Search Event
672 results
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Seminar
Introduction to stability conditions 2
March 9 (Wed) 16:00 - 17:30, 2022
Naoki Koseki (Postdoctoral Research Associate, School of Mathematics, University of Edinburgh, UK)
In 2002, Bridgeland defined the notion of stability conditions on a triangulated category, motivated by string theory and mirror symmetry. Since then, Bridgeland stability conditions have been found very useful not only in Mathematical Physics, but also in various areas of Pure Mathematics. In the first part, I will review basic background and open problems in the theory of Bridgeland stability conditions. In the second part, I will explain recent developments of the theory, especially its applications to algebraic geometry.
Venue: via Zoom
Event Official Language: English
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Seminar
Introduction to stability conditions 1
March 2 (Wed) 16:00 - 17:30, 2022
Naoki Koseki (Postdoctoral Research Associate, School of Mathematics, University of Edinburgh, UK)
In 2002, Bridgeland defined the notion of stability conditions on a triangulated category, motivated by string theory and mirror symmetry. Since then, Bridgeland stability conditions have been found very useful not only in Mathematical Physics, but also in various areas of Pure Mathematics. In the first part, I will review basic background and open problems in the theory of Bridgeland stability conditions. In the second part, I will explain recent developments of the theory, especially its applications to algebraic geometry.
Venue: via Zoom
Event Official Language: English
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Seminar
How to understand Earth science system using data science
February 25 (Fri) 16:00 - 18:00, 2022
Kaman Kong (Postdoctoral Researcher, Computational Climate Science Research Team, RIKEN Center for Computational Science (R-CCS))
Hi everyone, my name is Kaman Kong. After I graduated from Nagoya University last April, I joined the computational climate science research team, R-CCS at Kobe. Although I have still not yet had the important results now, I would like to share my idea and future plan here. In this talk, different from the previous seminar, I would like to highlight how to use data science approaches to understand our Earth system science. In the first 60 minutes, I would like to share my research experiences in ecosystems, dust outbreaks, and atmospheric sciences and try to discuss their limitation in my study. After a 10-minute break, the 30 minutes will be spent discussing the potential methodology to overcome these limitations and new opportunities and challenges in Earth system science. (Part 1) In the first 60 minutes, I would like to talk about the relationships among ecosystems, dust outbreaks, and atmospheric conditions. I used the models of dust and ecosystem to explore seasonal variations of threshold wind speed, an index of soil susceptibility to dust outbreak, and its relations with land surface conditions, such as plant growth and soil moisture and temperature changes, in the Mongolian grasslands. On the other side, I am improving the weather forecast model to accurately predict dust emission and discuss its effects on the Earth system. Meanwhile, I am integrating the dust model into the ecosystem model. During this period, I realized there are many uncertainties of simulation. (Part 2) In the second 30 minutes, I will explain these limitations as I mentioned before and try to discuss how to solve these problems. For example, using deep learning to identify the green and brown plants separately for discussing their different effect on the dust model. And, used data assimilation (e.g., EnKF and Bayesian calibration) to improve the simulated performance of land surface parameters (e.g., soil moisture and vegetation).
Venue: via Zoom
Event Official Language: English
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Seminar
Stator dynamics of the bacterial flagellar motor
February 24 (Thu) 17:00 - 18:00, 2022
Ashley Nord (Researcher, Centre de Biologie Structurale, CNRS, France)
Rubén Pérez-Carrasco (Lecturer in Theoretical Systems Biology, Faculty of Natural Sciences, Department of Life Sciences, Imperial College London, UK)The bacterial flagellar motor is the membrane-embedded rotary molecular motor which turns the flagellum that provides thrust to many bacteria for swimming, swarming, and chemotaxis. This large multimeric complex, composed of a few dozen constituent proteins, is a hallmark of dynamic subunit exchange. The stator units are inner-membrane ion channels which dynamically bind to the cell wall and convert electrochemical energy into torque which is applied to the rotor. The dynamic exchange of stator units is a function of the viscous load on the flagellum, allowing the bacterium to adapt to its local environment, though the molecular mechanisms of this mechanosensitivity remain unknown. Previously, we have shown that stator units behave as a catch bond, a counterintuitive bond which becomes stronger under applied tension. Here, by actively perturbing the steady-state stator stoichiometry of individual motors, we reveal a stoichiometry-dependent asymmetry in stator remodeling kinetics. We interrogate the potential effect of next-neighbor interactions and local stator unit depletion and find that neither can explain the observed asymmetry. We then simulate and fit two mechanistically diverse models which recapitulate the asymmetry, finding assembly dynamics to be particularly well described by a two-state catch-bond mechanism.
Venue: via Zoom
Event Official Language: English
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Seminar
iTHEMS - R-CCS(FTRT) Joint Online Seminar: Second order chiral phase transition in three flavor quantum chromodynamics?
February 18 (Fri) 16:30 - 18:00, 2022
Gergely Fejös (Assistant Professor, Institute of Physics, Eötvös Loránd University, Hungary)
We calculate the renormalization group flows of all renormalizable interactions in the three dimensional Ginzburg--Landau potential for the chiral phase transition of three flavor quantum chromodynamics [1]. On the contrary to the common belief we find a fixed point in the system that is able to describe a second order phase transition in the infrared. This shows that longstanding assumptions on the transition order might be false. If the transition is indeed of second order, our results can also be interpreted as indirect evidence that the axial anomaly restores at the transition temperature.
Venue: via Zoom
Event Official Language: English
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Seminar
Hilbert transform and its applications to biology
February 17 (Thu) 10:00 - 11:00, 2022
Shingo Gibo (Postdoctoral Researcher, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS))
In chronobiology, the estimation of phase dynamics is important for measuring period and phase shift. However, it is difficult to precisely estimate the phase from time-series data when the frequency and the amplitude are nonstationary. Hilbert transform has been known as a signal processing method for decomposing time-series into the phase and the amplitude dynamics. This method allows us to analyze the phase from nonstationary time-series data. In this talk, I would like to introduce the basic concept of Hilbert transform and a few examples of its applications.
Venue: via Zoom
Event Official Language: English
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Workshop
Towards the Use of Data Assimilation for COVID-19 Investigations
February 14 (Mon) 13:00 - 17:30, 2022
Catherine Beauchemin (Deputy Program Director, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS))
Takemasa Miyoshi (Team Leader, Data Assimilation Research Team, RIKEN Center for Computational Science (R-CCS))This workshop aims to present recent investigations related to mathematical modeling of COVID-19 spread and impacts, and to foster the use of data assimilation techniques in future studies. It also aims to facilitate interactions and discussions among researchers from different fields such as epidemiology, economics, and mathematics. This workshop is jointly hosted by RIKEN Data Assimilation Research Team and by Nagoya University Graduate School of Mathematics, and supported by FY2021 RIKEN President's Discretionary Funds for COVID-19. A hybrid meeting is planned, but depending on the situation, an online version will be organized. Young researchers and students are encouraged to attend. Program: 13:00 - 13:10 Opening 13:10 - 14:00 Hiroshi Nishiura (Kyoto University) (35 min + 15 min Q&A) TBD 14:00 - 14:50 Catherine Beauchemin (RIKEN iTHEMS) (35 min + 15 min Q&A) The straight line: simple and effective 14:50 - 15:10 Break 15:10 - 16:00 Taisuke Nakata (The University of Tokyo) (35 min + 15 min Q&A) Balancing NPIs and Economic Activities 16:00 - 16:50 Qiwen Sun (RIKEN Data Assimilation Research Team, Nagoya University) (35 min + 15 min Q&A) Analysis of COVID-19 in Japan with Extended SEIR model and ensemble Kalman filter 16:50 - 17:30 Discussion
Venue: Hybrid Format (RIKEN R-CCS room 107 and Zoom)
Event Official Language: English
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Seminar
Stochastic operators: properties and applications
February 10 (Thu) 10:00 - 11:00, 2022
Gilberto Nakamura (Postdoctoral Researcher, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS))
Stochastic processes are widely used to model systems in which one or more variables fluctuate randomly. Problems arise when large sets of random variables are allowed to interact with each other, as is often the case with physical and biological systems. Stochastic operators provide a convenient framework for describing the interactions and evolution of the random variables. In this talk, I will discuss techniques and methods typically used in spin systems to deal with stochastic operators and their spectral analysis in the context of random processes. I will briefly review their properties and applications to biological systems. As practical examples, I will present some results of my research in infectious diseases and migration of glioma cells.
Venue: via Zoom
Event Official Language: English
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Seminar
Recent progress on dualities in W-superalgebras
January 28 (Fri) 16:00 - 18:00, 2022
Shigenori Nakatsuka (JSPS Fellow, Kavli Institute for the Physics and Mathematics of the Universe (Kavli IPMU), The University of Tokyo)
Vertex superalgebras are algebras which describe the chiral part of two dimensional superconformal field theory. A rich and fundamental class is provided by the affine vertex superalgebras associated with simple Lie superalgebras and the W-superalgebras obtained from them by cohomology parametrized by nilpotent orbits. Historically, the W-algebras associated with simple Lie algebras and principal nilpotent orbit have been studied intensively and are well-known to play an essential role in the quantum geometric Langlands program. In particular, they enjoy a duality, called the Feigin-Frenkel duality, which is a chiral analogue of the isomorphism between centers of the enveloping algebras of simple Lie algebras in Langlands duality. Recently, physicists found a suitable generalization for other types of nilpotent orbits from study on four dimensional supersymmetric gauge theory. In this talk, I will report the recent progress on our understanding of dualities in W-superalgebras since then in terms of several aspects: algebras, modules, and fusion rules.
Venue: via Zoom
Event Official Language: English
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Seminar
Galactic archaeology with r-process elements
January 28 (Fri) 10:00 - 11:30, 2022
Yutaka Hirai (JSPS Research Fellow, Department of Astronomy, Graduate School of Science, Tohoku University / JSPS Research Fellow (Visiting Scholar), Department of Physics, University of Notre Dame, USA)
Galactic archaeology studies the evolutionary histories of galaxies using information preserved in stars. Abundances of elements in stars are keys to understanding how the galaxies were evolved. It is, therefore, crucial to making it clear the origin of elements and the cycle of materials in galaxies. This talk will show the enrichment of heavy elements, including r-process elements, in dwarf galaxies and the Milky Way. Our high-resolution simulations of galaxies suggest that binary neutron star mergers play an important role in enriching r-process elements in dwarf galaxies and the Milky Way. I will also show that r-process enhanced stars in the Milky Way tend to form in dwarf galaxies previously accreted to the Milky Way. I will demonstrate that the abundance of r-process elements in stars can be used as an indicator for the early evolution of the Milky Way.
Venue: via Zoom
Event Official Language: English
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Seminar
A study of biological systems from topological point of view
January 20 (Thu) 10:00 - 11:00, 2022
Hiroyasu Miyazaki (Senior Research Scientist, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS))
A biological body can be regarded as a complicated network of chemical reactions. The chemical reaction network (CRN) is a (hyper)graph-theoretic model of such biological networks. Recently, in the joint work with Yuji Hirono, Takashi Okada and Yoshimasa Hidaka, we applied a topological method to the study of CRNs, and found a suitable way to simplify the networks. Since Professor Hirono has already explained our work in this seminar, I will try to explain it from a slightly different point of view. In the first half of the talk, I will review the entire work. In the second half, I will try to give a rough sketch of the mathematical method we used in the work.
Venue: via Zoom
Event Official Language: English
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Seminar
The Ohsawa-Takegoshi $L^2$ extension theorem and variations of Bergman kernels
January 14 (Fri) 16:00 - 18:00, 2022
Genki Hosono (Mathematical Institute, Graduate School of Science, Tohoku University)
In complex analysis and geometry, $L^2$ methods are very important and widely used. Recent studies show that the $L^2$ theory and the variational theory are closely related. In particular, the (optimal) $L^2$ extension theorem can be proved by subharmonicity of variations of Bergman kernels and vice versa. In this talk, I will explain the background, results, and key ideas of the proof. *Please contact Keita Mikami mailing address to get access to the Zoom meeting room.
Venue: via Zoom
Event Official Language: English
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Seminar
A comprehensive view of the SARS-CoV-2 infection process
January 13 (Thu) 10:00 - 11:00, 2022
Wataru Nishima (Scientist, New Mexico Consortium, Mexico)
Nishima et al. recently published a paper about a computational model of SARS-CoV-2 Spike Protein [1]. Although it is still a hypothesis due to the lack of direct experimental evidence, the story comprehensively explains the initial infection process of SARS-CoV-2 consistent with most of the empirical evidence. In the presentation, I would like to explain the overview of the infection process for the non-expert audience and how the hypothesis influences the current COVID-19 situation. If time permits, I would like to briefly explain the current plan of the iTHEMS-NMC COVID project, which is going to be the first case of undergoing an interdisciplinary collaboration framework between Japan and the US.
Venue: via Zoom
Event Official Language: English
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Seminar
Physics of nuclear bodies
January 6 (Thu) 10:00 - 11:00, 2022
Tetsuya Yamamoto (Specially Appointed Associate Professor, Institute for Chemical Reaction Design and Discovery, Hokkaido University)
Eukaryotic nucleus is not a uniform solution of DNA, but there are a number of nuclear bodies in the interchromatin spaces. There are growing number of experiments that suggest that nuclear bodies are assembled by liquid-liquid phase separation (LLPS). Condensates assembled by LLPS show coarsening or coalescence to decrease the surface energy. However, in some nuclear bodies, such as paraspeckles, nuclear stress bodies, and fibrillar centers in nucleoli, multiple condensates are stably dispersed and are not likely assembled by LLPS. The assembly mechanism of nuclear bodies is relevant to the regulation of the area of condensate surfaces, which are functional in some nuclear bodies, and the mobility of nuclear bodies. Hirose group (Osaka Univ.) has elucidated that nuclear bodies are scaffolded by a class of RNA, called architectural RNA (arcRNA), which forms complexes with RNA binding proteins. This implies that the assembly of nuclear bodies is governed RNA dynamics, such as transcription, degradation, and processing, and the sequence of bases of arcRNA. In the seminar, I will show how the base sequences and the dynamics of RNA are involved in the assembly of paraspeckles and fibrillar centers in nucleoli.
Venue: via Zoom
Event Official Language: English
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Seminar
Hidden Markov Models and their applications
December 23 (Thu) 10:00 - 11:00, 2021
Takashi Okada (Senior Research Scientist, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS))
The Hidden Markov models (HMM) have been used in a variety of fields for different purposes. I am going to review statistical inference methods associated with HMM & related biological problems. As an example of their applications, I'll also present my research on the SARS-CoV-2 evolution.
Venue: via Zoom
Event Official Language: English
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Seminar
Revisiting Standard Methods for Phylogenetic Tree Inference
December 16 (Thu) 10:00 - 11:00, 2021
Motomu Matsui (Research Associate, Graduate School of Science, The University of Tokyo)
Phylogenetic tree inference is the foundation to answer any biological questions, for example, how the living systems were established. However, the existing methods show poor performance to infer the phylogenetic tree when constructing an informative multiple sequence alignment (MSA) is difficult. In this talk, I will first review the current problems in phylogenetics, then introduce the graph splitting (GS), and edge perturbation (EP) method. The GS method rapidly reconstructs a protein superfamily-scale phylogenetic tree using a graph-based approach; evolutionary simulation showed that the GS method can accurately reconstruct phylogenetic trees when sequences substantially diverge. The EP method is the bootstrap-like method using pairwise sequence alignment (PSA) instead of MSA, which can provide reliable measurements on the estimated branches. In addition, we can rapidly and reliably reconstruct a phylogenetic tree with problematic MSA switching NJ+EP and GS+EP methods, because the EP method can be applied to the NJ method. These methods not only improve the accuracy of phylogenetic tree inference, but they also could open the door for revisiting phylogenetics.
Venue: via Zoom
Event Official Language: English
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Seminar
Magnetic field dependence of neutrino-driven core-collapse supernova models
December 10 (Fri) 14:00 - 15:00, 2021
Jin Matsumoto (Assistant Professor, Keio Institute of Pure and Applied Sciences (KiPAS), Graduate School of Science and Technology, Keio University)
Massive stars can explode and release huge energy (typically 10^51 erg) at the end of their life. It is one of the most energetic explosions in the Universe and is called a core-collapse supernova. The impact of the magnetic field on the explosion mechanisms of the core-collapse supernova is a long-standing mystery. Recently, we have updated our neutrino-radiation-hydrodynamics supernova code (3DnSNe, Takiwaki et al. 2016) to include magnetohydrodynamics (MHD). Using this code, we have performed three-dimensional MHD simulations for the evolution of non-rotating stellar cores focusing on the difference in the magnetic field of the progenitors. Initially, 20 and 27 solar mass pre-supernova progenitors are threaded by only the poloidal component of the magnetic field, which strength is 10^10 (weak) or 10^12 (strong) G. We find that the neutrino-driven explosion occurs in both the weak and strong magnetic field models. The neutrino heating is the main driver for the explosion in our models, whereas the strong magnetic field slightly supports the explosion. In my talk, I will introduce the details of this mechanism.
Venue: via Zoom
Event Official Language: English
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Seminar
Selective inference for testing trees and edges in hierarchical clustering and phylogeny
December 9 (Thu) 10:00 - 11:00, 2021
Hidetoshi Shimodaira (Professor, Graduate School of Informatics, Kyoto University / Team Leader, Mathematical Statistics Team, RIKEN Center for Advanced Intelligence Project (AIP))
Bootstrap resampling is quite useful for computing “confidence values” or “p-values” of trees and edges. However, they are biased and may lead to false positives (too many wrong discoveries) or false negatives (too few correct discoveries) depending on the “curvature” of the boundary surface of a hypothesis region in the data space. In addition, we face the issue of selection bias because we tend to use the dataset twice for hypothesis selection and its evaluation. I will explain these two types of bias and show methods to adjust the confidence values.
Venue: via Zoom
Event Official Language: English
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Seminar
The Conley index of topological dynamical systems
December 3 (Fri) 16:00 - 18:00, 2021
Yosuke Morita (Assistant Professor, Department of Mathematics, Kyoto University)
The study of topological dynamical systems, i.e. continuous self-homeomorphisms (or continuous flows) on topological spaces, is important in both pure mathematics and applications. To each isolated invariant subset of a topological dynamical system, we can assign an invariant called the Conley index, which is (roughly speaking) a based space that describes the dynamics around the isolated invariant subset. It is used not only in the study of topological dynamical systems themselves but also in Manolescu’s construction of the Seiberg-Witten-Floer homotopy type (a spectrum-valued (3+1)-dimensional TQFT). In this talk, I am planning to explain a new construction of Conley indices, which is entirely non-homotopical and uses only basic general topology. *Please contact Keita Mikami or Hiroyasu Miyazaki's mailing address to get access to the Zoom meeting room.
Venue: via Zoom
Event Official Language: English
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Seminar
Self-adjointness from quantum-classical correspondence
November 26 (Fri) 16:00 - 18:00, 2021
Koichi Taira (Assistant Professor, College of Science and Engineering Department of Mathematical Sciences, Ritsumeikan University)
Self-adjointness is a fundamental property of a linear operator in quantum mechanics. In physics, a self-adjoint operator is usually defined to be an operator which is own adjoint. However, this definition is in fact not satisfactory since a self-adjoint operator in this definition does not always have nice properties such as the spectral decomposition. Hence, in mathematics, a kind of completeness is also assumed in the definition of a self-adjoint operator. Here a natural question is how to judge whether an operator is self-adjoint. It has been believed that self-adjointness is closely related to completeness of the classical dynamics for a long time although a complete description of such relations has not been given so far. I am planning to talk about how self-adjointness is important in mathematical physics. Moreover, I will explain relations between self-adjointness and classical dynamics by introducing some examples. *Please contact Keita Mikami or Hiroyasu Miyazaki's mailing address to get access to the Zoom meeting room.
Venue: via Zoom
Event Official Language: English