Professor: Hisashi OKUMURA, Ph.D.
E-mail: hokumura[at]
Assistant Professor: Satoru ITOH, Ph.D.
E-mail: itoh[at]



Biomolecules such as proteins and peptides have complicated free-energy landscape with many local minima. The conventional canonical-ensemble molecular dynamics (MD) simulations tend to get trapped in a few of the local-minimum states. To overcome these difficulties, we have proposed new generalized-ensemble algorithms, such as replica-permutation method. We apply these methods to proteins and peptides and try to predict the native structures of proteins.
We are also interested in protein aggregates such as oligomers and amyloid fibrils, which are associated with more than 20 human neurodegenerative diseases. To understand formation and disruption of these protein aggregates, we perform MD simulations of these systems.



・H. Okumura and S. G. Itoh, Structural and fluctuational difference between two ends of Aβ amyloid fibril: MD simulation predicts only one end has open conformations, Sci. Rep. 6, 38422. (2016)
・H. Okumura and S. G. Itoh, Amyloid fibril disruption by ultrasonic cavitation: Nonequilibrium molecular dynamics simulations, J. Am. Chem. Soc. 136, 10549-10552. (2014)
・S. G. Itoh and H. Okumura, Replica-permutation method with the Suwa-Todo algorithm beyond the replica-exchange method, J. Chem. Theory Comput. 9, 570-581. (2013)

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