Distributed Simulations of DNA Multi-strand Dynamics

In a recent study, Spencer et al. 2021, we have proposed a computational modeling framework for DNA multi strand dynamics implemented using the agent- and rule-based modeling methodology. While this modeling methodology allows for compact representations for systems with large numbers of different species and complexes, such as the case of self-assembly systems, one of its main drawbacks concerns its scalability. Since each agent is individually represented and modeled in the system, the framework becomes slow when dealing with tens- and hundreds of thousands of individual components. In this study we introduce a method to parallelize the computational modeling process by distributing it over several CPU's. We show that such multi-thread models remain equivalent to their sequential counterpart, while the speedup of the computational process can reach even a one-fold increase.