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Team:Paris Saclay/PS-PCR/detailed description
From 2013.igem.org
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| Can be found in some power amplifiers and switches, but it's easier to buy them. | | Can be found in some power amplifiers and switches, but it's easier to buy them. | ||
|- | |- | ||
| - | ! scope="row"| | + | ! scope="row"| 1x BC547 transistor |
| TODO | | TODO | ||
| - | | You can get | + | | Or equivalent (for example 2N2222), can be found in many household gadgets like blinking key-rings or pens... |
| + | |- | ||
| + | ! scope="row"| 1x Atmega8 micro-controller | ||
| + | | TODO | ||
| + | | You can get one or two for free by requesting a sample (see for example [http://www.instructables.com/id/How-to-get-FREE-Atmel-Chips this link]). | ||
| + | |- | ||
| + | ! scope="row"| 1x USB-B female connector | ||
| + | | TODO | ||
| + | | You can unsolder them from items like USB hard drives, USB disk drives, USB printers... | ||
| + | |- | ||
| + | ! scope="row"| Connectors : 1xDIL6(or DIL2 if no extra thermistors), 1xDIL5 (ISP programmer header), 4x 2-pin screw headers | ||
| + | | TODO | ||
| + | | You can unsolder them from electronics, you can also buy longer ones and cut them into the needed smaller parts, or you can simply ignore them and solder your wires directly. | ||
| + | |- | ||
| + | ! scope="row"| 1x prototype board with some rigid small wires | ||
| + | | TODO | ||
| + | | Any Bakelite board will do the trick, you may even use cardboard. The wires can be easily found in household items, but perfect ones can be found near phone connection boxes after maintenance. | ||
| + | |- | ||
| + | ! scope="row"| 1x TODO POWER peltier element | ||
| + | | TODO | ||
| + | | Harder to find (USB fridges, some CPU cooling systems...), you may consider buying one. | ||
| + | |- | ||
| + | ! scope="row"| Lid heater : 1x Kapton heater or some kanthal wire or a 60W Peltier element | ||
| + | | TODO | ||
| + | | Any 12V heating device capable of boiling water will do the trick, if it fits in the lid. | ||
| + | |- | ||
| + | ! scope="row"| 1x 12V power supply, 200W or more | ||
| + | | TODO | ||
| + | | Can be easily found in older computers. | ||
| + | |- | ||
| + | ! scope="row"| 1x fan-cooled CPU thermal block | ||
| + | | TODO | ||
| + | | Can be easily found in older computers. | ||
| + | |- | ||
| + | ! scope="row"| 4x4x1.8cm aluminium block and 1mm aluminium plaques | ||
| + | | TODO | ||
| + | | Can be found in household items, except the block, which can be found or purchased from factory byproducts/trashes. | ||
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Revision as of 20:11, 28 September 2013
Contents |
PSPCR
The Paris-Saclay open source PCR thermal cycler project.
Introduction
PCR (Polymerase Chain Reaction) is a very useful procedure in the field of synthetic biology. However, this technique requires a device called a thermal cycler, which is designed to cycle the samples through different temperature steps. Commercial PCR thermal cyclers are traditionally very expensive, with prices starting at $2000, which makes them hard to afford for small labs and DIY projects.
This project aims at creating a thermal cycler for under 30€ with easily accessible parts.
Comparison with other projects
Some open source PCR thermal cycler projects already exist, but the aim of the PSPCR project is to provide a better and more affordable system, thus filling a gap in the list of existing projects.
| Project | Price | Discussion |
|---|---|---|
| [http://openpcr.org/ OpenPCR] | $649 | Heated lid, good performance, hard to manufacture. |
| [http://www.instructables.com/id/Arduino-PCR-thermal-cycler-for-under-85/ Arduino PCR] | $85 | No heated lid, room for only 2 tubes, fan-only cooling. |
| [http://lavaamp.wordpress.com/ Lava-Amp] | "pennies" | No data available, probably slow with no heated lid, 1 slot. |
| [http://www.instructables.com/id/Coffee-Cup-PCR-Thermocycler-costing-under-350/ Coffee Cup PCR] | $350 | 7 slots, no heated lid, fan-only cooling. |
| PSPCR | Under 30€ | Fast solid state heating/cooling, 16 slots, heated lid. |
Design overview
TODO inclure schema
Solid state heating/cooling
By using a [http://en.wikipedia.org/wiki/Peltier_effect#Peltier_effect peltier thermoelectric device], the system achieves fast heating and compressor-less cooling, enabling it to reach temperatures ranging from -3°C to 120°C in a relatively short time.
When powered, the Peltier block transfers heat from one of its sides to the other, thus cooling the former while heating the latter. The "heat pumping" direction can be flipped by reversing the direction of the current in the device.
One side of the Peltier is thermally attached to the sample holding aluminium block, while the other one is attached to a computer CPU fan-thermalized radiator. Since the fan keeps the radiator at near-room temperature, the Peltier device can pump heat from(to) it in order to heat(cool) the sample holding block.
Power control
In order to control the current inside the Peltier, and therefore the heat pumping power, the system uses PWM (Pulse Width Modulation). PWM is quite a simple technique : instead of continuously adjusting the current through the Peltier, it works by switching the peltier completely on and off using a high frequency (~1kHz) square signal. The ratio between the duration of the "on time" and the duration of the "off time" in a single signal period defines the mean power provided to the device : 1.0 meaning full power (Peltier always powered), 0.0 meaning zero power (device always off), 0.2 meaning 20% power (Peltier on 20% of the time, and off 80% of the time) for example. This method uses simple binary to control the Peltier power, allowing the usage of a digital micro-controller to drive the Peltier.
TODO image signal crénau
The direction of the current inside the Peltier is controlled using a power H-Bridge circuit. Our H-Bridge consists of two pairs of complementary power MOSFET transistors that can be selectively switched using digital signals in order to choose the direction of the current through the Peltier.
TODO : images 2 situations h-brige
Temperature sensing
Sample temperature feedback is done thanks to a thermistor attached to the sample holding block. A thermistor a resistor with a temperature-dependant value. By using a voltage divider, one can easily use it to obtain a measurable temperature-related voltage.
TODO schema
Digital interface
The digital control system is built around the Atmega8 inexpensive micro-controller which generates the PWM signal for the Peltier device, outputs current direction commands to the H-Bridge subsystem, acquires values from the temperature feedback sensors and provides an USB port for communication with a computer.
The whole system is controlled through the USB port by a computer running specifically designed software. The computer reads temperature feedbacks and sets the Peltier heat transfer direction and power. The software running on the computer provides a user interface allowing the user to select the PCR cycles to run.
Construction
Bill of materials
| Item | Price | Brotip |
|---|---|---|
| Resistors : 2x68R, 13x(or 9x if no extra thermistors)1k, 1x1k5, 1x2k2, 5x6k8, 3x100k, 2x300k | TODO | You can get them for free from electronics in any decent trash : they can be unsolder-ed from almost any household electronic device. There is a good tolerance on all those resistors, so don't panic if you don't have the exact value. |
| Diodes : 3x1N4148 | TODO | Since they can be replaced by any similar signal diode, they can be found for free in almost every household electronic device. D1 is optional, but if you don't use it, avoid programming your device while it is connected to the USB port, it may damage your programmer. |
| Capacitors : 2x22pF for crystal, 1x25v4.7µF stabilizing electrolytic. | TODO | The crystal capacitors can be chosen in the range 10pF-30pF. The stabilizing capacitor can be any capacitor rated at least 10v and 1µF. They can also be found for free in your local trash. |
| 1xLED | TODO | Choose your favorite color. They are also very common, and you can use either a 3mm or a 5mm LED. Easily found in household electronics. |
| 1x Quad comparator LM339N | TODO | Harder to find in household items, you may consider buying this one. It's still very cheap. |
| Power MOSFET transistors : 2xIRF540, 3xIRF9540 | TODO | Can be found in some power amplifiers and switches, but it's easier to buy them. |
| 1x BC547 transistor | TODO | Or equivalent (for example 2N2222), can be found in many household gadgets like blinking key-rings or pens... |
| 1x Atmega8 micro-controller | TODO | You can get one or two for free by requesting a sample (see for example [http://www.instructables.com/id/How-to-get-FREE-Atmel-Chips this link]). |
| 1x USB-B female connector | TODO | You can unsolder them from items like USB hard drives, USB disk drives, USB printers... |
| Connectors : 1xDIL6(or DIL2 if no extra thermistors), 1xDIL5 (ISP programmer header), 4x 2-pin screw headers | TODO | You can unsolder them from electronics, you can also buy longer ones and cut them into the needed smaller parts, or you can simply ignore them and solder your wires directly. |
| 1x prototype board with some rigid small wires | TODO | Any Bakelite board will do the trick, you may even use cardboard. The wires can be easily found in household items, but perfect ones can be found near phone connection boxes after maintenance. |
| 1x TODO POWER peltier element | TODO | Harder to find (USB fridges, some CPU cooling systems...), you may consider buying one. |
| Lid heater : 1x Kapton heater or some kanthal wire or a 60W Peltier element | TODO | Any 12V heating device capable of boiling water will do the trick, if it fits in the lid. |
| 1x 12V power supply, 200W or more | TODO | Can be easily found in older computers. |
| 1x fan-cooled CPU thermal block | TODO | Can be easily found in older computers. |
| 4x4x1.8cm aluminium block and 1mm aluminium plaques | TODO | Can be found in household items, except the block, which can be found or purchased from factory byproducts/trashes. |
Building the heating/cooling system
- Step 1 : stick a powerful Peltier device (100W+) to a CPU fan-thermalized radiator using thermally conductive paste.
- Step 2 : build the sample holder using a 4cm*4cm*1.6cm aluminium block pierced with 16 evenly-spaced holes. For perfect thermal contact, use this kind of drill : GaudiLabs PCR tube drill. If you don't have one, you can approximate the holes using increasingly small radius drills, and then smooth the holes. Another solution (used for the prototype shown here) is to drill simple cylindrical holes and put mineral oil for better thermal contact.
- Step 3 : stick the radiator&Peltier block to the sample holder with thermal paste and secure it in place in a thermally resistant but non-conductive way (not done yet for the first prototype shown here). Isolate the sides of the sample holder using a thermal insulator or cut a part of your smelly cooking glove to wrap it, this will limit lateral heat losses (not done yet in the first prototype shown here).
- Step 4 (Not yet implemented) : build the lid using a hinge and aluminium, and stick a less powerful Peltier element (~60W) or a Kapton heater or any other low power 12V heater so that it covers the sample holder when the lid is closed. You'll also have to stick another thermistor to it for lid temperature sensing purposes. This lid is useful for keeping the sample tops at 103 in order to prevent water condensation inside the PCR tubes.
Building the electronic control system
- Step 1 : build the electronics.
Notice : R24 to R27 are optional, add them only if you want to add other temperature sensors, otherwise, use a 4 pin header for SV2 (CTNs) with only the pins 9, 10, 11 and 12. The SV3 (GPIO) header is optional, use it only if you want to add custom electronics.
- Step 2 : Program the micro-controller.
Use the SV1 (ISP - In System Programming) header to program the chip by uploading the firmware. The firmware hex file to upload can be found in the Download section. You will need an ISP programmer like the cheap [http://www.fischl.de/usbasp/ USBasp]. You can then use [http://www.nongnu.org/avrdude/ avrdude] to upload the firmware. You must set the following flag bits (others must be reset to zero) : SPIEN, BOOTSZ0, BOOTSZ1.
The corresponding avrdude command to set the flags and upload the firmware is :
sudo avrdude -c usbasp -p m8 -U lfuse:w:0xff:m -U hfuse:w:0xd9:m -U flash:w:pspcr.hex
This command must be launched within the folder containing the downloaded pspcr.hex file.
- Step 3 : Wire everything together
| Connector | Wiring | Discussion |
|---|---|---|
| 1 - to sample block Peltier red wire
2 - to sample block Peltier black wire | If the Peltier cools the samples when it's supposed to heat them, flip those two wires. Don't use thin wires. |
| 1 & 2 - to lid heater leads | If you used a Peltier for the lid and if you notice that it's cooling instead of heating, flip those two wires. Don't use thin wires. |
| 11 & 12 - to sample block thermistor leads
9 & 10 - to lid thermistor leads 7 & 8 ; 5 & 6 ; 3 & 4 ; 1 & 2 - optional extra thermistors | If you don't plan to add extra thermistors, just ignore pins 1 to 8. |
| 1 - to power supply 12V out
2 - to power supply ground | If you flip them, the system will fry. |
| USB cable to a powered computer USB port. | Use an USB A to USB B cable, the shorter the better. Don't worry, the board draws very little USB power (~1mA max). |
Don't forget to wire the fan directly to the 12V power supply.
Installing the control software and calibrating
- Step 1 : Download and install the control software (see Download section).
- Step 2 : Calibrate the system.
The PSPCR system needs to be calibrated before use. A digital and precise (resolved down to or under 1°C) thermometer is required. In order to do the calibration, just launch the calibration software and follow the instructions.
Test
TODO
Download
TODO pspcr.hex, calibrator ...
Acknowledgements
TODO
Gallery
TODO
