jaxley.pumps.CaFaradayConcentrationChange

class CaFaradayConcentrationChange(name=None)

Bases: Pump

Update the intracellular calcium ion concentration depending on calcium current.

This channel implements Faraday’s first law of electrolysis to update the intracellular calcium concentration based on calcium current. Faraday’s law relates how a current (e.g., through a channel) impacts the number of ions. Mathematically:

\[n = \frac{I \cdot t}{F \cdot z}\]

Taking the derivative with respect to time:

\[\frac{dn}{dt} = \frac{I}{F \cdot z}\]

where:

• ( n ) is the amount of substance (number of moles),

• ( I ) is the current,

• ( t ) is time,

• ( F ) is the Faraday constant,

• ( z ) is the valence of the ion.

To obtain concentration ( c ) from the amount of substance ( n ), we divide by the volume:

\[\frac{dc}{dt} = \frac{1}{V} \cdot \frac{dn}{dt} = \frac{I}{F \cdot z \cdot V}\]

In Jaxley, the current is given in mS/cm2, so we first have to multiply the current by the surface area of a compartment.

The update is fully passive (i.e., there is no active pump). As such, it is even possible that ion concentration can become negative (because we do not enforce that calcium currents stop when no more ions are available).

Parameters:

name (str | None)

channel_params: dict[str, Array]

channel_states: dict[str, Array]

current_name: str

update_states(states, dt, v, params)

Update states if necessary (but this mechanism has no states to update).

Parameters:

• states (dict[str, Array])

• params (dict[str, Array])

compute_current(states, modified_state, params)

Return change of calcium concentration as the calcium current.

Parameters:

• states (dict[str, Array])

• params (dict[str, Array])

init_state(states, v, params, delta_t)

Initialize states of channel.

Parameters:

• states (dict[str, Array | ndarray | bool | number | bool | int | float | complex])

• v (Array | ndarray | bool | number | bool | int | float | complex)

• params (dict[str, Array | ndarray | bool | number | bool | int | float | complex])

• delta_t (float)

change_name(new_name)

Change the pump name.

Parameters:

new_name (str) – The new name of the pump.

Returns:

Renamed pump, such that this function is chainable.

property name: str | None

The name of the channel (by default, this is the class name).