Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/42989
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

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