Difference between revisions of "Spring 11:QRT-PCR"

Revision as of 18:28, 28 March 2011

Looking for weekly reports?

To-Do

• FIND & ORDER STUFF FOR HEATED LID
• get used to the new LabView code.
• test heating setup with sample vs block thermistor.
• find out data output format of labview program
• start investigating what kind of analysis I'll need to do in Python to the data

Weekly goals

• 3/25: Optics finished. Code started.
• 4/1: Heated lid finished.
• 4/8: Updated heat transfer function. Successful PCR.
• 4/15: QRT-PCR code finished.
• 4/22: Setup is ready for QRT-PCR. (i.e., the mechanical setup works)
• 4/29: Successful QRT-PCR from the side.
• 5/6: QRT-PCR from the top. Now which one was better?

Heated Lid research notes

OpenPCR first used nichrome wire and silicone tape sandwiched between two plates of aluminum...but it didn't work too well. They said it "smoked and burned out." However, they were designing for 16 samples, not just one (so we won't need to use as much wire). Also, we're not planning on using silicone tape. I still think it's worth trying.

Then they used a peltier device with an aluminum plate + thermal pad.

Another option: using a PCB. Instructions here.

Option 1: Nichrome wire

Researching nichrome wire... looks like NiChrome 80 is the best. Here is the datasheet. Now for calculations:

 I = 3A
 V = 15V
 n = length of wire (feet)
 rpf = resistance per foot (ohms/ft)
 
 I = V/R = V/(n*rpf)

 rpf and n are inversely proportional - and cost goes up with rpf. So we want to minimize that.
 reasonable values seem to be:
 rpf = 6.46
 n = 0.77 feet
 which means a 30 gauge wire, d = 0.0100 inches.

Okay, this turns out to be too long. If we're looking to use only one coil of wire, using nichrome is not feasible.

Option 2: Thermal foil

Mica, polyimide, silicon These are pretty expensive. Is it possible to just attach leads in random places to these foils, I wonder? That would make it cheaper. But as it is, they're more expensive than a TEC.

Option 3: PCB

Would it be fast enough? who knows.

 If you have such a specific spec that's not in the off the shelf units, that's a second argument (besides price) for making them yourself.

 I don't know about your mechanical design, but you may be more confident in making a heater out of a traditional circuit board-- it can easily handle 110 C, will be rigid, can be custom shaped with mounting holes, and you can dip it in a biocompatible coating if necessary. Final cost will be a few dollars (or lower), per board, exactly meeting your specs in terms of size, shape, voltage input, and power dissipation. 

 So you need 12 V input, and maybe 4-6 ohm resistance to get 20-30 W. Let's call it 5 ohms, and you'll then need 12/5 = 2.4 A available for the heater. 1 oz copper has resistance of *roughly* 0.05 ohms/inch in a 10 mil trace, so you need about 100 inches of wire. Suppose that you use 10 mil wires with 10 mil spacing, with a simple single-sided back-and-forth pattern. Then one wire plus spacing is 20 mil, and you can fit 50 wires per linear inch. If you have a 1.5" square, then in each linear inch, you get 1.5*50 wires = 75 wires per inch, and in 1.5 inches of that you get 1.5*75 wires = about 112 inches of wire total-- right on target.

Progress Notes

3/22/11

Getting the temperature calculation right earned me a level-up... meaning I got to graduate to the Current Version of the Code. Got a brief intro to it. It's pretty complicated.

3/20/11

Based on model system (blue LED + ND filter), I don't think gain is high enough. Increased gain of transimpedance amp from 2.5e4 to 2.5e5. Well, it didn't help that much. So it's back the way it was. In any case, we get a significant signal (~0.25 units amplitude) with the model system. Huzzah!

After much wrestling with simple math, the temperature sensing is largely working! yay

3/18/11

Optical setup appears to be working.

3/16/11

Added dichroic mirror.

Question: how can I verify the optical setup? it seems to respond to driving signal, not fluorescence.

TODO: put away 25mm lens