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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 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)
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)
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)
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)
At sufficiently high frequency and low temperature, the dielectric responses of glassy, crystalline, and molten ionic conductors all invariably exhibit nearly constant loss. This ubiquitous characteristic occurs in the short-time regime when the ions are still caged, indicating that it could be a determining factor of the mobility of the ions in conduction(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)