Applying the TPS method to modeling and simulation of biological systems

Deformable biological structures are typically modeled with the finite element method, but we have designed a much simpler impulse-based method called the "tethered particle system" (TPS). The TPS involves the use of discrete-event simulation to track the positions of a large number of particles. Two of these particles approaching to each other may collide and rebound off. The difference is that, provided they are "tethered", two separating particles may also collide and retract inwards. This constrains the distances between pairs of particles, allowing various deformable structures to be represented. In this article, we present the application of the TPS method to the simulation of different biological structures found in nerve cells: actin filaments, cell membranes and synapsin protein that bind with actin, mitochondria, and water particles which influence the motion of other structures. This includes advanced visualization methods.