Study of the conformation of polyelectrolyte aggregates using coarse-grained molecular dynamics simulations.

The conformation of polyelectrolyte aggregates as a function of the backbone rigidity is investigated by coarse-grained molecular dynamics simulation. The polyelectrolyte is represented by a bead-spring chain with charged side chains. The simulations start from the uniform distributions of the polyelectrolytes, and the resultant polyelectrolyte conformation after a few microseconds exhibits spherical self-aggregates, clusters, or bending bundle-like aggregates, depending on the backbone rigidity. The interaggregate structures on a large scale are featured by the static structure factor (SSF). The simulated SSFs of the bending bundle-like aggregates are consistent with those of the small angle X-ray scattering (SAXS) measurement so we successfully assign the microscopic structures of polyelectrolytes to the SAXS measurement. The power-law of the SSFs for the bundle conditions is steeper than that of the conventional cylinder model. The present study finds that such discrepancy in the power-law results from the bending of the bundle-like aggregates. In addition, the relaxation behavior includes slow dynamics. The present study proposes that such slow dynamics results from diffusion-limited aggregation and from gliding processes to reduce local metastable folding within the aggregates.

Molecular Dynamics Study for Channel Size Dependence of Shear Stress Between Droplet and Wall.

In this study, the channel size dependence of the shear stress between water droplets and solid walls in nm-order channel was analyzed. We considered a several different-sized and highly hydrophobic channel whose macroscopic contact angle was about 150 degrees. We have evaluated the shear stress and the normal pressure by molecular dynamics simulation. Analyzing shear stress and normal pressure based on the macroscopic model, we have discussed the difference between the macroscopic model based on hydrodynamics and the microscopic model. As a result, in the high hydrophobic case, it became clear that the shear stress depends on the channel size due to the large Laplace pressure. Furthermore, in the case that the channel size was less than 50 A, the normal pressure by the molecular simulation didn't agree with the expected value from the Young-Laplace equation. From this study it was clear that molecular simulation is needed when the channel size is less than 40 A.

Bottom-up construction of interaction models of non-Markovian dissipative particle dynamics.

We derive the equation of motion for non-Markovian dissipative particle dynamics (NMDPD) by introducing the history effects on the time evolution of the system. Our formulation is based on the generalized Langevin equation, which describes the motions of the centers of mass of clusters comprising microscopic particles. The mean, friction, and fluctuating forces in the NMDPD model are directly constructed from an underlying molecular dynamics (MD) system without any scaling procedure. For the validation of our formulation, we construct NMDPD models from high-density Lennard-Jones systems, in which the typical time scales of the coarse-grained particle motions and the fluctuating forces are not fully separable. The NMDPD models reproduce the temperatures, diffusion coefficients, and viscosities of the corresponding MD systems more accurately than the dissipative particle dynamics models based on a Markovian approximation. Our results suggest that the NMDPD method is a promising alternative for simulating mesoscale flows where a Markovian approximation is not valid.

Interfacial anisotropy in the transport of liquid crystals confined between flat, structureless walls: a molecular dynamics simulation approach.

Molecular dynamics simulations of uniaxial Gay-Berne ellipsoids as prolate liquid crystal molecules confined between two flat, structureless walls have been carried out in order to investigate anisotropy in their dynamic properties. Several physical quantities are profiled as a function of distance from a wall. The walls stimulate ellipsoids into different behaviors from those of the bulk system. The profiles of self-diffusion coefficients, which are distinguished in each direction of a director-based coordinate system, show that the ellipsoids are more diffusive parallel to the walls and less diffusive perpendicular to the walls with decreasing distance from the walls. According to the self-rotation coefficient and rotational viscosity profiles, ellipsoids are easy to rotate parallel to the walls and hard to rotate in the plane perpendicular to the walls. The analyses of velocity autocorrelation functions, angular velocity autocorrelation functions, director angular velocity autocorrelation functions, and their spectra are useful for the investigation of anisotropy near the walls. We conclude that the flat, structureless wall not only prevents ellipsoids from diffusing and rotating in the plane perpendicular to the walls, but also stimulates them to diffuse and rotate in the plane parallel to the walls.