Call for Application: RCCS Computational Resources FY2023 Second Half
Application Type: Category (B)
Application Open: Thursday, June 1, 2023.
Application Close: Friday, June 30, 2023 at 24:00.
Resource Available Period: October 2, 2023 to April 1, 2024 at 9:00.
NOTE: For Category (A) and (I) applications, please see this page for details.

Scientific results using RCCS

Au-Ag nanoclusters showing intense phosphorescence in cells

Luminescent metal nanoclusters are expected to exhibit unique physical properties in the cluster structure depending on the ligand structure, metal type, number of nuclei and arrangement. In this study, carbon-centered gold-silver (CAu6Ag2) clusters with N-heterocyclic carbene (NHC) ligands were designed and synthesized, and it was found that these clusters emit strong phosphorescence in solution, and the contribution of NHC ligands to phosphorescence emission was revealed by theoretical calculation. The luminescence rate constant was calculated by an analysis including spin-orbit interactions, and the quantum yield was discussed in terms of the energy barrier to the minimum energy crossing point. Furthermore, the phosphorescent gold-silver clusters with long luminescence lifetime were used for cellular imaging, which revealed the pathway of uptake into the cell and selective localization to specific organelles, confirming their superior functionality, which is different from the non-selective uptake of conventional phosphine ligands.
Z. Lei, M. Endo, H. Ube, T. Shiraogawa, P. Zhao, K. Nagata, X.-L. Pei, T. Eguchi, T. Kamachi, M. Ehara, T. Ozawa, M. Shionoya Nature Commun. 13, 4288-1-9 (2022).

“Bucket brigade” of remdesivir in RNA-dependent RNA polymerase of SARS-CoV-2

　The process of remdesivir uptake into the protein (RNA-dependent RNA polymerase) that replicates the gene of SARS-CoV-2 was revealed by molecular dynamics simulations. Remdesivir has a phosphate group with a negative charge, and the binding site of RNA polymerase has Mg2+ ions. In addition, RNA polymerase has lysine residues, which are positively charged, in a line toward the binding site. It was found that the lysine residue attracts the phosphate group of remdesivir and passes it to the next lysine residue sequentially, transporting the drug to the binding site like a bucket brigade.

S. Tanimoto, S. G. Itoh, and H. Okumura: Biophys. J. (2021), DOI: 10.1016/j.bpj.2021.07.026, “Bucket brigade” using lysine residues in RNA-dependent RNA polymerase of SARS-CoV-2

Molecular simulations of functional dynamics in biomolecular machines

Functional dynamics plays an important role when biomolecular machines fulfill their functions. For example, transporter proteins transport their substrates across the membrane by changing their conformation between inward-open and outward-open conformations. Although it is difficult to directly simulate millisecond functional time of these biomolecular machines whose total atoms amount to several hundred thousand, we use techniques such as metadynamics or transition path sampling to uncover molecular mechanism of the functioning moments.

K. Okazaki, D. Wöhlert, J. Warnau, H. Jung, Ö. Yildiz, W. Kühlbrandt and G. Hummer, Nat. Commun. 10, 1742 (2019)

Divergent applications of ab initio reaction dynamics and automated reaction path search

Analyses of ab initio MD trajectories for gold cluster structural transformation based on the global reaction route map clarify the dynamic reaction route going beyond the IRC pathways, leading to a new concept of "reaction path-jumping."

T. Tsutsumi, Y. Harabuchi, Y. Ono, S. Maeda, and T. Taketsugu, Phys. Chem. Chem. Phys., 20, 1364 (2018).

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Update Information

2023-05-08 May 11 (Thu) 9:00-17:00 NOUS maintenance

Application submission system NOUS will be unavailable from 9:00 to 17:00 on Thursday, May 11 due to the scheduled maintenance. Thank you for your understanding.
2023-03-31 Apr 4 (Mon) 10:50-12:15 Website temporarily suspended for maintenance

(Apr 3 13:07) Due to the delay of the maintenance work, the website was resumed at 13:03. Sorry for the inconvenience.
This website will be temporarily unavailable from 10:50 to 12:15 on Monday, April 3 due to the server maintenance.
2023-03-01 Mar 9 (Thu) 9:00-17:00 NOUS maintenance

Application submission system NOUS will be unavailable from 9:00 to 17:00 on Thursday, Mar 9 due to the scheduled maintenance. Thank you for your understanding.
2023-01-31 New system will be available from 10:00 on Feb. 1

We will start operation with the new system on February 1 (Wed) at 10:00.
The period from Feb 1 to the scheduled maintenance on Mar 6 (Mon) is a testing phase.
CPU points won't be consumed by submitted jobs.
2022-12-15 NOUS system failure (Dec 15) and maintenance (Dec 19-20, Dec 22)

The application system NOUS has been out of service since around noon on 12/15 (Thu).
NOUS will be unavailable twice next week on the following dates.

  • Dec 19 (Mon) 21:00 - Dec 20 (Tue) 3:00 (temporary maintenance)
  • Dec 22 (Thu) 12:00-13:00 (scheduled maintenance)

We apologize for the inconvenience and appreciate your understanding and cooperation.
(Dec 16 update) NOUS system failure occurred around the noon on Dec 15 was finally solved around 20:00 on Dec 15.
2022-10-25 Nov 10 (Thu) 9:00-17:00 NOUS maintenance

Application submission system NOUS will be unavailable from 9:00 to 17:00 on Thursday, Nov 10 due to the scheduled maintenance. Thank you for your understanding.
2022-10-25 Operation start date of the new system is postponed to January 2023 or later

We sincerely apologize for the inconvenience. Due to delays in securing materials, we can't start operation of the new system from December 1st. The new system is scheduled to be launched on January 2023 or later. We will report further details on this website as soon as they are finalized.
2022-10-11 Oct 13 (Thu) 12:00-13:00 NOUS maintenance

Application submission system NOUS will be unavailable from 12:00 to 13:00 on Thursday, Oct. 13 due to the maintenance. Thank you for your understanding.
2022-08-01 Aug. 9 (Tue) 9:00-17:00 NOUS scheduled maintenance

Application submission system NOUS will be unavailable from 9:00 to 17:00 on Tuesday, Aug. 9 due to the scheduled maintenance. The service might be resumed earlier than the scheduled time, 17:00.
2022-07-11 July 25(Mon) Network connection to RCCS unavailable for 5 minutes between 12:00-13:00

Due to the network maintenance work, access to RCCS will be unavailable for about 5 minutes between 12:00-13:00 on July 25 (Mon). Submitted/running jobs won't be affected by this maintenance work. However, you can't access to this website and login to the frontend nodes during the work (at most 5 minutes). Please avoid your data backing up work between 12:00-13:00.
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