ToyCaBindingSourceKinetic_SU2015_DCN

ToyCaBindingSourceKinetic_SU2015_DCN#

class braincell.ion.ToyCaBindingSourceKinetic_SU2015_DCN(size, temp=Quantity(309.15, 'K'), kf=Quantity(2., '1 / (mM * ms)'), kb=Quantity(0.5, 'kHz'), Btot=Quantity(1., 'mM'), ci_source=Quantity(0.002, 'mM / ms'), 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 a constant 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 ToyCaBindingKinetic_SU2015_DCN:

\[Ca_i + B \rightleftharpoons BC\]

and adds one constant source term on Ci:

\[\frac{d Ca_i}{dt}\Big|_{\text{source}} = s_{Ca}\]

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.
ci_source (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Constant source rate \(s_{Ca}\) added to dCi/dt. Defaults to 0.002 mM / ms.
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().

ToyCaBindingSourceKinetic_SU2015_DCN

Contents

ToyCaBindingSourceKinetic_SU2015_DCN#

Modeling

Infrastructure

Compilation