TABLE 1

Parameters used in the agent-based modela

SymbolMeaningUnitValue
or range
Comment(s)
NxNo. of voxels in the x direction100
NyNo. of voxels in the y direction100
NzNo. of voxels in the z direction100
l0Length of a voxel’s sideμm0.5The volume of each voxel is approximately that of one NTHI
bacterium (7).
kplankRate of diffusive movements
for the planktonic bacteria
1/s2.4Calculated using kplank = 6Dplank/l02, where Dplank = 0.2 μm2/s
and is the diffusion coefficient for the planktonic bacteria (7).
ktwitchRate of ballistic movement of NTHI
on extracellular DNA strands
induced by Tfp-mediated twitching
1/s0.12Calculated using, ktwitch = υtwitch/l0, where υtwitch is the linear velocity
of attached bacteria moving on the eDNA network. Estimated to
be similar to P. aeruginosa as studied in reference 30.
kturnRate of attached bacteria changing
direction
1/s0.02Estimated to be similar to P. aeruginosa as studied in reference 30.
The half-life of velocity autocorrelation is about 30 s, this gives
a rate constant of ln(2)/30 ≈ 0.023 s−1
kdivRate of division per nutrient density
(for both attached and planktonic
bacteria)
μm3/s0.0003Assuming 1 division per hour at a nutrient density of 1/μm3
kdeath*Rate of planktonic bacterial death1/s10−3−10−1Assuming faster than cell division, slower than movement
kattach*Rate of planktonic bacteria
becoming attached
1/s10−4−10−2Assuming faster than cell division, slower than movement
kdetach*Base rate of attached bacteria
becoming planktonic
1/s10−5−10−3Assuming similar to kdiv
kquorum*Additional rate of attached bacteria
becoming planktonic, when the
quorum sensing mechanism is
activated
1/s10−3−10−1Assuming >> kdiv
dquorum*(Manhattan) distance (in voxels) away
to use in the local density calculation
for quorum sensing
Δl1−4Sets the size of bacterial clusters
nquorum*Threshold to activate quorum sensing25–75%Total bacterial density within dquorum of a bacterium
knutrient*Rate of nutrient generation1/(μm3s)10−7−10−5Chosen to create a nutrient-starved state
nmax*Maximum nutrient density1/μm30.05−0.25Chosen to create a nutrient-starved state
  • a Parameters marked with an asterisk were optimized within the range shown. If the range is given in powers of 10, the optimization was done on a logarithmic scale.