ToyDiamFactorKinetic_SU2015_DCN

class braincell.ion.ToyDiamFactorKinetic_SU2015_DCN(size, temp=Quantity(309.15, 'K'), kf=Quantity(2., '1 / (mM * ms)'), kb=Quantity(0.5, 'kHz'), PumpTot=Quantity(1., 'mM * um'), depth=Quantity(1., 'um'), Co=None, Ci_initializer=Quantity(0.1, 'mM'), PumpBound_initializer=Quantity(0., 'mM * um'), solver='backward_euler', substeps=1, name=None, **channels)

Minimal geometry-factor toy with runtime-derived cytosolic strip factors.

Ci lives in a thin strip volume derived from the runtime midpoint diameter, while PumpFree and PumpBound live on a line-like membrane factor:

\[ \begin{align}\begin{aligned}cyto = \pi \cdot diam_{mid} \cdot depth\\pump\_area = \pi \cdot diam_{mid}\end{aligned}\end{align} \]

The mechanism then exercises a reversible reaction

\[Ca_i + PumpFree \rightleftharpoons PumpBound\]

together with the conserved pool

\[PumpFree + PumpBound = PumpTot \cdot pump\_area\]