An overview of genome-wide epistasis and co-selection analysis

2021年6月3日(木) 10:00 - 11:00

許 インイン (数理創造プログラム 基礎科学特別研究員)

This talk is a summary of research that have done by me and my team during 2016~2019. I was a postdoc researcher in Aalto university/Helsinki university in Finland. In the team, a worldwide active collaboration has happened between many fields including statistical physics, biology, computer science and statistics. The target is to analyze ultra-high dimensional large population genomic datasets of two major human pathogens, Streptococcus pneumoniae and Neisseria meningitidis, without phenotypic data. Interacting networks of resistance, virulence and core machinery genes are identified. Many different approaches have been invented and they can be generally applied to other datasets with similar mathematical setting. I will explain methods based on statistical model [1,2], mutual information [3], and theoretical performance analysis for statistical model [4]. In the end, I will briefly introduce a new phenomenon of random matrix which is discovered during the research process for statistical significance filtering [5]. *Please refer to the email to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

iTHEMS-phys Intro Meeting on June 1, 2021

2021年6月1日(火) 13:00 - 15:00

菊地 健吾 (数理創造プログラム 基礎科学特別研究員)
リナルディ エンリコ (Research Fellow, Physics Department, University of Michigan, USA)
横田 宏 (数理創造プログラム 特別研究員)

13:00-13:20 [JST] Kengo Kikuchi 13:20-13:40 [JST] Enrico Rinaldi 13:40-14:00 [JST] Hiroshi Yokota 14:00- Free discussion

会場: via Zoom

イベント公式言語: 英語

iTHEMS-phys Intro Meeting on May 31, 2021

2021年5月31日(月) 13:00 - 15:00

難波 亮 (数理創造プログラム 上級研究員)
大下 翔誉 (数理創造プログラム 基礎科学特別研究員)
横倉 祐貴 (数理創造プログラム 上級研究員)
長瀧 重博 (数理創造プログラム 副プログラムディレクター)

13:00-13:20 [JST] Ryo Namba 13:20-13:40 [JST] Naritaka Oshita (10 mins break) 13:50-14:10 [JST] Yuki Yokokura 14:10-14:30 [JST] Shigehiro Nagataki 14:30- Free discussion

会場: via Zoom

イベント公式言語: 英語

Magnetorotational Instability: Current Understanding and Perspective

2021年5月28日(金) 16:00 - 17:00

簑島 敬 (海洋研究開発機構 (JAMSTEC) 副主任研究員)

The differentially rotating flow can be destabilized in the presence of a weak magnetic field through the magnetorotational instability (MRI). The MRI is considered as a possible mechanism for outward angular momentum transport and subsequent mass accretion in accretion disks. Numerous studies have been devoted to understand its nature and judge whether it can supply the power sufficient for observed transport efficiency. For example, the MHD simulation studies have attempted to reveal the scaling of the MRI on numerical (e.g., resolution and domain size) as well as physical parameters (e.g., magnetic field intensity and configuration). In this talk, I would like to discuss current understanding and perspective of the MRI through theoretical and numerical studies. I will especially focus on the impact of transport coefficients (viscosity, resistivity, and their ratio) on the evolution of the MRI and disk.

会場: via Zoom

イベント公式言語: 英語

A Mathematical Model for Stem Cell Competition to Maintain a Cell Pool Injured by Radiation Exposure

2021年5月27日(木) 10:00 - 11:00

内之宮 光紀 (電力中央研究所)

Cancer risk of low-dose-rate ionizing radiation exposure is one of the most important issues in radiation protection. Tissue stem cells have been considered one of the targets of radiation-induced carcinogenesis. There has been a hypothesis that the carcinogenic effects of radiation can be reduced if damaged stem cells are eliminated via stem cell competition between damaged and intact stem cells. This would be particularly effective under very low-dose-rate conditions, where only a few stem cells in a stem cell pool are affected by radiation. In this presentation, I will introduce a simple mathematical model to discuss the influence of stem cell competition on the accumulation of radiation damage and show that the character of damaged cells and the size of the stem cell pool may affect the accumulation of radiation damage. *Please refer to the email to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

Theory of Anomalous Floquet Higher-Order Topology

2021年5月26日(水) 22:00 - 23:15

Rui-Xing Zhang (University of Maryland, College Park, USA)

Periodically-driven or Floquet systems can realize anomalous topological phenomena that do not exist in any equilibrium states of matter, whose classification and characterization require new theoretical ideas that are beyond the well-established paradigm of static topological phases. In this work, we provide a general framework to understand anomalous Floquet higher-order topological insulators (AFHOTIs), the classification of which has remained a challenging open question. In two dimensions (2D), such AFHOTIs are defined by their robust, symmetry-protected corner modes pinned at special quasienergies, even though all their Floquet bands feature trivial band topology. The corner-mode physics of an AFHOTI is found to be generically indicated by 3D Dirac/Weyl-like topological singularities living in the phase spectrum of the bulk time-evolution operator. Physically, such a phase-band singularity is essentially a "footprint" of the topological quantum criticality, which separates an AFHOTI from a trivial phase adiabatically connected to a static limit. Strikingly, these singularities feature unconventional dispersion relations that cannot be achieved on any static lattice in 3D, which, nevertheless, resemble the surface physics of 4D topological crystalline insulators. We establish the above higher-order bulk-boundary correspondence through a dimensional reduction technique, which also allows for a systematic classification of 2D AFHOTIs protected by point group symmetries. We demonstrate applications of our theory to two concrete, experimentally feasible models of AFHOTIs protected by C2 and D4 symmetries, respectively. Our work paves the way for a unified theory for classifying and characterizing Floquet topological matters. *Detailed information about the seminar refer to the email.

会場: via Zoom

イベント公式言語: 英語

iTHEMS-phys Intro Meeting on May 25, 2021

2021年5月25日(火) 13:00 - 15:00

杉浦 拓也 (数理創造プログラム 特別研究員)
土井 琢身 (理化学研究所 仁科加速器科学研究センター (RNC) 量子ハドロン物理学研究室 専任研究員)
筒井 翔一朗 (理化学研究所 仁科加速器科学研究センター (RNC) 量子ハドロン物理学研究室 基礎科学特別研究員)
後藤 郁夏人 (数理創造プログラム 基礎科学特別研究員)

13:00-13:20 [JST] Takuya Sugiura 13:20-13:40 [JST] Takumi Doi (10 mins break) 13:50-14:10 [JST] Schoichiro Tsutsui 14:10-14:30 [JST] Kanato Goto 14:30- Free discussion

会場: via Zoom

イベント公式言語: 英語

Loewner's theorem for maps on operator domains / The structure of maps on the space of all quantum pure states that preserve a fixed quantum angle

2021年5月24日(月) 16:00 - 18:10

森 迪也 (数理創造プログラム 基礎科学特別研究員)

This talk is divided into two independent topics. In the first part of my talk we consider the order structure of hermitian matrices. Given two matrix domains (open connected sets of n-by-n hermitian matrices), what is the general form of order isomorphisms between them? I will explain that there is a complete correspondence between the class of order isomorphisms and that of biholomorphic mappings. In the second part we consider the metric structure of the space P(H) of all quantum pure states (= the projective space of a complex Hilbert space H). Wigner's theorem asserts that every surjective isometry of P(H) onto itself is implemented by a unitary or an antiunitary operator. Uhlhorn generalized Wigner's theorem by showing that every bijective transformation of P(H) that preserves orthogonality is implemented by a unitary or an antiunitary operator. We consider some variants of Uhlhorn's result. The first part is joint work with P. Semrl (Univ. of Ljubljana), and the second part with G.P. Geher (Univ. of Reading). Only basic linear algebra is assumed in both parts.

会場: via Zoom

イベント公式言語: 英語

iTHEMS-phys Intro Meeting on May 24, 2021

2021年5月24日(月) 13:00 - 14:30

田屋 英俊 (数理創造プログラム 基礎科学特別研究員)
関野 裕太 (数理創造プログラム 訪問研究員)
邱 靖凱 (数理創造プログラム 上級研究員)

13:00-13:20 [JST] Hidetoshi Taya 13:20-13:40 [JST] Yuta Sekino 13:40-14:00 [JST] Ching-Kai Chiu 14:00- Free discussion

会場: via Zoom

イベント公式言語: 英語

Organ-to-organ two-way coupling contributes to the stabilization of circadian clock in Arabidopsis.

2021年5月20日(木) 10:00 - 11:00

上本 恭平 (京都大学 / 奈良先端科学技術大学院大学)

Circadian clocks increase plant fitness by anticipating periodic environmental changes using unstable temporal information perceived in each tissue/organ. However, little is known about how such local and noisy temporal information regulates global and coordinated plant growth. Here, we show that nutrient-mediated two-way communication between shoots and roots stabilizes circadian rhythms and aids plant growth. The photosynthetic product, sucrose, is transported from the shoot to the root, where it regulates the expression of a clock gene and nutrients uptake rhythms. A lack of nutrient rhythms destabilizes the shoot circadian rhythms and reduces the growth rate. Our mathematical model supports that two-way communication between organs reduces the heterogeneity of the circadian rhythm, thereby maintaining the robustness of the circadian clock in a noisy environment. As with feedback loops in other hierarchies, nutrient-mediated shoot-root interorgan communication of the circadian clock is advantageous for proper growth under fluctuating environmental conditions. *Please refer to the email to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

Journal Club: Intrinsically Disordered Region (IDR)

2021年5月19日(水) 13:00 - 14:00

足立 景亮 (数理創造プログラム 基礎科学特別研究員 / 理化学研究所 生命機能科学研究センター (BDR) 生体非平衡物理学理研白眉研究チーム 基礎科学特別研究員)

A class of protein domain, which is called intrinsically disordered region (IDR), is known to take no rigid three dimensional structure. Recent studies have shown that IDRs can show biological functions through phase separation, and it is important to clarify what kind of amino acid sequence of IDR leads to phase separation and what kind of mutation results in malfunction. In this journal club, I will discuss these topics by reviewing recent papers. *Detailed information about the seminar refer to the email.

会場: via Zoom

イベント公式言語: 英語

iTHEMS-phys Intro Meeting on May 18, 2021

2021年5月18日(火) 13:00 - 14:30

本郷 優 (Postdoctoral Research Associate, Physics Department, The University of Illinois at Chicago (UIC), USA)
伊藤 悦子 (理化学研究所 仁科加速器科学研究センター (RNC) ストレンジネス核物理研究室 協力研究員)
松本 信行 (理化学研究所 仁科加速器科学研究センター (RNC) 理研BNL研究センター 計算物理研究グループ 基礎科学特別研究員)

13:00-13:20 [JST] Masaru Hongo 13:20-13:40 [JST] Etsuko Itou 13:40-14:00 [JST] Nobuyuki Matsumoto 14:00- Free discussion

会場: via Zoom

イベント公式言語: 英語

iTHEMS-phys Intro Meeting on May 17, 2021

2021年5月17日(月) 13:00 - 14:30

初田 哲男 (数理創造プログラム プログラムディレクター)
原田 了 (数理創造プログラム 基礎科学特別研究員)
多田 司 (理化学研究所 仁科加速器科学研究センター (RNC) 量子ハドロン物理学研究室 副主任研究員)

13:00-13:20 [JST] Tetsuo Hatsuda 13:20-13:40 [JST] Akira Harada 13:40-14:00 [JST] Tsukasa Tada 14:00- Free discussion

会場: via Zoom

イベント公式言語: 英語

Geometry of canonical metrics on Kähler manifolds

2021年5月14日(金) 16:00 - 18:10

井上 瑛二 (数理創造プログラム 基礎科学特別研究員)

The aim of this talk is to report recent trends in Kähler geometry. Kähler geometry consists of two aspects: the one is algebraic geometry and the other is metric geometry.The first one hour is an introduction for non-mathematicians. I begin with a simple example of algebraic variety from ancient Greek, which I believe is the simplest example illustrating motivation for compact complex manifolds. On the other hand, I explain the first motivation for canonical metrics in Kähler geometry via Riemann’s uniformization theorem.The last one hour is an introduction to recent trends in Kähler geometry, especially Kähler-Einstein metrics. The existence of Kähler-Einstein metrics turns out to be related to geometry of degenerations of space, which is so called Yau-Tian-Donaldson conjecture. I explain various aspects of this topic. We encounter deep studies in metric geometry, birational geometry and non-archimedean geometry. I finally explain recent breakthrough on Kähler-Ricci flow.The goal of this talk is the starting point of my study. I briefly explain my study if time permits.

会場: via Zoom

イベント公式言語: 英語

Modeling Membrane Morphological Change during Autophagosome Formation

2021年5月14日(金) 10:00 - 11:00

境 祐二 (数理創造プログラム 客員研究員 / 東京大学 大学院医学系研究科 助教)

Membrane-bound organelles compartmentalize eukaryotic cells and adopt various characteristic shapes such as disk-shaped, tubules, spherical vesicles, and their intermediate structures. Organellar morphology is regulated by protein and lipid compositions. Because organellar shape directly relates to organellar function, it is important to understand the mechanisms regulating organelle morphology. In autophagy, the morphologies of the isolation membrane change from disk- to cup-shaped, closed spherical double-membrane structure. Eventually the membrane engulfs the cytoplasmic materials. In this study [1], we investigate the dynamics of the continuous membrane morphological transition in autophagy, which is governed by the spatiotemporal regulation of curvature generators. *Please refer to the email to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

Aperiodic and amorphous topological phases

2021年5月12日(水) 17:00 - 18:15

クリストファー・ボーン (数理創造プログラム 客員研究員 / 東北大学 材料科学高等研究所 (AIMR) 助教)

Key features of topological insulators and superconductors such as stable edge modes have been found in an increasingly broad class of materials and systems. In this talk, I will introduce a mathematical framework to study Hamiltonians and topological phases on a general class of (aperiodic/random) point atterns. Using techniques from noncommutative geometry, we then show how bulk topological invariants and the bulk-boundary correspondence can be rigorously established in such generic systems. This is based on joint work with Emil Prodan and Bram Mesland. *Detailed information about the seminar refer to the email.

会場: via Zoom

イベント公式言語: 英語

Emulation for lensing and clustering observables of the cosmological large-scale structure

2021年5月12日(水) 10:00 - 11:00

西道 啓博 (京都大学 基礎物理学研究所)

Recent developments in observational technologies open exciting opportunities to map out the detailed structure of the universe. Remarkably, the unique combination of imaging and spectroscopic galaxy surveys is now becoming well established as a standard analysis methodology for precision cosmology. While the former can access directly the underlying clustering of mass dominated by dark matter projected on the sky through the weak gravitational lensing effect, the latter provides us with the three dimensional map of the structure traced by galaxies. One can mitigate the galaxy-bias uncertainty, which has been the major obstacle for cosmology based on galaxy surveys, by jointly analyzing these effects. We still need, however, a robust and versatile theoretical and statistical framework to interpret these datasets. The Dark Quest project, launched in 2015, is a structure formation simulation campaign precisely for this purpose. We have developed an emulation tool, dubbed as Dark Emulator, based on a large database of simulated dark matter halos in virtual universes with different cosmologies efficiently sampled in six-dimensional parameter space. Dark Emulator employs a simple machine-learning architecture with Gaussian process at its core. It makes predictions of various statistical measures of dark matter halos, both lensing and clustering observables, for a given cosmological parameters in a few seconds on laptop computers without running a new simulation. This AI-aided tool, once supplemented with recipes for the halo-galaxy connection, is therefore applicable to real-data analyses as the theoretical template, which typically requires hundreds of thousands of function calls in the course of parameter inference. I will introduce this project and report the status of its application to Subaru HSC data. We are looking forward to seeing you online.

会場: via Zoom

イベント公式言語: 英語

Kullback-Leibler divergence and stochastic dynamics

2021年5月6日(木) 10:00 - 11:00

入谷 亮介 (数理創造プログラム 研究員)

*Detailed information about the seminar refer to the email.

イベント公式言語: 英語

Thermodynamic Uncertainty Relation Connects Physics, Information Science, and Biology

2021年4月28日(水) 13:30 - 16:00

長谷川 禎彦 (東京大学 大学院情報理工学系研究科 准教授)

Higher precision demands more resources. Although this fact is widely accepted, it has only recently been theoretically proved. The thermodynamic uncertainty relation serves as a theoretical basis for this notion, and it states that current fluctuations are bounded from below by thermodynamic costs, such as entropy production and dynamical activity. In this seminar, I show a strong connection between the thermodynamic uncertainty relation and information theory by deriving it through information inequality known as a Cramér-Rao bound, which provides the error bound for any statistical estimator. Moreover, by using a quantum Cramér-Rao bound, I derive a quantum extension of thermodynamic uncertainty relation, which holds for general open quantum systems. The thermodynamic uncertainty relation predicts the fundamental limit of biomolecular processes, and thus it can be applied to infer the entropy production, corresponding to the consumption of adenosine triphosphate, of biological systems in the absence of detailed knowledge about them. *Detailed information about the seminar refer to the email.

会場: via Zoom

イベント公式言語: 英語

第15回 MACSコロキウム・2021年度MACS学生説明会

2021年4月23日(金) 15:00 - 17:30

石川 博 (早稲田大学 理工学術院 基幹理工学部 情報理工学科 教授)

15:00- 石川 博 博士「機械に認識させるとはどういうことか」 16:05- 2021年度MACS学生説明会

会場: via Zoom

イベント公式言語: 日本語