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Parallelization of particle-based reaction-diffusion simulations using MPI.

Sikao Guo¹, Nenad Korolija², Kent Milfeld³

¹TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.

Biorxiv : the Preprint Server for Biology

|December 23, 2024

Summary

Particle-based reaction-diffusion simulations offer high-resolution insights into molecular self-assembly. A new parallel implementation of NERDSS software significantly improves computational efficiency for these complex systems.

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Area of Science:

Computational biology
Biophysics
Materials science

Background:

Particle-based reaction-diffusion models provide high-resolution simulations of molecular dynamics.
These models capture discrete, volume-excluding molecular behavior essential for self-assembly.
Existing methods face high computational costs, limiting their application.

Purpose of the Study:

To present a parallel implementation of the NERDSS software for particle-based reaction-diffusion simulations.
To evaluate the scalability and accuracy of the parallel implementation.
To provide an open-source, documented code for broader scientific use.

Main Methods:

Implemented parallel NERDSS using Message Passing Interface (MPI) and spatial domain decomposition.
Evaluated scalability for bimolecular reactions, complex self-assembly (trimeric, hexameric), and protein lattice formation in 2D and 3D.
Assessed parallel efficiency based on system size, reaction network, and timescales.

Main Results:

Achieved near-linear scaling for parallel NERDSS up to 96 processors.
Demonstrated accurate solutions across various simulation scenarios (reactions, assemblies, lattices).
Identified factors influencing parallel efficiency, with optimal scaling for smaller, slower systems.

Conclusions:

Parallel NERDSS offers a computationally efficient solution for high-resolution reaction-diffusion simulations.
The software enables accurate modeling of molecular self-assembly and complex structures.
Open-source release facilitates further development and application in biological and material systems.