Re: [DIYbio] Electronic requirements for redesign of Arduino PCR thermal cycler

Oh, nice idea! I wonder if even plastic capillaries at that scale are
conductive enough to work, I could see it being possible to make
"pinch-off" capillaries that you fill (by capillary action? :)) and
pinch, then lay on your micro-cycler made with a peltier, two heatsinks,
an LM35 temp sensor, and an Arduino micro or similar.

As usual with Peltiers, the big ask is current, so the complexity arises
from ensuring enough is delivered from a suitable power source through
the peltiers.

I wonder if a "constant heat flow" design couldn't be knocked together
with a heating element atop the fins on the reaction side, so heat is
conducted downwards through the fins to the tubes, and cooling is
achieved by ceasing to apply heat and letting the heatsink distribute
what remains. But, that's only marginally simpler than fixing up a
cooling fan to a simple heat-block anyway and just doing
coil-heating-air-cooling, which is possibly as efficient as these things
get until you start coming full-circle to convective PCR (pun welcomed
but not intended)..

On 27/02/15 08:35, Mac Cowell wrote:
> Also, just want to point out that if you fill capillary glass tranfer
> pipettes (typically like $20 for 100, with volumes selectable from
> 0.5-50uL), they fit perfectly in the valleys of many
> sawtooth-style sinks (cheap). The surface to volume ratio is such that I
> don't think a heated lid is necessary. Imaging from above is possible,
> potentially enabling qpcr-like applications.
>
> They are just a bit of a pain to work with.
>
> But the thermocycler is so simple in this case. Peltier, sawtooth heat
> sink with 5-10 ridges, mosfet for switching power, embedded
> thermocouple, microcontroller, and 5-10 glass capillaries, one per sample.
>
> Cheers
> Mac
>
> On Friday, February 27, 2015, Mac Cowell <mac@diybio.org
> <mailto:mac@diybio.org>> wrote:
>
> The reaction mixture will condense on the coldest part of the pcr
> tube, for instance, any surface not enclosed in the main heated
> block and exposed to ambient air.
>
> One solution is to establish a temperature gradient from the top of
> the cap to the block by touching the cap with a second hot surface,
> preferably hotter than the main block such radiative and conductive
> heat transfer from the heated lid raises the temperature of all
> surfaces of the pcr tube exposed to air above the current
> temperature of the block.
>
> But you don't need s Peltier to do this. You just need a heat source
> you can keep at a constant temperature guaranteed to be hotter than
> any of the pcr temps.
>
> It would be interesting to explore a hybrid design combining
> dynamic conductive heating in the tube block with constant radiative
> heating from a lamp or hot air flow positioned at just the right
> distance, instead of a heated lid in constant contact with the cap.
> Can the radiative heat source be set up to always add +20C to the
> exposed cap and 5-10 C to the reaction mixture? If so, perhaps such
> a design could lead to faster ramp times, by switching the radiator
> off during cooling.
>
> Does the transparent plastic most pcr tubes are made from absorb IR?
>
> Or maybe all that matters is if the reaction mixture absorbs the
> radiative energy. Not sure. Would pcr work in a transparent Quartz
> vessel in a freezer that was pulsed by a powerful IR source? Or
> would that be condensation city?
>
> Cheers
> Mac
>
> On Thursday, February 26, 2015, Andy Morgan
> <andrew.r.morgan@gmail.com
> <javascript:_e(%7B%7D,'cvml','andrew.r.morgan@gmail.com');>> wrote:
>
> Thanks for the heads up Josiah.
>
> That's a bit annoying, I was hoping that I could have the lid at
> the same temperature as the tubes, allowing me to run the whole
> thing off of just the one simple circuit described in the
> original instructable.
>
> Perhaps I'll look into using one peltier element for the base
> and another smaller one for the lid, although that might mean
> I'd have to hook up a whole other arduino board and solid state
> relay. Not to mention that all sounding a wee bit over my head.
> If I could hook them both up to the one arduino board that might
> be a little bit simpler though.
>
> I came across this design
> (http://2013.igem.org/Team:Paris_Saclay/PS-PCR/detailed_description)
> that was build (and apparently for only 30 euros!) using peltier
> elements, but the electronic schematics look intense.
>
> On Friday, February 27, 2015 at 2:12:14 PM UTC+13, Josiah Zayner
> wrote:
>
> Keeping the lid at a constant temp of ~90C will generally
> suffice. Most PCR machines hold the lid at 90C - 105C.
>
> I have tried doing the lid at same temperature as the tubes
> but received condensation. I think this might have been
> because of the different heat transfer rates? Maybe you can
> figure it out?
>
> Looking on eBay these days you can buy most of the parts for
> the Arduino thermalcycler for much cheaper than the $85USD
> pricetag (inexpensive Arduino boards &c). Also, keep on eye
> out on eBay for thermal cyclers. Sometimes people don't know
> what the actual equipment is so they just list it as brand
> and product names so searching directly for brand names
> help. I have found some for under $100 that work great
> though this is from the US, so who knows what you might find?
>
>
>
> Josiah
>
>
>
>
> On Thursday, February 26, 2015 at 3:02:09 PM UTC-8, Andy
> Morgan wrote:
>
> Ah it all becomes clear, I was wondering why they listed
> a 12V power supply AND a regular power cable.
>
> Thanks Simon.
>
> On Friday, February 27, 2015 at 8:22:16 AM UTC+13, Simon
> Field wrote:
>
> I presume the power supply is simply for the Arduino
> part of the project, which is unchanged from the
> original. In fact, the only thing that has changed
> is the heater. It's like swapping a 40 watt light
> bulb for a 100 watt light bulb. You don't have to
> change anything else.
>
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