{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T05:35:34Z","timestamp":1767591334982,"version":"3.48.0"},"reference-count":19,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T00:00:00Z","timestamp":1767571200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Commun. Netw."],"abstract":"<jats:p>Next to further miniaturization, the process of self-assembly has great potential for construction, computation, and even communication at the nanoscale. DNA-based self-assembly is an especially promising candidate as it is possible to create entire nanonetworks from just DNA from already existing and comparably cheap building blocks. As wet-lab experiments are still fairly expensive and complex, and self-assembly is hard to predict, simulation tools are crucial for the rapid prototyping of new ideas. However, current self-assembly simulators mainly focus on computational and construction aspects. In this paper, we present a new model for our NetTAS simulator, kTHAM, which simulates the possible interactions of very large numbers of DNA structures simultaneously and measures the process in real-time. This allows for a much more realistic analysis of DNA-based nanonetworks as compared to what is possible with other simulators and with the other models of NetTAS.<\/jats:p>","DOI":"10.3389\/frcmn.2025.1637220","type":"journal-article","created":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T05:31:12Z","timestamp":1767591072000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Towards realistic simulation of DNA-based molecular communication networks"],"prefix":"10.3389","volume":"6","author":[{"given":"Max","family":"Kaussow","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert","family":"Peters","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah","family":"Scheer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian","family":"Hyttrek","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefan","family":"Fischer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Florian","family":"Lau","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2026,1,5]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"2260","DOI":"10.1016\/j.comnet.2008.04.001","article-title":"Nanonetworks: a new communication paradigm","volume":"52","author":"Akyildiz","year":"2008","journal-title":"Comput. Netw."},{"key":"B2","first-page":"431","article-title":"A predictive model of menu performance","volume-title":"Proceedings of the SIGCHI conference on human factors in computing systems","author":"Cockburn","year":"2003"},{"key":"B3","doi-asserted-by":"publisher","first-page":"812","DOI":"10.1007\/s00453-015-9976-y","article-title":"The two-handed tile assembly model is not intrinsically universal","volume":"74","author":"Demaine","year":"2016","journal-title":"Algorithmica"},{"key":"B4","unstructured":"NetTAS\n          \n          \n            \n              Kaussow\n              M."},{"key":"B5","unstructured":"NetTAS gitlab\n          \n          \n            \n              Kaussow\n              M."},{"key":"B6","doi-asserted-by":"crossref","DOI":"10.1145\/3109453.3109458","article-title":"Computational requirements for nano-machines: there is limited space at the bottom","volume-title":"4th ACM international conference on nanoscale computing and communication","author":"Lau","year":"2017"},{"key":"B7","doi-asserted-by":"publisher","first-page":"100245","DOI":"10.1016\/j.nancom.2019.05.002","article-title":"Computation of decision problems within messages in dna-tile-based molecular nanonetworks","volume":"21","author":"Lau","year":"2019","journal-title":"Nano Commun. Netw."},{"key":"B8","volume-title":"Usability engineering","author":"Nielsen","year":"1994"},{"key":"B9","volume-title":"The design of everyday things","author":"Norman","year":"2013"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.1101.5151","article-title":"Simulation of self-assembly in the abstract tile assembly model with isu tas","author":"Patitz","year":"2011","journal-title":"arXiv Preprint arXiv:1101"},{"key":"B11","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1007\/s11047-013-9379-4","article-title":"An introduction to tile-based self-assembly and a survey of recent results","volume":"13","author":"Patitz","year":"2014","journal-title":"Nat. Comput."},{"key":"B12","volume-title":"Isu tas","author":"Patitz","year":"2018"},{"key":"B13","article-title":"Pytas","author":"Patitz","year":"2023"},{"key":"B14","volume-title":"DNA computing: new computing paradigms","author":"Paun","year":"2005"},{"key":"B15","doi-asserted-by":"publisher","first-page":"null","DOI":"10.1371\/journal.pbio.0020424","article-title":"Algorithmic self-assembly of dna sierpinski triangles","volume":"2","author":"Rothemund","year":"2004","journal-title":"PLOS Biol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1016\/0022-5193(82)90002-9","article-title":"Nucleic acid junctions and lattices","volume":"99","author":"Seeman","year":"1982","journal-title":"J. Theoretical Biology"},{"key":"B17","volume-title":"Algorithmic self-assembly of Dna","author":"Winfree","year":"1998"},{"key":"B18","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1038\/28998","article-title":"Design and self-assembly of two-dimensional dna crystals","volume":"394","author":"Winfree","year":"1998","journal-title":"Nature"},{"key":"B19","volume-title":"The xgrow simulator","author":"Winfree","year":"2013"}],"container-title":["Frontiers in Communications and Networks"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/frcmn.2025.1637220\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T05:31:15Z","timestamp":1767591075000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/frcmn.2025.1637220\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,5]]},"references-count":19,"alternative-id":["10.3389\/frcmn.2025.1637220"],"URL":"https:\/\/doi.org\/10.3389\/frcmn.2025.1637220","relation":{},"ISSN":["2673-530X"],"issn-type":[{"value":"2673-530X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,5]]},"article-number":"1637220"}}