We are currently doing validation of
virus capsid assembly using
a tetrahedron assembly system. Both models use same algorithm and
methods. Explicit comparison of simulation run and ODEs model in
tetrahedron assembly system is strightfoward and provides valuable
experience for virus capsid assembly. To help demonstrate use of the
system, we have provided a
version of this tetrahedron model with the code available for download.
In
order to run the simulation of tetrahedron assembly,
please follow the instructions below:
1. Customize tetrahedron 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 tetrahedron assembly model.
The time course curves of assemblies demonstrate a good overlap
between the simulation run and ODE model.
Simulation Run of
Tetrahedron Assembly
Fig. 1 Tetrahedron assembly simulation set up
dialog
Fig. 2 Assembly simulation initialization with 1000 subunits with 3
binding sites
Fig. 3 Close-up view of 4 assembly products after
40000 steps
The following figures show the comparison of results from
5 simulation run of tetrahedron
assembly at equilibrium by
our discrete event simulator with an equivalent differential equations
model. In our experiments, the
parameters are shown in Fig.1. The blue smooth curves represent
the intergrating of ODEs using MATALB package. The black dashed curves
represent the results from 5 different simulation runs. The setup of
differential equations can be found from the following link.
Fig.4 Time courses of monomer
Fig.5 Time courses of dimer
Fig.6 Time
courses of trimer
Fig.7 Time courses of
tetramer(tetrahedron)