Self-Attraction Removal from Oritatami Systems

Yo Sub Han, Hwee Kim, Trent A. Rogers, Shinnosuke Seki

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

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 ς 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.

Original languageEnglish
Pages (from-to)1047-1067
Number of pages21
JournalInternational Journal of Foundations of Computer Science
Volume30
Issue number6-7
DOIs
Publication statusPublished - 2019 Sep 1

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RNA
Genes
Molecules

All Science Journal Classification (ASJC) codes

  • Computer Science (miscellaneous)

Cite this

Han, Yo Sub ; Kim, Hwee ; Rogers, Trent A. ; Seki, Shinnosuke. / Self-Attraction Removal from Oritatami Systems. In: International Journal of Foundations of Computer Science. 2019 ; Vol. 30, No. 6-7. pp. 1047-1067.
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Self-Attraction Removal from Oritatami Systems. / Han, Yo Sub; Kim, Hwee; Rogers, Trent A.; Seki, Shinnosuke.

In: International Journal of Foundations of Computer Science, Vol. 30, No. 6-7, 01.09.2019, p. 1047-1067.

Research output: Contribution to journalArticle

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