Understanding of genome structures is critical to further our understanding of genome functions such as transcription, DNA replication and repair, and repression of gene expression. We investigate the hierarchical genome structures down from DNA, to nucleosomes, to chromatin fibers, up to chromosomes, by computer simulations of multiscale models. Figures illustrate a model of chromatin fiber (an array of nucleosomes linked with linker DNA) and a model cell nucleus consisting of decondensed chromosomes.

Biological cells have very crowded environments filled with various macromolecules including proteins, RNAs, cell organelles. Biochemical reactions occurring in such crowded environments could become quite distinct from those studied in buffer solutions as in traditional biochemistry. In order to provide proper understanding of biochemical processes in crowded cellular environments, we perform computer simulations of model systems. The figure on the left illustrates the simple model study of protein-protein association reactions in crowded environments.

There are many examples where crystallization induces a harmful effect in science and engineering. Ice crystallization in animals and plants in polar areas is detrimental to their lives, ice growth in frozen foods severely damages the textural quality, and the growth of kidney stone in human body brings an enormous pains in patients’ lives. Therefore, inhibition of crystallization is important in a variety of industrial, scientific, and medical applications. Using molecular models, we aim to understand the crystallization and its inhibition by certain anti-crystallization candidates.