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Intrinsic universality of co-transcriptional folding

Research Project

Project/Area Number 20K11672
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 60010:Theory of informatics-related
Research InstitutionThe University of Electro-Communications

Principal Investigator

Seki Shinnosuke  電気通信大学, 大学院情報理工学研究科, 准教授 (30624944)

Project Period (FY) 2020-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2022: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2021: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2020: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Keywords分子プログラミング / 共転写性フォールディング / RNAオリガミ / オリタタミモデル / 本質的計算完全性 / チューリングマシン / 分子自己組織化 / RNA共転写性フォールディング / オリタタミシステム / 折り畳みシステム / 2次元チューリングマシン / チューリング完全性 / Intrinsic simulation / 分子計算
Outline of Research at the Start

DNAからタンパク質を合成する際の中間媒体であるRNAは、生成時に複雑な構造に折り畳まれながら様々な情報処理を行うことが知られている。この現象「RNA Cotranscriptional folding (CF)」により試験管内で人工構造を生成する技術が2014年にScience誌上で発表された。この技術を更に発展させ構造生成のみならず人工的な情報処理をも可能にするために提唱された数理モデルが「折り畳みシステム」である。
折り畳みシステムは全ての計算可能関数を計算できる(チューリング完全性)。CF駆動汎用計算機の実現を目指し、本研究ではCFの計算能力を超えてその本質的挙動の理解を目指す。

Outline of Final Research Achievements

An RNA sequence folds while being transcribed, that is, synthesized sequentially from its DNA template. This so-called co-transcriptional folding plays vital roles in assembling structures and computing in-vivo. Geary et al. demonstrated experimentally how to program a specific tile-like structure into a template such that the corresponding RNA sequence folds co-transcriptionally into the target structure. A formal model called Oritatami aims at developing this architecture further towards computation. It has been proved capable of computing all computable functions. However, such Turing-universal oritatami systems (OS) were too complicated to be implemented in the laboratory. In this project, we have simplified a TUOS to a considerable extent. More importantly, we designed a compiler from a variant of Turing machine, which can be easily programmed, to an OS. As a result, oritatami programming have been sufficiently simplified for their actual implementations in the laboratory.

Academic Significance and Societal Importance of the Research Achievements

分子プログラミングは生体高分子の振る舞いの観察ではなく、我々の意図するように振る舞う高分子の設計を目的とする。オリタタミはこの分野において最も新しいモデルの一つである。抽象タイルアセンブリモデル(aTAM)は、理論研究がDNAベースの様々な分子計算システムの実装につながっており、理論と実験の協働がこの分野でうまく機能している好例である。aTAMは多数の高分子の凝集による自己組織化のモデルであり、オリタタミが扱うRNA1本鎖のフォールディングによる自己組織化とは本質的に異なる。生体内の計算はRNAが司っており、オリタタミの研究により生体内で自動構築、治療を行うシステムなどの実用化が期待される。

Report

(5 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Research-status Report
  • 2021 Research-status Report
  • 2020 Research-status Report
  • Research Products

    (31 results)

All 2024 2023 2022 2021 2020 Other

All Int'l Joint Research (8 results) Journal Article (13 results) (of which Int'l Joint Research: 9 results,  Peer Reviewed: 13 results,  Open Access: 3 results) Presentation (9 results) (of which Int'l Joint Research: 9 results,  Invited: 5 results) Book (1 results)

  • [Int'l Joint Research] ENS Lyon(フランス)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] Aarhus University(デンマーク)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] Aalto University(フィンランド)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] Kiel University(ドイツ)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] Ajou University(韓国)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] Ecole Normale Superieure de Lyon/Aix-Marseille Universite(フランス)

    • Related Report
      2022 Research-status Report
  • [Int'l Joint Research] Ajou University(韓国)

    • Related Report
      2022 Research-status Report
  • [Int'l Joint Research] ENS Lyon(フランス)

    • Related Report
      2021 Research-status Report
  • [Journal Article] Towards composable computations by RNA co-transcriptional folding: A proof-of-concept demonstration of nested loops in oritatami2024

    • Author(s)
      Fazekas Szilard Zsolt、Iwano Naoya、Kihara Yu、Matsuoka Ryuichi、Seki Shinnosuke、Takeuchi Hinano
    • Journal Title

      Theoretical Computer Science

      Volume: 999 Pages: 114550-114550

    • DOI

      10.1016/j.tcs.2024.114550

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Programmable single-stranded architectures for computing2023

    • Author(s)
      Kihara Yu、Seki Shinnosuke
    • Journal Title

      Natural Computing

      Volume: 22 Issue: 3 Pages: 563-585

    • DOI

      10.1007/s11047-023-09963-0

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Freezing 1-Tag Systems with States2023

    • Author(s)
      Fazekas Szilard Zsolt, Seki Shinnosuke
    • Journal Title

      Electronic Proceedings in Theoretical Computer Science

      Volume: 386 Pages: 82-95

    • DOI

      10.4204/eptcs.386.8

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] On algorithmic self-assembly of squares by co-transcriptional folding2022

    • Author(s)
      Szilard Zsolt Fazekas, Hwee Kim, Ryuichi Matsuoka, Shinnosuke Seki, Hinano Takeuchi
    • Journal Title

      Proceedings of the 33rd International Symposium on Algorithms and Computation (ISAAC 2022)

      Volume: LIPIcs 248

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Oritatami Systems Assemble Shapes No Less Complex Than Tile Assembly Model (ATAM)2022

    • Author(s)
      Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, Guillaume Theyssier
    • Journal Title

      Proceedings of the 39th International Symposium on Theoretical Aspects of Computer Science (STACS 2022)

      Volume: 219

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Square network on a word2021

    • Author(s)
      Fazekas Szilard Zsolt、Seki Shinnosuke
    • Journal Title

      Theoretical Computer Science

      Volume: 894 Pages: 121-134

    • DOI

      10.1016/j.tcs.2021.08.004

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] A general architecture of oritatami systems for simulating arbitrary finite automata2021

    • Author(s)
      Han Yo-Sub、Kim Hwee、Masuda Yusei、Seki Shinnosuke
    • Journal Title

      Theoretical Computer Science

      Volume: 870 Pages: 29-52

    • DOI

      10.1016/j.tcs.2020.12.014

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Linear Bounds on the Size of Conformations in Greedy Deterministic Oritatami2021

    • Author(s)
      Fazekas Szilard Zsolt、Kim Hwee、Matsuoka Ryuichi、Morita Reoto、Seki Shinnosuke
    • Journal Title

      International Journal of Foundations of Computer Science

      Volume: 32 Issue: 05 Pages: 575-596

    • DOI

      10.1142/s0129054121410082

    • Related Report
      2021 Research-status Report 2020 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Counting infinitely by oritatami co-transcriptional folding2021

    • Author(s)
      Maruyama Kohei、Seki Shinnosuke
    • Journal Title

      Natural Computing

      Volume: Not decided yet Issue: 2 Pages: 329-340

    • DOI

      10.1007/s11047-021-09842-6

    • Related Report
      2020 Research-status Report
    • Peer Reviewed
  • [Journal Article] A general architecture of oritatami systems for simulating arbitrary finite automata2021

    • Author(s)
      Yo-Sub Han, Hwee Kim, Yusei Masuda, Shinnosuke Seki
    • Journal Title

      Theoretical Computer Science

      Volume: Not decided yet

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Simple Intrinsic Simulation of Cellular Automata in Oritatami Molecular Folding Model2020

    • Author(s)
      Pchelina Daria、Schabanel Nicolas、Seki Shinnosuke、Ubukata Yuki
    • Journal Title

      Proceedings of the 14th Latin American Symposium on Theoretical Informatics (LATIN 2020)

      Volume: LNCS 12118 Pages: 425-436

    • DOI

      10.1007/978-3-030-61792-9_34

    • ISBN
      9783030617912, 9783030617929
    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Transcript design problem of oritatami systems2020

    • Author(s)
      Han Yo-Sub、Kim Hwee、Seki Shinnosuke
    • Journal Title

      Natural Computing

      Volume: 19 Issue: 2 Pages: 323-335

    • DOI

      10.1007/s11047-019-09776-0

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Special Issue Developments in Language Theory 2018 ? Preface2020

    • Author(s)
      Seki Shinnosuke
    • Journal Title

      International Journal of Foundations of Computer Science

      Volume: 31 Issue: 06 Pages: 663-665

    • DOI

      10.1142/s0129054120020025

    • Related Report
      2020 Research-status Report
    • Peer Reviewed
  • [Presentation] How complex shapes can RNA fold into?2023

    • Author(s)
      Shinnosuke Seki
    • Organizer
      17th International Conference on Reachability Problems (RP 2023)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Freezing 1-Tag Systems with States2023

    • Author(s)
      Szilard Zsolt Fazekas
    • Organizer
      16th International Conference on Automata and Formal Languages (AFL 2023)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] On algorithmic self-assembly of squares by co-transcriptional folding2022

    • Author(s)
      Ryuichi Matsuoka
    • Organizer
      33rd International Symposium on Algorithms and Computation (ISAAC 2022)
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] Single-stranded architectures for computing by RNA co-transcriptional folding2022

    • Author(s)
      Shinnosuke Seki
    • Organizer
      Moving and Computing 2022 (MaC 2022)
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Single-stranded architectures for computing by RNA co-transcriptional folding2022

    • Author(s)
      Shinnosuke Seki
    • Organizer
      Dagstuhl seminar 22381: Rational Design of Ribonucleic Acids
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Turedo a new computational model for molecular nanobots?2022

    • Author(s)
      Nicolas Schabanel
    • Organizer
      Computability in Europe 2022 (CiE 2022)
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Oritatami Systems Assemble Shapes No Less Complex Than Tile Assembly Model (ATAM)2022

    • Author(s)
      Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, Guillaume Theyssier
    • Organizer
      39th International Symposium on Theoretical Aspects of Computer Science (STACS 2022)
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] Simple Intrinsic Simulation of Cellular Automata in Oritatami Molecular Folding Model2020

    • Author(s)
      Daria Pchelina
    • Organizer
      14th Latin American Symposium on Theoretical Informatics
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research
  • [Presentation] N/A2020

    • Author(s)
      Shinnosuke Seki
    • Organizer
      19th International Conference on Unconvetional Computation and Natural Computation (COVID-19により中止)
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research / Invited
  • [Book] New Generation Computing special issue for Hagiya-sensei's 2^6 Birthday2022

    • Author(s)
      Shin-ya Nishizeki and Shinnosuke Seki
    • Total Pages
      338
    • Publisher
      Ohmsha, Springer
    • Related Report
      2022 Research-status Report

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Published: 2020-04-28   Modified: 2025-01-30  

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