Rapid creation, Monte Carlo simulation, and visualization of realistic 3D cell models

Methods in Molecular Biology

Volumn 500, Issue 1, 2009, Pages 237-287

  Czech, Jacob ^b   Dittrich, Markus ^b   Stiles, Joel R ^a  

^a CARNEGIE MELLON UNIVERSITY   (United States)

^b NONE

Author keywords

Blender; Cell architecture; Cell geometry; Cell modeling; Diffusion reaction; DReAMM; MCell; MDL; Stochastic

Indexed keywords

ANIMAL; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; DIFFUSION; HUMAN; METABOLISM; MONTE CARLO METHOD; PHYSIOLOGY; SYNAPSE; SYNAPSE VESICLE; SYNAPTIC TRANSMISSION; SYNAPTOSOME; THREE DIMENSIONAL IMAGING;

ANIMALS; COMPUTER SIMULATION; DIFFUSION; HUMANS; IMAGING, THREE-DIMENSIONAL; MODELS, NEUROLOGICAL; MONTE CARLO METHOD; PRESYNAPTIC TERMINALS; SYNAPSES; SYNAPTIC TRANSMISSION; SYNAPTIC VESICLES;

EID: 65649140885     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-525-1_9     Document Type: Article

References (17)

1. Tao, L. and Nicholson, C. (2004) Maximum geometrical hindrance to diffusion in brain extracellular space surrounding uniformly spaced convex cells. J. Theor. Biol. 229, 59-68.
2. Hrabe, J., Hrabetova, S., and Segeth, K. (2004) A model of effective diffusion and tortuosity in the extracellular space of the brain. Biophys. J. 87, 1606-1617.
3. Tao, A., Tao, L., and Nicholson, C. (2005) Cell cavities increase tortuosity in brain extracellular space. J. Theor. Biol. 234, 525-536.
4. Stiles, J. R., Van Helden, D., Bartol, T. M., Jr., Salpeter, E. E., and Salpeter, M. M. (1996) Miniature endplate current rise times
5. Stiles, J. R., Bartol, T. M., Jr., Salpeter, E. E., and Salpeter, M. M. (1998) Monte Carlo simulation of neurotransmitter release using MCell, a general simulator of cellular physiological processes, in Computational Neuroscience ( Bower, J. M., ed.), Plenum, New York, NY, pp. 279-284.
6. Stiles, J. R., Bartol, T. M., Salpeter, M. M., Salpeter, E. E., and Sejnowski, T. J. (2001) Synaptic variability: New insights from reconstructions and Monte Carlo simulations with MCell, in Synapses ( Cowan, W. M., Stevens, C. F., and Sudhof, T. C., eds.), Johns Hopkins University Press, Baltimore, MD, pp. 681-731.
7. Stiles, J. R. and Bartol, T. M. (2001) Monte Carlo methods for simulating realistic synaptic microphysiology using MCell, in Computational Neuroscience: Realistic Modeling for Experimentalists ( De Schutter, E., ed.), CRC Press, Boca Raton, FL, pp. 87-127.
8. Pawlu, C., DiAntonio, A., and Heckmann, M. (2004) Postfusional control of quantal current shape. Neuron 43, 607-618.
9. Stiles, J. R., Ford, W. C., Pattillo, J. M., Deerinck, T. E., Ellisman, M. H., Bartol, T. M., and Sejnowski, T. J. (2004) Spatially realistic computational physiology: Past, present, and future, in Parallel Computing: Software Technology, Algorithms, Architectures & Applications ( Joubert, G. R., Nagel, W. E., Peters, F. J., and Walter, W. V., eds.), Elsevier, Amsterdam, pp. 685-694.
10. Coggan, J. S., Bartol, T. M., Esquenazi, E., Stiles, J. R., Lamont, S., Martone, M. E., Berg, D. K., Ellisman, M. H., and Sejnowski, T. J. (2005) Evidence for ectopic neurotransmission at a neuronal synapse. Science 309, 446-451.
11. He, L., Wu, X. S., Mohan, R., and Wu, L. G. (2006) Two modes of fusion pore opening revealed by cell-attached recordings at a synapse. Nature 444, 102-105.
12. Kerr, R.A., Bartol, T.M., Kaminsky, B., Dittrich, M., Chang, J.J.C, Baden, S.B., Sejnowski, T.J., and Stiles, J.R. Fast Monte Carlo simulation methods for biological reaction-diffusion systems in solution and on surfaces. SIAM J. Sci. Comput. 30, 3126-3149.
13. Kerr, R. A., Levine, H., Sejnowski, T. J., and Rappel, W. J. (2006) Division accuracy in a stochastic model of Min oscillations in Escherichia coli. Proc. Natl. Acad. Sci. USA 103, 347-352.
14. Koh, X., Srinivasan, B., Ching, H. S., and Levchenko, A. (2006) A 3D Monte Carlo analysis of the role of dyadic space geometry in spark generation. Biophys. J. 90, 1999-2014.
15. www.mcell.psc.edu and pages therein.
16. www.blender.org.
17. Synapse Web, Kristen M. Harris, PI, http:// synapse-web.org/. The publicly available VRML file that contains the data for the reconstruction can be downloaded from www.synapse-web.org/anatomy/Ca1pyrmd/ radiatum/index.stm.