ToyCaPumpFactorKinetic_SU2015_DCN

ToyCaPumpFactorKinetic_SU2015_DCN#

class braincell.ion.ToyCaPumpFactorKinetic_SU2015_DCN(size, temp=Quantity(309.15, 'K'), kf=Quantity(2., '1 / (mM * ms)'), kb=Quantity(0.5, 'kHz'), k_rel=Quantity(0.05, 'kHz'), PumpTot=Quantity(1., 'mM * um'), kCa=Quantity(3.45e-07, '1 / C'), depth=Quantity(0.2, 'um'), cyt_volume=Quantity(3., 'um^3'), pump_area=Quantity(3., 'um^2'), Co=None, Ci_initializer=Quantity(0.1, 'mM'), PumpBound_initializer=Quantity(0., 'mM * um'), solver='rk4', substeps=5, name=None, **channels)#

Minimal factor-crossing toy with cytosolic and pump-area compartments.

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. Ci lives in a cytosolic volume factor while pump states live in an area-like factor. The toy keeps the state count minimal while exercising mixed-factor reaction, conservation, and current-driven source paths, plus an irreversible (one-way) release reaction.

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 + PumpFree -> PumpBound binding reaction. Defaults to 2.0 / (mM * ms).

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

  • k_rel (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Rate constant of the irreversible PumpBound -> PumpFree release reaction (no back-reaction; backward=None). Defaults to 0.05 / ms.

  • PumpTot (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Per-area total pump concentration used by the conserved pool PumpFree + PumpBound = PumpTot * pump_area. Defaults to 1.0 mM * um.

  • 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.

  • cyt_volume (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Constant cytosolic volume backing the cyto factor that Ci lives in. Defaults to 3.0 um**3. Unlike ToyDiamFactorKinetic_SU2015_DCN, this value is a plain constructor constant, not derived from compartment geometry.

  • pump_area (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Constant membrane area backing the pump_area factor that PumpFree/PumpBound live in. Defaults to 3.0 um**2. Also a plain constructor constant, not geometry-derived.

  • 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.

  • PumpBound_initializer (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Initializer for the PumpBound species. Defaults to 0.00 mM * um.

  • 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.

ToyCaBindingIcaSourceKinetic_SU2015_DCN

Sibling fixture with the same current-driven Ci source but a single, non-factor binding partner.

ToyDiamFactorKinetic_SU2015_DCN

Sibling fixture whose factors are derived from runtime compartment geometry instead of fixed constructor constants.

braincell.ion._base.KineticIon

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

Notes

PumpFree is the algebraic member of the conserved pool PumpFree + PumpBound = PumpTot * pump_area; it is recovered from PumpBound by subtraction rather than integrated directly. The second reaction, PumpBound -> PumpFree, has backward=None and is therefore irreversible: it drains PumpBound at rate k_rel * pump_area with no corresponding forward-binding contribution of its own.

The Ci source evaluates to zero when total_current is None (no channels attached), and otherwise to cyt_volume * (kCa / depth) * total_current * 1e4, with total_current read in mA/cm**2. This mirrors ToyCaBindingIcaSourceKinetic_SU2015_DCN’s source formula, additionally scaled by cyt_volume because Ci here lives in a volume factor rather than being unfactored. This class sets uses_total_current = True.