomáš (advisor) ; Valkunas, Leonas (referee) ; Szöcs, Vojtech (referee)
The work summarizes basic theory of relaxation, energy transfer and decoher- ence in photosynthetic molecular aggregates described as open quantum systems and basic theory of third order coherent non-linear spectroscopy. The work presents two methods for calculation of photo-induced dynamics of molecular aggregates. The methods relax certain approximations of the theories commonly used to model the relaxation and energy transfer in the molecular systems on the sub-picosecond time scale. The first theory derived in the formalism of para- metric projection operators accounts for correlations in a second-order non-linear response-function that are usually neglected in the formalism of master equations. The second theory represents stochastic model of exact dynamics via the cumulant expansion. The work also presents an analysis of importance of the secular and the Markov approximations in the description of dynamics derived in the second-order perturbation theory in the system-bath coupling with emphasis on the excitonic coherence lifetime.
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Self-regulating mechanisms of photosynthetic systems
Semerák, Matěj ; Mančal, Tomáš (advisor) ; Holá, Dana (referee)
Photosynthesis, a process utilising energy of arriving photons for driving electron transport chain creating transmembrane pH gradient, is a widespread way of subsistence in the nature. However, the intensity of sunlight can exceed the rate which the organisms are able to manage by their gadgetry. In this situation, essential protective mechanisms, safely draining the excess energy away, take a turn. Many theories about the principle and regulation of these functions have been developed and new still arise. It appears that the attention focuses mainly on the antenna complex LHCII. It is possible to state that with high probability, the protective processes are assured by several mechanisms, and quite a stable opinion prevails that crucial role in their activation is played by decreasing pH. That is logical since the more photons come, the more intensively the transport of protons across the membrane happens, thus ΔpH reflects the balance between ATP usage and the membrane apparatus illumination. Generally, the phenomenon is called NPQ (non-photochemical quenching), because it weakens the chlorophyll fluorescence. An important task is probably handled by carotenoids, mainly zeaxanthin, created by violaxanthin deepoxidase at low pH; it provides chlorophylls with energetical trap during excitation...
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Selforganization and optical properties of small molecular aggregates
Sláma, Vladislav ; Mančal, Tomáš (advisor) ; Chvosta, Petr (referee)
The work deals with the description of carotenoid aggregation in water solutions. The main interactions which are involved in aggregation were analyzed and an efficient way of description of carotenoid aggregation, which leads to a speed up the computation, has been introduced. In addition, two different methods for calculation probability distribution of catotenoids configurations in solutions with variable water concentration were elaborated, and their advantages and disadvantages were discussed. Absorption spectra were calculated from these distributions, and they were compared with the experimental results. The influence of water on formation of different types of aggregates, and its impact on the shape of absorption spectra was also discussed. Results of this study will be used as a base of other, more accurate, description of carotenoids aggregation, which will include other weaker interactions between carotenoids.
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Teorie agregátů fotosyntetických molekul: spektroskopie, struktura, přenosové jevy
Lalinský, Ján ; Mančal, Tomáš (advisor) ; Šanda, František (referee)
Title: Theory of aggregates of photosynthetic molecules: spectroscopy, structure, transport phenomena Author: Ján Lalinský Institute: Institute of Physics of Charles University Supervisor of the master thesis: RNDr. Tomáš Mančal, PhD., Institute of Physics of Charles University Abstract. A theory of absorption of light in an isotropic solution of molecules was formulated on the basis of electromagnetic theory of par- ticles with attention to relativistic nature of their interaction and its im- pact on the spectrum of circular dichroism. Calculations of the absorption spectra of simple systems were performed to demonstrate the properties of the mathematical model. Also calculations of the absorption spectra of the models of the bacteriochlorophyll dimer which were proposed as possible basic unit in the lamellar model of the interior of a chlorosome were performed. The experimental spectra of solution of non-aggregated bacteriochlorophyll were used to fit the parameters of the mathematical model of the molecule and for these parameters the spectra of the pro- posed models of a dimer were calculated. It has been found that the new non-electrostatic terms in the description of the mutual interaction of the parts of the molecule are negligible for calculations of ordinary absorption spectrum, but they have...
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Srovnání poruchových a neporuchových přístupů k teorii optické spektroskopie
Malý, Pavel ; Mančal, Tomáš (advisor) ; Pšenčík, Jakub (referee)
This thesis focuses on the comparison of perturbative and non-perturba-tive calculation of the third order polarization in two dimensional (2D) optical spec- troscopy. A two-level molecule and a coupled dimer are chosen as simple systems for which the 2D spectrum is calculated using explicit equations of motion for the reduced density matrix and integrating the response functions. The two approaches are compared qualitatively and quantitatively using obtained re- sults. The main difference found is the presence of higher order polarization contributions in non-perturbatively calculated spectrum. 1
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Přenos koherencí při relaxaci excitační energie v molekulárních agregátech
Olšina, Jan ; Mančal, Tomáš (advisor)
We study the time dependence of the density operator of molecular aggregates in contact with thermal bath, to find a proper approximation for the description of a coherence transfer influence on this evolution. It is based on results of the computer program, written by the author of the work. The program uses three methods of evaluation - the solution of the convolution Quantum Master Equation, and solution of the derived Redfield equations in Markov and subsequent Secular approximations. The temperature dependence and dependence on other parameters of the model are discussed on the basis of the obtained numerical results performed on an example of a trimer. The influence of coherence transfer on time-evolution superoperator of the trimer is discussed as well. The reasons why the Markov approximation fails for a wide spectrum of parameters are given. It is concluded that it is not suitable for the description of coherence transfer effects.
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Analytical Solutions of Two-Dimensional Schrödinger Equation
Tichý, Vladimír ; Skála, Lubomír (advisor) ; Šťovíček, Pavel (referee) ; Mančal, Tomáš (referee)
The goal of the dissertation is to find new method of solving two-dimensional Schrödinger equation in such cases, when the separation of the variables is not applicable. The results are applied to the two-dimensional Schrödinger equation with the potentials of the form of the quartic polynomial, of the sextic polynomial and of the quartic Morse potential. For these cases, the analytical formulae for the ground state wave functions and the corresponding energies have been found. For the specific class of the potentials of the form of the quartic polynomial, analytical formula for one of the excited states and for the corresponding energy have been found.
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