Simulation and study of large-scale bacteria-materials interactions via BioScape enabled by GPUs

Abstract

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.