CIMMS Lunchtime Series: Dynamical Hierarchy of Transitions in Chemical Reactions
and Protein Dynamics

Tamiki Komatsuzaki, Associate Professor, Nonlinear Science Laboratory, Department of Earth and Planetary Sciences, Faculty of Science, Kobe University, Institute for Molecular Science, Department of Theoretical Studies, JST/CREST, Japan

Why do reacting species climb through a saddle from one stable state to another? In other terms, what are the necessary and sufficient conditions to react for molecules? Most biological functions are considered to occur associated with jumps among the basins whose free energy differences are at the order of thermal energy a degree of freedom. Any simple thermodynamic picture may not clarify their robust occurrence of functions with a probability almost unity. The functions result from the collection of sequential chemical reactions crossing through many basins and saddles on the multidimensional energy landscapes. That is, to understand the necessary and sufficient conditions of reactions should shed light on the underlying principle of robust occurrence of functions in biomolecular systems. I would like to give an overview of our researches on hierarchical regularity in chaotic transitions by revisiting the long-standing transition state concept in chemical community through which all reacting species pass only once from the reactant to the product states and their perspectives relevance to mechanics of protein folding.