QEIRQ

A simulator of a confluent monolayer of cells that hold a simple internal state and may communicate when in contact.

Model

Cell states patterned after a multi-compartment epidemiological SEIRS model were renamed to match the cellular signaling context:

• Q - quiescent,
• E - excited,
• I - inducing
• R - refractory.

The following transitions are assumed:

 Q -> E_1 -> ... -> E_{nE} -> I_1 -> ... -> I_{nI} -> R_1 -> ... -> R_{nR} -> Q
      ------"Excited"-----    -----"Inducing"-----    ----"Refractory"----

The transition Q -> E_1 is induced by a neighboring cell in one of the "Inducing" states.

The model is parametrized by specifying the numbers of the E, I, and R subcompartments and four kinetic rate constants for (forward-only) transitions. The respective parameters are:

• e_subcompartments_count (nE in the scheme above),
• i_subcompartments_count (nI in the scheme above),
• r_subcompartments_count (nR in the scheme above),
• c_rate (receiving activation from a Q neighbor to become E_1),
• e_forward_rate (progression within and out of the "Excited" states),
• i_forward_rate (progression within and out of the "Inducing" states),
• r_forward_rate (progression within and out of the "Refractory" states).

The simulation protocol is specified by a sequence of the two commands:

• +front at column 0 -- triggers a new front of activity by turning cells in column 0 to state I_1,
• run -- runs a simulation in a specified time span with the output time interval specified in square brackets (e.g., run 0h...30m [5s]); when the output time interval is not specified (as in, e.g., run 0h...30m []), then no output files are produced.

The reactor geometry is set upon launching the simulator with command-line arguments.

Running

The simulator is implemented in Rust. To compile and run the executable binary, in terminal type:

cargo run --release -- --height 7 --width 100 --states-out --activity-out --images-out input/parameters.json input/two_initial_fronts.proto

For an explanation of the command-line arguments, type:

cargo run --release -- --help

If libglib2.0-dev and libcairo2-dev are installed, all dependencies should be retrieved and compiled on the fly prior to simulator compilation and execution.

Origin

QEIRQ is a simplification of our viral infection simulator, VIS-A-VIS (https://github.com/grfrederic/visavis).