arXiv subjects

Koichi Fujimoto

Publications and source records attributed to Koichi Fujimoto.

14 recordsLinked to original sources

arXiv2026

Antipolar Cell-cell Adhesion-causing Collective Motility Disorder

In this study, we aim to theoretically investigate antipolar cell-cell adhesion, in which adhesion sites are located on the opposite side of the leading edge of migrating cells, as a candidate for irregularly polarized adhesion that induces disorder in collective cell migration. We employ the cellular Potts model to simulate the effects of antipolar adhesion on collective migration driven by cell motility. Antipolar adhesion induces a collective motility disorder, which exhibits a disordered configuration in the motility direction, even when collective motion occurs in the absence of adhesion. Consequently, antipolar adhesion inhibits collective migration. The effect is in contrast to that of polar adhesion, which accelerates the directional intercellular order of cell motility. At a specific motility strength, a depinning transition emerges from a collective motility disorder to a collective motion. The collective motility disorder can be physically explained by the cooperative effect between antipolar adhesion and motility persistence within the mean-field approximation.

physics.bio-ph↗

arXiv2026

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.

q-bio.PE↗

arXiv2026

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.

q-bio.CB↗

arXiv2026

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.

physics.bio-ph↗

arXiv2024

Motion Ordering in Cellular Polar-polar and Polar-nonpolar Interactions

We examine the difference in motion ordering between cellular systems with and without information transfer to evaluate the effect of the polar--polar interaction through mutual guiding, which enables cells to inform other cells of their moving directions. We compare this interaction with the polar--nonpolar interaction through cell motion triggered by cellular contact, which cannot provide information on the moving directions. We model these interactions on the basis of the cellular Potts model. We calculate the order parameter of the polar direction in the interactions and examine the cell concentration and surface tension conditions of ordering. The results suggest that the polar--polar interaction through mutual guiding efficiently induces the motion ordering in comparison with the polar-nonpolar interaction for contact triggering, except in cases of weak driving. The results also show that the polar--polar interaction efficiently accelerates the collective motion compared with the polar--nonpolar interaction.

q-bio.CB↗

arXiv2021

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.

q-bio.CB↗

arXiv2020

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.

q-bio.CB↗

arXiv2019

Cell Motion Alignment as Polarity Memory Effect

The clarification of the motion alignment mechanism in collective cell migration is an important issue commonly in physics and biology. In analogy with the self-propelled disk, the polarity memory effect of eukaryotic cell is a fundamental candidate for this alignment mechanism. In the present paper, we theoretically examine the polarity memory effect for the motion alignment of cells on the basis of the cellular Potts model. We show that the polarity memory effect can align motion of cells. We also find that the polarity memory effect emerges for the persistent length of cell trajectories longer than average cell-cell distance.

q-bio.CB↗

arXiv2019

Curved surface geometry-induced topological change of an excitable planar wave

On the curved surfaces of living and nonliving materials, planar excitable waves frequently exhibit directional change and subsequently undergo a topological change; that is, a series of wave dynamics from fusion, annihilation to splitting. Theoretical studies have shown that excitable planar stable waves change their topology significantly depending on the initial conditions on flat surfaces, whereas the directional-change of the waves occurs based on the geometry of curved surfaces. However, it is not clear if the geometry of curved surfaces induces this topological change. In this study, we first show the curved surface geometry-induced topological changes in a planar stable wave by numerically solving an excitable reaction-diffusion equation on a bell-shaped surface. We determined two necessary conditions for inducing topological change: the characteristic length of the curved surface (i.e., height of the bell-shaped structure) should be larger than the width of the wave and than a threshold independent of the wave width. As for the geometrical mechanism of the latter, we found that a bifurcation of the globally minimum geodesics (i.e. minimal paths) on the curved surface leads to the topological change. These conditions imply that wave topology changes can be predicted on the basis of curved surfaces, whose structure is larger than the wave width.

nlin.PS↗

arXiv2008

Network Evolution of Body Plans

Segmentation in arthropod embryogenesis represents a well-known example of body plan diversity. Striped patterns of gene expression that lead to the future body segments appear simultaneously or sequentially in long and short germ-band development, respectively. Regulatory genes relevant for stripe formation are evolutionarily conserved among arthropods, therefore the differences in the observed traits are thought to have originated from how the genes are wired. To reveal the basic differences in the network structure, we have numerically evolved hundreds of gene regulatory networks that produce striped patterns of gene expression. By analyzing the topologies of the generated networks, we show that the characteristics of stripe formation in long and short germ-band development are determined by Feed-Forward Loops (FFLs) and negative Feed-Back Loops (FBLs) respectively. Network architectures, gene expression patterns and knockout responses exhibited by the artificially evolved networks agree with those reported in the fly Drosophila melanogaster and the beetle Tribolium castaneum. For other arthropod species, principal network architectures that remain largely unknown are predicted.

q-bio.MN↗

arXiv2005

Emergence of multiple time scales in coupled oscillators with plastic frequencies

A coupled-phase oscillator model where each oscillator has an angular velocity that varies due to the interaction with other oscillators is studied. This model is proposed to deepen the understanding of the relationship between the coexistence and the plasticity of time scales in complex systems. It is found that initial conditions close to a one cluster states self-organize into multiple clusters with different angular velocities. Namely, hierarchization of the time scales emerges through the multi-clustering process in phases. Analyses for the clusters solution, the stability of the solution and the mechanism determining the time scales are reported.

nlin.AO↗

arXiv2001

How Fast Elements can Affect Slow Dynamics

A chain of coupled chaotic elements with different time scales is studied. In contrast with the adiabatic approximation, we find correlations between faster and slower elements when the differences in the time scales of the elements lie within a certain range. For such correlations to occur, three features are essential: strong correlations among the elements allowing for both synchronization and desynchronization, bifurcation in the dynamics of the fastest element by the change of its control parameter, and the cascade propagation of the bifurcation. The relevance of our results to biological memory is briefly discussed.

nlin.CD↗

arXiv1999

Sensitive boundary condition dependence of noise-sustained structure

Sensitive boundary condition dependence (BCD) is reported in a convectively unstable system with noise, where the amplitude of generated oscillatory dynamics in the downstream depends sensitively on the boundary value. This BCD is explained in terms of the manner in which the co-moving Lyapunov exponent (characterizing the convective instability) decreases from upstream to downstream. It is shown that a fractal BCD appears if the dynamics that represent the spatial change of the fixed point includes transient chaotic dynamics. By considering as an example a one-way-coupled map lattice, this theory for BCD is demonstrated.

chao-dyn↗

arXiv1998

Noise-induced Input Dependence in a Convective Unstable Dynamical System

Unidirectionally coupled dynamical system is studied by focusing on the input (or boundary) dependence. Due to convective instability, noise at an up-flow is spatially amplified to form an oscillation. The response, given by the down-flow dynamics, shows both analogue and digital changes, where the former is represented by oscillation frequency and the latter by different type of dynamics. The underlying universal mechanism for these changes is clarified by the spatial change of the co-moving Lyapunov exponent, with which the condition for the input dependence is formulated. The mechanism has a remarkable dependence on the noise strength, and works only within its medium range. Relevance of our mechanism to intra-cellular signal dynamics is discussed, by making our dynamics correspond to the auto-catalytic biochemical reaction for the chemical concentration, and the input to the external signal, and the noise to the concentration fluctuation of chemicals.

chao-dyn↗