Papers - Kobayashi Yasuaki
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Emergent Complexity in a Light-Driven Self-Oscillatory Crystal: A Molecular Perspective on Autonomous Behavior and Stimulus-Modulated Motion Reviewed
Yoshiyuki, Kageyama, Yasuaki Kobayashi, Makiko Matsuura, Toshiaki Shimizu, Tomonori Ikegami, Norio Tanada,Daisuke Yazaki
Crystal Growth & Design 25 7543 - 7556 2025.09
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Patterning in stratified epithelia depends on cell-cell adhesion Reviewed
Yosuke Mai, Yasuaki Kobayashi, Hiroyuki Kitahata, Takashi Seo, Takuma Nohara, Sota Itamoto, Shoko Mai, Junichi Kumamoto, Masaharu Nagayama, Wataru Nishie, Hideyuki Ujiie, Ken Natsuga
Life Science Alliance 7 ( 9 ) 1 - 14 2024.07
Language：English Publishing type：Research paper (scientific journal)
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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.
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Hair follicle stem cell progeny heal blisters while pausing skin development Reviewed
Yu Fujimura, Mika Watanabe, Kota Ohno, Yasuaki Kobayashi, Shota Takashima, Hideki Nakamura, Hideyuki Kosumi, Yunan Wang, Yosuke Mai, Andrea Lauria, Valentina Proserpio, Hideyuki Ujiie, Hiroaki Iwata, Wataru Nishie, Masaharu Nagayama, Salvatore Oliviero, Giacomo Donati, Hiroshi Shimizu, Ken Natsuga
EMBO Reports 2021
Publishing type：Research paper (scientific journal)
Injury in adult tissue generally reactivates developmental programs to foster regeneration, but it is not known whether this paradigm applies to growing tissue. Here, by employing blisters, we show that epidermal wounds heal at the expense of skin development. The regenerated epidermis suppresses the expression of tissue morphogenesis genes accompanied by delayed hair follicle (HF) growth. Lineage tracing experiments, cell proliferation dynamics, and mathematical modeling reveal that the progeny of HF junctional zone stem cells, which undergo a morphological transformation, repair the blisters while not promoting HF development. In contrast, the contribution of interfollicular stem cell progeny to blister healing is small. These findings demonstrate that HF development can be sacrificed for the sake of epidermal wound regeneration. Our study elucidates the key cellular mechanism of wound healing in skin blistering diseases.
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Substrate membrane bearing close-packed array of micron-level pillars incrassates air-exposed three-dimensional epidermal equivalent model Reviewed
Junichi Kumamoto, Koji Fujimoto, Yasuaki Kobayashi, Kota Ohno, Masaharu Nagayama, Mitsuhiro Denda
Skin Research and Technology 2021
Publishing type：Research paper (scientific journal)
Background: We showed previously that a thick three-dimensional epidermal equivalent can be constructed with passaged keratinocytes on a patterned surface. Material and Methods: We first carried out computer simulations of a three-dimensional epidermal equivalent model built on close-packed arrays of 10 µm, 15 µm, 20 µm, 30 µm, and 60 µm diameter pillars. Based on these predictions, we evaluated epidermal equivalents built on a series of porous plastic membranes bearing arrays of pillars 15 µm, 20 µm, 25 µm, 30 µm, and 50 µm in diameter. Results: The simulations predicted that a model having near-physiological thickness would be formed on 15 ~ 30 µm pillars. In the results of in vitro study, the thickest epidermal equivalent was obtained on the 20 µm pillars. Epidermal differentiation markers, filaggrin and loricrin, were expressed at the upper layer of the epidermal equivalent model, and tight-junction proteins, claudin-1 and ZO-1, were expressed on the cell membranes. BrdU-positive cells were observed at the base and also at the top of the pillars. Conclusion: The results of the study suggested that mathematical modeling might be a useful tool to guide biological studies.
DOI： 10.1111/srt.13035
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Mathematical-model-guided development of full-thickness epidermal equivalent. Reviewed
Kumamoto J, Nakanishi S, Makita M, Uesaka M, Yasugahira Y, Kobayashi Y, Nagayama M, Denda S, Denda M
Scientific reports 8 ( 1 ) 17999 2018.12
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Interplay between epidermal stem cell dynamics and dermal deformation Reviewed
Kobayashi Y, Yasugahira Y, Kitahata H, Watanabe M, Natsuga K, Nagayama M
npj Computational Materials 4 45 2018.08
Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE PUBLISHING GROUP
Tissue growth is a driving force of morphological changes in living systems. Whereas the buckling instability is known to play a crutial role for initiating spatial pattern formations in such growing systems, little is known about the rationale for succeeding morphological changes beyond this instability. In mammalian skin, the dermis has many protrusions toward the epidermis, and the epidermal stem cells are typically found on the tips of these protrusions. Although the initial instability may well be explained by the buckling involving the dermis and the basal layer, which contains proliferative cells, it does not dictate the direction of these protrusions, nor the spatial patterning of epidermal stem cells. Here we introduce a particle-based model of self-replicating cells on a deformable substrate composed of the dermis and the basement membrane, and investigate the relationship between dermal deformation and epidermal stem cell pattering on it. We show that our model reproduces the formation of dermal protrusions directing from the dermis to the epidermis, and preferential epidermal stem cell distributions on the tips of the dermal protrusions, which the basic buckling mechanism fails to explain. We argue that cell-type-dependent adhesion strengths of the cells to the basement membrane are crucial factors influencing these patterns.
DOI： 10.1038/s41524-018-0101-z
Other Link： http://orcid.org/0000-0003-4966-963X
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Sustained dynamics of a weakly excitable system with nonlocal interactions Reviewed
Yasuaki Kobayashi, Hiroyuki Kitahata, Masaharu Nagayama
PHYSICAL REVIEW E 96 ( 2 ) 022213 2017.08
Language：English Publishing type：Research paper (scientific journal) Publisher：AMER PHYSICAL SOC
We investigate a two-dimensional spatially extended system that has a weak sense of excitability, where an excitation wave has a uniform profile and propagates only within a finite range. Using a cellular automaton model of such a weakly excitable system, we show that three kinds of sustained dynamics emerge when nonlocal spatial interactions are provided, where a chain of local wave propagation and nonlocal activation forms an elementary oscillatory cycle. Transition between different oscillation regimes can be understood as different ways of interactions among these cycles. Analytical expressions are given for the oscillation probability near the onset of oscillations.
DOI： 10.1103/PhysRevE.96.022213
Other Link： http://orcid.org/0000-0003-4966-963X
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Type XVII collagen coordinates proliferation in the interfollicular epidermis Reviewed
Mika Watanabe, Ken Natsuga, Wataru Nishie, Yasuaki Kobayashi, Giacomo Donati, Shotaro Suzuki, Yu Fujimura, Tadasuke Tsukiyama, Hideyuki Ujiie, Satoru Shinkuma, Hideki Nakamura, Masamoto Murakami, Michitaka Ozaki, Masaharu Nagayama, Fiona M. Watt, Hiroshi Shimizu
ELIFE 6 e26635 2017.07
Language：English Publishing type：Research paper (scientific journal) Publisher：ELIFE SCIENCES PUBLICATIONS LTD
Type XVII collagen (COL17) is a transmembrane protein located at the epidermal basement membrane zone. COL17 deficiency results in premature hair aging phenotypes and in junctional epidermolysis bullosa. Here, we show that COL17 plays a central role in regulating interfollicular epidermis (IFE) proliferation. Loss of COL17 leads to transient IFE hypertrophy in neonatal mice owing to aberrant Wnt signaling. The replenishment of COL17 in the neonatal epidermis of COL17-null mice reverses the proliferative IFE phenotype and the altered Wnt signaling. Physical aging abolishes membranous COL17 in IFE basal cells because of inactive atypical protein kinase C signaling and also induces epidermal hyperproliferation. The overexpression of human COL17 in aged mouse epidermis suppresses IFE hypertrophy. These findings demonstrate that COL17 governs IFE proliferation of neonatal and aged skin in distinct ways. Our study indicates that COL17 could be an important target of anti-aging strategies in the skin.
DOI： 10.7554/eLife.26635
Other Link： http://orcid.org/0000-0003-4966-963X
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Synchronization failure caused by interplay between noise and network heterogeneity Reviewed
Y. Kobayashi, H. Kori
CHAOS 26 ( 9 ) 094805 2016.09
Language：English Publishing type：Research paper (scientific journal) Publisher：AMER INST PHYSICS
We investigate synchronization in complex networks of noisy phase oscillators. We find that, while too weak a coupling is not sufficient for the whole system to synchronize, too strong a coupling induces a nontrivial type of phase slip among oscillators, resulting in synchronization failure. Thus, an intermediate coupling range for synchronization exists, which becomes narrower when the network is more heterogeneous. Analyses of two noisy oscillators reveal that nontrivial phase slip is a generic phenomenon when noise is present and coupling is strong. Therefore, the low synchronizability of heterogeneous networks can be understood as a result of the difference in effective coupling strength among oscillators with different degrees; oscillators with high degrees tend to undergo phase slip while those with low degrees have weak coupling strengths that are insufficient for synchronization. Published by AIP Publishing.
DOI： 10.1063/1.4954216
Other Link： http://orcid.org/0000-0003-4966-963X
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Mathematical model for calcium-assisted epidermal homeostasis Reviewed
Yasuaki Kobayashi, Yusuke Sawabu, Hiroyuki Kitahata, Mitsuhiro Denda, Masaharu Nagayama
JOURNAL OF THEORETICAL BIOLOGY 397 52 - 60 2016.05
Language：English Publishing type：Research paper (scientific journal) Publisher：ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
Using a mathematical model of the epidermis, we propose a mechanism of epidermal homeostasis mediated by calcium dynamics. We show that calcium dynamics beneath the stratum corneum can reduce spatio-temporal fluctuations of the layered structure of the epidermis. We also demonstrate that our model can reproduce experimental results that the recovery from a barrier disruption is faster when the disrupted site is exposed to air. In particular, simulation results indicate that the recovery speed depends on the size of barrier disruption. (C) 2016 The Authors. Published by Elsevier Ltd.
DOI： 10.1016/j.jtbi.2016.02.032
Other Link： http://orcid.org/0000-0003-4966-963X
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Mathematical Model of Epidermal Structure Reviewed
Yasuaki Kobayashi, Masaharu Nagayama
APPLICATIONS + PRACTICAL CONCEPTUALIZATION + MATHEMATICS = FRUITFUL INNOVATION 11 121 - 126 2016
Language：English Publishing type：Research paper (international conference proceedings) Publisher：SPRINGER-VERLAG TOKYO
Using a mathematical model of the epidermis, we investigate how the structure of the dermis affects the spatio-temporal pattern of the upper structure, especially the stratum corneum (SC). We find that, while large scale undulations greatly affects the upper structure, small scale undulations do not propagate into the upper structure, which is consistent with experimentally observed cross sections of the epidermis.
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Model for calcium-mediated reduction of structural fluctuations in epidermis Reviewed
Yasuaki Kobayashi, Hiroyuki Kitahata, Masaharu Nagayama
PHYSICAL REVIEW E 92 ( 2 ) 022709 2015.08
Language：English Publishing type：Research paper (scientific journal) Publisher：AMER PHYSICAL SOC
We propose a reaction-advection-diffusion model of epidermis consisting of two variables, the degree of differentiation and the calcium ion concentration, where calcium ions enhance differentiation. By analytically and numerically investigating this system, we show that a calcium localization layer formed beneath the stratum corneum helps reduce spatiotemporal fluctuations of the structure of the stratum corneum. In particular, spatially or temporally small-scale fluctuations in the lower structure are suppressed and do not affect the upper structure, due to acceleration of differentiation by calcium ions. Analytical expressions for the reduction rate of fluctuation amplitudes are shown.
DOI： 10.1103/PhysRevE.92.022709
Other Link： http://orcid.org/0000-0003-4966-963X
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Mathematical Model for Epidermal Homeostasis Reviewed
Yasuaki Kobayashi, Yusuke Sawabu, Satoshi Ota, Masaharu Nagayama
Mathematical Progress in Expressive Image Synthesis II 18 119 - 123 2015.06
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Reentrant transition in coupled noisy oscillators Reviewed
Yasuaki Kobayashi, Hiroshi Kori
PHYSICAL REVIEW E 91 ( 1 ) 012901 2015.01
Language：English Publishing type：Research paper (scientific journal) Publisher：AMER PHYSICAL SOC
We report on a synchronization-breaking instability observed in a noisy oscillator unidirectionally coupled to a pacemaker. Using a phase oscillator model, we find that, as the coupling strength is increased, the noisy oscillator lags behind the pacemaker more frequently and the phase slip rate increases, which may not be observed in averaged phase models such as the Kuramoto model. Investigation of the corresponding Fokker-Planck equation enables us to obtain the reentrant transition line between the synchronized state and the phase slip state. We verify our theory using the Brusselator model, suggesting that this reentrant transition can be found in a wide range of limit cycle oscillators.
DOI： 10.1103/PhysRevE.91.012901
Other Link： http://orcid.org/0000-0003-4966-963X
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Mathematical Modeling of Calcium Waves Induced by Mechanical Stimulation in Keratinocytes Reviewed
Yasuaki Kobayashi, Yumi Sanno, Akihiko Sakai, Yusuke Sawabu, Moe Tsutsumi, Makiko Goto, Hiroyuki Kitahata, Satoshi Nakata, Junichi Kumamoto, Mitsuhiro Denda, Masaharu Nagayama
PLOS ONE 9 ( 3 ) e92650 2014.03
Language：English Publishing type：Research paper (scientific journal) Publisher：PUBLIC LIBRARY SCIENCE
Recent studies have shown that the behavior of calcium in the epidermis is closely related to the conditions of the skin, especially the differentiation of the epidermal keratinocytes and the permeability barrier function, and therefore a correct understanding of the calcium dynamics is important in explaining epidermal homeostasis. Here we report on experimental observations of in vitro calcium waves in keratinocytes induced by mechanical stimulation, and present a mathematical model that can describe the experimentally observed wave behavior that includes finite-range wave propagation and a ring-shaped pattern. A mechanism of the ring formation hypothesized by our model may be related to similar calcium propagation patterns observed during the wound healing process in the epidermis. We discuss a possible extension of our model that may serve as a tool for investigating the mechanisms of various skin diseases.
DOI： 10.1371/journal.pone.0092650
Other Link： http://orcid.org/0000-0003-4966-963X