Figure 6.

Abundance and escape dynamics for a simple genetic switch simulated in the intracellular environment of a HeLa cell. (a) Mean particle abundance (solid line) and standard deviation (shaded area) were computed over 37 simulation replicates. The time for a mRNA to diffuse out of the nucleus and find a ribosome is two orders of magnitude larger than the time for a newly translated protein to return and bind to its originating gene. The mRNA abundance in the cytoplasm is the sum of free mRNA and mRNA bound to ribosomes. (b–e) First passage time distributions of diffusion between compartments and reaction sites for the complete HeLa cell geometry (blue) and with all obstructions removed (green). These simulations were performed with instantaneous reaction rates in order to measure the time for diffusion alone over 222 simulation replicates. mRNA diffuses from the gene site into the cytoplasm (b), from the cytoplasm to the ribosome (c), the protein diffuses back into the nucleus (d), and the protein binds to the gene (e).