SpringSim '09 Proceedings of the 2009 Spring Simulation Multiconference
Efficient, correct simulation of biological processes in the stochastic pi-calculus
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Efficient simulation of agent-based models on multi-GPU and multi-core clusters
Proceedings of the 3rd International ICST Conference on Simulation Tools and Techniques
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Biological systems encompass complexity that far surpasses many artificial systems. Modeling and simulation of large and complex biological systems is a computationally intensive challenge. We present a GPU based simulation framework in a reactive environment in 3D space, along with the modeling language, BioScape, in order to describe various biological processes. We also present an efficient computational framework to study the interactions enabled by the massively parallel processing capability of the GPUs. Our driving example is a bio-triggered drug delivery system for infection-resistant medical implants. The modeling and simulation framework presented here will help in identifying biological targets and materials to treat biomaterials associated bacterial infections. The computational framework will offer a deeper insight into various biological processes compared to traditional modeling via implicit differential equations, and help us observe the key events as they unfold.