Publications
The first publication in which MCell is named: Stiles, JR, et al. (1996). Miniature endplate current rise times <100 μs from improved dual recordings can be modeled with passive acetylcholine diffusion from a synaptic vesicle. Proc. Natl. Acad. Sci. USA 93:5747-5752.
The best reference for learning to use MCell: Stiles, JR, and Bartol, TM. (2001). Monte Carlo methods for simulating realistic synaptic microphysiology using MCell. In: Computational Neuroscience: Realistic Modeling for Experimentalists, ed. De Schutter, E. CRC Press, Boca Raton, pp. 87-127.
We ask that you cite the two papers above in all publications that make use of MCell.
Other publications from the MCell and DReAMM developers and outside users: If you know of any other publications, please let us know.
Anglister, L, Stiles, JR, and Salpeter, MM (1994) Acetylcholinesterase den sity and turnover number at frog neuromuscular junctions, with modeling of their role in synaptic function. Neuron 12: 783-794.
Bartol, T.M. Jr. (1992) PhD thesis, Cornell Univ.
Bartol Jr., T.M., Land, B.R., Salpeter, E.E., Salpeter, M.M. (1991) Monte Carlo simulation of MEPC generation in the vertebrate neuromuscular junction. Biophys. J. 59:1290-1307.
Casanova, H, Bartol, T, Berman, F, Birnbaum, A, Dongarra, J, Ellisman, M, Faerman, M, Gokcay, E, Miller, M, Obertelli, G, Pomerantz, S, Sejnowski, T, Stiles, J, and Wolski, R. (2004) The Virtual Instrument: Support for Grid-enabled MCell Simulations. Intern. J. High Performance Computing Applications 18:3-18.
Casanova, H, Bartol, TM, Stiles, J, and Berman, F. (2001) Distributing MCell simulations on the grid. Intern. J. High Performance Computing Applications 15:243-257.
Coggan, JS, Bartol, TM, Esquenazi, E, Stiles, JR, Lamont, S, Martone, ME, Berg, DK, Ellisman, MH, and Sejnowski, TJ. (2005) Evidence for ectopic neurotransmission at a neuronal synapse. Science 309:446-451.
Diamond, JS. Neuronal glutamate transporters limit activation of NMDA receptors by neurotransmitter spillover on CA1 pyramidal cells, J Neurosci. 2001 Nov 1;21(21):8328-38.
Diamond, JS. Deriving the glutamate clearance time course from transporter currents in CA1 hippocampal astrocytes: transmitter uptake gets faster during development. J Neurosci. 2005 Mar 16;25(11):2906-16.
Dilger, JP. Modeling synapse function in the presence of competitive antagonists. 2004 Biophysical Society Meeting.
Franks KM, Bartol TM Jr, Sejnowski TJ, A Monte Carlo model reveals independent signaling at central glutamatergic synapses. Biophys J. 2002 Nov;83(5):2333-48.
Franks KM, Sejnowski TJ. Complexity of calcium signaling in synaptic spines. Bioessays. 2002 Dec;24(12):1130-44.
Geiger, J.R.P., Roth, A., Taskin, B. & Jonas, P. (1999). Glutamate-mediated synaptic excitation of cortical interneurons. In: Ionotropic Glutamate Receptors in the CNS (vol. 141 of Handbook of Experimental Pharmacology), Eds. P. Jonas and H. Monyer. Springer-Verlag, Berlin, pp. 363-398.
Gomez, CM, Maselli, RA, Vohra, BP, Navedo, M, Stiles, JR, Charnet, P, Schott, K, Rojas, L, Keesey, J, Verity, A, Wollmann, RW, and Lasalde-Dominicci, J. (2002) Novel delta subunit mutation in slow-channel syndrome causes severe weakness by novel mechanisms. Ann. Neurol. 51:102-112.
Häusser, M., Nusser, Z. & Roth, A. (2000). Modelling synaptic transmission at granule cell-Purkinje cell synapses. European Journal of Neuroscience 12 Suppl. 11, 182.
Hrabe J, Hrabetova S (2003). A simple semi-quantitative tortuosity model explains the dead-space microdomain effect. Satellite Symposium to the Sixth IBRO World Congress of Neuroscience. Prague, July 15 - 27. Program p. 50.
Hrabe J, Hrabetova S, Segeth K (2004). A model of effective diffusion and tortuosity in the extracellular space of the brain. Biophysical Journal 87, 1606-1617.
Keller, DX, Sobczyk, A, Bartol, TM, Svoboda, K, Sejnowski, TJ (2004) Refined Monte Carlo models of NMDA receptor signaling. Soc. Neurosci. Abst.
Kinney, JP, Bartol, TM, Sejnowski, TJ (2004) Monte Carlo model of background glutamate spillover in the hippocampus. Soc. Neurosci. Abst.
Kerr, R, Bartol, TM, Stiles, JR, Kennedy, MB, and Sejnowski, TJ. (2004) MCell3: A next-generation simulator of cellular microphysiology. Soc. Neurosci. Abst.
Koh, X., Ching, H.S., Srinivasan, B. and Levchenko, A. An exact Monte Carlo simulation of signaling events in the cardiac myocyte. NIH BISTI Symposium ?Digital Biology: The Emerging Paradigm?, Bethesda, MD (2003)
Koh, X., Ching, H.S., Srinivasan, B. and Levchenko, A. An exact Monte Carlo simulation of signaling events in the cardiac myocyte. Proc. of the 4 International Conference on Systems Biology, St. Louis, MO (2003)
Lopreore, CL, Keller, DX, Bartol, TM, Sejnowski, TJ. (2003) A hybrid electro-diffusion model for neural signaling. Soc. Neurosci. Abst.
Lopreore, CL, Bartol, TM, and Sejnowski, TJ. (2004) An electrodiffusion model for ion motion in dendritic spines. Soc. Neurosci. Abst.
Mitsner, V, Eagleman, DM, Coenen, OJD, Bartol, TM, JonesYZ, Ellisman, MH, Sejnowski, TJ (2004) A Monte Carlo model of extracellular calcium dynamics in the cerebellar glomerulus. Soc. Neurosci. Abst.
Mitsner, V, Eagleman, DM, Coenen, OJD; Wood, K; Bartol, TM, Jones YZ, Ellisman, MH, Sejnowski, TJ. (2003) Depletion of extracellular calcium in the cerebellar glomerulus. Soc. Neurosci. Abst.
Nusser, Z., Roth, A., Schorge, S. & Häusser, M. (2000). Simulations of synaptic transmission in 3-D reconstructions of cerebellar neuropil. Society for Neuroscience Abstracts 26, 1122.
Overstreet, L.S., Westbrook, G.L. and Jones, M.V. (2002) Measuring and Modeling the Spatiotemporal Profile of GABA at the Synapse. In Transmembrane Transporters (e.d., M. Quick) Wiley, New York. P. 259-275.
Pattillo, JM, Meriney, SD, and Stiles, JR. (2004) Spatially realistic Monte Carlo simulations predict calcium dynamics underlying transmitter release at a neuromuscular active zone. Soc. Neurosci. Abst.
Pattillo, JM, Meriney, SD, and Stiles, JR. Design Principles of Neurotransmitter Exocytosis Predicted by Spatially Realistic Monte Carlo Simulations (submitted, Nature).
Pawlu C, DiAntonio A, Heckmann M (2004) Postfusional control of quantal current shape. Neuron 43, 607-618.
Rollenhagen, A., Söhl, L., Roth, A., Sätzler, K., Jonas, P., Frotscher, M. & Lübke, J. (2004). Three-dimensional morphology of a central excitatory synapse: the mossy fiber bouton. FENS Abstracts 2, A119.10.
Rollenhagen, A., Söhl, L., Roth, A., Ohana, O., Sätzler, K., Sakmann, B., Frotscher, M. & Lübke, J. (2003). Morphology of central synapses: from structure to function. Society for Neuroscience Abstracts 29, 122.1.
Roth, A., Nusser, Z. & Häusser, M. (2000). Monte Carlo simulations of synaptic transmission in detailed three-dimensional reconstructions of cerebellar neuropil. European Journal of Neuroscience 12 Suppl. 11, 14.
Roth, A., Wilkinson, J.A., Cottingham, C.A., Nusser, Z. & Häusser, M. (2001). Spatiotemporal dynamics of transmitter diffusion at excitatory synapses in the cerebellar cortex. Society for Neuroscience Abstracts 27, 155.6.
Shah, N and Dilger, JP. Monte Carlo simulation of buffered diffusion of ligands into a synapse. 2005 Biophysical Society Meeting.
Shah, N and Dilger, JP. How long does it take for your favorite drug to diffuse into and out of a tight spot? MAC2005 Conference, Nara, Japan.
Stiles, J.R. (1990) PhD thesis, Univ. Kansas.
The best reference for learning to use MCell:
Stiles, JR, and Bartol, TM. (2001) Monte Carlo methods for simulating realistic synaptic microphysiology using MCell. In: Computational Neuroscience: Realistic Modeling for Experimentalists, ed. De Schutter, E. CRC Press, Boca Raton, pp. 87-127. CD-ROM material available at http://www.compneuro.org/CDROM. We ask that you cite this paper in all publications that make use of MCell.
Stiles, JR, Bartol, TM, Jr, Salpeter, EE, and Salpeter, MM. 1998. Monte Carlo simulation of neurotransmitter release using MCell, a general simulator of cellular physiological processes. In: Computational Neuroscience, ed. Bower, JM. Plenum, NY. pp. 279-284.
Stiles, JR, Bartol, TM, Salpeter, MM, Salpeter, EE, and Sejnowski, TJ. (2001) Synaptic variability: new insights from reconstructions and Monte Carlo simulations with MCell. In: Synapses, ed. Cowan, WM, Stevens, CF, and Sudhof, TC. Johns Hopkins Univ. Press, Baltimore, pp. 681-731.
Stiles, JR, Ford, WC, Pattillo, JM, Deerinck, TE, Ellisman, MH, Bartol, TM, and Sejnowski, TJ. (2004) Spatially realistic computational physiology: past, present, and future. In: Parallel Computing: Software Technology, Algorithms, Architectures & Applications, ed. Joubert, G, et al. Elsevier, Amsterdam, pp. 685-694.
Stiles, JR, Kovyazina, IV, Salpeter, EE, and Salpeter, MM. (1999). The temperature sensitivity of miniature endplate currents is mostly governed by channel gating: evidence from optimized recordings and Monte Carlo simulations. Biophys. J. 77:1177-1187.
Stiles, JR, Van Helden, D, Bartol, TM, Jr., Salpeter, EE, and Salpeter, MM. 1996. Miniature endplate current rise times <100 μs from improved dual recordings can be modeled with passive acetylcholine diffusion from a synaptic vesicle. Proc. Natl. Acad. Sci. USA 93:5747-5752. We ask that you cite this paper in all publications that make use of MCell.
Tao L, Hrabetova S, Nicholson C (2002). Effect of brain extracellular space geometry on molecular diffusion revealed by Monte Carlo simulation. Program No. 763.1. 2002 Abstract Viewer/Itinerary Planner. Washington, DC: Society for Neuroscience. Online.
Tao L, Nicholson C (2003). Monte Carlo simulation reveals that tortuosity in the extracellular space formed by uniformly spaced convex cells is much smaller than measured in brain. Satellite Symposium to the Sixth IBRO World Congress of Neuroscience. Prague, July 15 - 27. Program p. 52.
Tao L, Nicholson C (2004). Maximum geometrical hindrance to diffusion in brain extracellular space surrounding uniformly spaced convex cells. Journal of Theoretical Biology 229, 59-68.
Tao A, Tao L, Nicholson C. (2005) Cell cavities increase tortuosity in brain extracellular space. Journal of Theoretical Biology 234, 525-536.
Wachman, ES, Poage, RE, Stiles, JR, Farkas, DL, and Meriney, SD. (2004) Spatial distribution of calcium entry evoked by single action potentials within the presynaptic active zone. J. Neurosci. 24:2877-2885.
Xue, JHY and Pennefather, PS (2003) A 3D computational approach to study calcium dynamics in bullfrog sympathetic neuron. 47th Biophysical society annual meeting. San Antonio, Texas, USA. #B258
