Nondeterministic seedless oritatami systems and hardness of testing their equivalence

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

doi:10.1007/s11047-017-9661-y

Nondeterministic seedless oritatami systems and hardness of testing their equivalence

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

Department of Computer Science

Research output: Contribution to journal › Article › peer-review

9 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 language	English
Pages (from-to)	67-79
Number of pages	13
Journal	Natural Computing
Volume	17
Issue number	1
DOIs	https://doi.org/10.1007/s11047-017-9661-y
Publication status	Published - 2018 Mar 1

Bibliographical note

Funding Information:
Han was supported by the International Cooperation Program managed by NRF of Korea (2017K2A9A2A08000270), the Basic Science Research Program through NRF funded by MEST (2015R1D1A1A01060097) and the Yonsei University Future-leading Research Initiative of 2016. Kim was supported by an NRF grant funded by the Korean Government (NRF-2013-Global Ph.D. Fellowship Program). The work of S.S. was supported in part by the JST Program to Disseminate Tenure Tracking System, MEXT, Japan, no. 6F36, and by a JSPS Grant-in-Aid for Research Activity Start-up no. 15H06212 and for Young Scientists (A) no. 16H05854.

Publisher Copyright:
© 2017, Springer Science+Business Media B.V., part of Springer Nature.

All Science Journal Classification (ASJC) codes

Computer Science Applications

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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.",

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Nondeterministic seedless oritatami systems and hardness of testing their equivalence

Abstract

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