{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T11:09:15Z","timestamp":1740136155344,"version":"3.37.3"},"reference-count":44,"publisher":"Springer Science and Business Media LLC","issue":"4","license":[{"start":{"date-parts":[[2015,11,25]],"date-time":"2015-11-25T00:00:00Z","timestamp":1448409600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2015,11,25]],"date-time":"2015-11-25T00:00:00Z","timestamp":1448409600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/100000083","name":"Directorate for Computer and Information Science and Engineering","doi-asserted-by":"publisher","award":["CCF-0829798"],"award-info":[{"award-number":["CCF-0829798"]}],"id":[{"id":"10.13039\/100000083","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Comput"],"published-print":{"date-parts":[[2016,12]]},"DOI":"10.1007\/s11047-015-9532-3","type":"journal-article","created":{"date-parts":[[2015,11,25]],"date-time":"2015-11-25T07:55:54Z","timestamp":1448438154000},"page":"611-634","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Activatable tiles for compact robust programmable molecular assembly and other applications"],"prefix":"10.1007","volume":"15","author":[{"given":"Urmi","family":"Majumder","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sudhanshu","family":"Garg","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas H.","family":"LaBean","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John H.","family":"Reif","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2015,11,25]]},"reference":[{"key":"9532_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: Symposium on theory of computing, 740\u2013748","DOI":"10.1145\/380752.380881"},{"issue":"15","key":"9532_CR2","doi-asserted-by":"publisher","first-page":"6054","DOI":"10.1073\/pnas.0808736106","volume":"106","author":"RD Barish","year":"2009","unstructured":"Barish RD, Schulman R, Rothemund PWK, Winfree E (2009) An information-bearing seed for nucleating algorithmic self-assembly. Proc Natl Acad Sci 106(15):6054\u20136059","journal-title":"Proc Natl Acad Sci"},{"key":"9532_CR3","unstructured":"Chen H-L, Cheng Q, Goel A, Huang M-D, de Espan\u00e9s PM (2004) Invadable self-assembly: combining robustness with efficiency. In: Proceedings of the fifteenth annual ACM-SIAM symposium on discrete algorithms (Philadelphia, PA, USA, 2004), SODA \u201904, Society for Industrial and Applied Mathematics, pp 890\u2013899"},{"key":"9532_CR4","unstructured":"Chen H-L, Doty D (2012) Parallelism and time in hierarchical self-assembly. In: Proceedings of the twenty-third annual ACM-SIAM symposium on discrete algorithms (2012), SODA \u201912, SIAM, pp 1163\u20131182"},{"key":"9532_CR5","unstructured":"Chen H-L, Goel A (2004) Error free self-assembly using error prone tiles. In: Ferretti C, Mauri G, Sandro C (eds) Proceedings of the Tenth International Workshop on DNA Computing, Milan, LNCS, Vol 3384. Springer, Heidelberg, pp 62\u201375"},{"issue":"3","key":"9532_CR6","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1007\/s11047-008-9073-0","volume":"7","author":"E Demaine","year":"2008","unstructured":"Demaine E, Demaine M, Fekete S, Ishaque M, Rafalin E, Schweller R, Souvaine D (2008) Staged self-assembly: nanomanufacture of arbitrary shapes with o(1) glues. Nat Comput 7(3):347\u2013370","journal-title":"Nat Comput"},{"issue":"43","key":"9532_CR7","doi-asserted-by":"publisher","first-page":"15275","DOI":"10.1073\/pnas.0407024101","volume":"101","author":"R Dirks","year":"2004","unstructured":"Dirks R, Pierce N (2004) Triggered amplification by hybridization chain reaction. Proc Natl Acad Sci USA 101(43):15275\u201315278","journal-title":"Proc Natl Acad Sci USA"},{"issue":"7","key":"9532_CR8","doi-asserted-by":"publisher","first-page":"1791","DOI":"10.1021\/nl0722830","volume":"8","author":"K Fujibayashi","year":"2008","unstructured":"Fujibayashi K, Hariadi R, Park SH, Winfree E, Murata S (2008) Toward reliable algorithmic self-assembly of DNA tiles: a fixed-width cellular automaton pattern. Nano Lett 8(7):1791\u20131797","journal-title":"Nano Lett"},{"key":"9532_CR9","doi-asserted-by":"crossref","unstructured":"Fujibayashi K, Murata S (2005) A method of error suppression for self-assembling DNA tiles. 10th International Workshop on DNA Computing, DNA10, vol 3384. Springer, Milan,   pp 113\u2013127","DOI":"10.1007\/11493785_10"},{"key":"9532_CR10","doi-asserted-by":"crossref","unstructured":"Fujibayashi K, Zhang DY, Winfree E, Murata S (2009) Error suppression mechanisms for DNA tile self-assembly and their simulation, pp 589\u2013612","DOI":"10.1007\/s11047-008-9093-9"},{"key":"9532_CR11","unstructured":"Garg S. Xgrow modified for activatable tiles. Available at \n                    https:\/\/github.com\/sudhanshugarg\/projects\/tree\/master\/xgrow-activatable"},{"issue":"2","key":"9532_CR12","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1021\/nn504556v","volume":"9","author":"S Garg","year":"2015","unstructured":"Garg S, Chandran H, Gopalkrishnan N, LaBean TH, Reif J (2015) Directed enzymatic activation of 1-d DNA tiles. ACS Nano 9(2):1072\u20131079","journal-title":"ACS Nano"},{"key":"9532_CR13","doi-asserted-by":"crossref","unstructured":"Gautam V, Haddow P, Kuiper M (2013) Reliable self-assembly by self-triggered activation of enveloped DNA tiles. In: Dediu A-H, Martn-Vide C, Truthe C, Vega-Rodrguez M (eds) Theory and practice of natural computing, vol.\u00a08273 of lecture notes in computer science. Springer, Berlin, pp 68\u201379","DOI":"10.1007\/978-3-642-45008-2_6"},{"key":"9532_CR14","doi-asserted-by":"crossref","unstructured":"Hendricks J, Padilla J, Patitz M, Rogers T (2013) Signal transmission across tile assemblies: 3d static tiles simulate active self-assembly by 2d signal-passing tiles. In: Soloveichik D, Yurke B (eds) DNA computing and molecular programming, vol.\u00a08141 of lecture notes in computer science. Springer International Publishing, pp\u00a090\u2013104","DOI":"10.1007\/978-3-319-01928-4_7"},{"key":"9532_CR15","doi-asserted-by":"crossref","unstructured":"Jang B, Kim Y-B, Lombardi F (2007) Error rate reduction in DNA self-assembly by non-constant monomer concentrations and profiling. In: Design, automation test in Europe conference exhibition, 2007. DATE \u201907, pp\u00a01\u20136","DOI":"10.1109\/DATE.2007.364398"},{"issue":"02","key":"9532_CR16","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1142\/S0129054114500087","volume":"25","author":"N Jonoska","year":"2014","unstructured":"Jonoska N, Karpenko D (2014) Active tile self-assembly, part 1: universality at temperature 1. Int J Found Comput Sci 25(02):141\u2013163","journal-title":"Int J Found Comput Sci"},{"issue":"02","key":"9532_CR17","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1142\/S0129054114500099","volume":"25","author":"N Jonoska","year":"2014","unstructured":"Jonoska N, Karpenko D (2014) Active tile self-assembly, part 2: self-similar structures and structural recursion. Int J Found Comput Sci 25(02):165\u2013194","journal-title":"Int J Found Comput Sci"},{"issue":"4","key":"9532_CR18","doi-asserted-by":"publisher","first-page":"609","DOI":"10.1016\/j.molcel.2004.10.019","volume":"16","author":"S Kamtekar","year":"2004","unstructured":"Kamtekar S, Berman AJ, Wang J, Lzaro JM, de Vega M, Blanco L, Salas M, Steitz TA (2004) Insights into strand displacement and processivity from the crystal structure of the protein-primed DNA polymerase of bacteriophage $$\\varphi$$29. Mol Cell 16(4):609\u2013618","journal-title":"Mol Cell"},{"key":"9532_CR19","doi-asserted-by":"crossref","unstructured":"Keenan A, Schweller R, Zhong X (2013) Exponential replication of patterns in the signal tile assembly model. In: Soloveichik D, Yurke B (eds) DNA Computing and molecular programming, vol.\u00a08141 of lecture notes in computer science. Springer International Publishing, pp\u00a0118\u2013132","DOI":"10.1007\/978-3-319-01928-4_9"},{"issue":"9","key":"9532_CR20","doi-asserted-by":"publisher","first-page":"1848","DOI":"10.1021\/ja993393e","volume":"122","author":"T LaBean","year":"2000","unstructured":"LaBean T, Yan H, Kopatsch J, Liu F, Winfree E, Reif J, Seeman N (2000) Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes. J Am Chem Soc 122(9):1848\u20131860","journal-title":"J Am Chem Soc"},{"key":"9532_CR21","doi-asserted-by":"crossref","unstructured":"Majumder U, Sahu S, LaBean T, Reif J (2006) Design and simulation of self-repairing DNA lattices. In: Mao C, Yokomori T, (eds) DNA computing, vol.\u00a04287 of lecture notes in computer science. Springer, Berlin, pp\u00a0195\u2013214","DOI":"10.1007\/11925903_15"},{"key":"9532_CR22","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/35035038","volume":"407","author":"C Mao","year":"2000","unstructured":"Mao C, Labean T, Reif J, Seeman N (2000) Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407:493\u2013496","journal-title":"Nature"},{"key":"9532_CR23","unstructured":"Murata S (2004) Self-assembling DNA tiles-mechanisms of error suppression. In: SICE 2004 annual conference, vol.\u00a03, pp\u00a02764\u20132767"},{"issue":"2","key":"9532_CR24","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1007\/s11047-011-9268-7","volume":"11","author":"J Padilla","year":"2012","unstructured":"Padilla J, Liu W, Seeman N (2012) Hierarchical self assembly of patterns from the robinson tilings: DNA tile design in an enhanced tile assembly model. Nat Comput 11(2):323\u2013338","journal-title":"Nat Comput"},{"key":"9532_CR25","unstructured":"Padilla J, Patitz M, Pena R, Schweller R, Seeman N, Sheline R, Summers S, Zhong X (2013) Asynchronous signal passing for tile self-assembly Fuel efficient computation and efficient assembly: fuel efficient computation and efficient assembly of shapes. In: Mauri G, Dennunzio A, Manzoni L, Porreca A (eds) Unconventional computation and natural computation, vol.\u00a07956 of lecture notes in computer science. Springer, Berlin, pp 174\u2013185"},{"key":"9532_CR26","unstructured":"Reif J, Sahu S, Yin P (2004) Compact error-resilient computational DNA tiling assemblies. In: Ferretti C,  Mauri G,  Zandron C (eds)  Tenth International Meeting on DNA Based Computers (DNA10), Milano, Italy, June 7-10, 2004. Lecture Notes in Computer Science, vol 3384. Springer-Verlag, New York, pp 293\u2013307.\u00a0Extended version appears as\u00a0invited chapter in text Nanotechnology: Science and Computation (2006) In: Chen J, Jonoska N, Rozenberg G (eds) Natural Computing. Springer, Germany, pp 79\u2013104"},{"issue":"46","key":"9532_CR27","doi-asserted-by":"publisher","first-page":"13924","DOI":"10.1021\/ja038058b","volume":"125","author":"DM Rosenbaum","year":"2003","unstructured":"Rosenbaum DM, Liu DR (2003) Efficient and sequence-specific DNA-templated polymerization of peptide nucleic acid aldehydes. J Am Chem Soc 125(46):13924\u201313925","journal-title":"J Am Chem Soc"},{"key":"9532_CR28","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1038\/nature04586","volume":"440","author":"P Rothemund","year":"2006","unstructured":"Rothemund P (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440:297\u2013302","journal-title":"Nature"},{"key":"9532_CR29","doi-asserted-by":"publisher","first-page":"424","DOI":"10.1371\/journal.pbio.0020424","volume":"2","author":"P Rothemund","year":"2004","unstructured":"Rothemund P, Papadakis N, Winfree E (2004) Algorithmic self-assembly of DNA sierpinski triangles. PLoS Biol 2:424\u2013436","journal-title":"PLoS Biol"},{"key":"9532_CR30","doi-asserted-by":"crossref","unstructured":"Sahu S, Reif J (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, vol.\u00a04287 of lecture notes in computer science. Springer, Berlin, pp\u00a0223\u2013238","DOI":"10.1007\/11925903_17"},{"issue":"52","key":"9532_CR31","doi-asserted-by":"publisher","first-page":"31235","DOI":"10.1074\/jbc.270.52.31235","volume":"270","author":"J Saturno","year":"1995","unstructured":"Saturno J, Blanco L, Salas M, Esteban JA (1995) A novel kinetic analysis to calculate nucleotide affinity of proofreading DNA polymerases: application to 29 DNA polymerase fidelity mutants. J Biol Chem 270(52):31235\u201331243","journal-title":"J Biol Chem"},{"issue":"4","key":"9532_CR32","doi-asserted-by":"publisher","first-page":"1581","DOI":"10.1137\/070680266","volume":"39","author":"R Schulman","year":"2009","unstructured":"Schulman R, Winfree E (2009) Programmable control of nucleation for algorithmic self-assembly. SIAM J Comput 39(4):1581\u20131616","journal-title":"SIAM J Comput"},{"key":"9532_CR33","doi-asserted-by":"crossref","unstructured":"Schulman R, Yurke B, Winfree E (2012) Robust self-replication of combinatorial information via crystal growth and scission. In: Proceedings of the national academy of sciences","DOI":"10.1073\/pnas.1117813109"},{"key":"9532_CR34","doi-asserted-by":"crossref","unstructured":"Soloveichik D, Winfree E (2006) Complexity of compact proofreading for self-assembled patterns. In: Carbone A, Pierce N (eds) DNA computing, vol.\u00a03892 of lecture notes in computer science. Springer, Berlin, pp\u00a0305\u2013324","DOI":"10.1007\/11753681_24"},{"issue":"4","key":"9532_CR35","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1016\/0022-2836(75)90269-7","volume":"91","author":"BJ Thompson","year":"1975","unstructured":"Thompson BJ, Escarmis C, Parker B, Slater W, Doniger J, Tessman I, Warner RC (1975) Figure-8 configuration of dimers of s13 and $$\\varphi \\times 174$$ replicative form DNA. J Mol Biol 91(4):409\u2013419","journal-title":"J Mol Biol"},{"key":"9532_CR36","doi-asserted-by":"publisher","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  40:1-41","journal-title":"Bell Syst Tech J"},{"key":"9532_CR37","unstructured":"Winfree E (1998) Algorithmic self-assembly of DNA. Ph.D. thesis, California Institute of Technology"},{"key":"9532_CR38","unstructured":"Winfree E (1998) Simulations of computing by self-assembly. California Institute of Technology technical report"},{"key":"9532_CR39","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1007\/3-540-30296-4_4","volume-title":"Nanotechnology: science and computation, natural computing series","author":"E Winfree","year":"2006","unstructured":"Winfree E (2006) Self-healing tile sets. In: Chen J, Jonoska N, Rozenberg G (eds) Nanotechnology: science and computation, natural computing series. Springer, Berlin, pp 55\u201378"},{"key":"9532_CR40","unstructured":"Winfree E, Bekbolatov R (2003) Proof reading tile sets: error correction for algorithmic self-assembly. In: Chen J, Reif J (eds) DNA Computing. Lecture Notes in Computer Science, vol 2943. Springer, Heidelberg, pp 126\u2013144"},{"issue":"5641","key":"9532_CR41","doi-asserted-by":"publisher","first-page":"1882","DOI":"10.1126\/science.1089389","volume":"301","author":"H Yan","year":"2003","unstructured":"Yan H, Park SH, Finkelstein G, Reif J, LaBean T (2003) DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science 301(5641):1882\u20131884","journal-title":"Science"},{"issue":"4","key":"9532_CR42","doi-asserted-by":"publisher","first-page":"1077","DOI":"10.1021\/ja109089q","volume":"133","author":"DY Zhang","year":"2011","unstructured":"Zhang DY (2011) Cooperative hybridization of oligonucleotides. J Am Chem Soc 133(4):1077\u20131086","journal-title":"J Am Chem Soc"},{"key":"9532_CR43","doi-asserted-by":"crossref","first-page":"1965","DOI":"10.1038\/ncomms2965","volume":"4","author":"DY Zhang","year":"2013","unstructured":"Zhang DY, Hariadi RF, Choi HM, Winfree E (2013) Integrating DNA strand-displacement circuitry with DNA tile self-assembly. Nat Commun 4:1965","journal-title":"Nat Commun"},{"issue":"48","key":"9532_CR44","doi-asserted-by":"publisher","first-page":"17303","DOI":"10.1021\/ja906987s","volume":"131","author":"DY Zhang","year":"2009","unstructured":"Zhang DY, Winfree E (2009) Control of DNA strand displacement kinetics using toehold exchange. J Am Chem Soc 131(48):17303\u201317314","journal-title":"J Am Chem Soc"}],"container-title":["Natural Computing"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s11047-015-9532-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s11047-015-9532-3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s11047-015-9532-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s11047-015-9532-3","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,14]],"date-time":"2020-05-14T00:17:41Z","timestamp":1589415461000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s11047-015-9532-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,11,25]]},"references-count":44,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2016,12]]}},"alternative-id":["9532"],"URL":"https:\/\/doi.org\/10.1007\/s11047-015-9532-3","relation":{},"ISSN":["1567-7818","1572-9796"],"issn-type":[{"type":"print","value":"1567-7818"},{"type":"electronic","value":"1572-9796"}],"subject":[],"published":{"date-parts":[[2015,11,25]]},"assertion":[{"value":"25 November 2015","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}]}}