セミナー

How to make a dataset for phylogeny and the background of mathematical theory

2021年9月9日(木) 10:00 - 11:00

矢﨑 裕規 (理化学研究所 数理創造プログラム (iTHEMS) 特別研究員)

Molecular phylogenetic analysis is a very important method of analysis for understanding the evolution of organisms and so on. The method of molecular phylogenetic analysis itself is often discussed, and you are probably familiar with the background of the analysis. The dataset to be analyzed is just as important as the analysis method. However, it is not well known how the data set is made and what the methodology behind it is. Therefore, I will outline the background to the creation of data sets.

会場: via Zoom

イベント公式言語: 英語

The Polarised ring of the Supermassive Black Hole in M87: EHT observations and theoretical modeling

2021年9月3日(金) 14:00 - 16:00

水野 陽介 (T.D. Lee Fellow / Associate Professor, Tsung-Dao Lee Institute, Shanghai Jiao Tong University, China)

The Event Horizon Telescope has mapped the central compact radio source of the elliptical galaxy M87 at 1.3 mm with unprecedented angular resolution. These images show a prominent ring with a diameter of ~40 micro-arcsecond, consistent with the size and shape of the lensed photon orbit encircling the “shadow” of a supermassive black hole. Recently EHT has provided new images of the polarised emission around the central black hole in M87 on event-horizon scale. This polarised synchrotron emission probes the structure of magnetic fields and the plasma properties near the black hole. We found that the net azimuthal linear polarisation pattern may result from organised, poloidal magnetic fields in the emission region. In a quantitative comparison with a large simulated polarimetric image library, we found that magnetically arrested accretion disks are favoured to explain polarimetric EHT observations. In this talk, I also briefly discuss about a new modelling study of M87 jets in the collimation and acceleration region.

会場: via Zoom

イベント公式言語: 英語

Journal Club: A quantitative quasispecies theory-based model of virus escape mutation under immune selection

2021年9月2日(木) 10:00 - 11:00

許 インイン (理化学研究所 数理創造プログラム (iTHEMS) 基礎科学特別研究員)

I would like to introduce the paper "a quantitative quasispecies theory-based model of virus escape mutation under immune selection", written by Hyung-June Woo and Jaques Reifman [1]. Paper abstract: Viral infections involve a complex interplay of the immune response and escape mutation of the virus quasispecies inside a single host. Although fundamental aspects of such a balance of mutation and selection pressure have been established by the quasispecies theory decades ago, its implications have largely remained qualitative. Here, we present a quantitative approach to model the virus evolution under cytotoxic T-lymphocyte immune response. The virus quasispecies dynamics are explicitly represented by mutations in the combined sequence space of a set of epitopes within the viral genome. We stochastically simulated the growth of a viral population originating from a single wild-type founder virus and its recognition and clearance by the immune response, as well as the expansion of its genetic diversity. Applied to the immune escape of a simian immunodeficiency virus epitope, model predictions were quantitatively comparable to the experimental data. Within the model parameter space, we found two qualitatively different regimes of infectious disease pathogenesis, each representing alternative fates of the immune response: It can clear the infection in finite time or eventually be overwhelmed by viral growth and escape mutation. The latter regime exhibits the characteristic disease progression pattern of human immunodeficiency virus, while the former is bounded by maximum mutation rates that can be suppressed by the immune response. Our results demonstrate that, by explicitly representing epitope mutations and thus providing a genotype–phenotype map, the quasispecies theory can form the basis of a detailed sequence-specific model of real-world viral pathogens evolving under immune selection. *Please refer to the email to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

Extended and interacting bound states in elemental superconductors

2021年9月1日(水) 16:00 - 17:15

Levente Rózsa (Condensed Matter Physics, University of Konstanz, Germany)

Combining magnetism with superconductivity leads to the emergence of localized states, including Majorana bound states predicted to be relevant for topological quantum computation. In this talk, I discuss how these bound states are influenced by the details of the electronic structure. It will be shown how the shape of the Fermi surface leads to a long-ranged anisotropic extension of Yu-Shiba-Rusinov states in the vicinity of magnetic impurities [1]. The same type of Fermi surface will be demonstrated to give rise to topologically trivial Caroli-de Gennes-Matricon bound states in vortex cores [2], with similar spatial profiles to those of topological Majorana bound states. The role of spin-orbit coupling will be discussed in the hybridization of Yu-Shiba-Rusinov bound states of dimers with ferromagnetic and antiferromagnetic spin alignments [3]. The general theoretical concepts will be illustrated by experimental realizations in specific materials. *Detailed information about the seminar refer to the email.

会場: via Zoom

イベント公式言語: 英語

Mathematical analysis of body temperature fluctuation during hibernation

2021年8月26日(木) 10:00 - 11:00

黒澤 元 (理化学研究所 数理創造プログラム (iTHEMS) 専任研究員)

Hibernation (tomin in Japanese) is a strategy for the organisms to survive in a severe season with limited food and water availability. During hibernation, the organisms drastically decrease their basal metabolisms, drop their body temperature (Tb) more than 10 degree, and become immobile. Interestingly, body temperature during hibernation does not remain constant at very low value, but greatly fluctuates with inconstant period of several days. Although there have been many studies about hibernation since the era of Aristotle, fundamental problems of hibernation remain elusive. Recently, we started to investigate Tb data during hibernation by using a method in acoustic engineering for the analysis of irregular time-series such as music. We succeeded in quantifying many individual data, and found that a simple model can reproduce well and forecast Tb data during hibernation. This is the collaboration with Yoshifumi Yamaguchi at Institute of Low Temperature Science, Hokkaido University and Shingo Gibo at iTHEMS.

会場: via Zoom

イベント公式言語: 英語

Application of Machine Learning on Many-Body Problems

2021年8月23日(月) 16:00 - 17:15

Daw-Wei Wang (Professor, Department of Physics, National Tsinghua University, Taiwan)

Time: 4pm ~ 5:15pm (JST); 9am ~ 10:15am (CET); 3pm ~ 4:15pm (Taiwan) In this talk, I will briefly introduce the application of machine learning methods on quantum many-body problems. It includes a self-supervised learning approach to decide the topological phase transition in the systems of ultracold atoms by using Time-of-Flight images only without knowing any priori knowledge [1]. We then develop the Random Sampling Neural Networks for the investigation of quantum many body ground state properties in the strong interacting regime by a model rtained in the weak interacting regime [2]. Finally, we provide an Quantum-Inspired-Recurrent Neural Network, which could give a precise long-time dynamics of a quantum many-body system, even the model is trained in the short-time regime. We hope to show the great possibility to use machine learning as a new tool to investigate the quantum many-body problems. *Detailed information about the seminar refer to the email.

会場: via Zoom

イベント公式言語: 英語

The damped circadian oscillator in cyanobacterium: kaiA-less oscillator

2021年8月19日(木) 10:00 - 11:00

河本 尚大 (大阪大学 太陽エネルギー化学研究センター 特任研究員)

Circadian clocks are conserved in almost all organisms and provide fitness advantages to their owners through scheduling biological processes at appropriate time of diurnal cycles. Cyanobacteria possess circadian clock genes named kaiA, kaiB and kaiC. The phosphorylation cycle of KaiC, driven by KaiA and KaiB, is assumed to be a core oscillator in the cyanobacterial clock, and it has been believed that all of the three genes are essential for circadian oscillations since their finding in 1998. However, we found that the kaiA-disrupted strains exhibited a faint damped oscillation. Measuring the bioluminescence rhythms of mutants revealed that the damped oscillation is generated by transcriptional-translational feedback of kaiBC, but not by the phosphorylation cycle of KaiC. In this talk, in addition to the mechanism of the kaiA-less oscillator, I will propose how it can be beneficial for the total circadian system in the cyanobacterium by analyzing the simple model of the two coupled oscillators.

会場: via Zoom

イベント公式言語: 英語

Application of AdS/CFT to non-equilibrium phenomena in external electric fields

2021年8月16日(月) 13:00 - 15:00

木下 俊一郎 (中央大学 理工学部 共同研究員)

The AdS/CFT correspondence is a useful tool for studying strongly-coupled gauge theories. According to this correspondence, the D3/D7 brane system in string theory is one of the simplest toy model dual to supersymmetric QCD-like gauge theory. In the dual field theory, the mesons, i.e., the quark-antiquark bound states are stable in vacuum when the quark is massive, while the dielectric breakdown occurs by pair production of quark-antiquark under strong electric fields. In this talk, I will review a series of our works of D3/D7 systems and show time-dependent, non-equilibrium phenomena driven by external electric fields such as suddenly increasing or rotating electric fields.

会場: via Zoom

イベント公式言語: 英語

From Yang-Mills theory to enumerative geometry on Calabi-Yau 4-folds

2021年8月6日(金) 16:00 - 18:10

ヤーロン・ツァオ (理化学研究所 数理創造プログラム (iTHEMS) 研究員)

Yang-Mills theory was studied from mathematical perspectives in the 1970s by Atiyah and his collaborators (notably Drinfeld, Hitchin, Singer). Subsequent breakthroughs were made on dimensions 3 and 4 by Floer and Donaldson (based on deep analytic results obtained by Uhlenbeck and Taubes) in the 1980s. In 1996, Donaldson and Thomas proposed to study Yang-Mills theories on dimensions bigger than 4. In higher dimensions, the analytic method is limited and algebro-geometric method is heavily used instead. This powerful tool usually enables us to compute partition functions and lead to amazing links to other invariants in enumerative geometry, e.g. Gromov-Witten and Gopakumar-Vafa invariants. In this talk, I will review some of these inspiring stories and discuss how my works on Calabi-Yau 4-folds fit into them.

会場: via Zoom

イベント公式言語: 英語

Rational design of autonomous, peptide-based ion channels

2021年8月5日(木) 10:00 - 11:00

新津 藍 (理化学研究所 開拓研究本部 (CPR) 杉田理論分子科学研究室 基礎科学特別研究員)

Designing artificial ion channel proteins has been a major challenge since rational design of membrane proteins is still in its infancy. To address this challenge, we aim to understand the most fundamental interaction in membrane proteins, helix-helix packing, using artificial peptides. Here, we rationally design, synthesise and characterise transmembrane peptides which self-assemble into stable channels. In this talk, I will present our computational de novo peptide design, structure modelling and molecular dynamics simulations, followed by biophysical experiments indicating structure and function of the designed channels. These works shed light on a sequence-to-structure/stoichiometry of membrane alpha-helices, which will aid more accurate membrane protein designs in future. *Please refer to the email to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

Quantum annealing and its fundamental aspects/ Quantum annealing and its application to real world

2021年8月4日(水) 13:30 - 16:00

大関 真之 (東北大学 大学院 情報科学研究科 教授 / 東京工業大学 科学技術創成研究院 教授 / 株式会社シグマアイ 代表取締役)

Talk A (13:30~14:30) Title: Quantum annealing and its fundamental aspects Abstract: We introduce a heuristic solver for combinatorial optimization problem, quantum annealing. The quantum annealing utilizes the quantum tunneling effect to search the ground state. In particular, the Ising model with the transverse field is employed for demonstration of the quantum annealing. Most of the combinatorial optimization problem can be described by the Ising model and they are solved by quantum annealing. A decade ago, the D-Wave systems Inc. succeeded in realizing the quantum annealing in their manufactured spin system. In this talk, the concept of quantum annealing and its implementation in the D-Wave quantum annealer are introduced. Talk B (14:40~15:40) Title: Quantum annealing and its application to real world Abstract: In this talk, we review the fundamental aspects of quantum annealing and show several applications to practical combinatorial optimization problems. In particular, in Japan, many researchers in industry are interested in practical applications of quantum annealing. We, Tohoku University, are performing various collaboration with many companies in Japan. The first example is to control automated guided vehicles in collaboration with DENSO. The second one is to list hotel recommendation on a web site with Recruit lifestyle. Other ones are also exhibited as far as possible. Let us discuss a future perspective of the quantum annealing in practical applications.

会場: via Zoom

イベント公式言語: 英語

Application of bioenergetics to microbial modeling

2021年7月29日(木) 10:00 - 11:00

瀬戸 繭美 (奈良女子大学 理学部 化学生物環境科学科 助教)

Bioenergetics, the study of thermodynamics as applied to biological systems, aims to understand how energy flows through a living system. Since thermodynamics provides a framework for predicting the progress of a spontaneous reaction and for harnessing the energy released, bioenergetics can help us to understand the ecological processes of chemotrophic microorganisms that harvest metabolic energy from various chemical reactions. In this talk, I will introduce a theoretical model as an attempt to describe the growth of chemotrophic microorganisms in terms of the interrelationships between microbial activities and the change in Gibbs energy of a system. Based on our findings and previous literature in the field, I will discuss ecological insights into microbial ecosystems thriving in low-energy environment.

会場: via Zoom

イベント公式言語: 英語

Overview of Tensor Networks in Machine Learning

2021年7月28日(水) 13:30 - 14:50

チビン・チョウ (理化学研究所 革新知能統合研究センター (AIP) テンソル学習チーム チームリーダー)

Tensor Networks (TNs) are factorizations of high dimensional tensors into networks of many low-dimensional tensors, which have been studied in quantum physics, high-performance computing, and applied mathematics. In recent years, TNs have been increasingly investigated and applied to machine learning and signal processing, due to its significant advances in handling large-scale and high-dimensional problems, model compression in deep neural networks, and efficient computations for learning algorithms. This talk aims to present a broad overview of recent progress of TNs technology applied to machine learning from perspectives of basic principle and algorithms, novel approaches in unsupervised learning, tensor completion, multi-task, multi-model learning and various applications in DNN, CNN, RNN and etc. We also discuss the future research directions and new trend in this area.

会場: via Zoom

イベント公式言語: 英語

Fallback Accretion in Binary Neutron Star Mergers

2021年7月9日(金) 16:00 - 17:30

石﨑 渉 (京都大学 基礎物理学研究所 ポスドク研究員)

The gravitational wave event GW170817 with a kilonova shows that a merger of two neutron stars ejects matter with radioactivity including r-process nucleosynthesis. A part of the ejecta inevitably falls back to the central object, possibly powering long-lasting activities of a short gamma-ray burst (sGRB), such as extended and plateau emissions. We investigate the fallback accretion with the r-process heating by performing one-dimensional hydrodynamic simulations and developing a semi-analytical model. We show that the usual fallback rate dM/dt \propto t^{-5/3} is halted by the heating. The characteristic halting timescale is $\sim 10^4$--$10^8$ sec for the GW170817-like r-process heating, which is long enough to continue the long-lasting emission of sGRBs. Furthermore, we propose a new interpretation of the recently reported re-brightening in the annual-scale X-ray light curve of GW170817. We model the fallback of the merger ejecta and construct a simple light curve model from the accreting ejecta. We find that the X-ray flux excess can be well explained by the fallback of the post-merger ejecta such as the disk wind from the accretion disk of the merger remnant rather than by the fallback of the dynamical ejecta. The duration of the constant luminosity phase conveys the initial fallback timescale t_0 in the past. Future observations in the next decades will probe the timescale of t_0 \sim 10--10^4 sec, around the time of extended emission in short gamma-ray bursts.

会場: via Zoom

イベント公式言語: 英語

Non-Unitary TQFTs from 3d N=4 Rank-0 SCFTs

2021年7月5日(月) 13:00 - 14:30

Myungbo Shim (Kyung Hee University, Republic of Korea)

We propose a novel procedure of assigning a pair of non-unitary topological quantum field theories (TQFTs), TFT_\pm[T_0], to a (2+1)D interacting N=4 superconformal field theory (SCFT) T_0 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, we propose that F = max{ -log |S^{(+)}_{0\alpha}| } = max{ -log |S^{(-)}_{0\alpha}| }, where F is the round three-sphere free energy of T_0 and S^{(\pm)}_{0\alpha} is the first column in the modular S-matrix of TFT_\pm. From the dictionary, we derive the lower bound on F, F > -log(\sqrt{(5-\sqrt{5})/10}) \simeq 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. We explicitly work out the (rank 0 SCFT)/(non-unitary TQFTs) correspondence for infinitely many examples. Before going to the technical part, we provide some background materials including some peculiar features in 3d gauge theories, some supersymmetries, anyons, and some modular data of MTC in this talk.

会場: via Zoom

イベント公式言語: 英語

An introduction to modular functions, conformal field theories, and moonshine phenomena

2021年7月2日(金) 16:00 - 18:10

及川 瑞稀 (理化学研究所 数理創造プログラム (iTHEMS) 大学院生リサーチ・アソシエイト / 理化学研究所 数理創造プログラム (iTHEMS) 研修生 / 東京大学 大学院数理科学研究科 博士課程)

Moonshine phenomena are certain mysterious connections between modular functions and finite groups. The first example is the celebrated monstrous moonshine, which connects the J-invariant and the Monster group. Surprisingly, this relationship can be well understood in terms of chiral conformal field theory. In this talk, I would like to explain what is chiral conformal field theory and how it gives moonshine phenomena. In the first part of the talk, the notion of modular function will be introduced and the precise statement of the monstrous moonshine will be given. Then the monstrous moonshine will be explained in terms of vertex operator algebra, a mathematical model of chiral conformal field theory. In the second part of the talk, we focus on the question: what is chiral conformal field theory mathematically? In addition to vertex operator algebras, other mathematical models of chiral conformal field theory, namely conformal nets and Segal conformal field theories, will be introduced. Recent progress on the relationship among these three models, including the Carpi--Kawahigashi--Longo--Weiner correspondence and the geometric realization of conformal nets will also be reviewed.

会場: via Zoom

イベント公式言語: 英語

How nucleus size affects chromatin motion? - Experimental measurements and a polymer physics theory

2021年7月1日(木) 10:00 - 11:00

坂上 貴洋 (青山学院大学 理工学部 物理・数理学科 准教授)

Chromatin moves dynamically inside the cell nucleus, and its motion is often correlated with gene functions such as DNA recombination and transcription. A recent study has shown that during early embryogenesis of the nematode, Caenorhabditis elegans, the chromatin motion markedly decreases with the cell stage. However, the underlying mechanism for this transition has yet to be elucidated. Here we systematically investigate the impact of nuclear size to demonstrate that it is indeed a decisive factor in chromatin mobility. We show that a simple theoretical description, which takes into account the length and time scales of chromatin polymer solution, can quantitatively describe the relationship between the nucleus size and the chromatin motion in vivo. Our results emphasize a regulatory role of nuclear size in restricting chromatin motion, and a generic polymer physics model plays a guiding role in capturing this essential feature. *Please refer to the email to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

Toward QCD-based description of dense baryonic matter

2021年6月29日(火) 13:00 - 14:30

藤本 悠輝 (Postdoctoral Scholars, Department of Physics, University of Washington, USA)

The equation of state (EoS) of dense baryonic/quark matter is the crucial ingredient for understanding neutron stars. I briefly review the current state of the high-density matter EoS based on the QCD perspectives. In this talk, I particularly focus on the perturbative QCD (pQCD) EoS, which was previously thought to be useless at realistic density because it is plagued by the large uncertainty. I introduce our recent analysis of the EoS calculated within the pQCD framework with the resummation [Fujimoto & Fukushima, 2011.10891]. I discuss our scheme for the Hard Dense Loop resummation, which turns out to reduce the uncertainty compared with the conventional pQCD estimate without resummation. Our result apparently extends the applicability of the QCD-based EoS down to densities realized inside neutron stars and infers a smooth matching with the baryonic EoS.

会場: via Zoom

イベント公式言語: 英語

Theory of Core-Collapse Supernovae

2021年6月25日(金) 16:00 - 17:00

原田 了 (理化学研究所 数理創造プログラム (iTHEMS) 基礎科学特別研究員)

会場: via Zoom

イベント公式言語: 英語

Precise WIMP Dark Matter Abundance and Standard Model Thermodynamics

2021年6月24日(木) 16:30 - 17:30

白井 智 (東京大学 カブリ数物連携宇宙研究機構 (Kavli IPMU) 特任助教)

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!

会場: via Zoom

イベント公式言語: 英語