Molecular fluid simulation for self-organized/self-assembled pattern formation by applying group theory

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To clarify a pattern formation mechanism resulting from self-organization or self-assembly of molecules, we have performed experimental observations, theoretical developments, and molecular dynamics simulations. We successfully visualized self-assembled patterns of DNA fragments on mica and highly oriented pyrolytic graphite surfaces by atomic force microscopy. In addition to a coarse-grained molecular dynamics simulation, a reaction-diffusion model is applied to represent slow growths of the self-assembled patterns, in which symmetries of surfaces can be implemented by symmetric functions resulting from irreducible representations of group theory. Consequently, various self-assembled patterns which depend on surface conditions could be simulated in the practical temporal and spatial scales in comparison with experiments. Some parameters sensitive to the surface conditions were found out.