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Internal protein motion in a rough model potential.

P Jangid1, R Metzler2,3, S Chaudhury1

  • 1Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, Maharashtra, India.

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|December 22, 2025
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Summary
This summary is machine-generated.

This study models anomalous diffusion in proteins using fractional Fokker-Planck and continuous-time random walk methods. High roughness enhances ergodicity breaking, leading to power-law increases in mean squared displacement over time.

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Area of Science:

  • Biophysics
  • Statistical Mechanics
  • Computational Biology

Background:

  • Proteins exhibit complex internal motions influencing biochemical functions.
  • Subdiffusive behavior is common in protein dynamics within rugged free energy landscapes.

Purpose of the Study:

  • Investigate anomalous diffusion in rough confining potentials, inspired by protein internal dynamics.
  • Analyze the impact of potential roughness on particle motion and ergodicity.

Main Methods:

  • Employed fractional Fokker-Planck equation and continuous-time random walk models.
  • Derived approximate expressions for mean displacement and mean squared displacement.
  • Examined ergodic properties and mean maximal excursion.

Main Results:

  • Identified three distinct dynamic regimes: free subdiffusion, roughness-impacted motion, and confinement-driven thermal plateau.
  • Demonstrated enhanced weak ergodicity breaking in high-roughness systems.
  • Showed time-averaged mean squared displacement increases as a power-law over time.

Conclusions:

  • Mean maximal excursion quantifies confinement extent, serving as a robust measure for subdiffusive dynamics.
  • Protein internal dynamics can be effectively modeled using anomalous diffusion frameworks.
  • Roughness significantly alters protein dynamics and ergodicity, impacting functional mechanisms.