@MASTERSTHESIS\{IMM2015-06898,
    author       = "J. K. Friis",
    title        = "Modelling and analyses of synthetic biology",
    year         = "2015",
    school       = "Technical University of Denmark, Department of Applied Mathematics and Computer Science",
    address      = "Richard Petersens Plads, Building 324, {DK-}2800 Kgs. Lyngby, Denmark, compute@compute.dtu.dk",
    type         = "",
    note         = "{DTU} supervisor: Michael R. Hansen, mire@dtu.dk, {DTU} Compute",
    url          = "http://www.compute.dtu.dk/English.aspx",
    abstract     = "The goal of the thesis is to investigate current means of modelling and analysing chemical reaction systems, in the context of synthetic biology. Synthetic cells that are proposed to act as electronic gates, called synthetic genetic devices, are simulated under different conditions in order to assess the adequacy of Gillespie’s direct method and Oded Maler’s proposed model for spatial dynamics.

Both of these models are examined and described in terms of their level of abstraction, i.e. how true-to-nature they are. Experiments are then conducted by utilising a tool proposed and developed for this thesis. The tool itself is designed, such that the models can later be refined and extended. It incorporates a current format for specifying the devices, making it suitable for biochemists to use.

It is concluded that Gillespie’s model is in fact sufficient for described the synthetic genetic devices considered in this thesis, under the right circumstances. The motion of the particles, the devices consist of, had a great impact on the simulated dynamic behaviour compared to the expected. This revealed how sensitive the devices are to the parameters of the given simulation."
}