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Koichi Fujimoto

Koichi Fujimoto contributes to research discovery and scholarly infrastructure.

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Biological Physics Cell Behavior cond-mat.soft nlin.AO nlin.CD Populations and Evolution Tissues and Organs

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preprint2026arXiv

3D mechano-geometric multicellular model of apical stem cell-driven plant morphogenesis

The orientation of cell division is a major determinant of three-dimensional plant morphogenesis. Whether and how a simple division orientation rule explains the establishment of symmetric body plans is a fundamental question. Testing such hypotheses is facilitated by a modeling framework that combines realistic three-dimensional cell mechanics, irreversible cell-wall growth, and a deformable tissue geometry. We recently introduced such a framework, a 3D mechano-geometric multicellular model of apical stem cell-driven morphogenesis. Here we document how the model is built from physiological and computational perspectives. We describe the triangulated thin-shell representation of cells, the treatment of turgor pressure, cell-wall elasticity and strain-driven wall growth, the cell-division algorithm together with its two pluggable division-rule implementations, and the remeshing operations that keep the triangulation well-conditioned as cells grow, divide, and deform. The aim of this paper is to make the present model accessible and customizable to experimental plant biologists.

preprint2026arXiv

Delayed control driven oscillations in plant roots

Arabidopsis roots show oscillatory growth patterns on homogeneous agar surfaces, whereas other plants, such as maize, do not. Although several explanations have been proposed, a simple and general model that makes testable predictions across species has been lacking. Roots sense gravity and correct their growth direction towards the vertical. Motivated by recent evidence for a time delay in this gravitropic correction, we develop a minimal nonlinear model based on the delay hypothesis that predicts whether a root oscillates or grows vertically downwards. The model identifies a fourfold relation between the delay and time period, robust across different response functions. Analysing images of Arabidopsis, we find that the mode of the oscillatory arc length is not significantly different between inclined and vertical growth conditions. The quantitative agreement between the experimentally measured oscillatory arc length and the arc length estimated from estimated root growth speed and response delay supports this fourfold delay-period rule for delay-driven root oscillations. The simplicity of our model allows for a direct comparison with data from diverse plant species.

preprint2026arXiv

Skewed weak and Pareto-tailed strong interactions accompany community diversity and complexity

Ecological communities are often characterized by many weak and few strong interspecific interactions, yet their quantitative structure, generative basis, and links to community-level properties remain poorly understood. Using two empirical datasets of plant--animal networks, we show that both trophic and mutualistic interaction strengths distribute skewed weak and Pareto-strong tails (SWAPS), as quantified by positive skewness and extreme value theory, respectively. We further find that interaction strengths are taxon-specific and largely constrained within taxa. In community assembly simulations based on a generalized Lotka--Volterra model, this taxonomic conservatism, together with multiple interaction types beyond trophic and mutualistic ones, is required for the emergence of SWAPS distribution. Notably, SWAPS distribution emerges not only at the species level but also across lineages, and its emergence accompanies increases in community diversity and complexity. Together, these results identify SWAPS distribution as a previously unrecognized interaction signature of ecological communities and provide a new perspective on the organization of community-level properties.

preprint2021arXiv

Collective Cell Movement in Cell-Scale Tension Gradient on Tissue Interface

In this paper, we examine the emergence of cell flow induced by a tension gradient on a tissue interface as in the case of the Marangoni flow on liquid interface. We consider the molecule density polarity of the heterophilic adhesion between tissues as the origin of the tension gradient. By applying the cellular Potts model, we demonstrate that polarization in concentration (i.e., intracellular localization) of heterophilic adhesion molecules can induce a cell flow similar to the Marangoni flow. In contrast to the ordinary Marangoni flow, this flow is oriented in the opposite direction to that of the tension gradient. The optimal range of adhesion strength is also identified for the existence of this flow.

preprint2020arXiv

A Mechanical Instability in Planar Epithelial Monolayers Leads to Cell Extrusion

In cell extrusion, a cell embedded in an epithelial monolayer loses its apical or basal surface and is subsequently squeezed out of the monolayer by neighboring cells. Cell extrusions occur during apoptosis, epithelial-mesenchymal transition, or pre-cancerous cell invasion. They play important roles in embryogenesis, homeostasis, carcinogenesis, and many other biological processes. Although many of the molecular factors involved in cell extrusion are known, little is known about the mechanical basis of cell extrusion. We used a three-dimensional (3D) vertex model to investigate the mechanical stability of cells arranged in a monolayer with 3D foam geometry. We found that when the cells composing the monolayer have homogeneous mechanical properties, cells are extruded from the monolayer when the symmetry of the 3D geometry is broken due to an increase in cell density or a decrease in the number of topological neighbors around single cells. Those results suggest that mechanical instability inherent in the 3D foam geometry of epithelial monolayers is sufficient to drive epithelial cell extrusion. In the situation where cells in the monolayer actively generate contractile or adhesive forces under the control of intrinsic genetic programs, the forces act to break the symmetry of the monolayer, leading to cell extrusion that is directed to the apical or basal side of the monolayer by the balance of contractile and adhesive forces on the apical and basal sides. Although our analyses are based on a simple mechanical model, our results are in accordance with observations of epithelial monolayers {\it in vivo} and consistently explain cell extrusions under a wide range of physiological and pathophysiological conditions. Our results illustrate the importance of a mechanical understanding of cell extrusion and provide a basis by which to link molecular regulation to physical processes.

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