Parameter files for SimFil
ParM:
parM-100Seg-1e-4 (default) --a 3.19 micron ParM filament, 0.5 microns from the nearest surface, made from 100 monomer rigid segments, time-step = 1e-4 seconds. This is the default parameter set and was used to generate the data in Figure 4 from Alberts (2008).
Actin:
actin-100Seg-1e-5 --a 3.0 µm actin filament made from 100 monomer rigid segments, time-step = 1e-5 seconds
actin-100Seg-1e-4 --an 3.0 µm actin filament made from 100 monomer rigid segments, time-step = 1e-4 seconds
actin-100Seg-1e-3 --an 3.0 µm actin filament made from 100 monomer rigid segments, time-step = 1e-3 seconds
actin-200Seg-1e-4 --a 4.9 µm actin filament made from 200 monomer rigid segments, time-step = 1e-4 seconds
actin-200Seg-1e-3 --a 4.9 µm actin filament made from 200 monomer rigid segments, time-step = 1e-3 seconds
actin-50Seg-1e-5 --a 3.1 µm actin filament made from 50 monomer rigid segments, time-step = 1e-5 seconds
actin-50Seg-1e-4 --a 3.1 µm actin filament made from 50 monomer rigid segments, time-step = 1e-4 seconds
Microtubules:
mt-120Seg-1e-5 --a 4.3 µm microtubule made from 120 tubulin dimers (end-to-end) segments, time-step = 1e-5 seconds
mt-120Seg-1e-4 --a 4.3 µm microtubule made from 120 tubulin dimers (end-to-end) segments, time-step = 1e-4 seconds. This is a bad parameter set with some coefficients beyond the usable range... load this parameter set to see an oscillatory failure of the PAIRS method with filaments. For a filament as stiff as an MT, we'd have to use longer segments at this large a time-step (as with the next parameter file).
mt-240Seg-1e-4 --a 6.7 µm microtubule made from 240 tubulin dimers (end-to-end) segments, time-step = 1e-4 seconds.
mt-15micron-240Seg-1e-4 --a 14.4 µm microtubule made from 240 tubulin dimers (end-to-end) segments, time-step = 1e-4 seconds.