DEVS-based design of spatial simulations of biological systems

Abstract

The application of the DEVS formalism to spatial simulations of biological systems is motivated by a need to keep software manageable, even when faced with complex models that may combine algorithms for potential fields, fluid dynamics, the interaction of proteins, or the reaction and diffusion of chemicals. We demonstrate DEVS-based design by applying the formalism to a "tethered particle system" (TPS), a model we designed to capture the motion of deformable biological structures. The paper focuses on the design of DEVS models using hierarchies and layers, and describes a recently-developed simulator that supports our approach. The DEVS-based TPS model, which has been used to simulate certain interactions in nerve cells, demonstrates the formalism's potential as a means of addressing the complexity of spatial biological models.