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Title: Excitation energy transfer in photosynthetic systems
Authors: Zheng, Fulu
Keywords: DRNTU::Science::Physics
Issue Date: 2018
Source: Zheng, F. (2018). Excitation energy transfer in photosynthetic systems. Doctoral thesis, Nanyang Technological University, Singapore.
Abstract: As one of the most significant natural processes providing food and energy for almost all life on the Earth, photosynthesis starts with sunlight absorption by specialized light harvesting complexes (LHCs) and the excitation energy is then transferred with nearly perfect efficiency to reaction centers (RCs). The extraordinary energy transfer efficiency in natural photosynthesis has been attracting increasing attention. Despite that extensive experimental and theoretical efforts have been devoted to studies of the excitation energy transfer in photosynthesis, the mystery of the extremely high energy transfer rate has not yet been well understood. An in-depth understanding of the underlying mechanisms for the energy transfer in photosynthesis can benefit the design of artificial photosynthetic devices. To this end, the current thesis conducts a systematic study of excitation energy transfer in various photosynthetic systems by employing hybrid theoretical methodologies. Electronic structures and pigment-environment interactions are key factors that determine the energy transfer in photosynthetic complexes. Compared to extensive investigations of such quantities for LHCs, relatively few studies have been proceeded to obtain these properties of RC complexes in which charge separation occurs. In order to fill in this gap, quantum chemistry calculations combined with molecular dynamics simulations are applied in this thesis to evaluate static quantities of the RC complex from purple bacteria Thermochromatium tepidum, including excitation energies, excitonic coupling, and spectral densities of the pigments. Effects of protein environments on the electronic structures are taken into account by treating atoms surrounding the pigments as point charges, producing reliable site energies of the RC pigments. In addition to helping interpret asymmetric charge separation pathways in the RCs, comprehensive electronic structures and spectral densities constructed in this thesis can be used in future explorations of dynamical processes in the RCs. Beyond static property calculations, simulations of energy transfer in different photosynthetic aggregates are then carried out in this thesis. In the preliminary stage, a relatively small complex, a chlorophyll (Chl) a dimer is modeled as the target system to investigate the competitive intra- and inter-chromophore energy transfer by employing the nonadiabatic excited-state molecular dynamics (NA-ESMD). The real time energy relaxation at an atomic level is monitored, and relaxation rates in the Chla dimer are obtained within the NA-ESMD framework. Thanks to the level splitting induced by the excitonic coupling, the overall energy relaxation in the Chla dimer is faster than that in the monomeric Chla. The NA-ESMD trajectories are also utilized to reveal energy relaxation pathways. The electronic transition density is applied to visualize the exciton redistribution on the pigments upon photoexcitation, disclosing detailed intra- and inter-molecular energy transfer mechanisms in natural photosynthetic systems. In addition to energy transfer in the Chla dimer, exciton diffusion in large-scale artificial B850 nanoarrays is simulated using the Dirac-Frenkel time-dependent variational principle combined with the Davydov trial state, aiming to study the excitation energy transfer in realistic photosynthetic systems typically composed of hundreds of pigments. An efficient program is developed and implemented on the state-of-the-art graphic processor units (GPUs). The excellent scaling properties of GPU architectures facilitate fully quantum mechanical simulations of energy transfer in huge systems. From coherent exciton-phonon dynamics in one-dimensional and two-dimensional nanoarrays, exciton delocalization is scrutinized by analyzing the coherence length and the superradiance enhancement factor. The mean square displacement is measured to characterize the exciton diffusion behavior, and a superdiffusive component is found in the exciton propagation. In summary, this thesis presents a comprehensive investigation of static as well as dynamics properties in natural and engineered photosynthetic systems by employing various theoretical methodologies, including the combined quantum chemistry calculations and classical molecular dynamics simulations, the mixed quantum-classical dynamics, and the fully quantum mechanical modelling. It is expected that findings obtained in this thesis provide advantageous insights on energy transfer processes in photosynthetic complexes and guiding principles on the design of manufactured photosynthetic devices.
DOI: 10.32657/10356/74118
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:MSE Theses

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