Anomalous diffusion in the interphase cell nucleus: The effect of spatial correlations of chromatin

The metabolism of a living cell requires a permanent transfer of molecules throughout the cell and beyond its bounds. Within cell nuclei, molecules are predominantly driven by diffusion, which is influenced by the chromatin network. We propose a quantity related to the pair correlation function to measure the diffusion-relevant clumpiness of chromatin. Using Monte Carlo lattice simulations, we investigate to what extent diffusion can be anomalous due to obstruction by the chromatin network. Chromatin is simulated by a wormlike chain on a lattice, which exhibits different types of loop-induced compartmentalization on a subchromosomal level. Our simulation results show that the proposed measure of clumpiness is suitable to quantify the compartmentalization of chromatin and to connect it to diffusion anomaly parameters, critical molecule sizes for trapping and the transition lengths at which diffusion becomes normal at long times. (C) 2010 American Institute of Physics. [doi:10.1063/1.3435345]