Figure 2. Reconstruction of the living chromatin environment using Monte Carlo computer simulation. (A) The nucleosome is represented as a 10-nm red sphere and fixed in a restricted space at a concentration of 0.1 mM (left) or 0.5 mM (right, corresponding to mitotic chromatin) randomly but in a manner that avoids any overlap. The EGFP-pentamer is represented as a 13-nm sphere (green). See also Videos S1 to S3. (B) A simple scheme of the simulation procedure. For the details, see text. (C) Tracing patterns of three 13-nm spheres (EGFP-pentamers) under various conditions. At 0.1 mM of fixed 10-nm spheres (nucleosomes), the 13-nm spheres (EGFP-pentamers) move around freely (left image). However, at 0.5 mM of fixed 10-nm spheres (nucleosomes), the 13-nm spheres (EGFP-pentamers) are unable to move far from their starting points (middle image). In the environment with a fluctuation of 0.5 mM of the 10-nm spheres (nucleosomes), the 13-nm spheres (EGFP-pentamers) can move around freely (right image), in contrast to the case of the fixed 10-nm spheres (nucleosomes, middle image). Each 10-nm red sphere (nucleosome) behaves like “a dog on a leash.” The leash length is 20 nm. The three different temporal trajectories of the 13-nm spheres (EGFP-pentamers) for 0.2 ms are indicated in blue, green, and red. (D) Cartoons showing that a protein (green) is stacked in a confined space of fixed nucleosomes (left), and the protein is able to move freely with fluctuation of the nucleosomes (right).