Self-Attraction Removal from Oritatami Systems

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

Research output: Contribution to journalArticlepeer-review

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

Bibliographical note

Funding Information:
grants CAREER-1553166 and CCF-1422152. Seki was supported in part by JST Program to Disseminate Tenure Tracking System No. 6F36 and JSPS KAKENHI Grant-in-Aids for Young Scientists (A) No. 16H05854 and for Challenging Research (Exploratory) No. 18K19779. Han, Kim, and Seki were supported also by the JSPS-NRF Bilateral Program (YB29004).

Funding Information:
Han was supported in part by National Research Foundation of Korea (NRF) Grants Nos. 2017K2A9A2A08000270 and 2015R1D1A1A01060097. Kim was supported in part by the NRF-2013-Global Ph.D. Fellowship Program and by the NIH grant R01 GM109459. Rogers was supported in part by the National Science Foundation (NSF) Graduate Research Fellowship Program No. DGE-1450079, and the NSF

All Science Journal Classification (ASJC) codes

  • Computer Science (miscellaneous)

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