Re: Copper beads as thermocycling "block" - Was: [DIYbio] What do open source PCRs need?

The well block that heats the pcr tubes seems a little tricky to fab. 

I think the wells have conical sides with a spherical tip at the bottom. I measured the wells in the cad file in the ninjapcr repo - the side walls slope about 8.8 degrees from the normal, and the well ends 0.45" from the surface of the block in a flat bottom that has a diameter of about .075" (~2/32").

The closest tooling I can find from mcmaster to cut something like that is with this $21 Tapered High-Speed Steel End Mill (10 Degree Taper, 3/32" Tip Diameter, 1/2" Length of Cut) for the conical section, and this $19 Ball-End High-Speed Steel Two-Flute End Mill (1/8" Mill Diameter, 3/8" Shank Diameter, 3/8" Length of Cut). $40 of tooling and not quite right.

Besides getting a batch of this milled by a machine shop, what are some other options for heating the tubes besides hot air or liquid?

Lab Armor sells these metal beads designed to replace liquid water baths for heating and cooling, but their opening price is $100+.

​

Perhaps we could build a box with peltiers + heat pumps on the top and bottom and perhaps forced air on the sides, and fill it with these metal beads. We could pack the pcr tubes inside the beads in the box and thermocycle the whole thing. It might not be fast, but perhaps it would be smooth and steady.

Spent a little time hunting around for cheaper alternatives with the same idea...

Found a listing on ebay for 1lb of (supposed) aluminum granules for $21 + shipping.

And a 100-pack of 1/32" diameter aluminum spheres on mcmaster for $12 (I think 5-10 packs would be needed? Not sure about sphere packing... are spheres optimal shape because the allow for the highest net density? or worst b/c they minimize surface contact with one another and thus thermal conduction?).

McMaster also sells Aluminum oxide grit as a media for abrasive blasting, $28 for 10 lbs of 18 mesh grit. I guess it would pack and conduct heat much differently than the smooth spheres (worse?), but it's much cheaper.

Lastly, I found an online retailer that supplies metals for jewelers and casters. They are selling 1 troy oz of ".999 pure" copper casting grain for $3. 16 tubes might need 10-20 times that mass.

Some quick googling suggest that aggregates of metals like these conduct heat much worse than solids... perhaps only 10-30%? as thermally conductive as it would be if it were solid. That said, pure copper is apparently 1.5-2x as thermally conductive as pure aluminum .

So in conclusion, perhaps $60 of copper beads surrounding tubes would perform "within range" of a milled aluminum block - and without requiring a finicky heated lid.

Just some fun ideas!

Mac

On Mon, Feb 8, 2016 at 11:32 PM Cathal (Phone) <cathalgarvey@cathalgarvey.me> wrote:

I am very impressed with ninjapcr;

* Cheaper design
* Uses stock Arduino firmware!
* Has ninja in the name

On 9 February 2016 01:42:36 GMT+00:00, Mac Cowell <mac@diybio.org> wrote:

Just saw another open pcr project - "ninjapcr". OpenPCR fork. 

http://pcr.tori.st/index.php/Main_Page.  

https://github.com/hisashin/NinjaPCR

On Tue, Feb 2, 2016 at 6:48 PM Nathan McCorkle <nmz787@gmail.com> wrote:

On Tue, Feb 2, 2016 at 6:05 PM, John Griessen <john@industromatic.com> wrote:

a fast ramping air PCR thermocycler that needs no lid because it also
shakes the contents, (which also contributes to ramp rate performance)?

Now you're encouraging/helping phase-change of liquid-to-gas... it would be worth checking for prior-art. Also shearing of the DNA, people might look at you cross-eyed if you so much as drop their sample tube, or mix it too fast with your pipette tip. You're going to have to confidently demonstrate you're not adding new variables to a protocol pipeline.

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