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

To understand the influence of geometrical constraints in the spatial distr ibution of cancer correlated "Double Minute chromosomes (DMs)" in human cel l nuclei, we applied computer simulations of the nuclear 3D structure in co mbination with a voxel based segmentation algorithm. With this approach we determined the overlap volumes and intensities of the DMs with the chromati n free space in the simulated nucleus. For this purpose, beginning from a s tart configuration, simulated linear chromosome chains together with the DM s were relaxed according to the Monte Carlo process. The simulations predic t a preferential positioning of DMs within the "peripheral" "Inter Chromati n Domain (ICD)" space.