Ruleset optimization on isomorphic oritatami systems

Yo Sub Han, Hwee Kim

Research output: Chapter in Book/Report/Conference proceedingConference contribution

7 Citations (Scopus)

Abstract

RNA cotranscriptional folding refers to the phenomenon in which an RNA transcript folds upon itself while being synthesized out of a gene. The oritatami system (OS) is a computation model of this phenomenon, which lets its sequence of beads (abstract molecules) fold cotranscriptionally by the interactions between beads according to its ruleset. We study the problem of reducing the ruleset size while maintaining the terminal conformations geometrically same. We first prove the hardness of finding the smallest ruleset, and suggest two approaches that reduce the ruleset size efficiently.

Original languageEnglish
Title of host publicationDNA Computing and Molecular Programming - 23rd International Conference, DNA 23, Proceedings
EditorsRobert Brijder, Lulu Qian
PublisherSpringer Verlag
Pages33-45
Number of pages13
ISBN (Print)9783319667980
DOIs
Publication statusPublished - 2017 Jan 1
Event23rd International Conference on DNA Computing and Molecular Programming, DNA 2017 - Austin, United States
Duration: 2017 Sep 242017 Sep 28

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume10467 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other23rd International Conference on DNA Computing and Molecular Programming, DNA 2017
CountryUnited States
CityAustin
Period17/9/2417/9/28

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

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  • Cite this

    Han, Y. S., & Kim, H. (2017). Ruleset optimization on isomorphic oritatami systems. In R. Brijder, & L. Qian (Eds.), DNA Computing and Molecular Programming - 23rd International Conference, DNA 23, Proceedings (pp. 33-45). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 10467 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-319-66799-7_3