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http://hdl.handle.net/1942/42699
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DC Field | Value | Language |
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dc.contributor.author | LAEREMANS, Wout | - |
dc.contributor.author | Segers, Midas | - |
dc.contributor.author | Voorspoels, Aderik | - |
dc.contributor.author | Carlon, Enrico | - |
dc.contributor.author | HOOYBERGHS, Jef | - |
dc.date.accessioned | 2024-03-27T09:08:41Z | - |
dc.date.available | 2024-03-27T09:08:41Z | - |
dc.date.issued | 2024 | - |
dc.date.submitted | 2024-03-25T08:00:18Z | - |
dc.identifier.citation | JOURNAL OF CHEMICAL PHYSICS, | - |
dc.identifier.uri | http://hdl.handle.net/1942/42699 | - |
dc.description.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. | - |
dc.language.iso | en | - |
dc.publisher | AIP publishing | - |
dc.subject | Physics - Soft Condensed Matter | - |
dc.subject | Physics - Soft Condensed Matter | - |
dc.subject | Physics - Statistical Mechanics | - |
dc.subject | Quantitative Biology - Biomolecules | - |
dc.subject.other | Physics - Soft Condensed Matter | - |
dc.subject.other | Physics - Statistical Mechanics | - |
dc.subject.other | Quantitative Biology - Biomolecules | - |
dc.title | Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs. cgDNA+ | - |
dc.type | Journal Contribution | - |
local.bibliographicCitation.jcat | A1 | - |
local.type.refereed | Refereed | - |
local.type.specified | Article | - |
local.bibliographicCitation.status | In press | - |
dc.identifier.arxiv | arXiv:2401.05208 | - |
dc.identifier.url | http://arxiv.org/abs/2401.05208v1 | - |
local.provider.type | ArXiv | - |
local.uhasselt.international | yes | - |
item.fulltext | With Fulltext | - |
item.fullcitation | LAEREMANS, Wout; Segers, Midas; Voorspoels, Aderik; Carlon, Enrico & HOOYBERGHS, Jef (2024) Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs. cgDNA+. In: JOURNAL OF CHEMICAL PHYSICS,. | - |
item.accessRights | Open Access | - |
item.contributor | LAEREMANS, Wout | - |
item.contributor | Segers, Midas | - |
item.contributor | Voorspoels, Aderik | - |
item.contributor | Carlon, Enrico | - |
item.contributor | HOOYBERGHS, Jef | - |
crisitem.journal.issn | 0021-9606 | - |
crisitem.journal.eissn | 1089-7690 | - |
Appears in Collections: | Research publications |
Files in This Item:
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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