BoundaryCondition
Indicate species boundary condition
Description
The BoundaryCondition
property indicates whether reactions affect a species
quantity.
When the BoundaryCondition
of a species is false
(default), the reactions can modify the species quantity. If a species is modified by
reactions, then rules (repeated assignment rule, rate rule, or algebraic rule) cannot
modify its value. SimBiology considers a reaction to modify a species when the net
stoichiometry for the species is non-zero. For example, the reaction
X -> 2*X
modifies
X, but the reaction X +
E -> Y + E
does
not modify E.
When the BoundaryCondition
of a species is true
,
then the value of the species is not changed by reactions during model simulation, even if
the net stoichiometry is non-zero. Set the BoundaryCondition
of a
species to true
if you want the species to participate in the reaction
but you want to determine the value of that species using a rule instead. For example, set
the BoundaryCondition
of species X to
true
to specify its value using a repeated assignment rule but also
to use species X in a reaction with MassAction
kinetics, for example, X + Y ->
Z
.
For details on how these two properties affect a species quantity during simulation, see How Species Amounts Change During Simulations.
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.ForHsp90_complex:GR_cyt + dex -> Hsp90_complex + GR_nuc + dex
dex
,In this exampleBoundaryCondition = true; ConstantAmount = false
dex
is modeled as a boundary condition with a rule to regulate the rate of change ofdex
in the system. Here, the quantity ofdex
is not determined by the rate of the second reaction but by a rate rule such aswhich is specified in the SimBiology® software asddex/dt = 0.001
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 totrue
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 |
Examples
References
Pratt, W.B., Galigniana, M.D., Morishima, Y., Murphy, P.J. (2004), Role of molecular chaperones in steroid receptor action, Essays Biochem, 40:41-58.