-
Notifications
You must be signed in to change notification settings - Fork 1
/
Fig1.par
127 lines (94 loc) · 3.68 KB
/
Fig1.par
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Victor V. Matveev, Richard Bertram and Arthur Sherman (2009)
% Ca2+ current vs. Ca2+ channel cooperativity of exocytosis
% Journal of Neuroscience, 29(39): 12196-12209.
%
% This CalC simulation script reproduces Fig. 1 of the manuscript
% Victor Matveev, January 8, 2010
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
verbose = 0
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
B.total = $2 % Single command-line parameter: total buffer concentration (uM)
Dist = 0.03 / sqrt(2) % Distance from calcium channel to sensor is 30 nm (0.03 um)
%%%% Create file names for data output (file) and binding gate initialization (ICfile)
file = $1 "_Btot" $2 "_Dist30nm_" N "x" N "x" M ".dat"
ICfile = file ".IC"
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
L = 1
volume 0 L 0 L 0 L
N = 50
M = 40
grid N N M
stretch z 0 0
stretch x 0 Dist
stretch y 0 Dist
stretch.factor = 1.05
Ca.source 0 0 0 ww ww ww
ww = 0.005
Ca.D = 0.2
Ca.bgr = 0.1
Run adaptive T1
current = ICA pA
Run adaptive T2
current = 0
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
buffer B
B.D = 0.05
B.KD = 1
B.kplus = 0.65
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
uptake = 0.004
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Ca2+ binding scheme: Felmy Neher Schneggenburger (2003)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
C := Ca[Dist,Dist,0] % Release is drive by [Ca2+] at 30nm from channel mouth
dX/dt = - 5 C kon X + koff X1
dX1/dt = 5 kon C X - koff X1 - 4 C kon X1 + 2 koff b X2
dX2/dt = 4 kon C X1 - 2 koff b X2 - 3 C kon X2 + 3 koff b^2 X3
dX3/dt = 3 kon C X2 - 3 koff b^2 X3 - 2 C kon X3 + 4 koff b^3 X4
dX4/dt = 2 kon C X3 - 4 koff b^3 X4 - C kon X4 + 5 koff b^4 X5
dX4/dt = 2 kon C X3 - 4 koff b^3 X4 - C kon X4 + 5 koff b^4 X5
dX5/dt = C kon X4 - 5 koff b^4 X5 - gamma X5
R := gamma X5 % Release rate
kon = 0.116 % Binding scheme rate constants
koff = 8.430
gamma = 6.96
b = 0.25 % cooperativity parameter
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
T1 = 1 % Duration of current pulse (ms)
T2 = 4 % "Silent" interval after current pulse (ms)
TM = T1 + T2 % Total duration of sumulation
Tmax Rmax max R 0 TM % Rmax = max release; Tmax = time of max release
Cmax max C 0 TM % Cmax = max of [Ca2+] at select distance from channel
CAmax max Ca[] 0 TM % CAmax = max volume-averaged [Ca2+]
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
ICA1 = 0.001 % minimal single-channel Ca2+ current
ICA2 = 1 % maximal single-channel Ca2+ current
steps = 40 % steps in the for-loop over Ca2+ current values
Log1 = log(ICA1)
Log2 = log(ICA2)
dlog = (Log2 - Log1) / steps
for Istep = -1 to steps step 1 %%%%%%% MAIN FOR-LOOP STATEMENT %%%%%%%
if Istep == -1 then
ICA = 0
else
ICA = exp(Log1 + Istep * dlog)
endif
if Istep == -1 % first iteration in the loop (step=-1): zero-current pre-pulse of 12 ms
T2 = 12
X(0) = 1
print ICfile "X(0)=" X % Store the gate binding states 12 ms after simulation start
append ICfile "X1(0)=" X1
append ICfile "X2(0)=" X2
append ICfile "X3(0)=" X3
append ICfile "X4(0)=" X4
append ICfile "Rmax0=" Rmax "; Tmax0=" Tmax "; Cmax0=" Cmax
print file
else
include ICfile
endif
%%%%% Data output: four columns [ ICa Rmax Cmax CAmax Tmax ]
parStr = ICA
append file parStr " " Rmax " " Cmax " " CAmax " " Tmax
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%