Living Reference Work Entry

Encyclopedia of Computational Neuroscience

pp 1-5

Date: Latest Version


  • Thomas M. BartolAffiliated withNeurobiology Laboratory, Salk Institute for Biological Studies
  • , Markus DittrichAffiliated withBiomedical Applications Groups, Pittsburgh Supercomputing Center, Carnegie Mellon University
  • , James R. FaederAffiliated withDepartment of Computational and Systems Biology, University of Pittsburgh School of Medicine Email author 


MCell (Monte Carlo Cell) is a program for simulating spatially resolved cell models using particle-based Monte Carlo algorithms.

Detailed Description

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 199 ...

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