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359 イベント

Coarsegrained molecular dynamics simulation via Langevin simulation
2022年4月14日10:00  11:00
横田 宏 (数理創造プログラム 特別研究員)
In the cell biology or biophysics, many mechanical properties of proteins or DNA are discussed. In order to consider the dynamics, coarsegrained molecular dynamics simulation (Langevin simulation) is useful. In this seminar, I will give you the introductory and methodology talk about the Langevin simulation.
会場: via Zoom
イベント公式言語: 英語

セミナー
iTHEMS  Kyoto University Joint Seminar: Singletrajectory map equation
2022年4月1日8:30  10:00
川本 達郎 (国立研究開発法人産業技術総合研究所 (AIST) 人工知能研究センター 研究員)
This seminar is a joint seminar of Blockchain research group in Kyoto University and EcoP WG in iTHEMS.
会場: via Zoom
イベント公式言語: 英語

Journal Club: Phase separation in a manycomponent system with random interactions
2022年3月31日10:00  11:00
足立 景亮 (理化学研究所 生命機能科学研究センター (BDR) 生体非平衡物理学理研白眉研究チーム 基礎科学特別研究員)
Several kinds of protein condensates have been observed in living cells, and the liquidliquid phase separation is regarded as a basic mechanism of the condensate formation. However, given that there are thousands of protein species in a cell, it is not clear how the number and the composition of distinct condensates are controlled. One of the physics approaches to this problem is considering a model of many components with random interactions. In this Journal Club, I will introduce a recent paper [1] that applies randommatrix theory to the phase separation dynamics.
会場: via Zoom
イベント公式言語: 英語

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Hydrodynamic theory of electron and spin transport
2022年3月30日13:30  15:00
多々良 源 (理化学研究所 創発物性科学研究センター (CEMS) スピン物性理論研究チーム チームリーダー)
Electron and spin transports in metals are theoretically studied from a hydrodynamic viewpoint by calculating momentum flux density as a linear response to an applied electric field. Dissipative (ohmic) fluid regime is considered. An angular momentum generation in chiral (Weyl) system and spin motive force (voltage generation) by magnetizationvorticity coupling in anomalous Hall system are discussed. The spin Hall effect is argued from the viewpoint of a spinvorticity coupling.
会場: via Zoom
イベント公式言語: 英語

セミナー
Local and global topology for Dirac points with multihelicoid surface states
2022年3月24日17:00  18:15
Dr. Tiantian Zhang (東京工業大学 理学院 特任助教)
Though topological invariants defined for topological semimetals are usually local ones, they also have a global nature. For example, the Z type local monopole charge C for Weyl points, has a global nature, telling us its influence to the rest of the Brillouin zone, giving rise to bulksurface correspondence associated with helical surface states. In Dirac systems, helical surface states are not guaranteed due to C=0. However, a new bulksurface correspondence associated with double/quadhelicoid surface states (DHSSs/QHSSs) can be obtained for Dirac points with the protection of a Z2 type monopole charge Q, which is defined in terms of the timereversal (T)glide (G) symmetry (TG)2= 1. Here we study the topology of Q for Z2 Dirac points and establish its bulksurface correspondence with strict proofs. We find that Q is equivalent to the Gprotected Z2 invariant v mathematically and physically in Z2 Dirac systems. This result is counterintuitive, since v is always trivial in Tpreserving gapped systems, and was thought to be illdefined in gapless systems. We offer a gaugeinvariant formula for Q, which is associated with DHSSs in both the spinless and spinful systems with single G. Q is formulated in a simpler form in spinless systems with two vertical G, associated with QHSSs, which is also entangled with fillingenforced topological band insulators in three space groups when a Tbreaking perturbation is introduced. Since Q is illdefined in spinful systems with two vertical G, QHSSs will not be held. Material candidate Li2B4O7 together with a list of possible space groups preserving QHSSs are also proposed for demonstration on our theory and further studies. *Detailed information about the seminar refer to the email.
会場: via Zoom
イベント公式言語: 英語

Criticality in stochastic SIR model for infectious diseases based on pathintegral approach
2022年3月24日10:00  11:00
安井 繁宏 (高知大学医学部 医療情報科学センター 助教)
The susceptibleinfectedremoved (SIR) model provides us with a basic scheme for the analysis of the epidemic infectious diseases such as the COVID19. In this presentation, we focus on the stochastic SIR model which describes the stochastic timeevolutions of the population sizes for the susceptible, infected, and removed individuals. We consider the master equation (Kolmogorov forward equation) for the infection transmission and recovery processes (SI>II and I>R), and transform it into the Hamiltonian formalism with the Fock space a la quantum physics. According to the DoiPeliti prescription, furthermore, we introduce the pathintegral formalism similar to the quantum field theory, and perform the perturbative and nonperturbative calculations for the timeevolution of the susceptible, infected, and removed populations. We find that the critical value Rc of the basic reproduction number, which determines the spreading or the convergence of the infectious diseases, can be modified by the stochastic effects in comparison to the Rc in the conventional deterministic SIR model.
会場: via Zoom
イベント公式言語: 英語

セミナー
Explore the possibility to control hurricanes
2022年3月18日16:00  18:00
Dr. Lin Li (理化学研究所 開拓研究本部 (CPR) 三好予測科学研究室 特別研究員)
Hurricanes, also known as tropical cyclones and typhoons, are the biggest and the most devastating storms on Earth. In this seminar, I will talk about the possibility to control hurricanes with existing human capability. Energetically speaking, controlling hurricanes is a very challenging task due to a large gap: hurricanes are gigantic heat engines with a power of around 10^{14} Watt, while the most powerful manmade engines have the power of only 10^{8} Watt. This sixordermagnitude gap is the major obstacle toward using existing engines to control hurricanes. To fill in this gap, we propose to utilize the chaotic nature of hurricanes, namely, the sensitivity of a chaotic system to its initial condition, to control hurricanes. In this presentation, I will first review the basics of hurricanes and existing chaos control methods, and then present my thoughts on hurricane control and preliminary results I acquired since joining Prediction Science Laboratory. Future directions on using reinforcement learning to control hurricanes will also be discussed. Since it is a very challenging task, I welcome any discussions, questions, and comments. I hope we can make the hurricaneriskfree future come earlier.
会場: via Zoom
イベント公式言語: 英語

Phylogenomics revealed one of the problems for phylogeny –The monophyly of Archaeplastida including land plant
2022年3月17日10:00  11:00
矢﨑 裕規 (数理創造プログラム 特別研究員)
There are many problems between large eukaryotic lineages. One of these is the monophyly of Archaeplastida to which land plants and other photosynthetic organisms belong. Although it has been believed that the Archaeplastida are monophyletic because they share common chloroplast structures, several largescale molecular phylogenetic analyses have failed to reproduce this phylogenetic relationship. In this study, by enhancing the taxon sampling of the data set, the monophyly of Archaeplastida was successfully reconstructed, showing that the taxa critical for the reconstruction are present. Through detailed molecular phylogenetic and statistical analyses, it was estimated that the lack of monophyly ofArchaeplastida is due to the specific evolutionary signals of certain taxa.
会場: via Zoom
イベント公式言語: 英語

セミナー
Extracting rules from trained machine learning models with applications in Bioinformatics
2022年3月11日16:00  18:00
Dr. Pengyu Liu (情報統合本部 (RIH) 医療データ数理推論チーム 特別研究員)
Recently, Machine learning methods have achieved great success in various areas. However, some machine learningbased models are not explainable (e.g., Artificial Neural Networks), which may affect the massive applications in medical fields. In this talk, we first introduce two approaches that extract rules from trained neural networks. The first one leads to an algorithm that extracts rules in the form of Boolean functions. The second one extracts probabilistic rules representing relations between inputs and the output. We demonstrate the effectiveness of these two approaches by computational experiments. Then we consider applying an explainable machine learning model to predict human Dicer cleavage sites. Human Dicer is an enzyme that cleaves premiRNAs into miRNAs. We develop an accurate and explainable predictor for the human Dicer cleavage site  ReCGBM. Computational experiments show that ReCGBM achieves the best performance compared with several existing methods. Further, we find that features close to the center of premiRNA are more important for the prediction.
会場: via Zoom
イベント公式言語: 英語

セミナー
Toward modeling complete supernova neutrino emissions
2022年3月11日16:00  17:00
諏訪 雄大 (東京大学 大学院総合文化研究科 宇宙地球部会 准教授 / 京都大学 基礎物理学研究所 基研特任准教授)
Neutrinos are guaranteed observable from the next Galactic supernova (SN). Optical lights and gravitational waves are also observable but can be difficult to observe if SN location in the galaxy and the explosion details are unsuitable. The key to the next coming SN observation will be understanding various physical quantities using neutrinos first and then connecting them to other signals. In particular, understanding neutrinos in the late time (> 1 sec after the onset of explosion) is essential, since physics in this time scale has much smaller uncertainties than that of the early time. We should construct a simple and understandable neutrino model based on the latetime emissions. It allows us to tackle the physics in the early phase like the explosion mechanism. In this talk, I will discuss the following topics: 1) how to model the complete neutrino emissions from the very early phase up to the last observable event. 2) what physical quantities (e.g., mass and radius of neutron stars) can be extracted from observations using large statistical neutrinos as physics probes. 3) how to use these extracted physical quantities to link with the explosion mechanism of SN and multimessenger observations.
会場: via Zoom
イベント公式言語: 英語

セミナー
Nonperturbative cavity/waveguide quantum electrodynamics and dissipative quantum phase transition
2022年3月10日13:30  15:00
蘆田 祐人 (東京大学 大学院理学系研究科 准教授)
Strong coupling between matter and quantized electromagnetic modes in cavity or waveguide may offer yet another approach of controlling equilibrium phases or dynamics of manybody systems. Recent developments have realized such strong lightmatter interaction in genuinely quantum and nonperturbative regimes, where conventional approximate theoretical methods cannot be applied in general. I will talk about how one can analyze strongly coupled quantum lightmatter systems at arbitrary interaction strengths on the basis of an asymptotically disentangling unitary transformation [1,2]. I discuss its application to construction of tightbinding Hamiltonians, dynamics of bound states in the continuum, and revisiting dissipative quantum phase transition in resistively shunted Josephson junctions [3].
会場: via Zoom
イベント公式言語: 英語

Independent regulation of multiple checkpoints in cellcycle network system Biological function originated in the law of localization
2022年3月10日10:00  11:00
望月 敦史 (京都⼤学 ウイルス･再⽣医学研究所 教授)
In cell cycle, G1S and G2M checkpoints are regulated by different protein complexes, Cdc2Cdc13 and Cdc2Cig2, respectively. For a normal mitosis, activity of two complexes should rise specifically at different timing. However, the complex formations share common species of proteins and activation reactions conform a complicated network. We study how independent regulation of two checkpoints is realized in the network system by “structural sensitivity analysis”, which was previously established by us. The analyses clarified that activities of two complexes are regulated by disjoint sets of reaction parameters in the system. A series of nontrivial behaviors are generated by “buffering structures with an intersection”, which can generally appear in chemical reaction network including complex formation.
会場: via Zoom
イベント公式言語: 英語

セミナー
Introduction to stability conditions 2
2022年3月9日16:00  17:30
小関 直記 (Postdoctoral Research Associate, School of Mathematics, University of Edinburgh, UK)
In 2002, Bridgeland defined the notion of stability conditions on a triangulated category, motivated by string theory and mirror symmetry. Since then, Bridgeland stability conditions have been found very useful not only in Mathematical Physics, but also in various areas of Pure Mathematics. In the first part, I will review basic background and open problems in the theory of Bridgeland stability conditions. In the second part, I will explain recent developments of the theory, especially its applications to algebraic geometry.
会場: via Zoom
イベント公式言語: 英語

セミナー
Introduction to stability conditions 1
2022年3月2日16:00  17:30
小関 直記 (Postdoctoral Research Associate, School of Mathematics, University of Edinburgh, UK)
In 2002, Bridgeland defined the notion of stability conditions on a triangulated category, motivated by string theory and mirror symmetry. Since then, Bridgeland stability conditions have been found very useful not only in Mathematical Physics, but also in various areas of Pure Mathematics. In the first part, I will review basic background and open problems in the theory of Bridgeland stability conditions. In the second part, I will explain recent developments of the theory, especially its applications to algebraic geometry.
会場: via Zoom
イベント公式言語: 英語

セミナー
How to understand Earth science system using data science
2022年2月25日16:00  18:00
Dr. Kaman Kong (理化学研究所 計算科学研究センター (RCCS) 複合系気候科学研究チーム 特別研究員)
Hi everyone, my name is Kaman Kong. After I graduated from Nagoya University last April, I joined the computational climate science research team, RCCS at Kobe. Although I have still not yet had the important results now, I would like to share my idea and future plan here. In this talk, different from the previous seminar, I would like to highlight how to use data science approaches to understand our Earth system science. In the first 60 minutes, I would like to share my research experiences in ecosystems, dust outbreaks, and atmospheric sciences and try to discuss their limitation in my study. After a 10minute break, the 30 minutes will be spent discussing the potential methodology to overcome these limitations and new opportunities and challenges in Earth system science. (Part 1) In the first 60 minutes, I would like to talk about the relationships among ecosystems, dust outbreaks, and atmospheric conditions. I used the models of dust and ecosystem to explore seasonal variations of threshold wind speed, an index of soil susceptibility to dust outbreak, and its relations with land surface conditions, such as plant growth and soil moisture and temperature changes, in the Mongolian grasslands. On the other side, I am improving the weather forecast model to accurately predict dust emission and discuss its effects on the Earth system. Meanwhile, I am integrating the dust model into the ecosystem model. During this period, I realized there are many uncertainties of simulation. (Part 2) In the second 30 minutes, I will explain these limitations as I mentioned before and try to discuss how to solve these problems. For example, using deep learning to identify the green and brown plants separately for discussing their different effect on the dust model. And, used data assimilation (e.g., EnKF and Bayesian calibration) to improve the simulated performance of land surface parameters (e.g., soil moisture and vegetation).
会場: via Zoom
イベント公式言語: 英語

セミナー
How is turbulence born: Spatiotemporal complexity and phase transition of transitional fluids
2022年2月24日17:00  18:15
Dr. HongYan Shih (Assistant Research Fellow, Institute of Physics, Academia Sinica, Taiwan)
How a laminar flow becomes turbulence has been an unsolved problem for more than a century and is important in various industrial applications. Recently precise measurements in pipe flow experiments showed nontrivial spatiotemporal complexity at the onset of turbulence. Based on numerical evidence from the hydrodynamics equations, we discovered the surprising fact that the fluid behavior at the transition is governed by the emergent predatorprey dynamics of the important longwavelength mode, leading to the mathematical prediction that the laminarturbulent transition is analogous to an ecosystem on the edge of extinction. This prediction demonstrates that the laminarturbulent transition is a nonequilibrium phase transition in the directed percolation universality class, and provides a unified picture of transition to turbulence emerging in systems ranging from turbulent convection to magnetohydrodynamics. *Detailed information about the seminar refer to the email.
会場: via Zoom
イベント公式言語: 英語

Stator dynamics of the bacterial flagellar motor
2022年2月24日17:00  18:00
Dr. Ashley Nord (Researcher, CNRS, Centre de Biologie Structurale, France)
Dr. Rubén PérezCarrasco (Lecturer in Theoretical Systems Biology, Faculty of Natural Sciences, Department of Life Sciences, Imperial College London, UK)The bacterial flagellar motor is the membraneembedded rotary molecular motor which turns the flagellum that provides thrust to many bacteria for swimming, swarming, and chemotaxis. This large multimeric complex, composed of a few dozen constituent proteins, is a hallmark of dynamic subunit exchange. The stator units are innermembrane ion channels which dynamically bind to the cell wall and convert electrochemical energy into torque which is applied to the rotor. The dynamic exchange of stator units is a function of the viscous load on the flagellum, allowing the bacterium to adapt to its local environment, though the molecular mechanisms of this mechanosensitivity remain unknown. Previously, we have shown that stator units behave as a catch bond, a counterintuitive bond which becomes stronger under applied tension. Here, by actively perturbing the steadystate stator stoichiometry of individual motors, we reveal a stoichiometrydependent asymmetry in stator remodeling kinetics. We interrogate the potential effect of nextneighbor interactions and local stator unit depletion and find that neither can explain the observed asymmetry. We then simulate and fit two mechanistically diverse models which recapitulate the asymmetry, finding assembly dynamics to be particularly well described by a twostate catchbond mechanism.
会場: via Zoom
イベント公式言語: 英語

セミナー
iTHEMS  RCCS(FTRT) Joint Online Seminar: Second order chiral phase transition in three flavor quantum chromodynamics?
2022年2月18日16:30  18:00
Prof. Gergely Fejos (Assistant Professor, Institute of Physics, Eötvös Loránd University, Hungary)
We calculate the renormalization group flows of all renormalizable interactions in the three dimensional GinzburgLandau potential for the chiral phase transition of three flavor quantum chromodynamics [1]. On the contrary to the common belief we find a fixed point in the system that is able to describe a second order phase transition in the infrared. This shows that longstanding assumptions on the transition order might be false. If the transition is indeed of second order, our results can also be interpreted as indirect evidence that the axial anomaly restores at the transition temperature.
会場: via Zoom
イベント公式言語: 英語

Spin transport in ultracold atomic gases
2022年2月18日14:00  15:00
関野 裕太 (理化学研究所 開拓研究本部 (CPR) 長瀧天体ビッグバン研究室 特別研究員)
In condensed matter physics, transport measurement has played crucial roles in understanding fascinating phenomena such as superconductivity and quantum Hall and Kondo effects. In this talk, we discuss the usefulness of spin transport as a probe for manybody properties in ultracold atoms. In the first part, we focus on the conductivity of alternating spin current, which includes information on superfluid gap, pseudogap, and topological phase transition. In the latter part, we consider mesoscopic spin transport between two Fermi gases weakly connected with each other. Our analysis suggests that the spin current is sensitive to whether the gases have pseudogaps, which are gaplike structures in densities of states just above the superfluid transition temperature. In this talk, we also mention similarities of ultracold atoms to neutron star matter.
会場: via Zoom
イベント公式言語: 英語

Hilbert transform and its applications to biology
2022年2月17日10:00  11:00
儀保 伸吾 (数理創造プログラム 特別研究員)
In chronobiology, the estimation of phase dynamics is important for measuring period and phase shift. However, it is difficult to precisely estimate the phase from timeseries data when the frequency and the amplitude are nonstationary. Hilbert transform has been known as a signal processing method for decomposing timeseries into the phase and the amplitude dynamics. This method allows us to analyze the phase from nonstationary timeseries data. In this talk, I would like to introduce the basic concept of Hilbert transform and a few examples of its applications.
会場: via Zoom
イベント公式言語: 英語
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