I have been trying to create a method to create a homogeneous agar solution.

What are appropriate techniques to ensure homogeneous solidification of an agar-based aqueous solution?

The new solution consists of distilled boiling water, $\pu{20 g/L}$ agar, $\pu{10 g/L}$ $\ce{NaCl}$ and $\pu{1 g/L}$ $\ce{CuSO4}$. An issue with the agar is that it only dissolves between 90-100C which makes it difficult to dissolve using a hot plate or other methods as it also needs to be homogeneous.

I've made progress speaking to both the microbiology and chemistry departments of my university. The current idea to make the solution homogeneous is to heat it in an autoclave set at 121C. This will also sterilize the solution making the phantom last longer. Unfortunately we have no 3L beakers to do it all in one go. They have plenty of 2L and some 5L beakers, but nothing that is 3L.

A new idea is to heat a round bottomed flask in the autoclave and then transfer the semi-cooled solution to a perspex container that will have a base on it. (flask and container shown in the photo below)


The problem is how do we ensure the solution is still relatively homogeneous and won't be full of air bubbles? Are there any simple ways to solve this?

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    $\begingroup$ do you have access to an ultrasound bath? you could hold it in there for a time, if the chemical can withstand the stress it could help removing air bubbles.. $\endgroup$ – Fl.pf. Jun 2 '17 at 13:24
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    $\begingroup$ I discussed this with one of the physics technical officers, microbiology does have the equipment but didn't think it was a great idea. They pushed the autoclave method instead. I'm not sure why, I might ask them again. $\endgroup$ – James Blackwell Jun 2 '17 at 13:26
  • $\begingroup$ If you are making a phantom for radiation physics / health physics then why not use 1 M nitric acid with the radioisotope in it or some other aqueous liquid from which precipitation is unlikely. Another option would be to look for an organic soluble form of the radionuclide if it is very long lived. Then mix it with styrene and pour the solution into a glass version of the phantom. Use redistilled styrene. Now seal it up and put it away for months for the styrene to slowly convert into polystyrene. This could give you a very long lasting phantom. $\endgroup$ – Nuclear Chemist Apr 15 '18 at 7:05

There are two aspects to consider for the intended "air bubble free" (or at least, "air bubble less") transfer from your container where the liquid is prepared into the container where the liquid is supposed to solidify:

  • Your first container shown is a round bottom flask. Initially, an increase in inclination of the flask will increase the flow of liquid out of the flask. If however the inclination is too high, the air that aims to refill the inner volume of the container, initially occupied by the liquid, will no longer continously enter the flask. Instead, there will be an alternation of sorting liquid and entering air; which may in turn yield air bubbles in the sorting liquid. Depending on the viscosity of the liquid, the air bubbles may remain in the liquid for quite some time. From the perspective to lower the potential air intake by the liquid during the transfer, a wide mouth bottle, or even a beaker were better suited than a round bottom flask.
  • The distance between the first and the receiving container. For your purpose, it is not good to pour the liquid directly into the receiver. To lower splash and splatter in the transfer by decantation, an easy aide is using a glass rod, like shown here:

enter image description here

(picture source)

In your instance, it may be more convenient to use a slab of glass / a pane of glass that is just beneath the mouth of the first container, and bridges all the distance to the receiving container; as schematically drawn below:

enter image description here

Here, intentionally the slab of glass is partially immersed in the liquid already present in the receiving container. If done in a coordinated team of two, one holding and moving gently the slab of glass, the second gently decantating the liquid onto this "chute", you might cast larger volumes into trough-shaped containers / fish tanks, too. Once solidified, you would cut-out the block / shape you need. Overall, it reminds me a little to ballistic gelatin...

  • $\begingroup$ Thank you for the detailed answer! I know the flask isn't ideal, but the perspex will deform inside the autoclave. The chemistry department were surprised they didn't have a 3L beaker too. I show the above method to my supervisor and see what he thinks. For something that seems so trivial to make at the start, it has quickly become difficult! We're trying to make a human tissue analogue. The issue with gelatin is it's animal based and breaks down very quickly. Agar will still break down, but should still hopefully last a couple of weeks if sufficiently sterilized and kept sealed. $\endgroup$ – James Blackwell Jun 2 '17 at 13:08
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    $\begingroup$ I worked with some gelatin-based phantoms (for RF) one summer during my MPhys. We didn't have trouble with them breaking down. I assume we added some sort of preservative, but can't remember (it was 15 years ago). We made a half head on its side and the brain and eye were gelatin (the skull wasn't, which led to intersting effects when lit from the brain side) $\endgroup$ – Chris H Jun 2 '17 at 13:49
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    $\begingroup$ ... I can't find anything relevant published by that group around the time I was there. I hoped I might be able to find a citation for the recipe. (The group was based Bristol University, led by Alan W Preece) $\endgroup$ – Chris H Jun 2 '17 at 13:56
  • $\begingroup$ @ChrisH Thanks for that! That was just what my supervisor said to me anyway, I think agar is a bit cheaper too. How long did you work with it for? Our biggest issue once this is made is trying to keep the phantom consistent for a couple of weeks and minimizing dehydration. $\endgroup$ – James Blackwell Jun 2 '17 at 15:43
  • $\begingroup$ @JamesBlackwell It was a summer job for about 8 weeks essentially as a technician. My task was building it (and the stand and sensors). The rest of the group were expecting to be able to use it for some (unspecified but not small) time after I left. I think the solution to dehydration was simply a nice flat layer of clingfilm on top once it had set; we embedded sensors in the gelatin so could probably leave the clingfilm on, but I can't remember. $\endgroup$ – Chris H Jun 2 '17 at 15:48

If you can accept discarding a little solution at the beginning and end of the flow, a narrow siphon tube touching the receiving container will deliver a reliably air free flow.

With an open valve near the exit of the tube, submerge most of the tube in the solution and close the valve. You can now withdraw the submerged tube leaving only enough submerged to drain the source container. With exit end below the level of the solution open the valve and the siphon will begin to flow. Discard the first bit which is likely to have a few bubbles, close the valve, then begin to fill your receiving container while keeping the tube in contact with the container. Once both ends of the siphon are submerged it is near impossible to introduce air as long as the rate of flow is low enough to avoid agitating the surface. As the source container approaches empty you risk picking up some air, with a reasonable length tube you can easily close the valve before the first air bubble exits the siphon.

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