Abstract
We applied replica-exchange molecular dynamics simulation to five fragments of amyloid-β peptide in order to study the mechanism of amyloid fibril formation. In this study, we calculated the free energy by focusing on how to form the β-structures to obtain the dominant structures. We classify the obtained β-structures and elucidate the order of β-structure assembly.
Acknowledgements
Some of the computations were performed on the supercomputers at the Institute for Molecular Science and Center for Computational Sciences, University of Tsukuba.