Figure 3.

Flow chart illustrating differences in experimental and MD approaches for validating depth-dependent quenching methodology. Because MD operates with a vastly superior number of potential quenchers of known depth and because the target distribution of the fluorophore is also explicitly known, the MD-based validation of data analysis is preferable to experiment-based validation. Examples of simulation-based validation of different aspects of DDFQ data analysis are shown in Fig. 4 (comparison of DA and PM) and Fig. 5 (comparison of results obtained with the extended DA procedure and underlying depth distribution of the model fluorophore).