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Cells do not keep growing and dividing forever. Eventually, they undergo cell death, in which cells lyse (burst)
and decay. PhysiCell supports two models of cell death: apoptosis and necrosis. Apoptosis is programmed
cell death, which contributes to regular growth and function. Necrosis, on the other hand, is unprogrammed
cell death due to injury or disease. PhysiCell users may choose the model(s) appropriate for their projects.
The apoptosis model has only 1 phase, called Apoptotic. It is modeled by the following equation:
is the rate at which the cell exits the apoptotic stage. The apopotosis model does not involve any growth
in cell size, though cells do shrink afterwards. The necrosis model has 2 phases: the swelling phase and the
lysed phase. The cell is in the swelling phase and grows in size until it reaches a certain volume, at which
point it lyses (bursts). After lysis, the cell shrinks (and potentially calcifies), entering the lysed phase.
2.1 Death Class
The death class stores basic death information for the simulation being run.
Death rate is, as expected, the rate at which cells die in a model, measured in
. The rates are stored
as a vector, with one rate per model.
models is a vector containing the death models used in the simulation. The two possible models are apoptosis
and necrosis. If a simulation uses both, then the two models are included in the models vector.
The parameters vector holds the death parameters for each model. These parameters are described in the
dead is a variable that is either ”true” or ”false” and exists for every cell. If this variable is true for a cell,
that cell is dead.
2.1.5 current death model index
The current death model index is the index of the current death model for dead cells. The index either
corresponds to the apoptotic model or the necrotic model.
2.2 Death Cycle Parameters
Death cycle parameters determine what conditions lead to cell death.
2.2.1 time units
The default time units in PhysiCell is minutes.
2.2.2 Unlysed fluid change rate
The unlysed fluid change rate is the rate of fluid change (cytoplasmic fluid) before cell lysis. It is measured
2.2.3 Lysed fluid change rate
The lysed fluid change rate is the rate of fluid change (cytoplasmic fluid) after cell lysis (after cell death). It
is measured in
2.2.4 Cytoplasmic biomass change rate
In contrast with the two fluid change rates above, the cytoplasmic biomass change rate is the rate of degra-
dation for solids in the cytoplasm other than the nucleus. It is also measured in
2.2.5 Nuclear biomass change rate
The nuclear biomass change rate is the rate of degradation for nucleus solids. It is measured in
2.2.6 Calcification rate
Calcification is the deposition of calcium salts. In the body, this commonly occurs in the formation of bone,
but it also occurs as a result of cell death. In PhysiCell, calcification rate is measured in
2.2.7 Relative rupture volume
Relative rupture volume is the amount by which the volume of a cell must change for it to lyse. It is
dependent on the original volume of the cell.
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