Scientific results using RCCS

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).

Asymmetry of amyloid fibrils: Molecular Dynamics Simulations

Alzheimer’s disease, one of dementia, is caused by amyloid fibrils of amyloid-β (Aβ) peptides. It has been known that the Aβ amyloid fibrils extend only in one direction, but the reason has not been clarified. We found that the structure and fluctuation of the Aβ amyloid fibrils differ between the right and left ends by molecular dynamics simulations and clarified that this is the reason for the unidirectionality of the amyloid-fibril elongation. This result will be applied to develop inhibitors for the causative substance of the Alzheimer's disease.

H. Okumura and S. G. Itoh, Sci. Rep. 6 (2016) 38422 (9 pages).

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Update Information

2020-04-16 In Response to the Novel Coronavirus

RCCS supercomputer is working as usual. Various applications and inquiries via email or the web UI are also accepted. On the other hand, it is difficult to respond to phone and postal mail, since many of our staff are working at home. Please ask us not by phone but via email ccadm_at_draco.ims.ac.jp (please change _at_ to @) or the comment form.
2020-04-21 Apr. 21 15:00-16:00 User information can't be modified

(Apr. 21 15:55) Maintenance completed.
2020-04-13 Apr. 13 Category I Application via NOUS

Category I application (internal applicants from IMS, NIBB, NIPS, ExCELLS) is now available in NOUS.
The application type name in NOUS is "IMS-RCCS-shonai".
2020-04-09 Category(A) submission reopened (Apr. 9)

Category (A) application can be submitted via NOUS from Apr. 9.
Please choose "IMS-RCCS-A" category from the list of category types. Further detailed information will become available under How to Apply / Report page time by time.
2020-04-06 Yearly Update (Apr. 6-8)

We are now in yearly update maintenance.
New user registration and various user setting change (SSH, login shell) is temporary closed now. They will be reopened in 4/8 afternoon. Please wait for a while.
(Apr. 8) Update was successfully finished and the operation began at Apr. 8 17:00 as scheduled.
2020-03-31 (Apr. 1-8) Temporary suspension of new application due to migration to NOUS

(Apr. 9) The new submission system NOUS is finally available.
 
2019-12-17 Jan. 29 0:00-2:00 Network temporarily unavailable

On Jan. 29 (2020), network connection to RCCS will be temporarily unavailable for ~60 minutes somewhere during the period of 0:00-2:00 AM.
2019-11-05 Dec. 4 before dawn: Network will be suspended

Internet connection to RCCS will be suspended for ~60 minutes during the period of Dec. 4 (Wed) 1:00-4:00 AM.
RCCS intranet won't get involved in this maintenance work. Therefore, already submitted jobs won't be affected.
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