Fast parallel algorithms for short-range molecular dynamics
Journal of Computational Physics
FoSSaCS '98 Proceedings of the First International Conference on Foundations of Software Science and Computation Structure
Implementation of a discrete event simulator for biological self-assembly systems
WSC '05 Proceedings of the 37th conference on Winter simulation
Proceedings of the 11th Annual conference on Genetic and evolutionary computation
Compartmental rule-based modeling of biochemical systems
Winter Simulation Conference
UPP'04 Proceedings of the 2004 international conference on Unconventional Programming Paradigms
Evolution and oscillation in p systems: applications to biological phenomena
WMC'04 Proceedings of the 5th international conference on Membrane Computing
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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.