Re: [DIYbio] Re: Low cost PCR(under development)

We have a prototype Open qPCR machine at the moment which is capable of ramping ramping 5-10 C/s at various parts of the temperature range. Final controlled ramps in the PCR region are likely to be more like 5-7 C/s. The main difference over the OpenPCR was much higher power density in the thermoelectric modules, which necessitates larger power supplies and higher current power switching components. Another difference was reduction in thermal mass of the heatblock by removing more excess material. A third change was a faster heat exchange rate with the air when cooling (i.e. larger heatsink and faster airflow). As Cathal pointed out this requires more engineering in heatblock consistency and thermal control.

All of this increases cost relative to the conservatively engineered OpenPCR. The increased cost may not be worth it for everyone, but I think there is certainly benefit to PCR cycles that take 30 minutes instead of 2 hours. Anyways hope this answers your question about how faster ramp rates are possible in heat block based thermocyclers. There are some more exotic designs that achieve even faster ramp rates with high speed airjets.

-Josh

On Mon, Jun 30, 2014 at 4:05 AM, Cathal Garvey <cathalgarvey@cathalgarvey.me> wrote:

There are two ramp rates; ramp while increasing, and ramp while
decreasing. Most machines can achieve 3-4C increasing because they just
use heating coils, but their decreasing temperature (accomplished with a
peltier, cooling fluid, etc.) may be lower.

IIRC, OpenPCR has a climbing ramp rate of 2-3C, and a reducing ramp rate
of 1C. Larger machines with fundamentally the same architecture (coil +
peltier) achieve higher rates merely by adding extra wattage.

Remember though, an additional consideration is how homogenous the
temperature change is through the block, and at what rate the
temperature change in the block is reflected in the tubes. There would
be little point doubling the ramp rate of the block if the tubes cooled
at an only marginally faster rate. Worse, doubling the ramp rate as
measured by the thermometer may look great on the charts and benchmarks,
but the block may be unevenly cooling and this can have real
consequences when you're expecting your samples to experience identical
conditions.

It's rare that you'll need decreasing ramp rates faster than 1C, in any
case. Have you a special experiment in mind?

On 30/06/14 10:59, Michael Shamberger wrote:
> OpenPcr has a ramp rate of 1 degree C/s.  I checked specs for some
> commercial versions and they have ramp rates of 3 or 4 degrees C/s.   What
> are they doing differently?
>

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