Nakakuki Laboratory
Kyushu Institute of Technology
Research
From Molecules to Organs — Understanding and Engineering Biological Systems
We explore biological systems across multiple scales, from molecular information processing to inter-organ networks. Control theory provides a common framework for modeling, analysis, and the design of these complex dynamical systems.
Research Approach
We view biological phenomena as dynamic systems governed by interactions among molecules, cells, and organs, with control theory as a common foundation. Through mathematical modeling, we analyze their dynamics and control principles and apply these insights to molecular information processing and biological control.
By integrating modeling, analysis, design, and control with simulations, data analysis, and molecular experiments, we seek common principles across biological scales and translate them into new applications.
Molecular Computing
Opening New Possibilities in Life Science through DNA- and RNA-Based Information Processing
DNA and RNA do more than store genetic information. By exploiting molecular binding and reaction dynamics, they can perform information-processing functions such as detection, decision-making, amplification, memory, and control. We design molecular circuits using mechanisms such as DNA strand displacement and analyze their dynamic behavior through both mathematical modeling and experiments.
Our goal goes beyond proof-of-concept demonstrations. We aim to develop molecular information-processing systems into practical technologies for high-sensitivity diagnostics, biosensing, autonomous molecular systems, and molecular robotics, with real-world applications in mind.
DNA Computing and Molecular Circuits
We design molecular circuits based on DNA strand-displacement reactions that perform computation and decision-making in response to molecular inputs. By incorporating concepts from control theory and dynamical systems, we are developing methodologies for predicting and designing complex molecular reaction networks.
Molecular Sensing and Diagnostic Applications
We develop molecular sensing technologies for biomolecules such as miRNAs by combining target recognition, signal amplification, and suppression of false detection. Our goal is to translate the principles of molecular computing into practical diagnostic and biosensing technologies.
Molecular Memory and Autonomous Molecular Systems
We study molecular memory and autonomous systems that retain past information and dynamically adapt their responses to environmental changes. Using programmable molecular reactions, we aim to reproduce advanced biological information-processing functions such as learning, memory, and forgetting.
Systems Biology and Control Theory
Understanding Biological Networks from Molecules and Cells to Organs through Mathematics:
Biological functions and diseases do not arise from a single molecule or organ alone, but from interactions among molecules, cells, tissues, and organs. We view these as dynamic networks and use mathematical models, simulations, data analysis, and control theory to uncover their behavior and the mechanisms underlying disease development.
We also aim to detect subtle changes that appear before disease onset for ultra-early diagnosis, and to develop new control and therapeutic strategies for guiding complex biological systems toward desirable states.
Inter-organ Networks
We develop mathematical models of how the liver, skeletal muscle, adipose tissue, the central nervous system, and other organs exchange information to maintain homeostasis. From a multiscale perspective, we study how inter-organ interactions contribute to metabolism and disease development.
Control and Learning of Biological Systems
We study control methods for large-scale biological systems consisting of multiple cells and organs using feedback control, optimization, reinforcement learning, and mean-field games. Our goal is to develop new control strategies that account not only for individual components, but also for the collective behavior of populations and networks.
From Fundamental Research to Real-World Implementation
We pursue a continuous research process, from uncovering the fundamental principles of biological systems to designing mathematical models and molecular circuits, validating them through experiments and data, and ultimately developing technologies that can benefit society. By integrating control theory, mathematical modeling, computer science, and molecular biology, we advance our research through close interaction between theory and experiment.
In molecular computing, we aim to move beyond proof-of-concept studies toward real-world implementation in areas such as diagnostics, biosensing, and autonomous molecular systems. In systems biology and control, we seek to translate our understanding of biological systems into ultra-early disease detection and new strategies for control and therapy.
Projects and Collaborations
We collaborate with research institutions and companies, pursuing a broad range of activities from fundamental research to real-world implementation.
Moonshot Goal 2:
A large-scale research program aiming for ultra-early prediction and prevention of disease
Molecular Explorer: A research project advancing the design and exploration of molecular robots
PARKS:
Supports the commercialization of university-based deep-tech innovations
Meisenkai:
An alumni organization supporting education and research at Kyushu Institute of Technology
KAKENHI: Competitive research funding supporting original and innovative academic research
Research Achievements
Please visit our Researcher Database for a complete list of publications and research activities.