Population genetics in microchannels

October 17 (Tue) at 16:00 - 17:00, 2023

Anzhelika Koldaeva (Postdoctoral Researcher, Biological Complexity Unit, Okinawa Institute of Science and Technology Graduate University (OIST))

Spatial constraints, such as rigid barriers, affect the dynamics of cell populations, potentially altering the course of natural evolution. In this paper, we investigate the population genetics of Escherichia coli proliferating in microchannels with open ends. Our analysis is based on a population model, in which reproducing cells shift entire lanes of cells toward the open ends of the channel. The model predicts that diversity is lost very rapidly within lanes but at a much slower pace among lanes. As a consequence, two mixed, neutral E. coli strains competing in a microchannel must organize into an ordered regular stripe pattern in the course of a few generations. These predictions are in quantitative agreement with our experiments. We also demonstrate that random mutations appearing in the middle of the channel are much more likely to reach fixation than those occurring elsewhere. Our results illustrate fundamental mechanisms of microbial evolution in spatially confined space.

Venue: via Zoom

Event Official Language: English

Do higher-order interactions promote coexistence in diverse ecological communities?

October 10 (Tue) at 10:00 - 11:00, 2023

Theo Gibbs (Ph.D. Student, Lewis-Sigler Institute for Integrative Genomics, Princeton University, USA)

A central assumption in most ecological models is that the interactions in a community operate only between pairs of species. However, two species may interactively affect the growth of a focal species. Although interactions among three or more species, called higher-order interactions, have the potential to modify our theoretical understanding of coexistence, ecologists lack clear expectations for how these interactions shape community structure. In this talk, I will analyze two different sets of assumptions for how higher-order interactions impact the dynamics of competing species and show that they lead to differing outcomes. When higher-order interactions are sampled from unconstrained probability distributions, they are unlikely to generate widespread coexistence. In fact, using an analytical technique from statistical physics, I will show many — though not all — of the qualitative rules derived for pairwise interactions still apply to the higher-order case. Higher-order interactions that have specific relationships with the underlying pairwise interactions, however, can stabilize coexistence in diverse communities. I will conclude by briefly discussing ongoing experimental work that seeks to determine whether or not the dynamics of annual plant communities are structured by higher-order interactions.

Venue: via Zoom

Event Official Language: English

Neutrino production in AGN cores: Constraints from Kinetic Plasma Simulations

October 6 (Fri) at 14:00 - 15:15, 2023

Amir Levinson (Professor, Tel Aviv University, Israel)

Accreting black holes power a variety of high-energy astrophysical systems. The activation and mode of operation of these engines has been subject of intensive research. In recent years the structure of the multi-flow emanating from the putative, giant black hole in the M87 galaxy was probed down to near horizon scales in unprecedented detail, shedding new light on the physics of accretion and the processes responsible for the formation and dissipation of relativistic jets by the black hole. I shall review recent progress in observational and theoretical studies of accreting black hole engines.

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

Event Official Language: English

Progenitors and Explosion Properties of Supernova Remnants Hosting Central Compact Objects

October 6 (Fri) at 10:00 - 11:30, 2023

Chelsea Braun (Ph.D. Student, Department of Physics and Astronomy, University of Manitoba, Canada)

Presented is a systematic, global study of Galactic supernova remnants (SNRs) hosting Central Compact Objects (CCOs) aimed at addressing their explosion properties and supernova progenitors. With the Chandra and XMM-Newton telescopes, a spatially resolved X-ray spectroscopy study is performed on seven SNRs that show evidence of shock-heated ejecta. Using an algorithm, we segmented each SNR in the sample into regions of similar surface brightness. These regions were fit with one- or two-component plasma shock model(s) in order to separate the forward-shocked interstellar medium from the reverse shock-heated ejecta which peak in the X-ray bands for elements including O, Ne, Mg, Si, S, Ar, Ca, and Fe. We subsequently derived the explosion properties for each SNR in the sample and found overall low explosion energies (<10^51 erg). To address their progenitor mass, we compare the measured abundances from our spectroscopic modelling to five of the most widely used explosion models and a relatively new electron-capture supernova model. Additionally, we explore degeneracy in the explosion energy and its effects on the progenitor mass estimates. However, no explosion models match all of the measured ejecta abundances for any of the SNRs in our sample. Therefore, we present our best progenitor mass estimates and find overall low progenitor masses (<=25 solar masses) and we highlight the discrepancies between the observed data and the theoretical explosion models.

Venue: via Zoom

Event Official Language: English

How is host-symbiont specificity determined? ---Host’s partner-choice mechanisms and symbiont’s motility

October 3 (Tue) at 16:00 - 17:00, 2023

Yoshitomo Kikuchi (Group Leader, Environmental Biofunction Research Group, National Institute of Advanced Industrial Science and Technology (AIST))

Microbial symbiosis is omnipresent in animals and plants, playing a crucial role in the evolution of these organisms. While some organisms have developed mechanisms for vertical symbiont transmission, in most cases, these microbial partners are acquired from the surrounding environment, where the enormously diverse microorganisms inhabit. How, then, do these hosts ensure specificity with their symbiotic partners among such diverse environmental microorganisms? And how has this host-symbiont specificity evolved? We are addressing these questions using the bean bug Riptortus pedestris as our model. The insect acquires Caballeronia insecticola from the soil and symbioses with it in the gut crypts. Recently, we revealed that the entrance to the gut symbiotic organ is a narrow tube, just a few micrometers in diameter, filled with a mucus-like matrix. This constricted region helps the host insect select the symbiotic bacterium from the many other soil microbes. Notably, to pass through the constricted region, Caballeronia shows a unique motility called “drill motility”, where the bacterium wraps its flagella around its body. In this presentation, I will introduce the evolutionary process of both host insects and symbiotic bacteria and will discuss the pivotal role played by bacterial motility in the context of host-symbiont specificity.

Venue: via Zoom

Event Official Language: English

Interactions between Algebraic Topology and Representation Theory by Toric Code

October 2 (Mon) - 4 (Wed), 2023

Minkyu Kim (Research Fellow, School of Mathematics, Korea Institute for Advanced Study (KIAS), Republic of Korea)

Toric code is an error correction code designed by Kitaev in late 1990’s, which contributes to the birth of topological quantum computation. The goal of these lectures is to introduce toric code and related mathematics. We will explain an interaction between low-dimensional topology and representation of Drinfeld double. Especially, we will encode several operations (e.g. braidings) on representations into topology and geometry on surfaces. If time allows, we will give an overview of how toric code arises from chain complexes, which will be the prequel of our talk at Tokyo-Seoul Conference on Oct 6. These lectures will be fundamental and concrete. We hope that the audience are familiar with basic concepts of finite groups and Hopf algebras. These lectures will be held from Oct 2 to Oct 4, each from 13:30 to 15:00, for a total of 3 lectures. Oct 2 (mon) Introduction to toric code. Oct 3 (tue) Introduction to non-abelian toric code. Oct 4 (wed) Further studies on toric code.

Venue: via Zoom / Seminar Room #359

Event Official Language: English

The 4th "Medicine and Mathematics" Workshop

September 29 (Fri) - 30 (Sat), 2023

We will have the 4rd workshop on "Medicine and Math" in Sendai (hybrid style) on Sep.29-30, 2023. Please join if you are interested in this interdisciplinary subject. Most of the talks are in Japanese except for session 4. For more information and registration, please visit the related links. For more information and registration, please visit the related links. Co-organized by: Center for Integrative Medicine and Physics, Kyoto University Institute for Advanced Study (KUIAS) Center for Science Adventure and Collaborative Research Advancement (SACRA), Kyoto University Tohoku Forum of Creativity, Tohoku University RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS)

Venue: TOKYO ELECTRON House of Creativity, Katahira Campus, Tohoku University / via Zoom

Response to sounds in the cochlea of the inner ear

September 26 (Tue) at 16:00 - 17:00, 2023

Takeru Ota (Assistant Professor, Division of Glocal Pharmacology, Department of Pharmacology, Graduate School of Medicine, Osaka University)

We hear sounds. The acoustic wave passes through the ear canal and oscillates the ear drum. The middle ear bones conduct the mechanical input into the cochlea, the primary sensory organ of hearing. A sensory epithelium, a sheet-like tissue inside the snail-like structure, decomposes the sound frequencies into each component along the coil. The sound stimulation evokes nanometer-scale motions in the epithelium which contains hair cells. The cells expose their hair bundles to endolymph, the extracellular solution characterized by high [K+]. The epithelium vibration changes the open probability of mechanosensitive channels on the bundles and modulates the ion entering from the fluid. Inner hair cells release neurotransmitters to the auditory nerves and outer hair cells shrink and elongate their soma depending on the receptor potentials. The electromotive response amplifies the vibration of the sensory epithelium and contributes to the faint sound sensitivity and sharp frequency selectivity. With developed technique, we observed the sound-evoked vibrations in the sensory epithelium. In this seminar, I will introduce the physiological background of the cochlear physics and the recent results.

Venue: via Zoom

Event Official Language: English

Thermal production eV dark matter with bose-enhancement

September 25 (Mon) at 15:00 - 16:30, 2023

Wen Yin (Assistant Professor, Department of Physics, Graduate School of Science, Tohoku University)

A very simple production mechanism of feebly interacting dark matter (DM) that rarely annihilates is thermal production, which predicts the DM mass around eV. This has been widely known as the hot DM scenario. Despite there are several observational hints from background lights suggesting a DM in this mass range, the hot DM scenario has been considered strongly in tension with the structure formation of our Universe. In this talk, I show that the previous conclusions are not always true depending on the reaction for bosonic DM because of the Bose-enhanced reaction at very low momentum. By utilizing a simple $1 \leftrightarrow 2$ decay/inverse decay process to produce DM, I demonstrate that eV range bosonic DM can be thermally produced in a cold manner from a hot plasma. I also discuss some caveats arising from this phenomenon in the freeze-in production of DM, and present a related system that can suppress the hot plasma with thermal reaction.

Venue: via Zoom

Event Official Language: English

First X-ray polarimetry of neutron stars with strong magnetic fields

September 25 (Mon) at 13:30 - 15:00, 2023

Toru Tamagawa (Chief Scientist, High Energy Astrophysics Laboratory, RIKEN Cluster for Pioneering Research (CPR))

We launched the world's first highly sensitive X-ray polarimetry satellite, IXPE, in December 2021. IXPE began observations in January 2022 and detected significant X-polarization from objects in all categories. The IXPE observations have opened a new window in astrophysics. In this talk, I will introduce IXPE and present the results of X-ray polarimetry observations of neutron stars with strong magnetic fields (magnetars and neutron star binaries). The neutron star observations show results quite different from our prior expectations and await further theoretical interpretation.

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

Event Official Language: English

Induced gravitational waves from inflaton oscillons

September 22 (Fri) at 14:00 - 15:30, 2023

Kaloian Dimitrov Lozanov (Project Researcher, Kavli Institute for the Physics and Mathematics of the Universe (Kavli IPMU), The University of Tokyo)

We present a new way to study cosmic inflation with gravitational waves. The gravitational signal is generated thanks to nonlinear structures in the inflaton field, called oscillons. This novel probe allows us to test models of inflation which are challenging to test with CMB experiments.

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

Event Official Language: English

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, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (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

Venue: 3rd floor public space, Main Research Building

Event Official Language: English