MCell Simulation of miniature endplate current generation at the neuromuscular junction. Image rendered with Pixar Photorealistic RenderMan.
Biological structures show tremendous complexity and diversity at the subcellular level.
For example, a single cubic millimeter of cerebral cortex may contain of order 5 billion interdigitated synapses of different shapes and sizes. Subcellular communication is based on a wide variety of chemical signaling pathways, and for a process like synaptic transmission encompasses neurotransmitter and neuromodulator molecules, proteins involved with exo- and endocytosis, receptor proteins, transport proteins, and oxidative and hydrolytic enzymes. Until recently, computational limits have precluded highly realistic 3D simulations of subcellular architecture and physiology. As a result, the contribution of actual ultrastructure to signaling variability and plasticity has gone largely unexplored, and quantitative modeling has been severely hampered. As shown at the left, MCell simulations are positioned at a biological scale above molecular dynamics but below whole cell and higher level studies.