Using the SRSim Software for Spatial and Rule-Based Modeling of Combinatorially Complex Biochemical Reaction Systems

  • Gerd Grünert
  • Peter Dittrich
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6501)


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.


Message Passing Interface Dissipative Particle Dynamic Reaction Rule Membrane Computing Spatial Simulation 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Gerd Grünert
    • 1
  • Peter Dittrich
    • 1
  1. 1.Jena Center for Bioinformatics, Bio Systems Analysis Group, Institute of Computer ScienceFriedrich Schiller University JenaJenaGermany

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