{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T11:09:39Z","timestamp":1740136179513,"version":"3.37.3"},"reference-count":20,"publisher":"Springer Science and Business Media LLC","issue":"3","license":[{"start":{"date-parts":[[2023,9,21]],"date-time":"2023-09-21T00:00:00Z","timestamp":1695254400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2023,9,21]],"date-time":"2023-09-21T00:00:00Z","timestamp":1695254400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/100006502","name":"Defense Sciences Office, DARPA","doi-asserted-by":"publisher","award":["W911NF-18-2-0032"],"award-info":[{"award-number":["W911NF-18-2-0032"]}],"id":[{"id":"10.13039\/100006502","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Comput"],"published-print":{"date-parts":[[2024,9]]},"DOI":"10.1007\/s11047-023-09964-z","type":"journal-article","created":{"date-parts":[[2023,9,21]],"date-time":"2023-09-21T08:02:27Z","timestamp":1695283347000},"page":"455-476","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Parallel pairwise operations on data stored in DNA: sorting, XOR, shifting, and searching"],"prefix":"10.1007","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4039-2814","authenticated-orcid":false,"given":"Arnav","family":"Solanki","sequence":"first","affiliation":[]},{"given":"Tonglin","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Marc","family":"Riedel","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,9,21]]},"reference":[{"key":"9964_CR1","doi-asserted-by":"publisher","first-page":"1021","DOI":"10.1126\/science.7973651","volume":"266","author":"LM Adleman","year":"1994","unstructured":"Adleman LM (1994) Molecular computation of solutions to combinatorial problems. Science 266:1021\u20131024","journal-title":"Science"},{"issue":"3","key":"9964_CR2","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1016\/j.bpj.2018.11.1580","volume":"116","author":"N Athreya","year":"2019","unstructured":"Athreya N, Milenkovic O, Leburton J-P (2019) Detection and mapping of dsDNA breaks using graphene nanopore transistor. Biophys J 116(3):292","journal-title":"Biophys J"},{"issue":"7","key":"9964_CR3","doi-asserted-by":"publisher","first-page":"1476","DOI":"10.1016\/j.bpj.2016.02.027","volume":"110","author":"DB Broadwater","year":"2016","unstructured":"Broadwater DB, Kim HD (2016) The effect of basepair mismatch on DNA strand displacement. Biophys J 110(7):1476\u20131484","journal-title":"Biophys J"},{"issue":"8","key":"9964_CR4","doi-asserted-by":"publisher","first-page":"456","DOI":"10.1038\/s41576-019-0125-3","volume":"20","author":"L Ceze","year":"2019","unstructured":"Ceze L, Nivala J, Strauss K (2019) Molecular digital data storage using DNA. Nat Rev Genet 20(8):456\u2013466. https:\/\/doi.org\/10.1038\/s41576-019-0125-3","journal-title":"Nat Rev Genet"},{"key":"9964_CR5","unstructured":"Chen T, Solanki A, Riedel M (2021) Parallel pairwise operations on data stored in DNA: sorting, shifting, and searching. In: 27th international conference on DNA computing and molecular programming (DNA 27). Schloss Dagstuhl-Leibniz-Zentrum f\u00fcr Informatik"},{"key":"9964_CR6","doi-asserted-by":"publisher","first-page":"1628","DOI":"10.1126\/science.1226355","volume":"337","author":"G Church","year":"2012","unstructured":"Church G, Gao Y, Kosuri S (2012) Next-generation digital information storage in DNA. Science (New York, N.Y.) 337:1628. https:\/\/doi.org\/10.1126\/science.1226355","journal-title":"Science (New York, N.Y.)"},{"key":"9964_CR7","volume-title":"Introduction to algorithms","author":"TH Cormen","year":"2009","unstructured":"Cormen TH, Leiserson CE, Rivest RL, Stein C (2009) Introduction to algorithms, 3rd edn. The MIT Press, London","edition":"3"},{"key":"9964_CR8","unstructured":"Doty D, Ong A (2021) Simulating 3-symbol turing machines with SIMD||DNA. arXiv preprint arXiv:2105.08559"},{"issue":"9","key":"9964_CR9","doi-asserted-by":"publisher","first-page":"948","DOI":"10.1109\/TC.1972.5009071","volume":"21","author":"MJ Flynn","year":"1972","unstructured":"Flynn MJ (1972) Some computer organizations and their effectiveness. IEEE Trans Comput 21(9):948\u2013960","journal-title":"IEEE Trans Comput"},{"issue":"8","key":"9964_CR10","doi-asserted-by":"publisher","first-page":"4271","DOI":"10.1103\/PhysRevA.38.4271","volume":"38","author":"J Krug","year":"1988","unstructured":"Krug J, Spohn H (1988) Universality classes for deterministic surface growth. Phys Rev A 38(8):4271","journal-title":"Phys Rev A"},{"issue":"1","key":"9964_CR11","first-page":"107","volume":"1","author":"W Li","year":"1987","unstructured":"Li W (1987) Power spectra of regular languages and cellular automata. Complex Syst 1(1):107\u2013130","journal-title":"Complex Syst"},{"key":"9964_CR12","doi-asserted-by":"crossref","unstructured":"Li L, Jiang W, Lu Y (2018) A modified Gibson assembly method for cloning large DNA fragments with high GC contents. Synth Metab Pathw Methods Protoc 203\u2013209","DOI":"10.1007\/978-1-4939-7295-1_13"},{"issue":"1","key":"9964_CR13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-018-07882-8","volume":"10","author":"K Liu","year":"2019","unstructured":"Liu K, Pan C, Kuhn A, Nievergelt AP, Fantner GE, Milenkovic O, Radenovic A (2019) Detecting topological variations of DNA at single-molecule level. Nat Commun 10(1):1\u20139","journal-title":"Nat Commun"},{"key":"9964_CR14","doi-asserted-by":"crossref","unstructured":"Radding C.M, Beattie K.L, Holloman W.K, Wiegand R.C (1977) Uptake of homologous single-stranded fragments by superhelical dna: Iv. branch migration. Journal of molecular biology 116(4), 825\u2013839","DOI":"10.1016\/0022-2836(77)90273-X"},{"issue":"3","key":"9964_CR15","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1109\/TMBMC.2016.2537301","volume":"1","author":"SA Salehi","year":"2015","unstructured":"Salehi SA, Jiang H, Riedel MD, Parhi KK (2015) Molecular sensing and computing systems. IEEE Trans Mol Biol Multi-Scale Commun 1(3):249\u2013264","journal-title":"IEEE Trans Mol Biol Multi-Scale Commun"},{"issue":"12","key":"9964_CR16","doi-asserted-by":"publisher","first-page":"5393","DOI":"10.1073\/pnas.0909380107","volume":"107","author":"D Soloveichik","year":"2010","unstructured":"Soloveichik D, Seelig G, Winfree E (2010) DNA as a universal substrate for chemical kinetics. Proc Natl Acad Sci 107(12):5393\u20135398. https:\/\/doi.org\/10.1073\/pnas.0909380107","journal-title":"Proc Natl Acad Sci"},{"key":"9964_CR17","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-15588-z","author":"S Tabatabaei","year":"2020","unstructured":"Tabatabaei S, Wang B, Athreya N, Enghiad B, Hernandez A, Fields C, Leburton J-P, Soloveichik D, Zhao H, Milenkovic O (2020) DNA punch cards for storing data on native DNA sequences via enzymatic nicking. Nat Commun. https:\/\/doi.org\/10.1038\/s41467-020-15588-z","journal-title":"Nat Commun"},{"issue":"1","key":"9964_CR18","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-020-15588-z","volume":"11","author":"SK Tabatabaei","year":"2020","unstructured":"Tabatabaei SK, Wang B, Athreya NBM, Enghiad B, Hernandez AG, Fields CJ, Leburton J-P, Soloveichik D, Zhao H, Milenkovic O (2020) DNA punch cards for storing data on native DNA sequences via enzymatic nicking. Nat Commun 11(1):1\u201310","journal-title":"Nat Commun"},{"key":"9964_CR19","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1007\/978-3-030-26807-7_12","volume-title":"DNA computing and molecular programming","author":"B Wang","year":"2019","unstructured":"Wang B, Chalk C, Soloveichik D (2019) SIMD||DNA: single instruction, multiple data computation with DNA strand displacement cascades. In: Thachuk C, Liu Y (eds) DNA computing and molecular programming. Springer, Cham, pp 219\u2013235"},{"issue":"6796","key":"9964_CR20","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1038\/35020524","volume":"406","author":"B Yurke","year":"2000","unstructured":"Yurke B, Turberfield AJ, Mills AP, Simmel FC, Neumann JL (2000) A DNA-fuelled molecular machine made of DNA. Nature 406(6796):605\u2013608","journal-title":"Nature"}],"container-title":["Natural Computing"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11047-023-09964-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11047-023-09964-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11047-023-09964-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,31]],"date-time":"2024-08-31T13:07:52Z","timestamp":1725109672000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s11047-023-09964-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,9,21]]},"references-count":20,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2024,9]]}},"alternative-id":["9964"],"URL":"https:\/\/doi.org\/10.1007\/s11047-023-09964-z","relation":{},"ISSN":["1567-7818","1572-9796"],"issn-type":[{"type":"print","value":"1567-7818"},{"type":"electronic","value":"1572-9796"}],"subject":[],"published":{"date-parts":[[2023,9,21]]},"assertion":[{"value":"15 August 2023","order":1,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 September 2023","order":2,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare that they have no conflict of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}]}}