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General aim of our research

We study the fundamental principles of living systems from the perspective of non-equilibrium physics and its potential applications in biology and related chemistry. Viewing living systems through a physics lens, we can perceive them as the most intricate chemical systems in nature. These systems derive chemical energy from gradients of ions or other energy materials and govern reactions at interfaces with multifaceted functionalities. Understanding such biological soft matter, endowed with unique physical properties, and orchestrating their functions, encompassing microscopic transport and autonomous motion, constitutes a pivotal challenge at the interface of physics and biology.

Non-equilibrium Soft Matter and Active Matter

Atoms and molecules move along a gradient of external fields as seen in electrophoresis, which is a motion of charged molecules relative to fluid along an electric field. One unexplored but relevant alternative is thermophoresis, the Soret effect, which makes a solute move along a temperature gradient. Thermophoresis has great potential in biology, especially from the origin of life problems to the pattern formation of molecules. We study trapping and selection of molecules that could be physically feasible in a simple way relying on temperature gradient. Selection of RNA via temperature gradient might be relevant to molecular evolution at the origin of life: Separation of RNA from the large library of RNA world might occur at the thermal vent of the deep ocean where a large temperature gradient is present.

Furthermore, molecular motors form functional complexes with the cytoskeleton to create cellular functions that would be unexpected from a single molecule dynamics. Understanding the physics of these autonomously moving elements, called active matter, is essential to understanding the principles of structure and dynamics at multicellular tissue scale. We study collective motion and its emergent order in high-density suspensions of bacteria and cytoskeletal microtubule/actin filaments driven by motor proteins as representative examples of active matter. Our primary focus is a peculiar class of active matter, stimulated from the lower scales, that exhibits turbulence-like structures (i.e. active turbulence). Growing attention is paid to controlling collective motion and its application for microfluidics.

Selected publications

Synthetic Biology and Artificial Cell Engineering

It is important not only to understand nonequilibrium phenomena that occur under out-of-equilibrium but also to address design principle of autonomous reactor capable of genetically-encoded protein expression, self-organization and eventually self-reproduction. In the last century. the top-down approach based on molecular biology has revealed that molecular networks underlying in many cellular systems. However, its design principle is still elusive, as the top-down approach does not provide the physical understanding of cellular basis. To overcome this bottleneck, we develop the study of artificial cells made of molecular components and lipid membrane as emerging platforms to characterize, by construction, the properties of living systems. Cell-free transcription-translation (TXTL) system offers several advantages for the bottom-up synthesis of cellular reactors. Scaling up their design within well- defined geometries remains challenging. We build a microfluidic system hosting TXTL reactions of a single reporter gene in thousands of microwells separated from an external buffer by a phospholipid membrane.

For engineering aspects, symmetry and symmetry breaking are fundamental concepts that form the basis not only in condened matter physics but also in biological phenomena. In cell migration and division, polarity is created in spherical cells and spontaneous symmetry breaking occurs. This process is regulated by a complex of cytoskeletal proteins and molecular motor proteins. However, the mechanism is not well understood from a mechanistic viewpoint. We adopt a bottom-up approach to create “artificial cells” as a simplified model of living cells, allowing us to control cell size, protein concentration, and cell membrane molecules, which is challenging in living cells. This strategy allows us to reconstruct the self-organization process of the cytoskeletal actin network, from continuous flow to periodic wave of active cytoskeletal networks, within cell-sized spaces.

Selected publications