Computer simulation of energy migration in the C-phycocyanin of the blue-green algae Agmenellum Quadruplicatum

Two methods for simulation of energy migration in the C-phycocyanin fragments of PBS were developed. Both methods are based on the statistical analysis of an excitation behavior in modeling complexes with a limited number (up to hundreds) of chromophores using the Monte-Carlo approach and calculation of migration rates for the system of linear balance equations. Energy migration rates were calculated in the case of C-phycocyanin of the blue-green algae Agmenellum quadruplicatum. The main channels of energy migration were determined in a monomer, trimer, hexamer, and in the rods consisting of 2-4 hexamers. The influence of the “screw” angle between two adjoining trimers of hexamer on the rates of energy migration and on its efficiencies in 1-4 hexamers was also estimated. The analysis was made for the average (random) and real orientation of chromophores in the C-phycocyanin. For both cases the optimal angle values were determined and the one for real C-phycocyanin structure was found to be very close (Δø ≤ 5°) to the optimal angle calculated.