%********************************************************************************** % % CalC version 7.7, script "simple.par", Victor Matveev, September 17, 2013 % % This script calculates Ca2+ from a single channel near a spherical obstacle % representing a vesicle, and produces a binary dump of concentration values, % to be plotted using MATLAB script "simple.m" % %================================================================================== volume 0 0.5 0 0.5 0 0.4 % Defines the diffusion volume, sobstacle 0.2 0.2 0.140 0.15 % Define a sperical obstacle or radius 150nm grid 60 60 60 % The spatial grid will have 60 nodes in each direction Ca.D = 0.22 % The diffusion coefficient of calcium is 0.22 um^2/ms Ca.bgr = 0.1 % Initial calcium concentration is 0.1 uM (uM = micromolar) Ca.source 0.2 0.1 0 % Defines the calcium channel/source location buffer Bm % Introducing a buffer named "Bm" Bm.D = 0.1 % Its diffusion coefficient is 0.1 um^2/ms, Bm.KD = 2 % its calcium affinity is 2 uM Bm.kminus = 0.1 % and calcium unbinding rate is 0.1/ms Bm.total = 1000 % The total (bound + unbound) concentration of buffer is 1 mM Run adaptive 3 % This defines the simulation itself, which consists of current = 0.1 pA % a 3 ms open channel interval with a channel current of 0.1 pA, plot binary Ca "_simple.dat" % Output file will be named "Ca_simple.dat"