Project topic posted by Michel Dumontier (Dumontier Lab Website)

Off Lattice 3D Particle Cell Simulation

The ability to simulate a biological system has the potential to deliver insights into the function of the system that are difficult to examine using an experimental system. Ordinary- and partial-differential equations are often used to describe the motion and interaction of populations of molecules. We use a different approach, a 3D particle simulation, so as to explicitly represent each molecule as a discrete entity, capable of biologically relevant interactions. While this approach allows stochastic processes to be nicely modeled, the tracking of individual molecules poses a problem for parallelism and ultimately, scalability. This project entails research, case study and proof of concept implementations of 3D particle simulators using an off-lattice solution (single precision floating point). Proof of concepts can be implemented in software (C/C++) or hardware for the IBM Cell Processor, CMC’s FPGA System on a Chip, or SGI’s Altix using the high level Mitrion C-Compiler. The formation of inter-disciplinary groups (either with other CS students or with Biology, Biochemistry, Chemistry, Engineering honours students) is strongly encouraged.