Yasuaki Hiwatari

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A method is introduced to construct a better approximation for the reaction coordinate for protein folding from known order parameters. The folding of a two-state off-lattice alpha helical Go-type protein is studied using molecular dynamics simulations. Folding times are computed directly from simulation, as well as theoretically using an equation derived(More)
We present several characteristics of ionic motion in glassy ionic conductors brought out by time series analysis of molecular dynamics (MD) simulation data. Time series analysis of data obtained by MD simulation can provide crucial information to describe, understand and predict the dynamics in many systems. The data have been treated by the singular(More)
Molecular dynamics simulations of lithium metasilicate (Li2SiO3) glass have been performed. Dynamic heterogeneity of lithium ions has been examined in detail over 4 ns at 700 K. Type A particles show slow dynamics in accordance with a long tail of waiting time distribution of jump motion and localized jumps within neighboring sites (fracton), while type B(More)
We have performed a multicanonical molecular dynamics simulation on a simple model protein. We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers. Since the hydrophobic interaction is considered to significantly affect protein folding, we particularly focus on the competition between effects of the Coulomb(More)
Molecular dynamics simulations of lithium metasilicate (Li(2)SiO(3)) glass have been performed. The motion of lithium ions is divided into slow (A) and fast (B) categories in the glassy state. The waiting time distribution of the jump motion of each component shows power law behavior with different exponents. Slow dynamics are caused by localized jump(More)
Molecular dynamics (MD) simulations of lithium metasilicate (Li2SiO3) in the glassy and supercooled liquid states have been performed to illustrate the decay with time of the cages that confine individual Li+ ions before they hop out to diffuse cooperatively with each other. The self-part of the van Hove function of Li+ ions, G(s)(r,t), is used as an(More)
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