{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,9,30]],"date-time":"2023-09-30T19:42:47Z","timestamp":1696102967642},"reference-count":17,"publisher":"World Scientific Pub Co Pte Lt","issue":"06n07","funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"crossref","award":["2017K2A9A2A08000270","2015R1D1A1A01060097"],"award-info":[{"award-number":["2017K2A9A2A08000270","2015R1D1A1A01060097"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"crossref"}]},{"name":"NRF-2013-Global Ph.D. Fellowship Program","award":["R01 GM109459"],"award-info":[{"award-number":["R01 GM109459"]}]},{"name":"National Science Foundation (NSF) Graduate Research Fellowship Program","award":["DGE-1450079","CAREER-1553166","CCF-1422152"],"award-info":[{"award-number":["DGE-1450079","CAREER-1553166","CCF-1422152"]}]},{"name":"JSPS KAKENHI Grant-in-Aids for Young Scientists","award":["16H05854"],"award-info":[{"award-number":["16H05854"]}]},{"name":"Challenging Research","award":["18K19779"],"award-info":[{"award-number":["18K19779"]}]},{"name":"JSPS-NRF Bilateral Program","award":["YB29004"],"award-info":[{"award-number":["YB29004"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Found. Comput. Sci."],"published-print":{"date-parts":[[2019,9]]},"abstract":"<jats:p> RNA cotranscriptional folding refers to the phenomenon in which an RNA transcript folds upon itself while being synthesized out of a gene by an RNA polymerase. Oritatami is a computational model of this phenomenon, which lets its sequence of beads (abstract molecules) taken from a finite alphabet [Formula: see text] fold cotranscriptionally via interactions between beads according to its rule set. In this paper, we study the problem of removing self-attractions, which lets a bead interact with another bead of the same kind, from a given oritatami system without changing its behavior. Self-attraction is one of the major challenges in the construction of intrinsic oritatami systems, which can simulate even the dynamics of all the oritatami systems. <\/jats:p>","DOI":"10.1142\/s0129054119400288","type":"journal-article","created":{"date-parts":[[2019,9,19]],"date-time":"2019-09-19T07:06:43Z","timestamp":1568876803000},"page":"1047-1067","source":"Crossref","is-referenced-by-count":2,"title":["Self-Attraction Removal from Oritatami Systems"],"prefix":"10.1142","volume":"30","author":[{"given":"Yo-Sub","family":"Han","sequence":"first","affiliation":[{"name":"Department of Computer Science, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul 03722, Republic of Korea"}]},{"given":"Hwee","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul 03722, Republic of Korea"}]},{"given":"Trent A.","family":"Rogers","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Computer Engineering, University of Arkansas, Fayetteville, AR, 72701, USA"}]},{"given":"Shinnosuke","family":"Seki","sequence":"additional","affiliation":[{"name":"Department of Computer and Network Engineering, University of Electro-Communications, 1-5-1, Chofugaoka, Chofu, Tokyo 1828585, Japan"}]}],"member":"219","published-online":{"date-parts":[[2019,9,19]]},"reference":[{"key":"S0129054119400288BIB002","first-page":"880","volume-title":"Proceedings of ACM-SIAM Symposium on Discrete Algorithms (SODA 2004)","author":"Aggarwal G.","year":"2004"},{"key":"S0129054119400288BIB003","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0808736106"},{"key":"S0129054119400288BIB004","series-title":"LIPIcs","first-page":"172","volume-title":"Proceedings of the 30th International Symposium on Theoretical Aspects of Computer Science (STACS 2013)","volume":"20","author":"Cannon S.","year":"2013"},{"key":"S0129054119400288BIB005","doi-asserted-by":"publisher","DOI":"10.1109\/FOCS.2012.76"},{"key":"S0129054119400288BIB007","doi-asserted-by":"publisher","DOI":"10.1007\/s11047-014-9430-0"},{"key":"S0129054119400288BIB008","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-11295-4_1"},{"key":"S0129054119400288BIB009","series-title":"LIPIcs","first-page":"43:1","volume-title":"Proceedings of the 41st International Symposium on Mathematical Foundations of Computer Science (MFCS 2016)","volume":"58","author":"Geary C.","year":"2016"},{"key":"S0129054119400288BIB010","doi-asserted-by":"publisher","DOI":"10.1126\/science.1253920"},{"key":"S0129054119400288BIB011","doi-asserted-by":"publisher","DOI":"10.1038\/nature18287"},{"key":"S0129054119400288BIB012","doi-asserted-by":"publisher","DOI":"10.1007\/s11047-017-9661-y"},{"key":"S0129054119400288BIB013","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-60252-3_13"},{"key":"S0129054119400288BIB014","doi-asserted-by":"publisher","DOI":"10.1109\/FOCS.2016.90"},{"key":"S0129054119400288BIB015","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-94812-6_22"},{"key":"S0129054119400288BIB016","doi-asserted-by":"publisher","DOI":"10.1142\/S0129054114400061"},{"key":"S0129054119400288BIB017","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0020424"},{"key":"S0129054119400288BIB018","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1117813109"},{"key":"S0129054119400288BIB020","doi-asserted-by":"publisher","DOI":"10.4204\/EPTCS.128.5"}],"container-title":["International Journal of Foundations of Computer Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0129054119400288","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,19]],"date-time":"2019-09-19T07:07:11Z","timestamp":1568876831000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0129054119400288"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,9]]},"references-count":17,"journal-issue":{"issue":"06n07","published-print":{"date-parts":[[2019,9]]}},"alternative-id":["10.1142\/S0129054119400288"],"URL":"https:\/\/doi.org\/10.1142\/s0129054119400288","relation":{},"ISSN":["0129-0541","1793-6373"],"issn-type":[{"value":"0129-0541","type":"print"},{"value":"1793-6373","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,9]]}}}