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Fluorescence excitation spectra of photosynthetic antennae
Materna, Filip ; Mančal, Tomáš (advisor) ; Alster, Jan (referee)
The aim of this thesis is to offer a brief overview of energetic transfer taking place in photosynthetic antenna systems by studying an example antenna and trying to simulate its behavior. Utilising modern literature, we describe the structure of photosynthetic antenna systems, their properties and the methods used to study them. We follow this by proposing a model of the kinetics of ener- getic states in the studied system. The theoretical section is followed by analysis of measured absorption and fluorescence excitation spectra of the actual chloro- phyll + carotenoid dimers with use of OriginPro2020 and Python3. With this knowledge, we have developed a simulation to fit our model to the experimental values. We utilize the Quantarhei Python3 package to calculate the absorption spectra and the FES spectrum is constructed by solving a system of differential equations proposed from the kinetics model and fitting the measured data. From there, we extract the efficiency of energy transfer in the dimer.
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Influence of intra-molecular vibrational modes on excitation energy transfer in molecular aggregates
Herman, Daniel ; Mančal, Tomáš (advisor) ; Zamastil, Jaroslav (referee)
The energy transfer in molecular aggregates is generally hard to describe in a simple yet effective manner. There is often a trade-off between the accuracy of simulated results and the level of understanding of the underlying physics. To understand the evolution of a system with electronic degrees of freedom, understanding the influence of the system's evolution on the evolution of the bath is also required. To obtain an insight into the bath evolution, we introduce an exact factorization of the density matrix elements representing an entangled state of the bath and the system. We leverage this factorization to derive iterative quantum master equations. Iterative treatment of bath evolution is then used to derive corrected memory kernel with correlation functions in a local basis with the assumption of linear harmonic oscillators as modes of the bath. This approach attempts to improve existing perturbative master equations in a regime of weak interaction between the system and the bath. To judge the improvement achieved, we apply the theory to systems with the finite bath of small size. 1
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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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Teorie elektron-fononové interakce v modelovém otevřeném kvantovém systému
Krčmář, Jindřich ; Mančal, Tomáš (advisor) ; Lipavský, Pavel (referee)
The aim of this work is to investigate projection operator method of deriva- tion of equations of motion for reduced density matrix and apply it to a model open quantum system. We gradually pass from quantum mechanical model of a molecule with one vibrational degree of freedom to an example of open quantum system relevant in the theory of nonlinear spectroscopy. In the thesis we present results of numerical simulations of the time evolution of the open quantum system performed with a program written for this purpose. We are specially concerned with simulations of the solution of the time-convolutionless generalized master equation up to the a second order of the perturbation expan- sion, and we show that under certain conditions it provides an exact solution of the problem. The text also contains derivation of the recurrence relations for the Franck-Condon factors for the most general case of two quantum harmonic oscillators in one space dimension, i. e. transformation matrix between two bases of the L2 (R) space determined by the solutions of the time-independent Schrödinger equation appropriate for these oscillators. 1
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Nelineární optická spektroskopie molekulárních komplexů
Linhart, Jan ; Mančal, Tomáš (advisor) ; Pšenčík, Jakub (referee)
Práce se zabývá teorií nelineární spektroskopie a projevy kvantové koherentní dynamiky v nelineární spektroskopii. Poskytuje stručný přehled spektroskopických metod se zaměřením na metodu pump-probe. Dále rozví- jíme teorii nelineární odezvy, přičemž vycházíme z obecného N-wave mixing experimentu, a dospíváme ke tvaru odezvové funkce třetího řádu vyjádřené pomocí Liouvillových drah. Pro vybrané modelové systémy sledujeme koher- entní efekty, které se projevují v 2D a pump-probe spektrech, a provádíme jejich porovnání. D·raz je kladen na objasnění jev· relaxace a excitonové koherence mezi dvěma excitovanými stavy molekulárního dimeru. 1
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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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