Three-dimensional angiogenesis modelling on the GPU

Angiogenesis, the formation of de novo blood vessels, has been implicated in many human diseases, including cancer, diabetes, and in recent years, neurodegenerative diseases. Study of the formation of microvasculature, therefore, has important implications in diagnosis and treatment of diseases. This paper describes how we combine a CPU-based Cellular Potts model of sprouting angiogenesis in three dimensions with medical imaging techniques and fluid dynamics equations to create an individual-based GPU accelerated angiogenesis simulation. The use of GPU, optimized for fast, highly parallel mathematical operations, provides an increase in simulation speed and balances resource requirements across hardware. Specifically, micro-CT scans of resin cast rat cerebral vasculature are segmented and imported to instantiate nascent endothelial cells in a homogeneous three-dimensional grid representing the area over which the simulation is performed. A growth factor source is added, and simulation of steady production and diffusion of the vascular endothelial growth factor (VEGF) is performed on the GPU on the NVidia Compute Unified Device Architecture (CUDA) programming platform. Motion of individual endothelial cells is then tracked over the lifetime of the simulation towards the source of growth factor.