DNA Melter Improvements
This page catalogs improvements made to the apparatus for the 20.309 DNA Melting Lab Module.
Contents
Forced Cooling
Refer to Wikipedia for a basic explanation of the H-bridge motor controller circuit, which can drive a motor forwards or backwards, or let it 'free-run'. The TEC works like a motor, in the sense that if you apply voltage in one direction, one side gets hot and one side gets cold; if you apply voltage in the other direction, the hot side and the cold side are reversed; if you apply no voltage, the TEC does nothing and eventually reaches room temperature.
We can use an H-bridge to allow both forced heating and forced cooling of the sample block, instead of being stuck with passive cooling. How it's controlled. TODO: circuit diagram and how the DAQ wiring has to change.
ACCOMPLISHED: got H-bridge to act the same as the relay, with an unmodified LabView VI. Wooo! Now need to get rid of noise in RTD and photodiode inputs from rapid switching.
Documentation of changes made to LabView VI
Monolithic Photodiode-Amplifier
Rather than rolling our own trans-impedance amplifiers, we can use the OPT101 integrated circuit, which contains both a photodiode and a million-gain amplifier. The OPT101 is mounted on a piece of perforated board, which fits inside an optical tube.
Route the output of the photodiode-amplifier through a high-pass filter and then through an additional amplifier of gain 10, for an overall gain of 10^7.
TODO: circuit diagram
Why is the high-pass filter necessary? Remember why the LED is driven at 5kHz, and how the lock-in amplifier reduces 1/f noise? That's wonderful, but the lock-in amplifier is implemented in software. It helps to have an additional filter in hardware, before the signal reaches the DAQ. The DAQ only has one analog-to-digital converter, which is shared by all the analog input channels. It has input limits of +/- 10V. If it receives inputs outside these limits on any one channel, it will get confused and give nonsensical readings on all channels. (If you get nonsensical temperature readings, but your RTD circuit is correct, check the output of your photodiode amplifier!) A simple high-pass filter helps avoid maxing out the DAQ with amplified low-frequency noise.
Physically Restrained Optical System
Because people have to carry their DNA melters from place to place, the optical system tends to get misaligned very easily, leading to noisy data. Here are some ways to make the system more stable:
- Use CL5 clamps to hold the heat sink in place on the breadboard.
- Bend down the leads of the TEC and tie them to the 'legs' of the heat sink with short pieces of wire. (By itself this doesn't help very much, but in combination with thermal grease, it makes a big difference.)
- Use cage rods to hold together the sample block, the photodiode, the filter, and the lenses of the fluorescence detector. To avoid conducting heat out of the sample block, add nylon standoffs to your cage rods.
- TODO: can I also attach the LED to the sample block?
- TODO: photos
- TODO: measure improvement in SNR with these
Effect of Non-Uniform Sample Temperature
TODO: run a really slow melting curve (probably heating only, because after a long time the sample will be photobleached to the point of uselessness). See if it gets rid of that sine-wave-looking component of the residuals.
Translating MATLAB Into Python
I translated the Simulating DNA Melting walk-through into Python. TODO: test on Athena and on 309 lab computers.
I'm working on translating the "Estimate DNA Melting Parameters" analysis code into Python. It is reallllllllllllllllllllllly slow. Also, on my laptop, you can't do that animation-y thing without bringing in the big guns (GTK et al). TODO: finish last bit of code. TODO: see if fitting can be sped up. TODO: see if animation will work on Athena or 309 lab computers.
