Team:Exeter/Modelling Parameter
Parameter Scanning
Introduction
Using our working simulation, we proposed to use it to scan the optimal input parameters and therefore infer the most desirable conditions in which to run our system. This means running the simulation over a variety of input values in either single parameter or simultaneous multiple parameter analysis. The internal mechanics of the simulation were tuned to be as accurate as we could feasibly make them from literature research or by assumption. This includes [INSERT THINGS HERE like assumptions] the estimated translational rate of the ribosomes in our cell free kit; the toehold-trigger interactions and stability(probability of joining and splitting) as well as the interaction of particles with the edge of the container. The numerical output used to quantify the performance of the system is based on the rate of production of reporter. For example, using the estimated translational rate of GFP by the ribosomes we can calculate a cumulative sum of the GFP produced in one “run” of the simulation for the given parameters. Using fluorescence standards, this could be converted to an RFU value which would then allow direct comparison with lab-obtained data. However on a performance rating basis to test our different parameters, absolute GFP should be a suitable method of quantifying output.
Parameters To Scan
First we must categorise the parameters that we can vary by their logical impact and desired value, manipulability in the lab and feasibility of implementation to a field test. The main parameters to consider were:
- Temperature
- This directly influences the kinetic energy of the particles, stability of hybridisation and activity of the transcriptional and translational machinery amongst other things
- Concentration of plasmid DNA
- The DNA allows the transcription of the toeholds and hence will be crucial in determining the minimum concentration of plasmid required for an adequate response from the reporter to be formed.
- Concentration of RNA trigger
- The component to be detected by our toeholds, it is the limiting factor in terms of the sensitivity of our test. From conversing with vets and farmers, this must be minimised to, whilst maximising the reporter output to make a robust test that works on samples containing lower concentrations of the trigger.
- Viscosity
- This is a parameter that directly impacts on the practicality of the field test version of the system. For example, increasing the viscosity would be equivalent simulating the cell free system in a gel type matrix rather than in a solution with viscosity similar to water. Conversely, decreasing the viscosity could perhaps inform on the optimal choice of solvent that the cell free system.