Dynamics in Condensed Molecular Systems

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In order to understand chemical reaction dynamics in condensed molecular systems, following topics were studied.(1) Sequence selection simulation. Protein sequence is designed in a specific way to realize consistency among interactions in order to facilitate the rapid folding from the unfolded stretched chain to the folded native conformation. A possible scenario is that sequences were selected to satisfy the consistency conditions through the Darwinian selection process in the evolutionary history. A computer simulation was conducted using the newly developed empirical potential to show the validity of the functional selection scenario in computer.(2) Analyses of kinetic partitioning in a lattice model of protein folding. When there are competing energy minima other than the native conformation, the folding dynamics should show kinetic partitioning behaviors which are not found in the simplest funnel potential. A lattice model was developed to analyze the partitioning phenomena and compared to the observed data of lysozyme.(3) Mesoscopic structure and dynamics of the dipole field in liquid water and its role in hydration. MD simulation of liquid water is analyzed by taking average not on each molecule but on each spatial position through which many molecules pass by. Unexpected mesoscopic structures are found in the dipole field averaged on each spatial position. Its dynamics and implications in hydration of biomolecules were studied.