ArticleJournal of computational chemistry2025
Parallelization of Particle-Based Reaction-Diffusion Simulations Using MPI.
Article in Journal of computational chemistry, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
- Update of
Authors and funding
7 authors.
Funding
Abstract
Particle-based reaction-diffusion offers a high-resolution alternative to the continuum reaction-diffusion approach, capturing the volume-excluding nature of molecules undergoing stochastic dynamics. This is essential for simulating self-assembly into higher-order structures like filaments, lattices, or macromolecular complexes. Applications of self-assembly are ubiquitous in chemistry, biology, and materials science, but these higher-resolution methods increase computational cost. Here, we present a parallel implementation of the particle-based NERDSS software using the message passing interface (MPI), achieving close to linear scaling for up to 96 processors. By using a spatial decomposition of the system across processors, our approach extends to very large simulation volumes. The scalability of parallel NERDSS is evaluated for reversible reactions and several examples of higher-order self-assembly in 3D and 2D, with all test cases producing accurate solutions. Parallel efficiency depends on the system size, timescales, and reaction network, showing optimal scaling for smaller assemblies with slower timescales. We provide parallel NERDSS code open-source, supporting development and extension to other particle-based reaction-diffusion software.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.