Correction factors for boundary diffusion in reaction-diffusion master equations.

Area of Science:

• Computational chemistry
• Biophysics
• Chemical kinetics

Background:

• The reaction-diffusion master equation (RDME) is a common tool for modeling spatial stochastic chemical kinetics.
• RDME-based trajectorial methods offer a balance between spatial detail and computational cost.
• Accurate reaction rates are crucial, especially with reactive boundaries or binary reactions, to avoid unphysical results.

Purpose of the Study:

• To develop an alternative approach for deriving correction factors in RDME models.
• To address inaccuracies arising from reactive or semi-permeable boundaries.
• To provide a method for reassessing reaction rates in RDME simulations.

Main Methods:

• Deriving correction factors by solving a closed set of steady-state moment equations.
• The approach avoids modifying absorption or reflection probabilities.
• Discussion of existing correction mechanisms for bimolecular reaction rates under different diffusion limits.

Main Results:

• A new method for calculating correction factors for RDME models with reactive boundaries.
• The proposed method is based on steady-state moments, offering a systematic way to improve model accuracy.
• The approach is applicable to various boundary conditions and reaction types.

Conclusions:

• The presented method provides a robust way to derive correction factors for RDME models.
• This approach enhances the reliability of simulations involving spatial stochastic chemical kinetics.
• The method offers potential for broader application in modeling complex reaction-diffusion systems.