A procedure is described to generate and optimize the lattice models for spectrally inhomogeneous photosynthetic antenna/reaction center (RC) particles. It is based on the genetic algorithm search for the pigment spectral type distributions on the lattice by making use of steady-state and time-resolved spectroscopic input data. Upon a proper fitness definition, a family of excitation energy transfer models can be tested for their compatibility with the available experimental data. For the case of the photosystem I core antenna (99 chlorophyll + primary electron donor pigment (P700)), three spectrally inhomogeneous three-dimensional lattice models, differing in their excitation transfer conditions, were tested. The relevant fit parameters were the pigment distribution on the lattice, the average lattice spacing of the main pool pigments, the distance of P700 and of long wavelength-absorbing (LWA) pigments to their nearest-neighbor main pool pigments, and the rate constant of charge separation from P700. For cyanobacterial PSI antenna/RC particles containing a substantial amount of LWA pigments, it is shown that the currently available experimental fluorescence data are consistent both with more migration-limited and with more trap-limited excitation energy transfer models. A final decision between these different models requires more detailed experimental data. From all search runs about 30 different relative arrangements of P700 and LWA pigments were found. Several general features of all these different models can be noticed: 1) The reddest LWA pigment never appears next to P700. 2) The LWA pigments in most cases are spread on the surface of the lattice not far away from P700, with a pronounced tendency toward clustering of the LWA pigments. 3) The rate constant k(P700) of charge separation is substantially higher than 1.2 ps-1, i.e., it exceeds the corresponding rate constant of purple bacterial RCs by at least a factor of four. 4) The excitation transfer within the main antenna pool is very rapid (less than 1 ps equilibration time), and only the equilibration with the LWA pigments is slow (about 10-12 ps). The conclusions from this extended study on three-dimensional lattices are in general agreement with the tendencies and limitations reported previously for a simpler two-dimensional array. Once more detailed experimental data are available, the procedure can be used to determine the relevant rate-limiting processes in the excitation transfer in such spectrally inhomogeneous antenna systems.
Trinkunas, G., & Holzwarth, A. R. (1996). Kinetic modeling of exciton migration in photosynthetic systems. 3. Application of genetic algorithms to simulations of excitation dynamics in three-dimensional photosystem I core antenna/reaction center complexes. Biophysical Journal, 71(1), 351–364. https://doi.org/10.1016/S0006-3495(96)79233-0