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Abstract. In the present study a model for the compactification of the 30 nm chromatin fibre into higher order structures is suggested. The idea is that basically every condensing agent (HMG/SAR, HP1, cohesin, condensin, DNA-DNA interaction . . . ) can be modeled as an effective attractive potential of specific chain segments. This way the formation of individual 1 Mbp sized rosettes from a linear chain could be observed. We analyse how the size of these rosettes depends on the number of attractive segments and on the segment length. It turns out that 8-20 attractive segments per 1 Mbp domain produces rosettes of 300-800 nm in diameter. Furthermore, our results show that the size of the rosettes is relatively insensitive to the segment length.

A present model of the higher-order chromosome organization suggests the organization of chromosome built up by loops. Here we focus on a single rosette-like part of the fiber and analyse the diffusion behaviour of small particles (corresponding to single proteins/protein complexes) and the accessibility of such particles in relation to the dynamic rosette structure. Surprisingly, although the diffusion pattern of the diffusing particles revealed free diffusion, an area of about 6-12 kbp in the innermost part of these domains becomes visible which is inaccessible even for small particles (corresponding to single proteins/protein complexes). A localisation of a promotor sequence in this area might silence the respective gene by the physical inaccessibility of this area for transcription factors. We conclude that the compartmentalisation of chromatin in domains of a specific dynamical three-dimensional (3D) structure might be of high functional importance.

We investigate a self-avoiding polymer chain anchored with one end at a hard wall. The chains are modeled using the continuous backbone mass model. The sampling of the conformations is done by molecular dynamics for chains of various sizes. Presented are results for several different interesting situations. We have investigated the pressure that grafted chains of various sizes exert on the wall and find good agreement with the theory, if the theory is extended to the self-avoiding case using the standard scaling laws. Force-elongation simulations are compared to polymer theory and the partition function for a grafted ideal chain is explicitly calculated. Again we find good agreement with the theory.