Figure 4.

Simulated data. Here, we show a superstate trajectory (in blue) generated using Gillespie algorithm for a system-FRET composite with two system states ${\sigma }_{1:2}$ and three photophysical states. Collectively, superstates ${\phi }_{1:3}$ correspond to photophysical states when the system resides in ${\sigma }_1$ and superstates ${\phi }_{4:6}$ correspond to photophysical states when the system resides in ${\sigma }_2$. The pink vertical lines mark the time points where transitions between the superstates occur. The variables $b_{1:7}$ and $h_{1:7}$ between each set of vertical lines represent the superstates and associated holding times, respectively. The green and red dots show the photon detections at times $T_1$ and $T_2$ in channels 1 and 2, respectively. The first photon is detected upon transition $b_3\to b_4$ (or ${\phi }_5\to {\phi }_4$), while the second photon is detected upon transition $b_6\to b_7$ (or ${\phi }_6\to {\phi }_4$). For this plot, we have used very fast system transition rates of ${\lambda }_{{\sigma }_1\to {\sigma }_2}=0.001$ ns⁻¹ and ${\lambda }_{{\sigma }_1\to {\sigma }_2}=0.002$ ns⁻¹ for demonstrative purposes only.