Access

TOP    Events & Outreach    R-CCS Cafe    The 252nd R-CCS Cafe (Sep 15, 2023)

The 252nd R-CCS Cafe (Sep 15, 2023)

Japanese
Details
Date Fri, Sep 15, 2023
Time 3:00 pm - 3:50 pm (3 pm - 3:50 pm Talks, 3:50 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

Ayato Takii

Complex Phenomena Unified Simulation Research Team
Postdoctoral Researcher

Sriram Srinivasa Raghavan

Computational Structural Biology Research Team
Postdoctoral Researcher

Talk Titles and Abstracts

1st Speaker: Ayato Takii


Title:
Real-world Flight Simulation for Flying Car Safety: Propeller Failure and Recovery
Abstract:
Electric vertical takeoff and landing vehicles (eVTOLs), also known as flying cars, are garnering significant interest as a part of the future transportation infrastructure. These vehicles demand stricter operating conditions and higher safety standards than ground vehicles. In particular, countermeasures against in-flight failures are crucial, and the potential consequences of accidents must be minimized. To accurately predict the behavior of flying cars and contribute to their design and development, real-world simulations using Computational Fluid Dynamics (CFD) are needed. In this presentation, the long-term flight of a flying car is simulated by unsteady flow computations involving fluid-rigid body interactions. Additionally, the impact of propeller failure on flight performance will be investigated and a recovery method will be proposed based on the results.

2nd Speaker: Sriram Srinivasa Raghavani


Title:
Automated Density Extraction of Isomorphous Difference map and Occupancy-estimation for Conformer Fitting
Abstract:
TR-SFX (Time-Resolved Serial Femtosecond Crystallography) is a powerful technique that enables the capture and analysis of time-evolved dynamics of residual motion across various crystal structures, thereby facilitating the visual inspection of reaction kinetics. A critical step in elucidating intermittent reaction states involves the analysis of the isomorphous difference map, which provides valuable information about the variations in atomic positions between different crystal structures.

In this study, a clustering-based methodology was employed to cluster difference electron densities and establish associations with adjacent residues. Singular Value Decomposition (SVD) techniques were additionally utilized to identify and rank residues exhibiting motion, quantified by their electron density sum. Moreover, a network representation was further employed to highlight connections between these mobile residues in protein. Our tool not only identifies important residues linked to reaction kinetics, but also employs structure factor extrapolation techniques to compute the occupancy of structural intermediates. Following the identification of the residues having significant difference density, we extracted their conformers from molecular dynamics trajectory. These extracted conformers were then subjected to refinement, enhancing conformational sampling space for generating triggered state structure validated by real space correlation coefficient.

Our approach significantly enhances the structural characterization process providing a deeper understanding of the dynamic behavior and reaction mechanisms within crystal structures. Through the combination of TR-SFX with molecular dynamics-based fitting, we enable more accurate and detailed investigations of reaction kinetics and structural changes.
This has wider implications in fields such as materials science, drug discovery, and catalysis, paving the way for transformative discoveries and applications.

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 6, 2023）