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Robust Prediction of the Dynamics of Biocircuits using Integrated First-Principles and Data-Driven Models

Research Project

Project/Area Number 18H01464
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 21040:Control and system engineering-related
Research InstitutionKeio University

Principal Investigator

Hori Yutaka  慶應義塾大学, 理工学部(矢上), 准教授 (10778591)

Project Period (FY) 2018-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥17,030,000 (Direct Cost: ¥13,100,000、Indirect Cost: ¥3,930,000)
Fiscal Year 2020: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Fiscal Year 2019: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2018: ¥8,190,000 (Direct Cost: ¥6,300,000、Indirect Cost: ¥1,890,000)
Keywords制御工学 / 生体分子システム / マイクロ流体 / マイクロ流路 / 遺伝子回路
Outline of Final Research Achievements

We developed a theoretical framework for analyzing and designing the dynamics of biomolecular systems using a mathematical model, and an experimental platform that efficiently supplements data necessary for constructing such models. Specifically, we developed a modeling framework that combines the first-principles model derived from physical laws with a machine learning model learned from experimental data. The proposed framework enabled robust prediction and analysis of systems' dynamics that takes into account the influence of environmental factors, which was difficult to capture with the first-principles model alone. A microfluidic system was also developed to generate a large number of parallel reaction systems with slightly different environmental factors and use for model identification.

Academic Significance and Societal Importance of the Research Achievements

生体分子システムの持つ様々な不確かさに対してロバスト性の高いモデルベースの反応設計法を提案したことで,多分子・多機能の分子システムのモデルベース開発が容易になる.これにより,反応ネットワークの作用機序をボトムアップ的なアプローチで探求する学術研究や,分子システムの工学応用を目指す研究開発が加速すると期待される.
また,生体分子の反応ネットワークが持つ数理的な構造や不確かさを,制御工学や機械学習の理論と関連させてシステム論的に捉えるためのフレームワークを提案した点は,システム科学の発展においても学術的な意義がある.

Report

(4 results)
  • 2021 Final Research Report ( PDF )
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • Research Products

    (20 results)

All 2021 2020 2019 2018

All Journal Article (3 results) (of which Peer Reviewed: 3 results) Presentation (17 results) (of which Int'l Joint Research: 6 results)

  • [Journal Article] Finite-Time Stability Analysis for Resource Limited Chemical Reactions2021

    • Author(s)
      Matsunaga Tomoki, Uemura Ryosuke, Hori Yutaka
    • Journal Title

      IEEE Control Systems Letters

      Volume: 5 Issue: 3 Pages: 815-820

    • DOI

      10.1109/lcsys.2020.3006052

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Bounding Transient Moments of Stochastic Chemical Reactions2019

    • Author(s)
      Yuta Sakurai, Yutaka Hori
    • Journal Title

      IEEE Control Systems Letters

      Volume: 3 Issue: 2 Pages: 290-295

    • DOI

      10.1109/lcsys.2018.2869639

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Analysing diffusion and flow-driven instability using semidefinite programming2019

    • Author(s)
      Yutaka Hori, Hiroki Miyazako
    • Journal Title

      Journal of The Royal Society Interface

      Volume: 16 Issue: 150 Pages: 20180586-20180586

    • DOI

      10.1098/rsif.2018.0586

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Presentation] 非線形最適レギュレータ問題に対するモデルフリー二段階設計による過渡学習性能の改善2021

    • Author(s)
      増元 由佳, 大川 佳寛, 佐々木 智丈, 堀 豊
    • Organizer
      計測自動制御学会第8回制御部門マルチシンポジウム
    • Related Report
      2020 Annual Research Report
  • [Presentation] Robust Instability Radius for Multi-agent Dynamical Systems with Cyclic Structure2021

    • Author(s)
      Shinji Hara, Tetsuya Iwasaki, Yutaka Hori
    • Organizer
      SICE International Symposium on Control Systems
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Robust Instability Analysis with Application to Neuronal Dynamics2020

    • Author(s)
      Shinji Hara, Tetsuya Iwasaki, Yutaka Hori
    • Organizer
      IEEE Conference on Decision and Control
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 数理最適化による反応移流拡散システムのパターン形成解析2020

    • Author(s)
      堀 豊, 宮廻 裕樹
    • Organizer
      第63回自動制御連合講演会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 空間周波数サブシステム分解に基づく細胞間分子通信システムの外乱応答解析2020

    • Author(s)
      小塚 太資, 堀 豊
    • Organizer
      第63回自動制御連合講演会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 温度計を内包したドロップレットによる DNA 回路の温度特性計測2020

    • Author(s)
      古志 飛,堀 豊
    • Organizer
      第4回分子ロボティクス年次大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] リソースに制約のある化学反応の有限時間安定性の解析法2020

    • Author(s)
      松永知樹,植村涼良,堀豊
    • Organizer
      第7回制御部門マルチシンポジウム
    • Related Report
      2019 Annual Research Report
  • [Presentation] 制御対象の事前情報を利用した出力フィードバック最適制御器の効率的な学習に向けて2020

    • Author(s)
      増元由佳,堀豊
    • Organizer
      第7回制御部門マルチシンポジウム
    • Related Report
      2019 Annual Research Report
  • [Presentation] 筋力学モデルの不確かさを定量化するためのパラメタ集合同定法2020

    • Author(s)
      森田梨紗子, 内山孝憲, 堀豊
    • Organizer
      第7回制御部門マルチシンポジウム
    • Related Report
      2019 Annual Research Report
  • [Presentation] Disturbance response analysis of cell-to-cell communication systems based on spatial frequency decomposition2019

    • Author(s)
      Taishi Kotsuka, Yutaka Hori
    • Organizer
      IFAC Conference on Foundations of Systems Biology in Engineering
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Semidefinite programming for Turing instability analysis in molecular communication networks2019

    • Author(s)
      Yutaka Hori, Hiroki Miyazako
    • Organizer
      IEEE Conference on Decision and Control
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Temperature controlled droplet reactors for parallel tuning of DNA circuits2019

    • Author(s)
      Asuka Koshi, Yutaka Hori
    • Organizer
      Winter q-bio
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 不確かさのある化学マスター方程式に対するWorst-case解析2019

    • Author(s)
      櫻井裕大, 堀豊
    • Organizer
      計測自動制御学会制御部門マルチシンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] 不確かな動的多項式システムに対する解集合の外部近似法2019

    • Author(s)
      植村涼良, 櫻井裕大, 堀豊
    • Organizer
      計測自動制御学会制御部門マルチシンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] DNA回路の反応場温度を並列最適化するためのドロップレット型リアクタ2019

    • Author(s)
      古志飛, 堀豊
    • Organizer
      第2回分子ロボティクス年次大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 分子通信により制御される細胞集団の外乱応答特性の解析2018

    • Author(s)
      小塚太資,堀豊
    • Organizer
      分子ロボティクス定例研究会
    • Related Report
      2018 Annual Research Report
  • [Presentation] A microfluidic actuator for dynamic control of chemical reactions2018

    • Author(s)
      Ayaka Wakamei, Yutaka Hori
    • Organizer
      SICE Annual Conference
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research

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Published: 2018-04-23   Modified: 2023-01-30  

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