%**********************************************************************************
%
%                   CalC version 5.4.0, script "FCT_main.par"
%                       Victor Matveev, January 4, 2005
%
%                    "Facilitation through Buffer Saturation: 
%                 Constraints on Endogenous Buffering Properties"
%                      V. Matveev, A. Sherman and R. Zucker
%                       Biophys. J. (2004) 86:2691-2709
% 
%     This file contains the main definitions used by all simulations,
%     except for the buffer's parameters which are defined in the parent script.
%__________________________________________________________________________________
%
%  Units are: micrometers (um) for space, ms for time, microM (uM) for concentration.
%  Note that definitions appearing in a CalC script may be included in arbitrary order.
%==================================================================================
%
% Geometry parameters are based on:
% Tang et al. (2000), p.2741: Ave. bouton diameter = 3 um
% (Biophys J 78: 2735-2751)   Active zone diameter 160 nm
%                             AZ lies in the center of a 2.56 um^2 area = pi (0.9 um)^2

geometry = conical     % Conical geometry: see Fig. 1.
                       % This instructs CalC to solve the equations in spherical 
                       % coordinates (radius - polar theta angle).

AZ.R = 0.08            % radius of the AZ (80 nm)
S.R = 0.9              % radius of the cone's base (900 nm)
R = 3 / 2              % radius of the bouton (1.5 um)

Theta = S.R / R;       % Angle corresponding to the conical volume edge (Fig. 1, bottom)
Alpha = AZ.R / R;      % Angle corresponding to the the active zone edge (Fig. 1, top)

volume 0 R 0 Theta     % Defines the conical volume in Fig. 1

Ca.source R 0 0 Alpha  % Ca2+ source is centered at the vertex ( (R,0) in spherical
                       %  coordinates), and has an angular span of Alpha  

current.shape square   % Specifies that the current is distributed uniformly over
                       % the area defined by the Alpha angle in the Ca.source statement 
                       % above, and is zero outside of that area (i.e., as opposed 
                       % to a smooth gaussian distribution).

grid 36 36             % Enough for an accuracy of a few percent
                       % The grid is non-uniform, and is denser near the active zone:
stretch.factor = 1.05  % Multiplication factor for each successive grid interval.
stretch r R R          % In "stretch (r,theta) A B", [A,B] is the interval of minimal
stretch theta 0 Alpha  % grid spacing; grid spacing is increased outside of [A,B]

%==================================================================================

buffer Buffer  % This introduces the endogenous buffer, and gives it a name "Buffer" (duh!)
               % Buffer parameters will be defined in the parent script

%==================================================================================

% Now define variables tracking [Ca2+] and [Buffer] at locations labeled "1" 
% through "3" in Fig. 1 (top inset)

depth = R - 0.02         
th1 = (AZ.R + 0.02) / R  % Angle coordinate of location "1", 20 nm lateral to AZ edge
th2 = (AZ.R + 0.06) / R  % Angle coordinate of location "2", 60 nm lateral to AZ edge
th3 = (AZ.R + 0.10) / R  % Angle coordinate of location "3", 100 nm lateral to AZ edge

% Actually, in above we should have divided by "depth", not "R", but this has little 
% effect on the results

Ca1 := Ca[depth,th1] ; Buffer1 := Buffer[depth,th1] 
Ca2 := Ca[depth,th2] ; Buffer2 := Buffer[depth,th2] 
Ca3 := Ca[depth,th3] ; Buffer3 := Buffer[depth,th3]  

%==================================================================================

Ca.D   =  0.22    % this defines the Ca diffusion coefficient (0.22 um^2/ms)
Ca.bgr =  0.0     % background Ca concentration = 0

M      = 0.01           % Pump rate, in um / ms (Methods, p. 7)
K_PUMP = 0.2            % Pump affinity, uM (ibid)

A = - M / Ca.D / K_PUMP % Constant that appears in the pump boundary condition 
                        % (see the CalC manual and Eq. 5 of the manuscript) 

Ca.bc Noflux Pump Noflux Noflux  % Only the top z-surface has a pump
bc.define Pump 1 A 0 K_INV       % See CalC manual for b.c. definition syntax
K_INV = 1 / K_PUMP                  

%==================================================================================

% Current per active zone (Note: "ICa" is a reserved keyword, that's why we use "I.Ca")

I.Ca = 11.7 pA  

% This value is the same as the one used in Tang et al. (2000), translated to 
% the case of a 1 ms-long square pulse.

% Finally, the simulation statements: five 1 ms-long pulses at 100 Hz, which
% yields an interpulse interval of 9 ms. 

fivePulse = 1                      % Unless constant "fivePulse" is redefined in the
                                   % parent script, simulate a five-pulse train:
if (fivePulse) then
   Run adaptive 1.0; current I.Ca  % 1 ms-long channel opening
   Run adaptive 9.0; current 0     % Interpulse interval
   Run adaptive 1.0; current I.Ca  % Repeat five times
   Run adaptive 9.0; current 0
   Run adaptive 1.0; current I.Ca
   Run adaptive 9.0; current 0
   Run adaptive 1.0; current I.Ca
   Run adaptive 9.0; current 0
   Run adaptive 1.0; current I.Ca
   Run adaptive 3.0; current 0
endif

%==================================================================================