Seminar Report
367 news

20210205
Seminar ReportBiology 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 mechanochemical dynamics of an epithelial sheet. He first reviewed experimental observation of the epithelial sheet dynamics with ERK signals and simple theoretical modeling of the mechanochemical dynamics. He then presented the main questions, stressing the importance of twodimensionality and parameter heterogeneity in tissue dynamics. In the method part, he introduced the hierarchical modeling which connects the particlebased 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

20210129
Seminar ReportiTHEMS Theoretical Physics Seminar by Prof. Nobutoshi Yasutake on January 28, 2021
On January 28, the iTHEMSphys 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 manybody problems and the hadronic matter as quantum manybody 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.

20210128
Seminar ReportInformation 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 replicapermutation method to obtain stable structures. He started off the talk with some introduction of proteins' stable structures. To avoid reaching nonglobally optimal structures, the replicaexchange method used to be applied; however, this method may be computationally expensive and less efficient in some circumstances. Later work has proposed the replicapermutation 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 ? 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)

20210125
Seminar ReportBiology 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

20210121
Seminar ReportBiology 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

20210120
Seminar ReportInformation 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 speciessite 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)

20210119
Seminar ReportFirst 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 timedependent driven quantum critical systems in (1+1) dimensions, which connects condensed matter physics and high energy physics. Dr. Wen started with two different freefermion 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 timedependent driven conformal field theories. The driven CFTs show that the periodical driving systems can possess heating and nonheating 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. Reported by ChingKai Chiu

20210114
Seminar ReportInformation 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 twolevel 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 FokkerPlank 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 Adachisan for his excellent talk!

20210114
Seminar ReportBiology 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 nonexperts, 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

20201224
Seminar ReportInformation Theory SG by Dr. Yukimi Goto on December 23, 2020
This week, Dr. Yukimi Goto gave us an introduction to the LiebRobinson bound. After reviewing several important preliminaries, such as Liouvillians for open quantum systems, she discussed the LiebRobinson 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 Gotosan for her great talk!

20201223
Seminar ReportBiology 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)

20201218
Seminar ReportBiology 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

20201218
Seminar ReportiTHEMSphys seminar by Takeru Yokota on December 17, 2020
On December 17, the iTHEMSphys seminar entitled "Classical liquids and functional renormalization group" given by Dr. Takeru Yokota (ISSP, U. Tokyo) was held. He has been working for the functionalrenormalizationgroupaided density functional theory (FRGDFT) for several years. Recently, he is applying this method to classical liquid. As a benchmark calculation, he applied to a onedimensional 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.

20201218
Seminar ReportMathPhys Joint Seminar by Dr. Naotaka Kubo on December 14, 2020
His talk was on the test of nonperturbative dynamics of threedimensional 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 worldvolume theory on branes in string/Mtheory. 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 M2brane worldvolume theories can be understood from the brane dynamics in type IIB string theory, which is the socalled HananyWitten move/transition. In particular, he mentioned that after the sequence of the HananyWitten transitions, one may predict if the original gauge theories have SUSY breaking under the RG flow. Then he concluded that all the worldvolume theories related by the HananyWitten transitions would flow to the same IR theory, and SUSY will be broken if antiD3branes are created. In the latter part of the talk, he argued the nonperturbative tests of duality cascades in threedimensional 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 DuistermaatHeckman 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 HananyWitten 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.

20201217
Seminar ReportBiology 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, Kominamisan! Shingo Gibo

20201216
Seminar ReportInformation 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 spin1/2 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)

20201216
Seminar ReportInformation 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)

20201215
Seminar ReportMath 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.

20201210
Seminar ReportBiology Seminar by Dr. Euki Yazaki on December 10, 2020
In iTHEMS Biology Seminar on December 10th, Dr. Euki Yazaki (iTHEMS) talked about recent techniques and problems in obtaining the largescale sequence data of eukaryotes. He first mentioned the importance of identifying and comparing the genome sequence in biology. Then, he illustrated the two representative sequencing methods, Sanger sequencing and nextgeneration sequencing (NGS). He clearly explained the features of these methods, highlighting the advantages of NGS in exploring largescale or novel sequences. In the latter part, he introduced a method using the graph theory to reconstruct the largescale genome data from the fragments of a sequence obtained by NGS. He lastly pointed out some problems in the current reconstruction method, and we discussed possible ideas to mitigate them after the talk. We are grateful to Euki for the stimulating talk! Kyosuke Adachi (BDR/iTHEMS)

20201209
Seminar ReportMath Seminar by Dr. Tianfeng Hou on November 13, 2020
On November 13, Tianfeng Hou, a new member of the team, gave a math seminar on the Monte Carlo study. In the first part, the speaker focuses on quasiMonte Carlo method and its probabilistic assessments. In the second part, the speaker explained reducedorder models and how they work in the hygrothermal model. He first showed his model works efficiently in the linear scenario. On the other hand, he explained that his model is not so efficient in some nonlinear scenario.

20201208
Seminar ReportInformation Theory SG by Dr. Akinori Tanaka on December 8, 2020 (Continuation of last week)
Continued from last week, Dr. Akinori Tanaka (Senior Research Scientist of iTHEMS and AIP) gave us a talk about the connection between the thermodynamic law and the algorithms of deep learning. He first reviewed the second law of thermodynamics in Langevin systems and the representation of stochastic gradient descent algorithms using Gaussian fluctuation. He then explained about Generative Adversarial Networks (GAN), which can be used in producing near realistic fake images. Based on mathematical correspondence, he discussed a possible application of the modified thermodynamic law to the algorithms of GAN. We are thankful to him for the exciting talk! Kyosuke Adachi (BDR/iTHEMS)

20201207
Seminar ReportFirst Information Theory SG by Dr. Akinori Tanaka on December 1, 2020
Kicking off the study group of information theory, Akinori Tanaka (Senior Research Scientist of iTHEMS and AIP) talked about the connection between Langevin equation and deep neural networks. He first showed that by analyzing Langevin equations one can derive the second law of thermodynamics which posits that the total entropy of the system should increase. He then delved into stochastic gradient descent (SDG) and showed how to apply it to train the neural network in general. We discussed too enthusiastically for him to finish his talk, and so we'll organize the second part next week (08 December 2020). We are all looking forward to discussing more, and thank you so much for the elegant talk! Ryosuke Iritani (iTHEMS)

20201207
Seminar ReportMath Seminar by Dr. Martin Skrodzki on November 30, 2020
Our colleague Martin Skrodzki gave a farewelltalk in iTHEMS Math seminar on November 30. The title of the talk was “Flat and spherical surface approximations”. He talked about two approaches to approximate surfaces by using flat objects and spherical objects. In the first part, he explained the approximation using flat objects. Naively, there are two approaches to approximate surfaces. One is local and the other is global. In local approach, we need to get extremely many samples. In global approach, it will produce extreme torsion of surfaces. To remedy these problems, we should think of medium approach, i.e., patching of small simple flat objects (like covering of manifolds). This is called Variational Shape Approximation (VSA). The VSA has three steps: seeding, flooding and updating (and we iterate these recursively). This method gives us a very nice approximation of surfaces, but it still has some defects. Indeed, The recursive process does not always converge, the result depends on initial random choice of seeding, and it also depends on the artificial choice of the number of proxies we use. Therefore, Martin and his collaborators refined the VSA, by adding new steps called “splitting”, “Merging” and “Switching”. These steps avoids all defects above. In the second part, he explained his project on approximating surfaces using spheres. He shows some extreme examples of surfaces which are not relevant for spherical approximation: cone and toilet paper. If you imagine a needleshaped cone, then its intersection with a ball will be very small. On the other hand, if you thing of rolled paper, then its intersection with a ball have too large area. However, if the surface we want to approximate satisfies a relevant condition, we can obtain a condition on the radius of the ball we use to approximate the surface. During the lecture, he proposed an interesting question on the maximum/minimal area of the intersection of the ball and the surface, and there was an exciting discussion including the audience.

20201207
Seminar ReportDMWG Seminar by Dr. Naka: Directional Direct Detection Experiments
Among the kinds of dark matter (DM) candidates, Weakly Interacting Massive Particle (WIMP) shows a strong model motivation. It achieves the current DM density naturally via the socalled thermal freezeout mechanism. The strength of the interaction between WIMP and the standard model particles should be finite, and various direct detection experiments have already excluded a large part of the favored parameter space. We are now in the phase to consider the next strategy. There are several directions to proceed. For example, annual and/or diurnal modulation of the event rate of the DMnucleon scattering. However, the expected modulation amplitude is so small that a few percent for annual modulation and less than 1% for the diurnal case. Kinds of ongoing experiments intensively search the modulation signature now, however, it is still difficult to confirm. Another possibility is to make use of directional information. One important advantage of the directional search is its power for background rejection. The DM signal should be more frequently found in the direction corresponding to the Galactic Center while the backgrounds are in different directional distributions. These differences enable us to reduce the number of scattering events required for claiming the detection from O(1e4) to O(100), compared to the conventional direct detection cases. Furthermore, it could potentially provide us with information about the velocity distribution function, of which precise understanding is a key to any kinds of direct detection experiments, as well as the scenarios explaining the evolution of our Galaxy. Hence, the directional search is an attractive idea to probe the nature of DM. Recently, such projects are launched, and still some technical issues to solve remain. We have to achieve the O(1e9)m scale resolution of the particle track, to confirm the scalability and stability, and to understand the ultralow background. Many projects are now tackling these problems. The new era for direct DM search now begins!

20201130
Seminar ReportBiology Seminar by Dr. Hidenori Tanaka on November 20, 2020
In iTHEMS Biology Seminar on November 20th, Dr. Hidenori Tanaka (Physics & Informatics Laboratories, NTT Research) gave us an exciting talk about physics principles in neural networks. He first reviewed the basic scheme of deep learning using neural networks. Then, he presented three questions regarding both neural science and machine learning and explained his recent works which address these questions. He stressed how physics principles like symmetry and conservation laws are useful in extracting minimal features of biological circuit models, improving algorithms to simplify neural networks, and predicting learning dynamics of neural networks. As his talk was clear and kind to both specialists and nonspecialists, there were various questions from the audience. Hidenori is a very active researcher, and I was happy to invite him as a guest speaker. Kyosuke Adachi (BDR/iTHEMS)

20201124
Seminar ReportMath Seminar by Dr. Takahiro Kitayama on November 16, 2020
On November 16, professor Takahiro Kitayama from University of Tokyo gave a talk entitled “Representations of fundamental groups and 3manifold topology” at the iTHEMS math seminar. In the first part, he introduced a central motivation of 3manifold topology: classify all 3manifolds up to diffeomorphisms. As one of the important tools, he introduced the fundamental groups of spaces. He reviewed several known results of the fundamental groups of manifolds. Next, he focused on essential surfaces and introduced Haken 3manifolds as an important class of 3manifolds. In particular, he introduced several examples of Haken and nonHaken manifolds. At the end of the first talk, he explained SL(2,C)representation spaces (character varieties) of the fundamental groups of 3manifolds. He mentioned that the representation space has been used as a fundamental tool to classify knots and 3manifolds. In the second part, he first mentioned CullerShalen, MorganShalen’s theorem which says that an ideal point of the SL(2,C)character variety of a given 3manifold M gives an essential surface of M. Friedl, Hara, Kitayama, and Nagel developed CS and MS’s theory for the Lie group SL(n,C). He explained the main idea to obtain all essential surfaces from ideal points of SL(n,C)character variety. In particular, he introduced the tautological representation depending on some affine curve of the SL(2,C)character variety, and an action of the fundamental group on some contractible simplicial complex called the BruhatTits building. Then by a standard argument of topology, he constructed some simplicial map f from the universal covering space of a given 3manifold to the BruhatTits building. By taking the inverse image of f(after ignoring trivial parts and dividing by the fundamental group of the 3manifold), he finally constructed an essential surface. Next, he also told us about a relation between (homotopy types of) boundary loops of essential surfaces of knot complements and slopes of sides of the Newton polygon obtained from Apolynomials. He said an essential idea of the result, which can detect whether the boundary of an essential surface obtained from an ideal point is boundary parallel or not. At the end of the second talk, as the leading coefficients of torsion functions, he gave a function c_{M, ψ} on the SL(n, C)character variety. After explaining DunfieldFriedlJackson’s conjecture, he gave a partial solution of the conjecture which is related to the finiteness of c_{M, ψ} on the ideal points.

20201116
Seminar ReportMathPhys joint Seminar by Dr. Naoto Shiraishi on November 10, 2020
On November 10, Dr. Naoto Shiraishi from Gakushuin University gave a talk entitled “Mathematics of thermalization in isolated quantum systems” at the iTHEMS MathPhys joint seminar. In the first part, he reviewed some results and problems of quantum thermalization. Besides, he explained the typicality of equilibrium states, the relaxation caused by large effective dimensions, and the weak/strong eigenstate thermalization hypothesis mathematically. In the second part, the speaker discussed the difficulty of the thermalization problems and some of his results. Mainly, he showed the absence of local conserved quantities in the S=1/2 XYZ chain with a magnetic field. The talk had many participants from in and out iTHEMS and many stimulating discussions.

20201109
Seminar ReportBiology Seminar by Dr. Takahiro Sakamoto on November 5, 2020
On November 5th, Takahiro Sakamoto from SOKENDAI gave a talk at the iTHEMS Biology Seminar. First, he gave a very nice introduction about the basics of population genetics, and then, he talked about his theoretical study about how genetic divergence proceeds when there is migration between two locally adapted subpopulations. He did very well in explaining his research, which is actually quite complicated, to nonexperts, and because of that there were many questions and fruitful discussions. Takahiro is a student from my previous lab and I had in mind to invite him at some point because I knew he is good at giving talks and that his research should be interesting to iTHEMS people. So I was pleasantly surprised that Okadasan invited him, and I was very glad to see that many people enjoyed his talk. Jeffrey Fawcett

20201109
Seminar ReportBiology Seminar by Dr. Jeffrey Fawcett on October 29, 2020
In iTHEMS biology seminar on October 29, Jeffery Fawcett (RIKEN iTHEMS) gave us a talk on genomic data analysis. He started from explaining basic concepts of evolution and explained a couple of important quantities in population genetics, such as nucleotide diversity and the site frequency spectrum, which can be used to infer an underlying evolutionary process from sampled DNA sequences. He also explained statistical methods to study population structures and illustrated one of the methods in a study of the history of Japanese populations, which was very interesting. He made a great effort into his presentation. His talk was very educational and informative, and both experts and nonexperts enjoyed his talk. Besides, the next biology seminar on 11/5 was on theoretical population genetics (I was actually the host), and Jeff helped us to prepare for the next week's seminar. Thank you very much, Jeff!  Takashi Okada

20201030
Seminar ReportiTHEMS Theoretical Physics Seminar on October 23, 2020
The iTHEMS Theoretical Physics Seminar is held on October 23, 2020. The speaker is Dr. Masanori Hanada in Department of Mathematics, the University of Surrey. The title is ”Toward simulating Superstring/Mtheory on a Quantum Computer”. He present a framework for simulating superstring/Mtheory on a quantum computer, based on holographic duality. Because holographicduality maps superstring/Mtheory to quantum field theories (QFTs), we can study superstring/Mtheory if we can put such QFTs on a quantum computer  but it still looks like a complicated problem, if we use a usual lattice regularization. Here he propose an alternative approach, which turns out to be rather simple: we map the QFT problems to matrix models, especially the supersymmetric matrix models such as the BerensteinMaldacenaNastase (BMN) matrix model. Supersymmetric matrix models have natural applications to superstring/Mtheory and gravitational physics, in an appropriate limit of parameters. Furthermore, for certain states in the BerensteinMaldacenaNastase (BMN) matrix model, several supersymmetric quantum field theories dual to superstring/Mtheory can be realized on a quantum device. It is straightforward to put the matrix models on a quantum computer, because they are just quantum mechanics of matrices, and the construction of QFTs is mapped to the preparation of certain states. He show the procedures are conceptually rather simple and efficient quantum algorithms can be applied. In addition, as a (kind of) byproduct, he provide a new formulation of pure YangMills on quantum computer. The seminar was held via the Zoom online conference systems, and more than 15 people including outside of iTHEMS attended the seminar.

20201023
Seminar ReportiTHEMS Theoretical Physics Seminar by Dr. Tokuro Fukui on October 22, 2020
On October 22, the iTHEMSphys seminar entitled "Realistic shell model and chiral threebody force” given by Dr. Tokuro Fukui (YITP, Kyoto U.) was held. He and his collaborators proposed the way to calculate matrix elements of the threebody nuclear force, and showed the importance and effects of the threebody nuclear force in mediumheavy nuclei, such as calcium and nickel isotopes, starting from the chiral nuclear force using the shell model calculation. During his seminar, he introduced their works from the introduction to stateofart results. The seminar was held via the Zoom online conference systems, and more than 25 people including outside of iTHEMS attended the seminar.

20201022
Seminar ReportBiology Seminar by Dr. Christos Merkatas on October 21, 2020
On October 21st, Dr. Christos Merkatas from Aalto University in Finland gave a talk at the iTHEMS Biology Seminar. His talk was entitled, “Bayesian Nonparametric Estimation of Random Dynamical Systems”. Suppose that the observed time series is small, and the noise process is nonGaussian. How can we reconstruct and predict the behavior of the system? Dr. Merkatas showed that the proposed Bayesian approach enables us to reconstruct and predict the system by inferring the number of unknown components and their variances. According to him, the method can be applied to the problems in physics, biology, and economy. Since some of the audiences including me were not familiar with his method, we asked many basic questions. The talk by Dr. Merkatas was great and also educative. Gen Kurosawa

20201021
Seminar ReportDMWG seminar by Dr. Rinaldi: Towards the cosmological signature of composite DM
There are lots of dark matter (DM) candidates of particles and/or nonparticles. One important requirement is that DM should be massive. When we consider the main origin of the visible mass in the Universe, it is the proton, i.e. a composite of threequarks bound by the strong interaction. Then we can realize the DM mass naturally if we introduce similar dynamics in the dark sector. The interaction between the dark and the standard model sector is different from that of DM selfinteraction, hence it is also safe under the cosmological requirements. Among the varieties of composite DM models, the stealth DM scenario is a wellmotivated one with minimal assumptions. It is different from other baryonic composite DM since it is developed for solving the problem of DM rather than for another mystery in the standard model. Let's consider the signatures in cosmological observations which we could expect for the stealth DM scenario. Since the structure of the stealth DM is similar to that of the standard model baryons, they should experience the confinedunconfined phase transition in the early Universe. If the phase transition is of the 1st order, numerous vacuum babbles are produced in the transition from the false to the true vacuum. The collision of these bubbles sources the lowfrequency gravitational waves (GWs) of a ~nHzmHz range. However, it is difficult to calculate the physics around the phase transition. Indeed, it is not obvious whether the phase transition occurs in the 1st order or not. When it is of the 1st order, the gravitational wave spectrum is determined using the temperature of the Universe at the phase transition. Dr. Rinaldi and the members of the Lattice Strong Dynamics collaboration have investigated the phase transition in the stealth DM scenario by applying the sophisticated calculation techniques developed for the stronglyinteracting sector in the standard model. They reveal that the lower bound of the 1st order phase transition temperature for the scenario, which is then directly converted to the lower bound on the frequency of the GW. The technique should enable us to study DM from multiple aspects as is shown in this talk. Furthermore, this is the beginning of a new interdisciplinary study in which DM becomes the portal to connect the strong dynamics and GW cosmology, which could further enhance our understanding of this world!

20201007
Seminar ReportMathPhys Joint Seminar by Toshihiro Ota on October 2, 2020
On October 2, Toshihiro Ota gave a talk at the iTHEMS MathPhys Joint Seminar. His whole talk was on the interrelation among integrable lattIce models, quiver gauge theories, and hidden TQFT structure. His first talk was a sort of lecture on TQFT and integrable lattice model at an elementary level. At the beginning of the first talk, he explained quantum mechanics (QM). Then as a variant of QM, he introduced an axiomatic definition of topological quantum field theory as a special class of quantum field theory. He also introduced lattice model which can be seen as a discrete version of quantum field theories. In particular, he mentioned the integrability of the 1dimensional Ising model. In the second talk, he focused on the correspondence between Wilson't Hooft lines in a class of quantum gauge theories and transfer matrices in the corresponding integrable lattice models. At first, he gave an explanation of “classical integrability” and “quantum integrability” for field theories. In the case of 2dimensional lattice model, he explained that the integrability is described by the YangBaxter equation. Then he moved on to the details of the correspondence. In the lattice model side of the correspondence, he described the transfer matrix in terms of ncopies of Loperators. Moreover, in order to compare to the gauge theory side, he took the trigonometric limit and rewrote the transfer matrix by “more fundamental” Loperators. The gauge theory side is in particular given by 4d N=2 nnode circular quiver theory. The theory is defined on a 4d twisted spacetime S^1 xε R^2 x R, and he gave an expression of the Wilson't Hooft line wrapping the circle S^1. As the main result of his joint work with Kazunobu Maruyoshi and Junya Yagi, he gave a relation between these Wilson’t Hooft lines and transfer matrices. Finally, he gave several comments related to integrability from TQFT in extra dimension.

20201002
Seminar ReportDMWG seminar by Dr. Ishiyama: a spectacular cosmological Nbody simulation
Visible components of our Universe, such as galaxies, show hierarchical structures. Such structures are always embedded in DM structures called "halos". In the early Universe, there exist small density fluctuations that eventually collapse to halos at some points by their selfgravity. Then, halos grow to form larger structures again by selfgravity and this is the origin of the structure of the current Universe. The largescale structure of halos as well as their inner structures contain information about the nature of the DM particle. Cosmological Nbody simulation is a powerful computational method to follow that structure formation, by solving multibody problems numerically. A halo, which is a clump of elementary DM particles, is treated as one smooth particle in Nbody simulation. Its prediction power is so strong that the calculation corresponding to the upcoming cosmological survey, for example, has long been awaited. However, its computational costs scale as the square of the particle number N (or N log N when some reduction methods are adopted) and it is almost impossible to cover everything we need. There are two strategies in the calculation: simulating a large volume with large particle mass, or a small volume with small particle mass. The former is suitable for studies that deal with the largescale structure while the latter has advantages in studying the properties of each halo. His group has conducted a large highresolution simulation project which enables us to study both of them. The Uchuu simulation, which uses the cubic of 12800 particles in a 2 Gpcscale simulation box, enables us to study largescale structures. The ShinUchuu simulation in the same project, which uses the cubic of 6400 particles in a 140 Mpcscale box, is provided aiming to study the inner structure of DM halos. Analyzing the simulated structure and halo properties, the matter power spectrum covering from the largest to the nonlinear regime is obtained. Also, the socalled massconcentration relation in a wide halo mass range is now available thanks to the project. There is another good news for DM hunters: the results of the simulation are open to the public. This should boost the DM study from many aspects!

20200925
Seminar ReportBiology Seminar by Dr. Kyosuke Adachi on September 23, 2020
On September 23rd, Kyosuke Adachi gave a talk at the iTHEMS Biology Seminar on phase transitions in Biology. He first introduced the concept of phase transition and its possible application to understanding a number of biological phenomena. Then, he talked about his research on modelling the structural transition of chromatin states, and also about equilibrium and nonequilibrium dynamics. His research is really nice in how it engages both biologists and physicists, and many people seemed to enjoy his talk. In particular, the topic of chromatin dynamics is an area many molecular biologists are interested in at the moment, and we will be looking forward to hearing about his progress in the future.

20200918
Seminar ReportBiology Seminar by Dr. Hye Jin Park on September 16, 2020
On 16th September, Hye Jin Park (Asia Pacific Center for Theoretical Physics; APCTP) gave us a talk about her work on ecoevolutionary dynamics. She specifically looked at what if there are novel mutations that generate a nonexistent phenotype (temporal emergence of different phenotypes) and how it affects the evolution of cyclic dominance. She took advantage of introducing novel phenotypes to construct phylogeneticalike trees, which contain some information for which types are similar or dissimilar. She found that similar types are unlikely to exhibit cyclic dominance. We discussed how we can apply the theory to real systems and what factors are important. Thank you so much, Hye Jin for the fantastic talk! Ryosuke Iritani

20200911
Seminar ReportMath Seminar by Dr. Ken Furukawa on September 8, 2020
On September 8, there was a math seminar by Dr. Ken Furukawa. He gave a talk entitled Maximal Regularity and Partial Differential Equations. In the first part of his talk, the speaker explained the maximal regularity of parabolic partial differential equations and various sufficient conditions for the maximal regularity. Especially he introduced some functional calculus to obtain the analytic semigroup. In the second part, the speaker explained his recent collaboration work on the primitive equation and its relationship to the NavierStokes equation. He first shows that we can formally obtain primitive equations from the NavierStokes equation on the thin domain. He then explained his recent collaboration work which justifies this formal derivation of the primitive equation and how the sufficient conditions in the first talk work.

20200909
Seminar ReportBiology Seminar by Dr. Masashi Tachikawa on September 9, 2020
On 9th September, Masashi Tachikawa (Kyoto University) gave us a talk on adaptive dynamics as a framework for evolutionary dynamics. He first gave us a quick overview for modeling evolution, and then introduced adaptive dynamics toolbox and pairwise invasibility plots to visualize traitsubstitution processes towards evolutionarily singular points. He finally talked about how to capture evolutionary branching (two morphs emerging) using envelope with a trait value being tuned asif a parameter. We all excitedly learned a lot from this talk. Thank you, Masashi! Ryosuke Iritani

20200904
Seminar ReportBiology Seminar by Dr. Miki Ebisuya on July 17, 2020
In 1638, Galileo Galilei proposed “the squarecube law”: the ratio of two volumes is greater than the ratio of their surfaces. This law enables us to understand why large animals like elephants need longer time to cool their body temperature than small ones like human. On July 17th, Miki Ebisuya at European Molecular Biology Laboratory (EMBL) explained why human needs longer time to develop her/his body than mouse, at the iTHEMS seminar. In fact, the speed of the segment formation ("taisetsu" in Japanese) of human is twice or three times as slow as that of mouse. By combining stateoftheart experiments and a model with two variables, her group discovered that the difference of tempos is due to the difference of biochemical parameters. The talk was clear and enjoyable. And it was accessible to the diverse audience. As a mathematician asked during the talk, their discovery raises a new fundamental question about why reactions in human are slower than those in mouse. The question might be also answered by the collaboration between biology and mathematics in a future.

20200903
Seminar ReportiTHEMS MathPhys joint seminar was held on August 31 and September 1, 2020
The iTHEMS MathPhys joint seminar was held on August 31st and September 1st, inviting Makiko Sasada from University of Tokyo and Kenichi Bannai from Keio university / RIKEN AIP. This was a series of lectures entitled “Geometric Perspective for the Theory of Hydrodynamic Limits”. They explained to us their recent joint work with Yukio Kametani on hydrodynamic limits from algebraic/geometric view point. On Day 1, Sasadasan gave an introduction to hydrodynamic limits, and explained the motivation of the joint work and the key ideas. One of the goals of the theory of hydrodynamic limits is to derive macroscopic dynamics from microscopic evolution equations rigorously. There have been many results to this problem, but all of them depend on specific microscopic models. The long term goal of this joint work is to construct an abstract and universal theory of hydrodynamic limits. One of the most important ingredients of the theory of hydrodynamic limits is the “decomposition of closed forms”, which have been obtained by Varadhan and other people using very technical argument depending on models. One of the aims of this work is to give a more general and clear understanding of this type of decompositions. Their strategy is as follows: the microscopic data can be divided into topological (geometric) part and stochastic (analytic) part. For discrete models, the former one is modeled by a directed graph, the set of states at each vertex, and the interaction through edges. A typical analytic datum is the jump rate, i.e., the frequency of interaction. They observed that some important feature of hydrodynamic limits depends only on the geometric data, and as a consequence, they could avoid adhoc analytic estimations. Moreover, they obtain a version of Varadhan’s decomposition in a very general setting. On Day 2, Bannaisan gave a precise mathematical formulation of their main results and proofs. As explained above, the geometric part of microscopic model is given by a directed graph, a pointed set of states, and a function which represents the interaction through edges. From this set of data, we can form a configuration space, each point of which corresponds to a possible state on the graph (The interaction data induce the transition structure on the configuration space). On the configuration space, they consider a special type of functions / forms called “uniformly local functions / forms”, and construct a cohomology theory (uniformly local cohomology) associated to them. Surprisingly, the uniformly local cohomology captures all conserved quantities (macroscopic observables). Moreover, from this fact, they can derive a local form version of Varadhan’s decomposition. An important ingredient of the proof is the group cohomology, which is often used in the field of number theory. They assume the existence of a free group action on the graph (which is valid in many important examples), and apply a general theory of group cohomology. It is very surprising that a fundamental result in hydrodynamic limits is derived from an abstract algebraic theory, and it will provide us a new and clear understanding of this field.

20200903
Seminar ReportBiology Short Talk by Dr. Ryosuke Iritani on September 2, 2020
On September 2, Ryosuke Iritani gave a lecture at iTHMES Biology Seminar. In this seminar, Ryo explained the principles of evolution in an easytounderstand way, using examples such as the diversification of pet dogs and cruciferous plants, and changes in the structure of the gecko's hands. Especially, the formulation of adaptive evolution using Fokker planck equarion was introduced. His seminar will be very useful as a basic knowledge of evolutionary biology and mathematical biology that will be covered in future seminars.

20200827
Seminar ReportBiology Seminar by Dr. Gen Kurosawa on August 26, 2020
On August 26th, Gen Kurosawa gave a talk at the iTHEMS Biology seminar. The main topic of the talk was biological timing, and he introduced his work on mathematical modelling of circadian rhythm and hibernation. In addition, he also talked about his current effort in trying to apply theories developed in biology to understand the transaction network between companies. He clearly made a lot of effort to make the seminar accessible and enjoyable to people without background knowledge, and I'm sure many people appreciated that.

20200822
Seminar ReportiTHEMS Theoretical Physics Seminar by Dr. Takuya Shimazaki on August 21, 2020
On August 21st (Fri.), Takuya Shimazaki (The University of Tokyo) gave an iTHEMSphys seminar on an application of the Lefschetz thimble method to the Schwinger mechanism, or a particle production problem caused by strong electric fields. In the seminar, he has demonstrated a new formulation to estimate the particle production rate. The new formulation gives a good result even in some regimes where one cannot use the Dykhne–Davis–Pechukas (DDP) formula (a commonly used approximation in a twolevel quantum system equivalent to the Schwinger mechanism). There were a lot of lively discussions, and the audience looked enjoying the seminar.

20200805
Seminar ReportBiology Seminar by Dr. Lukasz Kusmierz on August 5, 2020
On 5th August, Ph.D. Lukasz Kusmierz ( RIKEN Center for Brain Science ) gave a talk at the iTHEMS Biology Seminar. Dr. Kusmierz introduced us to his work that modeling of heavy tails in the distribution of synaptic weights in the brain. His modeling, called "Cauchy network" which is based on the Cauchy distribution, has been successful in recreating biologically distributions. It could serve as a useful framework for checking the effects of synaptic heavy tails in various scenarios. His research will be a major step forward in the future of neuroscience. Thank you very much, Lukasz!

20200805
Seminar ReportMath Seminar by Dr. Tadahiro Miyao
The iTHEMS Math seminar entitled "Stability of ferromagnetism in manyelectron systems”, by Dr. Tadahiro Miyao, was held on 31 July. In the first part, the speaker reviewed basic properties of electron and introduced the Hubbard model, which describes interacting electrons. In addition, he constructed a model independent framework describing stabilities of ferromagnetism in strongly correlated electron systems. Especially, he reinterpreted the famous MarshallLiebMattis theorem and Lieb’s theorem. Then he showed that Lieb’s theorem still holds true even if the electronphonon and electronphoton interactions are taken into account. As examples, he explained the HolsteinHubbard model and the Kondo lattice model. Finally, he also mentioned other stability classes and open problems. In the second part, the speaker introduced order preserving operator inequalities and many mathematical tools, such as the PerronFrobeniusFaris theorem, abstract reflection positivity, the holeparticle transformation, and so on. He also explained how these inequalities are applied to the mathematical study of ferromagnetism. Then Lieb's theorem of the Hubbard model and its stabilities were discussed in terms of the inequalities.

20200731
Seminar ReportBiology Seminar by Dr. Takashi Okada on July 29, 2020
On 29th July, Takashi Okada gave us a talk on his work on population genetics theory. He first explained that the classical WrightFisher demography cannot inherently consider the realistic situation in which the offspringnumber distribution is skewed. Second, he talked about what if we extend the WrightFisher demography to a skewed offspring number (power low distribution), showing us that the powerlow distribution can dramatically change the timescale of evolution (e.g., sojourn time of fixation of a neutral mutant) as well as large population size limits. We learned that even the classic theory arising from Sewall Wright and Ronald A Fisher entails mathematical expansion. Thank you so much, Takashi, for the great talk!

20200727
Seminar ReportSpecial DMWG seminar : The latest results from the XENON1T experiment
XENON1T collaboration has reported interesting results in June, which could be the signature of the physics beyond the standard model. We held a special DMWG seminar on July 22, inviting Prof. Yamashita, who is a specialist in the XENON1T data analysis, from Nagoya University. Many people from various research fields have registered and participated in this online seminar. The number of registrants is more than 180 while the participants than 100. We first would like to apologize to our guests, especially to whom could not attend the seminar although they have registered due to our trouble with the webinar system. XENON1T is an experiment aiming to detect the scattering between dark matter (DM) and a xenon nucleus. Xenon is one of the best targets material for WIMP (Weakly Interacting Massive Particle) because of its stability and the large atomic number. By setting the detector deep underground, the cosmicray scattering event, which is the main source of the background, is efficiently removed. The original experiment was started in 2005 (XENON10) and after several upgrades, XENON1T has completed its first observing run in 2018. The signature of the socalled nuclear recoil event is searched to detect WIMP. There is another type of event referred to as the electronic recoil event, which is also useful to detect other DM signatures, and this seminar focuses on such a kind of event. The target region of the DM parameter space is different between these two event types. The 285 electronic recoil events over the expected 217247 from the background are observed in the recoil energy range of 17keV during the 1st observing run of the XENON1T experiment. In this talk, Prof. Yamashita has explained the details of the analysis and the possible interpretation of the signature. Starting from the introductions about the possible background considered in the traditional analysis, the statistical treatments, and also the model fitting results are provided. There are several possibilities for explaining the excess: (i) tritium background, (ii) solar axion, (iii) anomalous neutrino magnetic moment, and (iv) bosonic DM. If the excess is explained by tritium (i), it means that we have detected the first tritium background events while others indicate the detection of the signatures of the new physics. Solar axion (ii) could fit the recoil spectrum beautifully, however, there may not be consistent with the results from astrophysical observations. The neutrino scenario (iii) is another possibility with less significance, and the significance of the bosonic DM scenario (iv) could not over the 3.0 sigma. The excess itself is convincing while it is difficult to conclude its origin. Abobementioned possibilities are planned to be tested with further upgrades of the XENON1T experiment, XENONnT. We should be excited about the results in the near future. Stay tuned!

20200720
Seminar ReportMath seminar by Dr. Yuichi Ike on July 15, 2020
We have all heard that "data is the new oil". But just like any fossil resource, data also has to be worked with to use it effectively. In his talk, titled "Topological data analysis from a practical and mathematical perspective", Dr. Yuichi Ike from Fujitsu highlighted several mathematical aspects of data processing as well as relevant applications in the health sector. In the first part of the talk, the audience was introduced to basic concepts of topological data analysis. The goal of this technique is to infer the shape of data  i.e. topological quantities such as the number of connected components, loops, cavities, etc.  from the input data points. While the shape is represented by the homology group in the continuous case, the discrete case calls for different methodology. One possible technique is the creation of persistence diagrams to identify critical components. In a general application workflow, these approaches appear as follows. From the input data, its persistent homology is computed, visualized via a persistence diagram, and finally passed on to experts for evaluation. This has applications in material sciences and time series analysis as well as medical settings. Here, a recent work of the speaker was able to reduce misclassifications in a diagnosis setting by up to 70%. The second part of the talk was devoted to the mathematical foundations of the presented work, namely on persistencelike distance on the sheaf category and displacement energy. Starting from elements in symplectic geometry, via a Morse theory for sheaves, the speaker integrated several mathematical fields. Finally, after introducing the nondisplacement theorem, the audience learned about several proofs in the field. Thus, the talk nicely tied current relevant applications to deep results in theoretical mathematics.

20200716
Seminar ReportBiology Seminar about "Application of geometry to protein structure analysis" on July 15, 2020
In Biology Seminar on 15th July, a graduate student Haru OonoNegami (Engineering department, University of Tokyo) talked about a general overview of the interdisciplinary topic between geometry and protein biology, as well as her own work on the proteinclassification algorithms based on topological properties. Understanding and predicting the function of structurally "similar" proteins is of pivotal importance to any field of biology. Her work extends previous studies that classify the topological structure of proteins in a computationally reasonable time still with a good accuracy. We audience, after her talk, excitedly discussed extensions and background problems behind her talk. Thank you so much for the great talk, Harusan!  Ryosuke Iritani
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