{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,13]],"date-time":"2025-05-13T22:32:53Z","timestamp":1747175573966,"version":"3.37.3"},"reference-count":21,"publisher":"Wiley","license":[{"start":{"date-parts":[[2013,1,1]],"date-time":"2013-01-01T00:00:00Z","timestamp":1356998400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"funder":[{"name":"European Community\u2019s Seventh Framework Programme","award":["249032"],"award-info":[{"award-number":["249032"]}]},{"DOI":"10.13039\/501100001732","name":"Danmarks Grundforskningsfond","doi-asserted-by":"publisher","award":["249032"],"award-info":[{"award-number":["249032"]}],"id":[{"id":"10.13039\/501100001732","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["249032"],"award-info":[{"award-number":["249032"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Computational and Mathematical Methods in Medicine"],"published-print":{"date-parts":[[2013]]},"abstract":"<jats:p>We propose an automaton, a theoretical framework that demonstrates how to improve the yield of the synthesis of branched chemical polymer reactions. This is achieved by separating substeps of the path of synthesis into compartments. We use chemical containers (chemtainers) to carry the substances through a sequence of fixed successive compartments. We describe the automaton in mathematical terms and show how it can be configured automatically in order to synthesize a given branched polymer target. The algorithm we present finds an optimal path of synthesis in linear time. We discuss how the automaton models compartmentalized structures found in cells, such as the endoplasmic reticulum and the Golgi apparatus, and we show how this compartmentalization can be exploited for the synthesis of branched polymers such as oligosaccharides. Lastly, we show examples of artificial branched polymers and discuss how the automaton can be configured to synthesize them with maximal yield.<\/jats:p>","DOI":"10.1155\/2013\/467428","type":"journal-article","created":{"date-parts":[[2013,12,31]],"date-time":"2013-12-31T16:01:31Z","timestamp":1388505691000},"page":"1-8","source":"Crossref","is-referenced-by-count":11,"title":["The MATCHIT Automaton: Exploiting Compartmentalization for the Synthesis of Branched Polymers"],"prefix":"10.1155","volume":"2013","author":[{"given":"Mathias S.","family":"Weyland","sequence":"first","affiliation":[{"name":"European Centre for Living Technology, S. Marco 2940, 30124 Venice, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Harold","family":"Fellermann","sequence":"additional","affiliation":[{"name":"Center for Fundamental Living Technology (FLinT), Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maik","family":"Hadorn","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Sorek","sequence":"additional","affiliation":[{"name":"The Lancet Lab, Department of Molecular Genetics, Weizmann Institute of Science, 76100 Rehovot, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Doron","family":"Lancet","sequence":"additional","affiliation":[{"name":"The Lancet Lab, Department of Molecular Genetics, Weizmann Institute of Science, 76100 Rehovot, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steen","family":"Rasmussen","sequence":"additional","affiliation":[{"name":"Center for Fundamental Living Technology (FLinT), Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense, Denmark"},{"name":"Santa Fe Institute, Santa Fe, NM 87501, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rudolf M.","family":"F\u00fcchslin","sequence":"additional","affiliation":[{"name":"European Centre for Living Technology, S. Marco 2940, 30124 Venice, Italy"},{"name":"Institute of Applied Mathematics and Physics, School of Engineering, Zurich University of Applied Sciences, 8401 Winterthur, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","reference":[{"key":"3","doi-asserted-by":"publisher","DOI":"10.1038\/nchem.1313"},{"issue":"6128","key":"4","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1126\/science.1229495","volume":"340","year":"2013","journal-title":"Science"},{"key":"5","doi-asserted-by":"publisher","DOI":"10.1126\/science.1132493"},{"key":"6","doi-asserted-by":"publisher","DOI":"10.1021\/ja906987s"},{"key":"7","doi-asserted-by":"publisher","DOI":"10.1126\/science.1200520"},{"key":"8","doi-asserted-by":"publisher","DOI":"10.1039\/c2lc41121k"},{"issue":"3, article e9886","key":"9","volume":"5","year":"2010","journal-title":"PloS ONE"},{"issue":"50","key":"10","doi-asserted-by":"crossref","first-page":"20320","DOI":"10.1073\/pnas.1214386109","volume":"109","year":"2012","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"1","key":"11","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1002\/cplu.201200275","volume":"78","year":"2013","journal-title":"ChemPlusChem"},{"issue":"19","key":"12","doi-asserted-by":"crossref","first-page":"15098","DOI":"10.1021\/la102689v","volume":"26","year":"2010","journal-title":"Langmuir"},{"key":"13","doi-asserted-by":"publisher","DOI":"10.1021\/la202648h"},{"issue":"11, article e50156","key":"14","volume":"7","year":"2012","journal-title":"PloS One"},{"key":"15","doi-asserted-by":"publisher","DOI":"10.1016\/j.biosystems.2012.01.005"},{"key":"16","doi-asserted-by":"publisher","DOI":"10.1039\/b907931a"},{"issue":"2","key":"17","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1093\/glycob\/3.2.97","volume":"3","year":"1993","journal-title":"Glycobiology"},{"issue":"11","key":"18","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1093\/glycob\/10.11.1157","volume":"10","year":"2000","journal-title":"Glycobiology"},{"issue":"11","key":"19","doi-asserted-by":"crossref","first-page":"2004","DOI":"10.1002\/1521-3773(20010601)40:11<2004::AID-ANIE2004>3.0.CO;2-5","volume":"40","year":"2001","journal-title":"Angewandte Chemie\u2014International Edition"},{"key":"20","doi-asserted-by":"publisher","DOI":"10.1016\/S1359-6446(03)02933-7"},{"key":"21","doi-asserted-by":"publisher","DOI":"10.1021\/bi9007726"},{"issue":"1","key":"23","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1162\/ARTL_a_00079","volume":"19","year":"2013","journal-title":"Artiffcial Life"},{"issue":"3","key":"24","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1162\/106454601753238636","volume":"7","year":"2001","journal-title":"Artificial Life"}],"container-title":["Computational and Mathematical Methods in Medicine"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/downloads.hindawi.com\/journals\/cmmm\/2013\/467428.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/journals\/cmmm\/2013\/467428.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/journals\/cmmm\/2013\/467428.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,22]],"date-time":"2017-06-22T01:03:40Z","timestamp":1498093420000},"score":1,"resource":{"primary":{"URL":"http:\/\/www.hindawi.com\/journals\/cmmm\/2013\/467428\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013]]},"references-count":21,"alternative-id":["467428","467428"],"URL":"https:\/\/doi.org\/10.1155\/2013\/467428","relation":{},"ISSN":["1748-670X","1748-6718"],"issn-type":[{"type":"print","value":"1748-670X"},{"type":"electronic","value":"1748-6718"}],"subject":[],"published":{"date-parts":[[2013]]}}}