TITLE Calcium ion accumulation with longitudinal and radial diffusion buffering and pumping
COMMENT
Modified from examples/nrniv/nmodl/cabpump.mod to match The
NEURON Book writeup and to include more comments
See examples/nrniv/nmodl/capump.mod for the pump by itself
PROCEDURE factors_cdp() sets up the scale factors
needed to model radial diffusion. These scale factors do not
have to be recomputed when diam or DCa is changed
The amount of calcium in an annulus is ca[i]*diam^2*vrat[i]
with ca[0] being the 2nd order correct concentration at the
exact edge and ca[Nannuli1] being the concentration at the
exact center.
Buffer concentration and rates are based on Yamada et al. 1989
model of bullfrog sympathetic ganglion cell.
ENDCOMMENT
NEURON {
SUFFIX cdp13
USEION ca READ cao, cai, ica WRITE cai, ica
: need to read cai to initialize buffer and
: calcium in the compartments
: cao and ica added for pump. Writes to ica
GLOBAL vrat
: vrat must be GLOBALsee
: INITIAL block, but TotalBuffer and TotalPump may be RANGE
: if it varies among compartments
RANGE cai0, TotalBuffer, TotalPump, ica_pmp
: pump current is ica_pmp
: TotalPump is density of pump sites
: Make it RANGE if it varies among sections
: pump current can be referenced as ica_pmp_cdp
}
DEFINE Nannuli 13 : number of concentric shells
: must be >= 2, at least shell and core
UNITS {
(molar) = (1/liter)
(mM) = (millimolar)
(um) = (micron)
(mA) = (milliamp)
(mol) = (1) : pump density is in mol/cm2
FARADAY = (faraday) (10000 coulomb)
PI = (pi) (1)
}
PARAMETER {
DCa = 0.223 (um2/ms)
: to change rate of buffering without disturbing equilibrium
: multiply the following two by the same factor
k1buf = 100 (/mMms)
k2buf = 0.1 (/ms)
TotalBuffer = 0.03 (mM)
cai0 = 50e6 (mM) : Requires explicit use in INITIAL block
k1 = 1 (/mMms)
k2 = 0.005 (/ms)
k3 = 1 (/ms)
k4 = 0.005 (/mMms)
: rates mean 50 nM is equilibrium
: to eliminate the pump, set TotalPump to 0 in hoc
TotalPump = 3e13 (mol/cm2)
}
ASSIGNED {
diam (um)
ica (mA/cm2)
cai (mM)
cao (mM) : here cao is assumed constant
ica_pmp (mA/cm2)
ica_pmp_last (mA/cm2) : used so pump not counted twice
parea (um) : surface area for pump
vrat[Nannuli] (1) : dimensionless. Value of vrat[i]
: is the volume of annulus i of a 1 um diameter cyl
: per unit length
: gets extra um2 when multiplied by diam^2 to give vol
Kd (/mM)
B0 (mM) : initial free buffer
}
CONSTANT {volo = 1e+10 (um2) } : need an extracellular volume
: 1 liter per um of length. Actual value not relevant
: since cao is constant
STATE {
: ca[0] is equivalent to cai
: ca[] are very small, so specify absolute tolerance
ca[Nannuli] (mM) <1e7>
CaBuffer[Nannuli] (mM) <1e5>
Buffer[Nannuli] (mM) <1e5>
pump (mol/cm2) <1e15> : free pump sites
pumpca (mol/cm2) <1e15> : pump sites with ca bound
}
BREAKPOINT {
SOLVE state METHOD sparse
ica_pmp_last = ica_pmp : used so pump not counted twice
ica = ica_pmp : pump current needed for cai
: calculation
}
LOCAL factors_done : like a static variable in C
INITIAL {
if (factors_done == 0) { : flag becomes 1 in the first seg
factors_done = 1 : all subsequent segs will have
factors() : vrat =0 unless vrat is GLOBAL
: vrat and frat have to be calculated
: only once
}
cai = cai0 : cai is set to cai0_ca_ion by default.
: This overrides
Kd = k1buf/k2buf
B0 = TotalBuffer/(1 + Kd*cai) : various initializations
FROM i=0 TO Nannuli1 {
ca[i] = cai
Buffer[i] = B0
CaBuffer[i] = TotalBuffer  B0
}
parea = PI*diam : defines pump area per unit length
pump = TotalPump/(1 + (cai*k1/k2)) : initial free sites
pumpca = TotalPump  pump : initial ca bound sites
}
COMMENT
Note, the above initializations may not give a true "rest"
If Ca currents are included, as these may affect cai. It
may be necessary to do an "initialization run" and do
SaveState (see The NEURON Book Chap 8.4)
factors() sets up factors needed for radial diffusion
modeled by Nannuli concentric compartments.
The outermost shell is half as thick as the other shells
so the concentration is spatially second order correct
at the surface of the cell.
The radius of the cylindrical core
equals the thickness of the outermost shell.
The intervening Nannuli2 shells each have thickness =
r/(Nannuli1). (Nannuli must be >= 2).
ca[0] is at the edge of the cell, ca[Nannuli1] is at the
center of the cell, and ca[i] for 0 < i < Nannuli1 is
midway through the thickness of each annulus.
ENDCOMMENT
LOCAL frat[Nannuli] : scales the rate constants for model
: geometry. Local since applies to all
: segments that have a caldif, but not
: of general interest to be global
PROCEDURE factors() {
LOCAL r, dr2
r = 1/2 :radius starts at edge (half diam)
dr2 = r/(Nannuli1)/2 :full thickness of outermost annulus
:half thickness of all others
vrat[0] = 0
frat[0] = 2*r
FROM i=0 TO Nannuli2 {
vrat[i] = vrat[i] + PI*(rdr2/2)*2*dr2 :interior half
r = r  dr2
frat[i+1] = 2*PI*r/(2*dr2) :exterior edge of annulus
: divided by distance between centers
: frat[i+1] equals A(i+1)/(deltar)
: where A is the shell surface area
r = r  dr2
vrat[i+1] = PI*(r+dr2/2)*2*dr2
:outer half of annulus
}
}
LOCAL dsq, dsqvol : can't define local variable in KINETIC
: block or use in COMPARTMENT
KINETIC state {
COMPARTMENT i, diam*diam*vrat[i] {ca CaBuffer Buffer}
: specifies shell volumes for state variables
: for all compartments. i is the index
: converts states to mass from concentration
COMPARTMENT (1e10)*parea {pump pumpca}
COMPARTMENT volo {cao}
: these COMPARTMENT statements and 1e10 needed
: for dimensional consistency
:LONGITUDINAL_DIFFUSION i, DCa*diam*diam*vrat[i] {ca}
: diffusion into neighboring sections
: i is the index, flux expression (DCa * crosssec A),
: variable (ca)
: pump
~ ca[0] + pump <> pumpca (k1*parea*(1e10), k2*parea*(1e10))
~ pumpca <> pump + cao (k3*parea*(1e10), k4*parea*(1e10))
CONSERVE pump + pumpca = TotalPump * parea * (1e10)
: ensures conservation. Helpful for accuracy
ica_pmp = 2*FARADAY*(f_flux  b_flux)/parea
: after each reaction the forward and backward fluxes
: are assigned to f_flux and b_flux automatically
: f_flux is ca that is pumped out
~ ca[0] << ((ica  ica_pmp_last)*PI*diam/(2*FARADAY))
: consider all currents except pump since pump
: effect on ca[0] was considered a few statements
: above. ica contains pump current ica_pmp from the
: previous time step, so subtract ica_pmp_last here.
: (ica_pmp is the "new" value, but ca[0] must be
: computed using the "old" value, i.e. ica_pmp_last)
: uses kinetic syntax in place of an ode where ica
: comes into the outer compartment from outside.
: Note, mass/time herenot concentration
FROM i=0 TO Nannuli2 { : radial diffusion
~ ca[i] <> ca[i+1] (DCa*frat[i+1], DCa*frat[i+1])
}
dsq = diam*diam
FROM i=0 TO Nannuli1 {
dsqvol = dsq*vrat[i]
~ ca[i] + Buffer[i] <> CaBuffer[i] (k1buf*dsqvol, k2buf*dsqvol)
}
: the dsqvol is needed to convert from conc to mass
cai = ca[0]
: updates cai from ca[0] so eca can be computed
: by NEURON
}
COMMENT
Be sure to use modlunit to do units checking
When inserted into a section,
ca_cadifus[], Buffer_cadifus[], and CaBuffercadifus[]
are available to the .hoc file and for plotting
if total buffer or DCa are nonuniform in the cell, make
them RANGE variables
ENDCOMMENT
