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Center for Mathematical Science and Advanced Technology (MAT)

Seminar Schedule

[MAT Seminar]

Date:
2020/11/18(Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Gen Li
Title:
Development of a bio-inspired underwater robot and an eel migration route optimization algorithm
Abstract:
In this presentation, I would like to report the progress of two ongoing projects.
(1) The first project is a bio-inspired underwater robot design. This robot mimics the swimming of a stingray, a fish with flat body and living near the sea bottom. Different from most fish, the stingray uses a very distinctive swimming style—it generates two undulating waves travelling along both sides of its flat body. The developed robot is able to swim forward in the same pattern, and further possess overwhelming maneuverability. A novel type of beneficial ground effect is also observed in the simulation of the stingray robot locomotion. The stingray robot is potential to become a new tool for ocean observation.
(2) The second project is the development of a Japanese eel migration route optimization algorithm. Though the migration route of larval eel has already been well-studied, the migration route of adult eel is still a mystery. While larval Japanese eels are carried by the ocean currents from their spawning area to various habitats, the adult eel has to overcome ocean currents to return to the spawning area for reproduction. Two very different algorithms of optimal migration route in strong current, Zermelo solution algorithm and wavefront expansion algorithm, will be introduced and discussed.

[MAT Seminar]

Date:
2020/11/11(Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Ettore Barbieri
Title:
A General Formula for Large Deformation Peeling? An update
Abstract:
Mechanical peeling under large bending displacements occurs in a considerable number of industrial processes and biological phenomena, and at different length scales, even nanoscale. Although the first works by Kendall on the theory of peeling date back to the 1970s, it has enjoyed a resurgence of interest due to modern applications, such as liquid-phase exfoliation for the large-scale production of graphene.
Justified by hydrodynamic peeling, I presented last year our (my collaborators and I) work on a critical shear rate estimation based on a small displacements approximation.
This year, instead, I will present several full analytical solutions of peeling under large displacements, by solving the nonlinear differential equations of the Euler's Elastica for various boundary conditions.
In doing so, I stumbled upon what it appears to be an intriguing result: the same formula for the work of the external force during peeling seems to apply to all cases, whether it is peeling due to a force with a fixed direction, or a follower force, as in the case of hydrodynamic peeling.
A corollary of this result is that the expression for the strain energy release rate, crucial to calculate the peeling force, becomes stunningly simple.

[MAT Seminar]

Date:
2020/11/04(Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Ushikubo Takayuki (Kochi Institute, JAMSTEC)
Title:
Oxygen isotope systematics of chondrules: Evidence for outward migration of sub-millimeter particles in the protoplanetary disk.
Abstract:
Chondrules are sub-millimeter-scale igneous silicate spherules that have experienced transient high temperature processes in the protoplanetary disk. They are a predominant component of chondritic meteorites. They are also found in comet Wild 2, indicating that chondrules were widely dispersed in the protoplanetary disk from the inner main asteroid belt to the Kuiper belt regions.
In-situ oxygen isotope studies by SIMS revealed that most chondrules have internally homogeneous oxygen isotope ratios even though individual chondrules have diverse oxygen isotope ratios of -10‰ to +2‰ in D17O (= d17O - 0.52 × d18O). Furthermore, characteristic correlations were recognized between oxygen isotope ratios (D17O) and Mg# (molar ratio, 100×MgO/(MgO+FeO)) in chondrules. These indicate that chondrule-forming melt had (almost) equilibrated with the ambient gas via evaporation and re-condensation during chondrule formation. Chondrules record oxygen isotopic composition and redox state of chondrule-forming environments.
In this seminar, I will present oxygen isotopic systematics (D17O vs. Mg#) and 26Al-26Mg chronology data of chondrules from ordinary chondrites (S-type asteroids), CM-related chondrites (C-type asteroids), Tagish Lake-related meteorites (D-type asteroids), and comet Wild 2 (Kuiper belt object). Systematic difference in the D17O-Mg# distributions of chondrules among different type parent bodies suggests that chondrules formed in different environments were not completely mixed in the protoplanetary disk before accretion, and that chondrules formed in the outermost part of the chondrule-forming regions were transported to the Kuiper belt region. I would like to discuss possible mechanism(s) of outward migration of sub-millimeter-scale particles in the protoplanetary disk.

[MAT Seminar]

Date:
2020/10/28(Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Oshima Ippei
Title:
Numerical and theoretical studies of particle flow in the gas flow around a turbine blade
Abstract:
Multi-scale and multi-phase phenomena occur in the steam turbine.
Numerous droplets are generated by condensation and atomization from the nozzle, and these droplets in gas flow deposit on the turbine blade. This is one of the degrading factors of the performance for the steam turbine. Therefore, it is important to understand and predict the behavior of the liquid phase in the turbine. In this seminar, I would like to introduce a theoretical model to predict the droplet motion around the turbine blade and show the validation result using 3D numerical simulation.

[MAT Seminar]

Date:
2020/10/21(Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Nomura Shun
Title:
Transparent granular suspension and its applications
Abstract:
Particle-fluid interactions are well observed for example in the multiphase flow and soil mechanics. Their complex behaviors are important for the material science or engineering field, thereby, modeled through the series of experiment. Sometimes, the inner dynamics of the materials are needed to develop the model and explain experimental results. Although the inner geometries of the particle contained suspensions or structured medias are difficult to observe during the model tests due to the opacity of the mixture or the material itself. However, we can observe the inside of the materials when the refractive index among the materials are miraculously matched and the materials are transparent, which is known as the Refractive Index matching method (RI). In this talk, the concept of RI is firstly presented, then the materials which can utilize RI method easily are introduced. After describing the material properties of the solid particles and viscous fluids for RI and the technical difficulties to develop the transparent field by RI, the potential topics which are going to be tackled by improving the techniques are introduced.

[MAT Seminar]

Date:
2020/10/14(Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Nishiura Daisuke
Title:
Rheological simulation of water-grain suspensions
Abstract:
I have 5 collaborative projects with industry this year. For each project, I am developing the simulation software using a particle method such as a DEM (discrete element method) and SPH (smoothed particle hydrodynamics). In this seminar, I would like to talk about the two kinds of simulation methods for representing the rheological behavior of water-grain suspension that was the achievement of industry collaboration. Although some contents are confidential according to the non-disclosure agreement, I will introduce the research and development progress of each project as far as I can talk.

[MAT Seminar]

Date:
2020/10/7(Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Furuichi Mikito
Title:
Improvement of parallel domain decomposition of DEPTH toward numerical analysis repository
Abstract:
We are developing the DEM based Parallel mulTi pHysics simulator (DEPTH) as the application of numerical analysis repository. The characteristic feature of our code is the distributed memory parallelization with flexible 2D rectangular (FR) domain decomposition (DD) with iterative load balancing method. The efficient parallel performance of DEPTH is confirmed by the performance comparison test with other DEM software LIGGGHT and ESyS-Particle. Our technologies enabled the largest granular dynamics simulation of practical relevance to date contained 2.4 billion particles of numerical sandbox experiment. However, our current target problems with over billion particles are only limited to the problems characterized by 2D rectangular geometry. The current 2D FR-DD technique generates the subdomains with the large aspect ratios for the non-rectangular particle distributions found in many practical science and engineering applications, such as a landslide and dam break with real topography, mud, concrete, and polymer flow in the engineering process and biomechanics. The large aspect ratio can produce a large number of ghost particles to degrade the parallel performance. To address this issue, the parallel domain decomposition method is improved. We allowed each row to have a different number of subdomains; our algorithm generated the optimal sizes of columns and rows to minimize the total number of ghost particles for given particle distribution. Also, we extend FR-DD to 3D. The performance improvements are analyzed by the numerical experiment. These major updates of DEPTH are useful for the new Earth simulator and Fugaku to solve the practical problems as a numerical analysis repository.

[MAT Seminar]

Date:
2020/9/30(Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Noguchi Satoshi
Title:
Geometric discretization of electromagnetics and numerical analysis of dielectric breakdown
Abstract:
I would like to start this presentation with a short self-introduction followed by the specifics of my previous and current research activities. My research interest is the formulation of numerical analysis of physical phenomena based on the geometric viewpoint. In this presentation, I will focus on geometric discretization of electromagnetics and numerical analysis of dielectric breakdown. Starting with the introduction of mathematical tools, differential forms, I would like to explain the geometric formulation of discrete electromagnetics. After that, as one of the applications of the formulation, I will talk about numerical analysis method of dielectric breakdown with results of numerical simulation of several example problems. The presentation will be concluded with my research plan.

[MAT Seminar]

Date:
2020/9/16(Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Arthur Bauville
Title:
Overpressure and pressure oscillations near faults triggered by tectonic nappe formation: insight from a numerical sandbox experiment
A. Bauville, P. Yamato, and S. M. Schmalholz
Abstract:
The pressure recorded by metamorphic rocks is a key data in the geodynamic reconstruction of convergent tectonic margins because it allows researchers to estimate the depth at which rocks were buried or exhumed. For pressure-to-depth conversions, the pressure is often interpreted as being lithostatic. In particular, the peak Pp and retrograde Pr pressures are often interpreted as evidence of the maximum burial and rapid exhumation, respectively.
However, in recent years this view has been challenged by theoretical, experimental, and field data. Theoretical considerations reveal that the mean stress σm can be as large as twice the lithostatic pressure (2 Plitho), and the first principal stress, σ1, can be as large as 3 Plitho in a homogeneous lithosphere in compression, while σm =2/3 Plitho, σ3 =1/3 Plitho in extension. Besides, the mean stress in weak elliptical inclusion can be as large as σ1. Yamato and Brun (2017), and Bauville and Yamato (2020) proposed that the distribution of Pp, Pr can be explained by a model where the rock is in compression at Pp, and in extension at Pr. However, the mechanism responsible for this switch from compression to extension has not been identified yet.
The deformation of the crust at convergent margins commonly triggers the formation of a tectonic nappe stack. In this contribution, we employ numerical methods to reveal the stress state during a nappe stack formation. The configuration of the numerical experiment is similar to a sandbox experiment with high basal friction. The simulations reveal that the stress of state near faults can result in pressure as high as 3 Plitho, and σ1 =5 Plitho. In addition, in this experiment, the stress state is compressional in the most basal nappe that is being formed, but mostly extensional in nappes higher in the stack. Thus, the common process of nappe formation and nappe stacking results in a stress state that presents large overpressure locally and a rapid switch from compression to extension. Thus, this model may explain the pressure evolution observed in natural metamorphic rocks without requiring deep burial or fast exhumation.

[MAT Seminar]

Date:
2020/9/9 (Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Seyed Reza Amini Niaki
Title:
Improving the accuracy of two-fluid sub-grid modeling of dense gas-solid fluidized flows
Abstract:
In gas-solid fluidization highly resolved simulations (HRS) with microscopic two-fluid modeling (mTFM) are frequently employed for deriving sub-grid closures for filtered parameters that are required in filtered formulations useful in large scale simulations of real flows. This work intends to contribute for improving the accuracy of underlying HRS raw data upon which the accuracy of sub-grid closures relies on, particularly regarding dense gas-solid fluidized flows. The accuracy of mTFM is improved by incorporating interparticle frictional effects. The accuracy of correlation to filtered parameters is improved by accounting for macro-scale conditions and by enforcing a three independent variable approach. HRS were performed in a periodic domain applying the mTFM of MFIX properly modified by the inclusion of a literature trustworthy interparticle friction model. Results showed that accounting for macro-scale conditions and for three independent variables considerably contributes for improving correlation resolution, while the effect of interparticle friction was only marginal.

[MAT Seminar]

Date:
2020/9/2 (Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Jian Chen
Title:
A parametric study of soil mixing under water based on discrete element simulations: geometric and operational factors
Abstract:
A mixing process is widely used for handling granular materials. In geotechnics, a mixing process is applied for ground improvement, concrete production, etc. Recently, its potential usage for mining or dredging has been discussed. In this study, we augmented and calibrated the DEM based Parallel mulTi-pHysics simulator (DEPTH), which is a DEM code capable of large scale simulations, to study the mechanical responses of the mixing process under water. For calibration, the resultant torques on the mixer head and the surface mixing patterns are compared. With the calibrated DEM models, we conduct a comprehensive parametric study to evaluate the influence from various geometrical and operational factors of the mixing process.

[MAT Seminar]

Date:
2020/8/26 (Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Kameyama Masanori (MAT)
Title:
Two-dimensional numerical experiments on thermal convection of highly compressible fluids with variable viscosity and thermal conductivity: Implications for mantle convection of super-Earths
Abstract:
We conduct a series of numerical experiments of thermal convection of highly compressible fluids in two-dimensional rectangular box or spherical annulus, in order to study the mantle convection on super-Earths. The thermal conductivity and viscosity are assumed to exponentially depend on depth and temperature, respectively, while the variations in thermodynamic properties (thermal expansivity and reference density) with depth are taken to be relevant for the super-Earths with 10 times the Earth's. From our experiments we identified a distinct regime of convecting flow patterns induced by the interplay between the adiabatic temperature change and the spatial variations in viscosity and thermal conductivity. That is, for the cases with strong temperature-dependent viscosity and depth-dependent thermal conductivity, a "deep stratosphere" of stable thermal stratification is formed at the base of the mantle, in addition to thick stagnant lids at their top surfaces. In the "deep stratosphere", the fluid motion is insignificant particularly in the vertical direction in spite of smallest viscosity owing to its strong dependence on temperature. We also found that the occurrence of "deep stratosphere" tends to be suppressed for the cases with spherical geometry, owing the reduction of the surface area with depth which helps increase the temperature gradient in the lowermost mantle.
Our finding may further imply that both the effects of adiabatic compression and those of spherical geometry of mantle are of crucial importance in understanding the mantle dynamics of massive super-Earths in the presence of spatial variations in physical properties.

[MAT Seminar]

Date:
2020/8/19 (Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Hori Takane
Title:
Development of a system to monitor and forecast earthquake preparation and generation processes in subduction zone
Abstract:
Firstly, I will introduce how I consider to construct a system to monitor and forecast earthquake preparation and generation processes in subduction zone. There are many components to be developed, of course. I will summarize the components and how I have been developing them with many collaborators in and outside JAMSTEC. Within many components, there is at least one component I need to develop by myself: a method for sequential forecasting of earthquake preparation processes. So I will next explain how I have examined it and how I consider to develop it within a few years.

[MAT Seminar]

Date:
2020/8/5 (Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Takehiro Miyagoshi
Title:
My plan for studies of geodynamo
Abstract:
In this seminar, I would like to introduce my three plans for studies of geodynamo. They are,
(1) geodynamo simulation with realistic low Ekman number Ek (the order of Ek is ~1E-9).
Here, Ek is the ratio of viscous force to the Coriolis force.
(2) Geomagnetic field variation caused by length-of-day variation. Especially, small period variation compared with the spin up time, saw shape variation of length-of-day, and multiple period of length-of-day variation.
(3) Effects of the change of the outer core thickness, motivated by room experiments of liquid iron.
I have another plan, (4) geodynamo caused by horizontal convection, but I will talk about this in the future seminar.

[MAT Seminar]

Date:
2020/07/29 (Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Hirose Shigenobu (VAiG)
Title:
Development of a public code for calculating opacities of multi-species gas mixture
Abstract:
Hydrodynamics of multi-species gas mixture with radiative heat transport is relevant in many research areas including atmospheric science, engineering and astrophysics. To perform numerical simulations of radiation hydrodynamics accurately, reliable opacities are required. However, compiling necessary data sources and computing opacities from them is a complicated and time-consuming task, and thus researchers tend to use public opacity databases while they are only available in limited cases. Therefore, we are developing a public code for computing opacities, which can be easily extended by users to include necessary opacity sources for their own purposes. In this talk, I'll explain how our code works with various types of opacity sources as well as its computational-science aspects such as parallelization and data format (HDF5).

[MAT Seminar]

Date:
2020/07/22 (Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Minoshima Takashi
Title:
All-speed and divergence-free scheme for accurate and robust MHD simulations
Abstract:
The MHD simulation is widely employed to study the macroscopic dynamics of magnetized fluids.
In the field of computational space physics and astrophysics, modern MHD simulation codes adopt an upwind-type, shock-capturing scheme to robustly and accurately capture shocks and discontinuities.
Although the scheme has brought striking progress in MHD simulations, there still remain numerical issues in practical simulations, for example, the robustness in multi-dimensional shocks and the accuracy of low speed flows.
The preservation of the solenoidal condition of the magnetic field is also an issue when one extends the one-dimensional scheme to multidimension.
In this talk we summarize our new numerical scheme for MHD simulations aiming to resolve these issues (Minoshima+19,20).
We achieve, for the first time, the development of the “all-speed” MHD scheme, that is, the scheme obtains an accurate solution of nearly incompressible MHD flows as well as capturing high speed shocks robustly.
Therefore, the new scheme is expected to be a powerful tool for MHD simulations including both high and low speed flows with the magnetic field.

[MAT Seminar]

Date:
2020/07/08 (Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Yamagishi Yasuko
Title:
Reconstruction of database system of research vessel operating state information
Abstract:
We have developed a database system for operating state information of research vessels belonging to JAMSTEC to provide useful information for planning future research cruises. We completed the database in March 2019 and it is available now on LAN of JAMSTEC. This database can provide the downtime of the research cruises from FY 2008 to FY 2018. We are now reconstructing the database system to estimate more accurate downtime and to add needed new data, e.g., research sea area, kinds of observations, and so on for causal analysis of the downtime. Firstly, we changed the definition of the start of the research cruise. Next, we added the period of some operations to downtime. In this seminar, we will show the improvement points of the database and the modification points of the stored data.

[MAT Seminar]

Date:
2020/07/01 (Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Yanagisawa Takatoshi (VERC, IMG)
Title:
Wandering of columnar vortices in rotating Rayleigh-Benard convection
Abstract:
Rayleigh–Beard convection constrained by a background rotation is one of the most fundamental systems in the study of fluid flows in the Earth. This system is recognized as an important model in the aspects of atmospheric flows, oceanic flows, and flows in the outer liquid core of the Earth. In the system, flow patterns are characterized by numerous columnar vortices. We made up a powerful turntable to investigate motions of vortices in rotating convection. By realizing long term tracking of vortices in a wide area, we elucidated that there are three time-scales relating to the behavior of vortices.

[MAT Seminar]

Date:
2020/06/24 (Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Kawamura Yoji
Title:
Phase reduction approach to synchronization of periodic fluid flows:
From Rayleigh-Benard convection to Karman vortex street
Abstract:
Nature provides a rich variety of rhythmic systems and synchronization phenomena. Synchronization of spatiotemporal rhythms in fluid systems is of particular interest. Such periodic fluid flows can be considered as limit-cycle solutions to incompressible Navier-Stokes equations. We have recently been developing a phase reduction method for time-periodic incompressible viscous fluid flows; the method enables us to describe the dynamics of a periodic flow using a single degree of freedom called the phase. A key quantity is the phase sensitivity function, which quantifies the phase response of a periodic flow to weak perturbations applied at each point and at each time. The phase reduction method drastically facilitates detailed theoretical analysis of the synchronization dynamics of periodic flows. In this talk, we consider the phase reduction approach to synchronization of Rayleigh-Benard convection [Kawamura, Phys. Rev. Research 1, 033130 (2019)], and subsequently develop a theoretical framework for the phase reduction of Karman vortex street.

[MAT Seminar]

Date:
2020/06/17 (Wednesday) 13:00 - 15:00
Language:
English
Speaker:
AGATA Ryoichiro
Title:
Bayesian inference for fault slip distributions based on ensemble modeling of the uncertainty of Green’s function
Abstract:
In fault slip estimation using observation data of crustal deformation and seismic ground motion, the prediction errors originated from the underground structure uncertainty is often a major contributor to the errors between the data and the model predictions. Yet, most studies on slip inversions neglected the model prediction errors or did not distinguish it from observation errors. Several methods proposed in the past decade that incorporated the model prediction errors explicitly in slip estimation commonly assumed Gaussian distribution for the stochastic property of the prediction errors to simplify the formulation. Besides, while these studies focused on estimation on slip distribution, but the information on underground structure should also be extracted from the data via an accurate estimation of the prediction errors. In this study, we develop a novel flexible Bayesian inference method for estimating fault slip that can incorporate non-Gaussian prediction errors more accurately, considering the uncertainty of the underground structure based on ensemble modeling of Green's function uncertainty. The framework also allows for estimation of the posterior probabilistic density function (PDF) of the parameters of the underground structure, by calculating the likelihood of each sample in the ensemble.
To validate the advantage of the proposed method, we performed simple numerical experiments of estimating fault slip rate distribution on a 2D thrust fault using synthetic data of surface displacement rates, in which the dip angle of the fault plane is the parameter to characterize the underground structure. The proposed method succeeded in estimating a posterior PDF of slip rate that is consistent with the true one, despite the uncertain and inaccurate information on the dip angle. The method also could estimate a posterior PDF of the dip angle that has a strong peak near the true angle. By contrast, the estimation results obtained using a conventional approach, which introduces regularization based on smoothing constraints and does not distinguish explicitly the prediction and observation errors, included a significant amount of the bias, which was not seen in those obtained using the proposed method. The experiments with different settings of the parameters suggested that inaccurate prior information on the underground structure with small uncertainty possibly results in significant bias in the estimation results of the posterior PDFs for slip rate, that for the underground structure, and the posterior predicted PDF of the displacement rates. The distribution shapes of the prediction errors for representative model parameters in some observation points are significantly asymmetric with large absolute values of the sample skewness, for which Gaussian approximation is not usually applied.

[MAT Seminar]

Date:
2020/06/10 (Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Hirobe Sayako
Title:
Numerical analysis for crack pattern formation
Abstract:
I am firstly going to introduce my previous and current research activities. My research interest is the irreversible pattern formation process and I have been focusing on the crack pattern formation in solid continuum so far. I am going to present the interesting crack patterns observed in the desiccation cracking and the quenched glass plate. These crack patterns have the typical length scales in spite that the cracks are formed in the homogeneous field. I will show some numerical analysis results for these crack pattern formations and introduce the idea for the mechanism of the determination of the length scale. I am also going to present the simulation for the dynamic fracture in residual stress field. The crack paths strongly depend on the distribution of the residual stress. For simulating this dynamic fracture behavior, we need numerical analysis method which can rigorously evaluate the release and redistribution of the residual stress due to fracture. Lastly, I will present my research plan.

[MAT Seminar]

Date:
2020/06/03 (Wednesday) 13:00 - 15:00
Language:
English
Speaker:
Oguni Kenji
Title:
Short self introduction and some comments on plasticity theory
Abstract:
I am going to start this presentation with a short self introduction to provide you with some idea about your new director of MAT. Then, some comments on plasticity theory will be given. I am going to address the 150-years-old misconceptions in the mathematical theory of plasticity. This inconvenient fact should be surprising enough for everybody out of the research field of plasticity and embarrassing enough for the researchers in the field of computational plasticity and other fields related to plasticity.

[MAT Seminar]

Date:
2020/03/25 (Wednesday) 13:00 - 15:00
Place:
MAT theater at 5th floor, IT Building, Yokohama Institute
Language:
English
Speaker:
Hori Muneo
Title:
Looking for good coordinate system
Abstract:
I am expecting the presence of a good coordinate system in which most efficient numerical analysis is made for a physical problem such as a wave equation of solid continuum. The use of principal directions for a second-order symmetric tensor is a clue of finding one if an orthogonal curvilinear coordinate system is formed. Several trials of finding a good coordinate system are explained.

[MAT Seminar]

Date:
2020/03/12 (Thursday) 13:00 - 15:00
Place:
MAT theater at 5th floor, IT Building, Yokohama Institute
Language:
English
Speaker:
Shunsuke Shimobayashi
Title:
Nucleation energy landscape of membrane-less organelles
Abstract:
This is the report of one-and-a-half year oversea dispatch research in Princeton University. Cells organize intracellular biochemical materials through compartmentalization into various organelles. In general, it has been considered that such compartmentalization requires a lipid bilayer membrane; however, the cell can also compartmentalize the materials without a lipid membrane via liquid-liquid phase separation (LLPS).
The membrane-less organelles repeat to form or dissolve in response to the endo/exogenous change of system parameters (ex. concentration, temperature and etc). In this seminar, I will talk about our recent efforts to prove the nucleation energy landscape of membrane-less organelles in living cells.

[MAT Seminar]

Date:
2020/03/11 (Wednesday) 13:00 - 15:00
Place:
MAT theater at 5th floor, IT Building, Yokohama Institute
Language:
English
Speaker:
Gen Li
Title:
Novel Mathematical and physical models reveal mechanisms behind complex phenomena in biology
Abstract:
In this presentation, the speaker would like to introduce several ongoing studies during the last 6 months on biomechanics, based on novel mathematical and physical models.
[Study 1: On the actuation mechanism of fish swimming] We developed a dedicated experimental-numerical inverse dynamics approach to calculate the lateral bending moment distributions for a large-amplitude undulatory swimmer that moves freely in 3D space. Our analysis on fish larvae shows that the actuation patterns are not only relatively simple but also strikingly similar.
[Study 2: On an effective approach to test drug effect on fish] The use of zebrafish larvae has aroused wide interest in the medical field. To quantify the influence of drugs on zebrafish larvae swimming behaviors and energetics, we have developed a novel methodology to exploit intravital changes based on observed zebrafish locomotion. The approach has potential to evaluate the influence of drugs on the aquatic animal’s behavior changes and thus support the development of new analgesic and neuroactive drugs.
[Study 3: On the fluid dynamics of a carnivorous plant] The aquatic bladderwort captures zooplankton in mechanically triggered underwater traps. With characteristic dimensions less than 1 mm, the trapping structures are among the smallest known to capture prey by suction—a mechanism that is not effective in the creeping-flow regime. To understand what makes suction feeding possible on the small scale of bladderwort traps, we characterized their suction flows experimentally and mathematically.
[Study 4: On the physical mechanism of burst-and-coast swimming of fish] This study addresses the physical mechanism of intermittent swimming by considering the burst-and-coast regime of fish swimming at different speeds. We show that fish modulate a unique intrinsic cycle to sustain the demanded speed by modifying the bursting to coasting ratio while maintaining the duration of the cycle constant. Numerical simulations suggest that the chosen kinematics correspond to energetically optimized gaits.

[MAT Seminar]

Date:
2020/03/04 (Wednesday) 13:00 - 15:00
Place:
MAT theater at 5th floor, IT Building, Yokohama Institute
Language:
English
Speaker:
Ettore Barbieri
Title:
Formation and Disruption of Conductive Networks in Pyroresistive Polymer Composites
Abstract:
Pyroresistive composites combine the insulating properties of polymers with the conductive ability of a second phase, such as metallic particles. At standard temperatures, the whole material conducts electricity. Upon heating, the polymer expands, and the conductive networks of particles break down, rendering the composite effectively an insulator. Flexible and controllable self-regulating heating devices use these materials. Applications include healthcare appliances, soft robotics, artificial skins and wearable electronics.
Several essential questions arise in the manufacturing of these materials. In this talk, I will address three in particular: at which temperature the composite stops conducting? What is the critical volume fraction of particles for conduction? Does the diameter of the particles influence the disruption of the network? To answer these questions, I will use computer simulations based on thermomechanics, graph theory, percolation theory, random adsorption algorithms and the DLVO theory for colloids.

[MAT Seminar]

Date:
2020/02/26 (Wednesday) 13:00 - 15:00
Place:
MAT theater at 5th floor, IT Building, Yokohama Institute
Language:
English
Speaker:
Ippei Oshima
Title:
Transversal Oscillation of an air-blasted liquid sheet
Abstract:
Abstract: The atomization phenomenon of an air-blasted liquid sheet, which is widely used for many applications, is not clear because of its complicated multi-scale and multi-phase characteristics. The transversal oscillation induced by the surrounding air flows affects the spray characteristics such as spray angle and droplet diameter. Therefore, it is required to understand the transversal oscillation phenomenon of the liquid sheet and predicting transversal oscillation characteristics.
In this presentation, I will introduce the visualization result obtained by a high-speed camera and the proposed new prediction model for the transversal wavelength of the liquid sheet based on the spanwise oscillation mechanism.

[MAT Seminar]

Date:
2020/02/12 (Wednesday) 13:00 - 15:00
Place:
MAT theater at 5th floor, IT Building, Yokohama Institute
Language:
English
Speaker:
Kuwano Osamu
Title:
Direct observation of flash temperature at frictional interface of synthetic quartz crystal during high-velocity sliding
Abstract:
Recent experiments conducted at sub‐seismic to seismic sliding velocities (mm/s to m/s) show the dramatic weakening in the friction coefficient for a wide variety of rock types due to mechanochemical effects by frictional heating. Consequently, several weakening mechanisms have been proposed depending on the type of rock specimens. Some of them are based on the sample observation and analysis after experiments. Direct observation of frictional contacts during an experiment is indisputable to constrain an elementary process at frictional contacts during slip. To measure the temperature distribution of frictional contact directly, we conducted the in-situ observation of frictional interface of synthetic quartz crystal using a high-speed camera. I'll talk about our recent experiments to obtain thermal images of a frictional interface.

[MAT Seminar]

Date:
2020/02/05 (Wednesday) 13:00 - 15:00
Place:
MAT theater at 5th floor, IT Building, Yokohama Institute
Language:
English
Speaker:
Hosono Natsuki
Title:
Smoothed Particle Hydrodynamics simulations on FP16
Abstract:
The smoothed particle hydrodynamics (SPH) is one of the most widely accepted numerical hydrodynamic schemes.
One serious disadvantage to SPH is its computational cost.
Hence, it is common to apply high-performance computing techniques to SPH.
Lately, the so-called "AI-specific" processors have been hitting the market.
An AI-specific processor is typically a peripheral device to CPU which has many co-processors which support arithmetic operations of half-precision floating point numbers (FP16) to reduce the costs for data transfer and arithmetic operations.
Hence, FP16 can also be attractive for scientific computing.
However, FP16 would make simulation accuracy worse, which can be a severe problem for scientific computing whose accuracy is of paramount importance.
Hence, the effectiveness of FP16 to scientific computing should be determined by the balance between reduction of time-to-solution and exacerbation of simulation quality.
However, there are almost no studies for SPH which survey the effect of precision on simulation accuracy.
In this work, we aimed at surveying the relationship between time-to-solution and simulation accuracy to determine whether FP16 is useful to SPH.
We carried out a test problem, 2D Couette flow with SPH and measured the accuracy and wallclock time by changing precision for floating point numbers.
As a result, we found that the terminal accuracy does not depend on the precision.

[MAT Seminar]

Date:
2020/01/29 (Wednesday) 13:00 - 14:30
Place:
MAT theater at 5th floor, IT Building, Yokohama Institute
Language:
English
Speaker:
Nomura Shun
Title:
Exposing test of concrete specimens in the deep sea
Abstract:
The recent research elucidated that the deep sea has a lot of potential to develop the natural resources of the oceanic energy. Additionally, there are lot of demand to monitor the ocean bottom dynamics to manage the submarine disasters. To increase resource productivity and/or improve monitoring accuracy, the submarine infrastructure with enough stability in long term is essential matter. To overcome potential issues, concrete material is preferential candidate, since it is cheap but presents sufficient stiffness. However, to utilize the concrete material in the deep sea, there are problematic since there are no data over 200 m depth of the sea. In this talk I explain the outline of exposing test in deep sea started from 2018.8. Then the material properties which was recovered from 3500 m depth in 2019.9 are briefly introduced.

[MAT Seminar]

Date:
2020/01/22 (Wednesday) 15:30 - 17:00
Place:
MAT theater at 5th floor, IT Building, Yokohama Institute
Language:
English
Speaker:
Daisuke Nishiura
Title:
Introduction of my industrial collaborative research
Abstract:
Now, I have 8 collaborative projects with outside JAMSTEC in addition to 5 projects collaborated with other JAMSTEC group. There are so many projects, but completed projects are not so many because the working time assigned to one project has less than one month in simple calculation. Although almost all projects are ongoing, I will briefly introduce the overview of each project focused on the industrial collaboration. After that, I will pick up one project among those projects and explain the details in this seminar.

[MAT Seminar]

Date:
2020/01/08 (Wednesday) 13:00 - 15:00
Place:
MAT theater at 5th floor, IT Building, Yokohama Institute
Language:
English
Speaker:
Ikkyu Aihara
Title:
Interaction Mechanisms Quantified from Empirical Data (A Case Study on Frog Choruses)
Abstract:
Interaction mechanism in the acoustic communication of actual frogs is investigated by combining mathematical modeling and empirical data. Here we use a mathematical model (a phase oscillator model) to describe the deterministic and stochastic features of frog choruses in which male frogs attempt to avoid call overlaps with each other due to acoustic interaction.
The mathematical model with a general interaction term is identified by a Bayesian approach from multiple audio recordings on the choruses of male Japanese tree frogs. Then, we quantify the magnitude of attention paid among the male frogs from the identified model.

In this presentation, I briefly introduce our empirical and theoretical studies on frog choruses, and then explain the details in the model identification from empirical data.