data simulator
The focus of the simulation is on empirically reproducing typical smFRET data. To this end, we evaluated experimental smFRET trajectories (from different detectors, dyes, biomolecules) regarding intensities & intensity distributions, noise characteristics, trace lengths etc. Based on this, we obtained parameters that quantitatively describe typical smFRET trajectories.
Using the experiment-derived parameters, each state trajectory is simulated in continuous time according to the supplied transition rate matrix. Next, the traces are discretised using a typical sampling rate of a camera-based smFRET setup. The intensity at time t is obtained by integration over the populations of each state occurring during the corresponding exposure time (thus yielding intermediate intensity levels if a state transition occurred during the exposure time). Optionally, degenerate states are introduced.
The following parameters are used to simulate real-world experiments:
- the transition rate matrix
- frame rate and bleach rate
- minimal and maximal trace length
- the Gaussian* distribution of the fluorescence intensity of each state (leading to not necessarily Gaussian FRET efficiency distributions)
- the number of traces
- possible blinking kinetics of the dyes
- two parameters controlling a possible per-trace variability of the intensity levels
* Although strictly speaking Poissonian, the photon counts observed in typical camera-based smFRET experiments (N>10) are very well modeled by Gaussian distributions.