Laboratory of Physical Ethology

Analysis of behaviors of protozoa and lower organism by physico-mathematical science
Research Theme
Searching for an elementary algorithm of behavioral intelligence that may be common from amoeba to human/ Biophysical study on amoeboid and ciliary movement/Study on active soft matter in relation to bio-mechanics
Research Keywords

ciliate, amoeba, slime mold, protozoa, nematode, live cell imaging, field work, evolutionary ecology, biomechanics, locomotion, memory and learning, mathematical modeling, computer simulation, nonlinear dynamics, active soft matter, Belousov-Zhabotinski reaction, pattern formation, scaling theory, network of biochemical reactions


Overview of Research and Education

Research Field: Physical ethology
Education Field: Soft Matter Biophysics
Research Contents: Soft matter physics that deals with soft and largely deformable materials is a necessary tool for mechanical understanding of motion, deformation and growth of biological systems such as cells, tissues and organisms. Based on these ideas, we are investigating characteristic and functional behaviors of various biological systems, by inventing unique experimental setup. Explicit themes in our lab are as follows.
(1) Ethology of protozoa (slime molds, ciliates, amoebae, etc.).
(2) Biophysical study on intracellular regulation of amoeboid and ciliary movement.
(3) Rheology of solutions of biopolymers such as actin filaments and microtubules.
(4) Animal behavior and biomechanics of nematodes.
(5) Mechanics of peristaltic crawling of snails and earthworms.
(6) Mechanical properties and functions of trees and bones.
(7) Mechanical modeling for development of multicellular organisms.
(8) Shape, function and development of transport networks in slime mold and the other living systems.



Research Institute for Electrical Science
N20 W10, Kita-ku, Sapporo, Japan
nakagaki* replace*with @ when sending e-mail.)

Representative Publications

T. Ohmura, Y. Nishigami†, A. Taniguchi, S. Nonaka, J. Manabe, T. Ishikawa, M. Ichikawa, Simple mechanosense and response of ciliate motion reveal the intrinsic habits of ciliates, Proc. Natl. Acad. Sci. USA, 115, 3231 (2018)

Nishigami, T. Ohmura, A. Taniguchi, S. Nonaka, J. Manabe, T. Ishikawa, M. Ichikawa, Influence of cellular shape on sliding behavior of ciliates, Commun. Integr. Biol., 11, e1506666 (2018)

Sato, I. Kunita, Y. Takikawa, D. Takeuchi, Y. Tanaka, T. Nakagaki and H. Orihara, Direct observation of orientation distributions of actin filaments in a solution undergoing shear banding, Soft Matter, 13, 2708-2716 (2017).

Akita,D., Kunita, I. Fricker, M. D., Kuroda, S., Sato, K., Nakagaki,T., Experimental models for Murray’s Law, J. Phys. D: Appl. Phys., 50, 024001 (2016)

Kunita,I., Yamaguchi,T., Tero,A., Akiyama,M., Kuroda,S., Nakagaki,T., A ciliate memorizes the geometry of a swimming arena, J. R. Soc. Interface 13: 20160155 (2016)

Sato, K., Hiraiwa, T., Maekawa, E., Isomura, A., Shibata, T. & Kuranaga, E., Left-right asymmetric cell intercalation drives directional collective cell movement in epithelial morphogenesis, Nat Commun. 6, 10074 (2015).

Sato, K., Hiraiwa, T. & Shibata, T., Cell Chirality Induces Collective Cell Migration in Epithelial Sheets, Phys. Rev. Lett., 115, 188102, (2015).