Yasuaki Hiwatari

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We report the results of a molecular dynamics study on the kinetic properties of a small off-lattice model of proteins. The model consists of a linear chain of monomers interacting via a number of potentials. These include hydrophobic, bond-angle, and torsion potentials. The ground-state conformation of the studied model is a beta-sheet motif. Molecular(More)
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 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)
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)
21 goes up. This seems quite reasonable in a nite size system with continuous degrees of freedom since in spite of the absence of a perfectly crystalline ground state only a few conngurations of the particles are expected to really minimize the Hamiltonian. The natural next step in this analysis should consist in trying to get the behaviour of quantities(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)
The relaxation dynamics of a complex interacting system can be drastically changed when mixing with another component having different dynamics. In this work, we elucidate the effect of the less mobile guest ions on the dynamics of the more mobile host ions in mixed alkali glasses by molecular-dynamics (MD) simulations. One MD simulation was carried out on(More)
In this paper we report the results of a numerical investigation of the glass transition phenomenon in a minimalist protein model. The inherent structure theory of Stillinger and Weber was applied to an off-lattice protein model with a native state beta-sheet motif. By using molecular dynamics simulations and the steepest descent method, sets of local(More)
The bridge function for liquid sodium at T=373 K is obtained by using the mean spherical approximation to extrapolate the pair distribution function (PDF), calculated in molecular dynamics (MD) simulations, beyond the half simulation box length for two sizes of the MD system. The bridge function is found to strongly depend on the total number of particles(More)