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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