Team:EPF-Lausanne/Modeling/BioreactorSim

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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 (Strickland2008), 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. File:File:Team-EPF-Lausanne beer lambert.png

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.


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

This page uses Web Workers to avoid freezing the page while performing its calculations. Please update your browser to use this simulator.
Please check if all values in the forms are correct (all fields are filled, numbers are numbers, etc...).
Bioreactor Lighting Simulator

This defines the size of the bioreactor. This can be anything from a few centimeters to a few meters (depends on the production scale).

As the model of the bioreactor is an infinite cylinder with infinite lighting strips, the light intensity needs of all strip needs to be defined in Watts per meter. This power will be uniformly distributed among the lights.

The bioreactor can have reflective walls which will keep more of the light inside of the bioreactor. Typical values for the frequencies we're working with are 0.9 (for aluminium and silver) and 0.4 (for gold)

This value determines how much of the light is absorbed by the culture. Typical values can range from 0.01-0.04.

The lights can be uniform (same amount of light in all directions) or directed (light will come out of in a small angle).

This simulator works by shooting rays out of each light source. The more rays are used, the longer the simulation will take, but the better the result will be.

Resolution of the simulation. Higher resolutions need more rays per lightsource to be accurate.

Number of Lights in the system. The more lights, the better and the more uniform the lighting. Will increase the computation time.

Number of rings of Lights in the system. This just changes the distribution of the lights.

Results
?%
Shows the light intensity in a slice of the bioreactor. This image uses the jet colormap. Red = saturated, green = partially saturated, blue = low/no lighting.
At any point in time, ?% of the cells are saturated in light (as the cells are shaken around the orbital shaker and the LOV domain has a long half-time, they don't need to be constantly saturated).
?% of the light was lost (absorbed by the walls or escaped through a transparent wall).