Center for Mathematical Science and Advanced Technology (MAT)

Seminar Schedule

[MAT Seminar]

Date:

2024/08/01(Thursday) 13:00-15:00

Language:

English

Location:

MAT Theater, 508, InformationTechnology Building 5F, Yokohama Institute for Earth Sciences (YES)

Speaker:

Tetsuya Hiraiwa (Institute of Physics, Academia Sinica, Taiwan)

Title:

Computer simulations on influence of mechanical perturbations due to actions of subnuclear molecules on chromatin organization and dynamics

Abstract:

Genetic information in a eukaryotic cell is stored in its chromatin, a polymer-like composite of DNA and proteins, densely packed within the nucleus. Physical spacing of chromatin is critical in regulating bio-chemical and transcriptional abilities of genes, and proper functionality of the genomic content depends on the nonrandom organization of chromatin. Meanwhile, in a living cell, other subnuclear molecules, such as enzymes like polymerase and topoisomerase, act to facilitate cellular functions. Mechanical perturbation due to such actions of molecules may affect the chromatin organization and dynamics. In this talk, I would like to explain our computer-simulation studies about such effect, based on polymer-physics concepts and the GPU-aided computations, where we focused on a type of actions of molecules that we call catch-and-release action and implemented in the way inspired by a class of molecules like topoisomerase-II. I will share with the participants the results of our simulations on how it affects chromatin organization and dynamics. The results clarified (i) that the mechanical perturbation of such actions can modulate the phase separation organizations of chromatin called heterochromatic and euchromatic regions [1], and (ii) that the mechanical perturbation enhances fluctuating dynamics of inclusions in chromatin through the newly-proposed dynamic mode of chromatin remodeling [2].

References ---
[1] R Das, T Sakaue, GV Shivashankar, J Prost, T Hiraiwa (2022) "How enzymatic activity is involved in chromatin organization", eLife 11, e79901
[2] R Das, T Sakaue, GV Shivashankar, J Prost, T Hiraiwa (2024) “Chromatin Remodeling Due to Transient-Link-and-Pass Activity Enhances Subnuclear Dynamics", Physical Review Letters 132, 058401.

[MAT Seminar]

Date:

2024/07/24(Wednesday) 13:00-15:00

Language:

English

Location:

MAT Theater, 508, InformationTechnology Building 5F, Yokohama Institute for Earth Sciences (YES)

ZoomURL:

https://us02web.zoom.us/j/84174291596?pwd=OkifY8FybgEAaDTXHlaoftPfIzWsOK.1

Speaker:

Vikash Churasia (OIST)

Title:

Shape Preserving Everting Motion of Orientable or Nonorientable, Knotless, and Knotted Bands

Abstract:

Eversion, the process of turning bodies inside out, is a fascinating phenomenon observed widely in nature that has intrigued elasticians and mathematicians for decades. We introduce a novel framework for achieving continuous, periodic, everting motions of both orientable and nonorientable, as well as knotless and knotted bands, extending beyond the eversion of simple objects like halved tennis balls and cylindrical tubes. Our analytical approach yields a traveling wave solution that describes this unique class of motions. Each motion is isometric, preserving inter-point distances on the band, and isoenergetic, maintaining constant elastic bending energy throughout the process. This shape-preserving motion enriches the known categories of band transformations, previously limited to rigid rotations and translations. Potential applications of this work include the development of adaptive materials and soft robotic systems with dynamically tunable properties, which could drive innovation across diverse fields such as medical, aerospace, and architectural engineering.

[MAT Seminar]

Date:

2024/07/17(Wednesday) 13:00-15:00

Language:

English

Location:

MAT Theater, 508, InformationTechnology Building 5F, Yokohama Institute for Earth Sciences (YES)

ZoomURL:

https://us02web.zoom.us/j/84174291596?pwd=OkifY8FybgEAaDTXHlaoftPfIzWsOK.1

Speaker:

Riccardo Muolo (Tokyo Tech)

Title:

Effects of higher-order interactions on synchronization dynamics: from phase reduction to chimera states

Abstract:

Synchronization is a ubiquitous emergent phenomenon in which an ensemble of elementary units behaves in unison due to their interactions. Given the pervasiveness of synchronization, understanding how it is achieved is a fundamental question. In particular, the nature of the interactions among oscillators has strong consequences on the transition to synchronization. To tackle this issue, it is convenient to consider phase models in which each oscillator is described solely in terms of a phase variable. According to phase reduction theory, the phase model captures the dynamics completely when the coupling among the oscillators is sufficiently weak. If one considers only pairwise interactions, the synchronization transition is described by the Kuramoto-type model. Despite the versatility of such an approach, the classical theory of synchronization is solely based on pairwise interactions, while, in many natural systems, the interactions are intrinsically higher-order (many-body) rather than pairwise. In fact, many examples show that a pairwise description is not sufficient to match the theory with observations and, additionally, higher-order interactions appear naturally when phase reduction is performed up to higher orders. It was also shown that extensions of the Kuramoto model including higher-order interactions exhibit an explosive transition to synchrony or collective chaos. I will start by introducing the phase reduction theory and highlight the universality of phase models. Then, after discussing the basics of higher-order interactions, I will present a recent work where we analyzed the collective dynamics of the simplest minimal extension of the Kuramoto-type phase model for identical globally coupled oscillators subject to two- and three-body interactions and showed how the many-body interactions greatly enriches the behaviors of the system. In the last part of the seminar, I will briefly introduce an intriguing type of synchronization patterns, in which coherent and incoherent oscillators coexist, called chimera states. Such patterns, studied, among others, by Kuramoto and Battogtokh, are known to be elusive and characterized by a very short life-time when the interactions are pairwise; however some of these limitations can be overcome in systems where higher-order interactions are present.

[MAT Seminar]

Date:

2024/07/09(Tuesday) 11:00 - 12:00

Language:

English

Location:

MAT Theater, 508, InformationTechnology Building 5F, Yokohama Institute for Earth Sciences (YES)

ZoomURL:

https://us02web.zoom.us/j/84174291596?pwd=OkifY8FybgEAaDTXHlaoftPfIzWsOK.1

Speaker:

Davide Bigoni (University of Trento, Italy)

Title:

Metamaterials knocking on material instabilities’ door

Abstract:

Homogenization of periodic elastic grids subject to axial prestress is introduced to obtain equivalent elastic materials exhibiting material instabilities, driven by the microstructure of the grid and its level of prestress. Instabilities include shear band fromation and Hopf bifurcation, thus leading to odd elasticity.
A design strategy is introduced for metamaterials displaying tailored instabilities. When the latter occur at the microscale, they are analyzed with a Floquet-Bloch wave technique, while analysis of macroinstabilities leads to the definition of an equivalent elastic material. This material can be obtained via homogenization theory for periodic elastic structures, subject to a state of axial prestress and incremental deformation involving axial and shear forces and bending moment. Macroinstabilities in the form of shear bands usually occur only for compressive prestress, so that the stability domain for the equivalent material results unbounded in tension. We show that it is possible to design a material for which the stability domain is bounded, in other words, for which shear bands may form under tensile loads. The architecture of this structure leads to multiple band gaps, flat bands, and Dirac cones. The possibility of a Hopf bifurcation is introduced, as related to the presence of follower loads, or nonholonomic constraints, or discontinuity in the constraint curvature. When this instability is implemented in a material, apparently work is produced in a closed strain cycle, so that conservation of energy is apparently violated. As mentioned, this violation is only apparent, as the material is able to “suck and release” energy from the environment. When a material is subject to a Hopf bifurcation, mechanical waves propagate through it without decaying, rather with amplification, because energy is extracted from the surroundings.

Speaker:

Diego Misseroni (University of Trento, Italy)

Title:

Origami Metamaterials and Structures: Theoretical Insights and Experimental Validation

Abstract:

Origami metamaterials provide a versatile framework for finely tuning mechanical properties through intricate folding arrangements. This seminar unveils two novel experimental setups tailored for probing Poisson effects in deployable metamaterials and delve into the mechanics of Kresling tubes.
The first setup focuses on assessing Poisson's ratio across diverse origami patterns: the standard Miura-ori, Eggbox, the newly devised Morph, and Trimorph pattern. Notably, our investigations showcase the unique capability of Morph pattern to reverse Poisson's ratio sign and exhibit entirely positive or negative values via topological transformations. Our comprehensive analysis, integrating theoretical predictions, simulations, and experimental data, underscores the remarkable tunability of Poisson's ratio in origami metamaterials, solidifying the alignment across these domains.
The second setup is dedicated to unraveling the mechanical intricacies of Kresling tubes, comprising even and odd numbers of Kresling units with both similar and dissimilar chirality. This setup features two fixtures enabling independent control of axial displacement (contraction/expansion) and twist, without imposing constraints on the chiral arrangement of individual cells within the Kresling origami array. The fundamental nature of this work makes it applicable to several field of engineering, including soft robotics and mechanical computing.

[MAT Seminar]

Date:

2024/05/24(Friday) 13:00 - 15:00

Language:

Japanese

Speaker:

Takashi Minoshima

Title:

BepiColombo and STELEO observations and numerical modelling of solar energetic particle events in March 2022.

Abstract:

Solar Energetic Particles (SEPs) are high-energy charged particles spanning from a few keV to several GeV, which are generated in association with energetic phenomena on the Sun (flares and CMEs), and then are ejected into interplanetary space. Given that SEPs offer insights into acceleration and transport mechanisms in collisionless plasmas, understanding their origin and dynamics is of great interest to space plasma physics and relevant fields (e.g., high-energy astrophysics and laser plasma physics). Furthermore, accurate prediction of the SEP profile is required for space weather operations, as SEPs exceeding 10 MeV pose primary threats to the space environment, including radio communication failure, malfunction and degradation of equipment onboard aircraft and satellites, and radiation exposure of astronauts during extravehicular activities. This is expected to become more and more important in the future as humanity expands its activity beyond the Earth’s magnetosphere.

Unraveling the SEP physics presents a formidable challenge. On the theoretical front, the rigorous description of SEPs requires a first-principle kinetic treatment while the system scale of the Sun-Earth environment is far beyond the magnetohydrodynamic scale. On the observational front, SEPs have been conventionally observed by in-situ measurement of an individual satellite, resulting in information about physical mechanisms of acceleration and transport of SEPs being convolved during their journey from the Sun to the observation point. Presently, many satellites are operating to measure SEPs at different radii and longitudes, giving a valuable opportunity to integrate theoretical modeling with multi-satellite observations to extract their physical knowledge.

M and X-class flares, along with subsequent CMEs, occurred on 28 and 30 March, 2022. The propagations of CMEs and background solar wind were reconstructed by the global MHD simulation of the heliosphere based on the ground-based interplanetary scintillation (IPS) observation, IPS-SUSANOO. Two associated SEP events were observed simultaneously by BepiColombo at 0.6 AU and STEREO A at 1 AU. Fortunately, both satellites were positioned approximately along the same Parker spiral. In both events, the Solar Particle Monitor onboard BepiColombo/MMO detected 40-200 MeV ions approximately within one hour after the flare, with their peak exhibiting velocity dispersion indicative of ballistic motion. Time-of-flight analysis suggests the expected starting point to be 0.5-0.7 AU from the BepiColombo, close to the Sun. This is corroborated by the same analysis of 1.8-10 MeV ions detected by the Low Energy Telescope (LET) onboard STEREO A. The BepiColombo Environment Radiation Monitor (BERM) detected 1.5 MeV ions, providing a comparative study with 1.8 MeV ions detected by LET. While the difference in their peak times suggests ballistic motion along the magnetic field, the decay profile observed by LET is more prolonged than that observed by BERM. This observation may imply an increase in scattering over time, potentially indicating a reduction in mean free path to below 0.1 AU, as inferred from focused transport simulations. In this paper, we will present detailed observations and numerical modelling results, and discuss potential scenarios for the transport of SEPs between BepiColombo and STEREO locations.

[MAT Seminar]

Date:

2024/05/22(Wednesday) 13:00 - 15:00

Language:

English

Speaker:

Ayumi Ozawa

Title:

Development and application of the phase-reduction theory for understanding interacting oscillatory systems

Abstract:

When oscillatory units interact, they often self-organize and exhibit nontrivial behavior. For example, they adjust their rhythms to each other and yield coherent oscillations. This phenomenon, called synchronization, has been observed in various systems, including the atmosphere-ocean system. In this talk, I will present my past and current research projects on interacting oscillatory systems and my research plan at JAMSTEC. The talk will be organized as follows. First, I will give an overview of my work. I will then focus on my research on feedback control of interacting oscillators. This study is motivated by a wide range of examples of desirable and undesirable synchronized oscillations. Previous studies indicated that a simple global feedback loop can suppress synchronized oscillations by desynchronization, i.e. making the oscillations asynchronous. Later, another study reported that a similar feedback loop may also induce oscillation quenching, where the oscillations of individual oscillators cease. However, it was unclear under what conditions which of the two, desynchronization or oscillation quenching, occurs. We therefore constructed and analyzed a simple mathematical model of oscillators under feedback by utilizing the phase-reduction theory, which allows us to describe the dynamics of one oscillator with a single variable, the phase. The model is simple enough to allow detailed analyses, but its dynamics is rich enough to exhibit both desynchronization and oscillation quenching. We obtained the phase diagrams of the collective state and proposed a methodology to tune the feedback. Next, I will briefly introduce my ongoing project on the collective dynamics of small aquatic animals that exhibit circular trajectories. Lastly, I will explain my main research project at JAMSTEC. In this project, I will develop a phase-reduction theory for delay partial differential equations and apply it to a model of synchronized sea-surface temperatures over two ocean currents to elucidate their interaction.

[MAT Seminar]

Date:

2024/05/15(Wednesday) 13:00 - 15:00

Language:

English

Speaker:

Go Eguchi

Title:

Fish schooling and drafting behaviors: Fish can adjust angle of attack and curvature of body to minimize the total force acting on its body

Abstract:

Fish schooling has various advantages, one of which is the improvement in hydrodynamic propulsive efficiency. It is said that wake flow induced by tail beat makes reverse Kármán vortices, follower fish could get the advantage of thrust because of the reduction of experienced flow velocity and local pressure. We verified the velocity field of wake flow when fish swim in parallel by using visualization method, Particle Image Velocimetry (PIV). The results demonstrated that the existence of a region of reduction flow velocity, but not enough to explain all the energy-saving in fish schooling. Therefore, we focused on the behaviors, “drafting”.
Drafting is the act of swimming with force transmission among individuals without any physical contact. For example, it has been reported that some fish can follow other individual while swimming with minimal tail beat. These drafting occur in front or side of other individual. We investigated this mechanism by stably reproducing drafting using actual fish and a flat plate or hydrofoil model. The velocity and pressure field around the fish and forces acting on fish body were verified three experimental approach, PIV, Computational Fluid Dynamics (CFD) and model experiments using two-axis load cell. These results showed that fish can balance the anterior-posterior and lateral direction forces acting on its body by having an angle of attack or adjusting curvature of body in response to changes in pressure and flow fields. It is suggested that this mechanism may applied to energy saving in fish schooling.
In this seminar, I introduce the above in detail. In the latter, I explain “Observation of fish schooling dynamics in fish preserve nets” which I have started working on as a postdoctoral researcher, and explain the research plan, and outline of the business trip scheduled for May 16-23.

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