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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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Signatures of vibronic modulation of small molecular aggregates in two-dimensional electronic spectra
Perlík, Václav ; Šanda, František (advisor) ; Alster, Jan (referee) ; Gelin, Maxim (referee)
We studied the effects of underdamped vibrational modes on excitonic energy transfer in small molecular aggregates by means of ultrafast nonlinear spectroscopy. We developed a vibronic dynamical model to account for the interplay of electronic and vibrational coherence during excitation transport. Our model was aimed to simulate signals of a broad class of linear and third order spectroscopies (absorption, fluorescence, transient absorption (TA), transient grating (TG), two-dimensional spectroscopy (2D)) in the visible domain andaccounts for anharmonic vibrations, sub-exponential relaxation and nonlinear electron-vibrational coupling. We subsequently applied the model for several case studies, such as carotenoid to bacteriochlorophyll excitation transfer in light-harvesting 2 complex (LH2) of purple bacteria, excitation transfer in perylene dyads or vibrational dynamics in hypericin. We have paid particular attention for detailed interpretation of lineshapes of 2D spectrograms employing, e.g. phase analysis and center line (CL) slopes with emphasis to study interplay of electronic, vibrational modulations, or finite excitation pulse durations.
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Signatures of vibronic modulation of small molecular aggregates in two-dimensional electronic spectra
Perlík, Václav ; Šanda, František (advisor) ; Alster, Jan (referee) ; Gelin, Maxim (referee)
We studied the effects of underdamped vibrational modes on excitonic energy transfer in small molecular aggregates by means of ultrafast nonlinear spectroscopy. We developed a vibronic dynamical model to account for the interplay of electronic and vibrational coherence during excitation transport. Our model was aimed to simulate signals of a broad class of linear and third order spectroscopies (absorption, fluorescence, transient absorption (TA), transient grating (TG), two-dimensional spectroscopy (2D)) in the visible domain andaccounts for anharmonic vibrations, sub-exponential relaxation and nonlinear electron-vibrational coupling. We subsequently applied the model for several case studies, such as carotenoid to bacteriochlorophyll excitation transfer in light-harvesting 2 complex (LH2) of purple bacteria, excitation transfer in perylene dyads or vibrational dynamics in hypericin. We have paid particular attention for detailed interpretation of lineshapes of 2D spectrograms employing, e.g. phase analysis and center line (CL) slopes with emphasis to study interplay of electronic, vibrational modulations, or finite excitation pulse durations.
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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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Modelling Spectral Fluctuations in Nonlinear Spectroscopy - Stochastic Liouville Equations and Beyond
Perlík, Václav ; Novotný, Tomáš (referee) ; Šanda, František (advisor)
In this work we model nonlinear coherent optical response of aggregate of two level molecules. Exciton hamiltonian parametrically depends on a stochastic process, which models orientation changes (conformation jumps) of molecules. Stochastic nonlinear exciton equations are derived and implemented in the program that calculates nonlinear optical spectra. Absorption and 2D photon echo of tetramer are investigated in detail for two models of stochastic uctuations of dipole moment. Coherence length of exciton is identied with peaks position in spectra. Fluctuations of coherence length are then observed in cross-peak dynamics in 2D spectra.
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