ModelDB: Models that contain MCell

Simulation Environment: MCell

Note: this list includes both models hosted here at ModelDB and models where have metadata and link to the sourcecode somewhere else. These may also be viewed separately; see the browse by simulator page.

Action potential-evoked Ca2+ signals in CA1 pyramidal cell presynaptic terminals (Hamid et al 2019)
Active zone model of Ca2+ secretion coupling (Keller et al. 2015)
AMPA receptor trafficking and its role in heterosynaptic plasticity (Antunes et al 2018)
Analytical modelling of temperature effects on an AMPA-type synapse (Kufel & Wojcik 2018)
Modeling temperature changes in AMPAR kinetics (Postlethwaite et al 2007)
Synaptic vesicle fusion model (Church et al 2021)

http://www.mcell.cnl.salk.edu/
MCell, makes it possible to incorporate high resolution ultrastructure into models of ligand diffusion and signaling, and has evolved from experimental and theoretical work of the MCell gang: Joel Stiles (Biomedical Applications, Pittsburgh Supercomputing Center), Miriam Salpeter (Neurobiology & Behavior, Cornell University), Edwin Salpeter (Department of Physics and Astronomy, Cornell University), and Thomas Bartol and Terrence Sejnowski (Computational Neurobiology Laboratory, Salk Institute).

Top authors for MCell:

Hamid E (2)
Church E (2)
Alford S (2)
Keller D (1)
Babai N (1)
Kochubey O (1)
Han Y (1)
Markram H (1)
Schürmann F (1)
Schneggenburger R (1)

Top concepts studied with MCell:

Synaptic Plasticity (2)
Detailed Neuronal Models (2)
Reaction-diffusion (1)
Action Potentials (1)
Depression (1)
Long-term Synaptic Plasticity (1)
Methods (1)
Temperature (1)
Short-term Synaptic Plasticity (1)
Neuromodulation (1)

Top neurons studied with MCell:

Hippocampus CA1 pyramidal GLU cell (1)
Medial Nucleus of the Trapezoid Body (MNTB) neuron (1)

Top references cited by these models:

Kerr RA, Bartol TM, Kaminsky B, Dittrich M, Chang JC, Baden SB, Sejnowski TJ, Stiles JR. (2008). FAST MONTE CARLO SIMULATION METHODS FOR BIOLOGICAL REACTION-DIFFUSION SYSTEMS IN SOLUTION AND ON SURFACES. SIAM journal on scientific computing : a publication of the Society for Industrial and Applied Mathematics. 30 (4)
Sätzler K, Söhl LF, Bollmann JH, Borst JG, Frotscher M, Sakmann B, Lübke JH. (2002). Three-dimensional reconstruction of a calyx of Held and its postsynaptic principal neuron in the medial nucleus of the trapezoid body. The Journal of neuroscience : the official journal of the Society for Neuroscience. 22 (3)
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. Proceedings of the National Academy of Sciences of the United States of America. 93 (3)
Asztely F, Erdemli G, Kullmann DM. (1997). Extrasynaptic glutamate spillover in the hippocampus: dependence on temperature and the role of active glutamate uptake. Neuron. 18 (3)
Robert A, Howe JR. (2003). How AMPA receptor desensitization depends on receptor occupancy. The Journal of neuroscience : the official journal of the Society for Neuroscience. 23 (3)