Figure 8.

The effect of the dark state population (p_dark) on the two-state maximum likelihood parameters. 5 sets of 100 30 ms-long photon trajectories with a photon count rate n = 50 ms^-1 were simulated using 4 model parameter sets. (A) E_F = 0.9, E_U = 0.6, k/n = 0.2 (light blue circle) and E_F = 0.9, E_U = 0.6, k/n = 0.6 (purple circle). (B) E_F = 0.7, E_U = 0.3, k/n = 0.2 (light green square) and E_F = 0.7, E_U = 0.3, k/n = 0.6 (orange square). p_F = 0.5, k_b = 500 ms^-1, and k_d = k_b(1- p_b)/p_b. Horizontal dashed lines indicate these model parameters. The red dashed curves in the left panels guide the effective FRET efficiencies in the fast blinking limit E_Fp_b + E_Dp_d and E_Up_b + E_Dp_d. The red dashed curve in the middle panels guides the relaxation rate between the bright and dark states (k_b + k_d). The errors are the average standard deviations obtained from the curvature of the likelihood function at the maximum.