Ayori Mitsutake

TL;DR: Molecular dynamics simulations of small proteins demonstrate that these conformational fluctuations directly affect the protein's instantaneous diffusivity D_{I}, and demonstrates the validity of the local Stokes-Einstein-type relation.

TL;DR: This work simulates the nonequilibrium ensemble dynamics of a biomolecule using the weighted ensemble method, which was introduced in molecular dynamics simulations by Huber and Kim and further developed by Zuckerman and co-workers, and finds that the most significant DM coordinate turns out to extract a dihedral angle of glycine.

TL;DR: This work applied relaxation mode analysis to folding simulations of a designed mutant of protein G, NuG2, to investigate its folding pathways and classified various characteristic states such as native, nativelike, intermediate, and random states and clarified two main folding pathways.

TL;DR: This paper proposes a simple and effective extension of the RMA method, referred to as the positive definite R MA method, to introduce the evolution time parameter robustly, and demonstrates the effectiveness of the method.

TL;DR: The results for designing amino-acid substitution of the 10-residue peptide, chignolin, to stabilize the misfolded structure are reviewed using developed relaxation mode analysis and the three-dimensional reference interaction site model theory to investigate stabilities with solvent effects.