Ruleset optimization on isomorphic oritatami systems

Yo Sub Han; Hwee Kim

doi:10.1007/978-3-319-66799-7_3

Ruleset optimization on isomorphic oritatami systems

Yo Sub Han, Hwee Kim

College of Computing

Research output: Chapter in Book/Report/Conference proceeding › Conference 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 language	English
Title of host publication	DNA Computing and Molecular Programming - 23rd International Conference, DNA 23, Proceedings
Editors	Robert Brijder, Lulu Qian
Publisher	Springer Verlag
Pages	33-45
Number of pages	13
ISBN (Print)	9783319667980
DOIs	https://doi.org/10.1007/978-3-319-66799-7_3
Publication status	Published - 2017
Event	23rd International Conference on DNA Computing and Molecular Programming, DNA 2017 - Austin, United States Duration: 2017 Sept 24 → 2017 Sept 28

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	10467 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Other

Other	23rd International Conference on DNA Computing and Molecular Programming, DNA 2017
Country/Territory	United States
City	Austin
Period	17/9/24 → 17/9/28

Bibliographical note

Publisher Copyright:
© 2017, Springer International Publishing AG.

All Science Journal Classification (ASJC) codes

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/978-3-319-66799-7_3

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

Han, Yo Sub ; Kim, Hwee. / Ruleset optimization on isomorphic oritatami systems. DNA Computing and Molecular Programming - 23rd International Conference, DNA 23, Proceedings. editor / Robert Brijder ; Lulu Qian. Springer Verlag, 2017. pp. 33-45 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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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.",

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Han, YS & 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. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 10467 LNCS, Springer Verlag, pp. 33-45, 23rd International Conference on DNA Computing and Molecular Programming, DNA 2017, Austin, United States, 17/9/24. https://doi.org/10.1007/978-3-319-66799-7_3

Ruleset optimization on isomorphic oritatami systems. / Han, Yo Sub; Kim, Hwee.
DNA Computing and Molecular Programming - 23rd International Conference, DNA 23, Proceedings. ed. / Robert Brijder; Lulu Qian. Springer Verlag, 2017. p. 33-45 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 10467 LNCS).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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AB - 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.

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Han YS, Kim H. Ruleset optimization on isomorphic oritatami systems. In Brijder R, Qian L, editors, DNA Computing and Molecular Programming - 23rd International Conference, DNA 23, Proceedings. Springer Verlag. 2017. p. 33-45. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-319-66799-7_3

Ruleset optimization on isomorphic oritatami systems

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