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New development of spatio-temporal molecular programming

Research Project

Project/Area Number 20H00618
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Review Section Medium-sized Section 62:Applied informatics and related fields
Research InstitutionTohoku University

Principal Investigator

Murata Satoshi  東北大学, 工学研究科, 教授 (10334533)

Co-Investigator(Kenkyū-buntansha) 川又 生吹  京都大学, 理学研究科, 准教授 (30733977)
安部 桂太  東北大学, 工学研究科, 助教 (00982860)
Project Period (FY) 2020-04-01 – 2025-03-31
Project Status Completed (Fiscal Year 2024)
Budget Amount *help
¥44,200,000 (Direct Cost: ¥34,000,000、Indirect Cost: ¥10,200,000)
Fiscal Year 2024: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Fiscal Year 2023: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2022: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2021: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
Fiscal Year 2020: ¥23,530,000 (Direct Cost: ¥18,100,000、Indirect Cost: ¥5,430,000)
Keywords時空間分子プログラミング / DNAコンピューティング / 反応拡散系 / 空間分子プログラミング / マテリアライゼーション / DNAコンピューティング
Outline of Research at the Start

本研究では,分子プログラミングの技術をもちいて,生物が実現しているような自由自在な化学反応場の時空間制御を実現する.近年,人工的な反応拡散系によるパターン形成の研究が注目を集めているが,分子の拡散を制御するという観点が欠けているためできたパターンがすぐに散逸してしまうという問題や,できたパターンを機能化するための方法論がないといった問題があり,応用に結び付いていない.そこで本研究では,化学反応場において分子の拡散を積極的に制御する方法,および,できたパターンから物理化学的機能を引き出す方法を開発することにより,こうした問題を解決し,時空間分子プログラミングの基盤技術を確立する.

Outline of Final Research Achievements

The goal of this study was to achieve spatio-temporal control of chemical reaction fields, as occurs in vivo, using molecular programming techniques. Research on pattern formation by artificial reaction-diffusion systems has recently attracted attention. However, there are problems, such as patterns quickly disappearing due to a lack of control over molecular diffusion and a lack of methodology to functionalize patterns. In this study, we developed methods to actively control molecular diffusion in a chemical reaction field and to express physicochemical functions from formed patterns. These methods establish fundamental technology for space-time molecular programming.

Academic Significance and Societal Importance of the Research Achievements

本研究では,時空間プログラミングに適した反応系として,DNA重合反応を利用する新しい反応拡散システムの設計論を確立した.これにより初期反応空間に存在する単純な非対称性から出発して段階的に反応空間を複雑化することが可能になった.また,反応空間全体を粘性媒体とすることにより,形成された局所的な分子構造(ゲル)のパターンが波打つ動的な現象を見出した.これらは人工の反応拡散系によるパターン形成を自在に制御するための基盤的な知見となるもので,将来的には人工臓器などの人工的な生体組織の創成に資するものである.

Report

(7 results)
  • 2024 Annual Research Report   Final Research Report ( PDF )
  • 2023 Annual Research Report
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • 2020 Comments on the Screening Results   Annual Research Report
  • Research Products

    (31 results)

All 2025 2024 2023 2022 2021 2020 Other

All Int'l Joint Research (1 results) Journal Article (12 results) (of which Int'l Joint Research: 7 results,  Peer Reviewed: 12 results,  Open Access: 12 results) Presentation (14 results) (of which Int'l Joint Research: 6 results,  Invited: 1 results) Book (3 results) Remarks (1 results)

  • [Int'l Joint Research] ソルボンヌ大学(Jean Perrin Laboratory)(フランス)

    • Related Report
      2023 Annual Research Report
  • [Journal Article] Intra- and Interbead Communications by an Anchored DNA Structure and Cascaded DNA Reactions2025

    • Author(s)
      Kawamata Ibuki、Yoshizawa Satoru、Abe Keita、Takinoue Masahiro、Nomura Shin-Ichiro M.、Murata Satoshi
    • Journal Title

      ACS Synthetic Biology

      Volume: 14 Issue: 4 Pages: 1121-1128

    • DOI

      10.1021/acssynbio.4c00709

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Micrometer‐Sized Liposome‐Based Systems: A Hierarchical Breakdown2025

    • Author(s)
      Hamada Shogo、Sugiyama Hironori、Zhang Yiting、Iwabuchi Shoji、Hiroi Soichiro、Maruyama Toshiki、Balaji Yuktesh、Kumagai Sota、Murata Satoshi、Toyota Taro
    • Journal Title

      ChemSystemsChem

      Volume: - Issue: 3

    • DOI

      10.1002/syst.202400074

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 分子ロボットの過去・現在・未来2025

    • Author(s)
      小長谷 明彦、村田 智
    • Journal Title

      Farumashia

      Volume: 61 Issue: 4 Pages: 297-301

    • DOI

      10.14894/faruawpsj.61.4_297

    • ISSN
      0014-8601, 2189-7026
    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Autonomous assembly and disassembly of gliding molecular robots regulated by a DNA-based molecular controller2024

    • Author(s)
      Ibuki Kawamata, Kohei Nishiyama, Daiki Matsumoto, Shosei Ichiseki, Jakia J. Keya, Kohei Okuyama, Masatoshi Ichikawa, Arif M. R. Kabir, Yusuke Sato, Daisuke Inoue, Satoshi Murata, Kazuki Sada, Akira Kakugo, Shin-ichiro M. Nomura
    • Journal Title

      Science Advances

      Volume: 10 Issue: 22

    • DOI

      10.1126/sciadv.adn4490

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Liquid DNA Coacervates form Porous Capsular Hydrogels via Viscoelastic Phase Separation on Microdroplet Interface2024

    • Author(s)
      Morita Masamune、Sakamoto Tetsuro、Nomura Shin‐ichiro M.、Murata Satoshi、Yanagisawa Miho、Takinoue Masahiro
    • Journal Title

      Advanced Materials Interfaces

      Volume: 11 Issue: 13 Pages: 2300898-2300898

    • DOI

      10.1002/admi.202300898

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Non-catalytic role of phosphoinositide 3-kinase in mesenchymal cell migration through non-canonical induction of p85β/AP2-mediated endocytosis2024

    • Author(s)
      Matsubayashi Hideaki T.、Mountain Jack、Takahashi Nozomi、Deb Roy Abhijit、Yao Tony、Peterson Amy F.、Saez Gonzalez Cristian、Kawamata Ibuki、Inoue Takanari
    • Journal Title

      Nature Communications

      Volume: 15 Issue: 1 Pages: 1-16

    • DOI

      10.1038/s41467-024-46855-y

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Multi-Reconfigurable DNA Origami Nanolattice Driven by the Combination of Orthogonal Signals2023

    • Author(s)
      Kotaro Watanabe, Ibuki Kawamata, Satoshi Murata, Yuki Suzuki
    • Journal Title

      JACS Au

      Volume: To appear Issue: 5 Pages: 1-8

    • DOI

      10.1021/jacsau.3c00091

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] From Molecular Robotics to Molecular Cybernetics: The First Step Toward Chemical Artificial Intelligence2023

    • Author(s)
      Kuzuya Akinori、Nomura Shin-Ichiro M.、Toyota Taro、Nakakuki Takashi、Murata Satoshi
    • Journal Title

      IEEE Transactions on Molecular, Biological and Multi-Scale Communications

      Volume: 9 Issue: 3 Pages: 354-363

    • DOI

      10.1109/tmbmc.2023.3304243

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies2023

    • Author(s)
      Karna Deepak、Mano Eriko、Ji Jiahao、Kawamata Ibuki、Suzuki Yuki、Mao Hanbin
    • Journal Title

      Nature Communications

      Volume: 14 Issue: 1 Pages: 6459-6459

    • DOI

      10.1038/s41467-023-41604-z

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Collective Cargo Transport and Sorting with Molecular Swarms2023

    • Author(s)
      Aubert-Kato Nathanael、Nitschke Geoff、Kawamata Ibuki、Kakugo Akira
    • Journal Title

      ALIFE 2023

      Volume: -

    • DOI

      10.1162/isal_a_00593

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Web Server with a Simple Interface for Coarse-grained Molecular Dynamics of DNA Nanostructures2021

    • Author(s)
      Yudai Yamashita, Kotaro Watanabe, Satoshi Murata, Ibuki Kawamata
    • Journal Title

      Chem-Bio Informatics Journal

      Volume: 21 Issue: 0 Pages: 28-38

    • DOI

      10.1273/cbij.21.28

    • NAID

      130008031759

    • ISSN
      1347-0442, 1347-6297
    • Year and Date
      2021-04-30
    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Cascaded pattern formation in hydrogel medium using the polymerisation approach2021

    • Author(s)
      Keita Abe, Satoshi Murata, Ibuki Kawamata
    • Journal Title

      Soft Matter

      Volume: 25 Issue: 25 Pages: 6160-6167

    • DOI

      10.1039/d1sm00296a

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Hydrogel cubes for building DNA-based reaction-diffusion system2024

    • Author(s)
      Keita Abe and Satoshi Murata
    • Organizer
      International Conference on DNA Computing and Molecular Programming (DNA30), Johns Hopkins U
    • Related Report
      2024 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Implementation of DNA oscillator to artificial cells for inter-cellular information processing2024

    • Author(s)
      Kazumo Takahashi, Ibuki Kawamata, Keita Abe, Hideaki Matsubayashi, Shin-Ichiro Nomura and Satoshi Murata
    • Organizer
      International Conference on DNA Computing and Molecular Programming (DNA30), Johns Hopkins U.
    • Related Report
      2024 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Autonomous control of assembling and disassembling of microtubules by DNA2024

    • Author(s)
      Ibuki Kawamata
    • Organizer
      Seminar at The Institute of Intelligent Systems and Robotics (ISIR), Paris, France
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 分子ロボティクス2023

    • Author(s)
      川又生吹
    • Organizer
      CBI学会2023大会  口頭発表 O08
    • Related Report
      2023 Annual Research Report
  • [Presentation] 人工生体分子で脂質膜間通信を目指す2023

    • Author(s)
      川又生吹, 佐藤 佑介, 小宮 健, 多田隈 尚史, 豊田 太郎
    • Organizer
      CBI学会2023大会 フォーカストセッション FS07
    • Related Report
      2023 Annual Research Report
  • [Presentation] 分岐したDNAモチーフを用いたゾル媒体中でのパターン形成2022

    • Author(s)
      緒方寛,安部桂太,川又生吹,村田智
    • Organizer
      第6回分子ロボティクス年次大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Pattern formation in sol media using branched DNA motifs2022

    • Author(s)
      Hiroshi Ogata, Keita Abe, Ibuki Kawamata, Satoshi Murata
    • Organizer
      CBI学会2022年大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Cascaded pattern formation in DNA based Reaction-diffusion system2021

    • Author(s)
      Keita Abe, Satoshi Murata and Ibuki Kawamata
    • Organizer
      FNANO 2021: 18th Annual Conference Foundations of Nanoscience
    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Cascaded Pattern Formation in DNA-based Reaction-Diffusion System2021

    • Author(s)
      Keita Abe, Satoshi Murata and Ibuki Kawamata
    • Organizer
      DNA27: International Conference on DNA computing and Molecular Programming
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] DNA-based reaction-diffusion system for cascaded pattern formation2021

    • Author(s)
      Keita Abe, Satoshi Murata and Ibuki Kawamata
    • Organizer
      第59回日本生物物理学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] DNA反応拡散系におけるパターン形成のカスケード化2020

    • Author(s)
      安部桂太,村田智,川又生吹
    • Organizer
      第4回分子ロボティクス年次大会(併催分子ロボット倫理シンポジウム)
    • Related Report
      2020 Annual Research Report
  • [Presentation] DNAの重合反応を応用した反応拡散系のプログラムによるハイドロゲル中でのパターン形成2020

    • Author(s)
      安部 桂太, 川又生吹, 村田 智
    • Organizer
      SICE分子ロボティクス研究会第2回オンライン定例研究会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 合成DNAによる反応拡散系のプログラムを用いたハイドロゲル中でのパターン形成2020

    • Author(s)
      安部桂太
    • Organizer
      第3回 非線形科学オンライン研究会(若手の会)
    • Related Report
      2020 Annual Research Report
  • [Presentation] Cascaded Pattern Formation in Hydrogel using Reaction-Diffusion System2020

    • Author(s)
      Keita ABE, Ibuki KAWAMATA, Shin-ichiro M. NOMURA, and Satoshi MURATA
    • Organizer
      26th International Conference on DNA Computing and Molecular Programming
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Book] Visions of DNA Nanotechnology at 40 for the Next 40: A Tribute to Nadrian C. Seeman2023

    • Author(s)
      Satoshi Murata (Editors: Natasha Jonoska, Erik Winfree)
    • Total Pages
      431
    • Publisher
      Springer
    • ISBN
      9789811998904
    • Related Report
      2023 Annual Research Report
  • [Book] 実験の自動化・自律化によるR&Dの効率化と運用方法 -AI、ロボット技術、ChatGPT、MI、ベイズ最適化、秘密計算など-2023

    • Author(s)
      川又生吹, 清水 稜, Richard J. Archer, 野村 M. 慎一郎(第10章5節)
    • Total Pages
      545
    • Publisher
      技術情報協会
    • ISBN
      9784861049941
    • Related Report
      2023 Annual Research Report
  • [Book] Molecular Robotics -An Introduction2022

    • Author(s)
      Satoshi Murata (Editor)
    • Total Pages
      296
    • Publisher
      Springer
    • ISBN
      9789811939860
    • Related Report
      2022 Annual Research Report
  • [Remarks] 分子ロボティクス研究室ウェブサイト/研究成果/反応拡散によるパターン形成

    • URL

      http://www.molbot.mech.tohoku.ac.jp/achievements/

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report

URL: 

Published: 2020-04-28   Modified: 2026-01-16  

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