2016.igem.org:Team:Manchester/Model/Analyse
Units and beer’s law
Why units must be same?
In the lab we could produce concentration vs time graphs, these were simulated using our model. We required the units for both to be the same so we could compare.
How we did this model?
For our model our concentrations should be measured in units like mM i.e a measure of the amount of compounds per volume. The model units come from the units used in the initial conditions, we used mM by having the concentrations in ug/ml from the lab and dividing by the molecular weight.
How we did this experimental?
The experimental team used a plate reader. The units showing concentration over time were optical density values, these can be converted into a concentration using beers law and a calibration experiment.
Calibration experiment
The calibration experiment was done with Abts h202 and hrp there was excess H202 so that the equilibrium was such that we could assume all the abts was oxidised. We did this for a range of initial conditions. We now knew the od values at steady state and the concentrations at steady state. And hence we could calibrate.
There were some extra complications because abts decays and the other reagents cause absorbance, these were taken into account initially but the change was negligible so it was ignored, this assumption could be relaxed in the future. This analysis allowed us to convert od values to ug/ml and hence mM.
Theory of beer's law
Beer’s law simply states that concentration in a unit like mM is proportional to absorbance measured in od value, a result from fluid mechanics leads to this phenomena specifically with the od scale.
The graph is for the described experiment .The dotted line uses the gradient and intercept from fitting. With these you can easily convert between the two.
How code works and Git
Relevant github link. All files discussed here are available for reference.
This code is a simple one. Absorbance values in od are read into matlab as well as the concentrations of abts oxidised form the calibration experiment. A straight line fit is then made. Now from this straight lines equation given one variable e.g. absorbance values (od) you can calculate the concentration in (ug/ml.) You could divide by mr to get the answer in mM.
