Death Training App for PhysiCell

Training application for "Death" concept in PhysiCell.

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Version 1.0 - published on 28 Jan 2020

doi:10.21981/KC63-CC04 cite this

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1 Background

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 Parameters

2.1 Death Class

The death class stores basic death information for the simulation being run.

2.1.1 rates

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.

2.1.2 models

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.

2.1.3 parameters

The parameters vector holds the death parameters for each model. These parameters are described in the

next section.

2.1.4 dead

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.

Cite this work

Researchers should cite this work as follows:

  • Furkan Kurtoglu (2020), "Death Training App for PhysiCell," (DOI: 10.21981/KC63-CC04).

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