Rule-based spatial modeling with diffusing, geometrically constrained molecules

Background: We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our approach molecules possess a location in the reactor as well as an orientation and geometry, while the reactions are carried out according to a list of implicitly specified reaction rules. Because the reaction rules can contain patterns for molecules, a combinatorially complex or even infinitely sized reaction network can be defined. For our implementation (based on LAMMPS), we have chosen an already existing formalism (BioNetGen) for the implicit specification of the reaction network. This compatibility allows to import existing models easily, i.e., only additional geometry data files have to be provided. Results: Our simulations show that the obtained dynamics can be fundamentally different from those simulations that use classical reaction-diffusion approaches like Partial Differential Equations or Gillespie-ty...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Gerd Gruenert, Bashar Ibrahim, Thorsten Lenser, Maiko Lohel, Thomas Hinze, Peter Dittrich
• Keywords: BMCBI 2010, Business, Reaction Network, Reaction Rules, Simulation