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Reactive Vortexes in a Naturally Activated Process: Non-Diffusive Rotational Fluxes at Transition State Uncovered by Persistent Homology by Manuchehrfar, Farid; Li, Huiyu; Ma, Ao; Liang, Jie is a scholarly article available to read on EtoBox.

What is Reactive Vortexes in a Naturally Activated Process: Non-Diffusive Rotational Fluxes at Transition State Uncovered by Persistent Homology about?

Dynamics of reaction coordinates during barrier-crossing are key to understand activated processes in complex systems such as proteins. The default assumption from Kramers physical intuition is that of a diffusion process. However, the dynamics of barrier-crossing in natural complex molecules are largely unexplored. Here we investigate the transition dynamics of alanine-dipeptide isomerization, the simplest complex system with a large number of non-reaction coordinates that can serve as an adequate thermal bath feeding energy into the reaction coordinates. We separate conformations along the time axis and construct the dynamic probability surface of reaction. We quantify its topological structure and rotational flux using persistent homology and differential form. Our results uncovered a region with strong reactive vortex in the configuration-time space, where the highest probability peak and the transition state ensemble are located. This reactive region contains strong rotational fluxes: Most reactive trajectories swirl multiple times around this region in the subspace of the two most-important reaction coordinates. Furthermore, the rotational fluxes result from cooperative movem

Author

Manuchehrfar, Farid; Li, Huiyu; Ma, Ao; Liang, Jie

Published

2022

Language

EN