TOP    Events & Outreach    R-CCS Cafe    The 270th R-CCS Cafe (Oct 4, 2024)

Details
Date Fri, Oct 4, 2024
Time 1:00 pm - 3:00 pm (1:00 pm - 1:40 pm Talks, 1:50 pm - 2:10 Discussions, 2:10 pm - Free discussion and coffee break)
City Kobe, Japan/Online
Place

Lecture Hall (6th floor) at R-CCS, Online seminar on Zoom

  • If you are not affiliated with R-CCS and would like to attend R-CCS Cafe, please email us at r-ccs-cafe[at]ml.riken.jp.
Language Presentation Language: English
Presentation Material: English
Speakers

Satoru Oishi

Computational Disaster Mitigation and Reduction Research Team, TeamLeader

photo: Satoru OISHI (Team Leader, Computational Disaster Mitigation and Reduction Research Team)

Mitsunori Ikeguchi

Molecular Design Computational Intelligence Unit, UnitLeader

Talk Titles and Abstracts

1st Speaker: Satoru Oishi

Title:
Development of Disaster Management Digital Twin through Data Transformation for Automated Hazard Simulation System
Abstract:
Japan has many natural disaster hazard potentials, such as the Nankai Trough mega earthquake, earthquakes directly under the Tokyo metropolitan area, wide-area flooding in the Tokyo metropolitan area and storm surge flooding in three major port cities. The Disaster Prevention Digital Twin, which is necessary for physics based numerical simulations to predict the impact of hazards on an entire city, breaks through the limitations of conventional damage estimation and realizes more scientific damage estimation. The objective of this research and development is an automatic generation system for the digital twin. As outputs using the automatically generated digital twin, we propose a probabilistic hazard map, a dynamic hazard map, and a superimposed earthquake, storm surge, and flood hazard map. Probabilistic hazard maps use simulations based on a large number of disaster hazard scenarios. The probabilistic hazard maps clearly distinguish between localized severe damage with very low frequency and small to medium-scale damage with high frequency in various locations, which is impossible with conventional methods that have low detail and resolution, and contribute to more efficient and effective disaster prevention planning. A dynamic hazard map is a dynamic visualization of simulation results based on disaster hazards that have taken place in other regions. By visualizing "what would happen if the same disaster takes place" just after the occurrence of a disaster in another area, the system fosters residents' awareness of disaster prevention and encourages them to take concrete measures, resulting in a sense of security. The superimposed earthquake-surge flood hazard map utilizes a physical simulation of the superposition of a large-scale earthquake and a large-scale flood disaster. This contributes to the study of the superposition, which is literally a national disaster, although it has not yet been experienced. Immediately after a disaster, critical structures such as nuclear power plants require careful safety confirmation. In some cases, it took a considerable amount of time before they were put back into service. It is necessary to use a digital twin of highly detailed structures to significantly shorten the time required for safety confirmation. In this presentation, these digital twins and the SaaS that automatically generates disaster prevention and mitigation information using these digital twins for hazard simulation will be explained.

2nd Speaker: Mitsunori Ikeguchi

Title:
Computational Analysis of Activation of Dimerized Epidermal Growth Factor Receptor Kinase Using the String Method and Markov State Model
Abstract:
Protein kinases are important drug targets. They are known to undergo conformational changes during activation. In this talk, I present MD simulations about the activation process of the epidermal growth factor receptor (EGFR). While phosphorylation plays a crucial role in the activation of many protein kinases, in the case of EGFR, asymmetric dimerization triggers activation. In this study, we analyzed the activation process of EGFR through asymmetric dimerization using MD simulations. Conventional MD simulations have time scale limitations, making it challenging to directly follow the activation process. Therefore, we used the String method, which obtains the minimum free energy path, and the Markov State Model (MSM) to capture the activation process of EGFR. These methods involve performing many relatively short MD simulations and integrating them to obtain the free energy landscape and long-term trajectories. We used the GENESIS MD package for the String method and many short MD simulations. As a result, we elucidated how interactions at the asymmetric dimer interface induce activation of the receiver domain. Additionally, kinetic Monte Carlo simulations over several milliseconds revealed the time scale of these structural changes.

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.

(Sep 24, 2024)