CdpStC_CAMOnly_MA2020_GoC

class braincell.ion.CdpStC_CAMOnly_MA2020_GoC(size, temp=Quantity(298.15, 'K'), Nannuli=10.9495, cainull=Quantity(4.5e-05, 'mM'), CAM_start=Quantity(0.03, 'mM'), K1Coff=Quantity(0.04, 'kHz'), K1Con=Quantity(5.4, '1 / (mM * ms)'), K2Coff=Quantity(0.00925, 'kHz'), K2Con=Quantity(15., '1 / (mM * ms)'), K1Noff=Quantity(2.5, 'kHz'), K1Non=Quantity(142.5, '1 / (mM * ms)'), K2Noff=Quantity(0.75, 'kHz'), K2Non=Quantity(175., '1 / (mM * ms)'), Co=None, Ci_initializer=None, species_initializers=None, solver='backward_euler', substeps=1, name=None, **channels)

Import of the calmodulin-only CdpStC_CAMOnly_MA20_GoC.mod.

Isolates the calmodulin (CaM) subnetwork of the imported Golgi-cell calcium pool so its binding kinetics can be validated independently of the pump and non-CaM buffers that CdpStC_MA2020_GoC also tracks. The scheme is a two-lobe CaM binding model: an independent C-lobe and N-lobe, each with two sequential, reversible calcium-binding steps, reaching the fully-loaded CAM4 state through four distinct binding orders.

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 25 degrees Celsius, converted to kelvin via u.celsius2kelvin before being stored.

• Nannuli (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Radial-shell count inherited from the NEURON multi-shell diffusion template. BrainCell tracks a single well-mixed Ci pool, so Nannuli only shapes the effective volume fraction returned by vrat (dr2 = 0.25 / (Nannuli - 1)); no shell diffusion is performed. Defaults to 10.9495.

• cainull (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Baseline/initial free calcium concentration Ci. Defaults to 45e-6 mM.

• CAM_start (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Initial concentration of apo-calmodulin, CAM0. Defaults to 0.03 mM.

• K1Coff (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Backward and forward rate constants of the first C-lobe binding step. Default 0.04 /ms and 5.4 /(mM*ms).

• K1Con (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Backward and forward rate constants of the first C-lobe binding step. Default 0.04 /ms and 5.4 /(mM*ms).

• K2Coff (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Backward and forward rate constants of the second C-lobe binding step. Default 0.00925 /ms and 15.0 /(mM*ms).

• K2Con (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Backward and forward rate constants of the second C-lobe binding step. Default 0.00925 /ms and 15.0 /(mM*ms).

• K1Noff (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Backward and forward rate constants of the first N-lobe binding step. Default 2.5 /ms and 142.5 /(mM*ms).

• K1Non (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Backward and forward rate constants of the first N-lobe binding step. Default 2.5 /ms and 142.5 /(mM*ms).

• K2Noff (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Backward and forward rate constants of the second N-lobe binding step. Default 0.75 /ms and 175.0 /(mM*ms).

• K2Non (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Backward and forward rate constants of the second N-lobe binding step. Default 0.75 /ms and 175.0 /(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 | None) – Initializer for the Ci species. Defaults to None, which falls back to cainull.

• species_initializers (dict[str, object] | None) – Per-species initializer overrides, keyed by one of this class’s ten differential species (Ci, CAM0, CAM1C, CAM2C, CAM1N2C, CAM1N, CAM2N, CAM2N1C, CAM1C1N, CAM4). Defaults to None (no overrides).

• solver (str) – Integrator name used for the reaction network. Defaults to "backward_euler", matching default_solver.

• substeps (int) – Number of solver substeps run inside one parent update. Defaults to 1, matching default_substeps.

• 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 species_initializers names a species outside the ten listed above, or if temp is explicitly passed as None, or substeps is less than 1 (the latter two raised by KineticIon._init_kinetic_ion()).

• AttributeError – Raised during state initialization or reset if this ion’s compartment geometry (diam_arc_mean) has not been attached yet.

See also

Calcium

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

CdpStC_NoCAM_MA2020_GoC

Sibling decomposition keeping the pump and non-CaM buffers while dropping this class’s CaM network.

CdpStC_MA2020_GoC

The undivided mechanism, combining this CaM network with the pump and non-CaM buffers.

braincell.ion._base.KineticIon

Template this class instantiates; documents the NMODL-style semantics shared by all Cdp* mechanisms.

Notes

Ported from GoC/ion/CdpStC_CAMOnly_MA20_GoC.mod, part of the cerebellar Golgi cell model of (Masoli et al., 2020) [4]. That file carries a title only, no credit block; the CaM subnetwork it isolates belongs to the CdpStC mechanism of Anwar, Hong & De Schutter [1], whose extended buffer parameters come from Schmidt et al. (2003) [2] and whose pump rate was tuned to data from Maeda et al. (1999) [3]. uses_total_current = False and sources = (): this pool has no calcium influx or pump of its own, so Ci is consumed by the twelve CaM reactions above and never resupplied. It is meant to be exercised in isolation, matching the .mod file’s role of validating the CaM subnetwork rather than serving as a standalone physiological pool.

The cam_unit factor scales the nine CaM-state species by a unit-magnitude, um**2-dimensioned array rather than by dsqvol again: the imported NMODL COMPARTMENT scaling applies once, to the shared cytosolic volume that Ci occupies, and must not be applied a second time to each CaM row.

CdpStC_NoCAM_MA2020_GoC hardcodes solver="backward_euler" and substeps=1 as literal defaults, as this class does, whereas CdpStC_MA2020_GoC instead defaults both to None and lets KineticIon._init_kinetic_ion() fall back to the same class-level default_solver and default_substeps; the observable defaults are identical either way.

References

[1]

Anwar, H., Hong, S., & De Schutter, E. (2012). Controlling Ca2+-activated K+ channels with models of Ca2+ buffering in Purkinje cells. The Cerebellum, 11(3), 681-693. doi:10.1007/s12311-010-0224-3

[2]

Schmidt, H., Stiefel, K. M., Racay, P., Schwaller, B., & Eilers, J. (2003). Mutational analysis of dendritic Ca2+ kinetics in rodent Purkinje cells: role of parvalbumin and calbindin D28k. The Journal of Physiology, 551(1), 13-32. doi:10.1113/jphysiol.2002.035824

[3]

Maeda, H., Ellis-Davies, G. C. R., Ito, K., Miyashita, Y., & Kasai, H. (1999). Supralinear Ca2+ signaling by cooperative and mobile Ca2+ buffering in Purkinje neurons. Neuron, 24(4), 989-1002. doi:10.1016/S0896-6273(00)81045-4

[4]

Masoli, S., Ottaviani, A., Casali, S., & D’Angelo, E. (2020). Cerebellar Golgi cell models predict dendritic processing and mechanisms of synaptic plasticity. PLOS Computational Biology, 16(12), e1007937. doi:10.1371/journal.pcbi.1007937