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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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Tensor Network-based Computational Methods for Strongly Correlated Molecular Quantum Mechanics
Brandejs, Jan ; Veis, Libor (advisor) ; Mančal, Tomáš (referee) ; Pitoňák, Michal (referee)
Despite an immense progress in recent decades, a precise treatment of strongly corre- lated molecular systems still remains a challenge as of today. To help solve this problem, we have developed a massively parallel implementation of DMRG, called MOLMPS. For nonrelativistic systems requiring accurate treatment of both static and dynamical corre- lation, we have extended MOLMPS by the means of the almost linear scaling DLPNO- TCCSD method. In relativistic domain, we are the first who employed the 4c-CCSD to add dynamical correlation on top of DMRG, yielding the 4c-TCCSD method. When tested on benchmarks like the π-conjugated anthracene tetramer with CAS(63,63) and the FeMoco cofactor with CAS(113,76). We showed a good parallel performance on up to about 2000 CPUs. On the example of Iron(II)-Porphyrin model, we showed that the DLPNO-TCCSD captures 99.9% of TCCSD correlation energy. Our spectroscopic study on heavy diatomics showed that the 4c-TCCSD approach increases the precision of underlying CCSD to the order of CCSD(T) and that it is a promising approach. The thesis discusses three different implementations of quantum chemical methods based on QC-DMRG. 1
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Coherence transfer during relaxation in molecular aggregates
Olšina, Jan ; Mančal, Tomáš (advisor) ; Skála, Lubomír (referee)
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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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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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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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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