Table 1.
Computational and experimental works mentioned in this review (partial account), listed under the scale of interest.
| Scale | Publication | Subject | Computational techniques | Experimental data |
|---|---|---|---|---|
| NCP | Fan et al. (2013) | Ionic dependence of aggregation | Langevin MD | FCS |
| Materese et al. (2009) | Ion condensation, NCP solvation | MD, PBE | PDB structure | |
| Buckwalter et al. (2017) | Sequence dependence of DNA curvature | MC | EM | |
| Rohs et al. (2009) | Sequence dependence of DNA electrostatics | PBE | PDB structures | |
| Shaytan et al. (2016) | Histone tail interaction | MD | ||
| Rychkov et al. (2017) | NCP Assembly | MD | SANS, FRET, AFM | |
| Davey et al. (2002) | NCP Solvation | NMR | ||
| Luger et al. (1997) | Nucleosome structure | X-ray crystallography | ||
| Bertin et al. (2004) | Histone tail interaction | SAXS | ||
| Nucleosome arrays | Diesinger and Heermann (2009); Diesinger et al. (2010) | Histone and nucleosome depletion | MC | FISH |
| Collepardo-Guevara and Schlick (2014) | NRL-produced patterns | MC | ||
| Kepper et al. (2008) | NRL-produced patterns | MC | Stretching experiments | |
| Norouzi and Zhurkin (2018) | Nucleosome array unwrapping | MC | FCS | |
| Stehr et al. (2008) | Inter-NCP interactions | MC | Data from various techniques | |
| Gan and Schlick (2010) | Ionic dependence of aggregation | PBE, DiSCO | Data on DNA bending | |
| Grigoryev et al. (2009) | Linker histones, ionic dependence | MC | EM | |
| Izadi et al. (2016) | Electrostatics, histone tails, linker DNA | PBE | Cryo-EM | |
| Koslover et al. (2010) | Linker DNA | Energy optimization | EM, FCS | |
| Bascom et al. (2016) | Loop formation | MC | 3C | |
| Entire genome | Ohno et al. (2019) | 3D genome architecture | Hi-CO method | Hi-C |
| Cauer et al. (2019) | Hi-C 3D reconstruction | Mathematical modeling | Hi-C | |
| Lieberman-Aiden et al. (2009) | Fractal globule | Polymer simulations | Hi-C | |
| Iashina et al. (2017) | Fractal globule | Mathematical analysis | SANS | |
| Ghosh and Jost (2018) | Chromosome modeling | Coarse-grained Polymer model | Hi-C | |
| Fudenberg et al. (2016) | TADs | Polymer model | Hi-C | |
| Giorgetti et al. (2014) | TADs | Polymer model | 3C, FISH | |
| Bianco et al. (2017) | TADs | Polymer model | 5C | |
| Ricci et al. (2015) | Nucleosome aggregation | STORM | ||
| Le Gratiet et al. (2018) | Chromatin organization in the nucleus | CIDS, Fluorescence |
Computational techniques and experimental data used are listed, when applicable.