torchcell.metabolism.flux_layer.CompartmentParameters

class CompartmentParameters(*, ph: dict[str, float] = <factory>, ionic_strength_m: dict[str, float] = <factory>, membrane_potential_mv: dict[str, float] = <factory>, reference_compartment: str = 'c', temperature_k: float = 303.15, source: str = 'Smith et al. 2026, Thermo-Flux, Table 1 (iMM904 parameter set); membrane potentials in mV, pH dimensionless.')

Bases: BaseModel

pH, ionic strength and membrane potential per compartment.

Values for S. cerevisiae iMM904 as tabulated by Thermo-Flux (Smith et al. 2026, Table 1): cytosol pH 7.0, mitochondrion pH 7.4, extracellular pH 5.0; ionic strength 0.25 M in all compartments; T = 298 K; membrane potential 60 mV across the plasma membrane and 160 mV across the mitochondrial membrane. They are defaults, not constants: another organism supplies its own, which is the entire organism-specific surface of the thermodynamic layer.

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].