Volume 188

iTHEMS Weekly News Letter

Event Schedule

Events for the 2nd week of March 2022

2022-03-03

Thursday, March 10, 8:00– 9:30 External Event: Fundamentals Fest, mini Pre-event on Science "Exploring and Bridging: The Potential of Basic Science"
Thursday, March 10, 10:00– 11:00 iTHEMS Biology Seminar
Thursday, March 10, 13:30– 15:00 NEW WG Seminar
Friday, March 11, 12:30- 13:30 Coffee Meeting
Friday, March 11, 16:00- 18:00 iTHEMS Math Seminar
Saturday, March 12, 13:00- 14:30 Special Lecture: 【Shigefumi Mori and Takashi Sakajo Special Talk】How is mathematics utilized in society? - Exploring the Essence of Mathematical Research

Seminar Report

iTHEMS Biology Seminar by Dr. Ashley Nord and Dr. Rubén Pérez-Carrasco on February 24, 2022

2022-03-01

Dr. Ashley Nord (Centre de Biologie Structurale/CNRS, France) and Dr. Rubén Pérez-Carrasco (Imperial College London, UK) gave a very interesting talk on the dynamics of stator units, the ion channels that generate torque for bacterial flagella.

In the first half of the presentation, Dr. Ashley explained how the stator units produce torque once they are bound to the flagellar structure. Their experiment was able a) to track magnetic nanoparticles attached to E. coli flagella, and b) to set two initial conditions for the number of bound stator units. The work differs from the traditional views of the field because it shows -- for the first time -- the existence of two sets of relaxation times for stator units [1,2].

In the second part of the talk, Dr. Rúben discussed various stochastic models with asymmetric relaxation times to describe the dynamics of stator units. According to estimates via approximate Bayesian computation, the extended catch bond model with additional bound states performed better than other alternatives. If confirmed, their conclusion could give important hints and improve our understanding of biochemical processes in flagellar motors.

Reported by Gilberto Nakamura

References

  1. Ruben Perez-Carrasco, et al, Relaxation time asymmetry in stator dynamics of the bacterial flagellar motor, bioRxiv 2021.07.05.451114 (2021), doi: 10.1101/2021.07.05.451114
  2. Ruben Perez-Carrasco, et al, Science Advances (2022)
Stator dynamics of the bacterial flagellar motor image

Seminar Report

Quantum Matter SG seminar by Dr. Hong-Yan Shih on February 24, 2022

2022-02-28

The Quantum Matter Study Group invited Dr. Hong-Yan Shih from Academia Sinica to talk about the phase transitions of turbulence dynamics. In the beginning, she introduced the turbulence and the phase transition between laminar flow and turbulence. Surprisingly, this phase transition shares a unified picture with the predator-prey system. Then, she showed the connection between this fluid dynamics and the biosystem with the same university class. It is an inspiring interdisciplinary study.

Reported by Ching-Kai Chiu

Upcoming Events

External Event

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Fundamentals Fest, mini Pre-event on Science "Exploring and Bridging: The Potential of Basic Science"

March 10 (Thu) at 8:00 - 9:30, 2022

Makiko Sasada (Visiting Scientist, Mathematical Statistics Team, RIKEN Center for Advanced Intelligence Project (AIP) / Associate Professor, Graduate School of Mathematical Sciences, The University of Tokyo)
Tetsuo Hatsuda (Program Director, iTHEMS)
Juichi Yamagiwa (Director-General, Research Institute for Humanity and Nature)

Unlike applied science and technology, basic science has a high degree of independence, making it difficult to have contact with society. In today's world where science and technology are maturing, there are many issues on how to bridge the gap between academic knowledge and society from the aspect of science/technology and ethics. However, there are not many opportunities to discuss such bridging activities. In this session, we would like to discuss the peculiarities and possibilities to bridge the basic science and society.

Program (Morning)
8:00-8:10 Introduction (What is the Fundamentals Fest)
8:10-8:40 Self-introduction by speakers
8:40-9:20 Discussion
9:20-9:30 Questions and Answers

Participation Fee: Free

See related links for details.

Venue: via YouTube Live

Event Official Language: Japanese

Seminar

Atsushi Mochizuki thumbnail

iTHEMS Biology Seminar

Independent regulation of multiple checkpoints in cell-cycle network system -Biological function originated in the law of localization-

March 10 (Thu) at 10:00 - 11:00, 2022

Atsushi Mochizuki (Professor, Institute for Frontier Life and Medical Sciences, Kyoto University)

In cell cycle, G1-S and G2-M checkpoints are regulated by different protein complexes, Cdc2-Cdc13 and Cdc2-Cig2, respectively. For a normal mitosis, activity of two complexes should rise specifically at different timing. However, the complex formations share common species of proteins and activation reactions conform a complicated network. We study how independent regulation of two checkpoints is realized in the network system by “structural sensitivity analysis”, which was previously established by us. The analyses clarified that activities of two complexes are regulated by disjoint sets of reaction parameters in the system. A series of non-trivial behaviors are generated by “buffering structures with an intersection”, which can generally appear in chemical reaction network including complex formation.

Venue: via Zoom

Event Official Language: English

Seminar

NEW WG Seminar

Nonperturbative cavity/waveguide quantum electrodynamics and dissipative quantum phase transition

March 10 (Thu) at 13:30 - 15:00, 2022

Yuto Ashida (Associate Professor, Graduate School of Science, The University of Tokyo)

Strong coupling between matter and quantized electromagnetic modes in cavity or waveguide may offer yet another approach of controlling equilibrium phases or dynamics of many-body systems. Recent developments have realized such strong light-matter interaction in genuinely quantum and nonperturbative regimes, where conventional approximate theoretical methods cannot be applied in general. I will talk about how one can analyze strongly coupled quantum light-matter systems at arbitrary interaction strengths on the basis of an asymptotically disentangling unitary transformation [1,2]. I discuss its application to construction of tight-binding Hamiltonians, dynamics of bound states in the continuum, and revisiting dissipative quantum phase transition in resistively shunted Josephson junctions [3].

References

  1. Y. Ashida, A. Imamoglu and E. Demler, Cavity Quantum Electrodynamics at Arbitrary Light-Matter Coupling Strengths, Phys. Rev. Lett (2021), doi: 10.1103/PhysRevLett.126.153603
  2. Yuto Ashida, Takeru Yokota, Atac Imamoglu, Eugene Demler, Nonperturbative Waveguide Quantum Electrodynamics, arXiv: 2105.08833
  3. K. Masuki, H. Sudo, M. Oshikawa and Y. Ashida, Absence versus Presence of Dissipative Quantum Phase Transition in Josephson Junctions, arXiv: 2111.13710

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Math Seminar

Extracting rules from trained machine learning models with applications in Bioinformatics

March 11 (Fri) at 16:00 - 18:00, 2022

Pengyu Liu (Postdoctoral Researcher, Medical Data Mathematical Reasoning Team, RIKEN Information R&D and Strategy Headquarters (R-IH))

Recently, Machine learning methods have achieved great success in various areas. However, some machine learning-based models are not explainable (e.g., Artificial Neural Networks), which may affect the massive applications in medical fields.

In this talk, we first introduce two approaches that extract rules from trained neural networks. The first one leads to an algorithm that extracts rules in the form of Boolean functions. The second one extracts probabilistic rules representing relations between inputs and the output. We demonstrate the effectiveness of these two approaches by computational experiments.

Then we consider applying an explainable machine learning model to predict human Dicer cleavage sites. Human Dicer is an enzyme that cleaves pre-miRNAs into miRNAs. We develop an accurate and explainable predictor for the human Dicer cleavage site -- ReCGBM. Computational experiments show that ReCGBM achieves the best performance compared with several existing methods. Further, we find that features close to the center of pre-miRNA are more important for the prediction.

Venue: via Zoom

Event Official Language: English

Special Lecture

[Shigefumi Mori and Takashi Sakajo Special Talk] How is mathematics utilized in society? - Exploring the Essence of Mathematical Research

March 12 (Sat) at 13:00 - 14:30, 2022

Tetsuo Hatsuda (Program Director, iTHEMS)
Takashi Sakajo (Professor, Department of Mathematics, Kyoto University)
Shigefumi Mori (Director-General, Kyoto University Institute for Advanced Study (KUIAS))

Venue: via Zoom

Event Official Language: Japanese

Upcoming Visitors

March 7 (Mon) - 11 (Fri), 2022

Issei Koga

Ph.D. Student, Department of Physics, Graduate School of Science, Kyushu University

March 7 (Mon) - 18 (Fri), 2022

Kazushige Ueda

Ph.D. Student, Department of Physics, Graduate School of Science, Kyushu University

Person of the Week

Masato Itami thumbnail

Self-introduction: Masato Itami

2022-03-02

My name is Masato Itami, and I have joined iTHEMS as a visiting scientist in March 2022. I love stochastic things by nature, so I am currently studying the universal form of stochastic equations of motion for fluctuating objects in non-equilibrium systems. I am looking forward to interacting with people from various fields. By the way, my hobby is chess, so if you like chess, let's play chess together while/without talking about science.

Paper of the Week

Week 1, March 2022

2022-03-03

Title: Advances in QED with intense background fields
Author: A. Fedotov, A. Ilderton, F. Karbstein, B. King, D. Seipt, H. Taya, G. Torgrimsson
arXiv: http://arxiv.org/abs/2203.00019v1

Title: Nuclear force with LapH smearing
Author: Takuya Sugiura, Yutaro Akahoshi, Tatsumi Aoyama, Takahiro M. Doi, Takumi Doi
arXiv: http://arxiv.org/abs/2202.12532v1

Title: Weighted one-level density of low-lying zeros of Dirichlet $L$-functions
Author: Shingo Sugiyama, Ade Irma Suriajaya
arXiv: http://arxiv.org/abs/2201.00326v1

Title: Zeros of derivatives of $L$-functions in the Selberg class on $\Re(s)<1/2$
Author: Sneha Chaubey, Suraj Singh Khurana, Ade Irma Suriajaya
arXiv: http://arxiv.org/abs/2202.12126v1

Title: Entropies in $μ$-framework of canonical metrics and K-stability, II -- Non-archimedean aspect: non-archimedean $μ$-entropy and $μ$K-semistability
Author: Eiji Inoue
arXiv: http://arxiv.org/abs/2202.12168v1

Title: Revealing time-resolved particle acceleration in the recurrent Nova RS Ophiuchi
Author: H.E.S.S. Collaboration (Naomi Tsuji)
arXiv: http://arxiv.org/abs/2202.08201v1

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