Recent progress in supercomputers has been enabling large-scale (~O(10 nm)) and/or long-time (~O(1 μs)) molecular dynamics (MD) calculations, where all-atom MD calculations provide us with microscopic insights into physico-chemical properties of self-assemblies of amphiphilic molecules in solution such as micelles, bilayers, and protein complexes. Here, we present a brief review of our recent calculations for these systems.

It is widely known that the dynamical and rheological properties of colloidal suspensions are under strong influence of hydrodynamic interactions among particles, but it is very difficult to elucidate their roles analytically. Thus, numerical simulation is a very powerful tool for studying them and a variety of numerical methods have been proposed. We developed a new method, which we named “Fluid Particle Dynamics”. Here we explain the basic principle of our method and show its application to the study of colloidal phase separation. Our study indicates not only the importance of hydrodynamic interactions but also the predictability of the dynamical behavior of colloidal suspensions.

One can call a simulation as “rheology simulation” if the simulation can deal with the calculation of the mechanical response of materials against flows and deformations. There exist two significant branches for such rheology simulation. In the industry, a widely used direction is the phenomenological approach, where the constitutive equation gives the rheological properties of the material. The other one is the molecular basis to calculate the rheological properties from the dynamics of the molecules. The latter will be mainly explained in this review with attention to some coarse-graining technologies, which are required to trace the molecular motion for a long time.

To study the shape and size of realistic polymer chains used in industry, it is difficult to apply all-atom molecular dynamics simulations due to the limitation of number of atoms and time scale of dynamics that can be handled. Therefore, instead of all-atom molecular dynamics, coarse-grained molecular dynamics simulations are often used to study the structure and dynamics of bulk polymer chains. After briefly introducing the concept of coarse-grained polymer chains, some examples of coarse-grained molecular dynamics simulations are presented. Specific examples include the study of size of single chain in homogenous polymer melts of linear and branched chain, deformation of the shape of polymer melts and grafted chain near the solid wall, and configuration of block copolymers in microphase separated structures.