Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

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Language：English   Publishing type：Research paper (scientific journal)  

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

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Language：English   Publishing type：Research paper (scientific journal)  

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

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Authorship：Last author   Language：Japanese   Publishing type：Research paper (scientific journal)  

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1039/D0CP00746C

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.7566/JPSJ.89.063901

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Language：Japanese   Publishing type：Research paper (scientific journal)  

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.3390/geosciences10020069

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1103/PhysRevE.101.012903

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Nature Publishing Group  

DOI： 10.1038/s41598-019-45367-w

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PubMed

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Academic Press  

DOI： 10.1016/j.jtbi.2019.01.002

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PubMed

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

This study presents a mathematical model of garden ants (Lasius japonicus) to examine how stochasticity in following pheromone trails influences group foraging efficiency. Simulations show that the optimal mix of deterministic and stochastic ants varies with environmental conditions: stable environments favor mildly stochastic ants, while variable ones benefit from highly stochastic individuals. The interplay between individual randomness and pheromone cues is key to optimizing foraging. When variability in pheromone sensitivity is included, stochasticity further enhances collective efficiency, suggesting it plays an important adaptive role in group behavior.

DOI： 10.1039/c8sm00517f

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Language：English   Publishing type：Research paper (scientific journal)  

Using the discrete element method, this study investigates splash processes caused by a grain impacting a randomly packed bed. The simulation results align well with previous experimental data on grain movement. The ejection angle and speed of individual grains vary depending on when they are ejected after impact. Notably, grains ejected early differ significantly from those ejected later: the vertical ejection-speed distribution changes over time from a power-law to a lognormal form. This shift may influence the subsequent trajectories of the ejected grains.

DOI： 10.1103/PhysRevE.95.022906

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：FRONTIERS MEDIA SA  

This study proposes coarse-grained elastic network models of DNA, called 1-particle-per-k-nucleotides (1PkN), to analyze the global dynamics of long DNA sequences while accounting for sequence-dependent geometry. These models were calibrated using anisotropic fluctuation data from a previous 1-particle-per-1-nucleotide (1P1N) model, which closely matched all-atom simulations. Among the variants, the 1P3N and 1P4N models effectively capture local dynamics, such as twisting motions. Designed for large-scale structures like 10-nm chromatin fibers or mitochondrial and phage DNA, the models enable efficient analysis with low computational cost. As a demonstration, the study analyzed the physical properties of entire human and Plasmodium falciparum mitochondrial genomes.

DOI： 10.3389/fphys.2017.00103

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PUBLIC LIBRARY SCIENCE  

This study quantifies the photomovement behavior of Euglena gracilis in response to light intensity gradients, aiming to better understand their role in bioconvection patterns. Two experiments were conducted. In the first, a capillary with cell suspension was exposed to different light intensities in two regions. The steady-state cell distribution showed a linear relationship with the light difference: more cells gathered in the brighter region at low mean intensity (1.25 μmol m⁻² s⁻¹), while the opposite occurred at high mean intensity (13.75 μmol m⁻² s⁻¹). In the second experiment, a shallow container was illuminated with stepwise light levels. Cells accumulated around a light intensity of approximately 3.8 μmol m⁻² s⁻¹, suggesting this value as the preferred intensity (Ic). These findings demonstrate that E. gracilis exhibits a clear response to light gradients, with behavior dependent on both the direction and strength of the light.

DOI： 10.1371/journal.pone.0168114

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Language：English   Publishing type：Research paper (scientific journal)  

This study investigates synchronized motion and mode bifurcation of two symmetric self-propelled objects—camphor disks—on an annular water channel, both numerically and experimentally. The model combines Newton’s equation of motion, driven by surface tension differences, with a reaction-diffusion equation for camphor concentration. Simulations revealed various dynamical behaviors, including four synchronized modes: reversal oscillation, stop-and-move rotation, equally spaced rotation, and clustered rotation. These modes were also observed experimentally by varying the channel diameter. The bifurcation and coexistence of these modes were analyzed in terms of disk number density. The results demonstrate that the model effectively captures key features of synchronization, collective motion, and mode transitions.

DOI： 10.1103/PhysRevE.92.022910

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PUBLIC LIBRARY SCIENCE  

This study develops simple elastic network models to explore the relationship between DNA structure and dynamics across various nucleotide sequences. First, an all-atom elastic network model is introduced that accurately reproduces temperature factor profiles observed in several DNA crystal structures. Next, a coarse-grained model is proposed, representing each nucleotide with a single node. This simplified model effectively captures detailed sequence-dependent dynamics similar to the all-atom model. Using normal-mode analysis on the coarse-grained model, the dynamics of many long DNA sequences (~150 base pairs) were extensively studied. The analysis revealed a positive correlation between the DNA’s nucleosome-forming ability and the strength of inter-strand fluctuations, providing insight into how dynamic properties influence DNA’s biological function.

DOI： 10.1371/journal.pone.0143760

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER PHYSICAL SOC  

This study explores the collective motion of symmetric self-propelled objects driven by surface tension differences, moving spontaneously around an annular water channel. The objects interact through a camphor layer on the water surface. Two distinct collective motion modes—discrete and continuous density waves—emerge depending on the number of objects. These modes are analyzed through their local and global dynamics, revealing differences in how camphor concentration distributes within the channel. The study concludes that the key distinction between the two modes lies in the driving mechanism: the force that pushes a camphor paper away from clusters, which generates and sustains the density waves.

DOI： 10.1103/PhysRevE.88.012911

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PUBLIC LIBRARY SCIENCE  

This study explores how molecular crowding on cell membranes affects biochemical signal transduction. Using a 2D model of receptors, signaling proteins, and target proteins, it shows that as target protein binding increases, signal flow (activation frequency) can follow three patterns: steadily increasing, bell-shaped, or S-shaped. Crowding causes signaling proteins to cluster around receptors, with target proteins surrounding these clusters during high signal flow. Stochastic analysis explains how excluded volume influences these behaviors, highlighting the key role of molecular crowding in membrane reactions.

DOI： 10.1371/journal.pone.0062218

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

This study investigates the collective behavior of self-propelled camphor boats moving in a one-dimensional channel, focusing on their tendency to form clusters or swarms. This clustering behavior, one of three experimentally observed types, is also reproduced through simulations using a simple theoretical model. The research analyzes the model to identify the mechanism behind clustering and the conditions that lead to its occurrence. Additionally, a method for quantifying clustering behavior is proposed, which could aid future experimental studies.

DOI： 10.1103/PhysRevE.85.055201

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER PHYSICAL SOC  

Reorientation of the segregation pattern of a binary granular mixture on a two-dimensional horizontally oscillating tray is numerically realized. The mixture consists of large and heavy particles and small and light particles, and the segregation pattern shows a transition between a striped pattern perpendicular to the oscillation and one parallel to the oscillating direction according to the change of area fractions of the two types of particle. The transition mechanism is discussed on the basis of a simplified one-dimensional dynamics.

DOI： 10.1103/PhysRevE.85.041304

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1103/PhysRevLett.108.158001

Web of Science

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Language：English   Publishing type：Research paper (scientific journal)  

This study numerically investigates effective stochastic resonance (SR) using a model of two coupled FitzHugh-Nagumo excitable elements exposed to noise with unequal amplitudes. Compared to previous models with single elements or equal noise amplitudes, this setup shows a stronger resonance response to external signals. The key concept introduced is "triggered excitation," where one noise-free element is excited synchronously with the external signal due to the triggering influence of another element fluctuating asynchronously. This mechanism is supported by deterministic simulations, helping to explain the enhanced SR observed in the system.

DOI： 10.1103/PhysRevE.84.021135

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

This study explores stochastic resonance using a model of two coupled particles exposed to noise with different amplitudes. It finds that under certain coupling strengths and noise conditions, one particle with very low or no noise can exhibit strong resonance to an external field, aided by the other particle experiencing high noise. This intense resonance arises from the unique interplay between the stochastically fluctuating particle and the other particle that responds classically to the external signal. The results highlight how heterogeneous noise levels and coupling can enhance resonance effects.

DOI： 10.1103/PhysRevE.82.051122

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER PHYSICAL SOC  

This study investigates the transition from free flow to a jammed state in a counter-chemotactic particle flow along a quasi-one-dimensional path. A key feature is the spontaneous formation of a path-blocking cluster (PBC) that blocks the path and causes jamming when particle density exceeds a threshold. Near this threshold, the PBC can intermittently collapse, restoring free flow. The size dynamics of the PBC control the overall particle flux. Using numerical simulations from a stochastic cellular automata model, the authors propose a Langevin equation to describe the PBC size evolution, capturing key behaviors observed. The findings suggest that the jammed state emerges through a saddle-node bifurcation in the system.

DOI： 10.1103/PhysRevE.82.015102

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Physical Society of Japan  

DOI： 10.1143/JPSJ.79.063002

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER PHYSICAL SOC  

We propose an inanimate system composed of camphor boats in an annular water channel in order to understand the collective motions. The boats move on the water surface spontaneously and interact with one another through the concentration of the camphor molecules on the water. We observed several modes of collective motion, e.g., behaviors analogous to traffic flow or an ant trail. Our system provides a convenient experimental setup for the investigation of a variety of collective motions.

DOI： 10.1103/PhysRevE.81.056210

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：The American Physical Society  

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：一般社団法人 日本物理学会  

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：日本学術会議 「機械工学委員会・土木工学・建築学委員会合同IUTAM分科会」  

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：一般社団法人 日本物理学会  

Quasi-one-dimensional bidirectional particle flow including the effect of chemotaxis is investigated through a modification of the John-Schadschneider-Chowdhury-Nishinari model. Specifically, we permit multiple lanes to be shared by both directionally traveling particles. The relation between particle density and flux is studied for several evaporation rates of pheromone, and the following results are obtained: i) in the low-particle-density range, the flux is enlarged by pheromone if the pheromone evaporation rate is sufficiently low, ii) in the high particle-density range, the flux is largest at a reasonably high evaporation rate and, iii) if the evaporation rate is at the level intermediate between the above two cases, the flux is kept small in the entire range of particle densities. The mechanism of these behaviors is investigated by observing the spatiotemporal evolution of particles and the average cluster size in the system.

DOI： 10.1143/JPSJ.78.073801

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：一般社団法人日本物理学会  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Physical Society of Japan  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：一般社団法人 日本物理学会  

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Physical Society of Japan  

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Physical Society of Japan  

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Physical Society of Japan  

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Physical Society of Japan  

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：一般社団法人 日本物理学会  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：社団法人応用物理学会  

DOI： 10.1143/JJAP.34.397

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Other Link： http://orcid.org/0000-0003-0867-8986

Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：日本鉱物科学会  

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：公益社団法人 日本表面科学会  

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Astronomical Society of Japan  

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：一般社団法人日本物理学会  

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Authorship：Last author   Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：一般社団法人日本物理学会  

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Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：物性研究刊行会  

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：一般社団法人 日本物理学会  

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Language：Japanese   Publisher：京都大学数理解析研究所  

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Language：Japanese  

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Language：Japanese   Publisher：京都大学数理解析研究所  

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Authorship：Lead author   Language：Japanese   Publisher：京都大学数理解析研究所  

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Language：Japanese   Publisher：一般社団法人 日本物理学会  

DOI： 10.11316/butsuri1946.49.18

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