I/V clamp electrod

[Raj]

Dear Reza,

Just changing the clamp voltage will already lead to a capacitive current, because the capacitance needs to be charged.

I set every possible conductance I could find to zero. This is a debugging strategy eliminate as many sources of confusion as you can find and try to address its cause. Then I could see that the problem was visible even without the calcium current present . Then when I found the cause I could add the calcium currrent back in and see if I solved your problem. I still think I did.

The right handside is 100 times bigger because it is in units of 10pA whereas your left handside is in nA. So divide the righthand side by 100, adjust the timestep and you should be fine.

Regards,
Raj

[reza_rzm]

Dear Raj,


I think this is my last question!!(i hope!)

If I plot SEVClamp.i and soma[0].i_cap*24058.317/100 together in one plot there is a pronounced difference when dt=0.025 which disappears with a smaller timestep, e.g. dt=0.0025 ms. I set
gkbar_hh2=0 gnabar_hh2=0 g_pas=0 pcabar_itGHK=0

That's right! (I didn't notice to dt!!! ) . I see the equal behavior for "SEVClamp.i " and "soma[0].i_cap*24058.317/100"

just, i don't know why do you devide by 100,

soma[0].i_cap --->unite:mA/cm2
area= 24058.317-->unite:um2

then soma[0].i_cap*24058.317

--->uinte= (value for current)*24058.317 *10^(-5) A

right? so why devide by 100!

Second,

After putting : pcabar_itGHK=2e-3
I still see good agreement between the currents.

between SEVClamp.i and (1 or 2 or ? )

1-soma[0].i_cap*24058.317/100
2-(soma[0].i_cap+soma[0].ica)*24058.317/100


Yours,
reza

[Raj]

just, i don't know why do you devide by 100

1nA = 100*10pA

So if your ica is given in units of 10pA/um2 and your area in um2 you have to divide the numerical value of the current you obtain by a hundred to get the current in nA.

between SEVClamp.i and (1 or 2 or ? )

1-soma[0].i_cap*24058.317/100
2-(soma[0].i_cap+soma[0].ica)*24058.317/100

The second option.

Regards,
Raj

[ted]

i don't know why do you devide by 100,

soma[0].i_cap --->unite:mA/cm2
area= 24058.317-->unite:um2

then soma[0].i_cap*24058.317

--->uinte= (value for current)*24058.317 *10^(-5) A

right?

At the risk of being drawn into an interminable exchange, here are my two bits.

Code: Select all

If current density is in mA/cm2 and area is in cm2,
here's how to find the units of the product:

mA    cm2   mA x cm2   mA   cm2   mA    1
--  x     = -------- =    x --- =    x --- = mA
cm2           cm2           cm2         1

But if area is in um2

mA    cm2   mA x um2   mA   um2   mA   um2     cm2
--  x     = -------- =    x --- =    x --- x --------
cm2           cm2           cm2        cm2   10^8 um2

(because 1 cm2 = 10^8 um2, so 1 cm2 / 10^8 um2 = 1)

Continuing
from this last expression --------^^^^^^^^^^^^^^^^^^^^
we have

mA    cm2   mA   um2     cm2       mA    10^6 nA   nA
--  x     =    x --- x -------- = ---- x ------- = ---
cm2              cm2   10^8 um2   10^8     mA      100

In other words, if current density is in mA/cm2 and area is in um2,
the numeric value of the product must be divided by 100 in order to 
get the net current in nA.

An aside:  for a single compartment model with surface area 100 um2,
the current density in mA/cm2 is numerically equal to net current
in nA.  That is, if leak current density is y mA/cm2, total leak
current is y nA.  This is why the single compartment model 
created by NEURON Main Menu / Build / single compartment
has surface area 100 um2.

That's all I have to say, other than thanks to my first chemistry teacher,
who taught us how to deal with units.

[reza_rzm]

Dear Ted and Raj!

Thank you very much.

I have learned so much from these posts.

Yours,

Reza