Modelling and stochastic simulation of synthetic biological Boolean gates
KeywordComputational modelling; Logic gates; Biological system modelling; Stochastic processes; Genetics; Mathematical model; Integrated circuit model
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AbstractSynthetic Biology aspires to design, compose and engineer biological systems that implement specified behaviour. When designing such systems, hypothesis testing via computational modelling and simulation is vital in order to reduce the need of costly wet lab experiments. As a case study, we discuss the use of computational modelling and stochastic simulation for engineered genetic circuits that implement Boolean AND and OR gates that have been reported in the literature. We present performance analysis results for nine different state-of-the-art stochastic simulation algorithms and analyse the dynamic behaviour of the proposed gates. Stochastic simulations verify the desired functioning of the proposed gate designs.
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CitationSanassy D, Fellerman H, Krasnogor N et al (2014) Modelling and stochastic simulation of synthetic biological Boolean gates. In: 2014 IEEE International Conference on High Performance Computing and Communications, 2014 IEEE 6th International Symposium of Cyberspace Safety and Security, 2014 IEEE 11th International Conference on Embedded Software and Systems (HPCC, CSS, ICESS). 20-22 Aug 2014 Paris, France: IEE: 404-408.
Link to publisher’s versionhttps://doi.org/10.1109/HPCC.2014.68
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