# セミナーレポート

2021-05-31

## Quantum Matter SG seminar by Dr. Rui-Xing Zhang on May 26, 2021

On May 26th, Dr. Rui-Xing Zhang from the University of Maryland gave a talk about the classification of anomalous floquet higher-order topological insulators. He started with a pedagogical introduction to floquet topological insulators, which possess robust boundary states. Notably, there are two types of non-trivial floquet topology. 1. The floquet bands inherit the topology of the static bands. 2. The non-trivial physics of the anomalous floquet topological insulators stems from dynamical phase bands. Dr. Zhang extended the idea of the second type to higher-order topological insulators, which have robust corner states or edge ones. Dr. Zhang specifically discussed the anomalous floquet topology for chiral symmetric systems preserving C2 rotation symmetry. Using this example, he generalized the classification of the topological phases to various point groups. We thank Dr. Zhang for giving this wonderful talk. Reported by Ching-Kai Chiu

2021-05-27

## iTHEMS Biology Seminar by Dr. Kouki Uchinomiya on May 27, 2021

On May 27 (JST), we had online talk by Dr. Kouki Uchinomiya at iTHEMS Biology Seminar. He was one of active members of RIKEN iTHES, and currently he is at Central Research Institute of Electric Power Industry in Tokyo. This time, Kouki talked about radiation and cancer risk. Radiation can cause DNA damage for which it can cause cancer in our body. In the field of radiation and cancer, there has been a mystery that cancer risk decreases as the dose rate of radiation (Gy/h) decreases while the total dose of radiation fixed. By incorporating the competition between the normal and the damaged cells by radiation into a simple mathematical model, he successfully explained the mysterious phenomena. His model revealed that the key parameters including a relative reproductive ability of the damaged cells determine the cancer risk. According to him, those parameters will be experimentally measured in the near future, and we understand that the model should contribute to the quantitative estimation of cancer risk by radiation. During and after the talk, there were stimulating discussions as for the philosophy behind his very simple model and a possible extension to the model with the effect of immune system. We enjoyed his concise talk very much. Thanks Kouki! Reported by Gen Kurosawa

2021-05-27

## Math Seminar by Dr. Michiya Mori on May 24, 2021

On May 24, there was an iTHEMS math seminar by Dr. Michiya Mori. In the first part, he explained his research on Lowebner theorems. He first described the notion of abstract order. He then introduced an order on the space of the hermitian matrix. He explained Molnar's results that the order-preserving map must be affine on a particular good subset of matrices. Lastly, he explained his results with his collaborator that a map on matrix domain is an order isomorphism if and only if it has a good extension to the upper half-space. In the second part, the speaker introduced the projective Hilbert space, the space of all quantum states, and Fubini-Study metric, an "argument" on the projective Hilbert space. He then introduced the result by Wigner that any bijective maps preserving Fubini-Study metric are unitary or anti-unitary. The speaker introduced Uhlhorn's variant of this result: if the dimension of the space is larger than three, any bijection preserving argument π/2 is unitary or anti-unitary. The speaker also explained that Gehér extended Uhlhorn's works for other cases, but there was one open case. The speaker explained his result with Gehér that the variant of the result by Uhlhorn holds for this last case. Reported by Keita Mikami

2021-05-24

## Journal Club of Information Theory SG by Dr. Kyosuke Adachi on May 19, 2021

On May 19, Dr. Kyosuke Adachi talked about “Amino acid sequence and protein phase separation” at the journal club of information theory study group. First, he introduced the history of protein states, from its structure observed with X-ray to intrinsically disordered region (IDR) and liquid-liquid phase separation. In this talk, the speaker focused on IDR and phase separations. Second, he explained some biological functions of phase separation, such as compartmentalization of specific molecules, facilitation of biochemical reaction, and stress response. And the talk moved a question of what kind of sequence feature determines phase properties. Mainly, the speaker discussed coarse-grained models, which are expected to determine phase properties. Finally, he mentioned the problem of how to classifying IDRs and the importance of the coarse-grained sequence. Thank you, Adachi-san, for the interesting talk! Reported by Yukimi Goto

2021-05-20

## Math Seminar by Dr. Iyan Mulia on April 22, 2021

On April 22, the iTHEMS Math seminar was held (Sorry for the delay of the report!). This time, we invited Dr. Iyan Mulia from RIKEN Cluster for Pioneering Research, Prediction Science Laboratory. The title of the talk was “Alternative tsunami observing and forecasting systems”. The main topic of the talk was his work about how to catch and predict tsunami. First, he proposed new approaches to construct tsunami observing systems. There exist various observing systems already, but they share a big problem that they are very expensive. Since observing systems need to be updated regularly, it is very important to reduce the cost. Iyan’s proposal is to make use of existing commercial vessels and airplanes. Since they already exist and form a dense network all over the world, it will suffice to let them observe the sea level altitude and transfer the information. Iyan and his collaborators already demonstrated in experiments that the proposed observing system is accurate enough to detect large tsunamis. Next, he moved to another topic. Once we observe the occurrence of tsunami, next step is to predict its impact in the areas near the coast. While there are conventional mathematical models which provide very accurate prediction, it needs relatively long time for calculation. This is a non-ignorable defect because it means the delay of the warning to residents. If we use linear models instead of the accurate model, the calculation becomes much faster but the accuracy of the prediction gets low. Iyan’s proposal is plug in the Machine Learning techniques to bridge these two models. He trained neural networks to predict the results of the accurate model from the results of the linear model. This method actually gives a satisfactory result: the prediction is very accurate and fast. If this method is accepted widely, it will be possible to predict the effect of tsunami very accurately in very short time. Reported by Hiroyasu Miyazaki

2021-05-14

## iTHEMS Biology Seminar by Prof. Yuji Sakai on May 14, 2021

In iTHEMS Biology Seminar on May 14th, Prof. Yuji Sakai (Univ. of Tokyo) talked about the theoretical model of the autophagosome. First, he explained the autophagosome formation process, where the disk-like and cup-like shapes of the membrane are observed. Then, he talked about the previous theories, where the spontaneous curvature is not considered. Next, he explained his theoretical model, in which the spontaneous curvature is induced and stabilized by the “curvature generator”. By minimizing the free energy in his model, he quantitatively reproduced the autophagosome formation via the disk and the cup. Finally, he mentioned the candidate of the curvature generator. His attractive talk induced various discussions and questions from the audience. Thank you very much for nice talk, Yuji! Reported by Hiroshi Yokota

2021-05-14

## Quantum Matter Seminar by Prof. Christopher Bourne on May 12, 2021

Quantum Matter Study Group invited Prof. Christopher Bourne to give a talk on aperiodic and amorphous topological phases on May 12th, 2021. In the beginning, he reviewed topological phases in lattice systems and introduced integer Chern numbers. To generalize the topological phases, we extend the lattice to Delone sets, including quasicrystal and amorphous solid. The main talk focused on the topological phases for those types of solid. He provided examples to show the amorphous patterns exhibit gapped phases. He showed that the invariants can be defined as noncommutative Chern number and computed the non-zero Chern number in the gapped phase. It is interesting to see that quasicrystal and amorphous solid share similar integer Chern numbers, and the idea can be further extended to different spatial dimensions with symmetries. We thank Prof. Bourne for giving a wonderful talk. Reported by Ching-Kai Chiu

2021-05-12

## DMWG Seinar by Dr. Nishimichi: Cosmology, the Fundamental for the DM on May 12, 2021

What we have known about dark matter (DM) is that it occupies ~25% of the energy density of our Universe. The precise determination of the cosmological parameter is crucially important for determining this abundance of DM. Another important point here is that one the value of those parameters are determined assuming a specific cosmological model, such as vanilla (i.e., the simplest) lambda CDM and so on. So we might have a different DM relic density if the assumption of the simplest Lambda-CDM breaks. Hence the examination of the cosmological parameters and the model behind them is important two-fold for DM physicists. The basic observable for the cosmological parameter is cosmic microwave background, the large-scale structure, and so on. Those data are huge at the raw level, and still so large at the scientific data level. In order to derive a handful of cosmological parameters from such data, one must calculate the so-called summary statistics. By matching the summary statistics in simulation data of specific cosmological models (vanilla lambda-CDM, for example) adopting MCMC techniques, we arrive at the cosmological parameter that we need. Note that there is always degeneracy between cosmological parameters derived from observational data. The matching between the observational and simulated summary statistics takes a lot of costs in the calculation. By adopting analytical formula, the calculation becomes much quicker while the precision decreases at some level. The emulator, which is developed in the Dark Quest Project, solves this computational problem. It enables us to speed up the calculation while keeping the precision. The degeneracy between the parameters also becomes accessible. The precise summary statistics such as halo mass function, halo-matter cross-correlation, and far more... is crucially important for DM study. Halo formation theory and weak lensing search are kinds of examples for applications. With this new fantastic open-source tool of Dark Quest Project, the future for DM search study emerges definitely. We are looking forward to seeing a lot of cutting-edge as well as steady works implemented with this item in the near future! Reported by Nagisa Hiroshima

2021-05-06

## iTHEMS Biology Seminar by Dr. Yukinori Nishigami on April 22, 2021

In iTHEMS biology seminar on April 22, Dr. Yukinori Nishigami (Hokkaido Univ.) gave us a talk about his research results, such as modeling the swimming behavior of unicellular organisms in their environment. First, Dr. Nishigami introduced us to the diversity of unicellular eukaryotes and the fact that they have their own specific movements. Many of the participants were amazed at how a small, single-celled organism can move in complex ways using flagella and other mechanisms, and how the cells themselves can move in complex ways. Next, he talked about the main topic: modeling the phenomenon of ciliate accumulation in a stable environment. Through careful observation and simulation, he modeled the movement and found that the movement of ciliates in such an environment is due to the simple principle of cell shape and mechanosensitivity of cilia. He presented a good example of modeling the behavior of unicellular organisms, which led to a lively discussion at the seminar. Thank you very much, Nishigami-san! Reported by Euki Yazaki

2021-04-28

## Information Theory SG Seminar by Prof. Yoshihiko Hasegawa on April 28, 2021

On April 28, Prof. Yoshihiko Hasegawa (Associate Professor, The University of Tokyo) gave us a talk on the thermodynamic uncertainty relation (TUR). In the first part of his talk, he started from a motivation to consider trade-off relations between energy and cost, showing biological examples. After reviewing general theory of stochastic thermodynamics and TUR for classical Markovian systems, he presented two recent works of him: one is to derive the TUR from information-theoretic method (i.e., the Cramer-Rao bound) and the second is to derive it from the fluctuation theorem. In the second part, he discussed quantum version of the TUR. After the review of quantum dynamics under measurement, he showed the quantum TUR for general open systems. He applied his theory to continuously measured systems and explained its physical meaning. There were a lot of interactive discussions during and after the talk. We really thank Prof. Hasegawa for his great talk. Reported by Ryusuke Hamazaki

2021-04-23

## Quantum Matter Seminar by Dr. Se Kwon Kim on April 21, 2021

On April 21st, Dr. Se Kwon Kim from KAIST gave a talk about unconventional spin transport in quantum materials. First, he gave an overview of spintronic physics. The advancements in spintronic techniques can potentially lead to new applications, such as quantum information science. Then, he showed the realization of magnonic topological insulators, which are Chern insulators with spin current but without electron charge current. Furthermore, he predicted that spin transport induces vortex flow in superconductors. We thank Dr. Kim for giving a wonderful talk. Reported by Ching-Kai Chiu

2021-04-22

## Math-Phys Joint Seminar by Prof. Takuju Zen on April 13, 2021

On April 13, Dr. Takuju Zen from Kochi University of Technology gave a talk entitled “Self-adjoint extension in quantum mechanics and non-Rydberg spectra of one-dimensional hydrogen atom” at the iTHEMS Math-Phys joint seminar. In the first part, he briefly explained the necessity of self-adjointness of operators in quantum mechanics and gave some important examples of such operators. Besides, he mentioned that the self-adjointness of Laplacian is equivalent to flux conservation in one dimension. Finally, he introduced studies of quantum particles on graphs. In the second part, the speaker discussed one dimensional Coulomb problem. Mainly, he noted that a simple self-adjoint extension of such hamiltonian could not be used. Then he provided a concrete procedure to study the solutions of one dimensional Coulomb problem and explained his interesting results. Reported by Yukimi Goto

2021-04-21

## iTHEMS Colloquium by Prof. Kenji Fukaya on April 16, 2021

On April 16, 2021, 13:30-15:00 (JST) 0:30-2:00(EDT), Professor Kenji Fukaya, Simons Center for Geometry and Physics, Stony Brook University, gave a colloquium talk by zoom. The title was "Mirror symmetry and KAM theory". His talk began at the origin of symplectic geometry, namely, the Hamiltonian dynamics. He reviewed completely integrable Hamiltonian systems, where the first integrals define foliation by half dimensional Lagrangian tori with linear flows. The KAM (Kolmogorov-Arnold-Moser) theory describes perturbation of this system and shows that almost all tori persist. Then Professor Fukaya explained the Lagrangian torus fibration found by Strominger-Yau-Zaslow, with the example of the complex projective space. For the complex projective n-space, the image of the moment map is an n-simplex and the regular fibers are Lagrangian n-tori. The inverse image of the boundary of the simplex corresponds to the singular fiber of the holomorphic fibration (the product of homogeneous coordinates) to a disk, By choosing a symplectic form, around the singular fiber of holomorphic fibration, there is defined the monodromy map by using the Hamiltonian flow of the Hamiltonian function that is the absolute value of the fibering. Professor Fukaya told that for this example in dim n = 2, the monodromy near the singular fiber exhibits the KAM theoretic behavior, but in dim n = 3, it is not the case with respect to the Fubini-Study symplectic form. However, he expects it can be the case with respect to the Calabi-Yau Kaehler form. This correspondence between symplectic manifolds (the torus fibration of the complex projective space) and complex manifolds (the holomorphic map to the disk) is an introductory example of the mirror symmetry. His talk might enter much deeper part related with homological mirror symmetry, but he stopped and concluded by saying that the KAM theory explains the transition from completely integrable systems to chaos and it should be possible to find alternative in mirror symmetry or field theory which will explain the transition from stable system to chaos. The talk of Professor Fukaya was really stimulating and his enthusiasm impressed the audience. Reported by Takashi Tsuboi

2021-04-16

## Quantum Matter Seminar by Dr. Mario Flory on April 14, 2021

On April 14th, from Instituto de Física Teórica, Universidad Autonoma de Madrid and Consejo Superior de Investigaciones Científicas, in Spain, Dr. Mario Flory gave a seminar talk about the connection between the AdS/CFT correspondence and condensed matter physics. In the first half of the talk, he briefly reviewed the ideas of the correspondence and its history. The most important breakthrough is that Juan Maldacena first proposed the AdS/CFT in the late '90s. It is known that the entropy of the black hole is proportional to its area, so that this feature suggests a holographic principle. The AdS/CFT correspondence serves a better understanding of this principle by connecting strongly coupled CFTs to classical gravity. In the second half, Dr. Flory addresses the important application of the correspondence to condensed matter physics. Because of the AdS/CFT correspondence, the problems of the Kondo model in condensed matter physics can be tackled by solving gravity problems. He specifically discussed the entanglement problem through the correspondence in detail. We thank Dr. Flory for giving an excellent talk. Reported by Thore Posske and Ching-Kai Chiu

2021-04-15

## iTHEMS Biology Seminar by Dr. Kyosuke Adachi on April 15, 2021

In iTHEMS Biology Seminar on April 15th, Kyosuke Adachi (BDR/iTHEMS) talked about the formation mechanism and the biological function of liquid condensates in eucaryotic cell. First, he explained the higher-order structure of the chromatin fiber. He focused on A compartment and B compartment, in which the high and low transcription activities are shown, respectively. Then, he talked about the biomolecular condensate which is the liquid droplet composed of proteins. He talked about the important interaction on the condensate creation and explained the theoretical model based on the mean field theory. Finally, he explained the role of the condensates on the transcription activity. The transcription occurs in the condensates of some proteins coexisting on the chromatin fiber. The audience enjoyed his attractive talk. Thank you very much for great talk, Kyosuke! Reported by Hiroshi Yokota

2021-04-15

## iTHEMS Biology Seminar by Prof. Catherine Beauchemin on April 8, 2021

In iTHEMS Biology Seminar on April 8th, Catherine Beauchemin (Deputy Program Director of RIKEN iTHEMS and Professor of Ryerson University) gave us an introductory talk on Markov chain Monte Carlo (MCMC) method. Many of theoretical scientists often use mathematical models, but it is difficult to correctly estimate parameter values of the model from experimental data. In this seminar, Catherine taught us the MCMC method is a powerful tool for parameter estimation using her recent research on cancer as an example. First, she explained four simple models of cancer growth. Then, using these models, she explained the basic idea and the detail process of the MCMC method. Her talk was very clear. I think that the seminar became helpful for the many attendees because the method can be applied to various fields of science and engineering. Merci beaucoup, Catherine! Reported by Shingo Gibo

2021-04-15

## Journal Club of Information Theory SG by Dr. Yukimi Goto on April 14, 2021

On 14th April, Dr. Yukimi Goto gave an introduction to trace inequalities and related topics in our journal club of the Information Theory Study Group. She started from a simple counter example of the triangle inequality for operators on Hilbert space, and introduced density matrices, von Neumann entropy and Wigner-Yanase skew information. Then, she explained the concept of jointly convex/concave functions and Wigner-Yanase-Dyson-Lieb theorem, and discussed the sub-additivity and strong sub-additivity of von Neumann entropy and its generalizations. Thank you, Goto-san, for interesting talk! Reported by Akinori Tanaka

2021-04-12

## Math Seminar by Dr. Kai Koike on April 7, 2021

On April 7, Dr. Kai Koike from Kyoto University gave a talk entitled “Long-time behavior of moving solids in a fluid and the kinetic theory of gases” at Math seminar. In the first part, he reviewed a moving boundary problem of gases. Then he introduced some interesting results in fluid dynamics and developments concerning his research. In the second part, the speaker explained his results about the long-time behavior of a point particle moving in a fluid. It is an explanation of related numerical results for a BGK model of the Boltzmann equation. Reported by Yukimi Goto

2021-04-05

## Math Seminar by Dr. Wataru Kai on March 22, 2021

On March 22, the last iTHEMS Math seminar in FY 2020 was held. This time, we invited Wataru Kai from Tohoku University. The title of the talk was “The Green-Tao theorem for number fields”. The main topic of the talk was his recent joint work with his collaborators about the Green-Tao theorem and its generalization. In the first part, he explained the historical background and the technology behind the proof of the Green-Tao theorem, which asserts that there are arbitrarily long arithmetic progressions of prime numbers. In the second part, he introduced algebraic numbers and algebraic integers, which generalize rational numbers and integers, respectively, and he explained how we can generalize the Green-Tao theorem to this situation. For example, if we think of numbers of the form a+b\sqrt{5}, these are algebraic numbers. Plotting them on the ab-plane, each of the numbers corresponds to a lattice point. We can draw a “shape” by choosing finite number of those lattices. Then, the generalized Green-Tao theorem asserts that, by applying scaling and parallel translation, we can make all of the chosen lattice points correspond to prime elements simultaneously. Here, prime element is a generalization of prime number in the world of algebraic numbers. He also explained that at some point of the proof of the generalized Green-Tao theorem, a classical technique well-known to algebraic number theorists plays a fundamental role. Reported by Hiroyasu Miyazaki

2021-04-02

## Biology Seminar by Dr. Yuji Hirono on April 1st, 2021

In iTHEMS biology seminar on April 1st, Yuji Hirono (Assistant Professor, Asia Pacific Center for Theoretical Physics, POSTECH, Korea) gave us a talk on chemical reaction networks. Hirono-san has been recently working on chemical reaction networks with Miyazaki-san, Hidaka-san, and me. In the seminar, he talked about a new method of studying chemical reaction networks from network topology. He first explained graph theoretical aspects of chemical reaction systems, and then explained how these tools can be used to characterize reaction systems. Then, he explained a method of simplifying/deforming chemical reaction systems without affecting steady-state properties. I am grateful to Hirono-san because I could improve my understanding of reaction systems through collaboration with him. Also, Hirono-san and I have been friends since we were undergraduates, and I am happy to work together. Thank you very much, Hirono-san! Reported by Takashi Okada

2021-03-26

## Biology Seminar by Dr. José Gutiérrez on March 25, 2021

On March 25th, José Gutiérrez from Chiba University gave a talk at iTHEMS Biology Seminar about the evolution and diversification of cycads ("sotetsu" in Japanese) in Mexico. He explained how the different species and populations of cycads are distributed in different areas of Mexico, and showed how this can be explained by changes in the climate and the adaptation of each species to the different environment. He then discussed some general ideas of how speciation and diversification can occur. It was probably the first time for many iTHEMS members to hear about research in Ecology, and I think many of us learned something new. We were also able to have a nice and fruitful discussion after the talk. Reported by Jeffrey Fawcett

2021-03-25

## Information Theory SG by Dr. Akinori Tanaka on March 24, 2021

On 24th March, Dr. Akinori Tanaka gave an introduction to the reinforcement learning (RL) in our journal club of the Information Theory Study Group. He started from simple examples of a maze and a chess game to introduce the fundamental variables (i.e., states, actions, and rewards) and their evolution as a Markov decision process.After explaining that the goal of the RL is to maximize the value function, he discussed policy improvement theorem with the application to the epsilon-greedy update. We thank Akinori for the great and clear talk!

2021-03-18

## Quantum Matter Seminar by Prof. Takahiro Morimoto on March 16, 2021

On March 16th, Prof. Takahiro Morimoto from the University of Tokyo gave an online talk on geometric nonlinear optical effects. First, he introduced topological states of matter and the notion of the Berry connection to the audience. He explained how these concepts lead to the quantization of observable quantities in the linear-response regime so that the audience learned the background to understand his main research works. After the introduction, he talked about several geometric nonlinear effects in topological states beyond the linear response theory. In particular, the shift current stems from the geometric nonlinear response, and the quantized circular photogalvanic effect can be realized in specific Weyl semimetals. In addition to the theoretical concepts, he also discussed experimental observations, such as perovskite-based solar cell materials and chiral multifold fermion compound RhSi. During and after the talk there were interactive discussions, and more than 25 participants attended this well-presented talk. -Chen-Hsuan Hsu and Ching-Kai Chiu

2021-03-05

## Quantum Matter Seminar by Prof. Jan Budich on March 3, 2021

We are happy to invite Prof. Han Budich from the Dresden University of Technology to give a talk on March 3rd. The topic is Exceptional Topology of Non-Hermitian Systems: from Theoretical Foundations to Novel Quantum Sensors. Prof. Budich started with the review of the topological phases. After the introduction, he introduced the emergence of the exceptional points from non-Hermitian systems. The exceptional points, which are similar to Weyl nodes, possess intrinsic topological properties. Later, he proposed a novel idea of the quantum sensor to probe topological features from non-Hermitian platforms. It is great to have this nice talk.

2021-02-26

## ABBL-iTHEMS Joint Seminar by Prof. Gordon Baym on February 22, 2021

On Feb. 22, our iTHEMS colleague, Gordon Baym, gave an online talk from Urbana-Champaign on the detection of the primordial neutrinos created in the early Universe. We are in the sea of those neutrinos at the present day with the neutrino density of about 56/cc for each neutrino species. Although neutrinos (anti-neutrinos) are left-handed (right-handed) in early Universe, both cosmic and galactic magnetic fields as well as the gravitational inhomogeneities can flip their spins with respect to the momentum, so that the helicities (spin projection along the direction of the momentum) of the relic neutrinos could be a new probe of cosmic gravitational and magnetic fields. More that 60 participants attended this interesting seminar and there were lively discussions during and after the talk.

2021-02-25

## Biology Seminar by Mr. Junichiro Iwasawa on February 18, 2021

On 18th February, we invited Junichiro Iwasawa from the University of Tokyo, who gave a talk about the unique study to identify the evolutionary constraints of drug-resistance in Escherichia coli using automated high-throughput laboratory experiments. He first talked about the background of drug resistance evolution and about the well-known / novel resistance-conferring genes for E. coli that were elucidated from their data. He then moved on to the details of the data analyses and explained the combined method of random forest regression and principal component analysis on the multi-omics data. We enjoyed a long discussion on every single detail of the impressive work. We especially thank him for accepting our invitation despite the tight schedule with his dissertation. Thank you again for the great talk! -Ryosuke Iritani

2021-02-25

## Biology Seminar by Dr. Hiroshi Yokota on February 25, 2021

In iTHEMS biology seminar on Feb. 25th, Dr. Hiroshi Yokota (iTHEMS) talked about the mechanism of the non-linear response of DNA under stretching force. In the introduction part, he mentioned the experimental technique using the magnetic tweezer to measure the extension of DNA under stretching force, and he also showed the experimental results of the non-linear response of DNA. He then explained the strategy to clarify the origin of non-linearity by applying mathematical modeling and statistical physics. Introducing the worm-like chain model, he transformed the Hamiltonian in an elegant way and analytically obtained the formula of the extension, which explains the experimental data. His description of the model was very clear, and there were many questions and discussions. We are thankful to Hiroshi for the intriguing talk. Kyosuke Adachi

2021-02-19

## Information Theory SG by Dr. Ryusuke Hamazaki on February 17, 2021

On 17th February, we had Ryusuke Hamazaki (from RIKEN Hakubi and iTHEMS) talking about the recent studies on the large deviation principle in our journal club of the Information Theory Study Group. He started off by demonstrating Bernoulli's process and how to compute the large deviations, and then defined the Level 2.5 large deviations in Markovian jump process, thereby providing the derivation of a recently proposed inequality (the thermodynamic uncertainty relation). Finally, he explained possible extensions to quantum systems. The talk received numerous questions in every single part, specifically from those interested in the derivation and application of the Level 2.5 large deviation. Thanks, Ryusuke, for the great and inspiring talk! Ryosuke Iritani (iTHEMS)

2021-02-17

## DMWG seinar by Dr. Sakai: Astrometory for DM search

The precise understanding of the local DM density, as well as its velocity distribution, is critical for dark matter (DM) search, especially for direct detection experiments. We need information about the global structure such as the position and rotation velocity of the Solar system when evaluating these quantities. Astrometry, which is a technique to measure the time dependence of the position of stars, powerfully probes the 3D gravitational structure of our Galaxy. There are two types of astrometric observations: the first one is based on optical (and infrared) photometry. The parallax is obtained by comparing two snapshots of the sky between two epochs. The Gaia mission is the representative for this kind of observation. Gaia reveals the structure of our Galaxy up to ~5kpc from the Sun. The mission is planned to continue the observation to extend our reach to ~10kpc, meaning that it should cover the Galactic Center in the near future. The second one is the VLBI observation. VLBI is an abbreviation of the very-long baseline interferometry. The spatial resolution of milli-arcsecond is achieved with VLBI techniques. However, the sensitivity is limited and long-lasting observations are required in general. In this sense, VLBI and optical photometry are complemental. One important discovery for DM search from VLBI astrometry is reported in this seminar. The VLBI observation of the Galactic disk region reveals the position of the Sun is closer to the Galactic Center compared to the conventional values used for a long time, and the rotation velocity is higher. This means that our Galaxy is heavier, i.e. contains much DM, and the relative velocity between DM particle and us is different, compared with the previous estimates. Also, the disk region does not reach the equilibrium yet. These facts should change the picture of our Galactic DM structure. New facilities for astrometric observations are now being planned and constructed. There are diverse possibilities for the synergy between DM search. The astrometry should give important indications such as the merger history of DM halo, dynamical interaction between the Milky Way and its satellite galaxies, the global structure of the Milky Way, and far more. We should stay tuned!

2021-02-17

## iTHEMS Theoretical Physics Seminar by Mr. Masaaki Tokieda on February 16, 2021

On February 16, the iTHEMS-phys seminar entitled "Quantum mechanical description of energy dissipation and application to heavy-ion fusion reactions" given by Mr. Masaaki Tokieda (Tohoku U.) was held. He introduced his work during graduate school, that is, considering dissipation and fluctuation to the quantum mechanics to unify the description of above the Coulomb barrier and sub-barrier reactions. He also applied the method to heavy-ion fusion reactions. The seminar was held via the Zoom online conference systems. More than 20 people, including outside from iTHEMS, attended the seminar. The discussion was quite lively, and it was continued for long, even after the seminar.

2021-02-15

## Biology Seminar by Dr. Keitaro Kume on February 12, 2021

In iTHEMS biology seminar on February 12, Keitaro Kume (Univ. of Tsukuba) gave us a talk about applying machine learning to the analysis of non-model organisms that are difficult to experiment with. First, Dr Kume introduced us about the brief mitochondrial evolution and several eukaryotes possessed not typical mitochondria as like Mitochondrion related organelle (MRO) which is highly degraded mitochondria. Next, he described the detection of mitochondrial localization signals and their applications, explaining that it is difficult to detect localization signals in mitochondria of non-model organisms, especially MROs. Finally, He obtained a large amount of data on MRO-localized proteins in non-model organisms, and through machine learning using the data as training data, he created a detector that can detect MRO-localized signals in such non-model organisms. He presented a good example of the connection between biological evolutionary research and machine learning, which led to a lively discussion at the seminar. Thank you very much, Kei!

2021-02-05

## iTHEMS Theoretical Physics Seminar by Dr. Di-Lun Yang on February 4, 2021

On February 4, the iTHEMS-phys seminar entitled "Quantum kinetic theory for chiral and spin transport in relativistic heavy ion collisions and core-collapse supernovae" given by Dr. Di-Lun Yang (Keio U.) was held. He has been working for the quantum kinetic theory. In his seminar, first, he introduced the general background of the quantum transport of the massless fermions and its anomaly. Then, he showed its application to the relativistic heavy-ion collisions and core-collapse supernovae. The seminar was held via the Zoom online conference systems. More than 20 people, including outside from iTHEMS, attended the seminar. The discussion was quite lively, and it was continued for long, even after the seminar.

2021-02-05

## Biology Seminar by Mr. Yoshifumi Asakura on February 4, 2021

In iTHEMS Biology Seminar on Feb. 4th, Yoshifumi Asakura (Kyoto University) talked about modeling of the mechano-chemical dynamics of an epithelial sheet. He first reviewed experimental observation of the epithelial sheet dynamics with ERK signals and simple theoretical modeling of the mechano-chemical dynamics. He then presented the main questions, stressing the importance of two-dimensionality and parameter heterogeneity in tissue dynamics. In the method part, he introduced the hierarchical modeling which connects the particle-based and continuum models with the cell tracking data. He showed that the models can reproduce the essential features of the tissue dynamics with ERK signals, and moreover, can be used for the quantitative prediction of the velocity field of cells. His presentation contained many beautiful movies of the epithelial sheet dynamics and model simulations. We are thankful to him for the nice talk! Kyosuke Adachi

2021-01-29

## iTHEMS Theoretical Physics Seminar by Prof. Nobutoshi Yasutake on January 28, 2021

On January 28, the iTHEMS-phys seminar entitled "Many body problems from quarks to stellar evolutions" given by Prof. Nobutoshi Yasutake (Chiba Institute of Technology/JAEA) was held. He has been working for the stelar evolutions as gravitational many-body problems and the hadronic matter as quantum many-body problems based on the Lagrangian schemes. Recently, he discussed hadronic matters properties using the color molecular dynamics. The seminar was held via the Zoom online conference systems. Around 20 people, including outside from iTHEMS, attended the seminar. The discussion was quite lively, and it was continued more than one hour even after the seminar.

2021-01-28

## Information Theory SG by Dr. Hiroshi Yokota on January 27, 2021

Today's journal club of the Information Theory Study Group had Hiroshi Yokota (iTHEMS) talk about the replica-permutation method to obtain stable structures. He started off the talk with some introduction of proteins' stable structures. To avoid reaching nonglobally optimal structures, the replica-exchange method used to be applied; however, this method may be computationally expensive and less efficient in some circumstances. Later work has proposed the replica-permutation method by which the candidates of the stable structures are permutated (shuffled) and relaxes the detailed balance condition. He drew an analogy with allocation problems of various volumed cups each filled with water. He finally talked about the application in a paper that examines amyloid 𝛽 oligomerization. The audience asked lots of questions about the algorithm per se, physical meaning, and even its potential applications. Thanks, Hiroshi, for the fantastic talk! I as well as arguably all the audience really enjoyed it! -Ryosuke Iritani (RIKEN iTHEMS)

2021-01-25

## Biology Seminar by Dr. Takashi Okada on January 21, 2021

On January 21st, Takashi Okada (RIKEN iTHEMS) gave a talk on Boolean networks at the iTHEMS Biology Seminar. He first introduced the basics of Boolean networks and their applications in Biology, and then talked about his recent work on information transfer in Boolean networks. Network is a theme that is common to almost all fields of Science and is relevant to most of us. Thus, his talk was very useful to get a basic idea of what Boolean network is and how it is applied. Not only the basic introduction, but also his recent work on information transfer was explained very clearly in simple terms, which made it possible for all of us to follow and enjoy. Thanks Takashi! - Jeffrey Fawcett

2021-01-21

## Biology Seminar by Dr. Koichiro Uriu on January 7, 2021

On January 7th, Dr. Koichiro Uriu gave a talk on one of the most important pattern formation in our body. Koichiro was an active member of iTHES, and is currently an assistant professor at Kanazawa Univ. Rhythmic (ON and OFF) and also spatial gene activity pattern, termed the segmentation clock underlies our body axis segmentation (“Taisetsu" in Japanese). Thus, robust gene activity oscillation propagates from the backward to the forward domain by which the segment is formed sequentially. In the seminar, Koichiro discussed the recovery processes of the segment formation after the removal of the drug which blocks oscillator coupling in a fish, called zebrafish. Curiously, experiments show that intermingled segments can occur in the body of the fish especially when the drug is removed at early stage. To understand the pattern recovery, he developed a physical model incorporating mechanics and genetic oscillations. During and after the talk, there were numerous questions from the audience because his talk was very interesting and also very clear. Thank you and see you, Koichiro! - Gen Kurosawa

2021-01-20

## Information Theory SG by Dr. Ryosuke Iritani on January 20, 2021

On January 20th, Dr. Ryosuke Iritani gave us a talk about his motivation to work with information theory. He first formulated the dynamics of species-site data in ecology as a Markov model. By reducing the model to a simpler one in an elegant way, he analytically obtained the evolution of the proportion of species. In addition, he discussed certain entropies that characterize the diversity of species and showed us the unique dynamics of the entropy in his model. His talk was clear as he explained mathematical concepts by using simple examples and illustrations, and there were questions and comments from several viewpoints. We are thankful to Ryosuke for the exciting talk! Kyosuke Adachi (BDR/iTHEMS)

2021-01-19

## First Quantum Matter Seminar by Dr. Xueda Wen on January 18, 2021

We are happy to invite Dr. Xueda Wen from Harvard University to give a talk on January 18th. This talk is the first seminar of the quantum matter study group. The topic is time-dependent driven quantum critical systems in (1+1) dimensions, which connects condensed matter physics and high energy physics. Dr. Wen started with two different free-fermion lattice Hamiltonians. The system is driven periodically and alternatively with these two Hamiltonians. Interestingly, this driven system leads to two distinct two phases. This straightforward introduction smoothly brought us to the study of time-dependent driven conformal field theories. The driven CFTs show that the periodical driving systems can possess heating and non-heating phases, and the phase transition boundary separates these two phases. Dr. Wen further talked about the generalization of driving CFTs and several unsolved problems. This talk is informative as well as interactive. Drs. Tada, Hongo, and Takasan asked several key questions, and Dr. Wen answered those questions clearly and informatively. We thank Dr. Wen for the great talk. --Ching-Kai Chiu

2021-01-14

## Information Theory SG by Dr. Kyosuke Adachi on January 13, 2021

On January 13, Dr. Kyosuke Adachi gave a talk entitled “Accelerated equilibration in classical stochastic systems” at the journal club of information theory study group. First, he reviewed the concept of shortcuts to adiabaticity (STA) and discussed a two-level system as a concrete example. Then it was explained that STA are fast routes to the final states in quantum systems. Second, he introduced the engineered swift equilibration (ESE) in classical stochastic systems, which is a classical counterpart of STA. Indeed, he explained that the Fokker-Plank equation has a similar structure to the Schroedinger equation, and the fast routes from the initial equilibrium state to the final equilibrium state are ESE. As examples of ESE, compression of Brownian particles, and evolutionary systems were given. Finally, he mentioned some interesting questions. The talk had many stimulating discussions. We are grateful to Adachi-san for his excellent talk!

2021-01-14

## Biology Seminar by Dr. Jeffrey Fawcett on January 14, 2021

In iTHEMS biology seminar on January 14, Jeffery Fawcett (RIKEN iTHEMS) gave us a talk on what genes are and how we can identify them. He started from the basics such as chromosomes, genes, and how proteins are produced from them. He then explained difficulties in defining a gene. This sounds very interesting because most of us (at least, I) naively think that we know what a gene is, even without knowing a precise definition of it. He also explained how we can predict the location of genes on the chromosomes. Jeff nicely presented keys ideas for non-experts, and all of us enjoyed his talk. I am also working on evolutionary biology, but I have never thought seriously about how genes are identified, and his talk became a nice introduction to this fascinating topic. Thank you very much, Jeff! - Takashi Okada

2020-12-24

## Information Theory SG by Dr. Yukimi Goto on December 23, 2020

This week, Dr. Yukimi Goto gave us an introduction to the Lieb-Robinson bound. After reviewing several important preliminaries, such as Liouvillians for open quantum systems, she discussed the Lieb-Robinson bound, which is a theorem for the bound on speed of information propagation. She then explained two notable applications of the bound, i.e., correlation decay and the entanglement area law for a gapped ground state in isolated quantum systems. We thank Goto-san for her great talk!

2020-12-23

## Biology Seminar by Dr. Shingo Iwami on December 22, 2020

In his seminar Dr. Iwami (Kyushu University) presented his mathematical model for coronavirus (新型コロナウイルス) in patients. The aim of the project was to determine why some papers disagreed on the efficacy of certain antiviral drugs to treat the coronavirus. Because the available data was limited, only a simple mathematical model was considered. The mathematical model only represents the fraction of cells remaining to be infected and the amount of virus. The curve for the virus in the model was fitted to the data of virus in the nasal swab of patients. From this analysis, Dr. Iwami's group could separate the patients into 3 types: with either slow, medium or fast decay of virus. He showed that in his model, only early treatment can be effective for all decay types. This can be one reason why two different clinical trials can find different results: if one trial includes late treatment then it can appear that the treatment is not effective. From the mathematical model, he suggested some changes in the criteria for patient inclusion into clinical trials to improve the ability to detect statistically significant effects for the antiviral drug. The seminar was very well attended, with many questions and discussions. Thank you Dr. Iwami for your great talk! - Catherine Beauchemin (iTHEMS)

2020-12-18

## Biology Seminar by Akane Hara on December 17, 2020

In today's biology seminar, we invited Akane Hara, a PhD student at Kyushu University, to have her talk about how pathogen infection can cause autoimmune diseases. Normally, the immune systems attack germs like viruses and bacteria to prevent their growth within the body. However, these germs may mimic themselves to our body system so that they can avoid the attack. As a result, the immune system is not able to tell the germs from our body parts, and so even after the removal of the germs, it harms our body mistakenly. Wondering why - or when - this is the case, she considered ordinary differential equations of the compartment models for virus, helper cells, and memory T cells, by explicitly considering cross immunity. She presented a mathematical condition for which autoimmune diseases may be present and/or severe. We discussed possible extensions of the mathematical models. Thank you so much for the great talk, Akane! Personally, I was a colleague with her at Kyushu University and so feel a bit emotional that she's completing her PhD very soon! -Ryosuke Iritani

2020-12-18

## iTHEMS-phys seminar by Takeru Yokota on December 17, 2020

On December 17, the iTHEMS-phys seminar entitled "Classical liquids and functional renormalization group" given by Dr. Takeru Yokota (ISSP, U. Tokyo) was held. He has been working for the functional-renormalization-group-aided density functional theory (FRG-DFT) for several years. Recently, he is applying this method to classical liquid. As a benchmark calculation, he applied to a one-dimensional exactly solvable system. The exact solution was sucessfully reproduced by the method. The seminar was held via the Zoom online conference systems. More than 20 people, including outside from iTHEMS, attended the seminar. The discussion was quite lively, and it was continued several hours even after the seminar.

2020-12-18

## Math-Phys Joint Seminar by Dr. Naotaka Kubo on December 14, 2020

His talk was on the test of non-perturbative dynamics of three-dimensional gauge theories from the perspective of brane dynamics in string theory. In the first half of his talk, he explained important ideas in quantum field theory at an elementary level, such as renormalization group (RG) flow, supersymmetry (SUSY), and world-volume theory on branes in string/M-theory. Combining these fundamental ideas, he moved on to the discussion of duality cascades in quantum gauge theories in four and three dimensions. Using branes in string theory, he demonstrated that the duality cascades in M2-brane world-volume theories can be understood from the brane dynamics in type IIB string theory, which is the so-called Hanany-Witten move/transition. In particular, he mentioned that after the sequence of the Hanany-Witten transitions, one may predict if the original gauge theories have SUSY breaking under the RG flow. Then he concluded that all the world-volume theories related by the Hanany-Witten transitions would flow to the same IR theory, and SUSY will be broken if anti-D3-branes are created. In the latter part of the talk, he argued the non-perturbative tests of duality cascades in three-dimensional supersymmetric gauge theories using partition functions of the theories. He first introduced the notion of partition functions of quantum field theories on S^3 and rephrased the conclusion given in the first part in the language of partition function. He then illustrated the general idea to exactly compute the partition function of supersymmetric gauge theories, which is an analogue of Duistermaat-Heckman formula and is called supersymmetric localization. He gave a dictionary between the viewpoint of brane configuration and the partition function of supersymmetric gauge theories. With such a dictionary, the Hanany-Witten transition of branes was rewritten by an equality between the partition functions. Moreover, one can directly check the duality cascades and SUSY breaking by calculating the partition functions. Finally, he showed the duality cascades and SUSY breaking in supersymmetric gauge theories by an explicit evaluation of partition functions, with comments on Fermi gas formalism and residue computation.

2020-12-17

## Biology Seminar by Dr. Yuri Kominami on November 27, 2020

In iTHEMS Biology Seminar on November 27th, Dr. Yuri Kominami from University of Tokyo gave us a talk about her experimental study on population dynamics of rotifer. It is often difficult to understand population dynamics of animals because the population is reflected by complex environmental conditions. In her study, by using rotifer as a model organism, she has succeeded in measuring the laboratory population size, the birth rate, and the life span in a controlled condition. In this seminar, she showed some of nontrivial results of her experiment. Her discoveries were very exciting for theoretical biologists, and we enjoyed active discussion. Thank you so much, Kominami-san! -Shingo Gibo

2020-12-16

## Information Theory SG by Dr. Ryusuke Hamazaki on December 16, 2020

In the journal club of Information Theory Study Group held on December 16th, Dr. Ryusuke Hamazaki (CPR/iTHEMS) gave us a talk about recent proposals of a quantum version of the Wasserstein distance. He first reviewed the commonly used quantities expressing the distance between probability distributions, i.e., the total variation distance and the relative entropy. After pointing out certain problems with these quantities, he introduced the classical Wasserstein distance of order 1 as a better definition of the distance and explained its representative properties like transportation inequality and tensorization property. Next, he introduced a quantum counterpart of the Wasserstein distance, which can apply to spin-1/2 quantum systems. In contrast to the total variation distance, the quantum Wasserstein distance has interesting properties like the invariance under permutation or local unitary transformation. Lastly, he explained an application of the quantum version of transportation inequality to the eigenvalue distribution. Reflecting the interdisciplinary subject of the talk, there were several questions and comments from both mathematical and physical viewpoints. We are grateful to Ryusuke for the great talk! Kyosuke Adachi (BDR/iTHEMS)

2020-12-16

## Information Theory SG by Dr. Koichiro Yoshino on December 16, 2020

As the first seminar speaker of the Information Theory study group, we invited Koichiro Yoshino (Teamleader of Robotics Project, RIKEN) to give a talk on natural language processing. First, he explained the statistical language model's basis, e.g. language model, distributed representations, etc, and then discussed his own works: 1) attribute transfer in word embedding space, 2) modeling sentence structure. Natural language processing is one of the good applicants of information theory, and we enjoyed his clear talk and discussions. Akinori Tanaka (iTHEMS/AIP)

2020-12-15

## Math Seminar by Dr. Hideki Inoue on December 7, 2020

On December 7, there was a math seminar by Dr. Hideki Inoue. His talk aims to introduce Levinson's Theorem and its recent progress. In the first part, he gave a brief survey talk on Levinson's theorem and its formulation. He then explained that Levinson's theorem, which can be proved analytically. He then introduced abstract scattering theory and operator algebras and how they applied to Levinson's theorem study. In the second part, he explained his recent results on Levinson's theorem. He showed a straightforward representation formula of the wave operator, a significant research target in the scattering theory. With this formula, he proved that one could prove Levinson's theorem by abstract theory. He also explained similar results on discrete operators.