MCell (Monte Carlo Cell) is a program for simulating spatially resolved cell models using particle-based Monte Carlo algorithms.
Biological processes at the cell level take place in small and often complex geometries and frequently involve only a small number of molecular players (tens to thousands). A prime example of a process in which this “microphysiology” plays a central role is neurotransmission at chemical synapses in the brain and in the peripheral nervous system (Stiles et al. 2001; Stiles and Bartol 2001). At such small subcellular scales, the familiar macroscopic concept of concentration breaks down and stochastic behavior dominates. MCell uses optimized Monte Carlo algorithms to track discrete molecules in space and time as they diffuse and interact with other effector molecules such as membrane channels, receptors, transporters, or enzymes (Bartol et al. 1991; Stiles and Bartol 2001; Kerr et al. 2008).
The first version of MCell, released in...
KeywordsMonte Carlo Algorithm Bimolecular Reaction Unimolecular Reaction Model Syntax Global Time Step
We gratefully acknowledge the funding from NIH/NIGMS grant P41GM103712. In addition we thank Jacob Czech for his help with the figure preparation; the members of the MCell development team, including Dipak Barua, Jacob Czech, Leonard Harris, Bob Kuczewski, and Jose Juan Tapia, for the helpful discussions; and Terry Sejnowski for the support and inspiration. We dedicate this entry to the memory of Joel R. Stiles.
- Stiles JR, Bartol TM (2001) Monte Carlo methods for simulating realistic synaptic microphysiology using MCell. In: De Schutter E (ed) Computational neuroscience: realistic modeling for experimentalists. CRC Press, Boca Raton, pp 87–127Google Scholar
- Stiles JR, Van Helden D, Bartol TM, Salpeter EE, Salpeter MM (1996) Miniature endplate current rise times less than 100 microseconds from improved dual recordings can be modeled with passive acetylcholine diffusion from a synaptic vesicle. Proc Natl Acad Sci USA 93:5747–5752PubMedCrossRefPubMedCentralGoogle Scholar
- Stiles JR, Bartol TM, Salpeter MM, Salpeter EE, Sejnowski TJ (2001) Synaptic variability: new insights from reconstructions and Monte Carlo simulation with MCell. In: Cowan M, Sudhof TC, Stevens CF (eds) Synapses. Johns Hopkins University Press, Baltimore/London, pp 681–731Google Scholar