Paper Citing NAMD - Abstract
Fujita, Takatoshi; Huh, Joonsuk; Saikin, Semion K.; Brookes, Jennifer C.; Aspuru-Guzik, Alan
Theoretical characterization of excitation energy transfer in chlorosome light-harvesting antennae from green sulfur bacteria
PHOTOSYNTHESIS RESEARCH, 120:273-289, JUN 2014
We present a theoretical study of excitation dynamics in the chlorosome antenna complex of green photosynthetic bacteria based on a recently proposed model for the molecular assembly. Our model for the excitation energy transfer (EET) throughout the antenna combines a stochastic time propagation of the excitonic wave function with molecular dynamics simulations of the supramolecular structure and electronic structure calculations of the excited states. We characterized the optical properties of the chlorosome with absorption, circular dichroism and fluorescence polarization anisotropy decay spectra. The simulation results for the excitation dynamics reveal a detailed picture of the EET in the chlorosome. Coherent energy transfer is significant only for the first 50 fs after the initial excitation, and the wavelike motion of the exciton is completely damped at 100 fs. Characteristic time constants of incoherent energy transfer, subsequently, vary from 1 ps to several tens of ps. We assign the time scales of the EET to specific physical processes by comparing our results with the data obtained from time-resolved spectroscopy experiments.
