Note from the ModelDB Adminsitrator: the below is a snapshot of Matveev's Calcium Calculator Simulation Scripts web page taken on April 13th, 2009. The 4th listed item contains the link for the code associated with Nguyen et al. 2005.

Calcium Calculator Simulation Script Files
CalC Download	CalC Manual	CalC Scripts	CalC Publications	Victor's Homepage

DEMO SCRIPTS Example script files with comments, in lieau of a tutorial. Hopefully, enough to get you started. Publication Scripts:

1.    L.N. Cornelisse, R.A.J. van Elburg, R.M. Meredith, R. Yuste, and H.D. Mansvelder (2007) High Speed Two-Photon Imaging of Calcium Dynamics in Dendritic Spines: Consequences for Spine Calcium Kinetics and Buffer Capacity. PLoS ONE 2(10): e1073. Full Text SCRIPTS

2.   O. Babich, V. Matveev, A. L. Harris, R. Shirokov (2007) Ca2+-dependent inactivation of CaV1.2 channels prevents Gd2+ block: does Ca2+ block the pore of inactivated channels? Journal of General Physiology, 129: 477-483. Abstract Full Text PDF SCRIPTS

3.   V. Matveev, R. Bertram, A. Sherman (2006) Residual Bound Ca2+ Can Account for the Effects of Ca2+ Buffers on Synaptic Facilitation Journal of Neurophysiology, 96: 3389-3397. Abstract Full Text PDF SCRIPTS

4.   Nguyen V, Mathias R, Smith GD (2005) A stochastic automata network descriptor for Markov chain models of instantaneously coupled intracellular Ca2+ channels. Bull Math Biol, 67(3):393-432. Abstract PDF script The script markov.par (linked above) demonstrates the use of Markov variables to simulate stochastic Ca2+ channel gating, examining the coupling of two stochastic Ca2+ channels with 4-state gating kinetics by Nguyen et al. (2005).

5.   V. Matveev, R.S. Zucker, A. Sherman (2004) Facilitation through Buffer Saturation: Constraints on Endogenous Buffering Properties Biophysical Journal, 86:2691-2709 Abstract Full Text PDF SCRIPTS

6.   V. Matveev, A. Sherman, R.S. Zucker, (2002) New and Corrected Simulations of Synaptic Facilitation Biophysical Journal, 83:1368-1373. Abstract Full Text PDF SCRIPTS

7.   Yamada, W.M., and R.S. Zucker (1992) Time course of transmitter release calculated from simulations of a calcium diffusion model. Biophysical Journal, 61:671-682. Abstract Full Text PDF script The script YamadaZucker.par (linked above) reproduces Fig. 3B of Yamada and Zucker (1992)

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This material is based upon work supported by the National Science Foundation grant 0417416 and 0817703.
Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author and do not necessarily reflect the views of the National Science Foundation

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Victor Matveev

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Last modified: Feb 15, 2009