Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs. cgDNA+
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| Format: | Preprint |
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2024
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| _version_ | 1866910427920728064 |
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| author | Laeremans, Wout Segers, Midas Voorspoels, Aderik Carlon, Enrico Hooyberghs, Jef |
| author_facet | Laeremans, Wout Segers, Midas Voorspoels, Aderik Carlon, Enrico Hooyberghs, Jef |
| contents | Coarse-grained models have emerged as valuable tools to simulate long DNA molecules while maintaining computational efficiency. These models aim at preserving interactions among coarse-grained variables in a manner that mirrors the underlying atomistic description. We explore here a method for testing coarse-grained vs. all-atom models using stiffness matrices in Fourier space ($q$-stiffnesses), which are particularly suited to probe DNA elasticity at different length scales. We focus on a class of coarse-grained rigid base DNA models known as cgDNA and its most recent version cgDNA+. Our analysis shows that while cgDNA+ follows closely the $q$-stiffnesses of the all-atom model, the original cgDNA shows some deviations for twist and bending variables which are rather strong in the $q \to 0$ (long length scale) limit. The consequence is that while both cgDNA and cgDNA+ give a suitable description of local elastic behavior, the former misses some effects which manifest themselves at longer length scales. In particular, cgDNA performs poorly on the twist stiffness with a value much lower than expected for long DNA molecules. Conversely, the all-atom and cgDNA+ twist is strongly length scale dependent: DNA is torsionally soft at a few base pair distances, but becomes more rigid at distances of a few dozens base pairs. Our analysis shows that the bending persistence length in all-atom and cgDNA+ is somewhat overestimated. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2401_05208 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs. cgDNA+ Laeremans, Wout Segers, Midas Voorspoels, Aderik Carlon, Enrico Hooyberghs, Jef Soft Condensed Matter Statistical Mechanics Biomolecules Coarse-grained models have emerged as valuable tools to simulate long DNA molecules while maintaining computational efficiency. These models aim at preserving interactions among coarse-grained variables in a manner that mirrors the underlying atomistic description. We explore here a method for testing coarse-grained vs. all-atom models using stiffness matrices in Fourier space ($q$-stiffnesses), which are particularly suited to probe DNA elasticity at different length scales. We focus on a class of coarse-grained rigid base DNA models known as cgDNA and its most recent version cgDNA+. Our analysis shows that while cgDNA+ follows closely the $q$-stiffnesses of the all-atom model, the original cgDNA shows some deviations for twist and bending variables which are rather strong in the $q \to 0$ (long length scale) limit. The consequence is that while both cgDNA and cgDNA+ give a suitable description of local elastic behavior, the former misses some effects which manifest themselves at longer length scales. In particular, cgDNA performs poorly on the twist stiffness with a value much lower than expected for long DNA molecules. Conversely, the all-atom and cgDNA+ twist is strongly length scale dependent: DNA is torsionally soft at a few base pair distances, but becomes more rigid at distances of a few dozens base pairs. Our analysis shows that the bending persistence length in all-atom and cgDNA+ is somewhat overestimated. |
| title | Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs. cgDNA+ |
| topic | Soft Condensed Matter Statistical Mechanics Biomolecules |
| url | https://arxiv.org/abs/2401.05208 |