fix nufeb/T6SS/lysis command

Syntax

fix ID group-ID nufeb/T6SS/lysis sub-ID lysis-rate sub-ratio

  • ID = user-assigned name for the fix

  • group-ID = ID of the group atoms to apply the fix to

  • sub-ID = substrate ID for organic substrate released by lysis

  • lysis-rate = rate at which lysed organism loses mass

  • sub-ratio = conversion ratio of lost mass to substrate produced

Examples

# lyse at a rate of 8 h^-1 and 20% of mass lost becomes substrate
fix lysis_intox het_intoxicated nufeb/T6SS/lysis sub 2e-3 0.2

Description

The atoms defined in group-ID will undergo lysis, resulting in a mass loss and the conversion of some of that mass into a substrate. The affected atoms are considered as heterotrophic bacteria, having a spherical shape (atom_style coccus).

The mass loss is calculated by the lysis-rate parameter, which is in units of inverse time.

\[m_{t+1} = m_{t}(1-r_{lys} \Delta_t)\]

where:

  • \(m_{t+1}\) is the mass of the atom after the time step

  • \(m_{t}\) is the mass of the atom before the time step

  • \(r_{lys}\) is the lysis rate

  • \(\Delta_t\) is the duration of the time step

A proportion of the lost mass is released as a substrate, given the ratio sub-ratio, with substrate specified by sub-ID.

The fix is called at each biological step (see run_style nufeb) to update atom and grid attributes.

The value of the sub-ID must be consistent with the name defined in the grid_style chemostat command.

This fix requires that NUFEB be installed/built by including the --enable-t6ss argument when installing via install.sh or by including make yes-t6ss as part of the build process.

Restrictions

This fix is not compatible with the following commands: