Computational Biology

My current research is described on the Autodesk Research Website. This page summarizes my work at Carleton University where, in 2009, I completed a master’s degree in biomedical engineering. Under the supervision of Prof. Gabriel Wainer, my research focused on the simulation of deformable biological structures.

Below is a simulation of a single presynaptic terminal of a nerve cell. There are hundreds of trillions of these in your brain. Inside are synaptic vesicles (green) that get bound together by synapsin protein (blue). Every 5 seconds or so in the video, a signal called an “action potential” breaks some of the vesicle-synapsin bonds and causes a few vesicles to fuse with the membrane.

To implement the simulation, I developed a method called the Tethered Particle System. As shown below, there are three basic types of interactions between particles: blocking collisions (two particles bouncing off one another); tethering collisions (two particles bouncing towards one another as if “tethered” by an invisible cord); and revolution (two particles spinning around one another).

These three simple interactions can be used to simulate complex systems, such as the self-assembly of vesicle clusters in presynaptic compartments.

The Tethered Particle System is similar to a method called Discrete Molecular Dynamics, though I was hoping to accommodate deformable structures at larger scales. See the examples below:

Feel free to download my thesis, or take a look at my related papers on the ARSLab Publications Page.