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R-CCS Cafe
The 255th R-CCS Cafe (Nov 6, 2023)
The 255th R-CCS Cafe (Nov 6, 2023)
JapaneseDate | Mon, Nov 6, 2023 |
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Time | 4:00 pm - 5:20 pm (4 pm - 5 pm Talks, 5 pm - Free discussion and coffee break) |
City | Kobe, Japan/Online |
Place | Lecture Hall (6th floor) at R-CCS, Online seminar on Zoom
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Language | Presentation Language: English Presentation Material: English |
Speakers |
Yasumichi Aoki Field Theory Research Team ![]() Yuji Sugita Computational Biophysics Research Team ![]() Kengo Nakajima Deputy Director, RIKEN Center for Computational Science ![]() |
Talk Titles and Abstracts
1st Speaker: Yasumichi Aoki
Title:
Field theory simulations to fundamental properties of matters
Abstract:
Mass of the visible matters in our universe is mostly composed of that of baryons, among which nucleons (protons and neutrons) are most abundant because they are the most stable baryons. A neutron decays into a proton with an electron and a neutrino through a beta decay. Proton is the stable lightest baryon, which will not decay at all, if the standard model of particle physics is the ultimate theory of matters. Therefore if the proton decay is observed, it is a smoking gun signal of the physics beyond the standard model.
Nucleon prpoerties are now being studied with realistic simulation parameters that matches to those in our physical real world thanks to the advancement of the computer, algorithms and software.
In this talk we will touch some of the recent advancements on the understanding of the properties of nucleons and a numerical technique which realized the improved precision of the quantities of interest.
2nd Speaker: Yuji Sugita
Title:
Coarse-grained modeling and simulation of protein and lipid dynamics
Abstract:
Computational modeling and simulations are powerful approaches to examine the structure-dynamics-function relationships of biomolecules. Due to the computational limitations, molecular dynamics simulations with atomistic models cannot describe slow biological processes. Here, we apply residue-level coarse-grained models for proteins and lipid molecules to study conformational dynamics of biomolecules in the cell. Structure-based approaches, such as the Go-model, are mainly employed for simulating protein dynamics, while physics-based approaches are partially used. We have also developed a heterogeneous domain-decomposition scheme for coarse-grained molecular dynamics simulations and carried out large-scale biological simulations on Fugaku. We have also developed new coarse-grained models of lipid molecules treating their electrostatic interactions explicitly. We plan to integrate the coarse-grained lipid models with the residue-level coarse-grained models for proteins and simulate large biological membranes or other slow biological processes near the membrane interfaces.
3rd Speaker: Kengo Nakajima
Title:
Integration of Simulation/Data/Learning and Beyond
Abstract:
Recently, supercomputing has been changing dramatically. Integration/convergence of Simulation/Data/Learning (S+D+L) is important towards Society 5.0 proposed by Japanese Government, which enables integration of cyber space & physical space. We propose an innovative method for computational science for sustainable promotion of scientific discovery by supercomputers in the Exascale Era by combining (Simulation + Data + Learning (S+D+L)) in the project, and have developed a software platform "h3-Open-BDEC" for integration of (S+D+L) and evaluate the effects of integration of (S+D+L) on the Wisteria/BDEC-01 system at the University of Tokyo.
In this talk, the speaker will give an overview of the activities of the h3-Open-BDEC project. Since this project will end this FY, the speaker would like to specifically talk about future developments.
Important Notes
- Please turn off your video and microphone when you join the meeting.
- The broadcasting may be interrupted or terminated depending on the network condition or any other unexpected event.
- The program schedule and contents may be modified without prior notice.
- Depending on the utilized device and network environment, it may not be able to watch the session.
- All rights concerning the broadcasted material will belong to the organizer and the presenters, and it is prohibited to copy, modify, or redistribute the total or a part of the broadcasted material without the previous permission of RIKEN.
(Oct 31, 2023)