Encyclopedia of Computational Neuroscience

Living Edition
| Editors: Dieter Jaeger, Ranu Jung


  • Thomas M. Bartol
  • Markus Dittrich
  • James R. Faeder
Living reference work entry
DOI: https://doi.org/10.1007/978-1-4614-7320-6_256-1


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...


Monte Carlo Algorithm Bimolecular Reaction Unimolecular Reaction Model Syntax Global Time Step 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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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.


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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Thomas M. Bartol
    • 2
  • Markus Dittrich
    • 3
  • James R. Faeder
    • 1
  1. 1.Department of Computational and Systems BiologyUniversity of Pittsburgh School of MedicinePittsburghUSA
  2. 2.Neurobiology LaboratorySalk Institute for Biological StudiesLa JollaUSA
  3. 3.Biomedical Applications Groups, Pittsburgh Supercomputing CenterCarnegie Mellon UniversityPittsburghUSA