Abstract
When building models that simulate biological systems at different levels of abstraction, we need to compare their output parameters with measurements from lab experiments. Before we can do that, we need a way to parameterise the models themselves. Here, we investigate parameterising an abstract computational model of plasmid circuits operated by DNA supercoiling (TORCComp), using a more detailed biophysical model (TORCPhys). TORCComp is built as a high speed low fidelity model, which will allow us to explore many variations of parameters in our modelled systems, at the higher abstract level of circuit components. This is aimed at increasing our ability to design supercoiling operated plasmid circuits. TORCPhys is a slower more detailed model, whose parameters are derived from physical concepts and lab experiments, designed to simulate the detailed action of a single circuit at the lower biomolecular level. It cannot be used as an exploratory tool for circuit construction due to longer run times. To explore the feasibility of using TORCPhys to parameterise TORCComp, here, we compare the models of a simple supercoiling controlled plasmid circuit operational in bacteria (Escherichia coli or Salmonella enterica) through the mappings of their states. We parameterise TORCComp based on parameter values that are physiologically observable in both lab experiments and TORCPhys, and also those that are not observable in the lab, but can be observed in TORC-Phys. Our results demonstrate the difficulty of parameterising a model based on limited highly contextual observations, and the difficulty of comparing models at different abstraction levels.