Figure 1.
An overview of tools discussed here that are used for the rule-based specification and particle-based evaluation (spatial or nonpatial) of multi-state biomolecules.
Figure 2.
Principles of particle-based modeling.
In particle-based modeling, each particle is tracked individually through the simulation. At any point, a particle only “sees” the rules that apply to it. This figure follows two molecular particles (one of type A in red, one of type B in blue) through three steps in a hypothetical simulation following a simple set of rules (given on the right). At each step, the rules that potentially apply to the particle under consideration are highlighted in that particle's colour.
Figure 3.
Screenshot from an MCell simulation of calcium signaling within the spine.
Although other types of calcium-regulated molecules were included in the simulations, only CaMKII molecules are visualized. They are shown in red when bound to calmodulin and in black when unbound. The simulation compartment is a reconstruction of a dendritic spine as presented by Kinney et al. [59]. The area of the postsynaptic density is shown in red, the spine head and neck in gray, and the parent dendrite in yellow. The figure was generated by visualizing the simulation results in Blender.
Table 1.
Examples of multi-state models of biological systems.