SimBiology^®

BoundaryCondition - Indicate species boundary condition

Description

The BoundaryCondition property indicates whether a species object has a boundary condition. If BoundaryCondition is true, the species quantity is determined by InitialAmount and/or a rule object, and not by the reaction rate equation. All SimBiology^® species are state variables regardless of BoundaryCondition or ConstantAmount property.

By default BoundaryCondition is false and the reaction rate equations determine the rate of change of a species quantity in the model. Boundary condition is used when a species is modeled as a participant of reactions but the species quantity is not determined by a reaction rate equation.

More Information

Consider the following two use cases of boundary conditions:

Modeling receptor-ligand interactions that affect the rate of change of the receptor but not the ligand. For example, in response to hormone, steroid receptors such as the glucocorticoid receptor (GR) translocate from the cytoplasm (cyt) to the nucleus (nuc). The hsp90/ hsp70 chaperone complex directs this nuclear translocation [Pratt 2004]. The natural ligand for GR is cortisol; the synthetic hormone dexamethasone (dex) is used in place of cortisol in experimental systems. In this system dexamethasone participates in the reaction but the quantity of dexamethasone in the cell is regulated using a rule. To simply model translocation of GR you could use the following reactions:
Formation of the chaperone–receptor complex,
```
Hsp90_complex + GR_cyt -> Hsp90_complex:GR_cyt
```
In response to the synthetic hormone dexamethasone (dex), GR moves from the cytoplasm to the nucleus.
```
Hsp90_complex:GR_cyt + dex -> Hsp90_complex + GR_nuc + dex
```
For dex,
```
 BoundaryCondition = true; ConstantAmount = false
```
In this example dex is modeled as a boundary condition with a rule to regulate the rate of change of dex in the system. Here, the quantity of dex is not determined by the rate of the second reaction but by a rate rule such as
```
ddex/dt = 0.001 
```
which is specified in the SimBiology software as
```
dex = 0.001
```
Modeling the role of nucleotides (for example, GTP, ATP, cAMP) and cofactors (for example, Ca⁺⁺, NAD⁺, coenzyme A). Consider the role of GTP in the activation of Ras by receptor tyrosine kinases.
```
Ras-GDP + GTP  -> Ras-GTP + GDP
```
```
For GTP, BoundaryCondition = true; ConstantAmount = true
```
Model GTP and GDP with boundary conditions, thus making them boundary species. In addition you can set the ConstantAmount property of these species to true to indicate that their quantity does not vary during a simulation.

Characteristics

Applies to	Object: species
Data type	`boolean`
Data values	`true` or `false`. The default value is `false.`
Access	Read/Write

Example

Create a model object
```
modelObj = sbiomodel ('my_model');
```
Add a species object and verify that boundary condition property setting is 'false' or 0.
```
speciesObj = addspecies(modelObj, 'glucose');
get(speciesObj, 'BoundaryCondition')
```
MATLAB^® returns
```
ans =

     0
```

Set boundary condition to 'true' and verify

set(speciesObj, 'BoundaryCondition', true);
get(speciesObj, 'BoundaryCondition')

MATLAB returns

ans =

     1

References