Volume 271

iTHEMS Weekly News Letter

Press Release

Shingo Iwami thumbnail

Success in Calculating Cluster Occurrence Probability for New Coronavirus Infections

2023-10-06

A research group led by Shingo Iwami (Professor, Graduate School of Science, Nagoya University / Visiting Scientist, RIKEN iTHEMS) in collaboration with the University of Oxford (UK), has achieved the world's first successful calculation of the probability of cluster occurrence due to new coronavirus infections.

For more details, please visit Nagoya University's website (in Japanese) or EurekAlert! (in English) through the related links.

Seminar Report

iTHEMS Biology Seminar by Yoshitomo Kikuchi on October 3, 2023

2023-10-04

In this seminar, I hosted Dr. Kikuchi from AIST, who delivered a lecture on the symbiosis between insects and microbes. In agriculture, the development of insecticide resistance in insects is a pressing issue, and one of the contributing factors is the presence of symbiotic bacteria within insects. His seminar experimentally demonstrated that insecticide-resistant bacteria residing in the soil can become symbiotic with insects by being ingested and adapting within the insect's gut.

Their discovery is of significant importance for understanding various causes of insect resistance. Notably, the insects they focus on have very narrow intestinal tunnels, with bacteria either capable or incapable of passing through. Furthermore, they discovered that to traverse these narrow tunnels, bacteria engage in a unique movement called "drill motility," where they wrap their flagella around their bodies and twist while moving.

This drill motility is a highly unique form of movement, and it is currently being researched in their project titled "The Reason why microbes are moving" from ecological, molecular biological, and physical perspectives. In the latter part of the seminar, advancements in the research related to this drill motility were discussed.

These studies on host-microbe interactions based on microbial behavior have evolved into a grand interdisciplinary research effort encompassing physics, mathematics, and informatics. Throughout the seminar, discussions were held regarding the fusion of mathematical sciences with biological research, making it a highly dynamic event.

Reported by Daiki Kumakura

Upcoming Events

Seminar

iTHEMS Biology Seminar

Do higher-order interactions promote coexistence in diverse ecological communities?

October 10 (Tue) at 10:00 - 11:00, 2023

Theo Gibbs (Ph.D. Student, Lewis-Sigler Institute for Integrative Genomics, Princeton University, USA)

A central assumption in most ecological models is that the interactions in a community operate only between pairs of species. However, two species may interactively affect the growth of a focal species. Although interactions among three or more species, called higher-order interactions, have the potential to modify our theoretical understanding of coexistence, ecologists lack clear expectations for how these interactions shape community structure. In this talk, I will analyze two different sets of assumptions for how higher-order interactions impact the dynamics of competing species and show that they lead to differing outcomes. When higher-order interactions are sampled from unconstrained probability distributions, they are unlikely to generate widespread coexistence. In fact, using an analytical technique from statistical physics, I will show many — though not all — of the qualitative rules derived for pairwise interactions still apply to the higher-order case. Higher-order interactions that have specific relationships with the underlying pairwise interactions, however, can stabilize coexistence in diverse communities. I will conclude by briefly discussing ongoing experimental work that seeks to determine whether or not the dynamics of annual plant communities are structured by higher-order interactions.

Venue: via Zoom

Event Official Language: English

Seminar

iTHEMS Biology Seminar

Population genetics in microchannels

October 17 (Tue) at 16:00 - 17:00, 2023

Anzhelika Koldaeva (Postdoctoral Researcher, Biological Complexity Unit, Okinawa Institute of Science and Technology Graduate University (OIST))

Spatial constraints, such as rigid barriers, affect the dynamics of cell populations, potentially altering the course of natural evolution. In this paper, we investigate the population genetics of Escherichia coli proliferating in microchannels with open ends. Our analysis is based on a population model, in which reproducing cells shift entire lanes of cells toward the open ends of the channel. The model predicts that diversity is lost very rapidly within lanes but at a much slower pace among lanes. As a consequence, two mixed, neutral E. coli strains competing in a microchannel must organize into an ordered regular stripe pattern in the course of a few generations. These predictions are in quantitative agreement with our experiments. We also demonstrate that random mutations appearing in the middle of the channel are much more likely to reach fixation than those occurring elsewhere. Our results illustrate fundamental mechanisms of microbial evolution in spatially confined space.

Reference

  1. A. Koldaeva, H.-F. Tsai, A. Q. Shen, and S. Pigolotti, Population genetics in microchannels, Proc. Natl. Acad. Sci. U.S.A. 119, e2120821119 (2022), doi: 10.1073/pnas.2120821119

Venue: via Zoom

Event Official Language: English

Workshop

Introduction to F-Theory

October 18 (Wed) - 20 (Fri), 2023

Shun'ya Mizoguchi (Associate Professor, High Energy Accelerator Research Organization (KEK))

This is the fifth event hosted by the Quantum Gravity Gatherings (QGG) Study Group at RIKEN iTHEMS. For this event, we have invited Professor Shun'ya Mizoguchi from KEK, Tsukuba, to deliver pedagogical lectures on the F-theory and its relation to particle physics. We aim for this event to provide insights to researchers in related fields.

Originally, heterotic string theory was a promising candidate for describing our world, as it naturally incorporated Grand Unified Theory (GUT) based on an exceptional gauge group. However, heterotic theory encounters challenges in moduli fixing. On the other hand, type II theory has an advantage in moduli fixing, but realizing GUT proves to be challenging. The F-theory describes the strongly coupled type IIB string theory, fully utilizing string dualities. This theory appears to realize both the moduli fixing and GUT. Consequently, F-theory plays a central role in string phenomenology. Shun'ya is a leading expert in these areas. We are fortunate to have the opportunity to learn numerous insights into string theory as well as particle physics.

This intensive lecture series is designed to be an interactive event. To facilitate this, the number of participants will be limited to approximately 30. The intensive talk will be given in a face-to-face blackboard style (in English, no online streaming) to encourage informal and lively Q&A discussions. The program will also include short talk sessions, where participants can present a 5-minute talk on a topic of their choice, including their research, reviews of specific works, or future study interests.

Venue: #435-437, 4F, Main Research Building, RIKEN

Event Official Language: English

Seminar

iTHEMS Math Seminar

A cluster algebra structure in the quantum cohomology ring of a quiver variety

October 24 (Tue) at 10:00 - 11:30, 2023

Yingchun Zhang (Postdoctoral Researcher, Institute for Advanced Study in Mathematics, Zhejiang University, China)

The Gromov-Witten theory of a quiver variety is expected to be preserved by quiver mutation according to Seiberg duality, which has been proved to be true for A-type and star-shaped quivers. Cluster algebra can be constructed for a given quiver via quiver mutation. The two subjects Gromov-Witten and cluster algebra seem to differ a lot. Howerver, when we move to the quantum cohomology ring of a quiver variety, Benini-Park-Zhao’s work “indicates” that there should be a cluster algebra structure in the quantum cohomology ring of the quiver variety. In this talk, I will introduce our recent work about the construction of such a cluster algebra structure in the quantum cohomology of a quiver variety. In particular, we will give a proof of the construction for A-type cluster algebra in quantum cohomology of a flag variety.
This is a joint work with Weiqiang He.

Venue: Seminar Room #359, 3F Main Research Building, RIKEN

Event Official Language: English

Seminar

iTHEMS Theoretical Physics Seminar

Topological Aspect of Adsorption Site Selectivity on Metal Surfaces

October 24 (Tue) at 13:30 - 15:00, 2023

Yuta Tsuji (Associate Professor, Faculty of Engineering Sciences, Kyushu University)

In this talk, the presenter will discuss which adsorption structure is preferred in the adsorption of atoms and molecules on metal surfaces based on the topology of the adsorption structures. The method of moments is used to analyze the electronic density of states of the surface. The third-order moment, which characterizes the skewness of the distribution of the electronic density of states, is related to the topology of the triangles at the adsorption interface. By further relating this to the change in energy of the system with the change in electron occupancy of the states, it is shown that it is possible to discuss the relationship between the type of metal and the topological features of the energetically stable adsorption structure.

Venue: Seminar Room #359, 3F Main Research Building, RIKEN / via Zoom

Event Official Language: English

Seminar

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iTHEMS Biology Seminar

Mathematical modelling of the host response to inhalational anthrax across different scales

October 31 (Tue) at 16:00 - 17:00, 2023

Bevelynn Williams (Postdoctoral Fellow, School of Mathematics, University of Leeds, UK)

Inhalational anthrax, caused by the bacterium Bacillus anthracis, is a disease with very high fatality rates. Due to the significant risk posed if the bacterium was to be intentionally used as a bioweapon, it is important to be able to defend against such an attack and to make optimal decisions about treatment strategies. Mechanistic mathematical models can help to quantify and improve understanding of the underlying mechanisms of the infection. In this talk, I will present a multi-scale mathematical model for the infection dynamics of inhalational anthrax. This approach involves constructing individual models for the intracellular, within-host, and population-level infection dynamics, to define key quantities characterising infection at each level, which can be used to link dynamics across scales. I will begin by introducing a model for the intracellular infection dynamics of B. anthracis, which describes the interaction between B. anthracis spores and host cells. The model can be used to predict the distribution of outcomes from this host-pathogen interaction. For example, it can be used to estimate the number of bacteria released upon rupture of an infected phagocyte, as well as the timing of phagocyte rupture and bacterial release. Next, I will show how these key outputs can be used to connect the intracellular model to a model of the infection at the within-host scale. The within-host model aims to provide an overall understanding of the early progression of the infection, and is parametrised with infection data from studies of rabbits and guinea pigs. Furthermore, this model allows the probability of infection and the time to infection to be calculated. Building a model that offers a realistic mechanistic description of these different animal responses to the inhalation of B. anthracis spores is an important step towards eventually extrapolating the model to describe the dynamics of human infection. This would enable predictions of how many individuals would become infected in different exposure scenarios and also on what timescale this would occur.

Venue: via Zoom / Hybrid Format (3F #359 and Zoom), Main Research Building, RIKEN

Event Official Language: English

Seminar

iTHEMS Theoretical Physics Seminar

Compact Star Solutions Beyond General Relativity

November 7 (Tue) at 13:30 - 15:00, 2023

Kota Numajiri (Ph.D. Student, Graduate School of Science, Nagoya University)

The neutron star solutions have been gathering attention. Their high compactness enables us to observationally access the information about extreme regimes of hadron physics. On the other hand, their strong gravity features bring up another possibility, gravity beyond general relativity (GR).
Although GR has been a great success until now, the present scenario for our universe still has several problems, such as dark sectors and the quantum description of gravity. To tackle these problems, the modified gravity theories have been discussed for decades. Their modifications are expected to become noticeable in strong gravity regimes like compact stars.
In this talk, I will discuss the configuration of the compact star solution under the F(R) gravity, one of the most popular and simplest modifications of GR. The background hydrostatic solutions are calculated with some F(R) models, which show non-trivial influences from the additional scalar DOF in this theory. The tidal deformation phenomenon is also considered to focus on another observable, tidal deformability. I will comment on how to utilize obtained observables to determine the gravity theory and the unknown equation of state simultaneously.

Venue: Seminar Room #359, 3F Main Research Building, RIKEN / via Zoom

Event Official Language: English

Seminar

Math-Phys Seminar

Vortex Reconnection in Classical and Quantum Fluids

November 10 (Fri) at 15:00 - 16:30, 2023

Yoshifumi Kimura (Professor, Graduate School of Mathematics, Nagoya University)

As a fundamental process in turbulence, vortex reconnection has been studied widely not only in classical fluids but also in quantum fluids. For the latter, the first real observation of vortex reconnection was rather recent, and since then active analyses have been continued. On the other hand, vortex reconnection in the former has a long history, and it is now studied intensively as a candidate for a solution to the problem of the regularity/Singularity of the Navier-Stokes equations, which is one of the seven millennium prize problems of the Clay Mathematical Institute.
In this talk, after introducing the problem, we will present some results of analysis and simulations of the dynamical system which has been proposed to describe a vortex reconnection of two vortex rings located symmetrically on two tilted planes [1], [2], [3]. Then it will be shown that this dynamical system can be written in noncanonical Hamiltonian form with Hamiltonian, H, and a Casimir invariant, C in the limit of zero viscosity [4].

References

  1. H.K. Moffatt and Y. Kimura, Towards a finite-time singularity of the Navier-Stokes equations. Part 1. Derivation and analysis of dynamical system, J. Fluid Mech. 861, 930 (2019), doi: 10.1017/jfm.2018.882
  2. H.K. Moffatt and Y. Kimura, Towards a finite-time singularity of the Navier-Stokes equations. Part 2. Vortex reconnection and singularity evasion, J. Fluid Mech. 870, R1 (2019), doi: 10.1017/jfm.2019.263
  3. H.K. Moffatt and Y. Kimura, Towards a finite-time singularity of the Navier-Stokes equations. Part 3. Vortex reconnection and singularity evasion, J. Fluid Mech. 967, R1 (2023), doi: 10.1017/jfm.2023.472
  4. P.J. Morrison and Y. Kimura, A Hamiltonian Description of Finite-Time Singularity in Euler’s Fluid Equation, Phys. Lett. A 484, 129078 (2023), doi: 10.1016/j.physleta.2023.129078

Venue: Seminar Room #359, 3F Main Research Building, RIKEN / via Zoom

Event Official Language: English

Workshop

Takashi Okada thumbnail

iTHEMS Graph-theory workshop: from basics to applications

November 13 (Mon) - 14 (Tue), 2023

Momoko Hayamizu (Assistant Professor, Faculty of Science and Engineering, School of Fundamental Science and Engineering, Waseda University / PRESTO Researcher, Japan Science and Technology Agency (JST))
Seiya Negami (Professor Emeritus, Yokohama National University)
Takashi Okada (Program-Specific Associate Professor, Institute for Life And Medical Sciences, Kyoto University)
Tasuku Soma (Associate Professor, Department of Statistical Inference and Mathematics, The Institute of Statistical Mathematics / Associate Professor, Statistical Science Program, The Graduate University for Advanced Studies (SOKENDAI))
Shun'ichi Azuma (Professor, Garduate School of Informatics, Kyoto University)

We will hold a two-day workshop on graph theory, which covers a variety of topics including basic concepts and theorems in graph-theory; graph-embedding; phylogenetic tree construction; chemical reaction networks; and cactus network theory.

The details are found in the website linked below.

Venue: #435-437, Main Research Building, RIKEN

Event Official Language: English

Colloquium

iTHEMS Colloquium

Bridging physics and society: A case study of collective memory dynamics by socio-econophysics approach

November 20 (Mon) at 15:00 - 16:30, 2023

Yukie Sano (Associate Professor, Institute of Systems and Information Engineering, University of Tsukuba)

The movements of individuals with free will are unpredictable, complex, and, needless to say, fundamentally distinct from the movements of matter. Furthermore, studying society, which forms collectives while engaging in intricate individual interactions, using mathematical models seems incredibly daunting. However, when analyzing empirical data, relatively simple mathematics often emerge in the distribution and dynamics of society at the level of collective behavior. Additionally, such mathematics often share commonalities with physical phenomena. With this background, research is progressing by applying ideas from physics to social-economic phenomena, a field known as socio-econophysics. In this presentation, I will introduce a mathematical model that addresses the decay of collective memory using access logs on the web as an example of research in socio-econophysics.

Venue: Okochi Hall, 1F Laser Science Laboratory, RIKEN / via Zoom

Event Official Language: English

Seminar

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ABBL-iTHEMS Joint Astro Seminar

Early Formation of Dark Matter Halos

November 24 (Fri) at 14:00 - 15:15, 2023

Derek Beattie Inman (Research Scientist, iTHEMS)

Cosmological observations have led to an extremely precise understanding of the large-scale structure of the Universe. A common assumption is to extrapolate large-scale properties to smaller scales; however, whether this is correct or not is unknown and many well-motivated early Universe scenarios predict substantially different structure formation histories. In this seminar I will discuss two scenarios where nonlinear structures form much earlier than is typically assumed. In the first case, the initial fluctuations are enhanced on small scales leading to either primordial black holes clusters or WIMP minihalos right after matter-radiation equality. In the second, I will show that an additional attractive dark force leads to structure formation even in the radiation dominated Universe. I will furthermore discuss possible observations of such early structure formation including changes to the cosmic microwave background, dark matter annihilation, and when the first galaxies form.

Venue: Seminar Room #359, 3F Main Research Building, RIKEN / via Zoom

Event Official Language: English

Workshop

Integrated Innovation Building (IIB) venue photo

Second Workshop on Fundamentals in Density Functional Theory (DFT2024)

February 20 (Tue) - 22 (Thu), 2024

The density functional theory (DFT) is one of the powerful methods to solve quantum many-body problems, which, in principle, gives the exact energy and density of the ground state. The accuracy of DFT is, in practice, determined by the accuracy of an energy density functional (EDF) since the exact EDF is still unknown. Currently, DFT has been used in many communities, including nuclear physics, quantum chemistry, and condensed matter physics, while the fundamental study of DFT, such as the first principle derivations of an accurate EDF and methods to calculate many observables from obtained densities and excited states. However, there has been little opportunity to have interdisciplinary communication.

On December 2022, we had the first workshop on this series (DFT2022) at Yukawa Institute for Theoretical Physics, Kyoto University, and several interdisiplinary discussions and collaborationd were started. To share such progresses and extend collaborations, we organize the second workshop. In this workshop, the current status and issues of each discipline will be shared towards solving these problems by meeting together among researchers in mathematics, nuclear physics, quantum chemistry, and condensed matter physics.

This workshop mainly comprises lectures/seminars on cutting-edge topics and discussion, while a half-day session composed of contributed talks is also planned.

This workshop is partially supported by iTHEMS-phys Study Group. This workshop is a part of the RIKEN Symposium Series.

The detailed information can be found in the workshop website.

Venue: 8F, Integrated Innovation Building (IIB), Kobe Campus, RIKEN / via Zoom

Event Official Language: English

Person of the Week

Yuto Yamamoto thumbnail

Self-introduction: Yuto Yamamoto

2023-10-06

I specialize in tropical geometry, a field of mathematics that naturally emerges when considering the limits of spaces with respect to some parameters. My primary research interest lies in calculating the limits of invariants of the spaces using tropical geometry. Despite being a relatively new field, tropical geometry has already demonstrated its applicability to other various sciences. During my time at iTHEMS, I look forward to exploring such applicational aspects of tropical geometry as well.

Person of the Week

Misako Tatsuuma thumbnail

Self-introduction: Misako Tatsuuma

2023-10-06

I'm Misako Tatsuuma, and I joined iTHEMS as a Research Scientist in October 2023. My research focuses on planetary formation theory. Specifically, I'm working on the formation process of planetesimals, which are kilometer-sized bodies like comets and asteroids, from micron-sized cosmic dust grains. This process is still not fully understood and has been extensively studied through observations, explorations, experiments, and simulations. My approach involves investigating the material strengths of dust aggregates using dust grain N-body simulations and comparing the results with explorational findings of comets and asteroids in our solar system. I got my Ph.D. in March 2022 at the University of Tokyo and subsequently began the JSPS fellow (PD) at Tokyo Institute of Technology. As for personal, I'm a mother of two and facing the ongoing challenge of balancing childcare and research.

Person of the Week

Shinichiro Fujii thumbnail

Self-introduction: Shinichiro Fujii

2023-10-05

My name is Shinichiro Fujii. I was originally a nuclear theorist. After finishing my PhD at Kyushu University in 2000, I joined RIKEN as a special postdoctral researcher. After that, I had several positions including associate professor at the University of Tokyo. After a period of unemployment at the age of 40 due to the term limit, I was hired by JST-CRDS as a fellow in 2013. I conducted research and survey activities to formulate Japan's science and technology policy for 5 years. After that, I was involved in the management of large national projects related to quantum computers and quantum communications, such as JST-ERATO, Q-LEAP and Moonshot Goal 6, at the University of Tokyo and Yokohama National University for 5 years. 23 years after beginning my career as a researcher at RIKEN, I am back to RIKEN as a coordinator in 2023. I would like to contribute to creating a better environment for researchers and enhancing the value of RIKEN.

Paper of the Week

Week 2, October 2023

2023-10-05

Title: The deconfinement phase transition in $Sp(2N)$ gauge theories and the density of states method
Author: David Mason, Biagio Lucini, Maurizio Piai, Enrico Rinaldi, Davide Vadacchino
arXiv: http://arxiv.org/abs/2310.02145v1

Title: Classification of High-Ordered Topological Nodes Towards MFBs in Twisted Bilayers
Author: Fan Cui, Congcong Le, Qiang Zhang, Xianxin Wu, Jiangping Hu, Ching-Kai Chiu
arXiv: http://arxiv.org/abs/2310.00662v1

Title: Berry's phase and quantum mechanical formulation of anomalous Hall effect
Author: Kazuo Fujikawa, Koichiro Umetsu
arXiv: http://arxiv.org/abs/2310.02052v1

Title: Possible inconsistency between phenomenological and theoretical determinations of charge symmetry breaking in nuclear energy density functionals
Author: Tomoya Naito, Gianluca Colò, Tetsuo Hatsuda, Haozhao Liang, Xavier Roca-Maza, Hiroyuki Sagawa
arXiv: http://arxiv.org/abs/2309.17060v1

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