Laboratory for Physics
on Bio-inspired Intelligent Systems
In our laboratory, we define that “Life = Matter x Information” (life is a material system that has information and can manipulate information by itself), and we are working on the construction of intelligent molecular systems inspired by biological systems and the elucidation of their physical mechanisms, by combining physics, information science, biomolecular science, and nano- and micro-engineering, using wet experiments and computer simulations. In particular, we are working on the biophysics and nanotechnology of informational molecule ‘DNA’ and artificial cells.
DNA not only has a beautiful and symmetric double helix structure, but also has a robust structure. In addition, based on the base sequence information, we can change mechanical properties such as shape and hardness, and also can design chemical reactions and dynamic phase separation. Nowadays, the thermodynamic behavior of DNA double helix formation can be easily predicted by a computer. In addition to static structures, non-equilibrium and dynamic behavior, including chemical reactions, can be designed.
DNA is a unique material with distinctive molecular and informational properties that span multiple scales. Single-stranded DNA is a soft string that bends at about 1 nm, but in the case of a double-helix structure, it can be regarded as a rigid rod in 60 nm scale. Using DNA nanotechnology, we can make 1 μm-scale robust structures. In addition, chromosomal DNA is 1 m in its relaxed coiled state, but is compacted in a few micrometers in a cell nucleus. It is a condensed but fluidic and dynamic gel state. In addition to being able to accurately hold tens of thousands of genes and large amounts of information in that small amount of material, it is also possible to make nanocomputers and nanodevices using hybridization reactions of DNA. DNA is the embodiment of the concept that “Life = Matter x Information”.
Furthermore, cells are microscopic droplets (capsules) with fL to pL in volume. In such a small scale, the interfacial tension and surface charge of the droplet, molecular size and crowding effects, molecular fewness and fluctuations in chemical reactions, and strong nonlinearity and non-equilibrium nature of chemical reaction give important effects on the chemical reaction systems, which is usually not seen in mL-size test tubes. In such a complex system, the question of how a living system achieves stable, efficient, accurate molecular information processing based on chemical reaction is interesting from the biological science point of view, but it is an important issue from a physical and computer science point of view, when we try to build nanometer-sized molecular computers.
From this point of view, we have been actively studying the following researches in recent years. Through these studies, we would like to know higher-order biological information systems such as DNA and chromosomes as basic science research, and then we are trying to approach the question of what life is, in terms of the boundary between life and matter and in terms of the emergence of intelligence. Also, from an engineering point of view, We also challenge the construction of nanocomputers and nano-/micro-machines that surpass the functions of living systems.
・Construction of artificial cell nuclei (artificial chromosomes) using DNA nanotechnology
・Biophysical research such as quantitative analysis of RNA using an artificial chromatin model, a mathematical model of chromosome phase separation, and reconstruction experiments
・Coarse-grained molecular dynamics simulation of DNA gels and DNA droplets
・Sequence design of DNA gel by reinforcement learning
・Construction of molecular computers and molecular memory with digital-molecular information conversion
・Construction of cell-like molecular robots based on DNA nanostructures
・Development of molecular robots that mimic macrophages (immune cells)
・Spontaneous ratchet transport of micro-materials using nanomicelle charging and particle crowding effect
・Computer-aided control of artificial cell reactors
・Tiny non-equilibrium open reactors
Please refer to the following pages for more information on our research achievements.
Molecular reactions are the basis of information processing in living systems. Therefore, if information processing systems can be created by molecular reactions, the secrets of information processing and autonomy of life may be revealed. We are constructing molecular computers by designing DNA sequences and cellular molecular robots integrating multiple elements.
The smallest unit of an organism is a cell, which is an ultramicrovessel made of a membrane called a cell membrane. We aim to understand the physics of living systems by constructing artificial cell models that mimic cell functions, as well as constructing microreactors that mimic cells.
Biopolymers and colloidal particles such as DNA/RNA, proteins, and lipids are classified into a group of materials called soft matter. In addition to elucidating the properties of soft matter, we are studying hybrid systems between electricity and electric systems, and active matter such as spontaneous collective transport phenomena of particles.