Simulating Growth Kinetics in a Data-Parallel 3D Lattice Photobioreactor

Though there have been many attempts to address growth kinetics in algal photobioreactors, surprisingly little have attempted an agent-based modelling (ABM) approach. ABM has been heralded as a method of practical scientific inquiry into systems of a complex nature and has been applied liberally in a range of disciplines including ecology, physics, social science, and microbiology with special emphasis on pathogenic bacterial growth. We bring together agent-based simulation with the Photosynthetic Factory (PSF) model, as well as certain key bioreactor characteristics in a visual 3D, parallel computing fashion. Despite being at small scale, the simulation gives excellent visual cues on the dynamics of such a reactor, and we further investigate the model in a variety of ways. Our parallel implementation on graphical processing units of the simulation provides key advantages, which we also briefly discuss. We also provide some performance data, along with particular effort in visualisation, using volumetric and isosurface rendering.

Adding Refined Isosurface Rendering and Shadow Mapping to vtkGPUVolumeRayCastMapper

In the medical simulation world the use of isosurfaces is a common action, as the information from some sources, e.g. CTs, is very well defined, and the isosurface can be easily set. Additionally, in any simulator shadows are a necessary addition to increase the users immersion as well as its depth perception. Unfortunately, the Visualization Toolkit does not offer these features, and so in this paper a modified vtkGPUVolumeRayCastMapper is presented. This modified version allows volumetric isosurface rendering as well as receiving shadows from polygons using the usual pipeline.