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

All Science Journal Classification (ASJC) codes

  • Computer Science (miscellaneous)

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