Note
The simulations and visualizations in this tutorial were generated using Blender 2.67 and CellBlender 1.0 RC. It may or may not work with other versions.
This tutorial uses the Lotka-Volterra oscillating system to demonstrate the difference between a diffusion-limited reaction and a "physiologic" reaction. The project files for the following two examples are available here. After downloading this file, unzip it anywhere on your computer. It contains two blend files (LV_diff_lim.blend and LV_phys.blend) inside of a directory called LV.
After opening LV_diff_lim.blend, we need to tell CellBlender where MCell is located. Under Project Settings, hit Set Path to MCell Binary, navigate to where you have downloaded MCell, select it, and hit the Set MCell Binary button. Next, hit the Run Simulation button. After the simulation has completed, hit the Read Viz Data button. Hit Alt-a to play through the visualization data.
A diffusion-limited reaction is a reaction which occurs whenever the species meet. In other words, the probability of reaction is 1 (or greater), and the only parameter limiting the reactions occurrence is the availability of the reactant species (and how often they meet). In CellBlender, this effect is achieved by making the rate constant so high as to push the probability of reaction to be greater than 1. Running with a small starting number of molecules from a point allows this model to show a firework pattern of the two oscillating species (B and C) as they move through the tube. If you look at the reaction data, there are no smooth regular oscillations as seen in the physiologic model.
After opening LV_phys.blend, we need to tell CellBlender where MCell is located, like we did in the previous example. Under Project Settings, hit Set Path to MCell Binary, navigate to where you have downloaded MCell, select it, and hit the Set MCell Binary button. Next, hit the Run Simulation button. After the simulation has completed, hit the Read Viz Data button. Hit Alt-a to play through the visualization data.
This is the same model as the diffusion-limited reaction except that it starts from well mixed conditions and the probabilities for the reactions are not greater than 1. Now, the visualization will show the molecules changing throughout the entire system (the tube will slowly change from B to C and back). In the reaction data the oscillations will be smooth and regular (and will closely match an ODE model given that this reaction adheres to well mixed conditions).
