Martini 3 Coarse-Grained Model of DNA for Heterogeneous Molecular Systems
- 1Department of Mechanical Engineering and Materials Science, Duke University, Durham
Abstract
DNA often functions in heterogeneous molecular systems containing proteins, lipids, polymers, and other materials. All-atom molecular dynamics simulations can be used to study DNA in these multicomponent systems, but computational cost limits the accessible system sizes and time scales. Coarse-grained models extend these scales, but existing DNA models are generally not designed for interactions with a broad range of other molecular species. To fill this gap, we develop a coarse-grained model of DNA designed for use with the Martini 3 force field. The model was parameterized through an iterative Bayesian optimization workflow, which used a scaled Wasserstein metric to compare distributions of local geometrical features and global structure from coarse-grained simulations against all-atom reference simulations. The optimized model captures key structural and mechanical properties of single- and double-stranded DNA across varying strand lengths and ionic conditions, while retaining compatibility with the broader Martini 3 ecosystem. This compatibility enables DNA to be integrated with a broad range of molecular systems, as we illustrate through simulations of double-stranded DNA bound to a transcription factor, cholesterol-tagged DNA duplex interacting with a lipid bilayer, a crossover-containing DNA nanostructure, and single-stranded DNA adsorbing onto graphene. Together, these results establish a transferable coarse-grained model of DNA for simulations of heterogeneous biomolecular and engineered systems.
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BibTeX
@misc{dargis2026martini,
title = {{Martini 3 Coarse-Grained Model of DNA for Heterogeneous Molecular Systems}},
author = {R. Dargis and G. Arya},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.14.751576},
url = {https://www.biorxiv.org/content/10.64898/2026.09.14.751576v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Martini 3 Coarse-Grained Model of DNA for Heterogeneous Molecular Systems
AU - R. Dargis
AU - G. Arya
PY - 2026
DA - 2026/09/14
PB - bioRxiv
DO - 10.64898/2026.09.14.751576
UR - https://www.biorxiv.org/content/10.64898/2026.09.14.751576v1
AB - DNA often functions in heterogeneous molecular systems containing proteins, lipids, polymers, and other materials. All-atom molecular dynamics simulations can be used to study DNA in these multicomponent systems, but computational cost limits the accessible system sizes and time scales. Coarse-grained models extend these scales, but existing DNA models are generally not designed for interactions with a broad range of other molecular species. To fill this gap, we develop a coarse-grained model of DNA designed for use with the Martini 3 force field. The model was parameterized through an iterative Bayesian optimization workflow, which used a scaled Wasserstein metric to compare distributions of local geometrical features and global structure from coarse-grained simulations against all-atom reference simulations. The optimized model captures key structural and mechanical properties of single- and double-stranded DNA across varying strand lengths and ionic conditions, while retaining compatibility with the broader Martini 3 ecosystem. This compatibility enables DNA to be integrated with a broad range of molecular systems, as we illustrate through simulations of double-stranded DNA bound to a transcription factor, cholesterol-tagged DNA duplex interacting with a lipid bilayer, a crossover-containing DNA nanostructure, and single-stranded DNA adsorbing onto graphene. Together, these results establish a transferable coarse-grained model of DNA for simulations of heterogeneous biomolecular and engineered systems.
ER -