Abstract
All the functionally important processes for proteins are activated processes. Understanding their mechanisms is of critical importance in both theory and applications. We use transition path sampling and a recently developed energy flow method to investigate the progress of the energy activation phase and transition barrier crossing. The method is applied to the prototypic biomolecular isomerization reaction of alanine dipeptide and we study a new mechanism of an activated process that reveals the existence of preferred energy flow channels during the activated process and strong coordination between potential and kinetic energies along with different coordinates.
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