Good Enough Coding in Science

2026年11月10日(火) 10:00 - 15:00

Igors Dubanevics (沖縄科学技術大学院大学 (OIST) 博士課程)

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.

会場: セミナー室 (359号室) 3階 359号室

イベント公式言語: 英語

Topological properties of empirical fitness landscapes from merge trees

2026年11月9日(月) 13:00 - 14:00

Igors Dubanevics (沖縄科学技術大学院大学 (OIST) 博士課程)

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.

会場: via Zoom / セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催

イベント公式言語: 英語

Collaborative Research with AI: Hyperplane Arrangements and Magnitude

2026年11月6日(金) 15:00 - 16:30

小泉 淳之介 (理化学研究所 数理創造研究センター (iTHEMS) 数理基礎部門 基礎科学特別研究員)

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.

会場: セミナー室 (359号室) 3階 359号室 / via Zoom

イベント公式言語: 英語

Explaining GRB features through MAD black hole spin-down

2026年11月6日(金) 14:00 - 15:00

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.

会場: 研究本館 2階　220号室 / via Zoom

イベント公式言語: 英語

Scaling regimes of the 1D Kuramoto-Sivashinsky equation

2026年11月5日(木) 17:00 - 18:30

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.

会場: via Zoom

イベント公式言語: 英語

Local Rules and Global Invariants in Vertebrate Organ Morphogenesis

2026年11月5日(木) 13:00 - 14:00

森下 喜弘 (理化学研究所 生命機能科学研究センター (BDR) 発生幾何研究チーム チームディレクター)

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.

会場: セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催 / via Zoom

イベント公式言語: 英語

Mathematical Application Research Team Meeting #20

2026年10月30日(金) 15:30 - 16:45

兒玉 悠弥 (鹿児島大学 大学院理工学研究科 助教)

Mathematical Application Research Team is delighted to welcome Prof. Kodama Yuya from Kagoshima University for an upcoming team meeting. We warmly invite everyone to join us to hear his talk. Title: Thompson's groups and knot theory Abstract: Thompson’s groups were introduced by Richard Thompson in the 1960s. They first appeared in mathematical logic, but they have since been studied in many other areas of mathematics. For example, they were rediscovered in homotopy theory, and some researchers have tried to use them in cryptography. In 2014, Vaughan Jones found an interesting connection between Thompson’s groups and knot theory. In this talk, I will first introduce Thompson’s groups and some of their connections with other areas. I will then explain the basic idea of Jones’s theory. If time permits, I will also mention my joint work with Takano of Osaka University.

会場: via Zoom / セミナー室 (359号室) 3階 359号室

イベント公式言語: 英語

Quantum Creation of the Universe: Reassessing the No-Boundary and Tunneling Proposals

2026年10月30日(金) 14:00 - 15:00

松井 宏樹 (大阪公立大学 数学研究所 特別研究員)

How was our Universe created? This is one of the most fundamental questions in cosmology. Quantum cosmology attempts to answer it by using a "wave function of the Universe," and for four decades the discussion has been dominated by two proposals: the no-boundary proposal of Hartle and Hawking, and the tunneling proposal of Vilenkin. The two predict very different initial states for our Universe, yet for a long time there was no common framework in which they could be exactly analyzed and compared. In this talk I will begin with a pedagogical introduction to the wave function of the Universe and to the Lorentzian path integral formulation based on Picard-Lefschetz theory, which makes the gravitational path integral well defined without the ambiguities of the traditional Euclidean approach and allows both proposals to be treated on the same footing. I will then present our recent results. Using Lefschetz-thimble analysis together with resurgence theory, we resolve the Stokes-line ambiguity that had obscured earlier analyses and show that the path integral uniquely yields the tunneling wave function rather than the no-boundary one. The no-boundary saddles nevertheless leave a trace: their contributions exactly cancel the Borel ambiguity of the perturbative quantum-gravity corrections around the tunneling saddle, demonstrating that resurgence is at work in quantum cosmology. I will also discuss quantum cosmology beyond four-dimensional general relativity, using two-dimensional Jackiw-Teitelboim gravity as an illustrative model.

会場: 研究本館 3階 359号室とZoomのハイブリッド開催 / via Zoom

イベント公式言語: 英語

Maximal Enhancements in Eight-Dimensional Non-Supersymmetric Heterotic Strings

2026年10月30日(金) 10:30 - 12:00

Yuefeng Liu (九州大学 高等研究院 学術研究員)

We classify maximally enhanced, rank-preserving non-supersymmetric heterotic strings in eight dimensions by studying orbifolds of supersymmetric heterotic strings on T^2.We first review the construction in nine dimensions, where it reproduces the 95 maximally semisimple enhancement points obtained from previous extended-Dynkin analyses. We then start from the maximally enhanced supersymmetric Narain points in eight dimensions and use Kac's theorem to enumerate candidate order-two inner actions, retaining only those that lift to consistent Narain-lattice shifts. This gives 1210 maximal enhancement points, of which 71 are tachyon-free, and 25 have neither tachyons nor shifted-sector massless scalars. For each entry we determine the gauge algebra and the low-lying scalar and fermion spectra, and for the tachyon-free cases we evaluate the one-loop cosmological constant. For the 25 subcases without shifted-sector massless scalars, we further compute the Hessian of the one-loop potential and test the refined de Sitter swampland conjecture.

会場: セミナー室 (359号室) (メイン会場) / via Zoom

イベント公式言語: 英語

Behaviorally Informed Institutional Design with Game Theory and LLMs

2026年10月29日(木) 14:30 - 15:30

森 隆太郎 (理化学研究所 脳神経科学研究センター (CBS) 計算論的集団力学連携ユニット 基礎科学特別研究員)

The event will start 30 minutes before initially announced. How can we design social institutions that account for how people actually make decisions? Behavioral research has revealed substantial heterogeneity in preferences and decision-making that traditional economic models often abstract away. Understanding these tendencies may open new possibilities for improving collective outcomes. In this talk, I present two projects addressing complementary aspects of this broader goal. First, I investigate how real-time interaction facilitates cooperation in a one-shot social dilemma, where purely self-interested behavior predicts only mutual defection. Experiments show that real-time interaction yields higher mutual cooperation, primarily through stronger reciprocity by followers. A game-theoretic model suggests that flexible decision timing helps people infer others' cooperative preferences from their actions and coordinate their responses. This illustrates how institutional tweaks can leverage existing cooperative tendencies. Second, I introduce Cross-Centaur, an LLM-based model of individual decision-making across diverse domains. We construct a dataset in which the same participants complete tasks spanning learning, decisions under risk and delay, reasoning, and social decision-making, and use it to fine-tune an LLM. The model uses behavior in one task to better predict the same individual's decisions in another, a step toward more flexible, generalizable models of decision-making. Together, these projects explore how understanding human decision-making may inform the design of better social institutions.

会場: セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催 / via Zoom

イベント公式言語: 英語

Towards the Geometric Beauty of Bonsai

2026年10月29日(木) 13:00 - 14:00

内海 忍 (理化学研究所 数理創造研究センター (iTHEMS) 数理展開部門 数理社会科学チーム 学振特別研究員PD)

I will present an overview of my ongoing and future research projects. Art has been a central element of human culture and society across regions and throughout history. However, the inherent subjectivity of aesthetic evaluation has long made it challenging to study art quantitatively and systematically within the mathematical sciences. My research tackles this challenge through bonsai—the art of recreating the grandeur of natural landscapes and majestic trees within a small pot. Often described as a “living art” and a “crystallization of Japanese aesthetics,” bonsai provides a unique opportunity to explore a fundamental question: How can we quantify something as seemingly subjective as beauty? The key methodology of this research involves the 3D digitization of actual bonsai using photogrammetry, followed by the extraction of their skeletal structures and their representation as 3D non-looped tree graphs. I then apply morphological and network analyses to investigate commonalities and differences in branching structures across bonsai of different styles and grades. Looking ahead, I will discuss future research directions, including how these analyses and mathematical models could be extended to quantitatively characterize traditional Japanese aesthetic principles (e.g., the beauty of subtraction and negative space), as well as what distinguishes the structures of artistically cultivated bonsai from those of naturally growing trees.

会場: セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催 / via Zoom

イベント公式言語: 英語

Exploring Noisy Quantum Thermodynamical Processes via the Depolarizing-Channel Approximation

2026年10月28日(水) 16:00 - 17:00

Jian Li (Ph.D. Student, Center for Theoretical Physics, Polish Academy of Sciences, Poland)

Noise and errors are unavoidable in any realistic quantum process, including processes designed to reduce noise and errors in the first place. In particular, quantum thermodynamical protocols for cooling can be significantly affected, potentially altering both their performance and efficiency. Analytically characterizing the impact of such errors becomes increasingly challenging as the system size grows, particularly in deep quantum circuits where noise can accumulate in complex ways. To address this, we introduce a general framework for approximating the cumulative effect of gate-dependent noise using a global depolarizing channel. We specify the regime in which this approximation provides a reliable description of the noisy dynamics. Applying our framework to the thermodynamical two-sort algorithmic cooling (TSAC) protocol, we analytically derive its asymptotic cooling limit in the presence of noise. Using the cooling limit, the optimal cooling performance is achieved by a finite number of qubits --- distinguished from the conventional noiseless TSAC protocol by an infinite number of qubits --- and fundamental bounds on the achievable ground-state population are derived. This approach opens new avenues for exploring noisy quantum thermodynamical processes.

会場: via Zoom

イベント公式言語: 英語

Born-Oppenheimer EFT: an unified description of ordinary and exotic quarkonia

2026年10月27日(火) 13:30 - 15:00

Nora Brambilla (Professor, TUM School of Natural Sciences, Technical University of Munich, Germany)

We show how the Born--Oppenheimer effective field theory (BOEFT) provides a unified description of ordinary and exotic quarkonia grounded on the non-relativistic expansions of QCD and supplemented with lattice QCD inputs. We show applications of the BOEFT to tetraquarks, pentaquarks, quarkonium hybrids and on threshold effects in the quarkonium spectrum. We present the insights that BOEFT delivers us on the mature of these XYZ exotics states.

会場: via Zoom

イベント公式言語: 英語

Birational rigidity of singular Fano threefolds

2026年10月23日(金) 14:00 - 16:00

張 繼剛 (理化学研究所 数理創造研究センター (iTHEMS) 数理基礎部門 基礎科学特別研究員)

Birationally rigid varieties form an important class of Fano varieties. A Fano variety is called birationally rigid if it is not birationally equivalent to any other Mori fibre space. Many well-known examples of birationally rigid smooth Fano threefolds have been known for a long time. However, the first example of a birationally rigid singular Fano threefold was found only recently by Krylov, Okada, Paemurru, and Park. Their example is a sextic double solid with only cA1 singularities. On the other hand, Paemurru proved that sextic double solids with cAn singularities are not birationally rigid when n is at least four. In our work, we generalized the method of Krylov, Okada, Paemurru, and Park to more general cDV singularities and found the first example of a birationally rigid Fano threefold with cD-type singularities. This is joint work with Jheng-Jie Chen and Takuzo Okada.

会場: via Zoom / 研究本館

イベント公式言語: 英語

An Origin Story for Money

2026年10月22日(木) 15:00 - 16:00

Stephen Marsland (Professor, Victoria University of Wellington, New Zealand)

In indirect reciprocity a reputation is used to enable donors to choose whether or not to provide costly help to potential recipients. Often this reputation is binary — good or bad — and is maintained by a third party who oversees all interactions. I will introduce extensions to this system that enables money to be viewed as a reputation and investigate how this helps us identify how systems of money may have first been invented.

会場: セミナー室 (359号室) (メイン会場) / via Zoom

イベント公式言語: 英語

Observability-based causal inference in linear stochastic systems with hidden inputs

2026年10月22日(木) 13:00 - 14:00

關澤 太樹 (理化学研究所 脳神経科学研究センター (CBS) 数理脳科学研究チーム 基礎科学特別研究員)

Causal inference from neural time series is confounded by correlations induced by hidden common inputs, a problem that is especially acute because the full set of variables shaping neural activity is rarely accessible. Prediction based measures such as Granger causality can therefore falsely attribute such dependencies to causal influence. Delay coordinate reconstruction, which is also closely connected to observability in control theory, provides a complementary route: in deterministic systems, downstream delays can reconstruct upstream causes, whereas the reverse does not generally hold. This asymmetry provides a signature of causal direction, as exploited by convergent cross mapping. In stochastic dynamics, however, dynamical and observation noise enter delay coordinates and prevent exact trajectory reconstruction. Here, we develop data driven criteria that extend this observability principle to partially observed stochastic systems. First, we show that observability can be tested by regression of time lagged covariance matrices, which removes direct noise contributions while preserving the observability relation. Second, we show that causal direction can be tested through inclusion of stochastic Koopman eigenvalues estimated from upstream and downstream delay coordinates, because downstream observations generically contain the dynamical components observable upstream. Numerical examples show that the proposed criteria recover causal direction and reject spurious dependencies induced by unobserved common inputs, including cases in which Granger causality and convergent cross mapping fail to distinguish common input from causal influence. Although motivated by neural recordings, the framework applies broadly to partially observed stochastic dynamical systems beyond neuroscience.

会場: 研究本館 3階 359号室とZoomのハイブリッド開催 / via Zoom

イベント公式言語: 英語

Data assimilation with the full covariance on a fault-tolerant quantum computer

2026年10月21日(水) 15:00 - 16:30

三好 建正 (理化学研究所 計算科学研究センター (R-CCS) データ同化研究チーム チームプリンシパル)

Data assimilation (DA) is the core of numerical weather prediction, estimating an accurate state of the weather model by combining forecast and observations. DA provides a general approach and is being applied to various problems beyond weather. The state estimation is a linear solve where the background error covariance B is essential. Since B is an N × N matrix with N ~ 10^8 to 10^9 for the weather model, the full B has never been used. For decades the community has approximated B by parameterized covariance models or by low-rank ensembles with localization and thereby discards genuine structures that we know exist from large-ensemble experiments. Fault-tolerant quantum computing (FTQC) could remove this constraint, since quantum linear system solvers scale polylogarithmically in N. However, the DA equations cannot be applied naively: the observation-space form squares the block-encoding normalization factor for observations with wide footprints, and the state-space form contains B^{-1}, whose condition number ~10^8. This talk presents a combined state-observation formulation that avoids both difficulties: it contains no B^{-1}, and its condition number is governed by the observation error covariance R rather than by B. Numerical experiments with the Lorenz-96 model reproduce the exact solution with the full B and outperform localized ensemble Kalman filters. The formulation assumes that B and the observation operator are provided as block-encoded oracles, and how to construct such oracles without ever storing the matrices is the open problem. A first concrete target is an end-to-end demonstration with Lorenz-96 on a quantum simulator with only seven data qubits, which I would like to discuss with the iTHEMS community.

会場: セミナー室 (359号室) (メイン会場) / via Zoom

イベント公式言語: 英語

Bubble wall dynamics from non-equilibrium quantum field theory

2026年10月21日(水) 13:30 - 15:00

Matthias Carosi (Postdoctoral Researcher, International Centre for Theoretical Physics Asia-Pacific (ICTP-AP), University of Chinese Academy of Sciences, China)

First-order phase transitions in the early universe are a unique probe of physics beyond the Standard Model, with potential implications for electroweak baryogenesis, the formation of primordial black holes, magnetogenesis and the production of dark matter. Upcoming gravitational wave detectors may capture the imprint of such transitions, but to extract theoretical insights from these signals requires a precise understanding of the underlying dynamics. In this talk, I show how the language of non-equilibrium quantum field theory, combined with the two-particle-irreducible effective action, provides a natural framework for describing the dynamics of a bubble after nucleation. After a brief introduction to the closed-time-path formalism, I derive the dynamical equations governing the bubble and the plasma and identify all sources of friction for the bubble expansion. This framework unifies the pre-existing approaches within a single, consistent description. In the ultrarelativistic regime, I demonstrate how to compute the friction induced by the pair production of heavy scalar particles.

会場: セミナー室 (359号室) 3階 359号室とZoomのハイブリッド開催 / via Zoom

イベント公式言語: 英語

Quantum Simulations of Entanglement in Jet Production and Structure Functions at the EIC

2026年10月20日(火) 15:30 - 17:00

Dima Kharzeev (Professor, Department of Physics, University of Connecticut, USA)

The Electron–Ion Collider (EIC) offers an opportunity to explore the quantum structure of hadronic matter and the role of entanglement in high-energy scattering. I will present our results on quantum simulations of entanglement in jet production and structure functions, highlighting how quantum computing can help investigate correlations in partonic dynamics. I will discuss the physical insights emerging from these simulations and their implications for connecting quantum information concepts with observables at the EIC.

会場: セミナー室 (359号室) (メイン会場) / via Zoom

イベント公式言語: 英語

Mini-Workshop: Quantum Frontiers — From Molecules to Quarks and the EIC

2026年10月20日(火) 9:45 - 17:00

== Mini-workshop Program == 9:45 - 10:15 Erik Loetstedt (RIKEN) Rovibrational energy levels of molecules by quantum computing 10:15 - 10:45 Ryusuke Hamazaki (RIKEN) Quantum many-body Mpemba effect through resonances 10:45 - 11:15 Yang-yang Tan (U. Tokyo) Generative Modeling of Stochastic Dynamics for Long-Time Evolution 11:15 - 11:45 Yan Lyu (RIKEN) Charmonia scattering from lattice QCD 11:45 - 13:00 Lunch 13:00 - 13:30 Arata Yamamoto (RIKEN) Quantum anomaly for benchmarking quantum computing 13:30 - 14:00 Tianyin Li (RIKEN) Efficient Quantum Simulations of Yang-Mills theory with Maximal-tree Gauge 14:00 - 14:30 Yahui Chai (RIKEN) Probing Resonances through Real-Time Particle Scattering 14:30 - 15:00 Ermal Rrapaj (LBL) Quantum Simulations of Two-Dimensional Non-Abelian Adjoint String Breaking 15:00 - 15:30 Coffee Break 15:30 - 17:00 Dima Kharzeev (U. Connecticut) Quantum Simulations of Entanglement in Jet Production and Structure Functions at the EIC

会場: セミナー室 (359号室) (メイン会場) / via Zoom

イベント公式言語: 英語