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Affiliation |
Faculty of Science Department of Mathematics |
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Title |
Associate Professor |
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Contact information |
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External Link |
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Kobayashi Yasuaki
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Research Areas 【 display / non-display 】
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Natural Science / Applied mathematics and statistics
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Natural Science / Biophysics, chemical physics and soft matter physics
From School 【 display / non-display 】
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The University of Tokyo Faculty of Science Graduated
- 2002.03
From Graduate School 【 display / non-display 】
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The University of Tokyo Graduate School of Science Department of Physics Doctor's Course Completed
2002.04 - 2007.03
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The University of Tokyo Faculty of Science Department of Physics Doctor's Course Completed
1998.04 - 2002.03
Employment Record in Research 【 display / non-display 】
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Josai University Faculty of Science Department of Mathematics Associate Professor
2024.04
External Career 【 display / non-display 】
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Hokkaido University Associate Professor
2019.03 - 2024.03
Papers 【 display / non-display 】
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On the reaction–diffusion type modelling of the self-propelled object motion Reviewed
Masaharu Nagayama, Harunori Monobe, Koya Sakakibara, Ken-Ichi Nakamura, Yasuaki Kobayashi, Hiroyuki Kitahata
Scientific Reports 13 ( 1 ) 2023.08
Publishing type：Research paper (scientific journal) Publisher：Springer Science and Business Media LLC
Abstract
In this study, we propose a mathematical model of self-propelled objects based on the Allen–Cahn type phase-field equation. We combine it with the equation for the concentration of surfactant used in previous studies to construct a model that can handle self-propelled object motion with shape change. A distinctive feature of our mathematical model is that it can represent both deformable self-propelled objects, such as droplets, and solid objects, such as camphor disks, by controlling a single parameter. Furthermore, we demonstrate that, by taking the singular limit, this phase-field based model can be reduced to a free boundary model, which is equivalent to the $$L^2$$-gradient flow model of self-propelled objects derived by the variational principle from the interfacial energy, which gives a physical interpretation to the phase-field model.DOI： 10.1038/s41598-023-39395-w
Other Link： https://www.nature.com/articles/s41598-023-39395-w
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Keisuke Imafuku, Hiroaki Iwata, Ken Natsuga, Makoto Okumura, Yasuaki Kobayashi, Hiroyuki Kitahata, Akiharu Kubo, Masaharu Nagayama, Hideyuki Ujiie
Cell Proliferation 2023.03
Publishing type：Research paper (scientific journal) Publisher：Wiley
DOI： 10.1111/cpr.13441
Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1111/cpr.13441
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A computational model of the epidermis with the deformable dermis and its application to skin diseases Reviewed
Kota Ohno, Yasuaki Kobayashi, Masaaki Uesaka, Takeshi Gotoda, Mitsuhiro Denda, Hideyuki Kosumi, Mika Watanabe, Ken Natsuga, Masaharu Nagayama
Scientific Reports 11 13234 2021.06
Authorship：Lead author Publishing type：Research paper (scientific journal)
The skin barrier is provided by the organized multi-layer structure of epidermal cells, which is dynamically maintained by a continuous supply of cells from the basal layer. The epidermal homeostasis can be disrupted by various skin diseases, which often cause morphological changes not only in the epidermis but in the dermis. We present a three-dimensional agent-based computational model of the epidermis that takes into account the deformability of the dermis. Our model can produce a stable epidermal structure with well-organized layers. We show that its stability depends on the cell supply rate from the basal layer. Modeling the morphological change of the dermis also enables us to investigate how the stiffness of the dermis affects the structure and barrier functions of the epidermis. Besides, we show that our model can simulate the formation of a corn (clavus) by assuming hyperproliferation and rapid differentiation. We also provide experimental data for human corn, which supports the model assumptions and the simulation result.
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Temporal coherency of mechanical stimuli modulates tactile form perception Reviewed
Masashi Nakatani, Yasuaki Kobayashi, Kota Ohno, Masaaki Uesaka, Sayako Mogami, Zixia Zhao, Takamichi Sushida, Hiroyuki Kitahata, Masaharu Nagayama
Scientific Reports 11 11737 2021.06
Authorship：Lead author Publishing type：Research paper (scientific journal)
The human hand can detect both form and texture information of a contact surface. The detection of skin displacement (sustained stimulus) and changes in skin displacement (transient stimulus) are thought to be mediated in different tactile channels; however, tactile form perception may use both types of information. Here, we studied whether both the temporal frequency and the temporal coherency information of tactile stimuli encoded in sensory neurons could be used to recognize the form of contact surfaces. We used the fishbone tactile illusion (FTI), a known tactile phenomenon, as a probe for tactile form perception in humans. This illusion typically occurs with a surface geometry that has a smooth bar and coarse textures in its adjacent areas. When stroking the central bar back and forth with a fingertip, a human observer perceives a hollow surface geometry even though the bar is physically flat. We used a passive high-density pin matrix to extract only the vertical information of the contact surface, suppressing tangential displacement from surface rubbing. Participants in the psychological experiment reported indented surface geometry by tracing over the FTI textures with pin matrices of the different spatial densities (1.0 and 2.0 mm pin intervals). Human participants reported that the relative magnitude of perceived surface indentation steeply decreased when pins in the adjacent areas vibrated in synchrony. To address possible mechanisms for tactile form perception in the FTI, we developed a computational model of sensory neurons to estimate temporal patterns of action potentials from tactile receptive fields. Our computational data suggest that (1) the temporal asynchrony of sensory neuron responses is correlated with the relative magnitude of perceived surface indentation and (2) the spatiotemporal change of displacements in tactile stimuli are correlated with the asynchrony of simulated sensory neuron responses for the fishbone surface patterns. Based on these results, we propose that both the frequency and the asynchrony of temporal activity in sensory neurons could produce tactile form perception.
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A reaction–diffusion particle model for clustering of self-propelled oil droplets on a surfactant solution Reviewed
Minsoo Kim, Mamoru Okamoto, Yusuke Yasugahira, Shinpei Tanaka, Satoshi Nakata, Yasuaki Kobayashi, Masaharu Nagayama
Physica D: Nonlinear Phenomena 425 132949 2021.06
Publishing type：Research paper (scientific journal)
We experimentally and numerically investigate collective behaviors of oil droplets floating on a surfactant solution in a narrow circular channel. A closed environment where a glass cover is placed on the channel shown that ethyl salicylate droplets on the surface of sodium dodecyl sulfate solution exhibit transient oscillatory dynamics, leading to the formation of a single cluster via the merging of sub-clusters. When the glass cover is removed, oscillatory behavior resumes, and the cluster breaks up. To understand these experimental findings, we introduce a mathematical model that combines equations of motion for droplets with a reaction–diffusion system, where droplet dynamics and the chemical reactions are considered on the one-dimensional surface, and the diffusion of chemicals in the air phase and the water phase is treated in the two-dimensional region. Our model successfully reproduces transient oscillations and the characteristics of cluster formation, and the effect of the glass cover. We argue that the attractive long-range interaction due to the global concentration profile of the solution suffices for the cluster formation.
Misc 【 display / non-display 】
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塑性変形可能な基底膜モデルを用いた毛包形成メカニズムの数理的考察—A mathematical study of the mechanism of hair follicle formation using a plastic deformable basement membrane model
奥村 真善美, 小林 康明, 長山 雅晴, 藤原 裕展, 安ヶ平 祐介, 大野 航太
計算工学講演会論文集 = Proceedings of the Conference on Computational Engineering and Science / 日本計算工学会 編 27 456 - 459 2022.06
Language：Japanese Publisher：日本計算工学会
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計算工学講演会論文集 Proceedings of the Conference on Computational Engineering and Science 24 5p 2019.05
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The epidermal barrier homeostasis in the mathematical model
計算工学講演会論文集 Proceedings of the Conference on Computational Engineering and Science 24 5p 2019.05
Presentations 【 display / non-display 】
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Dynamics and distribution of epidermal stem cells on a membrane Invited International conference
Yasuaki Kobayashi, Masaharu Nagayama
A3-NIMS Joint Workshop on Mathematical Biology, the National Institute of Mathematical Sciences, Daejeon, South Korea 2017.03
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Modeling of phase-shifted oscillatory signals driven by Hes7 oscillations
Yasuaki Kobayashi, Hiroshi Kori
5th Annual Winter q-bio Meeting in Kauai, Grand Hyatt Kauai, Hawaii, U.S.A. 2017.02
Event date： 2017.02
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Synchronization failure caused by interplay between noise and network heterogeneity
Yasuaki Kobayashi, Hiroshi Kori
International Conference Patterns and Waves 2016, Hokkaido University Confer- ence Hall, Sapporo, Japan 2016.08
Event date： 2016.08
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Synchronization failure caused by interplay between noise and network hetero- geneity
Yasuaki Kobayashi, Hiroshi Kori
NetSci2016: International School and Conference on Network Science, K-Hotel, Seoul, South Korea 2016.05
Event date： 2016.05
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Reentrant transition in coupled noisy oscillators
Yasuaki Kobayashi, Hiroshi Kori
International Workshop: New Frontiers in Nonlinear Sciences, Hotel KAN- RONOMORI, Niseko, Japan 2016.03
Event date： 2016.03
Scientific Research Funds Acquisition Results 【 display / non-display 】
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時空間パターンを形成する細胞シートの連続体モデル構築と解析
Grant number：22K03428 2022.04 - 2025.03
日本学術振興会 科学研究費助成事業 基盤研究(C)
小林 康明
Grant amount：\4030000 （ Direct Cost: \3100000 、 Indirect Cost：\930000 ）
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やわらかい組織の上で増殖する細胞系の連続体モデル構築と解析
Grant number：19K03629 2019.04 - 2023.03
日本学術振興会 科学研究費助成事業 基盤研究(C)
小林 康明
Grant amount：\4030000 （ Direct Cost: \3100000 、 Indirect Cost：\930000 ）
これまでのモデルに修正を加え，基底層と基底膜の接着の相互作用を，幹細胞の位置でデルタ関数的に大きくなるものから，幹細胞の位置にピークをもち連続的に減衰する関数に変更したモデルを考案し，数理モデルを導出した．このモデルの数値計算を行い，以前と同様に幹細胞の位置で上向きの突起が形成されることを示した.このモデルにおいて，接着強度が空間的に一様であっても一様状態が不安定化し，周期的な空間構造が発生することを明らかにした．線形安定性解析を行い，一様解が不安定化する波長と基底膜の物性，基底膜と基底層の接着強度の間の関係を求めた．幹細胞数と膜の弾性に対する相図を作成し，形成される突起の数と形状の分類を行った．
続いて基底層の細胞同士の接着を考慮した数理モデルの構築を行った．細胞密度と圧力の２変数の連続体モデルの解析を行い，細胞密度の変化によって空間一様な状態が不安定化し，周期構造が現れることを示した．細胞の収縮力と細胞密度の相図を示し，空間パターンを生じる細胞密度に上限と下限が存在することを示した．初期細胞密度が周期的に分布している場合，低波数では最終パターンの細胞集団数は波数に一致するが，高波数では一致せず一山の集団が生じることを示した．
また基底膜と接着を保ちつつ細胞分裂を繰り返す系の大変形を記述する数理モデルの構築を行った．これまでの数理モデルを，基底膜が塑性変形を伴う場合に拡張し，細胞分裂の力によって膜の大変形を引き起こすような現象をよく記述する結果を得ることに成功した．大変形を扱うことが可能になることで，乾癬のような真皮の形態変化を伴う病態をシミュレーションすることも可能になり，様々な応用が期待できる．