Seminar Report
337 news

20210421
Seminar ReportiTHEMS Colloquium by Prof. Kenji Fukaya on April 16, 2021
On April 16, 2021, 13:3015:00 (JST) 0:302:00(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 (KolmogorovArnoldMoser) theory describes perturbation of this system and shows that almost all tori persist. Then Professor Fukaya explained the Lagrangian torus fibration found by StromingerYauZaslow, with the example of the complex projective space. For the complex projective nspace, the image of the moment map is an nsimplex and the regular fibers are Lagrangian ntori. 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 FubiniStudy symplectic form. However, he expects it can be the case with respect to the CalabiYau 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

20210416
Seminar ReportQuantum 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 (University of Hamburg, Germany) and ChingKai Chiu

20210415
Seminar ReportiTHEMS 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 higherorder 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

20210415
Seminar ReportiTHEMS 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

20210415
Seminar ReportJournal 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 WignerYanase skew information. Then, she explained the concept of jointly convex/concave functions and WignerYanaseDysonLieb theorem, and discussed the subadditivity and strong subadditivity of von Neumann entropy and its generalizations. Thank you, Gotosan, for interesting talk! Reported by Akinori Tanaka

20210412
Seminar ReportMath Seminar by Dr. Kai Koike on April 7, 2021
On April 7, Dr. Kai Koike from Kyoto University gave a talk entitled “Longtime 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 longtime 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

20210405
Seminar ReportMath 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 GreenTao theorem for number fields”. The main topic of the talk was his recent joint work with his collaborators about the GreenTao theorem and its generalization. In the first part, he explained the historical background and the technology behind the proof of the GreenTao 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 GreenTao 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 abplane, each of the numbers corresponds to a lattice point. We can draw a “shape” by choosing finite number of those lattices. Then, the generalized GreenTao 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 GreenTao theorem, a classical technique wellknown to algebraic number theorists plays a fundamental role. Reported by Hiroyasu Miyazaki

20210402
Seminar ReportBiology 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. Hironosan has been recently working on chemical reaction networks with Miyazakisan, Hidakasan, 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 steadystate properties. I am grateful to Hironosan because I could improve my understanding of reaction systems through collaboration with him. Also, Hironosan and I have been friends since we were undergraduates, and I am happy to work together. Thank you very much, Hironosan! Reported by Takashi Okada

20210326
Seminar ReportBiology 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

20210325
Seminar ReportInformation 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 epsilongreedy update. We thank Akinori for the great and clear talk!

20210318
Seminar ReportQuantum 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 linearresponse 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 perovskitebased 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 wellpresented talk. Reported by ChenHsuan Hsu (CEMS, RIKEN) and ChingKai Chiu

20210305
Seminar ReportQuantum 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 NonHermitian 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 nonHermitian 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 nonHermitian platforms. It is great to have this nice talk.

20210226
Seminar ReportABBLiTHEMS Joint Seminar by Prof. Gordon Baym on February 22, 2021
On Feb. 22, our iTHEMS colleague, Gordon Baym, gave an online talk from UrbanaChampaign 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 (antineutrinos) are lefthanded (righthanded) 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.

20210225
Seminar ReportBiology 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 drugresistance in Escherichia coli using automated highthroughput laboratory experiments. He first talked about the background of drug resistance evolution and about the wellknown / novel resistanceconferring 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 multiomics 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

20210225
Seminar ReportBiology 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 nonlinear 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 nonlinear response of DNA. He then explained the strategy to clarify the origin of nonlinearity by applying mathematical modeling and statistical physics. Introducing the wormlike 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

20210219
Seminar ReportInformation 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)

20210217
Seminar ReportDMWG Seminar 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 verylong baseline interferometry. The spatial resolution of milliarcsecond is achieved with VLBI techniques. However, the sensitivity is limited and longlasting 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!

20210217
Seminar ReportiTHEMS Theoretical Physics Seminar by Mr. Masaaki Tokieda on February 16, 2021
On February 16, the iTHEMSphys seminar entitled "Quantum mechanical description of energy dissipation and application to heavyion 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 subbarrier reactions. He also applied the method to heavyion 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.

20210215
Seminar ReportBiology 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 nonmodel 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 nonmodel organisms, especially MROs. Finally, He obtained a large amount of data on MROlocalized proteins in nonmodel organisms, and through machine learning using the data as training data, he created a detector that can detect MROlocalized signals in such nonmodel 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!

20210205
Seminar ReportiTHEMS Theoretical Physics Seminar by Dr. DiLun Yang on February 4, 2021
On February 4, the iTHEMSphys seminar entitled "Quantum kinetic theory for chiral and spin transport in relativistic heavy ion collisions and corecollapse supernovae" given by Dr. DiLun 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 heavyion collisions and corecollapse 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.

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 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)

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.
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