Laboratory of Physical Ethology

Analysis of behaviors of protists and lower organisms 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.
(9) Ethological dynamics in diorama environments (

Laboratory of Physical Ethology (pdf)

Practical Subjects



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

Representative Publications

A. Taniguchi†, Y. Nishigami†, H. Kajiura-Kobayashi, D. Takao, D. Tamaoki, T. Nakagaki, S. Nonaka, S. Sonobe (†equally contributed): ”Light-sheet microscopy reveals dorsoventral asymmetric membrane dynamics of Amoeba proteus during pressure-driven locomotion”, Biology Open, 12, bio059671 (2023)

S. Echigoya, K. Sato, O. Kishida, T. Nakagaki, Y. Nishigami† (†corresponding author): ”Switching of behavioral modes and their modulation by a geometrical cue in the ciliate Stentor coeruleus”, Frontiers in Cell and Developmental Biology, 10, 1021469 (2022)

T. Aoki, N. Fujiwara, M. Fricker, T. Nakagaki: “A model for simulating emergent patterns of cities and roads on real-world landscape”, Scientific Reports, 12:10093, pp.1-12 (2022) DOI: 10.1038/s41598-022-13758-1

S. Kuroda, N. Uchida, T. Nakagaki: “Gait switching with phase reversal of locomotory waves in the centipede Scolopocryptos rubiginous”, Bioinspiration & Biomimetics, 17(2), 026005 (2022),

K. Matsumoto, Y. Nishigami, T. Nakagaki: “Binocular stereomicroscopy for deforming intact amoeba”, Optics Express, 30(2), 2424-2437(2022)

S. Okuda, K. Sato: “Polarized interfacial tension induces collective migration of cells, as a cluster, in a 3D tissue”, Biophysical Journal 121(10), 1856-1867(2022) DOI: 10.1016/j.bpj.2022.04.018

T. Ohmura, Y. Nishigami, A. Taniguchi, S. Nonaka, T. Ishikawa, M. Ichikawa: “Near-wall rheotaxis of the ciliate Tetrahymena induced by the kinesthetic sensing of cilia”, Science Advances, 7 (43), abi5878 (2021)

C. Gao, C. Liu, D. Schenz, X. Li, Z. Zhang, M. Jusup, Z. Wang, M. Beekman and T. Nakagaki: “Does being multi-headed make you better at solving problem? A survey of Physarum-based models and computations”, Physics of Life Reviews, Vol. 29, 1-26 (2019)

D. Schenz,Y. Nishigami, K. Sato, T. Nakagaki: “Uni-cellular integration of complex spatial information in slime moulds and ciliates”, Current Opinion in Genetics & Development, 57, 78-83 (2019) DOI: 10.1016/j.gde.2019.06.012

S. Daniel, S. Yasuaki, S. Kuroda, T. Nakagaki and K. Ueda : “A mathematical model for adaptive vein formation during exploratory migration of Physarum polycephalum: routing while scouting”, Journal of Physics: Applied Physics, 50 : 434001(14pp)- (2017)

S. Kuroda, S. Takagi, T. Saigusa and T. Nakagaki : “Physical ethology of unicellular organism”,Brain evolution by design -From Neural origin to cognitive architecture- (Ed. by S. Shigeno, Y. Murakami, T. Nomura) ISBN: 978-4-431-56467-6, Springer-Verlag : 3-23 (2017)

D. Akita, I. Kunita, M. D. Fricker, S. Kuroda, K. Sato and T. Nakagaki : “Experimental models for Murray’s law”, J. Phys. D: Appl. Phys., Vol. 50, 024001(11pp) (2017).