Using the SRSim Software for Spatial and Rule-Based Modeling of Combinatorially Complex Biochemical Reaction Systems
G Grunert and P Dittrich, MEMBRANE COMPUTING, 6501, 240-256 (2010).
The simulator software SRSim is presented here. It is constructed from the molecular dynamics simulator LAMMPS and a set of extensions for modeling rule-based reaction systems. The aim of this software is coping with reaction networks that are combinatorially complex as well as spatially inhomogeneous. On the one hand, there is a combinatorial explosion of necessary species and reactions that occurs when complex biomolecules are allowed to interact, e.g. by polymerization or phosphorilation processes. On the other hand, diffusion over longer distances in the cell as well as the geometric structures of sophisticated macromolecules can further influence the dynamic behavior of a system. Addressing the mentioned demands, the SRSim simulation system features a stochastic, particle based, spatial simulation of Brownian Dynamics in three dimensions of a rule-based reaction system.
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