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. Author manuscript; available in PMC: 2007 Oct 1.
Published in final edited form as: J Phys Chem B. 2006 Aug 24;110(33):16366–16376. doi: 10.1021/jp063367k

Figure 1.

Figure 1

Reduced two-state model used for HMM analysis of single-molecule photobleaching trajectories. The shaded oval region represents spectroscopically indistinguishable emissive (bright) states with inset circles representing distinct bright states. The shaded rectangle region represents spectroscopically indistinguishable nonemissive (dark) states with inset squares representing distinct dark states. Active states, whether dark or bright (A), are considered to be related by reversible physical processes such as isomerization or intersystem crossing. Damaged states (D) are considered to be chemically modified dark or bright states. Bleached states (B) are dark and entered irreversibly. If there is only one connection between the emitting and nonemitting states, then the system can be reduced to a two-state system. The use of hidden Markov models can make it possible to extract both the emitting and nonemitting hidden states given enough state transitions to characterize them.