Reaction systems, inspired by biochemical processes in living cells, form a computational model where system behaviour emerges from interactions of reactions governed by facilitation and inhibition. A distinctive feature of this model is the non-permanency of entities, which poses challenges for simulation using alternative frameworks such as Petri nets. In this paper, we extend the standard semantical framework of reaction systems by introducing duration for reactions, while preserving the non-permanency assumption. We develop a modular Petri net encoding that supports a compositional construction and enables an accurate simulation of the new semantics. This framework is particularly well-suited for practical applications such as modelling of aneurysm, where structural variability, transient biochemical conditions, and uncertain process duration are critical factors.