ToyCaBindingIcaSourceKinetic_SU2015_DCN

class braincell.ion.ToyCaBindingIcaSourceKinetic_SU2015_DCN(size, temp=Quantity(309.15, 'K'), kf=Quantity(2., '1 / (mM * ms)'), kb=Quantity(0.5, 'kHz'), Btot=Quantity(1., 'mM'), kCa=Quantity(3.45e-07, '1 / C'), depth=Quantity(0.2, 'um'), Co=None, Ci_initializer=Quantity(0.1, 'mM'), BC_initializer=Quantity(0., 'mM'), solver='rk4', substeps=5, name=None, **channels)

Minimal reversible calcium-binding toy with current-driven Ci source.

This is a BrainCell import-path validation fixture, not a model of a published mechanism – the SU2015_DCN suffix follows BrainCell’s naming convention only. The mechanism keeps the same reversible binding network as the earlier toy kinetic ions and drives Ci with inward-positive calcium current.

Parameters:

• size (int | Sequence[int] | integer | Sequence[integer]) – The size of the simulation target, typically the number of neurons or compartments. Forwarded unchanged to Calcium.

• temp (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Absolute temperature used by the Nernst equation in E. Defaults to 36 degrees Celsius, converted to kelvin via u.celsius2kelvin before being stored.

• kf (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Forward rate constant of the Ci + B -> BC reaction. Defaults to 2.0 / (mM * ms).

• kb (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Backward rate constant of the BC -> Ci + B reaction. Defaults to 0.5 / ms.

• Btot (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Total conserved concentration of B + BC. Defaults to 1.0 mM.

• kCa (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Current-to-flux scale factor used by the Ci source. Defaults to 3.45e-7 / coulomb.

• depth (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Shell depth used by the Ci source’s unit conversion. Defaults to 0.2 um.

• Co (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable | None) – Extracellular calcium concentration. Defaults to None, which falls back to Calcium.default_Co inside KineticIon._init_kinetic_ion().

• Ci_initializer (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Initializer for the Ci species. Defaults to 0.10 mM.

• BC_initializer (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Initializer for the BC species. Defaults to 0.00 mM.

• solver (str) – Integrator name used for the reaction network. Defaults to "rk4".

• substeps (int) – Number of solver substeps run inside one parent update. Defaults to 5.

• name (str | None) – Runtime ion instance name. Defaults to None.

• **channels – Channel instances to attach to this ion, forwarded unchanged to Calcium.

Raises:

ValueError – If temp is explicitly passed as None, or if substeps is less than 1. Both come from KineticIon._init_kinetic_ion().

See also

Calcium

Base calcium ion family this class attaches the reaction network to.

ToyCaBindingKinetic_SU2015_DCN

Same reaction network without any source term.

ToyCaBindingSourceKinetic_SU2015_DCN

Sibling fixture with a constant, rather than current-driven, source.

braincell.ion._base.KineticIon

Template this class instantiates; documents the NMODL-style semantics shared by all five toy fixtures.

Notes

The Ci source evaluates to zero when total_current is None (no channels attached), and otherwise to (kCa / depth) * total_current * 1e4, with total_current read in mA/cm**2 and the 1e4 factor converting that current density into the mM/ms units the source needs – the standard cross-sectional-area conversion used across BrainCell’s current-driven calcium sources. This class sets uses_total_current = True, so KineticIon()’s derivative hook always supplies a real total_current once at least one channel is attached, unlike CalciumFirstOrder.