Difference between revisions of "Spring 11:QRT-PCR"
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Kristin Kuhn (Talk | contribs) (→To-Do) |
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HEAT | HEAT | ||
| − | * | + | * order crimp-ons, then wire up heated lid. |
* get heat transfer equation b/w sample, block with heated lid | * get heat transfer equation b/w sample, block with heated lid | ||
* what is that last equation on the right of the code...? | * what is that last equation on the right of the code...? | ||
| Line 13: | Line 13: | ||
LIGHT | LIGHT | ||
* find new fiber optic / re-design setup / something to reduce that background | * find new fiber optic / re-design setup / something to reduce that background | ||
| + | * learn when LED is supposed to be on. I bet Steven can tell me this... bwahaha. | ||
* make sure LED matches heating cycle. (it's on when it needs to be) | * make sure LED matches heating cycle. (it's on when it needs to be) | ||
Revision as of 00:08, 8 April 2011
Looking for weekly reports?
Or LabView QRT-PCR version info?
Contents
To-Do
Last updated 19:49, 7 April 2011 (EDT)
HEAT
- order crimp-ons, then wire up heated lid.
- get heat transfer equation b/w sample, block with heated lid
- what is that last equation on the right of the code...?
LIGHT
- find new fiber optic / re-design setup / something to reduce that background
- learn when LED is supposed to be on. I bet Steven can tell me this... bwahaha.
- make sure LED matches heating cycle. (it's on when it needs to be)
CODE
- what is output format of Labview VI? what are we even DOING?
- then...what do I need to do with it? check out cool website below.
Questions
- can thermistor actually stick in sample? or should it just be near the lid?
- will I need to isolate the circuit, since it's drawing so much current (1-3 A)?
Weekly goals
as of 15:03, 4 April 2011 (EDT)
- 3/25: Optics finished. Code started.
- 4/1: Heated lid finished.
- 4/8: No really, heated lid finished. Updated heat transfer function. Kinda know LabView.
- 4/15: Successful PCR.
- 4/22: Optics are ready for QRT-PCR!
- 4/29: Successful QRT-PCR from the side.
- 5/6: QRT-PCR from the top. Now which one was better?
Research notes
Useful Links
- Resistance wire temperature table
- Calculations with resistance wire
- Simple Labview Tutorial
- QRT-PCR Tutorial
Progress Notes
4/6/11
Posted 17:13, 6 April 2011 (EDT)
Learned some more about LabView.....
I've constructed the heated lid. Now I just need to hook it up electrically. Which I can't do...without some guidance, since you gotta use something called acid flux with the NiChrome. okay.
The heater in the lid is a little too tall, so that the lid doesn't quite fit under the cap. Probably smaller-diameter washers could fix this. But for now, it doesn't need to be fixed.
I still don't know what the 2.712 TEC cooling problem is. I do know that it is not:
- the PWM controller.
- the Kp, Ki, or Kd values.
My next guess is that it has to do with this weird equation, which appears to convert temperature to volts? what? Yeah, I need to talk to Steven.
I currently need to talk to Steven about:
- soldering/wiring the NiChrome wire
- TEC cooling problem
4/4/11
Posted 17:13, 4 April 2011 (EDT)
I now know the reason for the background signal. The fiber optic cable is auto-fluorescing. BOO. It works okay for now (there is a small, but extant difference between H20 and SYBR+dsDNA), but in order to do any serious testing, I'll need to change the design. Or get a new fiber optic
It might, in fact, be time to get rid of the fiber optic all together. But I will also look around for fiber optics that really, really do not fluoresce.
Came up with a preliminary design for heated lid. Will verify with Steven.
v2.712 now uses thermistor equations instead of RTD. The correct temperature is produced. Hooray! However, The modeled temperature is quite wrong. More problematically, the TEC doesn't cool in this version (though it does in 2.52). This is probably due to the settings in 2.712 (i.e., it's comparing against the modeled temp instead of the real sample temp), as opposed to fundamental issues with the code. But I will talk to Steven about it.
4/1/11
Posted 15:50, 1 April 2011 (EDT)
Officially ordered 29-gauge wire.
The optics *do* detect a difference between water and SYBR dsDNA, but it's a fairly small difference. I think this small difference is due to the HUGE amount of background signal at the carrier frequency. Why is this happening? My current hypothesis is that the dichroic mirror is directly reflecting some light from the blue LED into the photodiode... but with the filters in place, this shouldn't be happening!
Question: how good are the filters we're using? Could they still be letting some other light through? (maybe we need another blue filter in front of the blue LED).
Steven went over with me some of the different existing versions of the LabView code. I will be working with versions 2.700 and later. Not all of them work. I will take notes on this; take a look at QRT-PCR:LabView-versions.
3/28/11
Turns out my calculations were all messed up before! With corrected calculations, and the data from [www.heatersplus.com], I decided on 29-gauge resistance wire for our heated lid.
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
