Creation of secretion/consumption

During secretion, the cell releases the substrate into the environment, and during consumption, it absorbs it from the environment.

To create a secretion/consumption, you need:

  1. Click LMB on the icon icon_secretion on the toolbar.

  2. Click LMB on the cell type that will secrete/absorb a specific substrate.

  3. Click LMB on the substrate that cells of the selected type will secrete/consume.

Secretion_creation


After this, a gray arrow will appear on the diagram, directed from the cell type to the substrate.

Secretion_reaction


To configure the parameters of the created secretion/consumption, you need to right-click on the arrow on the diagram indicating this secretion/consumption, and in the drop-down list, click LMB on the Edit button.

Edit_reaction


After this, in the window that appears, you need to set the parameters of the secretion/consumption:

Secretion_parameters


  • Title: name of secretion/consumption,

  • Comment: comment,

  • Substrate: name of the allocated/consumed substrate (unchangeable!),

  • Secretiom Rate: rate of secretion of a substance,

  • Secretiom Target: “saturation” value at which secretion stops,

  • Uptake Rate: rate of consumption of the substance,

  • Net export rate: constant level of secretion/consumption of substrate, independent of cell volume.

Warning

Positive values ​​of the Net export rate parameter correspond to constant secretion, and negative values ​​correspond to constant consumption.

Once all parameters have been set, click Ok.

Below is the formula for calculating the change in substrate concentration (p) in a three-dimensional lattice cell by one cell per unit time dt:

\[p(t+dt) = \frac{p(t) + D * (V_{\mathrm{cell}} / V) * S * T}{1 + D * (V_{\mathrm{cell}} / V) * (S + U)} \, + \, D \, * \frac{E}{V},\]

Where:

  • D - Diffusion dt from settings simulation,

  • Vcell - cell volume,

  • V - environment cell volume,

  • S - secretion rate of the substance (Secretion Rate),

  • T - “saturation” value at which secretion stops (Secretiom Target),

  • U - rate of consumption of the substance (Uptake Rate),

  • E - constant level of secretion/consumption of substrate, independent of cell volume (Net export rate).

In cases where all secretion/consumption parameters, except Net export rate (S, T, and U), have zero values, the formula can be simplified to the following form:

\[p(t+dt) = p(t) + \, D \, * \frac{E}{V}.\]

Чтобы удалить секрецию/потребление из модели, необходимо нажать на него ЛКМ и нажать клавишу Delete.

Если вы работаете в веб-версии BioUML, то для удаления нужно:

  1. Нажать на обозначение секреции/потребления ПКМ.

  2. В раскрывающемся списке нажать ЛКМ на Remove icon_remove_element.