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Shuji Ishihara

Publications and source records attributed to Shuji Ishihara.

At least 19 recordsLinked to original sources

Starvation suppression in dense scale-free metabolic networks: Dynamical mean-field analysis of catalytic reaction networks

Cellular metabolic networks exhibit scale-free topologies with power-law degree distributions across diverse organisms. Although such topologies are often linked to mutational robustness and evolutionary advantage, their role in metabolic dynamics remains unclear. Using dynamical mean-field theory, we derive an exact solution for an intracellular catalytic reaction model on dense random networks with arbitrary degree distributions. We show that the metabolic-starvation transition observed under nutrient-poor conditions for homogeneous degree distributions disappears when the out-degree distribution is scale-free. We also show a power-law in-degree distribution of the underlying catalytic reaction network gives rise to a power-law distribution of biomolecular abundances with the same exponent. Large-scale numerical simulations validate these predictions. Our results provide a theoretical framework linking network topology and metabolic dynamics.

cond-mat.stat-mech

Attraction-Induced Cluster Fragmentation and Local Alignment in Active Particle Systems

We numerically studied active Brownian particles with attractive interactions. Contrary to our intuition, the attractive force between particles disrupts the formation of a single cluster observed in motility-induced phase separation, giving rise to a multi-cluster state characterized by a power-law distribution of cluster sizes. Remarkably, the self-propulsion directions spontaneously align within each cluster, resulting in enhanced cluster motility despite the absence of alignment interactions. This study revealed the intricate role of attractive interactions in the aggregation of motile systems.

cond-mat.soft

Active Matter under Cyclic Stretch: Modeling Microtubule Alignment and Bundling

We investigate the behavior of self-propelled particles under cyclic stretching, inspired by the characteristic pattern dynamics observed in microtubule (MT) motility assays subjected to uniaxial cyclic substrate stretching. We develop a self-propelled particle model that incorporates the elastic energy acting on the filaments due to substrate deformation, successfully reproducing the experimentally observed MT patterns. Additionally, the general framework of the model enables systematic exploration of collective responses to various substrate deformations, offering potential applications in the manipulation of MT patterns and other active matter systems.

cond-mat.soft

Anti-aligning Self-propelled Model of Two Species: Emergence of Self-organized Heterogeneous Aligned and Clustered Order

Self-propelled particles with anti-aligning interactions generally do not form a polar order. However, in this Letter, we show that when multiple types of such particles coexist and interact through aligning interactions between different species, a global polar order can emerge through the formation of elongated clusters with alternating domains of each species. By developing a mean-field theory, we reveal the conditions for cluster formation and characterize the resulting patterns. Our findings highlight the critical role of inter-species interactions in the emergence of complex ordered states.

cond-mat.soft

Weakly nonlinear analysis of Turing pattern dynamics on curved surfaces

Pattern dynamics on curved surfaces are ubiquitous. Although the effect of surface topography on pattern dynamics has gained much interest, there is a limited understanding of the roles of surface geometry and topology in pattern dynamics. Recently, we reported that a static pattern on a flat plane can become a propagating pattern on a curved surface [Nishide and Ishihara, Phys. Rev. Lett. 2022]. By examining reaction-diffusion equations on axisymmetric surfaces, certain conditions for the onset of pattern propagation were determined. However, this analysis was limited by the assumption that the pattern propagates at a constant speed. Here, we investigate the pattern propagation driven by surface curvature using weakly nonlinear analysis, which enables a more comprehensive approach to the aforementioned problem. The analysis reveals consistent conditions of the pattern propagation similar to our previous results, and further predicts that rich dynamics other than pattern propagation, such as periodic and chaotic behaviors, can arise depending on the surface geometry. This study provides a new perspective on the relationship between surfaces and pattern dynamics and a basis for controlling pattern dynamics on surfaces.

nlin.PS

Oscillatory and chaotic pattern dynamics driven by surface curvature

Patterns on curved surfaces are ubiquitous, yet the influence of surface geometry on pattern dynamics remains elusive. We recently reported a new mechanism of pattern propagation in which a static pattern on a flat plane becomes a propagating pattern on a curved surface [Nishide and Ishihara, Phys. Rev. Lett. 2022]. Here, we address whether surface curvature can drive more complex pattern dynamics beyond propagation. By employing a combination of weakly nonlinear analysis and numerical simulation, we show that oscillatory and chaotic pattern dynamics can emerge by controlling the surface shapes. These findings highlight a new role of surface topography in pattern formation and dynamics.

nlin.CD

Active Deformable Cells Undergo Cell Shape Transition Associated with Percolation of Topological Defects

Cell deformability is an essential determinant for tissue-scale mechanical nature, such as fluidity and rigidity, and is thus crucial for understanding tissue homeostasis and stable developmental processes. However, numerical simulations for the collective dynamics of cells with arbitral cell deformations akin to mesenchymal, ameboid, and epithelial cells in a non-confluent situation need high computational costs and are still challenging. Here we propose a new method that allows us to study significantly larger numbers of cells than existing methods. Using the method, we investigated the densely packed active cell population interacting via excluded volume interactions, and discovered the emergence of two fluid phases in deformable cell populations, a soft-fluid phase with drastically deformed cell shapes and a fluid phase with circular cell shapes. The transition between these two phases is characterized by the percolation of topological defects, which is experimentally testable.

q-bio.TO

Pattern Propagation Driven by Surface Curvature

Pattern dynamics on curved surfaces are found everywhere in nature. The geometry of surfaces have been shown to influence dynamics and play a functional role, yet a comprehensive understanding is still elusive. Here, we report for the first time that a static Turing pattern on a flat surface can propagate on a curved surface, as opposed to previous studies, where the pattern is presupposed to be static irrespective of the surface geometry. To understand such significant changes on curved surfaces, we investigate reaction-diffusion systems on axisymmetric curved surfaces. Numerical and theoretical analyses reveal that both the symmetries of the surface and pattern participate in the initiation of pattern propagation. This study provides a novel and generic mechanism of pattern propagation that is caused by surface curvature, as well as insights into the general role of surface geometry.

nlin.PS

Surface-tension-driven coarsening in mass-conserved reaction-diffusion systems

Mass conservation in chemical species appears in a broad class of reaction-diffusion systems (RDs) and is known to bring about coarsening of the pattern in chemical concentration. Recent theoretical studies on RDs with mass conservation (MCRDs) reported that the interfacial curvature between two states contributes to the coarsening process, reminiscent of phase separation phenomena. However, since MCRDs do not presuppose a variational principle, it is largely unknown whether description of surface tension is operative or not. In this study, we numerically and theoretically explore the coarsening process of patterns in MCRDs in two and three dimensions. We identify the parameter regions where the homogeneous steady state becomes stable, unstable, and metastable. In the unstable region, pattern formation is triggered by usual Turing instability, whereas in the metastable region, nucleation-growth-type pattern formation is observed. In the later stage, spherical droplet patterns are observed in both regions, where they obey a relation similar to the Young-Laplace law and coarsen following the evaporation-condensation mechanism. These results demonstrate that in the presence of a conserved variable, a physical quantity similar to surface tension is relevant to MCRDs, which provides new insight into molecular self-assembly driven by chemical reactions.

cond-mat.stat-mech

Cytoskeleton polarity is essential in determining orientational order in basal bodies of multi-ciliated cells

Synchronous and directed ciliary beating in trachea allows transport and ejection of virus and dust from the body. This ciliary function depends on the coordinated configuration of basal bodies (root of cilia) in apical cell membrane. However, the mechanism for their formation remains unknown. In this study, we show that the polarity in apical microtubule bundles plays a significant role in the organization of basal bodies. A mathematical model incorporating polarity has been formulated which provides a coherent explanation and is able to reproduce experimental observations. We have clarified both necessity ('why polarity is required for pattern formation') and sufficiency ('how polarity works for pattern formation') of cytoskeleton polarity for correct pattering of basal bodies with verification by experimental data. This model further leads us to a possible mechanism for cellular chirality.

q-bio.CB

From cells to tissue: A continuum model of epithelial mechanics

A continuum model of epithelial tissue mechanics was formulated using cellular-level mechanical ingredients and cell morphogenetic processes, including cellular shape changes and cellular rearrangements. This model can include finite deformation, and incorporates stress and deformation tensors, which can be compared with experimental data. Using this model, we elucidated dynamical behavior underlying passive relaxation, active contraction-elongation, and tissue shear flow. This study provides an integrated scheme for the understanding of the mechanisms that are involved in orchestrating the morphogenetic processes in individual cells, in order to achieve epithelial tissue morphogenesis.

q-bio.TO

Collective dynamics of active filament complexes

Networks of biofilaments are essential for the formation of cellular structures that support various biological functions. For the most part, previous studies have investigated the collective dynamics of rod-like biofilaments; however, the shapes of the actual subcellular components are often more elaborate. In this study, we considered an active object composed of two active filaments, which represents the progression from rod-like biofilaments to complex-shaped biofilaments. Specifically, we numerically assessed the collective behaviors of these active objects in two dimensions and observed several types of dynamics depending on the density and the angle of the two filaments as shape parameters of the object. Among the observed collective dynamics, a moving density band that we named a `moving smectic' is introduced here for the first time. By analyzing the trajectories of individual objects and the interactions among them, this study demonstrated how interactions among active biofilaments with complex shapes could produce collective dynamics in a non-trivial manner.

physics.bio-ph

The Baldwin effect under multi-peaked fitness landscapes: Phenotypic fluctuation accelerates evolutionary rate

Phenotypic fluctuations and plasticity can generally affect the course of evolution, a process known as the Baldwin effect. Several studies have recast this effect and claimed that phenotypic plasticity acceler- ates evolutionary rate (the Baldwin expediting effect); however, the validity of this claim is still controversial. In this study, we investi- gate the evolutionary population dynamics of a quantitative genetic model under a multi-peaked fitness landscape, in order to evaluate the validity of the effect. We provide analytical expressions for the evolutionary rate and average population fitness. Our results indicate that under a multi-peaked fitness landscape, phenotypic fluctuation always accelerates evolutionary rate, but it decreases the average fit- ness. As an extreme case of the trade-off between the rate of evolution and average fitness, phenotypic fluctuation is shown to accelerate the error catastrophe, in which a population fails to sustain a high-fitness peak. In the context of our findings, we discuss the role of phenotypic plasticity in adaptive evolution.

q-bio.PE

Evolution of Genetic Redundancy : The Relevance of Complexity in Genotype-Phenotype Mapping

Genetic redundancy is ubiquitous and can be found in any organism. However, it has been argued that genetic redundancy reduces total population fitness, and therefore, redundancy is unlikely to evolve. In this letter, we study an evolutionary model with high-dimensional genotype-phenotype mapping (GPM) to investigate the relevance of complexity in GPM to the evolution of genetic redundancy. By applying the replica method to deal with quenched randomness, the redundancy dependence of the fitness is analytically obtained, which demonstrates that genetic redundancy can indeed evolve, provided that the GPM is complex. Our result provides a novel insight into how genetic redundancy evolves.

q-bio.PE

Cell Migration Model with Multiple Chemical Compasses

A simple model is proposed that describes the various morphodynamic principles of migrating cells from polar to amoeboidal motions. The model equation is derived using competing internal cellular compass variables and symmetries of the system. Fixed points for the $N = 2$ system are closely investigated to clarify how the competition among polaritors explains the observed morphodynamics. Response behaviors of cell--to--signal stimuli are also investigated. This model will be useful for classifying high-dimensional cell motions and investigating collective cellular behaviors.

q-bio.CB

Identifying dynamical systems with bifurcations from noisy partial observation

Dynamical systems are used to model a variety of phenomena in which the bifurcation structure is a fundamental characteristic. Here we propose a statistical machine-learning approach to derive lowdimensional models that automatically integrate information in noisy time-series data from partial observations. The method is tested using artificial data generated from two cell-cycle control system models that exhibit different bifurcations, and the learned systems are shown to robustly inherit the bifurcation structure.

q-bio.QM

Robustness under functional constraint: The genetic network for temporal expression in Drosophila neurogenesis

Precise temporal coordination of gene expression is crucial for many developmental processes. One central question in developmental biology is how such coordinated expression patterns are robustly controlled. During embryonic development of the Drosophila central nervous system, neural stem cells called neuroblasts sequentially express a group of genes in a definite order, which generates the diversity of cell types. By producing all possible regulatory networks of these genes and examining their expression dynamics numerically, we identify requisite regulations and predict an unknown factor to reproduce known expression profiles caused by loss-of-function or overexpression of the genes in vivo, as well as in the wild type. We then evaluate the stability of the actual Drosophila network for sequential expression. This network shows the highest robustness against parameter variations and gene expression fluctuations among the possible networks that reproduce the expression profiles. We propose a regulatory module composed of three kinds of regulations which is responsible for precise sequential expression. The present study suggests an underlying principle on how biological systems are robustly designed under functional constraint.

q-bio.MN

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