Fig 1. Examples of Tissue Forge modeling features.

A: Five superimposed snapshots of a double pendulum implemented in Tissue Forge. Bonded interactions (represented as green cylinders) explicitly describe the interaction between a particular pair of particles, while a constant force acts on the blue particles in the downward direction. The red particle is fixed. B: Four Tissue Forge clusters representing biological cells, each consisting of ten particles whose color demonstrates cluster membership. Potentials describe particle interactions by whether they are in the same cluster (i.e., intracellular) or different clusters i.e., intercellular. C: Tissue Forge simulation of chemical flux during fluid droplet collision. Each particle represents a portion of fluid that carries an amount of a diffusive chemical, the amount of which varies from zero (blue) to one (red). When two droplets carrying different initial chemical amounts collide, resulting droplets tend towards homogeneous chemical distributions.