Journal
IEEE JOURNAL ON SELECTED AREAS IN COMMUNICATIONS
Volume 31, Issue 12, Pages 868-878Publisher
IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC
DOI: 10.1109/JSAC.2013.SUP2.12130019
Keywords
Nanotechnology; bacteria-based nanonetworks; bacteria consortia; multiscale modeling; stochastic simulation; heterogeneous multicellular system; cyber-physical systems
Funding
- US National Science Foundation (NSF) [CPS-1135850]
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Bacteria-based networks are formed using native or engineered bacteria that communicate at nano-scale. This definition includes the micro-scale molecular transportation system which uses chemotactic bacteria for targeted cargo delivery, as well as genetic circuits for intercellular interactions like quorum sensing or light communication. To characterize the dynamics of bacterial networks accurately, we introduce BNSim, an open-source, parallel, stochastic, and multiscale modeling platform which integrates various simulation algorithms, together with genetic circuits and chemotactic pathway models in a complex 3D environment. Moreover, we show how this platform can be used to model synthetic bacterial consortia which implement a XOR function and aggregate nearby bacteria using light communication. Consequently, the results demonstrate how BNSim can predict various properties of realistic bacterial networks and provide guidance for their actual wet-lab implementations .
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