//genesis
//CaDifshell.g
/*************************** MS Model, Version 12 *********************
Avrama Blackwell kblackw1@gmu.edu
Rebekah Evans rcolema2@gmu.edu
Sriram dsriraman@gmail.com
*****************************************************************************/
//old calcium concentration - single time constant of decay
function add_CaConcen (buffername, a, b, cellpath)
str buffername,cellpath
float a,b
str compt
float len,dia,position
float Ca_tau,kb
float PI = 3.14159
float shell_thick={outershell_thickness}
foreach compt ({el {cellpath}/##[TYPE={compartment}]})
//make sure this is not an axon, and determine length and diameter
if (!{{compt} == {{cellpath}@"/axIS"} || {compt} == {{cellpath}@"/ax"}})
dia = {getfield {compt} dia}
position = {getfield {compt} position}
len = {getfield {compt} len}
end
//if the compartment is not a spine and its position is between [a,b]
if ({position >= a} && {position < b} )
// Sabatini's model. Sabatini, 2001,2004
create Ca_concen {compt}/{buffername} // create Ca_pool here!
if({dia} < 0.81e-6) // this is tertiary dendrites
kb = 96
elif (dia < 1.5e-6) // secondary dendrites
kb = 96
elif (dia < 1.8e-6) // primary dendrites
kb = 96
else // soma
kb = 200 // the setting for soma is arbitrary
end
if({dia} < 15e-6)
Ca_tau = 25e-3
else
Ca_tau = 100e-3 // adhoc setting to fit the model
end
// set Ca_tau according to diameters of dendrites
if ({shell_thick} > 0)
float inner_dia = dia - shell_thick*2
else
float inner_dia = 0
end
float shell_vol= {PI}*(dia*dia/4-inner_dia*inner_dia/4)*len
float surf = dia*{PI}*dia
if ({dia}>= 15e-6)
echo {compt} "shell vol,len,dia=" {shell_vol} {len} "dia=" {dia} "SA=" {surf}
end
setfield {compt}/{buffername} \
B {1.0/(2.0*96494*shell_vol*(1+kb))} \
tau {Ca_tau} \
Ca_base {Ca_basal} \
thick {shell_thick}
end
end
end
//new calcium concentration - various buffers, pumps and diffusion
function create_difshell (shellName, basal, compLen, r, shellThickness, mode)
str shellName
float basal
float compLen
float r, shellThickness
str mode
create difshell {shellName}
setfield {shellName} \
C {basal} \
Ceq {basal} \
D {dca} \ //D_Ca = 2e-6 (cm^2)(s^(-1))
val 2 \
leak 0 \
shape_mode {mode} \
len {compLen} \
dia {r*2} \ //outer diameter of the shell
thick {shellThickness}
end
function add_difbuffer_to_difshell (shellName, bname, btotal, kf, kb, d, compLen, r, shellThickness, mode)
str shellName, bname
float btotal, kf, kb, d, compLen, r
str mode
create difbuffer {shellName}{bname}
setfield {shellName}{bname} \
Btot {btotal} \
kBf {kf} \
kBb {kb} \
D {d} \
shape_mode {mode} \
len {compLen} \
dia {r*2} \
thick {shellThickness}
addmsg {shellName}{bname} {shellName} BUFFER kBf kBb Bfree Bbound
addmsg {shellName} {shellName}{bname} CONCEN C
end
function add_mmpump (shellName, surfaceArea, kcat, km, pname)
str shellName
float surfaceArea, kcat, km
str pname
create mmpump {shellName}{pname}
setfield {shellName}{pname} \
vmax {kcat*surfaceArea} \
val {2} \
Kd {km}
addmsg {shellName}{pname} {shellName} MMPUMP vmax Kd
addmsg {shellName} {shellName}{pname} CONCEN C
end
function make_fura (compt, totalshells, bufname, calname)
str compt
str calname
str bufname
int totalshells, i
create fura2 {compt}/{bnamefluor}
i=1
while (i < totalshells+1)
str bnx = {calname} @ {i}
//str bn = {bnx}{bufname}
//echo "Make fura" {bnx} {bnx}{bufname}
addmsg {compt}/{bnx}{bufname} {compt}/{bnamefluor} CONCEN Bfree Bbound vol
i=i+1
end
end
function make_volavg (compt, totalshells, calname)
str compt
str calname
int totalshells, i
create wgtavg {compt}/volavg
i=1
while (i < totalshells+1)
str bnx = {calname} @ {i}
addmsg {compt}/{bnx} {compt}/volavg ValueWgt C vol
i=i+1
end
end
function make_buffervolavg (compt, totalshells, calname, buffer)
str compt
str calname
str buffer
int totalshells, i
create wgtavg {compt}/{buffer}Vavg
i=1
while (i < totalshells+1)
str bnx = {calname} @ {i}
addmsg {compt}/{bnx}{buffer} {compt}/{buffer}Vavg ValueWgt Bbound vol
i=i+1
end
end
function add_caconcen_objects (calName, CELLPATH)
str calName, CELLPATH
str outermostShellName = {calName} @ 1
str compt
int totalshells
float thickness, totalthick, remaining
foreach compt ({el {CELLPATH}/##[TYPE={compartment}]})
float dia={getfield {compt} dia}
float rad = 0.5*{dia}
float len = {getfield {compt} len}
int numShells = 0 //initialize numShells at 0
//**********calculate how many shells are needed from the diameter and thickness
int i
totalthick=outershell_thickness
remaining=rad
for (i = 1; remaining>minthick; i=i+1)
remaining=rad-totalthick
totalthick=totalthick+outershell_thickness*thicknessincrease**i
//echo "shells="{i}, "remaining" {remaining}
end
totalshells=i-1
if (({substring {compt} 6 9} != "tert") || ({compt}=="/cell/tertdend1_1"))
echo {compt} "radius=" {rad} ", totalshells=" {totalshells}
end
//make shells and buffers using the number of shells calculated above.
float shellRadius = {rad}
thickness=outershell_thickness
for (i=1; i<= totalshells; i=i+1)
str shellname = {calName} @ {i}
create_difshell {compt}/{shellname} {Ca_basal} {len} {shellRadius} {thickness} {SHELL}
add_difbuffer_to_difshell {compt}/{shellname} {bname1} {btotal1} {kf1} {kb1} {d1} {len} {shellRadius} {thickness} {SHELL}
add_difbuffer_to_difshell {compt}/{shellname} {bname2} {btotal2} {kf2} {kb2} {d2} {len} {shellRadius} {thickness} {SHELL}
add_difbuffer_to_difshell {compt}/{shellname} {bname4} {btotal4} {kf4} {kb4} {d4} {len} {shellRadius} {thickness} {SHELL}
if ({calciumdye} > 0)
add_difbuffer_to_difshell {compt}/{shellname} {bnamefluor} {btotalfluor} {kffluor} {kbfluor} {dfluor} {len} {shellRadius} {thickness} {SHELL}
if ({calciumdye} == 4)
add_difbuffer_to_difshell {compt}/{shellname} {egtaname} {egtatot} {kfegta} {kbegta} {degta} {len} {shellRadius} {thickness} {SHELL}
end
end
shellRadius = shellRadius-thickness
if (i==totalshells-1)
thickness=shellRadius
else
thickness=thickness*thicknessincrease
end
end
reset > reset.txt //reset to set sa and vol for correct diffusion messages.
if (calciumdye == 1)
//add fura object to each compartment to calc fluorescence
make_fura {compt} {totalshells} {bnamefluor} {calName}
elif ({calciumdye} > 1)
//add wgtavg object for bound single wavelength indicator dye
make_buffervolavg {compt} {totalshells} {calName} {bnamefluor}
if ({calciumdye} == 4)
make_buffervolavg {compt} {totalshells} {calName} {egtaname}
end
end
//add wgtavg object to calculated Ca concentration without dyes
make_volavg {compt} {totalshells} {calName}
//diffusion between calcium and diffusible buffer shells
for (i=1; i < totalshells; i=i+1)
str sn = {calName} @ {i}
str innerSn = {calName} @ {i+1}
//echo "shell=" {compt}/{sn} "SA=" {getfield {compt}/{sn} surf_up}
addmsg {compt}/{sn} {compt}/{innerSn} DIFF_DOWN prev_C thick
addmsg {compt}/{innerSn} {compt}/{sn} DIFF_UP prev_C thick
addmsg {compt}/{sn}{bname2} {compt}/{innerSn}{bname2} DIFF_DOWN prev_free thick
addmsg {compt}/{innerSn}{bname2} {compt}/{sn}{bname2} DIFF_UP prev_free thick
addmsg {compt}/{sn}{bname4} {compt}/{innerSn}{bname4} DIFF_DOWN prev_free thick
addmsg {compt}/{innerSn}{bname4} {compt}/{sn}{bname4} DIFF_UP prev_free thick
if ({calciumdye} > 0)
addmsg {compt}/{sn}{bnamefluor} {compt}/{innerSn}{bnamefluor} DIFF_DOWN prev_free thick
addmsg {compt}/{innerSn}{bnamefluor} {compt}/{sn}{bnamefluor} DIFF_UP prev_free thick
if ({calciumdye} ==4)
addmsg {compt}/{sn}{egtaname} {compt}/{innerSn}{egtaname} DIFF_DOWN prev_free thick
addmsg {compt}/{innerSn}{egtaname} {compt}/{sn}{egtaname} DIFF_UP prev_free thick
end
end
end
//pump @ outershell
float surfaceArea = {getfield {compt}/{outermostShellName} surf_up}
//echo "shell=" {compt}/{outermostShellName}
//showfield {compt}/{outermostShellName} *
if ({compt} == "/cell/soma")
float kcat=kcatsoma
else
float kcat=kcatdend
end
add_mmpump {compt}/{outermostShellName} {surfaceArea} {kcat} {km} {MMpumpName}
float CaBase = {getfield {compt}/{outermostShellName} Ceq}
float vmax = kcat*surfaceArea
float vol = {getfield {compt}/{outermostShellName} vol}
float leak = {{vmax*CaBase}/{vol*{CaBase + km}}} // {{kcat*CaBase}/{outershell_thickness*{CaBase + km}}}
setfield {compt}/{outermostShellName} leak {leak}
//echo "mmpump" {compt} "kcat="{kcatsoma} "leak ="{leak}
end
end
