Search Event

Inferring Phylogenetic Networks in the Genomic Era

October 30 (Thu) 13:00 - 14:00, 2025

Sungsik Kong (Research Scientist, Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))

While phylogenetic trees (i.e., branching diagrams that depict the evolutionary history of different organisms) have been essential for understanding species evolution, they do not fully capture certain evolutionary processes, such as hybridization. In these cases, a phylogenetic network, which extends a phylogenetic tree by allowing two branches to merge into one and create reticulations, is needed. However, existing methods for estimating networks from genomic data become computationally prohibitive as dataset size and topological complexity increase. In this talk, I present the performance of popular computational methods that detect hybridization from genomic data as an alternative to the network inference, discussing their significance and limitations. I then explain how phylogenetic networks generalize trees to represent complex evolutionary histories and explore the biological interpretations that can be drawn from various branching patterns. Finally, I introduce PhyNEST (Phylogenetic Network Estimation using SiTe patterns), a novel method that efficiently and accurately infers phylogenetic networks directly from sequence data using composite likelihood. PhyNEST is implemented as an open-source Julia package and is available at https://github.com/sungsik-kong/PhyNEST.jl.

Venue: #359, 3F, Main Research Building (Main Venue) / via Zoom

Event Official Language: English

Sequence-encoded protein condensation: a statistical physics perspective

October 23 (Thu) 13:00 - 14:00, 2025

Kyosuke Adachi (Research Scientist, Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))

Event Official Language: English

Particle-in-Cell Simulations on Collisionless Shocks and Particle Acceleration in Black Hole Coronae

October 16 (Thu) 14:00 - 15:15, 2025

Nhat-Minh Ly (Ph.D. Student, Department of Physics, The University of Osaka)

Multiple nearby Active Galactic Nuclei have been reported as sources of high-energy neutrinos detected by the IceCube observatory. These results strongly suggest efficient proton acceleration to (sub-)PeV energies, likely within Black Hole (BH) coronae, given the lack of γ-ray counterparts. The acceleration mechanisms remain unconfirmed due to limited understanding of coronal environments and challenges in modeling hot, relativistic plasmas. Although diffusive shock acceleration (DSA) has been proposed, a self-consistent treatment incorporating detailed kinetic plasma effects has been lacking. In this study, we present the particle-in-cell (PIC) method as a first-principles approach to investigate particle acceleration by collisionless shocks under conditions inferred from multi-wavelength observations of BH coronae. Using large-scale 1D3V simulations, we surveyed shock parameters, focusing on underexplored effects such as initial ion–electron temperature ratios and trans-relativistic shock velocities, and found that collisionless shocks can form even in hot, low-Mach plasmas. These shocks accelerate protons up to ~100 TeV, consistent with the energies required for IceCube neutrino detections, across a wide range of coronal conditions. The shocks partition ~10% of dissipated energy into nonthermal protons and <1% into electrons, providing critical, observationally testable constraints on the plasma state of BH coronae.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

Why complexity persists: Evolutionary dynamics of the amylase locus in primates

October 16 (Thu) 12:30 - 13:45, 2025

Charikleia Karageorgiou (Postdoctoral Fellow, University at Buffalo, USA)

The amylase locus is among the most structurally variable regions of the human genome, frequently linked to starch digestion, metabolic traits, and dietary adaptation. Yet the causes of its recurrent duplication and exceptional variability remain unresolved. Why is this locus particularly prone to structural change? To address these questions, we analyzed 98 modern human genomes using long-read sequencing and optical mapping, alongside 53 high-quality primate assemblies. We identified 30 distinct amylase haplotypes in humans and documented more than 15 lineage-specific expansions and contractions across primates. Structural complexity appears to have been initiated by lineage-specific LTR insertions and subsequently shaped by non-allelic homologous recombination, with occasional contributions from microhomology-mediated break-induced replication. Independent duplications and salivary expression gains evolved repeatedly across primate lineages, but extensive within-species structural polymorphism is largely unique to humans. We further detected signatures of positive selection among primate paralogs, and dietary correlations with copy number suggest recurrent adaptive roles for amylase variation. The persistence of structural variation in this locus points to a unique combination of elevated mutational input, relaxed constraint, and ongoing selection, highlighting broader principles in the evolution of structurally unstable loci.

Venue: via Zoom / Seminar Room #359

Event Official Language: English

Topological Field Theory Coupled to Parameter Spaces

October 15 (Wed) 13:30 - 15:00, 2025

Takamasa Ando (Ph.D. Student, Yukawa Institute for Theoretical Physics, Kyoto University)

Topological quantum field theories (TQFTs) describe the IR fixed points of wide classes of gapped theories and are useful for studying many-body quantum phases of matter. In this talk, I will talk about TQFTs coupled to parameter spaces. I first explain the motivation for studying such TQFTs with parameter spaces from two perspectives: generalizing the description of the partition function with background gauge fields, and generalizing to invariants of many-body gapped phases over parameter spaces, known as the Berry phase. Then I will explain how these two are related by showing two physically motivated maps that connect them. The construction of these maps provides physical evidence for the Cobordism Hypothesis. I also discuss other related topics, such as the bulk-boundary correspondence. The talk is based on my ongoing work with Ryan Thorngren (UCLA).

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

Why do we sleep? — The Role of Calcium and Phosphorylation in Sleep

October 10 (Fri) 15:30 - 17:00, 2025

Hiroki R. Ueda (Professor, Systems Pharmacology, Graduate School of Medicine, The University of Tokyo / Professor, Department of Systems Biology, Institute of Life Science, Kurume University)

Sleep remains one of greatest remaining mysteries. At the Sleep 2012 conference, we conceived a shift from the concept of “sleep substances” to “wake substances” such as calcium, suggesting that sleep homeostasis may arise from the integration of wake-related activity. Inspired by Dr. Setsuro Ebashi’s work on calcium signaling, we investigated calcium’s role in sleep regulation. Using our Triple-CRISPR method (Sunagawa et al. 2016), we screened 25 genes related to calcium channels and pumps, revealing calcium as a brake on brain activity to promote sleep (Tatsuki et al. 2016). We also developed a tissue-clearing method CUBIC (Susaki et al. 2014; Tainaka et al. 2014) to visualize calcium’s effects on neural circuits. Further work showed that calcium-dependent enzymes, CaMKIIα/β kinases, act as calcium “memory” devices, with phosphorylation sites controlling sleep onset, duration, and termination (Tone et al. 2022). Other direct and indirect calcium-dependent phosphatases, Calcineurin and PP1 (sleep-promoting), and opposing kinases, PKA (wake-promoting), function as synaptic sleep switches (Wang et al. 2024). We also identified the ryanodine receptor 1, a calcium channel, as a molecular target of inhalational anesthetics, hinting at shared pathways between anesthesia and sleep (Kanaya et al. 2025). Lastly, we proposed the WISE (Wake Inhibition Sleep Enhancement) mechanism, where quiet wakefulness suppresses and deep sleep strengthens synaptic connections, explaining links between sleep, depression, and antidepressant effects (Kinoshita et al. 2025).

Venue: Okochi Hall (Main Venue) / via Zoom

Event Official Language: English

Homo lupo lupus est: Man is a wolf to wolves.

October 9 (Thu) 14:00 - 15:00, 2025

Carlos Sarabia (Postdoctoral Researcher, Evolutionary Population Genetics Lab, Institute of Evolutionary Biology (IBE-CSIC), Spain)

The gray wolf (Canis lupus) is one of the most emblematic wild species in human history: revered as a symbol of strength and wildness, although unforgivably persecuted as a competitor and pest. Across Europe and much of Eurasia, wolves would still dominate as apex predators... were it not for millennia of human pressure. Today, their evolutionary trajectory is shaped not only by climate fluctuations and habitat loss, but also by a uniquely flexible species boundary. Due to their unique karyotype, canids can admix freely with other related species, a capacity that both threatens the genetic integrity of wild canids like wolves and enriches our understanding of hybridization as a driver of adaptation. In this talk, we will explore recent studies on wolf demography under human pressure and climatic change, with particular attention to admixture with domestic dogs and the consequences for their survival in increasingly anthropized environments. Finally, we will observe how the wolf's distinctive genomic architecture makes it a powerful model for testing population genetics theoretical frameworks and for applying state-of-the-art computational tools, offering new insights into the understanding of evolution as a force for change.

Venue: via Zoom

Event Official Language: English

Quantum tunneling in the curved spacetime

October 2 (Thu) 13:30 - 15:00, 2025

Masahide Yamaguchi (Director, Center for Theoretical Physics of the Universe, Institute for Basic Science, Republic of Korea)

False vacuum decay is theorized to have occurred frequently throughout the history of the universe, particularly during first-order phase transitions associated with spontaneous symmetry breaking. The decay rate of such a vacuum is governed by Euclidean bounce solutions, which can exhibit a wide range of configurations, even under fixed boundary conditions. In the absence of gravitational effects, it was established over four decades ago—under reasonable assumptions—that the most symmetric bounce solution, namely the O(4)-symmetric one, minimizes the Euclidean action. This renders it the dominant tunneling path in flat spacetime. However, when gravitational effects are taken into account—as is essential in cosmological settings—all prior studies have assumed, without rigorous proof, that the O(4)-symmetric bounce continues to minimize the action. This has remained a longstanding unresolved problem for more than forty years. In this work, we address this issue by employing the anti-de Sitter/conformal field theory (AdS/CFT) correspondence to determine the configuration with the lowest Euclidean action in a metastable AdS false vacuum. Within the Euclidean formalism of Callan and Coleman, we identify the most probable decay channel of the AdS vacuum. The AdS/CFT duality enables us to sidestep the technical challenges intrinsic to metastable gravitational systems. We demonstrate that the Fubini bounce in conformal field theory—which is dual to the Coleman–de Luccia (CdL) bounce in AdS—indeed minimizes the Euclidean action among all finite bounce solutions in a conformal scalar field theory. Consequently, under certain conditions, we establish that the CdL bounce yields the lowest action among all relevant configurations, including both large and thin-wall limits. Time permitting, we also discuss the prefactor of the decay rate, as obtained from one-loop quantum corrections.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

What constitutes a gravitational wave in an expanding universe?

October 1 (Wed) 16:00 - 17:30, 2025

Yi-Zen Chu (Professor, Department of Physics, National Central University, Taiwan)

Our understanding of gravitational waves produced by isolated astrophysical systems is primarily based on gravitational perturbation theory off a flat spacetime background. This leads to the common identification of gravitational radiation with massless spin-2 waves. In this talk, I will argue that gravitational waves may no longer be solely "spin-2" in character once the background spacetime is our expanding universe instead. As a result of the mixing between gravitational and other degrees of freedom, scalar "spin-0" gravitational waves may exist during the radiation-dominated epoch of our universe; as well as during its current accelerated expansion phase -- provided the main driver is not the cosmological constant, but some extra "Dark Energy" field. Moreover, during the radiation-dominated era, spin-0 Cherenkov gravitational waves may even be generated if its material source were traveling faster than 1/\sqrt{3}.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

A Continuous Galactic Line Source of Axions: The Remarkable Case of 23Na

September 30 (Tue) 14:00 - 15:00, 2025

Wick C. Haxton (Professor, Department of Physics, University of California, Berkeley, USA)

While it is unusual for odd-A nuclear species to be abundant in massive stars, 23Na is an interesting exception. Typically 0.1 solar masses of 23Na is synthesized during the carbon burning phase of supernova and ONeMg white dwarf progenitors, then maintained at approximately 10^9 K for periods ranging up to 60,000 years. Under these conditions, 23Na can pump the thermal energy of the star into escaping axions: the mechanism is the Boltzmann occupation of and subsequent axion emission from the 440 keV level. We develop a galactic model to show that the resulting flux of line axions is continuous, arising from hundreds of contributing sources. As they travel through the intra-galactic magnetic field, some of these axions convert to detectable gamma rays. Consequently, future all-sky detectors like COSI will be able to set new limits on light axion-like particles. Other interesting aspects of these axions will be discussed.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

Spontaneous quasiparticle creation in an analogue preheating experiment

September 30 (Tue) 10:00 - 12:00, 2025

Amaury Micheli (Postdoctoral Researcher, Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))

Abstract: First, I will briefly outline the motivations and concepts that underpin the analogue gravity program. Next, I will provide a detailed description of a specific experiment designed to simulate various features of the cosmological reheating era. Finally, I will present our recent experimental results from this setup, where we demonstrated the parametric creation of quasiparticle pairs from the quantum vacuum, drawing an analogy with the preheating phase of reheating.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

The QCD phase diagram at finite densities

September 29 (Mon) 13:30 - 15:00, 2025

Franz Sattler (Postdoc, Faculty of Physics, Bielefeld University, Germany)

I discuss recent progress towards calculating the QCD phase diagram at finite density using the functional Renormalisation Group (fRG). After introducing the fRG as applied to QCD, I explain some of the challenges encountered in functional approaches to the QCD phase diagram. Many of these can be resolved by recent developments of new numerical methods. In particular, the application of numerical hydrodynamics to RG flows and resolution of momentum dependences allow us to make progress towards quantitative access to the region of the conjectured critical end-point (CEP) of the QCD phase diagram. An interesting result is the appearance of new phases characterised by spatial modulations (the moat regime) and inhomogeneous condensates at high densities from a self-consistent first-principles calculation. For the near future, a clear program emerges to further pinpoint the CEP and its possibly modified nature using the fRG.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

The evolution of conditional dispersal promotes cooperation

September 25 (Thu) 13:00 - 14:00, 2025

Iris Prigent (Ph.D. Student, Department of Ecology and Evolution, University of Lausanne, Switzerland)

Kin selection is an important mechanism for the evolution of cooperative behaviours across multiple taxa. While limited dispersal can foster kin selection by generating a genetic correlation between cooperating individuals, it also increases competition among relatives, constraining the evolution of cooperation. Prior theory has explored the co-evolution of dispersal and cooperation but typically assumes dispersal is independent of social cues. Here, we use mathematical modelling to examine whether socially-mediated dispersal, whereby individuals adjust their dispersal based on social context, can mitigate kin competition and thus enhance cooperation. We model the joint evolution of: (i) the probability of cooperating within social groups; and (ii) the probability of dispersing conditional on the number of individuals that have cooperated within the group, leading to a reaction norm for dispersal. We show that when the probability of dispersal increases with the number of cooperators, cooperation is favoured because it increases the fitness of relatives. The joint evolution of the two traits can lead to the differentiation of two types of individuals, one that always cooperates and another that never does. Although both types evolve dispersal norms such that they disperse more often when there are more cooperators in the group, cooperators evolve a steeper norm, reflecting greater sensitivity to their social environment. Our study shows that dispersal responses to the environment can vary between individuals based on their own social tendency, which can help explain why dispersal proclivities may differ between genotypes and between environments within a single population.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359 (Main Venue) / via Zoom

Event Official Language: English

Lecture 2 on "Modular Structures in N=4 supersymmetric Yang-Mills theory"

September 19 (Fri) 14:30 - 17:30, 2025

Daniele Dorigoni (Associate Professor, University of Durham, UK)

In this lecture series we present recent results in the study of exact correlation functions of half-BPS operators in N=4 supersymmetric Yang-Mills theory (SYM) averaged over the space-time insertion points. After presenting some basic properties of 1/2-BPS operators in N=4 SYM, we review how these integrated correlation functions can be obtained from a matrix model formulation of the N=4 path-integral. We then move to present two different integrated correlation functions of four superconformal primary operators of the stress-tensor multiplet which are holographically related to scattering amplitudes of 4-gravitons in type IIB superstring theory on an AdS_5 x S^5 background. We derive exact expressions both in the number of colours N, as well as in the complexified Yang-Mills coupling \tau. A key player in our discussion is electro-magnetic duality of N=4 SYM which provides strong constraints on the coupling dependence of such observables which, in particular, have to be real-analytic modular invariant functions of \tau. We then discuss the large-N fixed-\tau limit to show how these results can be interpreted on the dual stringy side. We also present some details on how these integrated correlator can be used to supplement the standard bootstrap approach leading to exciting coupling dependent bounds on the anomalous dimensions of non-protected operators in N=4 SYM, such as the Konishi operator. Lastly, we discuss an integrated correlation function involving two superconformal primary operators in the stress tensor multiplet in the presence of a half-BPS line defect operator, such as a Wilson line. Electro-magnetic duality is again fundamental in understanding the exact dependence from the coupling constant \tau. [OPTIONAL: If time and energy permit, I can also present some new results regarding integrated correlation functions of two light operators, dual to gravitons on the holographic side, and heavy giant graviton operators, dual to D3 branes extended on the background geometry]

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

Lecture 1 on "Modular Structures in N=4 supersymmetric Yang-Mills theory"

September 18 (Thu) 14:30 - 17:30, 2025

Daniele Dorigoni (Associate Professor, University of Durham, UK)

In this lecture series we present recent results in the study of exact correlation functions of half-BPS operators in N=4 supersymmetric Yang-Mills theory (SYM) averaged over the space-time insertion points. After presenting some basic properties of 1/2-BPS operators in N=4 SYM, we review how these integrated correlation functions can be obtained from a matrix model formulation of the N=4 path-integral. We then move to present two different integrated correlation functions of four superconformal primary operators of the stress-tensor multiplet which are holographically related to scattering amplitudes of 4-gravitons in type IIB superstring theory on an AdS_5 x S^5 background. We derive exact expressions both in the number of colours N, as well as in the complexified Yang-Mills coupling \tau. A key player in our discussion is electro-magnetic duality of N=4 SYM which provides strong constraints on the coupling dependence of such observables which, in particular, have to be real-analytic modular invariant functions of \tau. We then discuss the large-N fixed-\tau limit to show how these results can be interpreted on the dual stringy side. We also present some details on how these integrated correlator can be used to supplement the standard bootstrap approach leading to exciting coupling dependent bounds on the anomalous dimensions of non-protected operators in N=4 SYM, such as the Konishi operator. Lastly, we discuss an integrated correlation function involving two superconformal primary operators in the stress tensor multiplet in the presence of a half-BPS line defect operator, such as a Wilson line. Electro-magnetic duality is again fundamental in understanding the exact dependence from the coupling constant \tau. [OPTIONAL: If time and energy permit, I can also present some new results regarding integrated correlation functions of two light operators, dual to gravitons on the holographic side, and heavy giant graviton operators, dual to D3 branes extended on the background geometry]

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

Cross-species transcriptome analysis using Gromov-Wasserstein optimal transport

September 18 (Thu) 13:00 - 14:00, 2025

Yuya Tokuta (Program-Specific Researcher, Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University Institute for Advanced Study (KUIAS))

Sequence homology underpins cross-species analysis but cannot identify evolutionarily distinct genes that play analogous regulatory roles. Furthermore, ethical restrictions on human experiments necessitate analytical frameworks that translate insights from other animals to humans. To address these challenges, we developed Species-OT, a cross-species transcriptome analysis framework based on Gromov-Wasserstein optimal transport, which quantitatively compares the geometry of transcriptome distributions. Given a pair of bulk or single-cell RNA-sequencing datasets, Species-OT returns a gene-to-gene correspondence capturing probabilistic alignments of regulatory roles, and a transcriptomic distance quantifying overall divergence. Applied pairwise, Species-OT yields a transcriptomic discrepancy array and a hierarchical clustering tree analogous to a phylogenetic tree. We validated Species-OT using bulk RNA-seq data from human, mouse, and macaque germ cell specification as well as scRNA-seq data from pluripotent stem cells of six mammalian species. Species-OT identified evolutionarily related and distinct gene correspondences including biologically unexplored candidates, while transcriptomic discrepancies recapitulated expected species relationships. This is joint work with T. Nakamura, K. Fujiwara, M. Imamura, M. Nagano, M. Saitou, Y. Imoto, and Y. Hiraoka.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English

Multi-strangeness matter from ab initio calculations

September 16 (Tue) 13:30 - 15:00, 2025

Hui Tong (Post-doctoral Fellow, Helmholtz-Institut für Strahlen- und Kernphysik, University of Bonn, Germany)

Hypernuclei and hypernuclear matter connect nuclear structure in the strangeness sector with the astrophysics of neutron stars, where hyperons are expected to emerge at high densities and affect key astrophysical observables. We present the first ab initio calculations that simultaneously describe single- and double- hypernuclei from the light to medium-mass range, the equation of state for -stable hypernuclear matter, and neutron star properties. Despite the formidable complexity of quantum Monte Carlo (QMC) simulations with multiple baryonic degrees of freedom, by combining nuclear lattice effective field theory with a newly developed auxiliary-field QMC algorithm we achieve the first sign-problem free ab initio QMC simulations of hypernuclear systems containing arbitrary number of neutrons, protons, and hyperons, including all relevant two- and three-body interactions. This eliminates reliance on the symmetry-energy approximation, long used to interpolate between symmetric nuclear matter and pure neutron matter. Our unified calculations reproduce hyperon separation energies, yield a neutron star maximum mass consistent with observations, predict tidal deformabilities compatible with gravitational-wave measurements, and give a trace anomaly in line with Bayesian constraints. By bridging the physics of finite hypernuclei and infinite hypernuclear matter within a single ab initio framework, this work establishes a direct microscopic link between hypernuclear structure, dense matter composition, and the astrophysical properties of neutron stars.

Venue: Seminar Room #359 (Main Venue) / via Zoom

Event Official Language: English

Separability criteria for loops via the Goldman bracket

September 12 (Fri) 15:00 - 17:00, 2025

Aoi Wakuda (Ph.D. Student, Graduate School of Mathematical Sciences, The University of Tokyo)

In this talk, we give algebraic criteria using the Goldman bracket to determine whether two free homotopy classes of loops on an oriented surface have disjoint representatives. As an application, we determine the center of the Goldman Lie algebra of a pair of pants. We extend Kabiraj's method, which was originally limited to oriented surfaces filled by simple closed geodesics, and show that in this case, the center is generated by the class of loops homotopic to a point, and the classes of loops winding multiple times around a single puncture or boundary component.

Venue: via Zoom / #359, Seminar Room #359

Event Official Language: English

Identifying signatures of natural selection through the genome using mixed models

September 11 (Thu) 13:00 - 14:00, 2025

Lucas Sort (Postdoctoral Researcher, Mathematical Genomics RIKEN ECL Research Unit, Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))

Identifying signatures of selection has traditionally relied on detecting traces in modern day genomes. In particular, the length of linkage disequilibrium (LD) blocks in modern day genomes has often been used as an indicator of selection. However, in recent years, the emergence of ancient DNA has enabled new approaches to infer selection that directly use genetic data from the past and reconstruct the evolutionary history of genomes. In this presentation, I will introduce a methodological framework that was recently proposed to identify variants under selection across the genome: mixed models. Mixed models have long been applied in the Genome-Wide Association Study (GWAS) literature, as they effectively account for population structure and easily integrate confounders. In this context, I will present the framework and outline our plans to further improve current approaches.

Venue: via Zoom / Seminar Room #359

Event Official Language: English

Exciting Possibilities of Multi-Messenger Windows on Cosmic Accelerators

September 9 (Tue) 13:30 - 15:00, 2025

Koichiro Yasuda (Ph.D. Student, Department of Physics and Astronomy, University of California, Los Angeles, USA)

Active Galactic Nuclei (AGN) jets are among the most extreme particle accelerators in the universe and are thought to play a key role in the origin of ultra-high-energy cosmic rays. Yet, the physical processes inside these jets, particularly those involving heavy nuclei, remain poorly understood. In this talk, I will explore how nuclear and atomic processes in AGN jets can leave distinctive multi-messenger signatures, from neutrino production via nuclear decays to characteristic gamma-ray features from nuclear excitations. These phenomena offer a new window into the microscopic physics of nuclei under astrophysical extreme conditions, while also serving as macroscopic probes of jet composition and acceleration mechanisms. I will also discuss how upcoming observations, including neutrino flavor studies and MeV gamma-ray missions, could provide critical tests of these ideas and shed light on the role of nuclear physics in shaping cosmic accelerators.

Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359

Event Official Language: English