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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, 160 (14) (Art N° 144105) | 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+ closely follows 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 -> 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 that manifest themselves at longer length scales. In particular, cgDNA performs poorly on twist stiffness, with a value much lower than expected for long DNA molecules. Conversely, the all-atom and cgDNA+ twist are strongly length scale dependent: DNA is torsionally soft at a few base pair distances but becomes more rigid at distances of a few dozen base pairs. Our analysis shows that the bending persistence length in all-atom and cgDNA+ is somewhat overestimated. | Notes: | Carlon, E (corresponding author), Katholieke Univ Leuven, Soft Matter & Biophys Unit, Celestijnenlaan 200D, B-3001 Leuven, Belgium. enrico.carlon@kuleuven.be; jef.hooyberghs@uhasselt.be |
Keywords: | Elasticity;Base Pairing;DNA | Document URI: | http://hdl.handle.net/1942/42989 | ISSN: | 0021-9606 | e-ISSN: | 1089-7690 | DOI: | 10.1063/5.0197053 | ISI #: | 001198859200008 | Category: | A1 | Type: | Journal Contribution |
Appears in Collections: | Research publications |
Files in This Item:
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144105_1_5.0197053.pdf Restricted Access | Published version | 6.8 MB | Adobe PDF | View/Open Request a copy |
ACFrOgADTJO6gVyXDtc40FNA8itcTqLvSrt-jjemDnmr1IP6rKw0ApzWLCppWDrM3Qp1.pdf | Peer-reviewed author version | 1.73 MB | Adobe PDF | View/Open |
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