Bacterial ecospecies and ecoclines

December 5 (Thu) at 16:00 - 17:00, 2024

Daniel Falush (Professor, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, China)

All bacteria reproduce clonally but some species exchange DNA frequently enough that they have well mixed geographic gene pools, similar to those found in outbreeding animals and plants. Using data from multiple species we show that these “recombinogenic” bacteria also have genome-wide genetic structures generated by natural selection, including discrete “ecospecies” and continuous “ecoclines”. These structures reflect evolutionary strategies employed within natural populations, which can be dissected using the powerful techniques of molecular microbiology, providing a unique new view into the private lives of bacteria.

Venue: via Zoom / Seminar Room #359

Event Official Language: English

Deep Learning for Non-Perturbative Quantum Chromodynamics

December 4 (Wed) at 15:00 - 16:30, 2024

Fu-Peng Li (PhD Candidate, Key Laboratory of Quark and Lepton Physics (MOE) and Institute of Particle Physics, Central China Normal University, China)

Machine learning, particularly deep learning, is revolutionizing research across diverse disciplines, including physics. In this seminar, we explore the application of deep learning techniques to tackle challenges in non-perturbative Quantum Chromodynamics (QCD), one of the most complex areas in fundmental physics. I will present our preliminary explorations in this interdisciplinary field, focusing on: (i) identifying the equations of state for nuclear matter, (ii) developing a neural network-based quasi-particle model for QCD equations of state, (iii) extracting parton fragmentation functions, and (iv) determining heavy quark interaction potentials. Fu-Peng Li s a Ph.D. candidate in Theoretical Physics at Central China Normal University(CCNU) with an expected graduation in June 2025. His research interests lie at the intersection of nuclear physics and machine learning, with a focus on auto-differentiation, physics-informed neural networks (PINNs) for inverse problems, and the application of machine learning to non-perturbative Quantum Chromodynamics (QCD).

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

Event Official Language: English

High Energy Physics in the Quantum Era

December 2 (Mon) - 4 (Wed), 2024

This workshop is co-hosted by KEK Theory Center and RIKEN iTHEMS to inaugurate their new partnership in theoretical studies of high energy physics and related subjects with special emphasis on development and application of quantum technologies. The workshop aims for developing new connection between particle physics and quantum information/technologies. In the situation where significant progress is expected in the field of quantum information and technologies, it is quite important to discuss how such progress can be used in physics researches. Also, new techniques or new theoretical formulations of quantum field theory/quantum gravity may give deeper understanding of our quantum world. In this workshop, we would like to have world-leading researchers both from particle physics and quantum technologies, and drive lively discussions on future prospects. We are trying to limit the number of talks to be as minimal as possible, so that we have plenty of time for discussions. The workshop is in-person only.

Venue: Kobayashi Hall, KEK Tsukuba Campus

Event Official Language: English

Global Thermodynamics for Heat Conduction Systems

December 2 (Mon) at 14:00 - 15:30, 2024

Naoko Nakagawa (Professor, Ibaraki University)

Non-equilibrium phenomena are typically addressed through continuum descriptions based on local equilibrium and linear response theory, such as hydrodynamics. While effective, these approaches often overlook global characteristics. We propose Global Thermodynamics as a minimal-variable framework to describe weak non-equilibrium systems, focusing on two-phase coexistence under weak heat flux. By introducing a unique global temperature and extending entropy to non-equilibrium systems with a non-additive term, the framework predicts phenomena like metastable state stabilization—beyond the scope of traditional heat conduction equations. This talk will outline the framework, its key predictions, and validation efforts through numerical simulations and experiments. (This is a joint seminar with Informatin Theory Study Group.)

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

Event Official Language: English

White dwarf binary stars as physics laboratories

November 29 (Fri) at 14:00 - 15:15, 2024

Lucy McNeill (Postdoctoral Researcher, iTHEMS)

White dwarfs are the most common remnant of stellar evolution, and most often orbit a binary companion. Orbital decay from gravitational radiation and binary stellar evolution can proceed to mass transfer onto the white dwarf, which may result in a Type Ia supernova. While these reliable thermonuclear explosions are essential tools for observational cosmology, the nature of the progenitor binary (double white dwarf, or white dwarf + evolved star) is still not clear. Surprisingly, recent galaxy surveys revealed that most Type Ia supernova come from exploding white dwarfs below the Chandrasekhar limit of 1.4 solar mass. Plus, observations of Milky Way white dwarf binaries suggest unexpectedly hot temperatures in double white dwarf merger progenitors. I will summarise our recent developments on the stellar structure and orbital evolution of finite temperature, partially degenerate white dwarfs in binary systems. Tidal heating can explain how candidate white dwarf merger progenitors are generically hot, which places more restrictive conditions required for a double white dwarf merger.

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

Event Official Language: English

asymptotics in astrophysics SG session 4: helioseismology

November 29 (Fri) at 10:30 - 12:00, 2024

Ryota Shimada (Ph.D. Student, Department of Astronomy, Graduate School of Science, Kyoto University)

Constraining the distribution of internal magnetic fields through observations is considered to advance solar dynamo models aimed at understanding the 11-year cycle of solar magnetic activity. This paper [1] is on the frequency shift of standing acoustic waves inside the Sun caused by internal magnetic fields. Quasi-degenerate perturbation theory is applied to treat perturbation by magnetic fields. I’d like to discuss their methods and application in the session.

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

Event Official Language: English

Analysing and Visualising Single Cell Omits Data

November 28 (Thu) at 15:30 - 16:30, 2024

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

Single cell multimodal omics data are characterized by sparsity, noise, and high dimension. Incorporating information across modalities is challenging. We developed a non-negative matrix factorization based algorithm to identify latent factors that can facilitate improved cell-type clustering and visualizations for multimodal single cell omics count data. We then extend this algorithm to larger datasets and for different distributions of data in different modalities.

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

Event Official Language: English

Crop domestication

November 25 (Mon) at 15:00 - 17:00, 2024

Cheng-Ruei Lee (Professor, Institute of Ecology and Evolutionary Biology, National Taiwan University, Taiwan)
Jeffrey Fawcett (Senior Research Scientist, iTHEMS)

This is a joint seminar hosted by the Mathematical Biology lab of Kyushu University where Jeffrey Fawcett (iTHEMS) and Cheng-Ruei Lee (National Taiwan University) will give talks about plant domestication. Both talks will be aimed at students and will include some basic introduction of the topic. The seminar will be held on-site at Kyushu University and also by zoom so please free to register and join. Program: Title: Domestication and dispersal process of common buckwheat Speaker: Dr. Jeffrey Fawcett (RIKEN iTHEMS) Abstract: Crop domestication has not only been an ideal model to study how selection drives evolution, it is also tightly linked to past human activity and contains useful information that can improve plant breeding. Common buckwheat (Fagopyrum esculentum), which is used to make “soba” noodles in Japan, was domesticated from a wild progenitor species distributed in Southwest China. We have been using whole-genome sequences of several hundred cultivated accessions from around the world and some wild progenitor accessions to study its process of domestication and subsequent dispersal throughout Eurasia including Japan. In this talk, I will first provide an overview of the domestication and dispersal process of common buckwheat based on archaeological findings. I will then discuss the domestication and dispersal process and adaptive evolution of common buckwheat based on results of our population genetic analyses [1]. Title: The domestication and expansion history of mung bean and adzuki bean: evidence from population genomics Speaker: Prof. Cheng-Ruei Lee (National Taiwan University) Abstract: Who domesticated the crops we eat? When and where? What happened after domestication? How did crops spread across the world? These are the questions that have fascinated archaeologists for a long time. Using modern genomics techniques, we aim to answer these questions from a different angle. In mung bean (Vigna radiata), we uncovered a unique route of post-domestication range expansion. This route cannot be explained simply by human activities alone; instead, it is highly associated with the natural climates across Asia. We showed how the trans-continental climatic variability affected the range expansion of a crop and further influenced local agricultural practices and the agronomic properties of mung bean varieties. In adzuki (Vigna angularis), we obtained solid evidence of its domestication in Japan, most likely by the Jomons. We identified and validated the causal mutations for the seed coat color change during domestication. Contrary to the common belief that important yield-ensuring phenotypes (e.g., loss of pod shattering) should be selected early during domestication, we revealed a unique order of domestication trait evolution that cannot be observed from archaeological records directly [2]. Please register via the form by November 22nd (Fri.). We will share the Zoom link with online participants on the morning of the event day.

Venue: W1-C-909, Ito Campus, Kyushu University /

Event Official Language: English

The 27th MACS Colloquium

November 25 (Mon) at 14:45 - 18:00, 2024

Ryusuke Hamazaki (RIKEN Hakubi Team Leader, Nonequilibrium Quantum Statistical Mechanics RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research (CPR))
Teruaki Enoto (Associate Professor, Department of Physics, Division of Physics and Astronomy, Graduate School of Science, Kyoto University)

14:45-15:00 Teatime discussion 15:00-16:00 Talk by Dr. Ryusuke Hamazaki (RIKEN Hakubi Team Leader, Nonequilibrium Quantum Statistical Mechanics RIKEN Hakubi Research Team) 16:15-17:15 Talk by Dr. Teruaki Enoto (Associate Professor, Department of Physics, Division of Physics and Astronomy, Graduate School of Science, Kyoto University) 17:15-18:00 Discussion

Venue: Maskawa Hall, 1F, Maskawa Building for Education and Research

Event Official Language: Japanese

Solving inverse problem via latent variable optimization of diffusion models: An application to CT reconstruction

November 25 (Mon) at 14:00 - 15:00, 2024

Sho Ozaki (Assistant Professor, Graduate School of Science and Technology, Hirosaki University)

Inverse problems are widely studied in various scientific fields, including mathematics, physics, and medical imaging (such as CT and MRI reconstructions). In this talk, I will present a novel method for solving inverse problems using the diffusion model, with an application to CT reconstruction. The diffusion model, which is a core component of recent image-generative AI, such as Stable Diffusion and DALL-E3, is capable of producing high-quality images with rich diversity. The imaging process in CT (i.e., CT reconstruction) is mathematically an inverse problem. When the radiation dose is reduced to minimize a patient's exposure, image quality deteriorates due to information loss, making the CT reconstruction problem highly ill-posed. In the proposed method, the diffusion model, trained with a large dataset of high-quality images, serves as a regularization technique to address the ill-posedness. Consequently, the proposed method reconstructs high-quality images from sparse (low-dose) CT data while preserving the patient's anatomical structures. We also compare the performance of the proposed method with those of other existing methods, and find that the proposed method outperforms the existing methods in terms of quantitative indices.

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

Event Official Language: English

Theoretical analysis of High-dose/Refuge strategy for durability of pest control

November 21 (Thu) at 16:00 - 17:00, 2024

Sayaki Suzuki (Postdoctoral Researcher, Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies)

When using chemicals to control pathogens or pests, a problem that always arises is that parasites develop resistance to the chemicals. In many cases, the amount of chemical used must be reduced for using the chemicals sustainably. However, if certain conditions are met, a method is known that can suppress the development of resistance in diploid organisms such as pest insects. This is the high-dose/refuge strategy (HD/R) proposed by Comins (1977). This unique method combines high doses of pesticide spraying with ‘Refuge’ that are completely pesticide-free, and is a rare example of a successful method that actually fields. In this presentation, I will provide an overview of the HD/R strategy, a formulation that incorporates the entire life cycle of the insect, which was an issue that Comins had not yet resolved. And show the life cycle of the insect and the conditions under which the HD/R strategy is effective, based on the results of an approximation using a source-think model.

Venue: via Zoom

Event Official Language: English

Nuclear clustering phenomena revealed by knockout reaction

November 20 (Wed) at 15:30 - 17:00, 2024

Kazuki Yoshida (Assistant Professor, Research Center for Nuclear Physics, Osaka University)

Nuclear clustering is one of the unique phenomena in the nucleon many-body system. Historically, alpha formation has been known since the very early years of the nuclear physics, in the light and heavy mass regions. The former is known as the alpha clustering and its threshold rule, which was introduced by the Ikeda diagram in 1968. The latter has been known since the beginning of the nuclear physics as the alpha decay phenomena; the formation of alpha particles and their tunneling through the Coulomb barrier. Recently, the alpha clustering has been experimentally confirmed in the medium mass nuclei, 112-124Sn (Tin isotopes), using the alpha knockout reaction. Triggered by the experimental observation, the alpha knockout reaction is used as a reaction probe for the alpha clustering phenomena. In this talk, I will give an overview of the clustering phenomena and its reaction observables, in particular I will introduce the idea that the alpha knockout reaction can be a probe for the alpha formation on the alpha decay nuclei. In general, this idea can be applied to probe the particle trapped in the potential resonance.

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

Event Official Language: English

Machine learning applications in neutron star physics

November 19 (Tue) at 15:00 - 16:30, 2024

Márcio Ferreira (Researcher, Physics Department, University of Coimbra, Portugal)

The equation of state and the internal composition of a neutron star are still unanswered questions in astrophysics. To constrain the different composition scenarios inside neutron stars, we rely on pulsars observations and gravitational waves detections. This seminar shows different applications of supervised/unsupervised machine learning models in neutron stars physics, such as: i) extract the equation of state; ii) infer the proton fraction; iii) detect the possible existence of a second branch in the mass-radius diagram; and iv) detect the presence of hyperons. Márcio Ferreira is a researcher at the Center for Physics at the University of Coimbra, Portugal, focusing on the application of machine learning to astrophysics and materials science. His work utilizes generative and descriptive models to address key questions in these fields. With a PhD in high energy physics and a Master’s in quantitative methods for finance, Márcio also merges his expertise in physics with an interest in financial market dynamics.​

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

Event Official Language: English

Entanglements & Applications

November 18 (Mon) at 9:30 - 15:00, 2024

Myfanwy Evans (Professor, Institute of Mathematics, University of Potsdam, Germany)
Stephen Hyde (Emeritus Professor, Materials Physics, Australian National University, Australia)
Toky Andriamanalina (Ph.D. Student, Institute of Mathematics, University of Potsdam, Germany)

9:30-10:30: Toky Andriamanalina Title: Untangling 3-periodic entanglements of filaments and nets Abstract: Entanglements of curves and nets can used to describe various biological and chemical structures, such as coordination polymers, liquid crystals, or DNA origami crystals. We recently developed new diagrammatic descriptions of 3-periodic entanglements. These new diagrams are drawn out of a projection along one axis of a unit cell of a 3-periodic structure. By using these diagrams, we define the notion of untangling number for 3-periodic structures, which is a measure of complexity of the entanglement. Thanks to this, it is now possible to characterise the least tangled structures that we call ground states, and in particular we show that the rod packings are the generic ground states of entanglements of curves. 10:30-11:00: coffee break 11:00 - 12:00: Stephen Hyde Title: Tangles... and untangles Abstract: Knots, braids, links, self-entangled nets, multiple catenated infinite nets... are examples of what we call, simply, “tangles”. They are relevant to molecular-scale (bio)materials, from duplexed ssRNA to metal-organic frameworks. We are interested in understanding: 1.Which tangles are “simple”? 2.How tangled is a tangle!? Our tangle toolkit is a simple one: we assemble helices into networks, allowing a broad spectrum of tangles to be built, from knots to tangled nets. Interesting “simple” tangles are entanglements of the edges of Platonic polyhedra [1] and entangled 2-periodic nets [2]. A proposed answer to point 2. above will be discussed. if there is time. The ideas are at present largely unpublished, and being working into a book to be published, we hope, in late 2025 [3]. 13:00 - 14:00: Myfanwy Evans Title: Can solvents tie knots? Helical folds of biopolymers in liquid environments. Abstract: Using a simulation technique based on the morphometric approach to solvation, we performed computer experiments which fold a short open flexible tube, modelling a biopolymer in aqueous environments, according to the interaction of the tube with the solvent alone. We find an array of helical geometries that self-assemble depending on the solvent conditions, including symmetric double helices where the strand folds back on itself and overhand knot motifs. Interestingly these shapes—in all their variety—are energetically favoured over the optimal helix. By differentiating the role of solvation in self–assembly our study helps illuminate the energetic background scenery in which all soluble biomolecules live. This event is organized with the Interdisciplinary Math Study Group.

Venue: Seminar Room #359

Event Official Language: English

iTHEMS Science Outreach Workshop 2024

November 15 (Fri) - 17 (Sun), 2024

This year's meeting on "Outreach of RIKEN iTHEMS 2024@Sendai&Zoom" will be held from FRI November 15 to SUN November 17, as a face-to-face meeting at TOKYO ELECTRON House of Creativity of Tohoku Forum for Creativity in cooperation with iTHEMS SUURI-COOL (Sendai) using ZOOM for the necessary part as well.

Venue: TOKYO ELECTRON House of Creativity, Katahira Campus, Tohoku University (Main Venue) / via Zoom

Event Official Language: Japanese

Finding Rules for Condensation of Disordered Protein Sequences

November 14 (Thu) at 16:00 - 17:00, 2024

Kyosuke Adachi (Research Scientist, iTHEMS)

Event Official Language: English

Emergence of wormholes from quantum chaos

November 12 (Tue) at 16:30 - 18:00, 2024

Gabriele Di Ubaldo (Postdoctoral Researcher, iTHEMS)

I will give a broad introduction to some aspects of quantum gravity and the so-called black hole information problem. I will introduce wormholes as novel contributions to the gravitational path integral and how they provide a solution to the black hole information problem. Wormholes, however, are rather mysterious and we don’t have a good microscopic understanding of them and why we should include them in the our theory. In particular, wormholes seem to imply that gravity is not a proper quantum system but rather an average over a statistical ensemble of quantum systems. I will then transition into my own work which addresses these questions in the context of holography. I will show how wormholes in 3D quantum gravity can emerge from quantum chaos in the dual 2D Conformal Field Theory, without averaging. Wormholes capture coarse-grained properties of the CFT and conversely an individual chaotic CFT can effectively behave as an averaged system. Furthermore we will be able to explicitly factorize wormholes to extract microscopic information on black hole microstates. To achieve this I will (briefly) introduce and use tools such as Random Matrix Theory, the Gutzwiller Trace formula and Berry’s diagonal approximation, and the theory of SL(2,Z) non-holomorphic modular forms.

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

Event Official Language: English

Forming primordial black holes

November 11 (Mon) at 14:00 - 15:30, 2024

Zachary Picker (Postdoctoral Researcher, University of California, Los Angeles, USA)

Primordial black holes (PBHs) are black holes which form in the early universe. Not only are PBHs good dark matter candidates, but they have a wide range of fascinating phenomenology (even if they are only a fraction of the dark matter). In this talk I will review a somewhat under-discussed aspect of the PBH gospel---their formation mechanisms. In fact, there is a wide variety of ways to form PBHs of different sizes and abundances, and many of our favorite BSM theories can have PBHs in their spectra. I will then discuss some of our particular upcoming research on PBH formation, where attractive Yukawa forces in a dark sector can lead to the early formation of dense dark structures called Fermi balls which can collapse to black holes, with novel cosmological implications.

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

Event Official Language: English

Mathematical modeling of circadian rhythm: temperature compensation and after effect

November 7 (Thu) at 16:00 - 17:00, 2024

Yuta Kitaguchi (Ph.D. Student, Graduate School of Natural Science & Technology, Kanazawa University)

Almost all organisms have a circadian clock. This circadian clock consists of negative transcriptional-translational feedback loops (TTFLs) between various circadian clock genes in cells. Collective gene expression rhythms in the central circadian pacemaker tissue regulate nearly 24-hour behavioral rhythms of organisms. The circadian clock has three characteristics: (1) autonomous oscillation, (2) temperature compensation of the period, and (3) entrainment to external cycles such as a light-dark cycle. In this presentation, I will talk about theoretical studies on temperature compensation, and the entrainment to light-dark cycles. For temperature compensation, I will show that only a few temperature-insensitive reactions in the complex TTFLs of the circadian clock are sufficient to maintain the circadian period under increasing temperature. For entrainment to the light-dark cycle, I will show the mechanism for after-effect where the period of the circadian clock in constant darkness correlates with that of a previously entrained light-dark cycle for several months.

Venue: via Zoom

Event Official Language: English