The average conformation of a flexible chain molecule in solution is coupled to the local solvent structure. In a dense solvent, local chain structure often mirrors the pure solvent structure, whereas, in a dilute solvent, the chain can strongly perturb the solvent structure which, in turn, can lead to either chain expansion or compression. Here we use Monte Carlo (MC) simulation to study such ...

We present a stochastic rotation dynamics model of amphiphilic molecules. Vesicle formation of amphiphilic molecules in a thermal fluctuating fluid is demonstrated in this paper. In the model, the interaction of amphiphilic molecules is represented by Lennard–Jones potentials, and stochastic rotation dynamics [T. Ihle, D.M. Kroll, Stochastic rotation dynamics: A Galilean-invariant mesoscopic mo...

Dynamics of charge (or charge distribution) solvation is a subject of considerable interest.’ Recent molecular dynamics (MD) computer simulation studies reveal that solvent relaxation occurs in two time regimes.2-7 During the initial regime, which can be described by a Gaussian function, the relaxation occurs very fast (25-150 fs). The fast regime contributes about 60%-80% towards the total rel...

We present a new method to create realistic paint simulation, utilizing the characteristics of paint, such as fluidity, diffusion, and absorption. We treat the painting elements separately as pigment, binder, solvent, and paper. Adopting smoothed-particle hydrodynamics (SPH) including a consideration of viscoelastic movement, we simulate the fluid motion of the paint and the solvent. To handle ...

A new method for calculating the total conformational free energy of proteins in water solvent is presented. The method consists of a relatively brief simulation by molecular dynamics with explicit solvent (ES) molecules to produce a set of microstates of the macroscopic conformation. Conformational energy and entropy are obtained from the simulation, the latter in the quasi-harmonic approximat...