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

June 3 (Thu) at 10:00 - 11:00, 2021

Yingying Xu (Special Postdoctoral Researcher, iTHEMS)

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.

Venue: via Zoom

Event Official Language: English

iTHEMS-phys Intro Meeting on June 1, 2021

June 1 (Tue) at 13:00 - 15:00, 2021

Kengo Kikuchi (Special Postdoctoral Researcher, iTHEMS)
Enrico Rinaldi (Research Fellow, Physics Department, University of Michigan, USA)
Hiroshi Yokota (Postdoctoral Researcher, iTHEMS)

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

Venue: via Zoom

Event Official Language: English

iTHEMS-phys Intro Meeting on May 31, 2021

May 31 (Mon) at 13:00 - 15:00, 2021

Ryo Namba (Senior Research Scientist, iTHEMS)
Naritaka Oshita (Special Postdoctoral Researcher, iTHEMS)
Yuki Yokokura (Senior Research Scientist, iTHEMS)
Shigehiro Nagataki (Deputy Program Director, iTHEMS)

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

Venue: via Zoom

Event Official Language: English

Magnetorotational Instability: Current Understanding and Perspective

May 28 (Fri) at 16:00 - 17:00, 2021

Takashi Minoshima (Researcher, Japan Agency for Marine-Earth Science and Technology (JAMSTEC))

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.

Venue: via Zoom

Event Official Language: English

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

May 27 (Thu) at 10:00 - 11:00, 2021

Kouki Uchinomiya (Central Research Institute of Electric Power Industry)

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.

Venue: via Zoom

Event Official Language: English

Theory of Anomalous Floquet Higher-Order Topology

May 26 (Wed) at 22:00 - 23:15, 2021

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.

Venue: via Zoom

Event Official Language: English

iTHEMS-phys Intro Meeting on May 25, 2021

May 25 (Tue) at 13:00 - 15:00, 2021

Takuya Sugiura (Postdoctoral Researcher, iTHEMS)
Takumi Doi (Senior Research Scientist, Quantum Hadron Physics Laboratory, RIKEN Nishina Center for Accelerator-Based Science (RNC))
Shoichiro Tsutsui (Special Postdoctoral Researcher, Quantum Hadron Physics Laboratory, RIKEN Nishina Center for Accelerator-Based Science (RNC))
Kanato Goto (Special Postdoctoral Researcher, iTHEMS)

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

Venue: via Zoom

Event Official Language: English

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

May 24 (Mon) at 16:00 - 18:10, 2021

Michiya Mori (Special Postdoctoral Researcher, iTHEMS)

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.

Venue: via Zoom

Event Official Language: English

iTHEMS-phys Intro Meeting on May 24, 2021

May 24 (Mon) at 13:00 - 14:30, 2021

Hidetoshi Taya (Special Postdoctoral Researcher, iTHEMS)
Yuta Sekino (Visiting Researcher, iTHEMS)
Ching-Kai Chiu (Senior Research Scientist, iTHEMS)

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

Venue: via Zoom

Event Official Language: English

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

May 20 (Thu) at 10:00 - 11:00, 2021

Kyohei Uemoto (Kyoto University / NARA Institute of Science and Technology)

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.

Venue: via Zoom

Event Official Language: English

Journal Club: Intrinsically Disordered Region (IDR)

May 19 (Wed) at 13:00 - 14:00, 2021

Kyosuke Adachi (Special Postdoctoral Researcher, iTHEMS / Special Postdoctoral Researcher, Nonequilibrium Physics of Living Matter RIKEN Hakubi Research Team, RIKEN Center for Biosystems Dynamics Research (BDR))

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.

Venue: via Zoom

Event Official Language: English

iTHEMS-phys Intro Meeting on May 18, 2021

May 18 (Tue) at 13:00 - 14:30, 2021

Masaru Hongo (Postdoctoral Research Associate, Physics Department, The University of Illinois at Chicago (UIC), USA)
Etsuko Itou (Contract Researcher, Strangeness Nuclear Physics Laboratory, RIKEN Nishina Center for Accelerator-Based Science (RNC))
Nobuyuki Matsumoto (Special Postdoctoral Researcher, Computing Group, RIKEN BNL Research Center, RIKEN Nishina Center for Accelerator-Based Science (RNC))

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

Venue: via Zoom

Event Official Language: English

iTHEMS-phys Intro Meeting on May 17, 2021

May 17 (Mon) at 13:00 - 14:30, 2021

Tetsuo Hatsuda (Program Director, iTHEMS)
Akira Harada (Special Postdoctoral Researcher, iTHEMS)
Tsukasa Tada (Vice Chief Scientist, Quantum Hadron Physics Laboratory, RIKEN Nishina Center for Accelerator-Based Science (RNC))

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

Venue: via Zoom

Event Official Language: English

Geometry of canonical metrics on Kähler manifolds

May 14 (Fri) at 16:00 - 18:10, 2021

Eiji Inoue (Special Postdoctoral Researcher, iTHEMS)

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.

Venue: via Zoom

Event Official Language: English

Modeling Membrane Morphological Change during Autophagosome Formation

May 14 (Fri) at 10:00 - 11:00, 2021

Yuji Sakai (Visiting Scientist, iTHEMS / Assistant Professor, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo)

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.

Venue: via Zoom

Event Official Language: English

Aperiodic and amorphous topological phases

May 12 (Wed) at 17:00 - 18:15, 2021

Christopher Bourne (Visiting Scientist, iTHEMS / Assistant Professor, Advanced Institute for Materials Research (AIMR), Tohoku University)

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.

Venue: via Zoom

Event Official Language: English

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

May 12 (Wed) at 10:00 - 11:00, 2021

Takahiro Nishimichi (Yukawa Institute for Theoretical Physics, Kyoto University)

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.

Venue: via Zoom

Event Official Language: English

Kullback-Leibler divergence and stochastic dynamics

May 6 (Thu) at 10:00 - 11:00, 2021

Ryosuke Iritani (Research Scientist, iTHEMS)

*Detailed information about the seminar refer to the email.

Event Official Language: English

Thermodynamic Uncertainty Relation Connects Physics, Information Science, and Biology

April 28 (Wed) at 13:30 - 16:00, 2021

Yoshihiko Hasegawa (Associate Professor, Department of Information and Communication Engineering, The University of Tokyo)

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.

Venue: via Zoom

Event Official Language: English

The 15th MACS Colloquium

April 23 (Fri) at 15:00 - 17:30, 2021

Hiroshi Ishikawa (Professor, Faculty of Science and Engineering, Waseda University)

15:00- Talk by Prof. Hiroshi Ishikawa 16:05- MACS Student Conference FY2021

Venue: via Zoom

Event Official Language: Japanese