Ibuki Kawamata

Profile Information

Affiliation: Division of Physics and Astronomy, Graduate School of Science, Kyoto University

Degree: 博士（情報理工学）(Mar, 2014, 東京大学大学院情報理工学研究科)

Researcher number: 30733977
J-GLOBAL ID: 201801005123148380
researchmap Member ID: B000333861

External link: https://ibuki-kawamata.org/

Research Interests

Research Areas

Informatics / Biological, health, and medical informatics / Molecular Cybernetics, Molecular computation, Molecular programming, DNA computer
Natural sciences / Bio-, chemical, and soft-matter physics / Active matter, DNA reaction diffusion system, DNA gel
Nanotechnology/Materials / Nanomaterials / DNA origami, DNA nanotechnology
Informatics / Robotics and intelligent systems / Molecular robotics

Research History

Dec, 2023 - Present

Associate Professor, Graduate School of Science Division of Physics and Astronomy, Kyoto University
Feb, 2020 - Nov, 2023

(Concurrent post) Assistant Professor, Natural Science Division, Faculty of Core Research, Ochanomizu University
Apr, 2016 - Nov, 2023

Assistant Professor, Department of Robotics, Graduate School of Engineering, Tohoku University
Apr, 2017 - Mar, 2018

(Visiting researcher), Technical University of Munich
Apr, 2014 - Mar, 2016

東北大学大学院工学研究科バイオロボティクス専攻
Apr, 2011 - Mar, 2014

JSPS Research Fellowships for Young Scientists(DC1)

Education

Apr, 2009 - Mar, 2014

東京大学大学院情報理工学系研究科コンピュータ科学
Apr, 2005 - Mar, 2009

東京大学理学部情報科学科

Committee Memberships

Jan, 2025 - Dec, 2026

Editor, New Generation Computing
- Nov, 2025

実行委員, 第13回ソフトマター研究会
- Oct, 2025

プログラム委員, CBI学会2025年大会
- Sep, 2025

シンポジウムオーガナイザー, 第63回日本生物物理学会年会シンポジウム「生物物理からのアクティブマターへのアプローチ」
- Sep, 2025

世話人, 第14回分子モーター討論会
- Mar, 2025

実行委員, 第8回分子ロボティクス年次大会
- Nov, 2024

Committee of Domestic Meeting, BIOMOD 2024
- Oct, 2024

プログラム委員, CBI学会2024年大会
Jul, 2024 - Sep, 2024

実行委員, 分子ロボティクス夏の学校2024
- Sep, 2024

Program Committee, the 30th International Conference on DNA Computing and Molecular Programming
Jun, 2024

代議員, 分子ロボティクス研究会
- Mar, 2024

ウェブ担当, 第7回分子ロボティクス年次大会
Mar, 2024

Workshop Organizer, Utilization of DNA nanotechnology
Nov, 2023

Steering Committee (Accounting), BIOMOD 2023
Nov, 2023

モデレーター, CBI学会2023年フォーカストセッションFS07「分子ロボティクス研究会」
- Oct, 2023

プログラム委員, CBI学会2023年大会
Sep, 2023

Program Committee, the 29th International Conference on DNA Computing and Molecular Programming (DNA29)
Sep, 2023

Local Organization Committee, the 29th International Conference on DNA Computing and Molecular Programming (DNA29)
Sep, 2023

主催, DNAナノ構造体のモデル化および可視化のためのソフトウェア講習
Jun, 2023 - Aug, 2023

実行委員, 分子ロボティクス夏の学校2023

Awards

Apr, 2025

NIKON JOICO AWARD 2024 優秀賞, NIKON
Feb, 2025

CBI学会若手奨励賞, CBI学会
Sep, 2024

世界最小の加工賞, 京都大学アカデミックデイ
Nov, 2023

Thorlabs Japan award
May, 2023

Lab on a Chip outstanding research award (RSC award), サブミクロンスケールのトラス型DNAナノ構造体の精密設計, CHEMINAS 47
Mar, 2016

若手奨励賞, 新学術領域分子ロボティクス領域会議
Oct, 2013

Excellent Poster Award, Chem-Bio Informatics Society (CBI) Annual Meeting 2013
Jun, 2010

ISNSCE Award, The 16th International Meeting on DNA Computing and Molecular Programming

Papers

Intra- and Interbead Communications by an Anchored DNA Structure and Cascaded DNA Reactions

Ibuki Kawamata, Satoru Yoshizawa, Keita Abe, Masahiro Takinoue, Shin-Ichiro M. Nomura, Satoshi Murata

ACS Synthetic Biology, Mar 14, 2025 Lead authorCorresponding author
Logic-Gated Modulation of Cell Migration via Mesoscale Mechanical Uncaging Effects

Deepak Karna, Shin Watanabe, Grinsun Sharma, Arpit Sharma, Yaorong Zheng, Ibuki Kawamata, Yuki Suzuki, Hanbin Mao

ACS Nano, 19(8) 8058-8069, Feb 21, 2025
Transmembrane DNA Sequence Signaling via Hybridization

Kai Yoshida, Keita Abe, Yusuke Sato, Ibuki Kawamata, Richard James Archer, Hideaki T. Matsubayashi, Shogo Hamada, Satoshi Murata, Shin-ichiro Nomura

Jul 16, 2024
Autonomous assembly and disassembly of gliding molecular robots regulated by a DNA-based molecular controller

Ibuki Kawamata, Kohei Nishiyama, Daiki Matsumoto, Shosei Ichiseki, Jakia J. Keya, Kohei Okuyama, Masatoshi Ichikawa, Arif Md. Rashedul Kabir, Yusuke Sato, Daisuke Inoue …

Science Advances, 10(22), May 31, 2024 Peer-reviewedLead author
Non-catalytic role of phosphoinositide 3-kinase in mesenchymal cell migration through non-canonical induction of p85β/AP2-mediated endocytosis

Hideaki T. Matsubayashi, Jack Mountain, Nozomi Takahashi, Abhijit Deb Roy, Tony Yao, Amy F. Peterson, Cristian Saez Gonzalez, Ibuki Kawamata, Takanari Inoue

Nature Communications, 15(1), Mar 23, 2024 Peer-reviewed
Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies

Deepak Karna, Eriko Mano, Jiahao Ji, Ibuki Kawamata, Yuki Suzuki, Hanbin Mao

Nature Communications, 14(1), Oct 13, 2023 Peer-reviewedCorresponding author
Multi-Reconfigurable DNA Origami Nanolattice Driven by the Combination of Orthogonal Signals

Kotaro Watanabe, Ibuki Kawamata, Satoshi Murata, Yuki Suzuki

JACS Au, 3(5) 1435-1442, Apr 27, 2023 Peer-reviewed
Collective Cargo Transport and Sorting with Molecular Swarms

Nathanael Aubert-Kato, Geoff Nitschke, Ibuki Kawamata, Akira Kakugo

The 2023 Conference on Artificial Life, 2023 Peer-reviewed
Self-replication and Mutation of Polymeric Molecules Simulated by Simplified Chemistry

Taisei Mori, Ibuki Kawamata, Satoshi Murata

2022 Tenth International Symposium on Computing and Networking Workshops (CANDARW), Nov, 2022 Peer-reviewed
Algorithmic Design of 3D Wireframe RNA Polyhedra

Antti Elonen, Ashwin Karthick Natarajan, Ibuki Kawamata, Lukas Oesinghaus, Abdulmelik Mohammed, Jani Seitsonen, Yuki Suzuki, Friedrich C. Simmel, Anton Kuzyk, Pekka Orponen

ACS Nano, Sep 30, 2022 Peer-reviewed
Lipid bilayer-assisted dynamic self-assembly of hexagonal DNA origami blocks into monolayer crystalline structures with designed geometries

Yuki Suzuki, Ibuki Kawamata, Kotaro Watanabe, Eriko Mano

iScience, 25(5) 104292-104292, May, 2022 Peer-reviewed
Algorithmic design of 3D wireframe RNA polyhedra

Antti Elonen, Ashwin K. Natarajan, Ibuki Kawamata, Lukas Oesinghaus, Abdulmelik Mohammed, Jani Seitsonen, Yuki Suzuki, Friedrich C. Simmel, Anton Kuzyk, Pekka Orponen

Apr 28, 2022
Autonomous and Programmable Strand Generator Implemented as DNA and Enzymatic Chemical Reaction Cascade

Ibuki Kawamata, Shin-ichiro M. Nomura, Satoshi Murata

New Generation Computing, 40(2) 723-736, Feb 27, 2022 Peer-reviewedLead authorCorresponding author
Web Server with a Simple Interface for Coarse-grained Molecular Dynamics of DNA Nanostructures

Yudai Yamashita, Kotaro Watanabe, Satoshi Murata, Ibuki Kawamata

Chem-Bio Informatics Journal, 21 28-38, Apr 30, 2021 Peer-reviewedLast authorCorresponding author
Chemo-Mechanical Modulation of Cell Motions Using DNA Nanosprings

Deepak Karna, Morgan Stilgenbauer, Sagun Jonchhe, Kazuya Ankai, Ibuki Kawamata, Yunxi Cui, Yao-Rong Zheng, Yuki Suzuki, Hanbin Mao

Bioconjugate Chemistry, 32(2) 311-317, Feb 17, 2021 Peer-reviewed
Online Biomolecular Design Competition Across University Boundaries

Satoshi MURATA, Akinori KUZUYA, Kei FUJIWARA, Junichi TAIRA, Ibuki KAWAMATA, Yusuke SATO, Masahiro TAKINOUE, Shin-ichiro M. NOMURA, Akira KAKUGO, Yutaka HORI …

Journal of JSEE, 69(4) 31-39, 2021 Peer-reviewed
Cascaded pattern formation in hydrogel medium using the polymerisation approach

Keita Abe, Satoshi Murata, Ibuki Kawamata

Soft Matter, 17(25) 6160-6167, 2021 Peer-reviewedLast authorCorresponding author
A large, square-shaped, DNA origami nanopore with sealing function on a giant vesicle membrane

Shoji Iwabuchi, Ibuki Kawamata, Satoshi Murata, Shin-ichiro M. Nomura

Chemical Communications, 57(24) 2990-2993, 2021 Peer-reviewed
DNA Ring Motif with Flexible Joints

Shiyun Liu, Satoshi Murata, Ibuki Kawamata

Micromachines, 11(11) 987-987, Oct 31, 2020 Peer-reviewedLast authorCorresponding author
Large Deformation of a DNA-Origami Nanoarm Induced by the Cumulative Actuation of Tension-Adjustable Modules.

Yuki Suzuki, Ibuki Kawamata, Kohei Mizuno, Satoshi Murata

Angewandte Chemie (International ed. in English), 59(15) 6230-6234, Apr 6, 2020 Peer-reviewedCorresponding author

Misc.

分子群ロボットの構築

川又生吹, 角五彰

ファルマシア, 61(4) 324-328, Apr, 2025
フォーカストセッションFS05 分子ロボティクス研究会「動け、細胞/人工細胞フォーラム」

多田隈尚史, 川又生吹, 佐藤佑介, 小宮健, 豊田太郎

CBI学会誌, 13(1) 12-13, 2025
Programming Pattern Formation by DNA Reaction-diffusion System with Designed Base Sequences

Keita ABE, Satoshi MURATA, Ibuki KAWAMATA

Seibutsu Butsuri, 65(1) 14-16, 2025
化学反応系によるリザバー計算 (解説)

川又生吹, 龔逸鳴

現代化学, 9(642) 9, 2024
研究最前線 "Autonomous assembly and disassembly of gliding molecular robots regulated by a DNA-based molecular controller"

川又生吹

分子サイバネティクスニュースレター,, 15 2, 2024
口頭発表O04 『分子ロボティクス-1-』

小宮健, 川又生吹, 多田隈尚史

CBI学会誌, 12(4) 27, 2024
実験自動化による人工多細胞体の作製と観察への取り組みと今後の展望

川又生吹, 清水稜, Richard J. Archer, 野村 M. 慎一郎

実験の自動化・自律化によるR&Dの効率化と運用方法, 523-538, Dec, 2023
DNA オリガミ法で作るナノ構造体

川又生吹

化学とマイクロ・ナノシステム学会誌, Oct, 2023 Lead authorLast authorCorresponding author
口頭発表O7 『分子ロボティクス/レギュラトリサイエンス』

川又生吹

CBI学会誌, 10 40, Dec, 2022 Lead authorLast authorCorresponding author
口頭発表O8 『創薬応用 (3)/分子ロボティクス』

本間光貴, 川又生吹

CBI学会誌, 10 41, Dec, 2022 Last author
第6回分子ロボティクス年次大会活動報告

川又生吹

学術変革領域（A) Molecular Cybernetics News Letter 分子サイバネティクスニュースレター, 8 8-9, Dec, 2022 Lead authorLast authorCorresponding author
Advancement of Computer-aided Design Software and Simulation tools for Nucleic acid Nanostructures and DNA Origami

Ibuki Kawamata

DNA Origami: Structures, Technology, and Applications, May, 2022 Lead authorLast authorCorresponding author
Development of Browser-Based Software for Intuitively Manipulating and Integrating DNA Nanostructures

Ibuki Kawamata, Sho Aradachi, Satoshi Murata

60th Annual Conference of the Society of Instrument and Control Engineers of Japan (SICE), Sep, 2021 Peer-reviewedLead authorCorresponding author
新刊情報 "DNA origami入門基礎から学ぶDNAナノ構造体の設計技法"

Molecular Cybernetics News Letter, 1 5, 2021
研究最前線 "Cascaded pattern formation in hydrogel medium using the polymerisation approach"

Molecular Cybernetics News Letter, 3 1, 2021
口頭発表３「ADME・毒性 / バイオインフォマティックス / 分子ロボティクス / その他」

夏目やよい, 川又生吹

CBI学会誌, 9(4) 37-37, 2021
<口頭発表3> 分子ロボティクス

佐藤佑介, 川又生吹, 小宮健

CBI学会誌, 8(4) 26-27, Dec, 2020
Programmable reactions and diffusion using DNA for pattern formation in hydrogel medium

Keita Abe, Ibuki Kawamata, Shin Ichiro, M. Nomura, Satoshi Murata

Molecular Systems Design and Engineering, 4 639-643, Jun 1, 2019
マイクロ流路デバイスによるゲル微粒子の合成とゲルオートマトンへの応用

西諒也, 川又生吹, 宮元展義

高分子学会予稿集(CD-ROM), 67(2) ROMBUNNO.1Pb020, Aug 29, 2018
Size Controllable Linear Self-Assembly Module of DNA Origami

LIU Shiyun, 安部桂太, 内田健央, 遠藤佑真, 秋田賢, 市堰翔成, 荒舘笙, 斎藤正崇, 吉川太陽, 福地成彦 …

形の科学シンポジウム講演予稿集(Web), 85th 23‐24 (WEB ONLY), Jun, 2018

Books and Other Publications

DNA origami入門: 基礎から学ぶDNAナノ構造の設計技法

川又生吹, 鈴木勇輝, 村田智 (Role: Joint author, 全13章中11章)

May, 2021
分子ロボティクス概論 : 分子のデザインでシステムをつくる

分子ロボティクス研究会, 村田, 智

CBI学会, 2019 (ISBN: 9784990907648)
DNA分子デザインのすべて : BIOMOD虎の巻

分子ロボティクス研究会

情報計算化学生物学会, 2016 (ISBN: 9784990907679)

Professional Memberships

Jun, 2024 - Present

物理学会
Apr, 2021 - Present

The Chem-Bio Informatics Society
化学とマイクロ・ナノシステム学会
生物物理学会
応用物理学会

Research Projects

分子シミュレーションと実験自動化による大規模DNA構造体設計手法の開発

科学研究費助成事業, 基盤研究(C), 日本学術振興会, Apr, 2022 - Mar, 2026

川又生吹
機械学習による解析に基づいたアクティブ生体分子システムの創発単年度研究助成

単年度研究助成, 公益財団法人池谷科学技術振興財団, Apr, 2025 - Mar, 2026

川又生吹
Development of Molecular Memory / Molecular Learning Circuits for Minimal Artificial Brain

Grants-in-Aid for Scientific Research, Grant-in-Aid for Transformative Research Areas (A), Japan Society for the Promotion of Science, Nov, 2020 - Mar, 2025
New development of spatio-temporal molecular programming

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (A), Japan Society for the Promotion of Science, Apr, 2020 - Mar, 2025
Molecular swarm robotics: Verifying working ability of molecular robots and their implementation in social contexts

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (A), Japan Society for the Promotion of Science, Apr, 2021 - Mar, 2024
Development of novel platform to rationally design DNA origami

Grants-in-Aid for Scientific Research, Grant-in-Aid for Early-Career Scientists, Japan Society for the Promotion of Science, Apr, 2018 - Mar, 2021

Kawamata Ibuki
Development of Artificial Membrane System by DNA Membrane Motif

Grants-in-Aid for Scientific Research, Grant-in-Aid for Challenging Research (Exploratory), Japan Society for the Promotion of Science, Jun, 2018 - Mar, 2020

Murata Satoshi
A study on molecular robotics blood glucose level control method with NOD mice

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (A), Japan Society for the Promotion of Science, Apr, 2017 - Mar, 2020

KONAGAYA Akihiko
Construction of Control System for Behavior Programming of Molecular Robots

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (A), Japan Society for the Promotion of Science, Apr, 2015 - Mar, 2019

Murata Satoshi
Motion generation based on cooperation of structured gel and chemical reaction field

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Japan Society for the Promotion of Science, Jun, 2012 - Mar, 2017

Hagiya Masami, KAWAMATA Ibuki, HAMADA Shogo
Design and implementation of programmable reaction diffusion system using nucleic acids

Grants-in-Aid for Scientific Research, Grant-in-Aid for Research Activity Start-up, Japan Society for the Promotion of Science, Aug, 2014 - Mar, 2016

Kawamata Ibuki
Development of molecular robotics based on DNA nanoengineering

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (S), Japan Society for the Promotion of Science, Apr, 2010 - Mar, 2015

MURATA Satoshi, KUZUYA Akinori, TAKINOUE Masahiro, SEKIYAMA Kosuke, NOMURA Shin-ichiro, FUJIMOTO Kenzo, TAKEUCHI Shyoji, KOBAYASHI Satoshi, KAWAMATA Ibuki, MORITA Masamune, HAMADA Shogo

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