Modeling Diffusion Between Regions with Different Diffusion Coefficients.

Area of Science:

• Biophysics
• Computational Biology
• Chemical Physics

Background:

• Biological systems feature spatial regions with distinct diffusion coefficients.
• Directly simulating the physical causes of varying diffusion is computationally expensive.
• Accurate simulation of molecular motion, particularly thermal diffusion, is crucial for understanding biological processes at equilibrium.

Purpose of the Study:

• To develop and present accurate methods for simulating thermal diffusion in systems with spatially varying diffusion coefficients.
• To address the challenge of modeling boundaries between regions with different diffusion rates.
• To ensure simulations reflect energy-neutral influences on molecular concentrations at equilibrium.

Main Methods:

• Developed transmission coefficients and probability equations for simulating thermal diffusion.
• Incorporated methods to account for free energy differences and volume exclusion by crowders.
• Implemented these simulation parameters within the Smoldyn particle-based simulation software.

Main Results:

• Demonstrated that reducing transmission probability into slow-diffusing regions correctly simulates thermal diffusion.
• Showed that this approach prevents artificial molecular accumulation, unlike fully permeable boundaries.
• Validated that energy-neutral factors like macromolecular crowding do not alter equilibrium molecular concentrations.

Conclusions:

• The presented transmission probability method accurately simulates thermal diffusion in heterogeneous environments.
• This approach is essential for realistic modeling of molecular motion in biological systems at equilibrium.
• The implementation in Smoldyn provides a valuable tool for computational biophysics research.