ToyCaBindingKinetic_SU2015_DCN

ToyCaBindingKinetic_SU2015_DCN#

class braincell.ion.ToyCaBindingKinetic_SU2015_DCN(size, temp=Quantity(309.15, 'K'), kf=Quantity(2., '1 / (mM * ms)'), kb=Quantity(0.5, 'kHz'), Btot=Quantity(1., 'mM'), 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 for KineticIon validation.

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 models one reversible buffering step:

\[Ca_i + B \rightleftharpoons BC\]

with the conserved pool:

\[B + BC = B_{tot}\]

B is solved algebraically from the conservation rule while Ci and BC are integrated as differential species.

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.

  • 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.

ToyCaBindingSourceKinetic_SU2015_DCN

Same reaction network plus a constant source on Ci.

ToyCaBindingIcaSourceKinetic_SU2015_DCN

Same reaction network plus a current-driven source on Ci.

braincell.ion._base.KineticIon

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

Notes

B is not a differential species: it is declared in species for readability, but conserves marks it as the algebraic member of the B + BC = Btot conservation relation, so its value is recovered from BC rather than integrated.