pwAddC


 m = pwAddC(m, *ID, *size, outside, spatialDim, name, unit, constant,
            designerProps, classname, description)
 m = pwAddC(m, interactive)

 Adds a compartment to the model, defined essentially by its ID and
 the size which can be a number or the name of a parameter.

 

Arguments for pwAddC

 m             struct       A model struct
 ID            ID           Compartment ID
 size          float/string Size of the compartment
 outside       ID           ID of the embracing compartment
 spatialDim    integer      Dimension of the compartment
 name          string
 unit          string
 constant      integer      constant size of compartment (1 yes, 0 no)
 designerProps array        [x y z w h r g b isVisible]
 classname     string       E.g. 'cytoplasm' or 'nucleus'
 description   string

 Alternative function call for interactive specification:
 interactive   bool    If true, the user is prompted to enter the properties
                       into a user interface.

 

Description

 Chemical reactions depend on the concentration of their reactants and products.
 If a molecule enters a different compartment, e.g. the nuclues, the concentration
 decrease in the cytoplasm may differ from the concentration increase in the
 nucleus. Hence, handling the compartment volume is a crucial aspect for the
 modeling of chemical reaction networks.

 PottersWheel treats all x variables as concentrations!
 Therefore, all plotted x trajectories are concentrations,
 even if the start value for a variable was given as an amount.

 If a system has two or more compartments, a reaction A -> B
 with rate constant k, A being in compartment c1 and B in c2
 leads to the following flux and change for the concentrations A and B:

  v     = (k * A) * c1 % flux (amount)
  dA/dt = - v /c1      % concentration change
  dB/dt =   v /c2

 Please open the dynamically generated ODE C file to see how PottersWheel
 processed the reactions of your system.

 Instead of a numeric value for the compartment size a parameter name
 can be specified. This is useful if the compartment size should
 be fitted.

 Currently, only the ID and size information are processed within
 PottersWheel. However, the other arguments are exported to SBML files.

 

Example

 m = pwAddC(m, 'cytoplasm', 1);
 m = pwAddC(m, 'nucleus',   1, 'cytoplasm');

See also

pwAddK
pwAddR
pwAddX
pwAddK
pwGetEmptyModel