Physical and Chemical Computing & Molecular Intelligence

We are conducting research on “physical and chemical computing,” a new computational method that uses not only electronic computers but also materials, physical systems, and natural phenomena such as molecules, particles, fluids, quantum, and living organisms. We are pioneering new computational principles such as the development of nano-sized molecular computers working in living organisms and molecular programming methods. For example, a molecular computer based on DNA computation reads information on a one-dimensional tape called a DNA sequence, and changes in the nanostructure of DNA are state transitions that can be computed, as well as spatio-temporal pattern formation through chemical reactions. A biochemical reaction network in a cell can be regarded as a calculation based on a molecular reaction circuit. In other words, the living system itself can be considered a kind of computer. The molecular reaction procedures to realize these reactions are a kind of algorithm, also called molecular programming, which is a design theory of information processing mechanisms at the molecular level.

We are also conducting research on “physical and chemical simulations,” in which materials, physical systems, and natural phenomena are simulated on electronic computers. With respect to systems such as molecular reactions, genetic circuits, complex fluids, self-driven particles, gels, and soft micromachines, we also aim to pioneer multi-physics simulations in which chemical reactions and physical phenomena are coupled. Systems such as molecular motion, chemical reactions, and DNA logic circuits can be modeled by systems of differential equations, and their behavior can be predicted and designed by simulation on a computer. Multiphysics simulation is useful in a variety of situations ranging from nanotechnology to bio-medical, agri- and eco-applications.

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(1) Physical and chemical simulation and numerical computation (molecular simulation, Monte Carlo simulation, fluid simulation, chemical reaction simulation, complex system simulation, ALife/Boid/Cellular Automata); (2) Molecular computing, molecular programming, DNA Computing, DNA Logic Circuits, Natural Computing, Biocomputing, Artificial Molecular Intelligence, Soft Robotics; (3) Bioinformatics

Synthetic Biology & Molecular Robotics

Understanding how living systems are created from non-living materials is undoubtedly an important open question not only in life science but also in material science. Therefore, by constructing primitive cell models that mimic cells, the smallest unit of living organisms, and artificial cells that adapt to their environment and evolve, we are trying to understand “what is life? and to pioneer the field of biophysics of ʻorganismsʼ not existing in nature, which explores possible life. While the conventional elemental reduction approach alone cannot provide insight into the behavior of an entire system in which life is life, the constructivist approach can be used to understand such phenomena. We also use cellular models to explore how robust biological information processing can be realized from fluctuating intracellular reactions.

Furthermore, by making full use of DNA nanotechnology (DNA gel, DNA oligomers), we aim to construct cell-mimetic molecular robots that can perform diagnostic and therapeutic procedures inside the body. Recently, we have focused on DNA droplets, which are a new state of DNA nanostructure assembly, and are constructing dynamic artificial cells and molecular robots based on their liquid-liquid phase separation behavior. For example, a DNA droplet computer that can diagnose diseases. In addition to these, we are also developing microreactors to perform genetic engineering and chemical analysis with high precision and efficiency.

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(1) primitive cell models, artificial cell construction, wet artificial life (Wet ALife), artificial living systems, origin of life, phase separation biology, biophysics of ʻorganismsʼ not existing in nature; (2) DNA nanotechnology, RNA nanotechnology, molecular robotics, DNA gel, DNA droplet, DNA oligami; (3) microreactor, μTAS, chemical chip, molecular sensor, bioMEMS

Biophysics & Living Soft Matter Physics

Biopolymers (biomacromolecules) and colloidal particles such as DNA/RNA, proteins, lipids, etc., which compose living systems, are called soft matter. Since they are soft, large, and having multiple degrees of freedom, they exhibit rich physical properties. An interesting point is that they can use the informatics space in addition to the physical-chemical space because they have information. It is also known that the ability to adapt to the environment, self-repair, self-replication, and evolution, which are origins of the nature of living systems, cannot be realized by simply mixing molecules, but can only be realized in a non-equilibrium open system, in which the flow of energy, matter, and information is appropriately controlled and molecular reactions are organically coordinated. However, research is still in its infancy. Therefore, we are exploring the formation of informative soft matter and hierarchical self-organization in non-equilibrium systems, as well as research on active matter, such as control by external fields such as electric fields, and autonomous motion and collective transport phenomena through coupling with energy metabolism by chemical reactions. We are also developing micromachines and soft robots based on these findings.
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(1) active matter, soft matter, microfluidics, biophysics; (2) non-equilibrium open systems, spatio-temporal order formation, self-organization; (3) electrical/chemical hybrids, intelligent systems, soft robotics