論文 - 國田　樹

Dynamic remodeling model based on chemotaxis of slime molds

Uza, M; Kunita, I

BIOINSPIRATION & BIOMIMETICS ( Bioinspiration and Biomimetics )  19 ( 5 )   2024年09月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

　概要を見る

Social infrastructure networks, essential for daily life and economic activities, encompass utilities such as water, electricity, roads, and telecommunications. Dynamic remodeling of these systems is crucial for responding to continuous changes, unexpected events, and increased demand. This study proposes a new dynamic remodeling model inspired by biological mechanisms, focusing on a model based on the chemotaxis of slime molds. Slime molds adapt spontaneously to environmental changes by remodeling through the growth and degeneration of tubes. This capability can be applied to optimizing and dynamic remodeling social infrastructure networks. This study elucidated the chemotactic response characteristics of slime molds using biological experiments. The mold’s response was observed by considering changes in the concentration of chemicals as environmental changes, confirming that slime molds adapt to environmental changes by shortening their periodic cycles. Subsequently, based on this dynamic response, we propose a new dynamic model (oscillated Physarum solver, O-PS) that extends the existing Physarum solver (PS). Numerical simulations demonstrated that the O-PS possesses rapid and efficient path-remodeling capabilities. In particular, within a simplified maze network, the O-PS was confirmed to have the same shortest-path searching ability as the PS, while being capable of faster remodeling. This study offers a new approach for optimizing and dynamically remodeling social infrastructure networks by mimicking biological mechanisms, enabling the rapid identification of solutions considering multiple objectives under complex constraints. Furthermore, the variation in convergence speed with oscillation frequency in the O-PS suggests flexibility in responding to environmental changes. Further research is required to develop more effective remodeling strategies.

• この論文にアクセスする

  DOI
• 関連情報を調べる
  PubMed

Estimating individual exposure to predation risk in group-living baboons, Papio anubis.

Suire A, Kunita I, Harel R, Crofoot M, Mutinda M, Kamau M, Hassel JM, Murray S, Kawamura S, Matsumoto-Oda A

PloS one ( Public Library of Science (PLoS) )  18 ( 11 ) e0287357 - e0287357   2023年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

　概要を見る

In environments with multiple predators, vulnerabilities associated with the spatial positions of group-living prey are non-uniform and depend on the hunting styles of the predators. Theoretically, coursing predators follow their prey over long distances and attack open areas, exposing individuals at the edge of the group to predation risk more than those at the center (marginal predation). In contrast, ambush predators lurk unnoticed by their prey and appear randomly anywhere in the group; therefore, isolated individuals in the group would be more vulnerable to predators. These positions of vulnerability to predation are expected to be taken by larger-bodied males. Moreover, dominant males presumably occupy the center of the safe group. However, identifying individuals at higher predation risk requires both simultaneous recording of predator location and direct observation of predation events; empirical observations leave ambiguity as to who is at risk. Instead, several theoretical methods (predation risk proxies) have been proposed to assess predation risk: (1) the size of the individual ‘unlimited domain of danger’ based on Voronoi tessellation, (2) the size of the ‘limited domain of danger’ based on predator detection distance, (3) peripheral/center position in the group (minimum convex polygon), (4) the number and direction of others in the vicinity (surroundedness), and (5) dyadic distances. We explored the age-sex distribution of individuals in at-risk positions within a wild baboon group facing predation risk from leopards, lions, and hyenas, using Global Positioning System collars. Our analysis of the location data from 26 baboons revealed that adult males were consistently isolated at the edge of the group in all predation risk proxies. Empirical evidence from previous studies indicates that adult male baboons are the most frequently preyed upon, and our results highlights the importance of spatial positioning in this.

• この論文にアクセスする

  DOI
• 関連情報を調べる
  PubMed

A Three-Dimensional Scanning System for Digital Archiving and Quantitative Evaluation of Arabidopsis Plant Architectures.

Kunita I, Morita MT, Toda M, Higaki T

Plant & cell physiology     2021年05月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

• この論文にアクセスする

  DOI
• 関連情報を調べる
  PubMed

シロイヌナズナ草姿の立体再構成

國田 樹, 金城 愛梨, 戸田 真志, 檜垣 匠

ＰＬＡＮＴ　ＭＯＲＰＨＯＬＯＧＹ ( 日本植物形態学会 )  33 ( 1 ) 67 - 69   2021年

掲載種別: 研究論文（学術雑誌）

　概要を見る

<p>植物のかたちとその変化を正確に把握するためには，非破壊的な立体再構成技術が不可欠である．我々はモデル植物の代表であるシロイヌナズナを主な解析対象とし，植物科学を専門とする研究室でも容易に取得することのできる省スペースかつ安価な植物の立体再構成システムを開発した．本システムは，ローテーターの上で低速回転するシロイヌナズナを固定カメラにより複数方向から撮影し，視体積交差法に基づいて草姿を立体再構築する．大きさと形状が既知の立体模型を用いて立体再構成精度を検証したところ，およそ1°間隔で360枚程度撮影すれば，サブミリオーダーかつ形状再現度の高い立体再構成像が得られることがわかった．本システムはシロイヌナズナの表現型解析の推進に寄与することが期待される．</p>

• この論文にアクセスする

  DOI
• 関連情報を調べる
  CiNii Research J-GLOBAL

Millimeter-sized belt-like pattern formation of actin filaments in solution by interacting with surface myosin in vitro

Kentaro Ozawa, Hirotaka Taomori, Masayuki Hoshida, Itsuki Kunita, Shigeru Sakurazawa, Hajime Honda

Biophysics and Physicobiology ( Biophysics and Physicobiology )  16   1 - 8   2019年01月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

• この論文にアクセスする

  DOI

Behavioural differentiation induced by environmental variation when crossing a toxic zone in an amoeba

Kunita I.

Journal of Physics D: Applied Physics ( Journal of Physics D: Applied Physics )  50 ( 35 )   2017年08月

掲載種別: 研究論文（学術雑誌）

• この論文にアクセスする

  DOI

Integrating perfusable vascular networks with a three-dimensional tissue in a microfluidic device.

Nashimoto Y, Hayashi T, Kunita I, Nakamasu A, Torisawa YS, Nakayama M, Takigawa-Imamura H, Kotera H, Nishiyama K, Miura T, Yokokawa R

Integrative biology : quantitative biosciences from nano to macro   9 ( 6 ) 506 - 518   2017年06月

掲載種別: 研究論文（学術雑誌）

• この論文にアクセスする

  DOI
• 関連情報を調べる
  PubMed

ENGINEERING A THREE-DIMENSIONAL TISSUE MODEL WITH A PERFUSABLE VASCULATURE IN A MICROFLUIDIC DEVICE

6． Yuji Nashimoto, Itsuki Kunita, Akiko Nakamasu, Yu-suke Torisawa, Masamune Nakayama, Hisako Takigawa-Imamura, Hidetoshi Kotera, Koichi Nishiyama, Takashi Miura, Ryuji Yokokawa

30TH IEEE INTERNATIONAL CONFERENCE ON MICRO ELECTRO MECHANICAL SYSTEMS (MEMS 2017) ( IEEE )    592 - 595   2017年01月 [ 査読有り ]

掲載種別: 研究論文（国際会議プロシーディングス）

• この論文にアクセスする

  DOI

Direct observation of orientation distributions of actin filaments in a solution undergoing shear banding

Sato K.

Soft Matter ( Soft Matter )  13 ( 14 ) 2708 - 2716   2017年01月

掲載種別: 研究論文（学術雑誌）

• この論文にアクセスする

  DOI

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 ( IOP PUBLISHING LTD )  50 ( 2 )   2017年01月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

　概要を見る

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.

• この論文にアクセスする

  DOI

A ciliate memorizes the geometry of a swimming arena.

Kunita I, Yamaguchi T, Tero A, Akiyama M, Kuroda S, Nakagaki T

Journal of the Royal Society, Interface   13 ( 118 )   2016年05月

掲載種別: 研究論文（学術雑誌）

• この論文にアクセスする

  DOI
• 関連情報を調べる
  PubMed

血管新生現象を利用した組織-マイクロ流路間の接続と灌流培養への取り組み

梨本裕司, 國田樹, 中益朗子, 鳥澤勇介, 中山雅宗, 今村(滝川)寿子, 小寺秀俊, 西山功一, 三浦岳, 横川隆司

化学とマイクロ・ナノシステム ( その他の出版社 )  15   19 - 22   2016年03月

掲載種別: 研究論文（その他学術会議資料等）

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 ( その他の出版社 )  5   270(1-8)   2014年06月

掲載種別: 研究論文（その他学術会議資料等）

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 ( その他の出版社 )  11   20140205   2014年04月

掲載種別: 研究論文（その他学術会議資料等）

Ethological Response to Periodic Stimulation in Chara and Blepharisma

Itsuki Kunita, Sho Sato, Tetsu Saigusa, Toshiyuki Nakagaki

Natural Computing and Beyond ( その他の出版社 )  6   1 - 13   2013年04月

掲載種別: 研究論文（その他学術会議資料等）

Adaptive Path Finding and Transport Network Formation by the Amoeba-Like Organism Physarum

Itsuki Kunita, Kazunori Yoshihara, Atsushi Tero, Kentaro Ito, Shiu Fan Lee, Mark D. Fricker, Toshiyuki Nakagaki

Natural Computing and Beyond ( その他の出版社 )  6   14 - 29   2013年04月

掲載種別: 研究論文（その他学術会議資料等）

Shear banding in an F-actin solution

Itsuki Kunita, Katsuhiko Sato, Yoshimi Tanaka, Yoshinori Takikawa, Hiroshi Orihara, Toshiyuki Nakagaki

Physical Review Letters ( その他の出版社 )  109 ( 24 ) 248303(1-4)   2012年12月

掲載種別: 研究論文（その他学術会議資料等）

Visualization of Local Winding Propagations on an Actin Filament in an in vitro Motility Assay System

Shigeru Sakurazawa, Hana Sakata, Itsuki Kunita

Journal of Computer Chemistry, Japan ( その他の出版社 )  11 ( 1 ) 43 - 48   2012年05月

掲載種別: 研究論文（その他学術会議資料等）

Up-and-down movement of a sliding actin filament in the in vitro motility assay

Itsuki Kunita, Shigeru Sakurazawa, Hajime Honda

BioSystems ( その他の出版社 )  103 ( 1 ) 79 - 84   2011年01月

掲載種別: 研究論文（その他学術会議資料等）

Winding Propagation on Actin Filament in an in vitro Motility Assay System

Itsuki Kunita

Journal of Computer Chemistry, Japan ( その他の出版社 )  9 ( 3 ) 127 - 134   2010年08月

掲載種別: 研究論文（その他学術会議資料等）