MARKOV STATE MODEL

Markov State Models (MSMs) partition molecular dynamics trajectories into kinetically distinct conformational states, then estimate transition rates. The stationary distribution satisfies π_i ∝ e^{-F_i/k_BT}. The folding rate is the slowest relaxation eigenvalue of the transition matrix. The committor function p_fold(i) gives each state's probability of folding before unfolding.