The Stochastic drift-diffusion (DrDiff) framework can determine the coordinate-dependent diffusion coefficient D(Q), the drift velocity v(Q) and the free-energy landscape F(Q) using a given single-molecule trajectory Q(t) as input. It can also resolve the mean first passage time and mean transition path time from trajectory and calculate the first passage time and the transition path time by Kramers' theory using D(Q) and F(Q) previously settled.
References:
Stochastic diffusion framework determines the free-energy landscape and rate from single-molecule trajectory. Ronaldo J. Oliveira. The Journal of Chemical Physics, Volume 149, Issue 23, Page 234107, 2018. https://aip.scitation.org/doi/10.1063/1.5052142
Drift-diffusion (DrDiff) framework determines kinetics and thermodynamics of two-state folding trajectory and tunes diffusion models. Frederico Campos Freitas, Angelica Nakagawa Lima, Vinicius de Godoi Contessoto, Paul C. Whitford and Ronaldo Junio de Oliveira, Journal Of Chemical Physics, v. 151, n. 11, 13 p., 2019. https://aip.scitation.org/doi/10.1063/1.5113499
Snapshot with transitions between two states, alongside the D(Q), F(Q) and v(Q) for prion protein (PrP) analysis.
