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http://hdl.handle.net/1942/42699
Title: | Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs. cgDNA+ | Authors: | LAEREMANS, Wout Segers, Midas Voorspoels, Aderik Carlon, Enrico HOOYBERGHS, Jef |
Issue Date: | 2024 | Publisher: | AIP publishing | Source: | JOURNAL OF CHEMICAL PHYSICS, | Status: | In press | Abstract: | 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. | Keywords: | Physics - Soft Condensed Matter;Physics - Statistical Mechanics;Quantitative Biology - Biomolecules | Document URI: | http://hdl.handle.net/1942/42699 | Link to publication/dataset: | http://arxiv.org/abs/2401.05208v1 | ISSN: | 0021-9606 | e-ISSN: | 1089-7690 | Category: | A1 | Type: | Journal Contribution |
Appears in Collections: | Research publications |
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File | Description | Size | Format | |
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2401.05208v1.pdf | Non Peer-reviewed author version | 1.7 MB | Adobe PDF | View/Open |
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