Chromosome structure predicted by a polymer model

Human chromosomes were simulated by a polymer model in the presence of an excluded-volume interaction. The polymer chain of each chromosome was arranged into loops and several consecutive loops formed subcompartments. We observed the formation of distinct chromosome territories with separated chromosome arms and subcompartments in agreement with recent experiments. Mean spatial distances between markers agree with measurements under different preparation conditions. Different scaling properties were found depending on the genomic distance regarded. The radial density, the position of genes, and the overlap of chromosome arms and subcompartments agree with experimental results. The parallelization of the Monte Carlo and Brownian dynamics algorithms and a method for the computation of confocal images is described, which allows a direct comparison with results from confocal light microscopy.