Nakagaki Toshiyuki
| Research Institute for Electronic Science Research Center of Mathematics for Social Creativity | Professor |
| Research Institute for Electronic Science Green Nanotechnology Research Center | Professor |
| Center for Human Nature Artificial Intelligence and Neuroscience | Professor |
Last Updated :2025/07/05
■Researcher basic information
Degree
Profile Information
Toshiyuki Nakagaki is a professor of Mathematical and Physical Ethology in Research Center of Mathematics for Social Creativity, Research Institute for Electronic Science (RIES), Hokkaido University (Sapporo, Japan). Currently he is director of RIES. He graduated from Faculty of Pharmaceutical Science, Hokkaido University (Bachelor in 1987, Master in 1989) and worked in Pfizer Inc. (Central Research Center, Nagoya, Japan) for 5 years. After quitting the job in Pfizer Inc., he entered Nagoya University (Graduate School of Human Informatics) and got a Ph.D in biophysics in 1997 while working as a part-time teacher in a correspondence high school. The thesis title was ‘Amoeboid cell behaviors based on self-organization of nonlinear chemical oscillators’. His post-doc research was done in Bio-mimetic Control Research Center, RIKEN institute, Japan and a study on ‘maze-solving by an amoeba’ was published. He became an associate professor in Hokkaido University in 2000 and conducted an experimental and mathematical study on how an amoeba of slime mold designed multi-functional transport network. After being a professor in Faculty of Complex and Intelligent Systems, Future University Hakodate in 2010, he came to his current position in 2013.
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Educational Organization
- Master's degree program, Graduate School of Life Science
- Doctoral (PhD) degree program, Graduate School of Life Science
■Career
Career
- Oct. 2013 - Present
Hokkaido University, Research Institute for Electronic Science, professor - Apr. 2017 - Mar. 2021
Hokkaido University, Research Institute for Electronic Science, Director, Japan - Apr. 2010 - Sep. 2013
Future University Hakodate, Faculty of Systems Information Science, professor - Nov. 2000 - Mar. 2010
Hokkaido University, Research Institute for Electronic Science, associate professor - Apr. 2000 - Oct. 2000
RIKEN Institute, Frontier Post-doc researcher - Apr. 1997 - Mar. 2000
RIKEN Institute, Bio-Mimetic Control Research Center, Special Post-doc researcher for Basic Science - Apr. 1995 - Mar. 1997
Aichi KYOKURYO correspondence high school, part-time teacher - Apr. 1989 - May 1994
Pfizer Inc., Central Research Center Nagoya, scientist
Educational Background
Position History
■Research activity information
Awards
Papers
- Measurement of protoplasmic streaming over the entire body of Physarum plasmodium, and estimation of the transport and mixing of protoplasma through the intricate vein network
Yo Sato, Charles Fosseprez, Yukinori Nishigami, Katsuhiko Sato, Hiroshi Orihara, Toshiyuki Nakagaki
Biophysics and Physicobiology, 22, 1, e220002, Biophysical Society of Japan, 2025, [Last author, Corresponding author], [Domestic magazines]
English, Scientific journal, Transport networks spanning the entire body of an organism are key infrastructures for achieving a functional system and facilitating the distribution of nutrients and signals. The large amoeba-like organism Physarum polycephalum has gained attention as a useful model for studying biological transport networks owing to its visible and rapidly adapting vein structure. Using particle-tracking velocimetry, we measured the flow velocity of protoplasmic streaming over the entire body of Physarum plasmodia during the development of its intricate vein network. Based on these measurements, we estimated how the protoplasm is transported and mixed throughout the body. Our findings suggest that the vein network significantly enhances effective mixing of the protoplasm throughout the organism, which may have important physiological implications for nutrient distribution and signaling. - Dynamics of centipede locomotion revealed by large-scale traction force microscopy
J. P. Rieu, H. Delanoë-Ayari, C. Barentin, T. Nakagaki, S. Kuroda
Journal of Royal Society Interface, 21, 20230439, 20230450, May 2024, [Peer-reviewed]
English, Scientific journal - Cellular Ethological Dynamics in Diorama Environments
Yukinori Nishigami, Itsuki Kunita, Katsuhiko Sato, Toshiyuki Nakagaki
Journal of the Physical Society of Japan, 15 Dec. 2023, [Peer-reviewed], [Last author, Corresponding author]
Scientific journal - Caenorhabditis elegans transfers across a gap under an electric field as dispersal behavior.
Takuya Chiba, Etsuko Okumura, Yukinori Nishigami, Toshiyuki Nakagaki, Takuma Sugi, Katsuhiko Sato
Current biology : CB, 33, 13, 2668, 2677, 14 Jun. 2023, [Peer-reviewed], [International Magazine]
English, Scientific journal, Interactions between different animal species are a critical determinant of each species' evolution and range expansion. Chemical, visual, and mechanical interactions have been abundantly reported, but the importance of electric interactions is not well understood. Here, we report the discovery that the nematode Caenorhabditis elegans transfers across electric fields to achieve phoretic attachment to insects. First, we found that dauer larvae of C. elegans nictating on a substrate in a Petri dish moved directly to the lid through the air due to the electrostatic force from the lid. To more systematically investigate the transfer behavior, we constructed an assay system with well-controlled electric fields: the worms flew up regardless of whether a positive or negative electric field was applied, suggesting that an induced charge within the worm is related to this transfer. The mean take-off speed is 0.86 m/s, and the worm flies up under an electric field exceeding 200 kV/m. This worm transfer occurs even when the worms form a nictation column composed of up to 100 worms; we term this behavior "multiworm transfer." These observations led us to conclude that C. elegans can transfer and attach to the bumblebee Bombus terrestris, which was charged by rubbing with flower pollen in the lab. The charge on the bumblebee was measured with a coulomb-meter to be 806 pC, which was within the range of bumblebee charges and of the same order of flying insect charges observed in nature, suggesting that electrical interactions occur among different species. - Light-sheet microscopy reveals dorsoventral asymmetric membrane dynamics of Amoeba proteus during pressure-driven locomotion
Atsushi Taniguchi, Yukinori Nishigami, Hiroko Kajiura-Kobayashi, Daisuke Takao, Daisuke Tamaoki, Toshiyuki Nakagaki, Shigenori Nonaka, Seiji Sonobe
Biology Open, 12, 2, 30 Jan. 2023, [Peer-reviewed], [International Magazine]
English, Scientific journal, Amoebae are found all around the world and play an essential role in the carbon cycle in the environment. Therefore, the behavior of amoebae is a crucial factor when considering the global environment. Amoebae change their distribution through amoeboid locomotion, which are classified into several modes. In the pressure-driven mode, intracellular hydrostatic pressure generated by the contraction of cellular cortex actomyosin causes the pseudopod to extend. During amoeboid locomotion, the cellular surface exhibits dynamic deformation. Therefore, to understand the mechanism of amoeboid locomotion, it is important to characterize cellular membrane dynamics. Here, to clarify membrane dynamics during pressure-driven amoeboid locomotion, we developed a polkadot membrane staining method and performed light-sheet microscopy in Amoeba proteus, which exhibits typical pressure-driven amoeboid locomotion. It was observed that the whole cell membrane moved in the direction of movement, and the dorsal cell membrane in the posterior part of the cell moved more slowly than the other membrane. In addition, membrane complexity varied depending on the focused characteristic size of the membrane structure, and in general, the dorsal side was more complex than the ventral side. In summary, the membrane dynamics of Amoeba proteus during pressure-driven locomotion are asymmetric between the dorsal and ventral sides. This article has an associated interview with the co-first authors of the paper. - Editorial: Ethological dynamics in diorama environments.
Toshiyuki Nakagaki, Audrey Dussutour, Laurence Wilson, Takuji Ishikawa
Frontiers in cell and developmental biology, 11, 1347957, 1347957, 2023, [Lead author], [International Magazine]
English - Switching of behavioral modes and their modulation by a geometrical cue in the ciliate Stentor coeruleus
Syun Echigoya, Katsuhiko Sato, Osamu Kishida, Toshiyuki Nakagaki, Yukinori Nishigami
Frontiers in Cell and Developmental Biology, 10, 1021469, 1021469, 01 Nov. 2022, [Peer-reviewed], [International Magazine]
English, Scientific journal, Protists ubiquitously live in nature and play key roles in the food web chain. Their habitats consist of various geometrical structures, such as porous media and rigid surfaces, affecting their motilities. A kind of protist, Stentor coeruleus, exhibits free swimming and adhering for feeding. Under environmental and culture conditions, these organisms are often found in sediments with complex geometries. The determination of anchoring location is essential for their lives. However, the factors that induce the behavioral transition from swimming to adhering are still unknown. In this study, we quantitatively characterized the behavioral transitions in S. coeruleus and observed the behavior in a chamber with dead ends made by a simple structure mimicking the environmental structures. As a result, the cell adheres and feeds in narrow spaces between the structure and the chamber wall. It may be reasonable for the organism to hide itself from predators and capture prey in these spaces. The behavioral strategy for the exploration and exploitation of spaces with a wide variety of geometries in their habitats is discussed. - A model for simulating emergent patterns of cities and roads on real-world landscapes.
Takaaki Aoki, Naoya Fujiwara, Mark Fricker, Toshiyuki Nakagaki
Scientific reports, 12, 1, 10093, 10093, 16 Jun. 2022, [Last author], [International Magazine]
English, Scientific journal, Emergence of cities and road networks have characterised human activity and movement over millennia. However, this anthropogenic infrastructure does not develop in isolation, but is deeply embedded in the natural landscape, which strongly influences the resultant spatial patterns. Nevertheless, the precise impact that landscape has on the location, size and connectivity of cities is a long-standing, unresolved problem. To address this issue, we incorporate high-resolution topographic maps into a Turing-like pattern forming system, in which local reinforcement rules result in co-evolving centres of population and transport networks. Using Italy as a case study, we show that the model constrained solely by topography results in an emergent spatial pattern that is consistent with Zipf's Law and comparable to the census data. Thus, we infer the natural landscape may play a dominant role in establishing the baseline macro-scale population pattern, that is then modified by higher-level historical, socio-economic or cultural factors. - Dynamic Control of Microbial Movement by Photoswitchable ATP Antagonists
Sampreeth Thayyil, Yukinori Nishigami, Md. Jahirul Islam, P. K. Hashim, Ken'ya Furuta, Kazuhiro Oiwa, Jian Yu, Min Yao, Toshiyuki Nakagaki, Nobuyuki Tamaoki
Chemistry – A European Journal, 28, 30, e202200807, Wiley, 25 May 2022, [Peer-reviewed], [International Magazine]
English, Scientific journal, Adenosine triphosphate (ATP) is the energy source for various biochemical processes and biomolecular motors in living things. Development of ATP antagonists and their stimuli-controlled actions offer a novel approach to regulate biological processes. Herein, we developed azobenzene-based photoswitchable ATP antagonists for controlling the activity of motor proteins; cytoplasmic and axonemal dyneins. The new ATP antagonists showed reversible photoswitching of cytoplasmic dynein activity in an in vitro dynein-microtubule system due to the trans and cis photoisomerization of their azobenzene segment. Importantly, our ATP antagonists reversibly regulated the axonemal dynein motor activity for the force generation in a demembranated model of Chlamydomonas reinhardtii. We found that the trans and cis isomers of ATP antagonists significantly differ in their affinity to the ATP binding site. - Gait switching with phase reversal of locomotory waves in the centipede Scolopocryptops rubiginosus
Shigeru Kuroda, Nariya Uchida, Toshiyuki Nakagaki
Bioinspiration and Biomimetics, 17, 2, 026005, 026005, IOP Publishing, 01 Mar. 2022, [Last author], [International Magazine]
English, Scientific journal,Abstract
Crawling using locomotory waves is a common method of locomotion for limbless and many-legged invertebrates and stimulates the biomimetic engineering of flexible locomotion. It is generally believed that the direction of locomotory waves is fixed for a given species. However, we found that a centipede,Scolopocryptops rubiginosus , flexibly generated its gait to allow for locomotory waves that varied in direction, depending on (i) locomotion speed and (ii) the physical conditions of terrain. We also found a new type of centipede’s swimming gait unlike eel-like way known so far which is using posteriorly traveling waves of horizontal body undulation. The gait patterns of the centipede were examined in various conditions and analyzed how the waves switched in detailed. We showed that gait patterns were associated with control of stride length rather than stride frequency. Discussion was made on a possible scenario of the gait transition in the centipede compatible with our observations. This finding may give a hint at bio-inspired control of flexible gait switching in response to irregular terrain. - Binocular stereo-microscopy for deforming intact amoeba
Kenji Matsumoto, Yukinori Nishigami, Toshiyuki Nakagaki
Optics Express, 30, 2, 2424, 2437, The Optical Society, 17 Jan. 2022, [Peer-reviewed], [Last author], [International Magazine]
English, Scientific journal, A powerful and convenient method for measuring three-dimensional (3D) deformation of moving amoeboid cells will assist the progress of environmental and cytological studies as protists amoebae play a role in the fundamental environmental ecosystem. Here we develop an inexpensive and useful method for measuring 3D deformation of single protists amoeba through binocular microscopy and a newly proposed algorithm of stereo-scopy. From the movies taken from the left and right optical tubes of the binocular microscope, we detect the 3D positions of many intrinsic intracellular vesicles and reconstruct cellular surfaces of amoeboid cells in 3D space. Some observations of sampled behaviors are shown in a single-celled organism of Amoeba proteus. The resultant surface time series is then analyzed to obtain surface velocity, curvature and volume increasing rates of pseudo-pods for characterizing the movements of amoeboid cells. The limitations and errors of this method are also discussed. - Thermal Conductivity and Thermal Diffusivity of Slime Mold (Physarum Polycephalum)
Syou Maki, Shigeru Kuroda, Seiji Fujiwara, Seiichi Tanaka, Eka Erzalia, Mizuki Kato, Katsumasa Higo, Toshiaki Arata, Toshiyuki Nakagaki
Biomedical Journal of Scientific & Technical Research, 31, 3, 24140, 24145, Biomedical Research Network, LLC, 22 Oct. 2020, [Peer-reviewed], [Last author]
English, Scientific journal - Uni-cellular integration of complex spatial information in slime moulds and ciliates
Daniel Schenz, Yukinori Nishigami, Katsuhiko Sato, Toshiyuki Nakagaki
Current Opinion in Genetics and Development, 57, 78, 83, Aug. 2019, [Peer-reviewed], [Last author, Corresponding author], [International Magazine]
English, Scientific journal - Dynamic gait transition in theScolopendromorpha scolopocryptops rubiginosus L. Kochcentipede
Shigeru Kuroda, Nariya Uchida, Toshiyuki Nakagaki
Cold Spring Harbor Laboratory, May 2018, [Last author] - モジホコリ
高木 清二, 佐藤 勝彦, 中垣 俊之
生物工学, 96, 8, 488, 492, 2018, [Invited], [Last author]
Japanese, Research society - Does being multi-headed make you better at solving problems? A survey of Physarum-based models and computations
Chao Gao, Chen Liu, Daniel Schenz, Xuelong Li, Zili Zhang, Marko Jusup, Zhen Wang, Madeleine Beekman, Toshiyuki Nakagaki
Physics of Life Reviews, 29, 1, 26, Elsevier B.V., 2018, [Peer-reviewed], [Last author], [International Magazine]
English, Scientific journal - A mathematical model for adaptive vein formation during exploratory migration of Physarum polycephalum: routing while scouting
Daniel Schenz, Yasuaki Shima, Shigeru Kuroda, Toshiyuki Nakagaki, Kei-Ichi Ueda
JOURNAL OF PHYSICS D-APPLIED PHYSICS, 50, 43, 434001, Nov. 2017, [Peer-reviewed]
English, Scientific journal - Behavioural differentiation induced by environmental variation when crossing a toxic zone in an amoeba
Itsuki Kunita, Kei-Ichi Ueda, Dai Akita, Shigeru Kuroda, Toshiyuki Nakagaki
JOURNAL OF PHYSICS D-APPLIED PHYSICS, 50, 35, 354002, Sep. 2017, [Peer-reviewed], [Last author]
English, Scientific journal - Response to various periods of mechanical stimuli in Physarum plasmodium
Takuya Umedachi, Kentaro Ito, Ryo Kobayashi, Akio Ishiguro, Toshiyuki Nakagaki
JOURNAL OF PHYSICS D-APPLIED PHYSICS, 50, 25, Jun. 2017, [Peer-reviewed], [Last author]
English, Scientific journal - Current reinforcement model reproduces center-in-center vein trajectory of Physarum polycephalum
Dai Akita, Daniel Schenz, Shigeru Kuroda, Katsuhiko Sato, Kei-ichi Ueda, Toshiyuki Nakagaki
DEVELOPMENT GROWTH & DIFFERENTIATION, 59, 5, 465, 470, Jun. 2017, [Peer-reviewed], [Last author, Corresponding author], [Domestic magazines]
English, Scientific journal - Automated analysis of Physarum network structure and dynamics
Mark D. Fricker, Dai Akita, Luke L. M. Heaton, Nick Jones, Boguslaw Obara, Toshiyuki Nakagaki
JOURNAL OF PHYSICS D-APPLIED PHYSICS, 50, 25, 254005, Jun. 2017, [Peer-reviewed], [Last author]
English, Scientific journal - Studies of the phase gradient at the boundary of the phase diffusion equation, motivated by peculiar wave patterns of rhythmic contraction in the amoeboid movement of Physarum polycephalum
Makoto Iima, Hiroshi Kori, Toshiyuki Nakagaki
JOURNAL OF PHYSICS D-APPLIED PHYSICS, 50, 15, Apr. 2017, [Peer-reviewed], [Last author]
English, Scientific journal - Direct observation of orientation distributions of actin filaments in a solution undergoing shear banding
K. Sato, I. Kunita, Y. Takikawa, D. Takeuchi, Y. Tanaka, T. Nakagaki, H. Orihara
SOFT MATTER, 13, 14, 2708, 2716, Apr. 2017, [Peer-reviewed]
English, Scientific journal - The role of noise in self-organized decision making by the true slime mold Physarum polycephalum
Bernd Meyer, Cedrick Ansorge, Toshiyuki Nakagaki
PLOS ONE, 12, 3, e0172933, Mar. 2017, [Peer-reviewed], [Last author], [International Magazine]
English, Scientific journal - Experimental models for Murray's law
Dai Akita, Itsuki Kunita, Mark D. Fricker, Shigeru Kuroda, Katsuhiko Sato, Toshiyuki Nakagaki
JOURNAL OF PHYSICS D-APPLIED PHYSICS, 50, 2, 024001, Jan. 2017, [Peer-reviewed], [Last author, Corresponding author]
English, Scientific journal - Physical ethology of unicellular organism
S. Kuroda, S. Takagi, T. Saigusa, T. Nakagaki
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, [Peer-reviewed], [Last author, Corresponding author]
English, Scientific journal - Physical ethology of single-celled organism
Toshiyuki Nakagaki
INTERNATIONAL JOURNAL OF PSYCHOLOGY, 51, 574, 574, Jul. 2016
English, Symposium - A ciliate memorizes the geometry of a swimming arena
Itsuki Kunita, Tatsuya Yamaguchi, Atsushi Tero, Masakazu Akiyama, Shigeru Kuroda, Toshiyuki Nakagaki
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 13, 118, 20160155, May 2016, [Peer-reviewed], [Last author, Corresponding author], [International Magazine]
English, Scientific journal - 粘菌の用不用適応能に倣った形状最適化設計法の検討
吉原一詞, 中垣俊之
土木学会論文集 A2(応用力学)(Web), 72, 2, 3, 11, 2016, [Invited], [Last author, Corresponding author]
Japanese - Allometry in Physarum plasmodium during free locomotion: size versus shape, speed and rhythm
Shigeru Kuroda, Seiji Takagi, Toshiyuki Nakagaki, Tetsuo Ueda
JOURNAL OF EXPERIMENTAL BIOLOGY, 218, 23, 3729, 3738, Dec. 2015, [Peer-reviewed], [International Magazine]
English, Scientific journal - Periodic traction in migrating large amoeba of Physarum polycephalum
Jean-Paul Rieu, Helene Delanoe-Ayari, Seiji Takagi, Yoshimi Tanaka, Toshiyuki Nakagaki
Journal of the Royal Society Interface, 12, 106, May 2015, [Peer-reviewed], [Last author], [International Magazine]
English, Scientific journal - Attempts to retreat from a dead-ended long capillary by backward swimming in Paramecium
Itsuki Kunita, Shigeru Kuroda, Kaito Ohki, Toshiyuki Nakagaki
FRONTIERS IN MICROBIOLOGY, 5, 270, 270, Jun. 2014, [Peer-reviewed], [Last author], [International Magazine]
English, Scientific journal - Common mechanics of mode switching in locomotion of limbless and legged animals
Shigeru Kuroda, Itsuki Kunita, Yoshimi Tanaka, Akio Ishiguro, Ryo Kobayashi, Toshiyuki Nakagaki
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 11, 95, 20140205, 20140205, Jun. 2014, [Peer-reviewed], [Last author], [International Magazine]
English, Scientific journal - Current-reinforced random walks for constructing transport networks
Qi Ma, Anders Johansson, Atsushi Tero, Toshiyuki Nakagaki, David J.T. Sumpter
Journal of the Royal Society Interface, 10, 80, 06 Mar. 2013, [Peer-reviewed]
English, Scientific journal - A Design Principle of the Decentralized Control and its Applications
Ryo Kobayashi, Toshiyuki Nakagaki, Akio Ishiguro
11TH INTERNATIONAL CONFERENCE OF NUMERICAL ANALYSIS AND APPLIED MATHEMATICS 2013, PTS 1 AND 2 (ICNAAM 2013), 1558, 2440, 2443, 2013, [Peer-reviewed]
English, International conference proceedings - Adaptive path-finding and transport network formation by the amoeba-like organism {\it Physarum}
Itsuki Kunita, Kazunori Yoshihara, Atsushi Tero, Kentaro Ito, Chiu Fan Lee, Mark D. Fricker, Toshiyuki Nakagaki
Natural Computing and Beyond, Proceedings in Information and Communications Technology (PICT), Springer-Verlag,, 6, 14, 29, 2013, [Peer-reviewed], [Last author, Corresponding author]
English, International conference proceedings - Ethological response to periodic stimulation in {\it Chara} and {\it Brepharisma}
Itsuki Kunita, Sho Sato, Tetsu Saigusa, Toshiyuki Nakagaki
Natural Computing and Beyond, Proceedings in Information and Communications Technology (PICT), Springer-Verlag, 6, 3, 13, 2013, [Peer-reviewed], [Last author, Corresponding author]
English, International conference proceedings - Shear Banding in an F-Actin Solution
Itsuki Kunita, Katsuhiko Sato, Yoshimi Tanaka, Yoshinori Takikawa, Hiroshi Orihara, Toshiyuki Nakagaki
PHYSICAL REVIEW LETTERS, 109, 24, 248303, 248303, Dec. 2012, [Peer-reviewed], [Last author], [International Magazine]
English, Scientific journal - Peristaltic transport and mixing of cytosol through the whole body of Physarum plasmodium
Makoto Iima, Toshiyuki Nakagaki
MATHEMATICAL MEDICINE AND BIOLOGY-A JOURNAL OF THE IMA, 29, 3, 263, 281, Sep. 2012, [Peer-reviewed], [Last author]
English, Scientific journal - Tactic direction determined by the interaction between oscillatory chemical waves and rheological deformation in an amoeba
Kei-Ichi Ueda, Seiji Takagi, Toshiyuki Nakagaki
PHYSICAL REVIEW E, 86, 1, 011927, Jul. 2012, [Peer-reviewed], [Last author]
English, Scientific journal - Mechanics of peristaltic locomotion and role of anchoring
Yoshimi Tanaka, Kentaro Ito, Toshiyuki Nakagaki, Ryo Kobayashi
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 9, 67, 222, 233, Feb. 2012, [Peer-reviewed]
English, Scientific journal - Transport and mixing of chemicals inside the body of a micro-organism
Makoto Iima, Toshiyuki Nakagaki
Journal of Mathematical Medicine and Biology, 29, 263, 281, 2012, [Peer-reviewed], [Last author]
English, Scientific journal - Fluid-Filled Soft-Bodied Amoeboid Robot Inspired by Plasmodium of True Slime Mold
Takuya Umedachi, Ryo Idei, Toshiyuki Nakagaki, Ryo Kobayashi, Akio Ishiguro
ADVANCED ROBOTICS, 26, 7, 693, 707, 2012, [Peer-reviewed]
English, Scientific journal - Novel control principle based on the discrepancy function
Ryo Kobayashi, Toshiyuki Nakagaki, Akio Ishiguro
RIMS Kokyuroku Bessatsu, B31, 61, 77, Kyoto University, 2012
English, Symposium - Traffic optimization in railroad networks using an algorithm mimicking an amoeba-like organism, Physarum plasmodium
Shin Watanabe, Atsushi Tero, Atsuko Takamatsu, Toshiyuki Nakagaki
BIOSYSTEMS, 105, 3, 225, 232, Sep. 2011, [Peer-reviewed], [Last author]
English, Scientific journal - Structure and formation of ant transportation networks
Tanya Latty, Kai Ramsch, Kentaro Ito, Toshiyuki Nakagaki, David J. T. Sumpter, Martin Middendorf, Madeleine Beekman
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 8, 62, 1298, 1306, Sep. 2011, [Peer-reviewed]
English, Scientific journal - Flow-induced channel formation in the cytoplasm of motile cells
Robert D. Guy, Toshiyuki Nakagaki, Grady B. Wright
PHYSICAL REVIEW E, 84, 1, Jul. 2011, [Peer-reviewed]
English, Scientific journal - Cellular Computation Realizing Intelligence of Slime Mold Physarum Polycephalum
Yoshimi Tanaka, Toshiyuki Nakagaki
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 8, 3, 383, 390, Mar. 2011, [Peer-reviewed], [Last author]
English - Mathematical model for contemplative amoeboid locomotion
Kei-Ichi Ueda, Seiji Takagi, Yasumasa Nishiura, Toshiyuki Nakagaki
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 83, 2, 021916, 28 Feb. 2011, [Peer-reviewed], [Last author]
English, Scientific journal - A Soft Deformable Amoeboid Robot Inspired by Plasmodium of True Slime Mold
Takuya Umedachi, Koichi Takeda, Toshiyuki Nakagaki, Ryo Kobayashi, Akio Ishiguro
INTERNATIONAL JOURNAL OF UNCONVENTIONAL COMPUTING, 7, 6, 449, 462, 2011, [Peer-reviewed]
English, Scientific journal - Convergence properties for the Physarum solver
Kentaro Ito, Anders Johansson, Toshiyuki Nakagaki, Atsushi Tero
arXiv:1101.5249v1[math.OC] 27 Jan 2011, Jan. 2011
English, Research society - Kinetic study of anti-viral ribavirin uptake mediated by hCNT3 and hENT1 in Xenopus laevis oocytes
Takashi Yamamoto, Mitsuru Sugawara, Takashi Kikukawa, Seiji Miyauchi, Masahiro Yamaguchi, Atsushi Tero, Seiji Takagi, Toshiyuki Nakagaki
BIOPHYSICAL CHEMISTRY, 147, 1-2, 59, 65, Mar. 2010, [Peer-reviewed], [Last author]
English, Scientific journal - Fully decentralized control of a soft-bodied robot inspired by true slime mold
Takuya Umedachi, Koichi Takeda, Toshiyuki Nakagaki, Ryo Kobayashi, Akio Ishiguro
BIOLOGICAL CYBERNETICS, 102, 3, 261, 269, Mar. 2010, [Peer-reviewed]
English - Development of an Amoeboid Soft-bodied Robot That Exploits Law of Conservation of Protoplasmic Mass
武田光一, 梅舘拓也, 中垣俊之, 小林亮, 石黒章夫
第22回自律分散システム・シンポジウム, 30 Jan. 2010
Japanese, Research society - The Birth of Physarum Computing
Toshiyuki Nakagaki
INTERNATIONAL JOURNAL OF UNCONVENTIONAL COMPUTING, 6, 2, 75, 77, 2010, [Peer-reviewed]
English - Taming Large Degrees of Freedom A Case Study with an Amoeboid Robot
Takuya Umedachi, Koichi Takeda, Toshiyuki Nakagaki, Ryo Kobayashi, Akio Ishiguro
2010 IEEE INTERNATIONAL CONFERENCE ON ROBOTICS AND AUTOMATION (ICRA), 3787, 3792, 2010, [Peer-reviewed]
English, International conference proceedings - Foraging Behaviors and Potential Computational Ability of Problem-Solving in an Amoeba
Toshiyuki Nakagaki
NATURAL COMPUTING, 2, 42, 54, 2010, [Peer-reviewed]
English, Scientific journal - Rules for Biologically Inspired Adaptive Network Design
Atsushi Tero, Seiji Takagi, Tetsu Saigusa, Kentaro Ito, Dan P. Bebber, Mark D. Fricker, Kenji Yumiki, Ryo Kobayashi, Toshiyuki Nakagaki
SCIENCE, 327, 5964, 439, 442, Jan. 2010, [Peer-reviewed], [Last author, Corresponding author]
English, Scientific journal - A Method Inspired by Physarum for Solving the Steiner Problem
Aisushi Tero, Toshiyuki Nakagaki, Kazutaka Toyabe, Kenji Yumiki, Ryo Kobayashi
INTERNATIONAL JOURNAL OF UNCONVENTIONAL COMPUTING, 6, 2, 109, 123, 2010, [Peer-reviewed]
English, Scientific journal - A Soft-bodied Fluid-driven Amoeboid Robot Inspired by Plasmodium of True Slime Mold
Takuya Umedachi, Koichi Takeda, Toshiyuki Nakagaki, Ryo Kobayashi, Akio Ishiguro
IEEE/RSJ 2010 INTERNATIONAL CONFERENCE ON INTELLIGENT ROBOTS AND SYSTEMS (IROS 2010), 2401, 2406, 2010, [Peer-reviewed]
English, International conference proceedings - Risk management in spatio-temporally varying field by true slime mold
Kentaro Ito, David Sumpter, Toshiyuki Nakagaki
NOLTA (Nonlinear Theory and Application) journal, IEICE., 1, 1, 26, 36, The Institute of Electronics, Information and Communication Engineers, 2010, [Peer-reviewed], [Last author]
English, Scientific journal, Revealing how lower organisms solve complicated problems is a challenging research area, which could reveal the evolutionary origin of biological information processing. Here we report on the ability of a single-celled organism, true slime mold, to find a smart solution of risk management under spatio-temporally varying conditions. We designed test conditions under which there were three food-locations at vertices of equilateral triangle and a toxic light illuminated the organism on alternating halves of the triangle. We found that the organism behavior depended on the period of the repeated illumination, even though the total exposure time was kept the same . A simple mathematical model for the experimental results is proposed from a dynamical system point of view. We discuss our results in the context of a strategy of risk management by Physarum. - 真正粘菌変形体から着想を得た自律分散制御方策の実験的検証
梅舘拓也, 武田光一, 中垣俊之, 小林 亮, 石黒章夫
計測自動制御学会論文集, 46, 11, 706, 712, The Society of Instrument and Control Engineers, 2010, [Peer-reviewed]
Japanese, Scientific journal, This paper presents a fully decentralized control inspired by plasmodium of true slime mold and its validity using a soft-bodied amoeboid robot. The notable features of this paper are twofold: (1) the robot has truly soft and deformable body stemming from real-time tunable springs and a balloon, the former is utilized as an outer skin of the body and the latter serves as protoplasm; and (2) a fully decentralized control using coupled oscillators with completely local sensory feedback mechanism is realized by exploiting the long-distance physical interaction between the body parts induced by the law of conservation of protoplasmic mass. Experimental results show that this robot exhibits truly supple locomotion without relying on any hierarchical structure. The results obtained are expected to shed new light on design scheme for autonomous decentralized control system. - Understanding Autonomous Decentralized Control of Many-Degree-of-Freedom from Amoeboid Locomotion
武田光一, 梅舘拓也, 中垣俊之, 小林亮, 石黒章夫
第15回創発システム・シンポジウム, P02 83, 86, 08 Aug. 2009
Japanese, Research society, 第15回創発システム・シンポジウム ベストポスター優秀賞 - Development of a Soft and Supple Robot Inspired from True Slime
武田 光一, 北村 太一, 梅舘 拓也, 中垣 俊之, 小林 亮, 石黒 章夫
第21回自律分散システム・シンポジウムProceedings, 22 Jan. 2009
English, Research society - Adaptive biological networks
Mark D. Fricker, Lynne Boddy, Toshiyuki Nakagaki, Daniel P. Bebber
Understanding Complex Systems, 2009, 51, 70, 2009, [Peer-reviewed]
English, Scientific journal - Foraging Behaviors and Potential Computational Ability of Problem-Solving in an Amoeba.
Toshiyuki Nakagaki
Natural Computing - 4th International Workshop on Natural Computing, IWNC 2009, Himeji, Japan, September 2009, Proceedings, 42, 54, Springer, 2009, [Peer-reviewed] - A Modular Robot Driven by Protoplasmic Streaming
Takuya Umedachi, Thichi Kitamura, Koichi Takeda, Toshiyuki Nakagaki, Ryo Kobayashi, Akio Ishiguro
DISTRIBUTED AUTONOMOUS ROBOTIC SYSTEMS 8, 193, +, 2009, [Peer-reviewed]
English, International conference proceedings - Protoplasmic Computing to Memorize and Recall Periodic Environmental Events
Atsushi Tero, Tetsu Saigusa, Toshiyuku Nakagaki
NATURAL COMPUTING, PROCEEDINGS, 1, 213, 221, 2009
English, International conference proceedings - An Autonomous Decentralized Control of a Soft and Supple Robot Inspired from True Slime Mold
北村 太一, 梅舘 拓也, 武田 光一, 中垣 俊之, 小林 亮, 石黒 章夫
計測自動制御学会SI部門講演会SI2008予稿集, 139, 140, 05 Dec. 2008
Japanese, Research society - Computational Ability of Cells based on Cell Dynamics and Adaptability
Toshiyuki Nakagaki, Atsushi Tero, Ryo Kobayashi, Isamu Onishi, Tomoyuki Miyaji
NEW GENERATION COMPUTING, 27, 1, 57, 81, Nov. 2008, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal - A Fully Decentralized Morphology Control of an Amoeboid Robot by Exploiting the Law of Conservation of Protoplasmic Mass
Akio Ishiguro, Takuya Umedachi, Taichi Kitamura, Toshiyuki Nakagaki, Ryo Kobayashi
IEEE/RSJ 2008 International Conference on Intelligent RObots and Systems, 22 Sep. 2008, [Peer-reviewed]
English, International conference proceedings - Failure to the shortest path decision of an adaptive transport network with double edges in Plasmodium system
Tomoyuki Miyaji, Isamu Ohnishi, Atsushi Tero, Toshiyuki Nakagaki
International Journal of Dynamical Systems and Differential Equations, 1, 3, 210, 219, Jul. 2008, [Peer-reviewed], [Last author]
English, Scientific journal - Flow-network adaptation in Physarum amoebae
Atsushi Tero, Kenji Yumiki, Ryo Kobayashi, Tetsu Saigusa, Toshiyuki Nakagaki
THEORY IN BIOSCIENCES, 127, 2, 89, 94, Jun. 2008, [Peer-reviewed], [Last author, Corresponding author]
English, Scientific journal - Locomotive mechanism of Physarum plasmodia based on spatiotemporal analysis of protoplasmic streaming
Kenji Matsumoto, Seiji Takagi, Toshiyuki Nakagaki
BIOPHYSICAL JOURNAL, 94, 7, 2492, 2504, Apr. 2008, [Peer-reviewed], [Last author]
English, Scientific journal - Flow rate driven by peristaltic movement in plasmodial tube of Physarum polycephalum
Hiroyasu Yamada, Toshiyuki Nakagaki
COLLECTIVE DYNAMICS: TOPICS ON COMPETITION AND COOPERATION IN THE BIOSCIENCES, 1028, 210, +, 2008, [Peer-reviewed], [Last author]
English, International conference proceedings - Intelligent behaviors of amoeboid movement based on complex dynamics of soft matter
Toshiyuki Nakagaki, Robert D. Guy
SOFT MATTER, 4, 1, 57, 67, 2008, [Peer-reviewed], [Last author, Corresponding author]
English, Scientific journal - Amoebae anticipate periodic events
Tetsu Saigusa, Atsushi Tero, Toshiyuki Nakagaki, Yoshiki Kuramoto
PHYSICAL REVIEW LETTERS, 100, 1, 018101, Jan. 2008, [Peer-reviewed], [Corresponding author]
English, Scientific journal - Minimum-risk path finding by an adaptive amoebal network
Toshiyuki Nakagaki, Makoto Iima, Tetsuo Ueda, Yasumasa Nishiura, Tetsu Saigusa, Atsushi Tero, Ryo Kobayashi, Kenneth Showalter
PHYSICAL REVIEW LETTERS, 99, 6, 068104, Aug. 2007, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal - Dispersion relation in oscillatory reaction-diffusion systems with self-consistent flow in true slime mold
H. Yamada, T. Nakagaki, R. E. Baker, P. K. Maini
JOURNAL OF MATHEMATICAL BIOLOGY, 54, 6, 745, 760, Jun. 2007, [Corresponding author]
English, Scientific journal - A mathematical model for adaptive transport network in path finding by true slime mold
Atsushi Tero, Ryo Kobayashi, Toshiyuki Nakagaki
JOURNAL OF THEORETICAL BIOLOGY, 244, 4, 553, 564, Feb. 2007, [Peer-reviewed], [Last author]
English, Scientific journal - Effects of amount of food on path selection in the transport network of an amoeboid organsim
Toshiyuki Nakagaki, Tetsu Saigusa, Atsushi Tero, Ryo Kobayashi
Proceedings of Int. Symp. On Topological Aspects of Critical Systems and Networks (World Scientific Publishing Co.), 94, 100, 2007, [Lead author, Corresponding author] - Indecisive behavior of amoeba crossing an environmental barrier
Seiji Takagi, Yasumasa Nishiura, Toshiyuki Nakagaki, Tetsuo Ueda, Kei-ichi Ueda
Proceedings of Int. Symp. On Topological Aspects of Critical Systems and Networks (World Scientific Publishing Co.), 86, 93, 2007 - Mathematical model for rhythmic protoplasmic movement in the true slime mold
Ryo Kobayashi, Atsushi Tero, Toshiyuki Nakagaki
JOURNAL OF MATHEMATICAL BIOLOGY, 53, 2, 273, 286, Aug. 2006, [Peer-reviewed], [Last author]
English, Scientific journal - Super water-repellent surfaces with fractal structures and their potential application to biological studies
Hu Yan, Hatsuki Shiga, Etsuro Ito, Toshiyuki Nakagaki, Seiji Takagi, Tetsuo Ueda, Kaoru Tsujii
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS, 284, 490, 494, Aug. 2006, [Peer-reviewed]
English, Scientific journal - Physarum solver: A biologically inspired method of road-network navigation
A Tero, R Kobayashi, T Nakagaki
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 363, 1, 115, 119, Apr. 2006, [Last author, Corresponding author]
English, Scientific journal - Spatiotemporal symmetry in rings of coupled biological oscillators of Physarum plasmodial slime mold
A Takamatsu, R Tanaka, H Yamada, T Nakagaki, T Fujii, Endo, I
PHYSICAL REVIEW LETTERS, 87, 7, 0781021-4., Aug. 2001, [Peer-reviewed]
English, Scientific journal - Maze-solving by an amoeboid organism
T Nakagaki, H Yamada, A Toth
NATURE, 407, 6803, 470, 470, Sep. 2000, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal - Interaction between cell shape and contraction pattern in the Physarum plasmodium (vol 84, pg 195, 2000)
T Nakagaki, H Yamada, T Ueda
BIOPHYSICAL CHEMISTRY, 87, 1, 85, 86, Sep. 2000, [Peer-reviewed], [Lead author, Corresponding author]
English - Modulation of cellular rhythm and photoavoidance by oscillatory irradiation in the Physarum plasmodium
T Nakagaki, H Yamada, T Ueda
BIOPHYSICAL CHEMISTRY, 82, 1, 23, 28, Nov. 1999, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal - Reaction-diffusion-advection model for pattern formation of rhythmic contraction in a giant amoeboid cell of the Physarum Plasmodium
T Nakagaki, H Yamada, M Ito
JOURNAL OF THEORETICAL BIOLOGY, 197, 4, 497, 506, Apr. 1999, [Peer-reviewed], [Lead author, Corresponding author]
English, Scientific journal - Pattern formation of a reaction-diffusion system with self-consistent flow in the amoeboid organism Physarum plasmodium
H Yamada, T Nakagaki, M Ito
PHYSICAL REVIEW E, 59, 1, 1009, 1014, Jan. 1999, [Peer-reviewed]
English, Scientific journal - Action spectrum for sporulation and photoavoidance in the plasmodium of Physarum polycephalum, as modified differentially by temperature and starvation
T Nakagaki, S Umemura, Y Kakiuchi, T Ueda
PHOTOCHEMISTRY AND PHOTOBIOLOGY, 64, 5, 859, 862, Nov. 1996, [Peer-reviewed], [Lead author]
English, Scientific journal - Phase switching of oscillatory contraction in relation to the regulation of amoeboid behavior by the Plasmodium of Physarum polycephalum
T Nakagaki, T Ueda
JOURNAL OF THEORETICAL BIOLOGY, 179, 3, 261, 267, Apr. 1996, [Peer-reviewed], [Lead author]
English, Scientific journal - NONSPECIFIC ACTIVITY OF (+/-)CP-96,345 IN MODELS OF PAIN AND INFLAMMATION
A NAGAHISA, R ASAI, Y KANAI, A MURASE, M TSUCHIYANAKAGAKI, T NAKAGAKI, TC SHIEH, K TANIGUCHI
REGULATORY PEPTIDES, 46, 1-2, 433, 436, Jul. 1993
English, Scientific journal - NONSPECIFIC ACTIVITY OF (+/-) CP-96,345 IN MODELS OF PAIN AND INFLAMMATION
A NAGAHISA, R ASAI, Y KANAI, A MURASE, M TSUCHIYANAKAGAKI, T NAKAGAKI, T SHIEH, K TANIGUCHI
REGULATORY PEPTIDES, 107, 2, S122, S122, Sep. 1992
English - ULTRAVIOLET ACTION SPECTRUM FOR INTRACELLULAR FREE CA-2+ INCREASE IN HUMAN EPIDERMAL-KERATINOCYTES
T NAKAGAKI, J ODA, H KOIZUMI, T FUKAYA, C YASUI, T UEDA
CELL STRUCTURE AND FUNCTION, 15, 4, 175, 179, Aug. 1990, [Peer-reviewed], [Lead author]
English, Scientific journal - DYNAMIC ORGANIZATION OF ATP AND BIREFRINGENT FIBRILS DURING FREE LOCOMOTION AND GALVANOTAXIS IN THE PLASMODIUM OF PHYSARUM-POLYCEPHALUM
T UEDA, T NAKAGAKI, T YAMADA
JOURNAL OF CELL BIOLOGY, 110, 4, 1097, 1102, Apr. 1990, [Peer-reviewed]
English, Scientific journal - ACTION SPECTRA FOR SUPEROXIDE GENERATION AND UV AND VISIBLE-LIGHT PHOTOAVOIDANCE IN PLASMODIA OF PHYSARUM-POLYCEPHALUM
T UEDA, Y MORI, T NAKAGAKI, Y KOBATAKE
PHOTOCHEMISTRY AND PHOTOBIOLOGY, 48, 5, 705, 709, Nov. 1988, [Peer-reviewed]
English, Scientific journal - CHANGES IN CAMP AND CGMP CONCENTRATION, BIREFRINGENT FIBRILS AND CONTRACTILE ACTIVITY ACCOMPANYING UV AND BLUE-LIGHT PHOTOAVOIDANCE IN PLASMODIA OF AN ALBINO STRAIN OF PHYSARUM-POLYCEPHALUM
T UEDA, Y MORI, T NAKAGAKI, Y KOBATAKE
PHOTOCHEMISTRY AND PHOTOBIOLOGY, 47, 2, 271, 275, Feb. 1988, [Peer-reviewed]
English, Scientific journal - Patterns in intracellular ATP distribution and rhythmic contraction in relation to amoeboid locomotion in the plasmodium of Physarum polycephalum
Tetsuo Ueda, Toshiyuki Nakagaki, Yonosuke Kobatake
Protoplasma, Suppl 1, 51, 56, 1988, [Peer-reviewed]
English
Other Activities and Achievements
- やや複雑な状況における原生生物の行動 : 変形体性粘菌の例を中心に—Behavior of protists in some rather complicated situation : Focusing on the example of plasmodial slime mold—特集 無神経な行動生態学
越後谷 駿, 西上 幸範, 佐藤 勝彦, 中垣 俊之, 日本生態学会誌 = Japanese journal of ecology / 日本生態学会誌編集委員会 編, 74, 2, 203, 213, Sep. 2024
京都 : 日本生態学会誌編集委員会, Japanese - “Biophysics” and “Biomechanics”
NAKAGAKI Toshiyuki, Seibutsu Butsuri, 64, 5, 231, 231, 2024
The Biophysical Society of Japan General Incorporated Association, Japanese - Environment-adaptive transport network in Physarum plasmodium
中垣俊之, 佐藤勝彦, 西上幸範, BSJ-Review, 13, C, 151, 153, Aug. 2022, [Peer-reviewed], [Invited], [International Magazine]
公益社団法人 日本植物学会, Japanese - ホジキン-ハクスレー模型に見る数学と生物学の頼もしい出会い—特集 境界の数理 : 異分野と接するところ
中垣 俊之, 数学セミナー, 61, 7, 18, 23, Jul. 2022
東京 : 日本評論社, Japanese - 粘菌のジオラマ行動力学 : 迷路の中の採餌行動を例に—特集 菌類の世界 : きのこ・カビ・酵母
中垣 俊之, ユリイカ = Eureka, 54, 6, 277, 281, May 2022
東京 : 青土社, Japanese - Mathematical sciences by an amoeboid organism
Nakagaki Toshiyuki, JSAP Annual Meetings Extended Abstracts, 2019.2, 5, 5, 04 Sep. 2019
The Japan Society of Applied Physics, Japanese - A Social Aggregation of Caenorhabditis elegans and its behavioral mechanism
越智翔大, 中垣俊之, 中垣俊之, 佐藤勝彦, 佐藤勝彦, Nematological Research, 49, 2, 2019 - Physarum inspires research beyond biomimetic algorithms: Reply to comments on “Does being multi-headed make you better at solving problems?”
Chao Gao, Chen Liu, Daniel Schenz, Xuelong Li, Zili Zhang, M. Jusup, Zhen Wang, Madeleine Beekman, Toshiyuki Nakagaki, Physics of Life Reviews, 29, 51, 54, 2019, [International Magazine]
Elsevier B.V., English - MEASUREMENT OF THERMAL CONDUCTIVITY AND THERMAL DIFFUSIVITY OF SLIME MOLD BY USING A SHORT HOT WIRE METHOD
藤原誠之, 黒田茂, 牧祥, 田中誠一, 荒田敏昭, 森本正太郎, 宇田川周子, 谷本能文, 中垣俊之, Thermophysical Properties, 39th, 40‐42, 13 Nov. 2018
Japanese - 泳ぐ神経細胞といわれる繊毛虫の適応行動と制御
中垣俊之, 山口達也, 日本生体医工学会大会プログラム・抄録集(Web), 57th, ROMBUNNO.OS2‐5‐1‐4 (WEB ONLY), 19 Jun. 2018
Japanese - 線虫Caenorhabditis elegansの集団分散行動
越智翔大, 中垣俊之, 佐藤勝彦, 中垣俊之, 佐藤勝彦, 日本動物行動学会大会発表要旨集, 37th, 54, 2018
Japanese - Adaptive behavior in ciliate that is a so-called swimming neuron
NAKAGAKI TOSHIYUKI, YAMAGUCHI TATSUYA, Transactions of Japanese Society for Medical and Biological Engineering, 56, 0, S166, S166, 2018
<p>A ciliate, Paramecium, is often called a swimming neuron as the electrophysiological studies done after 1960s have indicated the similar properties of membrane potential to that in neuron. A model equation for dynamics of membrane potential was proposed and is of Hodgkin-Huxley type that was originally proposed for squid neuron. Because ciliary motion that produces swimming force in ciliate is tightly regulated by the membrane potential, we expect that any kinds of behaviors, for instance, smart behaviors adaptive to environment, are organized by some modulation of model equation for membrane potential. Here we will introduce an adaptive behavior of a ciliate and discuss a possible mechanism of the adaptability based on the model equation for membrane potential. </p>, Japanese Society for Medical and Biological Engineering, Japanese - Artificial Intelligence and Natural Intelligence
中垣 俊之, 情報処理, 57, 10, 948, 949, 15 Sep. 2016
情報処理学会, Japanese - A method of network design adaptive to environmental conditions, based on current-reinforcement rule of living systems
中垣俊之, 電子情報通信学会技術研究報告, 116, 180(CCS2016 16-28), 1‐2, 02 Aug. 2016
Japanese - F‐アクチン溶液のシアバンディング
瀧川佳紀, 國田樹, 佐藤勝彦, 田中良巳, 折原宏, 中垣俊之, 高分子学会予稿集(CD-ROM), 64, 2, ROMBUNNO.3PD002, 25 Aug. 2015
Japanese - On the Way to Physical Ethology
Toshiyuki Nakagaki, 人工知能 = journal of the Japanese Society for Artificial Intelligence, 30, 4, 525, 531, 01 Jul. 2015
人工知能学会 ; 2014-, Japanese - 自律分散システムとロコモーション 脚式と非脚式の這行ロコモーションにおける運動モードスイッチングの共通力学
黒田茂, 田中良巳, 中垣俊之, 計測と制御, 54, 4, 248, 253, 10 Apr. 2015
The Society of Instrument and Control Engineers, Japanese - 単細胞生物の物理エソロジー : 輸送現象論から読み解く賢さのしくみ (特集 イグノーベル賞)
中垣 俊之, 化学と工業 = Chemistry & chemical industry, 68, 4, 342, 344, Apr. 2015
日本化学会, Japanese - Common Mechanics in Crawling Locomotion of Limbless and Legged Animals
KURODA Shigeru, TANAKA Yoshimi, NAKAGAKI Toshiyuki, Journal of The Society of Instrument and Control Engineers, 54, 4, 248, 253, 2015
The Society of Instrument and Control Engineers, Japanese - F‐アクチン溶液に形成されるシアバンディング
武内大輔, 瀧川佳紀, 折原宏, 佐藤勝彦, 田中良巳, 國田樹, 中垣俊之, レオロジー討論会講演要旨集, 62nd, 104, 105, 15 Oct. 2014
Japanese - 達人対談 単細胞だってナメるなよ 粘菌の達人 中垣俊之 北海道大学電子科学研究所生命動態研究分野教授vs.ビートたけし
中垣 俊之, ビートたけし, 新潮45, 33, 4, 272, 283, Apr. 2014
新潮社, Japanese - シート状真正粘菌の成長パターンの粘性流体指理論を用いた解析
及川典子, 田中良巳, 野口貴大, 中垣俊之, 日本物理学会講演概要集, 69, 1, 293, 293, 05 Mar. 2014
The Physical Society of Japan (JPS), Japanese - 27aAR-7 Analysis of the growth pattern of sheet-like Physarum polycephalum with the viscous fingering model
Oikawa Noriko, Tanaka Yoshimi, Noguchi Takahiro, Nakagaki Toshiyuki, Meeting Abstracts of the Physical Society of Japan, 69, 0, 293, 293, 2014
The Physical Society of Japan, Japanese - F‐アクチン溶液のシアバンディング
瀧川佳紀, 折原宏, 佐藤勝彦, 田中良巳, 國田樹, 中垣俊之, レオロジー討論会講演要旨集, 61st, 344, 345, 25 Sep. 2013
Japanese - 粘菌の収縮ダイナミクスに関する1次元位相振動子モデル
飯間信, 郡宏, 中垣俊之, 日本物理学会講演概要集, 68, 2, 241, 241, 26 Aug. 2013
The Physical Society of Japan (JPS), Japanese - Modulation of decision-making by environmental fluctuations in Physarum plasmodium
國田樹, 上田肇一, 中垣俊之, 自律分散システム・シンポジウム資料, 25th, 39, 42, 25 Jan. 2013
Japanese - Allometoric properties of the true slime mold during free locomotion: speed, shape and rhythm
黒田茂, 高木清二, 中垣俊之, 上田哲男, 自律分散システム・シンポジウム資料, 25th, 35, 38, 25 Jan. 2013
Japanese - A one-dimensional phase diffusion equation for peristaltic pumping of tadpole shape slimemold
Iima Makoto, Kori Hiroshi, Nakagaki Toshiyuki, Meeting Abstracts of the Physical Society of Japan, 68, 0, 241, 241, 2013
The Physical Society of Japan, Japanese - 26aXZC-9 Shear banding in F-actin solution
Tanaka Yoshimi, Meeting Abstracts of the Physical Society of Japan, 68, 0, 419, 419, 2013
The Physical Society of Japan, Japanese - HI, I'M PHYSARUM, A SINGLE-CELLED INTELLIGENT AMOEBA!
中垣 俊之, 斉藤 俊行, たくさんのふしぎ, 332, 1冊., Nov. 2012
福音館書店, Japanese - 第8回南方熊楠ゼミナール 基調講演 粘菌からのぞく行動知の起源 : 学際的視点から
中垣 俊之, 熊楠works, 0, 39, 4, 13, 15 Apr. 2012
南方熊楠顕彰会, Japanese - Analysis of fungal networks
Luke Heaton, Boguslaw Obara, Vincente Grau, Nick Jones, Toshiyuki Nakagaki, Lynne Boddy, Mark D. Fricker, Fungal Biology Reviews, 26, 1, 12, 29, Apr. 2012
English, Introduction scientific journal - プロジェクト「生物ロコモーションに学ぶ大自由度システム制御の新展開」
小林亮, 中垣俊之, 石黒章夫, 応用数理, 22, 1, 62, 64, 27 Mar. 2012
The Japan Society for Industrial and Applied Mathematics, Japanese - 収縮ダイナミクスをもつ1次元粘菌モデルにおける輸送機能の発現
飯間信, 郡宏, 中垣俊之, 日本物理学会講演概要集, 67, 1, 423, 423, 05 Mar. 2012
The Physical Society of Japan (JPS), Japanese - 知性とは何か人間と自然のこれからを粘菌に訊く
中垣 俊之, 広告, 第53巻2号、通巻389号, 116, 117, 2012 - Honor speech
中垣 俊之, Japanese Journal of Physiological Psychology and Psychophysiology, 30, 2, 103, 104, 2012
Japanese Society for Physiological Psychology and Psychophysiology, Japanese - 27aBJ-11 Transport mechanism of a one-dimensional slimemold model with peristaltic pumping dynamics
Iima Makoto, Kori Hiroshi, Nakagaki Toshiyuki, Meeting Abstracts of the Physical Society of Japan, 67, 0, 423, 423, 2012
The Physical Society of Japan, Japanese - Project "Innovations in Controlling Hyper Redundant and Flexible Systems Inspired by Biological Locomotion"(Laboratories)
Kobayashi Ryo, Nakagaki Toshiyuki, Ishiguro Akio, Bulletin of the Japan Society for Industrial and Applied Mathematics, 22, 1, 62, 64, 2012
The Japan Society for Industrial and Applied Mathematics, Japanese - Performance of Information Processing in a Primitive Organism of True Slime Mold : A Note on How Behavioral Intelligence Develop from Physical Nature
NAKAGAKI Toshiyuki, KOBAYASHI Ryo, Toshiyuki Nakagaki, Ryo Kobayashi, Journal of Japanese Society for Artificial Intelligence, 26, 5, 482, 493, 01 Sep. 2011
人工知能学会, Japanese - 真性粘菌内流動における蠕動運動の役割について
飯間信, 中垣俊之, 日本物理学会講演概要集, 66, 2, 300, 300, 24 Aug. 2011
The Physical Society of Japan (JPS), Japanese - Smart Network of True Slime Mold
ITO Kentaro, NAKAGAKI Toshiyuki, Seibutsu Butsuri, 51, 4, 178, 181, 25 Jul. 2011
The origin of information processing is a fundamental problem in evolutionary biology. True slime mold, <i>Physarum</i>, has become a model organism for study of problem solving by single-celled organisms. Here we report its ability to find a smart network by describing its aptitude in maze solving, multi purpose optimization for transportation network and risk management in a spatio-temporally varying field. We discuss these results in the context of a risk management strategy.<br>, The Biophysical Society of Japan General Incorporated Association, Japanese - Physico-chemical mechanism of tactic movement in an amoeba
Ueda Kei-Ichi, Takagi Seiji, Nakagaki Toshiyuki, RIMS Kokyuroku, 1751, 1751, 109, 112, Jul. 2011
Kyoto University, Japanese - 真正粘菌変形体の環境適応性(非平衡系の物理-非平衡ゆらぎと集団挙動-,研究会報告)
上田 肇一, 高木 清二, 西浦 廉政, 中垣 俊之, 物性研究, 96, 1, 93, 94, 2011
この論文は国立情報学研究所の電子図書館事業により電子化されました。, 物性研究刊行会, Japanese - 21aJD-4 Role of peristaltic pumping in tadpole-shape slime mold
Iima Makoto, Nakagaki Toshiyuki, Meeting Abstracts of the Physical Society of Japan, 66, 0, 300, 300, 2011
The Physical Society of Japan, Japanese - How Do Intelligent Behaviours Develop?: Lessons from a Single-Celled Organism
中垣 俊之, The Journal of oriental studies, 50, 1, 165, 193, 2011
東洋哲学研究所, Japanese - Experimental Verification of Fully Decentralized Control Inspired by Plasmodium of True Slime Mold
梅舘拓也, 武田光一, 中垣俊之, 小林亮, 石黒章夫, 計測自動制御学会論文集, 46, 11, 706, 712, 30 Nov. 2010
This paper presents a fully decentralized control inspired by plasmodium of true slime mold and its validity using a soft-bodied amoeboid robot. The notable features of this paper are twofold: (1) the robot has truly soft and deformable body stemming from real-time tunable springs and a balloon, the former is utilized as an outer skin of the body and the latter serves as protoplasm; and (2) a fully decentralized control using coupled oscillators with completely local sensory feedback mechanism is realized by exploiting the long-distance physical interaction between the body parts induced by the law of conservation of protoplasmic mass. Experimental results show that this robot exhibits truly supple locomotion without relying on any hierarchical structure. The results obtained are expected to shed new light on design scheme for autonomous decentralized control system., The Society of Instrument and Control Engineers, Japanese - 粘菌の迷路解きから得られた適応ネットワーク共通原理の新展開~都市間ネットワークや癌の血管新生のコントロールについて~
手老篤史, 中垣俊之, 小林亮, 日本応用数理学会年会講演予稿集, 2010, 273, 274, Sep. 2010
Japanese - 粘菌の記憶と迷いのエソロジカルダイナミクス (第6回生物数学の理論とその応用--RIMS研究集会報告集)
中垣 俊之, 数理解析研究所講究録, 1704, 1704, 165, 171, Aug. 2010
京都大学数理解析研究所, Japanese - 原形質量保存則を活用した流体駆動型アメーバ様ソフトロボット
武田光一, 梅舘拓也, 中垣俊之, 小林亮, 石黒章夫, 日本機械学会ロボティクス・メカトロニクス講演会講演論文集(CD-ROM), 2010, ROMBUNNO.1A1-E20, E20(1)"-"1A1-E20(4)", 13 Jun. 2010
This paper presents a soft-bodied fluid-driven amoeboid robot inspired by plasmodium of true slime mold. Significant features of this robot are twofold: (1) the robot has fluidic circuit (i.e., nylon tubes filled with fluid) and truly soft and deformable body stemming from real-time tunable springs, the former serves as protoplasm and the latter is used for elastic actuators; and (2) a fully decentralized control using coupled oscillators with completely local sensory feedback mechanism is realized by exploiting the long-distance physical interaction between the body parts induced by the law of conservation of protoplasmic mass. Experimental result shows that this robot exhibits truly supple locomotion without relying on any hierarchical structure. The result obtained is expected to shed new light on design scheme for autonomous decentralized control system., The Japan Society of Mechanical Engineers, Japanese - アメーバのエソロジー(生物物理若手の会第49回夏の学校,研究会報告)
中垣 俊之, 物性研究, 94, 2, 238, 239, 05 May 2010
この論文は国立情報学研究所の電子図書館事業により電子化されました。, 物性研究刊行会, Japanese - 適応ダイナミクスに基づく細胞の計算能力
中垣俊之, 手老篤史, 小林亮, 物性研究, 93, 6, 911, 934, 05 Mar. 2010
生物システムがどのように問題を解いているかを学ぶことが、新しい計算方法をデザインすることに役立つかもしれない。単純な単細胞生物における情報処理は興味深い。なぜなら、単純な情報処理系を用いて約10億年の年月を生き抜いて来たからである。ここでは、よく研究されている一つのモデル系について議論する。それは、巨大なアメーバ様生物である真正粘菌フィザルムPhysarumの変形体である。このアメーバは、迷路や最短ネットワーク問題を解くように、組み合わせ最適化問題の近似解を見つけることができる。このレポートで、我々は、このアメーバによる問題解決とそのアメーバ行動から抽出された計算法について述べる。フィザルムに基づいてデザインされたアルゴリズムは、単純でありかつ、なかなか有用であるようだ。, 物性研究刊行会, Japanese - 適応ダイナミクスに基づく細胞の計算能力(第54回物性若手夏の学校(2009年度),講義ノート)
中垣 俊之, 手老 篤史, 小林 亮, 物性研究, 93, 6, 911, 934, 05 Mar. 2010
この論文は国立情報学研究所の電子図書館事業により電子化されました。生物システムがどのように問題を解いているかを学ぶことが、新しい計算方法をデザインすることに役立つかもしれない。単純な単細胞生物における情報処理は興味深い。なぜなら、単純な情報処理系を用いて約10億年の年月を生き抜いて来たからである。ここでは、よく研究されている一つのモデル系について議論する。それは、巨大なアメーバ様生物である真正粘菌フィザルムPhysarumの変形体である。このアメーバは、迷路や最短ネットワーク問題を解くように、組み合わせ最適化問題の近似解を見つけることができる。このレポートで、我々は、このアメーバによる問題解決とそのアメーバ行動から抽出された計算法について述べる。フィザルムに基づいてデザインされたアルゴリズムは、単純でありかつ、なかなか有用であるようだ。, 物性研究刊行会, Japanese - 適応ダイナミクスに基づく細胞の計算能力 (第54回 物性若手夏の学校(2009年度))
中垣 俊之, 手老 篤史, 小林 亮, 物性研究, 93, 6, 911, 934, Mar. 2010
生物システムがどのように問題を解いているかを学ぶことが、新しい計算方法をデザインすることに役立つかもしれない。単純な単細胞生物における情報処理は興味深い。なぜなら、単純な情報処理系を用いて約10億年の年月を生き抜いて来たからである。ここでは、よく研究されている一つのモデル系について議論する。それは、巨大なアメーバ様生物である真正粘菌フィザルムPhysarumの変形体である。このアメーバは、迷路や最短ネットワーク問題を解くように、組み合わせ最適化問題の近似解を見つけることができる。このレポートで、我々は、このアメーバによる問題解決とそのアメーバ行動から抽出された計算法について述べる。フィザルムに基づいてデザインされたアルゴリズムは、単純でありかつ、なかなか有用であるようだ。, 物性研究刊行会, Japanese - 流体回路による大域的相互作用を活用した自律分散制御~アメーバ様ソフトロボットを用いた実験的検証~
武田光一, 出井遼, 梅舘拓也, 中垣俊之, 小林亮, 石黒章夫, 日本ロボット学会学術講演会予稿集(CD-ROM), 28th, ROMBUNNO.3N2-7, 2010
Japanese - 1A1-E20 A Fluid-driven Amoeboid Robot That Exploits Law of Conservation of Protoplasmic Mass
TAKEDA Koichi, UMEDACHI Takuya, NAKAGAKI Toshiyuki, KOBAYASHI Ryo, ISHIGURO Akio, The Proceedings of JSME annual Conference on Robotics and Mechatronics (Robomec), 2010, 0, _1A1, E20_1-_1A1-E20_4, 2010
This paper presents a soft-bodied fluid-driven amoeboid robot inspired by plasmodium of true slime mold. Significant features of this robot are twofold: (1) the robot has fluidic circuit (i.e., nylon tubes filled with fluid) and truly soft and deformable body stemming from real-time tunable springs, the former serves as protoplasm and the latter is used for elastic actuators; and (2) a fully decentralized control using coupled oscillators with completely local sensory feedback mechanism is realized by exploiting the long-distance physical interaction between the body parts induced by the law of conservation of protoplasmic mass. Experimental result shows that this robot exhibits truly supple locomotion without relying on any hierarchical structure. The result obtained is expected to shed new light on design scheme for autonomous decentralized control system., The Japan Society of Mechanical Engineers, Japanese - 真正粘菌変形体をモチーフとした大自由度ソフトロボットの自律分散制御
梅舘拓也, 武田光一, 中垣俊之, 小林亮, 石黒章夫, 計測自動制御学会システム・情報部門学術講演会講演論文集(CD-ROM), 2009, ROMBUNNO.2C2-2, 24 Nov. 2009
Japanese - Experimental Verification of a Soft-bodied Robot with Large D.O.F. Inspired by True Slime Mold
武田光一, 北村太一, 梅舘拓也, 中垣俊之, 小林亮, 石黒章夫, 日本機械学会ロボティクス・メカトロニクス講演会講演論文集(CD-ROM), 2009, ROMBUNNO.2A2-F22, 24 May 2009
Japanese - イグノーベル賞授賞式顛末記
中垣俊之, 69, 31, 33, 2009 - 単細胞生物の情報処理
中垣俊之, 手老篤史, 三枝徹, 小林亮, 伊藤賢太郎, 日本生体医工学会大会プログラム・論文集(CD-ROM), 48th, ROMBUNNO.OS-14-1, 2009
Japanese - 2A2-F22 Experimental Verification of a Soft-bodied Robot with Large D. O. F. Inspired by True Slime Mold
TAKEDA Koichi, KITAMURA Taichi, UMEDACHI Takuya, NAKAGAKI Toshiyuki, KOBAYASHI Ryo, ISHIGURO Akio, The Proceedings of JSME annual Conference on Robotics and Mechatronics (Robomec), 2009, 0, _2A2, F22_1-_2A2-F22_4, 2009
This paper presents a soft-bodied amoeboid robot inspired by true slime mold. Significant features of this robot are twofold: (1) the robot has highly soft and deformable body stemming from real-time tunable springs and a balloon, the former is utilized as an outer skin of the body and the latter serves as protoplasm; and (2) a fully decentralized control using coupled oscillators with completely local sensory feedback mechanism is realized by exploiting the long-distance interaction between the body parts stemming from the law of conservation of protoplasmic mass. Experimental results show that this robot exhibits highly supple locomotion without relying on any hierarchical structure. The results obtained are expected to shed a new light on design methodology for autonomous decentralized control system., The Japan Society of Mechanical Engineers, Japanese - Autonomous Decentralized Control of an Amoeboid Robot by Exploiting Global Interaction Stemming from Protoplasm
北村太一, 梅舘拓也, 武田光一, 中垣俊之, 小林亮, 石黒章夫, 日本ロボット学会学術講演会予稿集(CD-ROM), 26th, ROMBUNNO.3H1-05, 09 Sep. 2008
Japanese - Dynamics and control for smart behaviors in an amoeba
中垣俊之, 三枝徹, 手老篤史, 小林亮, システム制御情報学会研究発表講演会講演論文集(CD-ROM), 52nd, 147, 148, 16 May 2008
Japanese - Mechanism and control for intelligent behaviors in an amoeba
Nakagaki Toshiyuki, Tero Atsushi, Saigusa Tetsu, Kobayashi Ryo, Proceedings of the Annual Conference of the Institute of Systems, Control and Information Engineers, 8, 0, 51, 51, 2008
We report here intelligent behaviors in an amoeboid organism of Physarum plasmodium. Topics reported are ability to solve some geometrical puzzles, ability to anticipate periodic climate changes and a kind of contemplative behavior. The ability is evaluated by biological experiments and mathematical models for a mechanism of intelligence are considered., The Institute of Systems, Control and Information Engineers, Japanese - アメーバの迷路解きに学ぼう (特集 現象を視る--〈現象数理科学〉への誘い)
手老 篤史, 小林 亮, 中垣 俊之, 数理科学, 46, 1, 7, 11, Jan. 2008
サイエンス社, Japanese - Maze-solving by true slime molds
小林 亮, 手老 篤史, 中垣 俊之, Cell technology., 26, 7, 769, 773, Jul. 2007
秀潤社, Japanese - Path finding method by true slime mold
手老 篤史, 中垣 俊之, 小林 亮, Materials integration, 20, 5, 55, 60, May 2007
ティー・アイ・シィー, Japanese - 知の創造から知の活用へ―北大創成科学共同研究機構 アメーバに学ぶ経路探索の方法
手老篤史, 中垣俊之, 小林亮, Mater Integr, 20, 5, 55, 60, 25 Apr. 2007
Japanese - 真正粘菌変形体の予想と想起~振動子を用いた学習と記憶のメカニズム~
手老篤史, 三枝徹, 中垣俊之, 物性研究, 87, 4, 613, 614, 20 Jan. 2007
物性研究刊行会, Japanese - Anticipation of periodic environmental changes in an amoeba
Tetsu Saigusa, Toshiyuki Nakagaki, NOISE AND FLUCTUATIONS, 922, 655, +, 2007
English - 生物に学ぶ最短経路探索アルゴリズム(生命リズムと振動子ネットワーク)
手老 篤史, 中垣 俊之, 小林 亮, 物性研究, 87, 4, 583, 583, 2007
この論文は国立情報学研究所の電子図書館事業により電子化されました。研究会報告, 物性研究刊行会, Japanese - 真正粘菌変形体の予想と想起 : 振動子を用いた学習と記憶のメカニズム(生命リズムと振動子ネットワーク)
手老 篤史, 三枝 徹, 中垣 俊之, 物性研究, 87, 4, 613, 614, 2007
この論文は国立情報学研究所の電子図書館事業により電子化されました。研究会報告, 物性研究刊行会, Japanese - 真正粘菌変形体の運動と情報処理について
小林 亮, 手老 篤史, 中垣 俊之, KOBAYASHI Ryo, TERO Atsushi, NAKAGAKI Toshiyuki, 盛岡応用数学小研究集会報告集, 2006, 26, 35, 01 Jan. 2007
自然界はさまざまな「かたち」で満ちている。それらの「かたち」（＝構造）はすべて何らかの自然のしくみによって自発的に形成されたものである｡我々はそれぞれの構造に対し､なぜそれが形成されたかを問うことができる。そして多くの場合その答えは自明ではなく､十分に研究対象となり得るものである｡実際､結晶成長･流体のパターン･粉粒体のパターン･化学反応波のつくるパターン等は､非線形科学の研究対象として恰好の材料を提供してきた｡ 上記のような無生物の構造形成に対しなぜを問うた場合には､それがいかにして形成されたかが説明されれば､満足が得られるであろう｡それに対し､生物の構造形成に対しなぜを問う場合は多少事情が異なる｡生物の構造には､ほとんどの場合｢機能｣が関係しているからである｡それゆえ､その構造がいかに生物の生存や増殖に有利であるか､という説明が一つの答えになるわけである。もちろん無生物の場合と同じように､その構造がいかにして形成されたかという説明も、もう一つの答えである。このように生物の構造形成においては常に｢機能｣や｢情報処理｣という要素がからんでいて、それが無生物の場合と異なる点であり､また面白い点でもある｡ さて、本稿で扱う真正粘菌変形体は、何ら分化した器官を持たないアメーバ生物で、それゆえ環境のセンシング･判断･運動を体全体で滞然一体となって行っている。すなわち｢感じる体､考える体､行動する体｣である｡その体制は高度に均質なサブシステムからなっているので､均質な要素からなる系の集団運動から情報機能が創発するしくみを解明するにはまたとないモデル系であると言えよう。, 岩手大学人文社会科学部, Japanese - Dynamics of transport network in slime mold
中垣俊之, 手老篤史, 小林亮, 生体・生理工学シンポジウム論文集, 21st, 97, 100, 17 Nov. 2006
Japanese - 真正粘菌変形体の振動パターンのモデリング (非線形現象のモデル化とその数理解析 RIMS研究集会報告集)
手老 篤史, 小林 亮, 中垣 俊之, 数理解析研究所講究録, 1522, 1522, 72, 81, Oct. 2006
京都大学数理解析研究所, Japanese - 真正粘菌変形体による最適ネットワーク (第2回生物数学の理論とその応用 RIMS研究集会報告集)
手老 篤史, 小林 亮, 中垣 俊之, 数理解析研究所講究録, 1499, 1499, 159, 166, Jul. 2006
京都大学数理解析研究所, Japanese - 生物における構造形成と情報処理 -真正粘菌をモデル生物として-
小林 亮, 手老 篤史, 中垣 俊之, 総合講演・企画特別講演アブストラクト, 2006, 1, 89, 98, 2006
一般社団法人 日本数学会, Japanese - Mathematical Models of the Motion and Information Processing of the plasmodium of Physarum polycephalum
小林亮, 手老篤史, 中垣俊之, 日本結晶成長学会誌, 32, 3, 236, 237, 17 Aug. 2005
Experiments of cell fusion and partial separation of the plasmodium of Physarum polycephalum is demonstrated. We introduce a mathematical model of coupled oscillator system with one conserved quantity, which will reproduce the experimental results well qualitatively., The Japanese Association for Crystal Growth (JACG), Japanese - A coupled-oscillator model with a conservation law for the rhythmic amoeboid movements of plasmodial slime molds
A Tero, R Kobayashi, T Nakagaki, PHYSICA D-NONLINEAR PHENOMENA, 205, 1-4, 125, 135, Jun. 2005
English - Collective movement of epithelial cells on a collagen gel substrate
H Haga, C Irahara, R Kobayashi, T Nakagaki, K Kawabata, BIOPHYSICAL JOURNAL, 88, 3, 2250, 2256, Mar. 2005
English - Collective movement of epithelial cells on collagen gel substrate
H Haga, C Irahara, R Kobayashi, T Nakagaki, K Kawabata, BIOPHYSICAL JOURNAL, 88, 1, 429A, 429A, Jan. 2005
English, Summary international conference - How does an amoeba tackle some geometrical puzzles?
Toshiyuki Nakagaki, Proceedings SICE Annual Conference, 3537, 3542, 2005 - 18aD01 Mathematical Models of the Motion and Information Processing of the plasmodium of Physarum polycephalum(NCCG-35)
Kobayashi R, Tero A, Nakagaki T, Journal of the Japanese Association for Crystal Growth, 32, 3, 236, 237, 2005
Experiments of cell fusion and partial separation of the plasmodium of Physarum polycephalum is demonstrated. We introduce a mathematical model of coupled oscillator system with one conserved quantity, which will reproduce the experimental results well qualitatively., The Japanese Association for Crystal Growth, Japanese - Obtaining multiple separate food sources: behavioural intelligence in the Physarum plasmodium
T Nakagaki, R Kobayashi, Y Nishiura, T Ueda, PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 271, 1554, 2305, 2310, Nov. 2004
English - Sequences of symmetry-breaking in phyllotactic transitions
H Yamada, R Tanaka, T Nakagaki, BULLETIN OF MATHEMATICAL BIOLOGY, 66, 4, 779, 789, Jul. 2004
English - 真正粘菌変形体の運動と形態形成の数理モデル (Pattern formation and asymptotic geometric structure in reaction-diffusion systems)
小林 亮, 中垣 俊之, 手老 篤史, 数理解析研究所講究録, 1356, 1356, 128, 131, Feb. 2004
京都大学数理解析研究所, Japanese - Smart network solutions in an amoeboid organism
T Nakagaki, H Yamada, M Hara, BIOPHYSICAL CHEMISTRY, 107, 1, 1, 5, Jan. 2004
English - 1SC01 Experiments and mathematical modeling for the phase dynamics of oscillation of the plasmodium of true slime mold
Kobayashi R, Tero A, Nakagaki T, Seibutsu Butsuri, 44, 0, S5, 2004
The Biophysical Society of Japan General Incorporated Association, Japanese - Morphology and physiological functions of communication network in an amoeboid organism.
中垣俊之, システム・情報部門学術講演会講演論文集, 2003, 15, 20, 11 Nov. 2003
Japanese - 粘菌変形体の流路ネットワークの形態形成 (複雑流体の数理3 研究集会報告書)
中垣 俊之, 小林 亮, 数理解析研究所講究録, 1305, 1305, 1, 7, Feb. 2003
京都大学数理解析研究所, Japanese - 真性粘菌変形体の運動の数理モデル (複雑流体の数理3 研究集会報告書)
小林 亮, 中垣 俊之, 数理解析研究所講究録, 1305, 1305, 8, 14, Feb. 2003
京都大学数理解析研究所, Japanese - Oscillation patterns in cytoplasmic networks of the Physarum plasmodium
H Yamada, T Nakagaki, TRAFFIC AND GRANULAR FLOW'01, 563, 568, 2003
English - Effective design of transportation network by an amoeba
Nakagaki T, Ueda T, Seibutsu Butsuri, 43, 0, S113, 2003
The Biophysical Society of Japan General Incorporated Association, English - Behaviors of true slime mold regarded as coupled oscillators
Nakagaki T, Kobayashi R, Meeting Abstracts of the Physical Society of Japan, 58, 0, 254, 254, 2003
The Physical Society of Japan, Japanese - Macroscopic behavior and cellular computation in an amoeboid organism.
中垣俊之, 電気学会産業システム情報化研究会資料, IIS-02, 23-33, 29, 32, 04 Dec. 2002
Japanese - Morphogenesis of transportation network based on cellular rhythms in true slime mold.
中垣俊之, 生体・生理工学シンポジウム論文集, 17th, 373, 376, 09 Sep. 2002
Japanese - Morphogenesis of transportation network based on cellular rhythms in true slime mold
NAKAGAKI Toshiyuki, 生体・生理工学シンポジウム論文集, 17, 373, 376, 09 Sep. 2002
Japanese - 「生物リズムの理論的基礎と多様性」について 振動するのか,定常値に落ち着くのか,それが問題だ(原標題は英語)
中垣俊之, 日本時間生物学会会誌, 8, 1, 32, 37, May 2002
Japanese - To be oscillatory or stationary, that is a question
中垣 俊之, 日本時間生物学会会誌: Journal of Chronobiology, 8, 1, 32, 37, 01 May 2002
Japanese - Patterns and Computing in the Amoeba-like Organism.
小林亮, 中垣俊之, 理論応用力学講演会講演論文集, 51st, 183, 184, 22 Jan. 2002
Japanese - Smart behavior of true slime mold in a labyrinth
T Nakagaki, RESEARCH IN MICROBIOLOGY, 152, 9, 767, 770, Nov. 2001
English, Book review - 迷路を解く巨大アメーバ細胞 粘菌
中垣俊之, 山田裕康, 生物物理, 41, 5, 244, 246, Oct. 2001
The Biophysical Society of Japan General Incorporated Association, Japanese - Solving a Maze by the Amoeboid Cell of True Slime Mold
NAKAGAKI Toshiyuki, YAMADA Hiroyasu, Seibutsu Butsuri, 41, 5, 244, 246, 25 Sep. 2001
The Biophysical Society of Japan General Incorporated Association, Japanese - Path finding by tube morphogenesis in an amoeboid organism
T Nakagaki, H Yamada, A Toth, BIOPHYSICAL CHEMISTRY, 92, 1-2, 47, 52, Aug. 2001, [Lead author]
English - リング状に結合した粘菌振動子系における時空間振動パターン
高松敦子, 田中玲子, 山田裕康, 中垣俊之, 藤井輝夫, 遠藤勲, 自律分散システム・シンポジウム資料, 13th, 411, 414, 26 Jan. 2001
Japanese - 振動子の結合形態と位相パターン 粘菌のネットワーク形態ダイナミクスの解析をめざして
山田裕康, 中垣俊之, 田中玲子, 高松敦子, 自律分散システム・シンポジウム資料, 13th, 421, 424, 26 Jan. 2001
Japanese - 粘菌振動子系の解析 対称系のHopf分岐理論の適用
田中玲子, 山田裕康, 中垣俊之, 高松敦子, 自律分散システム・シンポジウム資料, 13th, 415, 420, 26 Jan. 2001
Japanese - Do single-cell organisms have intelligence? Slime mould, for one, can solve a maze and find food
Toshiyuki Nakagaki, Times Higher Educatio Supplement, 1479, March 23, 24, 2001 - Amoeboid organisms may be more clever than we thought!
Toshiyuki Nakagaki, Newsletter of RIKEN Frontier Research System, February, 8, 12, 2001 - Solving a maze by true slime mold
Nakagaki T, Seibutsu Butsuri, 41, 0, S3, 2001
The Biophysical Society of Japan General Incorporated Association, English - Transition of phyllotaxis through symmetry breaking of reflection
Yamada H, Tanaka R, Nakagaki T, Meeting Abstracts of the Physical Society of Japan, 56, 0, 286, 286, 2001
The Physical Society of Japan, Japanese - Network Formation and Cellular Rhythms in the Physarum plaswodium.
中垣俊之, 山田裕康, 日本化学会非線形反応と協同現象シンポジウム, 10th, 28, 29, 18 Nov. 2000
Japanese - 粘菌の収縮リズムと数理モデル (反応拡散系:生物・化学における現象とモデル)
中垣 俊之, 山田 裕康, 数理解析研究所講究録, 1167, 65, 68, Aug. 2000
京都大学数理解析研究所, Japanese - Interaction between cell shape and contraction pattern in the Physarum plasmodium
T Nakagaki, H Yamada, T Ueda, BIOPHYSICAL CHEMISTRY, 84, 3, 195, 204, May 2000
English - Morphology and Behaviour of the Physarum Plasmodium.
山田裕康, 中垣俊之, 自律分散システム・シンポジウム資料, 12th, 303, 306, 21 Jan. 2000
Japanese - Morphology and Behaviour of the Physarum Plasmodium
YAMADA Hiroyasu, NAKAGAKI Toshiyuki, 自律分散システム・シンポジウム資料 = SICE Symposium on Decentralized Autonomous Systems, 12, 303, 306, 21 Jan. 2000
Japanese - Rhythmic contraction and its fluctuations in an amoeboid organism of the Physarum plasmodium.[Quantum Information (]G0002[)](共著)
Toshiyuki Nakagaki, Hiroyasu Yamada, World Scientific Publisher Co., 107, 124, 2000
World Scientific Publisher Co. - Geometry of tube-network in the Physarum plasmodium
Nakagaki T, Yamada H, Seibutsu Butsuri, 40, 0, S99, 2000
The Biophysical Society of Japan General Incorporated Association, Japanese - Structure of tubes and endoplasmic flow in the true slime mould
Yamada H, Nakagaki T, Meeting Abstracts of the Physical Society of Japan, 55, 0, 258, 258, 2000
The Physical Society of Japan, Japanese - Network formation and oscillation pattern of endoplasmic veins in the plasmodium of true slime mould
Yamada H, Nakagaki T, Meeting Abstracts of the Physical Society of Japan, 55, 0, 247, 247, 2000
The Physical Society of Japan, Japanese - Dispersion relations to oscillatory reaction-diffusion systems with the self-consistent flow
Hiroyasu Yamada, Toshiyuki Nakagaki, 24 Jun. 1999
Dispersion curves to a oscillatory reaction-diffusion system with the
self-consistent flow have obtained by means of numerical calculations. The flow
modulates the shape of dispersion curves and characteristics of traveling
waves. The point of inflection which separates the dispersion curves into two
branches corresponding to trigger and phase waves, moves according to the value
of the advection constant. The dynamics of phase wave in
reaction-diffusion-advection equations has been studied by limit cycle
perturbations. The dispersion relation obtained from the phase equation shows
that the competition between diffusion and advection constants modulates the
oscillation frequency from the bulk oscillation in the long-wave dynamics. Such
a competition implies that phase waves with the flow have a wider variety of
dynamics than waves without the flow., Technical report - 粘菌変形体の反応拡散移流モデルにおける非線型分散関係
山田裕康, 中垣俊之, 伊藤正美, 日本物理学会講演概要集, 54, 1, 639, 639, 15 Mar. 1999
The Physical Society of Japan (JPS), Japanese - Patten Formation of Rhythmic Contraction with Vein-Network Morphology of the Protoplasmic Streaming in the Physarum Plasmodium
YAMADA Hiroyasu, NAKAGAKI Toshiyuki, ITO Masami, 自律分散システム・シンポジウム資料 = SICE Symposium on Decentralized Autonomous Systems, 11, 109, 114, 18 Jan. 1999
Japanese - 粘菌変形体の収縮リズムパターンと行動
中垣俊之, 数理生物ニュースレター, 29, 63, 78, 1999 - Pattern Formation of Rhythmic Contraction with Vein-Network Morphology of the Protoplasmic Streaming in the Physarum Plasmodium.
山田裕康, 中垣俊之, 伊藤正美, 自律分散システム・シンポジウム資料, 11th, 109, 114, Jan. 1999
Japanese - 25aPS-30 Plane waves for λ-ω system with advection terms of phase gradients
YAMADA H, NAKAGAKI T, Meeting Abstracts of the Physical Society of Japan, 54, 0, 227, 227, 1999
The Physical Society of Japan, Japanese - 28a-P-11 Nonlinear Dispersion Relation for a Reaction-Diffusion-Advection Model of the Physarum Plasmodium
Yamada H, Nakagaki T, Itoh M, Meeting Abstracts of the Physical Society of Japan, 54, 0, 639, 639, 1999
The Physical Society of Japan, Japanese - Reaction-diffusion-advection model for pattern formation of rhythmic contraction in a giant amoeboid cell of the Physarum
NAKAGAKI Toshiyuki, YAMADA Hiroyasu, ITO Masami, 生体・生理工学シンポジウム論文集, 13, 437, 440, 09 Sep. 1998
English - 粘菌変形体収縮運動の時空パターン形成における原形質流動の効果 III
山田裕康, 中垣俊之, 伊藤正美, 日本物理学会講演概要集, 53, 2, 856, 856, 05 Sep. 1998
The Physical Society of Japan (JPS), Japanese - 粘菌変形体における管状構造のネットワーク形成
中垣 俊之, 山田 裕康, 形の科学会誌 = Bulletin of the Society for Science on Form, 13, 1, 56, 57, Jun. 1998
Japanese - Effects of Protoplasmic Streaming on Pattern Formation of Cyclic Contraction in Physarum Plasmodium. II.
山田裕康, 中垣俊之, 伊藤正美, 日本物理学会講演概要集(年会), 53, 1, 729, Mar. 1998
Japanese - Model for pattern formation of rhythmic contraction in the Physarum plasmodium : Non-locally coupled map lattice model
NAKAGAKI Toshiyuki, YAMADA Hiroyasu, ITO Masami, 自律分散システム・シンポジウム資料 = SICE Symposium on Decentralized Autonomous Systems, 10, 5, 8, 20 Jan. 1998
Japanese - Model for Patten Formation of Rhythmic Contraction in the Physarum Plasmodium II : Reaction-Diffusion-Advection Model
YAMADA Hiroyasu, NAKAGAKI Toshiyuki, ITO Masami, 自律分散システム・シンポジウム資料 = SICE Symposium on Decentralized Autonomous Systems, 10, 9, 12, 20 Jan. 1998
Japanese - Pattern formation of reaction-diffusion model having self-determined flow in relation to amoeboid behaviour.(共著)
Hiroyasu Yamada, Toshiyuki Nakagaki, Masami Ito, RIKEN Review, 19, 148, 1998 - Formation of network of tubular structure in slime mold plasmodium.
中垣俊之, 山田裕康, 形の科学会報, 13, 1, 56, 57, 1998
Japanese - Model for Pattern Formation of Rhythmic Contraction in the Physarum Plasmodium. II. Reaction-Diffusion-Advection Model.
山田裕康, 中垣俊之, 伊藤正美, 自律分散システム・シンポジウム資料, 10th, 9, 12, Jan. 1998
Japanese - Model for pattern formation of rhythmic contraction in the Physarum plasmodium. Non-locally coupled map lattice model.
中垣俊之, 山田裕康, 伊藤正美, 自律分散システム・シンポジウム資料, 10th, 5, 8, Jan. 1998
Japanese - Effects of Protoplasmic Streaming on Pattern Formation of Cyclic Contraction in Physarum Plasmodium III
YAMADA H, NAKAGAKI T, ITO M, Meeting Abstracts of the Physical Society of Japan, 53, 0, 856, 856, 1998
The Physical Society of Japan, Japanese - Effects of Protoplasmic Streaming on Pattern Formation of Cyclic Contraction in Physarum Plasmodium II
YAMADA H, NAKAGAKI T, ITO M, Meeting Abstracts of the Physical Society of Japan, 53, 0, 729, 729, 1998
The Physical Society of Japan, Japanese - Amoeboid behaviors viewed from self-organization of coupled oscillators in the Physarum plasmodium.
中垣俊之, 山田裕康, 伊藤正美, 情報処理学会シンポジウム論文集, 97, 10, 31, 37, Dec. 1997
Japanese - Action spectroscopic evidence for phytochrome in the photo-morphogenesis of the Physarum plasmodium
KAKIUCHI Y, NAKAGAKI T, KOYA S, UEDA T, Biophysics, 37, S185, Oct. 1997
The Biophysical Society of Japan General Incorporated Association, Japanese - Amoeboid behavior viewed from self-organization of coupled collective oscillators
NAKAGAKI Toshiyuki, YAMADA Hiroyasu, ITO Masami, 生体・生理工学シンポジウム論文集, 12, 161, 164, 04 Sep. 1997
Japanese - Amoeboid behavior viewed from self-organization of coupled collective oscillators.
中垣俊之, 山田裕康, 伊藤正美, 生体・生理工学シンポジウム論文集, 12th, 161, 164, Sep. 1997
Japanese - Effects of Protoplasmic Streaming on Pattern Formation of Cyclic Contraction in Physarum Plasmodium.
山田裕康, 中垣俊之, 日本物理学会講演概要集(分科会), 1997, 855, Sep. 1997
Japanese - Reaction diffusion advection model in contraction rhythm of slime mold plasmodium.
山田裕康, 中垣俊之, 伊藤正美, 形の科学会報, 12, 3, 20, 21, 1997
Japanese - 8a-P-12 Effects of Protoplasmic Streaming on Pattern Formation of Cyclic Contraction in Physarum Plasmodium
YAMADA Hiroyasu, NAKAGAKI Toshiyuki, Meeting Abstracts of the Physical Society of Japan, 52, 0, 855, 855, 1997
The Physical Society of Japan, Japanese - Phase swtching of oscillaory contraction in relation to global regulation of amoeboid behavior by the plasnodium of Physarum polycephalum.
中垣俊之, 上田哲男, 日本生物物理学会年会講演予稿集, 33rd, S69, Aug. 1995
Japanese - NONSPECIFIC ACTIVITY OF (+/-)-CP-96,345 IN MODELS OF PAIN AND INFLAMMATION
A NAGAHISA, R ASAI, Y KANAI, A MURASE, M TSUCHIYANAKAGAKI, T NAKAGAKI, TC SHIEH, K TANIGUCHI, BRITISH JOURNAL OF PHARMACOLOGY, 107, 2, 273, 275, Oct. 1992
English - Article about mathematical model of slime mold
T. Nakagaki, R. Kobayashi, Y. Nishiura, The Asahi Shinbun （Evening Edition） Apr 19, 2005 - Learn from slime mold of optimal route
T. Nakagaki, R. Kobayashi, Y. Nishiura, The Asahi Shinbun （Evening Edition） Apr 19, 2005 - Cell Info.-NSC Workshop "Looking for a dynamic life statue of slime mold"
T. Ueda, T. Nakagaki, Y. Nishiura, Ryo. Kobayashi, Hokkaido University (Sapporo) (Feb 25-26, 2002) - NSC-Cell Info. Symposium on “Cell Dynamics And Physiological Functions In Physarum”
Tetsuo Ueda, Toshiyuki Nakagaki, Yasumasa Nishiura, Ryo Kobayashi, Hokkaido University (Sapporo) (Mar 25-26, 2002) - The 10th RIES-Hokudai International Symposium on "綾"
Ichiro Tsuda, Akira Ishibashi, Kuniharu Ijiro, Tetsuo Ueda, Keiji Sasaki, Yuzuru Sato, Toshiyuki Nakagaki, Yasumasa Nishiura, Yutaka Yamaguchi, Hokkaido University (Sapporo) (Dec 8-9, 2008)
Books and other publications
- 障害をしゃべろう! : 『コトノネ』が考えた、障害と福祉のこと
里見, 喜久夫, 新, 雅史, いがらし, みきお, 石川, 直樹, 稲垣, 栄洋, 大友, 良英, 大嶋, 栄子, 岡, 檀, 小川, 洋子, 空門, 勇魚, 照屋, 勇賢, 中垣, 俊之 (大学教員), 中島, 隆信, 中屋敷, 均, 藤原, 辰史, 森山, 徹, 松村, 圭一郎, 山田, 太一
青土社, Oct. 2021, 9784791774159, 279p, Japanese - Natural computing and beyond : Winter School Hakodate 2011, Hakodate, Japan, March 2011 and 6th International Workshop on Natural Computing, Tokyo, Japan, March 2012, Proceedings
Yasuhiro Suzuki, 中垣 俊之
Springer, 2013, 9784431543930, viii, 153 p., English - ゴルビツキー/スチュアート対称性の破れとパターン形成の数理
Golubitsky Martin, Stewart Ian Nicholas, 山田 裕康, 高松 敦子, 中垣 俊之, 田中 玲子
丸善, 2003, 4621072552, xxiv, 562p, Japanese
Affiliated academic society
Research Themes
- 人工･天然バイオ界面現象の理解に基づく生体親和性材料の設計・合成
CORE2-Aラボ
Apr. 2025 - Mar. 2026
田中賢, 林智広, 中垣俊之, 西上幸範, 大村拓也, 櫻井保志, 井関隆之
人と知と物質で未来を創るクロスオーバーアライアンス, 2025C002 - 繊毛虫・アメーバの集団的空間探査と空間活用のアルゴリズムの解明
科学研究費助成事業
Oct. 2021 - Mar. 2026
棟朝雅晴, 田中良巳, 佐藤勝彦, 國田樹
日本学術振興会, 学術変革領域研究（A）, 北海道大学, Principal investigator - ジオラマ環境で覚醒する原生知能を定式化する細胞行動力学
科学研究費助成事業
Oct. 2021 - Mar. 2026
石川拓司, 紫加田知幸, 柴小菊, 篠原恭介, 菊池謙次, 石本健太, 飯間信
日本学術振興会, 学術変革領域研究（A）, 北海道大学, Principal investigator - Advanced Bioimaging Support
Grants-in-Aid for Scientific Research
2016 - 2021
KANO Masanobu, Kano Masanobu, Ueno Naoto, Maruyama Megumi, Mano Shoji, Watanabe Takaki, Hiraoka Yasushi, Komoto Shinya, Miyazawa Atsuo, Sadato Norihiro, Shimanuki Mizuki, Imamura Takeshi, Nonaka Shigenori, Fujimori Toshihiko, Matsuda Michiyuki, Nabekura Junichi, Inaba Kazuo, Higashiyama Tetsuya, Nemoto Tomomi, Okada Yasushi, Furuta Toshiaki, Sugaya Yuki, Nakagaki Toshiyuki, Mitsuoka Kaoru, Sakamoto Hirotaka, Nakamura Kei-ichiro, Koike Masato, Furuse Mikio, Fukazawa Yugo, Watanabe Masahiko, Aoki Shigeki, Kasai Kiyoto, Uchida Seiichi, Yasunaga Takuo, Higaki Takumi, Oda Yoshihisa, Kimori Yoshitaka, Hasezawa Seiichiro
ABiS established a bioimaging support network with National Institute for Physiological Sciences and National Institute for Basic Biology as core institutions, and provided cutting-edge light microscopy, electron microscopy, magnetic resonance imaging, and image analysis technologies to Grant-in-Aid for Scientific Research recipients. Applications was received from most of the categories of Grant-in-Aid for Scientific Research in Biology, thus providing support to a wide range of research fields. The number of applications was 1,506 over 6 years. Some of the results were published in 396 papers (as of March 31, 2022), contributing to the promotion of Grant-in-Aid projects that require advanced bioimaging technology.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas ― Platforms for Advanced Technologies and Research Resources, National Institute for Physiological Sciences, 16H06280 - Fluctuation and Rheology of Soft Matter in Nonequilibrium Steady States
Grants-in-Aid for Scientific Research
Jun. 2013 - Mar. 2018
Orihara Hiroshi
Shear flow can change not only the structure of soft matter but also the nature of fluctuation and response by breaking the time-reversal symmetry. We constructed a system combining a rheometer and a confocal laser scanning microscope to mainly observe non-equilibrium structures and fluctuations under shear flow. We successfully observed anomalous fluctuation and response in nematic liquid crystal and colloidal systems, which are brought about by non-conservative forces characteristic to non-equilibrium systems. As for the liquid crystal, we analyzed the results in terms of the Ericksen-Leslie theory and furthermore derived a modified fluctuation-dissipation relation.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Hokkaido University, 25103006 - 数理科学と生体生命情報科学との連携による生命知の基本アルゴリズムの探求
Grant-in-aid for Scientific Research
Apr. 2014 - Mar. 2017
中垣俊之
Japan society for promotion of science, Principal investigator, Competitive research funding - Microrheology of non-Newtonian fluids under shear flow
Grants-in-Aid for Scientific Research
Apr. 2014 - Mar. 2017
Hiroshi Orihara, NAKAGAKI TOSHIYUKI
Soft matter such as polymers and liquid crystals has microscopic structures, which interplay with flow. We have investigated the effect of the structure on the rheological properties related to shear flow by applying microrheology. First, we observed both orientation and shear flow fluctuations at equilibrium to obtain the cross-correlation function between them, and elucidated the existence of interplay. Furthermore, we compared the experiment with a theoretical result derived from the Ericksen-Leslie Theory. Next, we observed sheared particles dispersed in a xthantan solution and found an anomalous diffusion due to the molecular interaction.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, 26289032 - 細胞運動における細胞レオロジーと応力場のクロストーク
Grant-in-aid for Scientific Research
Apr. 2013 - Mar. 2015
中垣俊之
Japan society for promotion of science, Principal investigator, Competitive research funding - 単細胞生物に学ぶ生命知の基本アルゴリズム
研究助成
Apr. 2013 - Mar. 2014
中垣 俊之
秋山記念生命科学振興財団, Principal investigator, Competitive research funding - 生物輸送ネットワークのダイナミクス
戦略的国際科学技術協力推進事業
Apr. 2011 - Mar. 2014
中垣 俊之
科学技術振興機構, Principal investigator, Competitive research funding - 生物ロコモーションに学ぶ大自由度システムの新展開
戦略的創造研究推進事業
Apr. 2008 - Mar. 2013
小林亮
科学技術振興機構, Competitive research funding - Analysis of propulsion and transport by the interaction between self-driven boundary motion and associated flow
Grants-in-Aid for Scientific Research
2011 - 2013
IIMA Makoto, NAKAGAKI Toshiyuki, KORI Hiroshi
Synchronization of spring-loaded cylinders in uniform flow was analyzed numerically. In the regime of Reynolds number where vortex separation is observed, synchronization of two cylinders with different natural frequencies was observed. The coupling function of phase model of this system was obtained by the data of the motions of the center of mass. Peristaltic pumping of true slime mold was also analyzed. Model consisting of chemical transport and boundary motion and model consisting of simple phase equation with Neumann boundary condition with non-zero gradient were analyzed. Characteristic spatio-temporal pumping pattern was reproduced.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), Hiroshima University, 23540433 - Experimentalevaluationofevolutionarydevelopmentofmemory abilityanditsanalysisbynonlineardynamics.
Grants-in-Aid for Scientific Research
Apr. 2008 - Mar. 2012
NAKAGAKI Toshiyuki, SAIGUSA Tetsu
Bio-systems are nature-made machine for information processing. To study how they workis interesting from a scientific point of view and is important from a technological point ofview. In this project, we focus on a model organism of Physarum plasmodium as one of themost elementary creature. The organism’s capacity of information processing is evaluatedby an experiment and its algorithm is proposed. We found that a cell can anticipate aperiodic environmental event and recall it later, and that the capacity can be realized by acollective motion of biochemical poly-rhythmic oscillations. We suggested that the capacityof this kind may be common widely in phyllogenetic tree from protozoa to plant and animal.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Principal investigator, Competitive research funding, 20300105 - Study on the strong interaction among spatially localized patterns in dissipative systems
Grants-in-Aid for Scientific Research
2009 - 2012
NISHIURA Yasumasa, UEDA Keiichi, TERAMOTO Takashi, IIMA Makoto, NAKAGAKI Toshiyuki, TAKAGI Seiji, EI Shinichiro, NAGAYAMA Masaharu
Spatially localized traveling patterns appear ubiquitously in nature such as neural system, gas-discharge phenomena, chemical reaction, binary convection, and motion of true slime mold. They display a variety of dynamic patterns like annihilation, coalescence,and splitting via collisions or interaction with environments. For the comprehensive understanding of these phenomena, we combine several theoretical and numerical approaches like local bifurcation analysis of higher codimension, numerical path-tracking, and reduction to finite dimensional systems, which allow us to clarify the mathematical mechanism controlling behind those dynamics.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), 21340019 - Optimization in Natural System: ants, bees and slime moulds
Research Grant
Sep. 2007 - Aug. 2010
SUMPTER David
Human Frontier Science Program, Competitive research funding - Mathematical Study of Pattern Formation and Information in Biological Systems
Grants-in-Aid for Scientific Research
2007 - 2010
KOBAYASHI Ryo, NAKAGAKI Toshiyuki, MIURA Takashi
We demonstrated experimentally that the plasmodium of Physarum polycephalum can promote formation of networks equivalent to the transportation network such as railroad system. We presented a new method of network design by constructing mathematical models. Also, we proposed models which describe how information works in the determining process of the geometry of early cleavage and in the formation of branching structure such as lung and blood vessel. We developed mathematical methods that can describe the mechanism combining biological pattern formation and information.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hiroshima University, 19340023 - トポロジー理工学の創成
21世紀COEプログラム
Apr. 2004 - Mar. 2008
丹田 聡
文部科学省, Competitive research funding - 粘菌アルゴリズム:制約条件付き最適化問題の生物模倣型解法
科学研究費助成事業
Apr. 2006 - 2007
中垣 俊之, 小林 亮
アメーバ生物である粘菌変形体は、何ら分化した器官を持たないので、環境のセンシング・判断・運動を体全体で渾然一体となって行う。感じる体、判断する体である。その体は高度に均質なサブシステムからなっている。したがって、均質な要素からなる系の集団運動から情報機能が創発するしくみを解明するにはまたとないモデル系である。この利点を最大限に活かして、粘菌の最適化アルゴリズムの抽出に取り組み、以下の成果を得た。
1)小さい餌場所を数個程度あちこちに配置すると粘菌はネットワーク形態を成して全ての餌場所にありついた。このネットワークは、全長が短くなるような性質を有しており、時々、真に最短なルートしめした。これにヒントを得て、一般的なスタイナー問題(平面上に任意の個数の点が任意の場所にある場合、全ての点を結ぶ最短経路を求める問題)を解く計算法を考案し、パラメタサーチと性能評価をくりかえし、ソルバーを提案できた。
2)都市間交通(道路や鉄道など)ネットワークの持つべき性質である、全長の最短性、任意の二つの餌場所間の連絡性、事故による管の断線に対する連結補償性に関して、これら三つの性質の重みを変えて自在に設計するような粘菌型計算法を提案できた。
粘菌の計算能力はまだまだ底が知れないこともわかった。今後、この実験系をさらに利用することにより、新たな生物型計算法のヒントが得られるものと期待できる。そのような発展的糸口を与えることが、本萌芽研究により成し遂げられた。
日本学術振興会, 萌芽研究, 北海道大学, Principal investigator, Competitive research funding, 18650054 - 生物に学ぶ動的ネットワーク最適化問題の研究
科学研究費助成事業
2006 - 2007
小林 亮, 中垣 俊之
真正粘菌変形体は原始的な神経系さえ持たない、単純な体制を持った多核単細胞生物であるが、迷路を解いたり最短経路問題を解く能力があることが、中垣らによって示されている。彼らが迷路を解く際には最終的なルートに管を残すという形を取るが、単純に迷路を解くというだけでなく、餌の量の多さによって多重にルートを残したり、単独の管を残したりと、状況に応じた反応をしている。我々はこのことを実験的に明らかにし、それを再現する数理モデルを提出した。
また、真正粘菌変形体は多くの餌を提示された場合には、それらをできるだけ総長が短い経路でつなぐが、これは数理的にいえばスタイナー問題を近似的に解いていることに他ならない。NP完全問題であるスタイナー問題は、最短経路探索問題よりも遙かに困難な問題であり、まともに解けば計算時間の指数的発散という問題に直面するわけであるが、ここでも真正粘菌変形体は「知性」を発揮している。我々はPhysarum Solverを以下のように拡張することにより、スタイナー問題を近似的に解く方法を開発した。まず与えられた点を含む凸包を細かいネットワークで覆い、短い時間間隔ごとに2頂点のペアをランダムに選び(実際はまず一方を選び、他方はそれからなるべく遠い頂点を選ぶ)、それにPhysarum Solverを適用するのである。このようにすると、スタイナー最小木ではないが、それと位相的に等価な経路を求めることができる。これを元にスタイナー点の位置を緩和することにより、スタイナー最小木に到達できるのである。少なくとも正解がわかる程度に頂点数が少ない場合についてはほぼ確実に正解に到達することがシミュレーションによって確かめられた。
日本学術振興会, 萌芽研究, 広島大学, 18654022 - Emergence of cellular intelligence based on selection of various dynamic pattems
Grants-in-Aid for Scientific Research
2006 - 2007
TAKAGI Seiji, UEDA Tetsuo, NAKAGAKI Toshiyuki
1. Recognition of the difference in the fractal dimension of a solid surface by the Physarum plasmodium.
We investigated rhythmic motions of the plasmodium on an area between fractal and smooth surfaces. Initial synchronous oscillation switched to anti-phase oscillation between the parts of the plasmodium on the fractal and smooth surface areas.
2. Emergence of various spatiotemporal patterns of thickness oscillation.
The emergence and transitions of various spatiotemporal patterns of thickness oscillation.
The emergence and transitions of various spatiotemporal patterns of thickness oscillation were studied in the freshly isolated protoplasm of the Physarum plasmodium. New patterns, such as standing waves, chaotic pattern and rotating spirals, developed successively before the well-documented synchronous pattern appeared.
3. Locomotive Mechanism of Physarum Plasmodia
We investigate how an amoeba mechanically moves its own center of gravity using the model organism Physarum plasmodium. Time-dependent velocity fields of protoplasmic streaming over the whole plasmodia were measured with a particle image velocimetry program developed for this work. Combining these data with measurements of the simultaneous movements of the plasmodia revealed a simple physical mechanism of locomotion.
4. A new kind of behavior
We found a new kind of behavior that seems to be 'contemplative' in the Physarum plasmodium. The plasmodium migrating in a narrow lane stops moving for a period of time when it encounters the presence of a chemical repellent. After stopping period, the organism suddenly begins to move again in one of three different ways depending on the repellent concentration, namely penetration, splitting into two fronts and turning back. A model based on reaction-diffusion equations, or Gray-Scott model, succeeds to reproduce the experimental observation.
5. Mechanism of signal integration
To investigate the mechanism of intracellular signal integration, stimulus-responses of the plasmodium were studied at the levels of receptor membrane and cell behavior. Signals of attractants and repellents do not interfere at the receptor level, while avoidance response shifts up to 100 times higher repellent concentration as the attractant concentration increases. We proposed a simple molecular mechanism of information integration which can reproduce the experimental results well.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), Hokkaido University, 18500229 - Solving Geometrical Puzzles by the True Slime Mold and Its Intracellular Computational Algorithm
Grants-in-Aid for Scientific Research
Apr. 2003 - 2006
UEDA Tetsuo, NAKAGAKI Toshiyuki, TAKAGI Seiji, NISHIURA Yasumasa, KOBAYASHI Ryo
With use of the single giant amoeboid cell of the Physarum plasmodium, we performed unconventional experiments concerning cellular intelligence and also constructed mathematical models based on nonlinear intracellular dynamics for clarifying computational algorithm. (1) The organism solved such geometrical puzzles as maze problems, Steiner problems, Fermart problems. (2) The formation of vein networks was governed by the trade-off among minimum path-length, assurance for not-breaking apart, and minimum danger, etc. (3) Mathematical models were constructed based on a coupled oscillators where the conservation of mass and the regional difference of the visco-elastic properties were taken into account. The model simulated synchronous oscillation patterns observed in the Physarum. (4) A mathematical model was constructed by taking into adaptive mechanism for the formation of veins. The model simulated maze solving by the Physarum, Steiner problems and Fermart problems.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Hokkaido University, Principal investigator, Competitive research funding, 15300098 - 生物における管のネットワークのダイナミクスの数理的研究
科学研究費助成事業
2004 - 2005
小林 亮, 中垣 俊之
中垣らは、真正粘菌変形体が迷路を解いたり、最短経路探索問題を解く能力があることを、2000年にNatureに発表した。我々は真正粘菌変形体がどのようにこれらの問題を解いているのかを観察し、それを数理的に記述することにより、グラフ上の最短経路探索問題を解く新しいシステム□Physarum Solver-を開発した。
各エッジに長さが与えられた連結無向グラフにおいて2つのノード間の最も短いパスを見いだすのが、最短経路探索問題であるが、迷路の問題はこのような形で記述される。
グラフを水道管のネットワークとみなし、2つのノードの一方から水を流し込み、他のノードから水が流れ出るという状況を考えると、水の流れの様子はネットワーク上のPoisson方程式を解くことで求めることができる。粘菌では原形質流動の流量に対し管の太さが適応的に変化するという性質があり、このことが迷路を解くことを可能にしていると考えられる。これに倣って、流量に対し管の太さが適応的に変化するようにモデルを構成すると、ある管は時間とともに太くなり、ある管は細くなるといった変化が生じる。そして、最終的に残った管が迷路の解を与えるのである。いずれの場合も、袋小路の部分は直ちに消えるが、適応的な変化を与える関数形によって、競合的なパスの漸近挙動は異なる。関数が線形である場合には、どのような初期値に対しても必ず最終的に最短経路が得られることが、シミュレーションにより確認された(簡単なグラフの場合には数学的証明も可能)。このPhysarum Solverでは計算時間がノード数の約1.32乗に比例しており、最短経路探査苦悶を解くアルゴリズムとしてはかなり速いものであり、しかも必ず最短経路に到達できるという長所がある。カーナビゲーションやインターネットにおける経路探索への応用が考えられる。
日本学術振興会, 萌芽研究, 広島大学, 16654017 - Dynamic mechanism of maze-solving and cell architecture in Physarum
Grants-in-Aid for Scientific Research
Apr. 2001 - 2002
NAKAGAKI Toshiyuki, UEDA Tetsuo
We reported that an amoeboid organism can solve a sort of optimization problem by using pattern formation of cellular rhythms.
We presented evidence that the giant amoeboid organism, the true slime mold, constructed a network appropriate for maximizing nutrient uptake. The body of the plasmodium of Physarum polycephalum contains a network of tubular elements by means of which nutrients and chemical signals circulate through the organism. When food pellets were presented at different points on the plasmodium it accumulated at each pellet with a few tubes connecting the plasmodial concentrations. The geometry of the network depended on the positions of the food sources. Statistical analysis showed that the network geometry met the multiple requirements of a smart network : short total length of tubes, close connections among all the branches (a small number of transit food-sites between any two food-sites) and tolerance of accidental disconnection of the tubes. These findings indicate that the plasmodium can achieve a better solution to the problem of network configuration than is provided by the shortest connection of Steiner's minimum tree.
Morphogenesis of the tube structure is induced depending on spatio-temporal patterns of cellular rhythms including mechanical, biochemical and electrical oscillations. Namely, geometrical morphology of the network is determined by the oscillation patterns. Chemical stimulation of the food to the organism leads to transition of the oscillation patterns since slight changes in oscillation frequency and cellular stiffness are induced around the stimulated site. Mechanism of the path finding by the organism is proposed in terms of pattern formation of the cellular rhythms. Along this line, a mathematical model for self-organization of transport network was proposed and discussed.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), HOKKAIDO UNIVERSITY, Principal investigator, Competitive research funding, 13831001 - Emergence of intelligence by cell shape changes in a giant amoeboid cell of the true slime mold Physarum
Grants-in-Aid for Scientific Research
2001 - 2002
UEDA Tetsuo, NAGASAKI Toshiyuki
A living cell is an intelligent chemical system which works dynamically by complex chemical reactions. The objective of the present research is to elucidate the cellular organization in terms of molecular synchronization with the aim to propose a new guideline for manufacturing functionality materials. We use a large amoeboid organism, the plasmodium of the true slime mold Physarum polycephalum, and study mechanisms of (1) organization of time order, (2) optimal design of cell shape, and (3) dynamical synchronization by simulation.
1. Organization of time order
By analyzing a long-term changes in the cell shape, 7 oscillatory components are found, periods ranging from a few secnds to 10h. All other oscillatory phenomena, such as cell cycle, morphogenesis, and periodic streaming of protoplasm, agree with the some one of the 7 periodicity. The following geometric progression holds among the periods Ti : Ti+1/Ti=7.5 and Ti+2/Ti+1=2.8 with I=1,2,3.
2. Optimal design of transportation vein network :
When many food-sources were placed at different locations on the uniformly spreading organism, the protoplasm gathers at the food and veins remained from various networks. Geometry of the network is analyzed statistically, and found that the network geometry meets multiple requirements for effective network ; short total length of tubes, close connection (small number of transit food-sites between any two food-sites) and fault-tolerance against an accidental disconnection of tubes.
3. Methematical modeling of the dynamic behavior by the slime mold
The proposed mathematical model is a set of nonlinear partial differential equations which take into account the flow of protoplasm and interaction among chemical oscillations via diffusion and hydrostatic oressure generated by tension generation. This model is successful to simulate typical patterns observed experimentally, as well as the accumulation of attractive locomotion to food-site (favorite site) and mound formation in crowed conditions.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), HOKKAIDO UNIVERSITY, 13650266 - 代謝・運動リズムのシンクロナイゼーションに基づくアメーバ様細胞の情報システム設計
科学研究費助成事業
2001 - 2002
上田 哲男, 中垣 俊之
原始的な巨大アメーバ細胞である粘菌変形体は、外部環境に応じて形状変化を伴う多言種多様な行動をとる。細胞インテリジェンスの創発の観点から、粘菌変形体におけるリズムの階層性ならびに管形状の合理性を実験的に見出し、シミュレーションによりリズム素子のシンクロナイゼーション機構を解明した。
粘菌リズムの階層性と規則性:粘菌の変形に伴う7つの多重リズムを見出し、その周期は、次のように2重の等比数列をなす。T_
粘菌の輸送ネットワークの最適性:寒天ゲル上に複数の餌を与えると、粘菌は全ての餌場所をたかだか二三本の管で結ぶような管ネットワークを形成した。このネットワークの幾何学的形を統計的に解析し、機能的なネットワークが持つべき複数の基準:全長の最短性、餌場所間の密な結合、事故による管の断線に対する連結補償性をすべて満足していることを示した。すなわち粘菌変形体のネットワークはインテリジェントで、最適性を満たしている。
粘菌の動的挙動の数理モデリング:粘菌変形体を、原形質の要素が自励振動し、原形質ゲルが内部のゾルを取り囲みシート状に広がっているものとみなし、時間空間的に相互作用しながら発展する粘菌の数理モデルを構築した。硬さパラメータの位置依存性により、同心円状に広がる粘菌でみられる同調した振動や、フェニルアラニン存在下あるいは高温下における粘菌でみられる全体としては協調しない振動を再現できた。
日本学術振興会, 特定領域研究, 北海道大学, 13022202 - 分子シンクロナイゼーションを発現するミクロ領域における構造と物性に関する研究
科学研究費助成事業
1999 - 2000
原 正彦, 山崎 裕一, 中嶋 健, 中垣 俊之
1.ナノレオロジー測定システムの構築
単一分子を原子間力顕微鏡のカンチレバーと金属単結晶基板の間に挟み、任意の波形で分子の延伸と圧縮を繰返すカンチレバー操作用ピエゾ駆動部の構築ならびにその試料調整法を検討した。また、カンチレバーによる単一分子の延伸と圧縮に対して、同位相同周期で分子が反応する場合の観測結果に加えて、圧縮するとさらに引力(分子が縮む力)が働く逆位相現象が確認された。
2.単一分子リフォールディング現象のシミュレーション
上述の現象は分子自体がある延伸長の領域で自発的にリフォールディング(3次元的再構成)とアンフォールディングを繰返していることに相当すると考えられる。
そこで、フォースカーブ測定から実測されたように、分子のバネ定数が延伸長に依存する系(分子のバネ定数が不連続に変化する系)を仮定してシミュレーションを試みたところ、実験結果を再現する波形が得られ、本研究におけるプローブ手法によって単一分子を対象としたナノレオロジー計測の可能性が示唆された。
また本ナノレオロジー計測システムを用いて、単一高分子鎖の伸張実験、両末端をSH置換したポリスチレンでの再現性のあるデータを取得している。
以上の成果は、本研究におけるプローブ手法が、分子シンクロナイゼーションに関する、個々の分子に対するレオロジーに代表される動的現象に対して重要な知見を与えることを示している。
日本学術振興会, 特定領域研究(A), 理化学研究所, 11167282 - 粘菌行動の反応拡散移流モデルに学ぶシステムの自己組織化
科学研究費助成事業
1999 - 2000
中垣 俊之
我々は、アメーバ様細胞である粘菌変形体が、迷路の経路探索問題の最短解を見出すことができることを発見した。迷路いっぱいに広がる粘菌に、餌を二ヶ所に与えると、行き止まりの経路に伸びている粘菌が衰退し、餌場所を繋ぐ経路にのみ管を残した。この管の配置は、出口を結ぶ全ての経路を示している。これは、見方を変えれば迷路の解をすべてあげつらっていることになる。さらに、時間が経つと、餌場所を繋ぐ管のうち長いものから衰退し、最後には最も短い管だけが残った。この経路は迷路の最短経路である。衰退した部分は、餌場所へ運ばれ餌を包み込んだ。これにより、粘菌は迷路のような複雑な状況でも、二つの餌場所から効率よく養分を吸収できるだろう。粘菌は、経路の長さという評価基準で、迷路の全ての解を序列付けることができた。粘菌の計算能力の高さが伺われる。このような粘菌の迷路探索機構は、反応拡散方程式のパターン形成としてモデル化できることを示した。粘菌の変形運動は、局所的に発生する自励的化学リズムの織り成す時空パターンに基づくことが分った。
粘菌を用いた実験を行うことにより解を求めるという粘菌コンピューターの可能性が生まれた。計算量の爆発を伴う組合せ最適化問題への適用が期待される。粘菌は、原形質と呼ばれる物質の塊であるから、粘菌の計算能力が明らかになれば、物質による情報機能の再構成などの機能性材料の設計原理に新たな方向となる。また、生物情報処理機構の研究に全く新しい切り口を与えた。単細胞生物のこのような高い情報機能は、脳にみる高次情報機能の一つの進化的起源として極めて興味深い。
日本学術振興会, 奨励研究(A), 理化学研究所, Principal investigator, Competitive research funding, 11750222
