CdpStC_NoCAM_MA2020_GoC

class braincell.ion.CdpStC_NoCAM_MA2020_GoC(size, temp=Quantity(298.15, 'K'), Nannuli=10.9495, cainull=Quantity(4.5e-05, 'mM'), mginull=Quantity(0.59, 'mM'), Buffnull1=Quantity(0., 'mM'), rf1=Quantity(0.0134329, '1 / (mM * ms)'), rf2=Quantity(0.0397469, 'kHz'), Buffnull2=Quantity(60.9091, 'mM'), rf3=Quantity(0.1435, '1 / (mM * ms)'), rf4=Quantity(0.0014, 'kHz'), BTCnull=Quantity(0., 'mM'), b1=Quantity(5.33, '1 / (mM * ms)'), b2=Quantity(0.08, 'kHz'), DMNPEnull=Quantity(0., 'mM'), c1=Quantity(5.63, '1 / (mM * ms)'), c2=Quantity(0.000107, 'kHz'), PVnull=Quantity(0.08, 'mM'), m1=Quantity(107., '1 / (mM * ms)'), m2=Quantity(0.00095, 'kHz'), p1=Quantity(0.8, '1 / (mM * ms)'), p2=Quantity(0.025, 'kHz'), kpmp1=Quantity(0.003, '1 / (mM * ms)'), kpmp2=Quantity(1.75e-05, 'kHz'), kpmp3=Quantity(7.255e-05, 'kHz'), TotalPump=Quantity(1.e-09, 'mol / cm^2'), Co=None, Ci_initializer=None, species_initializers=None, solver='backward_euler', substeps=1, name=None, **channels)

BrainCell-factored calcium pool: pump, non-CaM buffers, no CaM.

Keeps the pump and non-calmodulin buffer subnetworks of the imported Golgi-cell CdpStC calcium pool while dropping the calmodulin (CaM) reactions of CdpStC_CAMOnly_MA2020_GoC entirely. Unlike its sibling classes, this one is not itself a direct port of a .mod file: no CdpStC_NoCAM_MA20_GoC.mod exists in the imported source tree. It is a BrainCell-factored base whose literal parameter set matches BC/ion/CdpStC_MA25_BC.mod and SC/ion/CdpStC_RI21_SC.mod – both of which are exactly this GoC CdpStC mechanism with the CaM subnetwork commented out – so it exists to be shared by CdpStC_MA2025_BC and CdpStC_RI2021_SC rather than to stand for a distinct published mechanism. The CAM reactions were removed, not replaced by different kinetics.

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; only shapes the single effective volume fraction vrat. 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.

• mginull (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Baseline/initial magnesium concentration mg. Defaults to 0.59 mM.

• Buffnull1 (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Total concentration of the first generic buffer, Buff1 + Buff1_ca. Defaults to 0.0 mM.

• rf1 (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Forward and backward rate constants of the Buff1 binding step. Default 0.0134329 /(mM*ms) and 0.0397469 /ms.

• rf2 (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Forward and backward rate constants of the Buff1 binding step. Default 0.0134329 /(mM*ms) and 0.0397469 /ms.

• Buffnull2 (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Total concentration of the second generic buffer, Buff2 + Buff2_ca. Defaults to 60.9091 mM.

• rf3 (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Forward and backward rate constants of the Buff2 binding step. Default 0.1435 /(mM*ms) and 0.0014 /ms.

• rf4 (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Forward and backward rate constants of the Buff2 binding step. Default 0.1435 /(mM*ms) and 0.0014 /ms.

• BTCnull (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Total concentration of the BTC indicator dye buffer, BTC + BTC_ca. Defaults to 0.0 mM.

• b1 (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Forward and backward rate constants of the BTC binding step. Default 5.33 /(mM*ms) and 0.08 /ms.

• b2 (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Forward and backward rate constants of the BTC binding step. Default 5.33 /(mM*ms) and 0.08 /ms.

• DMNPEnull (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Total concentration of the caged-calcium buffer DMNPE, DMNPE + DMNPE_ca. Defaults to 0.0 mM.

• c1 (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Forward and backward rate constants of the DMNPE binding step. Default 5.63 /(mM*ms) and 0.107e-3 /ms.

• c2 (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Forward and backward rate constants of the DMNPE binding step. Default 5.63 /(mM*ms) and 0.107e-3 /ms.

• PVnull (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Total concentration of parvalbumin, PV + PV_ca + PV_mg. Defaults to 0.08 mM.

• m1 (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Forward and backward rate constants of the PV calcium binding step. Default 1.07e2 /(mM*ms) and 9.5e-4 /ms.

• m2 (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Forward and backward rate constants of the PV calcium binding step. Default 1.07e2 /(mM*ms) and 9.5e-4 /ms.

• p1 (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Forward and backward rate constants of the PV magnesium binding step. Default 0.8 /(mM*ms) and 2.5e-2 /ms.

• p2 (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Forward and backward rate constants of the PV magnesium binding step. Default 0.8 /(mM*ms) and 2.5e-2 /ms.

• kpmp1 (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Forward and backward rate constants of the pump + Ci -> pumpca binding step. Default 3e-3 /(mM*ms) and 1.75e-5 /ms.

• kpmp2 (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Forward and backward rate constants of the pump + Ci -> pumpca binding step. Default 3e-3 /(mM*ms) and 1.75e-5 /ms.

• kpmp3 (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Rate constant of the irreversible extrusion step, pumpca -> pump. Defaults to 7.255e-5 /ms.

• TotalPump (Array | ndarray | bool | number | bool | int | float | complex | Quantity | Callable) – Areal pump-site density; the conserved sum of pump + pumpca per unit membrane area. Defaults to 1e-9 mol/cm2.

• 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 fourteen differential species (Ci, mg, Buff1, Buff1_ca, Buff2, Buff2_ca, BTC, BTC_ca, DMNPE, DMNPE_ca, PV, PV_ca, PV_mg, pump). Defaults to None (no overrides); unset buffer/PV species default to their steady-state occupancy at cainull/mginull, and pump defaults to TotalPump.

• 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 fourteen 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, or from parea/dsq, 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_CAMOnly_MA2020_GoC

Sibling decomposition keeping only the CaM network this class omits.

CdpStC_MA2020_GoC

The undivided mechanism, combining this pump/buffer network with the CaM network.

CdpStC_MA2025_BC

Thin basket-cell subclass reusing this class’s network unchanged.

CdpStC_RI2021_SC

Thin stellate-cell subclass reusing this class’s network unchanged.

braincell.ion._base.KineticIon

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

Notes

This class has no source .mod file of its own; see the extended summary. Its credits are those of the GoC CdpStC mechanism it factors, part of the cerebellar Golgi cell model of (Masoli et al., 2020) [4]: Anwar, Hong & De Schutter [1] as the reference for the mechanism, the extended buffer parameters from Schmidt et al. (2003) [2], and the pump rate tuned to data from Maeda et al. (1999) [3]. uses_total_current = True and one Source drives Ci from the channel current supplied at each step: _ci_source_flux returns zero when no current is supplied, and otherwise total_current * pi * diam_arc_mean / (2 * faraday_constant). NEURON’s raw GoC ica is efflux-positive, but BrainCell channel currents follow the repo-wide inward-positive convention, so a positive total_current here increases Ci.

One Conserve constrains pump + pumpca = TotalPump * parea, with pumpca recovered algebraically rather than integrated; pump is the only pump state among the fourteen differential species.

Buffer- and PV-bound species initialize at the equilibrium occupancy implied by their dissociation constants and cainull/mginull (see _ss_buffer_free, _ss_buffer_bound, _ss_pv_free, _ss_pv_ca, _ss_pv_mg), not at zero, so steady state is reached without a long settling transient.

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