Fig. 13. Ideal and non-ideal FRET simulations. (A) Experimental FRET efficiencies for transfer from a single Cy3.5 to a variable number of Cy5.5s arrayed in a plane compared with ideal simulations assuming dynamic dipoles. For the simulations the distance between the Cy3.5 and the plane is assumed to be 8.6 nm, while the distances between Cy5.5s is 5.6 nm. (B) Non-ideal simulations using the MD-derived spacings and orientations. One calculation assumes all dyes are present (100% Sim) while the other assumes a DNA structural assembly yield of 90%. See Fig. 27 for a schematic of the structure from which this data is derived. Reprinted with permission from ref. 103 Copyright 2021 American Chemical Society.