Biomedical subjects

Hisashi Okumura

Publications and source records attributed to Hisashi Okumura.

6 recordsLinked to original sources

PubMed2006

Equation of state and structural properties of the Weeks-Chandler-Andersen fluid.

Molecular dynamics simulations have been carried out for the equation of state and percolation properties of the Weeks-Chandler-Andersen (WCA) system in its fluid phase as functions of density and temperature. The compressibility factor Z collapses well for the various isotherms, using an effective particle diameter for the WCA particle which is (in the usual WCA reduced units) sigma(e)=2(16)(1+T)(16), where T is the temperature. A corresponding "effective" packing fraction is zeta(e)=pisigma(e) (3)N6V, for N particles in volume V, which therefore scales out the effects of temperature. Using zeta(e) the simulation derived Z can be fitted to a simple analytic form which is similar to the Carnahan-Starling hard sphere equation of state and which is valid at all temperatures and densities where the WCA fluid is thermodynamically stable. The data, however, are not scalable onto the hard sphere equation of state for the complete packing fraction range. We explored the continuum percolation behavior of the WCA fluids. The percolation distance sigma(p) for the various states collapses well onto a single curve when plotted as sigma(p)sigma(e) against zeta(e). The ratio sigma(p)sigma(e) exhibits a monotonic decrease with increasing zeta(e) between the percolation line for permeable spheres and the glass transition limit, where sigma(p)sigma(e) approximately 1. The percolation packing fraction was calculated as a function of effective packing fraction and fitted to an empirical expression. The local coordination number at the percolation threshold showed a transition between the soft core and hard core limits from ca. 2:74 to 1:5, as previously demonstrated in the literature for true hard spheres. A number of simple analytic expressions that represent quite well the percolation characteristics of the WCA system are proposed.

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PubMed2006

Multibaric-multithermal ensemble molecular dynamics simulations.

We present new generalized-ensemble molecular dynamics simulation algorithms, which we refer to as the multibaric-multithermal molecular dynamics. We describe three algorithms based on (1) the Nosé thermostat and the Andersen barostat, (2) the Nosé-Poincaré thermostat and the Andersen barostat, and (3) the Gaussian thermostat and the Andersen barostat. The multibaric-multithermal simulations perform random walks widely both in the potential-energy space and in the volume space. Therefore, one can calculate isobaric-isothermal ensemble averages in wide ranges of temperature and pressure from only one simulation run. We test the effectiveness of the multibaric-multithermal algorithm by applying it to a Lennard-Jones 12-6 potential system.

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PubMed2004

Comparisons between molecular dynamics and hydrodynamics treatment of nonstationary thermal processes in a liquid.

Molecular dynamics (MD) and Navier-Stokes hydrodynamics have been performed to model thermal relaxation processes arising from an initially established nonequilibrium stationary state. A nanoscale two-layer Lennard-Jones (LJ) liquid system was constructed in which the two parts were initially at a different temperature, with a narrow transitional zone between the two layers that was spatially linear in temperature. The highest-temperature layer had widths of five or 20 LJ particle diameters. The hydrodynamics model used parametrized MD-derived transport coefficients and the LJ equation of state as input functions. The temporal and spatial temperature and density profiles produced by the two methods show good agreement, indicating that a hydrodynamics description is reliable even for nonstationary phenomena down to the scale of a few molecular diameters. We found that at certain locations the Navier-Stokes solution predicted that the pressure and temperature profiles relaxed in a damped oscillatory manner, which we could discern despite the fluctuations in the MD data.

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PubMed2004

Monte Carlo simulations in generalized isobaric-isothermal ensembles.

We present three generalized isobaric-isothermal ensemble Monte Carlo algorithms, which we refer to as the multibaric-multithermal, multibaric-isothermal, and isobaric-multithermal algorithms. These Monte Carlo simulations perform random walks widely in volume space and/or in potential energy space. From only one simulation run, one can calculate isobaric-isothermal-ensemble averages in wide ranges of pressure and temperature. We demonstrate the effectiveness of these algorithms by applying them to the Lennard-Jones 12-6 potential system with 500 particles.

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PubMed2003

Nonequilibrium molecular dynamics simulations of a bubble.

Molecular dynamics simulations are performed to investigate the microscopic dynamics of a bubble when liquids are locally heated. We successfully observe that the heated atoms scatter the neighboring nonheated atoms and make a bubble, and then the bubble is cooled and compressed by the surrounding liquids. The bubble dynamics in this process agrees with the results of the Rayleigh-Plesset equation which describes the dynamics of a bubble in terms of macroscopic hydrodynamics. In this way, we clarify that the hydrodynamic description is reliable even for a microscopic bubble.

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PubMed2003

Bulk viscosity in the case of the interatomic potential depending on density.

We derive a formula for the bulk viscosity zeta in a density-dependent-potential system. This is a generalization of the bulk-viscosity formula for the density-independent-potential system which has been proposed recently by us. In our formulas, the bulk viscosity is expressed by using microscopic quantities such as interatomic potentials and pair distribution functions. This has an outstanding advantage of providing the relation between such microscopic information and a macroscopic quantity zeta. On the other hand, in all formulas proposed previously, zeta is expressed in terms of pressure, a macroscopic quantity, and it is difficult to discuss this relation. We apply our formula to a model liquid metal in which the interatomic potential varies with density. Our calculated results show that zeta increases in the density region where the interatomic potential changes from one type to another. These results agree qualitatively with the experimental results about liquid mercury.

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