Introduction

Our group conducts advanced research in control theory and mathematical optimization, aiming to apply these frameworks to emerging fields such as synthetic biology and molecular robotics. We seek to systematize and accelerate the design of artificial biomolecular systems. Central to this effort is the development of an integrated platform that unites mathematical and computational modeling, biological knowledge, and device engineering. This includes the construction of experimental testbeds such as microfluidic devices that seamlessly link theory with practice, ultimately enabling a structured approach to designing engineering systems based on microbes and biomolecules.

■Theoretical and Experimental Platforms
・Research Objective: Development of a multi-layer microfluidic chemical stimulator using an L-2L ladder digital-to-analogue converter for modulating chemical concentrations.
- Title: L-2L ladder digital-to-analogue converter for dynamics generation of chemical concentrations, Chatani Tomohito, Shiraishi Suguru, Miyazako Hiroki, Onoe Hiroaki, Hori Yutaka （Royal Society Open Science） 10 （ 4 ） Apr. 2023
・Research Objective: To develop a method for calculating the robust instability radius in linear feedback systems and apply it to neuronal dynamics.
- Title: Robust Instability Analysis with Application to Neuronal Dynamics, Hara Shinji, Iwasaki Tetsuya, Hori Yutaka （2020 59th IEEE Conference on Decision and Control (CDC)） 6156-6161 Dec. 2020
■Biomolecular Circuit Design and Analysis
・Research Objective: To analyze the exact instability margin and achieve minimum-norm strong stabilization by maximizing the phase change rate in single-input-single-output linear time-invariant systems.
- Title: Exact Instability Margin Analysis and Minimum-Norm Strong Stabilization—Phase Change Rate Maximization, Hara Shinji, Kao Chung-Yao, Khong Sei Zhen, Iwasaki Tetsuya, Hori Yutaka （IEEE Transactions on Automatic Control） 69 （ 4 ） 2084-2099 Apr. 2024
・Research Objective: To propose and demonstrate a microfiber-shaped programmable material with stimuli-responsive and nonresponsive hydrogels for applications in biomimetics and soft robotics.
- Title: Microfiber-Shaped Programmable Materials with Stimuli-Responsive Hydrogel, Takeuchi Nobuki, Nakajima Shunsuke, Yoshida Koki, Kawano Ryuji, Hori Yutaka, Onoe Hiroaki （Soft Robotics） 9 （ 1 ） 89-97 Feb. 2022
・Research Objective: To analyze the robust instability margin of parametrized linear time-invariant systems and apply the findings to the repressilator in synthetic biology.
- Title: Instability margin analysis for parametrized LTI systems with application to repressilator, Hara Shinji, Iwasaki Tetsuya, Hori Yutaka （Automatica） 136 110047 Feb. 2022
■Optimization and Control Theory
・Research Objective: To propose an algebraic optimization approach for analyzing finite-time stability of resource-limited chemical reactions and to compute bounds on the duration of normal operation.
- Title: Finite-Time Stability Analysis for Resource Limited Chemical Reactions, Matsunaga Tomoki, Uemura Ryosuke, Hori Yutaka （IEEE Control Systems Letters） 5 （ 3 ） 815-820 Jul. 2021
・Research Objective: To propose mathematical optimization algorithms for determining the stability or instability of reaction-diffusion-advection systems using semidefinite programming.
- Title: Analysing diffusion and flow-driven instability using semidefinite programming, Hori Yutaka, Miyazako Hiroki （Journal of The Royal Society Interface） 16 （ 150 ） 20180586 Jan. 2019
・Research Objective: To analyze the robust stability of networked dynamical systems with generalized frequency variables and apply the findings to gene regulatory networks.
- Title: Robust stability analysis for LTI systems with generalized frequency variables and its application to gene regulatory networks, Hara Shinji, Iwasaki Tetsuya, Hori Yutaka （Automatica） 105 96-106 Jul. 2019
■Microfluidics and Chemical Modulation
Research Objective: The objective of this research is to develop theoretical and experimental platforms to analyze and design the dynamics of stochastic biomolecular reactions using feedback control theory, genetic engineering, and microfluidic devices.
Research Objective: The objective of this research is to develop both theoretical and experimental platforms to analyze and design the dynamics of stochastic biomolecular reactions by combining feedback control theory and genetic engineering.
■Stochastic and Molecular Systems
・Research Objective: To demonstrate the usefulness of phase change rate maximization in analyzing robust instability in multiagent systems and applying it to practical systems like magnetic levitation and repressilators.
- Title: Exact Instability Margin Analysis and Minimum-Norm Strong Stabilization—Phase Change Rate Maximization, Hara Shinji, Kao Chung-Yao, Khong Sei Zhen, Iwasaki Tetsuya, Hori Yutaka （IEEE Transactions on Automatic Control） 69 （ 4 ） 2084-2099 Apr. 2024
・Research Objective: To review fundamental theory and computational tools for the modeling, analysis, and design of stochastic biomolecular systems.
- Title: Modeling and Analysis of Stochastic Reaction Kinetics in Biomolecular Systems, Hori Yutaka （New Generation Computing） 38 （ 2 ） 367-377 May. 2020
・Research Objective: To propose a computationally tractable algebraic condition for analyzing Turing instability in molecular communication networks.
- Title: Semidefinite programming for Turing instability analysis in molecular communication networks, Hori Yutaka, Miyazako Hiroki （2019 IEEE 58th Conference on Decision and Control (CDC)） 1874-1880 Dec. 2019
■Biological Systems and Sensors
・Research Objective: To analyze the ability of cell-to-cell communication systems to attenuate impulsive disturbances with various spatial frequency profiles.
- Title: Disturbance response analysis of cell-to-cell communication systems based on spatial frequency decomposition, Kotsuka Taishi, Hori Yutaka （IFAC-PapersOnLine） 52 （ 26 ） 65-69
・Research Objective: To develop a computational framework for designing stochastic biocircuits with specified levels of intrinsic noise using statistical metrics.
- Title: Optimization-based synthesis of stochastic biocircuits with statistical specifications, Sakurai Yuta, Hori Yutaka （Journal of The Royal Society Interface） 15 （ 138 ） 20170709 Jan. 2018
・Research Objective: To uncover the mechanism for macrophages to acquire a stable response at high cell density through simulations of cell-cell communication via IFN-beta.
- Title: Time evolution of microenvironment around cells regulated by the secretion activity and culture density of the cells, Yamagishi Mai, Hori Yutaka, Uemura Sotaro, Ohara Osamu, Shirasaki Yoshitaka （2017 International Symposium on Micro-NanoMechatronics and Human Science (MHS)） 1-5 Dec. 2017
■Mechanical Systems and Actuators
・Research Objective: To develop a locally bendable stimuli-responsive hydrogel actuator with axially patterned functional materials using a valve-controlled microfluidic device.
- Title: Locally Bendable Stimuli-Responsive Hydrogel Actuator with Axially Patterned Functional Materials, Takeuchi Nobuki, Nakajima Shunsuke, Kawano Ryuji, Hori Yutaka, Onoe Hiroaki （2020 IEEE 33rd International Conference on Micro Electro Mechanical Systems (MEMS)） 243-244 Jan. 2020
■Signal Processing and Communication
・Research Objective: To propose a method for analyzing signal distortion in molecular communication channels using frequency response.
- Title: Analysis of Signal Distortion in Molecular Communication Channels Using Frequency Response, Kitada Shoichiro, Kotsuka Taishi, Hori Yutaka （New Generation Computing） 42 （ 2 ） 253-270 Jun. 2024
・Research Objective: To propose a method for analyzing the stability of large-scale multi-agent molecular communication systems using a system theoretic model and transfer functions.
- Title: Stability Analysis for Large-Scale Multi-Agent Molecular Communication Systems, Kotsuka Taishi, Hori Yutaka （IEEE Transactions on NanoBioscience） 23 （ 3 ） 507-517 Jul. 2024
・Research Objective: To propose a framework for analyzing the frequency response of one-dimensional molecular communication channels in bounded environments.
- Title: Frequency response of diffusion-based molecular communication channels in bounded environment, Kotsuka Taishi, Hori Yutaka （2022 European Control Conference (ECC)） 327-332 Jul. 2022
■Biological and Environmental Analysis
・Research Objective: To investigate how the co-existence of various macromolecules in cell-size spaces modulates protein localization and biochemical networks.
- Title: Multimolecular Competition Effect as a Modulator of Protein Localization and Biochemical Networks in Cell‐Size Space, Nishikawa Saki, Sato Gaku, Takada Sakura, Kohyama Shunshi, Honda Gen, Yanagisawa Miho, Hori Yutaka, Doi Nobuhide, Yoshinaga Natsuhiko, Fujiwara Kei （Advanced Science） 11 （ 6 ） Feb. 2024
・Research Objective: To analyze the collective behavior of dynamic multi-agent systems using graphical and analytical approaches under the generalized cyclic pursuit mechanism.
- Title: Graphical and Analytical Approaches for Analyzing Collective Behavior of Dynamic Multi-Agent Systems Governed by Generalized Cyclic Pursuit Mechanism, Kwak Taeheon, Kim Yeongjae, Hori Yutaka, Kim Tae-Hyoung （IEEE Access） 11 140481-140495
・Research Objective: To develop a mathematical model that predicts microalgal growth profiles based on light flux and medium concentration for effective cultivation planning.
- Title: A parametric logistic equation with light flux and medium concentration for cultivation planning of microalgae, Kambe Kazuki, Hirokawa Yasutaka, Koshi Asuka, Hori Yutaka （Journal of The Royal Society Interface） 19 （ 191 ） Jun. 2022
■Quantitative Handling of Uncertainty
・Research Objective: To propose a convex optimization approach for quantifying the steady state moments of molecular copy counts in stochastic chemical reactions.
- Title: A convex approach to steady state moment analysis for stochastic chemical reactions, Sakurai Yuta, Hori Yutaka （2017 IEEE 56th Annual Conference on Decision and Control (CDC)） 1206-1211 Dec. 2017

Areas of Research

・Control Engineering, Systems Engineering, Synthetic Biology, Molecular Robotics

Social Contributions

・Enhancing the design and analysis of molecular systems can accelerate innovations in biotechnology and medicine, leading to more efficient healthcare solutions.
・Improving the understanding and design of artificial biochemical systems in microorganisms can lead to significant advancements in synthetic biology, impacting various medical and industrial applications.