Spatial and Stochastic Cellular Modeling with the Smoldyn Simulator

This chapter describes how to use Smoldyn, which is a computer program for modeling cellular systems with spatial and stochastic detail. Smoldyn represents each molecule of interest as an individual point-like particle. These simulated molecules diffuse, interact with surfaces (e.g., biological membranes), and undergo chemical reactions much as they would in real biochemical systems. Smoldyn has been used to model signal transduction within bacterial cells, pheromone signaling between yeast cells, bacterial carboxysome function, diffusion in crowded spaces, and many other systems. A new “rule-based modeling” feature automatically generates chemical species and reactions as they arise in simulations due to protein modifications and complexation. Smoldyn is easy to use, quantitatively accurate, and computationally efficient. It is generally best for systems with length scales between nanometers and several microns, time scales from tens of nanoseconds to tens of minutes, and up to about 10⁵ individual molecules. Smoldyn runs on Macintosh, Linux, or Windows systems, is open source, and can be downloaded from http://www.smoldyn.org.