Nondeterministic seedless oritatami systems and hardness of testing their equivalence

Yo Sub Han, Hwee Kim, Makoto Ota, Shinnosuke Seki

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

4 Citations (Scopus)


The oritatami system (OS) is a model of computation by cotranscriptional folding, being inspired by the recent experimental succeess of RNA origami to self-assemble an RNA tile cotranscriptionally.The OSs implemented so far, including binary counter and Turing machine simulator, are deterministic, that is, uniquely fold into one conformation, while nondeterminism is intrinsic in biomolecular folding.We introduce nondeterminism to OS (NOS) and propose an NOS that chooses an assignment of Boolean values nondeterministically and evaluates a logical formula on the assignment.This NOS is seedless in the sense that it does not require any initial conformation to begin with like the RNA origami.The NOS allows to prove the co-NP hardness of deciding, given two NOSs, if there exists no conformation that one of them folds into but the other does not.

Original languageEnglish
Title of host publicationDNA Computing and Molecular Programming - 22nd International Conference, DNA 2016, Proceedings
EditorsYannick Rondelez, Damien Woods
PublisherSpringer Verlag
Number of pages16
ISBN (Print)9783319439938
Publication statusPublished - 2016
Event22nd International Conference on Computing and Molecular Programming, DNA 2016 - Munich, Germany
Duration: 2016 Sep 42016 Sep 8

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9818 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Other22nd International Conference on Computing and Molecular Programming, DNA 2016

Bibliographical note

Funding Information:
Kim was supported by NRF Grant funded by the Korean Government (NRF-2013-Global Ph.D. Fellowship Program). The work of S. S. was supported in part by JST Program to Disseminate Tenure Tracking System, MEXT, Japan, No. 6F36, and by JSPS Grant-in-Aid for Research Activity Start-up No. 15H06212 and for Young Scientists (A) No. 16H05854.

Publisher Copyright:
© Springer International Publishing Switzerland 2016.

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)


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