{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,17]],"date-time":"2024-06-17T15:57:54Z","timestamp":1718639874486},"reference-count":35,"publisher":"Springer Science and Business Media LLC","issue":"3","license":[{"start":{"date-parts":[[2008,7,9]],"date-time":"2008-07-09T00:00:00Z","timestamp":1215561600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Nat Comput"],"published-print":{"date-parts":[[2009,9]]},"DOI":"10.1007\/s11047-008-9093-9","type":"journal-article","created":{"date-parts":[[2008,7,7]],"date-time":"2008-07-07T22:33:15Z","timestamp":1215469995000},"page":"589-612","source":"Crossref","is-referenced-by-count":31,"title":["Error suppression mechanisms for DNA tile self-assembly and their simulation"],"prefix":"10.1007","volume":"8","author":[{"given":"Kenichi","family":"Fujibayashi","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David Yu","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erik","family":"Winfree","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Satoshi","family":"Murata","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,7,9]]},"reference":[{"key":"9093_CR1","doi-asserted-by":"crossref","unstructured":"Adleman L, Cheng Q, Goel A, Huang M-D (2001) Running time and program size for self-assembled squares. In: STOC\u201901: Proceedings of the 33rd annual ACM symposium on theory of computing. ACM Press, New York, NY, pp 740\u2013748","DOI":"10.1145\/380752.380881"},{"key":"9093_CR2","doi-asserted-by":"crossref","first-page":"2586","DOI":"10.1021\/nl052038l","volume":"5","author":"RD Barish","year":"2005","unstructured":"Barish RD, Rothemund PWK, Winfree E (2005) Two computational primitives for algorithmic self-assembly: copying and counting. Nano Lett 5:2586\u20132592","journal-title":"Nano Lett"},{"key":"9093_CR3","doi-asserted-by":"crossref","unstructured":"Baryshnikov Y, Coffman E, Seeman N, Yimwadsana T (2006) Self-correcting self-assembly: growth models and the Hammersley process. In: Carbone A, Pierce NA (eds) DNA Computing 11, vol. 3892 of LNCS. Springer-Verlag, Berlin, pp 1\u201311","DOI":"10.1007\/11753681_1"},{"key":"9093_CR4","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1006\/jmbi.1998.1769","volume":"279","author":"I Biswas","year":"1998","unstructured":"Biswas I, Yamamoto A, Hsieh P (1998) Branch migration through DNA sequence heterology. J Mol Biol 279:795\u2013806","journal-title":"J Mol Biol"},{"key":"9093_CR5","doi-asserted-by":"crossref","unstructured":"Chen H-L, Goel A (2005) Error free self-assembly using error prone tiles. In: Ferretti C, Mauri G, Zandron C (eds) DNA Computing 10, vol 3384 of LNCS. Springer-Verlag, Berlin, pp 1\u201311","DOI":"10.1007\/11493785_6"},{"key":"9093_CR6","unstructured":"Chen H-L, Cheng Q, Goel A, Huang M-D, de Espanes PM (2004) Invadable self-assembly: combining robustness with efficiency. In: SODA \u201904: Proceedings of the 15th annual ACM-SIAM symposium on discrete algorithms. SIAM, Philadelphia, PA, pp 890\u2013899"},{"key":"9093_CR7","doi-asserted-by":"crossref","first-page":"2913","DOI":"10.1021\/nl070793o","volume":"7","author":"H-L Chen","year":"2007","unstructured":"Chen H-L, Schulman R, Goel A, Winfree E (2007) Reducing facet nucleation during algorithmic self-assembly. Nano Lett 7:2913\u20132919","journal-title":"Nano Lett"},{"key":"9093_CR8","doi-asserted-by":"crossref","unstructured":"Cook M, Rothemund PWK, Winfree E (2004) Self-assembled circuit patterns. In: Chen J, Reif JH (eds) DNA Computing 9, vol 2943 of LNCS. Springer-Verlag, Berlin, pp 91\u2013107","DOI":"10.1007\/978-3-540-24628-2_11"},{"key":"9093_CR9","doi-asserted-by":"crossref","first-page":"15275","DOI":"10.1073\/pnas.0407024101","volume":"101","author":"RM Dirks","year":"2004","unstructured":"Dirks RM, Pierce NA (2004) Triggered amplification by hybridization chain reaction. Proc Natl Acad Sci USA 101:15275\u201315278","journal-title":"Proc Natl Acad Sci USA"},{"key":"9093_CR10","doi-asserted-by":"crossref","first-page":"3211","DOI":"10.1021\/bi00064a003","volume":"32","author":"T-J Fu","year":"1993","unstructured":"Fu T-J, Seeman NC (1993) DNA double-crossover molecules. Biochemistry 32:3211\u20133220","journal-title":"Biochemistry"},{"key":"9093_CR11","doi-asserted-by":"crossref","unstructured":"Fujibayashi K, Murata S (2005) A method of error suppression for self-assembling DNA tiles. In: Ferretti C, Mauri G, Zandron C (eds) DNA Computing 10, vol 3384 of LNCS. Springer-Verlag, Berlin, pp 113\u2013127","DOI":"10.1007\/11493785_10"},{"key":"9093_CR12","doi-asserted-by":"crossref","first-page":"2021","DOI":"10.1073\/pnas.91.6.2021","volume":"91","author":"IG Panyutin","year":"1994","unstructured":"Panyutin IG, Hsieh P (1994) The kinetics of spontaneous DNA branch migration. Proc Natl Acad Sci USA 91:2021\u20132025","journal-title":"Proc Natl Acad Sci USA"},{"key":"9093_CR13","doi-asserted-by":"crossref","first-page":"1819","DOI":"10.1002\/j.1460-2075.1995.tb07170.x","volume":"14","author":"IG Panyutin","year":"1995","unstructured":"Panyutin IG, Biswas I, Hsieh P (1995) A pivotal role for the structure of the Holliday junction in DNA branch migration. EMBO J 14:1819\u20131826","journal-title":"EMBO J"},{"key":"9093_CR14","doi-asserted-by":"crossref","unstructured":"Reif JH (1999) Local parallel biomolecular computation. In: Rubin H, Wood DH (eds) DNA based computers III, vol 48 of DIMACS. AMS Press, Providence, RI, pp 217\u2013254","DOI":"10.1090\/dimacs\/048\/17"},{"key":"9093_CR15","doi-asserted-by":"crossref","unstructured":"Reif JH, Sahu S, Yin P (2005) Compact error-resilient computational DNA tiling assemblies. In: Ferretti C, Mauri G, Zandron C (eds) DNA Computing 10, vol 3384 of LNCS. Springer-Verlag, Berlin, pp 293\u2013307","DOI":"10.1007\/11493785_26"},{"key":"9093_CR16","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1006\/jmbi.2000.3573","volume":"297","author":"LP Reynaldo","year":"2000","unstructured":"Reynaldo LP, Vologodskii AV, Neri BP, Lyamichev VI (2000) The kinetics of oligonucleotide replacements. J Mol Biol 297:511\u2013520","journal-title":"J Mol Biol"},{"key":"9093_CR17","doi-asserted-by":"crossref","unstructured":"Rothemund PWK, Winfree E (2000) The program-size complexity of self-assembled squares (extended abstract). In: STOC\u201900: Proceedings of the thirty-second annual ACM symposium on theory of computing. ACM Press, New York, NY, pp 459\u2013468","DOI":"10.1145\/335305.335358"},{"key":"9093_CR18","first-page":"2041","volume":"2","author":"PWK Rothemund","year":"2004","unstructured":"Rothemund PWK, Papadakis N, Winfree E (2004) Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biol 2: 2041\u20132053","journal-title":"PLoS Biol"},{"key":"9093_CR19","doi-asserted-by":"crossref","unstructured":"Sahu S, Reif JH (2006) Capabilities and limits of compact error resilience methods for algorithmic self-assembly in two and three dimensions. In: Mao C, Yokomori T (eds) DNA Computing 12, vol 4287 of LNCS. Springer-Verlag, Berlin, pp 223\u2013238","DOI":"10.1007\/11925903_17"},{"key":"9093_CR20","doi-asserted-by":"crossref","unstructured":"Schulman R, Winfree E (2005) Programmable control of nucleation for algorithmic self-assembly. In: Ferretti C, Mauri G, Zandron C (eds) DNA Computing 10, vol 3384 of LNCS. Springer-Verlag, Berlin, pp 319\u2013328. Extended abstract in DNA Computing 10; preprint of the full paper is cond-mat\/0607317 on http:\/\/arXiv.org","DOI":"10.1007\/11493785_28"},{"key":"9093_CR21","doi-asserted-by":"crossref","first-page":"15236","DOI":"10.1073\/pnas.0701467104","volume":"104","author":"R Schulman","year":"2007","unstructured":"Schulman R, Winfree E (2007) Synthesis of crystals with a programmable kinetic barrier to nucleation. Proc Natl Acad Sci USA 104:15236\u201315241","journal-title":"Proc Natl Acad Sci USA"},{"key":"9093_CR22","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1504\/IJNT.2005.008074","volume":"2","author":"NC Seeman","year":"2005","unstructured":"Seeman NC (2005) The challenge of structural control on the nanoscale: Bottom-up self-assembly of nucleic acids in 3D. Int J Nanotechnol 2:348\u2013370","journal-title":"Int J Nanotechnol"},{"key":"9093_CR23","doi-asserted-by":"crossref","unstructured":"Soloveichik D, Winfree E (2004) Complexity of self-assembled shapes. SIAM J Comput 36:1544\u20131569, 2007. Extended abstract in LNCS 3384: 344-354 (2004); preprint is cs.CC\/0412096 on http:\/\/arXiv.org","DOI":"10.1137\/S0097539704446712"},{"key":"9093_CR24","doi-asserted-by":"crossref","unstructured":"Somei K, Kaneda S, Fujii T, Murata S (2006) A microfluidic device for DNA tile self-assembly. In: Carbone A, Pierce NA (eds) DNA Computing 11, vol 3892 of LNCS. Springer-Verlag, Berlin, pp 325\u2013335","DOI":"10.1007\/11753681_25"},{"key":"9093_CR25","doi-asserted-by":"crossref","unstructured":"Turberfield AJ, Yurke B, Mills AP Jr (2000) DNA hybridization catalysts and molecular tweezers. In: Winfree E, Gifford DK (eds) DNA based computers V, vol 54 of DIMACS. AMS Press, Providence, RI, pp 171\u2013182","DOI":"10.1090\/dimacs\/054\/14"},{"key":"9093_CR26","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/j.1538-7305.1961.tb03975.x","volume":"40","author":"H Wang","year":"1961","unstructured":"Wang H (1961) Proving theorems by pattern recognition II. Bell Syst Tech J 40:1\u201342","journal-title":"Bell Syst Tech J"},{"key":"9093_CR27","first-page":"23","volume-title":"Proceedings of the symposium on the mathematical theory of automata.","author":"H Wang","year":"1963","unstructured":"Wang H (1963) Dominoes and the AEA case of the decision problem. In: Fox J (ed) Proceedings of the symposium on the mathematical theory of automata. Polytechnic Press, Brooklyn, NY, pp 23\u201355"},{"key":"9093_CR28","doi-asserted-by":"crossref","first-page":"227","DOI":"10.3109\/10409239109114069","volume":"26","author":"JG Wetmur","year":"1991","unstructured":"Wetmur JG (1991) DNA probes: applications of the principles of nucleic acid hybridization. Crit Rev Biochem Mol Biol 26:227\u2013259","journal-title":"Crit Rev Biochem Mol Biol"},{"key":"9093_CR29","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1126\/science.1962191","volume":"254","author":"GM Whitesides","year":"1991","unstructured":"Whitesides GM, Mathias JP, Seto CT (1991) Molecular self-assembly and nanochemistry: a chemical strategy for the synthesis of nanostructures. Science 254:1312\u20131319","journal-title":"Science"},{"key":"9093_CR30","doi-asserted-by":"crossref","unstructured":"Winfree E (1996) On the computational power of DNA annealing and ligation. In: Lipton RJ, Baum EB (eds) DNA based computers, vol 27 of DIMACS. AMS Press, Providence, RI, pp 199\u2013221","DOI":"10.1090\/dimacs\/027\/09"},{"key":"9093_CR31","unstructured":"Winfree E (1998) Simulations of computing by self-assembly. CaltechCSTR:1998.22. California Institute of Technology"},{"key":"9093_CR32","doi-asserted-by":"crossref","unstructured":"Winfree E, Bekbolatov R (2004) Proofreading tile sets: error correction for algorithmic self-assembly. In: Chen J, Reif JH (eds) DNA Computing 9, vol 2943 of LNCS. Springer-Verlag, Berlin, pp 126\u2013144","DOI":"10.1007\/978-3-540-24628-2_13"},{"key":"9093_CR33","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/28998","volume":"394","author":"E Winfree","year":"1998","unstructured":"Winfree E, Liu F, Wenzler LA, Seeman NC (1998) Design and self-assembly of two-dimensional DNA crystals. Nature 394:539\u2013544","journal-title":"Nature"},{"key":"9093_CR34","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1023\/A:1023928811651","volume":"4","author":"B Yurke","year":"2003","unstructured":"Yurke B, Mills AP Jr (2003) Using DNA to power nanostructures. Genet Program Evol Machines 4:111\u2013122","journal-title":"Genet Program Evol Machines"},{"key":"9093_CR35","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1038\/35020524","volume":"406","author":"B Yurke","year":"2000","unstructured":"Yurke B, Turberfield AJ, Mills AP Jr, Simmel FC, Nuemann JL (2000) A DNA-fuelled molecular machine made of DNA. Nature 406:605\u2013608","journal-title":"Nature"}],"container-title":["Natural Computing"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s11047-008-9093-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s11047-008-9093-9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s11047-008-9093-9","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,31]],"date-time":"2019-05-31T23:46:03Z","timestamp":1559346363000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s11047-008-9093-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,7,9]]},"references-count":35,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2009,9]]}},"alternative-id":["9093"],"URL":"https:\/\/doi.org\/10.1007\/s11047-008-9093-9","relation":{},"ISSN":["1567-7818","1572-9796"],"issn-type":[{"value":"1567-7818","type":"print"},{"value":"1572-9796","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,7,9]]}}}