Nondeterministic seedless oritatami systems and hardness of testing their equivalence

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

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

The oritatami system (OS) is a model of computation by cotranscriptional folding, being inspired by the recent experimental success of RNA origami to self-assemble an RNA tile cotranscriptionally. The OSs implemented so far, including the 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 the OS and propose a nondeterministic OS (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 like the RNA origami. The NOS enables proving the coNP-hardness of deciding, given two NOSs, if there exists no conformation that one of them folds but the other does not.

Original languageEnglish
Pages (from-to)67-79
Number of pages13
JournalNatural Computing
Volume17
Issue number1
DOIs
Publication statusPublished - 2018 Mar 1

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RNA
Conformations
Hardness
Testing
Turing machines
Tile
Simulators

All Science Journal Classification (ASJC) codes

  • Computer Science Applications

Cite this

Han, Yo-Sub ; Kim, Hwee ; Ota, Makoto ; Seki, Shinnosuke. / Nondeterministic seedless oritatami systems and hardness of testing their equivalence. In: Natural Computing. 2018 ; Vol. 17, No. 1. pp. 67-79.
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Nondeterministic seedless oritatami systems and hardness of testing their equivalence. / Han, Yo-Sub; Kim, Hwee; Ota, Makoto; Seki, Shinnosuke.

In: Natural Computing, Vol. 17, No. 1, 01.03.2018, p. 67-79.

Research output: Contribution to journalArticle

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