Minimization of universal oritatami system and its limit

• Project/Area Number: 18K19779
• Research Category: Grant-in-Aid for Challenging Research (Exploratory)
• Allocation Type: Multi-year Fund
• Review Section: Medium-sized Section 60:Information science, computer engineering, and related fields
• Research Institution: The 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)
• Co-Investigator(Kenkyū-buntansha): Fazekas Szilard 秋田大学, 理工学研究科, 講師 (70725382)
• Project Period (FY): 2018-06-29 – 2020-03-31
• Project Status: Completed (Fiscal Year 2019)
• Budget Amount: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000); Fiscal Year 2019: ¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000); Fiscal Year 2018: ¥3,510,000 (Direct Cost: ¥2,700,000、Indirect Cost: ¥810,000)
• Keywords: 分子自己組織化 / 共転写性フォールディング / チューリング完全性 / 分子自己組織化理論 / 最適化 / 折り畳みシステム

Outline of Final Research Achievements

A single-stranded sequence of RNA folds upon itself into an intricate structure while being synthesized (transcribed) from a template DNA sequence. This phenomenon called cotranscriptional folding has been utilized to self-assemble an artificial structure. In order to develop this technology further for artificial general-purpose computations, the mathematical model “oritatami system (OS)” has been proposed. The OS is known to be Turing universal, that is, be capable of computing all computable functions, but the OS proposed to prove this universality was too complicated to be implemented in-vitro. In this project, we have engineered a drastically simpler Turing universal OS. We also approached the limit of simplification from the opposite side by discovering several conditions under which the OS loses the Turing universality.

Academic Significance and Societal Importance of the Research Achievements

分子工学の分野は近年劇的な進展を遂げ、様々な構造や計算機構をDNAの反応により実現することが可能になってきている。DNAはしかしその安定性ゆえに反応活性をあげるために環境温度の変化を必要とし、それがこれら技術の生体応用を難しくしている。本課題が取り扱うRNA共転写性フォールディング（CF）は、生体内での情報処理に欠かせない現象であり、2014年にGearyらは人工タイル構造をCFにより試験管内で自己組織化させることに成功した。本課題は数理モデルを用いてCFの計算能力を明らかにする。CF駆動の計算機が実現すれば例えば疾病の治癒プログラムを遺伝子に埋め込むことで生体内での自動治癒が可能となる。

Research Products

• [Int'l Joint Research] Ecole Normal Superieure de Lyon/Ecole Normal Superieure de Paris/Aix-Marseille Universite(フランス)
• [Int'l Joint Research] California Institute of Technology/Massachusettes Institute of Technology/University of South Florida(米国)
• [Int'l Joint Research] Yonsei University(韓国)
• [Int'l Joint Research] Ecole Normale Superieure de Lyon(フランス)
• [Journal Article] Counting Infinitely by Oritatami Co-transcriptional Folding (2020)
  • Author(s): Maruyama Kohei、Seki Shinnosuke
  • Journal Title: Proceedings of the 46th International Conference on Current Trends in Theory and Practice of Informatics Volume: 12011 Pages: 566-575
  • DOI: 10.1007/978-3-030-38919-2_46
  • ISBN: 9783030389185, 9783030389192
  • Peer Reviewed
• [Journal Article] Simple Intrinsic Simulation of Cellular Automata in Oritatami Molecular Folding Model (2020)
  • Author(s): Daria Pchelina, Nicolas Schabanel, Shinnosuke Seki, Yuki Ubukata
  • Journal Title: Proceedings of the 14th Latin American Symposium on Theoretical Informatics Volume: -
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] A General Architecture of Oritatami Systems for Simulating Arbitrary Finite Automata (2019)
  • Author(s): Han Yo-Sub、Kim Hwee、Masuda Yusei、Seki Shinnosuke
  • Journal Title: Proceedings of the 24th International Conference on Implementation and Applications of Automata (CIAA 2019) Volume: 11601 Pages: 146-157
  • DOI: 10.1007/978-3-030-23679-3_12
  • ISBN: 9783030236786, 9783030236793
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Single-Stranded Architectures for Computing (2019)
  • Author(s): Seki Shinnosuke
  • Journal Title: Proceedings of the 23rd International Conference on Developments in Langauge Theory Volume: 11647 Pages: 41-56
  • DOI: 10.1007/978-3-030-24886-4_3
  • ISBN: 9783030248857, 9783030248864
  • Peer Reviewed
• [Journal Article] Self-Attraction Removal from Oritatami Systems (2019)
  • Author(s): Han Yo-Sub、Kim Hwee、Rogers Trent A.、Seki Shinnosuke
  • Journal Title: International Journal of Foundations of Computer Science Volume: 30 Issue: 06n07 Pages: 1047-1067
  • DOI: 10.1142/s0129054119400288
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] On the Power of Oritatami Cotranscriptional Folding with Unary Bead Sequence (2019)
  • Author(s): Fazekas Szilard Zsolt、Maruyama Kohei、Morita Reoto、Seki Shinnosuke
  • Journal Title: Proceedings of the 15th Annual Conference on Theory and Applications of Models of Computation (TAMC 2019, Kitakyushu, Japan, April 13-16, 2019) Volume: 11436 Pages: 188-207
  • DOI: 10.1007/978-3-030-14812-6_12
  • ISBN: 9783030148119, 9783030148126
  • Peer Reviewed
• [Journal Article] A general architecture of oritatami systems for simulating arbitrary finite automata (2019)
  • Author(s): Yo-Sub Han, Hwee Kim, Yusei Masuda, Shinnosuke Seki
  • Journal Title: Proceedings of the 24th International Conference on Implementation and Applications of Automata (CIAA 2019, Kosice, Slovakia, July 22-25, 2019) Volume: 印刷中
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Self-attraction removal from oritatami systems (2019)
  • Author(s): Yo-Sub Han, Hwee Kim, Treng A. Rogers, Shinnosuke Seki
  • Journal Title: International Journal of Foundations of Computer Science Volume: 印刷中
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Oritatami: a computational model for molecular co-transcriptional folding (2019)
  • Author(s): Cody Geary, Pierre-Etienne Meunier, Nicolas Schabanel, Shinnosuke Seki
  • Journal Title: International Journal of Molecular Sciences Volume: 印刷中
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Know When to Fold ’Em: Self-assembly of Shapes by Folding in Oritatami (2018)
  • Author(s): Demaine Erik D.、Hendricks Jacob、Olsen Meagan、Patitz Matthew J.、Rogers Trent A.、Schabanel Nicolas、Seki Shinnosuke、Thomas Hadley
  • Journal Title: Proceedings of the 24th International Conference on DNA Computing and Molecular Programming (DNA24, Jinan, China, Oct. 8-12, 2018) Volume: 11145 Pages: 19-36
  • DOI: 10.1007/978-3-030-00030-1_2
  • ISBN: 9783030000295, 9783030000301
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Transcript Design Problem of Oritatami Systems (2018)
  • Author(s): Han Yo-Sub、Kim Hwee、Seki Shinnosuke
  • Journal Title: Proceedings of the 24th International Conference on DNA Computing and Molecular Programming (DNA24, Jinan, China, Oct. 8-12, 2018) Volume: 11145 Pages: 139-154
  • DOI: 10.1007/978-3-030-00030-1_9
  • ISBN: 9783030000295, 9783030000301
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Proving the Turing Universality of Oritatami Co-Transcriptional Folding (2018)
  • Author(s): Cody Geary, Pierre-Etienne Meunier, Nicolas Schabanel, Shinnosuke Seki
  • Journal Title: Proceedings of the 29th International Symposium on Algorithms and Computation (ISAAC 2018, Jiaoxi, Taiwan, Dec. 16-19, 2018) Volume: 123
  • DOI: 10.4230/LIPICS.ISAAC.2018.23
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Towards the Algorithmic Molecular Self-assembly of Fractals by Cotranscriptional Folding (2018)
  • Author(s): Masuda Yusei、Seki Shinnosuke、Ubukata Yuki
  • Journal Title: Proceedings of the 23rd International Conference on Implementation and Applications of Automata (CIAA 2018, Charlottetown, Canada, July 30-Aug. 2, 2018) Volume: 10977 Pages: 261-273
  • DOI: 10.1007/978-3-319-94812-6_22
  • ISBN: 9783319948119, 9783319948126
  • Peer Reviewed
• [Presentation] Counting infinitely by oritatami co-transcriptional folding (2020)
  • Author(s): Kohei Maruyama
  • Organizer: SOFSEM2020: 46th International Conference on Current Trends in Theory and Practice of Informatics
  • Int'l Joint Research
• [Presentation] A General Architecture of Oritatami Systems for Simulating Arbitrary Finite Automata (2019)
  • Author(s): Shinnosuke Seki
  • Organizer: CIAA 2019: 24th International Conference on Implementation and Applications of Automata
  • Int'l Joint Research
• [Presentation] Single stranded architectures for computing (2019)
  • Author(s): Shinnosuke Seki
  • Organizer: DLT2019: 23rd International Conference on Developments in Language Theory
  • Int'l Joint Research / Invited
• [Presentation] On the Power of Oritatami Cotranscriptional Folding with Unary Bead Sequence (2019)
  • Author(s): Kohei Maruyama, Reoto Morita
  • Organizer: TAMC2019: 15th Annual Conference on Theory and Applications of Models of Computation
  • Int'l Joint Research
• [Presentation] On the Power of Oritatami Cotranscriptional Folding with Unary Bead Sequence (2019)
  • Author(s): Reoto Morita, Kohei Maruyama
  • Organizer: 15th Annual Conference on Theory and Applications of Models of Computation (TAMC 2019)
  • Int'l Joint Research
• [Presentation] A general architecture of oritatami systems for simulating arbitrary finite automata (2019)
  • Author(s): Yusei Masuda, Shinnosuke Seki
  • Organizer: 24th International Conference on Implementation and Applications of Automata (CIAA 2019)
  • Int'l Joint Research
• [Presentation] Single-stranded architectures for computing (2019)
  • Author(s): Shinnosuke Seki
  • Organizer: 23rd International Conference on Developments in Language Theory (DLT 2019)
  • Int'l Joint Research / Invited
• [Presentation] Proving the Turing Universality of Oritatami Co-Transcriptional Folding (2018)
  • Author(s): Nicolas Schabanel
  • Organizer: 29th International Symposium on Algorithms and Computation (ISAAC 2018)
  • Int'l Joint Research
• [Presentation] Know When to Fold ’Em: Self-assembly of Shapes by Folding in Oritatami (2018)
  • Author(s): Nicolas Schabanel
  • Organizer: 24th International Conference on DNA Computing and Molecular Programming (DNA 24)
  • Int'l Joint Research
• [Presentation] Transcript Design Problem of Oritatami Systems (2018)
  • Author(s): Hwee Kim
  • Organizer: 24th International Conference on DNA Computing and Molecular Programming (DNA 24)
  • Int'l Joint Research
• [Presentation] Towards the Algorithmic Molecular Self-assembly of Fractals by Cotranscriptional Folding (2018)
  • Author(s): Yusei Masuda, Yuki Ubukata
  • Organizer: 23rd International Conference on Implementation and Applications of Automata (CIAA 2018)
  • Int'l Joint Research
• [Book] Proceedings of the 18th International Confenrence on Unconventional Computation and Natural Computation (2019)
  • Author(s): Ian McQuillan, Shinnosuke Seki
  • Total Pages: 287
  • Publisher: Springer
  • ISBN: 9783030193102
• [Book] Proceedings of the 22nd International Conference on Developments in Language Theory (DLT 2018) (2018)
  • Author(s): Mizuho Hoshi, Shinnosuke Seki
  • Total Pages: 568
  • Publisher: Springer
  • ISBN: 9783319986531
• [Remarks] Cellular automata simulation by oritatami system
  • URL: https://apps.apple.com/us/app/caos-simulator/id1488203962
• [Funded Workshop] UCNC2019: 18th International Conference on Unconventional Computation and Natural Computation (2019)
• [Funded Workshop] 22nd International Conference on Developments in Language Theory (2018)