Seminar

Journal Club: Intrinsically Disordered Region (IDR)

May 19 (Wed) 13:00 - 14:00, 2021

Kyosuke Adachi (Special Postdoctoral Researcher, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS) / Special Postdoctoral Researcher, Nonequilibrium Physics of Living Matter RIKEN Hakubi Research Team, RIKEN Center for Biosystems Dynamics Research (BDR))

A class of protein domain, which is called intrinsically disordered region (IDR), is known to take no rigid three dimensional structure. Recent studies have shown that IDRs can show biological functions through phase separation, and it is important to clarify what kind of amino acid sequence of IDR leads to phase separation and what kind of mutation results in malfunction. In this journal club, I will discuss these topics by reviewing recent papers. *Detailed information about the seminar refer to the email.

Venue: via Zoom

Event Official Language: English

iTHEMS-phys Intro Meeting on May 18, 2021

May 18 (Tue) 13:00 - 14:30, 2021

Masaru Hongo (Postdoctoral Research Associate, Physics Department, The University of Illinois at Chicago (UIC), USA)
Etsuko Itou (Contract Researcher, Strangeness Nuclear Physics Laboratory, RIKEN Nishina Center for Accelerator-Based Science (RNC))
Nobuyuki Matsumoto (Special Postdoctoral Researcher, Computing Group, RIKEN BNL Research Center, RIKEN Nishina Center for Accelerator-Based Science (RNC))

13:00-13:20 [JST] Masaru Hongo 13:20-13:40 [JST] Etsuko Itou 13:40-14:00 [JST] Nobuyuki Matsumoto 14:00- Free discussion

Venue: via Zoom

Event Official Language: English

iTHEMS-phys Intro Meeting on May 17, 2021

May 17 (Mon) 13:00 - 14:30, 2021

Tetsuo Hatsuda (Program Director, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS))
Akira Harada (Special Postdoctoral Researcher, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS))
Tsukasa Tada (Vice Chief Scientist, Quantum Hadron Physics Laboratory, RIKEN Nishina Center for Accelerator-Based Science (RNC))

13:00-13:20 [JST] Tetsuo Hatsuda 13:20-13:40 [JST] Akira Harada 13:40-14:00 [JST] Tsukasa Tada 14:00- Free discussion

Venue: via Zoom

Event Official Language: English

Geometry of canonical metrics on Kähler manifolds

May 14 (Fri) 16:00 - 18:10, 2021

Eiji Inoue (Special Postdoctoral Researcher, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS))

The aim of this talk is to report recent trends in Kähler geometry. Kähler geometry consists of two aspects: the one is algebraic geometry and the other is metric geometry.The first one hour is an introduction for non-mathematicians. I begin with a simple example of algebraic variety from ancient Greek, which I believe is the simplest example illustrating motivation for compact complex manifolds. On the other hand, I explain the first motivation for canonical metrics in Kähler geometry via Riemann’s uniformization theorem.The last one hour is an introduction to recent trends in Kähler geometry, especially Kähler-Einstein metrics. The existence of Kähler-Einstein metrics turns out to be related to geometry of degenerations of space, which is so called Yau-Tian-Donaldson conjecture. I explain various aspects of this topic. We encounter deep studies in metric geometry, birational geometry and non-archimedean geometry. I finally explain recent breakthrough on Kähler-Ricci flow.The goal of this talk is the starting point of my study. I briefly explain my study if time permits.

Venue: via Zoom

Event Official Language: English

Modeling Membrane Morphological Change during Autophagosome Formation

May 14 (Fri) 10:00 - 11:00, 2021

Yuji Sakai (Visiting Scientist, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS) / Assistant Professor, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo)

Membrane-bound organelles compartmentalize eukaryotic cells and adopt various characteristic shapes such as disk-shaped, tubules, spherical vesicles, and their intermediate structures. Organellar morphology is regulated by protein and lipid compositions. Because organellar shape directly relates to organellar function, it is important to understand the mechanisms regulating organelle morphology. In autophagy, the morphologies of the isolation membrane change from disk- to cup-shaped, closed spherical double-membrane structure. Eventually the membrane engulfs the cytoplasmic materials. In this study [1], we investigate the dynamics of the continuous membrane morphological transition in autophagy, which is governed by the spatiotemporal regulation of curvature generators. *Please refer to the email to get access to the Zoom meeting room.

Venue: via Zoom

Event Official Language: English

Aperiodic and amorphous topological phases

May 12 (Wed) 17:00 - 18:15, 2021

Christopher Bourne (Visiting Scientist, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS) / Assistant Professor, Advanced Institute for Materials Research (AIMR), Tohoku University)

Key features of topological insulators and superconductors such as stable edge modes have been found in an increasingly broad class of materials and systems. In this talk, I will introduce a mathematical framework to study Hamiltonians and topological phases on a general class of (aperiodic/random) point atterns. Using techniques from noncommutative geometry, we then show how bulk topological invariants and the bulk-boundary correspondence can be rigorously established in such generic systems. This is based on joint work with Emil Prodan and Bram Mesland. *Detailed information about the seminar refer to the email.

Venue: via Zoom

Event Official Language: English

Emulation for lensing and clustering observables of the cosmological large-scale structure

May 12 (Wed) 10:00 - 11:00, 2021

Takahiro Nishimichi (Yukawa Institute for Theoretical Physics, Kyoto University)

Recent developments in observational technologies open exciting opportunities to map out the detailed structure of the universe. Remarkably, the unique combination of imaging and spectroscopic galaxy surveys is now becoming well established as a standard analysis methodology for precision cosmology. While the former can access directly the underlying clustering of mass dominated by dark matter projected on the sky through the weak gravitational lensing effect, the latter provides us with the three dimensional map of the structure traced by galaxies. One can mitigate the galaxy-bias uncertainty, which has been the major obstacle for cosmology based on galaxy surveys, by jointly analyzing these effects. We still need, however, a robust and versatile theoretical and statistical framework to interpret these datasets. The Dark Quest project, launched in 2015, is a structure formation simulation campaign precisely for this purpose. We have developed an emulation tool, dubbed as Dark Emulator, based on a large database of simulated dark matter halos in virtual universes with different cosmologies efficiently sampled in six-dimensional parameter space. Dark Emulator employs a simple machine-learning architecture with Gaussian process at its core. It makes predictions of various statistical measures of dark matter halos, both lensing and clustering observables, for a given cosmological parameters in a few seconds on laptop computers without running a new simulation. This AI-aided tool, once supplemented with recipes for the halo-galaxy connection, is therefore applicable to real-data analyses as the theoretical template, which typically requires hundreds of thousands of function calls in the course of parameter inference. I will introduce this project and report the status of its application to Subaru HSC data. We are looking forward to seeing you online.

Venue: via Zoom

Event Official Language: English

Kullback-Leibler divergence and stochastic dynamics

May 6 (Thu) 10:00 - 11:00, 2021

Ryosuke Iritani (Research Scientist, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS))

*Detailed information about the seminar refer to the email.

Event Official Language: English

Thermodynamic Uncertainty Relation Connects Physics, Information Science, and Biology

April 28 (Wed) 13:30 - 16:00, 2021

Yoshihiko Hasegawa (Associate Professor, Department of Information and Communication Engineering, The University of Tokyo)

Higher precision demands more resources. Although this fact is widely accepted, it has only recently been theoretically proved. The thermodynamic uncertainty relation serves as a theoretical basis for this notion, and it states that current fluctuations are bounded from below by thermodynamic costs, such as entropy production and dynamical activity. In this seminar, I show a strong connection between the thermodynamic uncertainty relation and information theory by deriving it through information inequality known as a Cramér-Rao bound, which provides the error bound for any statistical estimator. Moreover, by using a quantum Cramér-Rao bound, I derive a quantum extension of thermodynamic uncertainty relation, which holds for general open quantum systems. The thermodynamic uncertainty relation predicts the fundamental limit of biomolecular processes, and thus it can be applied to infer the entropy production, corresponding to the consumption of adenosine triphosphate, of biological systems in the absence of detailed knowledge about them. *Detailed information about the seminar refer to the email.

Venue: via Zoom

Event Official Language: English

Alternative tsunami observing and forecasting systems

April 22 (Thu) 16:00 - 18:10, 2021

Iyan Mulia (Research Scientist, Prediction Science Laboratory, RIKEN Cluster for Pioneering Research (CPR))

Dedicated tsunami observing systems are mostly expensive and are often not sustainable. Therefore, alternative approaches should be implemented to overcome the issues. We introduced innovative ways to observe tsunamis using existing instrumentation available on unconventional platforms such as commercial vessels and airplanes. Our study demonstrated that the accuracy of the proposed observing systems is adequate for detecting large tsunamis offshore. The use of such systems is expected to provide more cost-effective and sustainable observations for the future. Additionally, we also developed a tsunami forecasting system based on machine learning to improve or complement the conventional methods that typically require considerable computational resources. On the contrary, the main appealing feature of the machine learning is the computational speed that would be suitable for a real-time prediction of tsunami inundation or flooding. We found that the application of machine learning can significantly improve the computing time without sacrificing the accuracy compared to the conventional methods.

Venue: via Zoom

Event Official Language: English

The rheotaxis mechanism of swimming ciliates

April 22 (Thu) 10:00 - 11:00, 2021

Yukinori Nishigami (Research Institute for Electronic Science, Hokkaido University)

The swimming unicellular organisms, which live in freshwater, need to resist currents in the environment. Without this ability, their habitat changes with the flow, and they cannot survive in nature for a long time. It is reported that a kind of swimming microorganism, Paramecium, exhibits upstream swimming in 1904. However, the mechanism of the behavior has been still unclear. To elucidate the mechanism, we observed the behavior of a ciliate in a flow field and performed numerical fluid calculations. My results suggest that the rheotaxis is realized by cell shape and inhibition of ciliary beating near the wall. *Please refer to the email to get access to the Zoom meeting room.

Venue: via Zoom

Event Official Language: English

Unconventional Spin Transport in Quantum Materials

April 21 (Wed) 17:00 - 18:15, 2021

Se Kwon Kim (Korea Advanced Institute of Science and Technology (KAIST), Republic of Korea)

Recent advancements in spintronic techniques originally developed for spin-based devices now enable us to study fundamental spin physics of various quantum materials with unprecedented spin-current control and measurement, opening a new area of theoretical and experimental investigation of quantum systems. In this talk, we will introduce this emerging research area of spin transport in quantum materials which is fueled by the global interest in quantum information science. As examples, we will discuss our discovery of magnonic topological insulators realized by 2D magnets [1-3], which shows how spintronic techniques can be used for probing elusive quantum materials, and our prediction of long-range spin transport mediated by a vortex liquid in superconductors [4], which shows that quantum materials can provide novel platforms for efficient spin-transport devices. We will conclude the talk by offering a future outlook on quantum spintronics. *Detailed information about the seminar refer to the email.

Venue: via Zoom

Event Official Language: English

Liquid condensates in cell nucleus

April 15 (Thu) 10:00 - 11:00, 2021

Kyosuke Adachi (Special Postdoctoral Researcher, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS) / Special Postdoctoral Researcher, Nonequilibrium Physics of Living Matter RIKEN Hakubi Research Team, RIKEN Center for Biosystems Dynamics Research (BDR))

I will give a talk in a journal club style. I will introduce recent papers regarding liquid-liquid phase separation in cells. In cell biology, several types of liquid condensates of proteins/RNAs have been found recently. The functions of such condensates and the physical mechanism of controlling the liquid state are intensely discussed. In this talk, I will focus on liquid condensates in the cell nucleus and review recent experimental results. *Please refer to the email to get access to the Zoom meeting room.

Venue: via Zoom

Event Official Language: English

What "Holography" is and how to use it

April 14 (Wed) 17:00 - 18:15, 2021

Mario Flory (Instituto de Fisica Teorica, Universidad Autonoma de Madrid, Spain)

In this talk, I will give an introduction to the holographic principle and the Anti-de Sitter/Conformal Field Theory (AdS/CFT) correspondence. I will also discuss the role that quantum entanglement plays in this correspondence via the Ryu-Takayanagi formula which maps the calculation of entanglement entropy to a geometric problem of extremal surfaces. Then, I will present a holographic model of a Kondo like effect as an example of how the AdS/CFT correspondence can be employed in practice. *Detailed information about the seminar refer to the email.

Venue: via Zoom

Event Official Language: English

Journal Club: Trace inequalities and their applications

April 14 (Wed) 14:30 - 15:30, 2021

Yukimi Goto (Special Postdoctoral Researcher, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS))

In this talk, I will explain trace inequalities and related topics. Mainly, I focus on results concerning quantum entropy. This talk is an elementary introduction to that subjects. *Detailed information about the seminar refer to the email.

Venue: via Zoom

Event Official Language: English

Self-adjoint extension in quantum mechanics and non-Rydberg spectra of one-dimensional hydrogen atom

April 13 (Tue) 16:00 - 18:10, 2021

Takuju Zen (Professor, School of Environmental Science and Engineering, Kochi University of Technology)

We offer a beginner’s guide to the functional-analytical techniques in quantum mechanics, and cover its application to the 1D Coulomb problem. It is shown that the wave function at the diverging point of the Coulomb potential is mathematically described by three-parameter family of generalized connection conditions. A scheme is devised to physically implement the generalized conditions, which provides the way to experimentally realize non-Rydberg spectra in 1D Hydrogen atom. Schedule: Part 1, Self-adjoint extension of Hilbert space operator Part 2, 1D Coulomb problem

Venue: via Zoom

Event Official Language: English

Simple models of cancer growth, MCMC parameter estimation and identifiability

April 8 (Thu) 10:00 - 11:00, 2021

Catherine Beauchemin (Deputy Program Director, RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS) / Professor, Department of Physics, Ryerson University, Canada)

I would like to introduce some basic concepts about (very simple) mathematical model of cancer growth, the basic math behind parameter estimation via Markov chain Monte Carlo (MCMC) based on Bayes' theorem, and the different diagnostics you can use to know if the parameters are correctly estimated. I will use a recent example with cancer data in mice. I think this seminar can be interesting to mathematicians (because of the models and the math behind the parameter estimation, but the math is very basic!), to physicists (especially those that have to do some parameter estimation), and to biologists (the cancer model/data and the parameter estimation). I think it will also be interesting to the information theory and prediction science people. MCMC parameter estimation based on physical models is more valuable in my field than machine learning, so I think those interested in machine learning but maybe are not so familiar with MCMC should join to consider them as an alternative approach in certain contexts. *Please refer to the email to get access to the Zoom meeting room.

Venue: via Zoom

Event Official Language: English

Long-time behavior of moving solids in a fluid and the kinetic theory of gases

April 7 (Wed) 16:00 - 18:10, 2021

Kai Koike (JSPS Fellow, Graduate School of Engineering, Kyoto University)

Understanding dynamics of solids in a fluid is a fundamental problem in fluid dynamics. Due to the growing interest in engineering in out-of-equilibrium situations, moving boundary problems for kinetic equations such as the Boltzmann equation have become an active area of research. In the first part of the talk, I shall explain recent, especially mathematical, developments in this field. Then in the second part, I'd like to explain my results concerning the long-time behavior of a point particle moving in a 1D viscous compressible fluid. These results aim to give some explanation of related numerical simulations for a BGK model of the Boltzmann equation.

Venue: via Zoom

Event Official Language: English

Structural reduction of chemical reaction networks based on topology

April 1 (Thu) 10:00 - 11:00, 2021

Yuji Hirono (Junior Research Group Leader/Assistant Professor, Research Division, Asia Pacific Center for Theoretical Physics, Republic of Korea)

Chemical reactions form a complex network in living cells and they play vital roles for physiological functions. An amusing question is how the structure of a reaction network is linked to its chemical functionalities. I’ll talk about a method of the reduction of chemical reaction networks, which is convenient for extracting important substructures. Mathematical concepts such as homology and cohomology groups are found to be useful for characterizing the shapes of reaction networks and for tracking the changes of them under reductions. For a given chemical reaction network, we identify topological conditions on its subnetwork, reduction of which preserves the steady state of the remaining part of the network.

Venue: via Zoom

Event Official Language: English

Evolutionary conservativeness and diversification of cycads: Understanding the evolution of living fossils

March 25 (Thu) 10:00 - 11:00, 2021

José Said Gutiérrez-Ortega (Assistant Professor, Institute for Excellence in Educational Innovation, Chiba University)

The cycads are a lineage of gymnosperms that represent an example of biological stasis success. Despite their early origin in the seed plant evolution, they survived multiple events of mass extinction and could diversify in modern tropical ecosystems during the Cenozoic, especially in countries known for their great biodiversity such as Mexico. What factors have allowed their persistence and diversification despite their conservative nature? I have studied the cycad genus Dioon, a group of 17 species occurring in habitats ranging from tropical forests to arid zones in Mexico and Honduras. Phylogenetic and phylogeographic analyses revealed that the diversification of Dioon has been driven by the long-term process of aridification of Mexico since the Miocene. The lineages that shifted from mesic forests to arid zones show leaf trait variations beneficial against water stress; this feature can be also observed at the inter-population level when comparing mesic versus arid sister pairs. What mechanism allows this aridification-driven diversification? Using population genetics and ecological niche modeling on sister lineage pairs, I have revealed that lineages at arid zones might tolerate arid environments, but within the arid habitat, they retain the same ancestral niche also observed on their mesic sisters. The surrounding areas that are suboptimal for their niches serve as barriers against gene flow: this promotes allopatric speciation. This research has revealed that the mechanism that allows the diversification process in Dioon involves three factors: 1) a habitat shift due to aridification, 2) niche conservatism that facilitates geographic isolation, 3) gaining unique morphological and anatomical features that help to counteract water stress, probably through long-term stabilizing selection. This research highlights the importance of biological conservatism in evolution, and how “living fossils” can still diversify into modern ecosystems.

Venue: via Zoom

Event Official Language: English