3D lattice model of For3p-mediated actin cable dynamics in fission yeast cells

In the simulation, the cell has the shape of a cylinder with a hemispherical cap at each end, and is partitioned into a 3D rectangular lattice. Actin monomers are modeled as a continuous concentration field. Formin For3p dimers are modeled as discrete particles performing random walks on the lattice. Cortical binding sites for For3p are randomly placed at the cell tips. For3p dimers bind to cortical sites and processively polymerize actin subunits into filament bundles (actin cables). The actin cables undergo retrograde flow towards the cell center, driven by the actin polymerization at the cell cortex. For3p dimers randomly detach from the cortical sites with a rate which depends on the processivity parameter and the actin polymerization rate. The detached formins are passively transported to the cell center by actin cable retrograde flow. Close to the cell center, both the actin cable and the associated formins disassemble
into the cytoplasm.

Click here to download the executable jar file.

Input parameters
[Actin] (μM), # of For3p dimers
concentration of actin and the number of For3p dimers in the cell
DA, DF and kplusA, kplusF
diffusion coefficients of actin and For3p; association rate constant of actin and For3p
rminusAmax, tauAage
aged actin filament disassembly rate, ageing time
rminusFmax, tauFage
aged For3p dissociation rate from cable, ageing time
For3p processivity
processivity parameter of For3p
Num of cables and patches total number of actin cables (half on each cell tip) and patches
Cell length and radius total length of the cell and the radius of the cell tube
Parameter file a directory containing the parameter file "init.dat" will be created automatically

Running the program: Once the program is launched, change the parameter values or use the default, and then click the "Initialize" button, which becomes "Start" after clicking. Then hit the "Start" button to run the simulation. The graphics are updated every 0.2 seconds. Several windows will pop up once the simulation is started:

Actin cables with For3p dots: snapshot showing actin concentration along four randomly chosen cables, together with the For3p associtated along the actin cables. Click on a lattice site to see the values of the field corresponding to each lattice site.

For3p dimers in cytoplasm: snapshot showing discrete For3p dimers in a 2D slice at the center of the cell. Click on a lattice site to see the values of the field corresponding to each lattice site.

Actin in cytoplasm: snapshot of actin monomer concentration in the cytoplasm in a 2D slice at the center of the cell. Click on a lattice site to see the values of the field corresponding to each lattice site.

Actin density in cytoplasm: time averaged actin concentration profile along the long axis of the cell.

Tip For3p for different cables: four curves showing the number of For3p dimers associated with four randomly chosen cable tips, as a function of time.

More options are available in the parameter file "init.dat". To make use of this parameter file, download the jar file, and double click (or type "java -jar actinCable.jar" in a terminal window) to launch the program. Upon clicking the "Initialize" button, a directory "actinData" containing the file "init.dat" will be created in the same directory as the jar file. Use a text editor to open init.dat and change the values of the parameters (e.g., true to false). Save the init.dat file and click New->Reset, or launch the program again in order for the new parameters to take effect.

This project used the Open Source Physics (OSP) library for graphics and user control.

Wang and Vavylonis, PloS ONE (2008)

Updated Apr 9, 2008.