The 8th Asia-Pacific Conference on Few-Body Problems in Physics (APFB2020)

March 1 (Mon) - 5 (Fri), 2021

The next Asia-Pacific conference on few-body problems in physics (APFB2020) will be held at KANAZAWA BUNKA HALL, Kanazawa, Japan, from 1 to 5 March 2021. RIKEN iTHEMS is a co-host of this conference together with RIKEN Nishina Center, Kyushu Univ., Osaka Univ. and Tohoku Univ. The registration deadline for the online participation is Feb. 25, 2021.

Venue: KANAZAWA BUNKA HALL

Event Official Language: English

Origin of non-linearity of large deformation on DNA stretched

February 25 (Thu) at 10:00 - 11:00, 2021

Hiroshi Yokota (Postdoctoral Researcher, iTHEMS)

Since DNA in a cell is mechanically stretched or rotated by many proteins, the mechanical response of DNA in vitro is expected to be basic point for understanding its behavior. When DNA is stretched by relatively high force, the length of DNA shows the nonlinear response. In this talk, I introduce the theoretical treatment of DNA stretching in high force region based on polymer physics.

Venue: via Zoom

Event Official Language: English

The Evolution of Primordial Neutrino Helicities under Gravitational and Magnetic Fields and Implications for their Detection

February 22 (Mon) at 10:00 - 11:30, 2021

Gordon Baym (Senior Visiting Scientist, iTHEMS / Professor Emeritus, University of Illinois, USA)

Feb.22 (Mon) 10:00am-11:30am (JST) Primordial neutrinos decoupled in the early universe in helicity eigenstates. As I will discuss, two effects -- dependent on neutrinos having a non-zero mass -- can modify their helicities as they propagate through the cosmos. First, finite mass neutrinos have a magnetic moment and thus their spins, but not their momenta, precess in cosmic and galactic magnetic fields. The second is the propagation of neutrinos past cosmic matter density fluctuations, which bend their momenta, and bend their spins by a smaller amount. (The latter is a general relativistic effect.) Both effects turn a fraction of left-handed neutrinos into right-handed neutrinos, and right-handed antineutrinos into left-handed. If neutrino magnetic moments approach that suggested by the XENON1T experiment as a possible explanation of their excess of low energy electron events -- a value well beyond the moment predicted by the standard model -- helicities of relic Dirac (but not Majorana) neutrinos could be considerably randomized. I finally will discuss the implications of neutrino helicity rotation, as well as their Dirac vs. Majorana nature, on their detection rates via the Inverse Tritium Beta Decay reaction.

Venue: via Online

Event Official Language: English

High-throughput laboratory evolution with machine learning reveals constraints for drug resistance evolution

February 18 (Thu) at 10:00 - 11:00, 2021

Junichiro Iwasawa (Ph.D. Student, Department of Physics, Graduate School of Science, The University of Tokyo)

The understanding of evolution is crucial to tackle the problem of antibiotic resistance which is a growing health concern. Although the lack of sufficient data has long hindered the mechanism of evolution, laboratory evolution experiments equipped with high-throughput sequencing/phenotyping are now gradually changing this situation. The emerging data from recent laboratory evolution experiments have revealed repeatable features in evolutionary processes, suggesting the existence of constraints on evolutionary outcomes [1,2]. Despite its importance for understanding evolution, however, we still lack a systematic investigation for evolutionary constraints. In this seminar, I would like to talk about two projects on the investigation of evolutionary constraints using data acquired from laboratory evolution of Escherichia coli. In the first half, I will explain how to extract an effective latent space for probing constraints in resistance evolution using gene expression data. We will further discuss what kind of structure exists in this space [3]. In the latter half, I will talk about our recent study on how to construct a predictive model for evolution using the information of evolutionary constraints.

Venue: via Zoom

Event Official Language: English

The 14th MACS Colloquium

February 17 (Wed) at 15:00 - 17:30, 2021

Yoshihiro Kaneko (Associate Professor, Division of Earth and Planetary Sciences, Graduate School of Science, Kyoto University)

15:00- Talk by Prof. Yoshihiro Kaneko 16:05- MACS Report Meeting FY2019 16:30- Discussion of each study group

Venue: via Zoom

Event Official Language: Japanese

Journal Club: Large deviation statistics of Markovian quantum systems

February 17 (Wed) at 13:00 - 14:30, 2021

Ryusuke Hamazaki (Senior Research Scientist, iTHEMS / RIKEN Hakubi Team Leader, Nonequilibrium Quantum Statistical Mechanics RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research (CPR))

Large deviation is a mathematical framework to treat “rare events” in random processes [1]. In this journal club, I talk about recent development of large deviation analysis in open Markovian quantum systems [2,3]. I first introduce the notion of large deviation statistics using the simple independent and identically distributed random variables. I then review recent development of level 2.5 large deviation statistics for classical Markovian jump processes and its application to thermodynamic uncertainty relation [4]. Finally, I discuss how the classical results are extended to quantum regime. *Detailed information about the seminar refer to the email.

Venue: via Zoom

Event Official Language: English

Blockchain in Kyoto 2021

February 17 (Wed) - 18 (Thu), 2021

Language: Some parts will be in Japanese. The International Conference on Blockchains and their Applications aims at bringing together researchers and practitioners from various communities of science and technology working on areas related to FinTech, Crypto-asset, and Blockchain. For more information, please refer to the related links.

Venue: Hybrid Format (International Conference Room I, Clock Tower Centennial Hall, Kyoto University and Online)

Event Official Language: English

Public Lecture for Darwin Day

February 17 (Wed) at 9:00 - 10:00, 2021

Catherine Beauchemin (Deputy Program Director, iTHEMS / Professor, Department of Physics, Ryerson University, Canada)

Japan, February 17, 2021, 09:00 AM JST Canada/USA, Feb 16, 2021, 07:00 PM Eastern Time Through mutations and genetic reassortment, a virus can mutate and the resulting virus variants can evade our drugs, our vaccines, and our body's own immune response. Using specific viruses like influenza, HIV or SARS-CoV-2 (the virus responsible for COVID-19) as examples, I will introduce the basics of how viruses replicate, and the processes via which mutations arise. *Detailed information about the seminar refer to the Prof. Beauchemin’s email.

Venue: via Zoom

Event Official Language: English

Mapping the Milky Way by VLBI Astrometry

February 16 (Tue) at 13:30 - 15:00, 2021

Nobuyuki Sakai (Korea Astronomy and Space Science Institute (KASI), Republic of Korea)

Astrometry is the only way to obtain 6D (position-velocity) phase space information for astronomical objects. The unique capability allows us to examine the past, present, and future of the Milky Way. Firstly, I will introduce history and basics of astrometry. Secondly, I will overview astrometric projects in the world. Thirdly, I will highlight recent astrometric results about the Galactic structure. Lastly, I will introduce astrometric research in Korea as well as future astrometric projects and sciences in 2020s and 30s.

Venue: via Zoom

Event Official Language: English

Quantum mechanical description of energy dissipation and application to heavy-ion fusion reactions

February 16 (Tue) at 13:00 - 14:30, 2021

Masaaki Tokieda (Graduate students, Department of Physics, Tohoku University)

For theoretical description of heavy-ion fusion reactions, two different models have been used depending on the incident energy. At energies above the Coulomb barrier, importance of energy dissipation and fluctuation has been deduced from scattering experiments. To describe them phenomenologically, the classical Langevin equation has successfully been applied. At energies below the Coulomb barrier, on the other hand, the quantum coupled-channels method with a few number of internal states has been applied, and it has succeeded in explaining sub-barrier fusion reactions. While each method succeeds in each energy range, a unified description of heavy-ion fusion reactions from sub-barrier energies to above barrier energies is still missing. To achieve this, we need to treat dissipation and fluctuation quantum mechanically. In order to describe dissipation and fluctuation quantum mechanically, we have applied ideas of open quantum systems to heavy-ion fusion reactions. I will talk about recent development in this talk. First I will introduce a model Hamiltonian to treat dissipation and fluctuation quantum mechanically, and explain its character and a strategy for numerical studies. I will then apply the model to a fusion problem, and discuss a role of energy dissipation during quantum tunneling. Finally I will discuss a possible future direction for a unified description of heavy-ion fusion reactions.

Venue: via Zoom

Event Official Language: English

A machine learning approach for prediction of mitochondrial proteins in non-model organisms

February 12 (Fri) at 10:00 - 11:00, 2021

Keitaro Kume (Assistant Professor, Faculty of Medicine, University of Tsukuba)

The evolution of the repertoire of proteins localized to organelles is important for understanding the evolutionary process of organelles. However, experimental methods for identifying organelle-localized proteins have been established only for model organisms and some organisms. Therefore, prediction methods using sequence data obtained from genome and transcriptome analyses, which are relatively easy to obtain, are useful. However, such prediction methods had also been established only for model organisms. In this talk, I will introduce our study in which a machine learning method was used to obtain protein candidates localized to mitochondrion-related organelles in non-model organisms.

Venue: via Zoom

Event Official Language: English

The 12th RIKEN-Kyoto University Joint Data Assimilation Workshop

February 10 (Wed) at 13:30 - 16:30, 2021

Language: Japanese/English Participation deadline: Tuesday, February 9, 2021

Venue: via Online

Event Official Language: Japanese

Quantum kinetic theory for chiral and spin transport in relativistic heavy ion collisions and core-collapse supernovae

February 4 (Thu) at 13:00 - 14:30, 2021

Di-Lun Yang (Assistant Professor, Faculty of Science and Technology, Keio University)

Recently, the anomalous transport phenomena of relativistic fermions associated with chirality and spin induced by external fields have been greatly explored in different areas of physics. Notably, such phenomena are in connection to various quantum effects such as quantum anomalies and spin-orbit interaction. The quark gluon plasmas produced from relativistic heavy ion collisions (HIC) and the core-collapse supernovae (CCSN) are both the systems in extreme conditions with high temperature or density and the presence of strong magnetic and vortical fields. Meanwhile, the abundance of light quarks and neutrinos as relativistic fermions created therein accordingly makes these two systems ideal test grounds for studying such exotic transport phenomena. Inversely, the anomalous transport may also give rise to unexpected impacts on the evolution of both systems. However, to analyze such dynamical quantum effects, a novel quantum transport theory delineating the evolution of chirality imbalance and spin has to be introduced. In this talk, I will discuss recent developments and applications of the quantum kinetic theory for chiral and spin transport in the context of HIC and CCSN.

Venue: via Zoom

Event Official Language: English

System identification of mechano-chemical epithelial sheet dynamics

February 4 (Thu) at 10:00 - 11:00, 2021

Yoshifumi Asakura (Ph.D. Student, Graduate School of Biostudies, Kyoto University)

Collective migration of epithelial cells is a fundamental process of multi-cellular organisms. Our recent study using live imaging with FRET-based biosensor discovered that cell migration within an epithelial sheet is oriented by traveling waves of ERK activation. However, it is still elusive how the cells make a decision on migration direction by integrating mechano-chemical signals. Here, we performed reverse-engineering approach to extract a hidden control mechanism in the epithelial sheet dynamics in a data-driven manner. Our model has an ability to forecast cell migration quantified in time-lapse images. Therefore, our approach would be powerful to understand mechano-chemical epithelial sheet dynamics.

Venue: via Zoom

Event Official Language: English

Mathematics of magic angles for bilayer graphene

February 3 (Wed) at 20:00 - 21:15, 2021

Simon Becker (Ph.D. Student, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK)

20:00pm ~ 21:15pm on Feb. 03th, 2021 (JST) 11:00am ~ 12:15am on Feb. 03th, 2021 (UK) Magic angles are a hot topic in condensed matter physics: when two sheets of graphene are twisted by those angles the resulting material is superconducting. Please do not be scared by the physics though: I will present a very simple operator whose spectral properties are thought to determine which angles are magical. It comes from a recent PR Letter by Tarnopolsky–Kruchkov–Vishwanath. The mathematics behind this is an elementary blend of representation theory (of the Heisenberg group in characteristic three), Jacobi theta functions and spectral instability of non-self-adjoint operators (involving Hoermander’s bracket condition in a very simple setting). The results will be illustrated by colourful numerics which suggest some open problems. This is joint work with M. Embree, J. Wittsten, and M. Zworski.

Venue: via Zoom

Event Official Language: English

Many body problems from quarks to stellar evolutions

January 28 (Thu) at 13:30 - 15:00, 2021

Nobutoshi Yasutake (Associate Professor, Chiba Institute of Technology)

The many-body problems are major problems that need to be clarified not only in nuclear physics, but also in astronomy. In this seminar, I introduce stellar evolutions as gravitational many-body problems, and also hadronic matter as quantum many-body problems, based on the Lagrangian schemes. The macroscopic stars and the microscopic hadronic matter look completely different issues. But in this seminar, I introduce the similarities between the two problems. For hadronic matter, we adopt the color molecular dynamics to understand the behaviors and properties of hadronic matter in the framework of QCD. Although molecular dynamics can not be the first-principle, they are sometimes useful to understand many-body quantum properties. In this talk, we introduce the current status of our color molecular dynamics.

Venue: via Zoom

Event Official Language: English

Numerical inference of the molecular origin of the cyanobacterial circadian rhythm

January 28 (Thu) at 10:00 - 11:00, 2021

Shin-ichi Koda (Assistant Professor, Institute for Molecular Science)

The cyanobacterial clock proteins, KaiA, KaiB, and KaiC, are known as the simplest biological clock; Just by mixing them with ATP in a test tube, self-sustaining oscillation with a nearly 24h temperature-compensated period is reconstituted. To elucidate the molecular mechanisms of this oscillator, experimental studies have revealed and investigated in detail various elementary reactions/processes, ranging from local chemical reactions of ligands to global (dis)assembly of the proteins. Yet, proposing molecularly detailed mechanisms of the clock functions is still difficult because almost all experimentally measurable quantities are the results of complicated interplays between many elementary processes, i.e. independent measurement of an elementary process is difficult. In this talk, I will present a numerical approach to obtain the rate constants of the elementary processes from experimental data [1, 2]. First, a reaction model consisting of rate equations of the elementary processes is built. Then, their rate constants and temperature dependence are inferred by simultaneously fitting model outputs to multiple types of experimental data (such as phosphorylation reactions and ATPase activity) at various temperatures. On the basis of the inferred parameter values, we can quantitatively discuss how the clock functions arise from the interplays between elementary processes. As an example, I will present a potential molecular mechanism of the temperature compensation of period.

Venue: via Zoom

Event Official Language: English

Journal Club: Sampling the stable structures based on replica-permutation method

January 27 (Wed) at 13:00 - 14:30, 2021

Hiroshi Yokota (Postdoctoral Researcher, iTHEMS)

When we want to search the (meta)stable structures of the macromolecules such as protein, the combination of molecular dynamics simulation and replica exchange method (REM) is useful. In REM, sampling is performed by exchanging replicas (copies) of the system having different temperatures when this process is accepted based on Metropolis algorithm. In this method, the exchange can be rejected, which leads to the decrease in the sampling efficiency. To obtain more efficient sampling than that of REM, Itoh and Okumura proposed replica-permutation method (RPM) in which the replicas are permutated to perform sampling based on Suwa-Toudou algorithm. In this Journal club, I will introduce RPM and some examples of its application.

Event Official Language: English

Introduction to Boolean modeling and Boolean networks as information processing units

January 21 (Thu) at 10:00 - 11:00, 2021

Takashi Okada (Senior Research Scientist, iTHEMS)

Boolean networks are widely used in physics, biology, social science, and computer science. In this talk, I will introduce the basics of Boolean networks and give an overview of Biological applications. Then, I will discuss information transfer in Boolean networks and discuss optimal design principles. The latter part of the talk is based on joint work with Fumito Mori (Kyushu Univ).

Venue: via Zoom

Event Official Language: English

Information theory in ecology: Markov chain, Venn diagram, Kronecker (and Cartesian graph) products, and Tsallis entropy

January 20 (Wed) at 13:00 - 14:00, 2021

Ryosuke Iritani (Research Scientist, iTHEMS)

This is more like an introductory talk on how I was motivated to work with information theory, and include unpublished data. Ecologists have been long interested in understanding diversity (divergence) of natural ecosystems. One possible way of accounting for diversity is to use a species' presence/absence table across spatial locations (species-location table), in which we record 1 if a focal species is present in a given site (otherwise 0). Recent interest lies in assessing how diversity (e.g., the number of species) changes with time: for instance, extinction and colonization of species may result in the modification of such tables with time. However, we are yet to have theoretical toolkits to model the dynamics of spcies-site tables. In this talk, I will introduce my model (in collaboration with R. Hamazaki, S. Tatsumi, and M Cadotte) of the dynamics of species-site tables based on Markovian stochastic processes. Specifically, our apporach allows us to analytically obtain the solution of the full stochastic dynamics by means of localizing the dynamics to a single site and then expanding it towards the global sites with Kronecker's prodcut (in linear algebra) or Cartesian product (in graph theory). Intuition obtains from illustrating the dynamics onto Venn diagram, where we draw several sets (corresponding to locations) and binary numbers (corresponding to presence-absence data) and consider random walks on Venn diagram acorss sets; also this Venn diagram based interpretation is mathematically underpinned by Cartesian product of graphs. Finally I will briefly talk about how we assess diversity of ecosystems using Tsallis entropy (or the generalized Shannon entropy).

Venue: via Zoom

Event Official Language: English