Diffusion crossover of protein molecules: Two-step coarse-graining and oscillating memory.

Area of Science:

• Physics
• Biophysics
• Computational Biology

Background:

• Anomalous diffusion requires a detailed microscopic framework.
• Understanding protein diffusion dynamics is crucial in biophysics.

Purpose of the Study:

• To develop a consistent microscopic framework for anomalous diffusion.
• To model protein diffusion dynamics using coarse-graining.

Main Methods:

• A two-step coarse-graining procedure was employed.
• Protein molecules were modeled as generalized Brownian particles.
• Interactions were harmonic, coupled to a thermal bath.

Main Results:

• The power-law memory kernel was approximated by damped oscillator response functions.
• Oscillatory behavior was observed on sub-picosecond timescales.
• Protein molecules showed ballistic diffusion up to ~0.3 ps and subdiffusion up to 100 ps.

Conclusions:

• The model provides insights into protein diffusion mechanisms.
• Upward-tail behavior in mean-square displacement was observed.
• The dynamics were extended to the super-diffusive regime.