Seminar
1063 events
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Seminar
Genome and Sex Chromosome Analyses of Japanese Frogs Carrying Both XY and ZW Chromosomes Within the Same Species
February 27 (Thu) 16:00 - 17:00, 2025
Yukako Katsura (Assistant Professor, Center for the Evolutionary Origins of Human Behavior, Kyoto University)
The evolution of sex chromosomes, particularly sex chromosome turnover, is a complex and fascinating topic in genetics and evolutionary biology. Sex chromosome turnover refers to the process in which the sex chromosome system changes from XY to ZW (or vice versa), or in which sex chromosomes with different evolutionary origins emerge within the same system (e.g., from one XY system to another XY system). To study sex chromosome turnover, we focus on the Japanese frog (Glandirana rugosa), which possesses both XY and ZW sex chromosomes within the same species, and investigate the molecular mechanisms behind the turnover in the frog (Review: Hayashi et al. JB 2024). Previously, we sequenced the nuclear genome of the ZZ frog (Katsura et al. LSA 2021) and identified sex-linked genes in two populations of the XY and ZW frogs (Miura et al. Mol Ecol 2022). It has been suggested that sex chromosomes originating from at least three different chromosomal lineages have independently emerged within this species. The frogs have a total of 13 chromosomes, and in two populations (Tokai/Eastern Central Japan and Hokuriku-Tohoku/North-Western Japan), chromosome 7 has morphologically differentiated into both ZW and XY chromosomes. However, in other populations, sex chromosomes do not show any morphological differentiation. In this seminar, I introduce the background of our sex chromosome study and present the results of sequence comparisons of morphologically differentiated XY and ZW chromosomes, as well as findings from our analyses of populations, genome, and transcriptome.
Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359
Event Official Language: English
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Seminar
Quantum-Centric Supercomputing Software
February 26 (Wed) 13:00 - 14:00, 2025
Hanhee Paik (Head of IBM Quantum Japan, IBM Quantum)
A quantum-centric supercomputer represents the next generation of computing, combining a quantum computer with a classical supercomputer. It leverages error mitigation and error correction techniques to deliver results within practical timeframes. When fully developed, this system relies on advanced middleware to seamlessly integrate quantum circuits with classical computing resources. In this presentation, we will introduce IBM Quantum’s middleware for quantum-centric supercomputers, highlighting collaborative projects with our research partners.
Venue: Seminar Room #359 (Main Venue) / via Zoom
Event Official Language: English
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Seminar
Exploiting hidden low-rank structures in quantum field theories
February 24 (Mon) 13:00 - 14:30, 2025
Hiroshi Shinaoka (Associate Professor, Department of Physics, Saitama University)
Tensor networks are a powerful tool for compressing wave functions and density matrices of quantum systems in physics. Recent developments have shown that tensor network techniques can efficiently compress many functions beyond these traditional objects. Notable examples include the solutions to turbulence in Navier–Stokes equations [1] and the computation of Feynman diagrams [2,3]. These advancements have heralded a new era in the use of tensor networks for expediting the resolution of various complex equations in physics. This talk will provide an overview of our work utilizing tensor networks for computations based on quantum field theories. First, we will introduce the Quantics/quantized Tensor Train (QTT) representation [3,4] for compressing the space-time dependence of correlation functions in quantum systems [5], leveraging inherent length-scale separation for efficient representation. Second, we will present a robust tool named "Quantics Tensor Cross Interpolation" [6], which learns a quantics low-rank representation of a given function. Applications include the computation of Brillouin zone integrals [6] and integration of complex self-energy Feynman diagrams for multiorbital electron-phonon impurity models [7]. Finally, we will introduce new algorithms [8] and open-source libraries [9] for tensor cross interpolation.
Venue: via Zoom / Hong Kong University Science and Technology
Event Official Language: English
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Seminar
Ubiquity of geometric Brascamp--Lieb data
February 21 (Fri) 15:00 - 17:00, 2025
Hiroshi Tuji (JSPS Research Fellow PD, Graduate School of Science and Engineering, Saitama University)
This talk is based on a joint work with Neal Bez (Nagoya university) and Anthony Gauvan (Saitama university). The Brascamp--Lieb inequality is a futher general inequality involving some data (we call it the Brascamp--Lieb datum), which has been studied in harmonic analysis and convex geometry. For instance, the Hölder inequality and the Young convolution inequality are particular cases. In this talk, we have an interest in geometric Brascamp--Lieb data, which are specific data satisfying nice properties, for which the best constant of the Brascamp--Lieb inequality is well-understood. Our goal in this talk is to show that geomtric Brascamp--Lieb data are dense in general Brascamp--Lieb data in certain sence. Our result substantially follows from the work by Garg, Gurvits, Oliveira and Wigderson.
Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359
Event Official Language: English
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Seminar
Exploring the evolutionary fate of a mutualistic community using automated microbial culture system
February 20 (Thu) 16:00 - 17:00, 2025
Junya Sunagawa (Ph.D. Student, Graduate School of Life Science, Hokkaido University)
Microbes are ubiquitous around the world, forming systems where they interact through competition or cooperation. Especially in the form of cooperation, exchange of essential metabolites, known as metabolic cross-feeding, plays a fundamental role in the assembly of microbial communities. An extreme case of metabolic cross-feeding is an obligate mutualism, where one organism can only grow with the help of a partner supplying metabolites (e.g., amino acid). When they face environmental stresses such as antibiotics, it is unclear whether the benefit that causes the formation of obligate ecological mutualism may benefit (or cost) the members to increases (inhibits) resistance through interactions at the evolutionary scale. Another fascinating question is whether an additional benefit (e.g., an enzyme that helps the community persistence against environmental change) will select the community to increase the resistance. Here, I will report my ongoing research progress of obligate cross-feedings involving β-lactamase and discuss the conditions where the benefit can overcome the cost of the obligate interaction. I have started to address this issue by conducting laboratory evolution experiments with an automated culture system which can automatically adjust the strength of the stress (i.e., concentration of the antibiotics), so that the focal microbes have to get evolved. I will also share my story about building this automated culture system.
Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359
Event Official Language: English
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Seminar
How to define a Majorana fermion?
February 20 (Thu) 13:00 - 14:30, 2025
Kazuo Fujikawa (Professor Emeritus, The University of Tokyo)
It is fundamental in particle physics if the neutrino is a Dirac fermion or a Majorana fermion, and the seesaw model gives naturally a Majorana neutrino in an extension of the Standard Model. However, the commonly used chirality changing \(pseudo-C symmetry \) \(\nu^{\tilde C}_L=C\overline{\nu_L}^T\) of a chiral fermion is not defined in Lagrangian field theory. Precisely speaking, the neutrinoless double beta decay is not described by the pseudo-C symmetry. The Majorana neutrino obtained after a Bogoliubov-type canonical transformation, which is the one originally defined by Majorana using a Dirac-type fermion, describes consistently all the properties expected for the Majorana neutrino. Physical implication of this fact is briefly discussed.
Venue: Seminar Room #359 (Main Venue) / via Zoom
Event Official Language: English
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Seminar
The Topology, Geometry and Physics of non-Hausdorff manifolds
February 19 (Wed) 15:00 - 17:00, 2025
O'Connell David (Ph.D. Student, Okinawa Institute of Science and Technology Graduate University (OIST))
Non-Hausdorff manifolds are manifolds containing "doubled points" that cannot be separated by disjoint open sets. In this talk we will survey some mathematical and physical results surrounding these unusual spaces. As a theme, we will start with their fundamental description as a topological space, and slowly add in more and more structure of interest until we can meaningfully phrase questions of physics. On the mathematical side, we will see descriptions of non- Hausdorff manifolds as colimits of ordinary manifolds, which allows us to describe their geometric features without appealing to arbitrarily- existent partitions of unity. On the physical side, we will consider the inclusion of non-Hausdorff manifolds in a naïve 2d Lorentzian path integral for gravity, and (time permitting) explain how construct quantum fields on a non-Hausdorff background. Ultimately, we will see that these latter two arguments suggest that non-Hausdorff manifolds may be more appropriate than the standard "Trousers space" for the modelling of topology change in Lorentzian signature.
Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359
Event Official Language: English
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Seminar
New topological quantum order in 2D lattices from non-invertible symmetries
February 18 (Tue) 15:00 - 16:00, 2025
Ayan Mukhopadhyay (Associate Professor, Valparaiso University, Chile)
I will introduce an exactly solvable 2D lattice model which reveals a large number of distinct topological phases with non-invertible (generalized) symmetries. In all these topological phases, which have topological ground state degeneracy, a commutative stabilizer monoid of Hermitian operators leave the ground state invariant and can also distinguish *all* local excitations, (These symmetries are indeed symmetry operations.) There exists novel confined fractonic excitations which change the nature of deconfined excitatons profoundly. The fusion rules form an associative but noncommutative. non-Abelian and non-unital category, and are distinct for each of these phases. A class of these phases are adiabatically connected to a limit which can be described in terms of generalized free field theories. I will describe systematic ways to construct such phases. I will also discuss phases which do not have generalized free field limits. These phases have novel forms of non-local entanglement as many of them share the same topological entanglement entropy. They also violate the entanglement bootstrap axioms. When the phases do not have a generalized free field limit, the violation of the entanglement bootstrap axioms can happen for arbitrary large subregions signifying new forms of long-range entanglement.
Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359
Event Official Language: English
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Seminar
Operator-algebraic approach to point processes
February 14 (Fri) 15:00 - 17:00, 2025
Ryosuke Sato (JSPS Postdoctoral Research Fellow, Faculty of Science and Engineering, Chuo University)
A point process is a mathematical description of a particle system with random interactions, and it naturally appears in various areas of mathematical physics and mathematics, including statistical mechanics, random matrix theory, combinatorics, and representation theory. In particular, a random particle system with repulsive interactions is associated with a determinantal point process, in which the correlation of any number of particles is expressed in terms of the two-particle correlation via a determinant. Furthermore, this determinantal structure enables an algebraic analysis using CAR algebras, which are operator algebras determined by canonical anti-commutation relations. In the first half of the talk, we will review the relationship between determinantal point processes and operator algebras, with a focus on why operator algebras naturally lend themselves to analyses in probability theory and statistical mechanics. In the second half, based on recent work, we will examine the dynamic relationship between point processes and operator algebras, discussing how dynamics on CAR algebras give rise to stochastic processes on determinantal point processes.
Venue: Seminar Room #359 (Main Venue) / via Zoom
Event Official Language: English
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Seminar
Linking quantum error correction and gauge theories with quantum reference frames
February 14 (Fri) 10:30 - 11:30, 2025
Philipp Hoehn (Assistant Professor, Okinawa Institute of Science and Technology Graduate University (OIST))
Redundancy is the hallmark of both quantum error correction and gauge theories. In this talk, I will show that this analogy is not merely a coincidence but that there is a deeper underlying structural relationship. The key ingredient to this observation is quantum reference frames (QRFs), which constitute a universal tool for dealing with symmetries in quantum systems. They define a split between redundant and physical information in gauge systems, thereby establishing a notion of encoding in that context. This leads to an exact dictionary between (group-based) quantum error correcting codes and QRF setups. In stabilizer codes, this uncovers a correspondence between errors and QRFs: every maximal set of correctable errors generates a unique QRF, and each QRF is associated with a unique class of correctable errors. This allows for a reinterpretation of the Knill-Laflamme condition and novel insights into the relation between correctability and redundancy. The dictionary also reveals a novel error duality, based on Pontryagin duality, and somewhat akin to electromagnetic duality. Time permitting, I will illustrate these findings in surface codes, which can be understood as both codes and lattice gauge theories. These findings may find use in code design and quantum simulations of gauge theories.
Venue: #345-347, 3F, Main Research Building
Event Official Language: English
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Seminar
Application of genetics and genomics to breeding
February 13 (Thu) 16:00 - 17:30, 2025
Jeffrey Fawcett (Senior Research Scientist, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS))
Humans have domesticated and modified several plants and animals over the course of history to achieve food security. However, drastic changes are required in order to meet the needs of a growing population while facing global warming. In particular, utilizing and improving the productivity of unutilized or underutilized resources such as minor crops, aquatic species, and insects are thought to be essential. Here, I will provide an overview of how humans have been modifying organisms by selective breeding, the role of genetics and genomics in modern selective breeding, and the challenges we are currently facing. This talk will be aimed at non-experts/non-biologists and will cover the basics of genetics.
Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359
Event Official Language: English
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Seminar
Mathematical Studies on Human Cooperation
February 12 (Wed) 15:00 - 17:00, 2025
Yohsuke Murase (Research Scientist, Discrete Event Simulation Research Team, RIKEN Center for Computational Science (R-CCS))
Cooperation is a fundamental part of human society. But from an evolutionary perspective, it remains a puzzle—why do people help others even when it costs them? In theory, selfish individuals should have an advantage over cooperators. To explain how cooperative behaviors evolved, researchers have proposed several mechanisms, among which direct and indirect reciprocity play key roles in human interactions. In this talk, I will present my research on the evolution of cooperation, focusing on these two mechanisms. I will begin with an introduction to game theory and evolutionary game theory, which help us understand how people make decisions in strategic situations. Then, I will discuss my study on the repeated Prisoner’s Dilemma, where we discovered a new class of strategies through mathematical analysis and large-scale computations [1]. Finally, I will talk about my research on indirect reciprocity, a process where people cooperate based on reputation [2].
Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359
Event Official Language: English
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Seminar
Investigating the Crust Urca Process in Accretion Neutron Stars: Implications for Superburst Ignition and Hot Cooling Curve of MAXI J0556-332
February 7 (Fri) 16:00 - 17:15, 2025
Hao Huang (Ph.D. Student, Institute of Modern Physics, China)
This seminar investigates the Urca cooling strength of the 63Fe-63Mn pair, which varies due to uncertainties in the spin-parity of 63Fe, relevant to the Island of Inversion at N = 40. We present simulations that analyze the impact of this cooling mechanism on the thermal evolution of neutron star crusts, focusing on superburst ignition and anomalous hot quiescent phase cooling of MAXI J0556-332. Additionally, we explore the potential crust Urca process through the anomalous cooling curve of MAXI J0556-332, fitting observational data to determine neutron star mass and radius preferences. Preliminary results suggest that neutron stars with a crust Urca process tend to have smaller masses and larger radii, highlighting the need for precise β-decay measurements to further understand these phenomena.
Venue: Hybrid Format (3F #359 and Zoom), Main Research Building
Event Official Language: English
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Seminar
Fireworks in the cosmos: The Hidden Power of Nuclear Reactions
February 7 (Fri) 14:00 - 15:15, 2025
Irin Sultana (Ph.D. Student, Department of Physics, Central Michigan University, USA)
Neutron stars in low-mass X-ray binaries, accreting hydrogen- or helium-rich material from a companion star, frequently exhibit thermonuclear runaways on their surfaces known as Type-I X-ray bursts (XRBs). These bursts are powered by nuclear processes, such as the triple-$\alpha$ process, the $\alpha p$ process, and the rapid proton capture process, which play a critical role in model-observation comparisons. In this study, we investigate the impact of nuclear reaction uncertainties on XRBs using the ONEZONE model (Cyburt et al., 2016), considering different accreted compositions and accretion rates for the binary systems that are within the range of observed burst sources. The study is carried out in two stages. First, we determine the burst ignition conditions by simulating the settling of the accreted material with a full reaction network and a semi-analytical model. Second, we perform a sensitivity analysis by varying proton- and alpha-induced reaction rates in JINA REACLIBV2.2 within their estimated uncertainties. We explore the influence of these reactions on the XRBs light curve and the final abundances. The findings highlight key nuclear reactions that significantly affect XRB observables and the final abundances produced, offering guidance for future experimental efforts to improve our understanding of the uncertainties in the reaction rates involved in XRBs.
Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359
Event Official Language: English
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Seminar
A coarse-grained model of disordered RNA for simulations of biomolecular condensates
February 6 (Thu) 16:00 - 17:00, 2025
Ikki Yasuda (Ph.D. Student, Graduate School of Science and Technology, Keio University)
Protein-RNA condensates are involved in a range of cellular activities. Coarse-grained molecular models of intrinsically disordered proteins have been developed to shed light on and predict single-chain properties and phase separation. An RNA model compatible with such models for disordered proteins would enable the study of complex biomolecular mixtures involving RNA. Here, we present a sequence-independent coarse-grained, two-bead-per-nucleotide model of disordered, flexible RNA based on a hydropathy scale. We parameterize the model, which we term CALVADOS-RNA, using a combination of bottom-up and top-down approaches to reproduce local RNA geometry and intramolecular interactions based on atomistic simulations and in vitro experiments. The model semi-quantitatively captures several aspects of RNA-RNA and RNA-protein interactions. We examined RNA-RNA interactions by comparing calculated and experimental virial coefficients, and non-specific RNA-protein interaction by studying reentrant phase behavior of protein-RNA mixtures. We demonstrate the utility of the model by simulating the formation of mixed condensates consisting of the disordered region of MED1 and RNA chains, and the selective partitioning of disordered regions from transcription factors into these, and compare the results to experiments. Despite the simplicity of our model we show that it captures several key aspects of protein-RNA interactions and may therefore be used as a baseline model to study several aspects of the biophysics and biology of protein-RNA condensates.
Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359
Event Official Language: English
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Seminar
Mathematics of the Future, Science of the Future: Large Language Models and Their Applications
February 6 (Thu) 14:00 - 16:00, 2025
Akiyoshi Sannai (Program-Specific Associate Professor, Graduate School of Science, Kyoto University)
In recent years, the rapid development of large language models (LLMs) such as ChatGPT has given many researchers a strong impression that these systems truly exhibit “intelligence.” In this presentation, we first review the evolution of AI research, explaining how large language models go beyond conventional machine learning by enabling more “general” forms of learning. We then highlight the importance of “sensors” and “mathematical capability” as key factors that allow AI to autonomously carry out scientific tasks such as problem analysis, hypothesis generation, and proofs in fields like mathematics and physics. We also examine how proof assistants can address the issue of hallucinations in LLM outputs, and discuss the role of combinatorial creativity in accelerating interdisciplinary research. Finally, we introduce our “AI Mathematician” agent project, demonstrating how integrating large language models with proof assistants can open new horizons in mathematical sciences.
Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359
Event Official Language: English
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Seminar
Master equations for general non-Markovian processes: the Hawkes process and beyond
February 5 (Wed) 16:30 - 18:00, 2025
Kiyoshi Kanazawa (Associate Professor, Division of Physics and Astronomy, Graduate School of Science, Kyoto University)
The Markovian process is one of the most important classes of stochastic processes. The Markovian process is defined as a stochastic process whose time evolution is independent of the system's entire history and has been extensively studied using the master equation and Fokker-Planck equation approaches. In contrast, non-Markovian processes -- where time evolution depends on the full history of the system -- have not been systematically explored, except for a few special cases, such as semi-Markovian processes. In this talk, we present a recent master-equation approach to general non-Markovian jump processes [1-4]. Beginning with a general non-Markovian jump process, we derive the corresponding master equation through a Markovian-embedding approach. The Markovian embedding is a scheme to add a sufficient number of auxiliary variables to convert a non-Markovian model to a high-dimensional Markovian model. For the case of our model, the one-dimensional non-Markovian model is shown to be equivalent to a Markovian stochastic field theory, and we derive the field master equation correspondingly [4]. As an application, we examine the nonlinear Hawkes process, a history-dependent and self-exciting model frequently used in studying complex systems [1-3]. Additionally, we explore the stochastic thermodynamic framework for general jump processes [5] as another example.
Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359
Event Official Language: English
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Seminar
Introduction to the stochastic process and its application in physics
February 4 (Tue) - 5 (Wed) 2025
Kiyoshi Kanazawa (Associate Professor, Division of Physics and Astronomy, Graduate School of Science, Kyoto University)
The stochastic process is a popular tool for broad disciplines, such as physics, biophysics, chemistry, neuroscience, economics, and finance. In this lecture course, I will provide an elementary introduction to stochastic processes in physics without assuming rigorous background knowledge of probability theories. Most of the basic topics in stochastic processes will be covered in this lecture course, such as (1) the one-to-one correspondence between stochastic differential equations and master equations, (2) their standard forms, (3) Ito's lemma, and (4) the perturbation theories (the system-size expansion). I will also present its application to statistical physics, such as (5) kinetic theory and (6) a microscopic derivation of the Langevin equation from hard-sphere Hamiltonian dynamics in the dilute gas limit. My goal is to help the audience calculate most of the main calculations by their own hands by providing detailed explanations without abbreviations. This lecture is based on my Japanese notebook, available on my webpage (see the link below). Schedule: (Tue., Feb. 4) 13:00-14:30, 14:45-16:15, 16:30-18:00 (Wed., Feb. 5) 10:30-12:00, 13:00-14:30, 14:45-16:15
Venue: Hybrid Format (3F #359 and Zoom), Seminar Room #359
Event Official Language: English
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Seminar
Can AI understand Hamiltonian mechanics?
January 31 (Fri) 16:00 - 17:00, 2025
Tae-Geun Kim (Ph.D. Student, Department of Physics, Yonsei University, Republic of Korea)
With recent breakthroughs in deep learning, particularly in areas like natural language processing and image recognition, AI has shown remarkable abilities in understanding complex patterns. This raises a fundamental question: Can AI grasp the core concepts of physics that govern the natural world? In this talk, as a first step towards addressing this question, we will discuss the possibility of AI understanding Hamiltonian mechanics. We will first introduce the concept of operator learning, a novel technique that allows AI to learn mappings between infinite-dimensional spaces, and its application to Hamiltonian mechanics by reformulating it within this framework. Then, we will test whether AI can derive trajectories in phase space given an arbitrary potential function, without relying on any equations or numerical solvers. We will then showcase our findings, demonstrating AI's capability to predict phase space trajectories under certain constraints. Finally, we will discuss the limitations, future research directions, and the potential for AI to contribute to scientific discovery.
Venue: via Zoom
Event Official Language: English
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Seminar
D-modules and the Riemann-Hilbert correspondence as a foundation for mixed Hodge modules
January 31 (Fri) 14:00 - 16:00, 2025
Takahiro Saito (Assistant Professor, Faculty of Science and Engineering, Chuo University)
Algebraic analysis is a field which began with the study of differential equations in an algebraic framework, known as D-modules. The Riemann-Hilbert correspondence lies at the heart of this field, which bridges the worlds of analysis and geometry. Thanks to this, some geometric problems can be studied by using D-module theory, and vice versa. Based on D-module theory, Morihiko Saito introduced the concept of mixed Hodge modules, realizing Hodge theory on constructible sheaves, which brings us a functorial treatment of Hodge theory and various applications. In this talk, we will begin with the linear differential equations on the complex plane and introduce monodromy, regularity and Deligne's Riemann-Hilbert correspondence. Then, as a generalization of it, I will explain the basics of the theory of D-modules and the Riemann-Hilbert correspondence. Finally, I will describe the role they play in the theory of Hodge modules and recent progress in this area. For the audience's background knowledge, I will assume basic complex function theory. I will start with a simple example, so people outside the field are welcome.
Venue: Seminar Room #359 (Main Venue) / via Zoom
Event Official Language: English
1063 events