イベント検索
655 件
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セミナー
Origin of non-linearity of large deformation on DNA stretched
2021年2月25日(木) 10:00 - 11:00
横田 宏 (理化学研究所 数理創造プログラム (iTHEMS) 特別研究員)
Since DNA in a cell is mechanically stretched or rotated by many proteins, the mechanical response of DNA in vitro is expected to be basic point for understanding its behavior. When DNA is stretched by relatively high force, the length of DNA shows the nonlinear response. In this talk, I introduce the theoretical treatment of DNA stretching in high force region based on polymer physics.
会場: via Zoom
イベント公式言語: 英語
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セミナー
The Evolution of Primordial Neutrino Helicities under Gravitational and Magnetic Fields and Implications for their Detection
2021年2月22日(月) 10:00 - 11:30
ゴードン・ベイム (理化学研究所 数理創造プログラム (iTHEMS) 客員主管研究員 / Professor Emeritus, University of Illinois, USA)
Feb.22 (Mon) 10:00am-11:30am (JST) Primordial neutrinos decoupled in the early universe in helicity eigenstates. As I will discuss, two effects -- dependent on neutrinos having a non-zero mass -- can modify their helicities as they propagate through the cosmos. First, finite mass neutrinos have a magnetic moment and thus their spins, but not their momenta, precess in cosmic and galactic magnetic fields. The second is the propagation of neutrinos past cosmic matter density fluctuations, which bend their momenta, and bend their spins by a smaller amount. (The latter is a general relativistic effect.) Both effects turn a fraction of left-handed neutrinos into right-handed neutrinos, and right-handed antineutrinos into left-handed. If neutrino magnetic moments approach that suggested by the XENON1T experiment as a possible explanation of their excess of low energy electron events -- a value well beyond the moment predicted by the standard model -- helicities of relic Dirac (but not Majorana) neutrinos could be considerably randomized. I finally will discuss the implications of neutrino helicity rotation, as well as their Dirac vs. Majorana nature, on their detection rates via the Inverse Tritium Beta Decay reaction.
会場: via Online
イベント公式言語: 英語
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セミナー
High-throughput laboratory evolution with machine learning reveals constraints for drug resistance evolution
2021年2月18日(木) 10:00 - 11:00
岩澤 諄一郎 (東京大学 大学院理学系研究科物理学専攻 博士課程)
The understanding of evolution is crucial to tackle the problem of antibiotic resistance which is a growing health concern. Although the lack of sufficient data has long hindered the mechanism of evolution, laboratory evolution experiments equipped with high-throughput sequencing/phenotyping are now gradually changing this situation. The emerging data from recent laboratory evolution experiments have revealed repeatable features in evolutionary processes, suggesting the existence of constraints on evolutionary outcomes [1,2]. Despite its importance for understanding evolution, however, we still lack a systematic investigation for evolutionary constraints. In this seminar, I would like to talk about two projects on the investigation of evolutionary constraints using data acquired from laboratory evolution of Escherichia coli. In the first half, I will explain how to extract an effective latent space for probing constraints in resistance evolution using gene expression data. We will further discuss what kind of structure exists in this space [3]. In the latter half, I will talk about our recent study on how to construct a predictive model for evolution using the information of evolutionary constraints.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Quantum mechanical description of energy dissipation and application to heavy-ion fusion reactions
2021年2月16日(火) 13:00 - 14:30
時枝 正明 (東北大学 大学院理学研究科 物理学専攻 博士課程)
For theoretical description of heavy-ion fusion reactions, two different models have been used depending on the incident energy. At energies above the Coulomb barrier, importance of energy dissipation and fluctuation has been deduced from scattering experiments. To describe them phenomenologically, the classical Langevin equation has successfully been applied. At energies below the Coulomb barrier, on the other hand, the quantum coupled-channels method with a few number of internal states has been applied, and it has succeeded in explaining sub-barrier fusion reactions. While each method succeeds in each energy range, a unified description of heavy-ion fusion reactions from sub-barrier energies to above barrier energies is still missing. To achieve this, we need to treat dissipation and fluctuation quantum mechanically. In order to describe dissipation and fluctuation quantum mechanically, we have applied ideas of open quantum systems to heavy-ion fusion reactions. I will talk about recent development in this talk. First I will introduce a model Hamiltonian to treat dissipation and fluctuation quantum mechanically, and explain its character and a strategy for numerical studies. I will then apply the model to a fusion problem, and discuss a role of energy dissipation during quantum tunneling. Finally I will discuss a possible future direction for a unified description of heavy-ion fusion reactions.
会場: via Zoom
イベント公式言語: 英語
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セミナー
A machine learning approach for prediction of mitochondrial proteins in non-model organisms
2021年2月12日(金) 10:00 - 11:00
久米 慶太郎 (筑波大学 医学医療系 助教)
The evolution of the repertoire of proteins localized to organelles is important for understanding the evolutionary process of organelles. However, experimental methods for identifying organelle-localized proteins have been established only for model organisms and some organisms. Therefore, prediction methods using sequence data obtained from genome and transcriptome analyses, which are relatively easy to obtain, are useful. However, such prediction methods had also been established only for model organisms. In this talk, I will introduce our study in which a machine learning method was used to obtain protein candidates localized to mitochondrion-related organelles in non-model organisms.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Quantum kinetic theory for chiral and spin transport in relativistic heavy ion collisions and core-collapse supernovae
2021年2月4日(木) 13:00 - 14:30
Di-Lun Yang (慶應義塾大学 理工学部 助教)
Recently, the anomalous transport phenomena of relativistic fermions associated with chirality and spin induced by external fields have been greatly explored in different areas of physics. Notably, such phenomena are in connection to various quantum effects such as quantum anomalies and spin-orbit interaction. The quark gluon plasmas produced from relativistic heavy ion collisions (HIC) and the core-collapse supernovae (CCSN) are both the systems in extreme conditions with high temperature or density and the presence of strong magnetic and vortical fields. Meanwhile, the abundance of light quarks and neutrinos as relativistic fermions created therein accordingly makes these two systems ideal test grounds for studying such exotic transport phenomena. Inversely, the anomalous transport may also give rise to unexpected impacts on the evolution of both systems. However, to analyze such dynamical quantum effects, a novel quantum transport theory delineating the evolution of chirality imbalance and spin has to be introduced. In this talk, I will discuss recent developments and applications of the quantum kinetic theory for chiral and spin transport in the context of HIC and CCSN.
会場: via Zoom
イベント公式言語: 英語
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セミナー
System identification of mechano-chemical epithelial sheet dynamics
2021年2月4日(木) 10:00 - 11:00
浅倉 祥文 (京都大学 大学院生命科学研究科 博士課程)
Collective migration of epithelial cells is a fundamental process of multi-cellular organisms. Our recent study using live imaging with FRET-based biosensor discovered that cell migration within an epithelial sheet is oriented by traveling waves of ERK activation. However, it is still elusive how the cells make a decision on migration direction by integrating mechano-chemical signals. Here, we performed reverse-engineering approach to extract a hidden control mechanism in the epithelial sheet dynamics in a data-driven manner. Our model has an ability to forecast cell migration quantified in time-lapse images. Therefore, our approach would be powerful to understand mechano-chemical epithelial sheet dynamics.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Numerical inference of the molecular origin of the cyanobacterial circadian rhythm
2021年1月28日(木) 10:00 - 11:00
甲田 信一 (分子科学研究所 計算分子科学研究領域 助教)
The cyanobacterial clock proteins, KaiA, KaiB, and KaiC, are known as the simplest biological clock; Just by mixing them with ATP in a test tube, self-sustaining oscillation with a nearly 24h temperature-compensated period is reconstituted. To elucidate the molecular mechanisms of this oscillator, experimental studies have revealed and investigated in detail various elementary reactions/processes, ranging from local chemical reactions of ligands to global (dis)assembly of the proteins. Yet, proposing molecularly detailed mechanisms of the clock functions is still difficult because almost all experimentally measurable quantities are the results of complicated interplays between many elementary processes, i.e. independent measurement of an elementary process is difficult. In this talk, I will present a numerical approach to obtain the rate constants of the elementary processes from experimental data [1, 2]. First, a reaction model consisting of rate equations of the elementary processes is built. Then, their rate constants and temperature dependence are inferred by simultaneously fitting model outputs to multiple types of experimental data (such as phosphorylation reactions and ATPase activity) at various temperatures. On the basis of the inferred parameter values, we can quantitatively discuss how the clock functions arise from the interplays between elementary processes. As an example, I will present a potential molecular mechanism of the temperature compensation of period.
会場: via Zoom
イベント公式言語: 英語
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セミナー
What are genes and how can we find them?
2021年1月14日(木) 10:00 - 11:00
ジェフリ・フォーセット (理化学研究所 数理創造プログラム (iTHEMS) 上級研究員)
Although 'gene' is a word that is used frequently in the society, most people probably do not know what genes actually are. In fact, its definition is not so straightforward. In this talk, I will first give a historical perspective and our current understanding of what genes are and what they look like. Then, I will talk about 'gene prediction'. Once we obtain the DNA (genome) sequence data of a given species, we must 'find' the genes within the genome. This involves computational prediction utilizing probabilistic models and various sources of external evidence. I will briefly explain how this is done.
会場: via Zoom
イベント公式言語: 英語
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セミナー
From local resynchronization to global pattern recovery in the zebrafish segmentation clock
2021年1月7日(木) 10:00 - 11:00
瓜生 耕一郎 (金沢大学 生命理工学類 助教)
Tissue-scale developmental patterns are often generated by local cellular interactions and global tissue deformation. An example is gene expression rhythms in vertebrate, termed the segmentation clock. The oscillatory spatial pattern of the segmentation clock across a tissue determines the timing of body segment formation. In this seminar, we discuss pattern recovery in the zebrafish segmentation clock after perturbation in oscillator coupling. To predict pattern recovery in embryos, we develop a physical model that describes both cell mechanics and genetic oscillations. We show that the physical model explains experimentally observed intermingled segmental defects, and their axial distributions in different embryonic developmental stages. Our analysis suggests that pattern recovery in developing tissues occurs at two scales; local pattern formation and transport of these patterns through tissue morphogenesis.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Classical liquids and functional renormalization group
2020年12月17日(木) 13:00 - 14:30
横田 猛 (東京大学 物性研究所 特別研究員)
Development of methods for classical statistical mechanics is desired for accurate predictions of the structures and thermodynamic properties of liquids. A powerful framework to describe classical liquids is density functional theory (DFT). In the quantum case, there have been recent attempts to develop accurate methods with combining DFT and the functional renormalization group (FRG), which is another framework to deal with many-body systems utilizing evolution equations, and such approaches are expected to work also in the classical case. In this presentation, I will talk about a new approach for classical liquids aided by FRG. The formalism and some ideas to incorporate higher-order correlation functions to systematically improve the accuracy will be shown. I will also present a numerical demonstration in a one-dimensional exactly solvable system and discuss the results by comparing to other conventional methods such as the hypernetted chain.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Conserved charges in gravity and entropy
2020年12月10日(木) 13:00 - 14:30
青木 愼也
We propose a manifestly covariant definition of a conserved charge in gravity. We first define a charge density from the energy momentum tensor with a Killing vector, if exists in the system, and calculate the energy (and angular momentum) of the black hole by a volume integral. Our definition of energy leads to a correction of the known mass formula of a compact star, which includes the gravitational interaction energy and is shown to be 68\% of the leading term in some case. Secondly we propose a new method to define a conserved charge in the absence of Killing vectors, and argue that the conserved charge can be regarded as entropy, by showing the 1st law of thermodynamic for a special case. We apply this new definition to the expanding universe, gravitational plane waves and the black hole. We discuss future directions of our research.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Scattering theory for half-line Schrödinger operators: analytic and topological results
2020年12月7日(月) 16:00 - 18:10
井上 秀樹 (名古屋大学)
Levinson’s theorem is a surprising result in quantum scattering theory, which relates the number of bound states and the scattering part of the underlying quantum system. For the last about ten years, it has been proved for several models that once recast in an operator algebraic framework this relation can be understood as an index theorem for the Møller wave operators. Resulting index theorems are called topological version of Levinson’s theorem or shortly topological Levinson’s theorem. In this talk, we first review the background and the framework of our investigation. New analytical and topological results are provided for Schrödinger operators on the half-line. This talk is based on my Ph.D thesis.
会場: via Zoom
イベント公式言語: 英語
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外部イベント
Presented by iTHEMS & academist 君は本当にブラックホールを知っているか？
2020年12月6日(日) 14:00 - 16:00
長瀧 重博 (理化学研究所 数理創造プログラム (iTHEMS) 副プログラムディレクター / 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 主任研究員)
井上 芳幸 (理化学研究所 数理創造プログラム (iTHEMS) 客員主管研究員 / 大阪大学 大学院理学研究科 宇宙地球科学専攻 准教授)
横倉 祐貴 (理化学研究所 数理創造プログラム (iTHEMS) 上級研究員)～最新理論や観測結果からノーベル物理学賞解説まで！ 現役物理学者に学ぶ最新ブラックホール入門～ 2020年ノーベル物理学賞は、ブラックホールの理論と観測に貢献したロジャー・ペンローズ博士、ラインハルト・ゲンツェル博士、アンドレア・ゲズ博士の3名が受賞した。近年もブラックホール合体からの重力波やブラックホール撮像といったホットな話題を提供し続けるブラックホールだが、皆さんは本当にブラックホールのことを知っているだろうか？ 最先端のブラックホール研究者が、その正体と謎を解説する。
会場: via Online
イベント公式言語: 日本語
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セミナー
KPZ equation, attractive bosons, and the Efimov effect
2020年12月3日(木) 13:00 - 14:30
西田 祐介 (東京工業大学 理学院 物理学系 准教授)
The Kardar-Parisi-Zhang (KPZ) equation for surface growth has been a paradigmatic model in nonequilibrium statistical physics. In particular, it in dimensions higher than two undergoes a roughening transition from smooth to rough phases with increasing the nonlinearity. It is also known that the KPZ equation can be mapped onto quantum mechanics of attractive bosons with a contact interaction, where the roughening transition corresponds to a binding transition of two bosons with increasing the attraction. Such critical bosons in three dimensions actually exhibit the Efimov effect, where a three-boson coupling turns out to be relevant under the renormalization group so as to break the scale invariance down to discrete one. On the basis of these facts linking the two distinct subjects in physics, we predict that the KPZ roughening transition in three dimensions shows either the discrete scale invariance or no intrinsic scale invariance.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Flat and spherical surface approximations
2020年11月30日(月) 16:00 - 17:30
スクロツキ マーティン (理化学研究所 数理創造プログラム (iTHEMS) 客員研究員 / Fellow, German Academic Scholarship Foundation, Germany)
State-of-the-art acquisition devices produce surface representations of increasingly high resolution. While these detailed representations are important for production, they are problematic e.g. when exchanging drafts via the internet or when a quick rendering for comparison is necessary. In the first part of the talk, I will present results and further research questions from a paper I recently co-authored on 'Variational Shape Approximation'. This approach aims at linearizing the input surface and representing it via a set of localized planar segments. In the second part of the talk, I will present some ongoing research on surface representations via balls. This work started with constructions from spherical neodym magnets and provided a set of mathematical questions. These investigations are joint work with FU Berlin and OIST.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Rotifer can be a good model organism for theoretical biology
2020年11月27日(金) 10:00 - 11:00
小南 友里 (東京大学 大学院農学生命科学研究科 特任助教)
Rotifers are cylindrical zooplankton which constitute the phylum Rotifera. They have organs and tissues including ganglia, muscles, digestive organs, ovaries, and sensory organs in their <1mm body. Rotifers are suitable for the study on the population dynamics and longevity due to their short generation time. Furthermore the most attractive characteristic of the rotifers is asexual propagation, makes it easy to obtain clonal cultures. The genomic and transcriptomic database are developed and molecular biological techniques such as RNAi for using rotifers have been established. In this seminar, other attractive characteristics of rotifer as a model organism for theoretical biology and great studies using rotifers will be introduced. Our recent results of investigating the effects of calorie condition on longevity will be discussed.
会場: via Zoom
イベント公式言語: 英語
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コロキウム
The Unreasonable Effectiveness of Quantum Theory in Mathematics
2020年11月26日(木) 10:00 - 11:30
Robbert Dijkgraaf (Director, Institute for Advanced Study in Princeton, USA)
November 26 at 10:00-11:30, 2020 (JST) November 25 at 20:00-21:30, 2020 (EST) The physical concepts of quantum theory, in particular of quantum gravity and string theory, have proven to be extremely powerful in addressing deep problems in pure mathematics, from knot invariants to algebraic geometry. Is there such a thing as “quantum mathematics”? Should we add Feynman diagrams, strings, branes and black holes to the language of mathematics?
会場: via Zoom
イベント公式言語: 英語
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セミナー
Symmetry and conservation laws in neural networks
2020年11月20日(金) 10:00 - 11:00
Hidenori Tanaka (Group Leader & Senior Scientist, Physics & Informatics Laboratories, NTT Research, Inc., USA / Visiting Scholar, Stanford University, USA)
Symmetry is the central guiding principle in the exploration of the physical world but has been underutilized in understanding and engineering neural networks. We first identify simple yet powerful geometrical properties imposed by symmetry. Then, we apply the theory to answer a series of following important questions: (i) What, if anything, can we quantitatively predict about the complex learning dynamics of real-world deep learning models driven by real-world datasets? (ii) How can we make deep learning models more efficient by removing parameters without disconnecting information flow? (iii) How can we distill experimentally testable neuroscientific hypotheses by reducing the complexity of deep learning models mimicking the brain? Overall, our approach demonstrates how we can harness the principles of symmetry and conservation laws to reduce deep learning models' complexity and make advances in the science and engineering of biological and artificial neural networks.
会場: via Zoom
イベント公式言語: 英語
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セミナー
Representations of fundamental groups and 3-manifold topology
2020年11月16日(月) 16:00 - 18:10
北山 貴裕 (東京大学 大学院数理科学研究科 准教授)
In 3-dimensional topology the great progress during the last two decades revealed that various properties of 3-manifolds are well understood from their fundamental groups. I will give an introduction to the study of splittings of 3-manifolds along surfaces, with an emphasis on an application of group representations. A fundamental and difficult problem in general is to find surfaces essentially embedded in a given 3-manifold. I will explain how such surfaces are detected by deformations of representations of the fundamental group, and what information of detected surfaces is described in terms of topological invariants derived from representations.
会場: via Zoom
イベント公式言語: 英語