Spider silk big data drives the creation of targeted biopolymers -from polymerization to biodegradation-

September 20 (Wed) at 13:30 - 15:00, 2023

Keiji Numata (Professor, Graduate School of Engineering, Kyoto University)

Our Material DX research project (http://pixy.polym.kyoto-u.ac.jp/ku_numata/index.html) is dedicated to addressing challenges in the design and synthesis of polymeric materials. Our primary objective is to establish a comprehensive material research and technical platform built upon a polymer database. Our efforts center on the creation and advancement of bioadaptive materials featuring biological functionalities and physical properties.1,2 Within the domain of polymer science, the integration of material informatics (MI) for establishing correlations between material structure and properties, along with the utilization of extensive databases, has not witnessed substantial advancement in recent times. Structural protein such as spider silk is an eco- and bio-friendly polymer as well as one of the key factors to realize the unique properties and functions of natural tissues and organisms.3,4 However, use of structural proteins as structural materials in human life is still challenging. Spider silks are among the toughest known materials and thus provide models for renewable, biodegradable and sustainable biopolymers. However, the entirety of their diversity still remains elusive, and silks that exceed the performance limits of industrial fibers are constantly being discovered. We obtained transcriptome assemblies from 1,098 species of spiders to comprehensively catalog silk gene sequences and measured the mechanical, thermal, structural, and hydration properties of the dragline silks of 446 species.5 The combination of these silk protein genotype-phenotype data revealed essential contributions of multicomponent structures in high-performance dragline silks as well as numerous amino acid motifs contributing to each of the measured properties. We hope that our global sampling, comprehensive testing, integrated analysis and open data will provide a solid starting point for future biomaterial designs.

Venue: Seminar Room #359 (Main Venue) / via Zoom

Event Official Language: English

Predicting future biodiversity with species distribution models: current applications, persistent issues, and where to go from here

September 19 (Tue) at 16:00 - 17:00, 2023

Jamie M. Kass (Associate Professor, Graduate School of Science, Tohoku University)

There is much current interest in macroecology to make predictions of future biodiversity patterns in order to inform both regional and global priorities for conservation and sustainability of ecosystem functions and services. Species distribution models use data on species' occurrence records, environmental predictor variables, and sometimes other data sources to estimate niche relationships and distribution extents—these models can also be combined to make biodiversity estimates. As the field of species distribution modeling has grown considerably over the past two decades, many approaches now exist to build models, evaluate their performance, and use them to make predictions for unsampled areas and times. I will provide an overview of current techniques to predict future distributions of species and biodiversity, detail some issues with these techniques concerning uncertainty and realism of predictions, and contribute my humble thoughts on where the field should go from here.

Venue: via Zoom

Event Official Language: English

Classification of Meromorphic Spin 2-dimensional Conformal Field Theories of Central Charge 24

September 19 (Tue) at 15:00 - 16:30, 2023

Möller Sven (Group Leader, Department of Mathematics, University of Hamburg, Germany)

We classify the self-dual (or holomorphic) vertex operator superalgebras (SVOAs) of central charge 24, or in physics parlance the purely left-moving, spin 2-dimensional conformal field theories with just one primary field. There are exactly 969 such SVOAs under suitable regularity assumptions and the assumption that the shorter moonshine module VB^# is the unique self-dual SVOA of central charge 23.5 whose weight-1/2 and weight-1 spaces vanish. Additionally, there might be self-dual SVOAs arising as "fake copies" of VB^# tensored with a free fermion F. We construct and classify the self-dual SVOAs by determining the 2-neighbourhood graph of the self-dual (purely bosonic) VOAs of central charge 24 and also by realising them as simple-current extensions of a dual pair containing a certain maximal lattice VOA. We show that all SVOAs besides VB^# x F and potential fake copies thereof stem from elements of the Conway group Co_0, the automorphism group of the Leech lattice. By splitting off free fermions F, if possible, we obtain the classification for all central charges less than or equal to 24. This is based on joint work with Gerald Höhn (arXiv:2303.17190)

Venue: Seminar Room #359

Event Official Language: English

Quantum skyrmion Hall effect

September 14 (Thu) at 17:00 - 18:15, 2023

Ashley Cook (Group Leader, Correlations and Topology, Max Planck Institute for the Physics of Complex Systems and Max Planck Institute for Chemical Physics of Solids, Germany)

Field: condensed matter physics Keywords: topology, electron-based quantum skyrmions, spin, Berry curvature Abstract: Topological skyrmion phases of matter are recently-introduced topological phases of electronic systems in equilibrium, in which a system with more than one degree of freedom (e.g. spin and orbital degrees of freedom) realizes a topological state for a subset of the degrees of freedom (e.g. only spin). For topological skyrmion phases of spin, this topology is relevant even if spin is not conserved due to non-negligible atomic spin-orbit coupling, and is distinguished by a skyrmion forming in the spin texture over the Brillouin zone, distinct from a skyrmion forming in the texture of the projector onto occupied states over the Brillouin zone. We present results on three band Bloch Hamiltonians realizing this non-trivial spin topology, and outline some bulk-boundary correspondence features, such as gapless edge states corresponding to zero net charge—but finite spin angular momentum—pumped across the bulk gap. Tracing out the orbital degree of freedom, we can identify this spin pumping with pumping of spin point charges, and local curvature of the k-space spin skyrmion with a Berry curvature of these spin point charges. That is, the spin pumping is identified with pumping of spin magnetic skyrmions, which reduce to point magnetic charges after tracing out the orbital degree of freedom. We therefore identify topological skyrmion phases as lattice counterparts of quantized transport of quantum magnetic skyrmions, a quantum skyrmion Hall effect. This indicates that the theory of the quantum Hall effect must be generalized, by relaxing the assumption of point charges.

Venue: via Zoom

Event Official Language: English

Quasi-BPS categories

September 13 (Wed) at 10:00 - 11:30, 2023

Yukinobu Toda (Professor, Kavli Institute for the Physics and Mathematics of the Universe (Kavli IPMU), The University of Tokyo)

In this talk, I will explain the notion of "Quasi-BPS category". This is the (yet to be defined) category which categorifies BPS invariants on Calabi-Yau 3-folds, and plays an important role in categorical wall-crossing in Donaldson-Thomas theory. I will explain the motivation of quasi-BPS categories, give definition in the case of symmetric quivers with potential (a local model of CY 3-folds), and their properties. If time permits, I will explain quasi-BPS categories for local K3 surfaces and their relation to derived categories of hyperkahler manifolds. This is a joint work in progress with Tudor Padurariu.

Venue: Seminar Room #359

Event Official Language: English

Parameter Fitting for Glucose Homeostasis - Searching for Methods to Predict and Diagnose

September 12 (Tue) at 16:00 - 17:00, 2023

Gabriel Gress (Specially Appointed Research Fellow, Mathematical Science Group, Advanced Institute for Materials Research (AIMR), Tohoku University)

The human body regulates glucose through a complex web of biological interactions, for which state-of-the-art models require dozens of variables and parameters to even emulate. But while we've had devices to measure glucose levels as far back as the 1980's, nearly all of the remaining variables and parameters cannot be measured directly to this day. While continuous glucose monitors have greatly improved the health of diabetic patients, there are still many barriers in the diagnosis of at-risk patients as well as accurately dispersing insulin to counteract future trends in glucose levels. While glucose readings are only a small window into one of many factors of how the human body maintains glucose homeostasis, we search for ways to leverage the high-frequency and high-volume data to improve the state of diagnosis and prediction in diabetic patients.

Venue: Hybrid Format (3F #359 and Zoom), Main Research Building

Event Official Language: English

Collective Plasma Effects in Relativistic Radiation-Mediated Blast Waves

September 8 (Fri) at 14:00 - 15:15, 2023

Arno Vanthieghem (Princeton-NINS Postdoctoral Research Fellow, Department of Astrophysical Sciences, Princeton University, USA)

Relativistic radiation-mediated shocks (RRMS) dictate the early emission in numerous transient sources such as supernovae, low luminosity gamma-ray bursts, binary neutron star mergers, and tidal disruption events. These shock waves are mediated by Compton scattering and copious electron-positron pair creation. It has been pointed out that a high pair multiplicity inside the shock transition leads to a lepton-baryon velocity separation, prone to plasma instabilities. The interaction of the different species with this radiation-mediated microturbulence can lead to coupling and heating that is unaccounted for by current single-fluid models. Here, we present a theoretical analysis of the hierarchy of plasma microinstabilities growing in an electron-ion plasma loaded with pairs and subject to a radiation force. Our results are validated by particle-in-cell simulations that probe the nonlinear regime of the instabilities and the lepton-baryon coupling in the microturbulent electromagnetic field. Based on this analysis, we derive a reduced transport equation for the particles that demonstrates anomalous coupling of the species and heating in a Joule-like process by the joined contributions of the decelerating turbulence, radiation force, and electrostatic field. We will then discuss the effect of finite magnetization on the general dynamics and recent efforts toward a more self-consistent description of the coupling. In general, our results suggest that radiation-mediated microturbulence could have important consequences for the radiative signatures of RRMS.

Venue: via Zoom

Event Official Language: English

The Cosmic Gravitational Microwave Background

September 6 (Wed) at 15:00 - 16:30, 2023

Jan Schuette-Engel (Postdoctoral Researcher, iTHEMS)

The thermal plasma in the early universe produced a guaranteed stochastic gravitational wave (GW) background, which peaks today in the microwave regime and was dubbed the cosmic gravitational microwave background (CGMB). I show that the CGMB spectrum encodes fundamental information about particle physics and gravity at ultra high energies. In particular, one can determine from the CGMB spectrum the maximum temperature of the universe and the effective degrees of freedom at the maximum temperature. I also discuss briefly how quantum gravity effects arise in the CGMB spectrum as corrections to the leading order result.

Venue: Hybrid Format (3F #359 and Zoom), Main Research Building

Event Official Language: English

Lab-Theory Standing Talk #2

September 5 (Tue) at 13:00 - 13:50, 2023

Yusaku Nishimiya (Research Part-time Worker II, Ion Beam Breeding Group, RIKEN Nishina Center for Accelerator-Based Science (RNC))

Venue: 3rd floor public space, Main Research Building

Event Official Language: English

The 19th High Performance Computing Physics (HPC-Phys) Workshop

August 31 (Thu) at 13:30 - 17:30, 2023

Computational science is indispensable research method in various fields in physics. On the other hand, there is technical challenge in massive numerical simulations, such as optimization for each computational system and proper choice of computational method, and it is desirable to promote interdisciplinary collaborations between different fields. This series of workshops is organized to enhance such interdisciplinary activities among wide area of computational physics. The 19th workshop will be held with the following program: Program 13:30-13:35 Introduction 13:35-14:25 Tomonori Shirakawa : "Simulation of quantum computation using tensor network method" 14:25-15:15 Misa Ogata : "New computational method using Lagrangian construction for equilibrium shape of 2-dimensional stars" 15:15-15:35 Break 15:35-16:25 Rico Pohle : "Semi-classical Monte Carlo and molecular dynamics simulations of spin coherent states" 16:25-17:15 Ken-Ichi Ishikawa : "Algorithms for Lattice Quantum Chromodynamics" 17:15-17:30 Discussions (17:30- Informal social gathering)

Venue: Welfare and Conference Bldg. 2F Meeting Room, RIKEN Wako Campus

Event Official Language: Japanese

MNISQ: A Large-Scale Quantum Circuit Dataset for Machine Learning on/for Quantum Computers in the NISQ era

August 29 (Tue) at 14:00 - 15:30, 2023

Leonardo Placidi (Ph.D. Student, Graduate School of Engineering Science, Osaka University)

We introduce the first large-scale dataset, MNISQ, for both the Quantum and the Classical Machine Learning community during the Noisy Intermediate-Scale Quantum era. MNISQ consists of 4,950,000 data points organized in 9 subdatasets. Building our dataset from the quantum encoding of classical information (e.g., MNIST dataset), we deliver a dataset in a dual form: in quantum form, as circuits, and in classical form, as quantum circuit descriptions (quantum programming language, QASM). In fact, also Machine Learning research related to quantum computers undertakes a dual challenge: enhancing machine learning by exploiting the power of quantum computers, while also leveraging state-of-the-art classical machine learning methodologies to help the advancement of quantum computing. Therefore, we perform circuit classification on our dataset, tackling the task with both quantum and classical models. In the quantum endeavor, we test our circuit dataset with Quantum Kernel methods, and we show excellent results with up to 97% accuracy. In the classical world, the underlying quantum mechanical structures within the quantum circuit data are not trivial. Nevertheless, we test our dataset on three classical models: Structured State Space sequence model (S4), Transformer, and LSTM. In particular, the S4 model applied on the tokenized QASM sequences reaches an impressive 77% accuracy. These findings illustrate that quantum circuit-related datasets are likely to be quantum advantageous, but also that state-of-the-art machine learning methodologies can competently classify and recognize quantum circuits. We finally entrust the quantum and classical machine learning community.

Venue: #345, 3F, Main Research Building, RIKEN Wako Campus (Main Venue) / via Zoom

Event Official Language: English

Landscape structure drives eco-evolution in host parasite systems

August 24 (Thu) at 16:00 - 17:00, 2023

Jhelam Deshpande (Ph.D. Student, Biodiversity: dynamics, interactions and conservation team, Institute of Evolutionary Science of Montpellier, France)

As all biological and many artificial systems, hosts and their parasites are most often spatially structured. Besides this highly relevant spatial context, parasites may change through time due to to evolutionary processes, including mutation and selection. These facts imply that we must study host-parasite systems taking into account space and evolution. Past work has mainly focused on simple spatial structures, but how parasites evolve in realistically complex landscapes remains unclear, hampering the translation of theoretical predictions to real ecological systems.Therefore, we here develop an eco-evolutionary metapopulation model of host-parasite interactions in which hosts and parasites disperse through realistically complex spatial graphs. Parasite virulence, a parasite life-history trait of central importance that here impacts host reproduction, is able to evolve. Our model therefore captures the eco-evolutionary feedback loop between host demography and parasite evolution in space. In order to gain a general understanding of parasite eco-evolution in space, we analyse our model for spatial networks that represent terrestrial (represented by random-geometric graphs; RGG) and riverine aquatic (represented by optimal channel networks; OCN) landscapes. We find that evolved virulence is generally a function of host dispersal, with a unimodal relationship in aquatic and a saturating relationship in terrestrial landscape, and this is driven by higher order network properies. Consistent with previous work, we show that our results are driven by kin selection, because dispersal and landscape structure impact both patterns of relatedness and availability of susceptible hosts. Our model yields readily testable predictions, including that terrestrial parasites should be more virulent than aquatic parasites are low dispersal rates and vice versa as dispersal increases. These differences in evolved virulence directly lead to differences in system stability, with more virulent parasites more often leading to host extinction. Thus, in this study we highlight the role of landscape structure in driving eco-evolutionary dynamics of parasites.

Venue: via Zoom

Event Official Language: English

Exploring 2D Quantum Spacetime Based on Causal Dynamical Triangulations

August 21 (Mon) - 23 (Wed), 2023

Yuki Sato (Associate Professor, National Institute of Technology, Tokuyama College)

This is the fourth event by the Quantum Gravity Gatherings (QGG) Study Group at RIKEN iTHEMS. For this event we have invited Prof. Yuki Sato, National Institute of Technology, Tokuyama College, to give pedagogical lectures on the causal dynamical triangulations approach to quantum gravity. We wish this event to provide insights to researchers in related fields. The causal dynamical triangulations formalism appears to be one of the most promising constructive approaches to quantum gravity: possessing deep links with the asymptotic safety programme and Hořava-Lifshitz gravity, causal dynamical triangulations appears to avoid many of the well-known pathologies characteristic of its Euclidean analogue. As an example the emergence of spacetime geometry remains possible in various spacetime dimensions. While many of the results in higher dimensions are understood only at the numerical level, the analytical study of the approach in two spacetime dimensions is relatively well developed; Yuki Sato is a leading expert on these latter developments and we are very lucky he has agreed to present the understanding of 2D causal spacetime coming from this approach in a manner consistent with the Quantum Gravity Gatherings philosophy. This intensive lecture series is intended to be a lively and participatory event, not just a listening experience. For this reason, the number of participants will be limited to about 30 with priority given to graduate students and young post-docs; the intensive talk will be given in a face-to-face blackboard style (in English, no online streaming) to allow for informal and lively Q&A discussions. The program will also include short talk sessions, where interested participants can give a 5 min talk on a topic of their choice (their research, reviews on some works, what they want to study in the future, etc.). Registration is available via the dedicated website.

Venue: #435-437, 4F, Main Research Building

Event Official Language: English

Mating system of buckwheat

August 17 (Thu) at 16:00 - 17:00, 2023

Jeffrey Fawcett (Senior Research Scientist, iTHEMS)

Buckwheat (soba in Japanese) has a slightly unusual mating system called heterostylous self-incompatibility where two types of individuals coexist, one that produces flowers with a long style (female part of the flower) and short stamen (male part of the flower), and the other that produces flowers with a short style and long stamen. Mating is only successful when it occurs between the different types of individuals. It is a bit similar to sexual dimorphism where males and females coexists but in this case all individuals have both male and female organs. In this talk, I will introduce the basics of this mating system in buckwheat and some work we have been doing. In particular, I will talk about its genetic architecture and some parallels observed with other plants in which a similar mating system evolved independently. The talk will be aimed at non-experts so non-biologists are also welcome to attend.

Venue: via Zoom

Event Official Language: English

Dark matter heating vs vortex creep heating in old neutron stars

August 7 (Mon) at 13:30 - 15:00, 2023

Motoko Fujiwara (Postdoctoral Researcher, Theoretical Particle Physics Group, Technical University of Munich, Germany)

Old isolated neutron stars have been gathering attention as targets to probe Dark Matter (DM) through temperature observations. DM will anomalously heat neutron stars through its gravitational capture and annihilation process, which predicts surface temperature as T_s ~ (1 − 3) × 10^3 K for t > 10^6 years. We may put constraints on DM-nucleon scattering cross section by finding even colder neutron stars. This story, however, assumed that there is no relevant heating source for old neutron stars. In this talk, we discuss the creep motion of vortex lines in the neutron superfluid of the inner crust as the heating mechanism. This creep mechanism is inherent in the structure of neutron stars. The heating luminosity is proportional to the time derivative of the angular velocity of the pulsar rotation, and the proportional constant J has an approximately universal value for each neutron star. If this vortex creep heating is quantitatively relevant against DM heating, this mechanism may cause a serious background to probe DM. The J parameter can be determined from the temperature observation of old neutron stars because the heating luminosity is balanced with the photon emission in the late time. We study the latest data of neutron star temperature observation and find that these data indeed give similar values of J, in favor of the assumption that these neutron stars are heated by the frictional motion of vortex lines. Besides, these values turn out to be consistent with the theoretical calculations of the vortex-nuclear interaction. Integarting all the results, we evaluate the vortex creep heating and conclude its significance against DM heating.

Venue: Seminar Room #359 (Main Venue) / via Zoom

Event Official Language: English

Quasi-local holography in 3d quantum gravity

August 4 (Fri) at 14:00 - 15:30, 2023

Etera Livine (Research Director CNRS, Ecole Normale Supérieure de Lyon, France)

Since the idea appeared in black hole physics, the concept of holography has become a guiding principle for quantum gravity. It is the notion that the dynamics of the geometry of a region of space-time can be entirely encoded in a theory living on its boundary. Although such holographic dualities have been well-developed in an asymptotical context, it remains a challenge to realize it exactly at finite distances. I will draw a possible route in 3d quantum gravity, by showing a duality between the Ponzano-Regge path integral for 3d quantum gravity as a topological field theory and the 2d (inhomogeneous) Ising model. This leads to an intriguing geometrical interpretation of the Ising critical couplings and opens the door to a possibly rich interplay between 3d quantum gravity and 2d condensed matter built out of holographic dualities.

Venue: Seminar Room #359 (Main Venue) / via Zoom

Event Official Language: English

Evidence against a strong first-order phase transition in neutron star cores: impact of new data

August 1 (Tue) at 13:30 - 15:00, 2023

Len Brandes (Ph.D. Student, Technical University of Munich, Germany)

Information on the phase structure of strongly interacting matter at high baryon densities can be gained from observations of neutron stars and their detailed analysis. Bayesian inference methods are used to set constraints on the speed of sound in the interior of neutron stars, based on recent multimessenger data in combination with low-density constraints based on chiral effective field theory and perturbative QCD constraints at asymptotically high densities. A detailed re-analysis is performed in order to clarify the influence of the latter constraints on the inference procedure. The impact of the recent new heavy (2.35 M_sol) black widow pulsar PSR J0952-0607 and of the unusually light supernova remnant HESS J1731-347 is inspected. One of the consequences of including PSR J0952-0607 in the database is a further stiffening of the equation-of-state, resulting in a 2.1 solar-mass neutron star in a reduced central density of less than five times the equilibrium density of normal nuclear matter. A systematic Bayes factor assessment quantifies the evidence (or non-evidence) for small sound speeds, necessary for a strong first-order phase transition, within the range of densities realized in the core of neutron stars. Given the presently existing database, it can be concluded that the occurrence of a strong first-order phase transition in the core of even a 2.1 solar-mass neutron star is unlikely, while a continuous crossover cannot be ruled out.

Venue: via Zoom (Main Venue) / Seminar Room #132

Event Official Language: English

Clifford Group and Unitary Designs under Symmetry

July 31 (Mon) at 14:00 - 15:30, 2023

Yosuke Mitsuhashi (Ph.D. student, Department of Applied Physics, Graduate School of Engineering, The University of Tokyo)

We have generalized the well-known statement that the Clifford group is a unitary 3-design into symmetric cases by extending the notion of unitary design. Concretely, we have proven that a symmetric Clifford group is a symmetric unitary 3-design if and only if the symmetry constraint is described by some Pauli subgroup. We have also found a complete and unique construction method of symmetric Clifford groups with simple quantum gates for Pauli symmetries. For the overall understanding, we have also considered physically relevant U(1) and SU(2) symmetry constraints, which cannot be described by a Pauli subgroup, and have proven that the symmetric Clifford group is a symmetric unitary 1-design but not a 2-design under those symmetries. Our findings are numerically verified by computing the frame potentials, which measure the difference in randomness between the uniform ensemble on the symmetric group of interest and the symmetric unitary group. This work will open a new perspective into quantum information processing such as randomized benchmarking, and give a deep understanding to many-body systems such as monitored random circuits.

Venue: #345-347, Main Research Building, RIKEN Wako Campus (Main Venue) / via Zoom

Event Official Language: English

Higher Algebra in Geometry

July 31 (Mon) - August 10 (Thu), 2023

Hiro Lee Tanaka (Assistant Professor, Department of Mathematics, Texas State University, USA)

In these lectures, we will shed light on modern tools of higher algebra, where the traditional structures of algebra yield themselves only after controlled deformations. We will introduce infinity-categories, spectra, operads, and other standard tools of the last decade. The main applications will be to encode various higher-algebraic structures that inevitably arise in, and shed light on, geometry and topology. If time permits, we will illustrate how spectra naturally arise in geometric invariants. The audience is imagined to consist of mathematicians interested in applications of infinity-categorical tools -- so a broad range of geometers (including topologists) and algebraists. From Lecture Two onward, I will assume basic knowledge of algebraic topology (e.g., the material of Hatcher) and homological algebra. These lectures will be held between July 31 and August 10, each from 10:30 to 12:00, for a total of 8 lectures. 1st Week: Jul 31(mon), Aug 1(tue) - 3(thu) - Introduction to ideas of higher algebra in geometry, for a general audience. - Introduction to infinity-categories and to spectra. 2nd Week: Aug 7(mon) - 10(thu) - Examples in geometry and topology, including invariants of Legendrian links and generating functions. - Future Directions. Profile: Hiro Lee Tanaka is an assistant professor in the Department of Mathematics. After receiving his Ph.D. from Northwestern University and completing postdoctoral work at Harvard University, he conducted research at the Mathematical Sciences Research Institute in Berkeley, California, and at the Isaac Newton Institute in Cambridge, England. His research aims to fuse the higher structures in modern algebra with geometries emerging from both classical mechanics and supersymmetric field theories. Beyond research, Tanaka engages in efforts to create more equitable and supportive environments throughout the mathematics community.

Venue: #435-437, Main Research Building / via Zoom

Event Official Language: English