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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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Electronic structure calculations of biologically relevant transition metal complexes
Matoušek, Mikuláš ; Veis, Libor (advisor) ; Mančal, Tomáš (referee)
Porphyrins are an important class of biomolecules, which are heavily studied, both ex- perimentally and computationally. But, despite the intensive efforts, for many questions we still aren't able to consistently find an agreement between theory and experiment. One of the still unresolved issues is the character of the ground state of the Fe(II)-porphyrin molecule. We used a model of the Fe(II)-porphyrin molecule to study the effects of geometrical changes on the spin states. By carrying out extensive DMRG-CASSCF cal- culations topped with TCCSD correlation treatment we are able to link the effects of these geometrical changes to the experimental results, and predict a quintet ground state for the isolated Fe(II)-porphyrin molecule. Also, using a ligated porphyrin belonging to the iron porphyrin carbene class of molecules, we demonstrate by combining the CASSCF and AC0 methods that geometrical changes outside the porphyrin core cannot be over- looked. 1
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Role of system-bath interaction time-scales in photosynthetic excitation energy transfer
Malý, Pavel ; Mančal, Tomáš (advisor) ; Croce, Roberta (referee) ; Polívka, Tomáš (referee)
ROLE ASOVÉ 'KÁLY INTERAKCE SYSTÉM-LÁZE VE FOTOSYNTETICKÉM P ENOSU EXCITANÍ ENERGIE Tato práce se věnuje vlivu rychlého a pomalého molekulárno pohybu na přenos excitační energie ve fotosyntetick- ých světlosběrných komplexech. Vyvinuli jsme nový teoretický popis vnitromolekulárních vibračních mod· a zjistili jsme, že jejich resonance s energetickými rozdíly mezi fotosyntetickými pigmenty m·že vést ke zrychlení přenosu energie. Použitím jednomolekulární spektroskopie jsme pozorovali jak pomalé změny bílkovinné konformace mohou zcela změnit stav světlosběrného komplexu LHCII vyšších rostlin. Také jsme vyvinuli novou experimentální techniku, dvoupulzní ultrarychlou jednomolekulární spektroskopii. S její pomocí m·žeme pozorovat jak pomalý pohyb bílkoviny bakteriální antény LH2 ovlivňuje ultrarychlou relaxaci energie uvnitř komplexu. Konstrukcí jednotného modelu pro ultrarychlé objemové a jednomolekulární experimenty se nám podařilo zakomponovat rychlou a pomalou časovou škálu molekulárního pohybu do jednoho pohledu na fotosyntetický sběr světla.
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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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