# Event Schedule

## Events for the 4th week of November 2021

2021-11-18

Monday, November 22, 13:30– 15:00 Brownian Motion

Monday, November 25, 13:30– 15:00 NEW WG Seminar

Friday, November 26, 12:30- Coffee Meeting

# Hot Topic

## Farewell message from Dr. Jason Chang

2021-11-16

Our colleague Jason Chang moves on to a new carrier at LinkedIn as of November 14th. We all will miss him and wish him the best of luck in his latest endeavor. Here is a message from Jason:

*It was truly a pleasure to be part of iTHEMS.I have matured so much during this time through all the opportunities that have been made available to me because of how much iTHEMS has supported me in the decisions that I made.I certainly will miss everyone as well.I will move on to a data science position at LinkedIn.If anyone from iTHEMS is curious or has interest in transitioning to some industry position especially around the Bay Area, feel free to reach out to me.I will be more than happy to help with the process and introduce the person to the right recruiters as well.I believe I can convince LinkedIn to let me continue research in quantum algorithms for around 1 day / week as well.So perhaps in the end, I am not going away as far as one might think.The world is quite small after all.My direct manager at LinkedIn was Aida’s postdoc when I was her graduate student.One never knows which doors life decides to open.*

*Kind Regards,Jason*

# Seminar Report

## iTHEMS Biology Seminar by Dr. Takaharu Mori on November 4, 2021

2021-11-17

On Nov 4th 2021, Dr. Takaharu Mori from Molecular Science Lab (Sugita Lab), RIKEN gave an online talk, entitled, "Protein structure modeling from cryo-electron microscopy data". He talked about the theoretical method to determine three-dimensional structures of biomolecules at near-atomic resolution, using a molecular dynamics (MD) simulation and also microscopy data. In addition, he showed their combined approach of coarse-grained model and all-atom model. According to him, Bayesian inference and machine learning are useful for the determination of biomolecule's 3D structure which can be the seeds of future collaborations between us. During the seminar, there were many discussions with iTHEMS members especially about the theoretical method to use recent microscopy data. We enjoyed his talk very much. Thanks, Mori-san!

Reported by Gen Kurosawa

Protein structure modeling from cryo-electron microscopy data

November 4 at 13:30 - 14:30, 2021

# Seminar Report

## iTHEMS Math Seminar by Prof. Naichung Conan Leung on November 5, 2021

2021-11-15

Professor Conan Leung gave an introductory talk to mirror symmetry. He first started with the discussion on the sum of inner angles of a triangle to illustrate the difference between our familiar Euclidean spaces and spaces with nontrivial curvature. He then introduced the notion of complex numbers and how it is related to solving polynomial equations in algebra. Recalling that gravity theory and quantum theory having very different nature of behaviour, he introduced super string theory as a potential unification of these two theories and its great impact to the study of modern mathematics, e.g. enumerative geometry, geometry of special holonomy. Finally he introduced mirror symmetry and how to understand it from the perspective of Fourier transform following a proposal of Strominger, Yau and Zaslow.

Reported by Yalong Cao

Geometry and Physics of Mirror Symmetry

November 5 at 16:00 - 18:00, 2021

# Seminar Report

## iTHEMS Biology Seminar by Dr. Jae Kyoung Kim on November 11, 2021

2021-11-17

On Nov 11th 2021, Prof. Jae Kyoung Kim from KAIST, South Korea gave an online talk at iTHEMS. The title of the talk is “Toward mathematical medicine: development of a new drug and digital medicine for sleep disorders”. In the seminar, Dr. Kim talked about mathematical model (e.g. IBM) of our daily rhythms when environment within cells is crowded by lipids, and its implication for obesity. In addition, he showed their successful collaboration with Pfizer and Samsung medical center. The talk thrilled us very much. There were many intensive discussions with iTHEMS members and also experimental biologists from outside. Thanks, Jae!

Reported by Gen Kurosawa

Toward mathematical medicine: development of a new drug and digital medicine for sleep disorders

November 11 at 12:30 - 13:30, 2021

# Seminar Report

## iTHEMS Math Seminar by Prof. Todor Milanov on November 12, 2021

2021-11-15

Professor Todor Milanov gave a talk on his recent research on K-theoretic GW theory. He first recalled the definition of Gromov-Witten invariants and its K-theoretic generalization. Then he mentioned how to use genus 0 GW invariants to define quantum product on the usual cohomology group of a symplectic manifold. Such formulation has deep connection to integrable systems. He then introduced his research results, including a proof of the fact that small J-function in quantum cohomology of a Fano manifold can be obtained as a limit q -->1 of the small J-function in quantum K-theory.

Reported by Yalong Cao

Confluence for the K-theoretic J-function

November 12 at 16:00 - 18:00, 2021

# Seminar Report

## NEW WG Seminar by Prof. Naoto Nagaosa on November 15, 2021

2021-11-18

Naoto Nagaosa (Tokyo/RIKEN) gave a talk on "Geometry in optical responses of quantum materials." Geometry and topology provide new insight into optical responses of solids and are of interdisciplinary interest in physics. After an excellent review on this topic made over the past decade, Naoto mainly discussed (i) shift current in noncentrosymmetric quantum materials driven by Berry phases, and (ii) Riemannian geometry in nonlinear optical responses. About 50 physicists from various fields have joined the seminar and enjoyed fruitful discussions during and after the seminar.

Reported by Hidetoshi Taya

Geometry in optical responses of quantum materials

November 15 at 13:30 - 15:00, 2021

# Upcoming Events

## Colloquium

### The 17th MACS Colloquium

November 19 at 15:00 - 18:00, 2021

Prof. Momoko Hayamizu (Assistant Professor, Faculty of Science and Engineering, School of Fundamental Science and Engineering, Waseda University / PRESTO Researcher, Japan Science and Technology Agency (JST))

Dr. Shigeru Kuratani (Chief Scientist, Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR) / Team Leader, Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR))

15:00- Talk by Prof. Momoko Hayamizu

16:15- Talk by Dr. Shigeru Kuratani

17:15- Discussion

Venue: via Zoom

Event Official Language: Japanese

## Seminar

### The graph removal lemma

November 19 at 16:00 - 18:00, 2021

Dr. Shinichiro Seki (Assistant Professor, Aoyama Gakuin University)

We have recently proved an extension of the Green-Tao theorem on arithmetic progressions to number fields, in collaboration with Kai, Mimura, Munemasa and Yoshino. (Kai gave a talk on this result in March.) There are several promising approaches in this area, including ergodic theory and Fourier analysis, but we used a combinatorial tool, the relative hypergraph removal lemma proved by Conlon, Fox and Zhao.

In the first half of this talk, I will give a survey of Szemerédi's regularity lemma and the graph removal lemma, and explain how to extend the removal lemma to the case of (weighted) hypergraphs.

In the second half of this talk, I will present Fox's result on a quantitative version of the graph removal, and discuss the prospects for future research.

*Please contact Keita Mikami's mail address to get access to the Zoom meeting room.

Venue: via Zoom

Event Official Language: English

## Seminar

### Imaging Theory of Optical Microscopy: Basic to Super Resolution

November 25 at 13:30 - 15:00, 2021

Prof. Ryosuke Oketani (Assistant Professor, Physical Chemistry, Department of Chemistry, Faculty of Sciences, Kyushu University)

Optical microscopy is one of the sophisticated techniques to manipulate light based on well-established theories, as well as a powerful tool to observe living micro-organisms. The developments are still ongoing to overcome their limitations in observation. Recently, the invention of several super-resolution techniques has overcome the limit in spatial resolution caused by the wave nature of light.

In this presentation, I discuss the theories behind optical microscopy. My talk starts with basic wave optics to explain how a lens forms and magnifies an image in a conventional microscope. Then, I introduce laser scanning microscopy as an alternative form to the microscope. At last, as a recent development, I discuss several super-resolution techniques, which utilize interesting theory to improve spatial resolution.

Venue: via Zoom

Event Official Language: English

## Seminar

### Simulation-based inference for multi-type cortical circuits

November 29 at 13:30 - 15:00, 2021

Dr. Enrico Rinaldi (Research Fellow, Physics Department, University of Michigan, USA)

In many scientific fields, ranging from astrophysics to particle physics and neuroscience, simulators for dynamical systems generate a massive amount of data. One of the crucial tasks scientists are spending their precious time on is comparing observational data to the aforementioned simulations in order to infer physically relevant parameters and their uncertainties, based on the model embedded in the simulator. This poses a problem because the likelihood function for realistic simulations of complex physical systems is intractable. Simulation-based inference techniques attack this problem using machine learning tools and probabilistic programming. I will start with an overview of the problem and explain the general application of simulation-based inference methods. Then I will describe an application of the methods to a model of neurons in the visual cortex of mice."

Venue: via Zoom

Event Official Language: English

# Upcoming Visitor

November 30 - December 4, 2021 ## Prof. Katsuki AokiResearch Assistant Professor, Yukawa Institute for Theoretical Physics, Kyoto University Visiting Place: RIKEN Wako Campus |

# Paper of the Week

## Week 3, November 2021

2021-11-18

Title: Evaluation of origin of the driving force for loop formation in a chromatin fiber

Author: Hiroshi Yokota, Masashi Tachikawa

arXiv: http://arxiv.org/abs/2111.08881v1

Title: Impacts of Jets and Winds From Primordial Black Holes

Author: Volodymyr Takhistov, Philip Lu, Kohta Murase, Yoshiyuki Inoue, Graciela B. Gelmini

arXiv: http://arxiv.org/abs/2111.08699v1

Title: Generalized harmonic analysis reveals a frequency modulated timer regulates mammalian hibernation

Author: Shingo Gibo, Yoshifumi Yamaguchi, Gen Kurosawa

doi: https://doi.org/10.1101/2021.11.12.468369

Title: Nucleon Axial Form Factor from Domain Wall on HISQ

Author: Aaron S. Meyer, Evan Berkowitz, Chris Bouchard, Chia Cheng Chang, M. A. Clark, Ben Hörz, Dean Howarth, Christopher Körber, Henry Monge-Camacho, Amy Nicholson, Enrico Rinaldi, Pavlos Vranas, André Walker-Loud

arXiv: http://arxiv.org/abs/2111.06333v1

Title: Emergence of Hilbert Space Fragmentation in Ising Models with a Weak Transverse Field

Author: Atsuki Yoshinaga, Hideaki Hakoshima, Takashi Imoto, Yuichiro Matsuzaki, Ryusuke Hamazaki

arXiv: http://arxiv.org/abs/2111.05586v1

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