Exciton simulations of the optical properties of several photosynthetic light-harvesting complexes

İşeri, Erkut İnan
The work presented in this thesis was aimed to investigate the structure-function relationship of several photosynthetic Light-Harvesting Complexes (LHCs) including Chlorophyll Protein 29 (CP29) and Light-Harvesting Complex II (LHCII) of green plants, and Fenna-Matthews-Olson (FMO) complex of green sulfur bacterium Chlorobium tepidum. Based on the exciton calculations, a model was proposed to the electronic excited states (EES) of both CP29 and LHCII complexes by incorporating a considerable part of the current information offered by structure determination, mutagenesis analysis and spectroscopy in the modeling. The essential parameters for characterizing the excited states, Qy dipole orientations and site energies were assigned by suggesting a model that can explain both the key features of the linear (polarized) absorption spectra and the time scales of the energy transfer processes in CP29 and LHCII. The idea of offering structural information through setting connection between the spectroscopy and the spectral simulations were supported by the presented results on CP29 and LHCII. New spectroscopic measurements (absorption, linear dichroism (LD) and circular dichroism), carried out at 4 K on the FMO complex were presented, and also the LD spectrum was corrected for the degree of orientation of the sample, in order to provide comparison of not only the shape but also the size of the simulated and experimental spectra. The EES structure of the FMO complex was studied by simulating the measured optical spectra with more realistic model than the previously applied models. Simulations have been carried out with a computer program based on exciton model, which includes inhomogeneous, homogeneous and lifetime broadenings explicitly.


ERGUCYENER, C; AYGUN, S; Ataman, Osman Yavuz; TEMIZER, A (1988-01-01)
Mercury speciation in aqueous solutions containing inorganic mercury and methylmercury has been demonstrated using electrochemical separation prior to determination by cold-vapour atomic absorption spectrometry. Approximately 95% of the inorganic mercury was electro-deposited on a Pt electrode at –0.1 V, whereas for methylmercury –0.2 V or even more negative potentials were required. Organic mercury was determined by NaBH4 reduction after electrochemical separation. Inorganic mercury was determined in the o...
Optical characterization of silicon based hydrogenated amorphous thin films by un-visible and infrared measurements
Kılıç, İlker; Katırcıoğlu, Bayram; Department of Physics (2006)
Various carbon content hydrogenated amorphous silicon carbide (a-Si1ŁxCx:H) and hydrogenated amorphous silicon (a-Si:H) thin films have been deposited on various substrates by using plasma enhanced chemical vapour deposition (PECVD) technique. Transmission spectra of these films have been determined within UV-Visible region and the obtained data were analysed to find related physical constants such as; refractive indices, thicknesses, etc. Fourier transform infrared (FT-IR) spectrometry technique has been u...
Anharmonic line shift and linewidth of the Raman modes in TlInS2 layered crystals
Yuksek, NS; Hasanlı, Nızamı; Aydinli, A (Wiley, 2004-01-01)
The temperature dependence of the unpolarized Raman spectra from TlInS2 layered crystal was measured between 10 and 300 K. The analysis of the experimental data showed that the temperature dependences of wavenumbers and linewidths are well described by considering the contributions from thermal expansion and lattice anharmonicity. The purely anharmonic contribution (phonon-phonon coupling) was found to be due to three-phonon processes. This work demonstrates that the two Raman modes at 280.9 and 292.3 cm(-1...
Terahertz Transmission Through Patterened Vanadium Oxide Thin Films on Dielectric Substrates
AKKAYA, MAHİNUR; Demirhan, Y.; Yuce, H.; Aygun, G.; Ozyuzer, L.; SABAH, CUMALİ; Altan, Hakan (SCITEPRESS, AV D MANUELL, 27A 2 ESQ, SETUBAL, 2910-595, PORTUGAL; 2017-03-01)
Patterned and unpatterned films of vanadium oxide grown on dielectric substrates such as fused silica and sapphire were grown and analysed by varying the temperature using terahertz time domain spectroscopy. After investigating the critical transition temperature near 340K, a well-known cross-shaped pattern was studied to observe any resonances upon transmission. Due to the poor conductivity of the films the frequency selective nature of the structure was not observed, however an etalon effect could be seen...
Photoelectron, compton and characteristic x-ray escape from an HPGe detector in the range 8-52 keV
Yilmaz, E; Can, Cüneyt (Wiley, 2004-11-01)
Escape of photoelectrons, Compton-scattered photons and Ge x-rays from an HPGe detector was studied as a function of energy in the range 8-52 keV. A variable-energy source producing Cu, Rb, Mo, Ag, Ba. and Tb x-rays was used. All three mechanisms for energy loss were observed in the same experiment for Ba and Tb, while only x-ray and photoelectron escapes were evident in the spectra for Ag, Mo, Rb, and Cu. Spectral features and possible mechanisms for partial energy deposition were investigated. A Monte Car...
Citation Formats
E. İ. İşeri, “Exciton simulations of the optical properties of several photosynthetic light-harvesting complexes,” Ph.D. - Doctoral Program, Middle East Technical University, 2004.