基本情報

所属

• 電子科学研究所　附属社会創造数学研究センター

職名

• 教授

学位

• 博士(学術)（名古屋大学）
• 修士(薬学)（北海道大学）
• 学士(薬学)（北海道大学）

ホームページURL

http://mpel.es.hokudai.ac.jp

J-Global ID

• 200901014599160980

プロフィール

• 1963年愛知県生まれ。昭和６２年北海道大学薬学部卒、平成元年同大薬学研究科修士修了、製薬企業に就職し５年間勤務したのち退社。名古屋大学人間情報学研究科博士課程に入学、その間、通信制高校非常勤講師を兼務しながら、平成９年に同博士修了し学術博士となる。理化学研究所研究員を経て、平成１２年北海道大学電子科学研究所助教授、平成２２年公立はこだて未来大学システム情報科学部教授を務め、平成２５年北海道大学電子科学研究所教授となり、平成２９年４月から令和３年３月まで同所長。専門は物理エソロジー。2008年イグノーベル賞認知科学賞、2010年イグノーベル賞交通計画賞、2010年NHK番組「爆笑問題の日本の教養」による爆ノーベル賞、2011年函館市長賞。趣味は、庭での野菜作りと園芸。

研究キーワード

• 原生生物行動学   物理エソロジー   実験及び理論細胞生物学   

研究分野

• ライフサイエンス / 生物物理学 / 物理エソロジー

担当教育組織

•  修士課程　生命科学院
•  博士課程　生命科学院

職歴

• 2013年10月 - 現在 北海道大学 電子科学研究所 教授
• 2017年04月 - 2021年03月 北海道大学 電子科学研究所 所長
• 2010年04月 - 2013年09月 公立はこだて未来大学 システム情報科学部 教授
• 2000年11月 - 2010年03月 北海道大学 電子科学研究所 准教授
• 2000年04月 - 2000年10月 理化学研究所 フロンティア研究員
• 1997年04月 - 2000年03月 理化学研究所 バイオミメティックコントロール研究センター 基礎科学特別研究員
• 1995年04月 - 1997年03月 愛知県立旭陵高等学校 非常勤講師
• 1989年04月 - 1994年05月 ファイザー製薬（株） 名古屋中央研究所 研究員

学歴

• 1994年04月 - 1997年03月   名古屋大学   人間情報学研究科   物質・生命・情報学専攻
• 1987年04月 - 1989年03月   北海道大学   薬学研究科   製薬化学専攻
• 1982年04月 - 1987年03月   北海道大学   薬学部   製薬化学専攻

所属学協会

• 日本数理生物学会   形の科学会   日本生物物理学会   日本時間生物学会   日本原生生物学会   

研究活動情報

論文

• Cellular Ethological Dynamics in Diorama Environments

  Yukinori Nishigami, Itsuki Kunita, Katsuhiko Sato, Toshiyuki Nakagaki

  Journal of the Physical Society of Japan 2023年12月15日 [査読有り][通常論文]
  
• 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 2023年06月14日 [査読有り]
   

  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 2023年01月30日 [査読有り][通常論文]
  
• 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  2022年11月01日 [査読有り][通常論文]
  
• 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 2022年05月25日 [査読有り]
  
• Gait switching with phase reversal of locomotory waves in the centipede Scolopocryptops rubiginosus

  Shigeru Kuroda, Nariya Uchida, Toshiyuki Nakagaki

  Bioinspiration & Biomimetics 17 2 026005 - 026005 2022年03月01日 

  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  2022年01月17日 [査読有り][通常論文]
  
• 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 2020年10月22日 [査読有り][通常論文]
  
• 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 2019年08月 [査読有り][通常論文]
   

  © 2019 Elsevier Ltd Single-celled organisms show a fascinating faculty for integrating spatial information and adapting their behaviour accordingly. As such they are of potential interest for elucidating fundamental mechanisms of developmental biology. In this mini-review we highlight current research on two organisms, the true slime mould Physarum polycephalum and the ciliates Paramecium and Tetrahymena. For each of these, we present a case study how applying physical principles to explain behaviour can lead to the understanding of general principles possibly relevant to developmental biology.
• Dynamic gait transition in theScolopendromorpha scolopocryptops rubiginosus L. Kochcentipede

  Shigeru Kuroda, Nariya Uchida, Toshiyuki Nakagaki

  Cold Spring Harbor Laboratory 2018年05月 [査読無し][通常論文]
  
• 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年 [査読無し][招待有り]
  
• 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 2018年 [査読有り][通常論文]
   

  Physarum polycephalum, a single-celled, multinucleate slime mould, is a seemingly simple organism, yet it exhibits quasi-intelligent behaviour during extension, foraging, and as it adapts to dynamic environments. For these reasons, Physarum is an attractive target for modelling with the underlying goal to uncover the physiological mechanisms behind the exhibited quasi-intelligence and/or to devise novel algorithms for solving complex computational problems. The recent increase in modelling studies on Physarum has prompted us to review the latest developments in this field in the context of modelling and computing alike. Specifically, we cover models based on (i) morphology, (ii) taxis, and (iii) positive feedback dynamics found in top-down and bottom-up modelling techniques. We also survey the application of each of these core features of Physarum to solving difficult computational problems with real-world applications. Finally, we highlight some open problems in the field and present directions for future research.
• 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  2017年11月 [査読有り][通常論文]
   

  Exploring free space (scouting) efficiently is a non-trivial task for organisms of limited perception, such as the amoeboid Physarum polycephalum. However, the strategy behind its exploratory behaviour has not yet been characterised. In this organism, as the extension of the frontal part into free space is directly supported by the transport of body mass from behind, the formation of transport channels (routing) plays the main role in that strategy. Here, we study the organism's exploration by letting it expand through a corridor of constant width. When turning at a corner of the corridor, the organism constructed a main transport vein tracing a centre-in-centre line. We argue that this is efficient for mass transport due to its short length, and check this intuition with a new algorithm that can predict the main vein's position from the frontal tip's progression. We then present a numerical model that incorporates reaction-diffusion dynamics for the behaviour of the organism's growth front and current reinforcement dynamics for the formation of the vein network in its wake, as well as interactions between the two. The accuracy of the model is tested against the behaviour of the real organism and the importance of the interaction between growth tip dynamics and vein network development is analysed by studying variants of the model. We conclude by offering a biological interpretation of the well-known current reinforcement rule in the context of the natural exploratory behaviour of Physarum polycephalum.
• 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  2017年09月 [査読有り][通常論文]
   

  Organisms choose from among various courses of action in response to a wide variety of environmental conditions and the mechanism by which various behaviours are induced is an open question. Interesting behaviour was recently reported: that a unicellular organism of slime mold Physarum polycephalum known as an amoeba had multiple responses (crossing, returning, etc) when the amoeba encounters a zone with toxic levels of quinine, even under carefully controlled conditions. We here examined this elegant example in more detail to obtain insight into behavioural differentiation. We found that the statistical distribution of passage times across a quinine zone switch from unimodal to bimodal (with peaks corresponding to fast crossing and no crossing) when a periodic light stimulation to modulate a biorhythm in amoeba is applied homogeneously across the space, even under the same level of chemical stimuli. Based on a mathematical model for cell movement in amoeba, we successfully reproduced the stimulation-induced differentiation, which was observed experimentally. These dynamics may be explained by a saddle structure around a canard solution. Our results imply that the differentiation of behavioural types in amoeba is modified step-by-step via the compounding of stimulation inputs. The complex behaviour like the differentiation in amoeba may provide a basis for understanding the mechanism of behaviour selection in higher animals from an ethological perspective.
• 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 2017年06月 [査読有り][通常論文]
   

  Response to mechanical stimuli is a fundamental and critical ability for living cells to survive in hazardous conditions or to form adaptive and functional structures against force(s) from the environment. Although this ability has been extensively studied by molecular biology strategies, it is also important to investigate the ability from the viewpoint of biological rhythm phenomena so as to reveal the mechanisms that underlie these phenomena. Here, we use the plasmodium of the true slime mold Physarum polycephalum as the experimental system for investigating this ability. The plasmodium was repetitively stretched for various periods during which its locomotion speed was observed. Since the plasmodium has inherent oscillation cycles of protoplasmic streaming and thickness variation, how the plasmodium responds to various periods of external stretching stimuli can shed light on the other biological rhythm phenomena. The experimental results show that the plasmodium exhibits response to periodic mechanical stimulation and changes its locomotion speed depending on the period of the stretching stimuli.
• 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 2017年06月 [査読有り][通常論文]
   

  Vein networks span the whole body of the amoeboid organism in the plasmodial slime mould Physarum polycephalum, and the network topology is rearranged within an hour in response to spatio-temporal variations of the environment. It has been reported that this tube morphogenesis is capable of solving mazes, and a mathematical model, named the current reinforcement rule', was proposed based on the adaptability of the veins. Although it is known that this model works well for reproducing some key characters of the organism's maze-solving behaviour, one important issue is still open: In the real organism, the thick veins tend to trace the shortest possible route by cutting the corners at the turn of corridors, following a center-in-center trajectory, but it has not yet been examined whether this feature also appears in the mathematical model, using corridors of finite width. In this report, we confirm that the mathematical model reproduces the center-in-center trajectory of veins around corners observed in the maze-solving experiment.
• 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  2017年06月 [査読有り][通常論文]
   

  We evaluate different ridge-enhancement and segmentation methods to automatically extract the network architecture from time-series of Physarum plasmodia withdrawing from an arena via a single exit. Whilst all methods gave reasonable results, judged by precision-recall analysis against a ground-truth skeleton, the mean phase angle (Feature Type) from intensity-independent, phase-congruency edge enhancement and watershed segmentation was the most robust to variation in threshold parameters. The resultant single pixel-wide segmented skeleton was converted to a graph representation as a set of weighted adjacency matrices containing the physical dimensions of each vein, and the inter-vein regions. We encapsulate the complete image processing and network analysis pipeline in a downloadable software package, and provide an extensive set of metrics that characterise the network structure, including hierarchical loop decomposition to analyse the nested structure of the developing network. In addition, the change in volume for each vein and intervening plasmodial sheet was used to predict the net flow across the network. The scaling relationships between predicted current, speed and shear force with vein radius were consistent with predictions from Murray's law. This work was presented at PhysNet 2015.
• 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 2017年04月 [査読有り][通常論文]
   

  The boundary of a cell is the interface with its surroundings and plays a key role in controlling the cell movement adaptations to different environments. We propose a study of the boundary effects on the patterns and waves of the rhythmic contractions in plasmodia of Physarum polycephalum, a tractable model organism of the amoeboid type. Boundary effects are defined as the effects of both the boundary conditions and the boundary shape. The rhythmicity of contraction can be modulated by local stimulation of temperature, light and chemicals, and by local deformation of cell shape via mechanosensitive ion channels as well. First, we examined the effects of boundary cell shapes in the case of a special shape resembling a tadpole, while requiring that the natural frequency in the proximity of the boundary is slightly higher and uniform. The simulation model reproduced the approximate propagated wave, from the tail to the head, while the inward waves were observed only near the periphery of the head section of the tadpole-shape. A key finding was that the frequency of the rhythmic contractions depended on the local shape of cell boundary. This implies that the boundary conditions of the phase were not always homogeneous. To understand the dependency, we reduced the two-dimensional model into a one-dimensional continuum model with Neumann boundary conditions. Here, the boundary conditions reflect the frequency distribution at the boundary. We described the analytic solutions and calculated the relationship between the boundary conditions and the wave propagation for a one-dimensional model of the continuous oscillatory field and a discrete coupled oscillator system. The results obtained may not be limited to cell movement of Physarum, but may be applicable to the other physical systems since the analysis used a generic phase diffusion equation.
• 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 2017年04月 [査読有り][通常論文]
   

  Shear banding is frequently observed in complex fluids. However, the configuration of macromolecules in solutions undergoing shear banding has not yet been directly observed. In this study, by using the fact that F-actin solutions exhibit shear banding and actin filaments are visualized by fluorescent labels, we directly observed the intrinsic states of an actin solution undergoing shear banding. By combining the 3D imaging of labeled actin filaments and particle image velocimetry (PIV), we obtained orientation distributions of actin filaments in both high and low shear rate regions, whose quantitative differences are indicated. In addition, by using the orientation distributions and applying stress expression for rod-like polymers, we estimated stress tensors in both high and low shear rate regions. This evaluation indicates that different orientation distributions of filamentous macromolecules can exhibit a common shear stress.
• 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 2017年03月 [査読有り][通常論文]
   

  Self-organized mechanisms are frequently encountered in nature and known to achieve flexible, adaptive control and decision-making. Noise plays a crucial role in such systems: It can enable a self-organized system to reliably adapt to short-term changes in the environment while maintaining a generally stable behavior. This is fundamental in biological systems because they must strike a delicate balance between stable and flexible behavior. In the present paper we analyse the role of noise in the decision-making of the true slime mold Physarum polycephalum, an important model species for the investigation of computational abilities in simple organisms. We propose a simple biological experiment to investigate the reaction of P. polycephalum to time-variant risk factors and present a stochastic extension of an established mathematical model for P. polycephalum to analyze this experiment. It predicts that-due to the mechanism of stochastic resonance D noise can enable P. polycephalum to correctly assess time-variant risk factors, while the corresponding noise-free system fails to do so. Beyond the study of P. polycephalum we demonstrate that the influence of noise on self-organized decision-making is not tied to a specific organism. Rather it is a general property of the underlying process dynamics, which appears to be universal across a wide range of systems. Our study thus provides further evidence that stochastic resonance is a fundamental component of the decision-making in self-organized macroscopic and microscopic groups and organisms.
• 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  2017年01月 [査読有り][通常論文]
   

  Transport networks are ubiquitous in multicellular organisms and include leaf veins, fungal mycelia and blood vessels. While transport of materials and signals through the network plays a crucial role in maintaining the living system, the transport capacity of the network can best be understood in terms of hydrodynamics. We report here that plasmodium from the large, single-celled amoeboid Physarum was able to construct a hydrodynamically optimized veinnetwork when evacuating biomass from confined arenas of various shapes through a narrow exit. Increasingly thick veins developed towards the exit, and the network spanned the arena via repetitive bifurcations to give a branching tree. The Hausdorff distance from all parts of the plasmodium to the vein network was kept low, whilst the hydrodynamic conductivity from distal parts of the network to the exit was equivalent, irrespective of the arena shape. This combination of spatial patterning and differential vein thickening served to evacuate biomass at an equivalent rate across the entire arena. The scaling relationship at the vein branches was determined experimentally to be 2.53-3.29, consistent with predictions from Murray's law. Furthermore, we show that mathematical models for self-organised, adaptive transport in Physarum simulate the experimental network organisation well if the scaling coefficient of the current-reinforcement rule is set to 3. In simulations, this resulted in rapid development of an optimal network that minimised the combined volume and frictional energy in comparison with other scaling coefficients. This would predict that the boundary shear forces within each vein are constant throughout the network, and would be consistent with a feedback mechanism based on a sensing a threshold shear at the vein wall.
• 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年 [査読有り][通常論文]
  
• Physical ethology of single-celled organism

  Toshiyuki Nakagaki

  INTERNATIONAL JOURNAL OF PSYCHOLOGY 51 574 - 574 2016年07月 [査読無し][通常論文]
  
• 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  2016年05月 [査読有り][通常論文]
   

  Previous studies on adaptive behaviour in single-celled organisms have given hints to the origin of their memorizing capacity. Here we report evidence that a protozoan ciliate Tetrahymena has the capacity to learn the shape and size of its swimming space. Cells confined in a small water droplet for a short period were found to recapitulate circular swimming trajectories upon release. The diameter of the circular trajectories and their duration reflected the size of the droplet and the period of confinement. We suggest a possible mechanism for this adaptive behaviour based on a Ca2+ channel. In our model, repeated collisions with the walls of a confining droplet result in a slow rise in intracellular calcium that leads to a long-term increase in the reversal frequency of the ciliary beat.
• 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） 72 2 3 - 11 2016年 [査読無し][招待有り]
  
• 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 2015年12月 [査読有り][通常論文]
   

  Physarum plasmodium is a giant unicellular organism whose length can vary by more than three orders of magnitude. Using plasmodia ranging in size from 100 mu m to 10 cm, we investigated the size dependency of their thickness distributions and locomotion speeds during free locomotion. (1) In the longitudinal direction, the organism is thickest close to the front, and decreases exponentially in thickness towards the rear. The slenderness ratio varies with body size according to a power law, such that large plasmodia are long and flat, whereas small plasmodia are short and thick. (2) The mean locomotion speed is proportional to the mean maximum thickness of the frontal part. By conducting a dimensional analysis, possible physical models are discussed. (3) The intrinsic period of the thickness oscillation, which is related to shuttle streaming (period 1-2 min), increases logarithmically with body size. (4) Various characteristics exhibit size-independent, long-period (20 +/- 10 min) oscillations, including speed, shape and intrinsic thickness oscillation period. These variations are closely coupled to formation of the entire cell shape, including undulation of thickness along the longitudinal axis and timing of branching of the frontal tip. Based on these experimental results and those reported previously, we propose a simple mathematical model for cell locomotion.
• 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 2015年05月 [査読有り][通常論文]
   

  The slime mould Physarum polycephalum is a giant multinucleated cell exhibiting well-known Ca2+-dependent actomyosin contractions of its vein network driving the so-called cytoplasmic shuttle streaming. Its actomyosin network forms both a filamentous cortical layer and large fibrils. In order to understand the role of each structure in the locomotory activity, we performed birefringence observations and traction force microscopy on excised fragments of Physarum. After several hours, these microplasmodia adopt three main morphologies: flat motile amoeba, chain types with round contractile heads connected by tubes and motile hybrid types. Each type exhibits oscillations with a period of about 1.5 min of cell area, traction forces and fibril activity (retardance) when fibrils are present. The amoeboid types show only peripheral forces while the chain types present a never-reported force pattern with contractile rings far from the cell boundary under the spherical heads. Forces are mostly transmitted where the actomyosin cortical layer anchors to the substratum, but fibrils maintain highly invaginated structures and contribute to forces by increasing the length of the anchorage line. Microplasmodia are motile only when there is an asymmetry in the shape and/or the force distribution.
• 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 2014年06月 [査読有り][通常論文]
   

  We have observed how the ciliate Paramecium attempts to retreat from the dead-end of a long capillary that is too narrow for turning. After many trial-and-error episodes of short-term backward swimming (SBS), which is the conventional avoidance behavior exhibited in free swimming when an obstacle is faced, long-term backward swimming (LBS) that lasted five to ten times longer was developed. LBS may have a beneficial effect for complete withdrawal from the capillary space, although in our experiment it was impossible for the organism to do so due to the capillary length. In order to identify a physically possible mechanism for LBS, we propose model equations for the membrane potential of Hodgkin Huxley type, which describe the control of ciliary movement. The physiological implications and physical mechanism of the development of LBS are discussed.
• 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  2014年06月 [査読有り][通常論文]
   

  Crawling using muscular waves is observed in many species, including planaria, leeches, nemertea, aplysia, snails, chitons, earthworms and maggots. Contraction or extension waves propagate along the antero-posterior axis of the body as the crawler pushes the ground substratum backward. However, the observation that locomotory waves can be directed forward or backward has attracted much attention over the past hundred years. Legged organisms such as centipedes and millipedes exhibit parallel phenomena; leg tips form density waves that propagate backward or forward. Mechanical considerations reveal that leg-density waves play a similar role to locomotory waves in limbless species, and that locomotory waves are used by a mechanism common to both legged and limbless species to achieve crawling. Here, we report that both mode switching of the wave direction and friction control were achieved when backward motion was induced in the laboratory. We show that the many variations of switching in different animals can essentially be classified in two types according to mechanical considerations. We propose that during their evolution, limbless crawlers first moved in a manner similar to walking before legs were obtained. Therefore, legged crawlers might have learned the mechanical mode of movement involved in walking long before obtaining legs.
• 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 2013年03月06日 [査読有り][通常論文]
   

  Biological systems that build transport networks, such as trail-laying ants and the slime mould Physarum, can be described in terms of reinforced random walks. In a reinforced random walk, the route taken by 'walking' particles depends on the previous routes of other particles. Here, we present a novel form of random walk in which the flow of particles provides this reinforcement. Starting from an analogy between electrical networks and random walks, we show how to include current reinforcement. We demonstrate that current-reinforcement results in particles converging on the optimal solution of shortest path transport problems, and avoids the selfreinforcing loops seen in standard density-based reinforcement models. We further develop a variant of the model that is biologically realistic, in the sense that the particles can be identified as ants and their measured density corresponds to those observed in maze-solving experiments on Argentine ants. For network formation, we identify the importance of nonlinear current reinforcement in producing networks that optimize both network maintenance and travel times. Other than ant trail formation, these random walks are also closely related to other biological systems, such as blood vessels and neuronal networks, which involve the transport of materials or information. We argue that current reinforcement is likely to be a common mechanism in a range of systems where network construction is observed. © 2013 The Authors.
• 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年 [査読有り][通常論文]
   

  Why can animals show amazingly sinuous and robust motion under unpredictable complex environments ? It is because animals have a large number of degrees of freedom in their bodies and can orchestrate them very well. Even for the most advanced robots today, such abilities are difficult to attain. In order to create animal-like robots, autonomous decentralized control (ADC) is the key concept that facilitates real-time control of a large number of degrees of freedom corresponding to the changing surroundings. We propose a simple design principle of ADC, which is termed as discrepancy control; then, we test it by implementing it in various types of robots.
• 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年 [査読有り][通常論文]
  
• 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年 [査読有り][通常論文]
  
• 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  2012年12月 [査読有り][通常論文]
   

  We report herein the first evidence that an F-actin solution shows shear banding, which is characterized by the spontaneous separation of homogeneous shear flow into two macroscopic domains of different definite shear rates. The constant shear stress observed in the F-actin solution is explained by the banded flow with volume fractions that obey the lever rule. Nonhomogenous reversible flows were observed in the F-actin solution with respect to upward and downward changes in the shear rate. This is the first time shear banding has been observed in a simple biomacromolecule. The biological implications and dynamic aspects of shear flow velocity characteristic patterns are discussed.
• 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 2012年09月 [査読有り][通常論文]
   

  We study how the net transport and mixing of chemicals occur in a relatively large amoeba, the true slime mold Physarum polycephalum. The shuttle streaming of the amoeba is characterized by a rhythmic flow of the order of 1 mu m/s in which the protoplasm streams back and forth. To explain the experimentally observed transport of chemicals, we formulate a simplified model to consider the mechanism by which net transport can be induced by shuttle (or periodic) motion inside the amoeba. This model is independent from the details of fluid property as it is based on the mass conservation law only. Even in such a simplified model, we demonstrate that sectional oscillations play an important role in net transport and discuss the effects of the sectional boundary motion on net transport in the microorganism.
• 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  2012年07月 [査読有り][通常論文]
   

  The survival of an organism can depend upon the direction in which it decides to move in response to changes in external conditions. Here we propose a physicochemical mechanism of the decision process for migration direction in the case of a giant amoebalike Physarum plasmodium. The tactical movement response could be changed by reversal of the phase wave of the rhythmic contractions that occur in any part of the plasmodium body when local stimulation is applied and the frequency of the rhythmic contractions is locally modulated in the stimulated region. The proposed model describes a physicochemical mechanism of coupling between the local modulation of frequency and the global transport of protoplasmic mass. The decision process is clarified from a rheological point of view.
• 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 2012年02月 [査読有り][通常論文]
   

  Limbless crawling is a fundamental form of biological locomotion adopted by a wide variety of species, including the amoeba, earthworm and snake. An interesting question from a biomechanics perspective is how limbless crawlers control their flexible bodies in order to realize directional migration. In this paper, we discuss the simple but instructive problem of peristalsis-like locomotion driven by elongation-contraction waves that propagate along the body axis, a process frequently observed in slender species such as the earthworm. We show that the basic equation describing this type of locomotion is a linear, one-dimensional diffusion equation with a time-space-dependent diffusion coefficient and a source term, both of which express the biological action that drives the locomotion. A perturbation analysis of the equation reveals that adequate control of friction with the substrate on which locomotion occurs is indispensable in order to translate the internal motion (propagation of the elongation-contraction wave) into directional migration. Both the locomotion speed and its direction (relative to the wave propagation) can be changed by the control of friction. The biological relevance of this mechanism is discussed.
• 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年 [査読有り][通常論文]
  
• 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年 [査読有り][通常論文]
   

  This paper presents a fluid-filled soft-bodied amoeboid robot inspired by the plasmodium of the true slime mold. The significant features of this robot are 2-fold. (i) The robot has a fluid circuit (i. e., cylinders and nylon tubes filled with fluid), and a truly soft and deformable body stemming from real-time tunable springs-the former seals protoplasm to induce global physical interaction between the body parts and the latter is used for elastic actuators. (ii) A fully decentralized control using coupled oscillators with a completely local sensory feedback mechanism is realized by exploiting the global physical interaction between the body parts stemming from the fluid circuit. The experimental results show that this robot exhibits adaptive locomotion without relying on any hierarchical structure. The results obtained are expected to shed new light on the design scheme for autonomous decentralized control systems. (C) Koninklijke Brill NV, Leiden and The Robotics Society of Japan, 2012
• Novel control principle based on the discrepancy function

  Ryo Kobayashi, Toshiyuki Nakagaki, Akio Ishiguro

  京都大学数理解析研究所講究録別冊 B31 61 - 77 京都大学 2012年 [査読無し][通常論文]
  
• 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 2011年09月 [査読有り][通常論文]
   

  Traffic optimization of railroad networks was considered using an algorithm that was biologically inspired by an amoeba-like organism, plasmodium of the true slime mold, Physarum polycephalum. The organism developed a transportation network consisting of a tubular structure to transport protoplasm. It was reported that plasmodium can find the shortest path interconnecting multiple food sites during an adaptation process (Nakagaki et al., 2001. Biophys. Chem. 92, 47-52). By mimicking the adaptation process a path finding algorithm was developed by Tero et al. (2007). In this paper, the algorithm is newly modified for applications of traffic distribution optimization in transportation networks of infrastructure such as railroads under the constraint that the network topology is given. Application of the algorithm to a railroad in metropolitan Tokyo, Japan is demonstrated. The results are evaluated using three performance functions related to cost, traveling efficiency, and network weakness. The traffic distribution suggests that the modified Physarum algorithm balances the performances under a certain parameter range, indicating a biological process. (C) 2011 Elsevier Ireland Ltd. All rights reserved.
• 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 2011年09月 [査読有り][通常論文]
   

  Many biological systems use extensive networks for the transport of resources and information. Ants are no exception. How do biological systems achieve efficient transportation networks in the absence of centralized control and without global knowledge of the environment? Here, we address this question by studying the formation and properties of inter-nest transportation networks in the Argentine ant (Linepithema humile). We find that the formation of inter-nest networks depends on the number of ants involved in the construction process. When the number of ants is sufficient and networks do form, they tend to have short total length but a low level of robustness. These networks are topologically similar to either minimum spanning trees or Steiner networks. The process of network formation involves an initial construction of multiple links followed by a pruning process that reduces the number of trails. Our study thus illuminates the conditions under and the process by which minimal biological transport networks can be constructed.
• Flow-induced channel formation in the cytoplasm of motile cells

  Robert D. Guy, Toshiyuki Nakagaki, Grady B. Wright

  PHYSICAL REVIEW E 84 1 2011年07月 [査読有り][通常論文]
   

  A model is presented to explain the development of flow channels within the cytoplasm of the plasmodium of the giant amoeba Physarum polycephalum. The formation of channels is related to the development of a self-organizing tubular network in large cells. Experiments indicate that the flow of cytoplasm is involved in the development and organization of these networks, and the mathematical model proposed here is motivated by recent experiments involving the observation of development of flow channel in small cells. A model of pressure-driven flow through a polymer network is presented in which the rate of flow increases the rate of depolymerization. Numerical solutions and asymptotic analysis of the model in one spatial dimension show that under very general assumptions this model predicts the formation of channels in response to flow.
• Cellular Computation Realizing Intelligence of Slime Mold Physarum Polycephalum

  Yoshimi Tanaka, Toshiyuki Nakagaki

  JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE 8 3 383 - 390 2011年03月 [査読有り][通常論文]
   

  A series of ethological experiments on the primitive unicellular amoeboid organism Physarum polycephalum has shown that it possesses an unexpectedly high ability of information processing. This organism can solve mazes and certain optimization problems, and can demonstrate both anticipatory and contemplative behavior. A number of mathematical models have been proposed to describe and understand this smart behavior. We survey the investigations that have been performed on the cell level.
• 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  2011年02月28日 [査読有り][通常論文]
   

  It has recently been reported that even single-celled organisms appear to be "indecisive" or "contemplative" when confronted with an obstacle. When the amoeboid organism Physarum plasmodium encounters the chemical repellent quinine during migration along a narrow agar lane, it stops for a period of time (typically several hours) and then suddenly begins to move again. When movement resumes, three distinct types of behavior are observed: The plasmodium continues forward, turns back, or migrates in both directions simultaneously. Here, we develop a continuum mathematical model of the cell dynamics of contemplative amoeboid movement. Our model incorporates the dynamics of the mass flow of the protoplasmic sol, in relation to the generation of pressure based on the autocatalytic kinetics of pseudopod formation and retraction (mainly, sol-gel conversion accompanying actin-myosin dynamics). The biological justification of the model is tested by comparing with experimentally measured spatiotemporal profiles of the cell thickness. The experimentally observed types of behavior are reproduced in simulations based on our model, and the core logic of the modeled behavior is clarified by means of nonlinear dynamics. An on-off transition between the refractory and activated states of the chemical reactivity that takes place at the leading edge of the plasmodium plays a key role in the emergence of contemplative behavior. © 2011 American Physical Society.
• 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年 [査読有り][通常論文]
   

  This paper presents a soft-bodied amoeboid robot inspired by plasmodium of true slime mold. The significant features of this robot are twofold: (1) the robot has truly soft and deformable body stemming from periodically expanding and contracting real-time tunable springs and a balloon, the former is used for an outer skin of the body and the latter serves as protoplasm in order to induce long-distance physical interaction between the body parts; and (2) a fully decentralized control using coupled oscillators with completely local sensory feedback mechanism is realized by exploiting the long-distance physical interaction. 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 how autonomous decentralized control may he designed.
• Convergence properties for the Physarum solver

  Kentaro Ito, Anders Johansson, Toshiyuki Nakagaki, Atsushi Tero

  arXiv:1101.5249v1[math.OC] 27 Jan 2011 2011年01月 [査読無し][通常論文]
  
• 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 2010年03月 [査読有り][通常論文]
   

  Transport across the cell membrane is crucial in drug delivery. However, the process is complicated because nucleoside derivatives that are commonly used its anti-viral drugs are transported through two different types of specific transporters: concentrative transporters and equilibrative transporters. Cross-disciplinary approaches involving both biological experiments and theoretical considerations are therefore necessary to study the transport of nucleoside analogues such as ribavirin. Here we constructed an experimental model system using the Xenopus laevis oocyte that expressed examples of both types of transporters: human concentrative nucleoside transporter 3 and human equilibrative transporter 1. We also performed a kinetic study. Experimental results showed that the transport of ribavirin could be reduced by inhibiting one of the two types of transporters, which seems to be counterintuitive. We therefore designed a simple mathematical model of the dynamics of ribavirin uptake and analyzed the model behaviors using a numerical simulation. The theoretical results reproduced the experimentally observed phenomena and suggested a possible mechanism for the process. Based on this mechanism, we predicted some potential methods for the effective uptake of ribavirin from a dynamics point of view. (C) 2010 Elsevier B.V. All rights reserved.
• 真正粘菌変形体から探る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

  日本ロボット学会学術講演会予稿集(CD-ROM) 102 3 261 - 269 2010年03月 [査読有り][通常論文]
   

  Animals exhibit astoundingly adaptive and supple locomotion under real world constraints. In order to endow robots with similar capabilities, we must implement many degrees of freedom, equivalent to animals, into the robots' bodies. For taming many degrees of freedom, the concept of autonomous decentralized control plays a pivotal role. However a systematic way of designing such autonomous decentralized control system is still missing. Aiming at understanding the principles that underlie animals' locomotion, we have focused on a true slime mold, a primitive living organism, and extracted a design scheme for autonomous decentralized control system. In order to validate this design scheme, this article presents a soft-bodied amoeboid robot inspired by the true slime mold. Significant features of this robot are twofold: (1) the robot has a truly soft and deformable body stemming from real-time tunable springs and protoplasm, the former is used for an outer skin of the body and the latter is to satisfy the law of conservation of mass; and (2) 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 stemming from the law of conservation of protoplasmic mass. Simulation results show that this robot exhibits highly supple and adaptive locomotion without relying on any hierarchical structure. The results obtained are expected to shed new light on design methodology for autonomous decentralized control system.
• 原形質量保存則を活用したアメーバ様ソフトロボットの実機開発

  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 2010年01月30日 [査読無し][通常論文]
  
• The Birth of Physarum Computing

  Toshiyuki Nakagaki

  INTERNATIONAL JOURNAL OF UNCONVENTIONAL COMPUTING 6 2 75 - 77 2010年 [査読有り][通常論文]
  
• 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年 [査読有り][通常論文]
   

  Animals exhibit astoundingly adaptive and supple locomotion under real world constraints. In order to endow robots with similar capabilities, we must implement large degrees of freedom, equivalent to animals, into the robots' bodies. For taming large degrees of freedom, the concept of autonomous decentralized control plays a pivotal role. However, a systematic way of designing such autonomous decentralized control system is still missing. Aiming at understanding the principles that underlie animals' locomotion, in our early studies, we focused on true slime mold, a primitive living organism, and extracted a decentralized control scheme. In order to validate this control scheme, this paper presents a soft-bodied amoeboid robot inspired by true slime mold. Significant features of this robot are twofold: (1) the robot has truly soft and deformable body stemming from real-time tunable springs and a balloon, the former is used for 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 stemming from both the softness of the body and 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.
• Foraging Behaviors and Potential Computational Ability of Problem-Solving in an Amoeba

  Toshiyuki Nakagaki

  NATURAL COMPUTING 2 42 - 54 2010年 [査読有り][通常論文]
   

  We study cell behaviors in the complex situations: multiple locations of food were simultaneously given. An amoeba-like organism of true slime mold gathered at the multiple food locations while body shape made of tubular network was totally changed. Then only a few tubes connected all of food locations through a network shape. By taking the network shape of body, the plasmodium could meet its own physiological requirements: as fast absorption of nutrient as possible and sufficient circulation of chemical signals and nutrients through a whole body. Optimality of network shape was evaluated in relation to a combinatorial optimization problem. Here we reviewed the potential computational ability of problem-solving in the amoeba, which was much higher than we'd though. The main message of this article is that we had better to change our stupid opinion that an amoeba is stupid.
• 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 2010年01月 [査読有り][通常論文]
   

  Transport networks are ubiquitous in both social and biological systems. Robust network performance involves a complex trade-off involving cost, transport efficiency, and fault tolerance. Biological networks have been honed by many cycles of evolutionary selection pressure and are likely to yield reasonable solutions to such combinatorial optimization problems. Furthermore, they develop without centralized control and may represent a readily scalable solution for growing networks in general. We show that the slime mold Physarum polycephalum forms networks with comparable efficiency, fault tolerance, and cost to those of real-world infrastructure networks-in this case, the Tokyo rail system. The core mechanisms needed for adaptive network formation can be captured in a biologically inspired mathematical model that may be useful to guide network construction in other domains.
• 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年 [査読有り][通常論文]
   

  We propose a new solver for the Steiner tree problem, inspired by a true shine mold Physarum polycephalum. This problem involves finding the network that connects multiple points on a plane through the shortest total length. Such a network is known as the Steiner minimum tree (SMT). The solution of this problem is important for the design of transport and communication networks, but is not easy to obtain because the computational time required increases rapidly with the number of points. Using Melzak's algorithm, it is almost impossible to find the best solution for more than thirty points. However, it is known that an amoeboid organism, Physarum plasmodium, can construct a network on in agar plate between many Points at which food is placed. Because the Physarum network sometimes has the same topology as the SMT, we have studied how this is achieved by constructing a mathematical model for the network dynamics, based on the physiological mechanism. Our investigation enables us to propose and discuss the prospects of a new method for solving the Steiner problem.
• 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年 [査読有り][通常論文]
   

  Animals exhibit astoundingly adaptive and supple locomotion under real world constraints. In order to endow robots with similar capabilities, we must implement many degrees of freedom, equivalent to animals, into the robots' bodies. For taming many degrees of freedom, the concept of autonomous decentralized control plays a pivotal role. However, a systematic way of designing such autonomous decentralized control system is still missing. Aiming at understanding the principles that underlie animals' locomotion, in our early studies, we focused on plasmodium of true slime mold, a primitive living organism, and extracted a design scheme for autonomous decentralized control system. In order to demonstrate the relevance of this design scheme, this paper presents a soft-bodied fluid-driven amoeboid robot inspired by plasmodium of true slime mold. The significant features of this robot are twofold: (1) the robot has fluidic circuit (i.e., cylinders and 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 stemming from the law of conservation of protoplasmic mass. The 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.
• 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 一般社団法人 電子情報通信学会 2010年 [査読有り][通常論文]
   

  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年 [査読有り][通常論文]
   

  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.
• アメーバ様ロコモーションから探る大自由度システムの自律分散制御方策

  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 2009年08月08日 [査読無し][通常論文]
   

  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
• 真正粘菌をモチーフとした大自由度ソフトロボットの実機開発

  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 2009年01月22日 [査読無し][通常論文]
  
• Adaptive biological networks

  Mark D. Fricker, Lynne Boddy, Toshiyuki Nakagaki, Daniel P. Bebber

  Understanding Complex Systems 2009 51 - 70 2009年 [査読有り][通常論文]
   

  Mycelial fungi and acellular slime molds grow as self-organized networks that explore new territory to search for resources, whilst maintaining an effective internal transport system in the face of continuous attack or random damage. These networks adapt during development by selective reinforcement of major transport routes and recycling of the intervening redundant material to support further extension. In the case of fungi, the predicted transport efficiency of the weighted network is better than evenly weighted networks with the same topology, or standard reference networks. Experimentally, nutrient movement can be mapped using radio-tracers and scintillation imaging, and shows more complex transport dynamics, with synchronized oscillations and switching between different pre-existing routes. The significance of such dynamics to the interplay between transport control and topology is not yet known. In a similar manner, the resilience of the network can be tested in silico and experimentally using grazing invertebrates. Both approaches suggest that the same structures that confer good transport efficiency also show good resilience, with the persistence of a centrally connected core. The acellular slime mold, Physarum polycephalum also forms efficient networks between food sources, with a good balance between total cost, transit distance and fault tolerance. In this case, network formation can be captured by a mathematical model driven by non-linear positive reinforcement of tubes with high flux, and decay of tubes with low flux. We argue that organization of these simple planar networks has been honed by evolution, and they may exemplify potential solutions to real-world compromises between search strategy, transport efficiency, resilience and cost in other domains. © 2009 Springer-Verlag Berlin Heidelberg.
• 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年 [査読有り][通常論文]
  
• 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年 [査読有り][通常論文]
   

  Self-reconfigurable robots are expected to exhibit various interesting abilities, such as adaptivity and fault tolerance. These remarkable abilities originate from the fact that their mechanical systems intrinsically possess very large degrees of freedom. This, however, causes a serious problem, i.e., controllability. To overcome this, autonomous decentralized control is expected to play a crucial role, as widely observed in living organisms. However, much is still not understood about how such decentralized control can be achieved. This is mainly because the logic connecting local behaviors to global behaviors is still not understood. In this study, we particularly focus on a very primitive living organism, slime mold (physarum polycepharum), since it is believed to employ a fully decentralized control based on coupled biochemical oscillators. We modeled a decentralized control algorithm based on coupled nonlinear oscillators and then implement this into a two-dimensional modular robot consisting of incompressible fluid (i.e., protoplasm) covered with an outer skin composed of a network of passive and real-time tunable springs. Preliminary simulation results showed that this modular robot exhibits significantly supple locomotion similar to amoeboid locomotion and that the exploitation of the "long-distant interaction" stemming from "the law of conservation of protoplasmic mass" performs some of the "computation" that the controller would otherwise have to carry out. As a consequence, adaptive amoeboid locomotion emerges without the need for any centralized control system. The results obtained are also expected to shed new light on how control and mechanical systems with large degrees of freedom should be coupled.
• Protoplasmic Computing to Memorize and Recall Periodic Environmental Events

  Atsushi Tero, Tetsu Saigusa, Toshiyuku Nakagaki

  NATURAL COMPUTING, PROCEEDINGS 1 213 - 221 2009年 [査読無し][通常論文]
   

  Single-celled organisms might be more intelligent than previously envisaged [1]-[5]. The acts of anticipating and recalling events are higher functions performed by the brains of higher animals; their evolutionary origins and the way they self-organize, however, remain open questions. Here we show that an amoeboid organism can anticipate the timing of periodic events. The plasmodium of the true slime mold Physarum polycephalum moves rapidly under favorable conditions, but stops moving when transferred to less-favorable conditions. For example, plasmodia exposed to low temperature and low humidity, presented in three consecutive pulses at constant intervals, reduced their locomotive speed in response to each episode. When favorable conditions were subsequently reintroduced, the plasmodia spontaneously reduced their locomotive speed at the point in time when the next unfavorable episode would have occurred. This implies that the plasmodia are able to anticipate impending environmental change. After this anticipatory response had been evoked several times, the locomotion of the plasmodia returned to normal speed; however, the slowing down could subsequently be induced by a single unfavorable pulse, implying recall of the periodicity that had been memorized. We have explored the mechanisms underlying this behavior from a dynamical systems perspective. Our results suggest that this primitive intelligence is of cellular origin and that simple dynamics might be sufficient to explain its emergence. abstract environment.
• 真正粘菌から探る大自由度ロボットの自律分散制御方策

  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 2008年12月05日 [査読無し][通常論文]
  
• 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 2008年11月 [査読有り][通常論文]
   

  Learning how biological systems solve problems could help to design new methods of computation. Information processing in simple cellular organisms is interesting, as they have survived for almost 1 billion years using a simple system of information processing. Here we discuss a well-studied model system: the large amoeboid Physarum plasmodium. This amoeba can find approximate solutions for combinatorial optimization problems, such as solving a maze or a shortest network problem. In this report, we describe problem solving by the amoeba, and the computational methods that can be extracted from biological behaviors. The algorithm designed based on Physarum is both simple and useful.
• 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 2008年09月22日 [査読有り][通常論文]
  
• 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 2008年07月 [査読有り][通常論文]
   

  In this paper we study a mathematical model describing behaviour of Physarum polycephalum proposed by Tero et al. (2007). In the case of linear adaptive term, it has been proved that the model must solve the shortest path problem mathematically rigorously on a general planar graph in Miyaji and Ohnishi (2007, 2008). However, in a laboratory, P. polycephalum sometimes makes a mistake, for example, when there is a 'double-edge' in a graph. We study the case mathematically to show both why and how P. polycephalum makes a mistake. © 2008, Inderscience Publishers.
• Flow-network adaptation in Physarum amoebae

  Atsushi Tero, Kenji Yumiki, Ryo Kobayashi, Tetsu Saigusa, Toshiyuki Nakagaki

  THEORY IN BIOSCIENCES 127 2 89 - 94 2008年06月 [査読有り][通常論文]
   

  Understanding how biological systems solve problems could aid the design of novel computational methods. Information processing in unicellular eukaryotes is of particular interest, as these organisms have survived for more than a billion years using a simple system. The large amoeboid plasmodium of Physarum is able to solve a maze and to connect multiple food locations via a smart network. This study examined how Physarum amoebae compute these solutions. The mechanism involves the adaptation of the tubular body, which appears to be similar to a network, based on cell dynamics. Our model describes how the network of tubes expands and contracts depending on the flux of protoplasmic streaming, and reproduces experimental observations of the behavior of the organism. The proposed algorithm based on Physarum is simple and powerful.
• Locomotive mechanism of Physarum plasmodia based on spatiotemporal analysis of protoplasmic streaming

  Kenji Matsumoto, Seiji Takagi, Toshiyuki Nakagaki

  BIOPHYSICAL JOURNAL 94 7 2492 - 2504 2008年04月 [査読有り][通常論文]
   

  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. The shuttle streaming of the protoplasm was not truly symmetric due to the peristalsis-like movements of the plasmodium. This asymmetry meant that the transport capacity of the stream was not equal in both directions, and a net forward displacement of the center of gravity resulted. The generality of this as a mechanism for amoeboid locomotion is discussed.
• 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年 [査読有り][通常論文]
   

  We report a theoretical analysis of protoplasmic streaming driven by peristaltic movement in an elastic tube of an amoeba-like organism. The plasmodium of Physarum polycephalum, a true slime mold, is a large amoeboid organism that adopts a sheet-like form with a tubular network. The network extends throughout the plasmodium and enables the transport and circulation of chemical signals and nutrients. This tubular flow is driven by periodically propagating waves of active contraction of the tube cortex, a process known as peristaltic movement. We derive the relationship between the phase velocity of the contraction wave and the flow rate, and we discuss the physiological implications of this relationship.
• Intelligent behaviors of amoeboid movement based on complex dynamics of soft matter

  Toshiyuki Nakagaki, Robert D. Guy

  SOFT MATTER 4 1 57 - 67 2008年 [査読有り][通常論文]
   

  We review how soft matter is self-organized to perform information processing at the cell level by examining the model organism Physarum plasmodium. The amoeboid organism, Physarum polycephalum, in the class of true slime molds, exhibits the intelligent behavior of foraging in complex situations. When placed in a maze with food sources at two exits, the organism develops tubular structures with its body which connect the food sources along the shortest path so that the rates of nutrient absorption and intracellular communication are maximized. This intelligent behavior results from the organism's control of a dynamic network through which mechanical and chemical information is transmitted. We review experimental studies that explore the development and adaptation of structures that make up the network. Recently a model of the dynamic network has been developed, and we review the formulation of this model and present some key results. The model captures the dynamics of existing networks, but it does not answer the question of how such networks form initially. To address the development of cell shape, we review existing mechanochemical models of the protoplasm of Physarum, present more general models of motile cells, and discuss how to adapt existing models to explore the development of intelligent networks in Physarum.
• Amoebae anticipate periodic events

  Tetsu Saigusa, Atsushi Tero, Toshiyuki Nakagaki, Yoshiki Kuramoto

  PHYSICAL REVIEW LETTERS 100 1 018101  2008年01月 [査読有り][通常論文]
   

  When plasmodia of the true slime mold Physarum were exposed to unfavorable conditions presented as three consecutive pulses at constant intervals, they reduced their locomotive speed in response to each episode. When the plasmodia were subsequently subjected to favorable conditions, they spontaneously reduced their locomotive speed at the time when the next unfavorable episode would have occurred. This implied the anticipation of impending environmental change. We explored the mechanisms underlying these types of behavior from a dynamical systems perspective.
• 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  2007年08月 [査読有り][通常論文]
   

  When two food sources are presented to the slime mold Physarum in the dark, a thick tube for absorbing nutrients is formed that connects the food sources through the shortest route. When the light-avoiding organism is partially illuminated, however, the tube connecting the food sources follows a different route. Defining risk as the experimentally measurable rate of light-avoiding movement, the minimum-risk path is exhibited by the organism, determined by integrating along the path. A model for an adaptive-tube network is presented that is in good agreement with the experimental observations.
• 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 2007年06月 [査読無し][通常論文]
   

  In the large amoeboid organism Physarum, biochemical oscillators are spatially distributed throughout the organism and their collective motion exhibits phase waves, which carry physiological signals. The basic nature of this wave behaviour is not well-understood because, to date, an important effect has been neglected, namely, the shuttle streaming of protoplasm which accompanies the biochemical rhythms. Here we study the effects of self-consistent flow on the wave behaviour of oscillatory reaction-diffusion models proposed for the Physarum plasmodium, by means of numerical simulation for the dispersion relation and weakly nonlinear analysis for derivation of the phase equation. We conclude that the flow term is able to increase the speed of phase waves (similar to elongation of wave length). We compare the theoretical consequences with real waves observed in the organism and also point out the physiological roles of these effects on control mechanisms of intracellular communication.
• 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 2007年02月 [査読有り][通常論文]
   

  We describe here a mathematical model of the adaptive dynamics of a transport network of the true slime mold Physarum polycephalum, an amoeboid organism that exhibits path-finding behavior in a maze. This organism possesses a network of tubular elements, by means of which nutrients and signals circulate through the plasmodium. When the organism is put in a maze, the network changes its shape to connect two exits by the shortest path. This process of path-finding is attributed to an underlying physiological mechanism: a tube thickens as the flux through it increases. The experimental evidence for this is, however, only qualitative. We constructed a mathematical model of the general form of the tube dynamics. Our model contains a key parameter corresponding to the extent of the feedback regulation between the thickness of a tube and the flux through it. We demonstrate the dependence of the behavior of the model on this parameter. (c) 2006 Elsevier Ltd. All rights reserved.
• 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年 [査読無し][通常論文]
  
• 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年 [査読無し][通常論文]
  
• 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 2006年08月 [査読有り][通常論文]
   

  The plasmodium of the true slime mold Physarum polycephalum is a large amoeboid organism that displays "smart" behavior such as chemotaxis and the ability to solve mazes and geometrical puzzles. These amoeboid behaviors are based on the dynamics of the viscoelastic protoplasm and its biochemical rhythms. By incorporating both these aspects, we constructed a mathematical model for the dynamics of the organism as a first step towards understanding the relation between protoplasmic movement and its unusual abilities. We tested the validity of the model by comparing it with physiological observation. Our model reproduces fundamental characteristics of the spatio-temporal pattern of the rhythmic movement: (1) the antiphase oscillation between frontal tip and rear when the front is freely extending; (2) the asynchronous oscillation pattern when the front is not freely extending; and (3) the formation of protoplasmic mounds over a longer time scale. Both our model and physiological observation suggest that cell stiffness plays a primary role in plasmodial behaviors, in contrast to the conventional theory of coupled oscillator systems.
• 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 2006年08月 [査読有り][通常論文]
   

  Super water repellency of solid surfaces can be realized by formation of fractal structures, which were verified and explained by various materials, such as alkylketene dimer (AKD), platinum-palladium alloy-covered AKD, and poly(alkylpyrrole), and also by comparison of fractal surfaces with smooth ones. Novel potential applications of the fractal solid surfaces to unique biological studies are suggested based on our previous and the present biological studies on fractal AKD surfaces. (c) 2005 Elsevier B.V. All rights reserved.
• Physarum solver – a biologically inspired method for road-network navigation -

  Atsushi Tero, Ryo Kobayashi, Toshiyuki Nakagaki

  Physica 363 1 115 - 119 2006年04月 [査読無し][通常論文]
   

  We have proposed a mathematical model for the adaptive dynamics of the transport network in an amoeba-like organism, the true slime mold Physarum polycephalum. The model is based on physiological observations of this species, but can also be used for path-finding in the complicated networks of mazes and road maps. In this paper, we describe the physiological basis and the formulation of the model, as well as the results of simulations of some complicated networks. The path-finding method used by Physarum is a good example of cellular computation. (c) 2006 Elsevier B.V. All rights reserved.
• 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.  2001年08月 [査読有り][通常論文]
   

  Spatiotemporal patterns in rings of coupled biological oscillators of the plasmodial slime mold, Physarum polycephalum, were investigated by comparing with results analyzed by the symmetric Hopf bifurcation theory based on group theory. In three-, four-, and five-oscillator systems, all types of oscillation modes predicted by the theory were observed including a novel oscillation mode, a half period oscillation, which has not been reported anywhere in practical systems. Our results support the effectiveness of the symmetric Hopf bifurcation theory in practical systems.
• Maze-solving by an amoeboid organism

  T Nakagaki, H Yamada, A Toth

  NATURE 407 6803 470 - 470 2000年09月 [査読有り][通常論文]
  
• 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 2000年09月 [査読有り][通常論文]
  
• 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 1999年11月 [査読有り][通常論文]
   

  We studied responses of cellular rhythm and light-induced movement to periodic irradiation in a unicellular amoeboid organism, the Physarum plasmodium. The intrinsic frequency of the contraction rhythm, which is based on biochemical oscillations, became synchronized with the frequency of periodic irradiation with light when both frequencies were close enough. In order to study the role of the synchronization in light-induced movement, periodic irradiation was applied to only part of the plasmodium. The rate of avoidance of light was modulated in the frequency band in which the synchronization occurred. The synchronization property of the contraction oscillation underlies the regulation of tactic movement in plasmodium. (C) 1999 Elsevier Science B.V. All rights reserved.
• 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 1999年04月 [査読有り][通常論文]
   

  The plasmodium of Physarum polycephalum is a large amoeboid organism showing rhythmic contraction everywhere within an organism, and moves by forming spatio-temporal patterns of the rhythmic contraction. We propose a reaction-diffusion-advection model for the pattern formation. This model is constructed under physiological suggestions that the chemical oscillator acts as a clock regulating the rhythmic contraction and interacts spatially not only by diffusion but also by advection of protoplasm. Behavior of the model is studied by numerical calculation, especially the effects of the advection term on a simple reaction-diffusion system. The advection effect reproduces experimentally observed phenomena of fluctuating propagation of the contraction wave. Concept of the reaction-diffusion-advection system is promising for modeling the mechanism of amoeboid behavior in the Physarum plasmodium. (C) 1999 Academic Press.
• 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 1999年01月 [査読有り][通常論文]
   

  The amoeboid organism, the plasmodium of Physarum polycephalum, moves by forming a spatiotemporal pattern of contraction oscillators. This biological system can be regarded as a reaction-diffusion system with spatial interaction via active flow of protoplasmic sol in the cell. We present a reaction-diffusion system with self-consistent flow on the basis of the physiological evidence that the flow is determined by contraction patterns in the plasmodium. Such a coupling of reaction, diffusion, and advection is characteristic of biological systems, and is expected to be related to control mechanisms of amoeboid behavior. Using weakly nonlinear : analysis, we show that the envelope dynamics obeys the complex Ginzburg-Landau (CGL) equation when a bifurcation occurs at finite wave number. The flow term affects the nonlinear term of the CGL equation through the critical wave number squared. A physiological role of pattern formation with the flow is discussed. [S1063-651X(99)11501-0].
• 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 1996年11月 [査読有り][通常論文]
   

  The plasmodium of the myxomycete Physarum polycephalum sporulates in bright natural environments, suggesting a relationship between photobehavior and sporulation. Thus, the action spectra for two light-dependent phenomena as well as the effects of other environmental conditions have been studied. Sporulation like photoavoidance responded to UVC (near 270 nm) and near IR (near 750 nm) in addition to the well-documented UVA (near 350 nm) and blue (near 460 nm) regions. Sporulation and photoavoidance had similar sensitivities in the shorter wavelengths, while the former was about 100 times more sensitive in near IR. The plasmodium moved away from light in a wide spectral range. Starvation and high temperature at 31 degrees C (25 degrees C in standard conditions) reduced photoavoidance to UVA and to blue light, respectively. A high fluence rate of WC suppressed the rhythmic contraction of the plasmodium, and the action spectrum peaked at 270 nm. These results indicate that the Physarum plasmodium may stay at brighter places not by positive phototaxis but by weakening the negative phototaxis to sunlight or by other possible taxes such as hydrotaxis. There may be at least four different photosystems in the plasmodium.
• 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 1996年04月 [査読有り][通常論文]
   

  The plasmodium of the true slime mould Physarum polycephalum is a large aggregate of protoplasm and behaves like an amoeboid cell, exhibiting rhythmic contraction everywhere within the organism. Phase dynamics of these oscillations were studied in relation to the global organization of amoeboid behavior, by analysing the thickness oscillation, isotonic tension and the motive force of the streaming. Usually the plasmodium showed synchrony, the phase of the oscillation being the same everywhere excepting the peripheral part. We found several situations where this in-phase relationship switched to anti-phase. This occurred either at the early stages of the plasmodial coalescence, or when a single plasmodium was nearly separated by partition, or when the streaming of the protoplasm was hindered by applying the hydrostatic pressure. Furthermore, the motive force of the protoplasmic streaming increased once the anti-phase relationship was established. In this way, the weak interactions among plasmodial parts induce the switching of phase relationship from in-phase to anti-phase, and this transition in turn acts to increase the interaction by promoting a rapid mixing of the protoplasm. This global feedback mechanism by phase switching should help maintain a large single plasmodium without separating into parts. The possible mechanism of phase switching is discussed in terms of coupled nonlinear oscillators. (C) 1996 Academic Press Limited.
• 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 1993年07月 [査読無し][通常論文]
  
• 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 1992年09月 [査読無し][通常論文]
  
• 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 1990年08月 [査読有り][通常論文]
  
• 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 1990年04月 [査読有り][通常論文]
  
• 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 1988年11月 [査読有り][通常論文]
  
• 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

  Tetsuo Ueda, Yoshihito Mori, Toshiyuki Nakagaki, Yonosuke Kobatake

  Photochem. Photobiol. 47 2 271 - 275 1988年02月 [査読有り][通常論文]
  
• 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年 [査読有り][通常論文]
  

書籍

• 粘菌 : かしこい単細胞

  中垣 俊之, 斉藤 俊行 
  福音館書店 2015年 (ISBN: 9784834081862)
• 粘菌 : 偉大なる単細胞が人類を救う

  中垣 俊之 
  文藝春秋 2014年 (ISBN: 9784166609840)
• 複雑系知能学への招待 : 未来大の研究現場から

  中垣 俊之 
  キャンパス・コンソーシアム函館 2014年
• 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年 (ISBN: 9784431543930)
• かしこい単細胞粘菌

  中垣 俊之, 斉藤 俊行 
  福音館書店 2012年
• 複雑系知能学への招待 : 未来大の研究現場から

  中垣 俊之 
  キャンパス・コンソーシアム函館(制作) 2012年
• 粘菌 : その驚くべき知性

  中垣 俊之 
  PHP研究所 2010年 (ISBN: 9784569777863)
• 細胞生理学

  Keener James P, Sneyd James, 中垣 俊之 
  日本評論社 2005年 (ISBN: 453578356X)
• システム生理学

  Keener James P, Sneyd James, 中垣 俊之 
  日本評論社 2005年 (ISBN: 4535783578)
• 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年 (ISBN: 4621072552)

その他活動・業績

• 粘菌変形体における環境依存的な輸送ネットワーク形成

  中垣俊之, 佐藤勝彦, 西上幸範 植物科学最前線 13 151 2022年08月 [査読有り][招待有り]
  
• 非定常短細線加熱法による真正粘菌の熱伝導率および熱拡散率の測定

  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 2018年11月13日 [査読無し][通常論文]
  
• 粘菌から生き物の賢さを学ぶ

  中垣俊之 高分子学会予稿集(CD-ROM) 67 (2) ROMBUNNO.1A10IL 2018年08月29日 [査読無し][通常論文]
  
• モジホコリ

  高木清二, 佐藤勝彦, 中垣俊之 生物工学会誌 96 (8) 488‐492 2018年08月25日 [査読無し][通常論文]
  
• 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) 2018年06月19日 [査読無し][通常論文]
  
• ムカデにおける動的な歩容の遷移について

  黒田茂, 内田就也, 中垣俊之 日本動物行動学会大会発表要旨集 37th 27 2018年 [査読無し][通常論文]
  
• 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年 [査読無し][通常論文]
  
• 生物材料インデックス モジホコリ

  髙木 清二, 佐藤 勝彦, 中垣 俊之 生物工学会誌 96 (8) 488 -492 2018年 [査読無し][通常論文]
  
• 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 生体医工学 56 (0) S166 -S166 2018年 [査読無し][通常論文]
   

  <p>繊毛虫は、しばしば泳ぐ神経細胞といわれる。1960年代以降の電気生理学研究によって、繊毛虫の膜電位応答が、神経細胞のそれと類似していることがわかってきたからである。その膜電位動態のモデル方程式が提案されており、それは、元々イカ神経細胞に対して提案されたホジキン・ハクスレー型のモデル方程式と同様である。推進力を出す繊毛運動は膜電位により調節されているので、どんな遊泳行動も、例えば環境への適応行動も、膜電位のモデル方程式のレベルで理解出来ると思われる。この発表では、ある繊毛虫の適応行動を紹介し、その機構をモデル方程式を用いて考察する。</p>
• 生物の用不用則に基づく機能的な形作り

  中垣俊之 第12回バイオものづくりシンポジウム 理研シンポジウム 平成29年 21,23 2017年 [査読無し][通常論文]
  
• 人工知能と自然知能

  中垣 俊之 情報処理 57 (10) 948 -949 2016年09月15日 [査読無し][通常論文]
  
• 生物の用不用則に基づく適応的なネットワーク設計

  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 2016年08月02日 [査読無し][通常論文]
  
• 這行ロコモーションにおける歩容とその遷移

  黒田茂, 中垣俊之 自律分散システム・シンポジウム(CD-ROM) 28th ROMBUNNO.2A2‐3 2016年01月21日 [査読無し][通常論文]
  
• テトラヒメナにおける空間形状への適応的遊泳

  中垣俊之 日本微生物生態学会大会(Web) 31st 73 (WEB ONLY) 2016年 [査読無し][通常論文]
  
• キャピラリー空間におけるゾウリムシの空間学習とそのメカニズム

  大木開登, 黒田茂, 國田樹, 中垣俊之 日本原生生物学会大会講演要旨集 48th 23 2015年11月06日 [査読無し][通常論文]
  
• 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 2015年08月25日 [査読無し][通常論文]
  
• 物理エソロジーの道すがら(<レクチャーシリーズ>つながりが創発するイノベーション〔第2回〕)

  中垣 俊之, Toshiyuki Nakagaki 人工知能 = journal of the Japanese Society for Artificial Intelligence 30 (4) 525 -531 2015年07月01日 [査読無し][通常論文]
  
• 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 2015年04月10日 [査読無し][通常論文]
  
• イグノーベル賞 3 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

  中垣俊之 化学と工業 68 (4) 342 -344 2015年04月01日 [査読無し][通常論文]
  
• 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 2015年04月 [査読無し][通常論文]
  
• 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 2015年 [査読無し][通常論文]
  
• 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 2014年10月15日 [査読無し][通常論文]
  
• 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 2014年04月 [査読無し][通常論文]
  
• 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 2014年03月05日 [査読無し][通常論文]
  
• 27aAR-7 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(27aAR 領域11,領域12合同 生物合同セッション1,領域11(物性基礎論・統計力学・流体物理・応用数学・社会経済物理))

  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 (0) 293 -293 2014年 [査読無し][通常論文]
  
• 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 2013年09月25日 [査読無し][通常論文]
  
• 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 2013年08月26日 [査読無し][通常論文]
  
• F‐アクチン溶液のシアバンディング

  田中良巳, 國田樹, 佐藤勝彦, 瀧川佳紀, 折原宏, 中垣俊之 日本物理学会講演概要集 68 (1) 419 2013年03月05日 [査読無し][通常論文]
  
• 環境揺らぎによる粘菌変形体の行動選択の変調

  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 2013年01月25日 [査読無し][通常論文]
  
• 自由移動中の真性粘菌変形体におけるアロメトリー:速さ,形,リズム

  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 2013年01月25日 [査読無し][通常論文]
  
• 生命の智をめぐって―アメーバからヒトまで―

  中垣俊之 日本老年麻酔学会プログラム・抄録集 25th 18 2013年 [査読無し][通常論文]
  
• 26aKL-6 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(生物合同2,領域11,領域12合同,領域11(統計力学,物性基礎論,応用数学,力学,流体物理))

  飯間 信, 郡 宏, 中垣 俊之 日本物理学会講演概要集 68 (0) 241 -241 2013年 [査読無し][通常論文]
  
• 26aXZC-9 F-アクチン溶液のシアバンディング(26aXZC 生物物理,領域12(ソフトマター物理,化学物理,生物物理))

  田中 良巳, 國田 樹, 佐藤 勝彦, 瀧川 佳紀, 折原 宏, 中垣 俊之 日本物理学会講演概要集 68 (0) 419 -419 2013年 [査読無し][通常論文]
  
• 単細胞生物に学ぶ最適なネットワーク

  手老篤史, 中垣俊之, 小林亮 分子シミュレーション討論会講演要旨集 26th 48 -49 2012年11月26日 [査読無し][通常論文]
  
• かしこい単細胞 粘菌 /

  中垣 俊之, 斉藤 俊行 たくさんのふしぎ (332) 1冊. 2012年11月 [査読無し][通常論文]
  
• アメーバの問題解決 －行動知の数理モデリング－

  中垣俊之 研究報告数理モデル化と問題解決（MPS） 2012 (9) 1 -1 2012年09月12日 [査読無し][通常論文]
  
• アメーバの生理心理学にむけて

  中垣俊之 生理心理学と精神生理学 30 (2) 103 -104 2012年08月31日 [査読無し][通常論文]
  
• 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 2012年04月15日 [査読無し][通常論文]
  
• 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 2012年04月 [査読無し][通常論文]
   

  Mycelial fungi grow as indeterminate adaptive networks that have to forage for scarce resources in a patchy and unpredictable environment under constant onslaught from mycophagous animals. Development of contrast-independent network extraction algorithms has dramatically improved our ability to characterise these dynamic macroscopic networks and promises to bridge the gap between experiments in realistic experimental microcosms and graph-theoretic network analysis, greatly facilitating quantitative description of their complex behaviour. Furthermore, using digitised networks as inputs, empirically-based minimal biophysical mass-flow models already provide a high degree of explanation for patterns of long-distance radiolabel movement, and hint at global control mechanisms emerging naturally as a consequence of the intrinsic hydraulic connectivity. Network resilience is also critical to survival and can be explored both . in silico by removing links in the digitised networks according to particular rules, or . in vivo by allowing different mycophagous invertebrates to graze on the networks. Survival depends on both the intrinsic architecture adopted by each species and the ability to reconnect following damage. It is hoped that a comparative approach may yield useful insights into not just fungal ecology, but also biologically inspired rules governing the combinatorial trade-off between cost, transport efficiency, resilience and control complexity for self-organised adaptive networks in other domains. © 2012 The British Mycological Society.
• 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 2012年03月27日 [査読無し][通常論文]
  
• 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 2012年03月05日 [査読無し][通常論文]
  
• 特別講演 アメーバの生理心理学に向けて

  中垣 俊之 生理心理学と精神生理学 30 (2) 103 -104 2012年 [査読無し][通常論文]
  
• 27aBJ-11 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(27aBJ 生物物理,領域12(ソフトマター物理,化学物理,生物物理))

  飯間 信, 郡 宏, 中垣 俊之 日本物理学会講演概要集 67 (0) 423 -423 2012年 [査読無し][通常論文]
  
• 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」(ラボラトリーズ)

  小林 亮, 中垣 俊之, 石黒 章夫 応用数理 22 (1) 62 -64 2012年 [査読無し][通常論文]
  
• 原生生物粘菌による組合せ最適化法―物理現象として見た行動知―

  中垣俊之, 小林亮 人工知能学会誌 26 (5) 482 -493 2011年09月01日 [査読無し][通常論文]
  
• 原生生物粘菌による組合せ最適化法 : 物理現象として見た行動知

  中垣 俊之, 小林 亮, Toshiyuki Nakagaki, Ryo Kobayashi 人工知能学会誌 = Journal of Japanese Society for Artificial Intelligence 26 (5) 482 -493 2011年09月01日 [査読無し][通常論文]
  
• 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 2011年08月24日 [査読無し][通常論文]
  
• 粘菌ネットワークの賢さ

  伊藤 賢太郎, 中垣 俊之 生物物理 51 (4) 178 -181 2011年07月25日 [査読無し][通常論文]
   

  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>
• 真正粘菌変形体の環境適応行動の数理モデル (第7回生物数学の理論とその応用--RIMS研究集会報告集)

  上田 肇一, 高木 清二, 中垣 俊之 数理解析研究所講究録 1751 (1751) 109 -112 2011年07月 [査読無し][通常論文]
  
• 科学の興亡(完結編)科学放談 環境破壊が今の地球を作った

  中川 貴雄, 中垣 俊之, 竹内 薫 新潮45 30 (7) 154 -165 2011年07月 [査読無し][通常論文]
  
• 真正粘菌変形体の環境適応性

  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年04月05日 [査読無し][通常論文]
  
• アメーバの行動にみる賢さとそれをもたらすダイナミクス

  中垣俊之 化学系学協会北海道支部冬季研究発表会講演要旨集 2011 2 -3 2011年02月01日 [査読無し][通常論文]
  
• 真正粘菌変形体から着想を得た自律分散制御方策

  梅舘拓也, 出井遼, 中垣俊之, 小林亮, 石黒章夫 越境する数学 CREST研究報告会 平成23年 40 2011年 [査読無し][通常論文]
  
• 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 越境する数学 CREST研究報告会 平成23年 26 -29 2011年 [査読無し][通常論文]
  
• 粘菌ネットワークの賢さ

  伊藤賢太郎, 中垣俊之 生物物理 51 (4) 178-181 (J-STAGE) 2011年 [査読無し][通常論文]
  
• 真正粘菌変形体によるネットワーク形成

  伊藤賢太郎, 手老篤史, 高木清二, 中垣俊之, 小林亮 越境する数学 CREST研究報告会 平成23年 39 2011年 [査読無し][通常論文]
  
• 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年 [査読無し][通常論文]
   

  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。
• 21aJD-4 真性粘菌内流動における蠕動運動の役割について(21aJD 領域12,領域11合同生物物理,領域12(ソフトマター物理,化学物理,生物物理))

  飯間 信, 中垣 俊之 日本物理学会講演概要集 66 (0) 300 -300 2011年 [査読無し][通常論文]
  
• 単細胞(原始的生命体)に学ぶ生命知のからくり (現代科学の焦点--生命・脳・心)

  中垣 俊之 東洋学術研究 50 (1) 165 -193 2011年 [査読無し][通常論文]
  
• 粘菌がつくる自己組織的な鉄道網

  高木清二, 中垣俊之 現代化学 (477) 48 -51 2010年12月01日 [査読無し][通常論文]
  
• イグ・ノーベル賞受賞 粘菌がつくる自己組織的な鉄道網

  高木 清二, 中垣 俊之 現代化学 (477) 48 -51 2010年12月 [査読無し][通常論文]
  
• 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 2010年11月30日 [査読無し][通常論文]
   

  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.
• 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 2010年09月 [査読無し][通常論文]
  
• 真正粘菌変形体にみられる環境適応性

  上田肇一, 高木清二, 中垣俊之 日本応用数理学会年会講演予稿集 2010 267 -268 2010年09月 [査読無し][通常論文]
  
• 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 2010年08月 [査読無し][通常論文]
  
• 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)" 2010年06月13日 [査読無し][通常論文]
   

  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.
• アメーバのエソロジー

  中垣俊之 物性研究 94 (2) 238 -239 2010年05月05日 [査読無し][通常論文]
  
• 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 2010年05月05日 [査読無し][通常論文]
   

  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。
• 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 2010年03月05日 [査読無し][通常論文]
   

  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。
• 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 2010年03月05日 [査読無し][通常論文]
   

  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。
• 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 2010年03月 [査読無し][通常論文]
   

  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。
• 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年 [査読無し][通常論文]
  
• 真正粘菌における振動パターンとネットワークの関係

  手老篤史, 中垣俊之, 小林亮 日本数理生物学会大会講演要旨集 20th 54 2010年 [査読無し][通常論文]
  
• 変動環境下における真正粘菌ネットワークの適応戦略

  伊藤賢太郎, 中垣俊之 日本数理生物学会大会講演要旨集 20th 138 2010年 [査読無し][通常論文]
  
• 真正粘菌に学ぶ適応ネットワークの共通原理

  手老篤史, 中垣俊之, 小林亮 生化学 ROMBUNNO.2W17-P-6 2010年 [査読無し][通常論文]
  
• 粘菌アルゴリズムを用いた首都圏鉄道網の輸送量最適化

  渡邊晋, 手老篤史, 高松敦子, 中垣俊之 日本数理生物学会大会講演要旨集 20th 55 2010年 [査読無し][通常論文]
  
• 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 2010年 [査読無し][通常論文]
  
• 1A1-E20 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 ロボティクス・メカトロニクス講演会講演概要集 2010 (0) _1A1 -E20_1-_1A1-E20_4 2010年 [査読無し][通常論文]
   

  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.
• 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 2009年11月24日 [査読無し][通常論文]
  
• 単細胞生物研究に見る北海道の「開拓者精神(フロンティア・スピリット)」

  中垣 俊之 うおんつブックレット 26 (316) 1 -19 2009年09月 [査読無し][通常論文]
  
• 「薬学」から「粘菌の迷路解き」へ

  中垣俊之 ファルマシア 45 (6) 547 -552 2009年06月01日 [査読無し][通常論文]
  
• 真正粘菌をモチーフとした大自由度ソフトロボットの実験的検証

  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 2009年05月24日 [査読無し][通常論文]
  
• 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年 [査読無し][通常論文]
  
• 2A2-F22 真正粘菌をモチーフとした大自由度ソフトロボットの実験的検証

  武田 光一, 北村 太一, 梅舘 拓也, 中垣 俊之, 小林 亮, 石黒 章夫 ロボティクス・メカトロニクス講演会講演概要集 2009 (0) _2A2 -F22_1-_2A2-F22_4 2009年 [査読無し][通常論文]
   

  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.
• 「薬学」から「粘菌の迷路解き」へ(話題)

  中垣 俊之 ファルマシア 45 (6) 547 -552 2009年 [査読無し][通常論文]
  
• 単細胞生物の時間記憶

  三枝徹, 中垣俊之 時間生物学 14 (2) 60 2008年10月20日 [査読無し][通常論文]
  
• 原形質による大域的相互作用を活用したアメーバ様ロボットの自律分散制御

  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 2008年09月09日 [査読無し][通常論文]
  
• アメーバの賢さのしくみと制御

  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 2008年05月16日 [査読無し][通常論文]
  
• 真正粘菌による迷路・最短ネットワーク・最適交通網問題の解法

  手老篤史, 中垣俊之, 小林亮 交通流のシミュレーションシンポジウム論文集 14th 41 -44 2008年 [査読無し][通常論文]
  
• 真正粘菌の時間記憶能

  三枝徹, 中垣俊之 日本比較生理生化学会大会予稿集 30th 23 2008年 [査読無し][通常論文]
  
• 現象を視る アメーバの迷路解きに学ぼう

  手老篤史, 小林亮, 中垣俊之 数理科学 46 (1) 7 -11 2008年01月01日 [査読無し][通常論文]
  
• アメーバの賢さのしくみと制御

  中垣 俊之, 手老 篤史, 三枝 徹, 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 8 (0) 51 -51 2008年 [査読無し][通常論文]
   

  アメーバ様生物粘菌の行動レベルにあらわれる賢さについて述べる。具体的な項目は、迷路やいくつかの幾何学的パズルを解く能力、周期的な環境変動を記憶学習する能力、逡巡行動（行動選択）などである。その能力の高さを実験により解明し、その機構を数理モデルから理解する。
• 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 2008年01月 [査読無し][通常論文]
  
• 粘菌による迷路の解法 (特集 生物振動:振動が生み出す情報は分子を超える)

  小林 亮, 手老 篤史, 中垣 俊之 細胞工学 26 (7) 769 -773 2007年07月 [査読無し][通常論文]
  
• 生物振動:振動が生み出す情報は分子を超える 粘菌による迷路の解法

  小林亮, 手老篤史, 中垣俊之 細胞工学 26 (7) 769 -773 2007年06月22日 [査読無し][通常論文]
  
• アメーバに学ぶ経路探索の方法 (特集 知の創造から知の活用へ--北大創成科学共同研究機構)

  手老 篤史, 中垣 俊之, 小林 亮 マテリアルインテグレ-ション 20 (5) 55 -60 2007年05月 [査読無し][通常論文]
  
• 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 2007年04月25日 [査読無し][通常論文]
  
• 生物に学ぶ最短経路探索アルゴリズム

  手老篤史, 中垣俊之, 小林亮 物性研究 87 (4) 583 -583 2007年01月20日 [査読無し][通常論文]
  
• 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 2007年01月20日 [査読無し][通常論文]
  
• Anticipation of periodic environmental changes in an amoeba

  Tetsu Saigusa, Toshiyuki Nakagaki NOISE AND FLUCTUATIONS 922 655 -+ 2007年 [査読無し][通常論文]
   

  The amoeboid organism of true slime mold, the plasmodium of Physarum polycephalum, had capacity of memorizing a periodic event. The organism. showed vigorous locomotion in the favorite conditions. When stimulation of the unfavorable conditions was given in a pulse-like regime and was repeated three times at interval of 60 minutes, the amoeba reduced the locomotion speed in response to each pulse. Even though the favorite conditions were kept to be constant after the periodic pulses, the amoeba spontaneously reduced the locomotion speed at the timing of next pulse (after 60 minutes). This means that the amoeba anticipated the next environmental change.
• 粘菌ネットワークの流量適応ダイナミクス

  中垣俊之, 手老篤史, 小林亮 交通流のシミュレーションシンポジウム講演概要集 13th 35 -36 2007年 [査読無し][通常論文]
  
• 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年 [査読無し][通常論文]
   

  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
• 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年 [査読無し][通常論文]
   

  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
• 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 2007年01月01日 [査読無し][通常論文]
   

  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。
• 粘菌の作る輸送ネットワークのダイナミクス

  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 2006年11月17日 [査読無し][通常論文]
  
• 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 2006年10月 [査読無し][通常論文]
  
• 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 2006年07月 [査読無し][通常論文]
  
• 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年 [査読無し][通常論文]
  
• リズムが創りだす生命のしくみ 粘菌の行動にみる賢さ そのリズム性運動と網目体形

  中垣俊之 科学 75 (12) 1393 -1395 2005年12月01日 [査読無し][通常論文]
  
• 粘菌の行動にみる賢さ--そのリズム性運動と網目体形 (特集=リズムが創りだす生命のしくみ)

  中垣 俊之 科学 75 (12) 1393 -1395 2005年12月 [査読無し][通常論文]
  
• 真正粘菌変形体の運動と情報処理のモデル

  小林亮, 手老篤史, 中垣俊之 日本結晶成長学会誌 32 (3) 236 -237 2005年08月17日 [査読無し][通常論文]
   

  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.
• 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 2005年06月 [査読無し][通常論文]
   

  Experiments on the fusion and partial separation of plasmodia of the true slime mold Physarum polycephalum are described, concentrating on the spatio-temporal phase patterns of rhythmic amoeboid movement. On the basis of these experimental results we introduce a new model of coupled oscillators with one conserved quantity. Simulations using the model equations reproduce the experimental results well. (c) 2005 Elsevier B.V. All rights reserved.
• 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 2005年03月 [査読無し][通常論文]
   

  Collective cell movement acts as an efficient strategy in many physiological events, including wound healing, embryonic development, and morphogenesis. We found that epithelial cells (Madin-Darby canine kidney cell) migrated collectively along one direction on a collagen gel substrate. Time-lapse images of Madin-Darby canine kidney cells cultured on type-I collagen gels and glass substrates were captured by phase contrast microscopy equipped with an incubation system. On the gel substrate, the directions of cell movement gradually converged on one direction as the number of cells increased, whereas the cells moved randomly on the glass substrate. We also observed "leader'' cells, which extended large lamellae and were accompanied by many "follower'' cells, migrating in the direction of oriented collagen fibers. The mean-squared displacement of each cell movement and the spatial correlation function calculated from the spatial distribution of cell velocity were obtained as functions of observation time. In the case of the gel substrate, the spatial correlation length increased gradually, representing the collectiveness of multicellular movement.
• 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 2005年01月 [査読無し][通常論文]
  
• How does an amoeba tackle some geometrical puzzles?

  Toshiyuki Nakagaki Proceedings SICE Annual Conference 3537 -3542 2005年 [査読無し][通常論文]
  
• 18aD01 真正粘菌変形体の運動と情報処理のモデル(数理科学におけるモデリングと結晶成長,結晶成長基礎シンポジウム,第35回結晶成長国内会議)

  小林 亮, 手老 篶史, 中垣 俊之 日本結晶成長学会誌 32 (3) 236 -237 2005年 [査読無し][通常論文]
   

  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.
• 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 2004年11月 [査読無し][通常論文]
   

  To evaluate performance in a complex survival task, we studied the morphology of the Physarum plasmodium transportation network when presented with multiple separate food sources. The plasmodium comprises a network of tubular elements through which chemical nutrient, intracellular signals and the viscous body are transported and circulated. When three separate food sources were presented, located at the vertices of a triangle, the tubular network connected them via a short pathway, which was often analogous to the mathematically shortest route known as Steiner's minimum tree (SMT). The other common network shape had high fault tolerance against accidental disconnection of the tubes and was known as cycle (CYC). Pattern selection appeared to be a bistable system involving SMT and CYC. When more than three food sources were presented, the network pattern tended to be a patchwork of SMT and CYC. We therefore concluded that the plasmodium tube network is a well designed and intelligent system.
• Sequences of symmetry-breaking in phyllotactic transitions

  H Yamada, R Tanaka, T Nakagaki BULLETIN OF MATHEMATICAL BIOLOGY 66 (4) 779 -789 2004年07月 [査読無し][通常論文]
   

  This paper studies the transition of phyllotactic patterns by a group-theoretic approach. Typical phyllotactic patterns are represented here as dotted patterns on a cylinder, where the cylinder is regarded as the stem of a plant and the dots are points where leaves branch from the stem. We can then classify the symmetries of the alternate and opposite phyllotaxis into four types of groups, and clarify sequences of symmetry-breaking among these groups. The sequences turn out to correspond to transition paths of phyllotactic patterns found in the wild. This result shows the usefulness of classification of phyllotactic patterns based on their group symmetries. Moreover, the breaking of reflection symmetry is found to be an important rule for real phyllotactic transitions. (C) 2003 Society for Mathematical Biology. Published by Elsevier Ltd. All rights reserved.
• 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 2004年02月 [査読無し][通常論文]
  
• Smart network solutions in an amoeboid organism

  T Nakagaki, H Yamada, M Hara BIOPHYSICAL CHEMISTRY 107 (1) 1 -5 2004年01月 [査読無し][通常論文]
   

  We present evidence that the giant amoeboid organism, the true slime mold, constructs 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. (C) 2003 Elsevier B.V. All rights reserved.
• 1SC01 真正粘菌変形体の振動の位相ダイナミクスにかんする実験とモデリング(生物時空間構造のダイナミクス : 階層を越えたアプローチ)

  小林 亮, 手老 篤史, 中垣 俊之 生物物理 44 (0) S5 2004年 [査読無し][通常論文]
  
• 真正粘菌変形体の運動と形態形成の数理モデル

  小林亮, 中垣俊之, 手老篤史 日本化学会非線形反応と協同現象シンポジウム 13th 9 -12 2003年12月06日 [査読無し][通常論文]
  
• あるアメーバ様生物が作るコミュニケーションネットワークの形と機能

  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 2003年11月11日 [査読無し][通常論文]
  
• 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 2003年02月 [査読無し][通常論文]
  
• 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 2003年02月 [査読無し][通常論文]
  
• Oscillation patterns in cytoplasmic networks of the Physarum plasmodium

  H Yamada, T Nakagaki TRAFFIC AND GRANULAR FLOW'01 563 -568 2003年 [査読無し][通常論文]
   

  The plasmodium of a true slime mould is an amoeboid organism with vein networks. We regard this organism as the system of biological oscillators on a graph and study collective behaviour on it.
• アメーバ様生物による輸送ネットワークの効率的な設計

  中垣 俊之, 上田 哲男 生物物理 43 (0) S113 2003年 [査読無し][通常論文]
  
• 22pWE-7 結合振動子系としてみた真正粘菌の挙動

  中垣 俊之, 小林 亮 日本物理学会講演概要集 58 (0) 254 -254 2003年 [査読無し][通常論文]
  
• アメーバ様生物粘菌の行動と計算

  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 2002年12月04日 [査読無し][通常論文]
  
• 粘菌の流路ネットワーク形成と細胞リズム

  中垣俊之 生体・生理工学シンポジウム論文集 17th 373 -376 2002年09月09日 [査読無し][通常論文]
  
• 粘菌の流路ネットワーク形成と細胞リズム

  中垣 俊之 生体・生理工学シンポジウム論文集 17 373 -376 2002年09月09日 [査読無し][通常論文]
  
• 「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 2002年05月 [査読無し][通常論文]
  
• 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 2002年05月01日 [査読無し][通常論文]
  
• 生物専攻課程に数理生理学を (フォーラム:現代数学の風景 数学への夢・数学に託す夢)

  中垣 俊之 数学のたのしみ (30) 43 -48 2002年04月 [査読無し][通常論文]
  
• アメーバ様生命体のパターンと計算について

  小林亮, 中垣俊之 理論応用力学講演会講演論文集 51st 183 -184 2002年01月22日 [査読無し][通常論文]
  
• Smart behavior of true slime mold in a labyrinth

  T Nakagaki RESEARCH IN MICROBIOLOGY 152 (9) 767 -770 2001年11月 [査読無し][通常論文]
   

  Even for humans it is not easy to solve a maze. But the plasmodium of true slime mold, an amoeba-like unicellular organism, has shown an amazing ability to do so. This implies that an algorithm and a high computing capacity are included in the unicellular organism. In this report, we discuss information processing in the microorganism to focus on the issue as to whether the maze-solving behavior is akin to primitive intelligence. (C) 2001 Editions scientifiques et medicales Elsevier SAS.
• 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 2001年10月 [査読無し][通常論文]
  
• 粘菌変形体の細胞リズムの生理

  中垣 俊之 日本時間生物学会会誌: Journal of Chronobiology 7 (2) 66 -66 2001年10月01日 [査読無し][通常論文]
  
• 迷路を解く巨大アメーバー細胞:粘菌

  中垣 俊之, 山田 裕康 生物物理 41 (5) 244 -246 2001年09月25日 [査読無し][通常論文]
  
• Path finding by tube morphogenesis in an amoeboid organism

  T Nakagaki, H Yamada, A Toth BIOPHYSICAL CHEMISTRY 92 (1-2) 47 -52 2001年08月 [査読無し][通常論文]
   

  We have studied how the plasmodium of Physarum polycephalum, a large amoeboid cell, is able to track the shortest path between two selected points in a labyrinth. When nutrients are supplied at these points to a sheet-like plasmodium extended fully in a maze, the organism forms a single tube which connects the two sites via the shortest route. During the path finding, plasmodial parts in dead ends of the maze shrink and finally the tube with the minimum-length is selected from the existing possibilities. A simple cellular mechanism based on interacting cellular rhythms may describe the experimental observations. (C) 2001 Elsevier Science B.V. All rights reserved.
• 迷路を解く単細胞生物

  中垣 俊之 遺伝 55 (3) 23 -25 2001年05月 [査読無し][通常論文]
  
• 粘菌の経路探索

  中垣俊之, 山田裕康 自律分散システム・シンポジウム資料 13th 425 -428 2001年01月26日 [査読無し][通常論文]
  
• 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 2001年01月26日 [査読無し][通常論文]
  
• 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 2001年01月26日 [査読無し][通常論文]
  
• 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 2001年01月26日 [査読無し][通常論文]
  
• 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年 [査読無し][通常論文]
  
• Amoeboid organisms may be more clever than we thought!

  Toshiyuki Nakagaki Newsletter of RIKEN Frontier Research System (February) 8 -12 2001年 [査読無し][通常論文]
  
• S1B03粘菌による迷路の解法

  中垣 俊之 生物物理 41 (0) S3 2001年 [査読無し][通常論文]
  
• 30aPS-33 折り返し対称性の破れによる葉序遷移

  山田 裕康, 田中 玲子, 中垣 俊之 日本物理学会講演概要集 56 (0) 286 -286 2001年 [査読無し][通常論文]
  
• 粘菌変形体における管ネットワークの形成と細胞リズム

  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 2000年11月18日 [査読無し][通常論文]
  
• 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 2000年08月 [査読無し][通常論文]
  
• Interaction between cell shape and contraction pattern in the Physarum plasmodium

  T Nakagaki, H Yamada, T Ueda BIOPHYSICAL CHEMISTRY 84 (3) 195 -204 2000年05月 [査読無し][通常論文]
   

  The relationship between cell shape and rhythmic contractile activity in the large amoeboid organism Physarum polycephalum was studied. The organism develops intricate networks of veins in which protoplasmic sol moved to and fro very regularly. When migrating on plain agar, the plasmodium extends like a sheet and develops dendritic veins toward the rear. After a particular stimulation, the vein organization changes into veinless or vein-network structures. In both structures, the mixing rate of the protoplasm, which is related to communication among contraction oscillators, decreased compared with that of the dendritic one. Accompanying these changes in vein structure, the spatio-temporal pattern of the rhythmic contraction changed into a small-structured pattern from a synchronized one. In the above process, cell shape affects the contraction pattern, but, conversely, the contraction pattern effects the cell shape. To demonstrate this, a phase difference in the rhythmic contraction was induced artificially by entraining the intrinsic rhythm to external temperature oscillations. New veins then formed along the direction parallel to the phase difference of the rhythm. Consequently, the vein organization of the cell interacts with the contractile activity to form a feedback loop in a mechanism of contraction pattern formation. (C) 2000 Elsevier Science B.V. All rights reserved.
• 真正粘菌変形体の形態形成と細胞行動

  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 2000年01月21日 [査読無し][通常論文]
  
• 真正粘菌変形体の形態形成と細胞行動

  山田 裕康, 中垣 俊之 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 2000年01月21日 [査読無し][通常論文]
  
• Rhythmic contraction and its fluctuations in an amoeboid organism of the Physarum plasmodium

  NAKAGAKI T. Quantum Information 107 -124 2000年 [査読無し][通常論文]
  
• 粘菌に細胞インテリジェンスを探る

  上田哲男, 中垣俊之, 山田裕康 電子科学研究 8 60 -61 2000年 [査読無し][通常論文]
  
• 1M1315 粘菌変形体の管ネットワークの幾何

  中垣 俊之, 山田 裕康 生物物理 40 (0) S99 2000年 [査読無し][通常論文]
  
• 25aPS-26 真正粘菌変形体の管構造と原形質流動

  山田 裕康, 中垣 俊之 日本物理学会講演概要集 55 (0) 258 -258 2000年 [査読無し][通常論文]
  
• 23pPSA-47 粘菌変形体の原形質流路形態と振動パターン

  山田 裕康, 中垣 俊之 日本物理学会講演概要集 55 (0) 247 -247 2000年 [査読無し][通常論文]
  
• 位相勾配の移流項を持つλ‐ω系の平面波(原標題は英語)

  山田裕康, 中垣俊之 日本物理学会講演概要集 54 (2) 227 1999年09月03日 [査読無し][通常論文]
  
• Dispersion relations to oscillatory reaction-diffusion systems with the self-consistent flow

  Hiroyasu Yamada, Toshiyuki Nakagaki 1999年06月24日 [査読無し][通常論文]
   

  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.
• 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 1999年03月15日 [査読無し][通常論文]
  
• 粘菌変形体におけるネットワーク形態に関連した収縮リズムのパターン形成

  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 = SICE Symposium on Decentralized Autonomous Systems 11 109 -114 1999年01月18日 [査読無し][通常論文]
  
• 粘菌変形体におけるネットワーク形態に関連した収縮リズムのパターン形成

  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 1999年01月 [査読無し][通常論文]
  
• 25aPS-30 Plane waves for λ-ω system with advection terms of phase gradients

  山田 裕康, 中垣 俊之 日本物理学会講演概要集 54 (0) 227 -227 1999年 [査読無し][通常論文]
  
• 28a-P-11 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 (0) 639 -639 1999年 [査読無し][通常論文]
  
• 粘菌変形体における収縮リズムのパターン形成モデル

  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 13 437 -440 1998年09月09日 [査読無し][通常論文]
  
• 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 1998年09月05日 [査読無し][通常論文]
  
• 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 1998年06月 [査読無し][通常論文]
  
• 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 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 1998年03月 [査読無し][通常論文]
  
• 粘菌変形体の収縮リズムにおける反応拡散移流モデル

  山田 裕康, 中垣 俊之, 伊藤 正美 形の科学会報 12 (3) 20 -21 1998年03月01日 [査読無し][通常論文]
  
• 粘菌の収縮リズムのパターン形成モデルI : 非局所結合写像モデルの構成と解析

  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 = SICE Symposium on Decentralized Autonomous Systems 10 5 -8 1998年01月20日 [査読無し][通常論文]
  
• 粘菌における収縮リズムのパターン形成モデルII : 反応拡散移流モデルの構成と解析

  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 = SICE Symposium on Decentralized Autonomous Systems 10 9 -12 1998年01月20日 [査読無し][通常論文]
  
• 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年 [査読無し][通常論文]
  
• 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 形の科学会報 13 (1) 56 -57 1998年 [査読無し][通常論文]
  
• 粘菌における収縮リズムのパターン形成モデル II 反応拡散移流モデルの構成と解析

  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 1998年01月 [査読無し][通常論文]
  
• 粘菌の収縮リズムのパターン形成モデル I 非局所結合写像モデルの構成と解析

  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 1998年01月 [査読無し][通常論文]
  
• 27p-Q-4 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 (0) 856 -856 1998年 [査読無し][通常論文]
  
• 30p-YB-4 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II

  山田 裕康, 中垣 俊之, 伊藤 正美 日本物理学会講演概要集 53 (0) 729 -729 1998年 [査読無し][通常論文]
  
• 結合振動子系の自己組織化としてみた粘菌の行動

  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 1997年12月 [査読無し][通常論文]
  
• 粘菌変形体の形態形成 : フィトクロム関与の証拠

  垣内 康孝, 中垣 俊之, 古家 奨, 上田 哲男 生物物理 37 S185 1997年10月 [査読無し][通常論文]
  
• 結合振動子系の自己組織化としてみたアメーバ様細胞の行動

  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 12 161 -164 1997年09月04日 [査読無し][通常論文]
  
• 結合振動子系の自己組織化としてみたアメーバ様細胞の行動

  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 1997年09月 [査読無し][通常論文]
  
• 粘菌変形体の形態形成 フィトクロム関与の証拠

  垣内康孝, 中垣俊之, 古家奨, 上田哲男 日本生物物理学会年会講演予稿集 35th S185 1997年09月 [査読無し][通常論文]
  
• 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

  山田裕康, 中垣俊之 日本物理学会講演概要集(分科会) 1997 855 1997年09月 [査読無し][通常論文]
  
• 粘菌変形体の収縮リズムにおける反応拡散移流モデル

  山田裕康, 中垣俊之, 伊藤正美 形の科学会報 12 (3) 20 -21 1997年 [査読無し][通常論文]
  
• 8a-P-12 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

  山田 裕康, 中垣 俊之 日本物理学会講演概要集 52 (0) 855 -855 1997年 [査読無し][通常論文]
  
• 粘菌の収縮リズムにおける多重振動状態間の経巡り

  中垣俊之, 上田哲男 日本生物物理学会年会講演予稿集 34th S188 1996年10月 [査読無し][通常論文]
  
• 粘菌変形体の行動発現に伴うリズムのダイナミクス

  梅村昇治, 中垣俊之, 垣内康孝, 上田哲男 日本生物物理学会年会講演予稿集 34th S70 1996年10月 [査読無し][通常論文]
  
• 粘菌における収縮リズムの位相スイッチングによる原形質流動と前動の調節

  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 1995年08月 [査読無し][通常論文]
  
• 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 1992年10月 [査読無し][通常論文]
   

  The non-peptide NK1 receptor antagonist, CP-96,345, and its 2R,3R enantiomer CP-96,344, which is not an NK1 receptor antagonist (IC50 > 10 muM), were evaluated for antinociceptive and anti-inflammatory activities in several classical models of pain and inflammation in the rat. Both CP-96,345 and CP-96,344 reduced carrageenin-induced paw oedema and hyperalgesia, and attenuated the second phase of formalin-induced paw licking with equal potency. These results indicate that NK1 antagonism is not responsible for the activity of (+/-)-CP-96,345 in the above animal models.
• 粘菌の数理モデルに関する記事

  中垣 俊之, 西浦 廉政, 小林 亮 朝日新聞（夕刊） 2005年04月19日 [査読無し][通常論文]
  
• 新科論 最適ルート粘菌に学ぶ

  中垣 俊之, 小林 亮, 西浦 廉政 朝日新聞（夕刊） 2005年04月19日 [査読無し][通常論文]
  
• Cell Info.-NSC ワークショップ ”粘菌のダイナミックな生命像を求めて”

  上田 哲男, 中垣 俊之, 西浦 廉政, 小林 亮 北海道大学 (札幌) (2002年02月25日～2002年02月26日) [査読無し][通常論文]
  
• NSC-Cell Info. Symposium on “Cell Dynamics And Physiological Functions In Physarum”

  Tetsuo Ueda, Toshiyuki Nakagaki, Yasumasa Nishiura, Ryo Kobayashi 北海道大学 (札幌) (2002年03月25日～2002年03月26日) [査読無し][通常論文]
  
• 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) (2008年12月08日～2008年12月09日) [査読無し][通常論文]
  

受賞

• 2011年 NHKテレビ番組「爆笑問題の日本の教養」 爆ノーベル賞
   

  受賞者: 中垣 俊之
• 2010年 函館市長賞
   

  受賞者: 中垣 俊之
• 2010年 イグノーベル賞 交通計画賞
   

  受賞者: 中垣 俊之
• 2008年 イグノーベル賞 認知科学賞
   

  受賞者: 中垣 俊之

共同研究・競争的資金等の研究課題

• 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

  日本学術振興会：科学研究費助成事業

  研究期間 : 2021年10月 -2026年03月 

  代表者 : 棟朝雅晴, 田中良巳, 佐藤勝彦, 國田樹
• 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

  日本学術振興会：科学研究費助成事業

  研究期間 : 2021年10月 -2026年03月 

  代表者 : 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
• 非平衡定常状態におけるソフトマターのゆらぎとレオロジー

  日本学術振興会：科学研究費助成事業

  研究期間 : 2013年06月 -2018年03月 

  代表者 : 折原 宏, 長屋 智之, 佐藤 勝彦, 日高 芳樹, 中垣 俊之

   

  せん断流は、ソフトマターの空間構造を一変させるだけでなく、時間反転対称性を破ることによりゆらぎや応答の性質をも変化させる。本研究ではレオメーターと共焦点レーザー顕微鏡を組み合わせた装置を製作し、主にせん断流下でソフトマターの非平衡構造とゆらぎの研究を行った。液晶、コロイド、アクチン水溶液等のソフトマターにせん断を印加し、ゆらぎと応答を測定した結果、非平衡系に特有な現象が観測された。例えば、せん断流下の液晶およびコロイド粒子系では非平衡系に特有な非保存力が出現し、異常なゆらぎや応答が観測された。液晶に関しては、液晶のダイナミクスを記述するエリクセン－レスリー理論を用いて実験結果を考察した。
• せん断流下における非ニュートン流体のマイクロレオロジー

  日本学術振興会：科学研究費助成事業

  研究期間 : 2014年04月 -2017年03月 

  代表者 : 折原 宏, 佐々木 裕司, 中垣 俊之

   

  高分子、液晶等のソフトマターはミクロな構造を持ち、この構造は流れと相互作用をする。本研究では、構造が特にせん断流と関係したレオロジー的性質に及ぼす影響をマイクロレオロジー的手法を用いることによって明らかにした。先ず、平衡状態におけるネマチック液晶の配向ゆらぎとせん断流れを同時に観測し、これらの相互相関関数を求めることによって、相互作用がゆらぎにおいても存在することを明らかにした。さらに、相関関数をレスリー・エリクセン理論から導出し、実験結果と比較した。次に、キサンタン水溶液にせん断を印加したときの分散粒子のブラウン運動を観測し、キサンタン分子間の相互作用に起因する拡散があることを明らかにした。
• 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

  日本学術振興会：科学研究費補助金

  研究期間 : 2014年04月 -2017年03月 

  代表者 : 中垣俊之
• 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

  日本学術振興会：科学研究費補助金

  研究期間 : 2013年04月 -2015年03月 

  代表者 : 中垣俊之
• 単細胞生物に学ぶ生命知の基本アルゴリズム

  秋山記念生命科学振興財団：研究助成

  研究期間 : 2013年04月 -2014年03月 

  代表者 : 中垣 俊之
• 生物輸送ネットワークのダイナミクス

  科学技術振興機構：戦略的国際科学技術協力推進事業

  研究期間 : 2011年04月 -2014年03月 

  代表者 : 中垣 俊之
• 生物ロコモーションに学ぶ大自由度システムの新展開

  科学技術振興機構：戦略的創造研究推進事業

  研究期間 : 2008年04月 -2013年03月 

  代表者 : 小林亮
• 自己駆動する境界運動と流れの相互作用による推進・輸送現象の解明

  日本学術振興会：科学研究費助成事業

  研究期間 : 2011年 -2013年 

  代表者 : 飯間 信, 中垣 俊之, 郡 宏

   

  複数のバネ支持円柱を一様流中に置いた場合，渦剥離を伴う場合でも同期が発生することを示し，その条件について数値的に調べた． 剥離渦によるバネ支持円柱の振動を一つの振動子と捉え,2つの振動子間の相互作用の結合関数を位相差の関数として計算データから得た. また粘菌の微小変形体の蠕動運動の発生要因として化学物質の輸送と振動が結合したモデルと境界での位相勾配を与えた位相振動子モデルを検討し，微小変形体に特有の蠕動運動パターンを再現することに成功した．
• 時間記憶能の系統進化に対する実験的評価と非線形動力学構造

  日本学術振興会：科学研究費補助金

  研究期間 : 2008年04月 -2012年03月 

  代表者 : 中垣 俊之
• 散逸系孤立波の相互作用理論の新展開

  日本学術振興会：科学研究費助成事業

  研究期間 : 2009年 -2012年 

  代表者 : 西浦 廉政, 上田 肇一, 寺本 敬, 飯間 信, 中垣 俊之, 高木 清二, 栄 伸一郎, 長山 雅晴

   

  空間的に局在し、自走する粒子解とよばれるパターンは神経パルス、ガス放電現象、2相対流問題、さらに真正粘菌ダイナミクス等に現れる。粒子解同士あるいは不均一媒質等の環境との強い相互作用で、これらは消滅、合体、分裂等の多彩なダイナミクスを示す。これらの統一的理解のために、高い余次元をもつ分岐特異点解析、数値的大域分岐解析、有限次元への縮約理論を組み合わせることにより、環境との相互作用を含む様々な衝突現象をその遷移ダイナミクスまで含めて明らかにした。
• Optimization in Natural System: ants, bees and slime moulds

  Human Frontier Science Program：Research Grant

  研究期間 : 2007年09月 -2010年08月 

  代表者 : SUMPTER David
• 生物における構造形成と情報に関する数理的研究

  日本学術振興会：科学研究費助成事業

  研究期間 : 2007年 -2010年 

  代表者 : 小林 亮, 中垣 俊之, 三浦 岳

   

  真正粘菌が鉄道網のような輸送ネットワークと等価なネットワークを形成する能力があることを実験的に示し、その数理モデルを構築することによって、ネットワークの新しい設計手法を提案した。また、卵割初期における空間的配位の決定や、肺や血管網の分岐構造の形成において、情報がどのような機序で働いているかを記述するモデルを提案した。これらの研究を通して、生物の構造形成と情報を結ぶしくみを記述する数理的手法を開発した。
• 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

  日本学術振興会：科学研究費補助金

  研究期間 : 2006年04月 -2008年03月 

  代表者 : 中垣 俊之
• トポロジー理工学の創成

  文部科学省：21世紀COEプログラム

  研究期間 : 2004年04月 -2008年03月 

  代表者 : 丹田 聡
• 生物に学ぶ動的ネットワーク最適化問題の研究

  日本学術振興会：科学研究費助成事業

  研究期間 : 2006年 -2007年 

  代表者 : 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。
• 多様な動的パターンの選択に基づく細胞インテリジェンスの創発

  日本学術振興会：科学研究費助成事業

  研究期間 : 2006年 -2007年 

  代表者 : 高木 清二, 上田 哲男, 中垣 俊之

   

  本研究課題の目的は真正粘菌の変形体を非平衡開放系で時間発展するシステムとしてとらえ、その高度な情報処理能力とその原理を調べ、生命現象を包括的に理解することである。主に以下の研究成果が得られた。 1.変形体によるフラクタル表面の認識 変形体は表面の物理的形状の違いを認識する事を明らかにした。ワックス(アルキルケテンダイマー)の表面にフラクタル次元が約2.3次元の部分と2次元の部分を作り、両方を同面積覆うように変形体を置いた結果、移植後細胞全体で同相同期していた振動はおよそ10分後にフラクタル次元の異なる表面の間で逆位相となった。 2.摘出内質ゾルの発展過程に現れる多様な動的パターン 巨大な変形体から嫡出した内質ゾルは調整後10分程度で収縮弛緩運動を開始し、その時空間パターンは時間経過とともに1)定在波、2)時空間カオス、3)回転ラセン波、4)同期パターンと発展する。同期パターンを示す変形体は管構造を形成し、同期パターンから回転ラセン波に遷移すると管構造が破壊される事が分かった。 3.原形質流動の流速場測定システムの構築 微小変形体を顕微鏡下で観察し、細胞内の原形質流動の流れ場と細胞の変形を同時に計測する画像解析システムを開発した。変形体の規則的な収縮弛緩運動、原形質流動および細胞の移動の相関を調べる事により、細胞運動のメカニズムを明らかにした。 4.複合刺激の情報統合機構 粘菌変形体に忌避・誘引の混合刺激を与えた際の応答を膜受容、収縮弛緩振動のダイナミクス、細胞行動レベルで調べ、細胞の情報統合機構を調べた。その結果共存する誘引物質濃度が高くなると共に忌避行動の現れる忌避刺激強度も高くなる事が分かった。また、変形体が行動判断を行う際、収縮弛緩周期よりもおよそ10倍長い周期の遅い位相変調ダイナミクスが顕在化し、そのリズムで位相波の方向が変化し、行動が決定されることが明らかになった。
• 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

  日本学術振興会：科学研究費助成事業

  研究期間 : 2004年 -2005年 

  代表者 : 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。
• 単細胞生物粘菌による幾何学的パズル問題の解決法と細胞内計算アルゴリズム

  日本学術振興会：科学研究費補助金

  研究期間 : 2003年04月 -2004年03月 

  代表者 : 中垣 俊之
• 粘菌における迷路解法と細胞システム構築の動的メカニズム

  日本学術振興会：科学研究費補助金

  研究期間 : 2001年04月 -2003年03月 

  代表者 : 中垣 俊之
• 巨大アメーバ・粘菌の形状変化に基づく細胞インテリジェンスの創発

  日本学術振興会：科学研究費助成事業

  研究期間 : 2001年 -2002年 

  代表者 : 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_/T_i=7.5、T_/T_=2.8ここにi=1,2,3である。このように粘菌の多重リズムは階層的時間秩序を示す。 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。
• 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

  日本学術振興会：科学研究費助成事業

  研究期間 : 2001年 -2002年 

  代表者 : 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_/T_i=7.5、T_/T_i=2.8 ここにi=1,2,3である。このように粘菌の多重リズムは階層的時間秩序を示す。 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。
• 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

  日本学術振興会：科学研究費補助金

  研究期間 : 1999年04月 -2001年03月 

  代表者 : 中垣 俊之
• 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

  日本学術振興会：科学研究費助成事業

  研究期間 : 1999年 -2000年 

  代表者 : 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。
• 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

  住友財団：基礎科学研究助成

  研究期間 : 1997年04月 -1998年03月 

  代表者 : 中垣 俊之

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