MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework.

Spatial heterogeneity can have dramatic effects on the biochemical networks that drive cell regulation and decision-making. For this reason, a number of methods have been developed to model spatial heterogeneity and incorporated into widely used modeling platforms. Unfortunately, the standard approaches for specifying and simulating chemical reaction networks become untenable when dealing with multistate, multicomponent systems that are characterized by combinatorial complexity.

Rapid creation, Monte Carlo simulation, and visualization of realistic 3D cell models.

Spatially realistic diffusion-reaction simulations supplement traditional experiments and provide testable hypotheses for complex physiological systems. To date, however, the creation of realistic 3D cell models has been difficult and time-consuming, typically involving hand reconstruction from electron microscopic images. Here, we present a complementary approach that is much simpler and faster, because the cell architecture (geometry) is created directly in silico using 3D modeling software like that used for commercial film animations.