This repository contains scripts to simulate smFRET model in the paper entitled "Time-Heterogeneity of the Förster Radius from Dipole Orientational Dynamics Impacts Single-Molecule FRET Experiments". Paper: https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.7.023014
README.md: Documentation for understanding and using simulation codes.
Each code is well commented with definitions of each parameter. Each code outputs a .rds file containing 4 columns of information extracted from the simulations. That is Bin_FRET = FRET, Bin_life_D = Lifetime, Var_life = Variance of Lifetime, ds = Dynamic Shift, and df = Donor fluorescence rate. The user can decide which values they are interested in plotting. To plot the simulations of a representative dye trajectory, simply plot the sequence of values for the donor positions (Dx1,Dx2,Dx3) or the acceptor positions (Ax1,Ax2,Ax3).
Script to simulate the anisotropic spring model in Section IIA and Figure 4A.
Script to simulate the anisotropic spring model in Section IIA and Figure 4C.
Script to simulate the elastic pendulum model in Section IIB and Figure 4E.
Script to simulate the elastic pendulum model with kappa, orientational dynamics, in Section IIC and Figure 4G.