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Scientific results using RCCS

Electronic structure informatics to search for hightly efficient photovoltaic materials using singlet fission

The transition from fossil fuels to environment-friendly and renewable sources of energy has become one of the central challenges for today’s society and across scientific disciplines. Though global energy studies report that there has been record-breaking growth in sustainable energy production, further improvements are desirable. Solar energy is a promising solution for the near future, owing to its availability and potentially high output.

In this study, an "electronic structure informatics" approach combining the semiempirical molecular orbital method, time-dependent density functional theory, and machine learning has been applied to rapidly search for materials that can be used as photovoltaic cell materials with high efficiency by multiple exciton generation using singlet fission from over 4 million derivatives based on indigo, a famous dye of natural origin. The obtained promising candidate molecules and their possible candidates were identified and compared with those not. Random forest classification of the chemical structures of the obtained promising and non-promising candidate molecules led to the discovery of chemical structure rules that effectively show singlet fission and the identification of candidate materials with symmetric chemical structures and sufficient synthesizability in the order of several hundred.

Weber F., Mori H., npj Comput. Mater., 8, 176 (2022).

Electronic structure informatics to search for hightly efficient photovoltaic materials using singlet fission

Weber F., Mori H., npj Comput. Mater., 8, 176 (2022).

The mechanism of divalent cation block of ion channel activity

Nervous activity is subjected to complex regulation by ion channels. In this study, we reproduced the divalent cations block in molecular dynamics simulation and elucidated the blocking mechanism. It was observed that introducing a hydrophilic environment into the channel lumen allows the stable existence of divalent cations. This retention of divalent cations makes it difficult for ions to permeate the ion channel. This result also provides new knowledge about the reproduction of polyvalent ions in molecular dynamics simulations.

K. Irie, Y. Oda, T. Sumikama, A. Oshima, Y. Fujiyoshi, Nat. Commun., 14, 4236 (2023).

The mechanism of divalent cation block of ion channel activity

K. Irie, Y. Oda, T. Sumikama, A. Oshima, Y. Fujiyoshi, Nat. Commun., 14, 4236 (2023).

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).

Au-Ag nanoclusters showing intense phosphorescence in cells

“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

“Bucket brigade” of remdesivir 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)

Molecular simulations of functional dynamics in biomolecular machines

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Update Information

2024-05-01	May 9 (Thu) 9:00-17:00 NOUS maintenance
Application submission system NOUS will be unavailable from 9:00 to 17:00 on Thursday, May 9 due to the scheduled maintenance. Thank you for your understanding. Read more about May 9 (Thu) 9:00-17:00 NOUS maintenance

2024-04-22	May 25(Sat) 0:00-1:30: access to system temporarily unavailable due to SINET maintenance
Due to the maintenance work of SINET, there will be at most two times of network disconnection for 15 minutes during 0:00-1:30 AM on May 25 (Sat). Network access to RCCS website or ccfep will be unavailable during the disconnection period. Submitted jobs are not affected by the network disconnection. Read more about May 25(Sat) 0:00-1:30: access to system temporarily unavailable due to SINET maintenance

2024-04-22

May 25(Sat) 0:00-1:30: access to system temporarily unavailable due to SINET maintenance

Due to the maintenance work of SINET, there will be at most two times of network disconnection for 15 minutes during 0:00-1:30 AM on May 25 (Sat). Network access to RCCS website or ccfep will be unavailable during the disconnection period. Submitted jobs are not affected by the network disconnection.

Read more about May 25(Sat) 0:00-1:30: access to system temporarily unavailable due to SINET maintenance

2024-03-21	Broken links (404 Not Found error) fixed
During the update of this website on Monday, February 5, IDs of English pages had changed. This resulted in a large number of broken internal links. Most of these problems occurred on links in English pages. We have reviewed and corrected all major pages and recently created pages. We apologize for any inconvenience caused. Read more about Broken links (404 Not Found error) fixed

2024-01-25	We will be switching web servers on February 5th.
We will be switching web servers between 9:00 and 10:00 on February 5th. Read more about We will be switching web servers on February 5th.

2024-01-24	Fixed a problem that prevented execution of GAMESS 2023R2
A problem that prevented execution of GAMESS 2023R2 due to a setting error has been resolved. We apologize for any inconvenience caused. Read more about Fixed a problem that prevented execution of GAMESS 2023R2

2024-01-11	GRRM 23 installed
GRRM 23 was installed. Installation path is /apl/GRRM/23. Application is required to use GRRM 23. Please refer to the following page (users only) for application procedure and notes. https://ccportal.ims.ac.jp/en/GRRM23 Read more about GRRM 23 installed

2024-01-10	Support for Victims of the Noto Peninsula Earthquake
To support researchers affected by the Noto Peninsula Earthquake occurred on January 1, 2024, RCCS is providing the following assistance. Application for FY2023 SH Category (B) Application for FY2023 SH Category (B) for FY2023 Category (A) users Extend deadline of application for FY2024 Category (B) Undergraduate students added as members (as a special case; please see this page) Additional CPU points request (the situation will be taken into consideration upon review process) The support program above is available only for the victims of the earthquake. For Categories (A) and (B) application, please submit directly from NOUS. If you have any questions, please feel free to contact us. Read more about Support for Victims of the Noto Peninsula Earthquake

2024-01-10

Support for Victims of the Noto Peninsula Earthquake

To support researchers affected by the Noto Peninsula Earthquake occurred on January 1, 2024, RCCS is providing the following assistance.

Application for FY2023 SH Category (B)
Application for FY2023 SH Category (B) for FY2023 Category (A) users
Extend deadline of application for FY2024 Category (B)
Undergraduate students added as members (as a special case; please see this page)
Additional CPU points request (the situation will be taken into consideration upon review process)

The support program above is available only for the victims of the earthquake. For Categories (A) and (B) application, please submit directly from NOUS. If you have any questions, please feel free to contact us.

Read more about Support for Victims of the Noto Peninsula Earthquake

2023-12-25	Start accepting applications for GRRM23 (scheduled to start on January 11, 2024)
We have started accepting applications for GRRM23, a program for an automated exploration of chemical reaction pathways, from December 19. Once your application is approved, you will be able to use GRRM23 on the RCCS computer. The service is scheduled to begin on January 11, 2024. Please refer to the following page (users only) for application procedure and notes. https://ccportal.ims.ac.jp/en/GRRM23 Read more about Start accepting applications for GRRM23 (scheduled to start on January 11, 2024)

2023-12-25

Start accepting applications for GRRM23 (scheduled to start on January 11, 2024)

We have started accepting applications for GRRM23,
a program for an automated exploration of chemical reaction pathways,
from December 19.
Once your application is approved,
you will be able to use GRRM23 on the RCCS computer.
The service is scheduled to begin on January 11, 2024.
Please refer to the following page (users only) for application procedure and notes.

https://ccportal.ims.ac.jp/en/GRRM23

Read more about Start accepting applications for GRRM23 (scheduled to start on January 11, 2024)

2023-12-07	GAMESS 2023 R2 (2023Sep30) installed
GAMESS 2023 R2 (2023Sep30) was installed. Installation directory is /apl/gamess/2023R2. Sample can be found at /apl/gamess/2023R2/samples. Installation procedure is described in this page. Read more about GAMESS 2023 R2 (2023Sep30) installed