A Computational Study of Excitation Energy Transfer in Photosynthetic Light-Harvesting Complexes
Date of Award
Doctor of Philosophy (PhD)
Photosynthetic organisms have evolved to harvest sunlight at incredible quantum efficiencies, some nearing 100%, and have adapted to become most efficient in their environmental light conditions. In this dissertation, the excitation energy transfer (EET) pathways in the peridinin-chlorophyll a-protein (PCP) complex from dinoflagellates are studied using tools from computational biology, including electron structure using complete active space configuration interaction (CAS-CI), and energy transfer using Forster resonance energy transfer (FRET) theory. To calculate accurate electronic couplings between donor (peridinin) and acceptor (chlorophyll a) pigments in PCP, a transition density cube (TDC) methodology is
introduced as an extension of the MOPAC 2012 electronic structure code. Using this methodology, the efficient S1 to Qy EET pathway in PCP was confirmed with several calculated lifetimes from 2 - 3 ps, and an alternate, but less efficient S2 to Qy EET pathway in PCP yielded several sub-fs lifetimes. Also in this dissertation, energy transfer in the chlorophyll a and b pigments was simulated via an internal conversion mechanism using nonadiabatic excited state molecular dynamics (NA-ESMD). Differences in the chlorophyll species were favorably compared to experimental results, and the transition density localization of each chlorophyll excited state was tracked throughout the simulations. Both of these studies provide insights for future work, including continued development of the TDC methodology, the addition of environmental factors in PCP with molecular dynamics, and a nonradiative study of the inter-molecular energy transfer in chlorophyll pigments using NA-ESMD.
Robert Blankenship, Palghat Ramachandran, Jung-Tsung Shen