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Understanding the effect of defective, interfering influenza virus

2021年10月14日(木) 10:00 - 11:00

カトゥリン・ボシゥメン (理化学研究所 数理創造プログラム (iTHEMS) 副プログラムディレクター)

Defective interfering virus particles (DIPs) are viruses that are defective in a very specific way that allows them to out-compete standard, non-defective virus. It is difficult to count DIPs because they can look too similar to standard virus. So instead, people are counting them based on their effect on suppressing the standard virus population. In this talk, I will explain the basic biology of virus replication, what are DIPs, and how they compete with standard virus. I will present our mathematical model (ordinary differential equation) that describes co-infection competition with DIPs and standard virus. I will use the mathematical model to show how experiments to count DIPs can give incorrect results, and I will propose some solutions.

会場: via Zoom

イベント公式言語: 英語

Speed limit for population dynamics

2021年10月7日(木) 10:00 - 11:00

足立 景亮 (理化学研究所 生命機能科学研究センター (BDR) 生体非平衡物理学理研白眉研究チーム 基礎科学特別研究員)

In statistical and quantum physics, the speed limit, i.e., upper bound for change rate, of time-dependent quantities has been discussed. In this talk, I will extend the concept of speed limit to ecological and evolutionary processes by considering the competitive Lotka-Volterra model and the quasi-species model. As an application of the speed limit, I will also discuss the universal constraint for the relaxation at the bifurcation point of such models.

会場: via Zoom

イベント公式言語: 英語

Donaldson-Thomas invariants, wall-crossing and categorifications

2021年10月1日(金) 16:00 - 18:10

戸田 幸伸 (東京大学 カブリ数物連携宇宙研究機構 (Kavli IPMU) 教授)

It is an important subject to study algebraic curves inside algebraic varieties, both in classical algebraic geometry and also enumerative geometry inspired by string theory. The Donaldson-Thomas theory is one of curve counting theories on Calabi-Yau 3-folds, and has developed in these 20 years from several aspects of mathematics and mathematical physics. Among them, the wall-crossing in derived category turned out to be a key phenomena in proving deep structures of generating series of Donaldson-Thomas invariants. In the first one hour, I will review the classical aspect of counting curves inside algebraic varieties, and explain how it leads to modern enumerative geometry such as Gromov-Witten invariants, Donaldson-Thomas invariants. In the second one hour, I will explain wall-crossing phenomena in Donaldson-Thomas theory, and its categorification in the case of the resolved conifold. *Please contact Keita Mikami's mail address to get access to the Zoom meeting room.

会場: via Zoom

イベント公式言語: 英語

Evolutionary dynamics of seasonal influenza viruses

2021年9月30日(木) 10:00 - 11:00

岡田 崇 (理化学研究所 数理創造プログラム (iTHEMS) 上級研究員)

Seasonal influenza viruses undergo rapid evolution, which allows them to escape from human-immune-system responses and infect humans repeatedly. In this talk, I present some counter-intuitive properties observed in time-series data of viral sequence variation and then discuss how these strange properties can be explained by extending the standard framework of population genetics.

会場: via Zoom

イベント公式言語: 英語

Finding Gravitational Waves from the Early Universe

2021年9月27日(月) 16:00 - 17:30

小松 英一郎 (Director, Max Planck Institute for Astrophysics, Germany)

The Cosmic Microwave Background (CMB) gives a photographic image of the Universe when it was still an “infant”. We have been using it to test our ideas about the origin of the Universe. The CMB research told us a remarkable story: the structure we see in our Universe such as galaxies, stars, planets, and eventually ourselves originated from tiny quantum fluctuations in the period of the early Universe called cosmic inflation. While we have accumulated strong evidence for this picture, the extraordinary claim requires extraordinary evidence. The last prediction of inflation that is yet to be confirmed is the existence of primordial gravitational waves whose wavelength can be as big as billions of light years. To this end we have proposed to JAXA a new satellite mission called LiteBIRD, whose primary scientific goal is to find signatures of gravitational waves in the polarisation of the CMB. In this presentation we describe physics of gravitational waves from inflation, and the LiteBIRD proposal.

会場: via Zoom

イベント公式言語: 英語

S-matrix Unitarity toward UV Completion

2021年9月13日(月) 13:30 - 15:00

泉 圭介 (名古屋大学 素粒子宇宙起源研究所 (KMI) 助教)

Einstein gravity is not renormalizable and does not hold perturbative unitarity at high energy. This is the main reason why the construction of quantum gravity is difficult. A conjecture was proposed by Llewellyn Smith, "renormalizablility and tree-unitarity at high energy give the same conditions for theories". This conjecture would be important because it shows that, if a theory is constructed s.t. unitarity is satisfied, renormalizablility holds automatically, and vice versa. Unfortunately, a counterexample was pointed out. If a theory involves higher derivatives, there exists a theory which is renormalizable but does not satisfy tree-unitarity. A candidate of quantum gravity, the quadratic gravity (R_{\mu\nu}^2 gravity), is one of the examples. Therefore, Llewellyn Smith's conjecture would not be useful for the discussion of quantum gravity. Then, we introduce a new conjecture, "renormalizablility and S-matrix unitarity (or often called pseudo-unitarity) at high energy give the same conditions for theories". In this talk, Llewellyn Smith's conjecture and our contribution to it will be explained. Then, our new conjecture will be introduced. Finally, it will be shown that our conjecture works well even in theories with higher derivatives.

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

RIKEN-Vancouver Joint Workshop on Quantum Computing

2021年8月24日(火) - 25日(水)

The main aim of this workshop is that the quantum people in RIKEN (iTHEMS and RQC) and Vancouver (Quantum BC) get together online to discuss scientific activities and explore future collaborations. Program: August 24, 2021 (8:30am - 1:00pm) Tokyo August 23, 2021 (4:30pm - 9:00pm) Vancouver Tetsuo Hatsuda (iTHEMS): Welcome + iTHEMS overview Yasunobu Nakamura (RQC): RQC overview Lukas Chrostowski (UBC): Quantum BC overview Shunji Matsuura (1QBit): Accurate state preparation on noisy quantum devices Olivia Di Matteo (UBC): Operational, gauge-free quantum tomography Yasunobu Nakamura (RQC): Towards superconducting quantum computing Jason Chang (iTHEMS): Improving Schroedinger equation implementations with gray code for adiabatic quantum computers Robert Raussendorf (UBC): Computationally universal phase of quantum matter Akira Furusawa (RQC): Large-scale quantum computing with quantum teleportation August 25, 2021 (8:30am - 1:30pm) Tokyo August 24, 2021 (4:30pm - 9:30am) Vancouver Etsuko Itou (iTHEMS): Digital quantum simulation for screening and confinement in gauge theory with a topological term Joe Salfi (UBC): Engineering long coherence times of spin-orbit qubits in silicon Seiji Yunoki (RQC): Quantum simulations for quantum many-body systems: Variational quantum algorithms and beyond Takumi Doi (iTHEMS): Hybrid quantum annealing via molecular dynamics Drew Potter (UBC): Simulating highly-entangled matter with quantum tensor networks Seigo Tarucha (RQC): High-fidelity quantum gates in silicon quantum computing Organizing Institutes: iTHEMS: RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program RQC: RIKEN Center for Quantum Computing Quantum BC Organizers: Tetsuo Hatsuda (iTHEMS) Yasunobu Nakamura (RQC) Shunji Matsuura (1QBit) Joseph Salfi (UBC) Erika Kawakami (RQC / RIKEN CPR) Neill Lambert (RIKEN CPR)

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

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

RIKEN iTHEMSのアウトリーチについての研究会 2021

2021年7月11日(日) - 12日(月)

2016年11月に理化学研究所の数理創造プログラム（interdisciplinary Theoretical and Mathematical Sciences Program）RIKEN iTHEMSが発足しました。RIKEN iTHEMSでは、「数理」を軸とする分野横断的手法により、宇宙・物質・生命の解明や、社会における基本問題の解決を目指しています。これまでの「ジャーナリスト・イン・レジデンス・プログラム」による交流の実績の上で、RIKEN iTHEMSの研究と社会の関連付けを探るとともに、今後のジャーナリストと研究者の双方向的関係の構築のための議論を行うアウトリーチについての研究会を開催いたします。これまで東京大学玉原国際セミナーハウスで開催してきましたが、昨年度に続き本年度も当該セミナーハウスは閉館ということで、ZOOMによる研究会として開催させていただきます。 世話人: 坪井 俊 理化学研究所 数理創造プログラム 副プログラムディレクター

会場: via Zoom

イベント公式言語: 日本語

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

Quantitative Population Dynamics in Interdisciplinary Biology

2021年7月8日(木) 10:30 - 12:00

岩見 真吾 (名古屋大学 大学院理学研究科 教授)

Through the course of life, from the moment of birth till death, an organism will achieve various states of equilibrium or ‘homeostasis’ which will inevitably encounter perturbations. The processes of cell growth, differentiation, infection, mutation, evolution and adaptation work together as a coordinated ‘system’, described by mathematical models for population dynamics, to maintain a healthy state. Any disruptions to this system leads to disease including infection, allergy, cancer, and aging. We are conducting interdisciplinary research to elucidate “Quantitative Population Dynamics” through the course of life with original mathematical theory and computational simulation, which are both our CORE approach. Our mathematical model-based approach has quantitatively improved a current gold-standard approach essentially relying on the statistical analysis of “snapshot data” during dynamic interaction processes in life sciences research. In this talk, I will explain how our interdisciplinary approach extends our understanding for complicated clinical data and apply real world problem with an example of the Novel Coronavirus Disease, COVID-19.

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

Period variability can provide valuable information in oscillatory systems

2021年6月24日(木) 10:00 - 11:00

森 史 (九州大学 大学院芸術工学研究院 デザイン人間科学部門 助教)

Biological clocks generate temporally precise oscillations although they are subjected to various types of noise. In other words, oscillations with only a small variability in the period are observed under action of noise. In this talk, I focus on period variability in coupled phase oscillators and complex oscillatory dynamical systems, and present the following topics:(i) A phase oscillator subjected to noise can become to generate more precise oscillations not only when it is synchronized with periodic signal but also when it is mutually synchronized with another phase oscillator with stronger noise. (ii) In complex oscillatory dynamical systems, period variability is sensitive to the choice of an output variable and output checkpoint; it can be reduced by an appropriate selection of them. (iii) Noise intensity and coupling strength in synchronized phase oscillators can be inferred from data about period variability. This talk is based on joint researches with Dr. Hiroshi Kori (Tokyo Univ) and Dr. Alexander Mikhailov (Kanazawa Univ). *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