Chemostat (not your grandpa's bioreactor)

So anyone who was at Grindfest knows that we jammed on designing a piece of lab equipment called a chemostat.
For those of you without access to wikipedia, a chemostat is a self regulating bioreactor that uses a microcontrolled pump to add nutrients to the liquid that has your bacteria in it. What makes it cool is that the pump is regulated by using a small laser that takes cell density readings and adjusts the flow of nutrients accordingly. This allows for longer and more controlled growth with less plateaus and crashes in replication of cells.

This means that the device is prime from doing biosynthesis and even forced evolution of bacteria.

Here is the most engineer frindly design that I could find in the 10 seconds of Googling
Notice that it has all the parts, but doesnt show how they attach to a microcontroller.

This is one of the most important tools that you can have if you are doing biosynthesis.
It also costs a lot of money. Most of the time, labs end up building their own.
Anyone interested in this should start with this document
Notice that this chemostat is not microporccesor controlled. That means you end up having to fiddle with it a lot
Conceptually, the design is not that hard. If done well, the enitre thing could fit inside a shoebox, run by an arduino


  • A minimum viable chemostat for us will be able to maintain a constant temperature and pH inside the vessel, add air, add food/chemical base as necessary, stir the liquid inside, and monitor the number of cells (optical density or OD).

    I'm not going to get too into detail on the design in this post because I could go on for a while, and we've yet to nail down the final details on dimensions/materials/etc. See this pdf:

    for an example of what most biologists would be using for a smallish pre-built vessel, minus all the other shit normally attached to it.

    So! The arduino is gonna need to monitor a pH probe, thermocouple, and OD sensor. It'll control pumps to dispense the media and base, and a heating element. All that data'll need to output & record to an external computer, with control to set and adjust those parameters. Also some sort of PID control algorithm for pH and temperature, so it won't overcompensate when adjusting those.

    All the input/output components are pretty standard, except the OD sensor, and that's where the fun is. No one really sells an in-process OD sensor, so if you want one, you either make it yourself, ignore the OD and hope for the best, or sit next to the chemostat taking samples manually.

    The sensor design is simple in're shooting yellow (600nm) light through the liquid and seeing how much gets through. From this you can infer how many cells there are, and act accordingly.

    The light source is probably gonna be a yellow LED, as yellow lasers are hella expensive. The receiver is a photodiode or something? I'm not good at electronics. There's a small path between them, and I mean maaaybe 1mm. At high densities we're gonna be getting ~1% transmittance through the liquid, so the receiver might need to compensate for that if it's using the light's energy for the output signal.

    Ideally the sensor package is at the end of a rigid tube that's <13mm wide so it can be inserted into a standard port, and also survive at 121C for sterilization. Just a solid tube, except a gap at the end for the light and liquid to pass through and interact in.

    There's a whole shitton more mechanical stuff on top of this to take care of, but it'll depend more on what we have available. I can cover more of that later.
  • So some thoughts on design specs. (kinda cliff noting from some skype conversations)
    Needs to be glass. And it needs to be small. This is not a production tool, this is a get it working tool. No reason to make 2 litres fo somethign that doesn't work. That's a different tool Also, if you keep it 50ml tube size of lower, then you actually can shine your light through your setup. Temperature can regulated by a small water bath and wouldn't need to be controlled by the arduino. It's not like bacteria have temperature spikes. Same thing for pH. Properly buffered, your media is not going to spike unless something is terribly wrong and then you are tossing your batch.

    This really simplifies everything. All of the sudden, we are really only looking at a 600nm laser/led and a photoreceptor. The arduino picks up the signal and adjusts the flow accordingly. This has your system with two tubes in and two two tubes out and only one input output for the arduino.

    Also, we have found cheaper lasers and maybe leds will work.\

    Now this keeps things really simple, but it still dips right into the cool aspect of not having to sit there and fiddle with your biosynth toy. If this doesn't sound awesome, you have never have done time points.

    Also, by placing a glass tube for the air in we also remove the need for the stir bar or blender attachment that you can see in some of these designs. However, the design we are looking for is basically like the one @yashgaroth put up there, but small and more powerful due to the automation of growth.

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