Scientific results using RCCS

“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).

Simulations of Catalytic Reactions on Surface

Amide compounds are widely used for fine chemicals, medical drugs, and agricultural chemicals. By using quantum chemical calculations on supercomputer, we clarified the origin of the catalytic activity of Nb2O5 surface which performs highly efficient amidation reactions.
P. Hirunsit, T. Toyao, S. M. A. H. Siddiki, K. Shimizu, M. Ehara, ChemPhysChem (2018).

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Update Information

2022-04-28 Response to the Clarification of "Deemed Export" Controls (from May 1, 2022)

Until Apr 30, 2022, only "Non-Residents" are the subject to Foreign Exchange and Foreign Trade Act Law (FEFTA). However, from May 1, 2022, "Resident" under the significant influence of "Non-Resident" (a person falling under the "Specific Categories") will also be the subject to FEFTA. (ref: qualification page) Even Japanese persons with Japanese nationality is not free from this issue. In response to this change, RCCS needs to take some actions. Please see below for details.
(May 16 update) application form on NOUS was updated. You can apply for new project now.
2022-04-27 May 12(Thu) 9:00-17:00 NOUS scheduled maintenance

Application submission system NOUS will be unavailable from 9:00 to 17:00 on Thursday, May 12 due to the scheduled maintenance. The service might be resumed earlier than the scheduled time, 17:00.
2022-04-04 Apr 24(Sun) 10:00-11:00 Network connection to RCCS unavailable (spare date: Apr 26)

Due to the network replacement work, network connection to RCCS will be temporarily unavailable on Apr 24 (Sun) 10:00-11:00. Submitted/running jobs won't be affected by this replacement work. However, access to this website and frontend nodes (ccfep) will be unavailable. The detailed schedule will be posted on this web site as soon as it is confirmed.
(Apr 26) replacement work on Apr 24 was successfully completed.
2022-03-08 Mar 16 12:00-13:00 NOUS temporarily unavailable

Due to the system maintenance, NOUS will be temporarily unavailable from 12:00 to 13:00 on Mar 16 (Wed). Thank you for your understanding and cooperation.
2022-02-04 (Mar 29 update) Mar 26(Sat) 10:00-13:00: network unavailable

Network access to RCCS will temporarily be unavailable due to the replacement of upstream network devices on the following periods.

  • Mar 26 (Sat) 10:00-13:00

The last replacement work on March was rescheduled for Mar 26 (Sat). Please beware of this rescheduling.
The RCCS system itself will not be affected by the issue; already submitted jobs won't be affected by this replacement. However, access to this website or frontend nodes (ccfep) will be unavailable. Please avoid performing data backups during or around these periods. Further information, impact time etc., will be updated as it becomes available. We are really sorry for the inconvenience.
2022-02-01 Feb 17 (Thu) 9:00-17:00 NOUS maintenance

Application submission system NOUS will be unavailable from 9:00 to 17:00 on Thursday, Feb. 17 due to the scheduled maintenance. The service might be resumed earlier than the scheduled time, 17:00.
2021-10-29 Nov 11(Thu) 9:00-17:00 NOUS scheduled maintenance

Application submission system NOUS will be unavailable from 9:00 to 17:00 on Thursday, Nov. 11 due to the scheduled maintenance. The service might be resumed earlier than the scheduled time, 17:00.
2021-08-19 Sep 22 (Wed) 0:30-1:30 AM: network access to RCCS temporarily unavailable

Due to the maintenance work, network access to RCCS will be unavailable for 30 minutes somewhere from 0:30 AM to 1:30 AM on Sep 22 (Wed). You can't login to the frontend nodes during the maintenance. Already submitted jobs won't be affected.
2021-08-18 Aug 26 (Thr) 9:00-17:00 NOUS scheduled maintenance

Application submission system NOUS will be unavailable from 9:00 to 17:00 on Thursday, Aug. 26 due to the sceduled maintenance. The service might be resumed earlier than the scheduled time, 17:00.
2021-07-13 July 13: temporary power failure of cooling system due to the lightning (Jul 20 update)

At around 18:50 on July 13th, temporary power failure of our cooling system (colling tower) occurred due to the lightning. Due to the trouble, this website went down and some of commands in RCCS system (such as showlim) had been unavailbale during July 13 20:00-21:00. Also, 6 of computation nodes went down. Those problems (excluding computation node ones) were fixed until July 13 22:00. File system, frontend nodes, and the other computation nodes were not seriously affected by the issue.
(Jul 20 update) CPU points of the following affected jobs were paid back.
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