Biomedical subjects

Y Hiwatari

Publications and source records attributed to Y Hiwatari.

At least 19 recordsLinked to original sources

PubMed2005

Time series analysis of ion dynamics in glassy ionic conductors obtained by a molecular dynamics simulation.

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 spectrum analysis (SSA), which is a method to extract information from noisy short time series and thus provide insight into the unknown or partially unknown dynamics of the underlying system that generated the time series. Phase-space plot reconstructed using the principal components of SSA exhibited complex but clear structures, suggesting the deterministic nature of the dynamics.

Journal Article↗

PubMed2004

Improved theoretical description of protein folding kinetics from rotations in the phase space of relevant order parameters.

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 by considering Brownian-type dynamics for the putative reaction coordinate. Theoretical estimates of the folding time using the number of native contacts (Qn) as a reaction coordinate were seen to differ quite significantly from the true folding time of the protein. By considering the properties of the bimodal free energy surface of this protein as a function of Qn and another relevant coordinate for folding Q (the total number of contacts), we show that by introducing a rotation in the phase space of the order parameters Q and Qn, we can construct a new reaction coordinate q that leads to a fivefold improvement in the estimate of the folding rate. This new coordinate q, resulting from the rotation, lies along the line connecting the unfolded and folded ensemble minima of the free energy map plotted as a function of the original order parameters Q and Qn. Possible reasons for the remaining discrepancy between the folding time computed theoretically and from folding simulations are discussed.

Computer Simulation↗

PubMed2004

Dynamics of caged ions in glassy ionic conductors.

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 at longer times. An improved understanding of its origin should benefit the research of ion conducting materials for portable energy source as well as the resolution of the fundamental problem of the dynamics of ions. We perform molecular dynamics simulations of glassy lithium metasilicate (Li2SiO3) and find that the length scales of the caged Li+ ions motions are distributed according to a Levy distribution that has a long tail. These results suggest that the nearly constant loss originates from "dynamic anharmonicity" experienced by the moving but caged Li+ ions and provided by the surrounding matrix atoms executing correlated movements. The results pave the way for rigorous treatments of caged ion dynamics by nonlinear Hamiltonian dynamics.

Journal Article↗

PubMed2003

Glass transition in an off-lattice protein model studied by molecular dynamics simulations.

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 potential energy minima were generated for the model over a range of temperatures. The mean potential energy of the inherent structures allowed to make rough estimates of the glass-transition temperature T(K). More accurately T(K) was computed by direct evaluations of the total and vibrational entropies. It is found that for the present model the thermodynamic ratio of the folding and glass-transition temperatures is 1.7 which is in good agreement with experimental observations.

Journal Article↗

PubMed2002

Molecular dynamics study of cage decay, near constant loss, and crossover to cooperative ion hopping in lithium metasilicate.

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 indicator of the cage decay. At 700 K, in the early time regime t of Li+ ions also increases very slowly with time approximately as t(0.1) and has weak temperature dependence. Such can be identified with the near constant loss (NCL) observed in the dielectric response of ionic conductors. At longer times, when the cage decays more rapidly as indicated by the increasing buildup of the intensity of G(s)(r,t) at the distance between Li+ ion sites, broadly crosses over from the NCL regime to another power law t(beta) with beta approximately 0.64 and eventually it becomes t(1.0), corresponding to long-range diffusion. Both t(beta) and t(1.0) terms have strong temperature dependence and they are the analogs of the ac conductivity [sigma(omega) proportional, variant omega(1-beta)] and dc conductivity of hopping ions. The MD results in conjunction with the coupling model support the following proposed interpretation for conductivity relaxation of ionic conductors: (1) the NCL originates from very slow initial decay of the cage with time caused by few independent hops of the ions because t(x1)< and are about the same for t of the fast ions increases much more rapidly for t>t(x2). The self-part of the van Hove function of Li+ reveals that first jumps for some Li+ ions, which are apparently independent free jumps, have taken place before t(x2). While after t(x2) the angle between the first jump and the next is affected by the other ions, again indicating cooperative jump motion. The dynamic properties are analogous to those found in supercooled colloidal particle suspension by confocal microscopy.

Journal Article↗

PubMed2002

Diffusive dynamics of protein folding studied by molecular dynamics simulations of an off-lattice model.

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 dynamics simulations focused on the time evolution of the reaction coordinate measuring the similarity of a given conformation with the native state. Folding time for the studied model is calculated following the diffusive-rate formula of Bryngelson and Wolynes [J. Phys. Chem. 93, 6902 (1989)] by using a computed separately configurational diffusion coefficient. Comparison of the folding time with the mean-first passage time obtained directly from folding simulations shows that the approximation depicting the dynamics of the reaction coordinate in protein folding as a diffusive motion on a free-energy landscape is quantitatively correct for the studied model.

Chemical Phenomena↗

PubMed2001

Finite-size dependence of the bridge function extracted from molecular dynamics simulations.

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 used in the simulation cell. This dependency leads to a spurious maximum of the static structure factor at long wavelengths, obtained from the reference hypernetted-chain approximation (RHNC) with the MD system used as a reference system (RHNC-MD). A simple self-consistent procedure, proposed to account for the finite-size effects in the bridge function, allows one to efficiently correct the RHNC-MD static structure factor for all unphysical manifestations.

Journal Article↗

PubMed2000

Monte carlo simulation of the mixed alkali effect with cooperative jumps

In our previous works on molecular dynamics (MD) simulations of lithium metasilicate (Li2SiO3), it has been shown that the long time behavior of the lithium ions in Li2SiO3 has been characterized by the component showing the enhanced diffusion (Levy flight) due to cooperative jumps. It has also been confirmed that the contribution of such component decreases by interception of the paths in the mixed alkali silicate (LiKSiO3). Namely, cooperative jumps of like ions are much decreased in number owing to the interception of the path for unlike alkali-metal ions. In the present work, we have performed a Monte Carlo simulation using a cubic lattice in order to establish the role of the cooperative jumps in the transport properties in a mixed alkali glass. Fixed particles (blockage) were introduced instead of the interception of the jump paths for unlike alkali-metal ions. Two types of cooperative motions (a pull type and a push type) were taken into account. Low-dimensionality of the jump path caused by blockage resulted in a decrease of a diffusion coefficient of the particles. The effect of blockage is enhanced when the cooperative motions were introduced.

Journal Article↗

PubMed1999

Characteristics of slow and fast ion dynamics in a lithium metasilicate glass.

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 motions and the long waiting time. On the other hand, the fast dynamics of the lithium ions in Li(2)SiO(3) are characterized as Lévy flight caused by cooperative jumps. Short intervals of jump events also occur in the fast dynamics in the short time region. Both the temporal and spatial terms contribute to the dynamics acceleration and the heterogeneity caused by these two kinds of dynamics is illustrated. The slow dynamics characteristics of the "glass transition" and in the "mixed alkali effect" are discussed.

Journal Article↗

PubMed1995