Seminar
716 events
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Seminar
RNA-Puzzles - the evaluation and automation of RNA 3D structure
November 24 (Thu) at 16:00 - 17:00, 2022
Zhichao (Chichau) Miao (Principal Investigator, Guangzhou Laboratory, China / Guangzhou Medical University, China)
RNA-Puzzles is a collective endeavour dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are predicted by various groups before the publication of the crystal structures. Systematic protocols for comparing models and crystal structures are described and analyzed. In RNA-Puzzles, we discuss a) the capabilities and limitations of current methods of 3D RNA structure based on sequences; b) the progress in RNA structure prediction; c) the possible bottlenecks that hold back the field; d) the comparison between the automated web server and human experts; e) the prediction rules, such as coaxial stacking; f) the prediction of structural details and ligand binding; g) the development of novel prediction methods; and h) the potential improvements to be made. Till now, 37 RNAs with crystal structures have been predicted, while many of them have achieved high accuracy in comparison with the crystal structures. We have summarized part of our results in three papers and two community-wide meetings. With the results in RNA-Puzzles, we illustrate that the current bottlenecks in the field may lie in the prediction of non-Watson-Crick interactions and the reconstruction of the global topology. Correct coaxial stacking and tertiary contacts are key for the prediction of RNA architecture, while ligand binding modes can only be predicted with low resolution. For the model evaluation, we present RNA-Puzzles toolkit, a computational resource including (i) decoy sets generated by different RNA 3D structure prediction methods, (ii) 3D structure normalization, analysis, manipulation, visualization tools and (iii) 3D structure comparison metric tools. With the increasing number of RNA structures being solved as well as the high-throughput biochemical experiments, RNA 3D structure prediction is becoming routine and accurate. Structure modelling may effectively help in understanding the viral RNA structures, including the SARS-CoV-2.
Venue: via Zoom
Event Official Language: English
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Seminar
Energy partition in Weibel-mediated shock waves: from Supernova Remnants to Gamma-Ray Bursts
November 24 (Thu) at 14:00 - 15:00, 2022
Arno Vanthieghem (Princeton-NINS Postdoctoral Research Fellow, Department of Astrophysical Sciences, Princeton University, USA)
Gamma-ray bursts and supernovae provide ideal environments for efficient energy channeling between different plasma species through collective processes such as collisionless shock waves. Extensively studied in astrophysical and laboratory environments, observations and kinetic simulations indicate strong electron heating in the precursor of collisionless shock waves propagating in unmagnetized electron-ion plasmas. We outline a theoretical model accounting for electron heating via a Joule-like process through the interplay between pitch-angle scattering in the microturbulence and the coherent electrostatic field induced by the difference in inertia between species. Using analytical kinetic estimates, semi-analytical Monte Carlo methods, and ab-initio Particle-In-Cell simulations, we demonstrate the validity of this model in the relativistic regime relevant to the afterglow emission of gamma-ray burst and extend it to characterize the electron-to-ion-temperature ratio in the downstream of nonrelativistic high-Mach numbers shock waves relevant for supernova remnants and laboratory experiments.
Venue: via Zoom
Event Official Language: English
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Seminar
Tetra and pentaquarks with multi-flavor contents
November 22 (Tue) at 13:30 - 15:00, 2022
Atsushi Hosaka (Professor, Research Center for Nuclear Physics, Osaka University)
Recent hadron experiments keep providing evidences of exotic hadrons with multi-quark components. These multiquarks are self-arranged into various configurations such as diquarks, hadronic molecules and so on. In this seminar, we discuss possible structures of tetra and pentaquarks with multi-flavor contents including recently observed T_cc, Pc and P_cs. Based on our recent studies in the quark model and hadron models, we discuss where and how different quark structures emerge.
Venue: Hybrid Format (Common Room 246-248 and Zoom)
Event Official Language: English
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Seminar
Mathematics of Post-Quantum Cryptography
November 18 (Fri) at 14:00 - 16:30, 2022
Yusuke Aikawa (Researcher, Information Technology R&D Center, Mitsubishi Electric Corporation)
Cryptography keeps our everyday information communications secure. Cryptography based on key sharing have been used mainly for military purposes since ancient times in human history, but with the advent of the Internet, cryptography that does not require key sharing has become necessary. In 1976, Diffie and Hellman proposed the concept of public key cryptography, which does not require key sharing among communicators. Since then, research on public key cryptography has progressed, involving not only computer science but also mathematics, and has become an essential technology for the society we live in. The security of public key cryptography is supported by computational hardness of problems derived from mathematics. For example, the integer factoring problem is a basis for the security of RSA cryptography, and the discrete logarithm problem is for elliptic curve cryptography. However, in 1994, Shor proposed an efficient quantum algorithm that solves these problems. This means that emergence of large-scale quantum computers will break RSA and elliptic curve cryptography we use today. For this reason, research on next-generation cryptography, so-called Post-Quantum Cryptography (PQC for short), is currently underway to prepare for a future in which quantum computers will emerge. In this talk, without assuming any knowledge of cryptography, I will give a brief overview of cryptography and the progress of PQC. The first half of the talk will mainly outline the relationship between mathematics and cryptography, while the second half will discuss isogeny-based cryptography, one of the promising PQC, with our recent results.
Venue: Hybrid Format (Common Room 246-248 and Zoom)
Event Official Language: English
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Seminar
Emergence of growth and dormancy from a kinetic model of the Escherichia coli central carbon metabolism
November 17 (Thu) at 18:00 - 19:00, 2022
Yusuke Himeoka (Assistant Professor, Universal Biology Institute, The University of Tokyo)
Physiological states of bacterial cells exhibit a wide spectrum of timescale. Under nutrient-rich conditions, most of the cells in an isogenic bacterial population grow at certain rates, while a small subpopulation sometimes stays in a dormant state where the growth rates slow down by orders of magnitude. For revealing the origins of such heterogeneity of timescales, we studied the kinetic model of Escherichia coli central carbon metabolism. We found that the model robustly exhibits both the growing- and the dormant state. Performing the model reduction, we have revealed the necessary conditions for the distinct behaviour, namely, the depletion of energy due to the futile cycle and its non-uniform impact on the kinetics because of the coexistence of the energy currency-coupled and uncoupled reactions as well as branching of the network.
Venue: via Zoom
Event Official Language: English
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Seminar
Merger and post-merger of binary neutron stars with a quark-hadron crossover equation of state
November 15 (Tue) at 15:00 - 17:01, 2022
Yongjia Huang (Ph.D. Student, University of Science and Technology of China, China)
The state of the ultra-dense matter remains one of the long-standing open questions. Neutron star (NS), as it cools down the eons ahead after the birth in the supernova explosion, provides an astrophysical laboratory to investigate the dense, strongly interacting nuclear matter at zero temperature. On the other hand, the most intense gravitational wave(GW) radiation is produced in regions of the strong gravitational field by coherent movements of masses with large compactness. Therefore, GW from binary neutron star(BNS) merger naturally contains the information from the ultra-dense matter. In this talk, I will introduce our recent work, "Merger and post-merger of binary neutron stars with a quark-hadron crossover equation of state ."Quark-hadron crossover(QHC) is one way of hadron-quark transition, which generally predicts a peak in sound speed vs. density, and so releases more pressure during the hadron-quark transition. I will first briefly summarize the features of QHC EOS and the BNS merger. I will then focus on how information on the hadron-quark transition shows in the GW and its spectrum during the BNS merger.
Venue: via Zoom
Event Official Language: English
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Seminar
Expanding Edges of Quantum Hall Systems in a Cosmology Language - Hawking Radiation from de Sitter Horizon in Edge Modes
November 11 (Fri) at 16:00 - 17:30, 2022
Masahiro Hotta (Assistant Professor, Department of Physics, Graduate School of Science, Tohoku University)
Expanding edge experiments are promising to open new physics windows of quantum Hall systems. In a static edge, the edge excitation, which is described by free fields decoupled with the bulk dynamics, is gapless, and the dynamics preserve conformal symmetry. When the edge expands, such properties need not be preserved. We formulate a quantum field theory in 1+1 dimensional curved spacetimes to analyze the edge dynamics. We propose methods to address the following questions using edge waveforms from the expanding region: Does the conformal symmetry survive? Is the nonlinear interaction of the edge excitations induced by edge expansion? Do the edge excitations interact with the bulk excitations? We additionally show that the expanding edges can be regarded as expanding universe simulators of two-dimensional dilaton-gravity models, including the Jackiw-Teitelboim gravity model. As an application, we point out that our theoretical setup might simulate emission of analog Hawking radiation with the Gibbons-Hawking temperature from the future de Sitter horizon formed in the expanding edge region.
Venue: #345-347, 3F, Main Research Building (Main Venue) / via Zoom
Event Official Language: English
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Seminar
Arithmetic dynamics on algebraic varieties
November 11 (Fri) at 14:00 - 16:30, 2022
Yosuke Matsuzawa (Associate Professor, Department of Mathematics, Graduate School of Science, Osaka Metropolitan University)
The study of self-maps of algebraic varieties is a relatively new and active area in mathematics. Such a self-map can be considered as a discrete dynamical system, and we can study the asymptotic properties of such systems from various points of views, including number theoretic viewpoint. I will introduce several problems in arithmetic dynamics and some of my results in this area.
Venue: Hybrid Format (Common Room 246-248 and Zoom)
Event Official Language: English
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Seminar
Sociogenesis: motivations and first steps
November 10 (Thu) at 16:00 - 17:00, 2022
Cédric Ho Thanh (Postdoctoral Researcher, Prediction Science Laboratory, RIKEN Cluster for Pioneering Research (CPR))
Sociogenesis is a project that aims to study emergent social behaviors of multi-agent systems. In its simplest form, and agent simply seeks to survive by consuming food and maximizing some happiness score. In this presentation, I will discuss some motivations and inspirations of this project, as well as the challenges to get an agent to survive on its own. I will then showcase some methods to evaluate the quality of agents and their underlying architecture beyond simply looking at their lifespan. I will then conclude with some potential applications. No prior knowledge in reinforcement/deep learning is required to attend this presentation. This work is still mostly at an exploratory stage, so discussions and inputs from the audience are more than welcome!
Venue: via Zoom
Event Official Language: English
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Seminar
Tensor renormalization group approach to quantum fields on a lattice
November 8 (Tue) at 13:30 - 15:00, 2022
Shinichiro Akiyama (Specially Appointed Assistant Professor, Quantum Software Project, The University of Tokyo)
Tensor renormalization group (TRG) approach is a variant of the real-space renormalization group to evaluate the path integral defined on the thermodynamic lattice, without resorting to any probabilistic interpretation for the given Boltzmann weight. Moreover, since the TRG can directly deal with the Grassmann variables, this approach can be formulated in the same manner for the systems with bosons, fermions, or both. These advantages of the TRG approach have been confirmed by the earlier studies of various lattice theories, which suggest that the TRG enables us to investigate the parameter regimes where it is difficult to access with the standard stochastic numerical methods, such as the Monte Carlo simulation. In this talk, explaining our recent applications of the TRG approach to several lattice models, we demonstrate the efficiency of the TRG as a tool to investigate lattice theories particularly in higher dimensions and future perspective.
Venue: Hybrid Format (Common Room 246-248 and Zoom)
Event Official Language: English
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Seminar
UHECR anisotropy: effects of the Galactic magnetic field on the UHECR correlation studies
November 4 (Fri) at 14:00 - 15:00, 2022
Ryo Higuchi (Special Postdoctoral Researcher, Astrophysical Big Bang Laboratory, RIKEN Cluster for Pioneering Research (CPR))
Telescope Array (TA) and Auger experiments reported anisotropies in the arrival direction of ultra-high-energy cosmic rays (UHECRs). In the current correlation studies between UHECRs and source candidates, the Auger experiment reported a correlation between the flux model of assumed sources and UHECR events and suggested a 10% contribution of starburst galaxies (SBGs) to the anisotropy of UHECRs. However, they do not consider the effect of coherent deflection by the galactic magnetic field (GMF), and they should significantly affect the results of the correlation studies. In this talk, we introduce a current study of UHECR anisotropy and the effect of GMF on them.
Venue: via Zoom
Event Official Language: English
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Seminar
Gamma-ray emission from the Sagittarius Dwarf Spheroidal galaxy due to millisecond pulsars
October 28 (Fri) at 17:00 - 18:00, 2022
Oscar Macias (Faculty of Science, University of Amsterdam, Netherlands)
The Fermi Bubbles are giant, gamma-ray emitting lobes emanating from the nucleus of the Milky Way discovered in ~1-100 GeV data collected by the Fermi Gamma-Ray Space Telescope. Previous work has revealed substructure within the Fermi Bubbles that has been interpreted as a signature of collimated outflows from the Galaxy's super-massive black hole. In this talk, I will show that much of the gamma-ray emission associated to the brightest region of substructure -- the so-called cocoon -- is likely due to the Sagittarius dwarf spheroidal (Sgr dSph) galaxy. This large Milky Way satellite is viewed through the Fermi Bubbles from the position of the Solar System. As a tidally and ram-pressure stripped remnant, the Sgr dSph has no on-going star formation, but I will demonstrate that the dwarf's millisecond pulsar (MSP) population can plausibly supply the observed gamma-ray signal. This finding plausibly suggests that MSPs produce significant gamma-ray emission amongst old stellar populations, potentially confounding indirect dark matter searches in regions such as the Galactic Centre, the Andromeda galaxy, and other massive Milky Way dwarf spheroidals.
Venue: via Zoom
Event Official Language: English
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Seminar
Measuring diversity: species similarity
October 28 (Fri) at 16:00 - 17:00, 2022
Tom Leinster (Professor, University of Edinburgh, UK)
Traditional measures of the diversity of an ecological community depend only on how abundant the species are, not the similarities or differences between them. To better reflect biological reality, species similarity should be incorporated. Mathematically, this corresponds to moving from probability distributions on sets to probability distributions on metric spaces. I will explain how to do this and how it can change ecological judgements. Finally, I will describe a surprising theorem on maximum diversity (joint with Meckes and Roff), which reveals close connections between maximum diversity and invariants of geometric measure.
Venue: via Zoom
Event Official Language: English
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Seminar
Migration dynamics and model of cells crawling on a matrix with cell-scale stiffness heterogeneity
October 27 (Thu) at 16:00 - 17:00, 2022
Hiroyuki Ebata (Assistant Professor, Graduate School of Science, Kyushu University)
In living tissues where cells migrate, spatial distribution of mechanical properties, especially matrix stiffness, are generally heterogenous with cell-scales ranging from 10 to 1000 μm. Since the cell migration in our body plays critical role in morphogenesis, wound healing, and cancer metastasis, it is essential to understand the migratory dynamics on the matrix with cell-scale stiffness heterogeneity. However, while cellular responses to homogeneous matrix have been extensively explored, studies of the cell motility with stiffness heterogeneity have been limited to the directional movement (durotaxis) driven by a simple stiffness gradient. Thus, we need to elucidate how cell migration is determined through the interaction among cell-scale stiffness heterogeneity and cellular responses such as dynamics of the cell-matrix adhesion site, the intracellular prestress, and cell shape. In this talk, we introduce our experiments on cell motility, shaping, adhesion, and traction forces at long time scales using microelastically patterned hydrogels that enable us to systematically control the cell-scale heterogeneity of the matrix-stiffness. Using microelastically patterned hydrogels, we showed that the cell exhibited a general mode of durotaxis depending on the shape and size of the stiff domains, which was coincided with the extraordinarily large fluctuation of the traction force. We proposed a cell migration model based on equations of a deformable self-propelled particle adopting an amoeboid swimmer-like velocity-shape relationship. By considering the cellular response to stiffness gradients, the model can reproduce general durotaxis driven by cell-scale heterogeneity of the matrix-stiffness.
Venue: via Zoom
Event Official Language: English
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Seminar
Measuring diversity: the axiomatic approach
October 21 (Fri) at 16:00 - 17:00, 2022
Tom Leinster (Professor, University of Edinburgh, UK)
Ecologists have been debating the best way to measure diversity for more than 50 years. The concept of diversity is relevant not only in ecology, but also in other fields such as genetics and economics, as well as being closely related to entropy. The question of how best to quantify diversity has surprising mathematical depth. I will argue that the best approach is axiomatic: to enable us to reason logically about diversity, the measures we use must satisfy certain mathematical conditions, and those conditions dramatically limit the choice of measures. This point will be illustrated with a theorem: using a simple model of ecosystems, the only diversity measures that behave logically are the Hill numbers, which are very closely related to the Rényi entropies of information theory.
Venue: via Zoom
Event Official Language: English
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Seminar
How can interspecific pollen transfer affect coexistence and evolution of sex ratio of two closely related plant species?
October 20 (Thu) at 16:00 - 17:00, 2022
Keiichi Morita (Ph.D. Student, School of Advanced Sciences Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies (SOKENDAI))
In co-flowering species with shared pollinators, interspecific pollen transfer (IPT) may occur, in which pollen grains are transferred between different species. Yet, it is unclear how the costs of IPT in reduced pollen grains (i.e., costs for males) and seed set (i.e., costs for females) can affect coexistence and evolution of sex ratio. We investigated the conditions for which two closely related plants can coexist and of evolution in sex ratio, by constructing a theoretical model that incorporates the dynamics of population, pollen export, pollen reception on an ovule, and seed production in two closely related plants with resource competition and IPT. The model analysis revealed that coexistence is likely with infrequent IPT, α, and weak interspecific resource competition, β, and high production rates of pollen, Am, and ovules, Af. Also, we found a trade-off where too low value of either Am or Af makes both species go extinct. Furthermore, even when α and β were small enough, too low Am and Af made extinction of both species likely, because of the Allee effect due to resource competition and interspecific pollen competition for a small number of ovules. Adaptive dynamics, analysis of evolutionary dynamics showed that sex ratio evolve to 1:1 as the optimum allocation of resource to produce pollen grains and ovules.
Venue: via Zoom
Event Official Language: English
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Seminar
Quantum nucleation of topological solitons
October 20 (Thu) at 13:30 - 15:00, 2022
Minoru Eto (Professor, Faculty of Science, Yamagata University)
The chiral soliton lattice is an array of topological solitons realized as ground states of QCD at finite density under strong magnetic fields or rapid rotation, and chiral magnets with an easy-plane anisotropy. In such cases, topological solitons have negative energy due to topological terms originating from the chiral magnetic or vortical effect and the Dzyaloshinskii-Moriya interaction, respectively. We study quantum nucleation of topological solitons in the vacuum through quantum tunneling in 2+1 and 3+1 dimensions, by using a complex ϕ4 (or the axion) model with a topological term proportional to an external field, which is a simplification of low-energy theories of the above systems. In 2+1 dimensions, a pair of a vortex and an anti-vortex is connected by a linear soliton, while in 3+1 dimensions, a vortex is string-like, a soliton is wall-like, and a disk of a soliton wall is bounded by a string loop. Since the tension of solitons can be effectively negative due to the topological term, such a composite configuration of a finite size is created by quantum tunneling and subsequently grows rapidly. We estimate the nucleation probability analytically in the thin-defect approximation and fully calculate it numerically using the relaxation (gradient flow) method. The nucleation probability is maximized when the direction of the soliton is perpendicular to the external field.
Venue: via Zoom
Event Official Language: English
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Seminar
An Introduction to Rough Geometry (with a view to Euclidean Gravity)
October 14 (Fri) at 14:00 - 16:30, 2022
Christy Koji Kelly (Special Postdoctoral Researcher, iTHEMS)
The mathematical formulation of Einstein gravity typically utilises differentiable manifolds as models of smooth spacetimes. In many scenarios, however, it is desirable to have coarser models of spacetime and a correspondingly rough theory of geometry applicable to these coarser spacetime structures. In 2D Euclidean quantum gravity, for instance, the use of Regge calculus allows one to treat triangulations as regularisations of smooth spacetimes. There has been much recent progress in the mathematical (rigorous) understanding of this theory which we briefly review. We also introduce a rich alternative framework for the study coarse Euclidean geometry in the form of metric geometry augmented by optimal transport theory. In particular we introduce several optimal transport theoretic curvatures and demonstrate that these recover the familiar smooth notions under suitable limits.
Venue: Hybrid Format (Common Room 246-248 and Zoom)
Event Official Language: English
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Seminar
Introduction to cepstrum analysis and its applications
October 13 (Thu) at 16:00 - 17:00, 2022
Shingo Gibo (Postdoctoral Researcher, iTHEMS)
Recent advances in experimental technique enable us to obtain many time-series data of biological oscillatory systems. These time-series are of various shapes, which means that the envelop of spectrum are also various. Cepstrum analysis is well-known method for evaluating the spectrum shapes in acoustic engineering. In this talk, I will introduce cepstrum analysis and its applications for analyzing biological oscillations.
Venue: via Zoom
Event Official Language: English
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Seminar
Ultra-Light Axion Dark Matter: Bose-Einstein condensates and superfluids in the sky
October 11 (Tue) at 13:30 - 15:00, 2022
Elisa G.M. Ferreira (Project Assistant Professor, Kavli Institute for the Physics and Mathematics of the Universe (Kavli IPMU), The University of Tokyo)
The nature of dark matter (DM) is one of the biggest mysteries in cosmology. There are many different models to explain the nature of this elusive component. In this talk I will present a class of dark matter models: ultra-light dark matter (ULDM) or ultra-light axions (ULA). I will show the different models present in the literature and classify them according to the way they behave on small scales. One of the most interesting features of this class of DM models is that it might condense in the interior of the halos of galaxies forming a Bose-Einstein condensate (BEC) or superfluid. This interesting quantum phenomena on macroscopic scales, and the wave nature of ULDM leads to different and interesting astrophysical consequences that can be probed on small scales. I will quickly review first the fuzzy dark matter model, one of the most well studied ULA models, where I will present its description, predictions and current bounds. Then I will introduce the DM superfluid model, where, upon condensation in the interior of galaxies, DM dynamics represents that of MOdified Newtonian Dynamics (MOND) on galactic scales. This behaviour can address some of the curiosities of the behaviour of DM on small scales. I plan to show the theoretical description of this model and its interesting phenomenology.
Venue: Hybrid Format (Common Room 246-248 and Zoom)
Event Official Language: English
716 events