# MODLUNIT : changing pump units to picomoles/cm2

## Physical System

Calcium pump

## Model

Calcium pump in previous exercise.

## Simulation

The units for the pump are inappropriate and should be changed from mol/cm2 to pmol/cm2.

To make the units consistent, we will have to change the factors indicated below in bold type.

`UNITS {
...
(mol) = (1)
}
PARAMETER {
width = .1 (um)
tau = 1 (ms)
k1 = 5e8 (/mM-s)
k2 = .25e6 (/s)
k3 = .5e3 (/s)
k4 = 5e0 (/mM-s)
cabulk = .1 (uM)
cao = 10 (mM)
cai = 1e-3 (mM)
pump0 = 3e-14 (mol/cm2)
}
STATE {
cam (uM) <1e-6>
pump (mol/cm2) <1e-16>
capump (mol/cm2) <1e-16>
}
KINETIC pmp {
~ cabulk <-> cam (width/tau, width/tau)
~ cam + pump <-> capump ((1e7)*k1, (1e10)*k2)
~ capump <-> cao + pump ((1e10)*k3, (1e10)*k4)
ica_pmp = (1e-7)*2*FARADAY*(f_flux - b_flux)
~ cam << (-(ica - ica_pmp)/(2*FARADAY)*(1e7))
CONSERVE pump + capump = (1e13)*pump0
COMPARTMENT width {cam} : volume has dimensions of um
COMPARTMENT (1e13) {pump capump} : area is dimensionless
COMPARTMENT 1(um) {cabulk}
COMPARTMENT (1e3)*1(um) {cao}
cai = (.001)*cam
}
`

## Exercises

0) In the course/capump directory, copy capump.mod to temp.mod and change the SUFFIX from capmp to capmp2
Verify that you are starting out with consistent units by running "modlunit temp".

1) Change pump0, pump, and capump to pmol/cm2. You may also wish to change the default value for pump0 (from 3e-12 to 3e-2) as well as the default absolute error tolerance for pump and capump.

Run "modlunit temp" and notice that pmol is undefined. You can replace the UNITS definition

            (mol)   =       (1)

with

            (pmol)  =       (pico)

and run "modlunit temp" again. Don't look at this note.

2) The reaction quantity for pump and cam is inconsistent when multiplied by their respective compartment sizes.

Spend at most 10 minutes fixing the units so that temp.mod is accepted by the modlunit command.

3) If you had trouble. Here is how to do it systematically.

4) Verify that the calcium current as a function of the internal calcium concentration is still the same as in the previous exercise.

NEURON hands-on course
Copyright © 1998, 1999 by N.T. Carnevale and M.L. Hines, all rights reserved.