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FCT_Fig5.par
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%**********************************************************************************
%
% CalC version 4.9.8, script "FCT_Fig5.par"
% Victor Matveev, January 19, 2004
%
% "Facilitation through Buffer Saturation:
% Constraints on Endogenous Buffering Properties"
% V. Matveev, A. Sherman and R. Zucker
% Biophys. J. (2004) 86:2691-2709
%
% This script produces the data for the parameter-sweep plots in Fig. 5 and 6A,
% and requires a command-line parameter specifying the buffering capacity (kappa0)
% For instance, to reproduce Figs. 5A and 6Ab, execute:
%
% calc FCT_Fig5.par 500
%
% the resulting file will be called "FCT_vs_Btotal_and_kon_kappa500", and will consist
% of 8 data columns, in the format "Btotal kon P1at1 P5at1 P1at2 P5at2 P1at3 P5at3",
% where "P1ati" is the size of the first [Ca2+] transient at site "i", etc. Then
% start gnuplot, and type
%
% splot 'FCT_vs_Btotal_and_kon_kappa500' u 1:2:($6/$5) w lines
%
% This will make a surface plot of the ratio of the 6th and 5st columns, equal to
% the P5/P1 value at site "2".
%==================================================================================
path = "" % If running under Windows, specify here the path to the
% directory containing the script imported below
file = path "FCT_main.par"
include file % Import the simulation parameters from the main script,
% which defines everything but the buffer's parameters:
%==================================================================================
kappa = $2 % The command-line parameter specifies the total buffering
% capacity
Buffer.D = 0.2 % Diffusion coefficient is 0.2 um^2/ms
kmin = 0.05 % The binding rate will vary from 0.05/(uM ms)
kmax = 1.00 % to 1/(uM ms)
dK = 0.05 % with steps of 0.05/(uM ms)
BTmin = 40 % The buffer concentration will be varied from 40 uM
BTmax = 1200 % to 1.2 mM, with steps of 40 uM (30 steps total)
dB = 100
for Buffer.total = BTmin to BTmax step dB % Iterations over Btotal concentration
% values: this is the outside loop
for Buffer.kplus = kmin to kmax step dK % Iterations over binding rate (a.k.a kplus
% a.k.a kon): this is the inside loop
Buffer.KD = Buffer.total / kappa % Buffer affinity is determined by its
% concentration and total capacity
%==================================================================================
% [Reminder: CalC script is a list of definitions, so all statements can appear in
% any order (with some exceptions: see the manual)]
P1at1 max Ca1 0 3 % First peak [Ca2+] transient at site "1" (distance=20 nm)
P5at1 max Ca1 40 43 % Last peak [Ca2+] transient at the same site
P1at2 max Ca2 0 3 % First peak [Ca2+] transient at site "2" (distance=60 nm)
P5at2 max Ca2 40 43 % Last peak [Ca2+] transient at the same site
P1at3 max Ca3 0 3 % First peak [Ca2+] transient at site "3" (distance=100 nm)
P5at3 max Ca3 40 43 % Last peak [Ca2+] transient at the same site
% Expression forming the name of the file:
outfile = "FCT_vs_Btotal_and_kon_kappa" kappa
if (Buffer.kplus == kmin) then
if (Buffer.total == BTmin) then print outfile ' ' % Initialize the file at first iteration
else
append outfile ' ' % Put an empty line after each outside
endif % iteration
endif
% Output the following data into the above file at each iteration:
append outfile Buffer.total " " Buffer.kplus " " ...
P1at1 " " P5at1 " " P1at2 " " P5at2 " " P1at3 " " P5at3
verbose = 0 % Suppress all simulation status statements
%==================================================================================