{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:18:31Z","timestamp":1792790311385,"version":"4.5.0"},"posted":{"date-parts":[[2026,9,16]]},"group-title":"Biophysics","reference-count":41,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"award":["2R01GM122979"],"award-info":[{"award-number":["2R01GM122979"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"name":"U.S. National Science Foundation","award":["CMMI-2323969"],"award-info":[{"award-number":["CMMI-2323969"]}],"id":[{"id":"https:\/\/ror.org\/021nxhr62","id-type":"ROR","asserted-by":"crossref"}]},{"name":"U.S. National Science Foundation","award":["ACI-2138259, 2138286, 2138307, 2137603, and 2138296"],"award-info":[{"award-number":["ACI-2138259, 2138286, 2138307, 2137603, and 2138296"]}],"id":[{"id":"https:\/\/ror.org\/021nxhr62","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>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.<\/jats:p>","DOI":"10.64898\/2026.09.14.751576","type":"posted-content","created":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T05:05:28Z","timestamp":1789621528000},"source":"Crossref","is-referenced-by-count":0,"title":["Martini 3 Coarse-Grained Model of DNA for Heterogeneous Molecular Systems"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3908-0442","authenticated-orcid":false,"given":"Rokas","family":"Dargis","sequence":"first","affiliation":[{"name":"Department of Mechanical Engineering and Materials Science, Duke University, Durham"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5615-0521","authenticated-orcid":false,"given":"Gaurav","family":"Arya","sequence":"additional","affiliation":[{"name":"Department of Mechanical Engineering and Materials Science, Duke University, Durham"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026092102400489000_2026.09.14.751576v1.1","first-page":"413101","article-title":"Close encounters with DNA","volume":"26","year":"2014","journal-title":"Journal of Physics: Condensed Matter"},{"key":"2026092102400489000_2026.09.14.751576v1.2","doi-asserted-by":"publisher","DOI":"10.1039\/c0cp02796k"},{"key":"2026092102400489000_2026.09.14.751576v1.3","doi-asserted-by":"publisher","DOI":"10.1017\/S0033583510000077"},{"key":"2026092102400489000_2026.09.14.751576v1.4","doi-asserted-by":"publisher","DOI":"10.1039\/c2sm25789k"},{"key":"2026092102400489000_2026.09.14.751576v1.5","doi-asserted-by":"crossref","first-page":"e2504780122","DOI":"10.1073\/pnas.2504780122","article-title":"Regulation of the ordinal DNA translocation cycle in bacteriophage \u03a629 through trans-subunit interactions","volume":"122","year":"2025","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"2026092102400489000_2026.09.14.751576v1.6","doi-asserted-by":"crossref","first-page":"17068","DOI":"10.1038\/natrevmats.2017.68","article-title":"DNA Nanotechnology","volume":"3","year":"2017","journal-title":"Nature Reviews Materials"},{"key":"2026092102400489000_2026.09.14.751576v1.7","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-bioeng-062117-120904"},{"key":"2026092102400489000_2026.09.14.751576v1.8","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2016.03.015"},{"key":"2026092102400489000_2026.09.14.751576v1.9","doi-asserted-by":"publisher","DOI":"10.1039\/c3cp53545b"},{"key":"2026092102400489000_2026.09.14.751576v1.10","doi-asserted-by":"publisher","DOI":"10.1063\/1.3552946"},{"key":"2026092102400489000_2026.09.14.751576v1.11","doi-asserted-by":"publisher","DOI":"10.1063\/1.4754132"},{"key":"2026092102400489000_2026.09.14.751576v1.12","doi-asserted-by":"crossref","first-page":"7812","DOI":"10.1021\/jp071097f","article-title":"The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations","volume":"111","year":"2007","journal-title":"The Journal of Physical Chemistry B"},{"key":"2026092102400489000_2026.09.14.751576v1.13","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1021\/jp036508g","article-title":"Coarse grained model for semiquantitative lipid simulations","volume":"108","year":"2004","journal-title":"The Journal of Physical Chemistry B"},{"key":"2026092102400489000_2026.09.14.751576v1.14","doi-asserted-by":"crossref","first-page":"3932","DOI":"10.1021\/acs.jctc.5b00286","article-title":"Martini Coarse-Grained Force Field: Extension to DNA","volume":"11","year":"2015","journal-title":"Journal of Chemical Theory and Computation"},{"key":"2026092102400489000_2026.09.14.751576v1.15","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1038\/s41592-021-01098-3","article-title":"Martini 3: A General Purpose Force Field for Coarse-Grained Molecular Dynamics","volume":"18","year":"2021","journal-title":"Nature Methods"},{"key":"2026092102400489000_2026.09.14.751576v1.16","doi-asserted-by":"crossref","first-page":"7555","DOI":"10.1021\/acs.jctc.2c00757","article-title":"Martini 3 Coarse-Grained Force Field for Carbohydrates","volume":"18","year":"2022","journal-title":"Journal of Chemical Theory and Computation"},{"key":"2026092102400489000_2026.09.14.751576v1.17","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1016\/j.bpj.2025.07.034","article-title":"Coarse-grained RNA model for the Martini 3 force field","volume":"125","year":"2026","journal-title":"Biophysical Journal"},{"key":"2026092102400489000_2026.09.14.751576v1.18","doi-asserted-by":"crossref","unstructured":"Wang, J. ; Yu, Z. ; Zhao, M. 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