%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Weber AM, Wong FK, Tufford AR, Schlichter LC, Matveev V, Stanley EF
% N-type Ca2+ channels carry the largest current:
% implications for nanodomains and transmitter release.
%
% Nature Neuroscience 13: 1348-1350.
%
% This CalC simulation script produces data needed for Figs. S6-S9
% Victor Matveev, August 8, 2012
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
verbose = 0
geometry = cylindrical
N = 300 % Grid size in r direction
K = 300 % Grid size in z direction
grid N K
stretch r 0 0
stretch z 0 0
stretch.factor = 1.02
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
for iter = 1 to 4 step 1 % Cycle through 4 conditions:
% iter=1: V=-65mV, N-type channel
% iter=2: V=-65mV, L-type channel
% iter=3: V=-40mV, N-type channel
% iter=4: V=-40mV, L-type channel
if (iter mod 2) then
ICa = CaL
suffix = '_L'
else
ICa = CaN
suffix = '_N'
endif
if iter < 3
V = 65
CaL = 0.22 pA
CaN = 0.31 pA
else
V = 40
CaL = 0.2 pA
CaN = 0.251 pA
endif
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
L = 2 % Volume size in r- and in z-directions
volume 0 L 0 L
Ca.D = 0.2
Ca.bgr = 0.05
Ca.source 0 0 0 % Single channel at the origin
T = 0.6 % Total simulation duration
run adaptive T
current ICa
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
kappa = 50 % Buffering capacity
buffer B
B.total = B.KD * kappa % Total concentration = kappa * KD = 50 uM
B.KD = 1 % Affinity = 1 uM
B.kplus = 0.5 % Binding rate
B.D = $2 % Change to 50 for mobile buffer
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
rfile = '1Dr_V' V '_Ca' suffix '_kappa_' kappa '_BD_' B.D '_' N x K '.dat'
plot 1D.mute Ca r 0 rfile
plot.1D.steps = 400