Seminar
701 events
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Seminar
Basic experimental considerations for analyzing gene expression
February 28 (Wed) at 13:00 - 14:00, 2024
Hirotaka Toh (JSPS PD Researcher, RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR))
Methods such as RNA-sequencing and ribosome profiling are indispensable tools for the comprehensive elucidation of the mechanisms underlying gene expression. A fundamental aspect that requires meticulous attention in the execution of these experiment is the extraction of intact RNA and Ribosomes. The integrity and purity of the extracted RNA is critical to ensure the accuracy and reliability of the sequencing data. In this seminar, I will introduce the basic but key points of the extraction process.
Venue: 3rd floor public space, Main Research Building
Event Official Language: English
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Seminar
Using a trapped ion quantum computer for hamiltonian simulations
February 28 (Wed) at 10:30 - 12:00, 2024
Enrico Rinaldi (Senior Research Scientist, Quantum Machine Learning and Algorithms, Quantinuum K.K.)
Trapped ion quantum computers, like the H-series quantum hardware by Quantinuum, robustly encode quantum information in long lived and precise qubits. However, utilizing the hardware efficiently requires a full-stack workflow from software libraries to hardware compilers. In this talk we introduce the relevant elements of this stack in the context of solving the quantum dynamics of a spin system on H-series hardware: we start from the definition of the Hamiltonian operator in the qubit Hilbert space using the open-source pytket python library and we define the quantum circuits in measurements to run, on a simulator first and on hardware later.
Venue: Seminar Room #359 (Main Venue) / via Zoom
Event Official Language: English
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Seminar
Plant hackers: galling insects extend their phenotypes on the trees by novel plant organogenesis
February 27 (Tue) at 16:00 - 17:00, 2024
Xin Tong (Special Postdoctoral Researcher, Cell Function Research Team, RIKEN Center for Sustainable Resource Science (CSRS))
When it comes to plant-insect interactions, insects are generally seen as pests like caterpillars eating vegetables or fruits. However, one group of insects, the galling insects can induce de novo organogenesis on the host plants which are often woody plants. Each galling insect species ‘designs’ its own gall as the extended phenotype which are so-called species-specific gall formation. Different from leaves and roots, galls represent unique plant organs swiftly formed in response to parasitic organisms, observed across diverse plant species. Yet, the precise mechanisms by which normal plant development is interrupted and redirected to form galls by galling organisms remain elusive. During the talk, I will share some discoveries and views related to aphid gall formation on the elm tree, which is the super host plant for more than 30 galling species, and further discussion about why an insect gall is not simple cell mass but well-organized structure, and how we could systematically understand insect gall formation.
Venue: Hybrid Format (3F #359 and Zoom), Main Research Building
Event Official Language: English
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Seminar
An Investment Banker’s Journey to the World of Physicists -Seeking the Truth in Economics and Finance
February 26 (Mon) at 15:30 - 17:00, 2024
Irena Vodenska (Professor, Boston University, USA)
I encountered many exciting opportunities to learn, grow intellectually, and teach during my educational, professional, and scientific journey. Life brings chances, and it is up to us to take or leave them. I took my chances, one of the fascinating ones being to embark on a scientific interdisciplinary research collaboration with physicists. My background is in economics and finance, and doing research with physicists has been fascinating from many different points of view, especially in light of being free from any ONE discipline, free to explore research possibilities to answer finance and economic questions based on a boundless horizon of possible solutions. I worked as an investment banker after my first graduate degree before returning to academia to continue chartering new pathways to research. During my work as a hedge fund manager and a NASDAQ market maker, I had an opportunity to witness firsthand, on the trading floor, the US market collapse sparked by the demise of the Long Term Capital Management in 1998 and later the European market plunge during the tragic events of the terrorist attack on New York City on September 11, 2001, when I lived and worked on Manhattan. Most world problems today are complex to solve with one discipline, as multidisciplinary THINKING is needed to cover various aspects of scientific inquiry. Experience is essential, translating real-world knowledge into academia even more so. I was fortunate to be in a position to build the bridge between investment banking and academia. Learning about the pioneer of Econophysics, Boston University Professor H. Eugene Stanley, was like discovering a gold mine for me. After an exciting investment banking experience in the 1990s and early 2000s, I left my investment banking job in New York City to join Professor Stanley’s research laboratory, a time I will cherish and remember as formative, enlightening, and transformative for the rest of my life. One may ask why physicists work with economists on financial economics problems. The answer is simple: physicists are naturally curious, inquisitive, and open to new ideas. Moreover, physicists and economists share the same language, the language of mathematics. The value of the achievement in econophysics research is the results and the empirical outcome based on data obtained with solid models grounded in natural and social science theory. It is not trivial to produce interdisciplinary research, but recognizing its necessity is already prominently featured in many universities’ strategic plans, including Boston University. Let me lay out several studies and results to give you a glimpse into the research I will discuss today. We analyze economic time series and panel data to understand their relationships and investigate whether some economic data could be informative of the behavior of others. We use a novel approach comprised of Complex Hilbert Principal Component Analysis (CHPCA), Rotational Random Shuffling (RRS), and Helmholtz-Hodge (HH) potential to unearth statistically significant co-movements and identify noteworthy economic and geopolitical events that might influence such co-movement dynamics. I will present results from four cases studied collaboratively with my international research collaborators over the last decade since 2013.
Venue: Seminar Room #359 (Main Venue) / via Zoom
Event Official Language: English
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Seminar
A Selective Survey of Ideas, Tools and Results in Constructive Field Theory
February 26 (Mon) at 13:00 - 14:30, 2024
Christy Koji Kelly (Special Postdoctoral Researcher, iTHEMS)
In this talk we discuss some aspects of constructive field theory with an emphasis on analytical and probabilistic methods and results. In particular after an overview of some points in the history of constructive QFT we plan to discuss some early achievements in axiomatic QFT, some features of the theory of distributions and the basic structure of the Wightman reconstruction theorem. We also introduce the Osterwalder-Schrader axioms and overview the strategy for the construction of nontrivial measures describing path-integrals for interacting QFTs. Depending on time constraints we might also discuss probabilistic tools (weak convergence of measures, the Bochner-Minlos theorem etc), Gaussian measures, UV regularity of simple QFTs and the construction of (infinite volume) Euclidean P(phi)_2 measures. The plan is to discuss some of these topics in some detail after the end of the official seminar.
Venue: via Zoom / Seminar Room #359
Event Official Language: English
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Seminar
Cellular-level left-right asymmetry, cell chirality, induces the chiral collective rotation of multicellular colony
February 15 (Thu) at 16:00 - 17:00, 2024
Tomoki Ishibashi (Special Postdoctoral Researcher, Laboratory for Physical Biology, RIKEN Center for Biosystems Dynamics Research (BDR))
Ryohei Nishizawa (Ph.D. Student, Graduate School of Frontier Biosciences, Osaka University)The left-right (LR) asymmetric morphology of organs is essential for the development and maintenance of their functions in various species. In recent years, it has become clear that the LR asymmetry of organs originates from cell chirality, the LR asymmetric nature at the cellular level [1]. However, it is unclear how the cell chirality generates the LR asymmetry at the multicellular level. Here we show a mechanism of LR asymmetry formation at the multicellular level based on cell chirality. We previously found that Caco-2 cells, a typical cultured epithelial cell line derived from human colon cancer, exhibit stereotypical and directional cell chirality; when Caco-2 cells are cultured as single cells, their nuclei and cytoplasm rotate in the clockwise direction at a rate of 50°/h [2]. Interestingly, when Caco-2 forms multicellular colonies, the colonies also undergo a collective clockwise rotation at 10º/h. We revealed that the actomyosin cytoskeleton is essential for the formation of the collective rotation [2]. We also found that Caco-2 cells formed lamellipodia and focal adhesions LR asymmetrically during the collective colony rotation, which may be responsible for the chiral collective motion. Interestingly, the disruption of microtubules reversed the direction of collective rotation. The LR asymmetric formation of lamellipodia and focal adhesions was also reversed by inhibition of microtubule polymerization. We will discuss the possible mechanism and the mathematical model where cell chirality induces multicellular chiral rotation depending on microtubules.
Venue: Seminar Room #359 (Main Venue) / via Zoom
Event Official Language: English
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Seminar
Chemical reaction network theory and the problem of reaction rate
February 8 (Thu) at 16:00 - 17:00, 2024
Tomoharu Suda (Postdoctoral Researcher, Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science (CSRS))
A chemical system can be described at different levels. When we focus on the population of chemical species, it is convenient to consider the system as consisting of a number of chemical reactions, which assumes the structure of a (hyper)graph together with the species. The chemical reaction network theory studies chemical systems described in such a way. It aims to elucidate the dynamics of overall chemical composition in terms of the associated graph structure. Notably, it applies not only to chemical systems but also to more general systems as long as the mathematical structure is compatible. In the first part of this talk, we will review the basic concepts and results of the theory, which mainly concern the existence and stability of the equilibrium. From the viewpoint of chemical kinetics, it is interesting to consider the rate of the overall reaction, which may be obtained by the total balance of chemical species. The second part of the talk will be devoted to this topic. Formulation of the problem and some results will be presented. In particular, chemical reaction networks with first-order reactions will be considered in detail.
Venue: Hybrid Format (3F #359 and Zoom), Main Research Building
Event Official Language: English
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Seminar
Relativistic Jet Simulations and Modeling on Horizon Scale
February 8 (Thu) at 13:00 - 14:30, 2024
Yosuke Mizuno (T.D. Lee Fellow / Associate Professor, Tsung-Dao Lee Institute, Shanghai Jiao Tong University, China)
Relativistic jets are launched in the vicinity of the central black holes and emit powerful radiation across the electromagnetic spectrum. According to our current understanding, relativistic jets are launched by directly tapping the rotational energy of spinning black holes via the so-called Blandford-Znajek process. In addition to the spin of the black hole, numerical simulations showed the amount of accreted magnetized flux has a major impact on the formation of relativistic jets. We have investigated the radiative signatures of self-consistently launched relativistic jets using 3D general relativistic magneto-hydrodynamical simulations and general relativistic radiative transfer calculations in horizon scale to the connection with large-scale structure. We discuss our findings and comparison with observations.
Venue: Seminar Room #359 (Main Venue) / via Zoom
Event Official Language: English
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Seminar
Recent advances in nuclear Density Functional Theory and applications to the nuclear response
February 6 (Tue) at 13:30 - 15:00, 2024
Gianluca Colò (Professor, Department of Physics, University of Milan, Italy / Professor, Sezione di Milano, INFN, Italy)
In this contribution, I will give an overall (and, of course, biased) view of the general status of DFT. I will stress that, in contrast to ab initio methods, DFT is the only framework that allows the study of excited states, including those lying at relatively high energy. Accordingly, I will focus on the nuclear response. After a reminder on the nuclear Giant Resonances and the link with the nuclear equation of state, I will discuss the projection methods to restore symmetries in the calculations of deformed systems. While symmetry-restored calculations are nowadays of common use in the study of ground-state properties and low-lying excitations, similar realistic investigations for the nuclear response are essentially missing in the literature. Recently, we have implemented an exact Angular Momentum Projection (AMP) on top of Skyrme-Random Phase Approximation (RPA) calculations in a projection after variation (PAV) scheme, for the first time. The results will be critically analysed in the case of the monopole response, also taking into account the experimental investigations that can be envisioned for well-deformed systems. If time allows, the nuclear response will be also discussed as a way to improve the current density functionals and ground them on ab initio nuclear theory. This seminar is co-hosted by Nuclear Many-body Theory Laboratory and Few-body Systems in Physics Laboratory, RIKEN Nishina Center for Accelerator-Based Science.
Venue: 2F Large Meeting Room, RIBF Building, RIKEN Wako Campus (Main Venue) / via Zoom
Event Official Language: English
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Seminar
Nuclear Energy-Density Functional Approach to Bridging Neutron-Rich Nuclei and Neutron Stars
February 5 (Mon) at 13:30 - 15:00, 2024
Kenichi Yoshida (Associate Professor, Research Center for Nuclear Physics, Osaka University)
Understanding the properties of neutron-rich nuclei has been a central subject in low-energy nuclear physics. The great interest lies not only in the pursuit of a variety of structures and the elucidation of the mechanisms of their occurrence but also in obtaining insights into the structure of the inner crust of neutron stars. With advances in neutron-star observation techniques, the structure of neutron stars has been becoming better understood. The data accumulated from these observations unveil properties of neutron-rich matter that are otherwise inaccessible through terrestrial experiments. In this talk, I will introduce an attempt to construct a nuclear energy-density functional (EDF) inspired by the observations and then demonstrate its applicability to nuclear structure problems, including mass and deformation. One intriguing aspect of neutron stars is the emergence of superfluidity, especially the occurrence of spin-triplet pairing. I will discuss the unconventional pairing in nuclei within the nuclear EDF framework and give perspectives on the study of the phase diagram of the superfluidity in neutron stars. This seminar is co-hosted by UKAKUREN.
Venue: Seminar Room #359 (Main Venue) / via Zoom
Event Official Language: English
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Seminar
Competition across scales in biology
January 31 (Wed) at 11:00 - 12:00, 2024
Sidhartha Goyal (Associate Professor, Department of Physics, University of Toronto, Canada)
Many biological phenomena emerge from interaction and competition between its parts. I will share some examples across biological scales where data-driven theory can reveal new rules of biological competition. At the molecular scale competition between mitochondrial genomes within budding yeast depends on genome architecture; dynamics of adaptive immunity in microbes reveal different modalities of competition and coexistence of bacteria and its phages; in mammals cellular reprogramming may be driven by elite clones, and tumor response to drugs is driven by "epigenetic" switching. Going beyond, I will present some ideas on understanding dynamical systems that govern cell fate dynamics and if competition may play a role in it. Short bio: Sidhartha Goyal got his PhD in Physics at Princeton in 2009 and then moved to Kavli Institute for Theoretical Physics, Santa Barbara for a postdoc. He got his first degree in Electrical Engineering from IIT Bombay. He is now an Associate Professor in the Physics Department at University of Toronto interested in collective phenomena in biology across scales.
Venue: via Zoom
Event Official Language: English
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Seminar
Quantum Enhancement in Dark Matter Detection with Quantum Computation
January 22 (Mon) at 16:00 - 18:00, 2024
Thanaporn Sichanugrist (Ph.D. Student, Graduate School of Mathematical Sciences, The University of Tokyo)
Shion Chen (Project Assistant Professor, International Center for Elementary Particle Physics (ICEPP), The University of Tokyo)Title: Wave-like Dark Matter Search Using Qubits Abstract: The rapid controllability required for quantum computers makes the currently proposed quantum bit modalities also attractive as electromagnetic field sensors. One of the promising applications is wave-like dark matter searches, where the electric field converted from the coherent dark matter excites the qubits, leading to detectable signals [Phys. Rev. Lett. 131, 211001]. The quantum coherence between the qubits can be utilized to enhance the signal rate in a multi-qubit system. By designing an appropriate quantum circuit to entangle the qubits, it was found that the signal rate can scale proportionally to $n_q^2$, with $n_q$ being the number of sensor qubits, rather than linearly with $n_q$ [arXiv: 2311.10413]. In the seminar, we overview the theoretical framework of the search, elaborate on the signal-enhancing mechanism driven by quantum entanglement with specific examples of the quantum circuits, and discuss how the scheme can be implemented in the platform of future fault-tolerant quantum computers. We also provide the introduction of the experimental realization, and report the status of the experimental works carried out in UTokyo/ICEPP.
Venue: via Zoom
Event Official Language: English
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Seminar
Knot Theory in Doubly Periodic Tangles and Applications
January 19 (Fri) at 15:00 - 16:30, 2024
Sonia Mahmoudi (Assistant Professor, Mathematical Science Group, Advanced Institute for Materials Research (AIMR), Tohoku University)
Doubly periodic entangled structures offer an interesting framework for modeling and investigating diverse materials and physical phenomena, from micro to large scales. Specifically, a doubly periodic tangle (DP tangle) is characterized as an embedding of an infinite number of curves in the thickened plane, derived as the lift of a link in the thickened torus to the universal cover. DP tangles play a crucial role in scientific research, particularly in fields such as materials science, molecular chemistry, and biology. Despite their widespread applications, a universally accepted mathematical description of DP tangles is currently lacking. One of the key challenges arises from the infinite possibilities in choosing a periodic cell (referred to as a motif) for a DP tangle, taking into account various periodic boundary conditions. In this presentation, we conduct a comprehensive examination of the concept of topological equivalence of DP tangles, offering insights into potential classifications and applications in the process.
Venue: Hybrid Format (3F #359 and Zoom), Main Research Building
Event Official Language: English
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Seminar
Quantum features in cosmological perturbations?
January 18 (Thu) at 14:15 - 15:00, 2024
Amaury Micheli (Postdoctoral Researcher, iTHEMS)
The statistical properties of the CMB anisotropies, reflecting the curvature inhomogeneities in the very early Universe, are very well accounted for by assuming that the inhomogeneities come from amplified vacuum fluctuations. This scenario makes the cosmological perturbations a possible observational window on the interplay between quantum degrees of freedom and gravity. I will review the discussions on the current presence or absence of quantum features in the perturbations, emphasising the quantum information approaches to this question, and comment on the observability of these features.
Venue: Hybrid Format (3F #359 and Zoom), Main Research Building
Event Official Language: English
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Seminar
Gravitational lensing on superposed curved spacetime
January 18 (Thu) at 13:30 - 14:15, 2024
Youka Kaku (Ph.D. Student, Graduate School of Science, Nagoya University)
In 2017, Bose et al. proposed a tabletop experiment to observe the gravitational effect induced by a spatially superposed mass source, particularly gravity-induced entanglement. This experiment is expected to be the first step in exploring the quantum nature of gravity. Also, there are ongoing efforts to extend their proposal to the relativistic region to observe the unique quantum nature of gravity. In this talk, I will investigate gravitational lensing in a weak gravitational field induced by a spatially superposed mass source. I will show the Einstein ring image of a quantum scalar field propagated on a superposed curved spacetime and compare it with the image of the semi-classical gravity case. This work is currently in progress and is a collaboration with Yasusada Nambu.
Venue: Hybrid Format (3F #359 and Zoom), Main Research Building
Event Official Language: English
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Seminar
Bayesian mechanics of classical, neural, and quantum systems
January 17 (Wed) at 16:30 - 17:45, 2024
Takuya Isomura (Unit Leader, Brain Intelligence Theory Unit, RIKEN Center for Brain Science (CBS))
(This is a joint seminar with iTHEMS Biology group.) Bayesian mechanics is a framework that addresses dynamical systems that can be conceptualised as Bayesian inference. However, the elucidation of requisite generative models is required for empirical applications to realistic self-organising systems. This talk introduces that the Hamiltonian of generic dynamical systems constitutes a class of generative models, thus rendering their Helmholtz energy naturally equivalent to variational free energy under the identified generative model. The self-organisation that minimises the Helmholtz energy entails matching the system's Hamiltonian with that of the environment, leading to an ensuing emergence of their generalised synchrony. In short, these self-organising systems can be read as performing variational Bayesian inference of the interacting environment. These properties have been demonstrated with coupled oscillators, simulated and living neural networks, and quantum computers. This notion offers foundational characterisations and predictions regarding asymptotic properties of self-organising systems exchanging with the environment, providing insights into potential mechanisms underlying emergence of intelligence.
Venue: Seminar Room #359 (Main Venue) / via Zoom
Event Official Language: English
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Seminar
Methods for neural decoding using machine learning, deep learning, and quantum-inspired algorithms
January 17 (Wed) at 15:00 - 16:15, 2024
Kei Majima (Researcher, National Institutes for Quantum Science and Technology (QST))
Note: The format of this event has changed from hybrid to Zoom only. However, you will still be able to watch it on the screen in Room #359 of the Main Research Building. (This is a joint seminar with iTHEMS Biology group.) Recent advances in machine learning have enabled the extraction of intrinsic information from neural activities, a field known as neural decoding. In this presentation, I will introduce several machine learning methods recently developed for neural decoding analysis: 1) a method for visualizing subjective images in the human mind based on brain activity [1], 2) a supervised algorithm designed for predicting discrete ordinal variables [2], and 3) a fast classical algorithm algorithm inspired by quantum computation for approximating principal component analysis (PCA) and canonical correlation analysis (CCA), potentially allowing for the analysis of vast-dimensional neural data [3]. Following these presentations, I am eager to engage in discussions with participants at the RIKEN Quantum Seminar regarding potential collaborations.
Venue: via Zoom
Event Official Language: English
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Seminar
Dust-driven instabilities in protoplanetary disks: toward understanding formation of planetesimals
January 17 (Wed) at 10:30 - 11:30, 2024
Ryosuke Tominaga (Special Postdoctoral Researcher, Star and Planet Formation Laboratory, RIKEN Cluster for Pioneering Research (CPR))
Planet formation starts from collisional growth of sub-micron-sized dust grains in a gas disk called a protoplanetary disk. They are expected to grow toward km-sized objects called planetesimals. The resulting planetesimals further coalesce by gravity and form planets. However, there are some barriers preventing planetesimal formation, which includes fast radial drift and collisional fragmentation of dust grains. To circumvent the barriers and to explain planetesimal formation, previous studies have proposed hydrodynamic instabilities of dusty-gas disks. The instabilities can cause dust clumping, and planetesimals form if the resulting clumps collapse self-gravitationally. We have been investigating the linear/nonlinear development of these dust-gas instabilities. We also found a new instability driven by collisional growth of dust, which can bridge a potential gap between the first dust growth and the later planetesimal formation via the previous instabilities. In this talk, I will introduce our work on the dust-driven instabilities and their impact on planetesimal formation.
Venue: Hybrid Format (3F #359 and Zoom), Main Research Building
Event Official Language: English
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Seminar
Does horizontal gene transfer stabilize cooperation in bacteria?
January 16 (Tue) at 16:00 - 17:00, 2024
Anna Dewar (Postdoctoral Researcher, Department of Biology, University of Oxford, UK)
Bacteria are highly social. Much of this sociality occurs through the production of cooperative ‘public goods’. Unlike in animals, bacterial genes are able to transfer horizontally between individuals, in addition to vertically via descendants. This widespread horizontal gene transfer has implications for the concept of relatedness and how cooperation is maintained in bacteria. It has been suggested that horizontal gene transfer, particularly via small segments of DNA called plasmids, could stabilize cooperation in bacteria. Transfer of a cooperative gene could turn non-cooperative ‘cheats’ into cooperators, preventing cheats from invading and destabilizing cooperation. We tested this with a comparative analysis across bacterial species. In contrast to the predictions of the hypothesis, we found that genes for cooperative traits were not more likely to be carried on either: (1) plasmids compared to chromosomes; or (2) plasmids that transfer at higher rates. Our results were supported by theoretical modelling which showed that, while horizontal gene transfer can help cooperative genes initially invade a population, it has less influence on the longer-term maintenance of cooperation.
Venue: via Zoom
Event Official Language: English
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Seminar
Probing structure of neutron stars through X-ray bursters
January 12 (Fri) at 14:00 - 15:15, 2024
Akira Dohi (Special Postdoctoral Researcher, Astrophysical Big Bang Laboratory, RIKEN Cluster for Pioneering Research (CPR))
Type-I X-ray bursts are rapidly brightening phenomena triggered by the nuclear burning of light elements near the surface of accreting neutron stars. Most of the X-ray bursters show irregular behavior of light curves. However, some X-ray bursters are somehow quite regular, i.e., constant recurrence time and constant shaper of light curves, and are often called Clocked bursters, which are powerful sites to probe uncertainties of many model parameters such as accretion rate, the composition of accreted matter, reaction rates, neutron star structure, and temperature. In this study, we focus on the uncertainties of the equation of states, which determines the latter two properties. Based on our numerical models covering whole areas of neutron stars, we will present their impact on X-ray burst light curves. Furthermore, we will discuss the possibility of constraining the equation of states from Clocked bursters such as GS 1826-24 and 1RXS J180408.9-342058.
Venue: Seminar Room #359 (Main Venue) / via Zoom
Event Official Language: English
701 events