actin

We are currently doing validation using a filament assembly system meant to represent a simple model of actin assembly. To help demonstrate use of the system, we have provided a version of this filament model with the code available for download. In order to run the simulation of actin assembly, please follow the instructions below:

1. Customize actin assembly simulation parameters through the dialog panel shown in Fig.1

2. Click "Load" button to load the simulation scene.

3. Click "run" button to run the simulation.

4. When quantitative output is needed, edit the Simulation.java and use class methods to customize the output.

The remainder of this page provides some illustrative snapshots and preliminary quantitative results from our filament assembly model. The results demonstrate the ability of the simulator to handle moderate-sized systems of filament assembly.

Simulation Run of Actin Assembly

actin simulation set up dialog

Fig. 1 Actin assembly simulation set up dialog

Fig. 2 Assembly simulation initialization with 500 subunits with 0 binding sites

Fig. 3 Close-up view of 4 subunits with 0 binding sites before the assembly simulation starts to run

Fig. 4 Close-up view of one subunit with two binding sites after the assembly simulation starts to run

Fig. 5 A collection of actin filaments of different sizes after 20000 steps

The following figure shows the comparison of results from the simulation of actin filament assembly at equilibrium by our discrete event simulator with an equivalent differential equations model. In our experiments, the parameters are shown in Fig.1. After the simulation reached equilbrium, the average number of filament of different sizes (A0 represents monomer without binding ability) calculated over some time from the simulator run fits well with the results from differential equation solutions. The setup of differential equations can be found from the following link.

Fig.6 Comparison of actin filament length distribution between two models at equilibrium