Local Rules and Global Invariants in Vertebrate Organ Morphogenesis

November 5 (Thu) 13:00 - 14:00, 2026

Yoshihiro Morishita (Team Director, Laboratory for Developmental Morphogeometry, RIKEN Center for Biosystems Dynamics Research (BDR))

Quantitative analysis of tissue deformation provides a direct route to uncovering the cellular and physical principles that generate organ shape. Using live imaging and tissue-scale deformation analysis in several vertebrate systems, we have been asking whether apparently complex morphogenetic processes can be understood in terms of relatively simple local rules and more global organizing principles. During chick forebrain morphogenesis, we found that cells polarize actomyosin in response to tissue stress in an SHH-dependent manner. Local contraction along the principal stress direction results in active tissue deformation predominantly in the orthogonal direction, suggesting a simple mechanosensitive rule linking tissue mechanics to anisotropic morphogenesis. A related curvature-dependent contraction rule implemented in a vertex-based mechanical model of curved epithelia generates a range of three-dimensional tissue shapes, including simple elongation, protrusion, and branching. Related observations during chick heart looping and zebrafish mandibular morphogenesis suggest that SHH-dependent polarization of cellular behavior and anisotropic tissue deformation may represent a recurring morphogenetic module across vertebrate organs. At a more global level, comparison of chick and Xenopus limb development revealed that tissue deformation dynamics become highly conserved after removing time-dependent differences in tissue size and aspect ratio. This suggests that morphogenetic dynamics may be more naturally described in appropriately rescaled, tissue-intrinsic coordinates than in the original Cartesian coordinates. Together, these studies suggest that organ morphogenesis can be approached through both local rules governing active cellular motion and global representations that reveal conserved tissue dynamics. I will conclude by discussing an open theoretical question motivated by our current simulations: whether transitions from simple elongation to protrusion and branching can be understood as tissue-scale mechanical instabilities, and whether a continuum or active-shell-like description can be derived to identify the key physical parameters controlling these morphological transitions.

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

Event Official Language: English

Scaling regimes of the 1D Kuramoto-Sivashinsky equation

November 5 (Thu) 17:00 - 18:30, 2026

Liubov Gosteva (Ph.D. Student, LPMMC, Université Grenoble Alpes, France)

The Kuramoto-Sivashinsky (KS) equation describes various phenomena exhibiting chaos and instabilities, including flames, reaction-diffusion processes, and thin liquid film flows. It resembles the Kardar-Parisi-Zhang (KPZ) equation, with the key difference being the negative "viscosity" in the KS equation. The KS equation is known to belong to the KPZ universality class: at large scales, its statistical properties are governed by the KPZ fixed point, characterized by the dynamical exponent $z=3/2$ and a known PDF of fluctuations. In this talk, I will analyze the stochastic KS equation using the functional renormalization group (FRG). In this framework, attractive fixed points of the FRG equation determine large-scale universal behavior, while unstable fixed points govern small-scale universal behavior. I will show that the two-point correlation function exhibits, besides the KPZ scaling at large scale, another universal scaling regime at small scale, with $z=1$. This scaling is very robust as it is intrinsic to the KS dynamics. It arises from the vanishing of the effective viscosity when evolving from its microscopic negative KS value, to its macroscopic effective positive KPZ value. I will also present results from direct numerical simulations, which confirm these findings.

Venue: via Zoom

Event Official Language: English

Explaining GRB features through MAD black hole spin-down

November 6 (Fri) 14:00 - 15:00, 2026

Aleksander Lenart (Ph.D. Student, Astronomical Observatory, Jagiellonian University, Poland)

Recent developments in numerical general relativity magnetohydrodynamics have shown that a fast-spinning black hole (BH) surrounded by a magnetically arrested disk (MAD) will lose its angular momentum due to jet energy extraction. The magnetic field in the disk causes turbulence, which significantly lowers the specific angular momentum of the matter. Therefore, the energy extraction dominates over angular momentum delivery, and the BH loses its spin. In a recent paper by my team, we applied those findings to the data of Gamma-ray Bursts (GRBs). Those sources are primarily produced in the high-mass star core-collapse, resulting in the creation of a compact central object like a BH or a magnetar. Some GRBs exhibit an extreme energy budget of>10^53 erg, which is above the maximum possible energy of a magnetar. Therefore, for some sources, the BH-powered emission is the only known mechanism that could explain observations. I will demonstrate how such a scenario allows us to model GRB light curves, and how it predicts the Dainotti correlation. The anti-correlation between the duration of the plateau phase in the light curve and its luminosity. I will discuss the typical masses of BHs that could have been created in GRB events and the possible connection with the gravitational wave observations.

Venue: #220, 2F, Main Research Building / via Zoom

Event Official Language: English

Collaborative Research with AI: Hyperplane Arrangements and Magnitude

November 6 (Fri) 15:00 - 16:30, 2026

Junnosuke Koizumi (Special Postdoctoral Researcher, Division of Fundamental Mathematical Science, RIKEN Center for Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS))

In this talk, I will present research I conducted in collaboration with AI in 2026. I will also give a live demonstration of how I use AI agents in my research and discuss the future of collaboration between AI and mathematicians.

Venue: #359, 3F, Seminar Room #359 / via Zoom

Event Official Language: English

Holography and Observables in Quantum Gravity

November 9 (Mon) - 13 (Fri) 2026

Keiichiro Furuya (Project Researcher, Kavli Institute for the Physics and Mathematics of the Universe (Kavli IPMU), The University of Tokyo)
Moshe Rozali (Professor, The University of British Columbia, Canada)
Tadashi Takayanagi (Professor, Yukawa Institute for Theoretical Physics, Kyoto University)
Mengyang Zhang (Project Researcher, Kavli Institute for the Physics and Mathematics of the Universe (Kavli IPMU), The University of Tokyo)
Martin Sasieta (Postdoctoral Researcher, University of California, Berkeley, USA)
Pawel Caputa (Professor, Stockholm University, Sweden)
Kristan Jensen (Professor, University of Victoria, Canada)
Kotaro Shinmyo (Ph.D. Student, Kyoto University)
七海 中村 (Ph.D. Student, Yukawa Institute for Theoretical Physics, Kyoto University)
Ahmed Abdalla (Ph.D. Student, University of California, Berkeley, USA)

In the past 20 years, there has been significant progress in our understanding of quantum gravity based on AdS/CFT. Recently, study of quantum gravity beyond AdS/CFT attracts a lot of attention, where there is no longer an asymptotically AdS boundary on which we can perform measurements with infinite accuracy. Thus it is important to understand observables in gravitational spacetimes with no asymptotic AdS boundaries, what an observer experiences and measures in such a spacetime,  and what is the microscopic theory that describes them.  This workshop aims to gather researchers in the this subject to exchange cutting edge ideas, aiming to establish new research directions and collaborations.

Venue: via Zoom / Okochi Hall / Thursday only, Suzuki Umetaro Hall

Event Official Language: English

Topological properties of empirical fitness landscapes from merge trees

November 9 (Mon) 13:00 - 14:00, 2026

Igors Dubanevics (Ph.D. Student, Okinawa Institute of Science and Technology Graduate University (OIST))

How evolution navigates sequence space depends on the shape of the fitness landscape. Viewed as a scalar field over a discrete genotype graph, theoretical landscapes range from single-peaked to rugged and fragmented, with very different mutational accessibility. Which shapes real biological sequences occupy remains an open empirical question. Deep mutational scanning now measures sequence–function maps across complete combinatorial regions of sequence space, but the resulting landscapes are large, noisy, and hard to compare across studies. Existing analyses typically reduce each dataset to a few summary statistics, discarding which peaks connect to which, and through which saddles. We are developing a two-layer toolkit for empirical sequence–function landscapes. A statistical layer models overdispersed sequencing counts directly to separate genuine phenotypic differences from measurement noise, pruning spurious topological features before analysis. A topological layer then summarises the landscape as a merge tree of peaks, saddles, and the high-fitness ridges that link them, using persistence as a natural scale to distinguish global structure from minor ruggedness. I will first illustrate this approach on the largest published combinatorially complete protein-coding landscape, spanning over 260,000 sequences. Filtering by measurement uncertainty and persistence simplifies an apparently rugged surface, revealing that major peaks remain connected through high-fitness saddles rather than isolated by deep valleys. I will then present preliminary findings from a comparative atlas of more than 150 combinatorially complete sequence–function landscapes spanning DNA, RNA, and protein. By comparing merge-tree structure across this collection, we ask whether high-fitness ridges that bypass rugged regions recur across unrelated sequences, and whether landscapes group by the biological function they encode.

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

Event Official Language: English

Good Enough Coding in Science

November 10 (Tue) 10:00 - 15:00, 2026

Igors Dubanevics (Ph.D. Student, Okinawa Institute of Science and Technology Graduate University (OIST))

Many of us write software for research without much training in software development. A quick script and a few clever fixes can get us surprisingly far—until the project grows, a collaborator joins, or, heaven forbid, a paper revision means rerunning everything six months later. AI coding assistants make creating and changing software easier, but a well-organised project helps both humans and AI work with it. So what does “well-organised” actually mean? That’s what this hands-on workshop is about. Through small, approachable examples, we’ll explore practical habits for collaboration, reproducible environments, testing whether code does what we intend, and automating repetitive tasks—and how to use AI coding assistants to support those habits. You’ll leave with a repository and tutorial you can adapt to your own research projects.

Venue: #359, 3F, Seminar Room #359

Event Official Language: English

Meeting on Outreach of Data Descriptive Science and Mathematical Sciences 2026@IMI Kyushu&Zoom

November 13 (Fri) - 15 (Sun) 2026

The Journalists-in-Residence Program started in 2010 in cooperation with the Mathematical Society of Japan, and since then by this program many journalists were invited to stay at the places of researchers. In order to accelerate the bilateral information exchange between researchers and journalists which has been developed in JIR program, we have been organizing meetings on outreach since 2011. These are meetings where researchers and science journalists, science writers, ... get together. Researchers explain their research to journalists, ... and science journalists and writers talk about their experiences. This year we have the “Meeting on Outreach of Data Descriptive Science and Mathematical Sciences 2026@IMI Kyushu&Zoom” by the support of Transformative Research Areas (A), 2022–2026 “Establishing data descriptive science and its cross-disciplinary applications” as explained below. For the participation, please send an e-mail to the organizer.

Venue: W1-D-413, IMI Auditorium, Ito Campus, Kyushu University (Main Venue) / via Zoom

Event Official Language: Japanese

MACS Study Group Introduction and Networking Session

November 13 (Fri) 14:45 - 18:30, 2026

14:45-15:00 Teatime Discussion 15:00-17:30 MACS Study Group Introduction and Networking Session (at each study group's booth) 17:30-18:30 Discussion

Venue: Science Seminar House (Map 9), Kyoto University

Event Official Language: Japanese

A non-negative matrix factorization-based approach to integrating multimodal omics data with automatically tuned hyperparameters

November 16 (Mon) 14:00 - 15:00, 2026

Dorothy Ellis (Postdoctoral Researcher, Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences (IMS))

Venue: via Zoom

Event Official Language: English

Real-time calculations for excited state tunneling

November 17 (Tue) 14:00 - 15:30, 2026

Thomas Steingasser (Postdoctoral Fellow, Institute of Theoretical Physics (IFT), Spain)

Quantum tunnelling is conventionally formulated through Euclidean instantons, obscuring the role of physical time and complicating non-vacuum initial states. I will review the steadyon picture, in which infinitesimally regulated real-time path integrals are controlled by complex saddles whose projections recover familiar instantons. I will summarize its applications to finite-temperature decay, resonance states and states carrying conserved Noether charge, highlighting an emerging unified description of tunnelling beyond the false vacuum.

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

Event Official Language: English

Quantum Simulation of Non-Equilibrium Dynamics in SU(2) and SU(3) Lattice Gauge Theories

November 24 (Tue) 15:00 - 16:30, 2026

Xiaojun Yao (Research Assistant Professor, University of Washington, USA)

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

Event Official Language: English

KEK(-iTHEMS) Theory Workshop 2026

November 25 (Wed) - 27 (Fri) 2026

Hirotaka Hayashi (Professor, Department of Physics, School of Science, Tokai University)
Hikaru Kawai (Visiting Professor, Nambu Yoichiro Institute of Theoretical and Experimental Physics (NITEP), Osaka Metropolitan University)
Takato Mori (Assistant Professor, Department of Physics, Faculty of Science, Rikkyo University)
Masaya Nakagawa (Assistant Professor, Department of Physics, Graduate School of Science, The University of Tokyo)
Masaki Shigemori (Professor, Department of Physics, Graduate School of Science, Nagoya University)
Tadashi Takayanagi (Professor, Yukawa Institute for Theoretical Physics, Kyoto University)
Norihiro Tanahashi (Program-Specific Associate Professor, Department of physics, Graduate School of Science, Kyoto University)
Tatsuya Yamaoka (Ph.D. Student, Department of Physics, Graduate School of Science, The University of Osaka)

The KEK Theory Workshop is an annual workshop on string theory and quantum field theory. Since 2014, it has been held every winter as an international workshop and has become one of the major annual events in the high-energy physics community in Japan. This year’s workshop will be held on site at the KEK Tsukuba Campus from November 25 to 27, and it will be jointly organized with RIKEN iTHEMS. The workshop this year aims to provide a forum for extensive discussions on recent developments in string theory, matrix models, gauge/gravity duality, black-hole microstates, lattice constructions of chiral gauge theories, and open quantum systems.

Venue: Seminar Hall, Building 3, KEK Tsukuba Campus

Event Official Language: English

Rare k-mers reveal centromere haplogroups underlying human diversity and cancer translocation

November 26 (Thu) 13:00 - 14:00, 2026

Yuichi Shiraishi (Chief, Division of Genome Analysis Platform Development, National Cancer Center Japan)

Centromeres are highly variable and rapidly evolving regions of the human genome, and are frequently implicated in various cancers. Human centromeres consist of highly repetitive DNA sequences known as α-satellite higher-order repeats (HORs), which makes their analysis using conventional genome sequencing approaches extremely challenging. Although long-read sequencing technologies now enable near-complete sequencing of centromeres, applying these methods to large numbers of samples remains difficult. As a result, our understanding of centromere diversity across populations and its role in chromosomal rearrangements in cancer has remained limited. In this study, by focusing on rare k-mer markers, we demonstrate that α-satellite HOR haplotypes cluster into genetically related haplogroups. We further developed a software tool, ascairn, to accurately infer these haplogroups from common short-read whole-genome sequencing (WGS) data. Applying our approach to a dataset of more than 3,300 human samples revealed extensive centromere diversity and geographic variation. We also applied the rare k-mer–based approach to centromere sequences from 104 Japanese individuals generated as part of the Japanese Pangenome Project. This analysis revealed characteristic patterns of centromere evolution in the Japanese population and provided new insights into Japanese-specific centromere variation. In addition, we used this method to investigate class-defining chromosomal translocations, specifically der(1;19), also known as 1p/19q co-deletion, in oligodendrogliomas. By analyzing 142 samples from TCGA, we hypothesized that the breakpoints occurred on the p-arm side of D1Z7 and the q-arm side of D19Z3. This hypothesis was subsequently validated through extensive long-read sequencing in two cases, indicating that der(1;19) results in a dicentric chromosome containing two functional centromeres. We also observed that chromosomal rearrangements preferentially occurred in haplotypes with longer repetitive arrays on either the q-arm or p-arm side of the centromere. Furthermore, we identified specific centromere haplogroups associated with either increased or decreased likelihoods of der(1;19) translocations. Our findings show that rare k-mer analysis is a powerful approach for investigating centromere complexity and clarifying the mechanisms underlying centromere-associated abnormalities in cancer.

Venue: via Zoom / Seminar Room #359

Event Official Language: English

Quantum Geometry from Matrices: Framework and Applications

November 30 (Mon) 15:00 - 16:30, 2026

Harold Steinacker (Senior Scientist, Faculty of Physics, University of Vienna, Austria)

I will discuss the general framework of matrix geometry, which is a version of quantum geometry defined by a set of almost-commuting matrices. This framework allows for an efficient description of manifolds embedded in some target or feature space, which is particularly efficient for high-dimensional manifolds. I will discuss some applications in data science as well as in fundamental physics, notably how spacetime and gravity can emerge from the IKKT or IIB matrix model in this framework.

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

Event Official Language: English

Chiral Anomaly, Neutral-Pion Lifetime and Axion–Photon Coupling

December 7 (Mon) 15:00 - 16:30, 2026

Xu Feng (Professor, Director, Institute of Theoretical Physics, School of Physics, Peking University, China)

The chiral anomaly provides one of the rare opportunities to test QCD in the confinement regime at the percent level and beyond. A prime example is the neutral pion lifetime: after two decades of PrimEx measurements reaching 1.5% precision, future experiments at an upgraded 22 GeV JLab aim at the sub-percent level, calling for a comparably precise first-principles QCD prediction. The same anomaly also governs the QCD contribution to the axion–photon coupling, a key quantity connecting axion models to experimental searches for one of the leading dark-matter candidates. In this talk, I will present our recent lattice QCD studies of these two quantities, going beyond the chiral limit.

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

Event Official Language: English

Hamiltonian simulation: Standard algorithms and recent developments

December 17 (Thu) 10:30 - 17:00, 2026

Kaoru Mizuta (Associate Professor, Center for Quantum Information and Quantum Biology, The University of Osaka)

This is a lecture-style seminar of quantum computation. The tentative schedule consists of three slots: 10:30-12:00, 13:30-15:00, and 15:30-17:00. Due to equipment limitations, the blackboard might not be visible on Zoom, so we recommend attending in person.

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

Event Official Language: English

Optimal transport: Thermodynamics, biological information processing and generative models

January 18 (Mon) 13:30 - 15:00, 2027

Sosuke Ito (Associate Professor, Graduate School of Science, The University of Tokyo)

This is a joint seminar co-hosted by Institute for Physics of Intelligence (iπ), UTokyo, and the Venue is #1042,10F of Science Bldg.1 Optimal transport theory is a useful theoretical framework for geometrically characterizing the distance between probability distributions. It is not only used in recent research on generative models but has also been applied to detect information-processing capabilities in biological systems from a statistical perspective, and to discuss thermodynamic efficiency. In this seminar, I will begin with an introduction to optimal transport theory, and also discuss our research on its various applications. More specifically, I will discuss the following topics: 1) The problem of minimizing entropy production within a finite time and its experimental testing. 2) The application of optimal transport to the training of generative models, specifically diffusion models, and their optimal protocols. 3) Quantifying information processing performance using optimal transport in biological signal transduction.

Venue: Faculty of Science Bldg.1, School of Science, The University of Tokyo, Hongo Campus (Main Venue) / via Zoom

Event Official Language: English

iTHEMS NOW & NEXT 2027

July 13 (Tue) - 15 (Thu) 2027

We will hold our annual gathering, **“iTHEMS NOW & NEXT 2027,” from July 13 to 15, 2027**. iTHEMS NOW & NEXT has traditionally been a two-day in-house event, providing an important opportunity for all iTHEMS members, including visiting researchers and new members, to gain a comprehensive overview of current activities across iTHEMS, to learn about research beyond their own fields, and to discuss where iTHEMS should go next. In 2027, we will **expand NOW & NEXT from two to three days** and, for the first time, invite leading researchers from outside iTHEMS across a broad range of research fields. While the first two days will retain the main character of our traditional in-house gathering, the extended three-day format is intended to create a broader opportunity for scientific exchange and, in particular, to enable leading researchers from outside iTHEMS to become better acquainted with our research activities and with the researchers who make up the iTHEMS community. As in previous years, the program will present activities across iTHEMS, including those of its divisions, research teams, working groups, and study groups, together with research presentations and poster sessions by iTHEMS members. Particular emphasis will be placed on communication across disciplinary and organizational boundaries and on identifying emerging research directions and opportunities for new collaborations. The additional third day will build on the presentations and discussions of the preceding two days and provide an opportunity for invited researchers to gain a deeper understanding of the breadth and strengths of research at iTHEMS and to interact directly with our members. We hope that these exchanges will not only introduce iTHEMS and its researchers more widely to leading scientists in different fields, but also bring new perspectives to our community and open possibilities for future scientific interactions and collaborations. Through this expanded three-day NOW & NEXT 2027, we hope to share where iTHEMS is now and where it is heading next, both within our own community and with leading researchers from outside iTHEMS, and to explore together new possibilities for the future development of iTHEMS.

Venue: 2F Large Conference Room, Administrative Headquarters, RIKEN Wako Campus (Main Venue) / via Zoom

Event Official Language: English