Towards a dynamical approach for the simulation of large scale, cancer correlated chromatin structures.

To understand the influence of geometrical constraints in the spatial distribution of cancer correlated "Double Minute chromosomes (DMs)" in human cell nuclei, we applied computer simulations of the nuclear 3D structure in combination with a voxel based segmentation algorithm. With this approach we determined the overlap volumes and intensities of the DMs with the chromatin free space in the simulated nucleus. For this purpose, beginning from a start configuration, simulated linear chromosome chains together with the DMs were relaxed according to the Monte Carlo process. The simulations predict a preferential positioning of DMs within the "peripheral" "Inter Chromatin Domain (ICD)" space.