Jun Yamamoto
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Research

A overview of my research projects.

Current projects

Three-dimensional rendering of a porous medium inside a cubic volume, with an inner sampling region.
A three-dimensional porous medium as a physical network.
01Physical structure · spectral theory · dynamics

Physical networks

How physical constraints impact network structure and dynamics, including how degree-volume disorder controls Laplacian eigenmode localization (Yamamoto, Bonamassa, and Pósfai 2026b, 2026a).

Current focusLaplacian eigenmode localization, diffusion, synchronization

A branching tree rooted at the center and expanding radially with degree heterogeneity.
A branching tree with heterogeneous branching.
02Scaling theory · criticality · hierarchy

Scaling theory for networks

Scaling laws and critical phenomena for networks with heterogeneous topologies (Yamamoto and Yakubo 2023; Yakubo, Shimojo, and Yamamoto 2024).

Current focusCrossover · percolation criticality

Schematic of phase oscillators coupled through a network.
Phase oscillators coupled through a network.
03Nonlinear dynamics · experiments

Network synchronization

How network structure and physical heterogeneity organize collective order in experimentally realized oscillator systems.

Current focusModular synchronization · spin oscillators

Past project

The completed projects are listed below. For a full list of publications, see the publications page.

Generator construction and box covering for a fractal scale-free network.
Generator construction and box covering used to analyze bifractality.
PublishedPhysical Review E · 2023

Bifractality of fractal scale-free networks

We showed that fractal scale-free networks are characterized by two distinct local fractal dimensions: one governing neighborhoods around hubs and another governing regions far from them. Our analytical and numerical results suggest that such bifractality is generic, leading us to conjecture that any network combining scale-free connectivity with fractal structure exhibits this behavior. (Yamamoto and Yakubo 2023).

Paper arXiv

A bifractal network colored by local spectral dimension, with a color scale.
Local spectral dimension across a bifractal network.
PublishedPhysical Review E · 2024

Random walks on bifractal networks

Building on bifractality, we showed that a random walk’s walk dimension remains position-independent, whereas the spectral dimension splits into two local values.

The result connects structural bifractality to transport properties: local structural scaling remains visible in return-to-origin probabilities (Yakubo, Shimojo, and Yamamoto 2024).

Paper arXiv

Panels showing a single triadic interaction and its extension to a structural network with regulatory nodes.
Structural and regulatory layers of a triadic-interaction network.
PublishedNature Communications · 2025

Mining triadic interactions

We considered diffusive dynamics in networks with triadic interactions in which a node can influence the connection between two other nodes. We demonstrated that such interactions can be mined from conditional correlations and mutual information between node triplets (Niedostatek et al. 2025).

Paper arXiv Code

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References

Niedostatek, Marta, Anthony Baptista, Jun Yamamoto, Jürgen Kurths, Ruben Sanchez Garcia, Ben D MacArthur, and Ginestra Bianconi. 2025. “Mining Higher-Order Triadic Interactions.” Nature Communications.
Yakubo, Kousuke, Gentaro Shimojo, and Jun Yamamoto. 2024. “Random Walks on Bifractal Networks.” Physical Review E 110 (6): 064318.
Yamamoto, Jun, Ivan Bonamassa, and Márton Pósfai. 2026a. “Laplacian Eigenmode Localization in Physical Complex Networks.” Manuscript Submitted.
———. 2026b. “Localization Transitions of Diffusion Dynamics in Physical Networks.” arXiv Preprint arXiv:2607.19486.
Yamamoto, Jun, and Kousuke Yakubo. 2023. “Bifractality of Fractal Scale-Free Networks.” Physical Review E 108 (2): 024302.
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