KCS

In biology and chemistry, self-assembly is a fundamentally important process that enables the formation of macromolecules and supramolecules, respectively. Because inter-atomic interactions determine the self-assembly processes, atomic differences in the unit molecules can lead to a dramatically different self-assembly process. A good example is the two fundamental classes in biology—nucleic acids and amino acids—that differ from each other within a class by only a few atoms. Thus, the molecular dynamics (MD) simulation that can distinguish each atom became a mainstream computational tool in self-assembly. In this talk, we will evaluate the current issues in the MD simulation of self-assembly based on the principles of physical chemistry. Specifically, we will show that the colligative properties of small model compounds such as osmotic pressure can serve as an ideal reference data to evaluate and enhance the accuracy of the intermolecular interactions quantitatively. Then, we will demonstrate that the newly optimized force field can dramatically improve the realism of the MD simulations of various biological systems, including protein folding, DNA condensation, and protein-DNA complexes.