The Molecular Workbench software allows developers to create interlinked simulations. This allows many simulations in just one applet, which I call a "mega" applet. The following example, which provides simulations of physical phenomena at different scales, shows how this works.
Here is another example of molecular dynamics simulations of pressure conveyance in different settings through fluids:
A Molecular Workbench "mega" applet provides rich user experiences similar to Web 2.0, which can be designed using the software's authoring system. This is similar to Macromedia's Flash software.