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Cellzilla adds several arrow forms to the list of Cellerator Arrow Forms that may be used in a model; these new arrows allow for interactions between constituents in different Cellzilla compartments.

Arrow Form Description
{X⟶X, Diffusion[DX,DX']} X diffuses between cells with permeability constant DX or a function f[i,j,k] where i and j are the from and to cell indices and k is the edge index. The arrow is the LongRightArrow, \[LongRightArrow], or ␛-->␛ (where means the escape key.) The optional second permeability constant (default is zero) is the outer-wall permeability.
{X⟶X, Transport[f]} X may be transported between cells according to the function f. The arrow is the LongRightArrow, \[LongRightArrow], or ␛-->␛ (where means the escape key.)
{X↦Y, IGRN[...]} X induces Y in a neighboring cell via a GRN reaction. The options to IGRN are identical to the options for a Cellerator GRN reaction.
{cell⟶cell,
 Grow[Spring[k,fk],
  GrowthRate[mu,fmu],
  Pressure[P,fP]]
Specification of growth. The variable cell must be the same as the value of "CellVariable" option to grow. fk and fmu are the names of functions f(i,j,k) (i,j,k=cell,cell,edge) and fP is the name of a function f(i) (i=cell number). In their definitions, thefunctions may depend on any model variable, e.g., as
fmu[i_,j_,k_]:= mu0+mu1(X[i][t]+x[j][t]); or pure functions may be used here as in
GrowthRate[mu,mu0+mu1(X[#1][t]+X[#2][t])&]. In any case the global time dependence must be explicitly stated, in the same way that a user defined rate constant that depends on a protein must explicitly state the time dependence.
{cell⟶cell+cell,
 model[v, μ, σ, w]}
Cell Division. model must be either "ErreraModel" or "Potential". The variable cell is the same as "CellVariable defined in the options grow. Cell division occurs when variable v (usually cell) but it can be any protein, e.g., in the model, passes the corresponding thresholds set for that cell. Thresholds are set randomly at the start of the simulation with mean μ and standard deviation σ (with a normal distribution). If the model is "Potential" then the weight vector may b be specified as the fourth option.

 



[4 May 2013]