Emergence of compact-disordered phase in a polymer Potts model
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arXiv
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| Format: | Preprint |
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2023
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| _version_ | 1866918016170590208 |
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| author | Nakanishi, Ryo Hukushima, Koji |
| author_facet | Nakanishi, Ryo Hukushima, Koji |
| contents | One of the central problems in epigenetics is how epigenetic modification patterns and chromatin structure are regulated in the cell nucleus. The polymer Potts model, a recently studied model of chromatins, is introduced with an offset in the interaction energy as a parameter, and the equilibrium properties are investigated using the mean-field analysis of the lattice model and molecular dynamics simulations of the off-lattice model. The results show that in common with both models, a phase emerges, which could be called the compact-disordered phase, in which the polymer conformation is compact and the epigenetic modification pattern is disordered, depending on the offset in the interaction energy and the fraction of the modified nucleosomes. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2310_00844 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | Emergence of compact-disordered phase in a polymer Potts model Nakanishi, Ryo Hukushima, Koji Soft Condensed Matter Statistical Mechanics Biological Physics One of the central problems in epigenetics is how epigenetic modification patterns and chromatin structure are regulated in the cell nucleus. The polymer Potts model, a recently studied model of chromatins, is introduced with an offset in the interaction energy as a parameter, and the equilibrium properties are investigated using the mean-field analysis of the lattice model and molecular dynamics simulations of the off-lattice model. The results show that in common with both models, a phase emerges, which could be called the compact-disordered phase, in which the polymer conformation is compact and the epigenetic modification pattern is disordered, depending on the offset in the interaction energy and the fraction of the modified nucleosomes. |
| title | Emergence of compact-disordered phase in a polymer Potts model |
| topic | Soft Condensed Matter Statistical Mechanics Biological Physics |
| url | https://arxiv.org/abs/2310.00844 |