Fluxes¶
-
mechanica.flux(a, b, species_name, k[, decay=0])¶ The basic passive (Fickian) flux type. This flux implements a passive transport between a species located on a pair of nearby objects of type a and b. See Spatial Transport and Flux for a detailed discussion.
Parameters: - a (type) – object type a
- b (type) – object type b
- species_name (string) – string, textual name of the species to perform a flux with
- k (number) – flux rate constant
- decay (number) – decay rate, optional, defaults to 0.
A Fick flux of the species \(S\) attached to object types \(A\) and \(B\) implements the reaction:
\[\begin{split}\begin{eqnarray} a.S & \leftrightarrow a.S \; &; \; k \left(1 - \frac{r}{r_{cutoff}} \right)\left(a.S - b.S\right) \\ a.S & \rightarrow 0 \; &; \; \frac{d}{2} a.S \\ b.S & \rightarrow 0 \; &; \; \frac{d}{2} b.S, \end{eqnarray}\end{split}\]\(B\) respectivly. \(S\) is a chemical species located at each object instances. \(k\) is the flux constant, \(r\) is the distance between the two objects, \(r_{cutoff}\) is the global cutoff distance, and \(d\) is the optional decay term.
-
mechanica.produce_flux(a, b, species_name, k, target[, decay=0])¶ An active flux that represents active transport, and is can be used to model such processes like membrane ion pumps. See Spatial Transport and Flux for a detailed discussion. Unlike the consume_flux, the produce flux uses the concentation of only the source to determine the rate.
Parameters: - a (type) – object type a
- b (type) – object type b
- species_name (string) – string, textual name of the species to perform a flux with
- k (number) – flux rate constant
- target (number) – target concentation of the \(b.S\) species.
- decay (number) – decay rate, optional, defaults to 0.
The produce flux implements the reaction:
\[\begin{split}\begin{eqnarray} a.S & \rightarrow b.S \; &; \; k \left(r - \frac{r}{r_{cutoff}} \right)\left(a.S - a.S_{target} \right) \\ a.S & \rightarrow 0 \; &; \; \frac{d}{2} a.S \\ b.S & \rightarrow 0 \; &; \; \frac{d}{2} b.S \end{eqnarray}\end{split}\]
-
mechanica.consume_flux(a, b, species_name, k, target_concentation[, decay=0])¶ An active flux that represents active transport, and is can be used to model such processes like membrane ion pumps. See Spatial Transport and Flux for a detailed discussion.
Parameters: - a (type) – object type a
- b (type) – object type b
- species_name (string) – string, textual name of the species to perform a flux with
- k (number) – flux rate constant
- target (number) – target concentation of the \(b.S\) species.
- decay (number) – decay rate, optional, defaults to 0.
The consume flux implements the reaction:
\[\begin{split}\begin{eqnarray} a.S & \rightarrow b.S \; &; \; k \left(1 - \frac{r}{r_{cutoff}}\right)\left(b.S - b.S_{target} \right)\left(a.S\right) \\ a.S & \rightarrow 0 \; &; \; \frac{d}{2} a.S \\ b.S & \rightarrow 0 \; &; \; \frac{d}{2} b.S \end{eqnarray}\end{split}\]