HMM for Langevin dynamics

(a) Potential of mean force used to describe the protein dynamics dictate by the FRET pair (donor and acceptor) distance attached to a protein.
(b) Probability distribution function in (a).
(c) Simulated photon trajectories recorded by donor (red) and acceptor (blue) channels. Microtime (the time lag between the laser pulse and the arrival of the photon) for each photon recorded in donor channel (d) and acceptor channel (e).
(f) Reconstructed donor-acceptor distance trajectory using hidden Markov model (HMM) with evenly spaced 21 states across the donor-acceptor distance.
(g) “True” donor-acceptor distance trajectory, generated by Langevin dynamics simulation on (a), used to simulate the photon trajectory in (c).