Mesoscale systems simulation

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.
We have established that a new simulation technique, mprDPD, is well poised to meet these multiple objectives, and are exploring its application and Systems Biology integration in the Hepatosys project.

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