Team:TU Delft-Leiden/Modeling

Modeling Overview

We developed models for each of the three different modules of our project: the conductive curli module, the extracellular electron transport (EET) module and the landmine detection module.
For the conductive curli module, we wanted to know if a conductive path between two electrodes of a chip filled with curli growing E. coli arise at a certain point in time. We also wanted to make quantitative predictions about the resistance between the two electrodes of our system in time.
For the EET module, our goal was to investigate the carbon metabolism providing the electrons for the EET module. Also, we want the EET pathway used by the cells in order to have a measurable electrical signal for our biosensor, see the gadget section of our wiki. Furthermore, in our modeling of the assembly of the EET complex, we wanted to predict how many EET complexes are formed under different initial conditions. We focused, in addition to the assembly mechanism, also on the apparent reduced cell viability.
For the landmine module, we tried to find a model which would be able to reproduce the response curves of both the landmine promoters, as found in [1].
For the EET and landmine modules, we used deterministic modeling. For the curli module, we used a stochastic modeling approach, and considered the system at the gene, cell and colony level. At the colony levvel, we employed percolation theory in order to predict if a conductive path between the two electrodes arise at a certain point in time and to predict at which time this happens. Our application of percolation theory to describe the formation of a conductive biological network represents a novel approach that has not been used in the literature before.

We used Matlab for most of the calculations; the scripts we made can be found in the code repository. We had great interactions with the Life Science and Microfluidics departments, which for the conductive curli module can be read here, for the EET module can be read here and for the landmine detection module can be read here.

References

[1] S. Yagur-Kroll, S. Belkin et al., “Escherichia Coli bioreporters for the detection of 2,4-dinitrotoluene and 2,4,6-trinitrotoluene”, Appl. Microbiol. Biotechnol. 98, 885-895, 2014.