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376 ニュース
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2021-09-17
セミナーレポート
NEW WG Seminar by Prof. Yuta Murakami on September 15, 2021
Yuta Murakami from Tokyo Institute of Technology told us about "High-harmonic generation in strongly correlated systems." High-harmonic generation (HHG) by strong AC electric fields is one of the hottest topics in cond-mat physics. After a brief overview of HHG in various materials such as gasses and semi-conductors and also recent experimental results in Mott insulators, Yuta explained his recent numerical studies on HHG in strongly correlated systems and clarified unique features of HHG arising from the strongly-correlated nature. About 30 people joined the seminar and we enjoyed fruitful discussions during and after the seminar. Reported by Hidetoshi Taya
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2021-09-17
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NEW WG Seminar by Prof. Matteo Baggioli on September 10, 2021
Matteo Baggioli (Jiao-Tong U. Shanghai) gave a talk on "Towards a description of amorphous solids and viscoelastic materials using effective field theory and holographic methods." Amorphous and viscoelastic materials appear in many places, not only in scientific problems but also in our daily life. Despite its ubiquity, there are many intriguing phenomena that are not yet understood, in particular, in the non-linear regime. In the talk, Matteo explained his recent attempts to formulate non-linear responses in amorphous and viscoelastic materials based on holographic and effective-field-theory techniques. Matteo also discussed open problems and future directions that we can pursue in the future. There were about 30 participants from various fields of physics, and we had fruitful discussions from a broad point of view during and even after the talk. Reported by Hidetoshi Taya
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2021-09-09
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iTHEMS Biology Seminar by Dr. Euki Yazaki on September 9, 2021
Molecular phylogenetic analysis is one of the most important analysis methods in biology. If used well, it can help us understand how organisms diversified and how genes evolved. The methods of molecular phylogenetic analysis are subject to debate, so we are familiar with the mathematical background. However, we are not so familiar with how the data sets for phylogenetic analysis are made up. In this Biology Seminar, the main alignment algorithms for making data sets were explained and discussed. Scoring is important in alignment algorithms, and there was a discussion on scoring for amino acid and nucleic acid mutations and scoring for gap penalties. The discussion on alignment distance was also heated. I hope the audience all enjoyed it. I would like to have another discussion on phylogenetic analysis and mathematical background next time. Thank you very much!
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2021-09-09
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ABBL-iTHEMS Joint Seminar by Dr. Yosuke Mizuno on September 3, 2021
Prof. Yosuke Mizuno (Tsung-Dao Lee Institute, Shanghai JiaoTong University) gave an excellent talk on "The Polarised ring ofthe Supermassive Black Hole in M87: EHT observations andtheoretical modeling". He introduced that the Event HorizonTelescope (EHT) had mapped the central compact radio source of theelliptical galaxy M87 at 1.3 mm with unprecedented angular resolution. Recently EHT provided new images of the polarised emissionaround the central black hole in M87 on event-horizon scale. Thispolarised synchrotron emission probes the structure of magnetic fieldsand the plasma properties near the black hole. He and hiscollaborators found that the net azimuthal linear polarisationpattern may result from organised, poloidal magnetic fields in the emission region. In a quantitative comparison with a large simulated polarimetric image library, he found that magnetically arrested accretion disks are favoured to explain polarimetric EHT observations. In this talk, he also discussed about a new modelling study of M87jets in the collimation and acceleration region. Reported by Shigehiro Nagataki
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2021-09-03
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Quantum Matter SG seminar by Dr. Levente Rózsa on September 1, 2021
Dr. Levente Rózsa gave a talk about Yu-Shiba-Rusinov (YSR) states and other localized states appearing in superconductors for Quantum Matter Study Group on September 1st, 2021. There are three distinct types of localized in-gap states in superconductors —- Majorana bound states, YSR states, and Caroli-de Genne-Matricon states. Dr. Rózsa first introduced Majorana bound states emerging in topological superconductors. Next, he talked about the anisotropic spacial distribution of the YSR states on the La surface (0001). The YSR state is a localized in-gap state induced by magnetic impurity in a superconductor. He showed that this anisotropy stems from the anisotropic Fermi surface. Furthermore, he discussed the localized states appearing in vortex cores are Caroli-de Genne-Matricon states, instead of Majorana bound states. He went through the experimental details and compared them with his theoretical simulation. The talk was well-organized and clear. We thank Dr. Rózsa for sharing his interesting research works. Reported by Thore Posske (University of Hamburg, Germany) and Ching-Kai Chiu
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2021-09-03
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iTHEMS Biology Seminar by Dr. Yingying Xu on September 2, 2021
In today's Biology Seminar, Yingying Xu (iTHEMS) introduced one paper arguing the quantitative explanation for immune-escape of virus by means of quasispecies dynamics models with Gillespie algorithm. She firstly explained the background information about the immune systems. She then taught us how the authors simulated the dynamics and made a comparison with experimental data. We finally discussed potential future directions to further development of quantitative modeling of chronic or acute infectious virus, highlighting a potential issue in estimating the mutation rate of virus. We learned a lot from this journal club, thank you so much for the great talk, Yingying! Reported by Ryosuke Iritani
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2021-08-30
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iTHEMS Biology Seminar by Dr. Gen Kurosawa on August 26, 2021
During this covid-19 crisis, we check our body temperature (Tb) every day since Tb is essential variable of our body. In fact, some organisms like humans try to keep Tb constant, but some other organisms chose completely different strategies, including hibernation (冬眠). On August 26, I talked about hibernation at the iTHEMS Biology Seminar. Hibernation is a strategy for the organisms, including a primate to survive in a severe season with limited food and water availability. Although there have been a lot of studies about hibernation since the era of Aristotle, fundamental problems of hibernation remain unknown. Recently, we started to investigate mathematically body temperature profile of hibernating hamsters. During hibernation, the organisms drastically decrease their basal metabolisms, drop their body temperature (Tb) more than 10 degree, and become immobile. Mysteriously, Tb during hibernation does not remain constant at very low value, but greatly fluctuates with inconstant period of several days. At the seminar, I showed that a simple model can reproduce well and forecast Tb data during hibernation. Thankfully, there were a lot of questions and suggestions about the method of time-series analysis, hibernating species, and so on which are precious to me. This study is the collaboration with Prof. Yoshifumi Yamaguchi at Institute of Low Temperature Science, Hokkaido Univ and Shingo Gibo at iTHEMS. I’m really enjoying this research. I am happy if the audiences enjoyed the seminar and forgot about the heat. Thanks!
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2021-08-25
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iTHEMS Biology Seminar by Dr. Naohiro Kawamoto on August 19, 2021
In iTHEMS Biology Seminar on August 19th, Dr. Naohiro Kawamoto (Osaka University) gave a talk on cyanobacterial circadian oscillations. It is known that three proteins (KaiA, KaiB and KaiC) are sufficient for generating self-sustained circadian oscillations in cyanobacterium. In this talk, Dr. Kawamoto experimentally showed that the lack of kaiA causes damped oscillation. Then, he analyzed the benefit of the damped circadian oscillation by using a simple mathematical model of the interaction between the damped and self-sustained oscillators. This analysis revealed that kaiA-less damped oscillator can resonate to another oscillatory process. Finally, he talked about evolution of related to evolution of circadian clock system for future work. After the talk, we enjoyed discussion about mathematical modeling of various types of coupled oscillators. Thank you very much, Naohiro! Reported by Shingo Gibo
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2021-08-25
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Quantum Matter SG seminar by Prof. Daw-Wei Wang on August 23, 2021
On August 23rd, 2021, Quantum Matter Study Group invited Prof. Daw-Wei Wang to give a talk on the application of machine learning in condensed matter physics. First, he briefly introduced learning and emphasized using supervised machine learning in condensed matter physics. The practical condensed matter problem he focused on is the physics of many-body systems since the many-body problem is challenging to solve. By randomly choosing small portions of a many-body Hamiltonian, machine learning can almost accurately predict the energy of the many-body system. Prof. Wang used the 1D Fermi-Hubbard model and the 1D Ising model to show the consistency between the learning prediction and the known solutions. The limitation of this approach is that the system size has to be fixed. To resolve this problem, he used the transfer learning approach to extend the prediction to a larger system size by learning from small systems. In the end, he talked about identifying the topological phase transition points by improving the machine learning approach in the literature. The talk is very comprehensive and informative. We thank Prof. Wang for giving a wonderful talk. Reported by Ching-Kai Chiu
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2021-08-18
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iTHEMS Math Seminar by Dr. Yalong Cao on August 6, 2021
The final Math Seminar of this semester was held on August 9th. This time, we invited our new colleague Dr. Yalong Cao as a speaker. First, he gave an overview of the celebrated Yang-MIlls theory in real dimensions 3 and 4. Next, it was explained that one can complexify the above Yang-Mills theory on Calabi-Yau 3 and 4-folds. The point is that in algebro-geometric setting, moduli spaces of Yang-Mills connections admit nice compactifications. Finally, he explained the connection between the above story and the enumerative geometry, specifically on counting (stable) coherent sheaves and complex ASD connections on Calabi-Yau 4-folds. He and his collaborators proposed a conjectural sheaf-theoretic interpretation of Klemm-Pandharipande’s BPS invariants of CY 4-folds defined using Gromov-Witten theory. Reported by Hiroyasu Miyazaki
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2021-08-17
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iTHEMS Theoretical Physics Seminar by Dr. Shunichiro Kinoshita on August 16, 2021
Shunichiro Kinoshita (Chuo U.) gave a talk on "Application of AdS/CFT to non-equilibrium phenomena in external electric fields. "After a brief introduction to the AdS/CFT correspondence, Shunichiro analyzed a holographic QCD system under strong electric fields constructed with D3/D7 branes. Shunichiro considered two kinds of electric-field configurations.The first one was a field with a sudden switching on (quenched setup). Shunichiro discussed how the confinement-deconfinement phase transition occurs and showed the possibility of deconfinement driven by turbulence. The second configuration was rotating electric fields. Shunichiro discussed how the frequency of the electric field affects the phase transition and argued the possibility of a novel state, distinct from the vacuum, for infinitesimally small electric fields with finite frequency. Reported by Hidetoshi Taya
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2021-08-10
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Information Theory SG Seminar by Prof. Masayuki Ohzeki on August 4, 2021
On August 4, Prof. Masayuki Ohzeki (Tohoku University/Tokyo Institute of Technology/Sigma-i Co., Ltd.) gave us a talk on the quantum annealing. In the first part, after a general introduction, he demonstrated how to use the D-Wave machine from our personal computers. It is remarkable that we can easily manipulate a number of quantum spins ourselves to solve an optimization problem. In the second part, he reviewed working principles for quantum annealing: he started from the original proposal in 1998 and explained more recent methods such as the reverse annealing. He also explained carefully the usefulness and the limits of the quantum annealing. After discussing the theoretical perspective and how the machine is implemented using the superconducting qubits, he presented the application of the quantum annealer to the real world. He showed his collaborations with many companies and how the quantum annealing can be used to solve real-life problems, such as the optimization of the evacuation routes or listing the hotel recommendation on the web. A lot of interactive discussions were made during and after the talk. We really thank Prof. Ohzeki for his great talk. Reported by Ryusuke Hamazaki
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2021-08-06
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iTHEMS Biology Seminar by Dr. Ai Niitsu on August 5, 2021
In iTHEMS biology seminar on August 5th, Dr. Ai Niitsu (RIKEN Theoretical Molecular Science Lab.) gave a talk about the membrane peptide design and computational modeling. First, she mentioned the recent machine learning approach for the prediction of the protein structures. Then, she pointed out that the prediction of the membrane related structure and stoichiometry of protein complexes is still challenging. Next, she explained the computational design of the coiled-coil peptides in membrane. The amino acid sequence of the peptide is determined so that the interchain interaction is satisfied. As a result, she obtained some stable transmembrane assemblies of the peptide. Along with the modelling of the peptide assemblies and their conductance estimate, she experimentally measured the conductance of the peptide channel in membrane by imposing various voltages. The high voltage induces the multi-conductance state, which differs from the low voltage case where a stable single channel was observed. Based on further computational modelling and experiments, that multi-conductance state was suggested to come from the change in the peptide structures and stoichiometry of a single pore. Her computational method and experimental results attract the audience interests and induce various discussions. Thank you very much for great talk, Ai! Reported by Hiroshi Yokota
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2021-08-02
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Information Theory SG Seminar by Dr. Qibin Zhao on July 28, 2021
In the Information Theory SG seminar on July 28th, Dr. Qibin Zhao gave us an exciting talk about the basics and applications of tensor networks (TNs) in machine learning. His talk was divided into three parts, (i) tensor methods for data representation, (ii) TNs in deep learning modeling, and (iii) frontiers and future trends. In the first part, he started with a graphical introduction of tensors and dimension reduction methods. He then presented the important question of how the imperfect data represented by tensors can be completed using the low-rank approximation, and introduced several possible approaches with impressive examples. Here he explained the TNs and decomposition methods in detail using diagrammatic notations, which can concisely express the tensor operations such as the contraction. In the second part, he talked about the useful application of TNs to model compression in machine learning. He illustrated the ways to represent the neural network model by tensors and to learn the weights through the contraction. Interestingly, the density matrix renormalization group (DMRG), which was originally proposed in the quantum physics field, may be used as a learning algorithm. In the last part, he showed an overview of recent topics on TNs and machine learning such as TNs for probabilistic modeling and supervised learning with projected entangled pair states (PEPS). Intriguingly, the topological structure of TNs can be optimized for a given image, and the learned topology significantly depends on the input data and is more complex than conventional simple structures such as lines, trees, or cycles. The clearly structured talk took us from the basics to the cutting-edge subjects, and there were many questions and discussions during the talk. We are deeply grateful to Dr. Qibin Zhao for his excellent talk on the fast-growing interdisciplinary field. Reported by Kyosuke Adachi
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2021-07-30
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iTHEMS Biology Seminar by Prof. Mayumi Seto on July 29, 2021
On July 29th, Mayumi Seto (Nara Women's University) gave a talk on the application of thermodynamics to microbial modeling. She first introduced some important concepts of adenosine tri-phosphate (ATP), its synthesis in biology, and chmotrophic interactions between microorganisms. She then moved on to mathematical models explicitly incorporating energy flows in the microbial interactions. She finally gave implications from her work for future and ongoing studies, and after the talk we casually discussed her exciting projects. For me, she was the person whom I met on the very first visitation at Kyushu University in 2009 when I was, as an undergrad student at another university, yet unsure to start my Ph.D. at Kyushu University or not, and I'm sure her kind and encouraging guidance was one of the decisive factors for me being here as a researcher. Thanks again for the fantastic talk, Mayumi! Reported by Ryosuke Iritani
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2021-07-12
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iTHEMS Colloquium by Prof. Shingo Iwami on July 8, 2021
In his presentation for the iTHEMS Colloquium, Prof. Shingo Iwami discussed the foundational approach of his research: using a mathematical model-based approach to link experimental data from ever-improving experimental measurement technology in order to tackle problems in Biology, particularly in hematology, infectious diseases, cancer, etc. He illustrated his research approach through several examples that ranged from HIV, Hepatitis C virus, and the new SARS corona virus (SARS-CoV-2). He highlighted some of the key challenges that are faced when trying to extract specific information from limited data, and how properly calibrated models can be used to simulate experiments that cannot be performed. He also talked about his plans for the future, and introduced the research team he newly formed at Nagoya University, the interdisciplinary Biology Laboratory or iBLab. Reported by Catherine Beauchemin
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2021-07-07
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iTHEMS Theoretical Physics Seminar by Dr. Myungo Shim on July 5, 2021
On July 5, Myungo Shim from Kyung Hee University, Korea, gave the iTHEMS-physics seminar on a correspondence between three-dimensional gauge theories. He proposed a novel procedure of assigning a pair of non-unitary topological quantum field theories (TQFTs), TFT±[T0], to a (2+1)D interacting N=4 superconformal field theory (SCFT) T0 of rank 0, i.e. having no Coulomb and Higgs branches. The topological theories arise from particular degenerate limits of the SCFT. Modular data of the non-unitary TQFTs are extracted from the supersymmetric partition functions in the degenerate limits. As a non-trivial dictionary, he proposed that F=max{−log|S(+)0α|}=max{−log|S(−)0α|}, where F is the round three-sphere free energy of T0 and S(±)0α is the first column in the modular S-matrix of TFT±. From the dictionary, he derived the lower bound on F, F≥−log(√5−√510)≃0.642965, which holds for any rank 0 SCFT. The bound is saturated by the minimal N=4 SCFT proposed by Gang-Yamazaki, whose associated topological theories are both the Lee-Yang TQFT. Before going to the technical part, he also provided some background materials including some peculiar features in 3d gauge theories, some supersymmetries, anyons, and some modular data of MTC in the talk. Reported by Toshihiro Ota
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2021-07-06
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iTHEMS Math Seminar by Mr. Mizuki Oikawa on July 2, 2021
On July 2 Mizuki Oikawa gave a talk at the iTHEMS math seminar. He talked about the interaction among modular functions, conformal field theories and moonshine phenomena. Below is a recap of his talk. The j-invariant is an example of modular form. Its coefficients in the q-expansion is closely related to a certain sporadic simple group (the monster group), and the relation can be understood via the theory of vertex operator algebras (VOA), which is a mathematical model of conformal field theory (CFT). This gives an example of moonshine phenomena. On the other hand, there is another mathematical framework for CFT, called the conformal net, which depends on the theory of von Neumann algebras. Carpi-Kawahigashi-Longo-Weiner gave a correspondence between a certain class of VOAs (which includes the monstrous moonshine VOA) and that of conformal nets. Recently, Tener gave a geometric realization of some VOAs and the corresponding conformal nets via Segal CFT. The talk was highly stimulating, and the audience asked many questions that arise from both mathematical and physical sides. Reported by Michiya Mori
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2021-07-06
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iTHEMS Biology Seminar by Prof. Takahiro Sakaue on July 1, 2021
On July 1st, Prof. Takahiro Sakaue (Aoyama Gakuin University) gave us a talk about chromatin dynamics in C. elegans embryos. He first introduced important factors for gene expression such as phase separation, topological constraints, and chromatin dynamics. After explaining how to see the chromatin dynamics under the microscope, he showed us interesting experimental results about the dependence of MSD on the nucleus radius. By considering polymer models, he showed that two kinds of typical length/time scales appear and discussed how the type of anomalous diffusion of chromatin is determined depending on the time/length scale. Moreover, he theoretically explained the observed nucleus-size dependence of MSD. We are grateful to Sakaue-san for the exciting talk! Reported by Kyosuke Adachi
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2021-07-01
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iTHEMS Theoretical Physics Seminar by Dr. Yuki Fujimoto on June 29, 2021
On June 29th, Yuki Fujimoto (The University of Tokyo) gave the iTHEMS-physics seminar on the equation of state (EoS) in the dense baryonic matter. The EoS of dense baryonic/quark matter is the crucial ingredient for understanding neutron stars. He nicely reviewed the current state of the high-density matter EoS based on the QCD perspectives. His recent work on the EoS calculated within the pQCD framework with the resummation [Fujimoto & Fukushima, 2011.10891] gives the Hard Dense Loop resummation formula which turns out to reduce the uncertainty compared with the conventional pQCD estimate without resummation. His approach extends the applicability of the QCD-based EoS down to densities realized inside neutron stars and infers a smooth matching with the baryonic EoS. The audience asked a lot of questions and had fruitful discussions. Reported by Etsuko Itou
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2021-06-29
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iTHEMS Theoretical Physics Seminar by Dr. Kanato Goto on June 21, 2021
On June 21st, Kanato Goto (RIKEN iTHEMS) gave the iTHEMS-physics seminar on the black hole information paradox. Recently, there is a proposal for the formula for a quantum black hole entropy, called the island formula, which is expected to reconcile the conflict between the thermal and quantum natures of the black hole. One may regard the island formula as a generalization of the so-called Ryu-Takayanagi formula for the entanglement entropy, but its derivation is yet to be clarified. In the talk, after reviewing the current status of the black hole information paradox, Kanato explained their work on a derivation of the island formula based on the replica method for the gravitational path integral. The audience asked a lot of questions and we really enjoyed the talk. Reported by Masaru Hongo
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2021-06-28
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DMWG Seminar by Dr. Satoshi Shirai on June 24, 2021
We are now living in the era of precision cosmology. The relic abundance of dark matter (DM) is now observationally well-determined, and its error is smaller than O(1)%. This means that the same or much higher precision is required when we make theoretical predictions. Weakly Interacting Massive Particle (WIMP) has long been the leading candidate for DM because of its beautiful mechanism to predict the observed relic abundance. WIMP is in the same thermal bath as the Standard Model particles in the beginning. At a certain point when the temperature of the Universe is smaller than the DM mass, it decouples to fix its number density. The yield of the DM is determined by its annihilation cross-section to the Standard Model sector. It seems that there is no ambiguity in the calculation of this process at first: the cross-section is purely theoretical and all the remainings are described in the Standard Model physics. However, the source of the uncertainty does remain in the Standard Model sector. The dilution of the number density of DM particle depends on the expansion rate of the Universe, which is determined by the Standard Model particles. The effective degree of freedom (d.o.f) of the relativistic species controls this factor. We have to deal with the non-equilibrium dynamics to precisely describe the time-evolution of the d.o.f, in which we need numerical approaches. In this talk, he introduced his work to update these calculations. By implementing the latest findings in the non-equilibrium dynamics in i) the neutrino decoupling, ii) the QCD phase transition, iii) the electroweak phase transition, and iv) the perturbative calculations, they found that the final d.o.f is smaller than the previous estimate in more than 1%. This is larger than the level of precision in observations. It is also important that the uncertainty is quantified by them. Another good news is that he makes the calculated d.o.f with its error publically available. With these updates, we now correctly know the points to probe DM! Reported by Nagisa Hiroshima
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2021-06-28
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Math Seminar by Dr. Kazuki Kannaka on June 18, 2021
There was a math seminar by Kazuki Kannaka on June 18. He gave an introductory talk on his research fields, representation theory and briefly explained his study. He first explained some basic definitions in representation theory. He then explained the mathematical tiling problem with the Lie group. In the second part, he explained how the distribution of the compact pseudo-Riemannian manifolds differs for parameters. He also introduced his example, which has a continuous spectrum. Reported by Keita Mikami
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2021-06-25
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Information Theory SG Seminar by Prof. Yoshiyuki Kabashima on June 23, 2021
With great honor, we have invited Prof. Yoshiyuki Kabashima to our information theory seminar to give a stimulating talk about “introduction to the replica method” on 23rd June. Replica method is a physics-based technique developed for analyzing disordered many-body problems, which is now becoming popular more in information science using the structural similarity between problems from these two different fields. Prof. Yoshiyuki Kabashima is a master of the replica method. He applied this method to many problems in information theory, such as CDMA, compressed sensing, clustering of networks, error correcting codes, etc. The talk contains two parts. In the first part, as an example of the concept, he explained the mathematical similarity of three problems whose origins are unrelated with one another--random energy model (Physics), error correcting codes (information theory) and random k-SAT problem (theoretical computer science). A unified perspective is the common structure of the three examples is the conditional distribution, and the key to solve the problems is the assessment of the average free energy. The replica method provides a systematic way to performing the configurational average. Even the mathematical justification is still an open problem, there is no known example to which the replica method leads to wrong results by appropriately taking into account the replica symmetry breaking if necessary. In the second part, Prof. Yoshiyuki Kabashima demonstrated the calculation of replica method using an example of random energy model of spin glass. This simple model has an exact solution without using the replica method. One can see how replica method can provide the correct solution by taking care of the assumptions of replica symmetry and 1-step replica symmetric breaking (1RSB) in different temperature ranges. In the end, he gave an expert perspective of large deviation statistics of replica method and 1RSB solution. Many excellent questions and stimulating discussions have happened during the 2.5-hour seminar. We absorbed by the world of “replicas”. We thank to Prof. Yoshiyuki Kabashima for giving us this great opportunity and hope new ideas of applications of the replica method appear in iTHEMS. Report by Yingying Xu
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2021-06-25
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iTHEMS Biology Seminar by Dr. Jeffrey Fawcett on June 10, 2021
On 10 June 2021, our iTHEMS member Jeffrey Fawcett gave a talk about “the origin and dispersal of buckwheat” at the Biology Seminar. Jeffery works on or has worked on a broad range of topics related to genomics, evolution, genetics, bioinformatics, and systems biology. This time, he talked about his recent worldwide collaboration work using genomic data of wild samples from China (around Yunnan, Sichuan, and Tibet) and cultivated samples from various parts of the world to understand “when”, “where”, and “how” buckwheat originated and then spread across the world and came to Japan. He explained the significance of studying "domestication", which can contribute to research on evolution, molecular breeding and implications for human history. Buckwheat, which soba noodles is made from, is now such a familiar everyday life related plant in Japan. We are surprised how such a genomic approach about soba revealed the history of ancient world and Japan and gave us a hint about the origin of Japanese people. We are looking forward to further discovery of this interesting research topic. Report by Yingying Xu
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2021-06-25
セミナーレポートiTHEMS Biology Seminar by Prof. Fumito Mori on June 24, 2021
In iTHEMS biology seminar on June 24, Fumito Mori (Assistant Professor, Faculty of Design, Kyushu University) gave us a talk on synchronization and variability of the periodicity. In the seminar, he introduced minimal models of coupled oscillators to discuss synchronization. Interestingly, the variability of the periodicity, in general, depends on which variables (or genes) we consider and on which timepoints we (or cells) measure the periodicity. He demonstrated this subtlety in the so-called repressilator system. He then discussed how noise and interaction parameters can be inferred from given data of periodicity. In the talk, he showed us many general results, which were very impressive to us. Finally, I am grateful to Mori-san because I asked him to do the seminar just two weeks before it, but he kindly accepted. Thank you very much for the fantastic talk, Mori-san! Reported by Takashi Okada
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2021-06-07
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iTHEMS Biology Seminar by Dr. Yingying Xu on June 3, 2021
On June 3rd, Yingying Xu who recently joined iTHEMS gave a talk at the Biology Seminar. She spoke about her past research on applying ideas from statistical physics to genetics, especially on what is called "epistasis". Statistics plays a crucial role in the study of genetics, and one of the main challenges now is to understand the combined effect of multiple mutations, which is often referred to as epistasis. This clearly requires input from statistical physics, so I was very excited to hear the progress made with people from statistical physics - Yingying and her colleagues being involved. Her talk was also very helpful for everyone to get an idea of how advanced statistics/mathematics is being applied to genetics. It was also great to see the expertise of Yingying, and we will be looking forward to further interaction with her. Reported by Jeffrey Fawcett
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2021-05-31
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Quantum Matter SG seminar by Dr. Rui-Xing Zhang on May 26, 2021
On May 26th, Dr. Rui-Xing Zhang from the University of Maryland gave a talk about the classification of anomalous floquet higher-order topological insulators. He started with a pedagogical introduction to floquet topological insulators, which possess robust boundary states. Notably, there are two types of non-trivial floquet topology. 1. The floquet bands inherit the topology of the static bands. 2. The non-trivial physics of the anomalous floquet topological insulators stems from dynamical phase bands. Dr. Zhang extended the idea of the second type to higher-order topological insulators, which have robust corner states or edge ones. Dr. Zhang specifically discussed the anomalous floquet topology for chiral symmetric systems preserving C2 rotation symmetry. Using this example, he generalized the classification of the topological phases to various point groups. We thank Dr. Zhang for giving this wonderful talk. Reported by Ching-Kai Chiu
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2021-05-27
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iTHEMS Biology Seminar by Dr. Kouki Uchinomiya on May 27, 2021
On May 27 (JST), we had online talk by Dr. Kouki Uchinomiya at iTHEMS Biology Seminar. He was one of active members of RIKEN iTHES, and currently he is at Central Research Institute of Electric Power Industry in Tokyo. This time, Kouki talked about radiation and cancer risk. Radiation can cause DNA damage for which it can cause cancer in our body. In the field of radiation and cancer, there has been a mystery that cancer risk decreases as the dose rate of radiation (Gy/h) decreases while the total dose of radiation fixed. By incorporating the competition between the normal and the damaged cells by radiation into a simple mathematical model, he successfully explained the mysterious phenomena. His model revealed that the key parameters including a relative reproductive ability of the damaged cells determine the cancer risk. According to him, those parameters will be experimentally measured in the near future, and we understand that the model should contribute to the quantitative estimation of cancer risk by radiation. During and after the talk, there were stimulating discussions as for the philosophy behind his very simple model and a possible extension to the model with the effect of immune system. We enjoyed his concise talk very much. Thanks Kouki! Reported by Gen Kurosawa
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2021-05-27
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Math Seminar by Dr. Michiya Mori on May 24, 2021
On May 24, there was an iTHEMS math seminar by Dr. Michiya Mori. In the first part, he explained his research on Lowebner theorems. He first described the notion of abstract order. He then introduced an order on the space of the hermitian matrix. He explained Molnar's results that the order-preserving map must be affine on a particular good subset of matrices. Lastly, he explained his results with his collaborator that a map on matrix domain is an order isomorphism if and only if it has a good extension to the upper half-space. In the second part, the speaker introduced the projective Hilbert space, the space of all quantum states, and Fubini-Study metric, an "argument" on the projective Hilbert space. He then introduced the result by Wigner that any bijective maps preserving Fubini-Study metric are unitary or anti-unitary. The speaker introduced Uhlhorn's variant of this result: if the dimension of the space is larger than three, any bijection preserving argument π/2 is unitary or anti-unitary. The speaker also explained that Gehér extended Uhlhorn's works for other cases, but there was one open case. The speaker explained his result with Gehér that the variant of the result by Uhlhorn holds for this last case. Reported by Keita Mikami
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2021-05-24
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Journal Club of Information Theory SG by Dr. Kyosuke Adachi on May 19, 2021
On May 19, Dr. Kyosuke Adachi talked about “Amino acid sequence and protein phase separation” at the journal club of information theory study group. First, he introduced the history of protein states, from its structure observed with X-ray to intrinsically disordered region (IDR) and liquid-liquid phase separation. In this talk, the speaker focused on IDR and phase separations. Second, he explained some biological functions of phase separation, such as compartmentalization of specific molecules, facilitation of biochemical reaction, and stress response. And the talk moved a question of what kind of sequence feature determines phase properties. Mainly, the speaker discussed coarse-grained models, which are expected to determine phase properties. Finally, he mentioned the problem of how to classifying IDRs and the importance of the coarse-grained sequence. Thank you, Adachi-san, for the interesting talk! Reported by Yukimi Goto
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2021-05-20
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Math Seminar by Dr. Iyan Mulia on April 22, 2021
On April 22, the iTHEMS Math seminar was held (Sorry for the delay of the report!). This time, we invited Dr. Iyan Mulia from RIKEN Cluster for Pioneering Research, Prediction Science Laboratory. The title of the talk was “Alternative tsunami observing and forecasting systems”. The main topic of the talk was his work about how to catch and predict tsunami. First, he proposed new approaches to construct tsunami observing systems. There exist various observing systems already, but they share a big problem that they are very expensive. Since observing systems need to be updated regularly, it is very important to reduce the cost. Iyan’s proposal is to make use of existing commercial vessels and airplanes. Since they already exist and form a dense network all over the world, it will suffice to let them observe the sea level altitude and transfer the information. Iyan and his collaborators already demonstrated in experiments that the proposed observing system is accurate enough to detect large tsunamis. Next, he moved to another topic. Once we observe the occurrence of tsunami, next step is to predict its impact in the areas near the coast. While there are conventional mathematical models which provide very accurate prediction, it needs relatively long time for calculation. This is a non-ignorable defect because it means the delay of the warning to residents. If we use linear models instead of the accurate model, the calculation becomes much faster but the accuracy of the prediction gets low. Iyan’s proposal is plug in the Machine Learning techniques to bridge these two models. He trained neural networks to predict the results of the accurate model from the results of the linear model. This method actually gives a satisfactory result: the prediction is very accurate and fast. If this method is accepted widely, it will be possible to predict the effect of tsunami very accurately in very short time. Reported by Hiroyasu Miyazaki
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2021-05-14
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iTHEMS Biology Seminar by Prof. Yuji Sakai on May 14, 2021
In iTHEMS Biology Seminar on May 14th, Prof. Yuji Sakai (Univ. of Tokyo) talked about the theoretical model of the autophagosome. First, he explained the autophagosome formation process, where the disk-like and cup-like shapes of the membrane are observed. Then, he talked about the previous theories, where the spontaneous curvature is not considered. Next, he explained his theoretical model, in which the spontaneous curvature is induced and stabilized by the “curvature generator”. By minimizing the free energy in his model, he quantitatively reproduced the autophagosome formation via the disk and the cup. Finally, he mentioned the candidate of the curvature generator. His attractive talk induced various discussions and questions from the audience. Thank you very much for nice talk, Yuji! Reported by Hiroshi Yokota
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2021-05-14
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Quantum Matter Seminar by Prof. Christopher Bourne on May 12, 2021
Quantum Matter Study Group invited Prof. Christopher Bourne to give a talk on aperiodic and amorphous topological phases on May 12th, 2021. In the beginning, he reviewed topological phases in lattice systems and introduced integer Chern numbers. To generalize the topological phases, we extend the lattice to Delone sets, including quasicrystal and amorphous solid. The main talk focused on the topological phases for those types of solid. He provided examples to show the amorphous patterns exhibit gapped phases. He showed that the invariants can be defined as noncommutative Chern number and computed the non-zero Chern number in the gapped phase. It is interesting to see that quasicrystal and amorphous solid share similar integer Chern numbers, and the idea can be further extended to different spatial dimensions with symmetries. We thank Prof. Bourne for giving a wonderful talk. Reported by Ching-Kai Chiu
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2021-05-12
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DMWG Seminar by Dr. Nishimichi: Cosmology, the Fundamental for the DM on May 12, 2021
What we have known about dark matter (DM) is that it occupies ~25% of the energy density of our Universe. The precise determination of the cosmological parameter is crucially important for determining this abundance of DM. Another important point here is that one the value of those parameters are determined assuming a specific cosmological model, such as vanilla (i.e., the simplest) lambda CDM and so on. So we might have a different DM relic density if the assumption of the simplest Lambda-CDM breaks. Hence the examination of the cosmological parameters and the model behind them is important two-fold for DM physicists. The basic observable for the cosmological parameter is cosmic microwave background, the large-scale structure, and so on. Those data are huge at the raw level, and still so large at the scientific data level. In order to derive a handful of cosmological parameters from such data, one must calculate the so-called summary statistics. By matching the summary statistics in simulation data of specific cosmological models (vanilla lambda-CDM, for example) adopting MCMC techniques, we arrive at the cosmological parameter that we need. Note that there is always degeneracy between cosmological parameters derived from observational data. The matching between the observational and simulated summary statistics takes a lot of costs in the calculation. By adopting analytical formula, the calculation becomes much quicker while the precision decreases at some level. The emulator, which is developed in the Dark Quest Project, solves this computational problem. It enables us to speed up the calculation while keeping the precision. The degeneracy between the parameters also becomes accessible. The precise summary statistics such as halo mass function, halo-matter cross-correlation, and far more... is crucially important for DM study. Halo formation theory and weak lensing search are kinds of examples for applications. With this new fantastic open-source tool of Dark Quest Project, the future for DM search study emerges definitely. We are looking forward to seeing a lot of cutting-edge as well as steady works implemented with this item in the near future! Reported by Nagisa Hiroshima
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2021-05-06
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iTHEMS Biology Seminar by Dr. Yukinori Nishigami on April 22, 2021
In iTHEMS biology seminar on April 22, Dr. Yukinori Nishigami (Hokkaido Univ.) gave us a talk about his research results, such as modeling the swimming behavior of unicellular organisms in their environment. First, Dr. Nishigami introduced us to the diversity of unicellular eukaryotes and the fact that they have their own specific movements. Many of the participants were amazed at how a small, single-celled organism can move in complex ways using flagella and other mechanisms, and how the cells themselves can move in complex ways. Next, he talked about the main topic: modeling the phenomenon of ciliate accumulation in a stable environment. Through careful observation and simulation, he modeled the movement and found that the movement of ciliates in such an environment is due to the simple principle of cell shape and mechanosensitivity of cilia. He presented a good example of modeling the behavior of unicellular organisms, which led to a lively discussion at the seminar. Thank you very much, Nishigami-san! Reported by Euki Yazaki
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2021-04-28
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Information Theory SG Seminar by Prof. Yoshihiko Hasegawa on April 28, 2021
On April 28, Prof. Yoshihiko Hasegawa (Associate Professor, The University of Tokyo) gave us a talk on the thermodynamic uncertainty relation (TUR). In the first part of his talk, he started from a motivation to consider trade-off relations between energy and cost, showing biological examples. After reviewing general theory of stochastic thermodynamics and TUR for classical Markovian systems, he presented two recent works of him: one is to derive the TUR from information-theoretic method (i.e., the Cramer-Rao bound) and the second is to derive it from the fluctuation theorem. In the second part, he discussed quantum version of the TUR. After the review of quantum dynamics under measurement, he showed the quantum TUR for general open systems. He applied his theory to continuously measured systems and explained its physical meaning. There were a lot of interactive discussions during and after the talk. We really thank Prof. Hasegawa for his great talk. Reported by Ryusuke Hamazaki
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2021-04-23
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Quantum Matter Seminar by Dr. Se Kwon Kim on April 21, 2021
On April 21st, Dr. Se Kwon Kim from KAIST gave a talk about unconventional spin transport in quantum materials. First, he gave an overview of spintronic physics. The advancements in spintronic techniques can potentially lead to new applications, such as quantum information science. Then, he showed the realization of magnonic topological insulators, which are Chern insulators with spin current but without electron charge current. Furthermore, he predicted that spin transport induces vortex flow in superconductors. We thank Dr. Kim for giving a wonderful talk. Reported by Ching-Kai Chiu
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2021-04-22
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Math-Phys Joint Seminar by Prof. Takuju Zen on April 13, 2021
On April 13, Dr. Takuju Zen from Kochi University of Technology gave a talk entitled “Self-adjoint extension in quantum mechanics and non-Rydberg spectra of one-dimensional hydrogen atom” at the iTHEMS Math-Phys joint seminar. In the first part, he briefly explained the necessity of self-adjointness of operators in quantum mechanics and gave some important examples of such operators. Besides, he mentioned that the self-adjointness of Laplacian is equivalent to flux conservation in one dimension. Finally, he introduced studies of quantum particles on graphs. In the second part, the speaker discussed one dimensional Coulomb problem. Mainly, he noted that a simple self-adjoint extension of such hamiltonian could not be used. Then he provided a concrete procedure to study the solutions of one dimensional Coulomb problem and explained his interesting results. Reported by Yukimi Goto
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2021-04-21
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iTHEMS Colloquium by Prof. Kenji Fukaya on April 16, 2021
On April 16, 2021, 13:30-15:00 (JST) 0:30-2:00(EDT), Professor Kenji Fukaya, Simons Center for Geometry and Physics, Stony Brook University, gave a colloquium talk by zoom. The title was "Mirror symmetry and KAM theory". His talk began at the origin of symplectic geometry, namely, the Hamiltonian dynamics. He reviewed completely integrable Hamiltonian systems, where the first integrals define foliation by half dimensional Lagrangian tori with linear flows. The KAM (Kolmogorov-Arnold-Moser) theory describes perturbation of this system and shows that almost all tori persist. Then Professor Fukaya explained the Lagrangian torus fibration found by Strominger-Yau-Zaslow, with the example of the complex projective space. For the complex projective n-space, the image of the moment map is an n-simplex and the regular fibers are Lagrangian n-tori. The inverse image of the boundary of the simplex corresponds to the singular fiber of the holomorphic fibration (the product of homogeneous coordinates) to a disk, By choosing a symplectic form, around the singular fiber of holomorphic fibration, there is defined the monodromy map by using the Hamiltonian flow of the Hamiltonian function that is the absolute value of the fibering. Professor Fukaya told that for this example in dim n = 2, the monodromy near the singular fiber exhibits the KAM theoretic behavior, but in dim n = 3, it is not the case with respect to the Fubini-Study symplectic form. However, he expects it can be the case with respect to the Calabi-Yau Kaehler form. This correspondence between symplectic manifolds (the torus fibration of the complex projective space) and complex manifolds (the holomorphic map to the disk) is an introductory example of the mirror symmetry. His talk might enter much deeper part related with homological mirror symmetry, but he stopped and concluded by saying that the KAM theory explains the transition from completely integrable systems to chaos and it should be possible to find alternative in mirror symmetry or field theory which will explain the transition from stable system to chaos. The talk of Professor Fukaya was really stimulating and his enthusiasm impressed the audience. Reported by Takashi Tsuboi
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2021-04-16
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Quantum Matter Seminar by Dr. Mario Flory on April 14, 2021
On April 14th, from Instituto de Física Teórica, Universidad Autonoma de Madrid and Consejo Superior de Investigaciones Científicas, in Spain, Dr. Mario Flory gave a seminar talk about the connection between the AdS/CFT correspondence and condensed matter physics. In the first half of the talk, he briefly reviewed the ideas of the correspondence and its history. The most important breakthrough is that Juan Maldacena first proposed the AdS/CFT in the late '90s. It is known that the entropy of the black hole is proportional to its area, so that this feature suggests a holographic principle. The AdS/CFT correspondence serves a better understanding of this principle by connecting strongly coupled CFTs to classical gravity. In the second half, Dr. Flory addresses the important application of the correspondence to condensed matter physics. Because of the AdS/CFT correspondence, the problems of the Kondo model in condensed matter physics can be tackled by solving gravity problems. He specifically discussed the entanglement problem through the correspondence in detail. We thank Dr. Flory for giving an excellent talk. Reported by Thore Posske (University of Hamburg, Germany) and Ching-Kai Chiu
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2021-04-15
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iTHEMS Biology Seminar by Dr. Kyosuke Adachi on April 15, 2021
In iTHEMS Biology Seminar on April 15th, Kyosuke Adachi (BDR/iTHEMS) talked about the formation mechanism and the biological function of liquid condensates in eucaryotic cell. First, he explained the higher-order structure of the chromatin fiber. He focused on A compartment and B compartment, in which the high and low transcription activities are shown, respectively. Then, he talked about the biomolecular condensate which is the liquid droplet composed of proteins. He talked about the important interaction on the condensate creation and explained the theoretical model based on the mean field theory. Finally, he explained the role of the condensates on the transcription activity. The transcription occurs in the condensates of some proteins coexisting on the chromatin fiber. The audience enjoyed his attractive talk. Thank you very much for great talk, Kyosuke! Reported by Hiroshi Yokota
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2021-04-15
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iTHEMS Biology Seminar by Prof. Catherine Beauchemin on April 8, 2021
In iTHEMS Biology Seminar on April 8th, Catherine Beauchemin (Deputy Program Director of RIKEN iTHEMS and Professor of Ryerson University) gave us an introductory talk on Markov chain Monte Carlo (MCMC) method. Many of theoretical scientists often use mathematical models, but it is difficult to correctly estimate parameter values of the model from experimental data. In this seminar, Catherine taught us the MCMC method is a powerful tool for parameter estimation using her recent research on cancer as an example. First, she explained four simple models of cancer growth. Then, using these models, she explained the basic idea and the detail process of the MCMC method. Her talk was very clear. I think that the seminar became helpful for the many attendees because the method can be applied to various fields of science and engineering. Merci beaucoup, Catherine! Reported by Shingo Gibo
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2021-04-15
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Journal Club of Information Theory SG by Dr. Yukimi Goto on April 14, 2021
On 14th April, Dr. Yukimi Goto gave an introduction to trace inequalities and related topics in our journal club of the Information Theory Study Group. She started from a simple counter example of the triangle inequality for operators on Hilbert space, and introduced density matrices, von Neumann entropy and Wigner-Yanase skew information. Then, she explained the concept of jointly convex/concave functions and Wigner-Yanase-Dyson-Lieb theorem, and discussed the sub-additivity and strong sub-additivity of von Neumann entropy and its generalizations. Thank you, Goto-san, for interesting talk! Reported by Akinori Tanaka
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2021-04-12
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Math Seminar by Dr. Kai Koike on April 7, 2021
On April 7, Dr. Kai Koike from Kyoto University gave a talk entitled “Long-time behavior of moving solids in a fluid and the kinetic theory of gases” at Math seminar. In the first part, he reviewed a moving boundary problem of gases. Then he introduced some interesting results in fluid dynamics and developments concerning his research. In the second part, the speaker explained his results about the long-time behavior of a point particle moving in a fluid. It is an explanation of related numerical results for a BGK model of the Boltzmann equation. Reported by Yukimi Goto
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2021-04-05
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Math Seminar by Dr. Wataru Kai on March 22, 2021
On March 22, the last iTHEMS Math seminar in FY 2020 was held. This time, we invited Wataru Kai from Tohoku University. The title of the talk was “The Green-Tao theorem for number fields”. The main topic of the talk was his recent joint work with his collaborators about the Green-Tao theorem and its generalization. In the first part, he explained the historical background and the technology behind the proof of the Green-Tao theorem, which asserts that there are arbitrarily long arithmetic progressions of prime numbers. In the second part, he introduced algebraic numbers and algebraic integers, which generalize rational numbers and integers, respectively, and he explained how we can generalize the Green-Tao theorem to this situation. For example, if we think of numbers of the form a+b\sqrt{5}, these are algebraic numbers. Plotting them on the ab-plane, each of the numbers corresponds to a lattice point. We can draw a “shape” by choosing finite number of those lattices. Then, the generalized Green-Tao theorem asserts that, by applying scaling and parallel translation, we can make all of the chosen lattice points correspond to prime elements simultaneously. Here, prime element is a generalization of prime number in the world of algebraic numbers. He also explained that at some point of the proof of the generalized Green-Tao theorem, a classical technique well-known to algebraic number theorists plays a fundamental role. Reported by Hiroyasu Miyazaki
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2021-04-02
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Biology Seminar by Dr. Yuji Hirono on April 1st, 2021
In iTHEMS biology seminar on April 1st, Yuji Hirono (Assistant Professor, Asia Pacific Center for Theoretical Physics, POSTECH, Korea) gave us a talk on chemical reaction networks. Hirono-san has been recently working on chemical reaction networks with Miyazaki-san, Hidaka-san, and me. In the seminar, he talked about a new method of studying chemical reaction networks from network topology. He first explained graph theoretical aspects of chemical reaction systems, and then explained how these tools can be used to characterize reaction systems. Then, he explained a method of simplifying/deforming chemical reaction systems without affecting steady-state properties. I am grateful to Hirono-san because I could improve my understanding of reaction systems through collaboration with him. Also, Hirono-san and I have been friends since we were undergraduates, and I am happy to work together. Thank you very much, Hirono-san! Reported by Takashi Okada
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2021-03-26
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Biology Seminar by Dr. José Gutiérrez on March 25, 2021
On March 25th, José Gutiérrez from Chiba University gave a talk at iTHEMS Biology Seminar about the evolution and diversification of cycads ("sotetsu" in Japanese) in Mexico. He explained how the different species and populations of cycads are distributed in different areas of Mexico, and showed how this can be explained by changes in the climate and the adaptation of each species to the different environment. He then discussed some general ideas of how speciation and diversification can occur. It was probably the first time for many iTHEMS members to hear about research in Ecology, and I think many of us learned something new. We were also able to have a nice and fruitful discussion after the talk. Reported by Jeffrey Fawcett
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2021-03-25
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Information Theory SG by Dr. Akinori Tanaka on March 24, 2021
On 24th March, Dr. Akinori Tanaka gave an introduction to the reinforcement learning (RL) in our journal club of the Information Theory Study Group. He started from simple examples of a maze and a chess game to introduce the fundamental variables (i.e., states, actions, and rewards) and their evolution as a Markov decision process.After explaining that the goal of the RL is to maximize the value function, he discussed policy improvement theorem with the application to the epsilon-greedy update. We thank Akinori for the great and clear talk!
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2021-03-18
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Quantum Matter Seminar by Prof. Takahiro Morimoto on March 16, 2021
On March 16th, Prof. Takahiro Morimoto from the University of Tokyo gave an online talk on geometric nonlinear optical effects. First, he introduced topological states of matter and the notion of the Berry connection to the audience. He explained how these concepts lead to the quantization of observable quantities in the linear-response regime so that the audience learned the background to understand his main research works. After the introduction, he talked about several geometric nonlinear effects in topological states beyond the linear response theory. In particular, the shift current stems from the geometric nonlinear response, and the quantized circular photogalvanic effect can be realized in specific Weyl semimetals. In addition to the theoretical concepts, he also discussed experimental observations, such as perovskite-based solar cell materials and chiral multifold fermion compound RhSi. During and after the talk there were interactive discussions, and more than 25 participants attended this well-presented talk. Reported by Chen-Hsuan Hsu (CEMS, RIKEN) and Ching-Kai Chiu
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