TOPIC: [Bacteria simulators]: BNSim

[Bacteria simulators]: BNSim 1 year 7 months ago #26

BNSim is multithread java simulator of Bacteria-based networks. These networks interconnect engineered bacteria that communicate at nanoscales. BNSim integrates three simulation methods: (i) the Gillespie’s stochastic simulation algorithm (SSA), which solves the chemical master equation in order to determine the time evolution of a chemical system; the extremely small granularity of events makes this approach unpractical for population-level problems; (ii) stochastic differential equations, used to model large-scale chemical system with a controlled level of approximation; (iii) a hybrid algorithm which integrates both the SSA and the approximated methods based on differential equations.
The approximated methods based on stichastic differential equations are used to model the behavior of species that are present in large quantities and generate scalability issues. It was estimated a speed increase of 5-7 orders of magnitude over the SSA approach.
In addition, a specific thread scheduler was implemented to balance the workload for simulating the intracellular dynamics and interactions of entities.

See also:
G. Wei, P. Bogdan, R. Marculescu, “Efficient Modeling and Simulation of Bacteria-Based Nanonetworks with BNSim”, IEEE Journal on Selected Areas in Communications, vol. 31, no. 12, 2013.
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