Domain Project

We are pleased to announce that our paper “Model-Driven Parallel and Distributed Stochastic Simulation of Chemical Reaction Networks” has been accepted for presentation at the 29th IEEE/ACM International Symposium on Distributed Simulation and Real Time Applications (DS-RT 2025).

This work addresses the challenge of simulating large-scale biochemical systems, which are inherently stochastic and computationally demanding. We introduce a model-driven framework that transforms high-level rule-based descriptions from BioNetGen into an intermediate representation based on the Actor Model. This representation naturally captures concurrency and enables automated generation of executable code for ROOT-Sim, a speculative parallel discrete-event simulation environment.

A key contribution of the paper is an exact parallel implementation of the Stochastic Simulation Algorithm (SSA). By partitioning reactions and introducing an event-exchange protocol, we ensure consistency and atomicity in reactant consumption across distributed nodes. Furthermore, refined rollback and reaction rescheduling mechanisms address correctness issues that arise during speculative execution.

Our experiments on established biochemical models, such as FcεRI, show that this approach yields substantial speedups over sequential methods, paving the way for efficient and scalable simulations of complex biochemical networks.

This acceptance marks another important step for the project in extending model-driven engineering, DSL transformations, and parallel simulation techniques toward real-world high-performance applications.