Seminar

Dynamic Scaling Analysis for Enzymatic Degradation and Network Growth of DNA Liquid Droplets

August 14 (Thu) 13:00 - 14:00, 2025

Michio Tateno (JSPS Overseas Research Fellow, Material Research Laboratory, University of California Santa Barbara, USA)

In this talk, I will introduce two novel pattern formation dynamics exhibited by phase-separated liquid droplets composed of DNA nanoparticles: 1) By enzymatically inactivating the phase-separation ability of the nanoparticles, we observed the process by which droplets gradually disappeared. Notably, the droplet-size distribution density remained unchanged, while only the total number of droplets decreased over time. 2) We also observed the formation of a novel two-dimensional wire-like network pattern, in which two types of droplets are arranged in a one-dimensional, alternating manner. We confirmed that the characteristic size of the network follows power-law growth over nearly two decades, with a universal growth exponent that is independent of droplet viscosity and inter-droplet wetting affinity. We analyze these results within the framework of the dynamic scaling hypothesis and discuss the physical mechanisms underlying these behaviors.

Event Official Language: English

Extended Kalman filter: Lecture 2

August 13 (Wed) 13:00 - 14:00, 2025

Venue: R511, Computational Science Research Building (Main Venue) / via Zoom

Event Official Language: English

Cosmological Collider with Boundary Interactions

August 7 (Thu) 16:00 - 17:30, 2025

Yi Wang (Professor, Department of Physics, Hong Kong University of Science and Technology, Hong Kong)

We first review cosmological collider physics. Namely, how the mass, spin, width and parity of the primordial particles during inflation may be read off from the density correlations in the CMB and the Large Scale Structure of the universe, and how this can be related to particle physics such as the Standard Model. After that, we will introduce relations between bulk and boundary terms in cosmological collider physics, and highlight a class of interactions which were overlooked in the literature.

Venue: via Zoom

Event Official Language: English

iTHEMS Biology welcomes another new member!

August 7 (Thu) 13:00 - 14:15, 2025

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

This meeting will be used to welcome another new members to the iTHEMS Biology Study Group: Dr. Sungsik Kong, who is joining iTHEMS Fundamental Division as a Research Scientist. He will give us a 15-20 min talk to introduce his research. If time permits, let's also use this time to catch up on each other's current research. I hope that many people will join us to welcome this new member and come meet him and hear about his research.

Venue: Changed to Zoom only

Event Official Language: English

DA Seminar: Prof. Dai Yamazaki and Hannah Cloke

August 6 (Wed) 15:00 - 16:30, 2025

Dai Yamazaki (Associate Professor, Institute of Industrial Science, The University of Tokyo)
Hannah Cloke (Professor, Department of Meteorology, University of Reading, UK)

The seminar will be jointly given by Associate Professor Dai Yamazaki (The university of Tokyo) and Professor Hannah Cloke (University of Reading). Speaker 1: Associate Professor Dai Yamazaki (Institute of Industrial Science, The University of Tokyo) Title: How can we achieve fast and realistic simulation of river and flood dynamics on the global scale? Abstract: Modeling river hydrodynamics across continental-scale basins is challenging due to their inherently multiscale nature. On one hand, we must account for the water budget along river systems that extend over 1,000 km. On the other hand, water movement within channels and floodplains is governed by topographic features smaller than 100 meters. The global river model CaMa-Flood addresses this complexity by employing the Catchment-based Macro-scale Floodplain modeling approach (CMF approach). This method approximates the relationship between water volume, flood extent, and water depth through sub-grid scale parameterizations. These parameters, derived from high-resolution satellite-based digital elevation models (DEMs) and hydrography datasets, enable realistic simulation of river discharge and flood stages—without explicitly resolving small-scale floodplain dynamics. To further accelerate simulations, recent developments in CaMa-Flood have introduced several performance optimizations, including MPI/OpenMP parallelization, SIMD vectorization, sparse matrix implementation, and a GPU-enabled Python version. These enhancements make the model more suitable for large-scale and near-real-time applications such as global flood monitoring and climate impact assessment. Speaker 2: Professor Hannah Cloke (Department of Meteorology, University of Reading) Title: Preparing for floods in an uncertain future

Venue: Hybrid Format (RIKEN R-CCS room 107 and Zoom) (Main Venue) / via Zoom

Event Official Language: English

Coupling AI and SMC-based algorithms: Inference of population structure from single genome sequencing analysis

August 6 (Wed) 14:00 - 15:00, 2025

Alba Nieto Heredia (Ph.D. Student, L'Institut de Systématique, Évolution, Biodiversité, France)

The unprecedented availability of whole genome sequences has transformed population genetics, allowing researchers to reconstruct past demographic histories with greater resolution. Among the most widely used approaches for this purpose are methods grounded in the Sequentially Markovian Coalescent (SMC) framework, which leverage patterns of coalescence with recombination to infer fluctuations in effective population size over time. These fluctuations inform about past population trends, especially for endangered populations and extinct species. However, despite their success, these methods often rest on simplifying assumptions. Most notably, random mating among all the individuals in a population (panmixia) assumption can lead to biased or misleading inferences when applied to populations with underlying genetic and/or geographical structure. For instance, changes in ancestral population size and population structure can lead to confounding signals in the historical coalescent rate, which presents an non identifiability problem, resulting in misleading interpretations that primarily affect the analysis in species of conservation interest. After revising and detecting as systematic bias in SMC-based algorithms associated to population structure, we investigate the power of emerging summary statistics derived from whole genome data, proposing a novel deep learning framework that integrates the latent information contained in SMC transition matrices to distinguish between signals of population structure and true demographic change. By transforming these matrices into image-like representations, we develop a method based on deep convolutional neural networks (CNNs) in combination with perceptrons to classify demographic histories and predict key parameters of structured models, applying strategies of transfer learning. This approach enables discrimination between structured and panmictic populations and further infers specific features of the underlying demographic model. By blending the strengths of the modelling of coalescence with recombination of SMC-based approaches, deep learning, and coalescent simulations, this methodology offers a new avenue for scalable demographic inference considering structured populations.

Venue: via Zoom / Seminar Room #359

Event Official Language: English

iTHEMS Cosmology Forum #4 - Evolving Cosmos: new physical insights from new spectroscopic data

August 4 (Mon) - 5 (Tue) 2025

Seshadri Nadathur (Associate Professor, University of Portsmouth, UK)
Andrei Cuceu (NASA Einstein Fellow, Lawrence Berkeley National Laboratory (LBNL), USA)
Gerrit Farren (Postdoc, Lawrence Berkeley National Laboratory (LBNL), USA)
Antonio De Felice (Associate Professor, Yukawa Institute for Theoretical Physics, Kyoto University)
Linda Blot (Project Assistant Professor, Kavli Institute for the Physics and Mathematics of the Universe (Kavli IPMU), The University of Tokyo)
Wen Yin (Associate Professor, Department of Physics, Graduate School of Science, Tokyo Metropolitan University)

iTHEMS Cosmology Forum Workshop is a series of short workshops, each focusing on an emerging topics in cosmology. The target audience is cosmologists, high-energy physicists and astronomers interested in learning about the subject, not just those who have already worked on the topic. The goal of the workshop is to provide working knowledge of the topic and leave dedicated time for discussions to encourage mutual interactions among participants. The fourth workshop is dedicated to new physics discoveries enabled by new spectroscopic data. Nearly three decades after the discovery of accelerated expansion, there is at last compelling data pointing away from the simple cosmological constant. The results of new data hint at evolving dark energy, but the statistical significance and physical interpretation are both far from clear. Furthermore, another anticipated new physics measurement of the neutrino mass has also proven difficult. With this workshop, we aim to interrogate both the statistical evidence for new physics as well as the theoretical implications if these new results are confirmed. This forum will consist of two days. The workshop will be in English. The workshops are organised by the iTHEMS Cosmology Forum working group, which is the successor of the Dark Matter Working Group at RIKEN iTHEMS. Important dates: July 18 - Registration deadline August 4th, 5th - Workshop Days Invited Speakers: Sesh Nadathur (University of Portsmouth) Andrei Cuceu (LBNL) Gerrit Farren (LBNL) Antonio De Felice (YITP) Linda Blot (IPMU) Wen Yin (TMU)

Venue: #435-437, 4F, Main Research Building

Event Official Language: English

LeanConjecturer: Automatic Generation of Mathematical Conjectures for Theorem Proving

August 1 (Fri) 16:00 - 18:00, 2025

Naoto Onda (Project Research Engineer, Research Administrative Division, Omron Sinic X Corporation)

We introduce LeanConjecturer, a pipeline for automatically generating university-level mathematical conjectures in Lean 4 using Large Language Models (LLMs). Our hybrid approach combines rule-based context extraction with LLM-based theorem statement generation, addressing the data scarcity challenge in formal theorem proving. Through iterative generation and evaluation, LeanConjecturer produced 12,289 conjectures from 40 Mathlib seed files, with 3,776 identified as syntactically valid and non-trivial, that is, cannot be proven by aesop tactic. We demonstrate the utility of these generated conjectures for reinforcement learning through Group Relative Policy Optimization (GRPO), showing that targeted training on domain-specific conjectures can enhance theorem proving capabilities. Our approach generates 103.25 novel conjectures per seed file on average, providing a scalable solution for creating training data for theorem proving systems. Our system successfully verified several non-trivial theorems in topology, including properties of semi-open, alpha-open, and pre-open sets, demonstrating its potential for mathematical discovery beyond simple variations of existing results.

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

Event Official Language: English

Targeting SARS-CoV-2 RNA: Insights for RNA-Directed Drug Discovery

July 31 (Thu) 13:00 - 14:30, 2025

Mariia Ivonina (Postdoctoral Fellow, Platform for Inter/Transdisciplinary Energy Research (Q-PIT), Kyushu University)

Traditional pharmacology fights virus infections by targeting proteins including enzymes, receptors, and structural proteins to break up the viral machinery. Nucleic acid-targeting therapies, on the other hand, can act directly on the genetic code of viruses, blocking their replication or translation in host cells. Coronaviruses and HIV are examples of RNA viruses that use a process called -1 programmed ribosomal frameshifting (-1 PRF) to produce their viral proteins. In this process, the translating ribosome is forced to shift into the alternative reading frame, replicating mRNA in the wrong order. Using small-molecule compounds to block this mechanism could be a promising way to neutralize such viruses. It is difficult to experimentally study the interactions between RNA and a drug candidate to understand where the drug binds and how it changes the shape of the viral RNA. I will discuss how Molecular Dynamics simulations are used to explore the conformational dynamics of mRNA structural elements and to investigate what happens when an antiviral agent binds to it. Additionally, I will show how the quantum-chemical orbital interaction analysis we developed, called Through-Space/Through-Bond Energy Decomposition Analysis (TS/TB-EDA), reveals which RNA nucleotides, at the atomic level, are critical for binding. This molecular modelling approach reveals strategies for targeting structured RNA elements — a crucial step toward expanding the arsenal of RNA-targeting therapeutics for future pandemics.

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

Event Official Language: English

Bridging applied math and quantum many-body physics and beyond via tensor methods

July 23 (Wed) 16:00 - 17:00, 2025

Hiroshi Shinaoka (Associate Professor, Department of Physics, Saitama University)

In modern physics, high-dimensional functions and operators naturally arise in a wide range of contexts, including turbulence simulations, parameter-dependent partial differential equations (PDEs), and quantum field theory. Efficient representations and computations with such high-dimensional objects pose major challenges across disciplines. Dimensionality reduction techniques such as the Quantics Tensor Train (QTT) [1] and Tensor Cross Interpolation (TCI) [2] were originally developed in applied mathematics. In our work, we have extended these methods to quantum many-body problems, demonstrating their effectiveness in handling complex high-dimensional structures in theoretical physics [3–10]. Given their generality, QTT and TCI are expected to find applications beyond quantum theory itself, in fields such as statistical field theory, model reduction, and control of complex systems, where similar high-dimensional structures emerge. This presentation will first review the computational bottlenecks that arise in quantum many-body simulations and other high-dimensional problems. Then, we will introduce QTT and TCI from a broader, method-oriented perspective, aiming to bridge applied mathematics and quantum theoretical physics.

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

Event Official Language: English

Supersymmetric field theories and homotopy theory

July 23 (Wed) 13:00 - 14:30, 2025

Mayuko Yamashita (Junior Research Faculty member, Perimeter Institute for Theoretical Physics, Canada)

I will give a general introduction and overview on the Segal-Stolz-Teichner program, which tries to relate supersymmetric field theories in physics with homotopy theory in mathematics.

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

Event Official Language: English

Mesoscopic transport via one-dimensional chain with Localized two-body loss

July 23 (Wed) 10:00 - 11:30, 2025

Kensuke Kakimoto (Ph.D. Student, Faculty of Science and Engineering, School of Fundamental Science and Engineering, Waseda University)

Mesoscopic transport has long served as a powerful probe into the quantum behavior of matter; however, the role of dissipation in such systems remains unresolved. In recent years, quantum simulations of mesoscopic systems with ultracold atomic gases have made significant progress, particularly through the use of optical tweezers to induce local dissipation via atom loss. In this talk, we discuss a two-terminal mesoscopic system in which two-body loss occurs locally at the center of a one-dimensional chain, modeling a dissipative quantum point contact. To analyze this setup, we employ the Keldysh Green’s function formalism in combination with a noise-field representation of Lindblad dynamics. Our analysis reveals that the dissipation strength depends on the occupation number of the central dissipative site, leading to a weaker suppression of particle current in the weakly dissipative regime compared to the case of one-body loss.

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

Event Official Language: English

A free probability approach to quantum chaos in random matrix ensembles

July 22 (Tue) 16:00 - 17:00, 2025

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

In free probability theory, quantum chaos is marked by “free independence” between observables at early and late times, causing certain statistical measures (cumulants) to vanish. Motivated by this, we study the statistics of a time-evolved operator in the Rosenzweig-Porter (RP) random matrix ensembles. Analyzing operator statistics for different spin operators across these regimes reveals close alignment with free probability predictions in the ergodic phase, contrasted by persistent deviations in the fractal and localized phases even at late times. Using the distance measures and statistical methods, we define and characterize the onset of the free time in the ergodic phase. The talk is based on arXiv: 2506.04520.

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

Event Official Language: English

Detectability of post-Newtonian classical and quantum gravity via quantum clock interferometry

July 22 (Tue) 14:00 - 15:00, 2025

Eyuri Wakakuwa (Associate Professor, Department of Mathematical Informatics, Graduate School of Informatics, Nagoya University)

Understanding physical phenomena at the intersection of quantum mechanics and general relativity remains a major challenge in modern physics. While various experimental approaches have been proposed to probe quantum systems in curved spacetime, most focus on the Newtonian regime, leaving post-Newtonian effects such as frame dragging largely unexplored. In this study, we propose and theoretically analyze an experimental scheme to investigate how post-Newtonian gravity affects quantum systems. We consider two setups: (i) a quantum clock interferometry configuration designed to detect the gravitational field of a rotating mass, and (ii) a scheme exploring whether such effects could mediate entanglement between quantum systems. Due to the symmetry of the configuration, the proposed setup is insensitive to Newtonian gravitational contributions but remains sensitive to the frame-dragging effect. Assuming the validity of the quantum equivalence principle, this approach may provide insights not only into the quantum nature of gravity but also into whether spacetime itself exhibits quantum properties. However, our analysis reveals that, within realistic experimental parameters, the expected effects are too small to be detected. We discuss possible interpretations of this undetectability, and its implications for tests of quantum gravity.

Venue: #445--447, 4F, Main Research Building (Main Venue) / via Zoom

Event Official Language: English

ComSHeL collaboration planning

July 22 (Tue) 14:00 - 15:00, 2025

The objective of this 3rd monthly meeting of the ComSHeL Study Group is to discuss specific collaborations we could undertake across our own Teams/Divisions on projects of common interest to take advantage of our complementary skills and expertise. We also want to consider how ComSHeL could help respond to specific calls for focus in certain research areas within RIKEN and the broader funding landscape.

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

Event Official Language: English

Peaks sphericity of non-Gaussian random fields

July 22 (Tue) 10:30 - 12:00, 2025

Michiru Uwabo (Ph.D. Student / JSPS Research Fellow DC, Faculty of Science, Ochanomizu University)

We formulate the statistics of peaks of non-Gaussian random fields and implement it to study the sphericity of peaks. For non-Gaussianity of the local type, we present a general formalism valid regardless of how large the deviation from Gaussian statistics is. For general types of non-Gaussianity, we provide a framework that applies to any system with a given power spectrum and the corresponding bispectrum in the regime in which contributions from higher-order correlators can be neglected. We present an explicit expression for the most probable values of the sphericity parameters, including the effect of non-Gaussianity on the profile. We show that the effects of small perturbative non-Gaussianity on the sphericity parameters are negligible, as they are even smaller than the subleading Gaussian corrections. In contrast, we find that large non-Gaussianity can significantly distort the peak configurations, making them much less spherical.

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

Event Official Language: English

Thermal evolution of accreting neutron stars

July 20 (Sun) 16:00 - 17:30, 2025

Martin Javier Nava-Callejas (Postdoc, Université Libre de Bruxelles, Belgium)

Neutron stars undergoing mass accretion at low-mass X-ray binary systems (LMXBs) represent an outstanding opportunity to test our current models for nuclear matter and its properties, in particular those related to thermonuclear reactions at the surface, as well as the evolution of their ashes via weak reactions. While some aspects are relatively well understood, there are others which call out for further attention or a re-examination of what we so far know. In this talk I will discuss the current state-of-art regarding the modelling of thermal evolution of these objects and will introduce a new method aimed to simplify the calculation of thermal evolution during accreting episodes.

Venue: via Zoom

Event Official Language: English

Gravity is Different - Counterexamples to the Wilsonian Paradigm of Low Effective Theory

July 18 (Fri) 14:00 - 15:30, 2025

Hirosi Ooguri (Fred Kavli Professor and Director, Walter Burke Institute for Theoretical Physics, California Institute of Technology, USA)

As the 7th meeting of the Mathematical Application Research Team, we invite Prof. Hirosi Ooguri to give a lecture.

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

Event Official Language: English

Modeling form growth in curved spaces using Riemannian L-systems

July 17 (Thu) 16:00 - 17:30, 2025

Christophe Godin (Research Derector, Inria, Univ Lyon, France)

In the past 50 years, the formalism of L-systems has been successfully used and developed to model the growth of filamentous and branching biological forms. These simulations take place in classical 2-D or 3-D Euclidean spaces. However, various biological forms actually grow in curved, non-Euclidean, spaces. This is for example the case of vein networks growing within curved leaf blades, of unicellular filaments, such as pollen tubes, growing on curved surfaces to fertilize distant ovules, of teeth patterns growing on folded epithelia of animals, of diffusion of chemical or mechanical signals at the surface of plant or animal tissues, etc. In this talk, I will describe how we extended the formalism of L-systems to model the growth of branching structures in curved spaces. We will discuss how the space may feedback on the growing form and contribute to shape. I will also look at examples, where the space in which the form is growing is not necessarily a surface embedded in the euclidean 3-dimensional space, but is rather a space intrinsically curved, i.e. curved but not embedded in any higher-dimensional space. The possibility to use these more abstract Riemannian spaces potentially opens new avenues for formalizing rules driving the morphogenesis of living forms.

Venue: via Zoom / SUURI-COOL (Kyushu)

Event Official Language: English

Self-organization mechanism of adaptive colony size sensing in ants

July 17 (Thu) 13:00 - 14:00, 2025

Kazuki Tsuji (Professor, Department of Environmental Sciences and Technology, University of the Ryukyus)

Social insects such as ants and termites are superorganisms, and traits of a colony change in a manner similar to the growth of an individual. The most common pattern is that reproductive castes are produced only when the colony size exceeds a certain threshold, which is well known to be adaptive. This means that social insects can “sense” their own colony size. However, how they achieve this even without visual information in a dark environment was yet largely unknown. We empirically tested the self-organization hypothesis on the proximate mechanism using ant colonies. In Diacamma colonies the monogynous queen is known to increase the effort devoted to queen pheromone–transmission behaviour (patrolling) as the colony grows, as if she perceives colony size. The negative feedback hypothesis assumes that through repeated physical contacts with workers the queen monitors the physiological state (fertility) of workers and increases her patrolling effort when she encounters more fertile workers. Supporting this hypothesis, we found that queens increased patrol effort in response to a higher ratio of fertile workers under the experimental condition of constant colony size. Furthermore, supplementary experiments suggested that cuticular hydrocarbons can mediate the observed queen–worker communication of fertility state. However, when the colony size exceeds a certain value, information transmission fails, resulting in the production of the next generation of reproductive caste. Such a self-organising mechanism of sensing colony size may also operate in other social insects living in small colonies.

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

Event Official Language: English