Some requirements of a mesoscale simulation tool for systems biology are that
- It cover 3D space scales up to micrometers, and timescales up to minutes.
- It is compatible with traditional reaction kinetics and mechanisms.
- It allows biomolecular property input and reaction input for all classes of relevant molecules and reactions.
- It handle collective spatial structures such as vesicles autonomously and consistently, dealing with their formation, stability and morphology changes.
- It produce the correct macroscopic limit of hydrodynamic and diffusive transport and give the right scaling of the transport properties of collective structures such as endosomes.
- It be generalizable to include active transpot mechanisms such as motor protein mediated transport.
- It can take advantage of existing kinetic databases and fluorescence image data.