Figure 5

A virtual FLIP experiment. In A, the principle of the biological FLIP experiment is shown. One given, labeled protein, that participates in one given biological structure (shown in green, since it is fluorescent at the beginning of the experiment) is bleached whenever it passes through a given region of the nucleus (Bleaching Zone, a region of the nucleus where the laser is turned to the bleaching mode). The overall fluorescence of the structure it then studied as a function of time. If the protein moves freely out of the structure and into the cytoplasm, then it will at some point passes through the bleaching zone, be bleached, and by random movement be incorporated again in the structure,. The overall fluorescence of the structure will therefore decrease with time. B and C: Result of two individual in silico FLIP experiments. The following parameters were used: Protein number: 216; Number ratio: 0.5; Size ratio: 3 and COS = 0.9999 for the experiment shown in B and COS = 0.99999 for the experiment shown in C. The bleaching probability value (see Implementation section) was set to 0.01. Those results were confirmed by 10 independent simulations that gave a very narrow range of output (not shown so that the behavior of one individual simulation can be easily seen).