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. Author manuscript; available in PMC: 2017 Oct 20.
Published in final edited form as: J Chem Theory Comput. 2016 Nov 7;12(12):5946–5959. doi: 10.1021/acs.jctc.6b00712

Figure 2.

Figure 2

Left: Illustration of hierarchical charge partitioning (HCP) for three levels of approximation. The greater the distance from the point of interest, the larger (higher level) is the component used in the approximation. Here, h1, h2 and h3 are the level 1 (group), level 2 (subunit) and level 3 (complexes) threshold distances, respectively. The charge distribution for each component at level 1 and beyond is represented by two approximate point charges,83 which are used for computations involving distant components. Right: Multi-level hierarchical partitioning of 40-nucleosome 30-nm chromatin fiber (see Figure 1) based on its natural structural organization: (a) The fiber is made up of 40 nucleosome complexes excluding the DNA, (b) each complex (level 3) is made up of 9 subunits (histones), (c) each subunit (level 2) is made up of 68–135 groups, and (d) each group (level 1) is made up of 7–32 atoms (level 0). The DNA is partitioned into segments of 32 nucleotides with each segment being treated as a complex with a single subunit. The images were rendered using VMD.14