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Updated: Aug 22, 2025

An Analog Macroscopic Technique for Studying Molecular Hydrodynamic Processes in Dense Gases and Liquids
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Reactive Vortexes in a Naturally Activated Process: Non-Diffusive Rotational Fluxes at Transition State Uncovered by

Farid Manuchehrfar1, Huiyu Li1, Ao Ma1

  • 1Center for Bioinformatics and Quantiative Biology and Richard and Loan Hill Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, Illinois60607, United States.

The Journal of Physical Chemistry. B
|November 8, 2022
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Summary
This summary is machine-generated.

Complex molecular reactions show non-diffusive barrier-crossing dynamics. Analysis of alanine dipeptide isomerization reveals a "reactive vortex" where trajectories swirl, challenging traditional diffusion models.

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Area of Science:

  • Chemical Physics
  • Biophysics
  • Computational Chemistry

Background:

  • Understanding activated processes in complex systems like proteins relies on reaction coordinate dynamics during barrier-crossing.
  • Kramers' theory typically assumes a diffusion-driven process, but dynamics in natural complex molecules remain under-explored.

Purpose of the Study:

  • To investigate the transition dynamics of barrier-crossing in alanine dipeptide isomerization, a model for complex molecular systems.
  • To explore non-diffusive dynamics and identify novel features in the reaction pathway.

Main Methods:

  • Analyzing alanine dipeptide isomerization as a simple complex system with a sufficient thermal bath.
  • Constructing the dynamic probability surface of reaction by separating conformations over time.
  • Quantifying topological structure and rotational flux using persistent homology and differential forms.

Main Results:

  • Identified a "reactive vortex" in configuration-time space, encompassing the highest probability peak and transition state ensemble.
  • Observed strong rotational fluxes within this region, with reactive trajectories swirling multiple times.
  • Attributed rotational fluxes to cooperative motion along isocommitter surfaces and orthogonal barrier-crossing.

Conclusions:

  • The study reveals non-diffusive dynamics in the barrier-crossing of a natural activation process.
  • The findings introduce the concept of "reactive vortex" regions, offering new insights into molecular reaction mechanisms.
  • Challenges the conventional diffusion-based understanding of barrier-crossing in complex molecular systems.