There is a newer version of this record available.

Software Open Access

pc4covid19/COVID19: Version 0.3.2: draft v3 prototype

Paul Macklin

COVID19 tissue simulator

Version: 0.3.2

Release date: 15 July 2020


This model simulates replication dynamics of SARS-CoV-2 (coronavirus / COVID19) in a layer of epithelium with an initial immune reaction. It is being rapidly prototyped and refined with community support (see below).

In this model, SARS-CoV-2 (coronavirus / COVID19) infects a single cell, or a solution of virions is administered to the extracellular space. The virus is uncoated to explose viral RNA, which synthesizes viral proteins that are assembled into a virion. Assembled virions are exported to the environment, where they can diffuse and infect other cells. In the extracellular space, virions adhere to ACE2 receptors and get internalized through endocytosis. Internalized ACE2 receptors release their virus cargo and are recycled back to the surface.

Resident macrophages ingest apototic cells and release a pro-inflammatory cytokine that recruits additional macrophages, neutrophils, and CD8+ T cells. CD8+ T cells chemotax towards cytokines released by infected cells and adhere. Cumulative CD8+ T cell contact time can induce apoptosis in infectd cells. Activated macrophages and neutrophils chemotaxis chemotax along chemokine and debris gradients and continue to phagocytose dead cells. Neutrophils also absorb free (extracellular) virus.

The model includes a basic pharmacodynamic response (to assembled virions) to cause cell apoptosis. Apoptosed cells release some or all of their internal contents, notably including virions.

Caveats and disclaimers:

This model is under active development using rapid prototyping:

  • It has not been peer reviewed.
  • It is intended to drive basic scientific research and public education at this stage.
  • It cannot be used for public policy decisions.
  • It cannot be used for individual medical decisions.

This model will be continually refined with input from the community, particularly experts in infectious diseases. The validation state will be updated as this progresses.

Key makefile rules:

make : compiles the project.

make clean : removes all .o files and the executable, so that the next "make" recompiles the entire project

make data-cleanup : clears out all simulation data

make reset : reset to default settings (restores config file)

More references


Model details:



Latest info: follow @PhysiCell and @MathCancer on Twitter (

See for the full change log.

Files (20.1 MB)
Name Size
20.1 MB Download
All versions This version
Views 874217
Downloads 567
Data volume 1.0 GB140.7 MB
Unique views 706210
Unique downloads 477


Cite as