RIKEN-IBS Joint Workshop on Mathematical Approaches to Nature: from High-energy Physics to Biology

10 Dec 2025, 09:50 → 12 Dec 2025, 18:15 Asia/Seoul

Seminar Room B440 (IBS Center for Theoretical Physics of the Universe)

RIKEN-IBS Joint Workshop on Mathematical Approaches to Nature: from High-energy Physics to Biology 2025

Overview

This workshop marks a collaborative workshop jointly organized by RIKEN (Japan) and the Institute for Basic Science (IBS, South Korea). The workshop aims to explore the unifying mathematical principles that underlie diverse natural phenomena—from the fundamental interactions governing the universe to the complex behaviors observed in living systems.

This inaugural workshop will serve as a pilot meeting, focusing mainly on theoretical and mathematical physics, including areas such as high-energy theory, particle physics, and cosmology. In addition, several talks from mathematics and theoretical biology will provide broader perspectives and help identify common conceptual frameworks across different disciplines.
In recent years, new mathematical and theoretical approaches have been driving progress in our understanding of both the micro- and macro-structure of nature. These developments illustrate the growing importance of cross-disciplinary perspectives, where ideas originating in physics often inspire methods in mathematics and biology, and vice versa.

By bringing together researchers from RIKEN, IBS, and related institutions, this workshop aims to initiate sustained collaboration between the two communities and to lay the foundation for future RIKEN–IBS Joint Workshops that will grow into a truly interdisciplinary series exploring the mathematical structures of nature.

Speakers

[RIKEN iTHEMS]
Shuntaro Aoki
Che-Yu Chen
Alvaro Pastor Gutierrez
Derek Inman
Puttarak Jai-akson
Christy Kelly
Amaury Micheli
Ryo Namba

Ryoko Oishi-Tomiyasu
Zhe Wang

Sungsik Kong
Gen Kurosawa

[IBS]
Sebastian Bahamonde
Boris Betancourt Kamenetskaia
Adil Jueid
Tomotaka Kuroda
Siyao Li
Fumiya Sano
Michiru Uwabo-Niibo

Shingo Gibo
Jaekyoung Kim

Organizers

Shuntaro Aoki (RIKEN iTHEMS), Gen Kurosawa (RIKEN iTHEMS), Ryo Namba (RIKEN iTHEMS), Yusuke Yamada (IBS), Masahide Yamaguchi (IBS), Yuto Yamamoto (RIKEN iTHEMS)

Hosted by

RIKEN (Japan), Institute for Basic Science (South Korea)

Wednesday 10 December

Welcome remark

Convener: Masahide Yamaguchi (IBS)

Day 1 Morning: Jae Kyoung Kim

Chair: Yusuke Yamada

1 Synergy between math modeling and AI to solve human health problems

With recent advances in experimental tools and wearable devices, it has become increasingly easy to collect large volumes of time-series data. In this talk, I will demonstrate how such data can be utilized to uncover the hidden structures within complex systems. First, I will introduce GOBI (General Model-based Inference), a simple yet scalable method designed for inferring regulatory networks from time-series data. GOBI can infer both gene regulatory and ecological networks, surpassing the capabilities of traditional causality detection methods such as Granger and CCM. Next, I will present Density-PINN (Physics-Informed Neural Network), a method that infers the shape of the time-delay distribution governing interactions within a network. This inferred distribution helps identify the number of pathways responsible for signaling responses to antibiotics, addressing a long-standing question about the primary sources of cell-to-cell heterogeneity under stress. Finally, I will explore how the combination of mathematical modeling and machine learning can be used to analyze big data of sleep-wake timesereis measured with smartwatches. This allowed us to develop personalized sleep-wake schedules that help mitigate daytime sleepiness and reduce the risk of depression. I will also touch on how these findings can be translated into a practical app for broader use.

Speaker: Prof. Jaekyoung Kim (IBS, KAIST)

Day 1 Morning: Boris Betancourt Kamenetskaia

Chair: Yusuke Yamada

2 Structure and formation of self-interacting dark matter stars

Dark matter makes up the majority of matter in the Universe and plays a central role in the formation of cosmic structures. Under appropriate conditions, it may also form compact, self-gravitating objects analogous to stars. In this talk, I will examine the possibility that such “dark stars” arise in scenarios where dark matter possesses self-interactions in addition to gravity. These interactions are crucial, as they enable dark matter to dissipate energy and condense on astrophysically relevant timescales, while purely collisionless dark matter would collapse too slowly to form bound objects. I will present estimates for the internal structure of these systems and discuss the conditions under which their formation within dark matter halos becomes viable.

Speaker: Dr Boris Betancourt Kamenetskaia (IBS)

BorisBetancourtKamenetskaia_PresentationRikenWorkshop.pdf

Day 1 Morning: Derek Inman

Chair: Yusuke Yamada

3 Dark Matter Halos at Very High Redshifts

Cosmic halo formation is typically expected to begin deep in the matter-dominated epoch of the Universe. However, this expectation rests on assuming standard initial conditions and dark matter properties. In this talk I will discuss two situations which relax these assumptions. In the first, I will discuss initial conditions with larger than anticipated small scale fluctuations, leading to halo formation just after matter radiation equality. In the second, I will consider dark sector interactions that cause halo formation in the radiation era through long-range attractive forces.

Speaker: Derek Inman (RIKEN iTHEMS)

12:15 Lunch break

Day 1 Early afternoon: Siyao Li

Chair: Boris Betancourt Kamenetskaia

4 Igniting the universe: How reheating bridged Inflation and the Hot Big Bang

The very beginning of our universe is believed to be a rapid and silent expansion, called Inflation, during which the universe stayed cold, empty, and dark without heat or light. However, before the familiar hot and dense universe (the Hot Big Bang) begins, something extraordinary had to happen: the universe needs to get ignition. This brief but turbulent transition, known as reheating, transformed the vast, cold field energy left by inflation into a hot sea of particles, setting the stage for all later cosmic evolution. Instead of a simple decay process, reheating can involve rich nonlinear dynamics, including explosive particle production, inhomogeneity and the emergence of solitons. These intense and chaotic processes may leave traces in the form of gravitational waves or subtle signatures in the early matter distribution, which are potentially to be detected by the future observations. In this talk, I will explore how the universe gain its warmth, how the complicated dynamics set the precise initial conditions for the Hot Big Bang, and why this hidden era matters for understanding the cosmic history we observe today.

Speaker: Dr Siyao Li (IBS)

Day 1 Early afternoon: Adil Jueid

Chair: Boris Betancourt Kamenetskaia

5 Role of particle physics in dark matter indirect searches

Speaker: Dr Adil Jueid (IBS)

15:30 Break

Day 1 Late afternoon: Zhe Wang

Chair: Siyao Li

6 From KdV hierarchy to 1/24

It was first observed by Witten and soon proved by Kontsevich that the two-point correlation function of the 2d quantum gravity theory is a solution of the KdV hierarchy. Since then, relationships between 2d topological field theories coupling with gravity and integrable hierarchies have been studied in a great detail. In this talk, I will explain a canonical correspondence between semisimple 2d topological field theories and bihamiltonian integrable hierarchies with central invariants equal to 1/24.

Speaker: Dr Zhe Wang (RIKEN iTHEMS)

Day 1 Late afternoon: Ryo Namba

Chair: Siyao Li

7 Exact WKB formulation of canonical quantization on time-dependent background

Divergence in perturbative expansions is where interesting physics takes place. Particle production on time-dependent backgrounds, as one such example, is interpreted as transition from one vacuum to another. In this talk, I establish that several conceptual issues in the conventional approach to particle production in cosmology may be eliminated by fully employing the exact WKB methodology, a resummation technique of the standard (divergent) WKB series solutions. Canonical quantization and defining vacuum are performed with respect to the resummed mode functions. The correct results are shown to be reproduced without resorting to special functions or approximations, if the quantity called the Voros coefficient, which plays an important role to renormalize the asymptotic vacuum states, is properly incorporated.

Speaker: Dr Ryo Namba (RIKEN iTHEMS)

RyoNamba_RIKEN-IBS-2025.pdf

Thursday 11 December

Day 2 Morning: Fumiya Sano

Chair: Ryo Namba

8 Quantum-to-classical transition in cosmology

Speaker: Fumiya Sano (IBS)

Fumiya Sano.pdf

Day 2 Morning: Alvaro Pastor Gutierrez

Chair: Ryo Namba

9 Dynamical symmetry breaking in purely chiral theories

Dynamical phenomena in purely chiral fermionic theories remain an open challenge across a wide range of fields, from condensed matter to high-energy physics. In this talk, I will discuss how dynamical symmetry breaking can be studied in a class of chiral gauge theories that includes the Georgi–Glashow model originally proposed in the context of grand unification. This family of theories is inaccessible to standard lattice simulations, and their dynamics therefore remain largely unexplored. Using the effective action formalism and the non-perturbative functional renormalization group, we derive the flows of four-fermion interactions, which encode resonant structures and provide information on condensate emergence and bound-state formation. Extending the setup to multiple generations, we connect to the loss of asymptotic freedom and explore the boundary of a conjectured conformal window. Our results indicate that, while most of theory space favors a dominant color-breaking condensate, there exists a strongly coupled regime in which the leading condensating channels fail and more intricate dynamics emerge. Finally, I will outline the first steps towards the deep infrared limit using scale-dependent field redefinitions and incorporating color confinement as well as studying the related phenomenon of symmetric mass generation. This talk is based on [arXiv:2507.21208] and [arXiv:2412.12254].

Speaker: Dr Alvaro Pastor Gutierrez (RIKEN iTHEMS)

Day 2 Morning: Shingo Gibo

Chair: Ryo Namba

10 Theoretical analysis of hibernation using mathematical modelling and machine learning

During seasons with little or no food, hibernators enter inactive states to survive in harsh environments. Due to its complexity, the mechanism of hibernation remains largely unknown. Recent advances in experimental technology have enabled monitoring of body temperature in hibernators for more than 100 days. In this study, we aim to reveal the mechanisms of hibernation by analyzing body temperature time-series data.

Syrian hamsters start hibernation in response to winter-like short photoperiods and low temperatures. During hibernation, their body temperature shows fluctuation between euthermia and hypothermia, but the rules governing these cycles have remained unclear. By applying statistical analysis, we showed that the frequency modulation (FM) model reproduces the experimental data. This analysis also revealed a circannual period in a hibernator thought not to have circannual rhythms.

It is also still unclear when they hibernate, as the duration of the pre-hibernation period varies among individuals. According to the bifurcation theory, systems recover more slowly from small perturbations near a bifurcation point, implying that the onset of hibernation can be predicted by analyzing fluctuations in body temperature. Using a machine learning approach, we successfully predict the onset of hibernation for most individuals.

Speaker: Dr Shingo Gibo (IBS)

12:15 Lunch break

Day 2 Early afternoon: Michiru Uwabo-Niibo

Chair: Shingo Gibo

11 Cosmic Neutrino Background

Speaker: Dr Michiru Uwabo-Niibo (IBS)

Day 2 Early afternoon: Shuntaro Aoki

Chair: Shingo Gibo

12 Signatures of New Physics in Primordial Cosmological Perturbations

The correlation functions of primordial cosmological perturbations encode valuable information about the early universe. In particular, higher-order correlations, known as non-Gaussianities, can reveal additional insights, including the mass and spin of heavy particles, through characteristic oscillatory signatures. Remarkably, such particles can have masses as large as the Hubble scale during inflation, far beyond the reach of terrestrial experiments. This approach to uncovering new particles through primordial non-Gaussianity is known as the cosmological collider program, and it has emerged as a promising avenue for probing physics beyond the Standard Model. In this talk, I will briefly outline the cosmological collider framework, comment on some recent developments, and discuss my own contributions to this growing field.

Speaker: Shuntaro Aoki (RIKEN)

ShuntaroAoki_RIKEN-IBS Joint Workshop.pdf

15:30 Break

Day 2 Late afternoon: Sungsik Kong

Shuntaro Aoki

13 Towards the Network of Life

Reticulate evolution is a major driver of genetic and phenotypic diversity in the natural world. With the proliferation of genomic data, interest in detecting historical reticulation has grown rapidly, coinciding with advances in statistical methods for identifying complex evolutionary histories. Phylogenetic networks provide a probabilistic framework for representing such processes (e.g., hybrid speciation and introgressive hybridization) and for uncovering historical connectivity and complex histories across life on our planet. In this talk, I present recent methodological advances for inferring phylogenetic networks from genome-scale data. I also discuss some challenges, methodological limitations, and future research directions in this field.

Speaker: Dr Sungsik Kong (RIKEN iTHEMS)

SungsikKong_Talk-Evol.pdf

Day 2 Late afternoon: Tomotaka Kuroda

Shuntaro Aoki

14 Cosmological perturbations in stochastic inflation

Speaker: Tomotaka Kuroda (IBS)

Friday 12 December

Day 3 Morning: Amaury Micheli

Chair: Sungsik Kong

15 Quantum correlations in interacting primordial inhomogeneities

The statistical properties of the CMB anisotropies, reflecting the curvature inhomogeneities in the early Universe, are very well accounted for by assuming that they emerged from amplified vacuum fluctuations. Being the result of a genuine quantum process, it is natural to wonder which properties of these primordial inhomogeneities are quantum, and which, if any, persisted until their observations despite interactions that decohered, i.e. classicalised, them. I will review the latest progress on these questions, emphasising the quantum information approaches.

References:
Martin, J., Micheli, A., & Vennin, V. (2022). Discord and decoherence.Journal of Cosmology and Astroparticle Physics, 2022(04), 051.
https://iopscience.iop.org/article/10.1088/1475-7516/2022/04/051

Micheli, A., & Peter, P. (2023). Quantum Cosmological Gravitational Waves? In C. Bambi, L. Modesto, & I. Shapiro (Eds), Handbook of Quantum Gravity (pp. 1-66).
https://link.springer.com/10.1007/978-981-19-3079-9_10-1

Martin, Jérôme, Amaury Micheli, and Vincent Vennin. 2023. ‘Comparing Quantumness Criteria’. Europhysics Letters 142 (1): 18001. https://doi.org/10.1209/0295-5075/acc3be.

Speaker: Amaury Micheli (RIKEN iTHEMS)

Seminar IBS Dec 11 2025.pdf

Day 3 Morning: Puttarak Jai-akson

Chair: Sungsik Kong

16 Carrollian structure and null hypersurface

Carrollian physics has recently emerged as a powerful framework for describing gravitational subsystems with null boundaries, playing a central role in settings such as flat-space holography and black-hole horizons. In this talk, I will review the development of Carrollian structures, beginning with their algebraic formulation and then connecting it to the geometric viewpoint of null hypersurfaces in general relativity. The aim is to show that the Carrollian framework provides a natural and unifying language for the physics of null hypersurfaces.

Speaker: Dr Puttarak Jai-akson (RIKEN iTHEMS)

IBS_iTHEMS_workshop.pdf

Day 3 Morning: Ryoko Oishi-Tomiyasu

Chair: Sungsik Kong

17 Generalized phyllotaxis patterns: from lattices to manifolds

In Turing’s study of reaction–diffusion systems, phyllotactic pattern formation was one of his motivations, especially in his later unpublished notes. His work introduced continuous and dynamic approaches to discretely given phyllotactic patterns, inspiring extensive analytical and numerical studies in reaction–diffusion systems. However, Turing himself did not investigate phyllotaxis on surfaces without rotational symmetry or in higher-dimensional spaces.
In our recent work, we propose a unified framework for generating phyllotactic point patterns on general surfaces, Euclidean spaces, and higher-dimensional manifolds with diagonalizable metrics. Our approach relies on algebraic and geometric ideas, including products of linear forms from the geometry of numbers and Lamé systems in orthogonal curvilinear coordinates, offering a complementary perspective to the continuum-based approach by Turing. This framework naturally generalizes the classical golden-angle method to more complex geometries (S. E. Graiff-Zurita & R. OT, 2024; joint work with a student in a 1-year program at Kyushu University). Time permitting, we also discuss the “missing link” between Turing’s reaction–diffusion research and discrete phyllotaxis patterns.

Speaker: Prof. Ryoko Oishi-Tomiyasu (Kyushu University, RIKEN iTHEMS)

12:15 Lunch break

Day 3 Early afternoon: Che-Yu Chen

Chair: Ryoko Oishi-Tomiyasu

18 Shadows of rotating black holes with consistent thermodynamics

Quantum effects in general induce scale dependence in the coupling constants. When applied to Kerr black holes with a running Newton coupling, the consistency of black hole thermodynamics requires that the Newton coupling have a specific dependence on the black hole parameters. In this work, we consider such a class of Newton couplings and look for the possible observational implications on the highly lensed images of the black holes. In addition to placing constraints on the parameter space of the model through the latest Sgr A* images, we find that the variations in the shape of shadows in a large portion of the parameter space can be qualitatively captured by a quantity solely defined by the event horizon. Most importantly, the consistency of thermodynamics suggests a lower bound on the shadow size, beyond which either horizon disappears, or the shadow cannot keep the standard D-shaped structure. The possibility that the black holes in this model could spin faster than the Kerr bound, and the physical implications of the resulting cuspy shadows, are also discussed. Reference: arXiv:2510.00708.

Speaker: Che-Yu Chen (RIKEN iTHEMS)

CheYuChen_2025IBS_ithems.pdf

Day 3 Early afternoon: Christy Kelly

Chair: Ryoko Oishi-Tomiyasu

19 Axioms for QFT

In this talk we review various axiomatic approaches to quantum field theory and the known connections between them.

Speaker: Dr Christy Kelly (RIKEN iTHEMS)

ChristyKelly_iTHEMS_IBS_QFTAxioms.pdf

15:30 Break

Day 3 Late afternoon: Sebastian Bahamonde

Chair: Che-Yu Chen

20 Dynamical Systems: Cosmology and Biology

Speaker: Dr Sebastian Bahamonde (IBS)

SebastianBahamondeTalk.pdf

Day 3 Late afternoon: Gen Kurosawa

Chair: Che-Yu Chen

21 How our body keeps time in the heat

Imagine that you are in a room without information of time. The room is in a cave so that temperature and light-intensity are constant over time. Can you wake up tomorrow or day after tomorrow? In fact, most humans can wake up tomorrow and day after tomorrow almost regularly. It is because we have daily rhythms in our body. Biological experiments have shown that not only humans but also other many species on the Earth have these daily rhythms. In this talk, I will introduce several unsolved problems related to these rhythms, along with some theoretical approaches from dynamical systems and theoretical physics, including the renormalization group method.

Speaker: Dr Gen Kurosawa (RIKEN iTHEMS)

20251209IBS-RIKEN_kurosawa.pdf

Concluding remark

Convener: Gen Kurosawa (RIKEN iTHEMS)