Why?

Once we are ready to build a bigger bioreactor, we want to be sure that the irradiance we apply to the cells is enough to activate LovTAP-VP16 but not higher, to avoid damage to the cells.

• Can we know this value for a given bioreactor size and lighting setup?

What?

We have written a raytracing algorithm, both in MATLAB and JavaScript. Knowing the characteristics of our light source and the absorbance spectrum of the cell culture, we can get, as we show, a good approximation of the irradiance in the whole bioreactor just applying the Beer-Lambert Law.

How?

Example of irradiance map

Assuming laminar flow, the cells at a particular layer in the flow will see this irradiance pattern. Using our other modelling tools we can predict the amount of LovTAP-VP16 in them that will be active.

We chose to represent the bioreactor as an infinitely long cylinder. This allows us to consider the problem in two dimensions, yet should stay realistic (the bioreactor will normally be at least two-times longer than its radius, so this model should quite accurately represent what's happening in the middle). From literature (Strickland 2008), we know that LovTAP saturates at 20 mW/cm² (note: lower intensities should still work, as saturation isn't necessary, we just want a significant proportion to be activated, but this should keep things easier to calculate).

The results are displayed in a picture at the bottom of the page. Everything that is dark red is fully saturated, but everything between red and green should be enough. The places where the picture is blue represents parts that aren't illuminated enough. However, as the activated LOV-domain has a half-life of 30-40s (and our protein's half-life should be quite close to this), and the bioreactor is operating as an orbital shaker (which results in chaotic movement, meaning every cell has a quasi-uniform probability of going anywhere in the bioreactor), the only thing that matters is that the coverage is high enough (note: "high enough" depends on several parameters, such as the shaker speed).

Parameters

The parameters we have used for the cell culture absorbance have been extracted from the measurements that can be found in this file: File:Team-EPF-Lausanne-cell-culture-absorbance-nanodrop.pdf.

The simulation was built around the Beer Lambert law for absorbance of a solution.

Validation

Comparison of the analytical solution to the one given by our raytrace model. They fit perfecly.

We have solved a geometrically simple setup: just an onmidirectional light in the center and no reflexions. Then we could compare it to the analytical solution.

Code

Here the MATLAB code we have used for this section: File:Team-EPF-Lausanne bioreactor matlab.zip.

Please play with our tool! (If you're unsure about the settings, just click run to use sane defaults).