its significant limitations, particularly the exclusion of pseudoknots and reliance on simplified rate models, anchor it firmly to a specific, now somewhat outdated, problem scope.

Modern researchers seeking to simulate more complex biomolecular systems would likely find more value in tools that incorporate broader physical models or leverage more contemporary computational approaches, rather than attempting to adapt this specific, constrained architecture.

While the general concept of structuring simulations around local dynamics on structured state spaces is broadly applicable, this paper's specific implementation is deeply coupled to its restricted DNA model, making direct repurposing challenging and potentially less fruitful than utilizing or developing tools designed for broader physical accuracy or leveraging modern computational architectures (e.g., parallelization).